Microorganisms

15 pages, 3265 KiB

Open AccessEditor’s ChoiceArticle

Solitary Bees Host More Bacteria and Fungi on Their Cuticle than Social Bees

by Markus Thamm, Fabienne Reiß, Leon Sohl, Martin Gabel, Matthias Noll and Ricarda Scheiner

Microorganisms 2023, 11(11), 2780; https://doi.org/10.3390/microorganisms11112780 - 16 Nov 2023

Cited by 1 | Viewed by 1667

Bees come into contact with bacteria and fungi from flowering plants during their foraging trips. The Western honeybee (Apis mellifera) shows a pronounced hygienic behavior with social interactions, while the solitary red mason bee (Osmia bicornis) lacks a social [...] Read more.

Bees come into contact with bacteria and fungi from flowering plants during their foraging trips. The Western honeybee (Apis mellifera) shows a pronounced hygienic behavior with social interactions, while the solitary red mason bee (Osmia bicornis) lacks a social immune system. Since both visit the same floral resources, it is intriguing to speculate that the body surface of a solitary bee should harbor a more complex microbiome than that of the social honeybee. We compared the cuticular microbiomes of A. mellifera (including three European subspecies) and O. bicornis for the first time by bacterial 16S rRNA and fungal ITS gene-based high-throughput amplicon sequencing. The cuticular microbiome of the solitary O. bicornis was significantly more complex than that of the social A. mellifera. The microbiome composition of A. mellifera subspecies was very similar. However, we counted significantly different numbers of fungi and a higher diversity in the honeybee subspecies adapted to warmer climates. Our results suggest that the cuticular microbiome of bees is strongly affected by visited plants, lifestyle and adaptation to temperature, which have important implications for the maintenance of the health of bees under conditions of global change. Full article

(This article belongs to the Section Veterinary Microbiology)

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22 pages, 2387 KiB

Open AccessEditor’s ChoiceArticle

Monophasic Variant of Salmonella Typhimurium Infection Affects the Serum Metabolome in Swine

by Guillaume Larivière-Gauthier, Annaëlle Kerouanton, Sophie Mompelat, Stéphanie Bougeard, Martine Denis and Philippe Fravalo

Microorganisms 2023, 11(10), 2565; https://doi.org/10.3390/microorganisms11102565 - 15 Oct 2023

Viewed by 1586

Abstract

Salmonella is the most relevant foodborne zoonotic agent found in swine, and its presence in French herds is significant. Its carriage is asymptomatic, which makes it difficult to detect during rearing, thus increasing the risk of its presence on pork meat. Studies have [...] Read more.

Salmonella is the most relevant foodborne zoonotic agent found in swine, and its presence in French herds is significant. Its carriage is asymptomatic, which makes it difficult to detect during rearing, thus increasing the risk of its presence on pork meat. Studies have shown that enteric infection in animals could be associated with changes in the serum metabolome composition, through the immune response or changes in the digestive microbiota composition. We hypothesized that these changes in the serum metabolome composition could be used as markers for the detection of asymptomatic animals infected by Salmonella. Using untargeted analysis by liquid chromatography coupled with mass spectrometry, we showed that significant differences in the composition of the serum metabolome could be detected between infected or noninfected animals both 1 and 21 days after experimental infection. This serum metabolome composition significantly changed during the 21 days postinfection in the infected animal groups, suggesting an evolution of the impact of infection with time. Despite this evolution, differences in the serum metabolome composition persisted between infected and noninfected animals 21 days after the initial infection. We also showed a possible difference between high-shedding and low-shedding animals 21 days postinfection. Finally, some of the variations in the metabolome were found to be significantly associated with variations of specific members of the fecal microbiota. Thus, excreting and asymptomatic animals, but also high-shedding animals, could be identified on the basis of their serum metabolome composition. Full article

(This article belongs to the Section Veterinary Microbiology)

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14 pages, 1894 KiB

Open AccessEditor’s ChoiceArticle

Heat-Labile Enterotoxin Decreases Macrophage Phagocytosis of Enterotoxigenic Escherichia coli

by Ian E. Hollifield, Natalya I. Motyka, Kaylynn A. Fernando and Jacob P. Bitoun

Microorganisms 2023, 11(8), 2121; https://doi.org/10.3390/microorganisms11082121 - 21 Aug 2023

Cited by 3 | Viewed by 1637

Abstract

Enterotoxigenic E. coli (ETEC) are endemic in low-resource settings and cause robust secretory diarrheal disease in children less than five years of age. ETEC cause secretory diarrhea by producing the heat-stable (ST) and/or heat-labile (LT) enterotoxins. Recent studies have shown that ETEC can [...] Read more.

Enterotoxigenic E. coli (ETEC) are endemic in low-resource settings and cause robust secretory diarrheal disease in children less than five years of age. ETEC cause secretory diarrhea by producing the heat-stable (ST) and/or heat-labile (LT) enterotoxins. Recent studies have shown that ETEC can be carried asymptomatically in children and adults, but how ETEC subvert mucosal immunity to establish intestinal residency remains unclear. Macrophages are innate immune cells that can be exploited by enteric pathogens to evade mucosal immunity, so we interrogated the ability of ETEC and other E. coli pathovars to survive within macrophages. Using gentamicin protection assays, we show that ETEC H10407 is phagocytosed more readily than other ETEC and non-ETEC isolates. Furthermore, we demonstrate that ETEC H10407, at high bacterial burdens, causes nitrite accumulation in macrophages, which is indicative of a proinflammatory macrophage nitric oxide killing response. However, at low bacterial burdens, ETEC H10407 remains viable within macrophages for an extended period without nitrite accumulation. We demonstrate that LT, but not ST, intoxication decreases the number of ETEC phagocytosed by macrophages. Furthermore, we now show that macrophages exposed simultaneously to LPS and LT produce IL-33, which is a cytokine implicated in promoting macrophage alternative activation, iron recycling, and intestinal repair. Lastly, iron restriction using deferoxamine induces IL-33 receptor (IL-33R) expression and allows ETEC to escape macrophages. Altogether, these data demonstrate that LT provides ETEC with the ability to decrease the perceived ETEC burden and suppresses the initiation of inflammation. Furthermore, these data suggest that host IL-33/IL-33R signaling may augment pathways that promote iron restriction to facilitate ETEC escape from macrophages. These data could help explain novel mechanisms of immune subversion that may contribute to asymptomatic ETEC carriage. Full article

(This article belongs to the Special Issue Enterotoxigenic Escherichia coli Infection and Vaccine-Mediated Immunity)

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17 pages, 3283 KiB

Open AccessEditor’s ChoiceArticle

Alpha-Gal Bound Aptamer and Vancomycin Synergistically Reduce Staphylococcus aureus Infection In Vivo

by Matthew K. Doherty, Claire Shaw, Leslie Woods and Bart C. Weimer

Microorganisms 2023, 11(7), 1776; https://doi.org/10.3390/microorganisms11071776 - 8 Jul 2023

Cited by 3 | Viewed by 1898

Abstract

Methicillin-resistant Staphylococcus aureus (MRSA) is a pervasive and persistent threat that requires the development of novel therapies or adjuvants for existing ones. Aptamers, small single-stranded oligonucleotides that form 3D structures and can bind to target molecules, provide one possible therapeutic route, especially when [...] Read more.

Methicillin-resistant Staphylococcus aureus (MRSA) is a pervasive and persistent threat that requires the development of novel therapies or adjuvants for existing ones. Aptamers, small single-stranded oligonucleotides that form 3D structures and can bind to target molecules, provide one possible therapeutic route, especially when presented in combination with current antibiotic applications. BALB/c α-1, 3-galactosyltransferase (−/−) knockout (GTKO) mice were infected with MRSA via tail vein IV and subsequently treated with the αSA31 aptamer (n = 4), vancomycin (n = 12), or αSA31 plus vancomycin (n = 12), with split doses in the morning and evening. The heart, lungs, liver, spleen, and kidneys were harvested upon necropsy for histological and qPCR analysis. All mice treated with αSA31 alone died, whereas 5/12 mice treated with vancomycin alone and 7/12 mice treated with vancomycin plus αSA31 survived the course of the experiment. The treatment of MRSA-infected mice with Vancomycin and an adjuvant aptamer αSA31 reduced disease persistence and dispersion as compared to treatment with either vancomycin SA31 alone, indicating the combination of antibiotic and specifically targeted αSA31 aptamer could be a novel way to control MRSA infection. The data further indicate that aptamers may serve as a potential therapeutic option for other emerging antibiotic resistant pathogens. Full article

(This article belongs to the Special Issue Staphylococcal Infections (Host and Pathogenic Factors) 3.0)

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21 pages, 9137 KiB

Open AccessEditor’s ChoiceArticle

Comparative Genomic Analysis of a Novel Vibrio sp. Isolated from an Ulcer Disease Event in Atlantic Salmon (Salmo salar)

by Maryam Ghasemieshkaftaki, Ignacio Vasquez, Aria Eshraghi, Anthony Kurt Gamperl and Javier Santander

Microorganisms 2023, 11(7), 1736; https://doi.org/10.3390/microorganisms11071736 - 2 Jul 2023

Cited by 2 | Viewed by 2249

Abstract

Ulcer diseases are a recalcitrant issue at Atlantic salmon (Salmo salar) aquaculture cage-sites across the North Atlantic region. Classical ulcerative outbreaks (also called winter ulcer disease) refer to a skin infection caused by Moritella viscosa. However, several bacterial species are [...] Read more.

Ulcer diseases are a recalcitrant issue at Atlantic salmon (Salmo salar) aquaculture cage-sites across the North Atlantic region. Classical ulcerative outbreaks (also called winter ulcer disease) refer to a skin infection caused by Moritella viscosa. However, several bacterial species are frequently isolated from ulcer disease events, and it is unclear if other undescribed pathogens are implicated in ulcer disease in Atlantic salmon. Although different polyvalent vaccines are used against M. viscosa, ulcerative outbreaks are continuously reported in Atlantic salmon in Canada. This study analyzed the phenotypical and genomic characteristics of Vibrio sp. J383 isolated from internal organs of vaccinated farmed Atlantic salmon displaying clinical signs of ulcer disease. Infection assays conducted on vaccinated farmed Atlantic salmon and revealed that Vibrio sp. J383 causes a low level of mortalities when administered intracelomic at doses ranging from 10⁷–10⁸ CFU/dose. Vibrio sp. J383 persisted in the blood of infected fish for at least 8 weeks at 10 and 12 °C. Clinical signs of this disease were greatest 12 °C, but no mortality and bacteremia were observed at 16 °C. The Vibrio sp. J383 genome (5,902,734 bp) has two chromosomes of 3,633,265 bp and 2,068,312 bp, respectively, and one large plasmid of 201,166 bp. Phylogenetic and comparative analyses indicated that Vibrio sp. J383 is related to V. splendidus, with 93% identity. Furthermore, the phenotypic analysis showed that there were significant differences between Vibrio sp. J383 and other Vibrio spp, suggesting J383 is a novel Vibrio species adapted to cold temperatures. Full article

(This article belongs to the Special Issue Bacterial Infections in Aquaculture of Farmed Fish: Pathogenesis, Pathophysiology, Molecular Diagnosis, and Control)

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12 pages, 1339 KiB

Open AccessEditor’s ChoiceArticle

Diversification of Bourbon Virus in New York State

by Rachel E. Lange, Alan P. Dupuis II and Alexander T. Ciota

Microorganisms 2023, 11(6), 1590; https://doi.org/10.3390/microorganisms11061590 - 15 Jun 2023

Cited by 1 | Viewed by 2112

Abstract

Bourbon virus (BRBV, family Orthomyxoviridae) is a tickborne virus recently detected in the United States (US). BRBV was first identified from a fatal human case in 2014 in Bourbon County, Kansas. Enhanced surveillance in Kansas and Missouri implicated Amblyomma americanum as the [...] Read more.

Bourbon virus (BRBV, family Orthomyxoviridae) is a tickborne virus recently detected in the United States (US). BRBV was first identified from a fatal human case in 2014 in Bourbon County, Kansas. Enhanced surveillance in Kansas and Missouri implicated Amblyomma americanum as the primary vector for BRBV. Historically, BRBV was only detected in the lower midwestern US, but since 2020 it has been reported in North Carolina, Virginia, New Jersey, and New York State (NYS). This study aimed to elucidate genetic and phenotypic characteristics of BRBV strains from NYS through whole genome sequencing and the assessment of replication kinetics in mammalian cultures and A. americanum nymphs. Sequence analysis revealed the existence of two divergent BRBV clades circulating in NYS. BRBV NY21-2143 is closely related to the midwestern BRBV strains but has unique substitutions in the glycoprotein. Two other NYS BRBV strains, BRBV NY21-1814 and BRBV NY21-2666, form a distinct clade unique from previously sequenced BRBV strains. Phenotypic diversification was also detected in NYS BRBV strains compared to each other and midwestern BRBV strains, with BRBV NY21-2143 displaying attenuation in rodent-derived cell culture and a fitness advantage in experimentally infected A. americanum. These data suggest genetic and phenotypic diversification of emergent BRBV strains circulating in NYS that could contribute to increased spread of BRBV in the northeastern US. Full article

(This article belongs to the Special Issue Emerging Research on Tick-Borne Pathogens and Diseases)

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16 pages, 2614 KiB

Open AccessEditor’s ChoiceArticle

Propidium Monoazide (PMAxx)-Recombinase Polymerase Amplification Exo (RPA Exo) Assay for Rapid Detection of Burkholderia cepacia Complex in Chlorhexidine Gluconate (CHX) and Benzalkonium Chloride (BZK) Solutions

by Soumana Daddy Gaoh, Ohgew Kweon and Youngbeom Ahn

Microorganisms 2023, 11(6), 1401; https://doi.org/10.3390/microorganisms11061401 - 26 May 2023

Cited by 5 | Viewed by 1886

Abstract

Both sterile and non-sterile pharmaceutical products, which include antiseptics, have been recalled due to Burkholderia cepacia complex (BCC) contamination. Therefore, minimizing the frequency of outbreaks may be conducive to the development of a quick and sensitive approach that can distinguish between live and [...] Read more.

