References

Barlow, Jacob T., Said R. Bogatyrev, and Rustem F. Ismagilov. 2020. “A quantitative sequencing framework for absolute abundance measurements of mucosal and lumenal microbial communities.” Nat. Commun. 11 (1): 1–13. https://doi.org/10.1038/s41467-020-16224-6.

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.

Cartwright, Charles P., Amanda J. Pherson, Ayla B. Harris, Matthew S. Clancey, and Melinda B. Nye. 2018. “Multicenter study establishing the clinical validity of a nucleic-acid amplification–based assay for the diagnosis of bacterial vaginosis.” Diagn. Microbiol. Infect. Dis. 92 (3): 173–78. https://doi.org/10.1016/j.diagmicrobio.2018.05.022.

Clausen, David S, and Amy D Willis. 2022. “Modeling Complex Measurement Error in Microbiome Experiments,” April. http://arxiv.org/abs/2204.12733.

Conover, W Jay. 2012. “The Rank Transformation-an Easy and Intuitive Way to Connect Many Nonparametric Methods to Their Parametric Counterparts for Seamless Teaching Introductory Statistics Courses.” Wiley Interdiscip. Rev. Comput. Stat. 4 (5): 432–38. https://doi.org/10.1002/wics.1216.

Contijoch, Eduardo J, Graham J Britton, Chao Yang, Ilaria Mogno, Zhihua Li, Ruby Ng, Sean R Llewellyn, et al. 2019. “Gut microbiota density influences host physiology and is shaped by host and microbial factors.” Elife 8 (January). https://doi.org/10.7554/eLife.40553.

David, Lawrence A, Arne C Materna, Jonathan Friedman, Maria I Campos-Baptista, Matthew C Blackburn, Allison Perrotta, Susan E Erdman, and Eric J Alm. 2014. “Host lifestyle affects human microbiota on daily timescales.” Genome Biol. 15 (7): R89. https://doi.org/10.1186/gb-2014-15-7-r89.

Fernandes, Andrew D, Jennifer NS Reid, Jean M Macklaim, Thomas A McMurrough, David R Edgell, and Gregory B Gloor. 2014. “Unifying the analysis of high-throughput sequencing datasets: characterizing RNA-seq, 16S rRNA gene sequencing and selective growth experiments by compositional data analysis.” Microbiome 2 (1): 15. https://doi.org/10.1186/2049-2618-2-15.

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.

Gelman, Andrew, Jennifer Hill, and Aki Vehtari. 2020. Regression and Other Stories. Cambridge University Press.

Gill, Christina, Janneke H. H. M. van de Wijgert, Frances Blow, and Alistair C. Darby. 2016. “Evaluation of Lysis Methods for the Extraction of Bacterial DNA for Analysis of the Vaginal Microbiota.” Edited by Peter E. Larsen. PLoS One 11 (9): e0163148. https://doi.org/10.1371/journal.pone.0163148.

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.

Goodrich, Ben, Jonah Gabry, Imad Ali, and Sam Brilleman. 2020. “Rstanarm: Bayesian Applied Regression Modeling via Stan.” https://mc-stan.org/rstanarm.

Graspeuntner, Simon, Nathalie Loeper, Sven Künzel, John F. Baines, and Jan Rupp. 2018. “Selection of validated hypervariable regions is crucial in 16S-based microbiota studies of the female genital tract.” Sci. Rep. 8 (1): 9678. https://doi.org/10.1038/s41598-018-27757-8.

Greenland, Sander, John Copas, David R. Jones, David Spiegelhalter, Kenneth Rice, Ben Armstrong, Stephen Senn, et al. 2005. “Multiple-bias modelling for analysis of observational data.” J. R. Stat. Soc. Ser. A Stat. Soc. 168 (2): 267–306. https://doi.org/10.1111/j.1467-985X.2004.00349.x.

Harrison, Joshua G., W. John Calder, Bryan Shuman, and C. Alex Buerkle. 2021. “The quest for absolute abundance: The use of internal standards for DNA‐based community ecology.” Mol. Ecol. Resour. 21 (1): 30–43. https://doi.org/10.1111/1755-0998.13247.

Hevroni, Gur, José Flores-Uribe, Oded Béjà, and Alon Philosof. 2020. “Seasonal and diel patterns of abundance and activity of viruses in the Red Sea.” Proc. Natl. Acad. Sci., November, 202010783. https://doi.org/10.1073/pnas.2010783117.

Holmes, Susan, and Wolfgang Huber. 2018. Modern Statistics for Modern Biology. Cambridge University Press.

Huttenhower, Curtis, Dirk Gevers, Rob Knight, Sahar Abubucker, Jonathan H. Badger, Asif T. Chinwalla, Heather H. Creasy, et al. 2012. “Structure, function and diversity of the healthy human microbiome.” Nature 486 (7402): 207–14. https://doi.org/10.1038/nature11234.

