Zmora, N., Suez, J. & Elinav, E. You are what you eat: diet, health and the gut microbiota. Nat. Rev. Gastroenterol. Hepatol. 16, 35–56 (2019).

Article  CAS  PubMed  Google Scholar 

Lamont, R. J., Koo, H. & Hajishengallis, G. The oral microbiota: dynamic communities and host interactions. Nat. Rev. Microbiol. 16, 745–759 (2018).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chen, Y. E., Fischbach, M. A. & Belkaid, Y. Skin microbiota–host interactions. Nature 553, 427–436 (2018).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Trevathan-Tackett, S. M. et al. A horizon scan of priorities for coastal marine microbiome research. Nat. Ecol. Evol. 3, 1509–1520 (2019).

Article  PubMed  Google Scholar 

Jansson, J. K. & Hofmockel, K. S. The soil microbiome—from metagenomics to metaphenomics. Curr. Opin. Microbiol. 43, 162–168 (2018).

Article  CAS  PubMed  Google Scholar 

Trivedi, P., Leach, J. E., Tringe, S. G., Sa, T. & Singh, B. K. Plant–microbiome interactions: from community assembly to plant health. Nat. Rev. Microbiol. 18, 607–621 (2020).

Article  CAS  PubMed  Google Scholar 

Thompson, L. R. et al. A communal catalogue reveals Earth’s multiscale microbial diversity. Nature 551, 457–463 (2017).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Jin, J. et al. High-throughput identification and quantification of single bacterial cells in the microbiota. Nat. Commun. 13, 863 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Olsen, G. J., Lane, D. J., Giovannoni, S. J., Pace, N. R. & Stahl, D. A. Microbial ecology and evolution: a ribosomal RNA approach. Annu. Rev. Microbiol. 40, 337–365 (1986).

Article  CAS  PubMed  Google Scholar 

Pace, N. R., Stahl, D. A., Lane, D. J. & Olsen, G. J. in Advances in Microbial Ecology 1–55 (Springer, 1986).

Mccaig, A. E., Glover, L. A. & Prosser, J. I. Molecular analysis of bacterial community structure and diversity in unimproved and improved upland grass pastures. Appl. Environ. Microbiol. 65, 1721–1730 (1999).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kroes, I., Lepp, P. W. & Relman, D. A. Bacterial diversity within the human subgingival crevice. Proc. Natl Acad. Sci. Usa. 96, 14547–14552 (1999).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Navas-Molina, J. A. et al. Advancing our understanding of the human microbiome using QIIME. Methods Enzymol. 531, 371–444 (2013).

Callahan, B. J., McMurdie, P. J. & Holmes, S. P. Exact sequence variants should replace operational taxonomic units in marker-gene data analysis. ISME J. 11, 2639–2643 (2017).

Article  PubMed  PubMed Central  Google Scholar 

Kembel, S. W., Wu, M., Eisen, J. A. & Green, J. L. Incorporating 16S gene copy number information improves estimates of microbial diversity and abundance. PLoS Comput. Biol. 8, e1002743 (2012).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Louca, S., Doebeli, M. & Parfrey, L. W. Correcting for 16S rRNA gene copy numbers in microbiome surveys remains an unsolved problem. Microbiome 6, 41 (2018).

Article  PubMed  PubMed Central  Google Scholar 

Vandeputte, D. et al. Quantitative microbiome profiling links gut community variation to microbial load. Nature 551, 507–511 (2017).

Article  CAS  PubMed  Google Scholar 

Props, R. et al. Absolute quantification of microbial taxon abundances. ISME J. 11, 584–587 (2017).

Article  PubMed  Google Scholar 

Rao, C. et al. Multi-kingdom ecological drivers of microbiota assembly in preterm infants. Nature 591, 633–638 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Nguyen, N., Warnow, T., Pop, M. & White, B. A perspective on 16S rRNA operational taxonomic unit clustering using sequence similarity. npj Biofilms Microbiomes 2, 16004 (2016).

Article  PubMed  PubMed Central  Google Scholar 

McDonald, D. et al. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J. 6, 610–618 (2012).

Article  CAS  PubMed  Google Scholar 

Cole, J. R. et al. Ribosomal Database Project: data and tools for high throughput rRNA analysis. Nucleic Acids Res. 42, D633–D642 (2014).

Article  CAS  PubMed  Google Scholar 

Quast, C. et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41, D590–D596 (2013).

Article  CAS  PubMed  Google Scholar 

Lan, F., Demaree, B., Ahmed, N. & Abate, A. R. Single-cell genome sequencing at ultra-high-throughput with microfluidic droplet barcoding. Nat. Biotechnol. 35, 640–646 (2017).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chijiiwa, R. et al. Single-cell genomics of uncultured bacteria reveals dietary fiber responders in the mouse gut microbiota. Microbiome 8, 1–14 (2020).

Article  Google Scholar 

Zheng, W. et al. High-throughput, single-microbe genomics with strain resolution, applied to a human gut microbiome. Science 376, eabm1483 (2022).

Article  CAS  PubMed  Google Scholar 

Lloréns-Rico, V., Simcock, J. A., Huys, G. R. B. & Raes, J. Single-cell approaches in human microbiome research. Cell 185, 2725–2738 (2022).

Article  PubMed  Google Scholar 

Callahan, B. J. et al. High-throughput amplicon sequencing of the full-length 16S rRNA gene with single-nucleotide resolution. Nucleic Acids Res. 47, e103 (2019).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kinoshita, Y., Niwa, H., Uchida-Fujii, E. & Nukada, T. Establishment and assessment of an amplicon sequencing method targeting the 16S-ITS-23S rRNA operon for analysis of the equine gut microbiome. Sci. Rep. 11, 1–12 (2021).

Article  Google Scholar 

Ogawa, T., Kryukov, K., Imanishi, T. & Shiroguchi, K. The efficacy and further functional advantages of random-base molecular barcodes for absolute and digital quantification of nucleic acid molecules. Sci. Rep. 7, 13576 (2017).

Article  PubMed  PubMed Central  Google Scholar 

Wang, Q., Garrity, G. M., Tiedje, J. M. & Cole, J. R. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 73, 5261–5267 (2007).

Article  CAS  PubMed  PubMed Central  Google Scholar