Citations & Image Credits

Methods, software, pipeline papers

Callahan, B.J., McMurdie, P.J., Rosen, M.J., Han, A.W., Johnson, A.J.A., & Holmes, S.P. (2016). DADA2: High-resolution sample inference from Illumina amplicon data. Nature Methods, 13, 581–583. https://doi.org/10.1038/nmeth.3869

Bolyen, E., Rideout, J.R., Dillon, M.R., et al. (2019). Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature Biotechnology, 37, 852–857. https://doi.org/10.1038/s41587-019-0209-9

Martin, M. (2011). Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal, 17(1), 10–12. https://doi.org/10.14806/ej.17.1.200

McMurdie, P.J., & Holmes, S. (2013). phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data. PLOS ONE, 8(4), e61217. https://doi.org/10.1371/journal.pone.0061217

McMurdie, P. J., & Holmes, S. (2014). Waste not, want not: why rarefying microbiome data is inadmissible. PLoS computational biology, 10(4), e1003531. https://doi.org/10.1371/journal.pcbi.1003531

Oksanen, J., et al. (2022). vegan: Community Ecology Package. R package version 2.6-2. https://CRAN.R-project.org/package=vegan

Di Tommaso, P., Chatzou, M., Floden, E.W., Barja, P.P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316–319. https://doi.org/10.1038/nbt.3820

Douglas, G.M., Maffei, V.J., Zaneveld, J.R., Yurgel, S.N., Brown, J.R., Taylor, C.M., et al. (2020). PICRUSt2 for prediction of metagenome functions. Nature Biotechnology, 38(6), 685–688. https://doi.org/10.1038/s41587-020-0548-6

Watts, S.C., Ritchie, S.C., Inouye, M., & Holt, K.E. (2019). FastSpar: rapid and scalable correlation estimation for compositional data. Bioinformatics, 35(6), 1064–1066. https://doi.org/10.1093/bioinformatics/bty734

Weinroth, M.D., Belk, A.D., Dean, C., et al. (2022). Considerations and best practices in animal science 16S ribosomal RNA gene sequencing microbiome studies. Journal of Animal Science, 100(2), skab346. https://doi.org/10.1093/jas/skab346

Research articles

Chen, F.C., & Li, W.H. (2001). Genomic divergences between humans and other hominoids and the effective population size of the common ancestor of humans and chimpanzees. Am J Hum Genet, 68(2), 444–456. https://doi.org/10.1086/318206

Liu, K., Yang, X., Zeng, M., Yuan, Y., Sun, J., He, P., et al. (2021). The Role of Fecal Fusobacterium nucleatum and pks+ Escherichia coli as Early Diagnostic Markers of Colorectal Cancer. Dis Markers, 2021, 1171239. https://doi.org/10.1155/2021/1171239

Richter, M., & Rosselló-Móra, R. (2009). Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A, 106(45), 19126–19131. https://doi.org/10.1073/pnas.0906412106

Sofi, M.H., Wu, Y., Ticer, T., Schutt, S., Bastian, D., Choi, H.J., et al. (2021). A single strain of Bacteroides fragilis protects gut integrity and reduces GVHD. JCI Insight, 6(3). https://doi.org/10.1172/jci.insight.136841

Wu, G., Zhao, N., Zhang, C., Lam, Y.Y., & Zhao, L. (2021). Guild-based analysis for understanding gut microbiome in human health and diseases. Genome Medicine, 13(1), 22. https://doi.org/10.1186/s13073-021-00840-y

Zhao, L., Wu, G., & Zhao, N. (2024). Guild-based approach for mitigating information loss and distortion issues in microbiome analysis. J Clin Invest, 134(17). https://doi.org/10.1172/jci185395

Reference databases

Quast, C., Pruesse, E., Yilmaz, P., et al. (2013). The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Research, 41(D1), D590–D596. https://doi.org/10.1093/nar/gks1219

McDonald, D., Jiang, Y., Balaban, M., et al. (2023). Greengenes2 unifies microbial data in a single reference tree. Nature Biotechnology, 41, 1630–1633. https://doi.org/10.1038/s41587-023-01845-1

Images and visualizations

All stock imagery licensed via Adobe Stock. Asset IDs used on this site include: 1920368934, 252259825, 254265838, 254272392, 138554024, 228279263

Plots created using ggplot2 (version 4.0.2), gganimate (version 1.0.11) in R (version 4.5.3)

Google. (2026). List of census names in handwritten script [AI image generator]. Google Gemini.

16S rRNA gene structure (variable and conserved regions, V1–V9, with 515F/806R primer locations)

Figure used on the Overview page. Source: ResearchGate. Retrieved from https://www.researchgate.net/figure/S-rRNA-gene-showing-the-V1-V9-varaibale-regions-and-conserved-regions-The-515F-806R_fig1_340622946