Both sterile and non-sterile pharmaceutical products, which include antiseptics, have been recalled due to Burkholderia cepacia complex (BCC) contamination. Therefore, minimizing the frequency of outbreaks may be conducive to the development of a quick and sensitive approach that can distinguish between live and dead loads of BCC. We have assessed an exo probe-based recombinase polymerase amplification (RPA) with 10 µM propidium monoazide (PMAxx) for selective detection of live/dead BCC cells in various concentrations of antiseptics (i.e., chlorhexidine gluconate (CHX) and benzalkonium chloride (BZK) solutions) after 24 h. The optimized assay conducted using a set of primer–probes targeting gbpT was performed at 40 °C for 20 min and shows a detection limit of 10 pg/µL of genomic DNA from B. cenocepacia J2315, equivalent to 10⁴ colony-forming units (CFU/mL). The specificity of a newly designed primer and probe was 80% (20 negatives out of 25). The readings for total cells (i.e., without PMAxx) from 200 µg/mL CHX using PMAxx-RPA exo assay was 310 relative fluorescence units (RFU), compared to 129 RFU with PMAxx (i.e., live cells). Furthermore, in 50–500 µg/mL BZK-treated cells, a difference in the detection rate was observed between the PMAxx-RPA exo assay in live cells (130.4–459.3 RFU) and total cells (207.82–684.5 RFU). This study shows that the PMAxx-RPA exo assay appears to be a valid tool for the simple, rapid and presumptive detection of live BCC cells in antiseptics, thereby ensuring the quality and safety of pharmaceutical products. Full article

(This article belongs to the Special Issue New Insights into Epidemiology, Detection and Characterization of Bacterial Pathogens 2.0)

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16 pages, 6862 KiB

Open AccessEditor’s ChoiceArticle

GAPDH Released from Lactobacillus johnsonii MG Enhances Barrier Function by Upregulating Genes Associated with Tight Junctions

by Mengying Lyu, Yuying Bai, Kanami Orihara, Kazuhiko Miyanaga and Naoyuki Yamamoto

Microorganisms 2023, 11(6), 1393; https://doi.org/10.3390/microorganisms11061393 - 25 May 2023

Cited by 6 | Viewed by 1747

Abstract

Extracellular glyceraldehyde-3-phosphate dehydrogenase (GAPDH) has multiple interactions with various gut epithelial components. For instance, GAPDH in Lactobacillus johnsonii MG cells interacts with junctional adhesion molecule-2 (JAM-2) in Caco-2 cells and enhances tight junctions. However, the specificity of GAPDH toward JAM-2 and its role [...] Read more.

Extracellular glyceraldehyde-3-phosphate dehydrogenase (GAPDH) has multiple interactions with various gut epithelial components. For instance, GAPDH in Lactobacillus johnsonii MG cells interacts with junctional adhesion molecule-2 (JAM-2) in Caco-2 cells and enhances tight junctions. However, the specificity of GAPDH toward JAM-2 and its role in the tight junctions in Caco-2 cells remain unclear. In the present study, we assessed the effect of GAPDH on tight junction regeneration and explored the GAPDH peptide fragments required for interaction with JAM-2. GAPDH was specifically bound to JAM-2 and rescued H₂O₂-damaged tight junctions in Caco-2 cells, with various genes being upregulated in the tight junctions. To understand the specific amino acid sequence of GAPDH that interacts with JAM-2, peptides interacting with JAM-2 and L. johnsonii MG cells were purified using HPLC and predicted using TOF–MS analysis. Two peptides, namely ¹¹GRIGRLAF¹⁸ at the N-terminus and ³²³SFTCQMVRTLLKFATL³³⁸ at the C-terminus, displayed good interactions and docking with JAM-2. In contrast, the long peptide ⁵²DSTHGTFNHEVSATDDSIVVDGKKYRVYAEPQAQNIPW⁸⁹ was predicted to bind to the bacterial cell surface. Overall, we revealed a novel role of GAPDH purified from L. johnsonii MG in promoting the regeneration of damaged tight junctions and identified the specific sequences of GAPDH involved in JAM-2 binding and MG cell interaction. Full article

(This article belongs to the Special Issue Screening and Functional Evaluation of Antiinflammatory Bacteria Strains)

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12 pages, 1810 KiB

Open AccessEditor’s ChoiceArticle

Candida albicans Adhesins Als1 and Hwp1 Modulate Interactions with Streptococcus mutans

by Loyse Martorano-Fernandes, James S. Goodwine, Antônio Pedro Ricomini-Filho, Clarissa J. Nobile and Altair Antoninha Del Bel Cury

Microorganisms 2023, 11(6), 1391; https://doi.org/10.3390/microorganisms11061391 - 25 May 2023

Cited by 5 | Viewed by 2094

Abstract

Candida albicans and Streptococcus mutans are known to synergistically interact with each other in the oral cavity. For example, glucosyltransferase B (GtfB), secreted by S. mutans, can bind to the C. albicans cell surface, promoting dual-species biofilm formation. However, the fungal factors [...] Read more.

Candida albicans and Streptococcus mutans are known to synergistically interact with each other in the oral cavity. For example, glucosyltransferase B (GtfB), secreted by S. mutans, can bind to the C. albicans cell surface, promoting dual-species biofilm formation. However, the fungal factors mediating interactions with S. mutans are unknown. The C. albicans adhesins Als1, Als3, and Hwp1 are key players in C. albicans single-species biofilm formation, but their roles, if any, in interacting with S. mutans have not been assessed. Here, we investigated the roles of the C. albicans cell wall adhesins Als1, Als3, and Hwp1 on forming dual-species biofilms with S. mutans. We assessed the abilities of the C. albicans wild-type als1Δ/Δ, als3Δ/Δ, als1Δ/Δ/als3Δ/Δ, and hwp1Δ/Δ strains to form dual-species biofilms with S. mutans by measuring optical density, metabolic activity, cell enumeration, biomass, thickness, and architecture of the biofilms. We observed that the C. albicans wild-type strain formed enhanced dual-species biofilms in the presence of S. mutans in these different biofilm assays, confirming that C. albicans and S. mutans synergistically interact in the context of biofilms. Our results reveal that C. albicans Als1 and Hwp1 are major players in interacting with S. mutans, since dual-species biofilm formation was not enhanced when the als1Δ/Δ or hwp1Δ/Δ strains were cultured with S. mutans in dual-species biofilms. Als3, however, does not seem to play a clear role in interacting with S. mutans in dual-species biofilm formation. Overall, our data suggest that the C. albicans adhesins Als1 and Hwp1 function to modulate interactions with S. mutans and could be potential targets for future therapeutics. Full article

(This article belongs to the Section Biofilm)

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15 pages, 1920 KiB

Open AccessEditor’s ChoiceArticle

Characterization of Bacterial Transcriptional Regulatory Networks in Escherichia coli through Genome-Wide In Vitro Run-Off Transcription/RNA-seq (ROSE)

by Pascal Schmidt, David Brandt, Tobias Busche and Jörn Kalinowski

Microorganisms 2023, 11(6), 1388; https://doi.org/10.3390/microorganisms11061388 - 25 May 2023

Cited by 3 | Viewed by 2057

Abstract

The global characterization of transcriptional regulatory networks almost exclusively uses in vivo conditions, thereby providing a snapshot on multiple regulatory interactions at the same time. To complement these approaches, we developed and applied a method for characterizing bacterial promoters genome-wide by in vitro [...] Read more.

The global characterization of transcriptional regulatory networks almost exclusively uses in vivo conditions, thereby providing a snapshot on multiple regulatory interactions at the same time. To complement these approaches, we developed and applied a method for characterizing bacterial promoters genome-wide by in vitro transcription coupled to transcriptome sequencing specific for native 5′-ends of transcripts. This method, called ROSE (run-off transcription/RNA-sequencing), only requires chromosomal DNA, ribonucleotides, RNA polymerase (RNAP) core enzyme, and a specific sigma factor, recognizing the corresponding promoters, which have to be analyzed. ROSE was performed on E. coli K-12 MG1655 genomic DNA using Escherichia coli RNAP holoenzyme (including σ70) and yielded 3226 transcription start sites, 2167 of which were also identified in in vivo studies, and 598 were new. Many new promoters not yet identified by in vivo experiments might be repressed under the tested conditions. Complementary in vivo experiments with E. coli K-12 strain BW25113 and isogenic transcription factor gene knockout mutants of fis, fur, and hns were used to test this hypothesis. Comparative transcriptome analysis demonstrated that ROSE could identify bona fide promoters that were apparently repressed in vivo. In this sense, ROSE is well-suited as a bottom-up approach for characterizing transcriptional networks in bacteria and ideally complementary to top-down in vivo transcriptome studies. Full article

(This article belongs to the Special Issue Advances in Bacterial Genetics)

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16 pages, 2142 KiB

Open AccessEditor’s ChoiceArticle

O-Polysaccharides of LPS Modulate E. coli Uptake by Acanthamoeba castellanii

by Ying Liu and Gerald Koudelka

Microorganisms 2023, 11(6), 1377; https://doi.org/10.3390/microorganisms11061377 - 24 May 2023

Cited by 3 | Viewed by 1991

Abstract

Protozoan grazing is a major cause of bacterial mortality and controls bacterial population size and composition in the natural environment. To enhance their survival, bacteria evolved many defense strategies to avoid grazing by protists. Cell wall modification is one of the defense strategies [...] Read more.

Protozoan grazing is a major cause of bacterial mortality and controls bacterial population size and composition in the natural environment. To enhance their survival, bacteria evolved many defense strategies to avoid grazing by protists. Cell wall modification is one of the defense strategies that helps bacteria escape from recognition and/or internalization by its predators. Lipopolysaccharide (LPS) is the major component of Gram-negative bacterial cell wall. LPS is divided into three regions: lipid A, oligosaccharide core and O-specific polysaccharide. O-polysaccharide as the outermost region of E. coli LPS provides protection against predation by Acanthamoeba castellanii; however, the characteristics of O-polysaccharide contribute to this protection remain unknown. Here, we investigate how length, structure and composition of LPS affect E. coli recognition and internalization by A. castellanii. We found that length of O-antigen does not play a significant role in regulating bacterial recognition by A. castellanii. However, the composition and structure of O-polysaccharide play important roles in providing resistance to A. castellanii predation. Full article

(This article belongs to the Special Issue Bacterial Cell Wall)

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17 pages, 4523 KiB

Open AccessEditor’s ChoiceArticle

Klebsiella aerogenes Adhesion Behaviour during Biofilm Formation on Monazite

by Arya Van Alin, Melissa K. Corbett, Homayoun Fathollahzadeh, M. Christian Tjiam, Andrew Putnis, Jacques Eksteen, Anna H. Kaksonen and Elizabeth Watkin

Microorganisms 2023, 11(5), 1331; https://doi.org/10.3390/microorganisms11051331 - 18 May 2023

Cited by 2 | Viewed by 1667

Abstract

The adsorption behaviour of micro-organisms during the initial attachment stage of biofilm formation affects subsequent stages. The available area for attachment and the chemophysical properties of a surface affect microbial attachment performance. This study focused on the initial attachment behaviour of Klebsiella aerogenes [...] Read more.

The adsorption behaviour of micro-organisms during the initial attachment stage of biofilm formation affects subsequent stages. The available area for attachment and the chemophysical properties of a surface affect microbial attachment performance. This study focused on the initial attachment behaviour of Klebsiella aerogenes on monazite by measuring the ratio of planktonic against sessile subpopulations (P:S ratio), and the potential role of extracellular DNA (eDNA). eDNA production, effects of physicochemical properties of the surface, particle size, total available area for attachment, and the initial inoculation size on the attachment behaviour were tested. K. aerogenes attached to monazite immediately after exposure to the ore; however, the P:S ratio significantly (p = 0.05) changed in response to the particle size, available area, and inoculation size. Attachment occurred preferentially on larger-sized (~50 µm) particles, and either decreasing the inoculation size or increasing the available area further promoted attachment. Nevertheless, a portion of the inoculated cells always remained in a planktonic state. K. aerogenes produced lower eDNA in response to the changed surface chemical properties when monazite was replaced by xenotime. Using pure eDNA to cover the monazite surface significantly (p ≤ 0.05) hindered bacterial attachment due to the repulsive interaction between the eDNA layer and bacteria. Full article

(This article belongs to the Special Issue Feature Papers in Microbial Biofilms)

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11 pages, 1031 KiB

Open AccessEditor’s ChoiceArticle

16S-23S rRNA Internal Transcribed Spacer Region (ITS) Sequencing: A Potential Molecular Diagnostic Tool for Differentiating Lactococcus garvieae and Lactococcus petauri

by Nadia Stoppani, Silvia Colussi, Paolo Pastorino, Marino Prearo, Simona Sciuto, Ilhan Altinok, Rafet Çağrı Öztürk, Mustafa Ture, Ana Isabel Vela, Maria del Mar Blanco, Charalampos Kotzamanidis, Konstantina Bitchava, Andigoni Malousi, Lucio Fariano, Donatella Volpatti, Pier Luigi Acutis and Jose Francisco Fernández-Garayzábal

Microorganisms 2023, 11(5), 1320; https://doi.org/10.3390/microorganisms11051320 - 17 May 2023

Cited by 13 | Viewed by 2695

Abstract

Lactococcus garvieae is the etiological agent of lactococcosis, a clinically and economically significant infectious disease affecting farmed rainbow trout. L. garvieae had been considered the only cause of lactococcosis for a long time; however, L. petauri, another species of the genus Lactococcus [...] Read more.

