Whole-genome sequencing and genomic analysis of four Akkermansia strains newly isolated from human feces

Abstract

Background: Numerous studies have demonstrated that Akkermansia is closely associated with human health. These bacteria colonize the mucus layer of the gastrointestinal tract and utilize mucin as their sole source of carbon and nitrogen. Akkermansia spp. exhibit potential as probiotics under specific conditions. However, the gene accumulation curve derived from pan-genome analysis suggests that the genome of Akkermansia strains remains open. Consequently, current genome mining efforts are insufficient to fully capture the intraspecific and interspecific characteristics of Akkermansia, necessitating continuous exploration of the genomic and phenotypic diversity of new isolates.

Methods: Based on this finding, we sequenced, assembled, and functionally annotated the whole genomes of four new human isolates from our laboratory: AKK-HX001, AKK-HX002, AKK-HX003, and AKK-HX004.

Results: Phylogenetic analysis revealed that all four isolates belonged to the AmII phylogroup, whereas the type strain DSM 22959 is classified within the AmI phylogroup. Moreover, 2,184 shared homologous genes were identified among the four isolates. Functional annotation using the COG, KEGG, and CAZy databases indicated that the functional genes of the four isolates were primarily associated with metabolism. Two antibiotic resistance genes were identified in AKK-HX001 and AKK-HX002, while three resistance genes were detected in AKK-HX003 and AKK-HX004. Additionally, each of the four isolates possessed two virulence genes and three pathogenicity genes, none of which were associated with pathogenicity. The prediction of mobile genetic elements indicated unequal distributions of GIs among the isolates, and a complete CRISPR system was identified in all isolates except AKK-HX003. Two annotated regions of secondary metabolite biosynthesis genes, both belonging to Terpene, were detected using the antiSMASH online tool.

Conclusion: These findings indicate that the four Akkermansia isolates, which belong to a phylogroup distinct from the model strain DSM 22959, exhibit lower genetic risk and may serve as potential probiotic resources for future research.

Keywords: Akkermansia; genomic analysis; genomic diversity; probiotics; whole-genome sequencing.

Figure 1

Circular maps of AKK-HX001, AKK-HX002, AKK-HX003, AKK-HX004. From the inside out, the order is GC Skews (GC Skew+: green, GC Skew−: purple), GC Content (black), CDS (blue), tRNA, rRNA, repeat_region, and tmRNA (A). The Venn diagram was based on the homologous genes and unique genes of the 4 Akkermansia isolates (B).

Figure 2

Phylogenetic tree based on 16S rRNA. The value of each branch node in the phylogenetic tree represents the percentage of bootstrap values from 1,000 repetitions (A). The heatmap was based on the ANI values. The values shown on the heatmap indicate the similarity between each of the two given genomes (B).

Figure 3

Stacked histogram of COG functional classification of 4 Akkermansia isolates. COG functions were categorized into 4 main groups: Information Storage and Processing: J-B, Cellular Processes and Signaling: D-X, Metabolism: C-Q, Poorly Characterized: R, S.

Figure 4

The stacked bar of KEGG functional classification of 4 Akkermansia isolates. Metabolism: Carbohydrate metabolism, Energy metabolism, Lipid metabolism, Nucleotide metabolism, Amino acid metabolism, Metabolism of other amino acids, Glycan biosynthesis and metabolism, Metabolism of cofactors and vitamins, Metabolism of terpenoids and polyketides, Biosynthesis of other secondary metabolites, Xenobiotics biodegradation and metabolism. Genetic Information Processing: Transcription, Translation, Folding, Sorting and degradation, Replication and repair, Chromosome. Environmental Information Processing: Membrane transport, Signal transduction. Cellular Processes: Transport and catabolism, Cell growth and death, Cellular community – Prokaryotes, Cell motility. Organismal Systems: Immune system, Endocrine system, Digestive system, Excretory system, Nervous system, Aging, Environmental adaptation. Human Diseases: Cancer: Overview, Cancer: Specific types, Infectious disease: Viral, Infectious disease: Bacterial, Neurodegenerative disease, Cardiovascular disease, Endocrine and metabolic disease, Drug resistance: Antimicrobial, Drug resistance: Antineoplastic.

Figure 5

Cyclic thermogram of CAZy annotations of the 4 Akkermansia isolates.

Figure 6

COG categories for the genomes encoding genes on genomic islands of 4 Akkermansia isolates.