High throughput sequencing reveals distinct microbial populations within the mucosal and luminal niches in healthy individuals

Ringel, Yehuda; Maharshak, Nitsan; Ringel–Kulka, Tamar; Wolber, Elizabeth A.; Sartor, R. Balfour; Carroll, Ian M.

doi:10.1080/19490976.2015.1044711

Cited by 156 publications

(141 citation statements)

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“…The absence of a representative microbial structure for different anatomical sites and inter-individual uniformity were also confirmed in the samples collected from the different anatomical sites of CD and UC patients. Similar observations have been recently reported by other groups using samples collected by biopsy or other tools [17,20]. Thus, the overall gut microbial community might be more dependent on inter-individual variation than on anatomical site.…”

Section: Discussionsupporting

confidence: 74%

“…However, many of these studies relied on easily accessible fecal samples obtained on a single occasion, which may not properly represent mucosa-associated bacterial populations [17,18]. The mucosa-associated microbiota is considered to affect epithelial and mucosal function to a greater degree than luminal bacteria and to contribute more significantly to the pathogenesis of IBD [13,17,32].…”

Section: Discussionmentioning

confidence: 99%

“…The mucosa-associated microbiota is believed to directly affect epithelial and mucosal function to a greater degree than luminal bacteria, and may be more deeply involved in the pathophysiology of IBD. However, studies investigating the gut microbiota of IBD have typically used fecal samples because they are easily collected, and only a few studies have investigated the mucosa-associated microbiota [17,19,20]. In addition, most previous studies of mucosa-associated microbiota have used samples collected by endoscopic biopsy, which is invasive and sometimes causes unexpected bleeding.…”

Section: Introductionmentioning

confidence: 99%

“…The gut microbiota consists of two separate populations, the luminal microbiota and the mucosa-associated microbiota [17,18]. The mucosa-associated microbiota is believed to directly affect epithelial and mucosal function to a greater degree than luminal bacteria, and may be more deeply involved in the pathophysiology of IBD.…”

Section: Introductionmentioning

confidence: 99%

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Analysis of endoscopic brush samples identified mucosa-associated dysbiosis in inflammatory bowel disease

et al. 2017

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Background The mucosa-associated gut microbiota directly modulates epithelial and mucosal function. In this study, we investigated the mucosa-associated microbial community in patients with inflammatory bowel disease (IBD), using endoscopic brush samples. Methods A total of 174 mucus samples from 43 patients with ulcerative colitis (UC), 26 with Crohn's disease (CD) and 14 non-IBD controls were obtained by gentle brushing of mucosal surfaces using endoscopic cytology brushes. The gut microbiome was analyzed using 16S rRNA gene sequencing. Results There were no significant differences in microbial structure among different anatomical sites (the ileum, cecum and sigmoid colon) within individuals. There was, however, a significant difference in microbial structure between CD, UC and non-IBD controls. The difference between CD and non-IBD controls was more marked than that between UC patients and non-IBD controls. a-Diversity was significantly lower in UC and CD patients than non-IBD controls. When comparing CD patients with non-IBD controls, the phylum Proteobacteria was significantly increased and the phyla Firmicutes and Bacteroidetes were significantly reduced. These included a significant increase in the genera Escherichia, Ruminococcus (R. gnavus), Cetobacterium, Actinobacillus and Enterococcus, and a significant decrease in the genera Faecalibacterium, Coprococcus, Prevotella and Roseburia. Comparisons between CD and UC patients revealed a greater abundance of the genera Escherichia, Ruminococcus (R. gnavus), Clostridium, Cetobacterium, Peptostreptococcus in CD patients, and the genera Faecalibacterium, Blautia, Bifidobacterium, Roseburia and Citrobacter in UC patients. Conclusions Mucosa-associated dysbiosis was identified in IBD patients. CD and UC may be distinguishable from the mucosa-associated microbial community structure.