Lactococcus garvieae is the etiological agent of lactococcosis, a clinically and economically significant infectious disease affecting farmed rainbow trout. L. garvieae had been considered the only cause of lactococcosis for a long time; however, L. petauri, another species of the genus Lactococcus, has lately been linked to the same disease. The genomes and biochemical profiles of L. petauri and L. garvieae have a high degree of similarity. Traditional diagnostic tests currently available cannot distinguish between these two species. The aim of this study was to use the transcribed spacer (ITS) region between 16S rRNA and 23S rRNA as a potential useful molecular target to differentiate L. garvieae from L. petauri, saving time and money compared to genomics methods currently used as diagnostic tools for accurate discrimination between these two species. The ITS region of 82 strains was amplified and sequenced. The amplified fragments varied in size from 500 to 550 bp. Based on the sequence, seven SNPs were identified that separate L. garvieae from L. petauri. The 16S-23S rRNA ITS region has enough resolution to distinguish between closely related L. garvieae and L. petauri and it can be used as a diagnostic marker to quickly identify the pathogens in a lactococcosis outbreak. Full article

(This article belongs to the Special Issue Bacterial Infections in Aquaculture of Farmed Fish: Pathogenesis, Pathophysiology, Molecular Diagnosis, and Control)

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12 pages, 1398 KiB

Open AccessEditor’s ChoiceArticle

Seroconversion of a Swine Herd in a Free-Range Rural Multi-Species Farm against HPAI H5N1 2.3.4.4b Clade Virus

by Francesca Rosone, Francesco Bonfante, Marcello Giovanni Sala, Silvia Maniero, Antonella Cersini, Ida Ricci, Luisa Garofalo, Daniela Caciolo, Antonella Denisi, Alessandra Napolitan, Monja Parente, Bianca Zecchin, Calogero Terregino and Maria Teresa Scicluna

Microorganisms 2023, 11(5), 1162; https://doi.org/10.3390/microorganisms11051162 - 28 Apr 2023

Cited by 17 | Viewed by 3663

Abstract

Starting from October 2021, several outbreaks of highly pathogenic avian influenza virus (HPAIV) subtype H5N1 were reported in wild and domestic birds in Italy. Following the detection of an HPAIV in a free-ranging poultry farm in Ostia, province of Rome, despite the lack [...] Read more.

Starting from October 2021, several outbreaks of highly pathogenic avian influenza virus (HPAIV) subtype H5N1 were reported in wild and domestic birds in Italy. Following the detection of an HPAIV in a free-ranging poultry farm in Ostia, province of Rome, despite the lack of clinical signs, additional virological and serological analyses were conducted on samples collected from free-ranging pigs, reared in the same holding, due to their direct contact with the infected poultry. While the swine nasal swabs were all RT-PCR negative for the influenza type A matrix (M) gene, the majority (%) of the tested pigs resulted serologically positive for the hemagglutination inhibition test and microneutralization assay, using an H5N1 strain considered to be homologous to the virus detected in the farm. These results provide further evidence of the worrisome replicative fitness that HPAI H5Nx viruses of the 2.3.4.4b clade have in mammalian species. Moreover, our report calls for additional active surveillance, to promptly intercept occasional spillover transmissions to domestic mammals in close contact with HPAI affected birds. Strengthened biosecurity measures and efficient separation should be prioritized in mixed-species farms in areas at risk of HPAI introduction. Full article

(This article belongs to the Special Issue Ecology of Influenza A Viruses: 2nd Edition)

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11 pages, 1602 KiB

Open AccessEditor’s ChoiceArticle

Prevalence and Antibiotic Resistance of Bacillus sp. Isolated from Raw Milk

by Patryk Adamski, Zuzanna Byczkowska-Rostkowska, Joanna Gajewska, Arkadiusz Józef Zakrzewski and Lucyna Kłębukowska

Microorganisms 2023, 11(4), 1065; https://doi.org/10.3390/microorganisms11041065 - 19 Apr 2023

Cited by 22 | Viewed by 6623

Abstract

Milk, due to its diversity in terms of its nutritional content, is an important element of the human diet, as well as a good medium for the development of bacteria. The genus Bacillus contains ubiquitous aerobic, rod-shaped, endospore-producing gram-positive bacteria. Representatives of the [...] Read more.

Milk, due to its diversity in terms of its nutritional content, is an important element of the human diet, as well as a good medium for the development of bacteria. The genus Bacillus contains ubiquitous aerobic, rod-shaped, endospore-producing gram-positive bacteria. Representatives of the Bacillus cereus group and the Bacillus subtilis group contribute to shortening the shelf life of milk and dairy products by degrading milk components and its additives. They also produce a number of heat-stable toxins and can cause a number of ailments, mainly in the digestive system. The aim of this research was to identify Bacillus sp. strains isolated from raw milk and to determine their antibiotic resistance. Strains isolated from raw milk samples (n = 45) were identified by MALDI-TOF MS. Ninety strains of Bacillus sp. were identified, for which the antibiotic resistance phenotype was determined. A total of 90 strains of Bacillus were classified in five groups (the Bacillus cereus group (n = 35), B. licheniformis (n = 7), the B. subtilis group (n = 29), B. pumilus (n = 16), and Bacillus sp. (n = 3). All isolates were susceptible to chloramphenicol and meropenem. The antibiotic resistance profiles of the tested groups of Bacillus spp. differed from each other, which is of particular concern in relation to multidrug-resistant representatives of the B. cereus group resistant to cefotaxime (94.29%), ampicillin (88.57%), rifampicin (80%), and norfloxacin (65.71%). Our study provides data on the prevalence and antibiotic sensitivity of Bacillus sp. In raw milk, suggesting a potential risk to health and the dairy industry. Full article

(This article belongs to the Special Issue Antibiotic Resistance and Virulence Factors of Bacteria Isolated from Food)

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15 pages, 1126 KiB

Open AccessEditor’s ChoiceArticle

Maternal Psychosocial Stress Is Associated with Reduced Diversity in the Early Infant Gut Microbiome

by Christopher L. Dutton, Felicien Masanga Maisha, Edward B. Quinn, Katherine Liceth Morales, Julie M. Moore and Connie J. Mulligan

Microorganisms 2023, 11(4), 975; https://doi.org/10.3390/microorganisms11040975 - 8 Apr 2023

Cited by 6 | Viewed by 3915

Abstract

The developing infant gut microbiome is highly sensitive to environmental exposures, enabling its evolution into an organ that supports the immune system, confers protection from infection, and facilitates optimal gut and central nervous system function. In this study, we focus on the impact [...] Read more.

The developing infant gut microbiome is highly sensitive to environmental exposures, enabling its evolution into an organ that supports the immune system, confers protection from infection, and facilitates optimal gut and central nervous system function. In this study, we focus on the impact of maternal psychosocial stress on the infant gut microbiome. Forty-seven mother–infant dyads were recruited at the HEAL Africa Hospital in Goma, Democratic Republic of Congo. Extensive medical, demographic, and psychosocial stress data were collected at birth, and infant stool samples were collected at six weeks, three months, and six months. A composite maternal psychosocial stress score was created, based on eight questionnaires to capture a diverse range of stress exposures. Full-length 16S rRNA gene sequences were generated. Infants of mothers with high composite stress scores showed lower levels of gut microbiome beta diversity at six weeks and three months, as well as higher levels of alpha diversity at six months compared to infants of low stress mothers. Longitudinal analyses showed that infants of high stress mothers had lower levels of health-promoting Lactobacillus gasseri and Bifidobacterium pseudocatenulatum at six weeks compared to infants of low stress mothers, but the differences largely disappeared by three to six months. Previous research has shown that L. gasseri can be used as a probiotic to reduce inflammation, stress, and fatigue, as well as to improve mental state, while B. pseudocatenulatum is important in modulating the gut–brain axis in early development and in preventing mood disorders. Our finding of reduced levels of these health-promoting bacteria in infants of high stress mothers suggests that the infant gut microbiome may help mediate the effect of maternal stress on infant health and development. Full article

(This article belongs to the Special Issue Gut Microbiota and Host Diseases)

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16 pages, 2785 KiB

Open AccessEditor’s ChoiceArticle

Protective Effect of Novel Lactobacillus plantarum KC3 Isolated from Fermented Kimchi on Gut and Respiratory Disorders

by Min-Seon Park, Yu-Jeong Kim, Han-Jae Shin, Yoo Jin Kwon, Jaeryang Chu, Inock Lee, Kyung Hwan Kim, Byoung Kook Kim, Seung-Hyung Kim, Hwi Won Seo and Tae-Won Kim

Microorganisms 2023, 11(4), 967; https://doi.org/10.3390/microorganisms11040967 - 7 Apr 2023

Cited by 6 | Viewed by 2823

Abstract

Probiotics have been shown to possess anti-inflammatory effects in the gut by directly reducing the production of pro-inflammatory cytokines and by secreting anti-inflammatory molecules. However, their systemic anti-inflammatory effects have not been thoroughly investigated. In this study, we aimed to develop probiotics that [...] Read more.

Probiotics have been shown to possess anti-inflammatory effects in the gut by directly reducing the production of pro-inflammatory cytokines and by secreting anti-inflammatory molecules. However, their systemic anti-inflammatory effects have not been thoroughly investigated. In this study, we aimed to develop probiotics that have efficacy in both intestinal and lung inflammation. Lactobacillus plantarum KC3 (KC3), which was isolated from kimchi, was selected as a pre-candidate based on its inhibitory effects on the production of pro-inflammatory cytokines in vitro. To further validate the effectiveness of KC3, we used ear edema, DSS-induced colitis, and ambient particulate-matter-induced lung inflammation models. First, KC3 exhibited direct anti-inflammatory effects on intestinal cells with the inhibition of IL-1β and TNF-α production. Additionally, KC3 treatment alleviated ear edema and DSS-induced colic inflammation, improving colon length and increasing the number of regulatory T cells. Beyond its local intestinal anti-inflammatory activity, KC3 inhibited pro-inflammatory cytokines in the bronchoalveolar fluid and prevented neutrophil infiltration in the lungs. These results suggest that KC3 could be a potential functional ingredient with respiratory protective effects against air-pollutant-derived inflammation, as well as for the treatment of local gut disorders. Full article

(This article belongs to the Special Issue Research on Decreasing the Intestinal Carriage of Antibiotic Resistant Bacteria)

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19 pages, 2548 KiB

Open AccessEditor’s ChoiceArticle

Gut Dysbiosis: A Target for Protective Interventions against Parkinson’s Disease

by Illyane S. Lima, Ana C. Pêgo, Ana C. Martins, Ana R. Prada, João Tomás Barros, Gracelino Martins and Raffaella Gozzelino

Microorganisms 2023, 11(4), 880; https://doi.org/10.3390/microorganisms11040880 - 29 Mar 2023

Cited by 7 | Viewed by 2857

Abstract

Sub-chronic inflammation, caused by age-related dysbiosis, primes the brain to neuroinflammation and neurodegenerative diseases. Evidence revealed that Parkinson’s disease (PD) might originate in the gut, demonstrating gastro-intestinal disturbances, as reported by PD patients long before developing motor symptoms. In this study, we conducted [...] Read more.

Sub-chronic inflammation, caused by age-related dysbiosis, primes the brain to neuroinflammation and neurodegenerative diseases. Evidence revealed that Parkinson’s disease (PD) might originate in the gut, demonstrating gastro-intestinal disturbances, as reported by PD patients long before developing motor symptoms. In this study, we conducted comparative analyses in relatively young and old mice maintained in conventional or gnotobiotic conditions. We aimed to confirm that the effects induced by age-related dysbiosis, rather than aging itself, sensitize to PD onset. This hypothesis was confirmed in germ-free (GF) mice, which proved resistant to the pharmacological induction of PD, regardless of their age. Contrary to conventional animals, old GF mice did not develop an inflammatory phenotype or an accumulation of iron in the brain, two catalysts sensitizing to disease onset. The resistance of GF mice to PD is reverted when colonized with stool collected from conventional old animals, but not if receiving bacterial content from young mice. Hence, changes in gut microbiota composition are a risk factor for PD development and can be targeted preventively by iron chelators, shown to protect the brain from pro-inflammatory intestinal priming that sensitizes to neuroinflammation and the development of severe PD. Full article

(This article belongs to the Special Issue Lifestyle, Gut Microbiota and Health)

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16 pages, 14269 KiB

Open AccessEditor’s ChoiceArticle

Predatory Strategies of Myxococcus xanthus: Prey Susceptibility to OMVs and Moonlighting Enzymes

by Allison S. Zwarycz, Thomas Page, Gabriela Nikolova, Emily J. Radford and David E. Whitworth

Microorganisms 2023, 11(4), 874; https://doi.org/10.3390/microorganisms11040874 - 29 Mar 2023

Cited by 7 | Viewed by 2265

Abstract

Predatory outer membrane vesicles (OMVs) secreted by myxobacteria fuse readily with the outer membranes of Gram-negative bacteria, introducing toxic cargo into their prey. Here we used a strain of the myxobacterium Myxococcus xanthus that produces fluorescent OMVs to assay the uptake of OMVs [...] Read more.

