Bifidobacteria are the predominant bacteria in the infant gut and have beneficial effects on host physiology. Infant cohort studies have demonstrated that a higher abundance of bifidobacteria in the gut is associated with a reduced risk of disease. Recently, bifidobacteria-derived metabolites, such as organic acid, have been suggested to play crucial roles in host physiology. This review focuses on an investigation of longitudinal changes in the gut microbiota and organic acid concentrations over 2 years of life in 12 Japanese infants and aims to identify bifidobacteria that contribute to the production of organic acid in healthy infants. Acetate, lactate, and formate, which are rarely observed in adults, are characteristically observed during breast-fed infancy. Bifidobacterium longum subspecies infantis and the symbiosis of Bifidobacterium bifidum and Bifidobacterium breve efficiently produce these organic acids through metabolization of human milk oligosaccharide (HMO) with different strategies. These findings confirmed that HMO-utilizing bifidobacteria play an important role in regulating the gut organic acid profiles of infants.

Sustainable livestock production requires reducing competition for food and feed resources and increasing the utilization of food by-products in livestock feed. This study describes the establishment of an anaerobic batch culture model to simulate pig microbiota and evaluate the effects of a food by-product, wakame seaweed stalks, on ex vivo microbial communities. We selected one of the nine media to support the growth of a bacterial community most similar in composition and diversity to that observed in pig donor feces. Supplementation with wakame altered the microbial profile and short-chain fatty acid composition in the ex vivo model, and a similar trajectory was observed in the in vivo pig experimental validation. Notably, the presence of wakame increased the abundance of Lactobacillus species, which may have been due to cross-feeding with Bacteroides. These results suggest the potential of wakame as a livestock feed capable of modulating the pig microbiome. Collectively, this study highlights the ability to estimate the microbiome changes that occur when pigs are fed a specific feed using an ex vivo culture model.

How bifidobacteria colonize and survive in the intestine is not fully understood. The administration of bifidobacteria to conventional mice can be used to evaluate their ability to colonize the intestine in the presence of endogenous gut microbiota. However, human-derived bifidobacteria do not readily colonize the intestines of conventional mice, and although colonization by Bifidobacterium breve UCC2003 has been achieved, the viability of such populations requires improvement. Therefore, we aimed to establish a colonization system with human-derived bifidobacteria of high viability in conventional mice using Bifidobacterium longum subsp. longum 105-A. Lactose, raffinose, and 1-kestose were identified as the preferred carbohydrate sources for the growth of this strain in culture. The administration of B. longum 105-A to conventional BALB/c mice fed these carbohydrates showed that diets containing 6% (w/w) raffinose or 1-kestose facilitated colonization with >10⁸ colony-forming units/g feces for 2 weeks. The population of this strain was more stable in the raffinose-fed group than in the 1-kestose-fed group. The ingestion of these prebiotics had a greater impact on the composition of the microbiota than the administration of B. longum 105-A. The ingestion of these prebiotics also increased the fecal concentrations of organic acids, which was indicative of greater intestinal fermentation. Collectively, we established a colonization system for B. longum 105-A with high viability in conventional mice by feeding the mice raffinose or 1-kestose. This system should be useful for elucidation of the mechanisms of colonization and survival of bifidobacteria in the intestines in the presence of the endogenous gut microbiota.

Lactiplantibacillus plantarum SN13T is a probiotic plant-derived lactic acid bacterium that can grow in various medicinal plant extracts. In this study, we fermented an aqueous extract of gardenia fructus, the fruit of a medicinal plant, with SN13T, such that the bioactivity of the extract was potentiated after fermentation to suppress the release of inflammatory mediators, such as nitric oxide (NO), reactive oxygen species (ROS), interleukin-6 (IL-6), and tumor necrosis factor-alpha (TNF-α), as well as downregulate inflammatory genes in lipopolysaccharides (LPS)-stimulated RAW 264.7 cells. This increased antioxidant and anti-inflammatory activity was mediated through bioconversion of the iridoid glycoside geniposide to its aglycone genipin via the supposed hydrolytic action of β-glucosidases harbored by SN13T. In the complete genome of SN13T, ten putative genes encoding β-glucosidases of glycosyl hydrolase (GH) family 1 organized among eight gene operons were identified. Transcriptional profiling revealed that two 6-phospho-β-glucosidase genes, pbg9 and SN13T_1925, located adjacently in the gene operon SN13T_1923, were transcribed significantly more than the remaining genes during fermentation of the gardenia extract. This suggests the role of these β-glucosidases in bioconversion of geniposide to genipin and the subsequent enhanced bioactivity of the gardenia fructus extract after fermentation with SN13T.

