Gut non-bacterial microbiota contributing to alcohol-associated liver disease

References

• Cholankeril G, Wong RJ, Hu M, Perumpail RB, Yoo ER, Puri P, Younossi ZM, Harrison SA, Ahmed A. 2017. Liver transplantation for nonalcoholic steatohepatitis in the US: temporal trends and outcomes. Dig Dis Sci. 62(10):2915–18. doi:10.1007/s10620-017-4684-x. PMID: 28744836
   Google Scholar
• Lee BP, Vittinghoff E, Dodge JL, Cullaro G, Terrault NA. 2019. National trends and long-term outcomes of liver transplant for alcohol-Associated liver disease in the United States. JAMA Intern Med. 179(3):340–348. doi:10.1001/jamainternmed.2018.6536. PMID: 30667468
   Google Scholar
• Mokdad AA, Lopez AD, Shahraz S, Lozano R, Mokdad AH, Stanaway J, Murray CJ, Naghavi M. 2014. Liver cirrhosis mortality in 187 countries between 1980 and 2010: a systematic analysis. BMC Med. 12(1):145. doi:10.1186/s12916-014-0145-y. PMID: 25242656
   Google Scholar
• Sheron N. 2016. Alcohol and liver disease in Europe–Simple measures have the potential to prevent tens of thousands of premature deaths. J Hepatol. 64(4):957–967. doi:10.1016/j.jhep.2015.11.006. PMID: 26592352
   Google Scholar
• Seitz HK, Bataller R, Cortez-Pinto H, Gao B, Gual A, Lackner C, Mathurin P, Mueller S, Szabo G, Tsukamoto H, et al. 2018. Alcoholic liver disease. Nat Rev Dis Primers. 4(1):16. PMID: 30115921. doi:10.1038/s41572-018-0014-7.
   Google Scholar
• Rivera Ca, Bradford BU, Seabra V, Thurman RG. 1998. Role of endotoxin in the hypermetabolic state after acute ethanol exposure. Am J Physiol. 275:G1252–8. PMID: 9843760. doi:10.1152/ajpgi.1998.275.6.G1252.
   Google Scholar
• Yan AW, Fouts DE, Brandl J, Starkel P, Torralba M, Schott E, Tsukamoto H, E. Nelson K, A. Brenner D, Schnabl B, et al. 2011. Enteric dysbiosis associated with a mouse model of alcoholic liver disease. Hepatology. 53(1):96–105. PMID: 21254165. doi:10.1002/hep.24018.
   Google Scholar
• Bajaj JS, Heuman DM, Hylemon PB, Sanyal AJ, White MB, Monteith P, Noble NA, Unser AB, Daita K, Fisher AR, et al. 2014. Altered profile of human gut microbiome is associated with cirrhosis and its complications. J Hepatol. 60(5):940–947. PMID: 24374295. doi:10.1016/j.jhep.2013.12.019.
   Google Scholar
• Leclercq S, Matamoros S, Cani PD, Neyrinck AM, Jamar F, Starkel P, Windey K, Tremaroli V, Bäckhed F, Verbeke K, et al. 2014. Intestinal permeability, gut-bacterial dysbiosis, and behavioral markers of alcohol-dependence severity. Proc Natl Acad Sci U S A. 111(42):E4485–93. PMID: 25288760. doi:10.1073/pnas.1415174111.
   Google Scholar
• Chen P, Miyamoto Y, Mazagova M, Lee KC, Eckmann L, Schnabl B. 2015. Microbiota protects mice against acute alcohol-induced liver injury. Alcohol Clin Exp Res. 39(12):2313–2323. doi:10.1111/acer.12900. PMID: 26556636
   Google Scholar
• Llopis M, Cassard AM, Wrzosek L, Boschat L, Bruneau A, Ferrere G, Puchois V, Martin JC, Lepage P, Le Roy T, et al. 2016. Intestinal microbiota contributes to individual susceptibility to alcoholic liver disease. Gut.65(5):830–839. PMID: 26642859. doi:10.1136/gutjnl-2015-310585.
   Google Scholar
• Wang L, Fouts DE, Starkel P, Hartmann P, Chen P, Llorente C, DePew J, Moncera K, Ho S, Brenner D, et al. 2016. Intestinal REG3 lectins protect against alcoholic steatohepatitis by reducing Mucosa-Associated microbiota and preventing bacterial translocation. Cell Host Microbe. 19(2):227–239. PMID: 26867181. doi:10.1016/j.chom.2016.01.003.
   Google Scholar
• Llorente C, Jepsen P, Inamine T, Wang L, Bluemel S, Wang HJ, Loomba R, Bajaj JS, Schubert ML, Sikaroodi M, et al. 2017. Gastric acid suppression promotes alcoholic liver disease by inducing overgrowth of intestinal enterococcus. Nat Commun. 8(1):837. PMID: 29038503. doi:10.1038/s41467-017-00796-x.
   Google Scholar
• Smirnova E, Puri P, Muthiah MD, Daitya K, Brown R, Chalasani N, Liangpunsakul S, Shah VH, Gelow K, Siddiqui MS, et al. 2020. Fecal microbiome distinguishes alcohol consumption from alcoholic hepatitis but does not discriminate disease severity. Hepatology. 72(1):271–286. PMID: 32056227. doi:10.1002/hep.31178.
   Google Scholar
• Volta U, Bonazzi C, Bianchi FB, Baldoni AM, Zoli M, Pisi E. 1987. IgA antibodies to dietary antigens in liver cirrhosis. Ric Clin Lab. 17:235–242. PMID: 3671996. doi:10.1007/BF02912537.
