There is growing optimism regarding the potential therapeutic and preventive benefits of regulating intestinal microbiota for various diseases. Diet is one of the most straightforward and safest methods for modulating the intestinal microbiota; however, considerable individual differences have been observed in the microbiota response to dietary interventions. These individual differences pose substantial challenges in application, which are primarily attributed to variations in the commensal flora and bacterial competition for nutrients. Our previous research indicated that the microscopic localization of bacteria provides valuable insights into the mechanisms by which specific intestinal bacterial species acquire nutrients within a competitive gut environment. Furthermore, our analysis revealed that the combination of bifidobacterial species and the nutrient source found in the localization analysis determined individual differences in microbiota response. These findings suggest that bacterial colonization facilitates the efficient, preferential, and presumably exclusive utilization of solid nutrient sources in the human gut. Moreover, the impact of a single nutrient source on the gut and human body may vary depending on the presence or absence of the primary species colonizing that source. In this review, we examined the micrometer-scale localization of intestinal bacteria and individual variability in microbiota responses to diet, drawing upon the results of our previous studies.

Lactiplantibacillus plantarum and Lactiplantibacillus pentosus are the commonly found dominant species in post-fermented Japanese tea. The dominant species of lactic acid bacteria (LAB) depends on the production area, regardless of the production method. However, the selection mechanism of these bacteria remains unknown. Therefore, we investigated the mechanism by which these LAB species are selected. We investigated the effects of pH and catechins on the growth of L. plantarum and L. pentosus isolated from two types of post-fermented Japanese teas. When the pH of the medium was adjusted with hydrochloric acid, the strains derived from Ishizuchi-kurocha grew at pH 4 to 10, whereas the strains derived from Awa-bancha grew at pH 3 to 10. In contrast, when the pH was adjusted using lactic acid, no growth was observed at pH 4. The pH of the fermented fluid of Ishizuchi-kurocha was approximately 4, suggesting that the growth of the LAB in Ishizuchi-kurocha was inhibited by the accumulation of lactic acid. Furthermore, when a mixture of green tea-derived catechins containing epicatechin, epigallocatechin, epicatechin gallate, and epigallocatechin gallate was added to the culture medium at a concentration of 1.0 mg/mL, Staphylococcus aureus growth was inhibited. However, the effect on L. plantarum or L. pentosus growth was negligible. Furthermore, when the catechins in the medium were analyzed using high-performance liquid chromatography after 24 hr incubation with LAB, the peak intensities of catechins, particularly catechin gallate, were decreased, and an unknown peak was observed. These results suggest that L. plantarum and L. pentosus metabolize catechins during tea leaf fermentation. During the fermentation of Ishizuchi-kurocha and Awa-bancha, at least, the catechins in them and decrease in pH due to mainly lactic acid accumulation are factors involved in LAB selection.

Humanized mouse models are widely used to investigate host–microbiota interactions, yet the extent to which host background contributes to engraftment fidelity remains incompletely defined. In this study, we transplanted fecal microbiota from healthy human donors into NCG and SGM3 mice and characterized engraftment using 16S rRNA sequencing. Both models exhibited reduced diversity relative to donors, but their colonization trajectories diverged. NCG recipients appeared closer to donors in β-diversity space, a pattern largely associated with the expansion of a limited set of opportunistic Proteobacteria such as Escherichia–Shigella and Citrobacter. In contrast, SGM3 mice displayed modestly higher α-diversity and retained a broader set of donor-associated genera, with selective enrichment of Bacillus, yet exhibited greater predicted functional divergence, with reductions in pathways related to ABC transport and carbohydrate metabolism. Several strictly anaerobic commensals, including Faecalibacterium, failed to colonize in either genotype. Collectively, these findings suggest that host genotype is associated with selective colonization of human fecal microbiota and support the utility of integrating compositional and functional criteria when selecting experimental models for translational microbiome research.

Urinary indoxyl sulfate (IS), a gut microbiota-derived uremic toxin, is associated with the adult gut microbiota and is elevated in children with autism spectrum disorder. However, its age-related trajectory and association with microbiota in healthy children remain uncharacterized. Therefore, we aimed to elucidate age-related changes in urinary IS in healthy children and to investigate the potential utility of urinary IS as a surrogate marker for their gut microbiota. We measured urinary IS/creatinine (Cr) ratios and analyzed the fecal gut microbiota composition (16S rRNA gene sequencing) in 102 healthy Japanese children aged 5 months to 12 years. Associations were assessed using Spearman’s correlation. An empirical age-adjustment model (inverse proportional) was developed to derive an age-adjusted IS/Cr ratio (actual/predicted), thereby removing the strong age dependence before re-evaluating correlations with gut microbiota. The unadjusted IS/Cr ratio showed a strong negative correlation with age (rs=−0.47, p<0.001) and declined markedly during early childhood, stabilizing at approximately 5 years. Weak correlations with microbiota metrics were observed before adjustment; however, the age-adjusted IS/Cr ratio showed no correlation with age (rs=−0.03, p=0.768). Notably, age adjustment revealed significant positive correlations between the IS/Cr ratio and the phylum Bacteroidota (rs=0.26, p=0.008) and strengthened the correlation with the genus Bacteroides (rs=0.31, p=0.002), associations that were not apparent before adjustment. Correcting for this age-dependent variation is crucial, after which the IS/Cr ratio can serve as a potential non-invasive surrogate marker reflecting the abundance of Bacteroidota, particularly the genus Bacteroides, in the pediatric gut microbiota.

