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Microorganisms
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The Role of the Gut Microbiome in Bacteria and Virus...
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The Role of the Gut Microbiome in Bacteria and Virus Infections

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Gut Microbiota".

Deadline for manuscript submissions: closed (30 June 2024) | Viewed by 4484

Special Issue Editors

Dr. Hideo Kato

E-Mail Website
Guest Editor
1. Department of Clinical Pharmaceutics, Graduate School of Medicine, Mie University, Mie 514-8507, Japan
2. Department of Pharmacy, Mie University Hospital, Mie 514-8507, Japan
Interests: clinical pharmaceutics; infectious disease; pharmacy
Special Issues, Collections and Topics in MDPI journals
Dr. Mao Hagihara

E-Mail Website
Guest Editor
Department of Molecular Epidemiology and Biomedical Sciences, Aichi Medical University, Aichi, Japan
Interests: pharmacokinetics; pharmacodynamics; antimicrobial; multi-drug resistant pathogen; therapeutic drug monitoring; in vivo study
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The number of studies on the human microbiome has increased over the last decade. In particular, gut commensal flora has been shown to contribute to influencing and maintianing body homeostasis by modulating immune reponses in the gastrointestinal system and other organs as a positive factor in human health. Dysbiosis of the gut microbiome can play a pathophysiological role in bacteria and virus infections via, for instance, abnormality of immunity and metabolism. On the other hand, some researchers have argued against an association between the abonormality of the gut microbiome and infections.

This Special Issue aims to discuss normalization of the gut microbiome in bacteria and virus infections.

Papers reporting original data from epidemiologic studies but also systematic reviews and meta-analyses are welcome for submission to this Special Issue, especially those providing basic studies to search novel mechanisms impacting the gut microbiome using bacterial and virus infection animal models.

We look forward to receiving your contributions.

Dr. Hideo Kato
Dr. Mao Hagihara
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • microbiome
  • gut
  • lung
  • bactereia
  • virus
  • clinical study
  • basic study

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Published Papers (2 papers)

