Inferred metagenomic comparison of mucosal and fecal microbiota from individuals undergoing routine screening colonoscopy reveals similar differences observed during active inflammation

Tang, Mei; Poles, Jordan; Leung, Jacqueline M.; Wolff, Martin; Davenport, Michael; Lee, Soo Ching; Lim, Yvonne A. L.; Chua, Kek Heng; Loke, P’ng; Cho, Ilseung

doi:10.1080/19490976.2014.1000080

Cited by 52 publications

(51 citation statements)

References 35 publications

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“…12545758 Additionally, epithelial cell function is affected to a greater extent by mucosally associated microbes 59–61 as measured herein, functional differences have been observed between mucosal and luminal microbiota, 62 and mucosal but not faecal microbiota may discriminate between disease status and health. 60 …”

Section: Discussionmentioning

confidence: 64%

Race-dependent association of sulfidogenic bacteria with colorectal cancer

Yazıcı

Wolf

Kim

et al. 2017

Gut

165

128

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Objective Colorectal cancer (CRC) incidence is higher in African Americans (AAs) compared with non-Hispanic whites (NHWs). A diet high in animal protein and fat is an environmental risk factor for CRC development. The intestinal microbiota is postulated to modulate the effects of diet in promoting or preventing CRC. Hydrogen sulfide, produced by autochthonous sulfidogenic bacteria, triggers proinflammatory pathways and hyperproliferation, and is genotoxic. We hypothesised that sulfidogenic bacterial abundance in colonic mucosa may be an environmental CRC risk factor that distinguishes AA and NHW. Design Colonic biopsies from uninvolved or healthy mucosa from CRC cases and tumour-free controls were collected prospectively from five medical centres in Chicago for association studies. Sulfidogenic bacterial abundance in uninvolved colonic mucosa of AA and NHW CRC cases was compared with normal mucosa of AA and NHW controls. In addition, 16S rDNA sequencing was performed in AA cases and controls. Correlations were examined among bacterial targets, race, disease status and dietary intake. Results AAs harboured a greater abundance of sulfidogenic bacteria compared with NHWs regardless of disease status. Bilophila wadsworthia-specific dsrA was more abundant in AA cases than controls. Linear discriminant analysis of 16S rRNA gene sequences revealed five sulfidogenic genera that were more abundant in AA cases. Fat and protein intake and daily servings of meat were significantly higher in AAs compared with NHWs, and multiple dietary components correlated with a higher abundance of sulfidogenic bacteria. Conclusions These results implicate sulfidogenic bacteria as a potential environmental risk factor contributing to CRC development in AAs.

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Section: Discussionmentioning

confidence: 64%

Race-dependent association of sulfidogenic bacteria with colorectal cancer

Yazıcı

Wolf

Kim

et al. 2017

Gut

165

128

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“…It is known that the microbial composition between stool and mucus is significantly different . For example, one study showed that mucus samples had a greater relative abundance of Proteobacteria and Fusobacteria than stool, although the stool had a greater proportion of Firmicutes and Bacteroidetes . Taken together, these data emphasize the need to investigate the different microbial niches within the gut, to comprehensively explore the gut microbiota and the impact of genotype or environment.…”

Section: Discussionmentioning

confidence: 99%

“…Crucially further studies should consider niche as both our qPCR and DGGE analysis of stool, colonic and small intestinal mucus highlighted differences in the microbial population among those niches. It is known that the microbial composition between stool and mucus is significantly different . For example, one study showed that mucus samples had a greater relative abundance of Proteobacteria and Fusobacteria than stool, although the stool had a greater proportion of Firmicutes and Bacteroidetes .…”

