Differentially Abundant Bacterial Taxa Associated with Prognostic Variables of Crohn’s Disease: Results from the IMPACT Study

Park, Soo-Kyung; Kim, Hanna; Choi, Chang Hwan; Im, Jong Pil; Myung, Jae; Eun, Chang Soo; Kim, Tae-Oh; Kang, Sang Bum; Bang, Ki Bae; Kim, Hyun Gun; Jung, Yunho; Yoon, Hyuk; Han, Dongsoo; Lee, Chil-Woo; Ahn, Kwang‐Soon; Kim, Hyung-Lae; Park, Dong Il

doi:10.3390/jcm9061748

Cited by 14 publications

(11 citation statements)

References 42 publications

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“…Some researchers did not find significant differences in the mucosa-associated bacteria between apparently normal and inflamed mucosa in IBD patients [ 15 , 66 , 100 , 127 , 128 , 147 ]. Conversely, other studies found gut microbiome differences between inflamed and non-inflamed regions in mucosal biopsies [ 19 , 44 , 72 , 78 , 120 , 125 , 134 , 144 ]. This difference was also observed in fungal communities of inflamed mucosa, which are distinguishable from those of the non-inflamed area [ 63 ].…”

Section: Resultsmentioning

confidence: 78%

Systematic Review: The Gut Microbiome and Its Potential Clinical Application in Inflammatory Bowel Disease

2021

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Inflammatory bowel disease (IBD) is a chronic relapsing–remitting systemic disease of the gastrointestinal tract. It is well established that the gut microbiome has a profound impact on IBD pathogenesis. Our aim was to systematically review the literature on the IBD gut microbiome and its usefulness to provide microbiome-based biomarkers. A systematic search of the online bibliographic database PubMed from inception to August 2020 with screening in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines was conducted. One-hundred and forty-four papers were eligible for inclusion. There was a wide heterogeneity in microbiome analysis methods or experimental design. The IBD intestinal microbiome was generally characterized by reduced species richness and diversity, and lower temporal stability, while changes in the gut microbiome seemed to play a pivotal role in determining the onset of IBD. Multiple studies have identified certain microbial taxa that are enriched or depleted in IBD, including bacteria, fungi, viruses, and archaea. The two main features in this sense are the decrease in beneficial bacteria and the increase in pathogenic bacteria. Significant differences were also present between remission and relapse IBD status. Shifts in gut microbial community composition and abundance have proven to be valuable as diagnostic biomarkers. The gut microbiome plays a major role in IBD, yet studies need to go from casualty to causality. Longitudinal designs including newly diagnosed treatment-naïve patients are needed to provide insights into the role of microbes in the onset of intestinal inflammation. A better understanding of the human gut microbiome could provide innovative targets for diagnosis, prognosis, treatment and even cure of this relevant disease.

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Section: Resultsmentioning

confidence: 78%

Systematic Review: The Gut Microbiome and Its Potential Clinical Application in Inflammatory Bowel Disease

2021

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“…As its activation has a wide range of implications, it is difficult to understand its meanings. The Lipopolysaccharide biosynthesis pathway has been suggested to be involved in the anti-inflammation of CD [ 33 ], and we think that this might also be true for UC in this study. We consider that the intestinal environment may be involved in reducing inflammation in Prevotella -rich clusters.…”

Section: Discussionmentioning

confidence: 54%

Gut Microbiota Associated with Clinical Relapse in Patients with Quiescent Ulcerative Colitis

