Microorganisms

18 pages, 4679 KiB

Open AccessArticle

MDR and Pre-XDR Clinical Mycobacterium tuberculosis Beijing Strains: Assessment of Virulence and Host Cytokine Response in Mice Infectious Model

by Mikhail V. Fursov, Egor A. Shitikov, Denis A. Lagutkin, Anastasiia D. Fursova, Elena A. Ganina, Tatiana I. Kombarova, Natalia S. Grishenko, Tatiana I. Rudnitskaya, Dmitry A. Bespiatykh, Nadezhda V. Kolupaeva, Viktoria V. Firstova, Lubov V. Domotenko, Anna E. Panova, Anatoliy S. Vinokurov, Vladimir A. Gushchin, Artem P. Tkachuk, Irina A. Vasilyeva, Vasiliy D. Potapov and Ivan A. Dyatlov

Microorganisms 2021, 9(8), 1792; https://doi.org/10.3390/microorganisms9081792 - 23 Aug 2021

Cited by 6 | Viewed by 3318

Abstract

Mycobacterium tuberculosis Beijing genotype associated with drug resistance is a growing public health problem worldwide. The aim of this study was the assessment of virulence for C57BL/6 mice after infection by clinical M. tuberculosis strains 267/47 and 120/26, which belong to the modern [...] Read more.

Mycobacterium tuberculosis Beijing genotype associated with drug resistance is a growing public health problem worldwide. The aim of this study was the assessment of virulence for C57BL/6 mice after infection by clinical M. tuberculosis strains 267/47 and 120/26, which belong to the modern sublineages B0/W148 and Central Asia outbreak of the Beijing genotype, respectively. The sublineages were identified by the analysis of the strains’ whole-genomes. The strains 267/47 and 120/26 were characterized as agents of pre-extensively drug-resistant (pre-XDR) and multidrug-resistant (MDR) tuberculosis, respectively. Both clinical strains were slow-growing in 7H9 broth compared to the M. tuberculosis H37Rv strain. The survival rates of C57BL/6 mice infected by 267/47, 120/26, and H37Rv on the 150th day postinfection were 10%, 40%, and 70%, respectively. Mycobacterial load in the lungs, spleen, and liver was higher and histopathological changes were more expressed for mice infected by the 267/47 strain compared to those infected by the 120/26 and H37Rv strains. The cytokine response in the lungs of C57BL/6 mice after infection with the 267/47, 120/26, and H37Rv strains was different. Notably, proinflammatory cytokine genes Il-1α, Il-6, Il-7, and Il-17, as well as anti-inflammatory genes Il-6 and Il-13, were downregulated after an infection caused by the 267/47 strain compared to those after infection with the H37Rv strain. Full article

(This article belongs to the Special Issue Advances and Challenges in Mycobacterium tuberculosis Research and Therapeutics Development)

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18 pages, 333 KiB

Open AccessArticle

Evaluation of Locally Isolated Entomopathogenic Fungi against Multiple Life Stages of Bactrocera zonata and Bactrocera dorsalis (Diptera: Tephritidae): Laboratory and Field Study

by Muhammad Usman, Waqas Wakil, Jaime C. Piñero, Shaohui Wu, Michael D. Toews and David Ian Shapiro-Ilan

Microorganisms 2021, 9(8), 1791; https://doi.org/10.3390/microorganisms9081791 - 23 Aug 2021

Cited by 17 | Viewed by 4081

Abstract

Fruit flies including Bactrocera zonata and B. dorsalis (Diptera: Tephritidae) are considered major pests of orchard systems in Pakistan. This study evaluated the laboratory virulence, sub-lethal effects, horizontal transmission, greenhouse, and field-cage efficacy of locally isolated entomopathogenic fungi (EPF) against B. zonata and [...] Read more.

Fruit flies including Bactrocera zonata and B. dorsalis (Diptera: Tephritidae) are considered major pests of orchard systems in Pakistan. This study evaluated the laboratory virulence, sub-lethal effects, horizontal transmission, greenhouse, and field-cage efficacy of locally isolated entomopathogenic fungi (EPF) against B. zonata and B. dorsalis. In virulence assays against third instars and adults, all 21 EPF isolates (Beauveria bassiana and Metarhizium anisopliae) tested were pathogenic and caused varying levels of mortality to the fruit flies. Based on the initial screening, four isolates (B. bassiana WG-21 and WG-18 and M. anisopliae WG-07 and WG-02) were selected for further study. The isolate WG-18 was the most virulent against larvae and adults of B. zonata and B. dorsalis followed by WG-21, WG-02, and WG-07. In both species, adults were more susceptible than larvae to all isolates, and pupae were the least susceptible. Isolates WG-18 and WG-21 strongly decreased female fecundity and fertility, the highest adult and larval mortality, and longest developmental time of larvae and pupae. Fungal conidia were disseminated passively from infected to healthy adults and induced significant mortality, particularly from infected males to non-infected females. In greenhouse and field-cage experiments, WG-18 and WG-21 were the most effective isolates in reducing adult emergence when applied to larvae and pupae of both fruit fly species. Our results indicate that B. bassiana isolates WG-18 and WG-21 were the most virulent against multiple life stages of B. zonata and B. dorsalis, and also exerted the strongest sub-lethal effects. Full article

9 pages, 777 KiB

Open AccessArticle

Rational Design for Enhanced Acyltransferase Activity in Water Catalyzed by the Pyrobaculum calidifontis VA1 Esterase

by Amanda Staudt, Henrik Terholsen, Jasmin Kaur, Henrik Müller, Simon P. Godehard, Ivaldo Itabaiana, Jr., Ivana C. R. Leal and Uwe T. Bornscheuer

Microorganisms 2021, 9(8), 1790; https://doi.org/10.3390/microorganisms9081790 - 23 Aug 2021

Cited by 8 | Viewed by 3552

Abstract

Biocatalytic transesterification is commonly carried out employing lipases in anhydrous organic solvents since hydrolases usually prefer hydrolysis over acyl transfer in bulk water. However, some promiscuous acyltransferases can catalyze acylation in an aqueous solution. In this study, a rational design was performed to [...] Read more.

Biocatalytic transesterification is commonly carried out employing lipases in anhydrous organic solvents since hydrolases usually prefer hydrolysis over acyl transfer in bulk water. However, some promiscuous acyltransferases can catalyze acylation in an aqueous solution. In this study, a rational design was performed to enhance the acyltransferase selectivity and substrate scope of the Pyrobaculum calidifontis VA1 esterase (PestE). PestE wild type and variants were applied for the acylation of monoterpene alcohols. The mutant PestE_I208A is selective for (–)-menthyl acetate (E-Value = 55). Highly active acyltransferases were designed, allowing for complete conversion of (–)-citronellol to citronellyl acetate. Additionally, carvacrol was acetylated but with lower conversions. To the best of our knowledge, this is the first example of the biocatalytic acylation of a phenolic alcohol in bulk water. In addition, a high citronellol conversion of 92% was achieved with the more environmentally friendly and inexpensive acyl donor ethyl acetate using PestE_N288F as a catalyst. PestE_N288F exhibits good acyl transfer activity in an aqueous medium and low hydrolysis activity at the same time. Thus, our study demonstrates an alternative synthetic strategy for acylation of compounds without organic solvents. Full article

(This article belongs to the Special Issue Advanced Biotechnology of Microbial Enzymes)

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16 pages, 4851 KiB

Open AccessArticle

Assessment of Carbon Substrate Catabolism Pattern and Functional Metabolic Pathway for Microbiota of Limestone Caves

by Suprokash Koner, Jung-Sheng Chen, Bing-Mu Hsu, Chao-Wen Tan, Cheng-Wei Fan, Tsung-Hsien Chen, Bashir Hussain and Viji Nagarajan

Microorganisms 2021, 9(8), 1789; https://doi.org/10.3390/microorganisms9081789 - 23 Aug 2021

Cited by 24 | Viewed by 4493

Abstract

Carbon utilization of bacterial communities is a key factor of the biomineralization process in limestone-rich curst areas. An efficient carbon catabolism of the microbial community is associated with the availability of carbon sources in such an ecological niche. As cave environments promote oligotrophic [...] Read more.

