Genomic and functional diversity of cultivated Bifidobacterium from human gut microbiota

Abstract

The genus Bifidobacterium widely exists in human gut and has been increasingly used as the adjuvant probiotics for the prevention and treatment of diseases. However, the functional differences of Bifidobacterium genomes from different regions of the world remain unclear. We here describe an extensive study on the genomic characteristics and function annotations of 1512 genomes (clustered to 849 non-redundant genomes) of Bifidobacterium cultured from human gut. The distribution of some carbohydrate-active enzymes varied among different Bifidobacterium species and continents. More than 36% of the genomes of B. pseudocatenulatum harbored biosynthetic gene clusters of lanthipeptide-class-iv. 99.76% of the cultivated genomes of Bifidobacterium harbored genes of bile salt hydrolase. Most genomes of B. adolescentis, and all genomes of B. dentium harbored genes involved in gamma-aminobutyric acid synthesis. B. longum subsp. infantis were characterized harboring most genes related to human milk oligosaccharide utilization. Significant differences between the distribution of antibiotic resistance genes among different species and continents revealed the importance to use antibiotics precisely in the clinical treatment. Phages infecting Bifidobacterium and horizontal gene transfers occurring in genomes of Bifidobacterium were dependent on species and region sources, and might help Bifidobacterium adapt to the environment. In addition, the distribution of Bifidobacterium in human gut was found varied from different regions of the world. This study represents a comprehensive view of characteristics and functions of genomes of cultivated Bifidobacterium from human gut, and enables clinical advances in the future.

Keywords: Bifidobacterium; Bile salt hydrolase; Gut microbiome; Horizontal gene transfers; Phages.

Fig. 1

Genomic diversity of cultivated Bifidobacterium in human gut. a, Phylogenetic tree of 1512 cultivated genomes of Bifidobacterium, based on GTDB annotation. The innermost circle is colored according to the species. The second circle is colored according to the continents from which strains were isolated. The third circle is colored according to the databases from which genomes were obtained. The fourth circle shows the GC content of genomes and the blue line represents a percentage of 62%. The outermost circle represents the genome length, with the red dashed line showing a genome size of 1.9 Mb and the light blue solid line showing a genome size of 2.5 Mb b, The number of genomes of Bifidobacterium collected from three databases, colored according to the species. c, Scatterplot of genomes of 849 non-redundant cultivated Bifidobacterium showing genome size and GC content. The cloud around points represents a simple encirclement of points, using geom_encircle in ggplot2 package of R. d, Principal Co-ordinates Analysis (PCoA) of taxonomic annotation of 849 Bifidobacterium genomes, based on ANI values among the genomes (p = 0.001, R² = 0.99917, calculated using Adonis test in R). The clouds around the clusters represents a 95% confidence interval. Panel b, c, and d are colored according to the species shown in panel a.

Fig. 2

Functional profile of cultivated Bifidobacterium (for 849 non-redundant genomes). a, The prevalence of some CAZyme families in B. adolescentis, B. pseudocatenulatum, and B. longum subsp. longum, colored according to the continent. The CAZymes with obvious differences among different continents in each species are shown. The prevalence represents the number of genomes harboring corresponding CAZyme relative to the total number of corresponding species in this continent. b, The distribution of BGCs in different species. The pie charts show the distribution of continents from which the genomes were obtained. The color of continents is shown in panel a. c, The distribution of genes related to GABA producing and bile salt hydrolysis harbored by each species. The sizes of bubbles and the number shown in the bubbles represent the prevalence of these genes in each species.

Fig. 3

Annotation of ARGs in the genomes of Bifidobacterium (for 849 non-redundant genomes). a, The distribution of annotated ARGs in Bifidobacterium. The genomes are annotated by their species and continents and the antibiotics are colored according to the importance of drug usage. b, The boxplot of number of ARGs harbored in genomes of different species, colored by their species. Each point represents a genome with annotated ARGs. c, The boxplot of number of ARGs harbored in genomes of different continents, colored by corresponding continent. Only the significant p-values are shown in the figure, calculated by paired wilcoxon test in R.

Fig. 4

Taxonomic and functional annotation of phages infecting Bifidobacterium (for 849 non-redundant genomes). a, Venn diagram and histogram showing distribution of VCs infecting Bifidobacterium of different species, colored according to their species. b, Venn diagram and histogram showing distribution of PFAMs of phages, colored according to their species. c-e, Venn diagram showing the distribution of PFAMs encoded by phages infecting B. longum subsp. longum (c), B. pseudocatenulatum (d), and B. adolescentis (e) from different continents, colored according to the continents.

Fig. 5

HGTs occurring in Bifidobacterium genomes (for 849 non-redundant genomes). a, The number of detected HGT genes classified based on the taxa supposed to be the source of the transfer. b, The number of genes derived from HGT events according to the COG annotation, colored by the COG types. c, The percentage of genes derived from HGT events in each genome, classified and colored according to the species. d, The percentage of genes derived from HGT events in each genome of B. adolescentis, B. bifidum, and B. longum subsp. longum, and B. pseudocatenulatum, classified and colored according to continents. P-values are shown in the figure, calculated by paired wilcoxon test in R.

Fig. 6

Distribution of cultivated Bifidobacterium in three different cohorts. Boxplot represents the proportion of each species in the abundance of these 15 Bifidobacterium species in a sample. Each point represents a sample, colored according to the cohorts. Significant differences between the proportion of the same species of different cohorts are marked on the right of the boxplot, calculated by paired wilcoxon test in R (*** represents P < 0.001).