Predatory outer membrane vesicles (OMVs) secreted by myxobacteria fuse readily with the outer membranes of Gram-negative bacteria, introducing toxic cargo into their prey. Here we used a strain of the myxobacterium Myxococcus xanthus that produces fluorescent OMVs to assay the uptake of OMVs by a panel of Gram-negative bacteria. M. xanthus strains took up significantly less OMV material than the tested prey strains, suggesting that re-fusion of OMVs with producing organisms is somehow inhibited. The OMV killing activity against different prey correlated strongly with the predatory activity of myxobacterial cells, however, there was no correlation between OMV killing activity and their propensity to fuse with different prey. It has previously been proposed that M. xanthus GAPDH stimulates the predatory activity of OMVs by enhancing OMV fusion with prey cells. Therefore, we expressed and purified active fusion proteins of M. xanthus glyceraldehyde-3-phosphate dehydrogenase and phosphoglycerate kinase (GAPDH and PGK; moonlighting enzymes with additional activities beyond their roles in glycolysis/gluconeogenesis) to investigate any involvement in OMV-mediated predation. Neither GAPDH nor PGK caused lysis of prey cells or enhanced OMV-mediated lysis of prey cells. However, both enzymes were found to inhibit the growth of Escherichia coli, even in the absence of OMVs. Our results suggest that fusion efficiency is not a determinant of prey killing, but instead resistance to the cargo of OMVs and co-secreted enzymes dictates whether organisms can be preyed upon by myxobacteria. Full article

(This article belongs to the Section Molecular Microbiology and Immunology)

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19 pages, 2571 KiB

Open AccessEditor’s ChoiceArticle

Alteration of Community Metabolism by Prebiotics and Medicinal Herbs

by Christine Tara Peterson, Josué Pérez-Santiago, Stanislav N. Iablokov, Dmitry A. Rodionov and Scott N. Peterson

Microorganisms 2023, 11(4), 868; https://doi.org/10.3390/microorganisms11040868 - 28 Mar 2023

Cited by 3 | Viewed by 2489

Abstract

Several studies have examined the impact of prebiotics on gut microbiota and associated changes in host physiology. Here, we used the in vitro cultivation of human fecal samples stimulated with a series of chemically related prebiotics and medicinal herbs commonly used in Ayurvedic [...] Read more.

Several studies have examined the impact of prebiotics on gut microbiota and associated changes in host physiology. Here, we used the in vitro cultivation of human fecal samples stimulated with a series of chemically related prebiotics and medicinal herbs commonly used in Ayurvedic medicine, followed by 16S rRNA sequencing. We applied a genome-wide metabolic reconstruction of enumerated communities to compare and contrast the structural and functional impact of prebiotics and medicinal herbs. In doings so, we examined the relationships between discrete variations in sugar composition and sugar linkages associated with each prebiotic to drive changes in microbiota composition. The restructuring of microbial communities with glycan substrates alters community metabolism and its potential impact on host physiology. We analyzed sugar fermentation pathways and products predicted to be formed and prebiotic-induced changes in vitamin and amino acid biosynthesis and degradation. These results highlight the utility of combining a genome-wide metabolic reconstruction methodology with 16S rRNA sequence-based community profiles to provide insights pertaining to community metabolism. This process also provides a rational means for prioritizing in vivo analysis of prebiotics and medicinal herbs in vivo to test hypotheses related to therapeutic potential in specific diseases of interest. Full article

(This article belongs to the Special Issue Gut Microbiota and Host Diseases)

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16 pages, 3230 KiB

Open AccessEditor’s ChoiceArticle

The Impact of Early Life Experiences and Gut Microbiota on Neurobehavioral Development in Preterm Infants: A Longitudinal Cohort Study

by Jie Chen, Hongfei Li, Tingting Zhao, Kun Chen, Ming-Hui Chen, Zhe Sun, Wanli Xu, Kendra Maas, Barry M. Lester and Xiaomei S. Cong

Microorganisms 2023, 11(3), 814; https://doi.org/10.3390/microorganisms11030814 - 22 Mar 2023

Cited by 6 | Viewed by 2601

Abstract

Objectives: The objective of this study is to investigate the impact of early life experiences and gut microbiota on neurobehavioral development in preterm infants during neonatal intensive care unit (NICU) hospitalization. Methods: Preterm infants were followed from NICU admission until their 28th postnatal [...] Read more.

Objectives: The objective of this study is to investigate the impact of early life experiences and gut microbiota on neurobehavioral development in preterm infants during neonatal intensive care unit (NICU) hospitalization. Methods: Preterm infants were followed from NICU admission until their 28th postnatal day or until discharge. Daily stool samples, painful/stressful experiences, feeding patterns, and other clinical and demographic data were collected. Gut microbiota was profiled using 16S rRNA sequencing, and operational taxonomic units (OTUs) were selected to predict the neurobehaviors. The neurobehavioral development was assessed by the Neonatal Neurobehavioral Scale (NNNS) at 36 to 38 weeks of post-menstrual age (PMA). Fifty-five infants who had NNNS measurements were included in the sparse log-contrast regression analysis. Results: Preterm infants who experienced a high level of pain/stress during the NICU hospitalization had higher NNNS stress/abstinence scores. Eight operational taxonomic units (OTUs) were identified to be associated with NNNS subscales after controlling demographic and clinical features, feeding patterns, and painful/stressful experiences. These OTUs and taxa belonging to seven genera, i.e., Enterobacteriaceae_unclassified, Escherichia-Shigella, Incertae_Sedis, Veillonella, Enterococcus, Clostridium_sensu_stricto_1, and Streptococcus with five belonging to Firmicutes and two belonging to Proteobacteria phylum. The enriched abundance of Enterobacteriaceae_unclassified (OTU17) and Streptococcus (OTU28) were consistently associated with less optimal neurobehavioral outcomes. The other six OTUs were also associated with infant neurobehavioral responses depending on days at NICU stay. Conclusions: This study explored the dynamic impact of specific OTUs on neurobehavioral development in preterm infants after controlling for early life experiences, i.e., acute and chronic pain/stress and feeding in the NICU. The gut microbiota and acute pain/stressful experiences dynamically impact the neurobehavioral development in preterm infants during their NICU hospitalization. Full article

(This article belongs to the Section Gut Microbiota)

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22 pages, 3800 KiB

Open AccessEditor’s ChoiceArticle

Comparative Genomic Analysis of Virulent Vibrio (Listonella) anguillarum Serotypes Revealed Genetic Diversity and Genomic Signatures in the O-Antigen Biosynthesis Gene Cluster

by Vimbai Irene Machimbirike, Ignacio Vasquez, Trung Cao, Joy Chukwu-Osazuwa, Oluwatoyin Onireti, Cristopher Segovia, Pongsak Khunrae, Triwit Rattanarojpong, Marije Booman, Simon Jones, Manuel Soto-Davila, Brian Dixon and Javier Santander

Microorganisms 2023, 11(3), 792; https://doi.org/10.3390/microorganisms11030792 - 20 Mar 2023

Cited by 5 | Viewed by 2875

Abstract

Vibrio anguillarum is the most frequent pathogen affecting fish worldwide. The only known virulent strains of V. anguillarum are serotypes O1, O2, and O3. Genetic differences between the serotypes that could shed insight on the evolution and serotype differences of this marine pathogen [...] Read more.

Vibrio anguillarum is the most frequent pathogen affecting fish worldwide. The only known virulent strains of V. anguillarum are serotypes O1, O2, and O3. Genetic differences between the serotypes that could shed insight on the evolution and serotype differences of this marine pathogen are unknown. Here, we fully sequenced and characterized a strain of V. anguillarum O1 (J382) isolated from winter steelhead trout (Oncorhynchus mykiss irideus) in British Columbia, Canada. Koch’s postulates using the O1 strain were replicated in naïve lumpfish (Cyclopterus lumpus) and compared to O2. Phenotypic and genotypic comparisons were conducted for serotypes O1, O2, and O3, using biochemical tests and bioinformatic tools, respectively. The genome of V. anguillarum O1 (J382) contains two chromosomes (3.13 Mb and 1.03 Mb) and two typical pJM1-like plasmids (65,573 and 76,959 bp). Furthermore, V. anguillarum O1 (J382) displayed resistance to colistin sulphate, which differs from serotype O2 and could be attributed to the presence of the ugd gene. Comparative genomic analysis, among the serotypes, showed that intra-species evolution is driven by insertion sequences, bacteriophages, and a different repertoire of putative ncRNAs. Genetic heterogeneity in the O-antigen biosynthesis gene cluster is characterized by the absence or the presence of unique genes, which could result in differences in the immune evasion mechanisms employed by the respective serotypes. This study contributes to understanding the genetic differences among V. anguillarum serovars and their evolution. Full article

(This article belongs to the Special Issue Microorganisms and Diseases Associated with Aquatic Animals)

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15 pages, 5622 KiB

Open AccessEditor’s ChoiceArticle

Isolation and Characterisation of Electrogenic Bacteria from Mud Samples

by György Schneider, Dorina Pásztor, Péter Szabó, László Kőrösi, Nandyala Siva Kishan, Penmetsa Appala Rama Krishna Raju and Rajnish Kaur Calay

Microorganisms 2023, 11(3), 781; https://doi.org/10.3390/microorganisms11030781 - 17 Mar 2023

Cited by 3 | Viewed by 3654

Abstract

To develop efficient microbial fuel cell systems for green energy production using different waste products, establishing characterised bacterial consortia is necessary. In this study, bacteria with electrogenic potentials were isolated from mud samples and examined to determine biofilm-formation capacities and macromolecule degradation. Matrix-assisted [...] Read more.

To develop efficient microbial fuel cell systems for green energy production using different waste products, establishing characterised bacterial consortia is necessary. In this study, bacteria with electrogenic potentials were isolated from mud samples and examined to determine biofilm-formation capacities and macromolecule degradation. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry identifications have revealed that isolates represented 18 known and 4 unknown genuses. They all had the capacities to reduce the Reactive Black 5 stain in the agar medium, and 48 of them were positive in the wolfram nanorod reduction assay. The isolates formed biofilm to different extents on the surfaces of both adhesive and non-adhesive 96-well polystyrene plates and glass. Scanning electron microscopy images revealed the different adhesion potentials of isolates to the surface of carbon tissue fibres. Eight of them (15%) were able to form massive amounts of biofilm in three days at 23 °C. A total of 70% of the isolates produced proteases, while lipase and amylase production was lower, at 38% and 27% respectively. All of the macromolecule-degrading enzymes were produced by 11 isolates, and two isolates of them had the capacity to form a strong biofilm on the carbon tissue one of the most used anodic materials in MFC systems. This study discusses the potential of the isolates for future MFC development applications. Full article

(This article belongs to the Special Issue New Electrogenic Microbes)

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15 pages, 841 KiB

Open AccessEditor’s ChoiceArticle

High-Resolution Taxonomic Characterization Reveals Novel Human Microbial Strains with Potential as Risk Factors and Probiotics for Prediabetes and Type 2 Diabetes

by Sarah A. Hendricks, Chantal A. Vella, Daniel D. New, Afiya Aunjum, Maximilian Antush, Rayme Geidl, Kimberly R. Andrews and Onesmo B. Balemba

Microorganisms 2023, 11(3), 758; https://doi.org/10.3390/microorganisms11030758 - 15 Mar 2023

Cited by 5 | Viewed by 2485

Abstract

Alterations in the composition of the gut microbiota is thought to play a key role in causing type 2 diabetes, yet is not fully understood, especially at the strain level. Here, we used long-read DNA sequencing technology of 16S-ITS-23S rRNA genes for high-resolution [...] Read more.

Alterations in the composition of the gut microbiota is thought to play a key role in causing type 2 diabetes, yet is not fully understood, especially at the strain level. Here, we used long-read DNA sequencing technology of 16S-ITS-23S rRNA genes for high-resolution characterization of gut microbiota in the development of type 2 diabetes. Gut microbiota composition was characterized from fecal DNA from 47 participants divided into 4 cohorts based on glycemic control: normal glycemic control (healthy; n = 21), reversed prediabetes (prediabetes/healthy; n = 8), prediabetes (n = 8), or type 2 diabetes (n = 10). A total of 46 taxa were found to be possibly related to progression from healthy state to type 2 diabetes. Bacteroides coprophilus DSM 18228, Bifidobacterium pseudocatenulatum DSM 20438, and Bifidobacterium adolescentis ATCC 15703 could confer resistance to glucose intolerance. On the other hand, Odoribacter laneus YIT 12061 may be pathogenic as it was found to be more abundant in type 2 diabetes participants than other cohorts. This research increases our understanding of the structural modulation of gut microbiota in the pathogenesis of type 2 diabetes and highlights gut microbiota strains, with the potential for targeted opportunistic pathogen control or consideration for probiotic prophylaxis and treatment. Full article

(This article belongs to the Special Issue Gut Microbiota in Disease)

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16 pages, 2308 KiB

Open AccessEditor’s ChoiceArticle

New Insights into the Physiology of the Propionate Producers Anaerotignum propionicum and Anaerotignum neopropionicum (Formerly Clostridium propionicum and Clostridium neopropionicum)

by Tina Baur and Peter Dürre

Microorganisms 2023, 11(3), 685; https://doi.org/10.3390/microorganisms11030685 - 7 Mar 2023

Cited by 3 | Viewed by 2693

Abstract

Propionate is an important platform chemical that is available through petrochemical synthesis. Bacterial propionate formation is considered an alternative, as bacteria can convert waste substrates into valuable products. In this regard, research primarily focused on propionibacteria due to high propionate titers achieved from [...] Read more.

Propionate is an important platform chemical that is available through petrochemical synthesis. Bacterial propionate formation is considered an alternative, as bacteria can convert waste substrates into valuable products. In this regard, research primarily focused on propionibacteria due to high propionate titers achieved from different substrates. Whether other bacteria could also be attractive producers is unclear, mostly because little is known about these strains. Therefore, two thus far less researched strains, Anaerotignum propionicum and Anaerotignum neopropionicum, were investigated with regard to their morphologic and metabolic features. Microscopic analyses revealed a negative Gram reaction despite a Gram-positive cell wall as well as surface layers for both strains. Furthermore, growth, product profiles, and the potential for propionate formation from sustainable substrates, i.e., ethanol or lignocellulosic sugars, were assessed. Results showed that both strains can oxidize ethanol to different extents. While A. propionicum only partially used ethanol, A. neopropionicum converted 28.3 mM ethanol to 16.4 mM propionate. Additionally, the ability of A. neopropionicum to produce propionate from lignocellulose-derived substrates was analyzed, leading to propionate concentrations of up to 14.5 mM. Overall, this work provides new insights into the physiology of the Anaerotignum strains, which can be used to develop effective propionate producer strains. Full article

(This article belongs to the Special Issue Physiology, Genetic and Industrial Applications of Clostridia)

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12 pages, 4470 KiB

Open AccessEditor’s ChoiceArticle

Nanoparticle Coatings on Glass Surfaces to Prevent Pseudomonas fluorescens AR 11 Biofilm Formation

by Daniele Marra, Irene Perna, Giulio Pota, Giuseppe Vitiello, Alessandro Pezzella, Giuseppe Toscano, Giuseppina Luciani and Sergio Caserta

Microorganisms 2023, 11(3), 621; https://doi.org/10.3390/microorganisms11030621 - 28 Feb 2023

Cited by 6 | Viewed by 2074

Abstract

Microbial colonization of surfaces is a sanitary and industrial issue for many applications, leading to product contamination and human infections. When microorganisms closely interact with a surface, they start to produce an exo-polysaccaridic matrix to adhere to and protect themselves from adverse environmental [...] Read more.

