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

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...

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Published inNature methods Vol. 20; no. 11; pp. 1672 - 1682
Main Authors Wu-Woods, Natalie J., Barlow, Jacob T., Trigodet, Florian, Shaw, Dustin G., Romano, Anna E., Jabri, Bana, Eren, A. Murat, Ismagilov, Rustem F.
Format Journal Article
LanguageEnglish
Published New York Nature Publishing Group US 01.11.2023
Nature Publishing Group
Subjects
631/1647/514
631/326/2565/2142
Acids
Animals
Bacteria
Bacteria - genetics
Bioinformatics
Biological Microscopy
Biological Techniques
Biomass
Biomedical and Life Sciences
Biomedical Engineering/Biotechnology
Biopsy
DNA
Feces
Gastrointestinal Tract
Genes
Genomes
High-Throughput Nucleotide Sequencing
Humans
Life Sciences
Mammals - genetics
Metagenome
Metagenomics
Metagenomics - methods
Methods
Microbiota
Microbiota - genetics
Microorganisms
Proteomics
RNA, Ribosomal, 16S - genetics
Taxonomy
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Summary: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. This work introduces microbial-enrichment methodology (MEM) that enables removal of host DNA in human intestinal biopsies and characterization of low-abundance microbial taxa down to 1%.
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N.J.W. and J.T.B conceived and optimized MEM. J.T.B designed sample collection and analyzed 16S sequencing. D.G.S. co-designed and performed human biopsy collection. N.J.W. and F.T. analyzed shotgun sequencing. A.E.R. performed library preparation. R.F.I. contributed to the design and implementation of the study and to obtaining funding. A.M.E. oversaw the bioinformatic analysis, contributed to the design and implementation of the study and to obtaining funding. B.J. supervised the clinical work, contributed to the design and implementation of the study and to obtaining funding. All authors edited the manuscript. A detailed author contribution statement is available in the SI.
Author Contribution Statement
ISSN:1548-7091
1548-7105
1548-7105
DOI:10.1038/s41592-023-02025-4