REFERENCES

1. Lozupone CA, Stombaugh JI, Gordon JI, Jansson JK, Knight R. Diversity, stability and resilience of the human gut microbiota. Nature 2012;489:220-30.

2. Bokulich NA, Chung J, Battaglia T, et al. Antibiotics, birth mode, and diet shape microbiome maturation during early life. Sci Transl Med 2016;8:343ra82.

3. Yassour M, Vatanen T, Siljander H, et al. Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability. Sci Transl Med 2016;8:343ra81.

4. Yatsunenko T, Rey FE, Manary MJ, et al. Human gut microbiome viewed across age and geography. Nature 2012;486:222-7.

5. Eggesbø M, Botten G, Stigum H, Nafstad P, Magnus P. Is delivery by cesarean section a risk factor for food allergy? J Allergy Clin Immunol 2003;112:420-6.

6. Milani C, Duranti S, Bottacini F, et al. The first microbial colonizers of the human gut: composition, activities, and health implications of the infant gut microbiota. Microbiol Mol Biol Rev 2017;81:e00036-17.

7. Sevelsted A, Stokholm J, Bønnelykke K, Bisgaard H. Cesarean section and chronic immune disorders. Pediatrics 2015;135:e92-8.

8. Jackson MA, Verdi S, Maxan ME, et al. Gut microbiota associations with common diseases and prescription medications in a population-based cohort. Nat Commun 2018;9:2655.

9. Yassour M, Jason E, Hogstrom LJ, et al. Strain-level analysis of mother-to-child bacterial transmission during the first few months of life. Cell Host Microbe 2018;24:146-154.e4.

10. Milani C, Mancabelli L, Lugli GA, et al. Exploring vertical transmission of bifidobacteria from mother to child. Appl Environ Microbiol 2015;81:7078-87.

11. Lagier JC, Dubourg G, Million M, et al. Culturing the human microbiota and culturomics. Nat Rev Microbiol 2018;16:540-50.

12. Bellais S, Nehlich M, Ania M, et al. Species-targeted sorting and cultivation of commensal bacteria from the gut microbiome using flow cytometry under anaerobic conditions. Microbiome 2022;10:24.

13. Fleming E, Pabst V, Scholar Z, et al. Cultivation of common bacterial species and strains from human skin, oral, and gut microbiota. BMC Microbiol 2021;21:278.

14. Naud S, Khelaifia S, Mbogning Fonkou MD, Dione N, Lagier JC, Raoult D. Proof of concept of culturomics use of time of care. Front Cell Infect Microbiol 2020;10:524769.

15. Diakite A, Dubourg G, Dione N, et al. Optimization and standardization of the culturomics technique for human microbiome exploration. Sci Rep 2020;10:9674.

16. Chang Y, Hou F, Pan Z, et al. Optimization of culturomics strategy in human fecal samples. Front Microbiol 2019;10:2891.

17. Kaeberlein T, Lewis K, Epstein SS. Isolating “uncultivable” microorganisms in pure culture in a simulated natural environment. Science 2002;296:1127-9.

18. Lugli GA, Milani C, Duranti S, et al. Isolation of novel gut bifidobacteria using a combination of metagenomic and cultivation approaches. Genome Biol 2019;20:96.

19. Kasendra M, Tovaglieri A, Sontheimer-Phelps A, et al. Development of a primary human small intestine-on-a-chip using biopsy-derived organoids. Sci Rep 2018;8:2871.

20. Kim HJ, Huh D, Hamilton G, Ingber DE. Human gut-on-a-chip inhabited by microbial flora that experiences intestinal peristalsis-like motions and flow. Lab Chip 2012;12:2165-74.

21. Shah P, Fritz JV, Glaab E, et al. A microfluidics-based in vitro model of the gastrointestinal human-microbe interface. Nat Commun 2016;7:11535.

22. Huh D, Torisawa YS, Hamilton GA, Kim HJ, Ingber DE. Microengineered physiological biomimicry: organs-on-chips. Lab Chip 2012;12:2156-64.

23. Hugenholtz F, de Vos WM. Mouse models for human intestinal microbiota research: a critical evaluation. Cell Mol Life Sci 2018;75:149-60.

24. Nguyen TL, Vieira-Silva S, Liston A, Raes J. How informative is the mouse for human gut microbiota research? Dis Model Mech 2015;8:1-16.

25. Mudd AT, Dilger RN. Early-life nutrition and neurodevelopment: use of the piglet as a translational model. Adv Nutr 2017;8:92-104.

26. Rose EC, Blikslager AT, Ziegler AL. Porcine models of the intestinal microbiota: the translational key to understanding how gut commensals contribute to gastrointestinal disease. Front Vet Sci 2022;9:834598.

27. Pabst R. The pig as a model for immunology research. Cell Tissue Res 2020;380:287-304.

28. Elzinga J, van der Oost J, de Vos WM, Smidt H. The use of defined microbial communities to model host-microbe interactions in the human gut. Microbiol Mol Biol Rev 2019;83:e00054-18.

29. Arumugam M, Raes J, Pelletier E, et al. Enterotypes of the human gut microbiome. Nature 2011;473:174-80.

30. Trosvik P, de Muinck EJ. Ecology of bacteria in the human gastrointestinal tract-identification of keystone and foundation taxa. Microbiome 2015;3:44.

31. Venema K, van den Abbeele P. Experimental models of the gut microbiome. Best Pract Res Clin Gastroenterol 2013;27:115-26.

32. Payne AN, Zihler A, Chassard C, Lacroix C. Advances and perspectives in in vitro human gut fermentation modeling. Trends Biotechnol 2012;30:17-25.

33. Huang W, Cho KY, Meng D, Walker WA. The impact of indole-3-lactic acid on immature intestinal innate immunity and development: a transcriptomic analysis. Sci Rep 2021;11:8088.

34. Zeng S, Patangia D, Almeida A, et al. A compendium of 32,277 metagenome-assembled genomes and over 80 million genes from the early-life human gut microbiome. Nat Commun 2022;13:5139.

35. Ventura M, Milani C, Turroni F, van Sinderen D. Envisioning emerging frontiers on human gut microbiota and its applications. Microb Biotechnol 2021;14:12-7.

Microbiome Research Reports
ISSN 2771-5965 (Online)

Portico

All published articles are preserved here permanently:

https://www.portico.org/publishers/oae/

Portico

All published articles are preserved here permanently:

https://www.portico.org/publishers/oae/