Comparative genomics of Escherichia coli isolated from patients with inflammatory bowel disease

<p>Abstract</p> <p>Background</p> <p>Inflammatory bowel disease (IBD) is used to describe a state of idiopathic, chronic inflammation of the gastrointestinal tract. The two main phenotypes of IBD are Crohn's disease (CD) and ulcerative colitis (UC). The major cause of IBD-associated mortality is colorectal cancer. Although both host-genetic and exogenous factors have been found to be involved, the aetiology of IBD is still not well understood. In this study we characterized thirteen <it>Escherichia coli </it>strains from patients with IBD by comparative genomic hybridization employing a microarray based on 31 sequenced <it>E. coli </it>genomes from a wide range of commensal and pathogenic isolates.</p> <p>Results</p> <p>The IBD isolates, obtained from patients with UC and CD, displayed remarkably heterogeneous genomic profiles with little or no evidence of group-specific determinants. No IBD-specific genes were evident when compared with the prototypic CD isolate, LF82, suggesting that the IBD-inducing effect of the strains is multifactorial. Several of the IBD isolates carried a number of extraintestinal pathogenic <it>E. coli </it>(ExPEC)-related virulence determinants such as the <it>pap</it>, <it>sfa</it>, <it>cdt </it>and <it>hly </it>genes. The isolates were also found to carry genes of ExPEC-associated genomic islands.</p> <p>Conclusions</p> <p>Combined, these data suggest that <it>E. coli </it>isolates obtained from UC and CD patients represents a heterogeneous population of strains, with genomic profiles that are indistinguishable to those of ExPEC isolates. Our findings indicate that IBD-induction from <it>E. coli </it>strains is multifactorial and that a range of gene products may be involved in triggering the disease.</p

Nutritional follow-up of patients with ulcerative colitis during periods of intestinal inflammatory activity and remission

CONTEXT: Ulcerative colitis is an inflammatory bowel disease involving superficial inflammation of the mucosa of the colon, rectum, and anus, sometimes including the terminal ileum. When in clinical activity, the disease is characterized by various daily evacuations containing blood, mucus and/or pus alternating periods of remission. OBJECTIVE: To compare nutritional parameters (dietary, biochemical and anthropometric) among patients with ulcerative colitis followed up on an outpatient basis over a period of 1 year and during periods of intestinal inflammatory activity and remission. METHODS: Sixty-five patients were studied over a period of 1 year and divided into two groups: group 1 with inflammatory disease activity (n = 24), and group 2 without disease activity (n = 41). Anthropometric measures, biochemical parameters, quantitative food intake, and qualitative food frequency were analyzed. RESULTS: A significant reduction in body mass index and weight and in the intake of energy, proteins, lipids, calcium, iron and phosphorus was observed in the group with inflammatory activity (group 1) when compared to the period of clinical remission. The most affected food groups were cereals, legumes, oils, and fats. In contrast, in group 2 significant differences in triceps and sub scapular skin fold thickness, total protein, hemoglobin and hematocrit were observed between the first and final visit. Calcium and vitamin B6 intake, as well as the consumption of legumes, meat and eggs, and sugar and sweets, was significantly higher than on the first visit. CONCLUSION: Patients with ulcerative colitis followed up on an outpatient basis tend to be well nourished. However, the nutritional aspects studied tend to worsen during the period of inflammatory disease activity.CONTEXTO: A retocolite ulcerativa inespecífica compreende uma das doenças inflamatórias intestinais, com características de inflamação superficial da mucosa do cólon, reto, ânus, podendo incluir o íleo terminal. Caracteriza-se por várias exonerações diárias, com a presença de sangue e/ou pus, cursando em períodos de atividade e remissão inflamatória intestinal. OBJETIVO: Comparar os parâmetros nutricionais (alimentares, bioquímicos e antropométricos) em pacientes com retocolite ulcerativa inespecífica acompanhados em ambulatório, durante a atividade e remissão da doença inflamatória, no período de 1 ano. MÉTODOS: Foram estudados 65 pacientes durante 1 ano e divididos em dois grupos: grupo 1 com atividade inflamatória da doença (n = 24) e grupo 2 sem atividade da doença (n = 41), e analisadas as medidas antropométricas, os exames bioquímicos, o consumo alimentar quantitativo e a frequência alimentar qualitativa. RESULTADOS: O grupo com atividade inflamatória (grupo 1) apresentou redução estatisticamente significante no índice de massa corpórea, peso, no consumo de energia, proteínas, lipídios, cálcio, ferro e fósforo, em relação ao período de remissão clínica. Os grupos alimentares com significado prejuízo foram os cereais, as leguminosas, os óleos e as gorduras. Já no grupo 2, foram observadas alterações com significância estatística na dobra cutânea tricipital e subescapular, nos valores de proteínas totais, hemoglobina e hematócrito da consulta inicial para a final. Encontrou-se consumo de cálcio e vitamina B6, assim como na ingestão do grupo das leguminosas, carnes e ovos, açúcares e doces maiores significativamente do que na consulta inicial. CONCLUSÃO: Pacientes com retocolite ulcerativa inespecífica, acompanhados em ambulatório, tendem a ser bem nutridos, mas na fase de atividade inflamatória da doença, há tendência na piora dos aspectos nutricionais estudados

Phylotype-level 16S rRNA analysis reveals new bacterial indicators of health state in acute murine colitis

Human inflammatory bowel disease and experimental colitis models in mice are associated with shifts in intestinal microbiota composition, but it is unclear at what taxonomic/phylogenetic level such microbiota dynamics can be indicative for health or disease. Here, we report that dextran sodium sulfate (DSS)-induced colitis is accompanied by major shifts in the composition and function of the intestinal microbiota of STAT1/and wild-type mice, as determined by 454 pyrosequencing of bacterial 16S rRNA (gene) amplicons, metatranscriptomics and quantitative fluorescence in situ hybridization of selected phylotypes. The bacterial families Ruminococcaceae, Bacteroidaceae, Enterobacteriaceae, Deferribacteraceae and Verrucomicrobiaceae increased in relative abundance in DSS-treated mice. Comparative 16S rRNA sequence analysis at maximum possible phylogenetic resolution identified several indicator phylotypes for DSS treatment, including the putative mucin degraders Akkermansia and Mucispirillum. The analysis additionally revealed strongly contrasting abundance changes among phylotypes of the same family, particularly within the Lachnospiraceae. These extensive phylotype-level dynamics were hidden when reads were grouped at higher taxonomic levels. Metatranscriptomic analysis provided insights into functional shifts in the murine intestinal microbiota, with increased transcription of genes associated with regulation and cell signaling, carbohydrate metabolism and respiration and decreased transcription of flagellin genes during inflammation. These findings (i) establish the first in-depth inventory of the mouse gut microbiota and its metatranscriptome in the DSS colitis model, (ii) reveal that family-level microbial community analyses are insufficient to reveal important colitis-associated microbiota shifts and (iii) support a scenario of shifting intra-family structure and function in the phylotype-rich and phylogenetically diverse Lachnospiraceae in DSS-treated mice