Metagenomic Characterization of the Human Intestinal Microbiota in Fecal Samples from STEC-Infected Patients

Background: Influenza predominantly causes respiratory diseases; however, gastrointestinal symptoms are not uncommonly reported, particularly among high-risk groups. Influenza virus RNA has been also detected in stools of patients infected with pandemic and seasonal influenza, however, the role and the clinical significance of intestinal infection has not been clearly demonstrated. Methods: Here, we used NGS technology to investigate molecular characterization of viral RNA shedding in feces of adults with active influenza infection. Paired nasal and fecal samples were collected from 295 patients showing to emergency department at Hamad Medical Corporation with flu-like symptoms during January 2018 and April 2019. Results: Among these, 90 nasal samples were positive for influenza, of which, 26 fecal samples were positive for influenza in real-time PCR and only five showed virus growth in both monolayer and 3D cell culture. Full genome sequencing of isolated viruses revealed some unique mutations that we are currently in the process of studying their effect on virus kinetics. Then, we investigated the potential impact of respiratory influenza infection on intestinal microbiota diversity and composition. Microbiome analysis results suggest that changes in gut microbiota composition in influenza-infected patients are significantly associated with (1) influenza virus type, and (2) the presence of viral RNA in intestines of infected patients. We also identified bacterial taxa for which relative abundance was significantly higher in the patients with severe respiratory symptoms. Conclusion: Altogether, our findings suggest that influenza viruses can affect intestinal environment either by direct intestinal infection or indirectly by modulating intestinal microbiota.

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Roadmap to functional characterization of the human intestinal microbiota in its interaction with the host

Journal of Pharmaceutical and Biomedical Analysis ◽

10.1016/j.jpba.2020.113751 ◽

2021 ◽

Vol 194 ◽

pp. 113751

Author(s):

Carolin A. Kolmeder ◽

Willem M. de Vos

Keyword(s):

Intestinal Microbiota ◽

Functional Characterization ◽

Human Intestinal Microbiota

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Probiotic Bacteria Influence the Composition and Function of the Intestinal Microbiota

Interdisciplinary Perspectives on Infectious Diseases ◽

10.1155/2008/175285 ◽

2008 ◽

Vol 2008 ◽

pp. 1-9 ◽

Cited By ~ 57

Author(s):

Paul W. O'Toole ◽

Jakki C. Cooney

Keyword(s):

Intestinal Microbiota ◽

Bacterial Species ◽

Analytical Techniques ◽

Probiotic Bacteria ◽

Mediated Effects ◽

Molecular Approaches ◽

Human Intestinal Microbiota ◽

Altered Immune Response ◽

And Function

Probiotics have a range of proposed health benefits for the consumer, which may include modulating the levels of beneficial elements in the microbiota. Recent investigations using molecular approaches have revealed a human intestinal microbiota comprising over 1000 phylotypes. Mechanisms whereby probiotics impact on the intestinal microbiota include competition for substrates, direct antagonism by inhibitory substances, competitive exclusion, and potentially host-mediated effects such as improved barrier function and altered immune response. We now have the microbial inventories and genetic blueprints to begin tackling intestinal microbial ecology at an unprecedented level of detail, aided by the understanding that dietary components may be utilized differentially by individual phylotypes. Controlled intervention studies in humans, utilizing latest molecular technologies, are required to consolidate evidence for bacterial species that impact on the microbiota. Mechanistic insights should be provided by metabolomics and other analytical techniques for small molecules. Rigorous characterization of interactions between the diet, microbiota, and probiotic bacteria will provide new opportunities for modulating the microbiota towards improving human health.

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Human intestinal microbiota: Characterization of a simplified and stable gnotobiotic rat model

Gut Microbes ◽

10.4161/gmic.2.1.14651 ◽

2011 ◽

Vol 2 (1) ◽

pp. 25-33 ◽

Cited By ~ 88

Author(s):

Natalie Becker ◽

Julia Kunath ◽

Gunnar Loh ◽

Michael Blaut

Keyword(s):

Intestinal Microbiota ◽

Rat Model ◽

Human Intestinal Microbiota

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Faculty Opinions recommendation of The effect of age and non-steroidal anti-inflammatory drugs on human intestinal microbiota composition.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1164825.626665 ◽

2009 ◽

Author(s):

Piero Vernia

Keyword(s):

Intestinal Microbiota ◽

Microbiota Composition ◽

Human Intestinal Microbiota ◽

Inflammatory Drugs ◽

Anti Inflammatory ◽

Effect Of Age

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Discovery of novel community-relevant small proteins in a simplified human intestinal microbiome

Microbiome ◽

10.1186/s40168-020-00981-z ◽

2021 ◽

Vol 9 (1) ◽

Author(s):

Hannes Petruschke ◽

Christian Schori ◽

Sebastian Canzler ◽

Sarah Riesbeck ◽

Anja Poehlein ◽

...

