A catalog of reference genomes from the human microbiome.
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.
Nelson
Karen E
KE
Weinstock
George M
GM
Highlander
Sarah K
SK
Worley
Kim C
KC
Creasy
Heather Huot
HH
Wortman
Jennifer Russo
JR
Rusch
Douglas B
DB
Mitreva
Makedonka
M
Sodergren
Erica
E
Chinwalla
Asif T
AT
Feldgarden
Michael
M
Gevers
Dirk
D
Haas
Brian J
BJ
Madupu
Ramana
R
Ward
Doyle V
DV
Birren
Bruce W
BW
Gibbs
Richard A
RA
Methe
Barbara
B
Petrosino
Joseph F
JF
Strausberg
Robert L
RL
Sutton
Granger G
GG
White
Owen R
OR
Wilson
Richard K
RK
Durkin
Scott
S
Giglio
Michelle Gwinn
MG
Gujja
Sharvari
S
Howarth
Clint
C
Kodira
Chinnappa D
CD
Kyrpides
Nikos
N
Mehta
Teena
T
Muzny
Donna M
DM
Pearson
Matthew
M
Pepin
Kymberlie
K
Pati
Amrita
A
Qin
Xiang
X
Yandava
Chandri
C
Zeng
Qiandong
Q
Zhang
Lan
L
Berlin
Aaron M
AM
Chen
Lei
L
Hepburn
Theresa A
TA
Johnson
Justin
J
McCorrison
Jamison
J
Miller
Jason
J
Minx
Pat
P
Nusbaum
Chad
C
Russ
Carsten
C
Sykes
Sean M
SM
Tomlinson
Chad M
CM
Young
Sarah
S
Warren
Wesley C
WC
Badger
Jonathan
J
Crabtree
Jonathan
J
Markowitz
Victor M
VM
Orvis
Joshua
J
Cree
Andrew
A
Ferriera
Steve
S
Fulton
Lucinda L
LL
Fulton
Robert S
RS
Gillis
Marcus
M
Hemphill
Lisa D
LD
Joshi
Vandita
V
Kovar
Christie
C
Torralba
Manolito
M
Wetterstrand
Kris A
KA
Abouellleil
Amr
A
Wollam
Aye M
AM
Buhay
Christian J
CJ
Ding
Yan
Y
Dugan
Shannon
S
FitzGerald
Michael G
MG
Holder
Mike
M
Hostetler
Jessica
J
Clifton
Sandra W
SW
Allen-Vercoe
Emma
E
Earl
Ashlee M
AM
Farmer
Candace N
CN
Liolios
Konstantinos
K
Surette
Michael G
MG
Xu
Qiang
Q
Pohl
Craig
C
Wilczek-Boney
Katarzyna
K
Zhu
Dianhui
D
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
D001426:Bacterial Proteins; D010455:Peptides