Microorganisms

12 pages, 1942 KiB

Open AccessArticle

Rare Plasmid-Mediated AmpC Beta-Lactamase DHA-1 Located on Easy Mobilized IS26-Related Genetic Element Detected in Escherichia coli from Livestock and Food in Germany

by Chiara Manfreda, Annemarie Kaesbohrer, Silvia Schmoger, Tanja Skladnikiewicz-Ziemer, Mirjam Grobbel and Alexandra Irrgang

Microorganisms 2024, 12(3), 632; https://doi.org/10.3390/microorganisms12030632 - 21 Mar 2024

Viewed by 1472

Abstract

AmpC beta-lactamases cause resistance to third-generation cephalosporins, including beta-lactamase inhibitors. In Escherichia coli from the German food production chain, the majority of AmpC beta-lactamase activity can be attributed to plasmid-mediated CMY-2 or overproduction of chromosomal AmpC beta-lactamase, but occasionally other enzymes like DHA-1 [...] Read more.

AmpC beta-lactamases cause resistance to third-generation cephalosporins, including beta-lactamase inhibitors. In Escherichia coli from the German food production chain, the majority of AmpC beta-lactamase activity can be attributed to plasmid-mediated CMY-2 or overproduction of chromosomal AmpC beta-lactamase, but occasionally other enzymes like DHA-1 are involved. This study investigated the prevalence of the AmpC beta-lactamase DHA-1 in ESBL/AmpC-producing E. coli (n = 4706) collected between 2016 and 2021 as part of a German antimicrobial resistance monitoring program along the food chain. Eight isolates (prevalence < 0.2%) were detected and further characterized by PFGE, transformation and conjugation experiments as well as short-read and long-read sequencing. All eight strains harbored bla_DHA-1 together with qnrB4, sul1 and mph(A) resistance genes on an IS26 composite transposon on self-transferable IncFII or IncFIA/FIB/II plasmids. During laboratory experiments, activation of the translocatable unit of IS26-bound structures was observed. This was shown by the variability of plasmid sizes in original isolates, transconjugants or transferred plasmids, and correspondingly, duplications of resistance fragments were found in long-read sequencing. This activation could be artificial due to laboratory handling or naturally occurring. Nevertheless, DHA-1 is a rare AmpC beta-lactamase in livestock and food in Germany, and its dissemination will be monitored in the future. Full article

(This article belongs to the Special Issue Antibiotic Resistance in Foodborne Bacteria)

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21 pages, 4110 KiB

Open AccessArticle

LPS-Dephosphorylating Cobetia amphilecti Alkaline Phosphatase of PhoA Family Divergent from the Multiple Homologues of Cobetia spp.

by Larissa Balabanova, Svetlana Bakholdina, Nina Buinovskaya, Yulia Noskova, Oksana Kolpakova, Vanessa Vlasova, Georgii Bondarev, Aleksandra Seitkalieva, Oksana Son and Liudmila Tekutyeva

Microorganisms 2024, 12(3), 631; https://doi.org/10.3390/microorganisms12030631 - 21 Mar 2024

Cited by 1 | Viewed by 1858

Abstract

A highly active alkaline phosphatase (ALP) of the protein structural family PhoA, from a mussel gut-associated strain of the marine bacterium Cobetia amphilecti KMM 296 (CmAP), was found to effectively dephosphorylate lipopolysaccharides (LPS). Therefore, the aim of this work was to perform a [...] Read more.

A highly active alkaline phosphatase (ALP) of the protein structural family PhoA, from a mussel gut-associated strain of the marine bacterium Cobetia amphilecti KMM 296 (CmAP), was found to effectively dephosphorylate lipopolysaccharides (LPS). Therefore, the aim of this work was to perform a comprehensive bioinformatics analysis of the structure, and to suggest the physiological role of this enzyme in marine bacteria of the genus Cobetia. A scrutiny of the CmAP-like sequences in 36 available Cobetia genomes revealed nine homologues intrinsic to the subspecies C. amphilecti, whereas PhoA of a distant relative Cobetia crustatorum JO1^T carried an inactive mutation. However, phylogenetic analysis of all available Cobetia ALP sequences showed that each strain of the genus Cobetia possesses several ALP variants, mostly the genes encoding for PhoD and PhoX families. The C. amphilecti strains have a complete set of four ALP families’ genes, namely: PhoA, PafA, PhoX, and two PhoD structures. The Cobetia marina species is distinguished by the presence of only three PhoX and PhoD genes. The Cobetia PhoA proteins are clustered together with the human and squid LPS-detoxifying enzymes. In addition, the predicted PhoA biosynthesis gene cluster suggests its involvement in the control of cellular redox balance, homeostasis, and cell cycle. Apparently, the variety of ALPs in Cobetia spp. indicates significant adaptability to phosphorus-replete and depleted environments and a notable organophosphate destructor in eco-niches from which they once emerged, including Zostera spp. The ALP clusterization and degree of similarity of the genus-specific biosynthetic genes encoding for ectoine and polyketide cluster T1PKS, responsible for sulfated extracellular polysaccharide synthesis, coincide with a new whole genome-based taxonomic classification of the genus Cobetia. The Cobetia strains and their ALPs are suggested to be adaptable for use in agriculture, biotechnology and biomedicine. Full article

(This article belongs to the Special Issue Genomics of Marine and Aquatic Bacteria: A Focus on Novel Taxa, Diversity and Biotechnological Potential)

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13 pages, 745 KiB

Open AccessReview

Exploring Viral–Host Protein Interactions as Antiviral Therapies: A Computational Perspective

by Sobia Idrees, Hao Chen, Nisha Panth, Keshav Raj Paudel and Philip M. Hansbro

Microorganisms 2024, 12(3), 630; https://doi.org/10.3390/microorganisms12030630 - 21 Mar 2024

Cited by 2 | Viewed by 2868

Abstract

The interactions between human and viral proteins are pivotal in viral infection and host immune responses. These interactions traverse different stages of the viral life cycle, encompassing initial entry into host cells, replication, and the eventual deployment of immune evasion strategies. As viruses [...] Read more.

The interactions between human and viral proteins are pivotal in viral infection and host immune responses. These interactions traverse different stages of the viral life cycle, encompassing initial entry into host cells, replication, and the eventual deployment of immune evasion strategies. As viruses exploit host cellular machinery for their replication and survival, targeting key protein–protein interactions offer a strategic approach for developing antiviral drugs. This review discusses how viruses interact with host proteins to develop viral–host interactions. In addition, we also highlight valuable resources that aid in identifying new interactions, incorporating high-throughput methods, and computational approaches, ultimately helping to understand how these tools can be effectively utilized to study viral–host interactions. Full article

(This article belongs to the Section Antimicrobial Agents and Resistance)

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12 pages, 3518 KiB

Open AccessArticle

Isolation and Characterization of a Novel Virulent Phage ASG01 of Aeromonas salmonicida and Its Cell Wall Hydrolase Activity

by Chen Li, Qiting Fang, Yangjun Zhang, Kunyan Li, Yaoguang Li, Rong Wang, Yuyuan Peng, Guofan Zhang, Liqiu Xia and Shengbiao Hu

Microorganisms 2024, 12(3), 629; https://doi.org/10.3390/microorganisms12030629 - 21 Mar 2024

Viewed by 1393

Abstract

Aeromonas salmonicida is an important pathogen that causes furunculosis in trout and salmon with high morbidity and mortality, resulting in significant economic losses in aquaculture. Overuse of antibiotics has led to the continuous emergence of drug-resistant strains. Hence, there is an urgent need [...] Read more.