et al. 2022

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The microbiota associated with relapse in patients with quiescent ulcerative colitis (qUC) remains unclear. Our objective was to analyze the fecal microbiota of Japanese patients with qUC and identify the relapse-associated microbiota. In this study, 59 patients with qUC and 59 healthy controls (HCs) were enrolled (UMIN 000019486), and their fecal microbiota was compared using 16S rRNA gene amplicon sequencing. We followed their clinical course up to 3.5 years and analyzed the relapse-associated microbiota. Potential functional changes in the fecal microbiota were evaluated using PICRUSt software and the Kyoto Encyclopedia of Genes and Genomes database. There were significant differences in fecal microbiota diversity between HC and qUC subjects, with 13 taxa characterizing each subject. Despite no significant difference in variation of microbiota in a single sample (α diversity) between patients in sustained remission and relapsed patients, the variation in microbial communities between samples (β diversity) was significantly different. Prevotella was more abundant in the sustained remission patients, whereas Faecalibacterium and Bifidobacterium were more abundant in the relapsed patients. We clustered the entire cohort into four clusters, and Kaplan–Meier analysis revealed the subsequent clinical course of each cluster was different. We identified 48 metabolic pathways associated with each cluster using linear discriminant analysis effect size. We confirmed the difference in microbiota between patients with qUC and HCs and identified three genera associated with relapse. We found that the clusters based on these genera had different subsequent clinical courses and activated different metabolic pathways.

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“…In addition, an increase of D-glucarate degradation I and the activation of biological mechanisms involved in polyamine and dTDP-N-acetylthomosamine biosynthesis were achieved only in the patients with a normal pouch. The identified pathways have in the bloom of the Enterobacteriaceae their top contributors [60]. More interestingly, when comparing the ileum of IPAA patients to normal ileum, no pathway was revealed.…”

Section: Discussionmentioning

confidence: 95%

Microbiome Analysis of Mucosal Ileoanal Pouch in Ulcerative Colitis Patients Revealed Impairment of the Pouches Immunometabolites

Palmieri

Castellana

Biscaglia

et al. 2021

Cells

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The pathogenesis of ulcerative colitis (UC) is unknown, although genetic loci and altered gut microbiota have been implicated. Up to a third of patients with moderate to severe UC require proctocolectomy with ileal pouch ano-anastomosis (IPAA). We aimed to explore the mucosal microbiota of UC patients who underwent IPAA. Methods: For microbiome analysis, mucosal specimens were collected from 34 IPAA individuals. Endoscopic and histological examinations of IPAA were normal in 21 cases, while pouchitis was in 13 patients. 19 specimens from the healthy control (10 from colonic and 9 from ileum) were also analyzed. Data were analyzed using an ensemble of software packages: QIIME2, coda-lasso, clr-lasso, PICRUSt2, and ALDEx2. Results: IPAA specimens had significantly lower bacterial diversity as compared to normal. The microbial composition of the normal pouch was also decreased also when compared to pouchitis. Faecalibacterium prausnitzii, Gemmiger formicilis, Blautia obeum, Ruminococcus torques, Dorea formicigenerans, and an unknown species from Roseburia were the most uncommon in pouch/pouchitis, while an unknown species from Enterobacteriaceae was over-represented. Propionibacterium acnes and Enterobacteriaceae were the species most abundant in the pouchitis and in the normal pouch, respectively. Predicted metabolic pathways among the IPAA bacterial communities revealed an important role of immunometabolites such as SCFA, butyrate, and amino acids. Conclusions: Our findings showed specific bacterial signature hallmarks of dysbiosis and could represent bacterial biomarkers in IPAA patients useful to develop novel treatments in the future by modulating the gut microbiota through the administration of probiotic immunometabolites-producing bacterial strains and the addition of specific prebiotics and the faecal microbiota transplantation.

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Differentially Abundant Bacterial Taxa Associated with Prognostic Variables of Crohn’s Disease: Results from the IMPACT Study

Cited by 14 publications

References 42 publications

Systematic Review: The Gut Microbiome and Its Potential Clinical Application in Inflammatory Bowel Disease

Systematic Review: The Gut Microbiome and Its Potential Clinical Application in Inflammatory Bowel Disease

Gut Microbiota Associated with Clinical Relapse in Patients with Quiescent Ulcerative Colitis

Microbiome Analysis of Mucosal Ileoanal Pouch in Ulcerative Colitis Patients Revealed Impairment of the Pouches Immunometabolites

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