scholarly journals Systematic characterization of human gut microbiome-secreted molecules by integrated multi-omics

2021 ◽  
Vol 1 (1) ◽  
Author(s):  
Bianca De Saedeleer ◽  
Antoine Malabirade ◽  
Javier Ramiro-Garcia ◽  
Janine Habier ◽  
Jean-Pierre Trezzi ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Complex Mixture ◽  
Host Cells ◽  
Methodological Framework ◽  
Secretion Systems ◽  
Human Gut ◽  
Healthy Human ◽  
Human Gut Microbiome ◽  
Health And Disease

AbstractThe human gut microbiome produces a complex mixture of biomolecules that interact with human physiology and play essential roles in health and disease. Crosstalk between micro-organisms and host cells is enabled by different direct contacts, but also by the export of molecules through secretion systems and extracellular vesicles. The resulting molecular network, comprised of various biomolecular moieties, has so far eluded systematic study. Here we present a methodological framework, optimized for the extraction of the microbiome-derived, extracellular biomolecular complement, including nucleic acids, (poly)peptides, and metabolites, from flash-frozen stool samples of healthy human individuals. Our method allows simultaneous isolation of individual biomolecular fractions from the same original stool sample, followed by specialized omic analyses. The resulting multi-omics data enable coherent data integration for the systematic characterization of this molecular complex. Our results demonstrate the distinctiveness of the different extracellular biomolecular fractions, both in terms of their taxonomic and functional composition. This highlights the challenge of inferring the extracellular biomolecular complement of the gut microbiome based on single-omic data. The developed methodological framework provides the foundation for systematically investigating mechanistic links between microbiome-secreted molecules, including those that are typically vesicle-associated, and their impact on host physiology in health and disease.

scholarly journals Enterotype Variations of the Healthy Human Gut Microbiome in Different Geographical Regions

2018 ◽  
Vol 14 (9) ◽  
pp. 560-573 ◽  
Author(s):  
Fauzul Mobeen ◽  
◽  
Vikas Sharma ◽  
Tulika Prakash ◽  
◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Human Gut ◽  
Healthy Human ◽  
Human Gut Microbiome ◽  
Geographical Regions

Global and temporal state of the human gut microbiome in health and disease

2021 ◽  
Author(s):  
Saeed Shoaie ◽  
Sunjae Lee ◽  
Mathieu Almeida ◽  
Gholamreza Bidkhori ◽  
Nicolas Pons ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Integrative Analysis ◽  
Human Gut ◽  
Human Gut Microbiome ◽  
Health And Disease ◽  
One Year ◽  
The Stability ◽  
Clinical Phenotyping ◽  
Sampling Times

Abstract The role of gut microbiota in humans is of great interest, and metagenomics provided the possibilities for extensively analysing bacterial diversity in health and disease. Here we explored the human gut microbiome samples across 19 countries, performing compositional, functional and integrative analysis. To complement these data and analyse the stability of the microbiome, we followed 86 healthy Swedish individuals over one year, with four sampling times and extensive clinical phenotyping. The integrative analysis of temporal microbiome changes shows the existence of two types of species with a tendency to vary in abundance with time, here called outflow and inflow species. Importantly, the former tends to be enriched in disease, while the latter is enriched in health. We suggest that the decrease of disease-associated outflow and the increase of health-associated inflow species with time may be a fundamental albeit previously unrecognized aspect of the homeostasis maintenance in a healthy microbiome.

Role of Human Gut Microbiome in Health and Disease

2021 ◽  
pp. 101-112
Author(s):  
Nazar Reehana ◽  
Mohamed Yousuff Mohamed Imran ◽  
Nooruddin Thajuddin ◽  
D. Dhanasekaran
Keyword(s):  
Gut Microbiome ◽  
Human Gut ◽  
Human Gut Microbiome ◽  
Health And Disease

scholarly journals Human genetic determinants of the gut microbiome and their associations with health and disease: a phenome-wide association study

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Hilde E. Groot ◽  
Yordi J. van de Vegte ◽  
Niek Verweij ◽  
Erik Lipsic ◽  
Jacco C. Karper ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Healthy Aging ◽  
Total Sample ◽  
Causal Link ◽  
Small Scale ◽  
Nucleotide Polymorphisms ◽  
Genetic Determinants ◽  
Human Gut ◽  
Human Gut Microbiome ◽  
Health And Disease