Carbon utilization of bacterial communities is a key factor of the biomineralization process in limestone-rich curst areas. An efficient carbon catabolism of the microbial community is associated with the availability of carbon sources in such an ecological niche. As cave environments promote oligotrophic (carbon source stress) situations, the present study investigated the variations of different carbon substrate utilization patterns of soil and rock microbial communities between outside and inside cave environments in limestone-rich crust topography by Biolog EcoPlate™ assay and categorized their taxonomical structure and predicted functional metabolic pathways based on 16S rRNA amplicon sequencing. Community level physiological profiling (CLPP) analysis by Biolog EcoPlate™ assay revealed that microbes from outside of the cave were metabolically active and had higher carbon source utilization rate than the microbial community inside the cave. 16S rRNA amplicon sequence analysis demonstrated, among eight predominant bacterial phylum Planctomycetes, Proteobacteria, Cyanobacteria, and Nitrospirae were predominantly associated with outside-cave samples, whereas Acidobacteria, Actinobacteria, Chloroflexi, and Gemmatimonadetes were associated with inside-cave samples. Functional prediction showed bacterial communities both inside and outside of the cave were functionally involved in the metabolism of carbohydrates, amino acids, lipids, xenobiotic compounds, energy metabolism, and environmental information processing. However, the amino acid and carbohydrate metabolic pathways were predominantly linked to the outside-cave samples, while xenobiotic compounds, lipids, other amino acids, and energy metabolism were associated with inside-cave samples. Overall, a positive correlation was observed between Biolog EcoPlate™ assay carbon utilization and the abundance of functional metabolic pathways in this study. Full article

(This article belongs to the Special Issue Microbe-Driven Migration and Transformation of Elements through the Earth’s Critical Zone)

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14 pages, 1821 KiB

Open AccessArticle

Effects of Age, Diet CP, NDF, EE, and Starch on the Rumen Bacteria Community and Function in Dairy Cattle

by Yangyi Hao, Yue Gong, Shuai Huang, Shoukun Ji, Wei Wang, Yajing Wang, Hongjian Yang, Zhijun Cao and Shengli Li

Microorganisms 2021, 9(8), 1788; https://doi.org/10.3390/microorganisms9081788 - 23 Aug 2021

Cited by 14 | Viewed by 3547

Abstract

To understand the effects of diet and age on the rumen bacterial community and function, forty-eight dairy cattle at 1.5 (M1.5), 6 (M6), 9 (M9), 18 (M18), 23 (M23), and 27 (M27) months old were selected. Rumen fermentation profile, enzyme activity, and bacteria [...] Read more.

To understand the effects of diet and age on the rumen bacterial community and function, forty-eight dairy cattle at 1.5 (M1.5), 6 (M6), 9 (M9), 18 (M18), 23 (M23), and 27 (M27) months old were selected. Rumen fermentation profile, enzyme activity, and bacteria community in rumen fluid were measured. The acetate to propionate ratio (A/P) at M9, M18, and M23 was higher than other ages, and M6 was the lowest (p < 0.05). The total volatile fatty acid (TVFA) at M23 and M27 was higher than at other ages (p < 0.05). The urease at M18 was lower than at M1.5, M6, and M9, and the xylanase at M18 was higher than at M1.5, M23, and M27 (p < 0.05). Thirty-three bacteria were identified as biomarkers of the different groups based on the linear discriminant analysis (LDA) when the LDA score >4. The variation partitioning approach analysis showed that the age and diet had a 7.98 and 32.49% contribution to the rumen bacteria community variation, respectively. The richness of Succinivibrionaceae_UCG-002 and Fibrobacter were positive correlated with age (r > 0.60, p < 0.01) and positively correlated with TVFA and acetate (r > 0.50, p < 0.01). The Lachnospiraceae_AC2044_group, Pseudobutyrivibrio, and Saccharofermentans has a positive correlation (r > 0.80, p < 0.05) with diet fiber and a negative correlation (r < −0.80, p < 0.05) with diet protein and starch, which were also positively correlated with the acetate and A/P (r > 0.50, p < 0.01). The genera of Lachnospiraceae_AC2044_group, Pseudobutyrivibrio, and Saccharofermentans could be worked as the target bacteria to modulate the rumen fermentation by diet; meanwhile, the high age correlated bacteria such as Succinivibrionaceae_UCG-002 and Fibrobacter also should be considered when shaping the rumen function. Full article

(This article belongs to the Special Issue Rumen Microbial Communities)

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30 pages, 5694 KiB

Open AccessReview

Hepatitis B Virus DNA Integration, Chronic Infections and Hepatocellular Carcinoma

by Maria Bousali, George Papatheodoridis, Dimitrios Paraskevis and Timokratis Karamitros

Microorganisms 2021, 9(8), 1787; https://doi.org/10.3390/microorganisms9081787 - 23 Aug 2021

Cited by 33 | Viewed by 9620

Abstract

Hepatitis B Virus (HBV) is an Old World virus with a high mutation rate, which puts its origins in Africa alongside the origins of Homo sapiens, and is a member of the Hepadnaviridae family that is characterized by a unique viral replication cycle. [...] Read more.

Hepatitis B Virus (HBV) is an Old World virus with a high mutation rate, which puts its origins in Africa alongside the origins of Homo sapiens, and is a member of the Hepadnaviridae family that is characterized by a unique viral replication cycle. It targets human hepatocytes and can lead to chronic HBV infection either after acute infection via horizontal transmission usually during infancy or childhood or via maternal–fetal transmission. HBV has been found in ~85% of HBV-related Hepatocellular Carcinomas (HCC), and it can integrate the whole or part of its genome into the host genomic DNA. The molecular mechanisms involved in the HBV DNA integration is not yet clear; thus, multiple models have been described with respect to either the relaxed-circular DNA (rcDNA) or the double-stranded linear DNA (dslDNA) of HBV. Various genes have been found to be affected by HBV DNA integration, including cell-proliferation-related genes, oncogenes and long non-coding RNA genes (lincRNAs). The present review summarizes the advances in the research of HBV DNA integration, focusing on the evolutionary and molecular side of the integration events along with the arising clinical aspects in the light of WHO’s commitment to eliminate HBV and viral hepatitis by 2030. Full article

(This article belongs to the Special Issue Molecular Biology of Hepatitis B Virus—from Basic Concepts to Therapeutic Targets)

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2 pages, 174 KiB

Open AccessComment

Comment on Favresse et al. Persistence of Anti-SARS-CoV-2 Antibodies Depends on the Analytical Kit: A Report for Up to 10 Months after Infection. Microorganisms 2021, 9, 556

by Johannes Schulte-Pelkum

Microorganisms 2021, 9(8), 1786; https://doi.org/10.3390/microorganisms9081786 - 23 Aug 2021

Cited by 3 | Viewed by 1808

Abstract

We thank the authors of the article [...] Full article

(This article belongs to the Special Issue COVID-19: Focusing on Epidemiologic, Virologic, and Clinical Studies)

15 pages, 3847 KiB

Open AccessArticle

Root-Associated Microbiomes, Growth and Health of Ornamental Geophytes Treated with Commercial Plant Growth-Promoting Products

by Gavriel Friesem, Noam Reznik, Michal Sharon Cohen, Nir Carmi, Zohar Kerem and Iris Yedidia

Microorganisms 2021, 9(8), 1785; https://doi.org/10.3390/microorganisms9081785 - 23 Aug 2021

Cited by 2 | Viewed by 2396

Abstract

The microbial community inhabiting a plant’s root zone plays a crucial role in plant health and protection. To assess the ability of commercial plant growth-promoting products to enhance the positive effects of this environment, two products containing beneficial soil bacteria and a product [...] Read more.

