title: A catalog of reference genomes from the human microbiome.
abstract: The human microbiome refers to the community of microorganisms, including prokaryotes, viruses, and microbial eukaryotes, that populate the human body. The National Institutes of Health launched an initiative that focuses on describing the diversity of microbial species that are associated with health and disease. The first phase of this initiative includes the sequencing of hundreds of microbial reference genomes, coupled to metagenomic sequencing from multiple body sites. Here we present results from an initial reference genome sequencing of 178 microbial genomes. From 547,968 predicted polypeptides that correspond to the gene complement of these strains, previously unidentified ("novel") polypeptides that had both unmasked sequence length greater than 100 amino acids and no BLASTP match to any nonreference entry in the nonredundant subset were defined. This analysis resulted in a set of 30,867 polypeptides, of which 29,987 (approximately 97%) were unique. In addition, this set of microbial genomes allows for approximately 40% of random sequences from the microbiome of the gastrointestinal tract to be associated with organisms based on the match criteria used. Insights into pan-genome analysis suggest that we are still far from saturating microbial species genetic data sets. In addition, the associated metrics and standards used by our group for quality assurance are presented.
authors.forename: Karen E
authors.initials: KE
authors.lastname: Nelson
authors.forename: George M
authors.initials: GM
authors.lastname: Weinstock
authors.forename: Sarah K
authors.initials: SK
authors.lastname: Highlander
authors.forename: Kim C
authors.initials: KC
authors.lastname: Worley
authors.forename: Heather Huot
authors.initials: HH
authors.lastname: Creasy
authors.forename: Jennifer Russo
authors.initials: JR
authors.lastname: Wortman
authors.forename: Douglas B
authors.initials: DB
authors.lastname: Rusch
authors.forename: Makedonka
authors.initials: M
authors.lastname: Mitreva
authors.forename: Erica
authors.initials: E
authors.lastname: Sodergren
authors.forename: Asif T
authors.initials: AT
authors.lastname: Chinwalla
authors.forename: Michael
authors.initials: M
authors.lastname: Feldgarden
authors.forename: Dirk
authors.initials: D
authors.lastname: Gevers
authors.forename: Brian J
authors.initials: BJ
authors.lastname: Haas
authors.forename: Ramana
authors.initials: R
authors.lastname: Madupu
authors.forename: Doyle V
authors.initials: DV
authors.lastname: Ward
authors.forename: Bruce W
authors.initials: BW
authors.lastname: Birren
authors.forename: Richard A
authors.initials: RA
authors.lastname: Gibbs
authors.forename: Barbara
authors.initials: B
authors.lastname: Methe
authors.forename: Joseph F
authors.initials: JF
authors.lastname: Petrosino
authors.forename: Robert L
authors.initials: RL
authors.lastname: Strausberg
authors.forename: Granger G
authors.initials: GG
authors.lastname: Sutton
authors.forename: Owen R
authors.initials: OR
authors.lastname: White
authors.forename: Richard K
authors.initials: RK
authors.lastname: Wilson
authors.forename: Scott
authors.initials: S
authors.lastname: Durkin
authors.forename: Michelle Gwinn
authors.initials: MG
authors.lastname: Giglio
authors.forename: Sharvari
authors.initials: S
authors.lastname: Gujja
authors.forename: Clint
authors.initials: C
authors.lastname: Howarth
authors.forename: Chinnappa D
authors.initials: CD
authors.lastname: Kodira
authors.forename: Nikos
authors.initials: N
authors.lastname: Kyrpides
authors.forename: Teena
authors.initials: T
authors.lastname: Mehta
authors.forename: Donna M
authors.initials: DM
authors.lastname: Muzny
authors.forename: Matthew
authors.initials: M
authors.lastname: Pearson
authors.forename: Kymberlie
authors.initials: K
authors.lastname: Pepin
authors.forename: Amrita
authors.initials: A
authors.lastname: Pati
authors.forename: Xiang
authors.initials: X
authors.lastname: Qin
authors.forename: Chandri
authors.initials: C
authors.lastname: Yandava
authors.forename: Qiandong
authors.initials: Q
authors.lastname: Zeng
