ArticleNature methods2023
Microbial-enrichment method enables high-throughput metagenomic characterization from host-rich samples.
Article in Nature methods, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Full-length 16S rRNA nanopore sequencing enables species resolution ofGut microbes · 2026Article
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- Comprehensive cross-cohort analysis reveals global gut microbiome signatures of celiac disease.Communications medicine · 2026Article
- Uniform bacterial genetic diversity along the gut.Nature communications · 2026Article
- Review
- Advancing Plant Microbiome Research Through Host DNA Depletion Techniques.Plant biotechnology journal · 2026Review
- Review
- Standardizing vaginal microbial profiling: evaluating swab materials, storage conditions, and host DNA depletion strategies.BMC microbiology · 2026Article
- Host depletion kits improve microbiome analyses in environmental samples: seagrass as a test case.ISME communications · 2026Article
- Evaluating urine volume and host depletion methods to enable genome-resolved metagenomics of the urobiome.Microbiome · 2025Article
- Challenges and Opportunities in Analyzing Cancer-Associated Microbiomes.Cancer research · 2025Review
- Inducible, but not constitutive, pancreatic REG/Reg isoforms are regulated by intestinal microbiota and pancreatic diseases.Mucosal immunology · 2025Article
- Benefits and challenges of host depletion methods in profiling the upper and lower respiratory microbiome.NPJ biofilms and microbiomes · 2025Article
- ChIP provides 10-fold microbial DNA enrichment from tissue while minimizing bias.Molecular biology reports · 2025Article
- Article
- Article
- A metagenomic catalogue of the ruminant gut archaeome.Nature communications · 2024Article
- Long journey of 16S rRNA-amplicon sequencing toward cell-based functional bacterial microbiota characterization.iMetaOmics · 2024Review
- Genome-resolved metagenomics: a game changer for microbiome medicine.Experimental & molecular medicine · 2024Review
- mEnrich-seq: methylation-guided enrichment sequencing of bacterial taxa of interest from microbiome.Nature methods · 2024Article
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Authors and funding
8 authors.
Funding
Abstract
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.
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