The microbial community inhabiting a plant’s root zone plays a crucial role in plant health and protection. To assess the ability of commercial plant growth-promoting products to enhance the positive effects of this environment, two products containing beneficial soil bacteria and a product containing plant extracts were tested on Zantedeschia aethiopica and Ornithogalum dubium. The products were tested in two different growing media: a soil and a soilless medium. The effects of these products on Pectobacterium brasiliense, the causal agent of soft rot disease, were also evaluated in vitro, and on naturally occurring infections in the greenhouse. The growing medium was found to have the strongest effect on the microbial diversity of the root-associated microbiome, with the next-strongest effect due to plant type. These results demonstrate that either a single bacterial strain or a product will scarcely reach the level that is required to influence soil microbial communities. In addition, the microbes cultured from these products, could not directly inhibit Pectobacterium growth in vitro. We suggest density-based and functional analyses in the future, to study the specific interactions between plants, soil type, soil microbiota and relevant pathogens. This should increase the effectiveness of bio-supplements and soil disinfestation with natural products, leading to more sustainable, environmentally friendly solutions for the control of bacterial plant diseases. Full article

(This article belongs to the Special Issue The Role of Soil Amendments in Shaping Soil and Plant-Associated Microbiomes)

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15 pages, 2104 KiB

Open AccessArticle

HERV-K Modulates the Immune Response in ALS Patients

by Giannina Arru, Grazia Galleri, Giovanni A. Deiana, Ignazio R. Zarbo, Elia Sechi, Marco Bo, Maria Piera L. Cadoni, Davide G. Corda, Claudia Frau, Elena R. Simula, Maria Antonietta Manca, Franca Galistu, Paolo Solla, Roberto Manetti, Gian Pietro Sechi and Leonardo A. Sechi

Microorganisms 2021, 9(8), 1784; https://doi.org/10.3390/microorganisms9081784 - 23 Aug 2021

Cited by 22 | Viewed by 5234

Abstract

Human endogenous retrovirus (HERV)-K env-su glycoprotein has been documented in amyotrophic lateral sclerosis (ALS), where HERV-K env-su _19–37 antibody levels significantly correlated with clinical measures of disease severity. Herein, we investigated further the humoral and cell-mediated immune response against specific antigenic peptides derived [...] Read more.

Human endogenous retrovirus (HERV)-K env-su glycoprotein has been documented in amyotrophic lateral sclerosis (ALS), where HERV-K env-su _19–37 antibody levels significantly correlated with clinical measures of disease severity. Herein, we investigated further the humoral and cell-mediated immune response against specific antigenic peptides derived from HERV-K in ALS. HERV-K env glycoprotein expression on peripheral blood mononuclear cells (PBMCs) membrane and cytokines and chemokines after stimulation with HERV-K env _19–37 and HERV-K env _109–126 were quantified in patients and healthy controls (HCs). HERV-K env glycoprotein was more expressed in B cells and NK cells of ALS patients compared to HCs, whereas HERV-K env transcripts were similar in ALS and HCs. In ALS patients, specific stimulation with HERV-K env _109–126 peptide showed a higher expression of IL-6 by CD19/B cells. Both peptides, however, were able to induce a great production of IFN-γ by stimulation CD19/B cells, and yielded a higher expression of MIP-1α and a lower expression of MCP-1. HERV-K env _19–37 peptide induced a great production of TNF-α in CD8/T cells. In conclusion, we observed the ability of HERV-K to modulate the immune system, generating mediators mainly involved in proinflammatory response. Full article

(This article belongs to the Special Issue Physiological and Pathophysiological Aspects of Endogenous Viruses)

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13 pages, 2385 KiB

Open AccessArticle

Removal of Phenols in Table Olive Processing Wastewater by Using a Mixed Inoculum of Candida boidinii and Bacillus pumilus: Effects of Inoculation Dynamics, Temperature, pH, and Effluent Age on the Abatement Efficiency

by Daniela Campaniello, Barbara Speranza, Clelia Altieri, Milena Sinigaglia, Antonio Bevilacqua and Maria Rosaria Corbo

Microorganisms 2021, 9(8), 1783; https://doi.org/10.3390/microorganisms9081783 - 23 Aug 2021

Cited by 1 | Viewed by 2168

Abstract

The main goal of this paper was to assess the ability of a combination of Candida boidinii and Bacillus pumilus to remove phenol in table olive processing water, as a function of some variables, like temperature, pH, a dilution of waste and the [...] Read more.

The main goal of this paper was to assess the ability of a combination of Candida boidinii and Bacillus pumilus to remove phenol in table olive processing water, as a function of some variables, like temperature, pH, a dilution of waste and the order of inoculation of the two microorganisms. At this purpose C. boidinii and B. pumilus were sequentially inoculated in two types of table olive processing water (fresh wastewater, FTOPW and wastewater stored for 3 months-aged wastewater, ATOPW). pH (6 and 9), temperature (10 and 35 °C) and dilution ratio (0, 1:1) were combined through a 2^k fractional design. Data were modeled using two different approaches: Multifactorial Analysis of Variance (MANOVA) and multiple regression. A higher removal yield was achieved by inoculating B. pumilus prior to the yeast (192 vs. 127 mg/L); moreover, an increased efficiency was gained at 35 °C (mean removal of 200 mg/L). The use of two statistic approach suggested a different weight of variables; temperature was a global variable, that is a factor able to affect the yield of the process in all conditions. On the other hand, an alkaline pH could increase the removal of phenol at 10 °C (25–43%). Full article

(This article belongs to the Special Issue Microbial Bioremediation)

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20 pages, 2863 KiB

Open AccessArticle

Remediation Strategies to Control Toxic Cyanobacterial Blooms: Effects of Macrophyte Aqueous Extracts on Microcystis aeruginosa (Growth, Toxin Production and Oxidative Stress Response) and on Bacterial Ectoenzymatic Activities

by Zakaria Tazart, Maura Manganelli, Simona Scardala, Franca Maria Buratti, Federica Nigro Di Gregorio, Mountasser Douma, Khadija Mouhri, Emanuela Testai and Mohammed Loudiki

Microorganisms 2021, 9(8), 1782; https://doi.org/10.3390/microorganisms9081782 - 23 Aug 2021

Cited by 10 | Viewed by 3162

Abstract

Increasing toxic cyanobacterial blooms in freshwater demand environmentally friendly solutions to control their growth and toxicity, especially in arid countries, where most drinking water is produced from surface reservoirs. We tested the effects of macrophyte allelochemicals on Microcystis aeruginosa and on the fundamental [...] Read more.

Increasing toxic cyanobacterial blooms in freshwater demand environmentally friendly solutions to control their growth and toxicity, especially in arid countries, where most drinking water is produced from surface reservoirs. We tested the effects of macrophyte allelochemicals on Microcystis aeruginosa and on the fundamental role of bacteria in nutrient recycling. The effects of Ranunculus aquatilis aqueous extract, the most bioactive of four Moroccan macrophyte extracts, were tested in batch systems on M. aeruginosa growth, toxin production and oxidative stress response and on the ectoenzymatic activity associated with the bacterial community. M. aeruginosa density was reduced by 82.18%, and a significant increase in oxidative stress markers was evidenced in cyanobacterial cells. Microcystin concentration significantly decreased, and they were detected only intracellularly, an important aspect in managing toxic blooms. R. aquatilis extract had no negative effects on associated bacteria. These results confirm a promising use of macrophyte extracts, but they cannot be generalized. The use of the extract on other toxic strains, such as Planktothrix rubescens, Raphidiopsis raciborskii and Chrysosporum ovalisporum, caused a reduction in growth rate but not in cyanotoxin content, increasing toxicity. The need to assess species-specific cyanobacteria responses to verify the efficacy and safety of the extracts for human health and the environment is highlighted. Full article

(This article belongs to the Special Issue Global Intensification of Cyanobacterial Blooms: The Driving Forces and Mitigation Approaches)

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10 pages, 1614 KiB

Open AccessArticle

Intestinal Colonization with Tropheryma whipplei—Clinical and Immunological Implications for HIV Positive Adults in Ghana

by Kirsten Alexandra Eberhardt, Fred Stephen Sarfo, Eva-Maria Klupp, Albert Dompreh, Veronica Di Cristanziano, Edmund Osei Kuffour, Richard Boateng, Betty Norman, Richard Odame Phillips, Martin Aepfelbacher and Torsten Feldt

Microorganisms 2021, 9(8), 1781; https://doi.org/10.3390/microorganisms9081781 - 22 Aug 2021

Cited by 2 | Viewed by 2470

Abstract

Background: Recent studies demonstrated higher prevalence rates of Tropheryma whipplei (T. whipplei) in HIV positive than in HIV negative subjects. However, associations with the immune status in HIV positive participants were conflicting. Methods: For this cross-sectional study, stool samples of 906 [...] Read more.

