References

Brooks, J Paul, David J Edwards, Michael D Harwich, Maria C Rivera, Jennifer M Fettweis, Myrna G Serrano, Robert A Reris, et al. 2015. “The truth about metagenomics: quantifying and counteracting bias in 16S rRNA studies.” BMC Microbiol. 15 (1): 66. https://doi.org/10.1186/s12866-015-0351-6.

Callahan, Benjamin J, Daniel B DiGiulio, Daniela S Aliaga Goltsman, Christine L Sun, Elizabeth K Costello, Pratheepa Jeganathan, Joseph R Biggio, et al. 2017. “Replication and refinement of a vaginal microbial signature of preterm birth in two racially distinct cohorts of US women.” Proc. Natl. Acad. Sci. U. S. A. 114 (37): 9966–71. https://doi.org/10.1073/pnas.1705899114.

Fettweis, Jennifer M., Myrna G. Serrano, Jamie Paul Brooks, David J. Edwards, Philippe H. Girerd, Hardik I. Parikh, Bernice Huang, et al. 2019. “The vaginal microbiome and preterm birth.” Nat. Med. 25 (6): 1012–21. https://doi.org/10.1038/s41591-019-0450-2.

Finucane, Mariel M., Thomas J. Sharpton, Timothy J. Laurent, and Katherine S. Pollard. 2014. “A Taxonomic Signature of Obesity in the Microbiome? Getting to the Guts of the Matter.” Edited by Markus M. Heimesaat. PLoS One 9 (1): e84689. https://doi.org/10.1371/journal.pone.0084689.

Galazzo, Gianluca, Niels van Best, Birke J. Benedikter, Kevin Janssen, Liene Bervoets, Christel Driessen, Melissa Oomen, et al. 2020. “How to Count Our Microbes? The Effect of Different Quantitative Microbiome Profiling Approaches.” Front. Cell. Infect. Microbiol. 10 (August). https://doi.org/10.3389/fcimb.2020.00403.

Gloor, Gregory B., Jean M. Macklaim, Vera Pawlowsky-Glahn, and Juan J. Egozcue. 2017. “Microbiome Datasets Are Compositional: And This Is Not Optional.” Front. Microbiol. 8 (November): 2224. https://doi.org/10.3389/fmicb.2017.02224.

Jian, Ching, Anne Salonen, and Katri Korpela. 2021. “Commentary: How to Count Our Microbes? The Effect of Different Quantitative Microbiome Profiling Approaches.” Front. Cell. Infect. Microbiol. 11 (March): 10–12. https://doi.org/10.3389/fcimb.2021.627910.

Kevorkian, Richard, Jordan T Bird, Alexander Shumaker, and Karen G Lloyd. 2018. “Estimating Population Turnover Rates by Relative Quantification Methods Reveals Microbial Dynamics in Marine Sediment.” Appl. Environ. Microbiol. 84 (1): e01443–17. https://doi.org/10.1128/AEM.01443-17.

Leopold, Devin R, and Posy E Busby. 2020. “Host Genotype and Colonist Arrival Order Jointly Govern Plant Microbiome Composition and Function.” Curr. Biol. 30 (16): 3260–3266.e5. https://doi.org/10.1016/j.cub.2020.06.011.

Lloyd, Karen G., Jordan T. Bird, Joy Buongiorno, Emily Deas, Richard Kevorkian, Talor Noordhoek, Jacob Rosalsky, and Taylor Roy. 2020. “Evidence for a Growth Zone for Deep-Subsurface Microbial Clades in Near-Surface Anoxic Sediments.” Appl. Environ. Microbiol. 86 (19): 1–15. https://doi.org/10.1128/AEM.00877-20.

Lozupone, Catherine A, Jesse Stombaugh, Antonio Gonzalez, Gail Ackermann, Janet K Jansson, Jeffrey I Gordon, Doug Wendel, Yoshiki Va, and Rob Knight. 2013. “Meta-analyses of studies of the human microbiota.” Genome Res., 1704–14. https://doi.org/10.1101/gr.151803.112.

Martin, Bryan D., Daniela Witten, and Amy D. Willis. 2020. “Modeling microbial abundances and dysbiosis with beta-binomial regression.” Ann. Appl. Stat. 14 (1): 94–115. https://doi.org/10.1214/19-AOAS1283.

McLaren, Michael R, Amy D Willis, and Benjamin J Callahan. 2019. “Consistent and correctable bias in metagenomic sequencing experiments.” Elife 8 (September): 46923. https://doi.org/10.7554/eLife.46923.

Wasserman, Larry. 2004. All of Statistics. Springer Texts in Statistics. New York, NY: Springer New York. https://doi.org/10.1007/978-0-387-21736-9.

Williamson, Brian D, James P Hughes, and Amy D Willis. 2021. “A multiview model for relative and absolute microbial abundances.” Biometrics, no. August 2019 (June): biom.13503. https://doi.org/10.1111/biom.13503.

Yeh, Yi-Chun, David M. Needham, Ella T. Sieradzki, and Jed A. Fuhrman. 2018. “Taxon Disappearance from Microbiome Analysis Reinforces the Value of Mock Communities as a Standard in Every Sequencing Run.” mSystems 3 (3): e00023–18. https://doi.org/10.1128/mSystems.00023-18.