Aeromonas salmonicida is an important pathogen that causes furunculosis in trout and salmon with high morbidity and mortality, resulting in significant economic losses in aquaculture. Overuse of antibiotics has led to the continuous emergence of drug-resistant strains. Hence, there is an urgent need to find an alternative environmentally friendly antimicrobial agent. In this study, we isolated a virulent phage of A. salmonicida, named ASG01, which belongs to the Myoviridae family and maintains lytic activity at a pH value range from 4 to 12 and in the temperature range from 30 °C to 60 °C. The whole genomic sequence of ASG01 showed 82% similarity to Aeromonas phage pAh6-C. The cell wall hydrolase (Cwh)-encoding gene from the genome of ASG01 was predicted and heterologously expressed. Notably, in the absence of additional phage genes, endogenous expression of Cwh could lyse E. coli cells and greatly inhibit the growth of tested fish pathogenic bacteria. The lytic activity of Cwh was eliminated when the predicted active site was mutated. These results indicate that Cwh of ASG01 possessed excellent lytic activity and a wide antibacterial spectrum, suggesting its potential as an effective enzybiotic. Full article

(This article belongs to the Section Microbial Biotechnology)

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19 pages, 6279 KiB

Open AccessArticle

Dinoflagellate Proton-Pump Rhodopsin Genes in Long Island Sound: Diversity and Spatiotemporal Distribution

by Huan Zhang, Kelly J. Nulick, Zair Burris, Melissa Pierce, Minglei Ma and Senjie Lin

Microorganisms 2024, 12(3), 628; https://doi.org/10.3390/microorganisms12030628 - 21 Mar 2024

Cited by 1 | Viewed by 1249

Abstract

Microbial proton-pump rhodopsin (PPR)-based phototrophy, a light-harvesting mechanism different from chlorophyll-based photosystems, may contribute significantly to solar energy entry into the marine ecosystem. PPR transforms solar energy into cellular energy that is used for various metabolic processes in the cells or flagellar movement. [...] Read more.

Microbial proton-pump rhodopsin (PPR)-based phototrophy, a light-harvesting mechanism different from chlorophyll-based photosystems, may contribute significantly to solar energy entry into the marine ecosystem. PPR transforms solar energy into cellular energy that is used for various metabolic processes in the cells or flagellar movement. Although rhodopsins or their encoding genes have been documented in a wide phylogenetic range of cultured dinoflagellates, information is limited about how widespread and how spatiotemporally dynamical dinoflagellate PPR (DiPPR) are in natural marine ecosystems. In this study, we investigated DiPPR in Long Island Sound (LIS), a temperate estuary of the Atlantic Ocean between Connecticut and Long Island, New York, USA. We isolated six novel full-length dinoflagellate proton-pump rhodopsin cDNAs, expanding the DiPPR database that is crucial to PPR research. Based on these new sequences and existing sequences of DiPPR, we designed primers and conducted quantitative PCR and sequencing to determine the abundance and diversity of DiPPR genes spatially and temporally throughout a year in the water samples collected from LIS. DiPPR genes were found year-round and throughout LIS but with higher abundances in the eutrophic Western Sound and in April and July. The gene diversity data suggest that there are at least five distinct rhodopsin-harboring groups of dinoflagellates throughout the year. The abundance of DiPPR genes, measured as copy number per mL of seawater, appeared not to be influenced by water temperature or nitrogen nutrient concentration but exhibited weak negative correlations with orthophosphate concentration and salinity and a positive correlation with the abundance of DiPPR-harboring dinoflagellates. This first quantitative profiling of PPR in natural plankton reveals the prevalence and dynamics of this plastid-independent photoenergy harvesting mechanism in a temperate estuary and provides efficient DiPPR primers potentially useful for future research. Furthermore, this study shed light on the potential role of DiPPR in phosphor nutrition and dinoflagellate population, which warrants further studies. Full article

(This article belongs to the Special Issue Research on Biology of Dinoflagellates)

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14 pages, 7882 KiB

Open AccessArticle

Metagenomic Insight into the Effect of Probiotics on Nitrogen Cycle in the Coilia nasus Aquaculture Pond Water

by Qi Mang, Jun Gao, Quanjie Li, Yi Sun, Gangchun Xu and Pao Xu

Microorganisms 2024, 12(3), 627; https://doi.org/10.3390/microorganisms12030627 - 21 Mar 2024

Viewed by 1205

Abstract

Recently, probiotics have been widely applied for the in situ remediation of aquatic water. Numerous studies have proved that probiotics can regulate water quality by improving the microbial community. Nitrogen cycling, induced by microorganisms, is a crucial process for maintaining the balance of [...] Read more.

Recently, probiotics have been widely applied for the in situ remediation of aquatic water. Numerous studies have proved that probiotics can regulate water quality by improving the microbial community. Nitrogen cycling, induced by microorganisms, is a crucial process for maintaining the balance of the aquatic ecosystem. Nevertheless, the underlying mechanisms by which probiotics enhance water quality in aquatic systems remain poorly understood. To explore the water quality indicators and their correlation with nitrogen cycling-related functional genes, metagenomic analysis of element cycling was performed to identify nitrogen cycling-related functional genes in Coilia nasus aquatic water between the control group (C) and the groups supplemented with probiotics in feed (PF) or water (PW). The results showed that adding probiotics to the aquatic water could reduce the concentrations of ammonia nitrogen (NH₄⁺-N), nitrite (NO₂⁻-N), and total nitrogen (TN) in the water. Community structure analysis revealed that the relative abundance of Verrucomicrobiota was increased from 30 d to 120 d (2.61% to 6.35%) in the PW group, while the relative abundance of Cyanobacteria was decreased from 30 d to 120 d (5.66% to 1.77%). We constructed a nitrogen cycling pathway diagram for C. nasus aquaculture ponds. The nitrogen cycle functional analysis showed that adding probiotics to the water could increase the relative abundance of the amoC_B and hao (Nitrification pathways) and the nirS and nosZ (Denitrification pathways). Correlation analysis revealed that NH₄⁺-N was significantly negatively correlated with Limnohabitans, Sediminibacterium, and Algoriphagus, while NO₂⁻-N was significantly negatively correlated with Roseomonas and Rubrivivax. Our study demonstrated that adding probiotics to the water can promote nitrogen element conversion and migration, facilitate nitrogen cycling, benefit ecological environment protection, and remove nitrogen-containing compounds in aquaculture systems by altering the relative abundance of nitrogen cycling-related functional genes and microorganisms. Full article

(This article belongs to the Section Environmental Microbiology)

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32 pages, 1235 KiB

Open AccessReview

Importance of Probiotics in Fish Aquaculture: Towards the Identification and Design of Novel Probiotics

by Edgar Torres-Maravilla, Mick Parra, Kevin Maisey, Rodrigo A. Vargas, Alejandro Cabezas-Cruz, Alex Gonzalez, Mario Tello and Luis G. Bermúdez-Humarán

Microorganisms 2024, 12(3), 626; https://doi.org/10.3390/microorganisms12030626 - 21 Mar 2024

Cited by 7 | Viewed by 4288

Abstract

Aquaculture is a growing industry worldwide, but it faces challenges related to animal health. These challenges include infections by parasites, bacteria, and viral pathogens. These harmful pathogens have devastating effects on the industry, despite efforts to control them through vaccination and antimicrobial treatments. [...] Read more.

Aquaculture is a growing industry worldwide, but it faces challenges related to animal health. These challenges include infections by parasites, bacteria, and viral pathogens. These harmful pathogens have devastating effects on the industry, despite efforts to control them through vaccination and antimicrobial treatments. Unfortunately, these measures have proven insufficient to address the sanitary problems, resulting in greater environmental impact due to the excessive use of antimicrobials. In recent years, probiotics have emerged as a promising solution to enhance the performance of the immune system against parasitic, bacterial, and viral pathogens in various species, including mammals, birds, and fish. Some probiotics have been genetically engineered to express and deliver immunomodulatory molecules. These promote selective therapeutic effects and specific immunization against specific pathogens. This review aims to summarize recent research on the use of probiotics in fish aquaculture, with a particular emphasis on genetically modified probiotics. In particular, we focus on the advantages of using these microorganisms and highlight the main barriers hindering their widespread application in the aquaculture industry. Full article

(This article belongs to the Special Issue Probiotics: The Current State of Scientific Knowledge)

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23 pages, 3266 KiB

Open AccessArticle

Evaluation of Pyrophosphate-Driven Proton Pumps in Saccharomyces cerevisiae under Stress Conditions

by Krishnan Sreenivas, Leon Eisentraut, Daniel P. Brink, Viktor C. Persson, Magnus Carlquist, Marie F. Gorwa-Grauslund and Ed W. J. van Niel

Microorganisms 2024, 12(3), 625; https://doi.org/10.3390/microorganisms12030625 - 20 Mar 2024

Cited by 1 | Viewed by 1317

Abstract

In Saccharomyces cerevisiae, pH homeostasis is reliant on ATP due to the use of proton-translocating ATPase (H⁺-ATPase) which constitutes a major drain within cellular ATP supply. Here, an exogenous proton-translocating pyrophosphatase (H⁺-PPase) from Arabidopsis thaliana, which uses inorganic [...] Read more.