Background: Recent studies demonstrated higher prevalence rates of Tropheryma whipplei (T. whipplei) in HIV positive than in HIV negative subjects. However, associations with the immune status in HIV positive participants were conflicting. Methods: For this cross-sectional study, stool samples of 906 HIV positive and 98 HIV negative individuals in Ghana were tested for T. whipplei. Additionally, sociodemographic parameters, clinical symptoms, medical drug intake, and laboratory parameters were assessed. Results: The prevalence of T. whipplei was 5.85% in HIV positive and 2.04% in HIV negative participants. Within the group of HIV positive participants, the prevalence reached 7.18% in patients without co-trimoxazole prophylaxis, 10.26% in subjects with ART intake, and 12.31% in obese participants. Frequencies of clinical symptoms were not found to be higher in HIV positive T. whipplei carriers compared to T. whipplei negative participants. Markers of immune activation were lower in patients colonized with T. whipplei. Multivariate regression models demonstrated an independent relationship of a high CD4+ T cell count, a low HIV-1 viral load, and an obese body weight with the presence of T. whipplei. Conclusions: Among HIV positive individuals, T. whipplei colonization was associated with a better immune status but not with clinical consequences. Our data suggest that the withdrawal of co-trimoxazole chemoprophylaxis among people living with HIV on stable cART regimen may inadvertently increase the propensity towards colonization with T. whipplei. Full article

(This article belongs to the Special Issue Tropheryma whipplei Infection and Whipple’s Disease)

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17 pages, 2553 KiB

Open AccessArticle

Bioinformatics Investigations of Universal Stress Proteins from Mercury-Methylating Desulfovibrionaceae

by Raphael D. Isokpehi, Dominique S. McInnis, Antoinette M. Destefano, Gabrielle S. Johnson, Akimio D. Walker, Yessenia A. Hall, Baraka W. Mapp, Matilda O. Johnson and Shaneka S. Simmons

Microorganisms 2021, 9(8), 1780; https://doi.org/10.3390/microorganisms9081780 - 21 Aug 2021

Cited by 1 | Viewed by 2649

Abstract

The presence of methylmercury in aquatic environments and marine food sources is of global concern. The chemical reaction for the addition of a methyl group to inorganic mercury occurs in diverse bacterial taxonomic groups including the Gram-negative, sulfate-reducing Desulfovibrionaceae family that inhabit extreme [...] Read more.

The presence of methylmercury in aquatic environments and marine food sources is of global concern. The chemical reaction for the addition of a methyl group to inorganic mercury occurs in diverse bacterial taxonomic groups including the Gram-negative, sulfate-reducing Desulfovibrionaceae family that inhabit extreme aquatic environments. The availability of whole-genome sequence datasets for members of the Desulfovibrionaceae presents opportunities to understand the microbial mechanisms that contribute to methylmercury production in extreme aquatic environments. We have applied bioinformatics resources and developed visual analytics resources to categorize a collection of 719 putative universal stress protein (USP) sequences predicted from 93 genomes of Desulfovibrionaceae. We have focused our bioinformatics investigations on protein sequence analytics by developing interactive visualizations to categorize Desulfovibrionaceae universal stress proteins by protein domain composition and functionally important amino acids. We identified 651 Desulfovibrionaceae universal stress protein sequences, of which 488 sequences had only one USP domain and 163 had two USP domains. The 488 single USP domain sequences were further categorized into 340 sequences with ATP-binding motif and 148 sequences without ATP-binding motif. The 163 double USP domain sequences were categorized into (1) both USP domains with ATP-binding motif (3 sequences); (2) both USP domains without ATP-binding motif (138 sequences); and (3) one USP domain with ATP-binding motif (21 sequences). We developed visual analytics resources to facilitate the investigation of these categories of datasets in the presence or absence of the mercury-methylating gene pair (hgcAB). Future research could utilize these functional categories to investigate the participation of universal stress proteins in the bacterial cellular uptake of inorganic mercury and methylmercury production, especially in anaerobic aquatic environments. Full article

(This article belongs to the Special Issue Bacterial Stress Response Mechanisms: Signal Perception, Transduction and Adaptation)

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11 pages, 3534 KiB

Open AccessArticle

Antimicrobial Peptide L18R Displays a Modulating Action against Inter-Kingdom Biofilms in the Lubbock Chronic Wound Biofilm Model

by Paola Di Fermo, Tecla Ciociola, Silvia Di Lodovico, Simonetta D’Ercole, Morena Petrini, Laura Giovati, Stefania Conti, Mara Di Giulio and Luigina Cellini

Microorganisms 2021, 9(8), 1779; https://doi.org/10.3390/microorganisms9081779 - 21 Aug 2021

Cited by 7 | Viewed by 2423

Abstract

Chronic wound infections represent an important health problem due to the reduced response to antimicrobial treatment of the pathogens organized in structured biofilms. This study investigated the effects of the previously described antifungal peptide L18R against three representative wound pathogens: Staphylococcus aureus, Pseudomonas [...] Read more.

Chronic wound infections represent an important health problem due to the reduced response to antimicrobial treatment of the pathogens organized in structured biofilms. This study investigated the effects of the previously described antifungal peptide L18R against three representative wound pathogens: Staphylococcus aureus, Pseudomonas aeruginosa, and Candida albicans. The antimicrobial activity of L18R was evaluated (i) against single planktonic microbial populations; (ii) on single, dual, and triadic species of biofilms in both the early stage and mature stage; and (iii) in the polymicrobial Lubbock chronic wound biofilm (LCWB) model, mimicking spatial microbial colonization. This study used the evaluation of CFUs, biofilm biomass detection, and confocal and scanning electron microscopy analysis. L18R showed a significant antimicrobial activity against planktonic microorganisms and was able to differentially reduce the biomass of monomicrobial biofilms. No reduction of biomass was observed against the polymicrobial biofilm. In mature LCWB, L18R caused a moderate reduction in total CFU number, with a variable effect on the different microorganisms. Microscopy images confirmed a predominant presence of P.aeruginosa and a lower percentage of C. albicans cells. These findings suggest a modulating action of L18R and recommend further studies on its potential role in chronic wound management in association with conventional antibiotics or alternative treatments. Full article

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

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20 pages, 4468 KiB

Open AccessArticle

From Water into Sediment—Tracing Freshwater Cyanobacteria via DNA Analyses

by Ebuka Canisius Nwosu, Patricia Roeser, Sizhong Yang, Lars Ganzert, Olaf Dellwig, Sylvia Pinkerneil, Achim Brauer, Elke Dittmann, Dirk Wagner and Susanne Liebner

Microorganisms 2021, 9(8), 1778; https://doi.org/10.3390/microorganisms9081778 - 21 Aug 2021

Cited by 16 | Viewed by 4349

Abstract

Sedimentary ancient DNA-based studies have been used to probe centuries of climate and environmental changes and how they affected cyanobacterial assemblages in temperate lakes. Due to cyanobacteria containing potential bloom-forming and toxin-producing taxa, their approximate reconstruction from sediments is crucial, especially in lakes [...] Read more.

