{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T17:38:34Z","timestamp":1791308314937,"version":"4.3.1"},"reference-count":63,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2010,10,28]],"date-time":"2010-10-28T00:00:00Z","timestamp":1288224000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Complex microbial populations are organized in relation to their environment. In the intestine, the inner lining (mucosa) is a potential focal point for such organization. The proximal murine colon contains mucosal folds that are known to be associated with morphologically distinct microbes. To identify these microbes, we used the technique of laser capture microdissection (LCM) to sample microbes associated with these folds (interfold region) and within the central lumen (digesta region). Using 16S rRNA gene tag pyrosequencing, we found that microbes in the interfold region were highly enriched for the phylum Firmicutes and, more specifically, for the families Lachnospiraceae and Ruminococcaceae. Other families such as Bacteroidaceae, Enterococcaceae and Lactobacillaceae were all enriched in the digesta region. This high-resolution system to capture and examine spatial organization of intestinal microbes should facilitate microbial analysis in other mouse models, furthering our understanding of host\u2013microbial interactions.<\/jats:p>","DOI":"10.1038\/ismej.2010.161","type":"journal-article","created":{"date-parts":[[2010,10,28]],"date-time":"2010-10-28T10:44:23Z","timestamp":1288262663000},"page":"627-638","source":"Crossref","is-referenced-by-count":256,"title":["Spatial organization of intestinal microbiota in the mouse ascending colon"],"prefix":"10.1093","volume":"5","author":[{"given":"Gerardo M","family":"Nava","sequence":"first","affiliation":[{"name":"Department of Pathology and Immunology, Washington University School of Medicine , St Louis, MO , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hans J","family":"Friedrichsen","sequence":"additional","affiliation":[{"name":"Department of Pathology and Immunology, Washington University School of Medicine , St Louis, MO , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thaddeus S","family":"Stappenbeck","sequence":"additional","affiliation":[{"name":"Department of Pathology and Immunology, Washington University School of Medicine , St Louis, MO , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2010,10,28]]},"reference":[{"key":"2024020218190965500_CR1","doi-asserted-by":"publisher","first-page":"1807","DOI":"10.1099\/ijs.0.65440-0","article-title":"Complete rpoB gene sequencing as a suitable supplement to DNA-DNA hybridization for bacterial species and genus delineation","volume":"58","author":"Adekambi","year":"2008","journal-title":"Int J Syst Evol Microbiol"},{"key":"2024020218190965500_CR2","first-page":"144","article-title":"A molecular technique for identification of bacteria using small subunit ribosomal RNA sequences","volume":"17","author":"Avaniss-Aghajani","year":"1994","journal-title":"Biotechniques"},{"key":"2024020218190965500_CR3","doi-asserted-by":"publisher","first-page":"1915","DOI":"10.1126\/science.1104816","article-title":"Host-bacterial mutualism in the human intestine","volume":"307","author":"Backhed","year":"2005","journal-title":"Science"},{"key":"2024020218190965500_CR4","doi-asserted-by":"publisher","first-page":"907","DOI":"10.1128\/IAI.01432-07","article-title":"Enteric salmonellosis disrupts the microbial ecology of the murine gastrointestinal tract","volume":"76","author":"Barman","year":"2008","journal-title":"Infect Immun"},{"key":"2024020218190965500_CR5","doi-asserted-by":"publisher","first-page":"330","DOI":"10.1016\/j.mcp.2006.03.006","article-title":"Fusobacterium necrophorum determined as abortifacient in sheep by laser capture microdissection and fluorescence in situ hybridization","volume":"20","author":"Boye","year":"2006","journal-title":"Mol Cell Probes"},{"key":"2024020218190965500_CR6","doi-asserted-by":"publisher","first-page":"367","DOI":"10.1016\/j.resmic.2008.04.006","article-title":"Viral diversity and dynamics in an infant gut","volume":"159","author":"Breitbart","year":"2008","journal-title":"Res Microbiol"},{"key":"2024020218190965500_CR7","doi-asserted-by":"publisher","first-page":"278","DOI":"10.1128\/AEM.01177-06","article-title":"Use of 16S rRNA and rpoB genes as molecular markers for microbial ecology studies","volume":"73","author":"Case","year":"2007","journal-title":"Appl