P461 Analysis of the mucosal microbiota from inflammatory bowel disease biopsy tissues using a custom 16s rRNA based phylogenetic microarray

Gupta, Anurag; Kang, Seungha; Wagner, Josef; McSweeney, Christopher S.; Morrison, Mark; Kirkwood, Carl D.; Macrae, F

doi:10.1016/s1873-9946(12)60480-2

Cited by 4 publications

(4 citation statements)

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“…2008; Gupta et al . 2014). Reductions of this bacterial group could substantially impact enterocyte nutrition and the maintenance of intestinal health (Flint et al.…”

Section: Resultsmentioning

confidence: 99%

Impact of cystic fibrosis disease on archaea and bacteria composition of gut microbiota

Miragoli

Federici

Ferrari

et al. 2016

FEMS Microbiology Ecology

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Cystic fibrosis is often associated with intestinal inflammation due to several factors, including altered gut microbiota composition. In this study, we analyzed the fecal microbiota among patients with cystic fibrosis of 10–22 years of age, and compared the findings with age-matched healthy subjects. The participating patients included 14 homozygotes and 14 heterozygotes with the delF508 mutation, and 2 heterozygotes presenting non-delF508 mutations. We used PCR-DGGE and qPCR to analyze the presence of bacteria, archaea and sulfate-reducing bacteria. Overall, our findings confirmed disruption of the cystic fibrosis gut microbiota. Principal component analysis of the qPCR data revealed no differences between homozygotes and heterozygotes, while both groups were distinct from healthy subjects who showed higher biodiversity. Archaea were under the detection limit in all homozygotes subjects, whereas methanogens were detected in 62% of both cystic fibrosis heterozygotes and healthy subjects. Our qPCR results revealed a low frequency of sulfate-reducing bacteria in the homozygote (13%) and heterozygote (13%) patients with cystic fibrosis compared with healthy subjects (87.5%). This is a pioneer study showing that patients with cystic fibrosis exhibit significant reduction of H2-consuming microorganisms, which could increase hydrogen accumulation in the colon and the expulsion of this gas through non-microbial routes.

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“…2008; Gupta et al . 2014). Reductions of this bacterial group could substantially impact enterocyte nutrition and the maintenance of intestinal health (Flint et al.…”

Section: Resultsmentioning

confidence: 99%

Impact of cystic fibrosis disease on archaea and bacteria composition of gut microbiota

Miragoli

Federici

Ferrari

et al. 2016

FEMS Microbiology Ecology

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“…Various studies have demonstrated no difference between IBD inflamed and noninflamed tissues from adults, using different tools, such as polymerase chain reactiondenaturing gradient gel electrophoresis (PCR-DGGE) [32], temporal temperature gradient gel electrophoresis (TTGE) [33,34], fluorescence in situ hybridization (FISH) [33], microarray analysis [35] and 16S rRNA-targeted metagenomics [13]. Moreover, Kansal et al recently studied the gut MM in a pediatric CD cohort with longitudinal…”

Section: Discussionmentioning

confidence: 99%

Fecal and mucosal microbiota profiling in pediatric inflammatory bowel diseases

Putignani

Oliva

Isoldi

et al. 2021

European Journal of Gastroenterology &Amp; Hepatology

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Background. An altered gut microbiota profile has been widely documented in inflammatory bowel diseases (IBD). Most studies are focused only on stool samples, and mainly in adult patients.We aimed to define the gut microbiota profile either by assessing fecal and colonic mucosa samples (inflamed or not) of pediatric IBD patients, Patients and Methods. Fecal and colonic samples from pediatric IBD (Crohn's Disease or Ulcerative Colitis) and controls (CTRLs) were selected. The relative abundance of bacteria, at phylum and genus/species levels, and bacterial diversity were determined through 16S rRNA sequence-based of fecal (FM) and mucosal microbiota (MM) analysis. Results. 59 children with IBD (26 Crohn's disease, 33 ulcerative colitis) and 39 controls were investigated. A clear separation between IBD and CTRLs in the overall composition of FM and MM was found, as well as a reduced bacterial richness in FM of IBD. At phylum level, abundance of Proteobacteria and Actinobacteria occurred in FM of IBD, while species with anti-inflammatory properties (i.e. Ruminococcus) were reduced. Fusobacterium prevailed in inflamed IBD areas in comparison to non-inflamed and CTRLs samples.Conclusions. Significant alterations in gut microbiota profile were shown in our IBD pediatric patients. Our data clearly indicate an abundance of species with a proinflammatory mucosal activity. An analysis of gut microbiota should be incorporated in designing future personalized treatment scenarios in IBD.