Sedimentary ancient DNA-based studies have been used to probe centuries of climate and environmental changes and how they affected cyanobacterial assemblages in temperate lakes. Due to cyanobacteria containing potential bloom-forming and toxin-producing taxa, their approximate reconstruction from sediments is crucial, especially in lakes lacking long-term monitoring data. To extend the resolution of sediment record interpretation, we used high-throughput sequencing, amplicon sequence variant (ASV) analysis, and quantitative PCR to compare pelagic cyanobacterial composition to that in sediment traps (collected monthly) and surface sediments in Lake Tiefer See. Cyanobacterial composition, species richness, and evenness was not significantly different among the pelagic depths, sediment traps and surface sediments (p > 0.05), indicating that the cyanobacteria in the sediments reflected the cyanobacterial assemblage in the water column. However, total cyanobacterial abundances (qPCR) decreased from the metalimnion down the water column. The aggregate-forming (Aphanizomenon) and colony-forming taxa (Snowella) showed pronounced sedimentation. In contrast, Planktothrix was only very poorly represented in sediment traps (meta- and hypolimnion) and surface sediments, despite its highest relative abundance at the thermocline (10 m water depth) during periods of lake stratification (May–October). We conclude that this skewed representation in taxonomic abundances reflects taphonomic processes, which should be considered in future DNA-based paleolimnological investigations. Full article

(This article belongs to the Special Issue Understanding Ancient Microbiomes)

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19 pages, 1711 KiB

Open AccessArticle

Features of the Opportunistic Behaviour of the Marine Bacterium Marinobacter algicola in the Microalga Ostreococcus tauri Phycosphere

by Jordan Pinto, Raphaël Lami, Marc Krasovec, Régis Grimaud, Laurent Urios, Josselin Lupette, Marie-Line Escande, Frédéric Sanchez, Laurent Intertaglia, Nigel Grimsley, Gwenaël Piganeau and Sophie Sanchez-Brosseau

Microorganisms 2021, 9(8), 1777; https://doi.org/10.3390/microorganisms9081777 - 20 Aug 2021

Cited by 9 | Viewed by 3054

Abstract

Although interactions between microalgae and bacteria are observed in both natural environment and the laboratory, the modalities of coexistence of bacteria inside microalgae phycospheres in laboratory cultures are mostly unknown. Here, we focused on well-controlled cultures of the model green picoalga Ostreococcus tauri [...] Read more.

Although interactions between microalgae and bacteria are observed in both natural environment and the laboratory, the modalities of coexistence of bacteria inside microalgae phycospheres in laboratory cultures are mostly unknown. Here, we focused on well-controlled cultures of the model green picoalga Ostreococcus tauri and the most abundant member of its phycosphere, Marinobacter algicola. The prevalence of M. algicola in O. tauri cultures raises questions about how this bacterium maintains itself under laboratory conditions in the microalga culture. The results showed that M. algicola did not promote O. tauri growth in the absence of vitamin B₁₂ while M. algicola depended on O. tauri to grow in synthetic medium, most likely to obtain organic carbon sources provided by the microalgae. M. algicola grew on a range of lipids, including triacylglycerols that are known to be produced by O. tauri in culture during abiotic stress. Genomic screening revealed the absence of genes of two particular modes of quorum-sensing in Marinobacter genomes which refutes the idea that these bacterial communication systems operate in this genus. To date, the ‘opportunistic’ behaviour of M. algicola in the laboratory is limited to several phytoplanktonic species including Chlorophyta such as O. tauri. This would indicate a preferential occurrence of M. algicola in association with these specific microalgae under optimum laboratory conditions. Full article

(This article belongs to the Special Issue Phytoplankton-Bacteria Interactions)

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18 pages, 1255 KiB

Open AccessArticle

Hybridized Zoonotic Schistosoma Infections Result in Hybridized Morbidity Profiles: A Clinical Morbidity Study amongst Co-Infected Human Populations of Senegal

by Cheikh B. Fall, Sébastien Lambert, Elsa Léger, Lucy Yasenev, Amadou Djirmay Garba, Samba D. Diop, Anna Borlase, Stefano Catalano, Babacar Faye, Martin Walker, Mariama Sene and Joanne P. Webster

Microorganisms 2021, 9(8), 1776; https://doi.org/10.3390/microorganisms9081776 - 20 Aug 2021

Cited by 13 | Viewed by 3346

Abstract

Hybridization of infectious agents is a major emerging public and veterinary health concern at the interface of evolution, epidemiology, and control. Whilst evidence of the extent of hybridization amongst parasites is increasing, their impact on morbidity remains largely unknown. This may be predicted [...] Read more.

Hybridization of infectious agents is a major emerging public and veterinary health concern at the interface of evolution, epidemiology, and control. Whilst evidence of the extent of hybridization amongst parasites is increasing, their impact on morbidity remains largely unknown. This may be predicted to be particularly pertinent where parasites of animals with contrasting pathogenicity viably hybridize with human parasites. Recent research has revealed that viable zoonotic hybrids between human urogenital Schistosoma haematobium with intestinal Schistosoma species of livestock, notably Schistosoma bovis, can be highly prevalent across Africa and beyond. Examining human populations in Senegal, we found increased hepatic but decreased urogenital morbidity, and reduced improvement following treatment with praziquantel, in those infected with zoonotic hybrids compared to non-hybrids. Our results have implications for effective monitoring and evaluation of control programmes, and demonstrate for the first time the potential impact of parasite hybridizations on host morbidity. Full article

(This article belongs to the Special Issue Schistosoma and Schistosomiasis)

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13 pages, 3153 KiB

Open AccessArticle

Comparative Pan-Genome Analysis of Oral Veillonella Species

by Izumi Mashima, Yu-Chieh Liao, Chieh-Hua Lin, Futoshi Nakazawa, Elaine M. Haase, Yusuke Kiyoura and Frank A. Scannapieco

Microorganisms 2021, 9(8), 1775; https://doi.org/10.3390/microorganisms9081775 - 20 Aug 2021

Cited by 8 | Viewed by 5348

Abstract

The genus Veillonella is a common and abundant member of the oral microbiome. It includes eight species, V. atypica, V. denticariosi, V. dispar, V. infantium, V. nakazawae, V. parvula, V. rogosae and V. tobetusensis. They possess [...] Read more.

The genus Veillonella is a common and abundant member of the oral microbiome. It includes eight species, V. atypica, V. denticariosi, V. dispar, V. infantium, V. nakazawae, V. parvula, V. rogosae and V. tobetusensis. They possess important metabolic pathways that utilize lactate as an energy source. However, the overall metabolome of these species has not been studied. To further understand the metabolic framework of Veillonella in the human oral microbiome, we conducted a comparative pan-genome analysis of the eight species of oral Veillonella. Analysis of the oral Veillonella pan-genome revealed features based on KEGG pathway information to adapt to the oral environment. We found that the fructose metabolic pathway was conserved in all oral Veillonella species, and oral Veillonella have conserved pathways that utilize carbohydrates other than lactate as an energy source. This discovery may help to better understand the metabolic network among oral microbiomes and will provide guidance for the design of future in silico and in vitro studies. Full article

(This article belongs to the Special Issue New Anaerobic Bacteria in Human Health and Disease)

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14 pages, 2068 KiB

Open AccessArticle

The Risk of Invasive Pneumococcal Disease Differs between Risk Groups in Norway Following Widespread Use of the 13-Valent Pneumococcal Vaccine in Children

by Brita Askeland Winje, Didrik Frimann Vestrheim, Richard Aubrey White and Anneke Steens

Microorganisms 2021, 9(8), 1774; https://doi.org/10.3390/microorganisms9081774 - 20 Aug 2021

Cited by 6 | Viewed by 2638

Abstract

The elderly and adults with medical risk conditions remain at high risk of invasive pneumococcal disease (IPD), highlighting the importance of adequate preventive efforts. In an observational population-based study in Norway (pop ≥ 5 years, 2009–2017) covering six years post-PCV13 implementation, we explored [...] Read more.

