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Gastrointestinal jumbo phages possess independent synthesis and utilization systems of NAD+

Authors: Li, Cunyuan; Liu, Kaiping; Gu, Chengxiang; Li, Ming; Zhou, Ping; Chen, Linxing; Sun, Shize; +5 Authors

Gastrointestinal jumbo phages possess independent synthesis and utilization systems of NAD+

Abstract

Jumbo phages, phages with genomes > 200 kbp, contain some unique genes for successful reproduction in their bacterial hosts. Due to complex and massive genomes analogous to those of small-celled bacteria, how jumbo phages complete their life cycle remains largely undefined.In this study, we assembled 668 high-quality jumbo phage genomes from over 15 terabytes (TB) of intestinal metagenomic data from 955 samples of 5 animal species (cow, sheep, pig, horse, and deer). Within them, we obtained a complete genome of 716 kbp in length, which is the largest phage genome so far reported in the gut environments. Interestingly, 174 out of the 668 jumbo phages were found to encode all genes required for the synthesis of NAD+ by the salvage pathway or Preiss-Handler pathway, referred to as NAD-jumbo phage. Besides synthesis genes of NAD+, these NAD-jumbo phages also encode at least 15 types of NAD+-consuming enzyme genes involved in DNA replication, DNA repair, and counterdefense, suggesting that these phages not only have the capacity to synthesize NAD+ but also redirect NAD+ metabolism towards phage propagation need in hosts. Phylogenetic analysis and environmental survey indicated NAD-jumbo phages are widely present in the Earth's ecosystems, including the human gut, lakes, salt ponds, mine tailings, and seawater.In summary, this study expands our understanding of the diversity and survival strategies of phages, and an in-depth study of the NAD-jumbo phages is crucial for understanding their role in ecological regulation. Video Abstract.

Keywords

DNA Replication, Sheep, Bacteria, Swine, Research, Deer, QR100-130, Genome, Viral, NAD, Jumbo phage, Gastrointestinal Microbiome, Microbial ecology, NAD+, Swine [MeSH] ; Bacteriophage ; Deer/virology [MeSH] ; Humans [MeSH] ; Bacteriophages/classification [MeSH] ; Metagenome ; Bacteria/genetics [MeSH] ; Gastrointestinal Microbiome [MeSH] ; Horses [MeSH] ; NAD/metabolism [MeSH] ; Animals [MeSH] ; DNA Replication [MeSH] ; Jumbo phage ; Phylogeny [MeSH] ; Genome, Viral/genetics [MeSH] ; Sheep [MeSH] ; Bacteriophages/isolation ; Animal gut ; Research ; Bacteriophages/genetics [MeSH] ; Cattle [MeSH] ; NAD ; Metagenomics [MeSH] ; Bacteria/virology [MeSH], Animal gut, Metagenome, Animals, Humans, Bacteriophages, Cattle, Metagenomics, Horses, Bacteriophage, Phylogeny

  • BIP!
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    popularity
    This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
    Top 10%
    influence
    This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
    Average
    impulse
    This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
    Average
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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
4
Top 10%
Average
Average
Green
gold