schliessen

Filtern

 

Bibliotheken

1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life

We present 1,003 reference genomes that were sequenced as part of the Genomic Encyclopedia of Bacteria and Archaea (GEBA) initiative, selected to maximize sequence coverage of phylogenetic space. These genomes double the number of existing type strains and expand their overall phylogenetic diversity... Full description

Journal Title: Nature biotechnology 2017-07, Vol.35 (7), p.676-683
Main Author: Mukherjee, Supratim
Other Authors: Seshadri, Rekha , Varghese, Neha J , Eloe-Fadrosh, Emiley A , Meier-Kolthoff, Jan P , Göker, Markus , Coates, R Cameron , Hadjithomas, Michalis , Pavlopoulos, Georgios A , Paez-Espino, David , Yoshikuni, Yasuo , Visel, Axel , Whitman, William B , Garrity, George M , Eisen, Jonathan A , Hugenholtz, Philip , Pati, Amrita , Ivanova, Natalia N , Woyke, Tanja , Klenk, Hans-Peter , Kyrpides, Nikos C
Format: Electronic Article Electronic Article
Language: English
Subjects:
Publisher: United States: Nature Publishing Group
ID: ISSN: 1087-0156
Zum Text:
SendSend as email Add to Book BagAdd to Book Bag
Staff View
recordid: cdi_osti_scitechconnect_1379902
title: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life
format: Article
creator:
  • Mukherjee, Supratim
  • Seshadri, Rekha
  • Varghese, Neha J
  • Eloe-Fadrosh, Emiley A
  • Meier-Kolthoff, Jan P
  • Göker, Markus
  • Coates, R Cameron
  • Hadjithomas, Michalis
  • Pavlopoulos, Georgios A
  • Paez-Espino, David
  • Yoshikuni, Yasuo
  • Visel, Axel
  • Whitman, William B
  • Garrity, George M
  • Eisen, Jonathan A
  • Hugenholtz, Philip
  • Pati, Amrita
  • Ivanova, Natalia N
  • Woyke, Tanja
  • Klenk, Hans-Peter
  • Kyrpides, Nikos C
subjects:
  • archeal genomics
  • bacterial genomics
  • Chromosome Mapping - standards
  • computational biology and bioinformatics
  • Database Management Systems
  • Databases, Genetic
  • Datasets as Topic
  • Encyclopedias as Topic
  • Genome, Archaeal - genetics
  • Genome, Bacterial - genetics
  • Genomes
  • genomics
  • High-Throughput Nucleotide Sequencing - standards
  • Knowledge Bases
  • Microbial genetics
  • Microbiological research
  • microbiology
  • Reference Values
  • Research
ispartof: Nature biotechnology, 2017-07, Vol.35 (7), p.676-683
description: We present 1,003 reference genomes that were sequenced as part of the Genomic Encyclopedia of Bacteria and Archaea (GEBA) initiative, selected to maximize sequence coverage of phylogenetic space. These genomes double the number of existing type strains and expand their overall phylogenetic diversity by 25%. Comparative analyses with previously available finished and draft genomes reveal a 10.5% increase in novel protein families as a function of phylogenetic diversity. The GEBA genomes recruit 25 million previously unassigned metagenomic proteins from 4,650 samples, improving their phylogenetic and functional interpretation. We identify numerous biosynthetic clusters and experimentally validate a divergent phenazine cluster with potential new chemical structure and antimicrobial activity. This Resource is the largest single release of reference genomes to date. Bacterial and archaeal isolate sequence space is still far from saturated, and future endeavors in this direction will continue to be a valuable resource for scientific discovery.