The elderly and adults with medical risk conditions remain at high risk of invasive pneumococcal disease (IPD), highlighting the importance of adequate preventive efforts. In an observational population-based study in Norway (pop ≥ 5 years, 2009–2017) covering six years post-PCV13 implementation, we explored the incidence and risk of IPD associated with age and comorbidities. We obtained the data on 5535 IPD cases from the Norwegian Surveillance System for Communicable Diseases and the population data from Statistics Norway. To define comorbidities, we obtained ICD-10 codes from the Norwegian Patient Registry for the cases and the Norwegian population. The average annual decrease in PCV13 IPD incidence was significant in all risk groups and decreased post-PCV13 introduction by 16–20% per risk group, implying a nondifferential indirect protection from the childhood vaccination. The IPD incidence remained high in the medical risk groups. The relative importance of medical risk conditions was 2.8 to 6 times higher in those aged 5–64 versus ≥65 years for all types of IPD, since age itself is a risk factor for IPD. In groups without medical risk, the risk of IPD was eight times higher in those aged ≥65 compared to those 5–64 years (RR 8.3 (95% CI 7.3–9.5)). Our results underscore the need for age- and risk-group-based prevention strategies. Full article

(This article belongs to the Section Public Health Microbiology)

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14 pages, 531 KiB

Open AccessReview

Multi-Drug Resistance Bacterial Infections in Critically Ill Patients Admitted with COVID-19

by Daniela Pasero, Andrea Pasquale Cossu and Pierpaolo Terragni

Microorganisms 2021, 9(8), 1773; https://doi.org/10.3390/microorganisms9081773 - 20 Aug 2021

Cited by 44 | Viewed by 4414

Abstract

Introduction. It is known that bacterial infections represent a common complication during viral respiratory tract infections such as influenza, with a concomitant increase in morbidity and mortality. Nevertheless, the prevalence of bacterial co-infections and secondary infections in critically ill patients affected by coronavirus [...] Read more.

Introduction. It is known that bacterial infections represent a common complication during viral respiratory tract infections such as influenza, with a concomitant increase in morbidity and mortality. Nevertheless, the prevalence of bacterial co-infections and secondary infections in critically ill patients affected by coronavirus disease 2019 (COVID-19) is not well understood yet. We performed a review of the literature currently available to examine the incidence of bacterial secondary infections acquired during hospital stay and the risk factors associated with multidrug resistance. Most of the studies, mainly retrospective and single-centered, highlighted that the incidence of co-infections is low, affecting about 3.5% of hospitalized patients, while the majority are hospital acquired infections, developed later, generally 10–15 days after ICU admission. The prolonged ICU hospitalization and the extensive use of broad-spectrum antimicrobial drugs during the COVID-19 outbreak might have contributed to the selection of pathogens with different profiles of resistance. Consequently, the reported incidence of MDR bacterial infections in critically ill COVID-19 patients is high, ranging between 32% to 50%. MDR infections are linked to a higher length of stay in ICU but not to a higher risk of death. The only risk factor independently associated with MDR secondary infections reported was invasive mechanical ventilation (OR 1.062; 95% CI 1.012–1.114), but also steroid therapy and prolonged length of ICU stay may play a pivotal role. The empiric antimicrobial therapy for a ventilated patient with suspected or proven bacterial co-infection at ICU admission should be prescribed judiciously and managed according to a stewardship program in order to interrupt or adjust it on the basis of culture results. Full article

(This article belongs to the Special Issue Complex Infectious Issues in Critically Ill Patients)

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11 pages, 396 KiB

Open AccessArticle

Latin American Origin Is Not Associated with Worse Outcomes among Hospitalized Patients with COVID-19 in a Public Healthcare System

by Silvia Otero-Rodriguez, Oscar Moreno-Pérez, Jose Manuel Ramos, Mar García, Vicente Boix, Sergio Reus, Diego Torrus, Pablo Chico-Sánchez, José Sánchez-Payá, Fernando Aldana-Macias, Joan Gil, Joaquín Portilla, Esperanza Merino and on behalf of COVID19 ALC Research Group

Microorganisms 2021, 9(8), 1772; https://doi.org/10.3390/microorganisms9081772 - 20 Aug 2021

Cited by 2 | Viewed by 2079

Abstract

Exploring differences in clinical outcomes based on race and origin among patients hospitalized for COVID-19 is a controversial issue. The ALC COVID-19 Registry includes all confirmed COVID-19 patients admitted to hospital from 3 March 2020 to 17 December 2020. The data were obtained [...] Read more.

Exploring differences in clinical outcomes based on race and origin among patients hospitalized for COVID-19 is a controversial issue. The ALC COVID-19 Registry includes all confirmed COVID-19 patients admitted to hospital from 3 March 2020 to 17 December 2020. The data were obtained from electronic health records in order to evaluate the differences in the clinical features and outcomes among European and Latin American patients. The follow-ups occurred after 156 days. A propensity score weighting (PSW) logistic regression model was used to estimate the odds ratio (OR, 95% CI) for Latin American origin and outcome associations. Of the 696 patients included, 46.7% were women, with a median age of 65 (IQR 53–67) years, 614 (88.2%) were European, and 82 (11.8%) were Latin American. Latin American patients were younger, with fewer comorbidities, and a higher incidence of extensive pneumonia. After adjusting for residual confounders, Latin American origin was not associated with an increased risk of death (PSW OR 0.85 (0.23–3.14)) or with the need for invasive mechanical ventilation (PSW OR 0.35 (0.12–1.03)). Latin American origin was associated with a shorter hospital stay, but without differences in how long the patient remained on mechanical ventilation. In a public healthcare system, the rates of death or mechanical ventilation in severe COVID-19 cases were found to be comparable between patients of European and Latin American origins. Full article

(This article belongs to the Special Issue Infectious Diseases: Clinical Diagnosis and Molecular Epidemiology)

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21 pages, 1554 KiB

Open AccessReview

Xylella fastidiosa in Olive: A Review of Control Attempts and Current Management

by Massimiliano Morelli, José Manuel García-Madero, Ángeles Jos, Pasquale Saldarelli, Crescenza Dongiovanni, Magdalena Kovacova, Maria Saponari, Alberto Baños Arjona, Evelyn Hackl, Stephen Webb and Stéphane Compant

Microorganisms 2021, 9(8), 1771; https://doi.org/10.3390/microorganisms9081771 - 19 Aug 2021

Cited by 59 | Viewed by 9918

Abstract

Since 2013, Xylella fastidiosa Wells et al. has been reported to infect several hosts and to be present in different areas of Europe. The main damage has been inflicted on the olive orchards of southern Apulia (Italy), where a severe disease associated with [...] Read more.

Since 2013, Xylella fastidiosa Wells et al. has been reported to infect several hosts and to be present in different areas of Europe. The main damage has been inflicted on the olive orchards of southern Apulia (Italy), where a severe disease associated with X. fastidiosa subspecies pauca strain De Donno has led to the death of millions of trees. This dramatic and continuously evolving situation has led to European and national (Italian and Spanish) measures being implemented to reduce the spread of the pathogen and the associated olive quick decline syndrome (OQDS). Research has been also carried out to find solutions to better and directly fight the bacterium and its main insect vector, Philaenus spumarius L. In the course of this frantic effort, several treatments based on chemical or biological substances have been tested, in addition to plant breeding techniques and integrated pest management approaches. This review aims to summarize the attempts made so far and describe the prospects for better management of this serious threat, which poses alarming questions for the future of olive cultivation in the Mediterranean basin and beyond. Full article

(This article belongs to the Special Issue Integrating Science on Xanthomonas and Xylella for Integrated Plant Disease Management)

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12 pages, 19052 KiB

Open AccessArticle

Connection between the Gut Microbiota of Largemouth Bass (Micropterus salmoides) and Microbiota of the Pond Culture Environment

by Qianfu Liu, Zini Lai, Yuan Gao, Chao Wang, Yanyi Zeng, Erchun Liu, Yongzhan Mai, Wanling Yang and Haiyan Li

Microorganisms 2021, 9(8), 1770; https://doi.org/10.3390/microorganisms9081770 - 19 Aug 2021

Cited by 24 | Viewed by 3497

Abstract

The vital role of the gut microbiota in fish growth, development, immunity, and health has been largely confirmed. However, the interaction between environmental microbiota and the gut microbiota of aquaculture species remains unclear. Therefore, we analyzed the gut microbiota of largemouth bass ( [...] Read more.

