Spatially distinct physiology of Bacteroides fragilis within the proximal colon of gnotobiotic mice.

Nature Microbiology
G P DonaldsonSarkis K Mazmanian

Abstract

A complex microbiota inhabits various microenvironments of the gut, with some symbiotic bacteria having evolved traits to invade the epithelial mucus layer and reside deep within the intestinal tissue of animals. Whether these distinct bacterial communities across gut biogeographies exhibit divergent behaviours is largely unknown. Global transcriptomic analysis to investigate microbial physiology in specific mucosal niches has been hampered technically by an overabundance of host RNA. Here, we employed hybrid selection RNA sequencing (hsRNA-Seq) to enable detailed spatial transcriptomic profiling of a prominent human commensal as it colonizes the colonic lumen, mucus or epithelial tissue of mice. Compared to conventional RNA-Seq, hsRNA-Seq increased reads mapping to the Bacteroides fragilis genome by 48- and 154-fold in mucus and tissue, respectively, allowing for high-fidelity comparisons across biogeographic sites. Near the epithelium, B. fragilis upregulated numerous genes involved in protein synthesis, indicating that bacteria inhabiting the mucosal niche are metabolically active. Further, a specific sulfatase (BF3086) and glycosyl hydrolase (BF3134) were highly induced in mucus and tissue compared to bacteria in the lumen....Continue Reading

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Citations

Oct 14, 2020·Environmental Microbiology Reports·Edward Ruby
Oct 13, 2020·Glycobiology·Andrew Bell, Nathalie Juge
Feb 6, 2021·Biological Chemistry·Daniel RyanAlexander J Westermann
Jan 1, 2021·Gut Microbes·Yijie GuoNobuhiko Kamada
Feb 19, 2021·Nature Reviews. Genetics·Alexander J Westermann, Jörg Vogel
Mar 7, 2021·International Journal of Medical Microbiology : IJMM·J Christian Pérez
Mar 28, 2021·Mucosal Immunology·Noëmie DanielBenoit Chassaing
May 19, 2021·Experimental & Molecular Medicine·Jian FangXiaohong Zhang
Jun 15, 2021·Translational Research : the Journal of Laboratory and Clinical Medicine·Cambrian Y LiuEugene B Chang
Feb 4, 2021·ACS Central Science·Justin E Silpe, Emily P Balskus
Sep 30, 2021·Gut Microbes·J Christian Pérez

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Datasets Mentioned

BETA
PRJNA438372

Methods Mentioned

BETA
RNA-Seq
hsRNA-Seq
PCR
environmental stress
density-gradient centrifugation
flow cytometry

Software Mentioned

edgeR
GLAM2Scan
FASTX
STRING
Prodigal
bedtools
MEME Suite
GLAM2
FlowJo
- Toolkit

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