ArticleThe ISME journal2019
Rethinking gut microbiome residency and the Enterobacteriaceae in healthy human adults.
Article in The ISME journal, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 75 papers.
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Who cites it
75 citing papers in PubMed.
- Microbiome ecology and antibiotic treatment failure: resistance spread, microbial competition and community engineering.Microbial genomics · 2026Review
- Interspecies interaction controlsProceedings of the National Academy of Sciences of the United States of America · 2026Article
- Characterization of the gut microbiome of wildFrontiers in microbiomes · 2026Article
- Strain displacement in microbiomes via ecological competition.Nature microbiology · 2025Article
- Comparative analysis of virulence genes, biofilm production, and antibiotic resistance in Escherichia coli from dogs and humans using rep-PCR.BMC veterinary research · 2025Article
- Evidence of ESBL plasmid transfer and selective persistence of multiple host-associatedApplied and environmental microbiology · 2025Article
- Clinical value of metagenomic next-generation sequencing in screening oropharyngeal colonization in patients undergoing allogeneic hematopoietic stem cell transplantation: a prospective observational study.Microbiology spectrum · 2025Observational
- Metabolic ecology of microbiomes: Nutrient competition, host benefits, and community engineering.Cell host & microbe · 2025Review
- Metagenomics reveals an increased proportion of anJournal of Zhejiang University. Science. B · 2025Article
- Vaccine-enhanced competition permits rational bacterial strain replacement in the gut.Science (New York, N.Y.) · 2025Article
- Recent Insights into the Evolving Role of the Gut Microbiome in Critical Care.Critical care clinics · 2025Review
- Cross-Sectional Comparative Analysis of Gut Microbiota in Spanish Adolescents with Mediterranean and Western Diets.Nutrients · 2025Article
- Strain phylogroup and environmental constraints shape Escherichia coli dynamics and diversity over a 20-year human gut time series.The ISME journal · 2025Article
- Residence-colonization trade-off and niche differentiation enable coexistence of Escherichia coli phylogroups in healthy humans.The ISME journal · 2025Article
- A proposed workflow to robustly analyze bacterial transcripts in RNAseq data from extracellular vesicles.Frontiers in microbiology · 2025Article
- Tracking the origin of bacterial DNA in blood: Indication of localized and sporadic transfer from other body sites.Gut microbes reports · 2025Article
- Exploring gut microbiota and its predicted functions in pulmonary tuberculosis: A multi-regional study using public 16S datasets.PloS one · 2025Article
- A plasmid-chromosome crosstalk in multidrug resistant enterobacteria.Nature communications · 2024Article
- Diagnosing and engineering gut microbiomes.EMBO molecular medicine · 2024Review
- Gut community structure as a risk factor for infection inmSystems · 2024Article
15 more citing papers are in PubMed but not listed here.
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Authors and funding
8 authors.
Funding
Abstract
Longitudinal human gut microbiome datasets generated using community-level, sequence-based approaches often report a sub-set of long-lived "resident" taxa that rarely, if ever, are lost. This result contrasts with population-level turnover of resident clones on the order of months to years. We hypothesized that the disconnect between these results is due to a relative lack of simultaneous discrimination of the human gut microbiome at both the community and population-levels. Here, we present results of a small, longitudinal cohort study (n = 8 participants) of healthy human adults that identifies static and dynamic members of the gut microbiome at the clone level based on cultivation/genetic discrimination and at the operational taxonomic unit/amplified sequence variant levels based on 16S rRNA sequencing. We provide evidence that there is little "stability" within resident clonal populations of the common gut microbiome bacterial family, Enterobacteriaceae. Given that clones can vary substantially in genome content and that evolutionary processes operate on the population level, these results question the biological relevance of apparent stability at higher taxonomic levels.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.