Cage and maternal effects on the bacterial communities of the murine gut

Abstract Findings from gut microbiome studies are strongly influenced by both experimental and analytical factors that can unintentionally bias their interpretation. Environment is also critical. Both co-housing and maternal effects are expected to affect microbiomes and have the potential to confou...

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Autores principales:	Gurdeep Singh, Andrew Brass, Sheena M. Cruickshank, Christopher G. Knight
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/dd2e2f3314e44cd681b20f0ea2334bf2
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spelling	oai:doaj.org-article:dd2e2f3314e44cd681b20f0ea2334bf22021-12-02T16:57:26ZCage and maternal effects on the bacterial communities of the murine gut10.1038/s41598-021-89185-52045-2322https://doaj.org/article/dd2e2f3314e44cd681b20f0ea2334bf22021-05-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-89185-5https://doaj.org/toc/2045-2322Abstract Findings from gut microbiome studies are strongly influenced by both experimental and analytical factors that can unintentionally bias their interpretation. Environment is also critical. Both co-housing and maternal effects are expected to affect microbiomes and have the potential to confound other manipulated factors, such as genetics. We therefore analysed microbiome data from a mouse experiment using littermate controls and tested differences among genotypes (wildtype versus colitis prone-mdr1a −/− ), gut niches (stool versus mucus), host ages (6 versus 18 weeks), social groups (co-housed siblings of different genotypes) and maternal influence. We constructed a 16S phylogenetic tree from bacterial communities, fitting random forest models using all 428,234 clades identified. Models discriminated all criteria except host genotype, where no community differences were found. Host social groups differed in abundant, low-level, taxa whereas intermediate phylogenetic and abundance scales distinguished ages and niches. Thus, a carefully controlled experiment treating evolutionary clades of microbes equivalently without reference to taxonomy, clearly identifies whether and how gut microbial communities are distinct across ecologically important factors (niche and host age) and other experimental factors, notably cage effects and maternal influence. These findings highlight the importance of considering such environmental factors in future microbiome studies.Gurdeep SinghAndrew BrassSheena M. CruickshankChristopher G. KnightNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-12 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Gurdeep Singh Andrew Brass Sheena M. Cruickshank Christopher G. Knight Cage and maternal effects on the bacterial communities of the murine gut
description	Abstract Findings from gut microbiome studies are strongly influenced by both experimental and analytical factors that can unintentionally bias their interpretation. Environment is also critical. Both co-housing and maternal effects are expected to affect microbiomes and have the potential to confound other manipulated factors, such as genetics. We therefore analysed microbiome data from a mouse experiment using littermate controls and tested differences among genotypes (wildtype versus colitis prone-mdr1a −/− ), gut niches (stool versus mucus), host ages (6 versus 18 weeks), social groups (co-housed siblings of different genotypes) and maternal influence. We constructed a 16S phylogenetic tree from bacterial communities, fitting random forest models using all 428,234 clades identified. Models discriminated all criteria except host genotype, where no community differences were found. Host social groups differed in abundant, low-level, taxa whereas intermediate phylogenetic and abundance scales distinguished ages and niches. Thus, a carefully controlled experiment treating evolutionary clades of microbes equivalently without reference to taxonomy, clearly identifies whether and how gut microbial communities are distinct across ecologically important factors (niche and host age) and other experimental factors, notably cage effects and maternal influence. These findings highlight the importance of considering such environmental factors in future microbiome studies.
format	article
author	Gurdeep Singh Andrew Brass Sheena M. Cruickshank Christopher G. Knight
author_facet	Gurdeep Singh Andrew Brass Sheena M. Cruickshank Christopher G. Knight
author_sort	Gurdeep Singh
title	Cage and maternal effects on the bacterial communities of the murine gut
title_short	Cage and maternal effects on the bacterial communities of the murine gut
title_full	Cage and maternal effects on the bacterial communities of the murine gut
title_fullStr	Cage and maternal effects on the bacterial communities of the murine gut
title_full_unstemmed	Cage and maternal effects on the bacterial communities of the murine gut
title_sort	cage and maternal effects on the bacterial communities of the murine gut
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/dd2e2f3314e44cd681b20f0ea2334bf2
work_keys_str_mv	AT gurdeepsingh cageandmaternaleffectsonthebacterialcommunitiesofthemurinegut AT andrewbrass cageandmaternaleffectsonthebacterialcommunitiesofthemurinegut AT sheenamcruickshank cageandmaternaleffectsonthebacterialcommunitiesofthemurinegut AT christophergknight cageandmaternaleffectsonthebacterialcommunitiesofthemurinegut
_version_	1718382594705326080

Cage and maternal effects on the bacterial communities of the murine gut

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