Microbial colonization of surfaces is a sanitary and industrial issue for many applications, leading to product contamination and human infections. When microorganisms closely interact with a surface, they start to produce an exo-polysaccaridic matrix to adhere to and protect themselves from adverse environmental conditions. This type of structure is called a biofilm. The aim of our work is to investigate novel technologies able to prevent biofilm formation by surface coatings. We coated glass surfaces with melanin-ZnO₂, melanin-TiO₂, and TiO₂ hybrid nanoparticles. The functionalization was performed using cold plasma to activate glass-substrate-coated surfaces, that were characterized by performing water and soybean oil wetting tests. A quantitative characterization of the antibiofilm properties was done using Pseudomonas fluorescens AR 11 as a model organism. Biofilm morphologies were observed using confocal laser scanning microscopy and image analysis techniques were used to obtain quantitative morphological parameters. The results highlight the efficacy of the proposed surface coating to prevent biofilm formation. Melanin-TiO₂ proved to be the most efficient among the particles investigated. Our results can be a valuable support for future implementation of the technique proposed here in an extended range of applications that may include further testing on other strains and other support materials. Full article

(This article belongs to the Special Issue Feature Papers in Microbial Biofilm Formation)

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10 pages, 960 KiB

Open AccessEditor’s ChoiceArticle

An Evaluation of Avian Influenza Virus Whole-Genome Sequencing Approaches Using Nanopore Technology

by Hon S. Ip, Sarah Uhm, Mary Lea Killian and Mia K. Torchetti

Microorganisms 2023, 11(2), 529; https://doi.org/10.3390/microorganisms11020529 - 19 Feb 2023

Cited by 6 | Viewed by 4611

Abstract

As exemplified by the global response to the SARS-CoV-2 pandemic, whole-genome sequencing played an important role in monitoring the evolution of novel viral variants and provided guidance on potential antiviral treatments. The recent rapid and extensive introduction and spread of highly pathogenic avian [...] Read more.

As exemplified by the global response to the SARS-CoV-2 pandemic, whole-genome sequencing played an important role in monitoring the evolution of novel viral variants and provided guidance on potential antiviral treatments. The recent rapid and extensive introduction and spread of highly pathogenic avian influenza virus in Europe, North America, and elsewhere raises the need for similarly rapid sequencing to aid in appropriate response and mitigation activities. To facilitate this objective, we investigate a next-generation sequencing platform that uses a portable nanopore sequencing device to generate and present data in real time. This platform offers the potential to extend in-house sequencing capacities to laboratories that may otherwise lack resources to adopt sequencing technologies requiring large benchtop instruments. We evaluate this platform for routine use in a diagnostic laboratory. In this study, we evaluate different primer sets for the whole genome amplification of influenza A virus and evaluate five different library preparation approaches for sequencing on the nanopore platform using the MinION flow cell. A limited amplification procedure and a rapid procedure are found to be best among the approaches taken. Full article

(This article belongs to the Special Issue Viral Metagenomic Analysis in Animals)

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14 pages, 1750 KiB

Open AccessEditor’s ChoiceArticle

Systematic Survey of Vibrio spp. and Salmonella spp. in Bivalve Shellfish in Apulia Region (Italy): Prevalence and Antimicrobial Resistance

by Maria Emanuela Mancini, Alessandra Alessiani, Adelia Donatiello, Antonella Didonna, Luigi D’Attoli, Simona Faleo, Gilda Occhiochiuso, Francesco Carella, Pietro Di Taranto, Lorenzo Pace, Valeria Rondinone, Annita Maria Damato, Rosa Coppola, Carmine Pedarra and Elisa Goffredo

Microorganisms 2023, 11(2), 450; https://doi.org/10.3390/microorganisms11020450 - 10 Feb 2023

Cited by 11 | Viewed by 2809

Abstract

The emergence of antimicrobial resistance (AMR) is increasingly common across the globe and aquatic ecosystems could be considered a reservoir of antibiotic-resistant bacteria. This study aimed to determine prevalence and antibiotic susceptibility of the potential pathogenic bacteria Salmonella spp. and Vibrio spp. in [...] Read more.

The emergence of antimicrobial resistance (AMR) is increasingly common across the globe and aquatic ecosystems could be considered a reservoir of antibiotic-resistant bacteria. This study aimed to determine prevalence and antibiotic susceptibility of the potential pathogenic bacteria Salmonella spp. and Vibrio spp. in bivalve molluscs intended for human consumption, collected over a period of 19 months along the northern coast of Apulia region. The AMR profile was also determined in non-pathogenic Vibrio species, common natural inhabitants of seawater and a useful indicator for the surveillance of AMR in the environment. The current study presents data on the AMR of 5 Salmonella and 126 Vibrio isolates by broth microdilution MIC. Multidrug resistance (MDR) was observed in one S. Typhimurium strain towards sulfamethoxazole, trimethoprim, tetracycline, gentamicin, and ampicillin and in 41.3% of the Vibrio strains, mostly towards sulphonamides, penicillin, and cephems. All Vibrio isolates were sensitive to azithromycin, chloramphenicol, tetracycline, amoxicillin/clavulanic acid, gentamicin, streptomycin, amikacin, and levofloxacin. The AMR phenomenon in the investigated area is not highly worrying but not entirely negligible; therefore, in-depth continuous monitoring is suggested. Results concerning the antibiotic agents without available specific clinical breakpoints could be useful to upgrade the MIC distribution for Vibrio spp. but, also, the establishment of interpretative criteria for environmental species is necessary to obtain a more complete view of this issue. Full article

(This article belongs to the Special Issue Seafood-Borne Pathogens)

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20 pages, 3387 KiB

Open AccessEditor’s ChoiceArticle

Metagenomic Analysis of Anaerobic Microbial Communities Degrading Short-Chain Fatty Acids as Sole Carbon Sources

by Daniela Becker, Denny Popp, Fabian Bonk, Sabine Kleinsteuber, Hauke Harms and Florian Centler

Microorganisms 2023, 11(2), 420; https://doi.org/10.3390/microorganisms11020420 - 7 Feb 2023

Cited by 7 | Viewed by 2428

Abstract

Analyzing microbial communities using metagenomes is a powerful approach to understand compositional structures and functional connections in anaerobic digestion (AD) microbiomes. Whereas short-read sequencing approaches based on the Illumina platform result in highly fragmented metagenomes, long-read sequencing leads to more contiguous assemblies. To [...] Read more.

Analyzing microbial communities using metagenomes is a powerful approach to understand compositional structures and functional connections in anaerobic digestion (AD) microbiomes. Whereas short-read sequencing approaches based on the Illumina platform result in highly fragmented metagenomes, long-read sequencing leads to more contiguous assemblies. To evaluate the performance of a hybrid approach of these two sequencing approaches we compared the metagenome-assembled genomes (MAGs) resulting from five AD microbiome samples. The samples were taken from reactors fed with short-chain fatty acids at different feeding regimes (continuous and discontinuous) and organic loading rates (OLR). Methanothrix showed a high relative abundance at all feeding regimes but was strongly reduced in abundance at higher OLR, when Methanosarcina took over. The bacterial community composition differed strongly between reactors of different feeding regimes and OLRs. However, the functional potential was similar regardless of feeding regime and OLR. The hybrid sequencing approach using Nanopore long-reads and Illumina MiSeq reads improved assembly statistics, including an increase of the N50 value (on average from 32 to 1740 kbp) and an increased length of the longest contig (on average from 94 to 1898 kbp). The hybrid approach also led to a higher share of high-quality MAGs and generated five potentially circular genomes while none were generated using MiSeq-based contigs only. Finally, 27 hybrid MAGs were reconstructed of which 18 represent potentially new species—15 of them bacterial species. During pathway analysis, selected MAGs revealed similar gene patterns of butyrate degradation and might represent new butyrate-degrading bacteria. The demonstrated advantages of adding long reads to metagenomic analyses make the hybrid approach the preferable option when dealing with complex microbiomes. Full article

(This article belongs to the Special Issue Microbial Communities in Anaerobic Digesters)

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15 pages, 1955 KiB

Open AccessEditor’s ChoiceArticle

Differential Effects of Viruses on the Growth Efficiency of Freshwater Bacterioplankton in Eutrophic Relative to Non-Eutrophic Lakes

by Angia Sriram Pradeep Ram and Télesphore Sime-Ngando

Microorganisms 2023, 11(2), 384; https://doi.org/10.3390/microorganisms11020384 - 2 Feb 2023

Cited by 3 | Viewed by 1529

Abstract

In aquatic environments, the consensus of viral impact on bacterial carbon metabolism with the nutrient environment as an important axis is limited. Henceforth, we explored the viral regulation of carbon-based bacterial growth efficiency (BGE) in a set of freshwater systems from French Massif [...] Read more.

In aquatic environments, the consensus of viral impact on bacterial carbon metabolism with the nutrient environment as an important axis is limited. Henceforth, we explored the viral regulation of carbon-based bacterial growth efficiency (BGE) in a set of freshwater systems from French Massif Central, which were broadly classified based on two trophic statuses: eutrophic and non-eutrophic lakes. Comparative analysis showed that microbial abundances (viruses and bacteria) were 3-fold higher in eutrophic compared with non-eutrophic lakes, and so were bacterial production and viral lytic infection. The observed variability in BGE (10–60%) was explained by the uncoupling between bacterial respiration and production. Viruses through selective lysis of susceptible host communities had an antagonistic impact on BGE in the eutrophic lakes, whereas the release of substrates via viral shunt exerted a synergistic influence on the carbon metabolism of non-targeted host populations in non-eutrophic lakes. The decisive effect of the two individual processes (i.e., lysis and substrate release) on BGE was supported by regressions of bacterial abundance as a function of bacterial production, which is considered as a proxy of top-down processes. The role of viruses through their negative impact via mortality and positive impact via substrate supply can eventually have implications on carbon transfer through bacterioplankton in freshwaters. Full article

(This article belongs to the Special Issue Microbiomes of Aquatic Organisms)

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17 pages, 1541 KiB

Open AccessEditor’s ChoiceArticle

C-di-AMP Is a Second Messenger in Corynebacterium glutamicum That Regulates Expression of a Cell Wall-Related Peptidase via a Riboswitch

by Sebastian J. Reich, Oliver Goldbeck, Tsenguunmaa Lkhaasuren, Dominik Weixler, Tamara Weiß and Bernhard J. Eikmanns

Microorganisms 2023, 11(2), 296; https://doi.org/10.3390/microorganisms11020296 - 23 Jan 2023

Cited by 2 | Viewed by 2371

Abstract

Cyclic di-adenosine monophosphate (c-di-AMP) is a bacterial second messenger discovered in Bacillus subtilis and involved in potassium homeostasis, cell wall maintenance and/or DNA stress response. As the role of c-di-AMP has been mostly studied in Firmicutes, we sought to increase the understanding of [...] Read more.

Cyclic di-adenosine monophosphate (c-di-AMP) is a bacterial second messenger discovered in Bacillus subtilis and involved in potassium homeostasis, cell wall maintenance and/or DNA stress response. As the role of c-di-AMP has been mostly studied in Firmicutes, we sought to increase the understanding of its role in Actinobacteria, namely in Corynebacterium glutamicum. This organism is a well-known industrial production host and a model organism for pathogens, such as C. diphtheriae or Mycobacterium tuberculosis. Here, we identify and analyze the minimal set of two C. glutamicum enzymes, the diadenylate cyclase DisA and the phosphodiesterase PdeA, responsible for c-di-AMP metabolism. DisA synthesizes c-di-AMP from two molecules of ATP, whereas PdeA degrades c-di-AMP, as well as the linear degradation intermediate phosphoadenylyl-(3′→5′)-adenosine (pApA) to two molecules of AMP. Here, we show that a ydaO/kimA-type c-di-AMP-dependent riboswitch controls the expression of the strictly regulated cell wall peptidase gene nlpC in C. glutamicum. In contrast to previously described members of the ydaO/kimA-type riboswitches, our results suggest that the C. glutamicum nlpC riboswitch likely affects the translation instead of the transcription of its downstream gene. Although strongly regulated by different mechanisms, we show that the absence of nlpC, the first known regulatory target of c-di-AMP in C. glutamicum, is not detrimental for this organism under the tested conditions. Full article

(This article belongs to the Special Issue Complex Signal Transduction Systems in Bacteria)

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22 pages, 4130 KiB

Open AccessEditor’s ChoiceArticle

Immunomodulatory and Antioxidant Properties of a Novel Potential Probiotic Bacillus clausii CSI08

by Ekaterina Khokhlova, Joan Colom, Annie Simon, Shahneela Mazhar, Guillermo García-Lainez, Silvia Llopis, Nuria Gonzalez, María Enrique-López, Beatriz Álvarez, Patricia Martorell, Marta Tortajada, John Deaton and Kieran Rea

Microorganisms 2023, 11(2), 240; https://doi.org/10.3390/microorganisms11020240 - 18 Jan 2023

Cited by 11 | Viewed by 6660

Abstract

Spore-forming bacteria of the Bacillus genus have demonstrated potential as probiotics for human use. Bacillus clausii have been recognized as efficacious and safe agents for preventing and treating diarrhea in children and adults, with pronounced immunomodulatory properties during several in vitro and clinical [...] Read more.