language: eng
source:
identifier: ISSN: 1087-0156
fulltext: no_fulltext
issn:
  • 1087-0156
  • 1546-1696
url: Link


@attributes
NO1
SEARCH_ENGINEprimo_central_multiple_fe
SEARCH_ENGINE_TYPEPrimo Central Search Engine
RANK2.774093
LOCALfalse
PrimoNMBib
record
control
sourceidgale_osti_
recordidTN_cdi_osti_scitechconnect_1379902
sourceformatXML
sourcesystemPC
galeidA498337414
sourcerecordidA498337414
originalsourceidFETCH-LOGICAL-1530t-a255d56ec1e8ea69a727ee97c5f1717709df28d9ba5427b693bca4bd00e8c0000
addsrcrecordideNqNkl2L1TAQhoso7roK_gIpXilsj0nbfF0uix8LCwt-XRqm6bQn0ibHJJX135t6jqsHbySQTJJnXjJvpiieUrKhpJGvXJc2jZT8XnFKWcsryhW_n2MiRUUo4yfFoxi_EkJ4y_nD4qSWnOSInBZf6DkhTRlwwIDOYDmi8zPG0g9lByZhsDCV4PoSgtkC5o2NfoKUEbzdrRfGf8cAI64paYtlCvgrnuyAj4sHA0wRnxzWs-LTm9cfL99V1zdvry4vrivKGpIqqBnrGUdDUSJwBaIWiEoYNlBBhSCqH2rZqw5YW4uOq6Yz0HY9IShNLoucFc_3uj4mq6OxCc3WeOfQJE0boRSpM_RiD-2C_7ZgTHq20eA0gUO_RE1V9ktxJtqMbvboCBNq6wafApg8epxt1sXB5vOLVsmmES1dE14eJWQm4W0aYYlRX314___szedj9vwvtluidRjzFO24TXGfcoQfSjTBx5h_Ve-CnSH80JTotVV0bhW9tkpGnx3cWLoZ-zvwd2_88eBOK9sKyebXBrDTv4o_AfKWxTs
sourcetypeOpen Access Repository
isCDItrue
recordtypearticle
pqid1908796574
display
typearticle
title1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life
creatorMukherjee, Supratim ; Seshadri, Rekha ; Varghese, Neha J ; Eloe-Fadrosh, Emiley A ; Meier-Kolthoff, Jan P ; Göker, Markus ; Coates, R Cameron ; Hadjithomas, Michalis ; Pavlopoulos, Georgios A ; Paez-Espino, David ; Yoshikuni, Yasuo ; Visel, Axel ; Whitman, William B ; Garrity, George M ; Eisen, Jonathan A ; Hugenholtz, Philip ; Pati, Amrita ; Ivanova, Natalia N ; Woyke, Tanja ; Klenk, Hans-Peter ; Kyrpides, Nikos C
creatorcontribMukherjee, Supratim ; Seshadri, Rekha ; Varghese, Neha J ; Eloe-Fadrosh, Emiley A ; Meier-Kolthoff, Jan P ; Göker, Markus ; Coates, R Cameron ; Hadjithomas, Michalis ; Pavlopoulos, Georgios A ; Paez-Espino, David ; Yoshikuni, Yasuo ; Visel, Axel ; Whitman, William B ; Garrity, George M ; Eisen, Jonathan A ; Hugenholtz, Philip ; Pati, Amrita ; Ivanova, Natalia N ; Woyke, Tanja ; Klenk, Hans-Peter ; Kyrpides, Nikos C ; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
descriptionWe present 1,003 reference genomes that were sequenced as part of the Genomic Encyclopedia of Bacteria and Archaea (GEBA) initiative, selected to maximize sequence coverage of phylogenetic space. These genomes double the number of existing type strains and expand their overall phylogenetic diversity by 25%. Comparative analyses with previously available finished and draft genomes reveal a 10.5% increase in novel protein families as a function of phylogenetic diversity. The GEBA genomes recruit 25 million previously unassigned metagenomic proteins from 4,650 samples, improving their phylogenetic and functional interpretation. We identify numerous biosynthetic clusters and experimentally validate a divergent phenazine cluster with potential new chemical structure and antimicrobial activity. This Resource is the largest single release of reference genomes to date. Bacterial and archaeal isolate sequence space is still far from saturated, and future endeavors in this direction will continue to be a valuable resource for scientific discovery.