The vital role of the gut microbiota in fish growth, development, immunity, and health has been largely confirmed. However, the interaction between environmental microbiota and the gut microbiota of aquaculture species remains unclear. Therefore, we analyzed the gut microbiota of largemouth bass (Micropterus salmoides) collected from subtropical ponds in southern China, as well as the pond water and aquatic sediment microbiota, using high-throughput sequencing of the 16S rRNA gene. Our results demonstrated significant differences in the compositions of pond water, sediment, and the gut microbiota of largemouth bass. Moreover, these compositions changed throughout the culture period. Only approximately 1% of the bacterial species in the pond sediment and gut microbiota were exchanged. However, the bacterial proportion of the gut microbiota from pond water microbiota was approximately 7% in samples collected in June and August, which increased markedly to 73% in October. Similarly, the proportion of bacteria in the pond water microbiota from the gut microbiota was approximately 12% in June and August, which increased to 45% in October. The study findings provide basic information for understanding the interactions between environmental microbiota and the gut microbiota of cultured fish, which may contribute to improved pond culture practices for largemouth bass. Full article

(This article belongs to the Special Issue The Microbiology of Natural and Artificial Aquatic Ecosystems)

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13 pages, 3346 KiB

Open AccessArticle

B7 Family Molecule VSIG4 Regulates Intestinal Anti-Enterohemorrhagic Escherichia coli Immunity by Altering Gut Flora Diversity

by Zhili He, Jiajia Li, Saisai Gong, Li Xing, Yakun Sun, Jianxin Wang, Tao Li, Nianzhi Ning, Liangyan Zhang, Wenjing Yu, Deyan Luo and Hui Wang

Microorganisms 2021, 9(8), 1769; https://doi.org/10.3390/microorganisms9081769 - 19 Aug 2021

Cited by 1 | Viewed by 2446

Abstract

As an essential member of the B7 family, V-set and immunoglobulin domain-containing 4 (VSIG4) is expressed explicitly in tissue-resident macrophages (TRMs) and plays an essential role in maintaining the homeostasis of the environmental immune system. Here, we demonstrate that gene-targeted VSIG4-deficient mice infected [...] Read more.

As an essential member of the B7 family, V-set and immunoglobulin domain-containing 4 (VSIG4) is expressed explicitly in tissue-resident macrophages (TRMs) and plays an essential role in maintaining the homeostasis of the environmental immune system. Here, we demonstrate that gene-targeted VSIG4-deficient mice infected with Enterohemorrhagic Escherichia coli (EHEC) display reduced bacterial burden. To reveal the role of VSIG4 in the fight against EHEC infection, we collected mice feces and used high-throughput 16S rRNA gene amplicons to detect changes in the flora. A total of 657330 sequences were sequenced on the PacBio platform, with an average length of 1498 bp. We found that VSIG4 deficiency could alter the gut microbiota by increasing diversity and shifting community composition. In particular, G_Akkermansia and G_Oscillo spiraceae increased significantly. These findings expand upon a prior observation that VSIG4 deficiency reduced EHEC colonization by changing the gut microbiota diversity and shifting community composition. Full article

(This article belongs to the Section Gut Microbiota)

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8 pages, 271 KiB

Open AccessArticle

Toxocara Seroprevalence and Risk Factor Analysis in Four Communities of the Wiwa, an Indigenous Tribe in Colombia

by Patrick Waindok, Simone Kann, Andrés Aristizabal, Juan Carlos Dib and Christina Strube

Microorganisms 2021, 9(8), 1768; https://doi.org/10.3390/microorganisms9081768 - 19 Aug 2021

Cited by 7 | Viewed by 2338

Abstract

The life of the indigenous Wiwa tribe in northeast Colombia is characterized by lacking access to clean drinking water and sanitary installations. Furthermore, free-roaming domestic animals and use of yucca and/or manioc as a primary food source favor the transmission of soil-transmitted helminths, [...] Read more.

The life of the indigenous Wiwa tribe in northeast Colombia is characterized by lacking access to clean drinking water and sanitary installations. Furthermore, free-roaming domestic animals and use of yucca and/or manioc as a primary food source favor the transmission of soil-transmitted helminths, e.g., Toxocara canis and Toxocara cati, the roundworms of dogs and cats. Infection may result in the clinical picture of toxocarosis, one of the most common zoonotic helminthoses worldwide. To estimate the Toxocara seroprevalence in four different villages of the Wiwa community, serum samples from 483 inhabitants were analyzed for anti-Toxocara-antibodies. Overall, 79.3% (383/483) of analyzed samples were seropositive. Statistically significant differences were observed between the four villages, as well as age groups (adults > adolescents > children), while sex had no effect. The high seropositivity rate demonstrates the risk of zoonotic roundworm infections and potential clinical disease in vulnerable indigenous inhabitants. Full article

(This article belongs to the Special Issue Zoonotic Parasites: Toxoplasma gondii, Trichinella spp., and Toxocara spp.)

17 pages, 4043 KiB

Open AccessArticle

Different Responses of Microbiota across Intestinal Tract to Enterococcus faecium HDRsEf1 and Their Correlation with Inflammation in Weaned Piglets

by Jin Zhou, Ji Luo, Shumin Yang, Qiling Xiao, Xiliang Wang, Zutao Zhou, Yuncai Xiao and Deshi Shi

Microorganisms 2021, 9(8), 1767; https://doi.org/10.3390/microorganisms9081767 - 19 Aug 2021

Cited by 12 | Viewed by 2644

Abstract

Enterococcus faecium HDRsEf1 (HDRsEf1) was identified to reduce the incidence of diarrhea in weaned piglets, but the mechanism has not been elucidated yet. Based on the fact that gut microbiota plays a crucial role in regulating inflammatory responses, the effects of HDRsEf1 on [...] Read more.

Enterococcus faecium HDRsEf1 (HDRsEf1) was identified to reduce the incidence of diarrhea in weaned piglets, but the mechanism has not been elucidated yet. Based on the fact that gut microbiota plays a crucial role in regulating inflammatory responses, the effects of HDRsEf1 on microbiota across the intestinal tract in weaned piglets were investigated. Microbiota from the luminal contents and the mucosa of the ileum, cecum, and colon of HDRsEf1-treated piglets were explored by 16S rRNA sequencing and qPCR. It was demonstrated that microbiota in different gut niches responded specifically to HDRsEf1, with major alterations occurring in the ileum and cecum. The total bacterial load of microbiota in ileal luminal contents and the relative abundance of Escherichia-Shigella in the ileal mucosa was significantly down-regulated by HDRsEf1 administration, while the relative abundance of butyrate-producing bacteria (including Clostridiaceae-1, Rumencoccidae, and Erysipelotrichaceae) in cecal luminal contents was significantly up-regulated. Moreover, the utilization of HDRsEf1 improved intestinal morphological development and reduced the inflammatory response, which were negatively correlated with the relative abundance of Escherichia-Shigella in the ileal mucosa and butyrate-producing bacteria in cecal luminal contents, respectively. Collectively, this study suggests that the administration of HDRsEf1 alters gut microbiota, thereby alleviating inflammation and improving intestinal morphological development in weaned piglets. Full article

(This article belongs to the Section Veterinary Microbiology)

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25 pages, 3485 KiB

Open AccessArticle

The Ever-Expanding Pseudomonas Genus: Description of 43 New Species and Partition of the Pseudomonas putida Group

by Léa Girard, Cédric Lood, Monica Höfte, Peter Vandamme, Hassan Rokni-Zadeh, Vera van Noort, Rob Lavigne and René De Mot

Microorganisms 2021, 9(8), 1766; https://doi.org/10.3390/microorganisms9081766 - 18 Aug 2021

Cited by 90 | Viewed by 10147

Abstract

The genus Pseudomonas hosts an extensive genetic diversity and is one of the largest genera among Gram-negative bacteria. Type strains of Pseudomonas are well known to represent only a small fraction of this diversity and the number of available Pseudomonas genome sequences is [...] Read more.

