Reproducible, Interactive, Scalable and Extensible Microbiome Data Science Using QIIME 2

Smith M, Yatsunenko T, Manary M, Trehan I, Mkakosya R, Cheng J . Gut microbiomes of Malawian twin pairs discordant for kwashiorkor. Science. 2013; 339(6119):548-54. PMC: 3667500. DOI: 10.1126/science.1229000. View

McDonald D, Clemente J, Kuczynski J, Rideout J, Stombaugh J, Wendel D . The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome. Gigascience. 2013; 1(1):7. PMC: 3626512. DOI: 10.1186/2047-217X-1-7. View

Callahan B, McMurdie P, Rosen M, Han A, Johnson A, Holmes S . DADA2: High-resolution sample inference from Illumina amplicon data. Nat Methods. 2016; 13(7):581-3. PMC: 4927377. DOI: 10.1038/nmeth.3869. View

Metcalf J, Xu Z, Weiss S, Lax S, Van Treuren W, Hyde E . Microbial community assembly and metabolic function during mammalian corpse decomposition. Science. 2015; 351(6269):158-62. DOI: 10.1126/science.aad2646. View

Gehring C, Sthultz C, Flores-Renteria L, Whipple A, Whitham T . Tree genetics defines fungal partner communities that may confer drought tolerance. Proc Natl Acad Sci U S A. 2017; 114(42):11169-11174. PMC: 5651740. DOI: 10.1073/pnas.1704022114. View

Gonzalez A, Navas-Molina J, Kosciolek T, McDonald D, Vazquez-Baeza Y, Ackermann G . Qiita: rapid, web-enabled microbiome meta-analysis. Nat Methods. 2018; 15(10):796-798. PMC: 6235622. DOI: 10.1038/s41592-018-0141-9. View

Franzosa E, McIver L, Rahnavard G, Thompson L, Schirmer M, Weingart G . Species-level functional profiling of metagenomes and metatranscriptomes. Nat Methods. 2018; 15(11):962-968. PMC: 6235447. DOI: 10.1038/s41592-018-0176-y. View

Barr T, Sureshchandra S, Ruegger P, Zhang J, Ma W, Borneman J . Concurrent gut transcriptome and microbiota profiling following chronic ethanol consumption in nonhuman primates. Gut Microbes. 2018; 9(4):338-356. PMC: 6219653. DOI: 10.1080/19490976.2018.1441663. View

Huber W, Carey V, Gentleman R, Anders S, Carlson M, Carvalho B . Orchestrating high-throughput genomic analysis with Bioconductor. Nat Methods. 2015; 12(2):115-21. PMC: 4509590. DOI: 10.1038/nmeth.3252. View

10.

VerBerkmoes N, Russell A, Shah M, Godzik A, Rosenquist M, Halfvarson J . Shotgun metaproteomics of the human distal gut microbiota. ISME J. 2008; 3(2):179-89. DOI: 10.1038/ismej.2008.108. View

11.

Kapono C, Morton J, Bouslimani A, Melnik A, Orlinsky K, Luzzatto Knaan T . Creating a 3D microbial and chemical snapshot of a human habitat. Sci Rep. 2018; 8(1):3669. PMC: 5829137. DOI: 10.1038/s41598-018-21541-4. View

12.

Schloss P, Westcott S, Ryabin T, Hall J, Hartmann M, Hollister E . Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol. 2009; 75(23):7537-41. PMC: 2786419. DOI: 10.1128/AEM.01541-09. View

13.

McMurdie P, Holmes S . phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One. 2013; 8(4):e61217. PMC: 3632530. DOI: 10.1371/journal.pone.0061217. View

14.

Pineda A, Kaplan I, Bezemer T . Steering Soil Microbiomes to Suppress Aboveground Insect Pests. Trends Plant Sci. 2017; 22(9):770-778. DOI: 10.1016/j.tplants.2017.07.002. View

15.

Rubin R, Koch G, Martinez A, Mau R, Bowker M, Hungate B . Developing climate-smart restoration: Can plant microbiomes be hardened against heat waves?. Ecol Appl. 2018; 28(6):1594-1605. DOI: 10.1002/eap.1763. View

16.

Gopalakrishnan V, Spencer C, Nezi L, Reuben A, Andrews M, Karpinets T . Gut microbiome modulates response to anti-PD-1 immunotherapy in melanoma patients. Science. 2017; 359(6371):97-103. PMC: 5827966. DOI: 10.1126/science.aan4236. View

17.

Wang M, Carver J, Phelan V, Sanchez L, Garg N, Peng Y . Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. Nat Biotechnol. 2016; 34(8):828-837. PMC: 5321674. DOI: 10.1038/nbt.3597. View

18.

Truong D, Franzosa E, Tickle T, Scholz M, Weingart G, Pasolli E . MetaPhlAn2 for enhanced metagenomic taxonomic profiling. Nat Methods. 2015; 12(10):902-3. DOI: 10.1038/nmeth.3589. View

19.

Bokulich N, Kaehler B, Rideout J, Dillon M, Bolyen E, Knight R . Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2's q2-feature-classifier plugin. Microbiome. 2018; 6(1):90. PMC: 5956843. DOI: 10.1186/s40168-018-0470-z. View

20.

Lee K, Pletcher S, Lynch S, Goldberg A, Cope E . Heterogeneity of Microbiota Dysbiosis in Chronic Rhinosinusitis: Potential Clinical Implications and Microbial Community Mechanisms Contributing to Sinonasal Inflammation. Front Cell Infect Microbiol. 2018; 8:168. PMC: 5974464. DOI: 10.3389/fcimb.2018.00168. View