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The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium inaugural meeting report

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The MetaSUB International Consortium·2016·Microbiome
DOI 10.1186/s40168-016-0168-z
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Abstract

The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium is a novel, interdisciplinary initiative comprised of experts across many fields, including genomics, data analysis, engineering, public health, and architecture. The ultimate goal of the MetaSUB Consortium is to improve city utilization and planning through the detection, measurement, and design of metagenomics within urban environments. Although continual measures occur for temperature, air pressure, weather, and human activity, including longitudinal, cross-kingdom ecosystem dynamics can alter and improve the design of cities. The MetaSUB Consortium is aiding these efforts by developing and testing metagenomic methods and standards, including optimized methods for sample collection, DNA/RNA isolation, taxa characterization, and data visualization. The data produced by the consortium can aid city planners, public health officials, and architectural designers. In addition, the study will continue to lead to the discovery of new species, global maps of antimicrobial resistance (AMR) markers, and novel biosynthetic gene clusters (BGCs). Finally, we note that engineered metagenomic ecosystems can help enable more responsive, safer, and quantified cities.

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Research works printed but not linked: 40

  1. The MetaSUB International Consortium: The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium inaugural meeting report. Microbiome 2016;4:24.
  2. Leung MH, Wilkins D, Li EK, Kong FK, Lee PK. Indoor-air microbiome in an urban subway network: diversity and dynamics. Appl Environ Microbiol. 2014;80:6760–70. · DOI · Paper page
  3. Robertson CE, Baumgartner LK, Harris JK, Peterson KL, Stevens MJ, Frank DN, Pace NR. Culture-independent analysis of aerosol microbiology in a metropolitan subway system. Appl Environ Microbiol. 2013;79(11):3485–93. · DOI
  4. Cao C, Jiang W, Wang B, Fang J, Lang J, Tian G, Jiang J, Zhu TF. Inhalable microorganisms in Beijing’s PM2.5 and PM10 pollutants during a severe smog event. Environ Sci Technol. 2014;48(3):1499–507. · DOI · Paper page
  5. Yooseph S, Andrews-Pfannkoch C, Tenney A, McQuaid J, Williamson S, Thiagarajan M, Brami D, Zeigler-Allen L, Hoffman J, Goll JB, Fadrosh D, Glass J, Adams MD, Friedman R, Venter JC. A metagenomic framework for the study of airborne microbial communities. PLoS One. 2013;8(12):e81862. · DOI
  6. Firth C, Bhat M, Firth MA, Williams SH, Frye MJ, Simmonds P, Conte JM, Ng J, Garcia J, Bhuva NP, Lee B, Che X, Quan PL, Lipkin WI. Detection of zoonotic pathogens and characterization of novel viruses carried by commensal Rattus norvegicus in New York City. MBio. 2014;5(5):e01933–14. · DOI · Paper page
  7. Conceição T, Diamantino F, Coelho C, de Lencastre H, Aires-de-Sousa M. Contamination of public buses with MRSA in Lisbon, Portugal: a possible transmission route of major MRSA clones within the community. PLoS One. 2013;8(11):e77812. · DOI
