Species-level functional profiling of metagenomes and metatranscriptomes

Nature Methods

Volumn 15, Issue 11, 2018, Pages 962-968

  Franzosa, Eric A ^a,b   McIver, Lauren J ^a,b   Rahnavard, Gholamali ^a,b   Thompson, Luke R ^c   Schirmer, Melanie ^a,b   Weingart, George ^a   Lipson, Karen Schwarzberg ^d   Knight, Rob ^c,e   Caporaso, J Gregory ^d   Segata, Nicola ^f   Huttenhower, Curtis ^a,b  

^a HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

^b BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^c UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^d NORTHERN ARIZONA UNIVERSITY   (United States)

^e UNIVERSITY OF CALIFORNIA   (United States)

^f UNIVERSITY OF TRENTO   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; GENETIC TRANSCRIPTION; HUMAN; METABOLISM; METAGENOME; MICROBIAL COMMUNITY; MICROBIOME; MULTIGENE FAMILY; NONHUMAN; BACTERIUM; CLASSIFICATION; GENE EXPRESSION PROFILING; GENETICS; HIGH THROUGHPUT SEQUENCING; ISOLATION AND PURIFICATION; MICROFLORA; SOFTWARE; SPECIES DIFFERENCE;

BACTERIAL PROTEIN; TRANSCRIPTOME;

BACTERIA; BACTERIAL PROTEINS; GENE EXPRESSION PROFILING; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; METAGENOME; MICROBIOTA; SOFTWARE; SPECIES SPECIFICITY; TRANSCRIPTOME;

EID: 85055773262     PISSN: 15487091     EISSN: 15487105     Source Type: Journal    
DOI: 10.1038/s41592-018-0176-y     Document Type: Article

References (51)