Abstract Small-scale studies have suggested a link between the human gut microbiome and highly prevalent diseases. However, the extent to which the human gut microbiome can be considered a determinant of disease and healthy aging remains unknown. We aimed to determine the spectrum of diseases that are linked to the human gut microbiome through the utilization of its genetic determinants as a proxy for its composition. 180 single nucleotide polymorphisms (SNPs) known to influence the human gut microbiome were used to assess the association with health and disease outcomes in 422,417 UK Biobank participants. Potential causal estimates were obtained using a Mendelian randomization (MR) approach. From the total sample analysed (mean age was 57 ± 8 years), 194,567 (46%) subjects were male. Median exposure was 66-person years (interquartile range 59–72). Eleven SNPs were significantly associated with 28 outcomes (Bonferroni corrected P value < 4.63·10−6) including food intake, hypertension, atopy, COPD, BMI, and lipids. Multiple SNP MR pointed to a possible causal link between Ruminococcus flavefaciens and hypertension, and Clostridium and platelet count. Microbiota and their metabolites might be of importance in the interplay between overlapping pathophysiological processes, although challenges remain in establishing causal relationships.

scholarly journals Defining a Healthy Human Gut Microbiome: Current Concepts, Future Directions, and Clinical Applications

2012 ◽  
Vol 12 (5) ◽  
pp. 611-622 ◽  
Author(s):  
Fredrik Bäckhed ◽  
Claire M. Fraser ◽  
Yehuda Ringel ◽  
Mary Ellen Sanders ◽  
R. Balfour Sartor ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Clinical Applications ◽  
Human Gut ◽  
Healthy Human ◽  
Future Directions ◽  
Human Gut Microbiome

Trust Your Gut: The Human Gut Microbiome in Health and Disease

2022 ◽  
pp. 53-96
Author(s):  
Hebatallah H. AboNahas ◽  
Amira M. G. Darwish ◽  
Hanaa F. Abd EL-kareem ◽  
Yousef H. AboNahas ◽  
Safaa A. Mansour ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Human Gut ◽  
Human Gut Microbiome ◽  
Health And Disease

scholarly journals Characterization of the SOS meta-regulon in the human gut microbiome

2014 ◽  
Vol 30 (9) ◽  
pp. 1193-1197 ◽  
Author(s):  
Joseph P. Cornish ◽  
Neus Sanchez-Alberola ◽  
Patrick K. O’Neill ◽  
Ronald O'Keefe ◽  
Jameel Gheba ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Human Gut ◽  
Human Gut Microbiome

scholarly journals Metaproteomics as a tool for studying the protein landscape of human-gut bacterial species

2021 ◽  
Author(s):  
Moses Stamboulian ◽  
Jamie Canderan ◽  
Yuzhen Ye
Keyword(s):  
Human Health ◽  
Gut Microbiome ◽  
De Novo ◽  
Bacterial Species ◽  
Individual Species ◽  
Human Gut ◽  
Human Gut Microbiome ◽  
Microbial Species ◽  
Microbial Organisms

AbstractHost-microbiome interactions and the microbial community have broad impact in human health and diseases. Most microbiome based studies are performed at the genome level based on next-generation sequencing techniques, but metaproteomics is emerging as a powerful technique to study microbiome functional activity by characterizing the complex and dynamic composition of microbial proteins. We conducted a large-scale survey of human gut microbiome metaproteomic data to identify generalist species that are ubiquitously expressed across all samples and specialists that are highly expressed in a small subset of samples associated with a certain phenotype. We were able to utilize the metaproteomic mass spectrometry data to reveal the protein landscapes of these species, which enables the characterization of the expression levels of proteins of different functions and underlying regulatory mechanisms, such as operons. Finally, we were able to recover a large number of open reading frames (ORFs) with spectral support, which were missed by de novo protein-coding gene predictors. We showed that a majority of the rescued ORFs overlapped with de novo predicted proteincoding genes, but on opposite strands or on different frames. Together, these demonstrate applications of metaproteomics for the characterization of important gut bacterial species. Results are available for public access at https://omics.informatics.indiana.edu/GutBac.Author summaryMany reference genomes for studying human gut microbiome are available, but knowledge about how microbial organisms work is limited. Identification of proteins at individual species or community level provides direct insight into the functionality of microbial organisms. By analyzing more than a thousand metaproteomics datasets, we examined protein landscapes of more than two thousands of microbial species that may be important to human health and diseases. This work demonstrated new applications of metaproteomic datasets for studying individual genomes. We made the analysis results available through the GutBac website, which we believe will become a resource for studying microbial species important for human health and diseases.

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