I suggest you also read these papers about primer choice and bias. There are many more, but these are a few highlights:
- Wasimuddin, Klaus Schlaeppi, Francesca Ronchi, Stephen L. Leib, Matthias Erb, and Alban Ramette. 2020. “Evaluation of Primer Pairs for Microbiome Profiling from Soils to Humans within the One Health Framework.” Molecular Ecology Resources, June. https://doi.org/10.1111/1755-0998.13215.
- Soergel, David A. W., Neelendu Dey, Rob Knight, and Steven E. Brenner. 2012. “Selection of Primers for Optimal Taxonomic Classification of Environmental 16S rRNA Gene Sequences.” The ISME Journal. https://doi.org/10.1038/ismej.2011.208.
- Darwish, Nadia, Jonathan Shao, Lori L. Schreier, and Monika Proszkowiec-Weglarz. 2021. “Choice of 16S Ribosomal RNA Primers Affects the Microbiome Analysis in Chicken Ceca.” Scientific Reports 11 (1): 11848. Choice of 16S ribosomal RNA primers affects the microbiome analysis in chicken ceca | Scientific Reports
- Fadeev, Eduard, Magda G. Cardozo-Mino, Josephine Z. Rapp, Christina Bienhold, Ian Salter, Verena Salman-Carvalho, Massimiliano Molari, Halina E. Tegetmeyer, Pier Luigi Buttigieg, and Antje Boetius. 2021. “Comparison of Two 16S rRNA Primers (V3-V4 and V4-V5) for Studies of Arctic Microbial Communities.” Frontiers in Microbiology 12 (February): 637526. Frontiers | Comparison of Two 16S rRNA Primers (V3–V4 and V4–V5) for Studies of Arctic Microbial Communities
- Heidrich, Vitor, Lilian T. Inoue, Paula F. Asprino, Fabiana Bettoni, Antonio C. H. Mariotti, Diogo A. Bastos, Denis L. F. Jardim, Marco A. Arap, and Anamaria A. Camargo. 2022. “Choice of 16S Ribosomal RNA Primers Impacts Male Urinary Microbiota Profiling.” Frontiers in Cellular and Infection Microbiology 12. Frontiers | Choice of 16S Ribosomal RNA Primers Impacts Male Urinary Microbiota Profiling.