Environ Microbiol"},{"key":"2024020218190965500_CR8","doi-asserted-by":"publisher","first-page":"D141","DOI":"10.1093\/nar\/gkn879","article-title":"The Ribosomal Database Project: improved alignments and new tools for rRNA analysis","volume":"37","author":"Cole","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"2024020218190965500_CR9","doi-asserted-by":"publisher","first-page":"812","DOI":"10.1099\/00207713-44-4-812","article-title":"The phylogeny of the genus Clostridium: proposal of five new genera and eleven new species combinations","volume":"44","author":"Collins","year":"1994","journal-title":"Int J Syst Bacteriol"},{"key":"2024020218190965500_CR10"},{"key":"2024020218190965500_CR11","doi-asserted-by":"publisher","first-page":"3376","DOI":"10.1128\/AEM.66.8.3376-3380.2000","article-title":"rpoB-based microbial community analysis avoids limitations inherent in 16S rRNA gene intraspecies heterogeneity","volume":"66","author":"Dahllof","year":"2000","journal-title":"Appl Environ Microbiol"},{"key":"2024020218190965500_CR12","doi-asserted-by":"crossref","first-page":"666","DOI":"10.1128\/iai.7.4.666-672.1973","article-title":"Microbial colonization of the intestinal epithelium in suckling mice","volume":"7","author":"Davis","year":"1973","journal-title":"Infect Immun"},{"key":"2024020218190965500_CR13","doi-asserted-by":"publisher","first-page":"532","DOI":"10.1002\/path.2006","article-title":"Validation of 16S rDNA sequencing in microdissected bowel biopsies from Crohn\u2032s disease patients to assess bacterial flora diversity","volume":"209","author":"De Hertogh","year":"2006","journal-title":"J Pathol"},{"key":"2024020218190965500_CR14","doi-asserted-by":"publisher","first-page":"67","DOI":"10.1084\/jem.122.1.67","article-title":"Indigenous, Normal, and Autochthonous Flora of the Gastrointestinal Tract","volume":"122","author":"Dubos","year":"1965","journal-title":"J Exp Med"},{"key":"2024020218190965500_CR15","volume-title":"Atlas of Protein Sequence and Structure","author":"Eck","year":"1966"},{"key":"2024020218190965500_CR16","doi-asserted-by":"publisher","first-page":"1635","DOI":"10.1126\/science.1110591","article-title":"Diversity of the human intestinal microbial flora","volume":"308","author":"Eckburg","year":"2005","journal-title":"Science"},{"key":"2024020218190965500_CR17","doi-asserted-by":"publisher","first-page":"57","DOI":"10.1007\/BF00038687","article-title":"Compositional dissimilarity as a robust measure of ecological distance","volume":"69","author":"Faith","year":"1987","journal-title":"Plant Ecol"},{"key":"2024020218190965500_CR18","doi-asserted-by":"publisher","first-page":"13780","DOI":"10.1073\/pnas.0706625104","article-title":"Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases","volume":"104","author":"Frank","year":"2007","journal-title":"Proc Natl Acad Sci USA"},{"key":"2024020218190965500_CR19","doi-asserted-by":"publisher","first-page":"1319","DOI":"10.1038\/ng.221","article-title":"Sequence variants in IL10, ARPC2 and multiple other loci contribute to ulcerative colitis susceptibility","volume":"40","author":"Franke","year":"2008","journal-title":"Nat Genet"},{"key":"2024020218190965500_CR20","doi-asserted-by":"publisher","first-page":"2691","DOI":"10.1128\/IAI.01570-08","article-title":"Perturbation of the small intestine microbial ecology by streptomycin alters pathology in a Salmonella enterica serovar typhimurium murine model of infection","volume":"77","author":"Garner","year":"2009","journal-title":"Infect Immun"},{"key":"2024020218190965500_CR21","doi-asserted-by":"publisher","first-page":"1355","DOI":"10.1126\/science.1124234","article-title":"Metagenomic analysis of the human distal gut microbiome","volume":"312","author":"Gill","year":"2006","journal-title":"Science"},{"key":"2024020218190965500_CR22","doi-asserted-by":"publisher","first-page":"747","DOI":"10.1038\/nature03034","article-title":"Spatial scaling of microbial eukaryote diversity","volume":"432","author":"Green","year":"2004","journal-title":"Nature"},{"key":"2024020218190965500_CR23","doi-asserted-by":"publisher","first-page":"235","DOI":"10.1038\/nmeth.1184","article-title":"Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex","volume":"5","author":"Hamady","year":"2008","journal-title":"Nat Methods"},{"key":"2024020218190965500_CR24","first-page":"e1","article-title":"Past: paleontological statistics software package for