Spore-forming bacteria of the Bacillus genus have demonstrated potential as probiotics for human use. Bacillus clausii have been recognized as efficacious and safe agents for preventing and treating diarrhea in children and adults, with pronounced immunomodulatory properties during several in vitro and clinical studies. Herein, we characterize the novel strain of B. clausii CSI08 (Munispore^®) for probiotic attributes including resistance to gastric acid and bile salts, the ability to suppress the growth of human pathogens, the capacity to assimilate wide range of carbohydrates and to produce potentially beneficial enzymes. Both spores and vegetative cells of this strain were able to adhere to a mucous-producing intestinal cell line and to attenuate the LPS- and Poly I:C-triggered pro-inflammatory cytokine gene expression in HT-29 intestinal cell line. Vegetative cells of B. clausii CSI08 were also able to elicit a robust immune response in U937-derived macrophages. Furthermore, B. clausii CSI08 demonstrated cytoprotective effects in in vitro cell culture and in vivo C. elegans models of oxidative stress. Taken together, these beneficial properties provide strong evidence for B. clausii CSI08 as a promising potential probiotic. Full article

(This article belongs to the Special Issue Probiotics and the Immune System: The Potential for Postimmunobiotics)

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26 pages, 5673 KiB

Open AccessEditor’s ChoiceArticle

The Development of the Bacterial Community of Brown Trout (Salmo trutta) during Ontogeny

by Katharina Keiz, Sebastian Ulrich, Jasmin Wenderlein, Patrick Keferloher, Anna Wiesinger, Klaus Neuhaus, Ilias Lagkouvardos, Helmut Wedekind and Reinhard K. Straubinger

Microorganisms 2023, 11(1), 211; https://doi.org/10.3390/microorganisms11010211 - 14 Jan 2023

Cited by 3 | Viewed by 2473

Abstract

Brown trout (Salmo trutta) is an important aquaculture species in Germany, but its production faces challenges due to global warming and a high embryo mortality. Climate factors might influence the fish’s bacterial community (BC) and thus increase embryo mortality. Yet, knowledge [...] Read more.

Brown trout (Salmo trutta) is an important aquaculture species in Germany, but its production faces challenges due to global warming and a high embryo mortality. Climate factors might influence the fish’s bacterial community (BC) and thus increase embryo mortality. Yet, knowledge of the physiological BC during ontogeny in general is scarce. In this project, the BC of brown trout has been investigated in a period from unfertilized egg to 95 days post fertilization (dpf) using 16S rRNA gene amplicon sequencing. Developmental changes differed between early and late ontogeny and major differences in BC occurred especially during early developmental stages. Thus, analysis was conducted separately for 0 to 67 dpf and from 67 to 95 dpf. All analyzed stages were sampled in toto to avoid bias due to different sampling methods in different developmental stages. The most abundant phylum in the BC of all developmental stages was Pseudomonadota, while only two families (Comamonadaceae and Moraxellaceae) occurred in all developmental stages. The early developmental stages until 67 dpf displayed greater shifts in their BC regarding bacterial richness, microbial diversity, and taxonomic composition. Thereafter, in the fry stages, the BC seemed to stabilize and changes were moderate. In future studies, a reduction in the sampling time frames during early development, an increase in sampling numbers, and an attempt for biological reproduction in order to characterize the causes of these variations is recommended. Full article

(This article belongs to the Special Issue Dietary Components and Gut Microbes in Fish)

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14 pages, 2140 KiB

Open AccessEditor’s ChoiceArticle

A 63-kDa Periplasmic Protein of the Endonuclear Symbiotic Bacterium Holospora obtusa Secreted to the Outside of the Bacterium during the Early Infection Process Binds Weakly to the Macronuclear DNA of the Host Paramecium caudatum

by Masahiro Fujishima, Hideaki Kawano and Isamu Miyakawa

Microorganisms 2023, 11(1), 155; https://doi.org/10.3390/microorganisms11010155 - 7 Jan 2023

Cited by 3 | Viewed by 2480

Abstract

The Gram-negative bacterium Holospora obtusa is a macronucleus-specific symbiont of the ciliate Paramecium caudatum. It is known that an infection of this bacterium induces high level expressions of the host hsp60 and hsp70 genes, and the host cell acquires both heat-shock and [...] Read more.

The Gram-negative bacterium Holospora obtusa is a macronucleus-specific symbiont of the ciliate Paramecium caudatum. It is known that an infection of this bacterium induces high level expressions of the host hsp60 and hsp70 genes, and the host cell acquires both heat-shock and high salt resistances. In addition, an infectious form of H. obtusa-specific 63-kDa periplasmic protein with a DNA-binding domain in its amino acid sequence is secreted into the host macronucleus after invasion into the macronucleus and remain within the nucleus. These facts suggest that binding of the 63-kDa protein to the host macronuclear DNA causes changes in the host gene expressions and enhances an environmental adaptability of the host cells. This 63-kDa protein was renamed as periplasmic region protein 1 (PRP1) to distinguish it from other proteins with similar molecular weights. To confirm whether PRP1 indeed binds to the host DNA, SDS-DNA PAGE and DNA affinity chromatography with calf thymus DNA and P. caudatum DNA were conducted and confirmed that PRP1 binds weakly to the P. caudatum DNA with a monoclonal antibody raised for the 63-kDa protein. Full article

(This article belongs to the Special Issue Paramecium as Modern Model System)

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9 pages, 269 KiB

Open AccessEditor’s ChoiceArticle

Intestinal Shedding of SARS-CoV-2 in Children: No Evidence for Infectious Potential

by Filomena Nogueira, Klara Obrova, Meryl Haas, Evelyn Tucek, Karin Kosulin, Michaela Fortschegger, Paola Fürhacker, Christina Walter, Lisa Größlinger, Susanne Peter, Julia Othman Hassan, Martin Probst, Hans Salzer and Thomas Lion

Microorganisms 2023, 11(1), 33; https://doi.org/10.3390/microorganisms11010033 - 22 Dec 2022

Cited by 3 | Viewed by 2937

Abstract

The clinical courses of COVID-19 in children are often mild and may remain undiagnosed, but prolonged intestinal virus shedding has been documented, thus potentially enabling fecal–oral transmission. However, the infectious potential of SARS-CoV-2 viruses excreted with feces has remained unclear. Here, we investigated [...] Read more.

The clinical courses of COVID-19 in children are often mild and may remain undiagnosed, but prolonged intestinal virus shedding has been documented, thus potentially enabling fecal–oral transmission. However, the infectious potential of SARS-CoV-2 viruses excreted with feces has remained unclear. Here, we investigated 247 stool specimens from 213 pediatric patients to assess the prevalence of intestinal SARS-CoV-2 shedding in hospitalized children without or with COVID-19 and determined the infectious capacity of stool-borne viruses. Upon RT-qPCR screening, the infectivity of virus-positive samples was tested in cell culture using the Vero-E6 permissive cell line. SARS-CoV-2 RNA was detected by RT-qPCR in 32 (13%) stool specimens, but the analysis of virus-positive samples in cell culture revealed no cytopathic effects attributable to SARS-CoV-2-related cell damage. Our findings do not support the notion of potential fecal–oral SARS-CoV-2 spreading, thus questioning the role of hygienic measures designed to prevent this mode of viral transmission. Full article

(This article belongs to the Section Virology)

26 pages, 3341 KiB

Open AccessEditor’s ChoiceArticle

Cross-Feeding and Enzymatic Catabolism for Mannan-Oligosaccharide Utilization by the Butyrate-Producing Gut Bacterium Roseburia hominis A2-183

by Abhishek Bhattacharya, Lovisa Majtorp, Simon Birgersson, Mathias Wiemann, Krishnan Sreenivas, Phebe Verbrugghe, Olivier Van Aken, Ed W. J. Van Niel and Henrik Stålbrand

Microorganisms 2022, 10(12), 2496; https://doi.org/10.3390/microorganisms10122496 - 16 Dec 2022

Cited by 4 | Viewed by 2761

Abstract

β-Mannan is abundant in the human diet and in hemicellulose derived from softwood. Linear or galactose-substituted β-mannan-oligosaccharides (MOS/GMOSs) derived from β-mannan are considered emerging prebiotics that could stimulate health-associated gut microbiota. However, the underlying mechanisms are not yet resolved. Therefore, this study investigated [...] Read more.

β-Mannan is abundant in the human diet and in hemicellulose derived from softwood. Linear or galactose-substituted β-mannan-oligosaccharides (MOS/GMOSs) derived from β-mannan are considered emerging prebiotics that could stimulate health-associated gut microbiota. However, the underlying mechanisms are not yet resolved. Therefore, this study investigated the cross-feeding and metabolic interactions between Bifidobacterium adolescentis ATCC 15703, an acetate producer, and Roseburia hominis A2-183 DSMZ 16839, a butyrate producer, during utilization of MOS/GMOSs. Cocultivation studies suggest that both strains coexist due to differential MOS/GMOS utilization, along with the cross-feeding of acetate from B. adolescentis E194a to R. hominis A2-183. The data suggest that R. hominis A2-183 efficiently utilizes MOS/GMOS in mono- and cocultivation. Notably, we observed the transcriptional upregulation of certain genes within a dedicated MOS/GMOS utilization locus (RhMosUL), and an exo-oligomannosidase (RhMan113A) gene located distally in the R. hominis A2-183 genome. Significantly, biochemical analysis of β-1,4 mannan-oligosaccharide phosphorylase (RhMOP130A), α-galactosidase (RhGal36A), and exo-oligomannosidase (RhMan113A) suggested their potential synergistic role in the initial utilization of MOS/GMOSs. Thus, our results enhance the understanding of MOS/GMOS utilization by potential health-promoting human gut microbiota and highlight the role of cross-feeding and metabolic interactions between two secondary mannan degraders inhabiting the same ecological niche in the gut. Full article

(This article belongs to the Special Issue Regulation and Workings of the Gastrointestinal Microbiota)

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20 pages, 3836 KiB

Open AccessEditor’s ChoiceArticle

Potential Probiotic Properties of Exopolysaccharide-Producing Lacticaseibacillus paracasei EPS DA-BACS and Prebiotic Activity of Its Exopolysaccharide

by Min-Gyu Lee, Huijin Joeng, Jaein Shin, Suin Kim, Chaeeun Lee, Youngbo Song, Byung-Hoo Lee, Hyoung-Geun Park, Tae-Ho Lee, Hai-Hua Jiang, Young-Sun Han, Bong-Gyeong Lee, Ho-Jin Lee, Min-Ju Park, Yun-Ju Jun and Young-Seo Park

Microorganisms 2022, 10(12), 2431; https://doi.org/10.3390/microorganisms10122431 - 8 Dec 2022

Cited by 15 | Viewed by 4579

Abstract

Exopolysaccharide (EPS)-producing Lacticaseibacillus paracasei EPS DA-BACS was isolated from healthy human feces and its probiotic properties, as well as the structure and prebiotic activity of the EPS from this strain were examined. EPS from L. paracasei EPS DA-BACS had a ropy phenotype, which [...] Read more.

Exopolysaccharide (EPS)-producing Lacticaseibacillus paracasei EPS DA-BACS was isolated from healthy human feces and its probiotic properties, as well as the structure and prebiotic activity of the EPS from this strain were examined. EPS from L. paracasei EPS DA-BACS had a ropy phenotype, which is known to have potential health benefits and is identified as loosely cell-bounded glucomannan-type EPS with a molecular size of 3.7 × 10⁶ Da. EPS promoted the acid tolerance of L. paracasei EPS DA-BACS and provided cells with tolerance to gastrointestinal stress. The purified EPS showed growth inhibitory activity against Clostridium difficile. L. paracasei EPS DA-BACS cells completely inhibited the growth of Bacillus subtilis, Pseudomonas aeruginosa, and Aspergillus brasiliensis, as well as showed high growth inhibitory activity against Staphylococcus aureus and Escherichia coli. Treatment of lipopolysaccharide-stimulated RAW 264.7 cells with heat-killed L. paracasei EPS DA-BACS cells led to a decrease in the production of nitric oxide, indicating the anti-inflammatory activity of L. paracasei EPS DA-BACS. Purified EPS promoted the growth of Lactobacillus gasseri, Bifidobacterium bifidum, B. animalis, and B. faecale which showed high prebiotic activity. L. paracasei EPS DA-BACS harbors no antibiotic resistance genes or virulence factors. Therefore, L. paracasei EPS DA-BACS exhibits anti-inflammatory and antimicrobial activities with high gut adhesion ability and gastrointestinal tolerance and can be used as a potential probiotic. Full article

(This article belongs to the Special Issue Environment Microorganisms and Their Enzymes with Biotechnological Application)

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12 pages, 22517 KiB

Open AccessEditor’s ChoiceArticle

Molecular Characterization of Octopamine/Tyramine Receptor Gene of Amitraz-Resistant Rhipicephalus (Boophilus) decoloratus Ticks from Uganda

by Patrick Vudriko, Rika Umemiya-Shirafuji, Dickson Stuart Tayebwa, Joseph Byaruhanga, Benedicto Byamukama, Maria Tumwebaze, Xuenan Xuan and Hiroshi Suzuki

Microorganisms 2022, 10(12), 2384; https://doi.org/10.3390/microorganisms10122384 - 30 Nov 2022

Cited by 1 | Viewed by 2356

Abstract

We previously reported the emergence of amitraz-resistant Rhipicephalus (Boophilus) decoloratus ticks in the western region of Uganda. This study characterized the octopamine/tyramine receptor gene (OCT/Tyr) of amitraz-resistant and -susceptible R. (B.) decoloratus ticks from four regions of Uganda. The [...] Read more.

