Duodenal Metatranscriptomics to Define Human and Microbial Functional Alterations Associated with Severe Obesity: A Pilot Study

Abstract

Obesity is a multifactorial disorder, and the gut microbiome has been suggested to contribute to its onset. In order to better clarify the role of the microbiome in obesity, we evaluated the metatranscriptome in duodenal biopsies from a cohort of 23 adult severely obese and lean control subjects using next generation sequencing. Our aim was to provide a general picture of the duodenal metatranscriptome associated with severe obesity. We found altered expressions of human and microbial genes in the obese compared to lean subjects, with most of the gene alterations being present in the carbohydrate, protein, and lipid metabolic pathways. Defects were also present in several human genes involved in epithelial intestinal cells differentiation and function, as well as in the immunity/inflammation pathways. Moreover, the microbial taxa abundance inferred by our transcriptomic data differed in part from the data that we previously evaluated by 16S rRNA in 13/23 individuals of our cohort, particularly concerning the Firmicutes and Proteobacteria phyla abundances. In conclusion, our pilot study provides the first taxonomic and functional characterization of duodenal microbiota in severely obese subjects and lean controls. Our findings suggest that duodenal microbiome and human genes both play a role in deregulating metabolic pathways, likely affecting energy metabolism and thus contributing to the obese phenotype.

Challenges and Perspective in Integrated Multi-Omics in Gut Microbiota Studies

“…Knowing that the metabolic activities of certain microbes could be suppressed by antagonists and so may not be actively involved in a given condition (phenotype), capturing such bacteria due to their sheer presence may give a false positive association. This is supported by studies that have reported that taxonomic abundance does not correspond to transcriptional activities [ 25 , 26 , 27 ]. The library construction, assembly, and reference databases of metagenomics for annotation employ biases that are difficult to understand [ 21 ].…”

“…For this reason, analyzing the mRNA produced by a microbe at a given time would be a better way to predict the metabolic activities and potential function(s) of the organism rather than making predictions based on its mere presence. Using metatranscriptomics, Granata et al [ 25 ] showed that carbohydrate, amino acid, and nucleotide metabolism are severely impaired in the duodenal microbiota of obese patients when compared to non-obese patients. Though the analytical technique is biased towards organisms with higher transcriptional rates, assigning mRNA reads to taxa could unveil critical functions contributed by keystone taxa.…”

Microbiota and Ocular Diseases

“…Shotgun sequencing profiles may present information about the potential function(s) of an entire microbial community at the gene level based on databases of microbial genomes with known sequences, yet the information yielded by this method may not accurately represent what is happening in the gut at a given time (Emerson et al, 2017). This is supported by studies of taxonomic abundance that do not correspond to transcriptional activities (Abu-Ali et al, 2018;Jia et al, 2019;Granata et al, 2020). Utilizing this method, distinct meibum microbial communities were identified in patients with meibomian gland dysfunction and in healthy controls, indicating different immune evasive virulence of the meibum microbiota (Zhao et al, 2020).…”

“…The same bacterial species has also been reported to fortify gut barrier functions by modulating mucin production in the gut, which may eventually prevent gut mucosal inflammation ( Graziani et al., 2016 ; Luissint et al., 2016 ). Using metatranscriptomics, Granata et al. (2020) showed that carbohydrate, amino acid, and nucleotide metabolism are severely impaired in the duodenal microbiota of obese patients compared to nonobese patients.…”

16S rRNA of Mucosal Colon Microbiome and CCL2 Circulating Levels Are Potential Biomarkers in Colorectal Cancer

“…Microbes play important roles in obesity. Previously, our group investigated the duodenal metatranscriptome in human obese and lean subjects, highlighting an obese-associated gut dysbiosis and human and bacterial genes both contributing to relevant dysfunctions in important metabolic pathways [ 17 , 18 ]. Regarding CRC alterations until now reported in the gut microbiota community or in single bacterial species in association with the tumor [ 19 ], in presence/absence of various risk factors among which increased adiposity, they have been mostly studied in murine models and/or in human fecal samples, but the human mucosal colon microbiome has still scarcely been investigated [ 20 , 21 , 22 , 23 ].…”