Temperature Gradient Gel Electrophoresis of Fecal 16S rRNA Reveals Active
            <i>Escherichia coli</i>
            in the Microbiota of Patients with Ulcerative Colitis

Sokol, Harry; Lepage, Patricia; Seksik, Philippe; Doré, Joël; Marteau, Philippe

doi:10.1128/jcm.02600-05

Cited by 134 publications

(106 citation statements)

References 29 publications

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“…Bacteria with high transcriptional activity might have a more important pathophysiological role than inactive bacteria. [22][23][24] We thus studied effects on the bacterial community at both the gene level (with relative 16S rRNA gene amplicon counts indicating abundance) and the transcript level (with relative 16S cDNA amplicon counts indicating general potential metabolic activity sensu Blazewicz et al 20 AB treatment similarly affects luminal and mucosal microbiota Both a diversity ( Fig. 3) and b diversity RDA plots (Fig.…”

Section: Discussionmentioning

confidence: 99%

Dynamic changes of the luminal and mucosa-associated gut microbiota during and after antibiotic therapy with paromomycin

Heinsen

Knecht

Neulinger³

et al. 2015

Gut Microbes

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(2015) Dynamic changes of the luminal and mucosa-associated gut microbiota during and after antibiotic therapy with paromomycin, Gut Microbes, 6:4, 243-254, DOI: 10.1080/19490976.2015 To link to this article: https://doi.org/10. 1080/19490976.2015 Keywords: 16S rRNA gene, antibiotics, lumen, microbiota, mucosaGut microbiota play a key role in the host's health system. Broad antibiotic therapy is known to disrupt the microbial balance affecting pathogenic as well as host-associated microbes. The aim of the present study was to investigate the influence of antibiotic paromomycin on the luminal and mucosa-associated microbiota at the DNA (abundance) and RNA (potential activity) level as well as to identify possible differences. The influence of antibiotic treatment on intestinal microbiota was investigated in 5 healthy individuals (age range: 20-22 years). All participants received the antibiotic paromomycin for 3 d. Fecal samples as well as sigmoidal biopsies were collected before and immediately after cessation of antibiotic treatment as well as after a recovery phase of 42 d. Compartment-and treatment statusspecific indicator operational taxonomic units (OTUs) as well as abundance-and activity-specific patterns were identified by 16S rRNA and 16S rRNA gene amplicon libraries and high-throughput pyrosequencing. Microbial composition of lumen and mucosa were significantly different at the DNA compared to the RNA level. Antibiotic treatment resulted in changes of the microbiota, affecting the luminal and mucosal bacteria in a similar way. Several OTUs were identified as compartment-and/or treatment status-specific. Abundance and activity patterns of some indicator OTUs differed considerably. The study shows fundamental changes in composition of gut microbiota under antibiotic therapy at both the potential activity and the abundance level at different treatment status. It may help to understand the complex processes of gut microbiota changes involved in resilience mechanisms and on development of antibiotic-associated clinical diseases.

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Section: Discussionmentioning

confidence: 99%

Dynamic changes of the luminal and mucosa-associated gut microbiota during and after antibiotic therapy with paromomycin

Heinsen

Knecht

Neulinger³

et al. 2015

Gut Microbes

View full text Add to dashboard Cite

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“…These bacteria have been isolated from ileal biopsy samples in ileal CD [55] and ulcerative colitis (UC) patients [56]. Treatment with mesalamine has shown to decrease the population of these bacteria.…”

Section: Gut Flora and Inflammatory Bowel Diseasementioning

confidence: 99%

Gut microbiome diversity in acute infective and chronic inflammatory gastrointestinal diseases in North India

