ObjectivesGut microbiota is a key component in obesity and type 2 diabetes, yet mechanisms and metabolites central to this interaction remain unclear. We examined the human gut microbiome’s functional composition in healthy metabolic state and the most severe states of obesity and type 2 diabetes within the MetaCardis cohort. We focused on the role of B vitamins and B7/B8 biotin for regulation of host metabolic state, as these vitamins influence both microbial function and host metabolism and inflammation.DesignWe performed metagenomic analyses in 1545 subjects from the MetaCardis cohorts and different murine experiments, including germ-free and antibiotic treated animals, faecal microbiota transfer, bariatric surgery and supplementation with biotin and prebiotics in mice.ResultsSevere obesity is associated with an absolute deficiency in bacterial biotin producers and transporters, whose abundances correlate with host metabolic and inflammatory phenotypes. We found suboptimal circulating biotin levels in severe obesity and altered expression of biotin-associated genes in human adipose tissue. In mice, the absence or depletion of gut microbiota by antibiotics confirmed the microbial contribution to host biotin levels. Bariatric surgery, which improves metabolism and inflammation, associates with increased bacterial biotin producers and improved host systemic biotin in humans and mice. Finally, supplementing high-fat diet-fed mice with fructo-oligosaccharides and biotin improves not only the microbiome diversity, but also the potential of bacterial production of biotin and B vitamins, while limiting weight gain and glycaemic deterioration.ConclusionStrategies combining biotin and prebiotic supplementation could help prevent the deterioration of metabolic states in severe obesity.Trial registration numberNCT02059538.

Symbiosis is a major force of evolutionary change, influencing virtually all aspects of biology, from population ecology and evolution to genomics and molecular/biochemical mechanisms of development and reproduction. A remarkable example is Wolbachia endobacteria, present in some parasitic nematodes and many arthropod species. Acquisition of genomic data from diverse Wolbachia clades will aid in the elucidation of the different symbiotic mechanisms(s). However, challenges of de novo assembly of Wolbachia genomes include the presence in the sample of host DNA: nematode/vertebrate or insect. We designed biotinylated probes to capture large fragments of Wolbachia DNA for sequencing using PacBio technology (LEFT-SEQ: Large Enriched Fragment Targeted Sequencing). LEFT-SEQ was used to capture and sequence four Wolbachia genomes: the filarial nematode Brugia malayi , w Bm, (21-fold enrichment), Drosophila mauritiana flies (2 isolates), w Mau (11-fold enrichment), and Aedes albopictus mosquitoes, w AlbB (200-fold enrichment). LEFT-SEQ resulted in complete genomes for w Bm and for w Mau. For w Bm, 18 single-nucleotide polymorphisms (SNPs), relative to the w Bm reference, were identified and confirmed by PCR. A limit of LEFT-SEQ is illustrated by the w AlbB genome, characterized by a very high level of insertion sequences elements (ISs) and DNA repeats, for which only a 20-contig draft assembly was achieved.

There are numerous factors involved in obesity progression and maintenance including systemic low-grade inflammation, adipose tissue dysfunction, or gut microbiota dysbiosis. Recently, a growing interest has arisen for vitamins' role in obesity and related disorders, both at the host and gut bacterial level. Indeed, vitamins are provided mostly by food, but some, from the B and K groups in particular, can be synthesized by the gut bacterial ecosystem and absorbed in the colon. Knowing that vitamin deficiency can alter many important cellular functions and lead to serious health issues, it is important to carefully monitor the vitamin status of patients with obesity and potentially already existing comorbidities as well as to examine the dysbiotic gut microbiota and thus potentially altered bacterial metabolism of vitamins. In this review, we examined both murine and human studies, to assess the prevalence of sub-optimal levels of several vitamins in obesity and metabolic alterations. This review also examines the relationship between vitamins and the gut microbiota in terms of vitamin production and the modulation of the gut bacterial ecosystem in conditions of vitamin shortage or supplementation. Furthermore, some strategies to improve vitamin status of patients with severe obesity are proposed within this review.

