Dim G, Pastore M, Marra F. Liver fibrosis in the context of nonalcoholic steatohepatitis: the role of adipokines. Minerva Gastroenterol Dietol. 2018;64(1):39–50. https://doi.org/10.23736/s1121-421x.17.02427-8.

Article  Google Scholar 

Rinella ME. Nonalcoholic fatty liver disease: a systematic review. JAMA. 2015;313(22):2263–73. https://doi.org/10.1001/jama.2015.5370.

Article  CAS  Google Scholar 

Brandl K, Schnabl B. Intestinal microbiota and nonalcoholic steatohepatitis. Curr Opin Gastroenterol. 2017;33(3):128–33. https://doi.org/10.1097/MOG.0000000000000349.

Article  CAS  Google Scholar 

Hoyles L, Fernandez-Real JM, Federici M, Serino M, Abbott J, Charpentier J, Heymes C, Luque JL, Anthony E, Barton RH, Chilloux J, Myridakis A, Martinez-Gili L, Moreno-Navarrete JM, Benhamed F, Azalbert V, Blasco-Baque V, Puig J, Xifra G, Ricart W, Tomlinson C, Woodbridge M, Cardellini M, Davato F, Cardolini I, Porzio O, Gentileschi P, Lopez F, Foufelle F, Butcher SA, Holmes E, Nicholson JK, Postic C, Burcelin R, Dumas ME. Molecular phenomics and metagenomics of hepatic steatosis in non-diabetic obese women. Nat Med. 2018;24(7):1070–80. https://doi.org/10.1038/s41591-018-0061-3.

Article  CAS  Google Scholar 

Denou E, Lolmede K, Garidou L, Pomie C, Chabo C, Lau TC, Fullerton MD, Nigro G, Zakaroff-Girard A, Luche E, Garret C, Serino M, Amar J, Courtney M, Cavallari JF, Henriksbo BD, Barra NG, Foley KP, McPhee JB, Duggan BM, O’Neill HM, Lee AJ, Sansonetti P, Ashkar AA, Khan WI, Surette MG, Bouloumie A, Steinberg GR, Burcelin R, Schertzer JD. Defective NOD2 peptidoglycan sensing promotes diet-induced inflammation, dysbiosis, and insulin resistance. EMBO Mol Med. 2015;7(3):259–74. https://doi.org/10.15252/emmm.201404169.

Article  CAS  Google Scholar 

Miura K, Yang L, van Rooijen N, Brenner DA, Ohnishi H, Seki E. Toll-like receptor 2 and palmitic acid cooperatively contribute to the development of nonalcoholic steatohepatitis through inflammasome activation in mice. Hepatology. 2013;57(2):577–89. https://doi.org/10.1002/hep.26081.

Article  CAS  Google Scholar 

Pierantonelli I, Rychlicki C, Agostinelli L, Giordano DM, Gaggini M, Fraumene C, Saponaro C, Manghina V, Sartini L, Mingarelli E, Pinto C, Buzzigoli E, Trozzi L, Giordano A, Marzioni M, Minicis S, Uzzau S, Cinti S, Gastaldelli A, Svegliati-Baroni G. Lack of NLRP3-inflammasome leads to gut-liver axis derangement, gut dysbiosis and a worsened phenotype in a mouse model of NAFLD. Sci Rep. 2017;7(1):12200. https://doi.org/10.1038/s41598-017-11744-6.

Article  CAS  Google Scholar 

Roh YS, Seki E. Toll-like receptors in alcoholic liver disease, non-alcoholic steatohepatitis and carcinogenesis. J Gastroenterol Hepatol. 2013;28(Suppl 1):38–42. https://doi.org/10.1111/jgh.12019.

Article  CAS  Google Scholar 

Bieghs V, Trautwein C. Innate immune signaling and gut-liver interactions in non-alcoholic fatty liver disease. Hepatobiliary Surg Nutr. 2014;3(6):377–85. https://doi.org/10.3978/j.issn.2304-3881.2014.12.04.

