Population structure discovery in meta-analyzed microbial communities and inflammatory bowel disease using MMUPHin

Microbiome studies of inflammatory bowel diseases (IBD) have achieved a scale for meta-analysis of dysbioses among populations. To enable microbial community meta-analyses generally, we develop MMUPHin for normalization, statistical meta-analysis, and population structure discovery using microbial t...

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Autores principales: Ma, Siyuan, Shungin, Dmitry, Mallick, Himel, Schirmer, Melanie, Nguyen, Long H., Kolde, Raivo, Franzosa, Eric, Vlamakis, Hera, Xavier, Ramnik, Huttenhower, Curtis
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2022
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9531436/
https://www.ncbi.nlm.nih.gov/pubmed/36192803
http://dx.doi.org/10.1186/s13059-022-02753-4
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author Ma, Siyuan
Shungin, Dmitry
Mallick, Himel
Schirmer, Melanie
Nguyen, Long H.
Kolde, Raivo
Franzosa, Eric
Vlamakis, Hera
Xavier, Ramnik
Huttenhower, Curtis
author_facet Ma, Siyuan
Shungin, Dmitry
Mallick, Himel
Schirmer, Melanie
Nguyen, Long H.
Kolde, Raivo
Franzosa, Eric
Vlamakis, Hera
Xavier, Ramnik
Huttenhower, Curtis
author_sort Ma, Siyuan
collection PubMed
description Microbiome studies of inflammatory bowel diseases (IBD) have achieved a scale for meta-analysis of dysbioses among populations. To enable microbial community meta-analyses generally, we develop MMUPHin for normalization, statistical meta-analysis, and population structure discovery using microbial taxonomic and functional profiles. Applying it to ten IBD cohorts, we identify consistent associations, including novel taxa such as Acinetobacter and Turicibacter, and additional exposure and interaction effects. A single gradient of dysbiosis severity is favored over discrete types to summarize IBD microbiome population structure. These results provide a benchmark for characterization of IBD and a framework for meta-analysis of any microbial communities. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-022-02753-4.
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spelling pubmed-95314362022-10-05 Population structure discovery in meta-analyzed microbial communities and inflammatory bowel disease using MMUPHin Ma, Siyuan Shungin, Dmitry Mallick, Himel Schirmer, Melanie Nguyen, Long H. Kolde, Raivo Franzosa, Eric Vlamakis, Hera Xavier, Ramnik Huttenhower, Curtis Genome Biol Method Microbiome studies of inflammatory bowel diseases (IBD) have achieved a scale for meta-analysis of dysbioses among populations. To enable microbial community meta-analyses generally, we develop MMUPHin for normalization, statistical meta-analysis, and population structure discovery using microbial taxonomic and functional profiles. Applying it to ten IBD cohorts, we identify consistent associations, including novel taxa such as Acinetobacter and Turicibacter, and additional exposure and interaction effects. A single gradient of dysbiosis severity is favored over discrete types to summarize IBD microbiome population structure. These results provide a benchmark for characterization of IBD and a framework for meta-analysis of any microbial communities. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-022-02753-4. BioMed Central 2022-10-03 /pmc/articles/PMC9531436/ /pubmed/36192803 http://dx.doi.org/10.1186/s13059-022-02753-4 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open AccessThis 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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Method
Ma, Siyuan
Shungin, Dmitry
Mallick, Himel
Schirmer, Melanie
Nguyen, Long H.
Kolde, Raivo
Franzosa, Eric
Vlamakis, Hera
Xavier, Ramnik
Huttenhower, Curtis
Population structure discovery in meta-analyzed microbial communities and inflammatory bowel disease using MMUPHin
title Population structure discovery in meta-analyzed microbial communities and inflammatory bowel disease using MMUPHin
title_full Population structure discovery in meta-analyzed microbial communities and inflammatory bowel disease using MMUPHin
title_fullStr Population structure discovery in meta-analyzed microbial communities and inflammatory bowel disease using MMUPHin
title_full_unstemmed Population structure discovery in meta-analyzed microbial communities and inflammatory bowel disease using MMUPHin
title_short Population structure discovery in meta-analyzed microbial communities and inflammatory bowel disease using MMUPHin
title_sort population structure discovery in meta-analyzed microbial communities and inflammatory bowel disease using mmuphin
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9531436/
https://www.ncbi.nlm.nih.gov/pubmed/36192803
http://dx.doi.org/10.1186/s13059-022-02753-4
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