Computational integration of genomic traits into 16S rDNA microbiota sequencing studies

Gene

Volumn 549, Issue 1, 2014, Pages 186-191

  Keller, Alexander ^a   Horn, Hannes ^a,b   Förster, Frank ^a   Schultz, Jörg ^a  

^a UNIVERSITY OF WÜRZBURG   (Germany)

^b UNIVERSITY OF WÜRZBURG   (Germany)

Author keywords

16S rDNA; Metabarcoding; Metagenomics; Molecular biodiversity; Molecular community ecology; Molecular functional ecology

Indexed keywords

DNA 16S; GENOMIC DNA; RIBOSOME RNA;

AMINO ACID SEQUENCE; ARTICLE; CLONE; COMMUNITY ECOLOGY; DNA BARCODING; DNA SEQUENCE; FLOWER; FOLLOW UP; GENETIC TRAIT; LOTUS CORNICULATUS; METAGENOME; MICROBIAL COMMUNITY; MICROBIAL DIVERSITY; MICROFLORA; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT LEAF; PRIORITY JOURNAL; PROTEIN FAMILY; PYROSEQUENCING; REFERENCE DATABASE;

16S RDNA; METABARCODING; METAGENOMICS; MOLECULAR BIODIVERSITY; MOLECULAR COMMUNITY ECOLOGY; MOLECULAR FUNCTIONAL ECOLOGY;

BACTERIA; COMPUTATIONAL BIOLOGY; DNA BARCODING, TAXONOMIC; DNA, BACTERIAL; DNA, RIBOSOMAL; GENETIC MARKERS; GENOME, BACTERIAL; GENOMICS; METAGENOMICS; MICROBIOTA; MULTIGENE FAMILY; REPRODUCIBILITY OF RESULTS; RNA, RIBOSOMAL, 16S;

EID: 84905740082     PISSN: 03781119     EISSN: 18790038     Source Type: Journal    
DOI: 10.1016/j.gene.2014.07.066     Document Type: Article

References (66)

