The Clostridium-infecting filamentous phage CAK1 genome analysis allows to define a new potential clade of Tubulavirales

• Published in: FEMS microbiology letters 2023-01, Vol.370
• Main Authors: Billaud, Maud, Petit, Marie-Agnès, Lossouarn, Julien
• Format: Article
• Language: English
• Subjects: Annotations; Bioinformatics; Clostridium; Genomes; Gram-positive bacteria; Life Sciences; Metagenomics; Phages
• ISSN: 1574-6968; 0378-1097; 1574-6968
• DOI: 10.1093/femsle/fnad099

Abstract What we know about Tubulavirales, i.e. filamentous phages, essentially comes from Gram-negative-infecting Inoviridae. However, metagenomics recently suggests filamentous phages are much more widespread and diverse. Here, we report the complete sequence and functional annotation of CAK1, a 6.6 kb filamentous phage that was shown to chronically infect Clostridium beijerinckii 30 years ago and only represents the second filamentous phage cultivated on a Gram-positive bacterium. CAK1 has a typical filamentous phage modular genome with no homologs in databases and we were interested to compare it with a pig gut filamentous phage metagenomics dataset that we previously assembled and for which many filamentous phages were predicted to infect Clostridium species by bioinformatics means. CAK1 is distantly related to nine of these sequences, two of which have been predicted as Clostridium-associated. In itself, this small cluster of CAK1-connected sequences sheds light on the diversity of filamentous phages that putatively infect Clostridium species, and probably many other Gram-positive genera. The Clostridium-infecting phage CAK1 genome analysis provides supplemental clues about the diversity of filamentous phages putatively associated to Clostridum and maybe other Gram-positive bacterial genera.