We previously reported the emergence of amitraz-resistant Rhipicephalus (Boophilus) decoloratus ticks in the western region of Uganda. This study characterized the octopamine/tyramine receptor gene (OCT/Tyr) of amitraz-resistant and -susceptible R. (B.) decoloratus ticks from four regions of Uganda. The OCT/Tyr gene was amplified from genomic DNA of 17 R. (B.) decoloratus larval populations of known susceptibility to amitraz. The amplicons were purified, cloned and sequenced to determine mutations in the partial coding region of the OCT/Tyr gene. The amplified R. (B.) decoloratus OCT/Tyr gene was 91–100% identical to the R. (B.) microplus OCT/Tyr gene. Up to 24 single nucleotide polymorphisms (SNPs) were found in the OCT/Tyr gene from ticks obtained from high acaricide pressure areas, compared to 8 from the low acaricide pressure areas. A total of eight amino acid mutations were recorded in the partial OCT/Tyr gene from ticks from the western region, and four of them were associated with amitraz-resistant tick populations. The amino acid mutations M1G, L16F, D41G and V72A were associated with phenotypic resistance to amitraz with no specific pattern. Phylogenetic analysis revealed that the OCT/Tyr gene sequence from this study clustered into two distinct groups that separated the genotype from high acaricide pressure areas from the susceptible populations. In conclusion, this study is the first to characterize the R. (B.) decoloratus OCT/Tyr receptor gene and reports four novel amino acid mutations associated with phenotypic amitraz resistance in Uganda. However, lack of mutations in the ORF of the OCT/Tyr gene fragment for some of the amitraz-resistant R. (B.) decoloratus ticks could suggest that other mechanisms of resistance may be responsible for amitraz resistance, hence the need for further investigation. Full article

(This article belongs to the Special Issue Advanced Research on Ticks and Tick-Borne Diseases)

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15 pages, 6666 KiB

Open AccessEditor’s ChoiceArticle

Bacilli in the International Space Station

by Andrea Quagliariello, Angela Cirigliano and Teresa Rinaldi

Microorganisms 2022, 10(12), 2309; https://doi.org/10.3390/microorganisms10122309 - 22 Nov 2022

Cited by 3 | Viewed by 4253

Abstract

Astronauts remote from Earth, not least those who will inhabit the Moon or Mars, are vulnerable to disease due to their reduced immunity, isolation from clinical support, and the disconnect from any buffering capacity provided by the Earth. Here, we explore potential risks [...] Read more.

Astronauts remote from Earth, not least those who will inhabit the Moon or Mars, are vulnerable to disease due to their reduced immunity, isolation from clinical support, and the disconnect from any buffering capacity provided by the Earth. Here, we explore potential risks for astronaut health, focusing on key aspects of the biology of Bacillus anthracis and other anthrax-like bacilli. We examine aspects of Bacillus cereus group genetics in relation to their evolutionary biology and pathogenicity; a new clade of the Bacillus cereus group, close related to B. anthracis, has colonized the International Space Station (ISS), is still present, and could in theory at least acquire pathogenic plasmids from the other B. cereus group strains. The main finding is that the genomic sequence alignments of the B. cereus group ISS strains revealed a high sequence identity, indicating they originated from the same strain and that a close look to the genetic variations among the strains suggesting they lived, or they are living, in a vegetative form in the ISS enough time to accumulate genetic variations unique for each single strains. Full article

(This article belongs to the Special Issue Microorganisms from Extreme Environments: Versatile Tools from Biotechnology to Space Colonization)

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19 pages, 3110 KiB

Open AccessEditor’s ChoiceArticle

Modulation of Virulence-Associated Traits in Aspergillus fumigatus by BET Inhibitor JQ1

by Anastasia Orekhova, Marta De Angelis, Andrea Cacciotti, Massimo Reverberi, Dante Rotili, Alessandra Giorgi, Virginia Protto, Graziana Bonincontro, Francesco Fiorentino, Victor Zgoda, Antonello Mai, Anna Teresa Palamara and Giovanna Simonetti

Microorganisms 2022, 10(11), 2292; https://doi.org/10.3390/microorganisms10112292 - 18 Nov 2022

Cited by 3 | Viewed by 1960

Abstract

Aspergillus fumigatus is a disease-causing, opportunistic fungus that can establish infection due to its capacity to respond to a wide range of environmental conditions. Secreted proteins and metabolites, which play a critical role in fungal–host interactions and pathogenesis, are modulated by epigenetic players, [...] Read more.

Aspergillus fumigatus is a disease-causing, opportunistic fungus that can establish infection due to its capacity to respond to a wide range of environmental conditions. Secreted proteins and metabolites, which play a critical role in fungal–host interactions and pathogenesis, are modulated by epigenetic players, such as bromodomain and extraterminal domain (BET) proteins. In this study, we evaluated the in vitro and in vivo capability of the BET inhibitor JQ1 to modulate the extracellular proteins and virulence of A. fumigatus. The abundance of 25 of the 76 extracellular proteins identified through LC-MS/MS proteomic analysis changed following JQ1 treatment. Among them, a ribonuclease, a chitinase, and a superoxide dismutase were dramatically downregulated. Moreover, the proteomic analysis of A. fumigatus intracellular proteins indicated that Abr2, an intracellular laccase involved in the last step of melanin synthesis, was absent in the JQ1-treated group. To investigate at which level this downregulation occurred and considering the ability of JQ1 to modulate gene expression we checked the level of ABR2, Chitinase, and Superoxide dismutase mRNA expression by qRT-PCR. Finally, the capacity of JQ1 to reduce the virulence of A. fumigatus has been proved using Galleria mellonella larvae, which are an in vivo model to evaluate fungal virulence. Overall, the promising activity exhibited by JQ1 suggests that A. fumigatus is sensitive to BET inhibition and BET proteins may be a viable target for developing antifungal agents. Full article

(This article belongs to the Special Issue Virulence Regulation and Drug-Resistance Mechanism of Fungal Infection)

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14 pages, 3835 KiB

Open AccessEditor’s ChoiceArticle

Lipoproteins Are Potent Activators of Nuclear Factor Kappa B in Mammary Epithelial Cells and Virulence Factors in Mycoplasma bovis Mastitis

by Peleg Schneider, Re’ella Brill, Iftach Schouten, Einat Nissim-Eliraz, Inna Lysnyansky and Nahum Yehuda Shpigel

Microorganisms 2022, 10(11), 2209; https://doi.org/10.3390/microorganisms10112209 - 8 Nov 2022

Cited by 3 | Viewed by 1989

Abstract

Mastitis due to Mycoplasma bovis is a worldwide problem, which leads to significant economic losses and affects animal welfare. However, the mechanisms by which M. bovis establishes and maintains intra-mammary infections (IMI) in dairy cows are largely unknown. To study in further detail [...] Read more.

Mastitis due to Mycoplasma bovis is a worldwide problem, which leads to significant economic losses and affects animal welfare. However, the mechanisms by which M. bovis establishes and maintains intra-mammary infections (IMI) in dairy cows are largely unknown. To study in further detail the pathogenesis of M. bovis IMI, time- and cost-effective experimental models are needed. To this end, we established and characterized an in vitro murine mammary alveolar epithelial (EpH4) cell-based model and an in vivo murine mastitis model. Our results showed that live and UV-treated M. bovis field strain 161791 and its lipid-associated membrane proteins (LAMP) activated nuclear factor kappa B (NF-kB) in EpH4 cells in a dose-dependent manner. In the murine mastitis model, temporal and spatial dynamics of inflammation in the mammary tissues were evident. Live M. bovis elicited diffuse inflammation affecting the whole challenged gland peaking at 48 h post infection (pi) in contrast to LAMP challenge, which elicited only focal inflammation peaking at 24 h and resolving at 48 h pi. Inflammation was characterized by massive neutrophil recruitment into the milk spaces and by elevated expression of the inflammatory mediators TNF-α, KC, iNOS and NF-kB dependent genes: A20 and IkBα. Moreover, the presence of intraepithelial bacterial communities in glands challenged with live M. bovis bacteria was shown. The developed models can be used efficiently for future characterization of M. bovis virulence factors and host immune response to IMI. Full article

(This article belongs to the Special Issue Mycoplasma Pathogenicity, Persistence and Virulence)

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17 pages, 4114 KiB

Open AccessEditor’s ChoiceArticle

The Emergence and Dynamics of Tick-Borne Encephalitis Virus in a New Endemic Region in Southern Germany

by Daniel Lang, Lidia Chitimia-Dobler, Malena Bestehorn-Willmann, Alexander Lindau, Marco Drehmann, Gabriele Stroppel, Helga Hengge, Ute Mackenstedt, Klaus Kaier, Gerhard Dobler and Johannes Borde

Microorganisms 2022, 10(11), 2125; https://doi.org/10.3390/microorganisms10112125 - 27 Oct 2022

Cited by 5 | Viewed by 1753

Abstract

Tick-borne encephalitis (TBE) is the most important viral tick-borne infection in Europe and Asia. It is emerging in new areas. The mechanisms of emergence are fairly unknown or speculative. In the Ravensburg district in southern Germany, TBE emerged, mainly over the last five [...] Read more.

Tick-borne encephalitis (TBE) is the most important viral tick-borne infection in Europe and Asia. It is emerging in new areas. The mechanisms of emergence are fairly unknown or speculative. In the Ravensburg district in southern Germany, TBE emerged, mainly over the last five years. Here, we analyzed the underlying epidemiology in humans. The resulting identified natural foci of the causal TBE virus (TBEV) were genetically characterized. We sampled 13 potential infection sites at these foci and detected TBEV in ticks (Ixodes ricinus) at eight sites. Phylogenetic analysis spurred the introduction of at least four distinct TBEV lineages of the European subtype into the Ravensburg district over the last few years. In two instances, a continuous spread of these virus strains over up to 10 km was observed. Full article

(This article belongs to the Special Issue Trends in Viral Zoonotic and Zooanthroponotic Diseases)

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13 pages, 2383 KiB

Open AccessEditor’s ChoiceArticle

Bile Acids: Major Regulator of the Gut Microbiome

by Chihyeok An, Hyeyeon Chon, Wanrim Ku, Sunho Eom, Mingyu Seok, Sangha Kim, Jaesun Lee, Daesung Kim, Sanghyuk Lee, Hoonsup Koo, Hyunjung Cho, Seungyun Han, Juik Moon, Miil Kang and Kihyun Ryu

Microorganisms 2022, 10(9), 1792; https://doi.org/10.3390/microorganisms10091792 - 6 Sep 2022

Cited by 18 | Viewed by 5149

Abstract

Bile acids are synthesized from cholesterol and play an important role in regulating intestinal microflora. The different degrees of hydrophobicity and acidity of individual bile acids may affect their antimicrobial properties. We examined the antimicrobial effects of different bile acids on various microorganisms [...] Read more.

Bile acids are synthesized from cholesterol and play an important role in regulating intestinal microflora. The different degrees of hydrophobicity and acidity of individual bile acids may affect their antimicrobial properties. We examined the antimicrobial effects of different bile acids on various microorganisms in vitro and confirmed whether these remain consistent in vivo. Using human bile acids, including ursodeoxycholic acid, cholic acid, chenodeoxycholic acid, deoxycholic acid, and lithocholic acid, a disc diffusion test was performed, and a rodent model was created to determine the antimicrobial effects of each bile acid. The fecal bacterial population was analyzed using a real-time polymerase chain reaction. Each bile acid showed different microbial inhibitory properties. The inhibitory activity of bile acids against microbiota which normally resides in the gastrointestinal tract and biliary system, was low; however, normal flora of other organs was significantly inhibited. Changes in microbial counts after bile acid administration in a rodent model differed in the colon and cecum. The in vivo and in vitro results show that the antimicrobial effects of bile acids against intestinal microbiota were similar. In conclusion, bile acids could be a novel treatment strategy to regulate gut microbiota. Full article

(This article belongs to the Special Issue Regulation and Workings of the Gastrointestinal Microbiota)

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23 pages, 5724 KiB

Open AccessEditor’s ChoiceArticle

Simultaneous Metabarcoding and Quantification of Neocallimastigomycetes from Environmental Samples: Insights into Community Composition and Novel Lineages

by Diana Young, Akshay Joshi, Liren Huang, Bernhard Munk, Christian Wurzbacher, Noha H. Youssef, Mostafa S. Elshahed, Christina D. Moon, Katrin Ochsenreither, Gareth W. Griffith, Tony M. Callaghan, Alexander Sczyrba, Michael Lebuhn and Veronika Flad

Microorganisms 2022, 10(9), 1749; https://doi.org/10.3390/microorganisms10091749 - 30 Aug 2022

Cited by 11 | Viewed by 4088

Abstract

Anaerobic fungi from the herbivore digestive tract (Neocallimastigomycetes) are primary lignocellulose modifiers and hold promise for biotechnological applications. Their molecular detection is currently difficult due to the non-specificity of published primer pairs, which impairs evolutionary and ecological research with environmental samples. [...] Read more.

