MetaSort untangles metagenome assembly by reducing microbial community complexity

Nature Communications

Volumn 8, Issue , 2017, Pages

  Ji, Peifeng ^a   Zhang, Yanming ^a   Wang, Jinfeng ^a   Zhao, Fangqing ^a  

^a INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; BACTERIUM; BIOINFORMATICS; COMPLEXITY; DATABASE; FLOW CYTOMETRY; GENETIC ANALYSIS; GENOME; MICROBIAL COMMUNITY; SOFTWARE;

BACTERIAL GENOME; FLOW CYTOMETRY; METAGENOME; METAGENOMICS; MICROBIAL COMMUNITY; MICROBIAL GENOME; MICROFLORA; NONHUMAN; BACTERIUM; BIOLOGY; DNA SEQUENCE; GENETICS; KELP; MICROBIOLOGY; PROCEDURES; SOFTWARE;

BACTERIA (MICROORGANISMS);

BACTERIA; COMPUTATIONAL BIOLOGY; GENOME, BACTERIAL; GENOME, MICROBIAL; KELP; METAGENOME; METAGENOMICS; MICROBIOTA; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 85010366301     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms14306     Document Type: Article

References (70)

1. Rinke, C., et al. Insights into the phylogeny and coding potential of microbial dark matter. Nature 499, 431-437 (2013).
2. Fitzsimons, M. S., et al. Nearly finished genomes produced using gel microdroplet culturing reveal substantial intraspecies genomic diversity within the human microbiome. Genome Res. 23, 878-888 (2013).
3. Peng, Y., Leung, H. C., Yiu, S. M., Chin, F. Y. Meta-IDBA: a de Novo assembler for metagenomic data. Bioinformatics 27, i94-i101 (2011).
4. Afiahayati, Sato, K., Sakakibara, Y. MetaVelvet-SL: an extension of the Velvet assembler to a de novo metagenomic assembler utilizing supervised learning. DNA Res. 22, 69-77 (2015).
5. Namiki, T., Hachiya, T., Tanaka, H., Sakakibara, Y. MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads. Nucleic acids res. 40, e155 (2012).
6. Albertsen, M., et al. Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nat. Biotechnol. 31, 533-538 (2013).
7. Wang, Y., Leung, H. C., Yiu, S. M., Chin, F. Y. MetaCluster 5.0: a two-round binning approach for metagenomic data for low-abundance species in a noisy sample. Bioinformatics 28, i356-i362 (2012).
8. Alneberg, J., et al. Binning metagenomic contigs by coverage and composition. Nat. Methods 11, 1144-1146 (2014).
9. Nielsen, H. B., et al. Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes. Nat. Biotechnol. 32, 822-828 (2014).
10. Kang, D. D., Froula, J., Egan, R., Wang, Z. MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities. PeerJ 3, e1165 (2015).
11. Dodsworth, J. A., et al. Single-cell and metagenomic analyses indicate a fermentative and saccharolytic lifestyle for members of the OP9 lineage. Nat. Commun. 4, 1854 (2013).
12. Bankevich, A., et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comp. Biol. 19, 455-477 (2012).
13. Lasken, R. S. Genomic sequencing of uncultured microorganisms from single cells. Nat. Rev. Microbiol. 10, 631-640 (2012).
14. Rodrigue, S., et al. Whole genome amplification and de novo assembly of single bacterial cells. PloS ONE 4, e6864 (2009).
15. Marcy, Y., et al. Nanoliter reactors improve multiple displacement amplification of genomes from single cells. PLoS Genet. 3, 1702-1708 (2007).
16. McLean, J. S., et al. Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum. Proc. Natl Acad. Sci. USA 110, E2390-E2399 (2013).
17. Nurk, S., et al. Assembling single-cell genomes and mini-metagenomes from chimeric MDA products. J. Comp. Biol. 20, 714-737 (2013).
18. Rinke, C., et al. Validation of picogram-and femtogram-input DNA libraries for microscale metagenomics. PeerJ 4, e2486 (2016).
19. Luo, R., et al. SOAPdenovo2: an empirically improved memory-efficient shortread de novo assembler. Gigascience 1, 18 (2012).