Section: Discussionmentioning

confidence: 99%

Gut eosinophils and their impact on the mucus‐resident microbiota

et al. 2019

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Summary The gut has the largest commensal bacterial population in the body and its composition can be impacted by host factors such as production of immunoglobulin A (IgA). Eosinophils in the gut have been implicated in the production of antibacterial factors and maintenance of IgA‐secreting plasma cells. We used an eosinophil‐deficient mouse (∆dblGATA‐1−/−) and littermate controls to investigate the role of eosinophils in the regulation of the microbiota, with particular emphasis on mucus‐resident species in the small and large intestine. We found no differences in IgA production or IgA‐expressing plasma cells between naive littermates in the small or large intestine. However, denaturing gel gradient electrophoresis revealed differences in the bacterial communities of the mucus and stools between wild‐type mice and ∆dblGATA‐1−/− mice, with the greatest separation between the mucus microbial communities. Mucus‐resident bacteria in ∆dblGATA‐1−/− mice had reduced diversity in the mucus compared with the stools. A quantitative PCR panel of selected bacteria showed that the most significant differences in the microbiota were between mucus‐resident bacteria and those in stool, such as the abundance of Clostridiales and Bacteroides. Our data implicate eosinophils in the regulation of the microbiota, especially the bacteria most hyperlocal to the gut barrier. Although we see differences between host genotypes in the overall microbial communities, further work is required to establish specifically which bacteria are different between these groups. Most importantly, the data revealed that the mucus and stool microbiota are discrete communities. Stool analysis alone may be insufficient to comprehensively explore and define the role of the gut microbiota in health and disease.

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“…Biopsies from the Mucosal Immunity of Ulcerative Colitis Patients Undergoing Therapy With Trichuris Suis Ova (MUCUS) (Trial ID: NCT01433471, https://clinicaltrials.gov) were collected from two trial subjects (ENR1 and ENR3) at three different time points (baseline, week 12 and week 24 post-treatment). Non-IBD control biopsies of the ileum and the sigmoid colon were obtained from patients referred to the Gastroenterology clinic at the Manhattan campus of the Veteran Affairs Hospital for average risk screening colonoscopy (19, 20). All FACS and 16S rRNA sequencing data were generated as previously described in (17).…”

Section: Methodsmentioning

confidence: 99%

Integrated Analysis of Biopsies from Inflammatory Bowel Disease Patients Identifies SAA1 as a Link Between Mucosal Microbes with TH17 and TH22 Cells

Tang¹,

Bowcutt²,

Leung³

et al. 2017

Inflammatory Bowel Diseases

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Background Inflammatory bowel diseases (IBD) are believed to be driven by dysregulated interactions between the host and the gut microbiota. Our goal is to characterize and infer relationships between mucosal T cells, the host tissue environment and microbial communities in IBD patients that will serve as basis for mechanistic studies on human IBD. Methods We characterized mucosal CD4+ T cells using flow cytometry, along with matching mucosal global gene expression and microbial communities data from 35 pinch biopsy samples from IBD patients. We analyzed these data sets using an integrated framework to identify predictors of inflammatory states and then reproduced some of the putative relationships formed among these predictors by analyzing data from the pediatric RISK cohort. Results We identified 26 predictors from our combined data set that were effective in distinguishing between regions of the intestine undergoing active inflammation and regions that were normal. Network analysis on these 26 predictors revealed SAA1 as the most connected node linking the abundance of the genus Bacteroides with the production of IL17 and IL22 by CD4+ T cells. These SAA1-linked microbial and transcriptome interactions were further reproduced with data from the pediatric IBD RISK cohort. Conclusion This study identifies expression of SAA1 as an important link between mucosal T cells, microbial communities and their tissue environment in IBD patients. A combination of FACS, gene expression and microbial profiling can distinguish between intestinal inflammatory states in IBD regardless of disease types.

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Inferred metagenomic comparison of mucosal and fecal microbiota from individuals undergoing routine screening colonoscopy reveals similar differences observed during active inflammation

Cited by 52 publications

References 35 publications

Race-dependent association of sulfidogenic bacteria with colorectal cancer

Race-dependent association of sulfidogenic bacteria with colorectal cancer

Gut eosinophils and their impact on the mucus‐resident microbiota

Integrated Analysis of Biopsies from Inflammatory Bowel Disease Patients Identifies SAA1 as a Link Between Mucosal Microbes with TH17 and TH22 Cells

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