   Google Scholar
• Abdel-Misih SR, Bloomston M. 2010. Liver anatomy. Surg Clin North Am. 90(4):643–653. doi:10.1016/j.suc.2010.04.017. PMID: 20637938
   Google Scholar
• Ger R. 1989. Surgical anatomy of the liver. Surg Clin North Am. 69(2):179–192. doi:10.1016/s0039-6109(16)44780-8. PMID: 2928899
   Google Scholar
• Albillos A, de Gottardi A, Rescigno M. 2020. The gut-liver axis in liver disease: pathophysiological basis for therapy. J Hepatol. 72(3):558–577. doi:10.1016/j.jhep.2019.10.003. PMID: 31622696
   Google Scholar
• Brescia P, Rescigno M. 2021. The gut vascular barrier: a new player in the gut-liver-brain axis. Trends Mol Med. 27(9):844–855. doi:10.1016/j.molmed.2021.06.007. PMID: 34229973
   Google Scholar
• Ghosh S, Whitley CS, Haribabu B, Jala VR. 2021. Regulation of intestinal barrier function by microbial metabolites. Cell Mol Gastroenterol Hepatol. 11(5):1463–1482. doi:10.1016/j.jcmgh.2021.02.007. PMID: 33610769
   Google Scholar
• Chopyk DM, Grakoui A. 2020. Contribution of the Intestinal microbiome and gut barrier to hepatic disorders. Gastroenterology. 159(3):849–863. doi:10.1053/j.gastro.2020.04.077. PMID: 32569766
   Google Scholar
• Ermund A, Schutte A, Johansson ME, Gustafsson JK, Hansson GC. 2013. Studies of mucus in mouse stomach, small intestine, and colon. I. Gastrointestinal mucus layers have different properties depending on location as well as over the Peyer’s patches. Am J Physiol Gastrointest Liver Physiol. 305(5):G341–7. doi:10.1152/ajpgi.00046.2013. PMID: 23832518
   Google Scholar
• Li H, Limenitakis JP, Fuhrer T, Geuking MB, Lawson MA, Wyss M, Brugiroux S, Keller I, Macpherson JA, Rupp S, et al. 2015. The outer mucus layer hosts a distinct intestinal microbial niche. Nat Commun. 6(1):8292. PMID: 26392213. doi:10.1038/ncomms9292.
   Google Scholar
• Kurashima Y, Kiyono H. 2017. Mucosal ecological network of epithelium and immune cells for gut homeostasis and tissue healing. Annu Rev Immunol. 35(1):119–147. doi:10.1146/annurev-immunol-051116-052424. PMID: 28125357
   Google Scholar
• Stevenson BR, Siliciano JD, Mooseker MS, Goodenough DA. 1986. Identification of ZO-1: a high molecular weight polypeptide associated with the tight junction (zonula occludens) in a variety of epithelia. J Cell Biol. 103(3):755–766. doi:10.1083/jcb.103.3.755. PMID: 3528172
   Google Scholar
• Furuse M, Hirase T, Itoh M, Nagafuchi A, Yonemura S, Tsukita S, Tsukita S. 1993. Occludin: a novel integral membrane protein localizing at tight junctions. J Cell Biol. 123(6):1777–1788. PMID: 8276896. doi:10.1083/jcb.123.6.1777.
   Google Scholar
• Furuse M, Fujita K, Hiiragi T, Fujimoto K, Tsukita S. 1998. Claudin-1 and −2: novel integral membrane proteins localizing at tight junctions with no sequence similarity to occludin. J Cell Biol. 141(7):1539–1550. doi:10.1083/jcb.141.7.1539. PMID: 9647647
   Google Scholar
• Odenwald MA, Turner JR. 2017. The intestinal epithelial barrier: a therapeutic target? Nat Rev Gastroenterol Hepatol. 14(1):9–21. doi:10.1038/nrgastro.2016.169. PMID: 27848962
   Google Scholar
• Rescigno M. 2011. The intestinal epithelial barrier in the control of homeostasis and immunity. Trends Immunol. 32(6):256–264. doi:10.1016/j.it.2011.04.003. PMID: 21565554
   Google Scholar
• Spadoni I, Zagato E, Bertocchi A, Paolinelli R, Hot E, Di Sabatino A, Caprioli F, Bottiglieri L, Oldani A, Viale G, et al. 2015. A gut-vascular barrier controls the systemic dissemination of bacteria. Science. 350(6262):830–834. PMID: 26564856. doi:10.1126/science.aad0135.
   Google Scholar
• Bouziat R, Jabri B. 2015. IMMUNOLOGY. Breaching the gut-vascular barrier. Science. 350(6262):742–743. doi:10.1126/science.aad6768. PMID: 26564835
   Google Scholar
• Gabele E, Dostert K, Hofmann C, Wiest R, Scholmerich J, Hellerbrand C, Obermeier F. 2011. DSS induced colitis increases portal LPS levels and enhances hepatic inflammation and fibrogenesis in experimental NASH. J Hepatol. 55(6):1391–1399. doi:10.1016/j.jhep.2011.02.035. PMID: 21703208
   Google Scholar
• El Kasmi KC, Anderson AL, Devereaux MW, Fillon SA, Harris JK, Lovell MA, Finegold MJ, Sokol RJ. 2012. Toll-like receptor 4-dependent Kupffer cell activation and liver injury in a novel mouse model of parenteral nutrition and intestinal injury. Hepatology. 55(5):1518–1528. doi:10.1002/hep.25500. PMID: 22120983
   Google Scholar
• Wang Y, Liu Y. 2021. Gut-liver-axis: barrier function of liver sinusoidal endothelial cell (LSEC). J Gastroenterol Hepatol. PMID: 33811372 10.1111/jgh.15512
   Google Scholar
• Wisse E. 1970. An electron microscopic study of the fenestrated endothelial lining of rat liver sinusoids. J Ultrastruct Res. 31(1–2):125–150. doi:10.1016/s0022-5320(70)90150-4. PMID: 5442603
   Google Scholar
• Monkemoller V, Oie C, Hubner W, Huser T, McCourt P. 2015. Multimodal super-resolution optical microscopy visualizes the close connection between membrane and the cytoskeleton in liver sinusoidal endothelial cell fenestrations. Sci Rep. 5(1):16279. doi:10.1038/srep16279. PMID: 26549018
   Google Scholar
• Poisson J, Lemoinne S, Boulanger C, Durand F, Moreau R, Valla D, Rautou P-E. 2017. Liver sinusoidal endothelial cells: physiology and role in liver diseases. J Hepatol. 66(1):212–227. doi:10.1016/j.jhep.2016.07.009. PMID: 27423426
   Google Scholar
• Ganesan LP, Mohanty S, Kim J, Clark KR, Robinson JM, Anderson CL, Desrosiers RC. 2011. Rapid and efficient clearance of blood-borne virus by liver sinusoidal endothelium. PLoS Pathog. 7(9):e1002281. doi:10.1371/journal.ppat.1002281. PMID: 21980295
   Google Scholar
• Simon-Santamaria J, Rinaldo CH, Kardas P, Li R, Malovic I, Elvevold K,McCourt P, Smedsrod B, Hirsch HH, Sorensen KK. 2014. Efficient uptake of blood-borne BK and JC polyomavirus-like particles in endothelial cells of liver sinusoids and renal vasa recta. PLoS One. 9(11):e111762. PMID: 25375646. doi:10.1371/journal.pone.0111762.
