Efficient recovery of complete gut phage genomes by combined short- and long-sequencing

Current metagenome-assembled human phage catalogs contained mostly fragmented genomes. Here, we developed a vigorous phage detection method involving phage enrichment and long-read sequencing and applied to 135 fecal samples. With ~10 times more efficient in obtaining complete genomes (~34%) than the Gut Virome Database, we identified the first megabasephage (~1.03Mb), and revealed the hidden diversity of the gut phageome including dozens of phages more prevalent than the crAssphages and Gubaphages.

[1]  Guoping Wang,et al.  Uncovering 1,058 novel human enteric DNA viruses through deep long-read third-generation sequencing and their clinical impact. , 2022, Gastroenterology.

[2]  Natalia N. Ivanova,et al.  Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome , 2021, Nature Microbiology.

[3]  Michael J. Tisza,et al.  A catalog of tens of thousands of viruses from human metagenomes reveals hidden associations with chronic diseases , 2021, Proceedings of the National Academy of Sciences.

[4]  P. Bork,et al.  Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation , 2021, Nucleic Acids Res..

[5]  P. Bork,et al.  A Previously Undescribed Highly Prevalent Phage Identified in a Danish Enteric Virome Catalog , 2021, mSystems.

[6]  Puzi Jiang,et al.  Treatment regimens may compromise gut-microbiome-derived signatures for liver cirrhosis. , 2021, Cell metabolism.

[7]  Silvio C. E. Tosatto,et al.  Pfam: The protein families database in 2021 , 2020, Nucleic Acids Res..

[8]  Xing-Ming Zhao,et al.  mMGE: a database for human metagenomic extrachromosomal mobile genetic elements , 2020, Nucleic Acids Res..

[9]  R. Finn,et al.  Massive expansion of human gut bacteriophage diversity , 2020, Cell.

[10]  N. Kyrpides,et al.  CheckV assesses the quality and completeness of metagenome-assembled viral genomes , 2020, Nature Biotechnology.

[11]  Ayal B. Gussow,et al.  Thousands of previously unknown phages discovered in whole-community human gut metagenomes , 2020, Microbiome.

[12]  M. Sullivan,et al.  The Gut Virome Database Reveals Age-Dependent Patterns of Virome Diversity in the Human Gut , 2020, Cell Host & Microbe.

[13]  Y. Furukawa,et al.  Metagenome Data on Intestinal Phage-Bacteria Associations Aids the Development of Phage Therapy against Pathobionts. , 2020, Cell host & microbe.

[14]  Luis Pedro Coelho,et al.  Statin therapy is associated with lower prevalence of gut microbiota dysbiosis , 2020, Nature.

[15]  M. Hattori,et al.  Long-read metagenomic exploration of extrachromosomal mobile genetic elements in the human gut , 2019, Microbiome.

[16]  Niranjan Nagarajan,et al.  Hybrid metagenomic assembly enables high-resolution analysis of resistance determinants and mobile elements in human microbiomes , 2019, Nature Biotechnology.

[17]  Jie Tan,et al.  PPR-Meta: a tool for identifying phages and plasmids from metagenomic fragments using deep learning , 2019, GigaScience.

[18]  M. Lercher,et al.  Evolview v3: a webserver for visualization, annotation, and management of phylogenetic trees , 2019, Nucleic Acids Res..

[19]  Yu Lin,et al.  Assembly of long, error-prone reads using repeat graphs , 2018, Nature Biotechnology.

[20]  Christine L. Sun,et al.  Clades of huge phages from across Earth’s ecosystems , 2019, bioRxiv.

[21]  Feng Li,et al.  MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies , 2019, PeerJ.

[22]  T. Sutton,et al.  Biology and Taxonomy of crAss-like Bacteriophages, the Most Abundant Virus in the Human Gut. , 2018, Cell host & microbe.

[23]  Brian C. Thomas,et al.  Megaphages infect Prevotella and variants are widespread in gut microbiomes , 2018, bioRxiv.

[24]  T. Sutton,et al.  Reproducible protocols for metagenomic analysis of human faecal phageomes , 2018, Microbiome.

[25]  C. Elson,et al.  Microbiota , 2010, Gut microbes.

[26]  Yang Young Lu,et al.  VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data , 2017, Microbiome.

[27]  David Torrents,et al.  Metformin alters the gut microbiome of individuals with treatment-naive type 2 diabetes, contributing to the therapeutic effects of the drug , 2017, Nature Medicine.

[28]  P. Pevzner,et al.  metaSPAdes: a new versatile metagenomic assembler. , 2017, Genome research.

[29]  S. Koren,et al.  Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation , 2016, bioRxiv.

[30]  S. Lynch,et al.  The Human Intestinal Microbiome in Health and Disease. , 2016, The New England journal of medicine.

[31]  Luis Pedro Coelho,et al.  Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper , 2016, bioRxiv.

[32]  Tim D Spector,et al.  Proton pump inhibitors alter the composition of the gut microbiota , 2015, Gut.

[33]  Jun Wang,et al.  Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota , 2015, Nature.

[34]  Matthew B. Sullivan,et al.  VirSorter: mining viral signal from microbial genomic data , 2015, PeerJ.

[35]  Björn Usadel,et al.  Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..

[36]  E. Cheek,et al.  Genome signature-based dissection of human gut metagenomes to extract subliminal viral sequences , 2013, Nature Communications.

[37]  S. Eddy,et al.  Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions , 2013, Nucleic acids research.

[38]  Peer Bork,et al.  Orthologous Gene Clusters and Taxon Signature Genes for Viruses of Prokaryotes , 2012, Journal of bacteriology.

[39]  Zhengwei Zhu,et al.  CD-HIT: accelerated for clustering the next-generation sequencing data , 2012, Bioinform..

[40]  Siu-Ming Yiu,et al.  IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth , 2012, Bioinform..

[41]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[42]  Paramvir S. Dehal,et al.  FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments , 2010, PloS one.

[43]  Miriam L. Land,et al.  Trace: Tennessee Research and Creative Exchange Prodigal: Prokaryotic Gene Recognition and Translation Initiation Site Identification Recommended Citation Prodigal: Prokaryotic Gene Recognition and Translation Initiation Site Identification , 2022 .

[44]  Robert C. Edgar,et al.  MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.

[45]  Anton J. Enright,et al.  An efficient algorithm for large-scale detection of protein families. , 2002, Nucleic acids research.

[46]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.