1. Albertsen M., Hugenholtz P., Skarshewski A., Nielsen K.L., Tyson G.W., Nielsen P.H. Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nat. Biotechnol. 2013, 31:533-538.
2. Ashburner M., Ball C.A., Blake J.A., Botstein D., Butler H., Cherry J.M., Davis A.P., Dolinski K., Dwight S.S., Eppig J.T., Harris M.A., Hill D.P., Issel-Tarver L., Kasarskis A., Lewis S., Matese J.C., Richardson J.E., Ringwald M., Rubin G.M., Sherlock G. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 2000, 25:25-29.
3. Begon M., Townsend C., Harper J. Ecology: From Individuals to Ecosystems 2009.
4. Beszteri B., Temperton B., Frickenhaus S., Giovannoni S.J. Average genome size: a potential source of bias in comparative metagenomics. ISME J. 2010, 4:1075-1077.
5. Caporaso J.G., Kuczynski J., Stombaugh J., Bittinger K., Bushman F.D., Costello E.K., Fierer N., Peña A.G., Goodrich J.K., Gordon J.I. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 2010, 7:335-336.
6. Caporaso J.G., Lauber C.L., Walters W.A., Berg-Lyons D., Huntley J., Fierer N., Owens S.M., Betley J., Fraser L., Bauer M., Gormley N., Gilbert J.A., Smith G., Knight R. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 2012, 6:1621-1624.
7. Chakraborty C., Doss C.G.P., Patra B.C., Bandyopadhyay S. DNA barcoding to map the microbial communities: current advances and future directions. Appl. Microbiol. Biotechnol. 2014, 98:3425-3436.
8. Chan J.Z.-M., Halachev M.R., Loman N.J., Constantinidou C., Pallen M.J. Defining bacterial species in the genomic era: insights from the genus Acinetobacter. BMC Microbiol. 2012, 12:302.
9. Chin C.-S., Alexander D.H., Marks P., Klammer A.A., Drake J., Heiner C., Clum A., Copeland A., Huddleston J., Eichler E.E., Turner S.W., Korlach J. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat. Methods 2013, 10:563-569.
10. Chou H.-H., Holmes M.H. DNA sequence quality trimming and vector removal. Bioinformatics 2001, 17:1093-1104.
11. Chun J., Lee J.-H., Jung Y., Kim M., Kim S., Kim B.K., Lim Y.-W. EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. Int. J. Syst. Evol. Microbiol. 2007, 57:2259-2261.
12. Clarridge J.E. Impact of 16S rRNA gene sequence analysis for identification of bacteria on clinical microbiology and infectious diseases. Clin. Microbiol. Rev. 2004, 17:840-862. (table of contents).
13. Drancourt M., Bollet C., Carlioz A., Martelin R., Gayral J.-P., Raoult D. 16S ribosomal DNA sequence analysis of a large collection of environmental and clinical unidentifiable bacterial isolates. J. Clin. Microbiol. 2000, 38:3623-3630.
14. Dröge J., McHardy A.C. Taxonomic binning of metagenome samples generated by next-generation sequencing technologies. Brief. Bioinform. 2012, 13:646-655.
15. Eisen J.A. Environmental shotgun sequencing: its potential and challenges for studying the hidden world of microbes. PLoS Biol. 2007, 5:e82.
16. Ernst R., Keller A., Landburg G., Grafe T.U., Linsenmair K.E., Roedel M.-O., Dziock F. Common ancestry or environmental trait filters: cross-continental comparisons of trait-habitat relationships in tropical anuran amphibian assemblages. Glob. Ecol. Biogeogr. 2012, 21:704-715.
17. Federhen S. The NCBI taxonomy database. Nucleic Acids Res. 2012, 40:D136-D143.
18. Finn R.D., Mistry J., Tate J., Coggill P., Heger A., Pollington J.E., Gavin O.L., Gunasekaran P., Ceric G., Forslund K., Holm L., Sonnhammer E.L.L., Eddy S.R., Bateman A. The Pfam protein families database. Nucleic Acids Res. 2010, 38:D211-D222.
19. Gentleman R.C., Carey V.J., Bates D.M., Bolstad B., Dettling M., Dudoit S., Ellis B., Gautier L., Ge Y., Gentry J., Hornik K., Hothorn T., Huber W., Iacus S., Irizarry R., Leisch F., Li C., Maechler M., Rossini A.J., Sawitzki G., Smith C., Smyth G., Tierney L., Yang J.Y., Zhang J. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004, 5:R80.
20. Gilbert J.A., Meyer F., Antonopoulos D., Balaji P., Brown C.T., Brown C.T., Desai N., Eisen J.A., Evers D., Field D., Feng W., Huson D., Jansson J., Knight R., Knight J., Kolker E., Konstantindis K., Kostka J., Kyrpides N., Mackelprang R., McHardy A., Quince C., Raes J., Sczyrba A., Shade A., Stevens R. Meeting report: the terabase metagenomics workshop and the vision of an Earth microbiome project. Stand. Genomic Sci. 2010, 3:243-248.
21. Guazzaroni M.-E., Beloqui A., Golyshin P.N., Ferrer M. Metagenomics as a new technological tool to gain scientific knowledge. World J. Microbiol. Biotechnol. 2009, 25:945-954.
22. Hebert P.D.N., Cywinska A., Ball S.L. Biological identifications through DNA barcodes. Proc. R. Soc. Lond. B Biol. Sci. 2003, 270:313-321.
