The Integrated Probiotic Database: a genomic compendium of bifidobacterial health-promoting strains

Abstract

Background: The World Health Organization defines probiotics as “live microorganisms, which when administered in adequate amounts confer a health benefit on the host”. In this framework, probiotic strains should be regarded as safe for human and animal consumption, i.e., they should possess the GRAS (generally recognized as safe) status, notified by the local authorities. Consistently, strains of selected Bifidobacterium species are extensively used as probiotic agents to prevent and ameliorate a broad spectrum of human and/or animal gastrointestinal disorders. Even though probiotic properties are often genus- or species-associated, strain-level differences in the genetic features conferring individual probiotic properties to commercialized bifidobacterial strains have not been investigated in detail. Methods: In this study, we built a genomic database named Integrated Probiotic DataBase (IPDB), whose first iteration consists of common bifidobacterial strains used in probiotic products for which public genome sequences were available, such as members of B. longum subsp. longum, B. longum subsp. infantis, B. bifidum, B. breve, and B. animalis subsp. lactis taxa. Furthermore, the IPDB was exploited to perform comparative genome analyses focused on genetic factors conferring structural, functional, and chemical features predicted to be involved in microbe-host and microbe-microbe interactions. Results and conclusion: Our analyses revealed strain-level genetic differences, underlining the importance of inspecting the strain-specific and outcome-specific efficacy of probiotics. In this context, IPDB represents a valuable resource for obtaining genetic information of well-established bifidobacterial probiotic strains.

Recommendations to Improve Quality of Probiotic Systematic Reviews With Meta-Analyses

“…Conclusions of SRMAs may be biased or misleading if heterogeneous interventions are pooled. In the probiotic field, current research supports the importance of considering individual strain differences when pooling studies . The main strength of using a strain-specific approach to assess efficacy is that clear conclusions on specific probiotic strains can be drawn, particularly when delivered in the same vehicle and dose …”

Identification of a prototype human gut Bifidobacterium longum subsp. longum strain based on comparative and functional genomic approaches

“…To assess unique features encoded by the PRL2022 genome that may for example enhance its fitness or gut-associated microbe-host/microbe-microbe interactions, a comparative genomics analysis was performed by considering the genomes of 10 B. longum subsp. longum strains currently included in commercially probiotic products ( Tarracchini et al, 2022 ). Specifically, to provide a fully representative PRL2022 genome sequence, the PRL2022 genome generated by combining sequencing data obtained from both Illumina sequencing (sequencing output of 556,485 short reads) and Oxford Nanopore MinION (sequencing output of 57,198 long reads) was used.…”

“…The PRL2022 genome together with various genomes of B. longum subsp. longum strains that are currently included in a variety of commercially available probiotic products ( Tarracchini et al, 2022 ; Supplementary Table S3 ), were subjected to a pangenome analysis pipeline (PGAP) ( Zhao et al, 2012b ). Predicted proteome of a specific B. longum subsp.…”

Designation of optimal reference strains representing the infant gut bifidobacterial species through a comprehensive multi‐omics approach

“…How to cite this article: Fontana, F., Alessandri, G., Tarracchini, C., Bianchi, M.G., Rizzo, S.M., Mancabelli, L. et al (2022) Designation of optimal reference strains representing the infant gut bifidobacterial species through a comprehensive multi-omics approach. Environmental Microbiology, 24(12), 5825-5839.…”

“…infantis and B. longum subsp. longum represent the most prevalent and abundant bifidobacterial species of the ‘infant‐like’ gut microbiota (Arboleya et al, 2016 ; Duranti et al, 2017 ; Milani et al, 2015 ; Tarracchini et al, 2022 ; Turroni et al, 2021 ; Turroni, Milani, Duranti, Ferrario, et al, 2018 ). Furthermore, scientific interest in bifidobacteria has led to extensive isolation efforts that now allow access to a large number of strains and their corresponding genomic sequences (Saturio et al, 2021 ; Turroni et al, 2022 ), rendering this genus a suitable example to perform phylogenomic studies.…”