   Google Scholar
• Oie CI, Wolfson DL, Yasunori T, Dumitriu G, Sorensen KK, McCourt PA,Ahluwalia BS, Smedsrod B. 2020. Liver sinusoidal endothelial cells contribute to the uptake and degradation of entero bacterial viruses. Sci Rep. 10(1):898. PMID: 31965000. doi:10.1038/s41598-020-57652-0.
   Google Scholar
• Yao Z, Mates JM, Cheplowitz AM, Hammer LP, Maiseyeu A, Phillips GS, Wewers MD, Rajaram MVS, Robinson JM, Anderson CL, et al. 2016. Blood-Borne lipopolysaccharide is rapidly eliminated by liver sinusoidal endothelial cells via high-density lipoprotein. J Immunol. 197(6):2390–2399. PMID: 27534554. doi:10.4049/jimmunol.1600702.
   Google Scholar
• Ganesan LP, Kim J, Wu Y, Mohanty S, Phillips GS, Birmingham DJ,Robinson JM, Anderson CL. 2012. FcgammaRIIb on liver sinusoidal endothelium clears small immune complexes. J Immunol. 189(10):4981–4988. PMID: 23053513. doi:10.4049/jimmunol.1202017.
   Google Scholar
• Deleve LD, Wang X, Guo Y. 2008. Sinusoidal endothelial cells prevent rat stellate cell activation and promote reversion to quiescence. Hepatology. 48(3):920–930. doi:10.1002/hep.22351. PMID: 18613151
   Google Scholar
• Xie G, Wang X, Wang L, Wang L, Atkinson RD, Kanel GC, Gaarde WA, DeLeve LD. 2012. Role of differentiation of liver sinusoidal endothelial cells in progression and regression of hepatic fibrosis in rats. Gastroenterology. 142(4):918–27e6. doi:10.1053/j.gastro.2011.12.017. PMID: 22178212
   Google Scholar
• Schaffner F, Poper H. 1963. Capillarization of hepatic sinusoids in man. Gastroenterology. 44(3):239–242. PMID: 13976646. doi:10.1016/S0016-5085(63)80130-4.
   Google Scholar
• Connolly MK, Bedrosian AS, Malhotra A, Henning JR, Ibrahim J, Vera V,Cieza-Rubio NE, Hassan BU, Pachter HL, Cohen S, et al. 2010. In hepatic fibrosis, liver sinusoidal endothelial cells acquire enhanced immunogenicity. J Immunol. 185(4):920–930. PMID: 20639479. doi:10.1002/hep.22351.
   Google Scholar
• Miyao M, Kotani H, Ishida T, Kawai C, Manabe S, Abiru H, Tamaki K. 2015. Pivotal role of liver sinusoidal endothelial cells in NAFLD/NASH progression. Lab Invest. 95(10):1130–1144. doi:10.1038/labinvest.2015.95. PMID: 26214582
   Google Scholar
• Human Microbiome PC. 2012. Structure, function and diversity of the healthy human microbiome. Nature. 486:207–214. PMID: 22699609. doi:10.1038/nature11234.
   Google Scholar
• Almeida A, Nayfach S, Boland M, Strozzi F, Beracochea M, Shi ZJ, Pollard KS, Sakharova E, Parks DH, Hugenholtz P, et al. 2021. A unified catalog of 204,938 reference genomes from the human gut microbiome. Nat Biotechnol. 39(1):105–114. PMID: 32690973. doi:10.1038/s41587-020-0603-3.
   Google Scholar
• Sender R, Fuchs S, Milo R. 2016. Are we really vastly outnumbered? revisiting the ratio of bacterial to host cells in humans. Cell. 164(3):337–340. doi:10.1016/j.cell.2016.01.013. PMID: 26824647
   Google Scholar
• Sender R, Fuchs S, Milo R. 2016. Revised estimates for the number of human and bacteria cells in the body. PLoS Biol. 14(8):e1002533. doi:10.1371/journal.pbio.1002533. PMID: 27541692
   Google Scholar
• Bajaj JS. 2019. Alcohol, liver disease and the gut microbiota. Nat Rev Gastroenterol Hepatol. 16(4):235–246. doi:10.1038/s41575-018-0099-1. PMID: 30643227
   Google Scholar
• Lang S, Schnabl B. 2020. Microbiota and fatty liver disease-the known, the unknown, and the future. Cell Host Microbe. 28(2):233–244. doi:10.1016/j.chom.2020.07.007. PMID: 32791115
   Google Scholar
• Szabo G. 2015. Gut-liver axis in alcoholic liver disease. Gastroenterology. 148(1):30–36. doi:10.1053/j.gastro.2014.10.042. PMID: 25447847
   Google Scholar
• Betrapally NS, Gillevet PM, Bajaj JS. 2016. Changes in the intestinal microbiome and alcoholic and nonalcoholic liver diseases: causes or effects? Gastroenterology. 150(8):1745–55e3. doi:10.1053/j.gastro.2016.02.073. PMID: 26948887
   Google Scholar
• Adolph TE, Grander C, Moschen AR, Tilg H. 2018. Liver-microbiome axis in health and disease. Trends Immunol. 39(9):712–723. doi:10.1016/j.it.2018.05.002. PMID: 29843959
   Google Scholar
• Peay KG, Kennedy PG, Talbot JM. 2016. Dimensions of biodiversity in the earth mycobiome. Nat Rev Microbiol. 14(7):434–447. doi:10.1038/nrmicro.2016.59. PMID: 27296482
   Google Scholar
• Seed PC. 2014. The human mycobiome. Cold Spring Harb Perspect Med. 5(5):a019810. doi:10.1101/cshperspect.a019810. PMID: 25384764
   Google Scholar
• Forbes JD, Bernstein CN, Tremlett H, Van Domselaar G, Knox NC. 2018. A fungal world: could the gut mycobiome be involved in neurological disease? Front Microbiol. 9:3249. PMID: 30687254. doi:10.3389/fmicb.2018.03249.
