Editorial: Role of Bifidobacteria in Human and Animal Health and Biotechnological Applications

Transcriptional landscape of the pMP7017 megaplasmid and its impact on the Bifidobacterium breve UCC2003 transcriptome

The 190 kb megaplasmid pMP7017 of Bifidobacterium breve JCM7017 represents the first conjugative and largest plasmid characterised within this genus to date. In the current study, we adopted an integrated approach combining transcriptomics, whole genome comparative analysis and metagenomic data mining to understand the biology of pMP7017 and related megaplasmids, and to assess the impact of plasmid-carriage on the host strain. The data generated revealed variations within basic features of promoter elements which correlate with a high level of transcription on the plasmid and highlight the transcriptional activity of genes encoding both offensive and defensive adaptations, including a Type IIL restriction-modification system, an anti-restriction system and four Type II toxin-antitoxin systems. Furthermore, a highly transcribed tmRNA, which likely provides translational support to the host strain, was identified, making pMP7017 the first plasmid of the Bifidobacterium genus and the smallest plasmid known to express a tmRNA. Analyses of synteny and variability among pMP7017 and related plasmids indicate substantial diversity in gene organisation and accessory gene cargo highlighting diverse (co-)evolution and potential host-specific rearrangements and adaptations. Systematic analysis of the codon usage profile of transcriptionally active pMP7017-encoded genes suggests that pMP7017 originated from (sub)species of Bifidobacterium longum. Furthermore, mining of metagenomic data suggests the presence of pMP7017-homologues in ~10% of microbiome samples, mostly infants and/or mothers from various geographical locations. Comparative transcriptome analysis of the B. breve UCC2003 chromosome in the presence or absence of pMP7017 revealed differential expression of genes representing 8% of the total gene pool. Genes involved in genetic information processing were exclusively upregulated, while altered expression of genes involved in biofilm production and polysaccharide biosynthesis was also observed.

A Natural Gas Fermentation Bacterial Meal (FeedKind®) as a Functional Alternative Ingredient for Fishmeal in Diet of Largemouth Bass, Micropterus salmoides

A 10-week growth study was conducted to evaluate the effect of a natural gas fermentation bacterial meal (FeedKind^®, FK) as a fishmeal (FM) alternative in largemouth bass (Micropterus salmoides) (48.0 ± 0.03 g). Four isonitrogenous and isoenergetic diets were formulated including one commercial control (C, 42% FM) and three experimental diets with gradient FK of 3% (FK3, 29%FM), 6% (FK6, 26%FM) and 9% (FK9, 23%FM), respectively. FK-fed groups showed significantly higher SR than that of C group. The WGR and SGR of fish fed FK3 and FK6 were significantly higher than those of FK9, but not statistical different from the C group. FK-fed groups showed higher apparent digestibility coefficients of dry matter and nutrients. Further, FK-fed groups increased the ratio of SOD/MDA in the plasma and liver, and the upregulation of intestinal Keap1 and downregulation of HIF1α was found in FK3. Furthermore, FK-fed groups showed higher microbial richness and diversity. Pearson correlation analysis found that antioxidant relevant biomarkers were negatively correlated with the relative abundance of certain potential beneficial bacteria. In conclusion, supplemented up to 3–6% FK replacing FM in a low FM diet of largemouth bass could increase growth, survival rate, antioxidant capacity, and improve gut microbiota.