Crisci, Marco Alberto; (2023) Lak megaphages: prevalence, taxonomy, and applications. Doctoral thesis (Ph.D), UCL (University College London).

Text Marco thesis lib.pdf - Accepted Version Access restricted to UCL open access staff until 1 July 2024. Download (56MB)

Abstract

Alternatively coded Lak megaphage genomes (>540 kbp) that replicate in Prevotella were recently resolved from human and baboon faecal metagenomes, along with partial genomes from pigs. This study used diagnostic and quantitative PCR to determine the wider prevalence and abundance of Lak phages in human and animal microbiomes, and the extent of codon reassignment. Lak phage genomes were taxonomically classified using computational tools. Furthermore, a recombinant Lak phage-encoded endolysin was produced to evaluate its therapeutic potential. Lak phages were detected in microbiomes from 9 different animal species (35% of those investigated), including pigs where they were significantly more abundant in the hindgut compared to the foregut. Lak phages were also detected in human periodontal plaques and vaginal samples from humans and pigs. From racehorse faecal DNA, genome-resolved metagenomics uncovered a 660 kbp Lak-like genome, which is the largest phage genome reported in a gut microbiome. Additional Lak-like phages were detected in pig, human and non-human primate gut metagenomes. Complete Lak-like genomes were assigned to the proposed family “Magnaviridae”, comprising of 4 discrete genera, 9 species and 23 strains. “Magnaviridae” is putatively placed in a new order “Grandevirales” which currently includes at least 45 huge phage genomes. Lak endolysins were predicted to have structural characteristics involved in peptidoglycan binding. Bacteriolytic activity of LysA1 against Prevotella melalinogenica was confirmed, providing evidence of self-delivery to the peptidoglycan, and experimental validation of phage recoding which is conserved in all Lak phages. Prevalence of related Lak genomes suggests dispersal between, and ubiquity in, Prevotella-rich enterotypes from humans and animals consuming fibrous diets. Lysis of Prevotella by Lak phages has potential relevance to periodontal disease, bacterial vaginosis, and production pig performance. Together, the results suggest that Lak phages may be adapted, ancient and persistent features of microbiomes.

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