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Microorganisms
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Advances in Host-Gut Microbiota
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Advances in Host-Gut Microbiota

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

Deadline for manuscript submissions: 31 October 2024 | Viewed by 2638

Special Issue Editor

Dr. Jean-Paul Motta

E-Mail Website
Guest Editor
Institute of Digestive Health Research, IRSD, INSERM U1220, Toulouse, France
Interests: host–microbiota interactions; mucosal biofilms; infectious and inflammatory gut disorders; microbiota ageing; intestinal epithelium
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue of Microorganisms will give an overview of current gut microbiota research being performed both in fundamental (CNRS) and applied host institutions (INSERM, CEA, INRAe), and with a particular focus on the impact of this research for human health perspectives. Current studies on how microbes influence host physiology and pathologies mostly rely on the taxonomic profiling of the gut microbiota from the mouth to anus, communities living close to the mucosa and in the lumen, and in different pathological situations. However, there are still important gaps in our understanding of the causal relationship between alterations in the microbiota (i.e., dysbiosis) and disease initiation/progression; hence, studies or reviews tackling this question will be welcomed in this Special Issue. Moreover, studies aimed at understanding, from an ecological perspective, how microbial communities interact with each other and their host environment represent an exciting research direction for the future, and will also be welcomed. In this Special Issue entitled “Advances in Host-Gut Microbiota”, we invite colleagues to contribute original research articles or reviews related to their multidisciplinary research, on topics including, but not limited to, the following:

Biologically relevant host–microbiota models, from in vitro to in vivo and ex vivo;
Structure and function of the microbiota;
Microbial community genetics, transcriptomics, proteomics and metabolomics;
Microbe–microbe interaction within host-associated microbial communities;
Metabolic interaction with the host;
Inflammatory diseases;
Interaction with the immune system;
Microbial biodegradation of nutrients and xenobiotics: role in drug response;
Microbial ecology;
Microbial biofilms interacting with host mucosa;
Microbial biogeography;
Microbial functions in the different habitats within the gut;
Metabolic flux analysis;
Analysis of functionalities by stable isotope probing (DNA, RNA, and protein);
Model systems for studying microbiome biology;
Novel technologies for the analysis of structure and function of the microbiota.

Dr. Jean-Paul Motta
Guest Editor

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

  • host–microbiota interactions
  • infectious and inflammatory gut disorders
  • microbiota ageing
  • intestinal epithelium

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Published Papers (4 papers)