Keyword(s):

Microbial Communities ◽

Intestinal Microbiota ◽

De Novo ◽

Bacterial Species ◽

Intestinal Microbiome ◽

Single Strain ◽

Small Proteins ◽

Human Intestinal Microbiota ◽

Wide Range

Abstract Background The intestinal microbiota plays a crucial role in protecting the host from pathogenic microbes, modulating immunity and regulating metabolic processes. We studied the simplified human intestinal microbiota (SIHUMIx) consisting of eight bacterial species with a particular focus on the discovery of novel small proteins with less than 100 amino acids (= sProteins), some of which may contribute to shape the simplified human intestinal microbiota. Although sProteins carry out a wide range of important functions, they are still often missed in genome annotations, and little is known about their structure and function in individual microbes and especially in microbial communities. Results We created a multi-species integrated proteogenomics search database (iPtgxDB) to enable a comprehensive identification of novel sProteins. Six of the eight SIHUMIx species, for which no complete genomes were available, were sequenced and de novo assembled. Several proteomics approaches including two earlier optimized sProtein enrichment strategies were applied to specifically increase the chances for novel sProtein discovery. The search of tandem mass spectrometry (MS/MS) data against the multi-species iPtgxDB enabled the identification of 31 novel sProteins, of which the expression of 30 was supported by metatranscriptomics data. Using synthetic peptides, we were able to validate the expression of 25 novel sProteins. The comparison of sProtein expression in each single strain versus a multi-species community cultivation showed that six of these sProteins were only identified in the SIHUMIx community indicating a potentially important role of sProteins in the organization of microbial communities. Two of these novel sProteins have a potential antimicrobial function. Metabolic modelling revealed that a third sProtein is located in a genomic region encoding several enzymes relevant for the community metabolism within SIHUMIx. Conclusions We outline an integrated experimental and bioinformatics workflow for the discovery of novel sProteins in a simplified intestinal model system that can be generically applied to other microbial communities. The further analysis of novel sProteins uniquely expressed in the SIHUMIx multi-species community is expected to enable new insights into the role of sProteins on the functionality of bacterial communities such as those of the human intestinal tract.

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Alterations in intestinal microbiota diversity, composition, and function in patients with sarcopenia

Scientific Reports ◽

10.1038/s41598-021-84031-0 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Lin Kang ◽

Pengtao Li ◽

Danyang Wang ◽

Taihao Wang ◽

Dong Hao ◽

...

Keyword(s):

Skeletal Muscle ◽

16S Rrna ◽

Intestinal Microbiota ◽

Muscle Growth ◽

Growth Function ◽

16S Rrna Sequencing ◽

Fecal Samples ◽

Lipopolysaccharide Biosynthesis ◽

Rrna Sequencing ◽

And Function

Abstract16S rRNA sequencing of human fecal samples has been tremendously successful in identifying microbiome changes associated with both aging and disease. A number of studies have described microbial alterations corresponding to physical frailty and nursing home residence among aging individuals. A gut-muscle axis through which the microbiome influences skeletal muscle growth/function has been hypothesized. However, the microbiome has yet to be examined in sarcopenia. Here, we collected fecal samples of 60 healthy controls (CON) and 27 sarcopenic (Case)/possibly sarcopenic (preCase) individuals and analyzed the intestinal microbiota using 16S rRNA sequencing. We observed an overall reduction in microbial diversity in Case and preCase samples. The genera Lachnospira, Fusicantenibacter, Roseburia, Eubacterium, and Lachnoclostridium—known butyrate producers—were significantly less abundant in Case and preCase subjects while Lactobacillus was more abundant. Functional pathways underrepresented in Case subjects included numerous transporters and phenylalanine, tyrosine, and tryptophan biosynthesis suggesting that protein processing and nutrient transport may be impaired. In contrast, lipopolysaccharide biosynthesis was overrepresented in Case and PreCase subjects suggesting that sarcopenia is associated with a pro-inflammatory metagenome. These analyses demonstrate structural and functional alterations in the intestinal microbiota that may contribute to loss of skeletal muscle mass and function in sarcopenia.

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Impact of Chronic Tetracycline Exposure on Human Intestinal Microbiota in a Continuous Flow Bioreactor Model

Antibiotics ◽

10.3390/antibiotics10080886 ◽

2021 ◽

Vol 10 (8) ◽

pp. 886

Author(s):

Youngbeom Ahn ◽

Ji Young Jung ◽

Ohgew Kweon ◽

Brian T. Veach ◽

Sangeeta Khare ◽

...

Keyword(s):

Molecular Analysis ◽

Intestinal Microbiota ◽

Continuous Flow ◽

Antimicrobial Drug ◽

Bioreactor Culture ◽

Analysis Techniques ◽

Human Intestinal Microbiota ◽

Traditional Cultures ◽

The Impact

Studying potential dietary exposure to antimicrobial drug residues via meat and dairy products is essential to ensure human health and consumer safety. When studying how antimicrobial residues in food impact the development of antimicrobial drug resistance and disrupt normal bacteria community structure in the intestine, there are diverse methodological challenges to overcome. In this study, traditional cultures and molecular analysis techniques were used to determine the effects of tetracycline at chronic subinhibitory exposure levels on human intestinal microbiota using an in vitro continuous flow bioreactor. Six bioreactor culture vessels containing human fecal suspensions were maintained at 37 °C for 7 days. After a steady state was achieved, the suspensions were dosed with 0, 0.015, 0.15, 1.5, 15, or 150 µg/mL tetracycline, respectively. Exposure to 150 µg/mL tetracycline resulted in a decrease of total anaerobic bacteria from 1.9 × 107 ± 0.3 × 107 down to 2 × 106 ± 0.8 × 106 CFU/mL. Dose-dependent effects of tetracycline were noted for perturbations of tetB and tetD gene expression and changes in acetate and propionate concentrations. Although no-observed-adverse-effect concentrations differed, depending on the traditional cultures and the molecular analysis techniques used, this in vitro continuous flow bioreactor study contributes to the knowledge base regarding the impact of chronic exposure of tetracycline on human intestinal microbiota.

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