This study explored the effects of different human milk oligosaccharides (HMOs), solely and in combination, on gut microbiota composition and metabolic activity (organic acid production), using anaerobic in vitro batch culture fermenters. The aim was to compare prebiotic effects of HMOs (2’FL, 3’FL, 3’SL, 6’SL, LNT, LNnT, and 1:1 ratio mixes of 2’FL/3’SL and 3’SL/LNT) in faecal samples from irritable bowel syndrome (IBS) donors and healthy controls, and to determine the best-performing HMO in IBS. Fluorescent in situ hybridisation coupled with flow cytometry was utilised to study microbiota changes in major colonic genera, and organic acid production was assessed by gas chromatography. IBS donors had different starting microbial profiles compared to healthy controls and lower levels of organic acids. In response to HMOs, there were alterations in both the control and IBS faecal microbiomes. In IBS donor fermenters, Bifidobacterium, Faecalibacterium, total bacterial numbers, and organic acid production significantly increased post-HMO intervention. When comparing the effect of HMO interventions on the microbiota and organic acid production, a mix of 3’SL/LNT HMOs may be the most promising intervention for IBS patients.

There has been a growing recognition of the significant role played by the human gut microbiota in altering the bioavailability as well as the pharmacokinetic and pharmacodynamic aspects of orally ingested xenobiotic and biotic molecules. The determination of species-specific contributions to the metabolism of biotic and xenobiotic molecules has the potential to aid in the development of new therapeutic and nutraceutical molecules that can modulate human gut microbiota. Here we present “GutBugDB,” an open-access digital repository that provides information on potential gut microbiome-mediated biotransformation of biotic and xenobiotic molecules using the predictions from the GutBug tool. This database is constructed using metabolic proteins from 690 gut bacterial genomes and 363,872 protein enzymes assigned with their EC numbers (with representative Expasy ID and domains present). It provides information on gut microbiome enzyme-mediated metabolic biotransformation for 1439 FDA-approved drugs and nutraceuticals. GutBugDB is publicly available at https://metabiosys.iiserb.ac.in/gutbugdb/.

Oral supplementation with probiotics, prebiotics, and synbiotics is a novel potential complementary therapy for addressing overweight and obesity through gut microbiota modulation. This systematic review provides a comprehensive summary of the existing evidence to guide future research. Literature searches were conducted in four databases to identify human trials published until May 2024 that examined the impact of probiotic, prebiotic, or synbiotic interventions on faecal microbiota composition changes in overweight and obese participants from Latin American and Caribbean populations (LACPs). Of the 13,090 identified records, five randomised controlled trials (RCTs) from Brazil, Mexico, and Chile met the inclusion criteria for this review. The included RCTs evaluated different forms of therapies over short-term interventions (6 or 8 weeks), with sample sizes ranging from 21 to 39 participants across the studies. Variations in the reported outcomes were observed due to differences in supplement formulation, dosage, population characteristics, and methodological heterogeneity. The findings indicate that the available data are inadequate to establish definitive conclusions regarding the impact of biotic treatments on gut microbiota profiles in LACP. Further research with larger sample sizes and precise microbiota analysis is required to elucidate the implications of dietary interventions on gut microbiota in obesity and related disorders.

The coronavirus disease 2019 (COVID-19) pandemic has caused health issues worldwide. Studies have suggested that modulation of the gut microbiota could attenuate the severity of COVID-19 symptoms. In light of this, we explored the effects of the prebiotic dietary fibre partially hydrolyzed guar gum (PHGG) on SARS-CoV-2 infection in a Syrian hamster model, hypothesizing that modulation of the gut microbiome and intestinal metabolites through PHGG administration would improve COVID-19 disease outcomes. Eight hamsters each were assigned to the PHGG administration and control groups. The PHGG group was given a diet supplemented with 5% PHGG for two weeks. Consequently, PHGG improved the host survival rate to 100% compared to 25% of the control group (P = 0.003) and attenuated morbid weight loss. Another non-infected set of hamsters was used for the analysis of the gut microbiome composition with 16S rRNA amplicon sequencing, serum, and faecal metabolites with GC–MS and LC–MS. PHGG altered the gut microbiome composition and increased the relative abundances of Ileibacterium, Bifidobacterium, and Prevotella. Furthermore, it elevated the concentrations of faecal valeric acid, propionic acid, ursodeoxycholic acid, and serum deoxycholic acid. Taken together, our data suggest that the prebiotic PHGG modulates gut metabolites and has the potential to reduce COVID-19 morbidity.