In Saccharomyces cerevisiae, pH homeostasis is reliant on ATP due to the use of proton-translocating ATPase (H⁺-ATPase) which constitutes a major drain within cellular ATP supply. Here, an exogenous proton-translocating pyrophosphatase (H⁺-PPase) from Arabidopsis thaliana, which uses inorganic pyrophosphate (PP_i) rather than ATP, was evaluated for its effect on reducing the ATP burden. The H⁺-Ppase was localized to the vacuolar membrane or to the cell membrane, and their impact was studied under acetate stress at a low pH. Biosensors (pHluorin and mQueen-2m) were used to observe changes in intracellular pH (pH_i) and ATP levels during growth on either glucose or xylose. A significant improvement of 35% in the growth rate at a pH of 3.7 and 6 g·L⁻¹ acetic acid stress was observed in the vacuolar membrane H⁺-PPase strain compared to the parent strain. ATP levels were elevated in the same strain during anaerobic glucose and xylose fermentations. During anaerobic xylose fermentations, co-expression of pHluorin and a vacuolar membrane H⁺-PPase improved the growth characteristics by means of an improved growth rate (11.4%) and elongated logarithmic growth duration. Our study identified a potential method for improving productivity in the use of S. cerevisiae as a cell factory under the harsh conditions present in industry. Full article

(This article belongs to the Section Microbial Biotechnology)

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15 pages, 6308 KiB

Open AccessArticle

Antimicrobial Effect of Copper Nanoparticles on Relevant Supragingival Oral Bacteria

by Nia Oetiker, Daniela Salinas, Joaquín Lucero-Mora, Rocío Orellana, Mariana Quiroz-Muñoz, Denisse Bravo and José M. Pérez-Donoso

Microorganisms 2024, 12(3), 624; https://doi.org/10.3390/microorganisms12030624 - 20 Mar 2024

Cited by 2 | Viewed by 2244

Abstract

Copper nanoparticles (Cu NPs) show promise in dentistry for combating bacterial dysbiosis and tooth decay. Understanding their effects on commensal versus pathogenic bacteria is vital for maintaining oral health balance. While Cu NPs demonstrate antibacterial properties against various oral bacteria, including common pathogens [...] Read more.

Copper nanoparticles (Cu NPs) show promise in dentistry for combating bacterial dysbiosis and tooth decay. Understanding their effects on commensal versus pathogenic bacteria is vital for maintaining oral health balance. While Cu NPs demonstrate antibacterial properties against various oral bacteria, including common pathogens associated with tooth decay, their impact on commensal bacteria requires careful examination. In our work, we analyzed three types of Cu NPs for their effects on the growth, viability, and biofilm formation of representative caries-associated and commensal oral bacteria. S. sanguinis showed high tolerance to all Cu NPs, while L. rhamnosus was highly sensitive. Oxide-Cu NPs exhibited a stronger inhibitory effect on pathobionts compared with commensal bacteria. Moreover, the biofilm formation of the key cariogenic bacteria S. mutans was reduced, with minimal negative effects on commensal species’ biofilm formation. All our results showed that CuO nanoparticles (CuO NPs) exhibit reduced toxicity toward commensal bacteria growth and development but have a strong impact on pathogens. This suggests their potential for targeted treatments against pathogenic bacteria, which could help in maintaining the balance of the oral bacterial community. Full article

(This article belongs to the Special Issue Antimicrobial Properties of Nanoparticle)

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10 pages, 590 KiB

Open AccessArticle

Antimicrobial Use during the SARS-CoV-2 Pandemic in a Greek Tertiary University Hospital

by Dimitrios Biros, Sempastian Filippas-Ntekouan, Diamantina Limperatou, Angelos Liontos, Rafail Matzaras, Konstantina-Helen Tsarapatsani, Nikolaos-Gavriel Kolios, Christiana Pappa, Maria Nasiou, Eleni Pargana, Ilias Tsiakas, Valentini Samanidou, Lazaros Athanasiou, Revekka Konstantopoulou, Haralampos Milionis and Eirini Christaki

Microorganisms 2024, 12(3), 623; https://doi.org/10.3390/microorganisms12030623 - 20 Mar 2024

Viewed by 1215

Abstract

In cases of SARS-CoV-2 hospitalization, despite low bacterial co-infection rates, antimicrobial use may be disproportionately high. Our aim was to quantify such usage in COVID-19 patients and identify factors linked to increased antibiotic use. We retrospectively studied patients with SARS-CoV-2 infection who were [...] Read more.

In cases of SARS-CoV-2 hospitalization, despite low bacterial co-infection rates, antimicrobial use may be disproportionately high. Our aim was to quantify such usage in COVID-19 patients and identify factors linked to increased antibiotic use. We retrospectively studied patients with SARS-CoV-2 infection who were hospitalized at our institution during the pandemic. In the initial two waves of the pandemic, antimicrobial use was notably high (89% in the first wave and 92% in the second), but it decreased in subsequent waves. Elevated procalcitonin (>0.5 μg/mL) and C-reactive protein (>100 mg/L) levels were linked to antibiotic usage, while prior vaccination reduced antibiotic incidence. Antimicrobial use decreased in the pandemic, suggesting enhanced comprehension of SARS-CoV-2′s natural course. Additionally, it was correlated with heightened SARS-CoV-2 severity, elevated procalcitonin, and C-reactive protein levels. Full article

(This article belongs to the Special Issue Healthcare-Associated Infections and Antimicrobial Therapy)

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11 pages, 596 KiB

Open AccessArticle

Association between Gut Microbiota and Muscle Strength in Japanese General Population of the Iwaki Health Promotion Project

by Yoshikuni Sugimura, Yichi Yang, Akira Kanda, Akihiro Mawatari, Yoshinori Tamada, Tatsuya Mikami, Shigeyuki Nakaji and Kazushige Ihara

Microorganisms 2024, 12(3), 622; https://doi.org/10.3390/microorganisms12030622 - 20 Mar 2024

Cited by 1 | Viewed by 1365

Abstract

The association between the gut microbiota and muscle strength has garnered attention in the context of mitigating muscle decline. However, many study subjects have been individuals with existing illnesses or the elderly only. This study aims to elucidate the association between the gut [...] Read more.

The association between the gut microbiota and muscle strength has garnered attention in the context of mitigating muscle decline. However, many study subjects have been individuals with existing illnesses or the elderly only. This study aims to elucidate the association between the gut microbiota and muscle strength indicators using grip strength/BMI in a large-scale study of community residents. The mean age of men (n = 442) and women (n = 588) was 50.5 (15.3) and 51.2 (15.9) years, respectively. The muscle strength indicator used was grip/BMI. The association between total read count and genus-level gut microbiota and muscle strength was analyzed. The mean grip/BMI was 1.8 (0.3) for men and 1.2 (0.2) for women. The genus of the gut microbiota that showed an association in both sexes was Eggerthella (men: β = 0.18, CI: 0.04–0.31, p = 0.009; women: β = 0.07, CI: 0.00–0.12, p = 0.028). Blautia, Eggerthella and Faecalibacterium were found to be significantly associated with grip/BMI in both the multiple regression analysis and Spearman’s correlation analysis after the multiple comparison adjustment. These results suggest that an increase in Blautia and Eggerthella, coupled with a decrease in Faecalibacterium, may contribute to muscle strengthening or the suppression of muscle weakness. Full article

(This article belongs to the Special Issue Effects of Gut Microbiota on Human Health and Disease)

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22 pages, 2948 KiB

Open AccessArticle

Dynamic Protein Phosphorylation in Streptococcus pyogenes during Growth, Stationary Phase, and Starvation

by Stefan Mikkat, Michael Kreutzer and Nadja Patenge

Microorganisms 2024, 12(3), 621; https://doi.org/10.3390/microorganisms12030621 - 20 Mar 2024

Cited by 2 | Viewed by 1519

Abstract

Phosphorylation of proteins at serine, threonine, and tyrosine residues plays an important role in physiological processes of bacteria, such as cell cycle, metabolism, virulence, dormancy, and stationary phase functions. Little is known about the targets and dynamics of protein phosphorylation in Streptococcus pyogenes [...] Read more.

