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Science. 2015 Sep 4;349(6252):1101-1106. doi: 10.1126/science.aac4812. Epub 2015 Jul 30.

Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samples.

Author information

1
Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel.
2
Immunology Department, Weizmann Institute of Science, Rehovot, Israel.
3
Department of Biological services, Weizmann Institute of Science, Rehovot, Israel.
4
Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel.
5
Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School and Broad Institute.
6
Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
#
Contributed equally

Abstract

Metagenomic sequencing increased our understanding of the role of the microbiome in health and disease, yet it only provides a snapshot of a highly dynamic ecosystem. Here, we show that the pattern of metagenomic sequencing read coverage for different microbial genomes contains a single trough and a single peak, the latter coinciding with the bacterial origin of replication. Furthermore, the ratio of sequencing coverage between the peak and trough provides a quantitative measure of a species' growth rate. We demonstrate this in vitro and in vivo, under different growth conditions, and in complex bacterial communities. For several bacterial species, peak-to-trough coverage ratios, but not relative abundances, correlated with the manifestation of inflammatory bowel disease and type II diabetes.

TRIAL REGISTRATION:

ClinicalTrials.gov NCT01892956.

PMID:
26229116
PMCID:
PMC5087275
DOI:
10.1126/science.aac4812
[Indexed for MEDLINE]
Free PMC Article

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