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.