authors.forename: Lan
authors.initials: L
authors.lastname: Zhang
authors.forename: Aaron M
authors.initials: AM
authors.lastname: Berlin
authors.forename: Lei
authors.initials: L
authors.lastname: Chen
authors.forename: Theresa A
authors.initials: TA
authors.lastname: Hepburn
authors.forename: Justin
authors.initials: J
authors.lastname: Johnson
authors.forename: Jamison
authors.initials: J
authors.lastname: McCorrison
authors.forename: Jason
authors.initials: J
authors.lastname: Miller
authors.forename: Pat
authors.initials: P
authors.lastname: Minx
authors.forename: Chad
authors.initials: C
authors.lastname: Nusbaum
authors.forename: Carsten
authors.initials: C
authors.lastname: Russ
authors.forename: Sean M
authors.initials: SM
authors.lastname: Sykes
authors.forename: Chad M
authors.initials: CM
authors.lastname: Tomlinson
authors.forename: Sarah
authors.initials: S
authors.lastname: Young
authors.forename: Wesley C
authors.initials: WC
authors.lastname: Warren
authors.forename: Jonathan
authors.initials: J
authors.lastname: Badger
authors.forename: Jonathan
authors.initials: J
authors.lastname: Crabtree
authors.forename: Victor M
authors.initials: VM
authors.lastname: Markowitz
authors.forename: Joshua
authors.initials: J
authors.lastname: Orvis
authors.forename: Andrew
authors.initials: A
authors.lastname: Cree
authors.forename: Steve
authors.initials: S
authors.lastname: Ferriera
authors.forename: Lucinda L
authors.initials: LL
authors.lastname: Fulton
authors.forename: Robert S
authors.initials: RS
authors.lastname: Fulton
authors.forename: Marcus
authors.initials: M
authors.lastname: Gillis
authors.forename: Lisa D
authors.initials: LD
authors.lastname: Hemphill
authors.forename: Vandita
authors.initials: V
authors.lastname: Joshi
authors.forename: Christie
authors.initials: C
authors.lastname: Kovar
authors.forename: Manolito
authors.initials: M
authors.lastname: Torralba
authors.forename: Kris A
authors.initials: KA
authors.lastname: Wetterstrand
authors.forename: Amr
authors.initials: A
authors.lastname: Abouellleil
authors.forename: Aye M
authors.initials: AM
authors.lastname: Wollam
authors.forename: Christian J
authors.initials: CJ
authors.lastname: Buhay
authors.forename: Yan
authors.initials: Y
authors.lastname: Ding
authors.forename: Shannon
authors.initials: S
authors.lastname: Dugan
authors.forename: Michael G
authors.initials: MG
authors.lastname: FitzGerald
authors.forename: Mike
authors.initials: M
authors.lastname: Holder
authors.forename: Jessica
authors.initials: J
authors.lastname: Hostetler
authors.forename: Sandra W
authors.initials: SW
authors.lastname: Clifton
authors.forename: Emma
authors.initials: E
authors.lastname: Allen-Vercoe
authors.forename: Ashlee M
authors.initials: AM
authors.lastname: Earl
authors.forename: Candace N
authors.initials: CN
authors.lastname: Farmer
authors.forename: Konstantinos
authors.initials: K
authors.lastname: Liolios
authors.forename: Michael G
authors.initials: MG
authors.lastname: Surette
authors.forename: Qiang
authors.initials: Q
authors.lastname: Xu
authors.forename: Craig
authors.initials: C
authors.lastname: Pohl
authors.forename: Katarzyna
authors.initials: K
authors.lastname: Wilczek-Boney
authors.forename: Dianhui
authors.initials: D
authors.lastname: Zhu
mesh_terms: D001419:Bacteria / Q000145:classification / Q000235:genetics; D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics; D044822:Biodiversity; D019295:Computational Biology; D030541:Databases, Genetic; D041981:Gastrointestinal Tract / Q000382:microbiology; D005798:Genes, Bacterial; D014644:Genetic Variation; D020745:Genome, Archaeal; D016680:Genome, Bacterial; D006801:Humans; D054892:Metagenome / Q000235:genetics*; D056186:Metagenomics / Q000379:methods / Q000592:standards; D009055:Mouth / Q000382:microbiology; D010455:Peptides / Q000737:chemistry / Q000235:genetics; D010802:Phylogeny; D012137:Respiratory System / Q000382:microbiology; D017422:Sequence Analysis, DNA / Q000592:standards; D012867:Skin / Q000382:microbiology; D014566:Urogenital System / Q000382:microbiology
chemical_list: D001426:Bacterial Proteins; D010455:Peptides