23. Hoefler B.C., Konganti K., Straight P.D. De novo assembly of the Streptomyces sp. strain Mg1 genome using PacBio single-molecule sequencing. Genome Announc. 2013, 1.
24. Huson D.H., Mitra S., Ruscheweyh H.J., Weber N., Schuster S.C. Integrative analysis of environmental sequences using MEGAN4. Genome Res. 2011, 21:1552-1560.
25. Junker R.R., Loewel C., Gross R., Dötterl S., Keller A., Blüthgen N. Composition of epiphytic bacterial communities differs on petals and leaves. Plant Biol. 2011, 13:918-924.
26. Kalyuzhnaya M.G., Lapidus A., Ivanova N., Copeland A.C., McHardy A.C., Szeto E., Salamov A., Grigoriev I.V., Suciu D., Levine S.R., Markowitz V.M., Rigoutsos I., Tringe S.G., Bruce D.C., Richardson P.M., Lidstrom M.E., Chistoserdova L. High-resolution metagenomics targets specific functional types in complex microbial communities. Nat. Biotechnol. 2008, 26:1029-1034.
27. Keddy P.A. Assembly and response rules: two goals for predictive community ecology. J. Veg. Sci. 1992, 3:157-164.
28. Keller A., Rödel M.-O.O., Linsenmair K.E., Grafe T.U. The importance of environmental heterogeneity for species diversity and assemblage structure in Bornean stream frogs. J. Anim. Ecol. 2009, 78:305-314.
29. Keller A., Grimmer G., Steffan-Dewenter I. Diverse microbiota identified in whole intact nest chambers of the red mason bee Osmia bicornis (Linnaeus 1758). PLoS One 2013, e78296.
30. Kunin V., Copeland A., Lapidus A., Mavromatis K., Hugenholtz P. A bioinformatician's guide to metagenomics. Microbiol. Mol. Biol. Rev. 2008, 72:557-578. (Table of Contents).
31. Lingner T., Asshauer K.P., Schreiber F., Meinicke P. CoMet-a web server for comparative functional profiling of metagenomes. Nucleic Acids Res. 2011, 39:W518-W523.
32. Mardis E.R. A decade's perspective on DNA sequencing technology. Nature 2011, 470:198-203.
33. Markowitz V.M., Chen I.-M.A., Chu K., Szeto E., Palaniappan K., Grechkin Y., Ratner A., Jacob B., Pati A., Huntemann M., Liolios K., Pagani I., Anderson I., Mavromatis K., Ivanova N.N., Kyrpides N.C. IMG/M: the integrated metagenome data management and comparative analysis system. Nucleic Acids Res. 2012, 40:D123-D129.
34. Mason O.U., Scott N.M., Gonzalez A., Robbins-Pianka A., Bælum J., Kimbrel J., Bouskill N.J., Prestat E., Borglin S., Joyner D.C., Fortney J.L., Jurelevicius D., Stringfellow W.T., Alvarez-Cohen L., Hazen T.C., Knight R., Gilbert J.A., Jansson J.K. Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill. ISME J. 2014, 8:1464-1475. 10.1038/ismej.2013.254.
35. McGill B.J., Enquist B.J., Weiher E., Westoby M. Rebuilding community ecology from functional traits. Trends Ecol. Evol. 2006, 21:178-185.
36. Mendes L.W., Kuramae E.E., Navarrete A.A., van Veen J.A., Tsai S.M. Taxonomical and functional microbial community selection in soybean rhizosphere. ISME J. 2014, 8:1577-1587. 10.1038/ismej.2014.17.
37. Metzker M.L. Sequencing technologies-the next generation. Nat. Rev. Genet. 2009, 11:31-46.
38. Meyer F., Paarmann D., D'Souza M., Olson R., Glass E.M., Kubal M., Paczian T., Rodriguez A., Stevens R., Wilke A., Wilkening J., Edwards R.A. The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 2008, 9:386.
39. Morgan J.L., Darling A.E., Eisen J.A. Metagenomic sequencing of an in vitro-simulated microbial community. PLoS One 2010, 5:e10209.
40. Ogata H., Goto S., Sato K., Fujibuchi W., Bono H., Kanehisa M. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 1999, 27:29-34.
41. Oksanen J., Kindt R., Legendre P., O'Hara B., Stevens M.H.H., Oksanen M.J., Suggests M. The vegan package. Community Ecol. Packag. 2007, 10:2008.
42. Overbeek R., Begley T., Butler R.M., Choudhuri J.V., Chuang H.-Y., Cohoon M., de Crécy-Lagard V., Diaz N., Disz T., Edwards R., Fonstein M., Frank E.D., Gerdes S., Glass E.M., Goesmann A., Hanson A., Iwata-Reuyl D., Jensen R., Jamshidi N., Krause L., Kubal M., Larsen N., Linke B., McHardy A.C., Meyer F., Neuweger H., Olsen G., Olson R., Osterman A., Portnoy V., Pusch G.D., Rodionov D.A., Rückert C., Steiner J., Stevens R., Thiele I., Vassieva O., Ye Y., Zagnitko O., Vonstein V. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res. 2005, 33:5691-5702.
43. Peterson J., Garges S., Giovanni M., McInnes P., Wang L., Schloss J.A., Bonazzi V., McEwen J.E., Wetterstrand K.A., Deal C., Baker C.C., Di Francesco V., Howcroft T.K., Karp R.W., Lunsford R.D., Wellington C.R., Belachew T., Wright M., Giblin C., David H., Mills M., Salomon R., Mullins C., Akolkar B., Begg L., Davis C., Grandison L., Humble M., Khalsa J., Little A.R., Peavy H., Pontzer C., Portnoy M., Sayre M.H., Starke-Reed P., Zakhari S., Read J., Watson B., Guyer M. The NIH human microbiome project. Genome Res. 2009, 19:2317-2323.