1. Shafquat, A., Joice, R., Simmons, S. L. & Huttenhower, C. Functional and phylogenetic assembly of microbial communities in the human microbiome. Trends Microbiol. 22, 261–266 (2014)
2. Fuhrman, J. A. Microbial community structure and its functional implications. Nature 459, 193–199 (2009)
3. Lloyd-Price, J., Abu-Ali, G. & Huttenhower, C. The healthy human microbiome. Genome Med. 8, 51 (2016)
4. Franzosa, E. A. et al. Sequencing and beyond: integrating molecular ‘omics’ for microbial community profiling. Nat. Rev. Microbiol. 13, 360–372 (2015)
5. Segata, N. et al. Metagenomic microbial community profiling using unique clade-specific marker genes. Nat. Methods 9, 811–814 (2012)
6. Sunagawa, S. et al. Metagenomic species profiling using universal phylogenetic marker genes. Nat. Methods 10, 1196–1199 (2013)
7. Silva, G. G., Green, K. T., Dutilh, B. E. & Edwards, R. A. SUPER-FOCUS: a tool for agile functional analysis of shotgun metagenomic data. Bioinformatics 32, 354–361 (2016)
8. Sharma, A. K., Gupta, A., Kumar, S., Dhakan, D. B. & Sharma, V. K. Woods: a fast and accurate functionalannotator and classifier of genomic and metagenomic sequences. Genomics 106, 1–6 (2015)
9. Petrenko, P., Lobb, B., Kurtz, D. A., Neufeld, J. D. & Doxey, A. C. MetAnnotate: function-specific taxonomic profiling and comparison of metagenomes. BMC Biol. 13, 92 (2015)
10. Bose, T., Haque, M. M., Reddy, C. & Mande, S. S. COGNIZER: a framework for functional annotation of metagenomic datasets. PLoS One 10, e0142102 (2015)
11. Kim, J., Kim, M. S., Koh, A. Y., Xie, Y. & Zhan, X. FMAP: functional mapping and analysis pipeline for metagenomics and metatranscriptomics studies. BMC Bioinformatics 17, 420 (2016)
12. Huson, D. H. et al. MEGAN Community Edition—interactive exploration and analysis of large-scale microbiome sequencing data. PLoS Comput. Biol. 12, e1004957 (2016)
13. Nayfach, S. et al. Automated and accurate estimation of gene family abundance from shotgun metagenomes. PLoS Comput. Biol. 11, e1004573 (2015)
14. Abubucker, S. et al. Metabolic reconstruction for metagenomic data and its application to the human microbiome. PLoS Comput. Biol. 8, e1002358 (2012)
15. Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature 486, 207–214 (2012)
16. Buchfink, B., Xie, C. & Huson, D. H. Fast and sensitive protein alignment using Diamond. Nat. Methods 12, 59–60 (2015)
17. Zhao, Y., Tang, H. & Ye, Y. RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data. Bioinformatics 28, 125–126 (2012)
18. Hauswedell, H., Singer, J. & Reinert, K. Lambda: the local aligner for massive biological data. Bioinformatics 30, i349–i355 (2014)
19. Truong, D. T., Tett, A., Pasolli, E., Huttenhower, C. & Segata, N. Microbial strain-level population structure and genetic diversity from metagenomes. Genome Res. 27, 626–638 (2017)
20. Scholz, M. et al. Strain-level microbial epidemiology and population genomics from shotgun metagenomics. Nat. Methods 13, 435–438 (2016)
21. Luo, C. et al. ConStrains identifies microbial strains in metagenomic datasets. Nat. Biotechnol. 33, 1045–1052 (2015)
22. Truong, D. T. et al. MetaPhlAn2 for enhanced metagenomic taxonomic profiling. Nat. Methods 12, 902–903 (2015)
23. Medini, D., Donati, C., Tettelin, H., Masignani, V. & Rappuoli, R. The microbial pan-genome. Curr. Opin. Genet. Dev. 15, 589–594 (2005)
24. Suzek, B. E., Wang, Y., Huang, H., McGarvey, P. B. & Wu, C. H. UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches. Bioinformatics 31, 926–932 (2015)
25. Galperin, M. Y., Makarova, K. S., Wolf, Y. I. & Koonin, E. V. Expanded microbial genome coverage and improved protein family annotation in the COG database. Nucleic Acids Res. 43, D261–D269 (2015)
26. Kanehisa, M., Sato, Y., Kawashima, M., Furumichi, M. & Tanabe, M. KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res. 44, D457–D462 (2016)
27. Finn, R. D. et al. The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res. 44, D279–D285 (2016)
28. Gene Ontology Consortium. Gene Ontology Consortium: going forward Nucleic Acids Res. 43, D1049–D1056 (2015)
29. Caspi, R. et al. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res. 44, D471–D480 (2016)
30. Lloyd-Price, J. et al. Strains, functions and dynamics in the expanded Human Microbiome Project. Nature 550, 61–66 (2017)
31. Sczyrba, A. et al. Critical assessment of metagenome interpretation—a benchmark of metagenomics software. Nat. Methods 14, 1063–1071 (2017)
32. Hamady, M. & Knight, R. Microbial community profiling for human microbiome projects: tools, techniques, and challenges. Genome Res. 19, 1141–1152 (2009)
33. Ravel, J. et al. Vaginal microbiome of reproductive-age women. Proc. Natl. Acad. Sci. USA 108, 4680–4687 (2011)
34. Thompson, L. R. et al. Metagenomic covariation along densely sampled environmental gradients in the Red Sea. ISME J. 11, 138–151,10.1038/ismej.2016.99 (2017)
35. Sunagawa, S. et al. Structure and function of the global ocean microbiome. Science 348, 1261359 (2015)
36. Swan, B. K. et al. Genomic and metabolic diversity of Marine Group I Thaumarchaeota in the mesopelagic of two subtropical gyres. PLoS One 9, e95380 (2014)
37. Thompson, L. R. et al. Phage auxiliary metabolic genes and the redirection of cyanobacterial host carbon metabolism. Proc. Natl. Acad. Sci. USA 108, E757–E764 (2011)
38. Integrative HMP (iHMP) Research Network Consortium. The Integrative Human Microbiome Project: dynamic analysis of microbiome-host omics profiles during periods of human health and disease. Cell Host Microbe 16, 276–289 (2014)
39. Franzosa, E. A. et al. Relating the metatranscriptome and metagenome of the human gut. Proc. Natl. Acad.Sci. USA 111, E2329–E2338 (2014)
40. Turnbaugh, P. J. et al. A core gut microbiome in obese and lean twins. Nature 457, 480–484 (2009)
41. Burke, C., Steinberg, P., Rusch, D., Kjelleberg, S. & Thomas, T. Bacterial community assembly based on functional genes rather than species. Proc. Natl. Acad. Sci. USA 108, 14288–14293 (2011)
42. Duran-Pinedo, A. E. et al. Community-wide transcriptome of the oral microbiome in subjects with and without periodontitis. ISME J. 8, 1659–1672 (2014)
43. Mason, O. U. et al. Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill. ISME J. 6, 1715–1727 (2012)
44. Pasolli, E., Truong, D. T., Malik, F., Waldron, L. & Segata, N. Machine learning meta-analysis of large metagenomic datasets: tools and biological insights. PLoS Comput. Biol. 12, e1004977 (2016)
45. UniProt Consortium. UniProt: a hub for protein information. Nucleic Acids Res. 43, D204–D212 (2015)
46. Huang, K. et al. MetaRef: a pan-genomic database for comparative and community microbial genomics. Nucleic Acids Res. 42, D617–D624 (2014)
47. Segata, N., Börnigen, D., Morgan, X. C. & Huttenhower, C. PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes. Nat. Commun. 4, 2304 (2013)
48. Edgar, R. C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26, 2460–2461 (2010)
49. Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012)
50. Ye, Y. & Doak, T. G. A parsimony approach to biological pathway reconstruction/inference for genomes and metagenomes. PLoS Comput. Biol. 5, e1000465 (2009)
51. Huang, W., Li, L., Myers, J. R. & Marth, G. T. ART: a next-generation sequencing read simulator. Bioinformatics 28, 593–594 (2012)