education and data analysis","volume":"4","author":"Hammer","year":"2001","journal-title":"Palaeont Elec"},{"key":"2024020218190965500_CR25","doi-asserted-by":"publisher","first-page":"148","DOI":"10.1038\/mi.2009.132","article-title":"Metagenomic analyses reveal antibiotic-induced temporal and spatial changes in intestinal microbiota with associated alterations in immune cell homeostasis","volume":"3","author":"Hill","year":"2009","journal-title":"Mucosal Immunol"},{"key":"2024020218190965500_CR26","volume-title":"Biology of the Laboratory Mouse","author":"Hummel","year":"1966"},{"key":"2024020218190965500_CR27","doi-asserted-by":"publisher","first-page":"4035","DOI":"10.1128\/AEM.71.7.4035-4043.2005","article-title":"Gut symbiotic bacteria of the genus Burkholderia in the broad-headed bugs Riptortus clavatus and Leptocorisa chinensis (Heteroptera: Alydidae)","volume":"71","author":"Kikuchi","year":"2005","journal-title":"Appl Environ Microbiol"},{"key":"2024020218190965500_CR28","doi-asserted-by":"publisher","first-page":"11070","DOI":"10.1073\/pnas.0504978102","article-title":"Obesity alters gut microbial ecology","volume":"102","author":"Ley","year":"2005","journal-title":"Proc Natl Acad Sci USA"},{"key":"2024020218190965500_CR29","doi-asserted-by":"publisher","first-page":"837","DOI":"10.1016\/j.cell.2006.02.017","article-title":"Ecological and evolutionary forces shaping microbial diversity in the human intestine","volume":"124","author":"Ley","year":"2006","journal-title":"Cell"},{"key":"2024020218190965500_CR30","doi-asserted-by":"publisher","first-page":"782","DOI":"10.1136\/gut.40.6.782","article-title":"Histochemistry of the surface mucous gel layer of the human colon","volume":"40","author":"Matsuo","year":"1997","journal-title":"Gut"},{"key":"2024020218190965500_CR31","doi-asserted-by":"publisher","first-page":"4537","DOI":"10.1128\/JCM.01537-06","article-title":"Identification of a novel, invasive, not-yet-cultivated Treponema sp. in the large intestine of pigs by PCR amplification of the 16S rRNA gene","volume":"44","author":"Molbak","year":"2006","journal-title":"J Clin Microbiol"},{"key":"2024020218190965500_CR32","doi-asserted-by":"publisher","first-page":"125","DOI":"10.1111\/j.1574-6941.2008.00497.x","article-title":"Selective stimulation of type I methanotrophs in a rice paddy soil by urea fertilization revealed by RNA-based stable isotope probing","volume":"65","author":"Noll","year":"2008","journal-title":"FEMS Microbiol Ecol"},{"key":"2024020218190965500_CR33","first-page":"3","article-title":"Genomic DNA isolation from different biological materials","volume":"353","author":"Park","year":"2007","journal-title":"Methods Mol Biol"},{"key":"2024020218190965500_CR34","first-page":"69","article-title":"Phylogenetic analysis by 16S ribosomal DNA sequence comparison reveals two unrelated groups of species within the genus Ruminococcus","volume":"129","author":"Rainey","year":"1995","journal-title":"FEMS Microbiol Lett"},{"key":"2024020218190965500_CR35","doi-asserted-by":"publisher","first-page":"2125","DOI":"10.1111\/j.1462-2920.2007.01369.x","article-title":"Diversity of the human gastrointestinal tract microbiota revisited","volume":"9","author":"Rajilic-Stojanovic","year":"2007","journal-title":"Environ Microbiol"},{"key":"2024020218190965500_CR36","doi-asserted-by":"publisher","first-page":"1166","DOI":"10.1111\/j.1365-2672.2004.02409.x","article-title":"Development of an extensive set of 16S rDNA-targeted primers for quantification of pathogenic and indigenous bacteria in faecal samples by real-time PCR","volume":"97","author":"Rinttila","year":"2004","journal-title":"J Appl Microbiol"},{"key":"2024020218190965500_CR37","doi-asserted-by":"publisher","first-page":"5870","DOI":"10.1128\/AEM.00963-06","article-title":"Lettuce for human consumption collected in Costa Rica contains complex communities of culturable oxytetracycline- and gentamicin-resistant bacteria","volume":"72","author":"Rodriguez","year":"2006","journal-title":"Appl Environ Microbiol"},{"key":"2024020218190965500_CR38","doi-asserted-by":"publisher","first-page":"76","DOI":"10.1038\/ni.1825","article-title":"Enteric defensins are essential regulators of intestinal microbial ecology","volume":"11","author":"Salzman","year":"2009","journal-title":"Nat Immunol"},{"key":"2024020218190965500_CR39","doi-asserted-by":"publisher","first-page":"1495","DOI":"10.1093\/ajcn\/23.11.1495","article-title":"Associations