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“…This dysbiosis, which is even more pronounced in a common complication in IBD, Clostridium difficile infection, is likely to be due to administration of antibiotics (89,90). At the species level, D. longicatena is also negatively associated with Crohn's disease (91) and positively with remission after surgery (92). Here, however, we showed that the Dorea FOS utilization locus is twice as abundant in the microbiomes of patients suffering from IBD than in those of healthy individuals.…”

Section: Discussionmentioning

confidence: 54%

Harvesting of Prebiotic Fructooligosaccharides by Nonbeneficial Human Gut Bacteria

Wang

Tauzin

Laville

et al. 2020

mSphere

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Prebiotic oligosaccharides, such as fructooligosaccharides, are increasingly being used to modulate the composition and activity of the gut microbiota. However, carbohydrate utilization analyses and metagenomic studies recently revealed the ability of deleterious and uncultured human gut bacterial species to metabolize these functional foods. Moreover, because of the difficulties of functionally profiling transmembrane proteins, only a few prebiotic transporters have been biochemically characterized to date, while carbohydrate binding and transport are the first and thus crucial steps in their metabolization. Here, we describe the molecular mechanism of a phosphotransferase system, highlighted as a dietary and pathology biomarker in the human gut microbiome. This transporter is encoded by a metagenomic locus that is highly conserved in several human gut Firmicutes, including Dorea species. We developed a generic strategy to deeply analyze, in vitro and in cellulo, the specificity and functionality of recombinant transporters in Escherichia coli, combining carbohydrate utilization locus and host genome engineering and quantification of the binding, transport, and growth rates with analysis of phosphorylated carbohydrates by mass spectrometry. We demonstrated that the Dorea fructooligosaccharide transporter is specific for kestose, whether for binding, transport, or phosphorylation. This constitutes the biochemical proof of effective phosphorylation of glycosides with a degree of polymerization of more than 2, extending the known functional diversity of phosphotransferase systems. Based on these new findings, we revisited the classification of these carbohydrate transporters.IMPORTANCE Prebiotics are increasingly used as food supplements, especially in infant formulas, to modify the functioning and composition of the microbiota. However, little is currently known about the mechanisms of prebiotic recognition and transport by gut bacteria, while these steps are crucial in their metabolism. In this study, we established a new strategy to profile the specificity of oligosaccharide transporters, combining microbiomics, genetic locus and strain engineering, and state-of-the art metabolomics. We revisited the transporter classification database and proposed a new way to classify these membrane proteins based on their structural and mechanistic similarities. Based on these developments, we identified and characterized, at the molecular level, a fructooligosaccharide transporting phosphotransferase system, which constitutes a biomarker of diet and gut pathology. The deciphering of this prebiotic metabolization mechanism by a nonbeneficial bacterium highlights the controversial use of prebiotics, especially in the context of chronic gut diseases.

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P461 Analysis of the mucosal microbiota from inflammatory bowel disease biopsy tissues using a custom 16s rRNA based phylogenetic microarray

Cited by 4 publications

References 0 publications

Impact of cystic fibrosis disease on archaea and bacteria composition of gut microbiota

Impact of cystic fibrosis disease on archaea and bacteria composition of gut microbiota

Fecal and mucosal microbiota profiling in pediatric inflammatory bowel diseases

Harvesting of Prebiotic Fructooligosaccharides by Nonbeneficial Human Gut Bacteria

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