title: Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samples.
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.
authors.affiliation: Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel.
authors.forename: Tal
authors.initials: T
authors.lastname: Korem
authors.affiliation: Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel.
authors.forename: David
authors.initials: D
authors.lastname: Zeevi
authors.affiliation: Immunology Department, Weizmann Institute of Science, Rehovot, Israel.
authors.forename: Jotham
authors.initials: J
authors.lastname: Suez
authors.affiliation: Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel.
authors.forename: Adina
authors.initials: A
authors.lastname: Weinberger
authors.affiliation: Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel.
authors.forename: Tali
authors.initials: T
authors.lastname: Avnit-Sagi
authors.affiliation: Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel.
authors.forename: Maya
authors.initials: M
authors.lastname: Pompan-Lotan
authors.affiliation: Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel.
authors.forename: Elad
authors.initials: E
authors.lastname: Matot
authors.affiliation: Department of Biological services, Weizmann Institute of Science, Rehovot, Israel.
authors.forename: Ghil
authors.initials: G
authors.lastname: Jona
authors.affiliation: Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel.
authors.forename: Alon
authors.initials: A
authors.lastname: Harmelin
authors.affiliation: Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel.
authors.forename: Nadav
authors.initials: N
authors.lastname: Cohen
authors.affiliation: Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School and Broad Institute.
authors.forename: Alexandra
authors.initials: A
authors.lastname: Sirota-Madi
authors.affiliation: Immunology Department, Weizmann Institute of Science, Rehovot, Israel.
authors.forename: Christoph A
authors.initials: CA
authors.lastname: Thaiss
authors.affiliation: Immunology Department, Weizmann Institute of Science, Rehovot, Israel.
authors.forename: Meirav
authors.initials: M
authors.lastname: Pevsner-Fischer
authors.affiliation: Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
authors.forename: Rotem
authors.initials: R
authors.lastname: Sorek
authors.affiliation: Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School and Broad Institute.
authors.forename: Ramnik
authors.initials: R
authors.lastname: Xavier
authors.affiliation: Immunology Department, Weizmann Institute of Science, Rehovot, Israel.
authors.forename: Eran
authors.initials: E
authors.lastname: Elinav
authors.affiliation: Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel.
authors.forename: Eran
authors.initials: E
authors.lastname: Segal
mesh_terms: D001419:Bacteria / Q000145:classification / Q000235:genetics / Q000254:growth & development*; D003924:Diabetes Mellitus, Type 2 / Q000382:microbiology*; D041981:Gastrointestinal Tract / Q000382:microbiology*; D016680:Genome, Bacterial; D006801:Humans; D015212:Inflammatory Bowel Diseases / Q000382:microbiology*; D054892:Metagenome; D056186:Metagenomics; D064307:Microbiota / Q000235:genetics / Q000502:physiology*