Microbial interactions and the homeostasis of the gut microbiome: the role of Bifidobacterium

Multi-omics technology reveals the changes in gut microbiota to stimulate aromatic amino acid metabolism in children with allergic rhinitis and constipation

Background

Comorbid allergic rhinitis and constipation (ARFC) in children are associated with gut microbiota (GM) dysbiosis and metabolic perturbations; however, the underlying mechanistic interplay remains unclear.

Objective

This multi-omics study aimed to characterize GM and fecal metabolomic signatures in preschool ARFC children and elucidate microbial-metabolite interactions driving dual symptomatology.

Methods

Fecal samples from 16 ARFC and 15 healthy control (HC) children underwent high-throughput absolute quantification 16S rRNA sequencing and untargeted metabolomics. Differential taxa and metabolites were identified via LEfSe and OPLS-DA (VIP > 1, false discovery rate (FDR) q < 0.05). Microbial-metabolite networks were reconstructed using genome-scale metabolic modeling and KEGG pathway analysis.

Results

The ARFC group exhibited distinct β-diversity (P = 0.031), marked by elevated Hungatella, Tyzzerella, and Bifidobacterium longum (P < 0.05). Metabolomics revealed upregulated aromatic amino acids (AAAs), neurotransmitters, and bile acids (FDR q < 0.05), with enrichment in tryptophan/tyrosine pathways (P < 0.01). Bioinformatic modeling linked Hungatella to tryptophan hydroxylase (EC:1.14.16.4), driving serotonin synthesis, and Tyzzerella to indoleamine 2,3-dioxygenase (EC:1.13.11.52), promoting kynurenine production. Bifidobacterium longum correlated with phenylalanine hydroxylase (EC:1.14.16.1), enhancing phenylalanine derivatives. A combined GM-metabolite diagnostic model demonstrated robust accuracy (AUC = 0.8).

Conclusion

GM dysbiosis in ARFC children activates AAA metabolism, generating neuroactive and pro-inflammatory metabolites that may exacerbate allergic and gastrointestinal symptoms. These findings highlight microbial-metabolite axes as therapeutic targets. Study limitations include cohort size and lack of disease-specific controls, necessitating validation in expanded cohorts.

Associations Between Microbiota Awareness, Healthy Eating Attitude, and Sociodemographic Factors in University Students

The global epidemic of diet-related chronic diseases emphasizes the significance of the human gut microbiota in dietary physiological effects and the etiology of chronic diseases. This research aimed to assess the relationship between microbiota awareness, healthy eating attitudes, and sociodemographic factors in university students. Two hundred forty-two university students participated in this descriptive and analytical study in Aydın and Ordu, Türkiye. University students completed a general information form, anthropometric measures, the Attitude Scale for Healthy Nutrition, the Microbiota Awareness Scale, and a probiotic and prebiotic food frequency questionnaire. In total, 48 (19.8%) male and 194 (80.2%) female students participated in the study. Nutrition and dietetics students had higher total scores and sub-factor scores in ASHN and microbiota awareness and lower body mass index compared to other departments (p < 0.05). A positive and significant correlation was found between the Attitude Scale for Healthy Nutrition and Microbiota Awareness Scale total scores. Conversely, a negative statistically significant correlation was observed between body mass index and the total score of the Microbiota Awareness Scale (p < 0.05). The frequency of probiotic and prebiotic food consumption was higher in nutrition and dietetics students compared to other departments. A higher Attitude Scale for Healthy Nutrition, studying in the nutrition and dietetic department, knowing the term microbiota, and self-assessment on microbiota knowledge as good were associated with increased awareness of microbiota (p < 0.05). Given this positive association, integrating healthy nutrition, microbiota, probiotics, and prebiotics into the educational curricula for all university departments, scientific conferences, and academic research may enhance microbiota awareness among university students.

Gut feelings on short-chain fatty acids to regulate respiratory health

Respiratory infections and diseases pose significant challenges to society and healthcare systems, underscoring the need for preventative and therapeutic strategies. Recent research in rodent models indicates that short-chain fatty acids (SCFAs), metabolites produced by gut bacteria, may offer medicinal benefits for respiratory conditions. In this opinion, we summarize the current literature that highlights the potential of SCFAs to enhance immune balance in humans. SCFAs have demonstrated the potential to decrease the risk of primary and secondary respiratory infections, modulate allergic airway exacerbations, and improve overall epithelial pathogen defenses. Therefore, we suggest that systemic SCFA levels could be targeted to support gut and respiratory health in specific groups, such as patients in hospital, women and their offspring, children, older adults, and athletes/military personnel.