Article  Google Scholar 

Cani PD, Amar J, Iglesias MA, Poggi M, Knauf C, Bastelica D, Neyrinck AM, Fava F, Tuohy KM, Chabo C, Waget A, Delmee E, Cousin B, Sulpice T, Chamontin B, Ferrieres J, Tanti JF, Gibson GR, Casteilla L, Delzenne NM, Alessi MC, Burcelin R. Metabolic endotoxemia initiates obesity and insulin resistance. Diabetes. 2007;56(7):1761–72.

Article  CAS  Google Scholar 

Verges B, Duvillard L, Lagrost L, Vachoux C, Garret C, Bouyer K, Courtney M, Pomie C, Burcelin R. Changes in lipoprotein kinetics associated with type 2 diabetes affect the distribution of lipopolysaccharides among lipoproteins. J Clin Endocrinol Metab. 2014;99(7):E1245-1253. https://doi.org/10.1210/jc.2013-3463.

Article  CAS  Google Scholar 

Berg RD, Wommack E, Deitch EA. Immunosuppression and intestinal bacterial overgrowth synergistically promote bacterial translocation. Arch Surg. 1988;123(11):1359–64.

Article  CAS  Google Scholar 

Amar J, Chabo C, Waget A, Klopp P, Vachoux C, Bermudez-Humaran LG, Smirnova N, Berge M, Sulpice T, Lahtinen S, Ouwehand A, Langella P, Rautonen N, Sansonetti PJ, Burcelin R. Intestinal mucosal adherence and translocation of commensal bacteria at the early onset of type 2 diabetes: molecular mechanisms and probiotic treatment. EMBO Mol Med. 2011;3(9):559–72. https://doi.org/10.1002/emmm.201100159.

Article  CAS  Google Scholar 

Garidou L, Pomie C, Klopp P, Waget A, Charpentier J, Aloulou M, Giry A, Serino M, Stenman L, Lahtinen S, Dray C, Iacovoni JS, Courtney M, Collet X, Amar J, Servant F, Lelouvier B, Valet P, Eberl G, Fazilleau N, Douin-Echinard V, Heymes C, Burcelin R. The Gut Microbiota Regulates Intestinal CD4 T Cells Expressing RORgammat and Controls Metabolic Disease. Cell Metab. 2015;22(1):100–12. https://doi.org/10.1016/j.cmet.2015.06.001.

Article  CAS  Google Scholar 

Pomie C, Blasco-Baque V, Klopp P, Nicolas S, Waget A, Loubieres P, Azalbert V, Puel A, Lopez F, Dray C, Valet P, Lelouvier B, Servant F, Courtney M, Amar J, Burcelin R, Garidou L. Triggering the adaptive immune system with commensal gut bacteria protects against insulin resistance and dysglycemia. Mol Metab. 2016;5(6):392–403. https://doi.org/10.1016/j.molmet.2016.03.004.

Article  CAS  Google Scholar 

Sookoian S, Salatino A, Castano GO, Landa MS, Fijalkowky C, Garaycoechea M, Pirola CJ. Intrahepatic bacterial metataxonomic signature in non-alcoholic fatty liver disease. Gut. 2020. https://doi.org/10.1136/gutjnl-2019-318811.

Article  Google Scholar 

Amar J, Serino M, Lange C, Chabo C, Iacovoni J, Mondot S, Lepage P, Klopp C, Mariette J, Bouchez O, Perez L, Courtney M, Marre M, Klopp P, Lantieri O, Dore J, Charles M, Balkau B, Burcelin R. Involvement of tissue bacteria in the onset of diabetes in humans: evidence for a concept. Diabetologia. 2011;54(12):3055–61. https://doi.org/10.1007/s00125-011-2329-8.

