@article{CosteaCoelhoSunagawaetal.2017,
  author    = {Costea, Paul I. and Coelho, Louis Pedro and Sunagawa, Shinichi and Munch, Robin and Huerta-Cepas, Jaime and Forslund, Kristoffer and Hildebrand, Falk and Kushugulova, Almagul and Zeller, Georg and Bork, Peer},
  title     = {Subspecies in the global human gut microbiome},
  series = {Molecular Systems Biology},
  volume    = {13},
  journal   = {Molecular Systems Biology},
  number    = {12},
  doi       = {10.15252/msb.20177589},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-172674},
  year      = {2017},
  abstract  = {Population genomics of prokaryotes has been studied in depth in only a small number of primarily pathogenic bacteria, as genome sequences of isolates of diverse origin are lacking for most species. Here, we conducted a large-scale survey of population structure in prevalent human gut microbial species, sampled from their natural environment, with a culture-independent metagenomic approach. We examined the variation landscape of 71 species in 2,144 human fecal metagenomes and found that in 44 of these, accounting for 72\% of the total assigned microbial abundance, single-nucleotide variation clearly indicates the existence of sub-populations (here termed subspecies). A single subspecies (per species) usually dominates within each host, as expected from ecological theory. At the global scale, geographic distributions of subspecies differ between phyla, with Firmicutes subspecies being significantly more geographically restricted. To investigate the functional significance of the delineated subspecies, we identified genes that consistently distinguish them in a manner that is independent of reference genomes. We further associated these subspecies-specific genes with properties of the microbial community and the host. For example, two of the three Eubacterium rectale subspecies consistently harbor an accessory pro-inflammatory flagellum operon that is associated with lower gut community diversity, higher host BMI, and higher blood fasting insulin levels. Using an additional 676 human oral samples, we further demonstrate the existence of niche specialized subspecies in the different parts of the oral cavity. Taken together, we provide evidence for subspecies in the majority of abundant gut prokaryotes, leading to a better functional and ecological understanding of the human gut microbiome in conjunction with its host.},
  language  = {en}
}
@article{MendeLetunicHuertaCepasetal.2017,
  author    = {Mende, Daniel R. and Letunic, Ivica and Huerta-Cepas, Jaime and Li, Simone S. and Forslund, Kristoffer and Sunagawa, Shinichi and Bork, Peer},
  title     = {proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes},
  series = {Nucleic Acids Research},
  volume    = {45},
  journal   = {Nucleic Acids Research},
  number    = {D1},
  doi       = {10.1093/nar/gkw989},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-171987},
  pages     = {D529-D534},
  year      = {2017},
  abstract  = {The availability of microbial genomes has opened many new avenues of research within microbiology. This has been driven primarily by comparative genomics approaches, which rely on accurate and consistent characterization of genomic sequences. It is nevertheless difficult to obtain consistent taxonomic and integrated functional annotations for defined prokaryotic clades. Thus, we developed proGenomes, a resource that provides user-friendly access to currently 25 038 high-quality genomes whose sequences and consistent annotations can be retrieved individually or by taxonomic clade. These genomes are assigned to 5306 consistent and accurate taxonomic species clusters based on previously established methodology. proGenomes also contains functional information for almost 80 million protein-coding genes, including a comprehensive set of general annotations and more focused annotations for carbohydrate-active enzymes and antibiotic resistance genes. Additionally, broad habitat information is provided for many genomes. All genomes and associated information can be downloaded by user-selected clade or multiple habitat-specific sets of representative genomes. We expect that the availability of high-quality genomes with comprehensive functional annotations will promote advances in clinical microbial genomics, functional evolution and other subfields of microbiology. proGenomes is available at http://progenomes.embl.de.},
  language  = {en}
}