Background: The correct identification of differentially abundant microbial taxa between experimental conditions is a methodological and computational challenge. Recent work has produced methods to deal with the high sparsity and compositionality characteristic of microbiome data, but independent benchmarks comparing these to alternatives developed for RNA-seq data analysis are lacking. Results: We compare methods developed for single-cell and bulk RNA-seq, and specifically for microbiome data, in terms of suitability of distributional assumptions, ability to control false discoveries, concordance, power, and correct identification of differentially abundant genera. We benchmark these methods using 100 manually curated datasets from 16S and whole metagenome shotgun sequencing. Conclusions: The multivariate and compositional methods developed specifically for microbiome analysis did not outperform univariate methods developed for differential expression analysis of RNA-seq data. We recommend a careful exploratory data analysis prior to application of any inferential model and we present a framework to help scientists make an informed choice of analysis methods in a dataset-specific manner.

In recent years, the concept of “microbial terroir” has been introduced in the frame of the more renowned notion of “vitivinicultural terroir,’ since several studies demonstrated that wine characteristics are related to regional microbial community compositions. Most of the existing research focused on grape berries microbiota, since it can directly impact wine quality. In this work we studied, for the first time through next-generation sequencing, the epiphytic bacterial community of vine bark and its relationships with grape microbiota. The study was carried out in two Italian wine appellations (situated in different regions) to explore the impact of biogeography, and the influence of two agronomical practices (biodynamic and conventional) was evaluated as well. Overall, our results show that grapevine bark harbors a rich epiphytic microbiota and displays a higher microbial biodiversity than grape berry. Moreover, this study suggests that geographic and anthropogenic factors impact both bark and grape bacteriomes, but to a different extent. The evidence of a “microbial terroir” seems to be even more marked in bark than in berries, possibly due to its permanence over time and to its physical proximity with soil. The importance of vine trunk bark, as potential source of inoculum for grapes and as interesting bacterial diversity habitat, is evidenced. This opens new fields of investigation, not only for researchers that aim at describing this little-known habitat within the vineyard, but also for stakeholders from the wine industry that want to understand the roles of microorganisms on the entire winemaking process, from vineyard to cellar.

Variations in gut microbiota might impact metabolism leading to body weight excess. We assessed the impact of a probiotic supplementation in pediatric obesity on weight, metabolic alterations, selected gut microbial groups, and functionality. Cross-over, double-blind, randomized control trial (BIFI-OBESE trial; NCT03261466). 101 youths (6-18 years, Tanner stage ≥2) with obesity and insulin-resistance on diet were randomized to 2 × 109 CFU/AFU/day of Bifidobacterium breve BR03 (DSM 16604) and B. breve B632 (DSM 24706) (51) or placebo (50) for 8 weeks with a 4-weeks wash-out period. All subjects (M/F 54/47) completed the first 8 weeks, and 82 (M/F 43/39) the last part without adverse events. Mixed-effects models revealed a carry-over effect on many variables in the entire study, narrowing the analysis to the first 8 weeks before the wash-out periods. All subjects improved metabolic parameters, and decreased weight and Escherichia coli counts. Probiotics improved insulin sensitivity at fasting (QUICKI, 0.013 CI95%0.0-0.03) and during OGTT (ISI, 0.654 CI95%-0.11-1.41). Cytokines, GLP1, and target microbial counts did not vary. Of 25 SCFAs, acetic acid and acetic acid pentyl-ester relative abundance remained stable in the probiotics, while increased in the placebo (p < 0.02). A signature of five butanoic esters identified three clusters, one of them had better glucose responses during probiotics. An 8 weeks treatment with B. breve BR03 and B632 had beneficial effects on insulin sensitivity in youths with obesity. Microbiota functionality could influence metabolic answers to probiotics. Long-term studies to confirm and enrich our findings are justified. Tailored probiotic treatments could be an additional strategy for obesity. NCT03261466.

Propionate is a short-chain fatty acid (SCFA) produced by gut microbiota through the fermentation of dietary fibers. Among the SCFAs, butyrate stands out and has been extensively studied for its beneficial effects; however, propionate has received less attention despite its relevant roles in immune modulation, metabolism, and mucosal homeostasis. This narrative review focuses on propionate’s effects on metabolism, inflammation, microbiota, and gastrointestinal diseases. Propionate acts as a signalling molecule through FFAR2/FFAR3 receptors and modulates immunity, energy metabolism, and gut–brain communication. It has beneficial effects in metabolic disorders, inflammatory bowel disease (IBD), and alcohol-related liver disease (ALD). However, excessive accumulation is linked to neurotoxicity, autism spectrum disorder (ASD), and mitochondrial dysfunction. Its effects are dose-dependent and tissue-specific, with both protective and harmful potentials depending on the context. Propionate use requires a personalized approach, considering the pathological context, host microbiota composition, and appropriate dosage to avoid adverse effects.

Autism spectrum disorders (ASDs) represent a diagnostic challenge with a still partially uncertain etiology, in which genetic and environmental factors have now been assessed. Among the hypotheses underlying the involvement of biological and environmental factors, the gut–brain axis is of particular interest in autism spectrum disorders. Several studies have highlighted the related incidence of particular gastrointestinal symptoms (GISs) in children suffering from ASDs. Probiotics have shown success in treating several gastrointestinal dysbiotic disorders; therefore, it is plausible to investigate whether they can alleviate behavioral symptoms as well. On these bases, a randomized double-blind crossover study with a placebo was conducted, evaluating the effects of a mixture of probiotics in a group of 61 subjects aged between 24 months and 16 years old with a diagnosis of ASD. Behavioral evaluation was performed through the administration of a questionnaire including a Parenting Stress Index (PSI) test and the Vineland Adaptive Behavior Scale (VABS). The Psycho-Educational Profile and the Autism Spectrum Rating Scale (ASRS) were also evaluated. Microbial composition analyses of fecal samples of the two groups was also performed. The study showed significant improvements in GISs, communication skills, maladaptive behaviors, and perceived parental stress level after the administration of probiotics. Microbiome alpha diversity was comparable between treatment arms and no significant differences were found, although beta diversity results were significantly different in the treatment group between T0 and T1 time points. Streptococcus thermophilus, Bifidobacterium longum, Limosilactobacillus fermentum, and Ligilactobacillus salivarius species were identified as some of the most discriminant taxa positively associated with T1 samples. This preliminary study corroborates the relationship between intestinal microbiota and ASD recently described in the literature.

Immune mechanisms contribute to the neuropathology of Alzheimer’s disease (AD) but the role of adaptive immune cells is unclear. Here we show that the brain CD8⁺ T cell compartment is dysregulated in AD patients and in the 3xTg-AD mouse model, accumulating activated CD103^– tissue-resident memory T cells that produce large amounts of granzyme K (GrK). These CD103^–CD8⁺ T cells originate from the circulation and migrate into the brain using LFA-1 integrin. Ablation of brain CD103^–CD8⁺ T cells in 3xTg-AD mice ameliorates cognitive decline and reduces neuropathology. GrK induces neuronal dysfunction and tau hyperphosphorylation in human and mouse cells via protease-activated receptor-1 (PAR-1), which is expressed at higher levels in the AD brain, revealing a key immune-mediated neurotoxic axis. We conclude that communication between CD8⁺ T cells and the nervous system is altered in AD, paving the way for therapies targeting T cell-dependent neurotoxic inflammation.