Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4

Metagenomic assembly enables new organism discovery from microbial communities, but it can only capture few abundant organisms from most metagenomes. Here we present MetaPhlAn 4, which integrates information from metagenome assemblies and microbial isolate genomes for more comprehensive metagenomic taxonomic profiling. From a curated collection of 1.01 M prokaryotic reference and metagenome-assembled genomes, we define unique marker genes for 26,970 species-level genome bins, 4,992 of them taxonomically unidentified at the species level. MetaPhlAn 4 explains ~20% more reads in most international human gut microbiomes and >40% in less-characterized environments such as the rumen microbiome and proves more…

• HT
  Harvard T.H. Chan School of Public Health
• CR
  Cancer Research UK

  Awards: A27140, C10674/A27140
• NI
  National Institutes of Health

  Awards: 1U01CA230551, R24DK110499, H2020, U19AI110820
• H2
  Horizon 2020 Framework Programme

  Awards: 818368, ONCOBIOME-825410 project, ONCOBIOME-825410, MASTER-818368 project, 825410
• NC
  National Cancer Institute

  Award: 1U01CA230551
• NI
  National Institute of Allergy and Infectious Diseases

  Award: U19AI110820
• NI
  National Institute of Diabetes and Digestive and Kidney Diseases

  Award: R24DK110499