   Google Scholar
• Ott SJ, Kuhbacher T, Musfeldt M, Rosenstiel P, Hellmig S, Rehman A, Drews O, Weichert W, Timmis KN, Schreiber S, et al. 2008. Fungi and inflammatory bowel diseases: alterations of composition and diversity. Scand J Gastroenterol. 43(7):831–841. PMID: 18584522. doi:10.1080/00365520801935434.
   Google Scholar
• Hillman ET, Lu H, Yao T, Nakatsu CH. 2017. Microbial ecology along the gastrointestinal tract. Microbes Environ. 32(4):300–313. doi:10.1264/jsme2.ME17017. PMID: 29129876
   Google Scholar
• Underhill DM, Iliev ID. 2014. The mycobiota: interactions between commensal fungi and the host immune system. Nat Rev Immunol. 14(6):405–416. doi:10.1038/nri3684. PMID: 24854590
   Google Scholar
• Hoffmann C, Dollive S, Grunberg S, Chen J, Li H, Wu GD, Lewis JD, Bushman FD. 2013. Archaea and fungi of the human gut microbiome: correlations with diet and bacterial residents. PLoS One. 8(6):e66019. doi:10.1371/journal.pone.0066019. PMID: 23799070
   Google Scholar
• Yeung F, Chen YH, Lin JD, Leung JM, McCauley C, Devlin JC, Hansen C, Cronkite A, Stephens Z, Drake-Dunn C, et al. 2020. Altered immunity of laboratory mice in the natural environment is associated with fungal colonization. Cell Host Microbe. 27(5):809–22e6. PMID: 32209432. doi:10.1016/j.chom.2020.02.015.
   Google Scholar
• Ukhanova M, Wang X, Baer DJ, Novotny JA, Fredborg M, Mai V. 2014. Effects of almond and pistachio consumption on gut microbiota composition in a randomised cross-over human feeding study. Br J Nutr. 111(12):2146–2152. doi:10.1017/S0007114514000385. PMID: 24642201
   Google Scholar
• David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE, Wolfe BE, Ling AV, Devlin AS, Varma Y, Fischbach MA, et al. 2014. Diet rapidly and reproducibly alters the human gut microbiome. Nature. 505(7484):559–563. PMID: 24336217. doi:10.1038/nature12820.
   Google Scholar
• Auchtung TA, Fofanova TY, Stewart CJ, Nash AK, Wong MC, Gesell JR, Auchtung JM, Ajami NJ, Petrosino JF. 2018. Investigating colonization of the healthy adult gastrointestinal tract by fungi. mSphere. 3(2). PMID: 29600282. doi:10.1128/mSphere.00092-18.
   Google Scholar
• Iliev ID, Funari VA, Taylor KD, Nguyen Q, Reyes CN, Strom SP, Brown J, Becker CA, Fleshner PR, Dubinsky M, et al. 2012. Interactions between commensal fungi and the C-type lectin receptor Dectin-1 influence colitis. Science. 336(6086):1314–1317. PMID: 22674328. doi:10.1126/science.1221789.
   Google Scholar
• Hallen-Adams HE, Kachman SD, Kim J, Legge RM, Martinez I. 2015. Fungi inhabiting the healthy human gastrointestinal tract: a diverse and dynamic community. Fungal Ecol. 15:9–17. PMID: WOS: 000356109500002. doi:10.1016/j.funeco.2015.01.006.
   Google Scholar
• Dollive S, Chen YY, Grunberg S, Bittinger K, Hoffmann C, Vandivier L, Cuff C, Lewis JD, Wu GD, Bushman FD, et al. 2013. Fungi of the murine gut: episodic variation and proliferation during antibiotic treatment. PLoS One. 8(8):e71806. PMID: 23977147. doi:10.1371/journal.pone.0071806.
   Google Scholar
• Schei K, Avershina E, Oien T, Rudi K, Follestad T, Salamati S, Ødegård RA. 2017. Early gut mycobiota and mother-offspring transfer. Microbiome. 5(1):107. doi:10.1186/s40168-017-0319-x. PMID: 28837002
   Google Scholar
• Willis KA, Purvis JH, Myers ED, Aziz MM, Karabayir I, Gomes CK, Peters BM, Akbilgic O, Talati AJ, Pierre JF, et al. 2019. Fungi form interkingdom microbial communities in the primordial human gut that develop with gestational age. FASEB J. 33(11):12825–12837. PMID: 31480903. doi:10.1096/fj.201901436RR.
   Google Scholar
• Yang AM, Inamine T, Hochrath K, Chen P, Wang L, Llorente C,Bluemel S, Hartmann P, Xu J, Koyama Y, et al. 2017. Intestinal fungi contribute to development of alcoholic liver disease. J Clin Invest. 127(7):2829–2841. PMID: 28530644. doi:10.1172/JCI90562.
   Google Scholar
• Lang S, Duan Y, Liu J, Torralba MG, Kuelbs C, Ventura‐Cots M, Abraldes JG, Bosques‐Padilla F, Verna EC, Brown RS, et al. 2020. Intestinal fungal dysbiosis and systemic immune response to fungi in patients with alcoholic hepatitis. Hepatology. 71(2):522–538. PMID: 31228214. doi:10.1002/hep.30832.
   Google Scholar
• Bajaj JS, Liu EJ, Kheradman R, Fagan A, Heuman DM, White M, Gavis EA, Hylemon P, Sikaroodi M, Gillevet PM, et al. 2018. Fungal dysbiosis in cirrhosis. Gut. 67(6):1146–1154. PMID: 28578302. doi:10.1136/gutjnl-2016-313170.
