Spatial Compartmentalization of the Microbiome between the Lumen and Crypts Is Lost in the Murine Cecum following the Process of Surgery, Including Overnight Fasting and Exposure to Antibiotics

MSystems
Alexander ZaborinJohn C Alverdy

Abstract

The cecum is a unique region in the mammalian intestinal tract in which the microbiome is localized to two compartments, the lumen and the crypts. The microbiome within crypts is particularly important as it is in direct contact with lining epithelial cells including stem cells. Here, we analyzed the microbiome in cecum of mice using multiple techniques including metagenomics. The lumen microbiome comprised Firmicutes and Bacteroidetes whereas the crypts were dominated by Proteobacteria and Deferribacteres, and the mucus comprised a mixture of these 4 phyla. The lumen microbial functional potential comprised mainly carbon metabolism, while the crypt microbiome was enriched for genes encoding stress resistance. In order to determine how this structure, assembly, and function are altered under provocative conditions, we exposed mice to overnight starvation (S), antibiotics (A), and a major surgical injury (partial hepatectomy [H]), as occurs with major surgery in humans. We have previously demonstrated that the combined effect of this "SAH" treatment leads to a major disturbance of the cecal microbiota at the bottom of crypts in a manner that disrupts crypt cell homeostasis. Here, we applied the SAH conditions and observed a loss...Continue Reading

References

Aug 1, 1972·Infection and Immunity·C P DavisD C Savage
Mar 1, 1996·Nature Biotechnology·S Tyagi, F R Kramer
Dec 11, 1999·Nucleic Acids Research·M Kanehisa, S Goto
Oct 30, 2001·Behavioural Brain Research·Y BenjaminiI Golani
May 10, 2005·International Journal of Systematic and Evolutionary Microbiology·Bronwyn R RobertsonAdrian Lee
Dec 8, 2005·Applied and Environmental Microbiology·Catherine Lozupone, Rob Knight
Apr 13, 2010·Nature Methods·J Gregory CaporasoRob Knight
Jun 11, 2010·Proceedings of the National Academy of Sciences of the United States of America·J Gregory CaporasoRob Knight
Mar 4, 2011·The Anatomical Record : Advances in Integrative Anatomy and Evolutionary Biology·Michel LaurinWilliam Parker
May 24, 2012·MBio·Thierry PédronPhilippe J Sansonetti
Jun 13, 2012·Nature Methods·Nicola SegataCurtis Huttenhower
Jun 30, 2012·Nature Methods·Johannes SchindelinAlbert Cardona
Oct 3, 2012·PLoS Computational Biology·Jonathan Friedman, Eric J Alm
Oct 1, 2013·Nature Methods·Joseph N PaulsonMihai Pop
Apr 4, 2014·Bioinformatics·Anthony M BolgerBjoern Usadel
Apr 23, 2014·BMC Microbiology·Christina SakarikouCarla Fontana
Aug 15, 2014·Nature Reviews. Microbiology·Pablo YarzaRamon Rosselló-Móra
Apr 22, 2015·The Journal of Veterinary Medical Science·Youhei MantaniHiroshi Kitagawa
Jul 17, 2015·American Journal of Physiology. Cell Physiology·Leon ZhengSean P Colgan
Dec 22, 2015·Communications for Statistical Applications and Methods·Seongho Kim
May 24, 2016·Nature Methods·Benjamin J CallahanSusan P Holmes
Dec 17, 2016·American Journal of Physiology. Gastrointestinal and Liver Physiology·Alexander ZaborinJohn C Alverdy
Jan 27, 2017·Microbiology and Molecular Biology Reviews : MMBR·Harry A DaileyMartin J Warren
Aug 12, 2017·Science·Mariana X ByndlossAndreas J Bäumler
Apr 8, 2018·The Biochemical Journal·Yugo TsuchiyaIvan Gout
Sep 29, 2018·Current Nutrition Reports·Edward S ChambersDouglas J Morrison
Nov 1, 2018·Nature Methods·Eric A FranzosaCurtis Huttenhower

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Citations

Dec 31, 2020·International Journal of Molecular Sciences·Marc Micó-CarneroCarmen Peralta
Mar 30, 2021·Microbes and Infection·Jen NguyenCarolina Tropini
May 23, 2021·Medical Microbiology and Immunology·Simone HerpBärbel Stecher
Nov 23, 2021·Environmental Science & Technology·Tyler D SowersKaren D Bradham

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Datasets Mentioned

BETA
PRJNA591641

Methods Mentioned

BETA
laser
amplicon sequencing
transmission electron microscopy
scanning electron microscopy
laser capture microdissection
PCR

Software Mentioned

Metaphlan2
Trimmomatic
SparCc
Humann2
phyloseq
BBMap
UniFrac
Agilent Mass Hunter
LASAF
BioCyc

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