Ji, Brian W., Ravi U. Sheth, Purushottam D. Dixit, Yiming Huang, Andrew Kaufman, Harris H. Wang, and Dennis Vitkup. 2019. “Quantifying spatiotemporal variability and noise in absolute microbiota abundances using replicate sampling.” Nat. Methods 16 (8): 731–36. https://doi.org/10.1038/s41592-019-0467-y.

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.

Karasov, Talia L., Manuela Neumann, Alejandra Duque-Jaramillo, Sonja Kersten, Ilja Bezrukov, Birgit Schröppel, Efthymia Symeonidi, et al. 2020. “The relationship between microbial population size and disease in the Arabidopsis thaliana phyllosphere.” bioRxiv. https://doi.org/10.1101/828814.

Kumar, M. Senthil, Eric V. Slud, Kwame Okrah, Stephanie C. Hicks, Sridhar Hannenhalli, and Héctor Corrada Bravo. 2018. “Analysis and correction of compositional bias in sparse sequencing count data.” BMC Genomics 19 (1): 799. https://doi.org/10.1186/s12864-018-5160-5.

Leek, Jeffrey T., Robert B. Scharpf, Héctor Corrada Bravo, David Simcha, Benjamin Langmead, W. Evan Johnson, Donald Geman, Keith Baggerly, and Rafael A. Irizarry. 2010. “Tackling the widespread and critical impact of batch effects in high-throughput data.” Nat. Rev. Genet. 11 (10): 733–39. https://doi.org/10.1038/nrg2825.

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.

Lloyd, Karen G., Megan K. May, Richard T. Kevorkian, and Andrew D. Steen. 2013. “Meta-analysis of quantification methods shows that archaea and bacteria have similar abundances in the subseafloor.” Appl. Environ. Microbiol. 79 (24): 7790–99. https://doi.org/10.1128/AEM.02090-13.

Lofgren, Lotus A., Jessie K. Uehling, Sara Branco, Thomas D. Bruns, Francis Martin, and Peter G. Kennedy. 2019. “Genome‐based estimates of fungal rDNA copy number variation across phylogenetic scales and ecological lifestyles.” Mol. Ecol. 28 (4): 721–30. https://doi.org/10.1111/mec.14995.

Love, Michael I, Wolfgang Huber, and Simon Anders. 2014. “Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.” Genome Biol. 15 (12): 550. https://doi.org/10.1186/s13059-014-0550-8.

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.

Mandal, Siddhartha, Will Van Treuren, Richard A. White, Merete Eggesbø, Rob Knight, and Shyamal D. Peddada. 2015. “Analysis of composition of microbiomes: a novel method for studying microbial composition.” Microb. Ecol. Heal. Dis. 26 (1): 27663. https://doi.org/10.3402/mehd.v26.27663.

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.

Morella, Norma M., Shangyang Christopher Yang, Catherine A. Hernandez, and Britt Koskella. 2018. “Rapid quantification of bacteriophages and their bacterial hosts in vitro and in vivo using droplet digital PCR.” J. Virol. Methods 259 (May): 18–24. https://doi.org/10.1016/j.jviromet.2018.05.007.

Nixon, Michelle Pistner, Jeffrey Letourneau, Lawrence David, Sayan Mukherjee, and Justin D. Silverman. 2022. “A Statistical Analysis of Compositional Surveys.” arXiv, January. http://arxiv.org/abs/2201.03616.

Props, Ruben, Frederiek-Maarten Kerckhof, Peter Rubbens, Jo De Vrieze, Emma Hernandez Sanabria, Willem Waegeman, Pieter Monsieurs, Frederik Hammes, and Nico Boon. 2017. “Absolute quantification of microbial taxon abundances.” ISME J. 11 (2): 584–87. https://doi.org/10.1038/ismej.2016.117.

Quinn, Thomas P., and Ionas Erb. 2020. “Interpretable Log Contrasts for the Classification of Health Biomarkers: a New Approach to Balance Selection.” Edited by Robert G. Beiko. mSystems 5 (2): 1–11. https://doi.org/10.1128/mSystems.00230-19.

Rao, Chitong, Katharine Z. Coyte, Wayne Bainter, Raif S. Geha, Camilia R. Martin, and Seth Rakoff-Nahoum. 2021. “Multi-kingdom ecological drivers of microbiota assembly in preterm infants.” Nature 591 (7851): 633–38. https://doi.org/10.1038/s41586-021-03241-8.

Regalado, Julian, Derek S. Lundberg, Oliver Deusch, Sonja Kersten, Talia Karasov, Karin Poersch, Gautam Shirsekar, and Detlef Weigel. 2020. “Combining whole-genome shotgun sequencing and rRNA gene amplicon analyses to improve detection of microbe–microbe interaction networks in plant leaves.” ISME J., May, 823492. https://doi.org/10.1038/s41396-020-0665-8.