Effects of Centella asiatica-isolated pectic polysaccharide on dextran sulfate sodium-induced colitis

Dietary supplementation of polysaccharides demonstrates strong therapeutic actions on inflammatory bowel disease (IBD). Centella asiatica (CA) has traditionally been used in Ayurveda and Chinese medicine. However, the effects of CA-isolated pectic polysaccharides on IBD remain unknown. This study determined the effect of a CA-isolated pectic polysaccharide on IBD. The crude polysaccharide (CA-CP), isolated from a hot-water extract of CA, is a typical pectic polysaccharide composed mainly of galacturonic acid (40.6 %), galactose (27.6 %), arabinose (13.5 %), and rhamnose (8.5 %). CA-CP improved clinical symptoms in a DSS-induced colitis murine model, including weight change (9.9-12.0 %), disease activity index (31.6-51.9 %), colon length (13.2-21.5 %), and spleen weight (21.8-26.3 %). CA-CP effectively regulated the levels of inflammatory and junctional factors by mediating the MAPK and NF-κB pathways. CA-CP partially alleviated DSS-induced crypt destruction, submucosal edema, inflammatory infiltration, and mucin secretion. The content of total short-chain fatty acids increased substantially (cecum 29.8-53.7 %, feces 75.4-109.3 %) with oral CA-CP administration compared to the DSS group. Cecal microbial community analysis revealed that CA-CP administration regulated DSS-induced colitis by reducing the abundance of Escherichia (5.0-10.9 %) and Clostridium (0.3-0.4 %), while increasing the abundance of Bacteroidetes (6.8-8.5 %), Ligilactobacillus (2.7-6.0 %), and Bilophilia (0.3-0.6 %). The findings provide fundamental data for developing novel functional therapeutic agents for the prevention and treatment of colitis, using CA-isolated pectic polysaccharides. Furthermore, to the best of our knowledge, our study is the first to demonstrate the effects of pectic polysaccharides isolated from CA on IBD.

Impact of Bifidobacterium longum Subspecies infantis on Pediatric Gut Health and Nutrition: Current Evidence and Future Directions

Background: the intestinal microbiota, a complex community vital to human health, is shaped by microbial competition and host-driven selective pressures. Among these microbes, Bifidobacterium plays a crucial role in early gut colonization during neonatal stages, where Bifidobacterium longum subspecies infantis (B. infantis) predominates and is particularly prevalent in healthy breastfed infants. Objectives: as we embark on a new era in nutrition of the pediatric population, this study seeks to examine the existing understanding regarding B. infantis, encompassing both preclinical insights and clinical evidence. Methods: through a narrative disceptation of the current literature, we focus on its genetic capacity to break down various substances that support its survival and dominance in the intestine. Results: using "omics" technologies, researchers have identified beneficial mechanisms of B. infantis, including the production of short-chain fatty acids, serine protease inhibitors, and polysaccharides. While B. infantis declines with age and in various diseases, it remains a widely used probiotic with documented benefits for infant and child health in numerous studies. Conclusions: the current scientific evidence underscores the importance for ongoing research and clinical trials for a deeper understanding of B. infantis's role in promoting long-term health.

Compendium of Bifidobacterium-based probiotics: characteristics and therapeutic impact on human diseases

