The gut microbiome plays a pivotal role in overall host health, yet the extent at which diet-derived microbial metabolites affect neurodevelopment and inflammation remains unclear. Here, we employed the robogut bioreactor system seeded with faecal samples from two healthy paediatric donors to generate microbial communities exposed to four different diets: low-fibre Western, high-fibre Western, Mediterranean, and Yanomami, as well as three fibre supplements: fruit and vegetable fibre, cereal fibre, and resistant starch fibre. Metabolites produced by these microbial communities were isolated and applied to germ-free zebrafish (Danio rerio) embryos to assess their effects on neurodevelopment and inflammatory gene expression under basal and stress-induced conditions. Despite minimal changes in microbial composition across diets and fibre sources, significant differences in short-chain fatty acid concentrations were observed. , Under basal conditions, metabolite treatments had limited effects on the expression of neural and inflammatory genes. Under stress conditions, metabolites from any diet mitigated stress-induced bdnf expression, suggesting a possible modulatory role of microbial metabolites on stress responses. Overall, these findings highlight the resilience of microbial communities to dietary changes and underscore the importance of microbial metabolite output and its donor-specific nature in influencing host neurodevelopment and immune responses.

This report summarizes key takeaways from the 11th International Yakult Symposium held in Amsterdam, the Netherlands, in October 2024. It provides an overview of insights obtained by the latest basic and clinical research, meta-analyses, and omics research, underscoring the relevance of the exposome, the outer and inner factors to which our bodies are exposed throughout our entire lifespan, in shaping the microbiota. The symposium addressed external factors such as diet (including probiotics and novel fermented foods), additives, pharmacologic agents, and physical environment, as well as the internal crosstalk between tissue or organ-specific microbial communities and their interactions with immune mediators, metabolic and neuroendocrine hormones, and their receptors. Collectively, the data presented during the symposium reinforced the understanding that health and disease are the result of the (im)balance of a tightly interconnected network rather than isolated axes. This was illustrated using examples of inflammatory and infectious diseases of the brain, mouth, gynaecologic tract, lungs, as well as of metabolic and mental states. Finally, a roundtable discussion on the current state of clinical trials in nutrition, including challenges and solutions was featured. The conclusion indicated that there is room for new developments and that hurdles need to be overcome, requiring continued collaboration across scientific disciplines.

Fermented dairy foods offer potential to improve gastrointestinal symptoms due to their functional characteristics (e.g., presence of potentially health-promoting microorganisms, and/or bioactives), which may improve quality of life (QoL). This study examined the effect of a Lactobacillus delbrueckii subsp. bulgaricus fermented skimmed milk powder (FSMP) on gastrointestinal health in healthy individuals with mild-to-moderate gastrointestinal symptoms. Subjects received 20 g/day of either the FSMP, skimmed milk powder (SMP), or maltodextrin for 8 weeks. QoL, faecal calprotectin, gut transit time, gas evacuations, stool consistency, dietary intake, and anthropometry were all assessed. Eighty-four participants (62% female, 34.9 ± 5.9 years) completed the trial. SMP improved anxiety (P = 0.015), discomfort (P = 0.002), and global (P = 0.010) domain scores vs. maltodextrin. Similarly, SMP improved discomfort (P = 0.007) and global (P = 0.023) domain score relative to FSMP. No other differences between groups post-intervention were observed (P > 0.05). Sub-analyses indicated those with more severe symptoms at baseline had more normal stool consistency (P = 0.016) and fewer gas evacuations (P = 0.008) in response to FSMP relative to maltodextrin. Overall, this exploratory analysis found an L. delbrueckii subsp. bulgaricus FSMP had limited effects on gastrointestinal health in this cohort.

Cellobiose, a β-(1 → 4)-linked disaccharide indigestible by humans, is a novel candidate prebiotic. Evidence from controlled human trials on its effects on the gut microbiota and metabolites remains limited. We conducted an exploratory randomised, double-blind, placebo-controlled trial in 37 healthy adults. Participants were allocated to three arms for 4 weeks, received 5 g/day and 10 g/day for cellobiose, oligofructose P95, or maltodextrin placebo. The primary endpoint was change in absolute abundance of Bifidobacterium and Lactobacillus (measured by 16S rRNA gene sequencing). Secondary endpoints included other taxa, diversity, faecal short-chain fatty acids (SCFAs) measured by gas chromatography–mass spectrometry and gastrointestinal (GI) tolerability. Cellobiose did not significantly change Bifidobacterium or Lactobacillus versus baseline or placebo (P > 0.05). Oligofructose P95 induced a borderline increase in Bifidobacterium (P = 0.049). Overall community composition remained unchanged. However, network analyses under cellobiose revealed tighter positive correlations among key genera. Faecal SCFA levels were not altered. GI symptom rates were low and similar across all arms. Cellobiose, at doses up to 10 g/day, is safe and well tolerated but did not enrich classic beneficial taxa. The findings suggest cellobiose drives subtle community shifts towards butyrate-producing bacteria.