of indigenous microorganisms with gastrointestinal mucosal epithelia","volume":"23","author":"Savage","year":"1970","journal-title":"Am J Clin Nutr"},{"key":"2024020218190965500_CR40","doi-asserted-by":"crossref","first-page":"240","DOI":"10.1128\/iai.10.1.240-250.1974","article-title":"Surface-surface associations in microbial communities populating epithelial habitats in the murine gastrointestinal ecosystem: scanning electron microscopy","volume":"10","author":"Savage","year":"1974","journal-title":"Infect Immun"},{"key":"2024020218190965500_CR41","doi-asserted-by":"publisher","first-page":"67","DOI":"10.1084\/jem.127.1.67","article-title":"The gastrointestinal epithelium and its autochthonous bacterial flora","volume":"127","author":"Savage","year":"1968","journal-title":"J Exp Med"},{"key":"2024020218190965500_CR42","doi-asserted-by":"crossref","first-page":"492","DOI":"10.1128\/iai.4.4.492-502.1971","article-title":"Anaerobic bacteria on the mucosal epithelium of the murine large bowel","volume":"4","author":"Savage","year":"1971","journal-title":"Infect Immun"},{"key":"2024020218190965500_CR43","doi-asserted-by":"publisher","first-page":"1183","DOI":"10.1038\/ismej.2008.76","article-title":"Micro-eukaryotic diversity of the human distal gut microbiota: qualitative assessment using culture-dependent and -independent analysis of faeces","volume":"2","author":"Scanlan","year":"2008","journal-title":"Isme J"},{"key":"2024020218190965500_CR44","doi-asserted-by":"publisher","first-page":"3564","DOI":"10.1128\/AEM.01409-08","article-title":"Campylobacter colonization of the Turkey intestine in the context of microbial community development","volume":"75","author":"Scupham","year":"2009","journal-title":"Appl Environ Microbiol"},{"key":"2024020218190965500_CR45","doi-asserted-by":"publisher","first-page":"318","DOI":"10.1136\/jcp.47.4.318","article-title":"Rapid techniques for DNA extraction from routinely processed archival tissue for use in PCR","volume":"47","author":"Sepp","year":"1994","journal-title":"J Clin Pathol"},{"key":"2024020218190965500_CR46","doi-asserted-by":"publisher","first-page":"16731","DOI":"10.1073\/pnas.0804812105","article-title":"Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients","volume":"105","author":"Sokol","year":"2008","journal-title":"Proc Natl Acad Sci USA"},{"key":"2024020218190965500_CR47","doi-asserted-by":"publisher","first-page":"1183","DOI":"10.1002\/ibd.20903","article-title":"Low counts of Faecalibacterium prausnitzii in colitis microbiota","volume":"15","author":"Sokol","year":"2009","journal-title":"Inflamm Bowel Dis"},{"key":"2024020218190965500_CR48","doi-asserted-by":"publisher","first-page":"167","DOI":"10.1016\/S0076-6879(02)56932-9","article-title":"Laser capture microdissection of mouse intestine: characterizing mRNA and protein expression, and profiling intermediary metabolism in specified cell populations","volume":"356","author":"Stappenbeck","year":"2002","journal-title":"Methods Enzymol"},{"key":"2024020218190965500_CR49","doi-asserted-by":"publisher","first-page":"253","DOI":"10.1136\/jcp.2006.037309","article-title":"Spatial organisation of microbiota in quiescent adenoiditis and tonsillitis","volume":"60","author":"Swidsinski","year":"2007","journal-title":"J Clin Pathol"},{"key":"2024020218190965500_CR50","doi-asserted-by":"publisher","first-page":"1131","DOI":"10.3748\/wjg.v11.i8.1131","article-title":"Spatial organization of bacterial flora in normal and inflamed intestine: a fluorescence in situ hybridization study in mice","volume":"11","author":"Swidsinski","year":"2005","journal-title":"World J Gastroenterol"},{"key":"2024020218190965500_CR51","doi-asserted-by":"publisher","first-page":"343","DOI":"10.1136\/gut.2006.098160","article-title":"Comparative study of the intestinal mucus barrier in normal and inflamed colon","volume":"56","author":"Swidsinski","year":"2007","journal-title":"Gut"},{"key":"2024020218190965500_CR52","doi-asserted-by":"publisher","first-page":"963","DOI":"10.1002\/ibd.20163","article-title":"Viscosity gradient within the mucus layer determines the mucosal barrier function and the spatial organization of the intestinal microbiota","volume":"13","author":"Swidsinski","year":"2007","journal-title":"Inflamm Bowel Dis"},{"key":"2024020218190965500_CR53","doi-asserted-by":"crossref","first-page":"1965","DOI":"10.1128\/aem.53.8.1965-1968.1987","article-title":"Demonstration of