  8. Reese AT, Savage A, Youngsteadt E, McGuire KL, Koling A, Watkins O, Frank SD, Dunn RR. Urban stress is associated with variation in microbial species composition-but not richness-in Manhattan. ISME J. 2015;10:751–60. doi: 10.1038/ismej.2015.152 . · DOI
  9. Alivisatos AP, Blaser MJ, Brodie EL, Chun M, Dangl JL, Donohue TJ, Dorrestein PC, Gilbert JA, Green JL, Jansson JK, Knight R, Maxon ME, McFall-Ngai MJ, Miller JF, Pollard KS, Ruby EG, Taha SA; Unified Microbiome Initiative Consortium. A unified initiative to harness Earth’s microbiomes. Science. 2015;350(6260):507–8. · DOI · Paper page
  10. Dubilier N, McFall-Ngai M, Zhao L. Microbiology: create a global microbiome effort. Nature. 2015;526(7575):631–4. · DOI
  11. Jones MB, Highlander SK, Anderson EL, Li W, Dayrit M, Klitgord N, abani MM, Seguritan V, Green J, Pride DT, Yooseph S, Biggs W, Nelson KE, Venter JC. Library preparation methodology can influence genomic and functional predictions in human microbiome research. Proc Natl Acad Sci U S A. 2015;112(45):14024–9. · DOI · Paper page
  12. Afshinnekoo E, Meydan C, Chowdhury S, Jaroudi D, Boyer C, Bernstein N, Maritz JM, Reeves D, Gandara J, Chhangawala S, Ahsanuddin S, Simmons A, Nessel T, Sundaresh B, Pereira E, Jorgensen E, Kolokotronis S, Kirchberger N, Garcia I, Gandara D, Dhanraj S, Nawrin T, Saletore Y, Alexander N, Vijay P, Hénaff EM, Zumbo P, Walsh M, O’Mullan GD, Tighe S, Dudley JT, Dunaif A, Ennis S, O’Halloran E, Magalhaes TR, Boone B, Jones AL, Muth TR, Paolantonio KS, Alter E, Schadt EE, Garbarino J, Prill RJ, Carlton JM, Levy S, Mason CE. Modern methods for delineating metagenomic complexity. Cell Sys. 2015;1(1):88. · DOI · Paper page
  13. Schatz MC, Phillippy AM. The rise of a digital immune system. Giga Sci. 2012;1(1):4. · DOI
  14. Mason CE, Porter S, Smith T. Characterizing Multi-omic data in systems biology. Adv Exp Med Biol. 2014;799:15–38. · DOI
  15. Ji P, Parks J, Edwards MA, Pruden A. Impact of water chemistry, pipe material and stagnation on the building plumbing microbiome. PLoS One. 2015;10(10):e0141087. · DOI
  16. Donia MS, Cimermancic P, Schulze CJ, Wieland Brown LC, Martin J, Mitreva M, Clardy J, Linington RG, and Fischbach MA. A systematic analysis of biosynthetic gene clusters in the human microbiome reveals a common family of antibiotics. Cell. 2014;158:1402–14. · DOI · Paper page
  17. Rosenfeld JA, Reeves D, Brugler MR, Narechania A, Simon S, Durrett R, Foox J, Shianna K, Schatz MC, Gandara J, Afshinnekoo E, Lam ET, Hastie AR, Chan S, Cao H, Saghbini M, Kentsis A, Planet PJ, Kholodovych V, Tessler M, Baker R, DeSalle R, Sorkin LN, Kolokotronis, Siddall ME, Amato G, Mason CE. Genome assembly and geospatial phylogenomics of the bed bug Cimex lectularius. Nat Commun. 2016;7, 10164. doi: 10.1038/ncomms10164 . · DOI
  18. Li S, Mason CE. The pivotal regulatory landscape of RNA modifications. Annu Rev Genomics Hum Genet. 2014;15:127–50. · DOI · Paper page
  19. Traxler MF, Kolter R. Natural products in soil microbe interactions and evolution. Nat Prod Rep. 2015;32:956–70. · DOI · Paper page
  20. Hu Y, Phelan V, Ntai I, Farnet CM, Zazopoulos E, Bachmann BO. Benzodiazepine biosynthesis in Streptomyces refuineus. Chem Biol. 2007;14:691–701. · DOI
  21. Dimise EJ, Widboom PF, Bruner SD. Structure elucidation and biosynthesis of fuscachelins, peptide siderophores from the moderate thermophile Thermobifida fusca. Proc Natl Acad Sci U S A. 2008;105:15311–6. · DOI