Studies characterising the immunoglobulin (Ig)-bound microbiota apply varying methodologies, making comparisons difficult. This scoping review synthesised evidence on Ig–microbiota binding patterns in maternal and infant contexts, identified recurrent Ig-bound and -unbound bacteria across studies, and highlighted knowledge gaps for further study. Nine articles investigating Ig–microbiota binding patterns in stool or breastmilk samples in mothers or infants were included. Ig–microbiota associations were influenced by sample type, Ig-subclass, genetics, and diet. The most important antibody was IgA, with partial functional redundancy with IgM, while IgG appeared more selective for pathobionts. Ig-bound taxa in early life included important commensals and pathobionts, with high levels of individuality. Ig–microbiota associations shifted with microbiome maturation, environmental and host factors, resembling adults at around 2 years of age. Transfer of Ig-bound Bifidobacterium through breastmilk may contribute to vertical transmission from mother to infant. Ig–microbiota associations also differed between health and disease states, beyond the overall microbiota. Results were limited by study numbers and a lack of methodological consistency. We propose the standardised term “Ig-Seq” in referring to the technique to study Ig–microbiota binding patterns, and suggest standardisation of laboratory protocols, bioinformatic pipelines, and statistical analyses to improve consistency in Ig-Seq.

The aim of this study is to describe the development and implementation of a novel Readiness to Change Nutritional Habits (RCNH) survey for use along with dietary assessment and gut microbiome profiling in a proof-of-concept study in individuals with early Alzheimer’s disease dementia (eAD), mild cognitive impairment (MCI), and healthy controls (HC). Overall, this methods paper contributes to emerging research examining how behavioural readiness for change can be integrated with dietary assessment and gut microbiome profiling to better understand the microbiome’s influence on the nervous system. This is a sub-study embedded within a multi-prong proof-of-concept, observational study mapping the gut microbiome in 45 participants (15 HC, 15 MCI, 15 eAD) at baseline, 3 months, and 6 months. The parent study collects gut microbiome profiles, dietary patterns, and cognitive assessments. The sub-study develops and administers the 32-item RCNH survey to characterize participants’ readiness to adopt nutritional change. This manuscript reports the RCNH survey, its development process, the sub-study protocol including data collection procedures, and planned exploratory analyses. This protocol presents a novel intervention to assess the gut microbiome, individual dietary patterns, and readiness to make lifestyle changes related to diet.

In this study, we analysed differences in the infant gut microbiome between breastfed and formula-fed infants using novel machine learning techniques. Breast milk, rich in bioactive agents, supports microbiota composition and immune development, while formulas aim to replicate its nutritional profile. We applied a methodology combining the DADA2 pipeline for 16S rRNA sequencing with the Recursive Ensemble Feature Selection (REFS) algorithm for biomarker discovery. We analysed three publicly available 16S rRNA datasets: PRJNA633365 (70 stool samples from China), PRJDB7295 (40 stool samples from the Philippines), and PRJNA562650 (40 stool samples from China). The discovery dataset (PRJNA633365) revealed 16 significant taxa out of 1,227, validated across the other two datasets. Next, we compared REFS performance with another feature selection algorithm, SelectKBest. Finally, we conducted a literature review to explore links between identified taxa and medical conditions. Additionally, we used MicrobiomeAnalyst to examine associations with diseases, diet, and lifestyle. Our results show differences in the bacterial composition between breastfed and formula-fed infants, and these findings were validated in two independent datasets. Future research should explore the functional roles of these taxa and consider regional and dietary variability to enhance understanding of microbiome dynamics and long-term health outcomes.