Article  CAS  Google Scholar 

Burcelin R, Serino M, Chabo C, Garidou L, Pomie C, Courtney M, Amar J, Bouloumie A. Metagenome and metabolism: the tissue microbiota hypothesis. Diabetes Obes Metab. 2013;15(Suppl 3):61–70. https://doi.org/10.1111/dom.12157.

Article  CAS  Google Scholar 

Balmer ML, Slack E, de Gottardi A, Lawson MA, Hapfelmeier S, Miele L, Grieco A, Van Vlierberghe H, Fahrner R, Patuto N, Bernsmeier C, Ronchi F, Wyss M, Stroka D, Dickgreber N, Heim MH, McCoy KD, Macpherson AJ. The liver may act as a firewall mediating mutualism between the host and its gut commensal microbiota. Sci Transl Med. 2014;6(237):237ra266. https://doi.org/10.1126/scitranslmed.3008618.

Article  CAS  Google Scholar 

Lelouvier B, Servant F, Paisse S, Brunet AC, Benyahya S, Serino M, Valle C, Ortiz MR, Puig J, Courtney M, Federici M, Fernandez-Real JM, Burcelin R, Amar J. Changes in blood microbiota profiles associated with liver fibrosis in obese patients: A pilot analysis. Hepatology (Baltimore, MD). 2016;64(6):2015–27. https://doi.org/10.1002/hep.28829.

Article  CAS  Google Scholar 

Loomba R, Seguritan V, Li W, Long T, Klitgord N, Bhatt A, Dulai PS, Caussy C, Bettencourt R, Highlander SK, Jones MB, Sirlin CB, Schnabl B, Brinkac L, Schork N, Chen CH, Brenner DA, Biggs W, Yooseph S, Venter JC, Nelson KE. Gut Microbiome-Based Metagenomic Signature for Non-invasive Detection of Advanced Fibrosis in Human Nonalcoholic Fatty Liver Disease. Cell Metab. 2017;25(5):1054-1062 e1055. https://doi.org/10.1016/j.cmet.2017.04.001.

Article  CAS  Google Scholar 

Schierwagen R, Alvarez-Silva C, Madsen MSA, Kolbe CC, Meyer C, Thomas D, Uschner FE, Magdaleno F, Jansen C, Pohlmann A, Praktiknjo M, Hischebeth GT, Molitor E, Latz E, Lelouvier B, Trebicka J, Arumugam M. Circulating microbiome in blood of different circulatory compartments. Gut. 2018. https://doi.org/10.1136/gutjnl-2018-316227.

Article  Google Scholar 

Fu A, Yao B, Dong T, Chen Y, Yao J, Liu Y, Li H, Bai H, Liu X, Zhang Y, Wang C, Guo Y, Li N, Cai S. Tumor-resident intracellular microbiota promotes metastatic colonization in breast cancer. Cell. 2022. https://doi.org/10.1016/j.cell.2022.02.027.

Article  Google Scholar 

Pushalkar S, Hundeyin M, Daley D, Zambirinis CP, Kurz E, Mishra A, Mohan N, Aykut B, Usyk M, Torres LE, Werba G, Zhang K, Guo Y, Li Q, Akkad N, Lall S, Wadowski B, Gutierrez J, Kochen Rossi JA, Herzog JW, Diskin B, Torres-Hernandez A, Leinwand J, Wang W, Taunk PS, Savadkar S, Janal M, Saxena A, Li X, Cohen D, Sartor RB, Saxena D, Miller G. The Pancreatic Cancer Microbiome Promotes Oncogenesis by Induction of Innate and Adaptive Immune Suppression. Cancer Discov. 2018;8(4):403–16. https://doi.org/10.1158/2159-8290.CD-17-1134.

