ArticleScientific reports2019
Deciphering the metabolic capabilities of Bifidobacteria using genome-scale metabolic models.
Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers.
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Who cites it
53 citing papers in PubMed.
- Nationwide cohort study reveals low bifidobacteria and distinct microbiota composition and function in Swedish newborns.Gut microbes · 2026Observational
- Dietary 4-Hydroxy-2,5-Dimethyl-3(2H)-Furanone Supplementation in Hu Sheep: Implications on Fecal and Rumen Microbiota.Animals : an open access journal from MDPI · 2026Article
- Longitudinal fecal amino acid profiles in extremely preterm infants: early-life determinants and associations with late-onset sepsis.Metabolomics : Official journal of the Metabolomic Society · 2026Article
- Molecular and Immunological Mechanisms Underlying the Anticancer Effects of Bifidobacterium.Probiotics and antimicrobial proteins · 2026Review
- Gut microbiota dysbiosis and altered fecal metabolome in patients with age-related cataract.Scientific reports · 2026Article
- Metabolic reprogramming of the infant gut by bifidobacteria-based probiotics drives exclusion of antibiotic-resistant pathobionts.Cell reports. Medicine · 2026Article
- Regulation of allergies across the body by microbial metabolites.Experimental & molecular medicine · 2026Review
- Feeding Type Shapes Infant Gut Microbiota and Metabolite Profiles in a Simulated Colonic Model.Microorganisms · 2026Article
- High-throughput single-cell isolation ofMicrobiology spectrum · 2026Article
- Expansion resistance against genotoxicFrontiers in microbiology · 2026Article
- The Japanese gut microbiome: ecology, uniqueness, and impact on health and disease.Proceedings of the Japan Academy. Series B, Physical and biological sciences · 2026Review
- The role of lactate metabolism in shaping intestinal microbiota and health.AIMS microbiology · 2026Review
- Host transcriptional responses to gut microbiome variation arising from urbanism.bioRxiv : the preprint server for biology · 2025Article
- Transition From a High-Sugar and Butter to a Standard Diet Leads to Cecal Dysbiosis, Disrupts Intestinal Homeostasis, and Favors Increased Ethanol Consumption and Preference.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2025Article
- Nanomedicine-Driven Modulation of the Gut-Brain Axis: Innovative Approaches to Managing Chronic Inflammation in Alzheimer's and Parkinson's Disease.International journal of molecular sciences · 2025Review
- Changes in the gut microbiota in mice exposed to chronic intermittent hypoxia.Journal of medical microbiology · 2025Article
- Inhibitory efficacy, production dynamics, and characterization of postbiotics of lactic acid bacteria.BMC microbiology · 2025Article
- Integrative genomic reconstruction reveals heterogeneity in carbohydrate utilization across human gut bifidobacteria.Nature microbiology · 2025Article
- Genome-scale metabolic model-guided systematic framework for designing customized live biotherapeutic products.NPJ systems biology and applications · 2025Review
- Integrative genomic reconstruction reveals heterogeneity in carbohydrate utilization across human gut bifidobacteria.bioRxiv : the preprint server for biology · 2025Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Bifidobacteria, the initial colonisers of breastfed infant guts, are considered as the key commensals that promote a healthy gastrointestinal tract. However, little is known about the key metabolic differences between different strains of these bifidobacteria, and consequently, their suitability for their varied commercial applications. In this context, the present study applies a constraint-based modelling approach to differentiate between 36 important bifidobacterial strains, enhancing their genome-scale metabolic models obtained from the AGORA (Assembly of Gut Organisms through Reconstruction and Analysis) resource. By studying various growth and metabolic capabilities in these enhanced genome-scale models across 30 different nutrient environments, we classified the bifidobacteria into three specific groups. We also studied the ability of the different strains to produce short-chain fatty acids, finding that acetate production is niche- and strain-specific, unlike lactate. Further, we captured the role of critical enzymes from the bifid shunt pathway, which was found to be essential for a subset of bifidobacterial strains. Our findings underline the significance of analysing metabolic capabilities as a powerful approach to explore distinct properties of the gut microbiome. Overall, our study presents several insights into the nutritional lifestyles of bifidobacteria and could potentially be leveraged to design species/strain-specific probiotics or prebiotics.
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