Objective. Although oral methotrexate (MTX) remains the anchor drug for rheumatoid arthritis (RA), up to 50% of patients do not achieve a clinically adequate outcome. In addition, there is a lack of prognostic tools for treatment response prior to drug initiation. This study was undertaken to investigate whether interindividual differences in the human gut microbiome can aid in the prediction of MTX efficacy in new-onset RA.Methods. We performed 16S ribosomal RNA gene and shotgun metagenomic sequencing on the baseline gut microbiomes of drug-naive patients with new-onset RA (n = 26). Results were validated in an additional independent cohort (n = 21). To gain insight into potential microbial mechanisms, we conducted ex vivo experiments coupled with metabolomics analysis to evaluate the association between microbiome-driven MTX depletion and clinical response.Results. Our analysis revealed significant associations of the abundance of gut bacterial taxa and their genes with future clinical response (q < 0.05), including orthologs related to purine and MTX metabolism. Machine learning techniques were applied to the metagenomic data, resulting in a microbiome-based model that predicted lack of response to MTX in an independent group of patients. Finally, MTX levels remaining after ex vivo incubation with distal gut samples from pretreatment RA patients significantly correlated with the magnitude of future clinical response, suggesting a possible direct effect of the gut microbiome on MTX metabolism and treatment outcomes.Conclusion. Taken together, these findings are the first step toward predicting lack of response to oral MTX in patients with new-onset RA and support the value of the gut microbiome as a possible prognostic tool and as a potential target in RA therapeutics.

Conjugation has classically been considered the main mechanism driving plasmid transfer in nature. Yet bacteria frequently carry so-called non-transmissible plasmids, raising questions about how these plasmids spread. Interestingly, the size of many mobilisable and non-transmissible plasmids coincides with the average size of phages (~40 kb) or that of a family of pathogenicity islands, the phage-inducible chromosomal islands (PICIs, ~11 kb). Here, we show that phages and PICIs from Staphylococcus aureus can mediate intra- and inter-species plasmid transfer via generalised transduction, potentially contributing to non-transmissible plasmid spread in nature. Further, staphylococcal PICIs enhance plasmid packaging efficiency, and phages and PICIs exert selective pressures on plasmids via the physical capacity of their capsids, explaining the bimodal size distribution observed for non-conjugative plasmids. Our results highlight that transducing agents (phages, PICIs) have important roles in bacterial plasmid evolution and, potentially, in antimicrobial resistance transmission.

Multidrug-resistant organisms (MDRO) are a major threat to public health. MDRO infections, including those caused by vancomycin-resistant Enterococcus (VRE), frequently begin by colonization of the intestinal tract, a crucial step that is impaired by the intestinal microbiota. However, the specific members of the microbiota that suppress MDRO colonization and the mechanisms of such protection are largely unknown. Here, using metagenomics and mouse models that mimic the patients’ exposure to antibiotics, we identified commensal bacteria associated with protection against VRE colonization. We further found a consortium of five strains that was sufficient to restrict VRE gut colonization in antibiotic treated mice. Transcriptomics in combination with targeted metabolomics and in vivo assays indicated that the bacterial consortium inhibits VRE growth through nutrient depletion, specifically by reducing the levels of fructose, a carbohydrate that boosts VRE growth in vivo. Finally, in vivo RNA-seq analysis of each strain of the consortium in combination with ex vivo and in vivo assays demonstrated that a single bacterium (Olsenella sp.) could recapitulate the effect of the consortium. Our results indicate that nutrient depletion by specific commensals can reduce VRE intestinal colonization, which represents a novel non-antibiotic based strategy to prevent infections caused by this multidrug-resistant organism.

Purpose of review Gluten is a complex mixture of highly immunogenic glutamine- and proline-rich proteins found in some cereals. In celiac disease (CeD), gluten triggers an autoimmune response due to its interaction with the human leukocyte antigen heterodimers that confer the genetic risk. The involvement of gluten in other disorders has also been investigated, but its role beyond CeD is still unclear. Here, we review the most recent evidence of the involvement of gluten in diseases and the opportunities of manipulating the gut microbiota to treat or prevent gluten-related conditions. Recent findings Most of the new studies have been conducted in the context of CeD, where important evidence has been gained on associations between the gut microbiota, genotype, and environmental factors such as breastfeeding and antibiotics. The role of the microbiota has been investigated in several prospective, observational and interventional studies with probiotics, which together showed that the gut microbiota could be targeted to ameliorate and aid in the prevention of CeD development. Summary Several studies have evidenced how genetic and environmental factors influence the gut microbiome with consequences in CeD. These findings could inspire the development of microbiota modulation strategies to support the prevention or treatment of CeD.

Tracking the journey of inulin, a soluble dietary fibre, reveals its fate and transformation by the gut microbiota to alleviate liver disease in mice.Dietary fibres are complex carbohydrates that nourish the gut microbiota and help shape host-microbe symbiosis. They cannot be fully degraded by human digestive enzymes, ensuring their availability for anaerobic fermentative bacteria in the large intestine. In return, commensal bacteria can produce beneficial fibre-derived metabolites that help regulate intestinal transit and reduce the risk of metabolic disease. However, the mechanisms that underlie this exchange of favours are likely influenced by the specific fibre type and the responsiveness of the host's gut microbiota to these dietary components. Indeed, the extent to which the gut microbiota contributes to the health benefits of dietary fibres is under debate, largely due to our limited knowledge of the mediating factors and mechanisms. Some human intervention trials with dietary fibre report improvements, for example, in type 2 diabetes. These are linked to increases in fibre-fermenting bacteria 1 . However, others report improvements in the host metabolic phenotype (for example, reductions in body weight and systemic inflammation) without induction of major changes to the gut microbiome, suggesting that the microbiota does not mediate the observed beneficial metabolic effects 2 .Writing in Nature Microbiology, Wei et al. report a mechanism by which inulin, a soluble fibre fermented by our gut microbiota, ameliorates non-alcoholic steatohepatitis (NASH). NASH is a liver disease that is characterized by inflammation and fat accumulation, and it is frequently associated with obesity and type 2 diabetes 3 . Gut microbiome alterations contribute to NASH. Microbiome-modulating strategies, such as inulin intake, could thus help prevent disease progression 3,4 . The authors employed an elegant strategy that combined stable-isotope probing, shotgun metagenomics and metabolomics to reveal that the gut commensal Parabacteroides distasonis uses inulin to produce pentadecanoic acid -an odd-chain saturated fatty acid that alleviates NASH in different mouse models (Fig. 1).The authors first compared the effects of two different fibre types in their mouse models of NASH -a soluble fibre (inulin) and an insoluble fibre (cellulose) -which are used differently by gut microbes. They found that inulin was more effective than cellulose in protecting against NASH, specifically through the attenuation of hepatic steatosis and fibrosis and the dampening of inflammation and oxidative stress. To identify the best inulin consumers in the gut microbiota and those responsible for these benefits, the authors tracked the incorporation of 13 C-labelled inulin into bacterial DNA using metagenome sequencing. The bulk of the 13 C-labelled species were Bacteroides (80%) and Parabacteroides (10%). Consistent with these findings, Bacteroides levels are frequently increased in response to dietary fibre in humans, which Check for updates