et al. 2016

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The disease profile in the Indian population provides a unique opportunity for studying the host microbiome interaction in both infectious (amebiasis) and autoimmune diseases like inflammatory bowel disease (IBD) from a similar environment and genetic background. Analysis of fecal samples from untreated amebic liver abscess (ALA) patients, Entamoeba histolytica (Eh)-negative and -positive asymptomatic individuals, and pus samples from naive ALA patients revealed a significant reduction in Lactobacillus in asymptomatic individuals (Eh ?ve) and ALA patients. Two anaerobic genera, namely Bacteroides and Peptostreptococcus, were detected in naive ALA pus samples. Analysis of fecal samples from amoebic colitis patients showed a significant decline in population of Bacteroides, Clostridium coccoides and leptum subgroup, Lactobacillus, Campylobacter, and Eubacterium, whereas a significant increase in Bifidobacterium was observed. Mucosa-associated bacterial flora analysis from IBD patients and healthy controls revealed a significant difference in concentration of bacteria among predominating and subdominating genera between ulcerative colitis (UC), Crohn's disease (CD) patients, and controls. In contrast to the mucosal studies, we found a significant increase in lactobacilli population in fecal samples of active UC patients. Another study revealed a significant decrease of Clostridium coccoides and leptum clusters in fecal samples of active UC patients along with decreased concentrations of fecal SCFAs, especially of nbutyrate, iso-butyrate, and acetate. We therefore found similar perturbations in gut microbiome in both infectious and autoimmune diseases, indicating inflammation to be the major driver for changes in gut microbiome.

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“…The biodiversity of active bacteria is reduced in UC patients compared to controls [77]. A decreased number of gastrointestinal health-promoting bacteria, Bacteroidetes and Lachnospiraceae, were found in surgical specimens from UC patients by rRNA sequence analysis compared to controls [76].…”

Section: Dysbiosis In Ucmentioning

confidence: 91%

“…Another study has shown a decrease of the beneficial Bifidobacteria in rectal biopsy specimens of UC patients, parallel to an increase of Clostridia and E. coli [78]. E. coli is also overrepresented among active fecal bacteria of UC patients, and is suggested to have a role in the development of colitis [77]. The number of Faecalibacterium prausnitzii, associated with mucosal protection, was also reduced in fecal samples of UC patients recovering from a relapse [79].…”

Section: Dysbiosis In Ucmentioning

confidence: 95%

Pathogenesis of Ulcerative Colitis and Crohn’s Disease: Similarities, Differences and a Lot of Things We Do Not Know Yet

Molnár¹

2014

J Clin Cell Immunol

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The pathogenesis of inflammatory bowel diseases (IBD), such as ulcerative colitis (UC) and Crohn's disease (CD) is complex, and our knowledge on the topic is constantly growing. The two disorders are distinct, yet overlap in their clinical manifestations and underlying causes. This review aims to provide a broad overview of the numerous pathogenetic factors that can lead to the development of IBD, focusing on novel findings and on the differences between UC and CD. Recent advances in genetics have identified new components in the pathogenesis, as an example, the importance of Th17 lymphocytes and the IL-17/IL-23 pathway have been highlighted in both diseases, apart from the previously known Th1-Th2 driven processes. Genetic background of increased permeability has been explored in UC, and the role of defective autophagy was recently described in CD. Genetic alterations can lead to an exaggerated immune response to the resident microbial flora. This microflora is altered in IBD patients, probably due to their reduced ability to stabilize its bacterial components and due to different environmental factors. An exhaustive exploration of environmental factors is particularly important, as they can be influential in many cases. The impact of smoking is the most established environmental factor, having deleterious effects in CD and protective in UC. Recent opinions on other factors, such as early appendectomy, diet, reduced vitamin D levels, the use of specific medications, breastfeeding, personal hygiene and psychological factors are also discussed. Epigenetics, a new field of research, links environmental factors to genetics. Understanding these factors is of great significance as changing lifestyles and improving life circumstances have started to increase the prevalence of IBD also in developing countries.

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Temperature Gradient Gel Electrophoresis of Fecal 16S rRNA Reveals Active Escherichia coli in the Microbiota of Patients with Ulcerative Colitis

Cited by 134 publications

References 29 publications

Dynamic changes of the luminal and mucosa-associated gut microbiota during and after antibiotic therapy with paromomycin

Dynamic changes of the luminal and mucosa-associated gut microbiota during and after antibiotic therapy with paromomycin

Gut microbiome diversity in acute infective and chronic inflammatory gastrointestinal diseases in North India

Pathogenesis of Ulcerative Colitis and Crohn’s Disease: Similarities, Differences and a Lot of Things We Do Not Know Yet

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