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Analysis of Gut Microbial Regulation of Host Gene Expression Along the Length of the Gut and Regulation of Gut Microbial Ecology

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Analysis of Gut Microbial Regulation of Host Gene Expression Along the Length of the Gut and Regulation of Gut Microbial Ecology Gut Online First, published on November 23, 2011 as 10.1136/gutjnl-2011-301104 Gut microbiota ORIGINAL ARTICLE Gut: first published as 10.1136/gutjnl-2011-301104 on 23 November 2011. Downloaded from Analysis of gut microbial regulation of host gene expression along the length of the gut and regulation of gut microbial ecology through MyD88 Erik Larsson,1,2 Valentina Tremaroli,1,2 Ying Shiuan Lee,1,2 Omry Koren,3 Intawat Nookaew,4 Ashwana Fricker,3 Jens Nielsen,4 Ruth E Ley,3 Fredrik Ba¨ckhed1,2 < Additional supplementary ABSTRACT materials are published online Background The gut microbiota has profound effects on Significance of this study only. To view these files please host physiology but local hostemicrobial interactions in visit the journal online (http:// gut.bmj.com). the gut are only poorly characterised and are likely to vary What is already known about the subject? from the sparsely colonised duodenum to the densely < 1Sahlgrenska Center for The gut harbours a vast ensemble of bacteria, Cardiovascular and Metabolic colonised colon. Microorganisms are recognised by the gut microbiota, encoding 150-fold more Research/Wallenberg pattern recognition receptors such as Toll-like receptors, genes than our own genome. Laboratory, Sahlgrenska which signal through the adaptor molecule MyD88. < The gut microbiota is altered in inflammatory University Hospital, Gothenburg, Methods To identify host responses induced by gut bowel disease and obesity. Sweden microbiota along the length of the gut and whether these 2Department of Molecular and < Germ-free mice are protected against inflamma- Clinical Medicine, University of required MyD88, transcriptional profiles of duodenum, tory bowel disease and diet-induced obesity. Gothenburg, Gothenburg, jejunum, ileum and colon were compared from germ-free < Toll-like receptors recognise microorganisms Sweden and conventionally raised wild-type and Myd88À/À mice. 3 and signal via MyD88. Department of Microbiology, The gut microbial ecology was assessed by 454-based Cornell University, Ithaca, New York, USA pyrosequencing and viruses were analysed by PCR. What are the new findings? < 4Department of Chemical and Results The gut microbiota modulated the expression of Provides an extensive survey of host responses Biological Engineering, Chalmers a large set of genes in the small intestine and fewer to the normal gut microbiota along the length of University of Technology, genes in the colon but surprisingly few microbiota- the gut. Gothenburg, Sweden regulated genes required MyD88 signalling. However, < Analysis of the gut microbial ecology along the Correspondence to MyD88 was essential for microbiota-induced colonic length of the gut. Dr Fredrik Ba¨ckhed, Wallenberg expression of the antimicrobial genes Reg3b and Reg3g < Demonstrates that Myd88-deficient mice Laboratory, Sahlgrenska in the epithelium, and Myd88 deficiency was associated harbour norovirus in the colonic epithelium. http://gut.bmj.com/ University Hospital, S-413 45 with both a shift in bacterial diversity and a greater Gothenburg, Sweden; How might it impact on clinical practice in the [email protected] proportion of segmented filamentous bacteria in the small intestine. In addition, conventionally raised Myd88À/À foreseeable future? < Revised 21 October 2011 mice had increased expression of antiviral genes in the Understanding the fundamental factors under- Accepted 23 October 2011 colon, which correlated with norovirus infection in the lying hostemicrobial interactions in the colonic epithelium. mammalian gut is essential for future studies Conclusion This study provides a detailed description of directed at targeting the gut microbiota in order on September 24, 2021 by guest. Protected copyright. tissue-specific host transcriptional responses to the to improve health. We also provide a web- normal gut microbiota along the length of the gut and accessible database, http://microbiota.wall.gu. demonstrates that the absence of MyD88 alters gut se, to investigate whether specific genes are microbial ecology. regulated by the gut microbiota and/or MyD88. This resource will facilitate the identification of microbially regulated genes for researchers interested in all aspects of gastroenterology. The human gut is home to trillions of bacteria (gut microbiota) that have co-evolved with us and established a finely tuned symbiosis.1 Their combined genomes (metagenome), which contain villus,5 increased vascularisation,6 recruitment of 150-fold more genes compared with our own lymphocytes7 and activation of the innate and genome, provide us with functions that we did not adaptive