Eiseman, B., Silen, W., Bascom, G. S. & Kauvar, A. J. Fecal enema as an adjunct in the treatment of pseudomembranous enterocolitis. Surgery 44, 854–859 (1958).

CAS  PubMed  Google Scholar 

Peppercorn, M. A. & Goldman, P. The role of intestinal bacteria in the metabolism of salicylazosulfapyridine. J. Pharmacol. Exp. Ther. 181, 555–562 (1972).

CAS  PubMed  Google Scholar 

Wilson, K. H. & Blitchington, R. B. Human colonic biota studied by ribosomal DNA sequence analysis. Appl. Environ. Microbiol. 62, 2273–2278 (1996).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Eckburg, P. B. et al. Diversity of the human intestinal microbial flora. Science 308, 1635–1638 (2005).

PubMed  PubMed Central  Article  Google Scholar 

Gill, S. R. et al. Metagenomic analysis of the human distal gut microbiome. Science 312, 1355–1359 (2006).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Ley, R. E. et al. Obesity alters gut microbial ecology. Proc. Natl Acad. Sci. USA 102, 11070–11075 (2005). Early work demonstrating that not only does obesity influence gut microbial ecology, but manipulation thereof could have a role in regulating energy balance.

CAS  PubMed  PubMed Central  Article  Google Scholar 

Turnbaugh, P. J. et al. The human microbiome project. Nature 449, 804–810 (2007).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Qin, J. et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464, 59–65 (2010).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature 486, 207–214 (2012). At the time, the Human Microbiome Project was the largest and most comprehensive effort to characterize the typical human microbiome across body sites, a pioneering effort that demonstrated considerable variation in community structure despite relative stability in metabolic pathways between healthy individuals.

Article  Google Scholar 

Yatsunenko, T. et al. Human gut microbiome viewed across age and geography. Nature 486, 222–227 (2012).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Kolde, R. et al. Host genetic variation and its microbiome interactions within the Human Microbiome Project. Genome Med. 10, 6 (2018).

PubMed  PubMed Central  Article  Google Scholar 

Lloyd-Price, J. et al. Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases. Nature 569, 655–662 (2019). One of a trio of initial manuscripts from the NIH Common Fund’s Integrative Human Microbiome Project, a large-scale initiative to densely phenotype and integrate clinical and multi-omic data in several conditions with established host–microbiome links (IBD, preterm labour and diabetes, respectively).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Rothschild, D. et al. Environment dominates over host genetics in shaping human gut microbiota. Nature 555, 210–215 (2018).

CAS  PubMed  Article  Google Scholar 

Mirzayi, C. et al. Reporting guidelines for human microbiome research: the STORMS checklist. Nat. Med. 27, 1885–1892 (2021).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Sinha, R. et al. Assessment of variation in microbial community amplicon sequencing by the Microbiome Quality Control (MBQC) project consortium. Nat. Biotechnol. 35, 1077–1086 (2017). A multi-institutional effort to characterize the impact of heterogeneous upstream data generation protocols and bioinformatic workflows that, if not considered, can undermine the comparability of disparate population-scale microbiome studies.

CAS  PubMed  PubMed Central  Article  Google Scholar 

Uffelmann, E. et al. Genome-wide association studies. Nat. Rev. Methods Prim. 1, 59 (2021).

CAS  Article  Google Scholar 

Mallick, H. et al. Experimental design and quantitative analysis of microbial community multiomics. Genome Biol. 18, 228 (2017).

PubMed  PubMed Central  Article  Google Scholar 

Tsilimigras, M. C. B. & Fodor, A. A. Compositional data analysis of the microbiome: fundamentals, tools, and challenges. Ann. Epidemiol. 26, 330–335 (2016).

PubMed  Article  Google Scholar 

Hong, M.-G., Pawitan, Y., Magnusson, P. K. E. & Prince, J. A. Strategies and issues in the detection of pathway enrichment in genome-wide association studies. Hum. Genet. 126, 289–301 (2009).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Claussnitzer, M. et al. A brief history of human disease genetics. Nature 577, 179–189 (2020).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Lozupone, C. A., Stombaugh, J. I., Gordon, J. I., Jansson, J. K. & Knight, R. Diversity, stability and resilience of the human gut microbiota. Nature 489, 220–230 (2012).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Lloyd-Price, J., Abu-Ali, G. & Huttenhower, C. The healthy human microbiome. Genome Med. 8, 51 (2016).

PubMed  PubMed Central  Article  Google Scholar 

Franzosa, E. A. et al. Sequencing and beyond: integrating molecular “omics” for microbial community profiling. Nat. Rev. Microbiol. 13, 360–372 (2015).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Bauermeister, A., Mannochio-Russo, H., Costa-Lotufo, L. V., Jarmusch, A. K. & Dorrestein, P. C. Mass spectrometry-based metabolomics in microbiome investigations. Nat. Rev. Microbiol. 20, 143–160 (2022).

CAS  PubMed  Article  Google Scholar 

Zhang, Y. et al. Metatranscriptomics for the human microbiome and microbial community functional profiling. Annu. Rev. Biomed. Data Sci. 4, 279–311 (2021).

PubMed  Article  Google Scholar 

Hamady, M. & Knight, R. Microbial community profiling for human microbiome projects: tools, techniques, and challenges. Genome Res. 19, 1141–1152 (2009).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Morgan, X. C. & Huttenhower, C. Chapter 12: human microbiome analysis. PLoS Comput. Biol. 8, e1002808 (2012).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Qin, J. et al. A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature 490, 55–60 (2012).

CAS  PubMed  Article  Google Scholar 

Nishiwaki, H. et al. Meta-analysis of gut dysbiosis in Parkinson’s disease. Mov. Disord. 35, 1626–1635 (2020).

CAS  PubMed  Article  Google Scholar 

Asnicar, F. et al. Microbiome connections with host metabolism and habitual diet from 1,098 deeply phenotyped individuals. Nat. Med. 27, 321–332 (2021).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Johnson, A. J. et al. Daily sampling reveals personalized diet-microbiome associations in humans. Cell Host Microbe 25, 789–802.e5 (2019). An in-depth exploration of the personalized links between dietary intake and gut microbial communities.

CAS  PubMed  Article  Google Scholar 

Choi, Y., Hoops, S. L., Thoma, C. J. & Johnson, A. J. A guide to dietary pattern-microbiome data integration. J. Nutr. 152, 1187–1199 (2022).

PubMed  Article  Google Scholar 

Qin, Y. et al. Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort. Nat. Genet. 54, 134–142 (2022).

CAS  PubMed  Article  Google Scholar 

Lopera-Maya, E. A. et al. Effect of host genetics on the gut microbiome in 7738 participants of the Dutch Microbiome Project. Nat. Genet. 54, 143–151 (2022).

CAS  PubMed  Article  Google Scholar 

Liu, X. et al. Mendelian randomization analyses support causal relationships between blood metabolites and the gut microbiome. Nat. Genet. 54, 52–61 (2022).

CAS  PubMed  Article  Google Scholar 

David, L. A. et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature 505, 559–563 (2014).

CAS  PubMed  Article  Google Scholar 

von Schwartzenberg, R. J. et al. Caloric restriction disrupts the microbiota and colonization resistance. Nature 595, 272–277 (2021).

Article  Google Scholar 

Sonnenburg, E. D. et al. Diet-induced extinctions in the gut microbiota compound over generations. Nature 529, 212–215 (2016). This study captures the interplay between dietary chemistry, microbial ecology and host health by demonstrating ways in which evolutionarily typical relationships can be disrupted (and restored).

CAS  PubMed  PubMed Central  Article