Characterization of the Duodenal Mucosal Microbiome in Obese Adult Subjects by 16S rRNA Sequencing

Abstract

The gut microbiota may have an impact on obesity. To date, the majority of studies in obese patients reported microbiota composition in stool samples. The aim of this study was to investigate the duodenal mucosa dysbiosis in adult obese individuals from Campania, a region in Italy with a very high percentage of obese people, to highlight microbial taxa likely associated with obesity. Duodenum biopsies were taken during upper gastrointestinal endoscopy in 19 obese (OB) and 16 lean control subjects (CO) and microbiome studied by 16S rRNA gene sequencing. Duodenal microbiome in our groups consisted of six phyla: Proteobacteria, Firmicutes, Actinobacteria, Fusobacteria, Bacteroidetes and Acidobacteria. Proteobacteria (51.1% vs. 40.1%) and Firmicutes (33.6% vs. 44.9%) were significantly (p < 0.05) more and less abundant in OB compared with CO, respectively. Oribacterium asaccharolyticum, Atopobium parvulum and Fusobacterium nucleatum were reduced (p < 0.01) and Pseudomonadales were increased (p < 0.05) in OB compared with CO. Receiver operating characteristic curve analysis showed Atopobium and Oribacterium genera able to discriminate with accuracy (power = 75% and 78%, respectively) OB from CO. In conclusion, increased Proteobacteria and decreased Firmicutes (Lachnospiraceae) characterized the duodenal microbiome of obese subjects. These data direct to further studies to evaluate the functional role of the dysbiotic-obese-associated signature.

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

“…The clinical and anamnestic data of each subject were collected by a clinician, whereas dietary habits were self-reported and recorded by a nutritionist. Thirteen subjects (7 OB and 6 CO), belonging to our cohort, had previously been investigated by our team using 16S rRNA sequencing to characterize their duodenal microbiome composition [ 24 ].…”

“…We collected blood samples and duodenal biopsy specimens from all enrolled individuals. The biopsy sample was taken during an upper gastrointestinal endoscopy performed for diagnostic testing, under sterile conditions to avoid contamination, as reported elsewhere [ 24 ]. Biopsies were immediately stored in a vial containing RNA Later, then cooled in dry ice and stored at −80 °C until RNA isolation for metatranscriptomics analysis.…”

“…In detail, the gut microbiota, and its approximately 3.3 million genes (the “microbiome”) [ 13 ], interact with the human genome and play a role in several functions, particularly in digesting food, preserving the gut mucosal barrier integrity, and priming the immune system, thus globally contributing to human health [ 16 , 17 ]. Thanks to the advent of next generation sequencing (NGS) techniques in the early 2000s [ 18 ], together with that of powerful tools for the bioinformatics processing of sequencing data [ 19 , 20 ], it has become possible to explore the gut microbiota composition in association with obesity [ 12 , 21 , 22 , 23 , 24 ]. However, given the large intra- and interindividual variability of the gut microbiota, about 20% of which is attributable to environmental factors and BMI [ 25 ], it is difficult to establish whether a microbiota is a “healthy” or “obese” one.…”

Nasopharyngeal Microbiome Signature in COVID-19 Positive Patients: Can We Definitively Get a Role to Fusobacterium periodonticum?

“…Among these, the microbiome composition at different levels (gut, lung, skin) was also investigated. Microbiome, the collective genomes of all microorganisms living in our body, in fact, can play a pivotal role in the development of several diseases ( Wang et al., 2017 ; Nardelli et al., 2020 ; Sacchetti and Nardelli, 2020 ; Scaglione et al., 2020 ). In fact, a perturbation of the microbial composition, named dysbiosis, could decrease the microbiota diversity, changing its composition, and promote an inflammatory environment favoring the coronavirus invasion and viral replication ( Antunes et al., 2020 ).…”

Can Dietary Fatty Acids Affect the COVID-19 Infection Outcome in Vulnerable Populations?

“…For example, stomach, duodenal, jejunum, and stool samples were collected from 8 heathy subjects; Proteobacteria were not detected in the stool but were present in the small intestinal samples (27). Other studies of small intestinal microbiota relied on the use of subjects undergoing esophagogastroduodenoscopy (28), such as for gastroesophageal reflux disease (29). Proteobacteria were detected in the duodenal samples, but it is not clear what role the medical condition may have played in these individuals.…”