Extensive transmission of microbes along the gastrointestinal tract
- European Molecular Biology Laboratory, Germany
- Université Paris-Est, France
- University of Luxembourg, Luxembourg
Abstract
The gastrointestinal tract is abundantly colonized by microbes, yet the translocation of oral species to the intestine is considered a rare aberrant event, and a hallmark of disease. By studying salivary and fecal microbial strain populations of 310 species in 470 individuals from five countries, we found that transmission to, and subsequent colonization of, the large intestine by oral microbes is common and extensive among healthy individuals. We found evidence for a vast majority of oral species to be transferable, with increased levels of transmission in colorectal cancer and rheumatoid arthritis patients and, more generally, for species described as opportunistic pathogens. This establishes the oral cavity as an endogenous reservoir for gut microbial strains, and oral-fecal transmission as an important process that shapes the gastrointestinal microbiome in health and disease.
Data availability
Raw sequencing data have been deposited in the European Nucleotide Archive under project accessions PRJNA289586 and PRJEB28422.
-
The Salivary Microbiome in Health and DiseaseEuropean Nucleotide Archive, PRJEB28422.
-
Human Gut Microbiome in a Multiplex Family Study of Type 1 Diabetes MellitusEuropean Nucleotide Archive, PRJNA289586.
-
The oral and gut microbiomes are perturbed in rheumatoid arthritis and partly normalized after treatment.European Nucleotide Archive, PRJEB6997.
-
FijiCOMP: saliva and stool metagenomesEuropean Nucleotide Archive, PRJNA217052.
-
Temporal and technical variability of human gut metagenomes.European Nucleotide Archive, PRJEB8347.
-
Potential of fecal microbiota for early-stage detection of colorectal cancer.European Nucleotide Archive, PRJEB6070.
-
Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes.European Nucleotide Archive, PRJNA289586.
Article and author information
Author details
Thomas Sebastian Benedikt Schmidt
Carine de Beaufort
Anna Heintz-Buschart
Funding
Fonds National de la Recherche Luxembourg (CORE/15/BM/10404093)
- Thomas Sebastian Benedikt Schmidt
- Matthew Robert Hayward
- Anna Heintz-Buschart
H2020 European Research Council (ERC-AdG-669830)
- Thomas Sebastian Benedikt Schmidt
- Simone S Li
- Oleksandr M Maistrenko
- Renato JC Alves
- Peer Bork
H2020 Marie Skłodowska-Curie Actions (661019)
- Matthew Robert Hayward
German Network Bioinformatics (de.NBI #031A537B)
- Georg Zeller
- Peer Bork
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Ethics
Human subjects: Informed consent was obtained from all study subjects for which novel data was generated; see respective previous publications for details (PMID: 27723761; PMID: 25432777; PMID: 25888008).
Reviewing Editor
- Max Nieuwdorp, AMC, Netherlands
Publication history
- Received: October 9, 2018
- Accepted: February 3, 2019
- Accepted Manuscript published: February 12, 2019 (version 1)
- Version of Record published: March 19, 2019 (version 2)
Copyright
© 2019, Schmidt et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
Metrics
-
- 12,109
- Page views
-
- 1,858
- Downloads
-
- 195
- Citations
Article citation count generated by polling the highest count across the following sources: Crossref, Scopus, PubMed Central.
Download links
A two-part list of links to download the article, or parts of the article, in various formats.
Downloads (link to download the article as PDF)
Open citations (links to open the citations from this article in various online reference manager services)
Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)
Extensive transmission of microbes along the gastrointestinal tract
eLife 8:e42693.
https://doi.org/10.7554/eLife.42693
Further reading
-
- Microbiology and Infectious Disease
eLife is pleased to present a Special Issue to highlight recent advances in the mechanistic understanding of microbiome function.
-
- Computational and Systems Biology
Biological age, distinct from an individual's chronological age, has been studied extensively through predictive aging clocks. However, these clocks have limited accuracy in short time-scales. Here we trained deep learning models on fundus images from the EyePACS dataset to predict individuals' chronological age. Our retinal aging clocking, 'eyeAge', predicted chronological age more accurately than other aging clocks (mean absolute error of 2.86 and 3.30 years on quality-filtered data from EyePACS and UK Biobank, respectively). Additionally, eyeAge was independent of blood marker-based measures of biological age, maintaining an all-cause mortality hazard ratio of 1.026 even when adjusted for phenotypic age. The individual-specific nature of eyeAge was reinforced via multiple GWAS hits in the UK Biobank cohort. The top GWAS locus was further validated via knockdown of the fly homolog, Alk, which slowed age-related decline in vision in flies. This study demonstrates the potential utility of a retinal aging clock for studying aging and age-related diseases and quantitatively measuring aging on very short time-scales, opening avenues for quick and actionable evaluation of gero-protective therapeutics.
