Genome plasticity shapes the ecology and evolution of Phocaeicola dorei and Phocaeicola vulgatus

Abstract

Phocaeicola dorei and Phocaeicola vulgatus are very common and abundant members of the human gut microbiome and play an important role in the infant gut microbiome. These species are closely related and often confused for one another; yet, their genome comparison, interspecific diversity, and evolutionary relationships have not been studied in detail so far. Here, we perform phylogenetic analysis and comparative genomic analyses of these two Phocaeicola species. We report that P. dorei has a larger genome yet a smaller pan-genome than P. vulgatus. We found that this is likely because P. vulgatus is more plastic than P. dorei, with a larger repertoire of genetic mobile elements and fewer anti-phage defense systems. We also found that P. dorei directly descends from a clade of P. vulgatus¸ and experienced genome expansion through genetic drift and horizontal gene transfer. Overall, P. dorei and P. vulgatus have very different functional and carbohydrate utilisation profiles, hinting at different ecological strategies, yet they present similar antimicrobial resistance profiles.

Keywords: Comparative genomics; Gut microbiome; Horizontal gene transfer; Pangenome; Phocaeicola.

Figure 1

Overview of the characteristics of the genomes of P. dorei and P. vulgatus. (Wilcoxon tests, ****: adj. p value < 0.0001, ns: non-significant). (A) Genome size comparison (total number of nucleotides). (B) Comparison between the number of predicted genes per genome. (C) Comparison between the GC content (%). (D, E) Completeness and Contamination level of the assemblies used in this study (%). (F) Genome size as a function of the number of predicted genes per genome. The lines correspond to linear regression for each species with 95% confidence intervals (R² = 0.901 and R² = 0.920 for P. dorei and P. vulgatus, respectively, t-test adj. p values < 0.0001). (G) Average cumulative number of conserved genes (plain lines) and total genes (dashed lines) as a function of added genomes in the pan-genome for P. dorei and P. vulgatus (averaged over 100 random combinations). Grey area correspond to standard deviation. (H) Distribution of gene lengths (in bases) for P. dorei and P. vulgatus.

Figure 2

Phylogeny and genomic comparison of P. dorei and P. vulgatus. (A) Phylogenetic tree (natural logarithmic scale) including metadata regarding host, country of origin, isolation from disease state, isolation from infants, and including all P. dorei and P. vulgatus assemblies used in this study. The blue and red bars indicate genome size relative to the average genome size of all assemblies. (B) Phylogenetic tree at the normal scale displaying only the average genome size. (C) Comparison of synteny between P. dorei and P. vulgatus reference genomes.

Figure 3

Mobile genetic elements and HGTs. P. dorei and P. vulgatus mobilome. (A) Number of proteins related to bacteriophage per genome. (B) Number of proteins related to IS per genome. (C) Number of proteins related to ICEs. (D) Number of proteins related to plasmids. (E) Number of CRISPR genes per genome. (F) Number of repeats per CRISPR gene per genome. (G) Number of genes associated with HGT. (H) Top 10 species associated with HGT in P. dorei. (I) Top 10 species associated with HGT in P. vulgatus.

Figure 4

COG categories comparison for P. dorei and P. vulgatus (****, Wilcoxon test, adj. p value < 0.0001. (***, Wilcoxon test, adj. p value < 0.001).

Figure 5

Carbohydrate enzyme profile of P. dorei and P. vulgatus. (A) Heat map showing the different CAZymes present in each assembly, with P. dorei and P. vulgatus genomes grouping separately (only GH families present in more than 4 genomes are shown here). (B) Heat map showing only GH families associated with HMO utilization genes according to^,. (C) Alpha diversity (Shannon index) of P. dorei and P. vulgatus GH families profile. (D) Number of genes per genome belonging to the GH family GH95 (1,2-α-L-fucosidase) (****, Wilcoxon test, adj. p value < 0.0001).

Figure 6

Antibiotic resistance profile of P. dorei and P. vulgatus. (A) Heat map of P. dorei and P. vulgatus assemblies showing the different antibiotic resistance genes present in each strain. (B) Comparison of the number of AMR genes present in the genomes of P. dorei and P. vulgatus. (C–E) AMR families with different abundances per genome in both species (Wilcoxon test, ****, adj. p value < 0.0001, ***, adj. p value < 0.001, **, adj. p value < 0.01, ns non-significant).