Phosphorylation of proteins at serine, threonine, and tyrosine residues plays an important role in physiological processes of bacteria, such as cell cycle, metabolism, virulence, dormancy, and stationary phase functions. Little is known about the targets and dynamics of protein phosphorylation in Streptococcus pyogenes, which possesses a single known transmembrane serine/threonine kinase belonging to the class of PASTA kinases. A proteomics and phosphoproteomics workflow was performed with S. pyogenes serotype M49 under different growth conditions, stationary phase, and starvation. The quantitative analysis of dynamic phosphorylation, which included a subset of 463 out of 815 identified phosphorylation sites, revealed two main types of phosphorylation events. A small group of phosphorylation events occurred almost exclusively at threonine residues of proteins related to the cell cycle and was enhanced in growing cells. The majority of phosphorylation events occurred during stationary phase or starvation, preferentially at serine residues. PASTA kinase-dependent cell cycle regulation processes found in related bacteria are conserved in S. pyogenes. Increased protein phosphorylation during the stationary phase has also been described for some other bacteria, and could therefore be a general feature in the physiology of bacteria, whose functions and the kinases involved need to be elucidated in further analyses. Full article

(This article belongs to the Section Systems Microbiology)

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12 pages, 310 KiB

Open AccessArticle

Impact of COVID-19 Pandemic on the Trends of Trichomonas vaginalis Infection in a Tertiary Hospital of Madrid, Spain

by Celia Bolumburu, Vega Zamora, María Muñoz-Algarra, Maria Luisa de la Cruz Conty, José Antonio Escario and Alexandra Ibáñez-Escribano

Microorganisms 2024, 12(3), 620; https://doi.org/10.3390/microorganisms12030620 - 20 Mar 2024

Cited by 1 | Viewed by 1398

Abstract

More than one million sexually transmitted infections (STIs) occur every day, and Trichomonas vaginalis is responsible for more than 156 million cases each year worldwide. Nevertheless, epidemiological studies of this parasite in Europe are scarce. The aim of this study was to evaluate [...] Read more.

More than one million sexually transmitted infections (STIs) occur every day, and Trichomonas vaginalis is responsible for more than 156 million cases each year worldwide. Nevertheless, epidemiological studies of this parasite in Europe are scarce. The aim of this study was to evaluate the impact that the COVID-19 pandemic may have had in the diagnosis and epidemiology of trichomoniasis. All available data from January 2018 to December 2021 for T. vaginalis isolation on gynecologic patients attending a Spanish Tertiary Hospital were analyzed. Pre-pandemic results (2018–2019) were compared to pandemic results (2020–2021). The pre-pandemic T. vaginalis prevalence in women was 1.15% (95% Confidence Interval, CI: 0.94–1.41), and significantly decreased in 2020–2021 (0.77%, 95% CI: 0.57–1.03; p = 0.025). Demographic nor clinical characteristics of women diagnosed with trichomoniasis did not statistically differ between the periods, although an increase in chlamydia co-infected patients was observed in the latest (from 8% in 2018–2019 to 19% in 2020–2021). This study has detected a decrease in the diagnosis of trichomoniasis; however, this is probably due to the increase in the healthcare pressure triggered by the pandemic. More than 75% of the cases diagnosed in 2021 occurred in the second half, which suggests that special attention should be given to the evolution in the coming years once normality has been restored in hospitals. Moreover, these results warn of the lack of routine diagnosis of trichomoniasis during pregnancy and the absence of specific protocols for possible co-infections, which could become a strategy to reduce the growing trend of STIs, including T. vaginalis detection, as an interesting marker of sexual risk behaviors. Full article

(This article belongs to the Special Issue Detection and Analysis of Clinical Microbial Infections)

14 pages, 302 KiB

Open AccessReview

Vaginal Microbiota and HPV in Latin America: A Narrative Review

by Eduardo Tosado-Rodríguez, Ian Alvarado-Vélez, Josefina Romaguera and Filipa Godoy-Vitorino

Microorganisms 2024, 12(3), 619; https://doi.org/10.3390/microorganisms12030619 - 20 Mar 2024

Cited by 1 | Viewed by 2151

Abstract

With the expansion of human microbiome studies in the last 15 years, we have realized the immense implications of microbes in human health. The human holobiont is now accepted, given the commensal relationships with bacteria, fungi, parasites, viruses, and human cells. The cervicovaginal [...] Read more.

With the expansion of human microbiome studies in the last 15 years, we have realized the immense implications of microbes in human health. The human holobiont is now accepted, given the commensal relationships with bacteria, fungi, parasites, viruses, and human cells. The cervicovaginal microbiota is a specific case within the human microbiome where diversity is lower to maintain a chemical barrier of protection against infections. This narrative review focuses on the vaginal microbiome. It summarizes key findings on how native bacteria protect women from disease or predispose them to damaging inflammatory processes with an emphasis on the role of HPV infections in Latin America, one of the world’s regions with the highest cervical cancer prevalence. Full article

(This article belongs to the Special Issue Vaginal Microbiome in Women's Health)

12 pages, 3156 KiB

Open AccessArticle

Utilization of Spent Coffee Grounds for Bioelectricity Generation in Sediment Microbial Fuel Cells

by Nurfarhana Nabila Mohd Noor, Ilwon Jeong, Seokjin Yoon and Kyunghoi Kim

Microorganisms 2024, 12(3), 618; https://doi.org/10.3390/microorganisms12030618 - 19 Mar 2024

Cited by 3 | Viewed by 1506

Abstract

This study examined the utilization of spent coffee grounds with different aqueous extraction methods for the bioelectricity generation from coastal benthic sediment through a sediment microbial fuel cell (SMFC) system. Different methods for the aqueous extraction of SCGs were evaluated, including rinsing and [...] Read more.

This study examined the utilization of spent coffee grounds with different aqueous extraction methods for the bioelectricity generation from coastal benthic sediment through a sediment microbial fuel cell (SMFC) system. Different methods for the aqueous extraction of SCGs were evaluated, including rinsing and drying of the SCG (SMFC-CRD), immersion, rinsing and drying (SMFC-CRID), drying alone (SMFC-CD), and untreated SCG (SMFC-C). The caffeine concentration in the SCG was significantly reduced using pretreatments, with SMFC-CRID achieving the lowest concentration of 0.021 ± 0.001 mg/g. SMFC-CRD contributed to the generation of the highest current density of 213.7 mA/m² during closed-circuit operation and exhibited the highest power density of 96.9 mW/m² in the polarization test, due to the suitable caffeine content of 0.275 ± 0.001 mg/g in the SCG. This study could provide a cost-effective method for reusing SCGs (i.e., 128 g) while generating bioelectricity as an alternative energy source. These results suggest that pretreatment with SCGs is essential for achieving optimal power density and reducing the caffeine concentration in the SMFC system. Full article

(This article belongs to the Special Issue Biotechnology for Environmental Remediation)

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15 pages, 7699 KiB

Open AccessReview

Back to the Future: Immune Protection or Enhancement of Future Coronaviruses

by Merit Bartels, Eric Sala Solé, Lotte M. Sauerschnig and Ger T. Rijkers

Microorganisms 2024, 12(3), 617; https://doi.org/10.3390/microorganisms12030617 - 19 Mar 2024

Viewed by 2126

Abstract

Before the emergence of SARS-CoV-1, MERS-CoV, and most recently, SARS-CoV-2, four other coronaviruses (the alpha coronaviruses NL63 and 229E and the beta coronaviruses OC43 and HKU1) had already been circulating in the human population. These circulating coronaviruses all cause mild respiratory illness during [...] Read more.

