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Diversity of Human-Associated Bifidobacterial Prophage Sequences.

ABSTRACT: Members of Bifidobacterium play an important role in the development of the immature gut and are associated with positive long-term health outcomes for their human host. It has previously been shown that intestinal bacteriophages are detected within hours of birth, and that induced prophages constitute a significant source of such gut phages. The gut phageome can be vertically transmitted from mother to newborn and is believed to exert considerable selective pressure on target prokaryotic hosts affecting abundance levels, microbiota composition, and host characteristics. The objective of the current study was to investigate prophage-like elements and predicted CRISPR-Cas viral immune systems present in publicly available, human-associated Bifidobacterium genomes. Analysis of 585 fully sequenced bifidobacterial genomes identified 480 prophage-like elements with an occurrence of 0.82 prophages per genome. Interestingly, we also detected the presence of very similar bifidobacterial prophages and corresponding CRISPR spacers across different strains and species, thus providing an initial exploration of the human-associated bifidobacterial phageome. Our analyses show that closely related and likely functional prophages are commonly present across four different species of human-associated Bifidobacterium. Further comparative analysis of the CRISPR-Cas spacer arrays against the predicted prophages provided evidence of historical interactions between prophages and different strains at an intra- and inter-species level. Clear evidence of CRISPR-Cas acquired immunity against infection by bifidobacterial prophages across several bifidobacterial strains and species was obtained. Notably, a spacer representing a putative major capsid head protein was found on different genomes representing multiple strains across B. adolescentis, B. breve, and B. bifidum, suggesting that this gene is a preferred target to provide bifidobacterial phage immunity.

SUBMITTER: Buckley D

PROVIDER: S-EPMC8705816 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Huanglongbing disease (HLB; yellow shoot disease) is a severe worldwide infectious disease for citrus family plants. The pathogen "Candidatus Liberibacter asiaticus" is an alphaproteobacterium of the Rhizobiaceae family that has been identified as the causative agent of HLB. The virulence of "Ca. Liberibacter asiaticus" has been attributed, in part, to prophage-carried genes. Prophage and prophage-like elements have been identified in 12 of the 15 available "Ca. Liberibacter asiaticus" genomes and are classified into three prophage types. Here, we reexamined all 15 "Ca. Liberibacter asiaticus" genomes using a de novo prediction approach and expanded the number of prophage-like elements from 16 to 33. Further, we found that all of the "Ca. Liberibacter asiaticus" genomes contained at least one prophage-like sequence. Comparative analysis revealed a prevalent, albeit previously unknown, prophage-like sequence type that is a remnant of an integrated prophage. Notably, this remnant prophage is found in the Ishi-1 "Ca. Liberibacter asiaticus" strain that had previously been reported as lacking prophages. Our findings provide both a resource for data and new insights into the evolutionary relationship between phage and "Ca. Liberibacter asiaticus" pathogenicity.IMPORTANCE Huanglongbing (HLB) disease is threatening citrus production worldwide. The causative agent is "Candidatus Liberibacter asiaticus." Prior work using mapping-based approaches identified prophage-like sequences in some "Ca. Liberibacter asiaticus" genomes but not all. Here, we utilized a de novo approach that expands the number of prophage-like elements found in "Ca. Liberibacter asiaticus" from 16 to 33 and identified at least one prophage-like sequence in all "Ca. Liberibacter asiaticus" strains. Furthermore, we identified a prophage-like sequence type that is a remnant of an integrated prophage-expanding the number of prophage types in "Ca. Liberibacter asiaticus" from 3 to 4. Overall, the findings will help researchers investigate the role of prophage in the ecology, evolution, and pathogenicity of "Ca. Liberibacter asiaticus."

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Diversity of Human-Associated Bifidobacterial Prophage Sequences.

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