Characterization of the Gastrointestinal Microbiota in Health and Inflammatory Bowel Disease

Abstract

The enteric bacterial flora play a key role in maintaining health. Inflammatory bowel disease is associated with quantitative and qualitative alterations in the microbiota. Early characterization of the microbiota involved culture-dependent techniques. The advent of metagenomic techniques, however, allows for structural and functional characterization using culture-independent methods. Changes in diversity, together with quantitative alterations in specific bacterial species, have been identified. The functional significance of these changes, and their pathogenic role, remain to be elucidated.

Biomarkers of Nutrient Bioactivity and Efficacy

“…In recent years, an important body of evidence has been generated about the participation of the gut microbiota in IBD, which has recently been reviewed extensively. 105,106 Dysbiosis in the broader sense is a deviation of the microbial community from its "normal" state, and in IBD, dysbiosis has been identified as a characteristic of mucosa-associated and/or fecal-associated microbiota of CD and UC patients. [107][108][109] Although a variety of changes in the repertoire of bacterial species present in the microbiota have been reported in both CD and UC, only 2 organisms have been most studied and found to be significantly associated with CD: Escherichia coli 110,111 and Mycobacterium avium subspecies tuberculosis.…”

“…112,113 To date, different studies have evaluated the potential role of microbiota changes in IBD recurrence, remission, and progression; although changes in diversity and quantitative alterations in specific bacterial species have been identified, there is still a debate about whether these changes precede or follow the development of IBD, and their functional significance remains to be elucidated. 105 To date, most of the knowledge that has been derived has relied on the characterization of the microbiota phylogenetic core based on 16s rRNA analyses by different techniques, including DNA-sequencing technologies. To have a better understanding of the functional consequences of these phylogenetic changes, more comprehensive metagenomic analyses including the analyses of functionally relevant genes or whole bacterial genomes, and also metatranscriptomic, metaproteomic, and metabolomic approaches, are being developed.…”

Metabolomics in the Clinical Diagnosis of Inflammatory Bowel Disease

“…In genetically susceptible hosts, alterations of the microbiota composition, the so-called dysbiosis, can lead to an activation of the mucosal immune system which can result in chronic inflammation of the intestine as observed in IBD [6][7][8][9] . In humans, the intestinal microbiota has been implicated in the pathogenesis of IBD by showing that (i) diversion of the fecal stream induces inflammatory remission and mucosal healing in the excluded intestinal segment [10] , (ii) the intestinal mucus barrier is altered in UC [11] , (iii) broad-spectrum antibiotics rapidly reduced metabolic activity of the microbiota and mucosal inflammation in UC [12] , (iv) the number of colon-associated mucolytic bacteria ( Ruminococcus gnavus and torques ) is increased [13] and (v) numbers of Faecalibacteria (Faecalibacterium prausnitzii) in the mucosa-associated microbiota or in fecal samples are decreased in IBD patients [14,15] .…”

The Modern View of the Pathogenesis and Laboratory Diagnostics of Ulcerative Colitis (Literature Review)

“…По мнению других авторов, вирулентные штаммы E. coli участву-ют в патогенезе ЯК [32]. Третья точка зрения: не все патогенные штаммы E. coli ассоциированы с ЯК [15]. По данным ряда исследований, известно, что токсин Clostridium difficile связан с обострением ВЗК [44].…”