identifier
0ISSN: 1087-0156
1EISSN: 1546-1696
2DOI: 10.1038/nbt.3886
3PMID: 28604660
languageeng
publisherUnited States: Nature Publishing Group
subjectarcheal genomics ; bacterial genomics ; Chromosome Mapping - standards ; computational biology and bioinformatics ; Database Management Systems ; Databases, Genetic ; Datasets as Topic ; Encyclopedias as Topic ; Genome, Archaeal - genetics ; Genome, Bacterial - genetics ; Genomes ; genomics ; High-Throughput Nucleotide Sequencing - standards ; Knowledge Bases ; Microbial genetics ; Microbiological research ; microbiology ; Reference Values ; Research
ispartofNature biotechnology, 2017-07, Vol.35 (7), p.676-683
rightsCOPYRIGHT 2017 Nature Publishing Group
lds50peer_reviewed
oafree_for_read
citedbyFETCH-LOGICAL-1530t-a255d56ec1e8ea69a727ee97c5f1717709df28d9ba5427b693bca4bd00e8c0000
citesFETCH-LOGICAL-1530t-a255d56ec1e8ea69a727ee97c5f1717709df28d9ba5427b693bca4bd00e8c0000
orcidid0000-0002-4577-8276 ; 0000-0002-4130-7784 ; 0000-0002-5144-6200 ; 0000-0002-2939-5398 ; 0000-0001-5386-7925 ; 0000-0001-9105-9814 ; 0000000241307784 ; 0000000229395398 ; 0000000191059814 ; 0000000153867925 ; 0000000245778276 ; 0000000251446200
links
openurl$$Topenurl_article
thumbnail$$Usyndetics_thumb_exl
backlink
0$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/28604660$$D View this record in MEDLINE/PubMed
1$$Uhttps://www.osti.gov/servlets/purl/1379902$$D View this record in Osti.gov
search
creatorcontrib
0Mukherjee, Supratim
1Seshadri, Rekha
2Varghese, Neha J
3Eloe-Fadrosh, Emiley A
4Meier-Kolthoff, Jan P
5Göker, Markus
6Coates, R Cameron
7Hadjithomas, Michalis
8Pavlopoulos, Georgios A
9Paez-Espino, David
10Yoshikuni, Yasuo
11Visel, Axel
12Whitman, William B
13Garrity, George M
14Eisen, Jonathan A
15Hugenholtz, Philip
16Pati, Amrita
17Ivanova, Natalia N
18Woyke, Tanja
19Klenk, Hans-Peter
20Kyrpides, Nikos C
21Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
title
01,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life
1Nature biotechnology
addtitleNat Biotechnol
descriptionWe present 1,003 reference genomes that were sequenced as part of the Genomic Encyclopedia of Bacteria and Archaea (GEBA) initiative, selected to maximize sequence coverage of phylogenetic space. These genomes double the number of existing type strains and expand their overall phylogenetic diversity by 25%. Comparative analyses with previously available finished and draft genomes reveal a 10.5% increase in novel protein families as a function of phylogenetic diversity. The GEBA genomes recruit 25 million previously unassigned metagenomic proteins from 4,650 samples, improving their phylogenetic and functional interpretation. We identify numerous biosynthetic clusters and experimentally validate a divergent phenazine cluster with potential new chemical structure and antimicrobial activity. This Resource is the largest single release of reference genomes to date. Bacterial and archaeal isolate sequence space is still far from saturated, and future endeavors in this direction will continue to be a valuable resource for scientific discovery.