   Google Scholar
• Hartmann P, Lang S, Zeng S, Duan Y, Zhang X, Wang Y, Bondareva M, Kruglov A, Fouts DE, Stärkel P, et al. 2021. Dynamic changes of the fungal microbiome in alcohol use disorder. Front Physiol. 12:699253. PMID: 34349667. doi:10.3389/fphys.2021.699253.
   Google Scholar
• Wu J, Wu D, Ma K, Wang T, Shi G, Shao J, Wang C, Yan G. 2020. Paeonol ameliorates murine alcohol liver disease via mycobiota-mediated Dectin-1/IL-1beta signaling pathway. J Leukoc Biol. 108(1):199–214. doi:10.1002/JLB.3MA0120-325RR. PMID: 32129526
   Google Scholar
• Brown GD, Gordon S. 2001. Immune recognition. A new receptor for beta-glucans. Nature. 413(6851):36–37. doi:10.1038/35092620. PMID: 11544516
   Google Scholar
• Kimberg M, Brown GD. 2008. Dectin-1 and its role in antifungal immunity. Med Mycol. 46(7):631–636. doi:10.1080/13693780802140907. PMID: 18608924
   Google Scholar
• Rogers NC, Slack EC, Edwards AD, Nolte MA, Schulz O, Schweighoffer E, Williams DL, Gordon S, Tybulewicz VL, Brown GD, et al. 2005. Syk-dependent cytokine induction by Dectin-1 reveals a novel pattern recognition pathway for C type lectins. Immunity. 22(4):507–517. PMID: 15845454. doi:10.1016/j.immuni.2005.03.004.
   Google Scholar
• Gross O, Gewies A, Finger K, Schafer M, Sparwasser T, Peschel C, Förster I, Ruland J. 2006. Card9 controls a non-TLR signalling pathway for innate anti-fungal immunity. Nature. 442(7103):651–656. doi:10.1038/nature04926. PMID: 16862125
   Google Scholar
• Kankkunen P, Teirila L, Rintahaka J, Alenius H, Wolff H, Matikainen S. 2010. (1,3)-beta-glucans activate both dectin-1 and NLRP3 inflammasome in human macrophages. J Immunol. 184(11):6335–6342. doi:10.4049/jimmunol.0903019. PMID: 20421639
   Google Scholar
• Gross O, Poeck H, Bscheider M, Dostert C, Hannesschlager N, Endres S, Hartmann G, Tardivel A, Schweighoffer E, Tybulewicz V, et al. 2009. Syk kinase signalling couples to the Nlrp3 inflammasome for anti-fungal host defence. Nature. 459(7245):433–436. PMID: 19339971. doi:10.1038/nature07965.
   Google Scholar
• Petrasek J, Bala S, Csak T, Lippai D, Kodys K, Menashy V, Barrieau M, Min S-Y, Kurt-Jones EA, Szabo G, et al. 2012. IL-1 receptor antagonist ameliorates inflammasome-dependent alcoholic steatohepatitis in mice. J Clin Invest. 122(10):3476–3489. PMID: 22945633. doi:10.1172/JCI60777.
   Google Scholar
• Sun S, Wang K, Sun L, Cheng B, Qiao S, Dai H, Shi W, Ma J, Liu H. 2020. Therapeutic manipulation of gut microbiota by polysaccharides of Wolfiporia cocos reveals the contribution of the gut fungi-induced PGE2 to alcoholic hepatic steatosis. Gut Microbes. 12(1):1830693. doi:10.1080/19490976.2020.1830693. PMID: 33106075
   Google Scholar
• Moyes DL, Wilson D, Richardson JP, Mogavero S, Tang SX, Wernecke J, Höfs S, Gratacap RL, Robbins J, Runglall M, et al. 2016. Candidalysin is a fungal peptide toxin critical for mucosal infection. Nature. 532(7597):64–68. PMID: 27027296. doi:10.1038/nature17625.
   Google Scholar
• Chu H, Duan Y, Lang S, Jiang L, Wang Y, Llorente C, Liu J, Mogavero S, Bosques-Padilla F, Abraldes JG, et al. 2020. The Candida albicans exotoxin candidalysin promotes alcohol-associated liver disease. J Hepatol. 72(3):391–400. PMID: 31606552. doi:10.1016/j.jhep.2019.09.029.
   Google Scholar
• Hill C, Guarner F, Reid G, Gibson GR, Merenstein DJ, Pot B, Morelli L, Canani RB, Flint HJ, Salminen S, et al. 2014. Expert consensus document. The international scientific association for probiotics and prebiotics consensus statement on the scope and appropriate use of the term probiotic. Nat Rev Gastroenterol Hepatol. 11(8):506–514. PMID: 24912386. doi:10.1038/nrgastro.2014.66.
   Google Scholar
• Barssotti L, Abreu I, Brandao ABP, Albuquerque R, Ferreira FG, Salgado MAC, Dias DDS, De Angelis K, Yokota R, Casarini DE, et al. 2021. Saccharomyces boulardii modulates oxidative stress and renin angiotensin system attenuating diabetes-induced liver injury in mice. Sci Rep. 11(1):9189. PMID: 33911129. doi:10.1038/s41598-021-88497-w.
   Google Scholar
• Albuquerque R, Brandao ABP, De Abreu I, Ferreira FG, Santos LB, Moreira LN, Taddei CR, Aimbire F, Cunha TS. 2019. Saccharomyces boulardii Tht 500101 changes gut microbiota and ameliorates hyperglycaemia, dyslipidaemia, and liver inflammation in streptozotocin-diabetic mice. Benef Microbes. 10(8):901–912. doi:10.3920/BM2019.0056. PMID: 31965836
   Google Scholar
• Yu L, Zhao XK, Cheng ML, Yang GZ, Wang B, Liu HJ, Hu YX, Zhu LL, Zhang S, Xiao ZW, et al. 2017. Saccharomyces boulardii administration changes gut microbiota and attenuates D-Galactosamine-induced liver injury. Sci Rep. 7(1):1359. PMID: 28465509. doi:10.1038/s41598-017-01271-9.