The human microbiota, a complex community of microorganisms residing in and on the human body, plays a crucial role in maintaining health and preventing disease. Bifidobacterium species have shown remarkable therapeutic potential across a range of health conditions, thus being considered optimal probiotic bacteria. This review provides insights into the concept of probiotics and explores the impact of bifidobacteria on human health, focusing on the gastrointestinal, respiratory, skeletal, muscular, and nervous systems. It also integrates information on the available genetic bases underlying the beneficial effects of each bifidobacterial probiotic species on different aspects of human physiology. Notably, Bifidobacterium-based probiotics have proven effective in managing gastrointestinal conditions such as constipation, antibiotic-associated diarrhea, irritable bowel syndrome (IBS), inflammatory bowel disease (IBD), and Helicobacter pylori infections. These benefits are achieved by modulating the intestinal microbiota, boosting immune responses, and strengthening the gut barrier. Moreover, Bifidobacterium species have been reported to reduce respiratory infections and asthma severity. Additionally, these probiotic bacteria offer benefits for skeletal and muscular health, as evidenced by Bifidobacterium adolescentis and Bifidobacterium breve, which have shown anti-inflammatory effects and symptom relief in arthritis models, suggesting potential in treating conditions like rheumatoid arthritis. Furthermore, probiotic therapies based on bifidobacterial species have shown promising effects in alleviating anxiety and depression, reducing stress, and enhancing cognitive function. Overall, this review integrates the extensive scientific literature now available that supports the health-promoting applications of probiotic Bifidobacterium species and underscores the need for further research to confirm their clinical efficacy across different body systems.

High-molecular-weight Fucoidan exerts an immune-enhancing effect in RAW 264.7 cells and cyclophosphamide-induced immunosuppression rat by altering the gut microbiome

High-molecular-weight fucoidan (Fucoidan P), sourced from Undaria pinnatifida exhibits several health benefits, including immunomodulation. However, the mechanisms underlying the immune-enhancing effects of Fucoidan P remain unclear. Here, we investigated the immune-enhancing effects and the potential mechanisms of Fucoidan P using RAW 264.7 macrophages and cyclophosphamide (CP)-induced immunosuppression rat model. In macrophages, Fucoidan P showed dose-dependent stimulation by increasing cell proliferation, nitric oxide production, and gene expression of inducible nitric oxide synthase, cyclooxygenase-2, and proinflammatory cytokines. These effects are mediated through the activation of the nuclear factor-kappa B (NF-κB) signaling pathway. Moreover, orally administered Fucoidan P was evaluated in immunosuppressed rats treated with CP. Fucoidan P administration increased hematological values and natural killer cell activity, and positively affected nitrite and prostaglandin E2 levels. The Fucoidan P treatment groups exhibited improved serum cytokine levels as well as splenic and intestinal cytokine mRNA expression compared to the model group. Fucoidan P also mitigated splenic damage and increased the phosphorylation of NF-κB and NF-κB inhibitor alpha (IκBα). Furthermore, Fucoidan P treatment altered the gut microbiota composition, enhancing the alpha diversity, evenness, and abundance of Bacteroidetes, which are associated with immune function. Taken together, our findings suggest that Fucoidan P exerts beneficial effects on immune function by activating NF-κB and modulating gut microbiota. These findings suggested its potential as a therapeutic agent for immune enhancement.

Probiotics in the New Era of Human Milk Oligosaccharides (HMOs): HMO Utilization and Beneficial Effects of Bifidobacterium longum subsp. infantis M-63 on Infant Health

A healthy gut microbiome is crucial for the immune system and overall development of infants. Bifidobacterium has been known to be a predominant species in the infant gut; however, an emerging concern is the apparent loss of this genus, in particular, Bifidobacterium longum subsp. infantis (B. infantis) in the gut microbiome of infants in industrialized nations, underscoring the importance of restoring this beneficial bacterium. With the growing understanding of the gut microbiome, probiotics, especially infant-type human-residential bifidobacteria (HRB) strains like B. infantis, are gaining prominence for their unique ability to utilize HMOs and positively influence infant health. This article delves into the physiology of a probiotic strain, B. infantis M-63, its symbiotic relationship with HMOs, and its potential in improving gastrointestinal and allergic conditions in infants and children. Moreover, this article critically assesses the role of HMOs and the emerging trend of supplementing infant formulas with the prebiotic HMOs, which serve as fuel for beneficial gut bacteria, thereby emulating the protective effects of breastfeeding. The review highlights the potential of combining B. infantis M-63 with HMOs as a feasible strategy to improve health outcomes in infants and children, acknowledging the complexities and requirements for further research in this area.