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16 pages, 10090 KiB  
Article
Gestational Interrelationships among Gut–Metabolism–Transcriptome in Regulating Early Embryo Implantation and Placental Development in Mice
by Shuai Lin, Yuqi Liang, Jingqi Geng, Yunfei Yan, Ruipei Ding and Maozhang He
Microorganisms 2024, 12(9), 1902; https://doi.org/10.3390/microorganisms12091902 - 17 Sep 2024
Abstract
Decidualization of the uterine endometrium is a critical process for embryo implantation in mammals, primarily occurring on gestational day 8 in pregnant mice. However, the interplay between the maternal gut microbiome, metabolism, and the uterus at this specific time point remains poorly understood. [...] Read more.
Decidualization of the uterine endometrium is a critical process for embryo implantation in mammals, primarily occurring on gestational day 8 in pregnant mice. However, the interplay between the maternal gut microbiome, metabolism, and the uterus at this specific time point remains poorly understood. This study employed a multi-omics approach to investigate the metabolic, gut microbiome, and transcriptomic changes associated with early pregnancy (gestational day 8 (E8)) in mice. Serum metabolomics revealed a distinct metabolic profile at E8 compared to controls, with the differential metabolites primarily enriched in amino acid metabolism pathways. The gut microbial composition showed that E8 mice exhibited higher alpha-diversity and a significant shift in beta-diversity. Specifically, the E8 group displayed a decrease in pathogenic Proteobacteria and an increase in beneficial Bacteroidetes and S24-7 taxa. Transcriptomics identified myriads of distinct genes between the E8 and control mice. The differentially expressed genes were enriched in pathways involved in alanine, aspartate, and glutamate metabolism, PI3K-Akt signaling, and the PPAR signaling pathway. Integrative analysis of the multi-omics data uncovered potential mechanistic relationships among the differential metabolites, gut microbiota, and uterine gene expression changes. Notably, the gene Asns showed strong correlations with specific gut S24-7 and metabolite L-Aspartatic acid, suggesting its potential role in mediating the crosstalk between the maternal environment and embryo development during early pregnancy. These findings provide valuable insights into the complex interplay between the maternal metabolome, the gut microbiome, and the uterine transcriptome in the context of early pregnancy, which may contribute to our understanding of the underlying mechanisms of embryo implantation and development. Full article
(This article belongs to the Special Issue Advances in Host-Gut Microbiota)
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17 pages, 2568 KiB  
Article
Sulfate-Reducing Bacteria Induce Pro-Inflammatory TNF-α and iNOS via PI3K/Akt Pathway in a TLR 2-Dependent Manner
by Sudha B. Singh, Cody A. Braun, Amanda Carroll-Portillo, Cristina N. Coffman and Henry C. Lin
Microorganisms 2024, 12(9), 1833; https://doi.org/10.3390/microorganisms12091833 - 5 Sep 2024
Abstract
Desulfovibrio, resident gut sulfate-reducing bacteria (SRB), are found to overgrow in diseases such as inflammatory bowel disease and Parkinson’s disease. They activate a pro-inflammatory response, suggesting that Desulfovibrio may play a causal role in inflammation. Class I phosphoinositide 3-kinase (PI3K)/protein kinase B [...] Read more.
Desulfovibrio, resident gut sulfate-reducing bacteria (SRB), are found to overgrow in diseases such as inflammatory bowel disease and Parkinson’s disease. They activate a pro-inflammatory response, suggesting that Desulfovibrio may play a causal role in inflammation. Class I phosphoinositide 3-kinase (PI3K)/protein kinase B (AKT) signaling pathway regulates key events in the inflammatory response to infection. Dysfunctional PI3K/Akt signaling is linked to numerous diseases. Bacterial-induced PI3K/Akt pathway may be activated downstream of toll-like receptor (TLR) signaling. Here, we tested the hypothesis that Desulfovibrio vulgaris (DSV) may induce tumor necrosis factor alpha (TNF-α) and inducible nitric oxide synthase (iNOS) expression via PI3K/Akt in a TLR 2-dependent manner. RAW 264.7 macrophages were infected with DSV, and protein expression of p-Akt, p-p70S6K, p-NF-κB, p-IkB, TNF-α, and iNOS was measured. We found that DSV induced these proteins in a time-dependent manner. Heat-killed and live DSV, but not bacterial culture supernatant or a probiotic Lactobacillus plantarum, significantly caused PI3K/AKT/TNF/iNOS activation. LY294002, a PI3K/Akt signaling inhibitor, and TL2-C29, a TLR 2 antagonist, inhibited DSV-induced PI3K/AKT pathway. Thus, DSV induces pro-inflammatory TNF-α and iNOS via PI3K/Akt pathway in a TLR 2-dependent manner. Taken together, our study identifies a novel mechanism by which SRB such as Desulfovibrio may trigger inflammation in diseases associated with SRB overgrowth. Full article
