Emu: species-level microbial community profiling of full-length 16S rRNA Oxford Nanopore sequencing data.
Journal
Nature methods
ISSN: 1548-7105
Titre abrégé: Nat Methods
Pays: United States
ID NLM: 101215604
Informations de publication
Date de publication:
07 2022
07 2022
Historique:
received:
30
04
2021
accepted:
10
05
2022
pubmed:
1
7
2022
medline:
12
7
2022
entrez:
30
6
2022
Statut:
ppublish
Résumé
16S ribosomal RNA-based analysis is the established standard for elucidating the composition of microbial communities. While short-read 16S rRNA analyses are largely confined to genus-level resolution at best, given that only a portion of the gene is sequenced, full-length 16S rRNA gene amplicon sequences have the potential to provide species-level accuracy. However, existing taxonomic identification algorithms are not optimized for the increased read length and error rate often observed in long-read data. Here we present Emu, an approach that uses an expectation-maximization algorithm to generate taxonomic abundance profiles from full-length 16S rRNA reads. Results produced from simulated datasets and mock communities show that Emu is capable of accurate microbial community profiling while obtaining fewer false positives and false negatives than alternative methods. Additionally, we illustrate a real-world application of Emu by comparing clinical sample composition estimates generated by an established whole-genome shotgun sequencing workflow with those returned by full-length 16S rRNA gene sequences processed with Emu.
Identifiants
pubmed: 35773532
doi: 10.1038/s41592-022-01520-4
pii: 10.1038/s41592-022-01520-4
pmc: PMC9939874
mid: NIHMS1870162
doi:
Substances chimiques
RNA, Ribosomal, 16S
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Research Support, N.I.H., Extramural
Langues
eng
Sous-ensembles de citation
IM
Pagination
845-853Subventions
Organisme : NINR NIH HHS
ID : R01 NR013497
Pays : United States
Organisme : NIAID NIH HHS
ID : R01 AI100914
Pays : United States
Organisme : NINDS NIH HHS
ID : R21 NS106640
Pays : United States
Organisme : NLM NIH HHS
ID : T15 LM007093
Pays : United States
Organisme : NIAID NIH HHS
ID : P01 AI152999
Pays : United States
Organisme : NIAID NIH HHS
ID : U01 AI124290
Pays : United States
Organisme : NIDDK NIH HHS
ID : P30 DK056338
Pays : United States
Organisme : NIAID NIH HHS
ID : K24 AI121296
Pays : United States
Informations de copyright
© 2022. The Author(s), under exclusive licence to Springer Nature America, Inc.
Références
Bioinformatics. 2018 Sep 1;34(17):2899-2908
pubmed: 29659695
Sci Transl Med. 2012 May 2;4(132):132ra52
pubmed: 22553250
Database (Oxford). 2020 Jan 1;2020:
pubmed: 32761142
Nucleic Acids Res. 2015 Jan;43(Database issue):D593-8
pubmed: 25414355
Nat Biotechnol. 2016 May;34(5):525-7
pubmed: 27043002
Genome Res. 2016 Dec;26(12):1721-1729
pubmed: 27852649
Nucleic Acids Res. 2013 Jan;41(Database issue):D590-6
pubmed: 23193283
Gigascience. 2017 Apr 1;6(4):1-6
pubmed: 28327957
Nat Biotechnol. 2017 Apr 11;35(4):316-319
pubmed: 28398311
FEMS Microbiol Rev. 2013 Sep;37(5):762-92
pubmed: 23789590
Genome Biol. 2019 Nov 28;20(1):257
pubmed: 31779668
BMC Microbiol. 2015 Mar 21;15:66
pubmed: 25880246
Heliyon. 2016 Sep 23;2(9):e00170
pubmed: 27699286
Bioinformatics. 2021 Jul 12;37(11):1600-1601
pubmed: 33079990
Nat Methods. 2019 Dec;16(12):1297-1305
pubmed: 31740818
Sci Data. 2016 Sep 27;3:160081
pubmed: 27673566
Microbes Infect. 1999 Apr;1(4):285-92
pubmed: 10602662
Comput Struct Biotechnol J. 2020 Jan 31;18:296-305
pubmed: 32071706
Appl Environ Microbiol. 2006 Jul;72(7):5069-72
pubmed: 16820507
Adv Exp Med Biol. 2016;902:83-93
pubmed: 27161352
Genome Res. 2011 Mar;21(3):487-93
pubmed: 21209072
Sci Rep. 2020 Jul 28;10(1):12580
pubmed: 32724214
Nat Biotechnol. 2019 Oct;37(10):1155-1162
pubmed: 31406327
Clin Microbiol Rev. 2016 Apr;29(2):223-38
pubmed: 26864580
Proc Natl Acad Sci U S A. 2011 Mar 15;108 Suppl 1:4680-7
pubmed: 20534435
Genome Biol. 2014 Mar 03;15(3):R46
pubmed: 24580807
Gigascience. 2016 Jan 28;5:4
pubmed: 26823973
Proc Natl Acad Sci U S A. 1977 Nov;74(11):5088-90
pubmed: 270744
Int J Mol Sci. 2019 Dec 31;21(1):
pubmed: 31906254
Nat Commun. 2019 Jul 11;10(1):3066
pubmed: 31296857
Microbiome. 2020 Aug 28;8(1):124
pubmed: 32859275
J Microbiol Methods. 2016 Mar;122:38-42
pubmed: 26812576
Nucleic Acids Res. 2014 Jan;42(Database issue):D633-42
pubmed: 24288368
J Physiol. 2017 Jan 15;595(2):451-463
pubmed: 27373840
Genome Biol. 2019 Jun 24;20(1):129
pubmed: 31234903
Nat Methods. 2022 Apr;19(4):429-440
pubmed: 35396482
Nucleic Acids Res. 2016 Jan 4;44(D1):D67-72
pubmed: 26590407
Sci Rep. 2016 Jul 14;6:29681
pubmed: 27411898
PeerJ. 2018 Aug 8;6:e5364
pubmed: 30123705
Bioinformatics. 2018 Sep 15;34(18):3094-3100
pubmed: 29750242
Nucleic Acids Res. 2016 Jan 4;44(D1):D733-45
pubmed: 26553804
Nat Methods. 2013 Jan;10(1):71-3
pubmed: 23160280
Microbiome. 2021 Jun 5;9(1):130
pubmed: 34090540
J Mol Biol. 1990 Oct 5;215(3):403-10
pubmed: 2231712
PeerJ. 2018 Jun 12;6:e5030
pubmed: 29910992
Nat Biotechnol. 2019 Aug;37(8):852-857
pubmed: 31341288
Nat Methods. 2021 Feb;18(2):165-169
pubmed: 33432244