  22. Ehrenberg R. Urban microbe come out of the shadows. Nature. 2015;522:399–400. doi: 10.1038/522399a . · doi:10.1038/522399a
  23. Hsu T, Joice R, Vallarino J, Abu-Ali G, Hartmann EM, Shafquat A, Dulong C, Baranowski C, Gevers D, Green JL, Morgan XC, Spengler JD, Huttenhower C. Urban transit system microbial communities differ by surface type and interaction with humans and environment. In Press
  24. Pendleton M, Sebra R, Pang AW, Ummat A, Franzen O, Rausch T, Stütz AM, Stedman W, Anantharaman T, Hastie A, Dai H, Fritz MH, Cao H, Cohain A, Deikus G, Durrett RE, Blanchard SC, Altman R, Chin CS, Guo Y, Paxinos EE, Korbel JO, Darnell RB, McCombie WR, Kwok PY, Mason CE, Schadt EE, Bashir A. Assembly and diploid architecture of an individual human genome via single-molecule technologies. Nat Methods. 2015;29. · DOI · Paper page
  25. Gilbert JA, Jansson JK, Knight R. The Earth Microbiome project: successes and aspirations. BMC Biol. 2014;12(1):69. · DOI · Paper page
  26. Filippidou S, Junier T, Wunderlin T, Lo CC, Li PE, Chain PS, Junier P. Under-detection of endospore-forming firmicutes in metagenomic data. Comput Struct Biotechnol J. 2015;13:299–306. doi: 10.1016/j.csbj.2015.04.002 . · DOI
  27. Vieira-Silva S, Rocha EP. The systemic imprint of growth and its uses in ecological (meta)genomics. PLoS Genet. 2010;6(1):e1000808. doi: 10.1371/journal.pgen.1000808 . · DOI · Paper page
  28. Felczykowska A, Krajewska A, Zielińska S, Los JM. Sampling, metadata and DNA extraction—important steps in metagenomic studies. Acta Biochim Pol. 2015;62(1):151–60. doi: 10.18388/abp.2014_916 . · DOI
  29. Cameron P, Corne DW, Mason CE, Rosenfeld J. Crowdfunding genomics and bioinformatics. Genome Biol. 2013;14(9):134. · doi:10.1186/gb-2013-14-9-134
  30. Dudley JT, Butte AJ. In silico research in the era of cloud computing. Nat Biotechnol. 2010;28(11):1181–5. · DOI
  31. Fisch KM, Meißner T, Gioia L, Ducom JC, Carland TM, Loguercio S, Su AI. Omics Pipe: a community-based framework for reproducible multi-omics data analysis. Bioinformatics. 2015;31(11):1724–8. · DOI
  32. La Rosa PS, Brooks JP, Deych E, Boone EL, Edwards DJ, Wang Q, Sodergren E, Weinstock G, Shannon WD. Hypothesis testing and power calculations for taxonomic-based human microbiome data. PLoS One. 2012;7(12):e52078. · DOI · Paper page
  33. http://www.ncbi.nlm.nih.gov/geo/
  34. Ilkka L, Almeida-King J, Kumanduri V, Senf A, Spalding JD, Ur-Rehman S, Saunders G, Kandasamy J, Caccamo M, Leinonen R, Vaughan R, Laurent T, Rowland F, Marin-Garcia P, Barker J, Jokinen P, Torres AC, Rambla De Argila J, Llobet OM, Medina I, Puy MS, Alberich M, De La Torre S, Navarro A, Paschall J, Flicek P. The European Genome-phenome Archive of human data consented for biomedical research. Nat Genet. 2015;47(7):692–95. · DOI · Paper page
  35. Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach J, Ansorge W, Ball CA, Causton HC, Gaasterland T, Glenisson P, Holstege FC, Kim IF, Markowitz V, Matese JC, Parkinson H, Robinson A, Sarkans U, Schulze-Kremer S, Stewart J, Taylor R, Vilo J, Vingron M. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet. 2001;29(4):365–71. · DOI · Paper page
  36. Rung J, Brazma A. Reuse of public genome-wide gene expression data. Nat Rev Genet. 2013;14(2):89–99. · DOI · Paper page