(This article belongs to the Special Issue Advances in Host-Gut Microbiota)
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14 pages, 3447 KiB  
Article
Two-Year Study on the Intra-Individual Dynamics of Gut Microbiota and Short-Chain Fatty Acids Profiles in Healthy Adults
by Anastasia Senina, Maria Markelova, Dilyara Khusnutdinova, Maria Siniagina, Olga Kupriyanova, Gulnaz Synbulatova, Airat Kayumov, Eugenia Boulygina and Tatiana Grigoryeva
Microorganisms 2024, 12(8), 1712; https://doi.org/10.3390/microorganisms12081712 - 20 Aug 2024
Viewed by 490
Abstract
While the gut microbiome has been intensively investigated for more than twenty years already, its role in various disorders remains to be unraveled. At the same time, questions about what changes in the gut microbiota can be considered as normal or pathological and [...] Read more.
While the gut microbiome has been intensively investigated for more than twenty years already, its role in various disorders remains to be unraveled. At the same time, questions about what changes in the gut microbiota can be considered as normal or pathological and whether communities are able to recover after exposure to negative factors (diseases, medications, environmental factors) are still unclear. Here, we describe changes in the gut microbiota composition and the content of short-chain fatty acids in adult healthy volunteers (n = 15) over a 24 month-period. Intraindividual variability in gut microbial composition was 40%, whereas the short chain fatty acids profile remained relatively stable (2-year variability 20%, inter-individual 26%). The changes tend to accumulate over time. Nevertheless, both short-term and long-term changes in the gut microbiome composition were significantly smaller within individuals than interindividual differences (two-year interindividual variability was 75%). Seasonal changes in gut microbiota were found more often in autumn and spring involving the content of minor representatives (less than 1.5% of the community in average) in the phyla Actinobacteriota, Firmicutes and Proteobacteria. Full article
(This article belongs to the Special Issue Advances in Host-Gut Microbiota)
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21 pages, 6051 KiB  
Systematic Review
The Role of Akkermansia muciniphila on Improving Gut and Metabolic Health Modulation: A Meta-Analysis of Preclinical Mouse Model Studies
by Leila Khalili, Gwoncheol Park, Ravinder Nagpal and Gloria Salazar
Microorganisms 2024, 12(8), 1627; https://doi.org/10.3390/microorganisms12081627 - 9 Aug 2024
Viewed by 636
Abstract
Akkermansia muciniphila (A. muciniphila) and its derivatives, including extracellular vesicles (EVs) and outer membrane proteins, are recognized for enhancing intestinal balance and metabolic health. However, the mechanisms of Akkermansia muciniphila’s action and its effects on the microbiome are not well [...] Read more.
Akkermansia muciniphila (A. muciniphila) and its derivatives, including extracellular vesicles (EVs) and outer membrane proteins, are recognized for enhancing intestinal balance and metabolic health. However, the mechanisms of Akkermansia muciniphila’s action and its effects on the microbiome are not well understood. In this study, we examined the influence of A. muciniphila and its derivatives on gastrointestinal (GI) and metabolic disorders through a meta-analysis of studies conducted on mouse models. A total of 39 eligible studies were identified through targeted searches on PubMed, Web of Science, Science Direct, and Embase until May 2024. A. muciniphila (alive or heat-killed) and its derivatives positively affected systemic and gut inflammation, liver enzyme level, glycemic response, and lipid profiles. The intervention increased the expression of tight-junction proteins in the gut, improving gut permeability in mouse models of GI and metabolic disorders. Regarding body weight, A. muciniphila and its derivatives prevented weight loss in animals with GI disorders while reducing body weight in mice with metabolic disorders. Sub-group analysis indicated that live bacteria had a more substantial effect on most analyzed biomarkers. Gut microbiome analysis using live A. muciniphila identified a co-occurrence cluster, including Desulfovibrio, Family XIII AD3011 group, and Candidatus Saccharimonas. Thus, enhancing the intestinal abundance of A. muciniphila and its gut microbial clusters may provide more robust health benefits for cardiometabolic, and age-related diseases compared with A. muciniphila alone. The mechanistic insight elucidated here will pave the way for further exploration and potential translational applications in human health. Full article
(This article belongs to the Special Issue Advances in Host-Gut Microbiota)
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