This study developed a synbiotic rice yogurt cake with a medium glycemic index by combining resistant starch-enhanced rice with Lactobacillus acidophilus. The effects of substrate concentration (20–40%), pullulanase enzyme activity (20–40 U/g), and hydrolysis time (4–8 hr) on resistant starch content were investigated. At a substrate concentration of 30%, an enzyme activity of 30 U/g, and a hydrolysis time of 6 hr, the optimal resistant starch content was 14.54 ± 0.96%. After being treated to enhance its resistant starch content, IR504 rice was mixed with milk and processed to produce rice milk. The rice milk was fermented for 12 hr at 37°C with a 3% inoculum ratio, yielding the highest L. acidophilus count of 5.62 × 10⁷ CFU/g. After freeze-drying, the synbiotic rice yogurt cake contained 3.8 × 10⁷ CFU/g L. acidophilus and 3.55 g/100 g resistant starch. Nutritional analysis showed 82.4 g carbohydrates, 6.78 g lipids, 8.90 g proteins, and 1.05% moisture per 100 g. This product achieved a lower estimated glycemic index of 69.32 ± 0.534 compared with non-resistant starch (77.74 ± 0.369). Microbiological tests confirmed safety standards were met, with undetectable Enterobacteriaceae (<10 CFU/g), Listeria monocytogenes (undetectable/25 g), and undetectable total mold. The predicted shelf life of the synbiotic rice yogurt cake was approximately 198 days under typical storage conditions at 30°C and L. acidophilus count of 4.8 × 10⁶ CFU/g. Therefore, the synbiotic rice yogurt cake can be used as a product supporting glycemic control while simultaneously providing a substrate for beneficial gut bacteria.

Lactococcus cremoris subsp. cremoris FC (L. cremoris FC) improves bowel movement; however, its associations with the intestinal microbiota remain unclear. To address this gap, this post hoc analysis of a four-week, placebo-controlled, parallel-group trial evaluates the associations between L. cremoris FC intake and gut microbiota profiles. We analyzed fecal samples from 83 healthy Japanese adults with mild constipation who received either placebo capsules containing corn starch (n=20) or L. cremoris FC capsules (50, 75, or 100 mg; n=21 each). Using 16S rRNA gene amplicon sequencing, we evaluated diversity and relative abundance and explored association patterns through Sparse InversE Covariance estimation for Ecological Association and Statistical Inference network analysis. Although no dose dependence was observed, alpha diversity decreased significantly in the L. cremoris FC 100 mg group, whereas beta diversity shifted significantly in the 50 mg group. Short-chain fatty acid producing genera, including Blautia, Anaerobutyricum, Anaerostipes, and Agathobaculum, showed higher relative abundances after intervention in both L. cremoris FC intake groups. Moreover, the relative abundance of Blautia was positively correlated with stool characteristics across post-intervention samples. Exploratory network analysis indicated altered statistical associations among bacterial taxa. Blautia and Roseburia showed higher centrality in the L. cremoris FC 100 mg group, whereas Bacteroides and Ruminococcus were more central in the placebo group. These findings suggest that L. cremoris FC intake was associated with coordinated alterations in microbial diversity, genus-level relative abundance, and association patterns, providing ecological insights into microbiota changes accompanying bowel improvement, though underlying mechanisms remain unclear.

Tongxie Yaofang (TXYF) is a classic formula for liver stagnation and spleen deficiency diarrhea, but its mechanisms involving the gut microbiota remain unclear. This study aimed to elucidate the mechanisms TXYF by integrating network pharmacology, molecular docking, and 16S rRNA gene sequencing. We employed network pharmacology and molecular docking to identify bioactive compounds, targets, and their associations with gut microbiota metabolites. Sequencing of the 16S rRNA gene revealed changes in the gut microbiota in a diarrheal mouse model after TXYF intervention. Thirty-nine active compounds (525 targets) were identified. Intersection analysis yielded 44 shared targets among TXYF, diarrhea, and gut microbiota metabolites. Molecular docking demonstrated favorable binding of the selected active compounds and representative gut microbiota-derived metabolites with the core targets GSK3B, TP53, and MAPK3. Sequencing of the 16S rRNA gene also showed that TXYF significantly modulated gut microbiota structure, notably altering abundances of Corynebacterium stationis, Proteus vulgaris, and Proteus mirabilis. TXYF treats diarrhea by modulating gut microbiota composition and maintaining microbial homeostasis via a multi-component, multi-target mechanism, supporting its potential as a microbiota-targeted therapy.