mucosa-associated microbial populations in the colons of mice","volume":"53","author":"Tannock","year":"1987","journal-title":"Appl Environ Microbiol"},{"key":"2024020218190965500_CR54","doi-asserted-by":"publisher","first-page":"2574","DOI":"10.1111\/j.1462-2920.2009.01982.x","article-title":"Towards the human intestinal microbiota phylogenetic core","volume":"11","author":"Tap","year":"2009","journal-title":"Environ Microbiol"},{"key":"2024020218190965500_CR55","doi-asserted-by":"publisher","first-page":"1237","DOI":"10.1177\/002215540205000911","article-title":"Methacarn fixation for genomic DNA analysis in microdissected, paraffin-embedded tissue specimens","volume":"50","author":"Uneyama","year":"2002","journal-title":"J Histochem Cytochem"},{"key":"2024020218190965500_CR56","doi-asserted-by":"crossref","first-page":"854","DOI":"10.4049\/jimmunol.115.3.854","article-title":"Intestinal uptake of macromolecules. III. Studies on the mechanism by which immunization interferes with antigen uptake","volume":"115","author":"Walker","year":"1975","journal-title":"J Immunol"},{"key":"2024020218190965500_CR57","doi-asserted-by":"crossref","first-page":"1223","DOI":"10.1016\/S0016-5085(19)32314-5","article-title":"Intestinal uptake of macromolecules. IV.--The effect of pancreatic duct ligation on the breakdown of antigen and antigen-antibody complexes on the intestinal surface","volume":"69","author":"Walker","year":"1975","journal-title":"Gastroenterology"},{"key":"2024020218190965500_CR58","first-page":"201","article-title":"Gastrointestinal host defence: importance of gut closure in control of macromolecular transport","volume":"70","author":"Walker","year":"1979","journal-title":"Ciba Found Symp"},{"key":"2024020218190965500_CR59","doi-asserted-by":"publisher","first-page":"5261","DOI":"10.1128\/AEM.00062-07","article-title":"Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy","volume":"73","author":"Wang","year":"2007","journal-title":"Appl Environ Microbiol"},{"key":"2024020218190965500_CR60","doi-asserted-by":"publisher","first-page":"653","DOI":"10.1002\/ibd.20783","article-title":"Twin studies reveal specific imbalances in the mucosa-associated microbiota of patients with ileal Crohn\u2032s disease","volume":"15","author":"Willing","year":"2009","journal-title":"Inflamm Bowel Dis"},{"key":"2024020218190965500_CR61","doi-asserted-by":"publisher","first-page":"12601","DOI":"10.1073\/pnas.230237997","article-title":"Genetic mosaic analysis based on Cre recombinase and navigated laser capture microdissection","volume":"97","author":"Wong","year":"2000","journal-title":"Proc Natl Acad Sci USA"},{"key":"2024020218190965500_CR62","doi-asserted-by":"publisher","first-page":"e3","DOI":"10.1371\/journal.pbio.0040003","article-title":"RNA viral community in human feces: prevalence of plant pathogenic viruses","volume":"4","author":"Zhang","year":"2006","journal-title":"PLoS Biol"},{"key":"2024020218190965500_CR63","doi-asserted-by":"publisher","first-page":"1639","DOI":"10.1111\/j.1365-2958.2006.05056.x","article-title":"A microbial world within us","volume":"59","author":"Zoetendal","year":"2006","journal-title":"Mol Microbiol"}],"container-title":["The ISME Journal"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/www.nature.com\/articles\/ismej2010161.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/www.nature.com\/articles\/ismej2010161","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/academic.oup.com\/ismej\/article-pdf\/5\/4\/627\/56547194\/41396_2011_article_bfismej2010161.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"http:\/\/www.nature.com\/articles\/ismej2010161.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"},{"URL":"https:\/\/academic.oup.com\/ismej\/article-pdf\/5\/4\/627\/56547194\/41396_2011_article_bfismej2010161.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,2,2]],"date-time":"2024-02-02T18:20:50Z","timestamp":1706898050000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/ismej\/article\/5\/4\/627\/7587834"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,10,28]]},"references-count":63,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2011,4,1]]}},"URL":"https:\/\/doi.org\/10.1038\/ismej.2010.161","relation":{},"ISSN":["1751-7362","1751-7370"],"issn-type":[{"value":"1751-7362","type":"print"},{"value":"1751-7370","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2011,4]]},"published":{"date-parts":[[2010,10,28]]}}}