B. infantis abundance in the infant gut may be associated with growth and health outcomes. However, these relationships have not been widely studied in settings where B. infantis is a dominant early-life commensal and growth faltering is prevalent. Here, we estimated associations between neonatal B. infantis abundance and anthropometric outcomes up to 6 months of age in generally healthy infants in Dhaka, Bangladesh; diarrhoea and hospitalizations (at 1–2 and 6 months) were secondary morbidity outcomes. B. infantis stool absolute abundance was quantified by qPCR; for each infant, the primary exposure was mean abundance (0–28 days). Length-for-age, weight-for-age, and weight-for-length z-scores were derived at birth, 2, 3, and 6 months. Neonatal B. infantis abundance had a bimodal distribution, with 63% of infants having detectable B. infantis by 28 days of age. Anthropometric z-score distributions were shifted down, with means below zero. Neonatal B. infantis abundance was not associated with any anthropometric outcome at 2, 3, or 6 months of age (n = 830), or with the risks of diarrhoea or hospitalizations. The lack of association of neonatal B. infantis abundance with growth outcomes suggests that promoting early B. infantis colonization is unlikely to improve growth in populations with postnatal faltering.

The microbiota–gut–brain axis (MGBA) has garnered considerable attention for its role in health, disease, and higher psychological processes. One area of particular importance is the relationship between the MGBA and stress. Although numerous animal models are suitable for research on stress, the number suitable for research on the impact of social stressors with translatability to humans is limited. The prairie vole is regarded as an ideal organism for probing the impact of social stress, as these animals not only exhibit social behaviours rare in mammals but also lack many drawbacks that come with using non-human primates. Moreover, the neurophysiological basis of their social behaviours is well characterized, and numerous studies have examined the impact of social stress, particularly social isolation, on these animals. However, only a limited number of studies have examined the prairie vole gastrointestinal system, intestinal microbiome, or MGBA. Consequently, this leaves ample opportunity for future research. In this review article, we summarize basic aspects of prairie vole ecology, behaviour, and neurophysiology, then review the limited but valuable body of research examining the gastrointestinal system and microbiome of prairie voles. Additionally, we note potential challenges and opportunities for future MGBA research utilizing prairie voles.

Researchers have studied gut microbiota changes following bariatric surgery (BS), but not gut diversity and function in patients who fail to reduce weight. Stool samples were collected from three groups of women: 15 women who did not lose weight after BS (“Yes” group), 9 overweight women without surgery, and 8 slim women (“No” group). 16S ribosomal RNA gene sequencing and PICRUSt2 were used for the analysis. The surgery and control groups had equal alpha and beta diversity, perhaps due to the high proportion of overweight participants (n = 24). All groupings were dominated by Bacteroidota and Bacillota. Barnesiellaceae decreased with BS, although Streptococcaceae remained frequent in overweight people. The iron supplementation group had High abundance of Atopobiaceae and Prevotellaceae. Barnesiellaceae abundance was considerably lower in both surgical groups (with and without iron supplementation) than in the no-iron and no-surgery groups. The ornithine degradation and haem biosynthesis routes use different metabolites than the glycine super system. Finally, the “Yes” group significantly upregulated PWY0–1241, PWY-5177, and PWY-5855 signaling pathways. In conclusion, gut bacteria and metabolic functions may predict weight loss after surgery better than diversity markers. The requirement for orthogonal validation assays is suggested by pathway analysis outperforming diversity metrics.

Oral administration of omega-3 polyunsaturated fatty acids (PUFAs) to rodents and humans is associated with an increase in gut bacteria that are predicted to synthesise short-chain fatty acids (SCFAs). We tested the hypothesis that physiological levels of omega-3 PUFAs in the distal intestinal lumen (1–50 μg/mL) are associated with increased SCFA synthesis in an in vitro fermentation model using faecal slurry from 10 healthy participants (mean age 30 years), with and without exogenous dietary fibres. SCFAs were measured by gas chromatography-flame ionisation detection (n = 10), and changes in bacterial composition were analysed by shotgun metagenomic sequencing (n = 6). In the presence of omega-3 PUFAs, there was a mean 9.3% (no inulin; P = 0.03) and 19.3% (+ 0.01 mg/mL inulin; P = 0.01) increase in total SCFA concentration at 24 h compared with paired control fermentations. Omega-3 PUFAs had a limited effect on the fermentation model microbiome in the absence of inulin. However, omega-3 PUFAs (50 μg/mL) were associated with increased abundance of Bifidobacteriaceae compared with paired control fermentations, if inulin (0.01 mg/mL) was present. Prebiotic activity of omega-3 PUFAs drives SCFA synthesis in an in vitro colonic fermentation model and is augmented by the soluble fibre inulin.