  37. Piwowar HA, Vision TJ, Whitlock MC. Data archiving is a good investment. Nature. 2011;473(7347):285. · DOI
  38. Rosenfeld J, Mason CE. Pervasive sequence patents cover the entire human genome. Genome Med. 2013;5(3):27. PMID: 23522065. · DOI
  39. Kopf A, Bicak M, Kottmann R, Schnetzer J, Kostadinov I, Lehmann K, Fernandez-Guerra A, Jeanthon C, Rahav E, Ullrich M, Wichels A, Gerdts G, Polymenakou P, Kotoulas G, Siam R, Abdallah RZ, Sonnenschein EC, Cariou T, O'Gara F, Jackson S, Orlic S, Steinke M, Busch J, Duarte B, Caçador I, Canning-Clode J, Bobrova O, Marteinsson V, Reynisson E, Loureiro CM, Luna GM, Quero GM, Löscher CR, Kremp A, DeLorenzo ME, Øvreås L, Tolman J, LaRoche J, Penna A, Frischer M, Davis T, Katherine B, Meyer CP, Ramos S, Magalhães C, Jude-Lemeilleur F, Aguirre-Macedo ML, Wang S, Poulton N, Jones S, Collin R, Fuhrman JA, Conan P, Alonso C, Stambler N, Goodwin K, Yakimov MM, Baltar F, Bodrossy L, Van De Kamp J, Frampton DM, Ostrowski M, Van Ruth P, Malthouse P, Claus S, Deneudt K, Mortelmans J, Pitois S, Wallom D, Salter I, Costa R, Schroeder DC, Kandil MM, Amaral V, Biancalana F, Santana R, Pedrotti ML, Yoshida T, Ogata H, Ingleton T, Munnik K, Rodriguez-Ezpeleta N, Berteaux-Lecellier V, Wecker P, Cancio I, Vaulot D, Bienhold C, Ghazal H, Chaouni B, Essayeh S, Ettamimi S, Zaid el H, Boukhatem N, Bouali A, Chahboune R, Barrijal S, Timinouni M, El Otmani F, Bennani M, Mea M, Todorova N, Karamfilov V, Ten Hoopen P, Cochrane G, L'Haridon S, Bizsel KC, Vezzi A, Lauro FM, Martin P, Jensen RM, Hinks J, Gebbels S, Rosselli R, De Pascale F, Schiavon R, Dos Santos A, Villar E, Pesant S, Cataletto B, Malfatti F, Edirisinghe R, Silveira JA, Barbier M, Turk V, Tinta T, Fuller WJ, Salihoglu I, Serakinci N, Ergoren MC, Bresnan E, Iriberri J, Nyhus PA, Bente E, Karlsen HE, Golyshin PN, Gasol JM, Moncheva S, Dzhembekova N, Johnson Z, Sinigalliano CD, Gidley ML, Zingone A, Danovaro R, Tsiamis G, Clark MS, Costa AC, El Bour M, Martins AM, Collins RE, Ducluzeau AL, Martinez J, Costello MJ, Amaral-Zettler LA, Gilbert JA, Davies N. Field D, Glöckner FO. The ocean sampling day consortium. Giga Sci. 2015;4:27. · DOI · Paper page
  40. Garbarino J, Mason CE. The power of engaging citizen scientists for scientific progress. J Microbiol Biol Educ. 2016;17(1):7–12. doi: 10.1128/jmbe.v17i1.1052 . · DOI

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Metadata

Authors
The MetaSUB International Consortium
Venue
Microbiome
Publisher
Springer Science and Business Media LLC
Published
2016-06-03
Volume
4
Issue
1
Pages
24-24
ISSN
2049-2618 (ISSN-L)
DOI
10.1186/s40168-016-0168-z
OpenAlex
W2531153203
Cited by
159
References
4
FWCI
13.63
Type
journal article
Language
en
Update notices
correction (2016-08-18)
Open access
gold
Licence
Funders
  • Alfred P. Sloan Foundation (2015-13964)
  • Irma T. Hirschl and Monique Weill-Caulier Charitable Trust (Mason001)
  • WorldQuant Foundation
  • Vallee Foundation (NA)
  • National Institutes of Health (F31GM111053, R25EB020393)

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The MetaSUB International Consortium. (2016). The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium inaugural meeting report. Microbiome. https://doi.org/10.1186/s40168-016-0168-z

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