ArticleNature communications2023
Culturing of a complex gut microbial community in mucin-hydrogel carriers reveals strain- and gene-associated spatial organization.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
17 citing papers in PubMed.
- Why probiotics fail: gut niche tension as the missing variable?Gut microbes · 2026Review
- Linkage of nucleotide and functional diversity varies across gut bacteria.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Exploring the predominant factors associated with shaping the cultivable swine gut microbiota of Wuzhishan piglets under in vitro cultivation conditions.BMC microbiology · 2026Article
- Uniform bacterial genetic diversity along the gut.Nature communications · 2026Article
- Spatial structure: shaping the ecology and evolution of microbial communities.FEMS microbiology reviews · 2026Review
- Hydrogel-based experimental models of the gastrointestinal tract.Microbiome · 2025Review
- Community coalescence reveals strong selection and coexistence within species in complex microbial communities.bioRxiv : the preprint server for biology · 2025Article
- Coarse-grained model of serial dilution dynamics in synthetic human gut microbiome.PLoS computational biology · 2025Article
- Metabolic ecology of microbiomes: Nutrient competition, host benefits, and community engineering.Cell host & microbe · 2025Review
- Enabling next-generation anaerobic cultivation through biotechnology to advance functional microbiome research.Nature biotechnology · 2025Review
- Accurate estimation of intraspecific microbial gene content variation in metagenomic data with MIDAS v3 and StrainPGC.Genome research · 2025Article
- Comprehensive profiling of genomic invertons in defined gut microbial community reveals associations with intestinal colonization and surface adhesion.Microbiome · 2025Article
- Predicting the first steps of evolution in randomly assembled communities.Nature communications · 2024Article
- Predicting the First Steps of Evolution in Randomly Assembled Communities.bioRxiv : the preprint server for biology · 2024Article
- Draft genome ofMicrobiology resource announcements · 2024Article
- Average Nucleotide Identity basedbioRxiv : the preprint server for biology · 2024Article
- Microbe-cellulose hydrogels as a model system for particulate carbon degradation in soil aggregates.ISME communications · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
Abstract
Microbial community function depends on both taxonomic composition and spatial organization. While composition of the human gut microbiome has been deeply characterized, less is known about the organization of microbes between regions such as lumen and mucosa and the microbial genes regulating this organization. Using a defined 117 strain community for which we generate high-quality genome assemblies, we model mucosa/lumen organization with in vitro cultures incorporating mucin hydrogel carriers as surfaces for bacterial attachment. Metagenomic tracking of carrier cultures reveals increased diversity and strain-specific spatial organization, with distinct strains enriched on carriers versus liquid supernatant, mirroring mucosa/lumen enrichment in vivo. A comprehensive search for microbial genes associated with this spatial organization identifies candidates with known adhesion-related functions, as well as novel links. These findings demonstrate that carrier cultures of defined communities effectively recapitulate fundamental aspects of gut spatial organization, enabling identification of key microbial strains and genes.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.