Roux-en-Y gastric bypass (RYGB) is efficient at inducing drastic albeit variable weight loss and type-2 diabetes (T2D) improvements in patients with severe obesity and T2D. We hypothesized a causal implication of the gut microbiota (GM) in these metabolic benefits, as RYGB is known to deeply impact its composition. In a cohort of 100 patients with baseline T2D who underwent RYGB and were followed for 5-years, we used a hierarchical clustering approach to stratify subjects based on the severity of their T2D (Severe vs Mild) throughout the follow-up. We identified via nanopore-based GM sequencing that the more severe cases of unresolved T2D were associated with a major increase of the class Bacteroidia, including 12 species comprising Phocaeicola dorei, Bacteroides fragilis , and Bacteroides caecimuris . A key observation is that patients who underwent major metabolic improvements do not harbor this enrichment in Bacteroidia, as those who presented mild cases of T2D at all times. In a separate group of 36 patients with similar baseline clinical characteristics and preoperative GM sequencing, we showed that this increase in Bacteroidia was already present at baseline in the most severe cases of T2D. To explore the causal relationship linking this enrichment in Bacteroidia and metabolic alterations, we selected 13 patients across T2D severity clusters at 5-years and performed fecal matter transplants in mice. Our results show that 14 weeks after the transplantations, mice colonized with the GM of Severe donors have impaired glucose tolerance and insulin sensitivity as compared to Mild-recipients, all in the absence of any difference in body weight and composition. GM sequencing of the recipient animals revealed that the hallmark T2D-severity associated bacterial features were transferred and were associated with the animals’ metabolic alterations. Therefore, our results further establish the GM as a key contributor to long-term glucose metabolism improvements (or lack thereof) after RYGB.

Severe obesity is associated with major tissue alterations and systemic low‐grade inflammation as well as with modifications of gut microbiota composition and functionality. Yet, there is increasing evidence revealing that the gut microbiota could influence metabolic health via the production of many microbiota‐derived metabolites which contribute to complex interorgan dialogs. Vitamins and more specifically B vitamins have been neglected in this context. Amongst them, Vitamin B7/biotin plays an important role in many physiological functions including carbohydrate and lipid metabolism. Although, biotin supplementation is suggested to improve glucose metabolism in type 2 diabetes (T2D), this vitamin has not been widely studied in metabolic disorders including subjects with severe obesity. We, here, investigated both the bacterial and host metabolism of biotin, using large scale data from the European cohort Metacardis and different murine models. Examining metagenomic data of gut microbiota from human with worsening stages of obesity and diet‐induced obesity in mice revealed deficiency in biotin microbial production and transport. This altered gut microbial metabolism was associated with metabolic and inflammatory deterioration in the human host. In the same subjects with severe obesity, we found suboptimal circulating levels of biotin and altered expression of biotin‐associated genes in adipose tissue. Then, we demonstrated the contribution of the gut microbiota to the host circulating biotin by a series of experiments performed in Germ‐free animals, antibiotic‐treated mice and after gut microbiota transfer (from human to mice). Furthermore, we studied gut microbiota biotin metabolism in the context of obesity management. First, bariatric surgery, which is known to improve metabolism and inflammation and to induce changes in gut microbiota composition, was associated with increased bacterial biotin producers together with improved systemic biotin in mice and humans. Second, the concomitant management of biotin status and dysbiosis in the context of installed obesity in mice was explored. The oral supplementation of mice with installed obesity with both biotin and a prebiotic fructoligosaccharide (FOS) led to limited weight gain and glycemic deterioration compared to animals with no supplementation. The mice supplemented by FOS and biotin also improved their bacterial biotin metabolism better than the other groups. Altogether, these results suggest the importance of biotin, and more generally B vitamins, in severe obesity and pave the way for future clinical investigation of biotin and prebiotic administration in humans to prevent obesity from transitioning to a more severe metabolic state.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Diet composition impacts metabolic health and is now recognized to shape the immune system, especially in the intestinal tract. Nutritional imbalance and increased caloric intake are induced by high-fat diet (HFD) in which lipids are enriched at the expense of dietary fibers. Such nutritional challenge alters glucose homeostasis as well as intestinal immunity. Here, we observed that short-term HFD induced dysbiosis, glucose intolerance and decreased intestinal RORγt+ CD4 T cells, including peripherally-induced Tregs and IL17-producing (Th17) T cells. However, dietary fiber supplementation of HFD-fed animals was sufficient to maintain RORγt+ CD4 T cell subsets and microbial species known to induce them, alongside having a beneficial impact on glucose tolerance. Dietary fiber-mediated normalization of Th17 cells and amelioration of glucose handling required the cDC2 dendritic cell subset in HFD-fed animals, while IL-17 neutralization limited fibers impact on glucose tolerance. Overall, we uncover a novel and pivotal role of cDC2 in the control of the immune and metabolic effects of dietary fibers in the context of HFD feeding.