Article  CAS  Google Scholar 

Jervis-Bardy J, Leong LE, Marri S, Smith RJ, Choo JM, Smith-Vaughan HC, Nosworthy E, Morris PS, O’Leary S, Rogers GB, Marsh RL. Deriving accurate microbiota profiles from human samples with low bacterial content through post-sequencing processing of Illumina MiSeq data. Microbiome. 2015;3:19. https://doi.org/10.1186/s40168-015-0083-8.

Article  Google Scholar 

Geller LT, Barzily-Rokni M, Danino T, Jonas OH, Shental N, Nejman D, Gavert N, Zwang Y, Cooper ZA, Shee K, Thaiss CA, Reuben A, Livny J, Avraham R, Frederick DT, Ligorio M, Chatman K, Johnston SE, Mosher CM, Brandis A, Fuks G, Gurbatri C, Gopalakrishnan V, Kim M, Hurd MW, Katz M, Fleming J, Maitra A, Smith DA, Skalak M, Bu J, Michaud M, Trauger SA, Barshack I, Golan T, Sandbank J, Flaherty KT, Mandinova A, Garrett WS, Thayer SP, Ferrone CR, Huttenhower C, Bhatia SN, Gevers D, Wargo JA, Golub TR, Straussman R. Potential role of intratumor bacteria in mediating tumor resistance to the chemotherapeutic drug gemcitabine. Science. 2017;357(6356):1156–60. https://doi.org/10.1126/science.aah5043.

Article  CAS  Google Scholar 

Geller LT, Straussman R. Intratumoral bacteria may elicit chemoresistance by metabolizing anticancer agents. Mol Cell Oncol. 2018;5(1):e1405139. https://doi.org/10.1080/23723556.2017.1405139.

Article  CAS  Google Scholar 

Costantini L, Magno S, Albanese D, Donati C, Molinari R, Filippone A, Masetti R, Merendino N. Characterization of human breast tissue microbiota from core needle biopsies through the analysis of multi hypervariable 16S-rRNA gene regions. Sci Rep. 2018;8(1):16893. https://doi.org/10.1038/s41598-018-35329-z.

Article  CAS  Google Scholar 

Jolliffe IT, Cadima J. Principal component analysis: a review and recent developments. Philos Trans A Math Phys Eng Sci. 2016;374(2065):20150202. https://doi.org/10.1098/rsta.2015.0202.

Article  Google Scholar 

Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett WS, Huttenhower C. Metagenomic biomarker discovery and explanation. Genome Biol. 2011;12(6):R60. https://doi.org/10.1186/gb-2011-12-6-r60.

Article  Google Scholar 

Douglas GM, Maffei VJ, Zaneveld JR, Yurgel SN, Brown JR, Taylor CM, Huttenhower C, Langille MGI. PICRUSt2 for prediction of metagenome functions. Nat Biotechnol. 2020;38(6):685–8. https://doi.org/10.1038/s41587-020-0548-6.

Article  CAS  Google Scholar 

Iwata-Reuyl D. Biosynthesis of the 7-deazaguanosine hypermodified nucleosides of transfer RNA. Bioorg Chem. 2003;31(1):24–43. https://doi.org/10.1016/s0045-2068(02)00513-8.

Article  CAS  Google Scholar 

McCarty RM, Somogyi A, Lin G, Jacobsen NE, Bandarian V. The deazapurine biosynthetic pathway revealed: in vitro enzymatic synthesis of PreQ(0) from guanosine 5’-triphosphate in four steps. Biochemistry. 2009;48(18):3847–52. https://doi.org/10.1021/bi900400e.

Article  CAS  Google Scholar 

Dunphy PJ, Phillips PG, Brodie AF. Separation and identification of menaquinones from microorganisms. J Lipid Res. 1971;12(4):442–9.

Article  CAS  Google Scholar 

Farrand SK, Taber HW. Physiological effects of menaquinone deficiency in Bacillus subtilis. J Bacteriol. 1973;115(3):1035–44. https://doi.org/10.1128/JB.115.3.1035-1044.1973.

Article  CAS  Google Scholar