ArticleEnvironmental microbiology2022
Designation of optimal reference strains representing the infant gut bifidobacterial species through a comprehensive multi-omics approach.
Article in Environmental microbiology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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12 citing papers in PubMed.
- Understanding the interaction between melatonin and bifidobacteria.Microbiome research reports · 2025Article
- The role of teichoic acids of bifidobacteria in driving the interaction with the human host.Frontiers in microbiology · 2025Article
- 'Wild Type'.Microbiology (Reading, England) · 2024Review
- Linking human milk oligosaccharide metabolism and early life gut microbiota: bifidobacteria and beyond.Microbiology and molecular biology reviews : MMBR · 2024Review
- Ecology- and genome-based identification of theApplied and environmental microbiology · 2024Article
- Molecular cross-talk among human intestinal bifidobacteria as explored by a human gut model.Frontiers in microbiology · 2024Article
- Genomic and ecological approaches to identify theFrontiers in microbiology · 2024Article
- Recent advances in enzymatic properties, preparation methods, and functions of glycoside hydrolase from Bifidobacterium: a review.World journal of microbiology & biotechnology · 2023Review
- Exploring Molecular Interactions between Human Milk Hormone Insulin and Bifidobacteria.Microbiology spectrum · 2023Article
- Sharing of Moonlighting Proteins Mediates the Symbiotic Relationship among Intestinal Commensals.Applied and environmental microbiology · 2023Article
- Identification of a prototype human gutFrontiers in microbiology · 2023Article
- Designation of optimal reference strains representing the infant gut bifidobacterial species through a comprehensive multi-omics approach.Environmental microbiology · 2022Article
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Authors and funding
19 authors.
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Abstract
The genomic era has resulted in the generation of a massive amount of genetic data concerning the genomic diversity of bacterial taxa. As a result, the microbiological community is increasingly looking for ways to define reference bacterial strains to perform experiments that are representative of the entire bacterial species. Despite this, there is currently no established approach allowing a reliable identification of reference strains based on a comprehensive genomic, ecological, and functional context. In the current study, we developed a comprehensive multi-omics approach that will allow the identification of the optimal reference strains using the Bifidobacterium genus as test case. Strain tracking analysis based on 1664 shotgun metagenomics datasets of healthy infant faecal samples were employed to identify bifidobacterial strains suitable for in silico and in vitro analyses. Subsequently, an ad hoc bioinformatic tool was developed to screen local strain collections for the most suitable species-representative strain alternative. The here presented approach was validated using in vitro trials followed by metagenomics and metatranscriptomics analyses. Altogether, these results demonstrated the validity of the proposed model for reference strain selection, thus allowing improved in silico and in vitro investigations both in terms of cross-laboratory reproducibility and relevance of research findings.
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