Diversity patterns of bacteriophages infecting Aggregatibacter and Haemophilus species across clades and niches

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  • Szymon P. Szafranski, Cluster Excellence RESIST EXC 2155, Hannover Medical School, Lower Saxony Ctr Biomed Engn Implant Res & Dev NI
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  • Mogens Kilian
  • Ines Yang, Lower Saxony Ctr Biomed Engn Implant Res & Dev NI, Hannover Medical School
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  • Gesa Bei Der Wieden, Lower Saxony Ctr Biomed Engn Implant Res & Dev NI, Hannover Medical School
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  • Andreas Winkel, Lower Saxony Ctr Biomed Engn Implant Res & Dev NI, Hannover Medical School
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  • Jan Hegermann, Cluster Excellence REBIRTH EXC 62, Hannover Medical School
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  • Meike Stiesch, Cluster Excellence RESIST EXC 2155, Lower Saxony Ctr Biomed Engn Implant Res & Dev NI, Hannover Medical School

Aggregatibacter and Haemophilus species are relevant human commensals and opportunistic pathogens. Consequently, their bacteriophages may have significant impact on human microbial ecology and pathologies. Our aim was to reveal the prevalence and diversity of bacteriophages infecting Aggregatibacter and Haemophilus species that colonize the human body. Genome mining with comparative genomics, screening of clinical isolates, and profiling of metagenomes allowed characterization of 346 phages grouped in 52 clusters and 18 superclusters. Less than 10% of the identified phage clusters were represented by previously characterized phages. Prophage diversity patterns varied significantly for different phage types, host clades, and environmental niches. A more diverse phage community lysogenizes Haemophilus infiuenzae and Haemophilus parainfiuenzae strains than Aggregatibacter actinomycetemcomitans and "Haemophilus ducreyi". Co-infections occurred more often in "H. ducreyi". Phages from Aggregatibacter actinomycetemcomitans preferably lysogenized strains of specific serotype. Prophage patterns shared by subspecies clades of different bacterial species suggest similar ecoevolutionary drivers. Changes in frequencies of DNA uptake signal sequences and guanine-cytosine content reflect phage-host long-term coevolution. Aggregatibacter and Haemophilus phages were prevalent at multiple oral sites. Together, these findings should help exploring the ecoevolutionary forces shaping virus-host interactions in the human microbiome. Putative lytic phages, especially phiKZ-like, may provide new therapeutic options.

Original languageEnglish
JournalISME Journal
Volume13
Issue10
Pages (from-to)2500-2522
Number of pages23
ISSN1751-7362
DOIs
Publication statusPublished - Oct 2019

    Research areas

  • UPTAKE SIGNAL SEQUENCES, DNA UPTAKE, ACTINOBACILLUS-ACTINOMYCETEMCOMITANS, ENORMOUS DIVERSITY, NATURAL COMPETENCE, PROPHAGES, GENOME, PHAGES, MICROBIOME, INFLUENZAE

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