Gut microbiota in the early stage of Crohn’s disease has unique characteristics

Abstract

Background Emerging evidence suggests that gut microbiota plays a predominant role in Crohn’s disease (CD). However, the microbiome alterations in the early stage of CD patients still remain unclear. The present study aimed to identify dysbacteriosis in patients with early CD and explore specific gut bacteria related to the progression of CD. Methods This study was nested within a longitudinal prospective Chinese CD cohort, and it included 18 early CD patients, 22 advanced CD patients and 30 healthy controls. The microbiota communities were investigated using high-throughput Illumina HiSeq sequencing targeting the V3–V4 region of 16S ribosomal DNA (rDNA) gene. The relationship between the gut microbiota and clinical characteristics of CD was analyzed. Results Differential microbiota compositions were observed in CD samples (including early and advanced CD samples) and healthy controls samples. Notably, Lachnospiracea_incertae_sedis and Parabacteroides were enriched in the early CD patients, Escherichia/Shigella, Enterococcus and Proteus were enriched in the advanced CD patients, and Roseburia, Gemmiger, Coprococcus, Ruminococcus 2, Butyricicoccus, Dorea, Fusicatenibacter, Anaerostipes, Clostridium IV were enriched in the healthy controls [LDA score (log10) > 2]. Furthermore, Kruskal–Wallis Rank sum test results showed that Blautia, Clostridium IV, Coprococcus, Dorea, Fusicatenibacter continued to significantly decrease in early and advanced CD patients, and Escherichia/Shigella and Proteus continued to significantly increase compared with healthy controls (P < 0.05). The PICRUSt analysis identified 16 remarkably different metabolic pathways [LDA score (log10) > 2]. Some genera were significantly correlated with various clinical parameters, such as fecal calprotectin, erythrocyte sedimentation rate, C-reactive protein, gland reduce, goblet cells decreased, clinical symptoms (P < 0.05). Conclusions Dysbacteriosis occurs in the early stage of CD and is associated with the progression of CD. This data provides a foundation that furthers the understanding of the role of gut microbiota in CD’s pathogenesis.

Intestinal epithelialAtg16l1influences pregnancy-induced fecal microbiota shifts in mice

“…Interestingly, many taxa that we found as increased or decreased in Atg16l1 ΔIEC pregnant mice in trimester 3 have been previously described to have a role in intestinal inflammation, specifically in Crohn’s disease. For instance, a significant reduction in the SCFA-producing bacteria Roseburia has been a consistent pattern of CD (Takahashi et al ., 1960; Shen et al ., 2018, 2022; Ma et al ., 2022), while the role of other members of the Lachnospiraceae family is more controversial (Vacca et al ., 2020). Of note, Lachnospiraceae UCG-001 , the same genus that we found reduced in Atg16l1 ΔIEC , has been negatively associated with CD in a recent study (Liu et al ., 2022).…”

“…Bacteroides acidifaciens has been characterized as a symbiotic organism that inhibits obesity, enhances insulin sensitivity in mice (Yang et al ., 2017), which however, was also associated to gut inflammation in mice models of colitis (Berry et al ., 2015; Staley et al ., 2023). Parabacteroides , which had a higher abundance in Atg16l1 ΔIEC pregnant mice at week 3 compared to controls, were found to be highly abundant in early CD patients (Ma et al ., 2022) and specifically Parabacteroides distasonis has been identified in intestinal microlesions of a severe CD patient (Yang et al ., 2019). Also, this bacterium was reported to induce depressive behavior in a mouse model of CD-like ileitis (Gomez-Nguyen et al ., 2021).…”

Comprehensive Probiogenomics Analysis of the Commensal Escherichia Coli CEC15 as a Potential Probiotic Strain

“…Metagenomics studies conducted in both experimental animal models and patients with intestinal in ammatory diseases have reported con icting results, with some studies showing a decrease in the Firmicutes phylum [122,123]. Interestingly, CEC15 administration showed a large reduction on Proteobacteria restoring levels of Firmicutes and increasing back the Firmicutes/Bacteroidetes ratio.…”

Special Issue “Gut Microbioma Structure and Functions in Human Health and Disease”: Editorial

“…How much a peculiar gut microbiota structure is then the cause, or the contributing cause, of disease, or to what extent is simply the consequence of a pathology, remains to be defined. Nevertheless, the possibility that the colonic microbiota can directly contribute to pathological manifestation is being reported increasingly frequently, for example, in inflammatory bowel disease [ 5 ]. Undeniably, however, we are at the beginning of a journey that we hope will soon lead us to a better understanding of how the different consortium structures that we observe when analysing the gut microbiota can become useful in a translational sense, providing us with elements on which to work with the aim of improving the health of patients.…”