Page 34 - Read Online

Page 12 of 13 Huang et al. Microbiome Res Rep 2024;3:30 https://dx.doi.org/10.20517/mrr.2024.14

3. Chang FY, Siuti P, Laurent S, et al. Gut-inhabiting Clostridia build human GPCR ligands by conjugating neurotransmitters with diet-
and human-derived fatty acids. Nat Microbiol 2021;6:792-805. DOI PubMed
4. Zhang J, Empl MT, Schwab C, et al. Gut microbial transformation of the dietary imidazoquinoxaline mutagen MelQx reduces its
cytotoxic and mutagenic potency. Toxicol Sci 2017;159:266-76. DOI PubMed PMC
5. Zhang J, Lacroix C, Wortmann E, et al. Gut microbial beta-glucuronidase and glycerol/diol dehydratase activity contribute to dietary
heterocyclic amine biotransformation. BMC Microbiol 2019;19:99. DOI PubMed PMC
6. Duncan SH, Hold GL, Harmsen HJM, Stewart CS, Flint HJ. Growth requirements and fermentation products of Fusobacterium
prausnitzii, and a proposal to reclassify it as Faecalibacterium prausnitzii gen. nov., comb. nov. Int J Syst Evol Microbiol
2002;52:2141-6. DOI PubMed
7. Qin J, Li R, Raes J, et al; MetaHIT Consortium. A human gut microbial gene catalogue established by metagenomic sequencing.
Nature 2010;464:59-65. DOI PubMed PMC
8. De Filippis F, Pasolli E, Ercolini D. Newly explored Faecalibacterium diversity is connected to age, lifestyle, geography, and disease.
Curr Biol 2020;30:4932-43.e4. DOI PubMed
9. Sokol H, Pigneur B, Watterlot L, et al. Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut
microbiota analysis of Crohn disease patients. Proc Natl Acad Sci U S A 2008;105:16731-6. DOI PubMed PMC
10. Quévrain E, Maubert MA, Michon C, et al. Identification of an anti-inflammatory protein from Faecalibacterium prausnitzii, a
commensal bacterium deficient in Crohn’s disease. Gut 2016;65:415-25. DOI PubMed PMC
11. Lenoir M, Martín R, Torres-Maravilla E, et al. Butyrate mediates anti-inflammatory effects of Faecalibacterium prausnitzii in
intestinal epithelial cells through Dact3. Gut Microbes 2020;12:1-16. DOI PubMed PMC
12. Martín R, Rios-Covian D, Huillet E, et al. Faecalibacterium: a bacterial genus with promising human health applications. FEMS
Microbiol Rev 2023;47:fuad039. DOI PubMed PMC
13. Miquel S, Leclerc M, Martin R, et al. Identification of metabolic signatures linked to anti-inflammatory effects of Faecalibacterium
prausnitzii. mBio 2015;6:e00300-15. DOI PubMed PMC
14. Heinken A, Khan MT, Paglia G, Rodionov DA, Harmsen HJ, Thiele I. Functional metabolic map of Faecalibacterium prausnitzii, a
beneficial human gut microbe. J Bacteriol 2014;196:3289-302. DOI PubMed PMC
15. Zhang J, Huang YJ, Yoon JY, et al. Primary human colonic mucosal barrier crosstalk with super oxygen-sensitive Faecalibacterium
prausnitzii in continuous culture. Med 2021;2:74-98.e9. DOI PubMed PMC
16. Zhang J, Huang YJ, Trapecar M, et al. An immune-competent human gut microphysiological system enables inflammation-modulation
by Faecalibacterium prausnitzii. NPJ Biofilms Microbiomes 2024;10:31. DOI PubMed PMC
17. Fofanova TY, Stewart CJ, Auchtung JM, et al. A novel human enteroid-anaerobe co-culture system to study microbial-host interaction
under physiological hypoxia. BioRxiv 2019:555755. DOI
18. Shin W, Wu A, Massidda MW, et al. A robust longitudinal co-culture of obligate anaerobic gut microbiome with human intestinal
epithelium in an anoxic-oxic interface-on-a-chip. Front Bioeng Biotechnol 2019;7:13. DOI PubMed PMC
19. Sakamoto M, Sakurai N, Tanno H, Iino T, Ohkuma M, Endo A. Genome-based, phenotypic and chemotaxonomic classification of
Faecalibacterium strains: proposal of three novel species Faecalibacterium duncaniae sp. nov., Faecalibacterium hattorii sp. nov. and
Faecalibacterium gallinarum sp. nov. Int J Syst Evol Microbiol 2022;72:005379. DOI PubMed
20. Zhang J, Hernandez-Gordillo V, Trapecar M, et al. Coculture of primary human colon monolayer with human gut bacteria. Nat Protoc
2021;16:3874-900. DOI PubMed PMC
21. Pang Z, Zhou G, Ewald J, et al. Using MetaboAnalyst 5.0 for LC-HRMS spectra processing, multi-omics integration and covariate
adjustment of global metabolomics data. Nat Protoc 2022;17:1735-61. DOI PubMed
22. Lambert SA, Jolma A, Campitelli LF, et al. The human transcription factors. Cell 2018;172:650-65. DOI PubMed
23. Matys V, Kel-Margoulis OV, Fricke E, et al. TRANSFAC and its module TRANSCompel: transcriptional gene regulation in
eukaryotes. Nucleic Acids Res 2006;34:D108-10. DOI PubMed PMC
24. Sadaghian Sadabad M, von Martels JZ, Khan MT, et al. A simple coculture system shows mutualism between anaerobic
faecalibacteria and epithelial Caco-2 cells. Sci Rep 2015;5:17906. DOI PubMed PMC
25. Wu D, Li Z, Zhang Y, et al. Proline uptake promotes activation of lymphoid tissue inducer cells to maintain gut homeostasis. Nat
Metab 2023;5:1953-68. DOI
26. Poyet M, Groussin M, Gibbons SM, et al. A library of human gut bacterial isolates paired with longitudinal multiomics data enables
mechanistic microbiome research. Nat Med 2019;25:1442-52. DOI
27. Bjerrum JT, Wang Y, Hao F, et al. Metabonomics of human fecal extracts characterize ulcerative colitis, Crohn’s disease and healthy
individuals. Metabolomics 2015;11:122-33. DOI PubMed PMC
28. Le Gall G, Noor SO, Ridgway K, et al. Metabolomics of fecal extracts detects altered metabolic activity of gut microbiota in ulcerative
colitis and irritable bowel syndrome. J Proteome Res 2011;10:4208-18. DOI
29. Honda K, Yanai H, Negishi H, et al. IRF-7 is the master regulator of type-I interferon-dependent immune responses. Nature
2005;434:772-7. DOI
30. Jefferies CA. Regulating IRFs in IFN driven disease. Front Immunol 2019;10:325. DOI PubMed PMC
31. Lukovac S, Belzer C, Pellis L, et al. Differential modulation by Akkermansia muciniphila and Faecalibacterium prausnitzii of host
peripheral lipid metabolism and histone acetylation in mouse gut organoids. mBio 2014;5:e01438-14. DOI PubMed PMC
32. Caballero-Flores G, Pickard JM, Núñez G. Microbiota-mediated colonization resistance: mechanisms and regulation. Nat Rev