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18 pages, 1573 KiB  
Article
Analysis of Cultured Gut Microbiota Using MALDI-TOF MS in COVID-19 Patients from Serbia during the Predominance of the SARS-CoV-2 Omicron Variant
by Aleksandra Patić, Gordana Kovačević, Vladimir Vuković, Ivana Hrnjaković Cvjetković, Mioljub Ristić, Biljana Milosavljević, Deana Medić, Milan Djilas, Jelena Radovanov, Aleksandra Kovačević, Tatjana Pustahija, Dragana Balać and Vladimir Petrović
Microorganisms 2024, 12(9), 1800; https://doi.org/10.3390/microorganisms12091800 - 30 Aug 2024
Viewed by 1342
Abstract
The currently dominant SARS-CoV-2 omicron variant, while causing mild respiratory symptoms, exhibits high transmissibility, drug resistance, and immune evasion. We investigated whether the presence of the SARS-CoV-2 affected the dynamics of fecal microbial composition isolated in culture in moderate COVID-19 patients. Blood, stool, [...] Read more.
The currently dominant SARS-CoV-2 omicron variant, while causing mild respiratory symptoms, exhibits high transmissibility, drug resistance, and immune evasion. We investigated whether the presence of the SARS-CoV-2 affected the dynamics of fecal microbial composition isolated in culture in moderate COVID-19 patients. Blood, stool, and medical records were collected from 50 patients with confirmed SARS-CoV-2 infection. Two samples were taken per patient, at disease onset (within 5 days) and after symptom resolution (30–35 days). The part of the gut microbiota identifiable using MALDI-TOF MS was analyzed, and inflammatory cytokines and blood markers were measured in serum. The analysis identified 566 isolates at the species level, including 83 bacterial and 9 fungal species. Our findings indicate a change in the gut microbiota composition isolated in culture during the initial phase of infection, characterized by the proliferation of opportunistic bacteria such as Enterococcus spp. and Citrobacter spp., at the expense of beneficial commensal bacteria from the genus Bacillus and Lactobacillus. Additionally, the enrichment of fungal pathogens in fecal samples collected 30 days after the cessation of disease symptoms might suggest a prolonged disruption of the gut microbiota even after the resolution of COVID-19 symptoms. This study contributes to a growing body of evidence on the systemic effects of SARS-CoV-2 and highlights the importance of considering gastrointestinal involvement in the management and treatment of COVID-19. Full article
(This article belongs to the Special Issue The Role of the Gut Microbiome in Bacteria and Virus Infections)
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22 pages, 2969 KiB  
Article
Ethanol-Producing Enterocloster bolteae Is Enriched in Chronic Hepatitis B-Associated Gut Dysbiosis: A Case–Control Culturomics Study
by Reham Magdy Wasfy, Babacar Mbaye, Patrick Borentain, Maryam Tidjani Alou, Maria Leticia Murillo Ruiz, Aurelia Caputo, Claudia Andrieu, Nicholas Armstrong, Matthieu Million and Rene Gerolami
Microorganisms 2023, 11(10), 2437; https://doi.org/10.3390/microorganisms11102437 - 28 Sep 2023
Cited by 6 | Viewed by 2751
Abstract
Background: Hepatitis B virus (HBV) infection is a global health epidemic that causes fatal complications, leading to liver cirrhosis and hepatocellular carcinoma. The link between HBV-related dysbiosis and specific bacterial taxa is still under investigation. Enterocloster is emerging as a new genus (formerly [...] Read more.
Background: Hepatitis B virus (HBV) infection is a global health epidemic that causes fatal complications, leading to liver cirrhosis and hepatocellular carcinoma. The link between HBV-related dysbiosis and specific bacterial taxa is still under investigation. Enterocloster is emerging as a new genus (formerly Clostridium), including Enterocloster bolteae, a gut pathogen previously associated with dysbiosis and human diseases such as autism, multiple sclerosis, and inflammatory bowel diseases. Its role in liver diseases, especially HBV infection, is not reported. Methods: The fecal samples of eight patients with chronic HBV infection and ten healthy individuals were analyzed using the high-throughput culturomics approach and compared to 16S rRNA sequencing. Quantification of ethanol, known for its damaging effect on the liver, produced from bacterial strains enriched in chronic HBV was carried out by gas chromatography–mass spectrometry. Results: Using culturomics, 29,120 isolated colonies were analyzed by Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry (MALDI–TOF); 340 species were identified (240 species in chronic HBV samples, 254 species in control samples) belonging to 169 genera and 6 phyla. In the chronic HBV group, 65 species were already known in the literature; 48 were associated with humans but had not been previously found in the gut, and 17 had never been associated with humans previously. Six species were newly isolated in our study. By comparing bacterial species frequency, three bacterial genera were serendipitously found with significantly enriched bacterial diversity in patients with chronic HBV: Enterocloster, Clostridium, and Streptococcus (p = 0.0016, p = 0.041, p = 0.053, respectively). However, metagenomics could not identify this enrichment, possibly concerning its insufficient taxonomical resolution (equivocal assignment of operational taxonomic units). At the species level, the significantly enriched species in the chronic HBV group almost all belonged to class Clostridia, such as Clostridium perfringens, Clostridium sporogenes, Enterocloster aldenensis, Enterocloster bolteae, Enterocloster clostridioformis, and Clostridium innocuum. Two E. bolteae strains, isolated from two patients with chronic HBV infection, showed high ethanol production (27 and 200 mM). Conclusions: Culturomics allowed us to identify Enterocloster species, specifically, E. bolteae, enriched in the gut microbiota of patients with chronic HBV. These species had never been isolated in chronic HBV infection before. Moreover, ethanol production by E. bolteae strains isolated from the chronic HBV group could contribute to liver disease progression. Additionally, culturomics might be critical for better elucidating the relationship between dysbiosis and chronic HBV infection in the future. Full article
(This article belongs to the Special Issue The Role of the Gut Microbiome in Bacteria and Virus Infections)
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