20. Leung, H. C., et al. A robust and accurate binning algorithm for metagenomic sequences with arbitrary species abundance ratio. Bioinformatics 27, 1489-1495 (2011).
21. McHardy, A. C., Martin, H. G., Tsirigos, A., Hugenholtz, P., Rigoutsos, I. Accurate phylogenetic classification of variable-length DNA fragments. Nat. Methods 4, 63-72 (2007).
22. Chang, C. C., Lin, C.-J. LIBSVM: a library for support vector machines. ACM Trans. Intel. Syst. Technol. 2, 27:21-27:27 (2011).
23. Wu, Y.W., Tang, Y. H., Tringe, S. G., Simmons, B. A., Singer, S. W. MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm. Microbiome 2, 26 (2014).
24. Luo, C., et al. ConStrains identifies microbial strains in metagenomic datasets. Nat. Biotechnol. 33, 1045-1052 (2015).
25. Huson, D. H., Auch, A. F., Qi, J., Schuster, S. C. MEGAN analysis of metagenomic data. Genome Res. 17, 377-386 (2007).
26. Nurk, S. M., D. Korobeynikov, A., Pevzner, P. A. metaSPAdes: a new versatile de novo metagenomics assembler. Preprint at arXiv: 1604.03071 (2016).
27. Peng, Y., Leung, H. C., Yiu, S. M., Chin, F. Y. IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics 28, 1420-1428 (2012).
28. Human Microbiome Project C. Structure, function and diversity of the healthy human microbiome. Nature 486, 207-214 (2012).
29. Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P., Tyson, G. W. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome res. 25, 1043-1055 (2015).
30. Ghylin, T. W., et al. Comparative single-cell genomics reveals potential ecological niches for the freshwater acI Actinobacteria lineage. ISME J. 8, 2503-2516 (2014).
31. Swan, B. K., et al. Prevalent genome streamlining and latitudinal divergence of planktonic bacteria in the surface ocean. Proc. Natl Acad. Sci. USA 110, 11463-11468 (2013).
32. Iverson, V., et al. Untangling genomes from metagenomes: revealing an uncultured class of marine Euryarchaeota. Science 335, 587-590 (2012).
33. Eid, J., et al. Real-time DNA sequencing from single polymerase molecules. Science 323, 133-138 (2009).
34. Chaisson, M. J., Tesler, G. Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory. BMC bioinform. 13, 238 (2012).
35. Martin, M., Portetelle, D., Michel, G., Vandenbol, M. Microorganisms living on macroalgae: diversity, interactions, and biotechnological applications. Appl. Microbiol. Biotechnol. 98, 2917-2935 (2014).
36. Gogarten, J. P., Townsend, J. P. Horizontal gene transfer, genome innovation and evolution. Nat. Rev. Microbiol. 3, 679-687 (2005).
37. Powell, S., et al. eggNOG v4.0: nested orthology inference across 3686 organisms. Nucleic acids res. 42, D231-D239 (2014).
38. Reuber, T. L., Walker, G. C. Biosynthesis of succinoglycan, a symbiotically important exopolysaccharide of Rhizobium meliloti. Cell 74, 269-280 (1993).
39. Ye, N., et al. Saccharina genomes provide novel insight into kelp biology. Nat. Commun. 6, 6986 (2015).
40. Egan, S., et al. The seaweed holobiont: understanding seaweed-bacteria interactions. FEMS Microbiol. Rev. 37, 462-476 (2013).
41. Cantarel, B. L., et al. The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics. Nucleic Acids Res. 37, D233-D238 (2009).
42. Doi, R. H., Kosugi, A. Cellulosomes: plant-cell-wall-degrading enzyme complexes. Nat. Rev. Microbiol. 2, 541-551 (2004).
43. van Teeseling, M. C., et al. Anammox Planctomycetes have a peptidoglycan cell wall. Nat. Commun. 6, 6878 (2015).
44. Jeske, O., et al. Planctomycetes do possess a peptidoglycan cell wall. Nat. Commun. 6, 7116 (2015).
45. Lindsay, M. R., et al. Cell compartmentalisation in planctomycetes: novel types of structural organisation for the bacterial cell. Arch. Microbiol. 175, 413-429 (2001).
