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Culturing of a complex gut microbial community in mucin-hydrogel carriers reveals strain- and gene-associated spatial organization
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...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10267222/ https://www.ncbi.nlm.nih.gov/pubmed/37316519 http://dx.doi.org/10.1038/s41467-023-39121-0 |
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author | Jin, Xiaofan Yu, Feiqiao B. Yan, Jia Weakley, Allison M. Dubinkina, Veronika Meng, Xiandong Pollard, Katherine S. |
author_facet | Jin, Xiaofan Yu, Feiqiao B. Yan, Jia Weakley, Allison M. Dubinkina, Veronika Meng, Xiandong Pollard, Katherine S. |
author_sort | Jin, Xiaofan |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-10267222 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-102672222023-06-15 Culturing of a complex gut microbial community in mucin-hydrogel carriers reveals strain- and gene-associated spatial organization Jin, Xiaofan Yu, Feiqiao B. Yan, Jia Weakley, Allison M. Dubinkina, Veronika Meng, Xiandong Pollard, Katherine S. Nat Commun Article 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. Nature Publishing Group UK 2023-06-14 /pmc/articles/PMC10267222/ /pubmed/37316519 http://dx.doi.org/10.1038/s41467-023-39121-0 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Article Jin, Xiaofan Yu, Feiqiao B. Yan, Jia Weakley, Allison M. Dubinkina, Veronika Meng, Xiandong Pollard, Katherine S. Culturing of a complex gut microbial community in mucin-hydrogel carriers reveals strain- and gene-associated spatial organization |
title | Culturing of a complex gut microbial community in mucin-hydrogel carriers reveals strain- and gene-associated spatial organization |
title_full | Culturing of a complex gut microbial community in mucin-hydrogel carriers reveals strain- and gene-associated spatial organization |
title_fullStr | Culturing of a complex gut microbial community in mucin-hydrogel carriers reveals strain- and gene-associated spatial organization |
title_full_unstemmed | Culturing of a complex gut microbial community in mucin-hydrogel carriers reveals strain- and gene-associated spatial organization |
title_short | Culturing of a complex gut microbial community in mucin-hydrogel carriers reveals strain- and gene-associated spatial organization |
title_sort | culturing of a complex gut microbial community in mucin-hydrogel carriers reveals strain- and gene-associated spatial organization |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10267222/ https://www.ncbi.nlm.nih.gov/pubmed/37316519 http://dx.doi.org/10.1038/s41467-023-39121-0 |
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