Li, X. V. et al. Immune regulation by fungal strain diversity in inflammatory bowel disease. Nature 603, 672–678 (2022).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Forster, S. C. et al. A human gut bacterial genome and culture collection for improved metagenomic analyses. Nat. Biotechnol. 37, 186–192 (2019).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Nayfach, S. et al. Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome. Nat. Microbiol. 6, 960–970 (2021).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Beghini, F. et al. Large-scale comparative metagenomics of Blastocystis, a common member of the human gut microbiome. ISME J. 11, 2848–2863 (2017).

PubMed  PubMed Central  Article  Google Scholar 

Karo-Atar, D. et al. Helminth-induced reprogramming of the stem cell compartment inhibits type 2 immunity. J. Exp. Med. 219, e20212311 (2022).

Zaiss, M. M. et al. The Intestinal Microbiota Contributes to the Ability of Helminths to Modulate Allergic Inflammation. Immunity 43, 998–1010 (2015).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Groussin, M. et al. Elevated rates of horizontal gene transfer in the industrialized human microbiome. Cell 184, 2053–2067.e18 (2021).

CAS  PubMed  Article  Google Scholar 

Almeida, A. et al. A new genomic blueprint of the human gut microbiota. Nature 1, 1 (2019).

Google Scholar 

Faith, J. J. et al. The long-term stability of the human gut microbiota. Science 341, 1237439 (2013).

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 

Schloissnig, S. et al. Genomic variation landscape of the human gut microbiome. Nature 493, 45–50 (2012).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Podlesny, D. et al. Metagenomic strain detection with SameStr: identification of a persisting core gut microbiota transferable by fecal transplantation. Microbiome 10, 1–15 (2022).

Article  Google Scholar 

De Filippis, F. et al. Distinct Genetic and Functional Traits of Human Intestinal Prevotella copri Strains Are Associated with Different Habitual Diets. Cell Host Microbe 25, 444–453.e3 (2019).

PubMed  Article  Google Scholar 

Thomas, A. M. & Segata, N. Multiple levels of the unknown in microbiome research. BMC Biol. 17–20 (2019).

Hitch, T. C. A. et al. Recent advances in culture-based gut microbiome research. Int. J. Med. Microbiol. 311, 151485 (2021).

Blaser, M. J. et al. Lessons learned from the prenatal microbiome controversy. Microbiome 9, 1–7 (2021).

Article  Google Scholar 

Walter, J. & Hornef, M. W. A philosophical perspective on the prenatal in utero microbiome debate. Microbiome 9, 1–9 (2021).

Article  Google Scholar 

de Goffau, M. C. et al. Human placenta has no microbiome but can contain potential pathogens. Nature 572, 329–334 (2019).

PubMed  PubMed Central  Article  Google Scholar 

De Agüero, M. G. et al. The maternal microbiota drives early postnatal innate immune development. Science 351, 1296–1302 (2016).

Article  Google Scholar 

Nuriel-Ohayon, M. et al. Progesterone Increases Bifidobacterium Relative Abundance during Late Pregnancy. Cell Rep. 27, 730–736.e3 (2019).

CAS  PubMed  Article  Google Scholar 

Shao, Y. et al. Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth. Nature 574, 117–121 (2019).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Mitchell, C. M. et al. Delivery Mode Affects Stability of Early Infant Gut Microbiota. Cell Rep. Med. 1, 100156 (2020).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Lawson, M. A. E. et al. Breast milk-derived human milk oligosaccharides promote Bifidobacterium interactions within a single ecosystem. ISME J. https://doi.org/10.1038/s41396-019-0553-2 (2019).

Stewart, C. J. et al. Temporal development of the gut microbiome in early childhood from the TEDDY study. Nature 562, 583–588 (2018).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Laursen, M. F., Bahl, M. I., Michaelsen, K. F. & Licht, T. R. First foods and gut microbes. Front. Microbiol. 8, 1–8 (2017).

Article  Google Scholar 

Costea, P. I. et al. Enterotypes in the landscape of gut microbial community composition. Nat. Microbiol. 3, 8–16 (2017).

PubMed  PubMed Central  Article  Google Scholar 

Hitch, T. C. A. et al. A taxonomic note on the genus Prevotella: Description of four novel genera and emended description of the genera Hallella and Xylanibacter. Syst. Appl. Microbiol. 45, 126354 (2022).