46. Wegner, C. E., et al. Expression of sulfatases in Rhodopirellula baltica and the diversity of sulfatases in the genus Rhodopirellula. Marine Genom. 9, 51-61 (2013).
47. Krohn-Molt, I., et al. Metagenome survey of a multispecies and algaassociated biofilm revealed key elements of bacterial-algal interactions in photobioreactors. Appl. environ. microbiol. 79, 6196-6206 (2013).
48. Kuleshov, V., et al. Synthetic long-read sequencing reveals intraspecies diversity in the human microbiome. Nat. Biotechnol. 34, 64-69 (2015).
49. Sharon, I., et al. Accurate, multi-kb reads resolve complex populations and detect rare microorganisms. Genome res. 25, 534-543 (2015).
50. Howe, A. C., et al. Tackling soil diversity with the assembly of large, complex metagenomes. Proc. Natl Acad. Sci. USA 111, 4904-4909 (2014).
51. Cleary, B., et al. Detection of low-abundance bacterial strains in metagenomic datasets by eigengenome partitioning. Nat. Biotechnol. 33, 1053-1060 (2015).
52. Hong, C., et al. PathoScope 2.0: a complete computational framework for strain identification in environmental or clinical sequencing samples. Microbiome 2, 33 (2014).
53. Nijkamp, J. F., Pop, M., Reinders, M. J., de Ridder, D. Exploring variationaware contig graphs for (comparative) metagenomics using MaryGold. Bioinformatics 29, 2826-2834 (2013).
54. Peng, G., Ji, P., Zhao, F. A novel codon-based de Bruijn graph algorithm for gene construction from unassembled transcriptomes. Genome Biol. 17, 232 (2016).
55. Kurtz, S., et al. Versatile and open software for comparing large genomes. Genome biol. 5, R12 (2004).
56. Wang, J., Gao, Y., Zhao, F. Phage-bacteria interaction network in human oral microbiome. Environ. microbiol. 18, 2143-2158 (2016).
57. Zhou, H., et al. CRISPRs provide broad and robust protection to oral microbial flora of gingival health against bacteriophage challenge. Protein Cell 6, 541-545 (2015).
58. Wang, J., et al. Metagenomic sequencing reveals microbiota and its functional potential associated with periodontal disease. Sci. Rep. 3, 1843 (2013).
59. Zhang, Y., Ji, P., Wang, J., Zhao, F. RiboFR-Seq: a novel approach to linking 16S rRNA amplicon profiles to metagenomes. Nucleic acids res. 44, e99 (2016).
60. Bolger, A. M., Lohse, M., Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114-2120 (2014).
61. Richter, M., Rossello-Mora, R. Shifting the genomic gold standard for the prokaryotic species definition. Proc. Natl Acad. Sci. USA 106, 19126-19131 (2009).
62. Seemann, T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30, 2068-2069 (2014).
63. Segata, N., Bornigen, D., Morgan, X. C., Huttenhower, C. PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes. Nat. Commun. 4, 2304 (2013).
64. Moriya, Y., Itoh, M., Okuda, S., Yoshizawa, A. C., Kanehisa, M. KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res. 35, W182-W185 (2007).
65. Yin, Y., et al. dbCAN: a web resource for automated carbohydrate-active enzyme annotation. Nucleic Acids Res. 40, W445-W451 (2012).
66. Wheeler, T. J., Eddy, S. R. nhmmer: DNA homology search with profile HMMs. Bioinformatics 29, 2487-2489 (2013).
67. Ciccarelli, F. D., et al. Toward automatic reconstruction of a highly resolved tree of life. Science 311, 1283-1287 (2006).
68. Edgar, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792-1797 (2004).
69. Price, M. N., Dehal, P. S., Arkin, A. P. FastTree 2-approximately maximumlikelihood trees for large alignments. PloS ONE 5, e9490 (2010).
70. Letunic, I., Bork, P. Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy. Nucleic Acids Res. 39, W475-W478 (2011).