Before the emergence of SARS-CoV-1, MERS-CoV, and most recently, SARS-CoV-2, four other coronaviruses (the alpha coronaviruses NL63 and 229E and the beta coronaviruses OC43 and HKU1) had already been circulating in the human population. These circulating coronaviruses all cause mild respiratory illness during the winter seasons, and most people are already infected in early life. Could antibodies and/or T cells, especially against the beta coronaviruses, have offered some form of protection against (severe) COVID-19 caused by infection with SARS-CoV-2? Related is the question of whether survivors of SARS-CoV-1 or MERS-CoV would be relatively protected against SARS-CoV-2. More importantly, would humoral and cellular immunological memory generated during the SARS-CoV-2 pandemic, either by infection or vaccination, offer protection against future coronaviruses? Or rather than protection, could antibody-dependent enhancement have taken place, a mechanism by which circulating corona antibodies enhance the severity of COVID-19? Another related phenomenon, the original antigenic sin, would also predict that the effectiveness of the immune response to future coronaviruses would be impaired because of the reactivation of memory against irrelevant epitopes. The currently available evidence indicates that latter scenarios are highly unlikely and that especially cytotoxic memory T cells directed against conserved epitopes of human coronaviruses could at least offer partial protection against future coronaviruses. Full article

(This article belongs to the Special Issue Coronaviruses: Past, Present, and Future)

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17 pages, 2607 KiB

Open AccessArticle

Comparative Analysis of Plant Growth-Promoting Rhizobacteria’s Effects on Alfalfa Growth at the Seedling and Flowering Stages under Salt Stress

by Xixi Ma, Cuihua Huang, Jun Zhang, Jing Pan, Qi Guo, Hui Yang and Xian Xue

Microorganisms 2024, 12(3), 616; https://doi.org/10.3390/microorganisms12030616 - 19 Mar 2024

Cited by 1 | Viewed by 1491

Abstract

Alfalfa (Medicago sativa L.), a forage legume known for its moderate salt–alkali tolerance, offers notable economic and ecological benefits and aids in soil amelioration when cultivated in saline–alkaline soils. Nonetheless, the limited stress resistance of alfalfa could curtail its productivity. This study [...] Read more.

Alfalfa (Medicago sativa L.), a forage legume known for its moderate salt–alkali tolerance, offers notable economic and ecological benefits and aids in soil amelioration when cultivated in saline–alkaline soils. Nonetheless, the limited stress resistance of alfalfa could curtail its productivity. This study investigated the salt tolerance and growth-promoting characteristics (in vitro) of four strains of plant growth-promoting rhizobacteria (PGPR) that were pre-selected, as well as their effects on alfalfa at different growth stages (a pot experiment). The results showed that the selected strains belonged to the genera Priestia (HL3), Bacillus (HL6 and HG12), and Paenibacillus (HG24). All four strains exhibited the ability to solubilize phosphate and produce indole-3-acetic acid (IAA) and 1-aminocyclopropane-1-carboxylate (ACC) deaminase. Among them, except for strain HG24, the other strains could tolerate 9% NaCl stress. Treatment with 100 mM NaCl consistently decreased the IAA production levels of the selected strains, but inconsistent changes (either enhanced or reduced) in terms of phosphate solubilization, ACC deaminase, and exopolysaccharides (EPS) production were observed among the strains. During the various growth stages of alfalfa, PGPR exhibited different growth-promoting effects: at the seedling stage, they enhanced salt tolerance through the induction of physiological changes; at the flowering stage, they promoted growth through nutrient acquisition. The current findings suggest that strains HL3, HL6, and HG12 are effective microbial inoculants for alleviating salt stress in alfalfa plants in arid and semi-arid regions. This study not only reveals the potential of indigenous salt-tolerant PGPR in enhancing the salt tolerance of alfalfa but also provides new insights into the mechanisms of action of PGPR. Full article

(This article belongs to the Special Issue Using Microorganisms to Increase Crop Productivity and Sustainability)

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17 pages, 5895 KiB

Open AccessArticle

Characterizing the Role of AosfgA and AofluG in Mycelial and Conidial Development in Arthrobotrys oligospora and Their Role in Secondary Metabolism

by Qianqian Liu, Na Bai, Shipeng Duan, Yanmei Shen, Lirong Zhu and Jinkui Yang

Microorganisms 2024, 12(3), 615; https://doi.org/10.3390/microorganisms12030615 - 19 Mar 2024

Cited by 3 | Viewed by 1073

Abstract

Arthrobotrys oligospora, a widespread nematode-trapping fungus which can produce conidia for asexual reproduction and form trapping devices (traps) to catch nematodes. However, little is known about the sporulation mechanism of A. oligospora. This research characterized the functions and regulatory roles of [...] Read more.

Arthrobotrys oligospora, a widespread nematode-trapping fungus which can produce conidia for asexual reproduction and form trapping devices (traps) to catch nematodes. However, little is known about the sporulation mechanism of A. oligospora. This research characterized the functions and regulatory roles of the upstream spore-producing regulatory genes, AosfgA and AofluG, in A. oligospora. Our analysis showed that AosfgA and AofluG interacted with each other. Meanwhile, the AofluG gene was downregulated in the ΔAosfgA mutant strain, indicating that AosfgA positively regulates AofluG. Loss of the AosfgA and AofluG genes led to shorter hyphae and more septa, and the ΔAosfgA strain responded to heat and chemical stresses. Surprisingly, the number of nuclei was increased in the mycelia but reduced in the conidia of the ΔAosfgA and ΔAofluG mutants. In addition, after nematode induction, the number and volume of vacuoles were remarkably increased in the ΔAosfgA and ΔAofluG mutant strains. The abundance of metabolites was markedly decreased in the ΔAosfgA and ΔAofluG mutant strains. Collectively, the AosfgA and AofluG genes play critical roles in mycelial development, and they are also involved in vacuole assembly, the stress response, and secondary metabolism. Our study provides distinct insights into the regulatory mechanism of sporulation in nematode-trapping fungi. Full article

(This article belongs to the Section Environmental Microbiology)

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15 pages, 3519 KiB

Open AccessArticle

Combined TCBS and CHROMagar Analyses Allow for Basic Identification of Vibrio vulnificus within a 48 h Incubation Period in the Coastal Baltic Sea

by Conor Christopher Glackin, Susann Dupke, Thota Sharath Chandra, David Riedinger and Matthias Labrenz

Microorganisms 2024, 12(3), 614; https://doi.org/10.3390/microorganisms12030614 - 19 Mar 2024

Viewed by 1953

Abstract

With rising infection rates in recent years, Vibrio vulnificus poses an increasing threat to public safety in the coastal brackish Baltic Sea. It is therefore important to monitor this organism and assess the V. vulnificus infection risk on a more regular basis. However, [...] Read more.

With rising infection rates in recent years, Vibrio vulnificus poses an increasing threat to public safety in the coastal brackish Baltic Sea. It is therefore important to monitor this organism and assess the V. vulnificus infection risk on a more regular basis. However, as the coastline of the Baltic Sea is 8000 km long and shared by nine nations, a convenient, fast, inexpensive, yet efficient V. vulnificus identification method is essential. We evaluated the effectiveness of a two-step agar-based approach consisting of successive Vibrio isolation and cultivation on thiosulphate-citrate-bile salt sucrose (TCBS) agar and CHROMagar™ Vibrio for V. vulnificus in comparison with V. cholerae, V. parahaemolyticus, and V. alginolyticus. Our study contains isolates from water and sediment across a broad expanse of the Baltic Sea including 13 locations and two different summers, the time of year during which Vibrio infections are usually much more frequent. Confirmation of isolate species identity was carried out using molecular analyses. The two-step agar plating method performed well across different locations and timeframes in correctly identifying V. vulnificus by more than 80%, but the sensitivity in other Vibrio species varied. Thus, our approach yielded promising results as a potential tool for early V. vulnificus detection across a broad timeframe and transect of the Baltic Sea and potentially other brackish environments. Full article

(This article belongs to the Section Environmental Microbiology)

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11 pages, 1306 KiB

Open AccessArticle

Characterization of the 3,4-Dichloroaniline Degradation Gene Cluster in Acinetobacter soli GFJ2

by Namiko Gibu, Daisuke Kasai, Saki Sato, Michiro Tabata, Alisa Vangnai and Masao Fukuda

Microorganisms 2024, 12(3), 613; https://doi.org/10.3390/microorganisms12030613 - 19 Mar 2024

Cited by 1 | Viewed by 1214

Abstract

3,4-Dichloroaniline (34DCA), a major metabolite of phenylurea herbicides, causes environmental contamination owing to its toxicity and recalcitrant properties. Acinetobacter soli strain GFJ2, isolated from soil potentially contaminated with herbicides, can degrade 34DCA. This study aimed to identify and characterize the 34DCA degradation gene [...] Read more.

