Annotated bacterial chromosomes from frame-shift-corrected long-read metagenomic data

被引：53

作者：

Arumugam, Krithika ^{[1
]}

Bagci, Caner ^{[2
,3
,4
]}

Bessarab, Irina ^{[5
]}

Beier, Sina ^{[2
]}

Buchfink, Benjamin ^{[6
]}

Gorska, Anna ^{[2
,3
,4
]}

Qiu, Guanglei ^{[1
]}

Huson, Daniel H. ^{[2
,7
]}

Williams, Rohan B. H. ^{[5
]}

机构：

[1] Nanyang Technol Univ, Singapore Ctr Environm Life Sci Engn, 60 Nanyang Dr,SBS 01N 27, Singapore 637551, Singapore

[2] Univ Tubingen, Dept Comp Sci, Sand 14, D-72076 Tubingen, Germany

[3] Max Planck Inst Dev Biol, Int Max Planck Res Sch Mol Organisms, Max Planck Ring 5, D-72076 Tubingen, Germany

[4] Eberhard Karls Univ Tubingen, Max Planck Ring 5, D-72076 Tubingen, Germany

[5] Natl Univ Singapore, Singapore Ctr Environm Life Sci Engn, 28 Med Dr, Singapore 117456, Singapore

[6] Max Planck Inst Dev Biol, Max Planck Ring 5, D-72076 Tubingen, Germany

[7] Natl Univ Singapore, Life Sci Inst, 28 Med Dr, Singapore 117456, Singapore

来源：

MICROBIOME | 2019年 / 7卷

基金：

新加坡国家研究基金会;

关键词：

Microbiome; Long-read sequencing; Microbial genomics; Sequence assembly; Frame-shifts; Algorithms; Software; GLYCOGEN-ACCUMULATING ORGANISMS; RIBOSOMAL-RNA; GENOME; SEARCH;

D O I：

10.1186/s40168-019-0665-y

中图分类号：

Q93 [微生物学];

学科分类号：

071005 ; 100705 ;

摘要：

BackgroundShort-read sequencing technologies have long been the work-horse of microbiome analysis. Continuing technological advances are making the application of long-read sequencing to metagenomic samples increasingly feasible.ResultsWe demonstrate that whole bacterial chromosomes can be obtained from an enriched community, by application of MinION sequencing to a sample from an EBPR bioreactor, producing 6 Gb of sequence that assembles into multiple closed bacterial chromosomes. We provide a simple pipeline for processing such data, which includes a new approach to correcting erroneous frame-shifts.ConclusionsAdvances in long-read sequencing technology and corresponding algorithms will allow the routine extraction of whole chromosomes from environmental samples, providing a more detailed picture of individual members of a microbiome.

引用

页数：13

共 30 条

[1] Gapped BLAST and PSI-BLAST: a new generation of protein database search programs [J].

Altschul, SF ;

Madden, TL ;

Schaffer, AA ;

Zhang, JH ;

Zhang, Z ;

Miller, W ;

Lipman, DJ .

NUCLEIC ACIDS RESEARCH, 1997, 25 (17) :3389-3402

[2]

[Anonymous], BIOINFORMATICS

[3] SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing [J].

Bankevich, Anton ;

Nurk, Sergey ;

Antipov, Dmitry ;

Gurevich, Alexey A. ;

Dvorkin, Mikhail ;

Kulikov, Alexander S. ;

Lesin, Valery M. ;

Nikolenko, Sergey I. ;

Son Pham ;

Prjibelski, Andrey D. ;

Pyshkin, Alexey V. ;

Sirotkin, Alexander V. ;

Vyahhi, Nikolay ;

Tesler, Glenn ;

Alekseyev, Max A. ;

Pevzner, Pavel A. .

JOURNAL OF COMPUTATIONAL BIOLOGY, 2012, 19 (05) :455-477

[4] metaxa2: improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data [J].

Bengtsson-Palme, Johan ;

Hartmann, Martin ;

Eriksson, Karl Martin ;

Pal, Chandan ;

Thorell, Kaisa ;

Larsson, Dan Goran Joakim ;

Nilsson, Rolf Henrik .

MOLECULAR ECOLOGY RESOURCES, 2015, 15 (06) :1403-1414

[5]

Benson DA, 2005, NUCLEIC ACIDS RES, V33, pD34, DOI [10.1093/nar/gki063, 10.1093/nar/gku1216]

[6] Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea [J].

Bowers, Robert M. ;

Kyrpides, Nikos C. ;

Stepanauskas, Ramunas ;

Harmon-Smith, Miranda ;

Doud, Devin ;

Reddy, T. B. K. ;

Schulz, Frederik ;

Jarett, Jessica ;

Rivers, Adam R. ;

Eloe-Fadrosh, Emiley A. ;

Tringe, Susannah G. ;

Ivanova, Natalia N. ;

Copeland, Alex ;

Clum, Alicia ;

Becraft, Eric D. ;

Malmstrom, Rex R. ;

Birren, Bruce ;

Podar, Mircea ;

Bork, Peer ;

Weinstock, George M. ;

Garrity, George M. ;

Dodsworth, Jeremy A. ;

Yooseph, Shibu ;

Sutton, Granger ;

Gloeckner, Frank O. ;

Gilbert, Jack A. ;

Nelson, William C. ;

Hallam, Steven J. ;

Jungbluth, Sean P. ;

Ettema, Thijs J. G. ;

Tighe, Scott ;

Konstantinidis, Konstantinos T. ;

Liu, Wen-Tso ;

Baker, Brett J. ;

Rattei, Thomas ;

Eisen, Jonathan A. ;

Hedlund, Brian ;

McMahon, Katherine D. ;

Fierer, Noah ;

Knight, Rob ;

Finn, Rob ;

Cochrane, Guy ;

Karsch-Mizrachi, Ilene ;

Tyson, Gene W. ;

Rinke, Christian ;

Lapidus, Alla ;

Meyer, Folker ;

Yilmaz, Pelin ;

Parks, Donovan H. ;

Eren, A. M. .

NATURE BIOTECHNOLOGY, 2017, 35 (08) :725-731

[7] Fast and sensitive protein alignment using DIAMOND [J].

Buchfink, Benjamin ;

Xie, Chao ;

Huson, Daniel H. .

NATURE METHODS, 2015, 12 (01) :59-60

[8] Abundance and ecophysiology of Defluviicoccus spp., glycogen-accumulating organisms in full-scale wastewater treatment processes [J].

Burow, Luke C. ;

Kong, Yunhong ;

Nielsen, Jeppe L. ;

Blackall, Linda L. ;

Nielsen, Per H. .

MICROBIOLOGY-SGM, 2007, 153 :178-185

[9] Recovery of an environmental chlamydia strain from activated sludge by co-cultivation with Acanthamoeba sp. [J].

Collingro, A ;

Poppert, S ;

Heinz, E ;

Schmitz-Esser, S ;

Essig, A ;

Schweikert, M ;

Wagner, M ;

Horn, M .

MICROBIOLOGY-SGM, 2005, 151 :301-309

[10] Search and clustering orders of magnitude faster than BLAST [J].

Edgar, Robert C. .

BIOINFORMATICS, 2010, 26 (19) :2460-2461

← 1 2 3 →