The genus Pseudomonas hosts an extensive genetic diversity and is one of the largest genera among Gram-negative bacteria. Type strains of Pseudomonas are well known to represent only a small fraction of this diversity and the number of available Pseudomonas genome sequences is increasing rapidly. Consequently, new Pseudomonas species are regularly reported and the number of species within the genus is constantly evolving. In this study, whole genome sequencing enabled us to define 43 new Pseudomonas species and provide an update of the Pseudomonas evolutionary and taxonomic relationships. Phylogenies based on the rpoD gene and whole genome sequences, including, respectively, 316 and 313 type strains of Pseudomonas, revealed sixteen groups of Pseudomonas and, together with the distribution of cyclic lipopeptide biosynthesis gene clusters, enabled the partitioning of the P. putida group into fifteen subgroups. Pairwise average nucleotide identities were calculated between type strains and a selection of 60 genomes of non-type strains of Pseudomonas. Forty-one strains were incorrectly assigned at the species level and among these, 19 strains were shown to represent an additional 13 new Pseudomonas species that remain to be formally classified. This work pinpoints the importance of correct taxonomic assignment and phylogenetic classification in order to perform integrative studies linking genetic diversity, lifestyle, and metabolic potential of Pseudomonas spp. Full article

(This article belongs to the Special Issue Genomics in Bacterial Taxonomy: Impact on the Genus Pseudomonas)

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15 pages, 3612 KiB

Open AccessReview

Update on the Mechanisms of Antibiotic Resistance and the Mobile Resistome in the Emerging Zoonotic Pathogen Streptococcus suis

by Manon Dechêne-Tempier, Corinne Marois-Créhan, Virginie Libante, Eric Jouy, Nathalie Leblond-Bourget and Sophie Payot

Microorganisms 2021, 9(8), 1765; https://doi.org/10.3390/microorganisms9081765 - 18 Aug 2021

Cited by 29 | Viewed by 4503

Abstract

Streptococcus suis is a zoonotic pathogen causing important economic losses in swine production. The most commonly used antibiotics in swine industry are tetracyclines, beta-lactams, and macrolides. Resistance to these antibiotics has already been observed worldwide (reaching high rates for macrolides and tetracyclines) as [...] Read more.

Streptococcus suis is a zoonotic pathogen causing important economic losses in swine production. The most commonly used antibiotics in swine industry are tetracyclines, beta-lactams, and macrolides. Resistance to these antibiotics has already been observed worldwide (reaching high rates for macrolides and tetracyclines) as well as resistance to aminoglycosides, fluoroquinolones, amphenicols, and glycopeptides. Most of the resistance mechanisms are encoded by antibiotic resistance genes, and a large part are carried by mobile genetic elements (MGEs) that can be transferred through horizontal gene transfer. This review provides an update of the resistance genes, their combination in multidrug isolates, and their localization on MGEs in S. suis. It also includes an overview of the contribution of biofilm to antimicrobial resistance in this bacterial species. The identification of resistance genes and study of their localization in S. suis as well as the environmental factors that can modulate their dissemination appear essential in order to decipher the role of this bacterium as a reservoir of antibiotic genes for other species. Full article

(This article belongs to the Special Issue Antimicrobial Resistance and Genetic Elements in Bacteria)

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28 pages, 455 KiB

Open AccessReview

Microbiome and Cancers of the Esophagus: A Review

by Yukiko Yano, Arash Etemadi and Christian C. Abnet

Microorganisms 2021, 9(8), 1764; https://doi.org/10.3390/microorganisms9081764 - 18 Aug 2021

Cited by 19 | Viewed by 4232

Abstract

Esophageal cancer (EC) is an aggressive malignant disease ranking amongst the leading causes of cancer deaths in the world. The two main histologic subtypes, esophageal squamous cell carcinoma (ESCC) and esophageal adenocarcinoma (EAC), have distinct geographic and temporal patterns and risk factor profiles. [...] Read more.

Esophageal cancer (EC) is an aggressive malignant disease ranking amongst the leading causes of cancer deaths in the world. The two main histologic subtypes, esophageal squamous cell carcinoma (ESCC) and esophageal adenocarcinoma (EAC), have distinct geographic and temporal patterns and risk factor profiles. Despite decades of research, the factors underlying these geo-temporal patterns are still not fully understood. The human microbiome has recently been implicated in various health conditions and disease, and it is possible that the microbiome may play an important role in the etiology of EC. Although studies of the microbiome and EC are still in their early stages, we review our current understanding of the potential links between ESCC, EAC, and bacterial communities in the oral cavity and esophagus. We also provide a summary of the epidemiology of EC and highlight some key challenges and future directions. Full article

(This article belongs to the Special Issue Bacteria and Esophageal Cancer)

19 pages, 3277 KiB

Open AccessArticle

Analysis of Human Gut Microbiota Composition Associated to the Presence of Commensal and Pathogen Microorganisms in Côte d’Ivoire

by Veronica Di Cristanziano, Fedja Farowski, Federica Berrilli, Maristella Santoro, David Di Cave, Christophe Glé, Martin Daeumer, Alexander Thielen, Maike Wirtz, Rolf Kaiser, Kirsten Alexandra Eberhardt, Maria J. G. T. Vehreschild and Rossella D’Alfonso

Microorganisms 2021, 9(8), 1763; https://doi.org/10.3390/microorganisms9081763 - 18 Aug 2021

Cited by 9 | Viewed by 3124

Abstract

Background: The human gut microbiota is a microbial ecosystem contributing to the maintenance of host health with functions related to immune and metabolic aspects. Relations between microbiota and enteric pathogens in sub-Saharan Africa are scarcely investigated. The present study explored gut microbiota composition [...] Read more.

Background: The human gut microbiota is a microbial ecosystem contributing to the maintenance of host health with functions related to immune and metabolic aspects. Relations between microbiota and enteric pathogens in sub-Saharan Africa are scarcely investigated. The present study explored gut microbiota composition associated to the presence of common enteric pathogens and commensal microorganisms, e.g., Blastocystis and Entamoeba species, in children and adults from semi-urban and non-urban localities in Côte d’Ivoire. Methods: Seventy-six stool samples were analyzed for microbiota composition by 16S rRDNA sequencing. The presence of adeno-, entero-, parechoviruses, bacterial and protozoal pathogens, Blastocystis, and commensal Entamoeba species, was analyzed by different molecular assays. Results: Twelve individuals resulted negative for any tested microorganisms, 64 subjects were positive for one or more microorganisms. Adenovirus, enterovirus, enterotoxigenic Escherichia coli (ETEC), and Blastocystis were frequently detected. Conclusions: The bacterial composition driven by Prevotellaceae and Ruminococcaceae confirmed the biotype related to the traditional dietary and cooking practices in low-income countries. Clear separation in UniFrac distance in subjects co-harboring Entamoeba hartmanni and Blastocystis was evidenced. Alpha diversity variation in negative control group versus only Blastocystis positive suggested its possible regulatory contribution on intestinal microbiota. Pathogenic bacteria and virus did not affect the positive outcome of co-harbored Blastocystis. Full article

(This article belongs to the Special Issue Gut Microbioma Structure and Functions in Human Health and Disease)

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