3,4-Dichloroaniline (34DCA), a major metabolite of phenylurea herbicides, causes environmental contamination owing to its toxicity and recalcitrant properties. Acinetobacter soli strain GFJ2, isolated from soil potentially contaminated with herbicides, can degrade 34DCA. This study aimed to identify and characterize the 34DCA degradation gene cluster responsible for the conversion of 34DCA to 4,5-dichlorocatechol in the strain GFJ2. Genome analysis revealed one chromosome and seven plasmids in GFJ2, comprising 21, 75, and 3309 copies of rRNA, 75 tRNA, and protein-encoding genes, respectively. A gene cluster responsible for 34DCA degradation was identified, comprising dcdA, dcdB, and dcdC, which encode dioxygenase, flavin reductase, and aldehyde dehydrogenase, respectively. Transcriptional analysis indicated that this gene cluster is constructed as an operon, induced during 34DCA utilization. The heterologous expression of dcdA and dcdB in Escherichia coli confirmed their activity in degrading 34DCA to an intermediate metabolite, converted to 4,5-dichlorocatechol via a reaction involving the dcdC gene product, suggesting their involvement in 34DCA conversion to 4,5-dichlorocatechol. Deletion mutants of dcdA and dcdB lost 34DCA degradation ability, confirming their importance in 34DCA utilization in GFJ2. This study provides insights into the genetic mechanisms of 34DCA degradation by GFJ2, with potential applications in the bioremediation of environments contaminated by phenylurea herbicides. Full article

(This article belongs to the Special Issue Microbial Biocatalysis and Biodegradation 2.0)

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11 pages, 3428 KiB

Open AccessArticle

Impact of Zero-Valent Iron Nanoparticles and Ampicillin on Adenosine Triphosphate and Lactate Metabolism in the Cyanobacterium Fremyella diplosiphon

by Yavuz S. Yalcin, Busra N. Aydin and Viji Sitther

Microorganisms 2024, 12(3), 612; https://doi.org/10.3390/microorganisms12030612 - 19 Mar 2024

Viewed by 1123

Abstract

In cyanobacteria, the interplay of ATP and lactate dynamics underpins cellular energetics; their pronounced shifts in response to zero-valent iron (nZVI) nanoparticles and ampicillin highlight the nuanced metabolic adaptations to environmental challenges. In this study, we investigated the impact of nZVIs and ampicillin [...] Read more.

In cyanobacteria, the interplay of ATP and lactate dynamics underpins cellular energetics; their pronounced shifts in response to zero-valent iron (nZVI) nanoparticles and ampicillin highlight the nuanced metabolic adaptations to environmental challenges. In this study, we investigated the impact of nZVIs and ampicillin on Fremyella diplosiphon cellular energetics as determined by adenosine triphosphate (ATP) content, intracellular and extracellular lactate levels, and their impact on cell morphology as visualized by transmission electron microscopy. While a significant increase in ATP concentration was observed in 0.8 mg/L ampicillin-treated cells compared to the untreated control, a significant decline was noted in cells treated with 3.2 mg/L nZVIs. ATP levels in the combination regimen of 0.8 mg/L ampicillin and 3.2 mg/L nZVIs were significantly elevated (p < 0.05) compared to the 3.2 mg/L nZVI treatment. Intracellular and extracellular lactate levels were significantly higher in 0.8 mg/L ampicillin, 3.2 mg/L nZVIs, and the combination regimen compared to the untreated control; however, extracellular lactate levels were the highest in cells treated with 3.2 mg/L nZVIs. Visualization of morphological changes indicated increased thylakoid membrane stacks and inter-thylakoidal distances in 3.2 mg/L nZVI-treated cells. Our findings demonstrate a complex interplay of nanoparticle and antibiotic-induced responses, highlighting the differential impact of these stressors on F. diplosiphon metabolism and cellular integrity. Full article

(This article belongs to the Special Issue New Methods in Microbial Research 3.0)

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19 pages, 5102 KiB

Open AccessArticle

A Novel Strain of Bacillus cereus with a Strong Antagonistic Effect Specific to Sclerotinia and Its Genomic and Transcriptomic Analysis

by Wanfu Ma, Jinhao Ding, Qingyun Jia, Qianru Li, Shanhai Jiao, Xupeng Guo, Chengming Fan, Yuhong Chen and Zanmin Hu

Microorganisms 2024, 12(3), 611; https://doi.org/10.3390/microorganisms12030611 - 19 Mar 2024

Cited by 1 | Viewed by 1454

Abstract

Sclerotinia, which is caused by Sclerotinia sclerotiorum, is a severe disease of oilseed rape, which is an important oil crop worldwide. In this study, we isolated a novel strain of Bacillus cereus, named B. cereus HF10, from the rhizosphere soil of [...] Read more.

Sclerotinia, which is caused by Sclerotinia sclerotiorum, is a severe disease of oilseed rape, which is an important oil crop worldwide. In this study, we isolated a novel strain of Bacillus cereus, named B. cereus HF10, from the rhizosphere soil of the reed on the seaside of Yagzhou Bay, Sanya city, Hainan Province, China. HF10 exhibited a significant antagonistic effect on Sclerotinia sclerotiorum, with an inhibition rate of 79%, and to other species in Sclerotinia, but no antagonistic effect was found on various other fungi or bacteria. HF10 had an 82.3% inhibitory effect on the S. sclerotiorum infection of oilseed rape leaves and a 71.7% control effect on Sclerotinia infection in oilseed rape based on in vitro and in vivo experiments, respectively. The genomics and transcriptomics of HF10 and its loss of the antifungal function mutant Y11 were analyzed, and the results provided insight into potential antifungal substances. Our work provides a novel strain, HF10, for developing a promising biological control agent against Sclerotinia, which infects oilseed rape and other plants. Full article

(This article belongs to the Special Issue Plant-Microbe Interaction State-of-the-Art Research in China)

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18 pages, 4661 KiB

Open AccessArticle

Identification of the Microbiome Associated with Prognosis in Patients with Chronic Liver Disease

by Kenta Yamamoto, Takashi Honda, Yosuke Inukai, Shinya Yokoyama, Takanori Ito, Norihiro Imai, Yoji Ishizu, Masanao Nakamura and Hiroki Kawashima

Microorganisms 2024, 12(3), 610; https://doi.org/10.3390/microorganisms12030610 - 19 Mar 2024

Viewed by 1419

Abstract

We investigated the prognostic role of the gut microbiome and clinical factors in chronic liver disease (hepatitis, cirrhosis, and hepatocellular carcinoma [HCC]). Utilizing data from 227 patients whose stool samples were collected over the prior 3 years and a Cox proportional hazards model, [...] Read more.

