RiboTagger: Fast and unbiased 16S/18S profiling using whole community shotgun metagenomic or metatranscriptome surveys

BMC Bioinformatics

Volumn 17, Issue , 2016, Pages

  Xie, Chao ^a,d   Goi, Chin Lui Wesley ^a   Huson, Daniel H ^a,b   Little, Peter F R ^a,c   Williams, Rohan B H ^a  

^a NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^b UNIVERSITY OF TÜBINGEN   (Germany)

^c NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^d Human Longevity Inc   (United States)

Author keywords

Microbial community profiling; Microbial ecology; Sequence analysis; Short subunit ribosomal RNA

Indexed keywords

ECOLOGY; MICROORGANISMS; NUCLEIC ACIDS; RNA; SURVEYS;

HIGH SENSITIVITY; HIGH THROUGHPUT; MICROBIAL COMMUNITIES; MICROBIAL ECOLOGY; RIBOSOMAL RNA; SEQUENCE ANALYSIS; SMALL SUBUNITS; VARIABLE REGIONS;

NUCLEIC ACID SEQUENCES;

RIBOSOME DNA; RNA 16S; RNA 18S; TRANSCRIPTOME;

BACTERIUM; BIOLOGY; DNA SEQUENCE; GENETICS; HIGH THROUGHPUT SEQUENCING; METAGENOME; METAGENOMICS; PROCEDURES; SOFTWARE;

BACTERIA; COMPUTATIONAL BIOLOGY; DNA, RIBOSOMAL; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; METAGENOME; METAGENOMICS; RNA, RIBOSOMAL, 16S; RNA, RIBOSOMAL, 18S; SEQUENCE ANALYSIS, DNA; SOFTWARE; TRANSCRIPTOME;

EID: 85006856675     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/s12859-016-1378-x     Document Type: Article

References (24)

1. Raes J, Bork P. Molecular eco-systems biology: towards an understanding of community function. Nat Rev Microbiol. 2008;6:693-9.
2. Harismendy O, et al. Evaluation of next generation sequencing platforms for population targeted sequencing studies. Genome Biol. 2009;10:R32.
3. Liu Z, Lozupone C, Hamady M, Bushman FD, Knight R. Short pyrosequencing reads suffice for accurate microbial community analysis. Nucleic Acids Res. 2007;35:e120.
4. Haas BJ, et al. Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res. 2011;21:494-504.
5. Hong S, Bunge J, Leslin C, Jeon S, Epstein SS. Polymerase chain reaction primers miss half of rRNA microbial diversity. ISME J. 2009;3:1365-73.
6. Albertsen M, Karst SM, Ziegler AS, Kirkegaard RH, Nielsen PH. Back to Basics--The Influence of DNA Extraction and Primer Choice on Phylogenetic Analysis of Activated Sludge Communities. PLoS ONE. 2015;10, e0132783.
7. Thomas T, Gilbert J, Meyer F. Metagenomics-a guide from sampling to data analysis. Microb Inform Exp. 2012;2:3.
8. Albertsen M, et al. Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nat Biotechnol. 2013;31:533-8.
9. Chistoserdova L. Is metagenomics resolving identification of functions in microbial communities? Microb Biotechnol. 2014;7:1-4.
10. Hartmann M, Howes CG, Abarenkov K, Mohn WW, Nilsson RH. V-Xtractor: an open-source, high-throughput software tool to identify and extract hypervariable regions of small subunit (16S/18S) ribosomal RNA gene sequences. J Microbiol Methods. 2010;83:250-3.
11. Lee JH, Yi H, Chun J. rRNASelector: a computer program for selecting ribosomal RNA encoding sequences from metagenomic and metatranscriptomic shotgun libraries. J Microbiol. 2011;49:689-91.
12. Bengtsson J, et al. Metaxa: a software tool for automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts in metagenomes and environmental sequencing datasets. Antonie Van Leeuwenhoek. 2011;100:471-5.
13. Bengtsson-Palme J, et al. METAXA2: improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data. Mol Ecol Resour. 2015;15:1403-14.
14. Leach AL, Chong JP, Redeker KR. SSuMMo: rapid analysis, comparison and visualization of microbial communities. Bioinformatics. 2012;28(5):679-86.
15. Logares R, et al. Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities. Environ Microbiol. 2014;16:2659-71.
16. Ramazzotti M, Berná L, Donati C, Cavalieri D. riboFrame: An Improved Method for Microbial Taxonomy Profiling from Non-Targeted Metagenomics. Front Genet. 2015;6:329.
17. Guo J, Cole JR, Zhang Q, Brown CT, Tiedje JM. Microbial Community Analysis with Ribosomal Gene Fragments from Shotgun Metagenomes. Appl Environ Microbiol. 2015;82(1):157-66.
18. Caporaso JG, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010;7:335-6.
19. Huson DH, et al. MEGAN Community Edition-Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data. PLoS Comput Biol. 2016;12, e1004957.
20. Cole JR, et al. Ribosomal Database Project: data and tools for high throughput rRNA analysis. Nucleic Acids Res. 2014;42(Database issue):D633-42.
21. Pruesse E, et al. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res. 2007;35:7188-96.
22. Giovannoni SJ, et al. Genome Streamlining in a Cosmopolitan Oceanic Bacterium. Science. 2005;309:1242-5.
23. Tikhonov M, Leach RW, Wingreen NS. Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution. ISME J. 2015;9:68-80.
24. DeSantis TZ, et al. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol. 2006;72:5069-72.