immune systems.8 have to evolve ourselves.23Recent data suggest The innate immune system recognises bacteria and that if this symbiosis is disrupted we are exposed to other infectious agents by pattern recognition recep- the increased risk of developing common diseases tors such as intracellular nucleotide-binding oligo- such as inflammatory bowel disease and obesity.4 merization domain-like receptors and Toll-like Germ-free mice provide a powerful tool to gain receptors (TLR).9 All TLR (except TLR3) as well as mechanistic insights into hostemicrobial interac- interleukin (IL) 1 and IL-18 signal via MyD88- This paper is freely available tions and their effect on host physiology. Coloni- dependent pathways, which activate nuclear factor online under the BMJ Journals fl unlocked scheme, see http:// sation of germ-free mice is associated with kappa B-driven pro-in ammatory signalling. Accord- gut.bmj.com/site/about/ profound morphological changes in the small ingly, MYD88 deficiency in humans is associated unlocked.xhtml intestine such as shortening and widening of the with increased susceptibility to pyogenic bacterial CopyrightLarsson E, Tremaroli Article V, Leeauthor YS, et al(or. Gut their(2011). employer) doi:10.1136/gutjnl-2011-301104 2011. Produced by BMJ Publishing Group Ltd (& BSG) under licence.1 of 8 Gut microbiota infections and Myd88-deficient mice have enhanced susceptibility each tissue separately using the expression console software Gut: first published as 10.1136/gutjnl-2011-301104 on 23 November 2011. Downloaded from and morbidity to most viral and bacterial experimental infections.10 (Affymetrix). CEL files and normalised data were deposited into The microbial ecology of the gut is governed by several the NCBI GEO repository, accession number GSE17438. Down- factors, such as age, diet and host genotype, and recent findings stream analyses were performed in Matlab using proprietary suggest an important role for the innate immune system.11 In scripts as and functions from the Bioinformatics toolbox. Genes particular, TLR5 has been shown to have a significant impact in were annotated against the ENSEMBL17 set of genes using the shaping the colonic gut microbiota, whereas TLR2 and TLR4 MoGene1.0STprobesetmappingprovidedusingBioMart.18 appear to play a minor role.12 13 Furthermore, in a mouse model Probesetsthatweremappedtomorethanonegenewereexcluded of non-obese diabetes, Myd88 deficiency is associated with whileredundantprobesetswereaveraged.Thisresultedinafinal altered microbial community composition that confers dataset of 22 073 unique genes, each associated with one or more protection against developing the disease.14 unambiguously mapped probe sets. Principal components analysis The function and architecture of the gut differs along its and hierarchical clustering (average linkage with Pearson’scorre- length: for example, nutrient absorption is most prevalent in the lation coefficient) was performed on the processed dataset. duodenum and jejunum, whereas the ileum is more immuno- Differential expression was evaluated in each tissue by calculating logically active.15 The colon is more of a fermentative reactor two-way analysis of variance (ANOVA) p values, including a test producing short chain fatty acids and is the major site of water for interaction, using colonisation status (germ-free or conven- reabsorption.15 However, little is known about how the host tionally raised) and genotype (Myd88À/À or wild type) as inde- responds to gut microbiota along the length of the gut. The pendent variables. This test was applied to each individual gene, concentration of bacteria increases along the length of the gut, and was followed by adjustment for multiple comparisons using from 104 cells/g in the duodenum to 1012 cells/g in the colon,15 theqvaluemethodproposedbyBenjaminiandHochberg.19 Gene and most published studies of gut microbial ecology have ontology (GO) statistics, based on ENSEMBL annotated terms and focused on the colon and feces, with less emphasis on the less their ancestors in the GO hierarchy, were calculated using Fisher’s populated and more inaccessible small intestine. The aim of our exact test. To account for multiple testing, we used permutation study was to identify the influence of innate immunity on simulations to determine that an enrichment p value threshold of À microbiota-induced host responses and microbial composition 10 4 resulted in a low fraction of false positives (<5%). Genes along the length of the gut; we used Myd88 deficiency as without annotated GO terms were excluded from the analysis. a model for the loss of innate immune signalling. cDNA synthesis and quantitative PCR MATERIALS AND METHODS An aliquot of 0.5 mg of total RNA was reverse transcribed (high Mice capacity cDNA reverse transcription kit; Applied Biosystems, Germ-free C57Bl6/J and Swiss Webster male mice (three to five Foster City, California, USA) and SYBR green-based
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