We investigated the prognostic role of the gut microbiome and clinical factors in chronic liver disease (hepatitis, cirrhosis, and hepatocellular carcinoma [HCC]). Utilizing data from 227 patients whose stool samples were collected over the prior 3 years and a Cox proportional hazards model, we integrated clinical attributes and microbiome composition based on 16S ribosomal RNA sequencing. HCC was the primary cause of mortality, with the Barcelona Clinic Liver Cancer staging system-derived B/C significantly increasing the mortality risk (hazard ratio [HR] = 8.060; 95% confidence interval [CI]: 3.6509–17.793; p < 0.001). Cholesterol levels < 140 mg/dL were associated with higher mortality rates (HR = 4.411; 95% CI: 2.0151–9.6555; p < 0.001). Incertae sedis from Ruminococcaceae showed a protective effect, reducing mortality risk (HR = 0.289; 95% CI: 0.1282 to 0.6538; p = 0.002), whereas increased Veillonella presence was associated with a higher risk (HR = 2.733; 95% CI: 1.1922–6.2664; p = 0.017). The potential of specific bacterial taxa as independent prognostic factors suggests that integrating microbiome data could improve the prognosis and treatment of chronic liver disease. These microbiome-derived markers have prognostic significance independently and in conjunction with clinical factors, suggesting their utility in improving a patient’s prognosis. Full article

(This article belongs to the Special Issue Advances in Human Microbiomes)

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14 pages, 2874 KiB

Open AccessArticle

Harmful and Harmless Soil-Dwelling Fungi Indicate Microhabitat Suitability for Off-Host Ixodid Ticks

by Claire E. Gooding, Layla Gould and Gerhard Gries

Microorganisms 2024, 12(3), 609; https://doi.org/10.3390/microorganisms12030609 - 19 Mar 2024

Viewed by 1436

Abstract

Following blood meals or questing bouts, hard ticks (Ixodidae) must locate moist off-host microhabitats as refuge. Soil-dwelling fungi, including entomopathogenic Beauveria bassiana (Bb), thrive in moist microhabitats. Working with six species of ixodid ticks in olfactometer bioassays, we tested the hypothesis [...] Read more.

Following blood meals or questing bouts, hard ticks (Ixodidae) must locate moist off-host microhabitats as refuge. Soil-dwelling fungi, including entomopathogenic Beauveria bassiana (Bb), thrive in moist microhabitats. Working with six species of ixodid ticks in olfactometer bioassays, we tested the hypothesis that ticks avoid Bb. Contrary to our prediction, nearly all ticks sought, rather than avoided, Bb-inoculated substrates. In further bioassays with female black-legged ticks, Ixodes scapularis, ticks oriented towards both harmful Bb and harmless soil-dwelling fungi, implying that fungi—regardless of their pathogenicity—signal habitat suitability to ticks. Only accessible Bb-inoculated substrate appealed to ticks, indicating that they sense Bb or its metabolites by contact chemoreception. Bb-inoculated substrate required ≥24 h of incubation before it appealed to ticks, suggesting that they respond to Bb metabolites rather than to Bb itself. Similarly, ticks responded to Bb-inoculated and incubated cellulose but not to sterile cellulose, indicating that Bb detection by ticks hinges on the Bb metabolism of cellulose. 2-Methylisoborneol—a common fungal metabolite with elevated presence in disturbed soils—strongly deterred ticks. Off-host ticks that avoid disturbed soil may lower their risk of physical injury. Synthetic 2-methylisoborneol could become a commercial tick repellent, provided its repellency extends to ticks in diverse taxa. Full article

(This article belongs to the Section Parasitology)

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21 pages, 2868 KiB

Open AccessArticle

Active Microbiota of Penaeus stylirostris Larvae: Partially Shaped via Vertical and Horizontal Transmissions and Larval Ontogeny

by Nolwenn Callac, Carolane Giraud, Dominique Pham, Dominique Ansquer, Nelly Wabete and Viviane Boulo

Microorganisms 2024, 12(3), 608; https://doi.org/10.3390/microorganisms12030608 - 19 Mar 2024

Viewed by 1333

Abstract

During their entire lifecycle, mariculture animals are farmed in water that contains various microorganisms with which they are in close associations. Microbial exchanges between the animals and their surrounding water can occur. However, little is known about the interactions between shrimp larvae and [...] Read more.

During their entire lifecycle, mariculture animals are farmed in water that contains various microorganisms with which they are in close associations. Microbial exchanges between the animals and their surrounding water can occur. However, little is known about the interactions between shrimp larvae and water, and more especially, about larval bacterial selection and microbiota modulation across ontogeny. To address this gap, using HiSeq sequencing targeting the V4 region of the 16S rRNA molecule, we investigated the active prokaryotic diversity and structure of healthy Penaeus stylirostris larvae and seawater. Comparisons between different larval stages revealed evidence of stage-specific microbiotas and biomarkers, a core microbiota common to all stages, and shared taxa between successive stages, suggesting vertical transmission of bacterial taxa. Comparisons between stage-specific microbiotas and core microbiotas with water storages highlighted that many taxa associated with the larvae were originally present in the natural seawater, underlining horizontal transmission of bacteria from water to larvae. As some of these lineages became active at specific larval stages, we suggest that larvae were able to modulate their microbiota. This study provides insight into larvae-microbiota interactions at the larval stage scale. Full article

(This article belongs to the Special Issue Holobionts in Aquaculture)

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12 pages, 2693 KiB

Open AccessArticle

Clinical Profile and Prognosis of Patients with Left-Sided Infective Endocarditis with Surgical Indication Who Are Not Operated

by María de Miguel, Javier López, Isidre Vilacosta, Carmen Olmos, Carmen Sáez, Gonzalo Cabezón, Pablo Zulet, Adrián Jerónimo, Daniel Gómez, Paloma Pulido, Adrián Lozano, Andrea Oña, Itziar Gómez-Salvador and J. Alberto San Román

Microorganisms 2024, 12(3), 607; https://doi.org/10.3390/microorganisms12030607 - 19 Mar 2024

Cited by 2 | Viewed by 1159

Abstract

Approximately a quarter of patients with infective endocarditis (IE) who have surgical indication only receive antibiotic treatment. Their short-term prognosis is dismal. We aimed to describe the characteristics of this group of patients to evaluate the mortality according to the cause of rejection [...] Read more.

Approximately a quarter of patients with infective endocarditis (IE) who have surgical indication only receive antibiotic treatment. Their short-term prognosis is dismal. We aimed to describe the characteristics of this group of patients to evaluate the mortality according to the cause of rejection and type of surgical indication and to analyze their prognostic factors of mortality. From 2005 to 2022, 1105 patients with definite left-sided IE were consecutively attended in three tertiary hospitals. Of them, 912 (82.5%) had formal surgical indication according to the most recent European Guidelines available in each period of the study and 303 (33%) only received medical treatment. These were older, had more comorbidities and higher in-hospital (46% vs. 24%; p < 0.001) and one year mortality (57.1% vs. 27.6%; p < 0.001) than operated patients. The main reason for surgical rejection was high surgical risk (57.1%) and the highest mortality when the cause were severe neurological conditions (76%). When the endocarditis team took the decision not to operate (25.5% of the patients), in-hospital (7%) and one-year mortality (17%) were low. In-hospital mortality associated with each surgical indication was 67% in heart failure, 53% in uncontrolled infection and 45% in prevention of embolisms (p < 0.001). Heart failure (OR: 2.26 CI95%: 1.29–3.96; p = 0.005), Staphylococcus aureus (OR: 3.17; CI95%: 1.72–5.86; p < 0.001) and persistent infection (OR: 5.07 CI95%: 2.85–9.03) are the independent risk factors of in-hospital mortality. One third of the patients with left-sided IE and formal surgical indication are rejected for surgery. In-hospital mortality is very high, especially when heart failure is the indication for surgery and when severe neurological conditions the reason for rejection. Short term prognosis of patients rejected by a specialized endocarditis team is favorable. Full article

(This article belongs to the Special Issue The Infective Endocarditis)

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14 pages, 1700 KiB

Open AccessArticle

Engineering a Lactobacillus Lysine Riboswitch to Dynamically Control Metabolic Pathways for Lysine Production in Corynebacterium glutamicum

by Qingwei Jiang, Feng Geng, Juan Shen, Ping Zhu, Zhaoxin Lu, Libang Zhou and Fengxia Lu

Microorganisms 2024, 12(3), 606; https://doi.org/10.3390/microorganisms12030606 - 18 Mar 2024

Viewed by 1586

Abstract

Knock-out of genes of metabolic pathways is conventionally used in the metabolic engineering of microorganisms, but it is not applicable for genes of essential pathways. In order to avoid undesirable effects caused by gene deletion, it is attractive to develop riboswitches to dynamically [...] Read more.