   Google Scholar
• Li M, Zhu L, Xie A, Yuan J. 2015. Oral administration of Saccharomyces boulardii ameliorates carbon tetrachloride-induced liver fibrosis in rats via reducing intestinal permeability and modulating gut microbial composition. Inflammation. 38(1):170–179. doi:10.1007/s10753-014-0019-7. PMID: 25227279
   Google Scholar
• Fernandez-Pacheco P, Ramos Monge IM, Fernandez-Gonzalez M, Poveda Colado JM, Safety A-VM. 2021. Evaluation of yeasts with probiotic potential. Front Nutr. 8:659328. PMID: 34095190. doi:10.3389/fnut.2021.659328.
   Google Scholar
• Santino I, Alari A, Bono S, Teti E, Marangi M, Bernardini A, Magrini L, Di Somma S, Teggi A. 2014. Saccharomyces cerevisiae fungemia, a possible consequence of the treatment of clostridium difficile colitis with a probioticum. Int J Immunopathol Pharmacol. 27(1):143–146. doi:10.1177/039463201402700120. PMID: 24674691
   Google Scholar
• Cherifi S, Robberecht J, Miendje Y. 2004. Saccharomyces cerevisiae fungemia in an elderly patient with Clostridium difficile colitis. Acta Clin Belg. 59(4):223–224. doi:10.1179/acb.2004.033. PMID: 15597730
   Google Scholar
• Henry S, D’Hondt L, Andre M, Holemans X, Canon JL. 2004. Saccharomyces cerevisiae fungemia in a head and neck cancer patient: a case report and review of the literature. Acta Clin Belg. 59(4):220–222. doi:10.1179/acb.2004.032. PMID: 15597729
   Google Scholar
• Cesaro S, Chinello P, Rossi L, Zanesco L. 2000. Saccharomyces cerevisiae fungemia in a neutropenic patient treated with Saccharomyces boulardii. Support Care Cancer. 8(6):504–505. doi:10.1007/s005200000123. PMID: 11094997
   Google Scholar
• Lu H, Lou H, Hu J, Liu Z, Chen Q. 2020. Macrofungi: a review of cultivation strategies, bioactivity, and application of mushrooms. Compr Rev Food Sci Food Saf. 19(5):2333–2356. doi:10.1111/1541-4337.12602. PMID: 33336985
   Google Scholar
• Huang J, Ou Y, Yew TW, Liu J, Leng B, Lin Z,Su Y, Zhuang Y, Lin J, Li X, et al. 2016. Hepatoprotective effects of polysaccharide isolated from Agaricus bisporus industrial wastewater against CCl(4)-induced hepatic injury in mice. Int J Biol Macromol. 82:678–686. PMID: 26454111. doi:10.1016/j.ijbiomac.2015.10.014.
   Google Scholar
• Li S, Li J, Zhang J, Wang W, Wang X, Jing H, Ren Z, Gao Z, Song X, Gong Z, et al. 2017. The antioxidative, antiaging, and hepatoprotective effects of Alkali-Extractable polysaccharides by agaricus bisporus. Evid Based Complement Alternat Med. 2017:7298683. PMID: 29104605. doi:10.1155/2017/7298683.
   Google Scholar
• Liu Y, Zheng D, Su L, Wang Q, Li Y. 2018. Protective effect of polysaccharide from Agaricus bisporus in Tibet area of China against tetrachloride-induced acute liver injury in mice. Int J Biol Macromol. 118:1488–1493. PMID: 29969638. doi:10.1016/j.ijbiomac.2018.06.179.
   Google Scholar
• Duan Z, Zhang Y, Zhu C, Wu Y, Du B, Ji H. 2020. Structural characterization of phosphorylated Pleurotus ostreatus polysaccharide and its hepatoprotective effect on carbon tetrachloride-induced liver injury in mice. Int J Biol Macromol. 162:533–547. PMID: 32565302. doi:10.1016/j.ijbiomac.2020.06.107.
   Google Scholar
• Bergh O, Borsheim KY, Bratbak G, Heldal M. High abundance of viruses found in aquatic environments. Nature. 1989;340(6233):467–468. doi:10.1038/340467a0. PMID: 2755508
   Google Scholar
• Cobian Guemes AG, Youle M, Cantu VA, Felts B, Nulton J, Rohwer F. 2016. Viruses as winners in the game of life. Annu Rev Virol. 3(1):197–214. doi:10.1146/annurev-virology-100114-054952. PMID: 27741409
   Google Scholar
• Shkoporov AN, Clooney AG, Sutton TDS, Ryan FJ, Daly KM, Nolan JA, McDonnell SA, Khokhlova EV, Draper LA, Forde A, et al. 2019. The human gut virome is highly diverse, stable, and individual specific. Cell Host Microbe. 26(4):527–41e5. PMID: 31600503. doi:10.1016/j.chom.2019.09.009.
   Google Scholar
• Shkoporov AN, Hill C. 2019. Bacteriophages of the human gut: the “known unknown” of the microbiome. Cell Host Microbe. 25(2):195–209. doi:10.1016/j.chom.2019.01.017. PMID: 30763534
   Google Scholar
• Roux S, Hallam SJ, Woyke T, Sullivan MB. 2015. Viral dark matter and virus-host interactions resolved from publicly available microbial genomes. Elife. 4 PMID: 26200428. doi:10.7554/eLife.08490.
   Google Scholar
• Krishnamurthy SR, Wang D. 2017. Origins and challenges of viral dark matter. Virus Res. 239:136–142. PMID: 28192164. doi:10.1016/j.virusres.2017.02.002.
   Google Scholar
• Clooney AG, Sutton TDS, Shkoporov AN, Holohan RK, Daly KM, O’Regan O, Ryan FJ, Draper LA, Plevy SE, Ross RP, et al. 2019. Whole-Virome analysis sheds light on viral dark matter in inflammatory bowel disease. Cell Host Microbe. 26(6):764–78e5. PMID: 31757768. doi:10.1016/j.chom.2019.10.009.
