The Inflammatory Bowel Disease Transcriptome and Metatranscriptome Meta-Analysis (IBD TaMMA) framework

Abstract

Inflammatory bowel disease (IBD) is a class of chronic disorders whose etiogenesis is still unknown. Despite the high number of IBD-related omics studies, the RNA-sequencing data produced results that are hard to compare because of the experimental variability and different data analysis approaches. We here introduce the IBD Transcriptome and Metatranscriptome Meta-Analysis (TaMMA) framework, a comprehensive survey of publicly available IBD RNA-sequencing datasets. IBD TaMMA is an open-source platform where scientists can explore simultaneously the freely available IBD-associated transcriptomics and microbial profiles thanks to its interactive interface, resulting in a useful tool to the IBD community.

Going Beyond Bacteria: Uncovering the Role of Archaeome and Mycobiome in Inflammatory Bowel Disease

“…As a matter of fact, in both mycobiome and archaeome contexts, the use of metatranscriptomics may help to better classify and annotate the fungal and archaeal composition of the gut microbiota, as we recently reported in IBD TaMMA (Massimino et al, 2021). However, much more effort in developing and improving both sequencing and cultivation approaches is required to make plausible the mycobiome and archaeome studies to unravel their physiological properties.…”

“…The majority of the studies reported so far elucidated the mycobiome composition in small sample-sized IBD patient cohorts, mainly on stools and exploiting targeted DNA sequencing and PCR (Mahmoudi et al, 2021). By contrast, IBD TaMMA (Massimino et al, 2021) highlighted CD and UC ilea both featuring an increased abundance of Glomerellales, Tremellales, and Hypocreales, coupled with decreased abundance of Schizosaccharomycetales. Some orders were instead differentially abundant in the two conditions.…”

“…While bacteriophages contribute to the maintenance of bacterial composition of the gut microbiota and changes in their abundances (virome dysbiosis) may affect bacteria diversity in the GI tract (Lin and Lin, 2019), the gut eukaryotic viruses (Taboada et al, 2021) may exert beneficial effects and directly impact the host's cells (Ungaro et al, 2019b). Gut virome dysbiosis was reported also in IBD patients and many studies profiled virome composition in the context of GI disease, as extensively reviewed elsewhere (Lin and Lin, 2019;Ungaro et al, 2019a;Massimino et al, 2021).…”

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Network Biology Approaches to Achieve Precision Medicine in Inflammatory Bowel Disease

“…In addition, despite the exponential increase in transcriptomics and metatranscriptomics studies in IBD in the past decade, such datasets are often limited by low patient numbers. Recently, a novel meta-analysis framework for transcriptome and metatranscriptome data in IBD has been introduced, called the IBD Transcriptome and Metatranscriptome Meta-Analysis (TaMMA) platform ( Massimino et al, 2021 ). The TaMMA platform collates and integrates transcriptomics (and metatranscriptomics) data from multiple IBD patient cohorts using a standardised pipeline that corrects batch effects and performs differential analysis of the data.…”