Ulva, an edible green alga, contains sulfated polysaccharides and oligosaccharides that possess immunomodulatory and anti-inflammatory properties. The objective of this study was to investigate the anti-allergic effects of Ulva-derived samples of polysaccharides (UP), oligosaccharides (UO), and residues (UR) on delayed-type hypersensitivity (DTH) in mice. Oral treatment of mice with UP, UO, and UR (250 mg/kg body weight) daily noticeably improved the DTH reaction as evidenced by attenuation of footpad swelling and cell infiltration at the allergen-challenge site. Although the Ulva samples had limited impacts on the production of serum total IgG, decreased concentrations of allergen-specific IgG and IgG_2a and an increased concentration of IgG₁ were observed in the treated mice. Moreover, treatment with them suppressed allergen-induced IFN-γ and TNF-α secretion and elevated IL-4 secretion. However, none of the Ulva sample treatments could modulate the production of IL-10. Concordantly, the in situ data reveal that the Ulva sample treatments suppressed IFN-γ and TNF-α expression at the allergen-injection site. These findings collectively suggest the potential of UP, UO, and UR as functional food candidates for the management of delayed-type hypersensitivity.

Chronic intestinal pseudo-obstruction (CIPO) is a rare intractable disease with limited treatment options. Small intestinal bacterial overgrowth (SIBO) often co-occurs with several diseases, including CIPO. While rifaximin (RFX) is effective in treating SIBO, its efficacy for CIPO remains unclear. Here, we aimed to investigate the efficacy and safety of RFX in adult patients with CIPO. Twelve patients were randomly assigned to receive RFX (400 mg three times daily, n=8) or a placebo (PBO, n=4) for 4 weeks. The global symptom score for abdominal bloating (GSS-bloating) and an original whole gastrointestinal symptoms score (O-WGSS) were collected, and a glucose hydrogen breath test (GHBT) and abdominal computed tomography (CT) were performed. No significant differences were observed in the primary endpoint. GSS-bloating improved by 75% and 25% in the PBO and RFX groups, respectively, and O-WGSS improved by 25% in both groups. No significant differences were observed in secondary and other endpoints, including the SIBO eradication rate in the GHBT and small intestinal volume on CT. In a post hoc analysis of SIBO-positive patients with CIPO (4/4 and 4/8 in the PBO and RFX groups), SIBO was eradicated in 25% and 75% of the patients (PBO and RFX groups, respectively) at the end of treatment, indicating a high eradication rate in the RFX group. Furthermore, the small intestinal gas volume decreased in the RFX group, and no severe adverse events occurred. Although no significant improvements were observed in subjective indicators, RFX may be beneficial in alleviating SIBO and reducing the small intestinal gas volume in SIBO-positive patients with CIPO.

The probiotic attributes of Lacticaseibacillus paracasei NY1301 were comprehensively characterized, and a comparison between the closely related LcA (Actimel) and LcY (Yakult) probiotic strains was conducted using genomic tools. All strains exhibited high genetic similarity and likely shared a common ancestor; differences were primarily expressed as minor chromosomal re-arrangements, substitutions, insertions, and deletions. Compared with LcY, NY1301 exhibited 125 single-nucleotide polymorphisms. NY1301 lacked virulence factors, antibiotic resistance genes, and mutations associated with antibiotic resistance and had a 46-kbp prophage. This prophage is spontaneously induced at low levels and remains in a non-lytic state under standard culture conditions. The observed causal adaptive mutations were likely related to niche adaptation within the respective laboratory or manufacturing processes that occurred during the maintenance of the strains. However, the phenotypic effects of these genomic differences remain unclear. To validate the safety of NY1301, we conducted an open-label trial with healthy participants who consumed excessive amounts of NY1301 (3.0 × 10¹¹ cfu) daily for 28 days. The results of this trial and those of other in vivo studies, coupled with the long history of human consumption without established risks to humans, provide strong evidence confirming the safety of NY1301.