Genome sequencing and probiotic properties of Lactobacillus Fermentum 3872

Introduction Due to the rise of multidrug-resistant forms of microbial pathogens, the development of alternative approaches for fighting infectious diseases is urgently needed. One such approach is the use of probiotics. Lactobacillus fermentum strain 3872 is a promising probiotic bacterium with a range of antibacterial properties. Methods Complete genome sequencing was achieved by using a hybrid approach, including Ion Torrent PGM, (producing up to 400 bp reads with low error rates), PacBio technology (generating long reads with higher error rates), as well as optical genomic mapping system (OpGen) allowing an independent verification of the assembly. Protein binding and bacterial attachment experiments were conducted by using an ELISA assay employing microtiter plates coated with collagen. Affinity purification was conducted using magnetic particles coated with collagen. Liquid State Mass-Spectrometry (LS-MS/MS) analysis was conducted at Cambridge Centre for Proteomics. Results The genome of Lactobacillus fermentum strain 3872 was found to consist of a circular chromosome (2,297,851 bases) and a plasmid, pLF3872 (32,641 bases). Genome sequencing of this strain revealed a number of specific features, potentially contributing to its beneficial probiotic properties, including a capability of producing a range of vitamins (e.g. as B1, B2, B5, B7 and B9). One remarkable feature of the genome is the presence of genes encoding putative adhesins with different specificities. In particular, a gene encoding a collagen-binding protein (CBP) was detected on the plasmid, which also contains a number of ‘selfish genes’ required for stable maintenance of the plasmid within the host. No other known L. fermentum strains contained this plasmid. The CBP structure was unique with a record number (five) of repetitive B domains, not found in similar proteins produced by other bacteria, including Staphylococcus aureus. As the B domains in similar proteins are known to form a stalk structure, the increased number of the units in this stalk is expected to improve interaction with the target host cells, increase stability of the protein and reduce a masking effect of the bacterial capsule. Strong binding of probiotic bacteria to host tissue collagen may lead to competitive exclusion of harmful pathogenic microorganisms using this receptor for attachment. The unique predicted features of the CBP of Lactobacillus fermentum 3872 prompted further investigation of its properties. The results of this study confirmed that the recombinant CBP protein of L. fermentum 3872, isolated after expression and purification from E. coli, binds to collagen 1. Moreover, we found that both CBP and L. fermentum compete with campylobacter for binding to this host cell receptor. Furthermore, using affinity purification system followed by LS MS/MS, we identified collagen-binding adhesins campylobacter. Discussion Combined with our observation that L. fermentum 3872 also possesses other factors involved in anti-campylobacter activity (e.g. by producing acidic environment), our findings provides a good basis for further investigation of this strain as a potential tool for fighting infections caused by campylobacter and other pathogens