Bacteriophages typically have small genomes 1 and depend on their bacterial hosts for replication 2 . Here we sequenced DNA from diverse ecosystems and found hundreds of phage genomes with lengths of more than 200 kilobases (kb), including a genome of 735 kb, which is-to our knowledge-the largest phage genome to be described to date. Thirty-five genomes were manually curated to completion (circular and no gaps). Expanded genetic repertoires include diverse and previously undescribed CRISPR-Cas systems, transfer RNAs (tRNAs), tRNA synthetases, tRNA-modification enzymes, translation-initiation and elongation factors, and ribosomal proteins. The CRISPR-Cas systems of phages have the capacity to silence host transcription factors and translational genes, potentially as part of a larger interaction network that intercepts translation to redirect biosynthesis to phage-encoded functions. In addition, some phages may repurpose bacterial CRISPR-Cas systems to eliminate competing phages. We phylogenetically define the major clades of huge phages from human and other animal microbiomes, as well as from oceans, lakes, sediments, soils and the built environment. We conclude that the large gene inventories of huge phages reflect a conserved biological strategy, and that the phages are distributed across a broad bacterial host range and across Earth's ecosystems.Phages-viruses that infect bacteria-are considered distinct from cellular life owing to their inability to carry out most biological processes required for reproduction. They are agents of ecosystem change because they prey on specific bacterial populations, mediate lateral gene transfer, alter host metabolism and redistribute bacterially derived compounds through cell lysis 2-4 . They spread antibiotic resistance 5 and disperse pathogenicity factors that cause disease in humans and animals 6,7 . Most knowledge about phages is based on laboratorystudied examples, the vast majority of which have genomes that are a few tens of kb in length. Widely used isolation-based methods select against large phage particles, and they can be excluded from phage concentrates obtained by passage through 100-nm or 200-nm filters 1 . In 2017, only 93 isolated phages with genomes that were more than 200 kb in length were published 1 . Sequencing of whole-community DNA can uncover phage-derived fragments; however, large genomes can still escape detection owing to fragmentation 8 . A new clade of human-and animal-associated megaphages was recently described on the basis of genomes that were manually curated to completion from metagenomic datasets 9 . This finding prompted us to carry out a more-comprehensive analysis of microbial communities to evaluate the prevalence, diversity and ecosystem distribution of phages with large genomes. Previously, phages with genomes of more than 200 kb have been referred to as 'jumbophages' 1 or, in the case of phages with genomes of more than 500 kb, as megaphages 9 . As the set reconstructed here span both size ranges we refer to them simply as 'huge phage...

Bacteriophages (phages) dramatically shape microbial community composition, redistribute nutrients via host lysis and drive evolution through horizontal gene transfer. Despite their importance, much remains to be learned about phages in the human microbiome. We investigated the gut microbiomes of humans from Bangladesh and Tanzania, two African baboon social groups and Danish pigs; many of these microbiomes contain phages belonging to a clade with genomes >540 kilobases in length, the largest yet reported in the human microbiome and close to the maximum size ever reported for phages. We refer to these as Lak phages. CRISPR spacer targeting indicates that Lak phages infect bacteria of the genus Prevotella. We manually curated to completion 15 distinct Lak phage genomes recovered from metagenomes. The genomes display several interesting features, including use of an alternative genetic code, large intergenic regions that are highly expressed and up to 35 putative transfer RNAs, some of which contain enigmatic introns. Different individuals have distinct phage genotypes, and shifts in variant frequencies over consecutive sampling days reflect changes in the relative abundance of phage subpopulations. Recent homologous recombination has resulted in extensive genome admixture of nine baboon Lak phage populations. We infer that Lak phages are widespread in gut communities that contain the Prevotella species, and conclude that megaphages, with fascinating and underexplored biology, may be common but largely overlooked components of human and animal gut microbiomes.

HighlightsPCR and genomeresolved 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