Cheng, M. & Ning, K. Stereotypes About Enterotype: the Old and New Ideas. Genomics, Proteom. Bioinforma. 17, 4–12 (2019).

Article  Google Scholar 

Knights, D. et al. Rethinking enterotypes. Cell Host Microbe 16, 433–437 (2014).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Bunesova, V., Lacroix, C. & Schwab, C. Mucin Cross-Feeding of Infant Bifidobacteria and Eubacterium hallii. Microb. Ecol. 75, 228–238 (2018).

CAS  PubMed  Article  Google Scholar 

Laursen, M. F., Bahl, M. I. & Licht, T. R. Settlers of our inner surface-factors shaping the gut microbiota from birth to toddlerhood. FEMS Microbiol. Rev. 45, 1–14 (2021).

Article  Google Scholar 

Bourriaud, C. et al. Lactate is mainly fermented to butyrate by human intestinal microfloras but inter-individual variation is evident. J. Appl. Microbiol 99, 201–212 (2005).

CAS  PubMed  Article  Google Scholar 

Robertson, R. C., Manges, A. R., Finlay, B. B. & Prendergast, A. J. The Human Microbiome and Child Growth – First 1000 Days and Beyond. Trends Microbiol 27, 131–147 (2019).

CAS  PubMed  Article  Google Scholar 

Pham, V. T., Lacroix, C., Braegger, C. P. & Chassard, C. Lactate-utilizing community is associated with gut microbiota dysbiosis in colicky infants. Sci. Rep. 7, 1–13 (2017).

Article  Google Scholar 

Fischbach, M. A. & Sonnenburg, J. L. Eating for two: How metabolism establishes interspecies interactions in the gut. Cell Host Microbe 10, 336–347 (2011).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Osbelt, L. et al. Klebsiella oxytoca causes colonization resistance against multidrug-resistant K. pneumoniae in the gut via cooperative carbohydrate competition. Cell Host Microbe 29, 1663–1679.e7 (2021).

CAS  PubMed  Article  Google Scholar 

Eberl, C. et al. E. coli enhance colonization resistance against Salmonella Typhimurium by competing for galactitol, a context-dependent limiting carbon source. Cell Host Microbe 29, 1680–1692.e7 (2021).

CAS  PubMed  Article  Google Scholar 

Stearns, J. C. et al. Bacterial biogeography of the human digestive tract. Sci. Rep. 1, 1–9 (2011).

Article  Google Scholar 

Donaldson, G. P., Lee, S. M. & Mazmanian, S. K. Gut biogeography of the bacterial microbiota. Nat. Rev. Microbiol. 14, 20–32 (2015).

PubMed  PubMed Central  Article  Google Scholar 

Zoetendal, E. G. et al. The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates. ISME J. 6, 1415–1426 (2012).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Barlow, J. T. et al. Quantitative sequencing clarifies the role of disruptor taxa, oral microbiota, and strict anaerobes in the human small-intestine microbiome. Microbiome 9, 1–17 (2021).

Article  Google Scholar 

Ryan, F. J. et al. Colonic microbiota is associated with inflammation and host epigenomic alterations in inflammatory bowel disease. Nat. Commun. 11, 1–12 (2020).

Article  Google Scholar 

Yang, M. et al. Mucosal-Associated Microbiota Other Than Luminal Microbiota Has a Close Relationship With Diarrhea-Predominant Irritable Bowel Syndrome. Front. Cell. Infect. Microbiol. 10, 1–12 (2020).

Article  Google Scholar 

Schroeder, B. O. Fight them or feed them: How the intestinal mucus layer manages the gut microbiota. Gastroenterol. Rep. 7, 3–12 (2019).

Article  Google Scholar 

Johansson, M. E. V., Sjövall, H. & Hansson, G. C. The gastrointestinal mucus system in health and disease. Nat. Rev. Gastroenterol. Hepatol. 10, 352–361 (2013).

CAS  PubMed  PubMed Central  Article  Google Scholar 

Kayama, H., Okumura, R. & Takeda, K. Interaction between the Microbiota, Epithelia, and Immune Cells in the Intestine. Annu. Rev. Immunol. 38, 23–48 (2020).

CAS  PubMed  Article  Google Scholar 

Liu, H. Y. et al. Distinct B cell subsets in Peyer’s patches convey probiotic effects by Limosilactobacillus reuteri. Microbiome 9, 198 (2021).

CAS