   Google Scholar
• Gregory AC, Zablocki O, Zayed AA, Howell A, Bolduc B, Sullivan MB. 2020. The gut virome database reveals age-dependent patterns of virome diversity in the human gut. Cell Host Microbe. 28(5):724–40e8. doi:10.1016/j.chom.2020.08.003. PMID: 32841606
   Google Scholar
• Camarillo-Guerrero LF, Almeida A, Rangel-Pineros G, Finn RD, Lawley TD. 2021. Massive expansion of human gut bacteriophage diversity. Cell. 184(4):1098–109e9. doi:10.1016/j.cell.2021.01.029. PMID: 33606979
   Google Scholar
• Wommack KE, Colwell RR. 2000. Virioplankton: viruses in aquatic ecosystems. Microbiol Mol Biol Rev. 64:69–114. PMID: 10704475. doi:10.1128/mmbr.64.1.69-114.2000.
   Google Scholar
• Dalmasso M, Hill C, Ross RP. 2014. Exploiting gut bacteriophages for human health. Trends Microbiol. 22(7):399–405. doi:10.1016/j.tim.2014.02.010. PMID: 24656964
   Google Scholar
• Manrique P, Bolduc B, Walk ST, van der Oost J, de Vos WM, Young MJ. 2016. Healthy human gut phageome. Proc Natl Acad Sci U S A. 113(37):10400–10405. doi:10.1073/pnas.1601060113. PMID: 27573828
   Google Scholar
• Ross A, Ward S, Hyman P. 2016. More is better: selecting for broad host range bacteriophages. Front Microbiol. 7:1352. PMID: 27660623. doi:10.3389/fmicb.2016.01352.
   Google Scholar
• Cahill J, Young R. 2019. Phage lysis: multiple genes for multiple barriers. Adv Virus Res. 103:33–70. PMID: 30635077. doi:10.1016/bs.aivir.2018.09.003.
   Google Scholar
• Howard-Varona C, Hargreaves KR, Abedon ST, Sullivan MB. 2017. Lysogeny in nature: mechanisms, impact and ecology of temperate phages. ISME J. 11(7):1511–1520. doi:10.1038/ismej.2017.16. PMID: 28291233
   Google Scholar
• Human Microbiome Jumpstart Reference Strains C. KE N, GM W, SK H, KC W, HH C, Wortman JR, Rusch DB, Mitreva M, Sodergren E, Chinwalla AT, et al. 2010. A catalog of reference genomes from the human microbiome. Science. 3285981: 994–999. 10.1126/science.1183605 PMID: 20489017
   Google Scholar
• Lengeling A, Mahajan A, Gally DL. 2013. Bacteriophages as pathogens and immune modulators?. mBio. 4(6):e00868–13. doi:10.1128/mBio.00868-13. PMID: 24222490
   Google Scholar
• Scotland SM, Smith HR, Willshaw GA, Rowe B. 1983. Vero cytotoxin production in strain of Escherichia coli is determined by genes carried on bacteriophage. Lancet. 2(8343):216. doi:10.1016/s0140-6736(83)90192-7. PMID: 6135046
   Google Scholar
• Tetz GV, Ruggles KV, Zhou H, Heguy A, Tsirigos A, Tetz V. 2017. Bacteriophages as potential new mammalian pathogens. Sci Rep. 7(1):7043. doi:10.1038/s41598-017-07278-6. PMID: 28765534
   Google Scholar
• Norman JM, Handley SA, Baldridge MT, Droit L, Liu CY, Keller BC, Kambal A, Monaco C, Zhao G, Fleshner P, et al. 2015. Disease-specific alterations in the enteric virome in inflammatory bowel disease. Cell. 160(3):447–460. PMID: 25619688. doi:10.1016/j.cell.2015.01.002.
   Google Scholar
• Ma Y, You X, Mai G, Tokuyasu T, Liu C. 2018. A human gut phage catalog correlates the gut phageome with type 2 diabetes. Microbiome. 6(1):24. doi:10.1186/s40168-018-0410-y. PMID: 29391057
   Google Scholar
• Monaco CL, Gootenberg DB, Zhao G, Handley SA, Ghebremichael MS, Lim ES, Lankowski A, Baldridge M, Wilen C, Flagg M, et al. 2016. Altered virome and bacterial microbiome in human immunodeficiency virus-associated acquired immunodeficiency syndrome. Cell Host Microbe. 19(3):311–322. PMID: 26962942. doi:10.1016/j.chom.2016.02.011.
   Google Scholar
• Nakatsu G, Zhou H, Wu WKK, Wong SH, Coker OO, Dai Z, Li X, Szeto C-H, Sugimura N, Lam TYT, et al. 2018. Alterations in enteric virome are associated with colorectal cancer and survival outcomes. Gastroenterology. 155(2):529–41e5. PMID: 29689266. doi:10.1053/j.gastro.2018.04.018.
   Google Scholar
• Koonin EV, Dolja VV, Krupovic M. 2021. The healthy human virome: from virus-host symbiosis to disease. Curr Opin Virol. 47:86–94. PMID: 33652230. doi:10.1016/j.coviro.2021.02.002.
   Google Scholar
• Jiang L, Lang S, Duan Y, Zhang X, Gao B, Chopyk J, Schwanemann LK, Ventura‐Cots M, Bataller R, Bosques‐Padilla F, et al. 2020. Intestinal virome in patients with alcoholic hepatitis. Hepatology. 72(6):2182–2196. PMID: 32654263. doi:10.1002/hep.31459.
   Google Scholar
• Rojo J, Simoes P, Krueger GR, Humberto CO, Ramon AM. 2003. Human herpesvirus-6 has no apparent influence on course of HCV hepatitis, but may complicate HBV hepatitis and alcoholic liver disease. A pilot study. Vivo. 17:29–33. PMID: 12655786.
   Google Scholar
• Yurlov KI, Masalova OV, Kisteneva LB, Khlopova IN, Samokhvalov EI, Malinovskaya VV,Parfyonov VV, Shuvalov AN, Kushch AA. 2021. Human herpesviruses increase the severity of hepatitis. Biology (Basel). 10. PMID: 34072365. doi:10.3390/biology10060483.
