Abstract
SummaryLak phages with alternatively coded ∼540 kbp genomes were recently reported to replicate in Prevotella in microbiomes of humans that consume a non-Western diet, baboons, and pigs. Here, we explore Lak phage diversity and broader distribution using diagnostic polymerase chain reaction and genome-resolved metagenomics. Lak phages were detected in 13 animal types, including reptiles, and are particularly prevalent in pigs. Tracking Lak through the pig gastrointestinal tract revealed significant enrichment in the hindgut compared to the foregut. We reconstructed 34 new Lak genomes, including six curated complete genomes, all of which are alternatively coded. An anomalously large (∼660 kbp) complete genome reconstructed for the most deeply branched Lak from a horse microbiome is also alternatively coded. From the Lak genomes, we identified proteins associated with specific animal species; notably, most have no functional predictions. The presence of closely related Lak phages in diverse animals indicates facile distribution coupled to host-specific adaptation.
Highlights
Prevotella and Bacteroides occupy similar ecological niches and compete for resources in gut microbiomes (Gorvitovskaia et al, 2016; Ley, 2016)
From the Lak genomes, we identified proteins associated with specific animal species; notably, most have no functional predictions
Lak phages detected in various animal microbiome samples by PCR PCR primer sets targeting genes for the major capsid protein (MCP), tail sheath monomer (TSM), and portal vertex protein (PVP) detected Lak in 112/194 samples from many animal gut microbiomes (Table 1, Tables S1 and S2)
Summary
Prevotella and Bacteroides (phylum Bacteroidetes) occupy similar ecological niches and compete for resources in gut microbiomes (Gorvitovskaia et al, 2016; Ley, 2016). Lak megaphages that replicate in Prevotella were recently discovered in human and baboon gut microbiomes using genome-resolved metagenomics (Devoto et al, 2019). To date, these phages are among the largest identified in gut microbiomes (>540 kbp genomes in length) and encode a tail sheath protein which (along with large terminase phylogeny) suggests a myovirus morphotype. Lak phage sequences were detected in Danish pig metagenomes abundant in Prevotella and in cow rumens at low abundance (Devoto et al, 2019). Lysis by Lak phages could alter the composition and abundance of Prevotella in the animal/human host, affecting microbial community structure and nutrient availability
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