Online Interactive Microbial Classification and Geospatial Distributional Analysis Using BioAtlas
In recent decades, the accumulation of data on 16s ribosomal RNA genes has yielded free and public databases such as SILVA, GreenGenes, The Ribosomal Database Project, and IMG, handling massive amounts of raw data and meta information. 16s rRNA gene contains hypervariable regions with great classification power. As a result, numerous classification tools have emerged including state-of-the-art tools such as Mothur, Qiime, and the 16s classifier. However, there is a gap between the sequence databases, the taxonomy profiling tools and available meta information such as geo/body-location information. Here, we present BioAtlas, and interactive web tool for searching, exploring, and analyzing prokaryotic distributions by integration of various resources of metagenomics databases. In the following section we show how to use BioAtlas to (1) search and explore prokaryote occurrences across the geospatial map of the world, (2) investigate and hunt for occurrences across generic user-generated surface-specific maps, with an example map of a human female, with data from Bouslimani et al., and (3) classify a user-given sequences dataset through our online platform for visual exploration of the spatial abundances of the identified microbes.
Key wordsTaxonomic classification 16s gene Ribosomal RNA Distributional analysis Microbiology Online tool Maps Data mining Integration Metadata
JBL is grateful for financial support from his VILLUM Young Investigator Grant. Funding for open access charge: VILLUM Young Investigator Grant of Jan Baumbach (Young Investigator Grant nr. 13154).
JBL is grateful for financial support from his Velux Foundation research grant (Research grant nr. 000121540), supporting his Ph.D. project.
Conflict of Interest Statement
- 1.Berney C, Ciuprina A, Bender S, Brodie J, Edgcomb V, Kim E, Rajan J, Parfrey LW, Adl S, Audic S et al (2017) Unieuk: time to speak a common language in protistology! J Eukaryot Microbiol 64(3):407–411Google Scholar
- 2.Bouslimani A, Porto C, Rath CM, Wang M, Guo Y, Gonzalez A, Berg-Lyon D, Ackermann G, Christensen GJM, Nakatsuji T et al (2015) Molecular cartography of the human skin surface in 3d. Proc Natl Acad Sci 112(17):E2120–E2129Google Scholar
- 3.Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI et al (2010) Qiime allows analysis of high-throughput community sequencing data. Nat Methods 7(5):335–336Google Scholar
- 4.Chaudhary N, Sharma AK, Agarwal P, Gupta A, Sharma VK (2015) 16s classifier: a tool for fast and accurate taxonomic classification of 16s rRNA hypervariable regions in metagenomic datasets. PLoS One 10(2):e0116106Google Scholar
- 5.Cole JR, Wang Q, Fish JA, Chai B, McGarrell DM, Sun Y, Brown CT, Porras-Alfaro A, Kuske CR, Tiedje JM (2013) Ribosomal database project: data and tools for high throughput rRNA analysis. Nucleic Acids Res 42(D1):D633–D642Google Scholar
- 6.de Queiroz K (1997) The linnaean hierarchy and the evolutionization of taxonomy, with emphasis on the problem of nomenclature. Aliso J Syst Evol Bot 15(2):125–144Google Scholar
- 7.DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL (2006) Greengenes, achimera-checked 16s rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72(7):5069–5072Google Scholar
- 8.Giovannoni SJ, Britschgi TB, Moyer CL, Field KG (1990) Genetic diversity in sargasso sea bacterioplankton. Nature 345(6270): 60–63Google Scholar
- 9.Lund JB, List M, Baumbach J (2017) Interactive microbial distribution analysis using bioatlas. Nucleic Acids Res. https://doi.org/10.1093/nar/gkx304
- 11.Mitchell A, Bucchini F, Cochrane G, Denise H, Hoopen Pt, Fraser M, Pesseat S, Potter S, Scheremetjew M, Sterk P et al (2015) Ebi metagenomics in 2016-an expanding and evolving resource for the analysis and archiving of metagenomic data. Nucleic Acids Res 44(D1):D595–D603CrossRefPubMedPubMedCentralGoogle Scholar
- 15.Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ et al (2009) Introducing mothur: open-source,platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75(23):7537–7541CrossRefPubMedPubMedCentralGoogle Scholar