subject
0archeal genomics
1bacterial genomics
2Chromosome Mapping - standards
3computational biology and bioinformatics
4Database Management Systems
5Databases, Genetic
6Datasets as Topic
7Encyclopedias as Topic
8Genome, Archaeal - genetics
9Genome, Bacterial - genetics
10Genomes
11genomics
12High-Throughput Nucleotide Sequencing - standards
13Knowledge Bases
14Microbial genetics
15Microbiological research
16microbiology
17Reference Values
18Research
issn
01087-0156
11546-1696
fulltextfalse
rsrctypearticle
creationdate2017
recordtypearticle
recordideNqNkl2L1TAQhoso7roK_gIpXilsj0nbfF0uix8LCwt-XRqm6bQn0ibHJJX135t6jqsHbySQTJJnXjJvpiieUrKhpJGvXJc2jZT8XnFKWcsryhW_n2MiRUUo4yfFoxi_EkJ4y_nD4qSWnOSInBZf6DkhTRlwwIDOYDmi8zPG0g9lByZhsDCV4PoSgtkC5o2NfoKUEbzdrRfGf8cAI64paYtlCvgrnuyAj4sHA0wRnxzWs-LTm9cfL99V1zdvry4vrivKGpIqqBnrGUdDUSJwBaIWiEoYNlBBhSCqH2rZqw5YW4uOq6Yz0HY9IShNLoucFc_3uj4mq6OxCc3WeOfQJE0boRSpM_RiD-2C_7ZgTHq20eA0gUO_RE1V9ktxJtqMbvboCBNq6wafApg8epxt1sXB5vOLVsmmES1dE14eJWQm4W0aYYlRX314___szedj9vwvtluidRjzFO24TXGfcoQfSjTBx5h_Ve-CnSH80JTotVV0bhW9tkpGnx3cWLoZ-zvwd2_88eBOK9sKyebXBrDTv4o_AfKWxTs
startdate201707
enddate201707
creator
0Mukherjee, Supratim
1Seshadri, Rekha
2Varghese, Neha J
3Eloe-Fadrosh, Emiley A
4Meier-Kolthoff, Jan P
5Göker, Markus
6Coates, R Cameron
7Hadjithomas, Michalis
8Pavlopoulos, Georgios A
9Paez-Espino, David
10Yoshikuni, Yasuo
11Visel, Axel
12Whitman, William B
13Garrity, George M
14Eisen, Jonathan A
15Hugenholtz, Philip
16Pati, Amrita
17Ivanova, Natalia N
18Woyke, Tanja
19Klenk, Hans-Peter
20Kyrpides, Nikos C
general
0Nature Publishing Group
1Springer Nature
scope
0CGR
1CUY
2CVF
3ECM
4EIF
5NPM
6AAYXX
7CITATION
8BSHEE
97X8
10OIOZB
11OTOTI
orcidid
0https://orcid.org/0000-0002-4577-8276
1https://orcid.org/0000-0002-4130-7784
2https://orcid.org/0000-0002-5144-6200
3https://orcid.org/0000-0002-2939-5398
4https://orcid.org/0000-0001-5386-7925
5https://orcid.org/0000-0001-9105-9814
6https://orcid.org/0000000241307784
7https://orcid.org/0000000229395398
8https://orcid.org/0000000191059814
9https://orcid.org/0000000153867925
10https://orcid.org/0000000245778276
11https://orcid.org/0000000251446200
sort
creationdate201707
title1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life
authorMukherjee, Supratim ; Seshadri, Rekha ; Varghese, Neha J ; Eloe-Fadrosh, Emiley A ; Meier-Kolthoff, Jan P ; Göker, Markus ; Coates, R Cameron ; Hadjithomas, Michalis ; Pavlopoulos, Georgios A ; Paez-Espino, David ; Yoshikuni, Yasuo ; Visel, Axel ; Whitman, William B ; Garrity, George M ; Eisen, Jonathan A ; Hugenholtz, Philip ; Pati, Amrita ; Ivanova, Natalia N ; Woyke, Tanja ; Klenk, Hans-Peter ; Kyrpides, Nikos C
facets
frbrtype5
frbrgroupidcdi_FETCH-LOGICAL-1530t-a255d56ec1e8ea69a727ee97c5f1717709df28d9ba5427b693bca4bd00e8c0000
rsrctypearticles
prefilterarticles
languageeng
creationdate2017
topic
0archeal genomics
1bacterial genomics
2Chromosome Mapping - standards
3computational biology and bioinformatics
4Database Management Systems
5Databases, Genetic
6Datasets as Topic
7Encyclopedias as Topic
8Genome, Archaeal - genetics
9Genome, Bacterial - genetics
10Genomes
11genomics
12High-Throughput Nucleotide Sequencing - standards
13Knowledge Bases
14Microbial genetics
15Microbiological research