Knock-out of genes of metabolic pathways is conventionally used in the metabolic engineering of microorganisms, but it is not applicable for genes of essential pathways. In order to avoid undesirable effects caused by gene deletion, it is attractive to develop riboswitches to dynamically control the metabolic pathways of microbial cell factories. In this regard, the aim of this study is to utilize the lysine riboswitch to control gene expressions of the biosynthetic pathways and by-pathways and thus improve lysine production in Corynebacterium glutamicum. To achieve this, a natural lysine riboswitch from Lactobacillus plantarum (LPRS) was first detected and then fused with RFP to test its functionality. After that, engineered lysine-activated (Lys-A) and lysine-repressed (Lys-R) riboswitches were successfully screened by dual genetic selection. Furthermore, the optimized A263 and R152 were applied to control the expression of aspartate kinase III and homoserine dehydrogenase in the lysine-producing strain C. glutamicum QW45, respectively. In contrast with QW45, the growth of the resulting A263-lysC mutant QW48 was similar to that of QW45; however, the growth of the resulting R357-hom mutant QW54 was slightly inhibited, indicating an inhibition of threonine biosynthesis caused by the riboswitch upon binding of intracellular lysine. Importantly, the lysine production of QW48 and QW54 was, respectively, 35% and 43% higher than that of the parent strain QW45, implying more metabolic flux directed into the lysine synthesis pathway. Finally, the engineered A263 and R357 were simultaneously applied to the same mutant QW55, which greatly improved lysine production. Thus, the approach demonstrated in this work could be principally used as a powerful tool to dynamically control any other undesired metabolic pathways. Full article

(This article belongs to the Section Microbial Biotechnology)

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11 pages, 2718 KiB

Open AccessArticle

One Step Forwards in Knowledge of Blossom Blight Brown Rot Disease: Monilinia spp. SSR Marker Database

by Raminta Antanynienė, Vidmantas Stanys and Birutė Frercks

Microorganisms 2024, 12(3), 605; https://doi.org/10.3390/microorganisms12030605 - 18 Mar 2024

Viewed by 1260

Abstract

A freely available Monilinia spp. marker database was created, containing microsatellite (SSR) data of the three most essential European fungal pathogens: M. fructigena, M. laxa, and M. fructicola. These pathogens cause brown rot blossom blight. Microsatellites were identified using the [...] Read more.

A freely available Monilinia spp. marker database was created, containing microsatellite (SSR) data of the three most essential European fungal pathogens: M. fructigena, M. laxa, and M. fructicola. These pathogens cause brown rot blossom blight. Microsatellites were identified using the bioinformatics tool Genome-wide Microsatellite Analyzing Toward Application (GMATA). The database provides information about SSR markers: forward and reverse sequences of the primers, fragment sizes, SSR motifs (and repeats), and the exact locations with the coordinates in the reference genome. This database currently contains information about 39,216 SSR motifs and 26,366 markers. In total, eight primers generated in silico were validated experimentally and they are marked in the database. All scientists can join this collaboration by adding their experimental data. This database is the initial start of organizing Monilinia spp. molecular data worldwide and, in the future, it could be extended by adding more molecular and genomic information. Full article

(This article belongs to the Special Issue Microbiome Research for Animal, Plant and Environmental Health)

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17 pages, 3561 KiB

Open AccessArticle

The Performance of a Modified Anode Using a Combination of Kaolin and Graphite Nanoparticles in Microbial Fuel Cells

by Lea Ouaknin Hirsch, Bharath Gandu, Abhishiktha Chiliveru, Irina Amar Dubrovin, Shmuel Rozenfeld, Alex Schechter and Rivka Cahan

Microorganisms 2024, 12(3), 604; https://doi.org/10.3390/microorganisms12030604 - 18 Mar 2024

Cited by 2 | Viewed by 1469

Abstract

The bacterial anode in microbial fuel cells was modified by increasing the biofilm’s adhesion to the anode material using kaolin and graphite nanoparticles. The MFCs were inoculated with G. sulfurreducens, kaolin (12.5 g·L⁻¹), and three different concentrations of graphite (0.25, [...] Read more.

The bacterial anode in microbial fuel cells was modified by increasing the biofilm’s adhesion to the anode material using kaolin and graphite nanoparticles. The MFCs were inoculated with G. sulfurreducens, kaolin (12.5 g·L⁻¹), and three different concentrations of graphite (0.25, 1.25, and 2.5 g·L⁻¹). The modified anode with the graphite nanoparticles (1.25 g·L⁻¹) showed the highest electroactivity and biofilm viability. A potential of 0.59, 0.45, and 0.23 V and a power density of 0.54 W·m⁻², 0.3 W·m⁻², and 0.2 W·m⁻² were obtained by the MFCs based on kaolin–graphite nanoparticles, kaolin, and bare anodes, respectively. The kaolin–graphite anode exhibited the highest Coulombic efficiency (21%) compared with the kaolin (17%) and the bare (14%) anodes. Scanning electron microscopy and confocal laser scanning microscopy revealed a large amount of biofilm on the kaolin–graphite anode. We assume that the graphite nanoparticles increased the charge transfer between the bacteria that are in the biofilm and are far from the anode material. The addition of kaolin and graphite nanoparticles increased the attachment of several bacteria. Thus, for MFCs that are fed with wastewater, the modified anode should be prepared with a pure culture of G. sulfurreducens before adding wastewater that includes non-exoelectrogenic bacteria. Full article

(This article belongs to the Special Issue Microbial Fuel Cells: An Update)

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20 pages, 3206 KiB

Open AccessArticle

Effect of the Inoculum-to-Substrate Ratio on Putative Pathogens and Microbial Kinetics during the Batch Anaerobic Digestion of Simulated Food Waste

by Saanu Victoria Otite, Bhushan P. Gandhi, Esther Agyabeng Fofie, Alfonso José Lag-Brotons, Lawrence I. Ezemonye, Alastair D. Martin, Roger W. Pickup and Kirk T. Semple

Microorganisms 2024, 12(3), 603; https://doi.org/10.3390/microorganisms12030603 - 18 Mar 2024

Cited by 2 | Viewed by 1634

Abstract

The effects of the inoculum (anaerobic digestion effluent) to substrate (simulated food waste) ratio (ISR) 4.00 to 0.25 on putative pathogens and microbial kinetics during batch mesophilic anaerobic digestion were investigated. Red fluorescent protein labelled (RFPAKN132) Escherichia coli JM105 was introduced as a [...] Read more.

The effects of the inoculum (anaerobic digestion effluent) to substrate (simulated food waste) ratio (ISR) 4.00 to 0.25 on putative pathogens and microbial kinetics during batch mesophilic anaerobic digestion were investigated. Red fluorescent protein labelled (RFPAKN132) Escherichia coli JM105 was introduced as a marker species, and together with the indigenous Clostridium sp., Enterococcus sp., Escherichia coli, and total coliforms were used to monitor pathogen death kinetics. Quantitative polymerase chain reaction was also used to estimate the bacterial, fungal, and methanogenic gene copies. All the ISRs eliminated E. coli and other coliforms (4 log₁₀ CFU/mL), but ISR 0.25 achieved this within the shortest time (≤2 days), while ISR 1.00 initially supported pathogen proliferation. Up to 1.5 log₁₀ CFU/mL of Clostridium was reduced by acidogenic conditions (ISR 0.25 and 0.50), while Enterococcus species were resistant to the digestion conditions. Fungal DNA was reduced (≥5 log₁₀ copies/mL) and was undetectable in ISRs 4.00, 2.00, and 0.50 at the end of the incubation period. This study has demonstrated that ISR influenced the pH of the digesters during batch mesophilic anaerobic digestion, and that acidic and alkaline conditions achieved by the lower (0.50 and 0.25) and higher (4.00 and 2.00) ISRs, respectively, were critical to the sanitisation of waste. Full article

(This article belongs to the Section Environmental Microbiology)

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Microorganisms, Volume 12, Issue 3 (March 2024) – 213 articles

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