Anaerobic fungi from the herbivore digestive tract (Neocallimastigomycetes) are primary lignocellulose modifiers and hold promise for biotechnological applications. Their molecular detection is currently difficult due to the non-specificity of published primer pairs, which impairs evolutionary and ecological research with environmental samples. We developed and validated a Neocallimastigomycetes-specific PCR primer pair targeting the D2 region of the ribosomal large subunit suitable for screening, quantifying, and sequencing. We evaluated this primer pair in silico on sequences from all known genera, in vitro with pure cultures covering 16 of the 20 known genera, and on environmental samples with highly diverse microbiomes. The amplified region allowed phylogenetic differentiation of all known genera and most species. The amplicon is about 350 bp long, suitable for short-read high-throughput sequencing as well as qPCR assays. Sequencing of herbivore fecal samples verified the specificity of the primer pair and recovered highly diverse and so far unknown anaerobic gut fungal taxa. As the chosen barcoding region can be easily aligned and is taxonomically informative, the sequences can be used for classification and phylogenetic inferences. Several new Neocallimastigomycetes clades were obtained, some of which represent putative novel lineages such as a clade from feces of the rodent Dolichotis patagonum (mara). Full article

(This article belongs to the Special Issue Unleashing the Hidden Potential of Anaerobic Fungi)

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10 pages, 258 KiB

Open AccessEditor’s ChoiceArticle

Role of Intracellular Pulmonary Pathogens during SARS-CoV-2 Infection in the First Pandemic Wave of COVID-19: Clinical and Prognostic Significance in a Case Series of 1200 Patients

by Matteo Guarino, Benedetta Perna, Francesca Cuoghi, Michele Domenico Spampinato, Alice Eleonora Cesaro, Francesca Manza, Adriana Pretula, Anastasio Grilli, Martina Maritati, Giacomo Caio, Aldo Carnevale, Maria Elena Flacco, Roberto De Giorgio and Carlo Contini

Microorganisms 2022, 10(8), 1636; https://doi.org/10.3390/microorganisms10081636 - 12 Aug 2022

Cited by 7 | Viewed by 2367

Abstract

Background: Since 2019, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic (COVID-19) has caused millions of deaths worldwide and is the second most serious pandemic after the Spanish flu. Despite SARS-CoV-2 infection having a dominant effect on morbidity and life-threatening outcomes, [...] Read more.

Background: Since 2019, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic (COVID-19) has caused millions of deaths worldwide and is the second most serious pandemic after the Spanish flu. Despite SARS-CoV-2 infection having a dominant effect on morbidity and life-threatening outcomes, the role of bacterial co-infection in patients with COVID-19 is poorly understood. The present study aimed to verify the existence of bacterial co-infections and their possible role as cofactors worsening COVID-19-related clinical manifestations. Methods: All patients with suspected SARS-CoV-infection, hospitalised in COVID-19 wards at the Sant’Anna University Hospital of Ferrara, were retrospectively included in this single-centre study and their specific bacterial serologies were assessed. Univariate and logistic regression analyses were performed. Results: A total of 1204 individual records were retrieved. Among them, 959 were excluded because of a negative nasopharyngeal swab or missing data; of the eligible 245 patients, 51 were co-infected. Compared to patients with SARS-CoV-2 infection alone, those with Chlamydia pneumoniae or Mycoplasma pneumoniae co-infections had worse respiratory/radiological features and more intensive care unit admissions. However, the co-infection did not result in a higher mortality rate. Conclusions: The present study, comparing clinical, laboratory and radiological findings between patients with COVID-19 vs. those with co-infections (C. pneumoniae or M. pneumoniae) showed that, on admission, these features were worse in co-infected patients, although the mortality rate did not differ between the two groups. Full article

(This article belongs to the Special Issue Advances in SARS-CoV-2 Infection)

13 pages, 955 KiB

Open AccessEditor’s ChoiceArticle

Controlling an Unprecedented Outbreak with Vancomycin-Resistant Enterococcus faecium in Germany, October 2015 to November 2019

by Jennifer K. Bender, Julia Hermes, Lutz T. Zabel, Sebastian Haller, Nadja Mürter, Hans-Peter Blank, Guido Werner, Ingo Hüttner and Tim Eckmanns

Microorganisms 2022, 10(8), 1603; https://doi.org/10.3390/microorganisms10081603 - 9 Aug 2022

Cited by 8 | Viewed by 3402

Abstract

Hospital outbreaks with vancomycin-resistant enterococci (VRE) pose a serious health threat and a challenge to infection prevention and control (IPC). We herein report on a VRE outbreak of unprecedented extent in Southern Germany (October 2015–November 2019). We used descriptive epidemiology and whole-genome sequencing [...] Read more.

Hospital outbreaks with vancomycin-resistant enterococci (VRE) pose a serious health threat and a challenge to infection prevention and control (IPC). We herein report on a VRE outbreak of unprecedented extent in Southern Germany (October 2015–November 2019). We used descriptive epidemiology and whole-genome sequencing (WGS) for a detailed outbreak investigation. Of the 2905 cases, 2776 (95.3%) were colonized, whereas from 127 (3.7%), VRE could be isolated from otherwise sterile body fluids or sites unlikely for enterococci colonization. Cases had a median age of 78 years (IQR 68–84) and 1339/2905 (46%) were female. The majority of isolates sequenced belonged to the clonal lineage ST80/CT1013 (212/397, 53%). Nosocomial transmission was observed as well as the constant import of VRE into the hospital. Extensive IPC measures were implemented and terminated the outbreak in late 2019, eventually. Our study shows that the combination of epidemiological and genomic analyses is indispensable for comprehensive outbreak investigations. The adaptation of IPC measures to these findings, their timely implementation, and strict execution also allow containment of large VRE outbreaks in hospital settings. Full article

(This article belongs to the Special Issue Nosocomial Pathogens and Antibiotic Resistance)

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10 pages, 977 KiB

Open AccessEditor’s ChoiceArticle

Whole Genome Sequencing and Molecular Analysis of Carbapenemase-Producing Escherichia coli from Intestinal Carriage in Elderly Inpatients

by Maria Giufrè, Giulia Errico, Monica Monaco, Maria Del Grosso, Michela Sabbatucci, Annalisa Pantosti, Marina Cerquetti, Michela Pagnotta, Manuela Marra, Maria Carollo, Angelo Rossini, Elena Fogato, Elisabetta Cesana, Flaminia Gentiloni Silverj, Dorjan Zabzuni and Marco Tinelli

Microorganisms 2022, 10(8), 1561; https://doi.org/10.3390/microorganisms10081561 - 3 Aug 2022

Cited by 4 | Viewed by 2026

Abstract

The spread of carbapenemase-producing (CP) Enterobacterales is currently a worldwide concern, especially in the elderly. Twelve CP-E. coli isolated from rectal swabs of colonized inpatients aged ≥65 years from four hospitals in two Italian cities (Milan and Rome) were analyzed by whole [...] Read more.

The spread of carbapenemase-producing (CP) Enterobacterales is currently a worldwide concern, especially in the elderly. Twelve CP-E. coli isolated from rectal swabs of colonized inpatients aged ≥65 years from four hospitals in two Italian cities (Milan and Rome) were analyzed by whole genome sequencing (WGS) to obtain multi-locus sequence typing (MLST), identification of carbapenemase-encoding genes, resistome, plasmid content, and virulence genes. MLST analysis showed the presence of 10 unrelated lineages: ST410 (three isolates from three different hospitals in two cities) and ST12, ST38, ST69, ST95, ST131, ST189, ST648, ST1288, and ST1598 (one isolate each). Most isolates (9/12, 75%) contained a serine-β-lactamase gene (5 bla_KPC-3, 2 bla_KPC-2, and 2 bla_OXA-181), while three isolates harbored a metallo-β-lactamase gene (two bla_NDM-5 and one bla_VIM-1). In most CP-E. coli, the presence of more than one plasmid was observed, with the predominance of IncF. Several virulence genes were detected. All isolates contained genes enhancing the bacterial fitness, such as gad and terC, and all isolates but one, fimH, encoding type 1 fimbriae. In conclusion, CP-E. coli clones colonizing elderly patients showed heterogeneous genetic backgrounds. We recommend strict surveillance to monitor and prevent the spread of successful, high-risk clones in healthcare settings. Full article

(This article belongs to the Special Issue ß-Lactamases 2.0)

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14 pages, 3296 KiB

Open AccessEditor’s ChoiceArticle

In Vitro and In Silico Analysis of the Inhibitory Activity of EGCG-Stearate against Herpes Simplex Virus-2

by James D. Stamos, Lee H. Lee, Calvin Taylor, Tony Elias and Sandra D. Adams

Microorganisms 2022, 10(7), 1462; https://doi.org/10.3390/microorganisms10071462 - 20 Jul 2022

Cited by 4 | Viewed by 3841

Abstract

About half a billion people worldwide are infected with herpes simplex virus-2 (HSV-2). Prolonged treatment with acyclovir (ACV) and its analogs leads to the development of resistant strains. The aim of this study was to investigate the antiviral potential of epigallocatechin gallate (EGCG) [...] Read more.

About half a billion people worldwide are infected with herpes simplex virus-2 (HSV-2). Prolonged treatment with acyclovir (ACV) and its analogs leads to the development of resistant strains. The aim of this study was to investigate the antiviral potential of epigallocatechin gallate (EGCG) from Camellia sinensis and a stable analog EGCG-stearate (EGCG-S) against HSV-2 in cultured Vero cells. Cell viability and cell proliferation assays were used to determine the non-cytotoxic concentrations on cultured Vero cells. HSV-2 with a green fluorescent protein (GFP) fusion protein of VP26 virions were treated with non-cytotoxic concentrations of EGCG and EGCG-S. The effects on infectivity and mechanisms were determined by plaque assay, attachment and penetration assays, confocal microscopy, qPCR, and in silico modeling analysis. Our results demonstrate that treatment of HSV-2 virions with EGCG and EGCG-S at a concentration of 75 µM showed greater than 99.9% inhibition by inhibiting the attachment of HSV-2 virions to host cells. The bioinformatic analysis indicated high binding affinity of EGCG-S for glycoprotein D; thus EGCG-S may block fusion of HSV-2 and the cell membrane, preventing entry of HSV-2 into the cell. Full article

(This article belongs to the Special Issue Emerging Viruses and Antiviral Drugs)

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16 pages, 2522 KiB

Open AccessEditor’s ChoiceArticle

Genome-Wide Study of Drug Resistant Mycobacterium tuberculosis and Its Intra-Host Evolution during Treatment

by Denis Lagutkin, Anna Panova, Anatoly Vinokurov, Alexandra Gracheva, Anastasia Samoilova and Irina Vasilyeva

Microorganisms 2022, 10(7), 1440; https://doi.org/10.3390/microorganisms10071440 - 17 Jul 2022

Cited by 7 | Viewed by 4463

Abstract

The emergence of drug resistant Mycobacterium tuberculosis (MTB) strains has become a global public health problem, while, at the same time, there has been development of new antimicrobial agents. The main goals of this study were to determine new variants associated with drug [...] Read more.

The emergence of drug resistant Mycobacterium tuberculosis (MTB) strains has become a global public health problem, while, at the same time, there has been development of new antimicrobial agents. The main goals of this study were to determine new variants associated with drug resistance in MTB and to observe which polymorphisms emerge in MTB genomes after anti-tuberculosis treatment. We performed whole-genome sequencing of 152 MTB isolates including 70 isolates as 32 series of pre- and post-treatment MTB. Based on genotypes and phenotypic drug susceptibility, we conducted phylogenetic convergence-based genome-wide association study (GWAS) with streptomycin-, isoniazid-, rifampicin-, ethambutol-, fluoroquinolones-, and aminoglycosides-resistant MTB against susceptible ones. GWAS revealed statistically significant associations of SNPs within Rv2820c, cyp123 and indels in Rv1269c, Rv1907c, Rv1883c, Rv2407, Rv3785 genes with resistant MTB phenotypes. Comparisons of serial isolates showed that treatment induced different patterns of intra-host evolution. We found indels within Rv1435c and ppsA that were not lineage-specific. In addition, Beijing-specific polymorphisms within Rv0036c, Rv0678, Rv3433c, and dop genes were detected in post-treatment isolates. The appearance of Rv3785 frameshift insertion in 2 post-treatment strains compared to pre-treatment was also observed. We propose that the insertion within Rv3785, which was a GWAS hit, might affect cell wall biosynthesis and probably mediates a compensatory mechanism in response to treatment. These results may shed light on the mechanisms of MTB adaptation to chemotherapy and drug resistance formation. Full article

(This article belongs to the Special Issue Mycobacterium tuberculosis Infection: Control & Treatment)

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18 pages, 887 KiB

Open AccessEditor’s ChoiceArticle

SARS-CoV-2 Amino Acid Mutations Detection in Greek Patients Infected in the First Wave of the Pandemic

by Niki Vassilaki, Konstantinos Papadimitriou, Anastasios Ioannidis, Nikos C. Papandreou, Raphaela S. Milona, Vassiliki A. Iconomidou and Stylianos Chatzipanagiotou

Microorganisms 2022, 10(7), 1430; https://doi.org/10.3390/microorganisms10071430 - 15 Jul 2022

Cited by 2 | Viewed by 2951

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a novel virus that belongs to the Coronoviridae family, emerged in December 2019, causing the COVID-19 pandemic in March 2020. Unlike previous SARS and Middle East respiratory syndrome (MERS) outbreaks, this virus has a higher transmissibility [...] Read more.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a novel virus that belongs to the Coronoviridae family, emerged in December 2019, causing the COVID-19 pandemic in March 2020. Unlike previous SARS and Middle East respiratory syndrome (MERS) outbreaks, this virus has a higher transmissibility rate, albeit a lower case fatality rate, which results in accumulation of a significant number of mutations and a faster evolution rate. Genomic studies on the mutation rate of the virus, as well as the identification of mutations that prevail and their impact on disease severity, are of great importance for pandemic surveillance and vaccine and drug development. Here, we aim to identify mutations on the SARS-CoV-2 viral genome and their effect on the proteins they are located in, in Greek patients infected in the first wave of the pandemic. To this end, we perform SARS-CoV-2 amplicon-based NGS sequencing on nasopharyngeal swab samples from Greek patients and bioinformatic analysis of the results. Although SARS-CoV-2 is considered genetically stable, we discover a variety of mutations on the viral genome. In detail, 18 mutations are detected in total on 10 SARS-CoV-2 isolates. The mutations are located on ORF1ab, S protein, M protein, ORF3a and ORF7a. Sixteen are also detected in patients from other regions around the world, and two are identified for the first time in the present study. Most of them result in amino acid substitutions. These substitutions are analyzed using computational tools, and the results indicate minor or major impact on the proteins’ structural stability, which could probably affect viral transmissibility and pathogenesis. The correlation of these variations with the viral load levels is examined, and their implication for disease severity and the biology of the virus are discussed. Full article

(This article belongs to the Section Virology)

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