16microbiology
17Reference Values
18Research
toplevelpeer_reviewed
creatorcontrib
0Mukherjee, Supratim
1Seshadri, Rekha
2Varghese, Neha J
3Eloe-Fadrosh, Emiley A
4Meier-Kolthoff, Jan P
5Göker, Markus
6Coates, R Cameron
7Hadjithomas, Michalis
8Pavlopoulos, Georgios A
9Paez-Espino, David
10Yoshikuni, Yasuo
11Visel, Axel
12Whitman, William B
13Garrity, George M
14Eisen, Jonathan A
15Hugenholtz, Philip
16Pati, Amrita
17Ivanova, Natalia N
18Woyke, Tanja
19Klenk, Hans-Peter
20Kyrpides, Nikos C
21Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
collection
0Medline
1MEDLINE
2MEDLINE (Ovid)
3MEDLINE
4MEDLINE
5PubMed
6CrossRef
7Academic OneFile (A&I only)
8MEDLINE - Academic
9OSTI.GOV - Hybrid
10OSTI.GOV
jtitleNature biotechnology
delivery
delcategoryRemote Search Resource
fulltextno_fulltext
addata
au
0Mukherjee, Supratim
1Seshadri, Rekha
2Varghese, Neha J
3Eloe-Fadrosh, Emiley A
4Meier-Kolthoff, Jan P
5Göker, Markus
6Coates, R Cameron
7Hadjithomas, Michalis
8Pavlopoulos, Georgios A
9Paez-Espino, David
10Yoshikuni, Yasuo
11Visel, Axel
12Whitman, William B
13Garrity, George M
14Eisen, Jonathan A
15Hugenholtz, Philip
16Pati, Amrita
17Ivanova, Natalia N
18Woyke, Tanja
19Klenk, Hans-Peter
20Kyrpides, Nikos C
aucorpLawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
formatjournal
genrearticle
ristypeJOUR
atitle1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life
jtitleNature biotechnology
addtitleNat Biotechnol
date2017-07
risdate2017
volume35
issue7
spage676
epage683
pages676-683
issn1087-0156
eissn1546-1696
notes
0AC02-05CH11231
1USDOE Office of Science (SC), Biological and Environmental Research (BER)
abstractWe present 1,003 reference genomes that were sequenced as part of the Genomic Encyclopedia of Bacteria and Archaea (GEBA) initiative, selected to maximize sequence coverage of phylogenetic space. These genomes double the number of existing type strains and expand their overall phylogenetic diversity by 25%. Comparative analyses with previously available finished and draft genomes reveal a 10.5% increase in novel protein families as a function of phylogenetic diversity. The GEBA genomes recruit 25 million previously unassigned metagenomic proteins from 4,650 samples, improving their phylogenetic and functional interpretation. We identify numerous biosynthetic clusters and experimentally validate a divergent phenazine cluster with potential new chemical structure and antimicrobial activity. This Resource is the largest single release of reference genomes to date. Bacterial and archaeal isolate sequence space is still far from saturated, and future endeavors in this direction will continue to be a valuable resource for scientific discovery.
copUnited States
pubNature Publishing Group
pmid28604660
doi10.1038/nbt.3886
tpages8
orcidid
0https://orcid.org/0000-0002-4577-8276
1https://orcid.org/0000-0002-4130-7784
2https://orcid.org/0000-0002-5144-6200
3https://orcid.org/0000-0002-2939-5398
4https://orcid.org/0000-0001-5386-7925
5https://orcid.org/0000-0001-9105-9814
6https://orcid.org/0000000241307784
7https://orcid.org/0000000229395398
8https://orcid.org/0000000191059814
9https://orcid.org/0000000153867925
10https://orcid.org/0000000245778276
11https://orcid.org/0000000251446200
oafree_for_read