Closely related Lak megaphages replicate in the microbiomes of diverse animals

Highlights
• PCR and genome-resolved metagenomics revealed Lak phages in 13 animal species
• Lak is abundant in the pig hindgut, with potential relevance to growth performance
• Thirty-four new Lak phage genomes present expanded size range and phylogeny
• Unique Lak protein families from specific microbiomes suggest animal host adaptation

Summary
Lak 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.