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Dietary fiber selectively regulates intestinal persistence of probiotic Bifidobacteria

ABSTRACT: Bifidobacteria is strongly associated with human health and dominates the gut microbiota of breast-fed infants. However, Bifidobacteria persists at high abundance in only a subset of individuals after weaning, and the factors that regulate intestinal persistence of Bifidobacteria are poorly understood. Here, we identified that a common dietary fiber, raffinose, supports Bifidobacteria persistence within complex microbiome communities. Raffinose-driven Bifidobacteria persistence is associated with disease resistance and restrained inflammation in mice. Altogether, our findings show that raffinose selectively regulates the intestinal persistence of Bifidobacteria, which may enable its sustained maintenance during microbiome diversification and thereby support prolonged probiotic functions.

ORGANISM(S): Mus musculus

PROVIDER: GSE330259 | GEO | 2026/08/31

REPOSITORIES: GEO

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Dietary fiber selectively regulates intestinal persistence of probiotic Bifidobacteria

Project description:Bifidobacteria is strongly associated with human health and dominates the gut microbiota of breast-fed infants. However, Bifidobacteria persists at high abundance in only a subset of individuals after weaning, and the factors that regulate intestinal persistence of Bifidobacteria are poorly understood. Here, we identified that a common dietary fiber, raffinose, supports Bifidobacteria persistence within complex microbiome communities. Raffinose-driven Bifidobacteria persistence is associated with disease resistance and restrained inflammation in mice. Altogether, our findings show that raffinose selectively regulates the intestinal persistence of Bifidobacteria, which may enable its sustained maintenance during microbiome diversification and thereby support prolonged probiotic functions.

2026-08-31 | GSE330838 | GEO

Dietary fiber selectively regulates intestinal persistence of probiotic Bifidobacteria [Fecal microbiota]

2026-08-31 | GSE330841 | GEO

probiotic metagenome strain:lactobacilli,bifidobacteria | breed:infant

Project description:probiotic metagenome strain:lactobacilli,bifidobacteria | breed:infant Metagenome

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RNA sequencing of CACO-2 cells incubated with bifidobacteria grown on human milk oligosaccharides.

Project description:Background: Breastfed human infants are predominantly colonized by bifidobacteria that thrive on human milk oligosaccharides (HMO). The two most predominant species of bifidobacteria in infant feces are Bifidobacterium breve (B. breve) and Bifidobacterium longum subsp. infantis (B. infantis), both avid HMO-consumer strains. Our laboratory has previously shown that B. infantis, when grown on HMO, increase adhesion to intestinal cells and increase the expression of the anti-inflammatory cytokine interleukin-10. The purpose of the current study was to investigate the effects of carbon source—glucose, lactose, or HMO—on the ability of B. breve and B. infantis to adhere to and affect the transcription of intestinal epithelial cells on a genome-wide basis. Results: HMO-grown B. infantis had higher percent binding to Caco-2 cell monolayers compared to B. infantis grown on glucose or lactose. B. breve had low adhesive ability regardless of carbon source. Despite differential binding ability, both HMO-grown strains significantly differentially affected the Caco-2 transcriptome compared to their glucose or lactose grown controls. HMO-grown B. breve and B. infantis both down-regulated genes in Caco-2 cells associated with chemokine activity. Conclusion: The choice of carbon source affects the interaction of bifidobacteria with intestinal epithelial cells. HMO-grown bifidobacteria reduce markers of inflammation, compared to glucose or lactose-grown bifidobacteria. In the future, the design of preventative or therapeutic probiotic supplements may need to include appropriately chosen prebiotics.

2017-02-10 | GSE63950 | GEO

RNA sequencing of CACO-2 cells incubated with Bifidobacteria breve grown on human milk oligosaccharides.