44. Powell S., Forslund K., Szklarczyk D., Trachana K., Roth A., Huerta-Cepas J., Gabaldón T., Rattei T., Creevey C., Kuhn M., Jensen L.J., von Mering C., Bork P. eggNOG v4.0: nested orthology inference across 3686 organisms. Nucleic Acids Res. 2014, 42:D231-D239.
45. Pruitt K.D., Tatusova T., Maglott D.R. NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 2007, 35:D61-D65.
46. Qu A., Brulc J.M., Wilson M.K., Law B.F., Theoret J.R., Joens L.A., Konkel M.E., Angly F., Dinsdale E.A., Edwards R.A., Nelson K.E., White B.A. Comparative metagenomics reveals host specific metavirulomes and horizontal gene transfer elements in the chicken cecum microbiome. PLoS One 2008, 3:e2945.
47. R Development Core Team R: A Language and Environment for Statistical Computing 2010, R Found. Stat. Comput., Vienna Austria.
48. Rastogi G., Sani R.K. Molecular techniques to assess microbial community structure, function, and dynamics in the environment. Microbes Microb. Technol. 2011, 29-57.
49. Rice P., Longden I., Bleasby A. EMBOSS: the European molecular biology open software suite. Trends Genet. 2000, 16(6):276-277. 10.1016/S0168-9525(00)02024-2.
50. Scholz M.B., Lo C.-C., Chain P.S.G. Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis. Curr. Opin. Biotechnol. 2012, 23:9-15.
51. Stackebrandt E., Ebers J. Taxonomic parameters revisited: tarnished gold standards. Microbiol. Today 2006, 33:152.
52. Stackebrandt E., Goebel B. Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Syst. Bacteriol. 1994, 44:846-849.
53. Tamames J., Moya A. Estimating the extent of horizontal gene transfer in metagenomic sequences. BMC Genomics 2008, 9:136.
54. Tatusov R.L., Fedorova N.D., Jackson J.D., Jacobs A.R., Kiryutin B., Koonin E.V., Krylov D.M., Mazumder R., Mekhedov S.L., Nikolskaya A.N., Rao B.S., Smirnov S., Sverdlov A.V., Vasudevan S., Wolf Y.I., Yin J.J., Natale D.A. The COG database: an updated version includes eukaryotes. BMC Bioinformatics 2003, 4:41.
55. Thompson J., Higgins D., Gibson T. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix. Nucleic Acids Res. 1994, 22(22):4673-4680. 10.1093/nar/22.22.4673.
56. Tringe S.G., Hugenholtz P. A renaissance for the pioneering 16S rRNA gene. Curr. Opin. Microbiol. 2008, 11:442-446.
57. Tringe S.G., von Mering C., Kobayashi A., Salamov A.A., Chen K., Chang H.W., Podar M., Short J.M., Mathur E.J., Detter J.C., Bork P., Hugenholtz P., Rubin E.M. Comparative metagenomics of microbial communities. Science 2005, 308:554-557.
58. Tyson G.W., Chapman J., Hugenholtz P., Allen E.E., Ram R.J., Richardson P.M., Solovyev V.V., Rubin E.M., Rokhsar D.S., Banfield J.F. Community structure and metabolism through reconstruction of microbial genomes from the environment 2004, 428:37-43.
59. Uchiyama I., Mihara M., Nishide H., Chiba H. MBGD update 2013: the microbial genome database for exploring the diversity of microbial world. Nucleic Acids Res. 2013, 41:D631-D635.
60. Valentini A., Pompanon F., Taberlet P. DNA barcoding for ecologists. Trends Ecol. Evol. 2009, 24:110-117.
61. Vizcaino M.I., Guo X., Crawford J.M. Merging chemical ecology with bacterial genome mining for secondary metabolite discovery. J. Ind. Microbiol. Biotechnol. 2014, 41:285-299.
62. Wang Q., Garrity G.M., Tiedje J.M., Cole J.R. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 2007, 73:5261-5267.
63. Webb C.O., Ackerly D.D., McPeek M.A., Donoghue M.J. Phylogenies and Community Ecology 2007.
64. Wu D., Hugenholtz P., Mavromatis K., Pukall R., Dalin E., Ivanova N.N., Kunin V., Goodwin L., Wu M., Tindall B.J., Hooper S.D., Pati A., Lykidis A., Spring S., Anderson I.J., D'haeseleer P., Zemla A., Singer M., Lapidus A., Nolan M., Copeland A., Han C., Chen F., Cheng J.-F., Lucas S., Kerfeld C., Lang E., Gronow S., Chain P., Bruce D., Rubin E.M., Kyrpides N.C., Klenk H.-P., Eisen J.A. A phylogeny-driven genomic encyclopaedia of bacteria and Archaea. Nature 2009, 462:1056-1060.
65. Yoon H.S., Price D.C., Stepanauskas R., Rajah V.D., Sieracki M.E., Wilson W.H., Yang E.C., Duffy S., Bhattacharya D. Single-cell genomics reveals organismal interactions in uncultivated marine protists. Science 2011, 332:714-717.
66. Zdobnov E.M., Apweiler R. InterProScan - an integration platform for the signature-recognition methods in InterPro. Bioinformatics 2001, 17:847-848.