Genomic Diversity Of Bifidobacterium Pseudocatenulatum And Its Effect On The Gut Microbiota Of Healthy Mice

Bifidobacterium pseudocatenulatum is one of the most predominant bifidobacterial species in the intestine of healthy adults.Besides,it is ubiquitous in people of all ages.Several strains belonging to this species have been shown to have probiotic functions like improving glycolipids metabolism,regulating immune balance,relieving anxiety and depression.In addition,this bifidobacterial species has shown potential in food industry for its features such as production of conjugated linolenic acid and phytase.Although many probiotic functions have been found within this species,its genomic diversity as well as genomic evolution has not been reported in the previous study which focused on the prevention and alleviation on disease by individual strains.The effect of B.pseudocatenulatum on healthy host are unknown.In this study,88 B.pseudocatenulatum strains were isolated from fecal samples of healthy people and animals in China.The genome drafts of these strains were sequenced by Illunima Hiseq platform.The genomic diversity and evolutionary relationship among these strains was analyzed by comparative genomic approaches.Strains classified in different clades were applied in animal experiment to explore the effect of B.pseudocatenulatum strains from different evolutionary clusters on the gut microbiota of healthy hosts,providing theoretical support for the application and development of this Bifidobacterium species.Several findings were obtained via comparative genomic analysis of the 88 B.pseudocatenulatum strains.Strains in this study showed the consistent GC content,genome size,number of ORF and tRNA with the B.pseudocatenulatum strains in NCBI database.Geographical region had influence on the phylogenetic relationship among strains belonging to this species whereas age and sex of the host were not likely to play roles on it.Moreover,B.pseudocatenulatum showed a relatively wide genomic diversity,indicating that it was able to obtain new genes continuously to better adapt to environment.Specifically,the genomic diversity of B.pseudocatenulatum could be seen in CAZymes coding genes,CRISPR-Cas system,prophage and antibiotic resistance genes.CAZymes coding genes not only showed a great impact on the evolutionary development of B.pseudocatenulatum species,but also reflected the age-related changes in human gut microbiota.The occurrence of CRISPR-Cas system and prophage within B.pseudocatenulatum was 68.18% and 54.55%,respectively.Their existence greatly enriched the pan-genome of this Bifidobacterium species and contributed to the genomic diversity in B.pseudocatenulatum directly.41 antibiotic resistance genes(ARGs)were found in the 88 B.pseudocatenulatum genomes,17 of which belong to the intrinsic ARGs in this species,and most of the remaining genes were not likely have the transfer potential.B.pseudocatenulatum strains were not likely to affect the water and food intake,body weight gain and the level of serum inflammatory factors.Only 2 B.pseudocatenulatum strains FGSYC12M4 and FHuNMY10M3 reduced the host serum LDL-C/HDL-C level significantly while the remaining strains didn't show significant effect on the serum lipids of healthy hosts.Gavage of B.pseudocatenulatum to healthy host affected the host's gut microbiota and its level of short-chain fatty acids(SCFAs).In terms of gut microbiota,the relative abundance of Actinobacteria,Bacteroidetes,Proteobacteria,Verrucomicrobia,and Firmicutes changed significantly after gavage.At the genus level,the relative abundance of Bifidobacterium,Lactobacillus,Akkermansia,Alisipes,Lachnoclostridium,Dubosiella,Turicibacter changed significantly and this change could last for one week after gavage.B.pseudocatenulatum significantly improved the concentration of acetate,butyrate and valerate but showed no significant effect on propionate content.Based on the animal experiment and genomic analysis,it was found that the effect of B.pseudocatenulatum on the gut microbiota of healthy hosts were not related to the evolutionary relationship among strains,but to the unique genes.Strains with higher colonization ability have more unique genes related to carbohydrate transport and metabolism.It is speculated that they obtain colonization advantages through substrate competition.FAHBZ9L5,the strain showed a lasting effect on the gut microbiota of healthy host,possessed the most unique genes at up to 297 and 2.01% of which related to bacteriophage functions.It is inferred that FAHBZ9L5 interacted with other intestinal microorganisms frequently to exert a lasting affect gut microbiota after one week after gavage withdrawl.