Gut microbiota signatures in inflammatory bowel disease

BACKGROUND

Inflammatory bowel diseases (IBD), including Crohn's disease (CD) and ulcerative colitis (UC), affect millions of people worldwide with increasing incidence.

OBJECTIVES

Several studies have shown a link between gut microbiota composition and IBD, but results are often limited by small sample sizes. We aimed to re-analyze publicly available fecal microbiota data from IBD patients.

METHODS

We extracted original fecal 16S rRNA amplicon sequencing data from 45 cohorts of IBD patients and healthy individuals using the BioProject database at the National Center for Biotechnology Information. Unlike previous meta-analyses, we merged all study cohorts into a single dataset, including sex, age, geography, and disease information, based on which microbiota signatures were analyzed, while accounting for varying technical platforms.

RESULTS

Among 2518 individuals in the combined dataset, we discovered a hitherto unseen number of genera associated with IBD. A total of 77 genera associated with CD, of which 38 were novel associations, and a total of 64 genera associated with UC, of which 28 represented novel associations. Signatures were robust across different technical platforms and geographic locations. Reduced alpha diversity in IBD compared to healthy individuals, in CD compared to UC, and altered microbiota composition (beta diversity) in UC and especially in CD as compared to healthy individuals were found.

CONCLUSIONS

Combining original microbiota data from 45 cohorts, we identified a hitherto unseen large number of genera associated with IBD. Identification of microbiota features robustly associated with CD and UC may pave the way for the identification of new treatment targets.

Characterization of Mucosa-Associated Microbiota in Formalin-Fixed, Paraffin-Embedded Tissues From Southern Thai Patients With Familial Adenomatous Polyposis

Familial adenomatous polyposis (FAP) is an autosomal dominant syndrome associated with germline mutations in the adenomatous polyposis coli (APC) gene. Patients eventually may develop colorectal cancer (CRC) if they are not diagnosed in the early stages. Dysbiosis is an important contributing factor to the complex events in carcinogenesis, which are poorly understood. First, 25 tissue samples from 13 patients with FAP at Songklanagarind Hospital were classified as nontumor (n = 18) or tumor tissues (n = 7). Following isolation, 5 DNA samples of insufficient quantity and quality were excluded. The 16S rRNA gene targeting the V3-V4 region was sequenced, and the sequencing data were analyzed using bioinformatics tools. The abundance of Romboutsia and Clostridium genera and Lachnospiraceae NK4A136 was significantly higher in tumor tissues than that in nonneoplastic samples. Furthermore, several bacterial genera, including Acinetobacter, Paracoccus, Brevundimonas, and Brevibacillus, were predominant or key taxa in nontumor mucosae. We found an alteration in the mucosa-associated microbiota composition of southern Thai patients that may have contributed to the tumorigenesis of FAP. These findings may improve the knowledge of the potential roles of microbes in FAP and aid the development of preventive measures for cancer development and progression through modulation of the gut microbiota.