Genome-scale metabolic modeling of the human milk oligosaccharide utilization by Bifidobacterium longum subsp. infantis

Bifidobacterium longum subsp. infantis is a representative and dominant species in the infant gut and is considered a beneficial microbe. This organism displays multiple adaptations to thrive in the infant gut, regarded as a model for human milk oligosaccharides (HMOs) utilization. These carbohydrates are abundant in breast milk and include different molecules based on lactose. They contain fucose, sialic acid, and N-acetylglucosamine. Bifidobacterium metabolism is complex, and a systems view of relevant metabolic pathways and exchange metabolites during HMO consumption is missing. To address this limitation, a refined genome-scale network reconstruction of this bacterium is presented using a previous reconstruction of B. infantis ATCC 15967 as a template. The latter was expanded based on an extensive revision of genome annotations, current literature, and transcriptomic data integration. The metabolic reconstruction (iLR578) accounted for 578 genes, 1,047 reactions, and 924 metabolites. Starting from this reconstruction, we built context-specific genome-scale metabolic models using RNA-seq data from cultures growing in lactose and three HMOs. The models revealed notable differences in HMO metabolism depending on the functional characteristics of the substrates. Particularly, fucosyl-lactose showed a divergent metabolism due to a fucose moiety. High yields of lactate and acetate were predicted under growth rate maximization in all conditions, whereas formate, ethanol, and 1,2-propanediol were substantially lower. Similar results were also obtained under near-optimal growth on each substrate when varying the empirically observed acetate-to-lactate production ratio. Model predictions displayed reasonable agreement between central carbon metabolism fluxes and expression data across all conditions. Flux coupling analysis revealed additional connections between succinate exchange and arginine and sulfate metabolism and a strong coupling between central carbon reactions and adenine metabolism. More importantly, specific networks of coupled reactions under each carbon source were derived and analyzed. Overall, the presented network reconstruction constitutes a valuable platform for probing the metabolism of this prominent infant gut bifidobacteria.IMPORTANCEThis work presents a detailed reconstruction of the metabolism of Bifidobacterium longum subsp. infantis, a prominent member of the infant gut microbiome, providing a systems view of its metabolism of human milk oligosaccharides.

Ecology- and genome-based identification of the Bifidobacterium adolescentis prototype of the healthy human gut microbiota

Bifidobacteria are among the first microbial colonizers of the human gut, being frequently associated with human health-promoting activities. In the current study, an in silico methodology based on an ecological and phylogenomic-driven approach allowed the selection of a Bifidobacterium adolescentis prototype strain, i.e., B. adolescentis PRL2023, which best represents the overall genetic content and functional features of the B. adolescentis taxon. Such features were confirmed by in vitro experiments aimed at evaluating the ability of this strain to survive in the gastrointestinal tract of the host and its ability to interact with human intestinal cells and other microbial gut commensals. In this context, co-cultivation of B. adolescentis PRL2023 and several gut commensals revealed various microbe-microbe interactions and indicated co-metabolism of particular plant-derived glycans, such as xylan.IMPORTANCEThe use of appropriate bacterial strains in experimental research becomes imperative in order to investigate bacterial behavior while mimicking the natural environment. In the current study, through in silico and in vitro methodologies, we were able to identify the most representative strain of the Bifidobacterium adolescentis species. The ability of this strain, B. adolescentis PRL2023, to cope with the environmental challenges imposed by the gastrointestinal tract, together with its ability to switch its carbohydrate metabolism to compete with other gut microorganisms, makes it an ideal choice as a B. adolescentis prototype and a member of the healthy microbiota of adults. This strain possesses a genetic blueprint appropriate for its exploitation as a candidate for next-generation probiotics.

The infant gut microbiota as the cornerstone for future gastrointestinal health

The early postnatal period represents a critical window of time for the establishment and maturation of the human gut microbiota. The gut microbiota undergoes dramatic developmental changes during the first year of life, being influenced by a variety of external factors, with diet being a major player. Indeed, the introduction of complementary feeding provides novel nutritive substrates and triggers a shift from milk-adapted gut microbiota toward an adult-like bacterial composition, which is characterized by an enhancement in diversity and proportions of fiber-degrading bacterial genera like Ruminococcus, Prevotella, Eubacterium, and Bacteroides genera. Inadequate gut microbiota development in early life is frequently associated with concomitant and future adverse health conditions. Thus, understanding the processes that govern initial colonization and establishment of microbes in the gastrointestinal tract is of great importance. This review summarizes the actual understanding of the assembly and development of the microbial community associated with the infant gut, emphasizing the importance of mother-to-infant vertical transmission events as a fundamental arrival route for the first colonizers.