2017-02-10 | GSE64017 | GEO

A Bifidobacteria-derived Tight adherence (Tad) pilus-associated protein signals colonic epithelial growth

Project description:Development of the human gut microbiota commences at birth, with bifidobacteria being among the first colonizers of the newborn gastrointestinal tract. To date, the genetic basis of Bifidobacterium colonization, persistence and dialogue with the host remains poorly understood. We previously identified tight adherence (Tad) pili from Bifidobacterium breve UCC2003 as an essential colonisation factor using murine models.We have identified the protein that mediates the proliferation response, and demonstrate that bifidobacteria contribute to the maturation of the naïve gut in early life through the production of specific extracellular protein structures under in vivo conditions. This bifidobacteria-derived signalling protein may represent one of the mechanisms by which members of the early colonising microbiota stimulate growth of the neonatal mucosa

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Project description:Clonal persistence dominates homeostatic intestinal IgA responses

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Maternal Probiotic Supplementation Effects on the Placenta-Brain Axis

Project description:The rate of probiotic usage by pregnant women in the US and Canada ranges from 1.3 to 3.6 %. Probiotic supplements are available without a prescription and have gained currency in treating a variety of ailment ranging from reducing risk of constipation, diarrhea, other gastrointestinal conditions, eczema, pre-term birth, and prevent adverse pregnancy outcomes, including gestational diabetes mellitus (GDM) and depression/anxiety. Three possible mechanisms by which maternal probiotic supplementation might influence the placenta are through 1) directly impacting possible bacteria residing in the placenta (placenta microbiome), 2) altering bacterial metabolites produced by gut microbiota within the mother that induce placental changes, and 3) maternal probiotics might affect the composition of the bacteria within the maternal gut that affects her immune cells and their responses to the heterologous placenta. For the second potential mechanism, bacterial metabolites that might influence placenta include short chain fatty acids (SCFAs), polyamines (PAs), and Vitamins B9 (Folic Acid) and 12 (Cobalamin), among others. This project aims to determine the effects maternal probiotic supplementation in mice might have on the fetal placenta. With the number of women taking over probiotic supplements increasing, further research is needed to determine how these bioactive agents may affect the placenta and health of the offspring.

2025-09-26 | GSE309308 | GEO

Integrative genomic reconstruction reveals heterogeneity in carbohydrate utilization across human gut bifidobacteria

Project description:Bifidobacteria are among the earliest colonizers of the human gut and are widely used as probiotics for their health-promoting properties. However, individual responses to probiotic supplementation may vary with strain type(s), microbiota composition, diet, or lifestyle conditions, highlighting the need for strain-level insight into bifidobacterial carbohydrate metabolism. Here, we systematically reconstructed 68 pathways involved in the utilization of mono-, di-, oligo-, and polysaccharides by analyzing the distribution of 589 curated metabolic functional roles (catabolic enzymes, transporters, transcriptional regulators) in 3083 non-redundant cultured Bifidobacterium isolates and metagenome-assembled genomes (MAGs) of human origin. Our analysis uncovered extensive inter- and intraspecies heterogeneity, including a distinct clade within the Bifidobacterium longum species capable of metabolizing starch. We also identified isolates of Bangladeshi origin that harbor unique gene clusters implicated in the breakdown of xyloglucan and human milk oligosaccharides. Thirty-eight predicted carbohydrate utilization phenotypes were experimentally validated in 30 geographically diverse Bifidobacterium isolates in vitro. Our large-scale genomic compendium expands the knowledge of bifidobacterial carbohydrate metabolism and can inform the rational design of probiotic and synbiotic formulations tailored to strain-specific nutrient preferences.

2024-08-08 | GSE239955 | GEO

Proteomic analysis of outer membrane vesicles from the probiotic strain Escherichia coli Nissle 1917

Project description:Escherichia coli Nissle 1917 (EcN) is a probiotic used for treatment of intestinal disorders. EcN improves gastrointestinal homeostasis and microbiota balance; however little is known about how this probiotic delivers effector molecules to the host. Outer membrane vesicles (OMVs) are constitutively produced by gram-negative bacteria and have a relevant role in bacteria-host interactions. Here we performed proteomic analysis of EcN OMVs. Using 1D SDSD-PAGE and highly sensitive LC-MS/MS analysis we identified 192 EcN vesicular proteins with high confidence in three independent experiments. Of these proteins, 18 were encoded by strain-linked genes and 57 were common to pathogen-derived OMVs. These proteins may contribute to the ability of this probiotic to colonize the human gut as they fulfil functions related to adhesion to host tissues, immune modulation or bacterial survival in host niches. This study describes the first global OMV proteome of a probiotic strain and provides evidence that probiotic-derived OMVs contain proteins that can target these vesicles to the host and mediate their beneficial effects on intestinal function.

2013-12-19 | PXD000367 | Pride

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