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Section: Discussionsupporting

confidence: 74%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Analysis of endoscopic brush samples identified mucosa-associated dysbiosis in inflammatory bowel disease

et al. 2017

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“…However, reliance on fecal sampling alone to answer some experimental questions has limitations. Fecal sampling cannot detect differences in microbial communities that are spatially separated along the length of the gut (Kohl et al, 2014a), and it may not distinguish between luminal and mucosa-associated bacterial communities (Galley et al, 2014;Ringel et al, 2015;Yasuda et al, 2015).…”

Section: Animal-microbe Symbioses Contribute To Host Ecology and Evolmentioning

confidence: 99%

A place for host–microbe symbiosis in the comparative physiologist's toolbox

Kohl

Carey

2016

Journal of Experimental Biology

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Although scientists have long appreciated that metazoans evolved in a microbial world, we are just beginning to appreciate the profound impact that host-associated microbes have on diverse aspects of animal biology. The enormous growth in our understanding of hostmicrobe symbioses is rapidly expanding the study of animal physiology, both technically and conceptually. Microbes associate functionally with various body surfaces of their hosts, although most reside in the gastrointestinal tract. Gut microbes convert dietary and host-derived substrates to metabolites such as short-chain fatty acids, thereby providing energy and nutrients to the host. Bacterial metabolites incorporated into the host metabolome can activate receptors on a variety of cell types and, in doing so, alter host physiology (including metabolism, organ function, biological rhythms, neural activity and behavior). Given that host-microbe interactions affect diverse aspects of host physiology, it is likely that they influence animal ecology and, if they confer fitness benefits, the evolutionary trajectory of a species. Multiple variables -including sampling regime, environmental parameters, host metadata and analytical methods -can influence experimental outcomes in host-microbiome studies, making careful experimental design and execution crucial to ensure reproducible and informative studies in the laboratory and field. Integration of microbiomes into comparative physiology and ecophysiological investigations can reveal the potential impacts of the microbiota on physiological responses to changing environments, and is likely to bring valuable insights to the study of host-microbiome interactions among a broad range of metazoans, including humans.

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Constitution of mucosa‐associated microbiota in the lower digestive tract does not change in early stage of non‐alcoholic fatty liver disease with fecal dysbiosis

et al. 2022

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Background and Aim Regarding the gut–liver axis, fecal dysbiosis is implicated in the pathogenesis of non‐alcoholic fatty liver disease (NAFLD). The significance of mucosa‐associated microbiota (MAM, which is present in the mucin layer covering the intestinal mucosa) has not been well explored. We aimed to clarify the characteristics of MAM in patients with NAFLD. Methods MAM were obtained from seven patients with early‐stage NAFLD and seven controls by colonoscopy in five locations (terminal ileum, cecum, ascending and sigmoid colon, and rectum) using mucosal brushes. The microbial 16S rDNA profiles of the MAM and fecal microbiota of patients in the NAFLD and control groups were analyzed. Results α‐diversities of fecal microbiota were decreased in patients with NAFLD (observed species, Shannon index, and Chao1: 174.57 vs 134.86, 5.51 vs 4.65, and 206.34 vs 167.91; P = 0.048, 0.067, and 0.087, respectively), and microbial composition analyses by principal coordinate analysis differed between the fecal microbiota of patients with NAFLD and those of controls (permutational analysis of variance [PERMANOVA] of weighted and unweighted: Pseud‐ F : 1.4179/ P ‐value: 0.05 and Pseud‐ F : 2.1497/ P ‐value: 0.049, respectively). However, α‐diversities or microbial composition of MAM in most parts of the intestine did not differ significantly between the NAFLD and control groups. Unclassified Rikenellaceae , Oscillospira, Odoribacter, unclassified clostridiales , and Holdemania were decreased in the feces of patients with NAFLD (determined by linear discriminant analysis effect size), but five (except Holdemania ) of the six genera were not decreased in the MAM of these patients. Conclusion In early‐stage NAFLD, MAM was uniform and relatively stable throughout the intestine, even when fecal dysbiosis appeared.

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High throughput sequencing reveals distinct microbial populations within the mucosal and luminal niches in healthy individuals

Abstract: The LM and MAM are distinct microbial ecosystems that differ significantly from each other in microbial diversity and composition. These two microbial niches should be investigated independently to better understand the role of the intestinal microbiota in health and disease.

Cited by 156 publications

References 32 publications

Analysis of endoscopic brush samples identified mucosa-associated dysbiosis in inflammatory bowel disease

Analysis of endoscopic brush samples identified mucosa-associated dysbiosis in inflammatory bowel disease

A place for host–microbe symbiosis in the comparative physiologist's toolbox

Constitution of mucosa‐associated microbiota in the lower digestive tract does not change in early stage of non‐alcoholic fatty liver disease with fecal dysbiosis

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