Rivera-Pinto, J., J. J. Egozcue, V. Pawlowsky-Glahn, R. Paredes, M. Noguera-Julian, and M. L. Calle. 2018. “Balances: a New Perspective for Microbiome Analysis.” Edited by Catherine Lozupone. mSystems 3 (4): e00053–18. https://doi.org/10.1128/mSystems.00053-18.

Silver, Nicholas, Steve Best, Jie Jiang, and Swee Lay Thein. 2006. “Selection of Housekeeping Genes for Gene Expression Studies in Human Reticulocytes Using Real-Time PCR.” BMC Mol. Biol. 7 (October): 33. https://doi.org/10.1186/1471-2199-7-33.

Srinivasan, Sujatha, Noah G. Hoffman, Martin T. Morgan, Frederick A. Matsen, Tina L. Fiedler, Robert W. Hall, Frederick J. Ross, et al. 2012. “Bacterial Communities in Women with Bacterial Vaginosis: High Resolution Phylogenetic Analyses Reveal Relationships of Microbiota to Clinical Criteria.” Edited by Adam J. Ratner. PLoS One 7 (6): e37818. https://doi.org/10.1371/journal.pone.0037818.

Stämmler, Frank, Joachim Gläsner, Andreas Hiergeist, Ernst Holler, Daniela Weber, Peter J. Oefner, André Gessner, and Rainer Spang. 2016. “Adjusting microbiome profiles for differences in microbial load by spike-in bacteria.” Microbiome 4 (1): 28. https://doi.org/10.1186/s40168-016-0175-0.

Stein, Richard R., Vanni Bucci, Nora C. Toussaint, Charlie G. Buffie, Gunnar Rätsch, Eric G. Pamer, Chris Sander, and João B. Xavier. 2013. “Ecological Modeling from Time-Series Inference: Insight into Dynamics and Stability of Intestinal Microbiota.” Edited by Christian von Mering. PLoS Comput. Biol. 9 (12): e1003388. https://doi.org/10.1371/journal.pcbi.1003388.

Tettamanti Boshier, Florencia A., Sujatha Srinivasan, Anthony Lopez, Noah G. Hoffman, Sean Proll, David N. Fredricks, and Joshua T. Schiffer. 2020. “Complementing 16S rRNA Gene Amplicon Sequencing with Total Bacterial Load To Infer Absolute Species Concentrations in the Vaginal Microbiome.” mSystems 5 (2): 1–14. https://doi.org/10.1128/mSystems.00777-19.

Tkacz, Andrzej, Marion Hortala, and Philip S. Poole. 2018. “Absolute quantitation of microbiota abundance in environmental samples.” Microbiome 6 (1): 110. https://doi.org/10.1186/s40168-018-0491-7.

Vandeputte, Doris, Gunter Kathagen, Kevin D’hoe, Sara Vieira-Silva, Mireia Valles-Colomer, João Sabino, Jun Wang, et al. 2017. “Quantitative microbiome profiling links gut community variation to microbial load.” Nature 551 (7681): 507. https://doi.org/10.1038/nature24460.

Vieira-Silva, Sara, João Sabino, Mireia Valles-Colomer, Gwen Falony, Gunter Kathagen, Clara Caenepeel, Isabelle Cleynen, Schalk van der Merwe, Séverine Vermeire, and Jeroen Raes. 2019. “Quantitative microbiome profiling disentangles inflammation- and bile duct obstruction-associated microbiota alterations across PSC/IBD diagnoses.” Nat. Microbiol. 4 (11): 1826–31. https://doi.org/10.1038/s41564-019-0483-9.

Wallace, Megan A., Kelsey A. Coffman, Clément Gilbert, Sanjana Ravindran, Gregory F. Albery, Jessica Abbott, Eliza Argyridou, et al. 2021. “The discovery, distribution, and diversity of DNA viruses associated with Drosophila melanogaster in Europe.” Virus Evol. 7 (1): 1–23. https://doi.org/10.1093/ve/veab031.

Wang, Yiwen, and Kim-Anh LêCao. 2020. “Managing batch effects in microbiome data.” Brief. Bioinform. 21 (6): 1954–70. https://doi.org/10.1093/bib/bbz105.

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.

Yuan, Sanqing, Dora B. Cohen, Jacques Ravel, Zaid Abdo, and Larry J. Forney. 2012. “Evaluation of Methods for the Extraction and Purification of DNA from the Human Microbiome.” Edited by Jack Anthony Gilbert. PLoS One 7 (3): e33865. https://doi.org/10.1371/journal.pone.0033865.

Zhang, Zhaojing, Yuanyuan Qu, Shuzhen Li, Kai Feng, Shang Wang, Weiwei Cai, Yuting Liang, et al. 2017. “Soil bacterial quantification approaches coupling with relative abundances reflecting the changes of taxa.” Sci. Rep. 7 (1): 1–11. https://doi.org/10.1038/s41598-017-05260-w.