Microbial-enrichment method enables high-throughput metagenomic characterization from host-rich samples.

Autor: Wu-Woods NJ; Biology and Bioengineering, California Institute of Technology, Pasadena, CA, USA., Barlow JT; Biology and Bioengineering, California Institute of Technology, Pasadena, CA, USA., Trigodet F; Department of Medicine, The University of Chicago, Chicago, IL, USA., Shaw DG; Department of Medicine, The University of Chicago, Chicago, IL, USA.; Committee on Immunology, The University of Chicago, Chicago, IL, USA.; Department of Pathology, The University of Chicago, Chicago, IL, USA., Romano AE; Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, USA., Jabri B; Department of Medicine, The University of Chicago, Chicago, IL, USA.; Committee on Immunology, The University of Chicago, Chicago, IL, USA.; Department of Pathology, The University of Chicago, Chicago, IL, USA., Eren AM; Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, USA.; Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany.; Alfred-Wegener-Institute for Marine and Polar Research, Bremerhaven, Germany.; Helmholtz Institute for Functional Marine Biodiversity, Oldenburg, Germany., Ismagilov RF; Biology and Bioengineering, California Institute of Technology, Pasadena, CA, USA. rustem.admin@caltech.edu.; Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, USA. rustem.admin@caltech.edu.
Jazyk: angličtina
Zdroj: Nature methods [Nat Methods] 2023 Nov; Vol. 20 (11), pp. 1672-1682. Date of Electronic Publication: 2023 Oct 12.
DOI: 10.1038/s41592-023-02025-4
Abstrakt: Host-microbe interactions have been linked to health and disease states through the use of microbial taxonomic profiling, mostly via 16S ribosomal RNA gene sequencing. However, many mechanistic insights remain elusive, in part because studying the genomes of microbes associated with mammalian tissue is difficult due to the high ratio of host to microbial DNA in such samples. Here we describe a microbial-enrichment method (MEM), which we demonstrate on a wide range of sample types, including saliva, stool, intestinal scrapings, and intestinal mucosal biopsies. MEM enabled high-throughput characterization of microbial metagenomes from human intestinal biopsies by reducing host DNA more than 1,000-fold with minimal microbial community changes (roughly 90% of taxa had no significant differences between MEM-treated and untreated control groups). Shotgun sequencing of MEM-treated human intestinal biopsies enabled characterization of both high- and low-abundance microbial taxa, pathways and genes longitudinally along the gastrointestinal tract. We report the construction of metagenome-assembled genomes directly from human intestinal biopsies for bacteria and archaea at relative abundances as low as 1%. Analysis of metagenome-assembled genomes reveals distinct subpopulation structures between the small and large intestine for some taxa. MEM opens a path for the microbiome field to acquire deeper insights into host-microbe interactions by enabling in-depth characterization of host-tissue-associated microbial communities.
(© 2023. The Author(s), under exclusive licence to Springer Nature America, Inc.)
Databáze: MEDLINE
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