   Google Scholar
• Tsai JP, Tseng KC, Lin MN, Su CC. 2019. A high seroprevalence of human herpesvirus type 8 already present in patients with chronic hepatitis before the development of cirrhosis. Pathology. 51(1):86–90. doi:10.1016/j.pathol.2018.10.005. PMID: 30497802
   Google Scholar
• Chou AL, Huang WW, Tsao SM, Li CT, Su CC. 2008. Human herpesvirus type 8 in patients with cirrhosis: correlation with sex, alcoholism, hepatitis B virus, disease severity, and thrombocytopenia. Am J Clin Pathol. 130(2):231–237. doi:10.1309/4FMBN316N4792UQ4. PMID: 18628092
   Google Scholar
• Hu J, Zhang X, Yu G, Cai H, Gu J, Hu M,Xiang D, Lian J, Yu L, Jia H, et al. 2019. Epstein-Barr virus infection is associated with a higher Child-Pugh score and may predict poor prognoses for patients with liver cirrhosis. BMC Gastroenterol. 19(1):94. PMID: 31215410. doi:10.1186/s12876-019-1021-1.
   Google Scholar
• Keen EC, Dantas G. 2018. Close encounters of three kinds: bacteriophages, commensal bacteria, and host immunity. Trends Microbiol. 26(11):943–954. doi:10.1016/j.tim.2018.05.009. PMID: 29909042
   Google Scholar
• Bajaj JS, Sikaroodi M, Shamsaddini A, Henseler Z, Santiago-Rodriguez T, Acharya C, Fagan A, Hylemon PB, Fuchs M, Gavis E, et al. 2021. ssInteraction of bacterial metagenome and virome in patients with cirrhosis and hepatic encephalopathy. Gut. 70(6):1162–1173. PMID: 32998876. doi:10.1136/gutjnl-2020-322470.
   Google Scholar
• Pirnay JP, Blasdel BG, Bretaudeau L, Buckling A, Chanishvili N, Clark JR,Corte-Real S, Debarbieux L, Dublanchet A, De Vos D, et al. 2015. Quality and safety requirements for sustainable phage therapy products. Pharm Res. 32(7):2173–2179. PMID: 25585954. doi:10.1007/s11095-014-1617-7.
   Google Scholar
• Cheroutre H, Madakamutil L. 2004. Acquired and natural memory T cells join forces at the mucosal front line. Nat Rev Immunol. 4(4):290–300. doi:10.1038/nri1333. PMID: 15057787
   Google Scholar
• Liu L, Gong T, Tao W, Lin B, Li C, Zheng X, Zhu S, Jiang W, Zhou R. 2019. Commensal viruses maintain intestinal intraepithelial lymphocytes via noncanonical RIG-I signaling. Nat Immunol. 20(12):1681–1691. doi:10.1038/s41590-019-0513-z. PMID: 31636462
   Google Scholar
• Gogokhia L, Buhrke K, Bell R, Hoffman B, Brown DG, Hanke-Gogokhia C, Ajami NJ, Wong MC, Ghazaryan A, Valentine JF, et al. 2019. Expansion of bacteriophages is linked to aggravated intestinal inflammation and colitis. Cell Host Microbe. 25(2):285–99e8. PMID: 30763538. doi:10.1016/j.chom.2019.01.008.
   Google Scholar
• Metzger RN, Krug AB, Eisenacher K. 2018. Enteric virome sensing-its role in intestinal homeostasis and immunity. Viruses. 10(4):146. doi:10.3390/v10040146. PMID: 29570694
   Google Scholar
• Broquet AH, Hirata Y, McAllister CS, MF K. 2011. RIG-I/MDA5/MAVS are required to signal a protective IFN response in rotavirus-infected intestinal epithelium. J Immunol. 186(3):1618–1626. doi:10.4049/jimmunol.1002862. PMID: 21187438
   Google Scholar
• Norman JM, Handley SA, Virgin HW. 2014. Kingdom-agnostic metagenomics and the importance of complete characterization of enteric microbial communities. Gastroenterology. 146(6):1459–1469. doi:10.1053/j.gastro.2014.02.001. PMID: 24508599
   Google Scholar
• Duan Y, Llorente C, Lang S, Brandl K, Chu H, Jiang L, White RC, Clarke TH, Nguyen K, Torralba M, et al. 2019. Bacteriophage targeting of gut bacterium attenuates alcoholic liver disease. Nature. 575(7783):505–511. PMID: 31723265. doi:10.1038/s41586-019-1742-x.
   Google Scholar
• Kortright KE, Chan BK, Koff JL, Turner PE. 2019. Phage therapy: a renewed approach to combat antibiotic-resistant bacteria. Cell Host Microbe. 25(2):219–232. doi:10.1016/j.chom.2019.01.014. PMID: 30763536
   Google Scholar
• Loc-Carrillo C, Abedon ST. 2011. Pros and cons of phage therapy. Bacteriophage. 1(2):111–114. doi:10.4161/bact.1.2.14590. PMID: 22334867
   Google Scholar
• DeLong EF. 1992. Archaea in coastal marine environments. Proc Natl Acad Sci U S A. 89(12):5685–5689. doi:10.1073/pnas.89.12.5685. PMID: 1608980
   Google Scholar
• Schleper C, Jurgens G, Jonuscheit M. 2005. Genomic studies of uncultivated archaea. Nat Rev Microbiol. 3(6):479–488. doi:10.1038/nrmicro1159. PMID: 15931166
   Google Scholar
• Auguet JC, Barberan A, Casamayor EO. 2010. Global ecological patterns in uncultured Archaea. ISME J. 4(2):182–190. doi:10.1038/ismej.2009.109. PMID: 19847207
   Google Scholar
• Pereira O, Hochart C, Auguet JC, Debroas D, Galand PE. 2019. Genomic ecology of Marine Group II, the most common marine planktonic Archaea across the surface ocean. Microbiologyopen. 8(9):e00852. doi:10.1002/mbo3.852. PMID: 31264806
   Google Scholar
• Santoro AE, Richter RA, Dupont CL. 2019. Planktonic marine archaea. Ann Rev Mar Sci. 11(1):131–158. doi:10.1146/annurev-marine-121916-063141. PMID: 30212260
   Google Scholar
• Albers SV, Meyer BH. 2011. The archaeal cell envelope. Nat Rev Microbiol. 9(6):414–426. doi:10.1038/nrmicro2576. PMID: 21572458
   Google Scholar
• Koga Y, Morii H. 2007. Biosynthesis of ether-type polar lipids in archaea and evolutionary considerations. Microbiol Mol Biol Rev. 71(1):97–120. doi:10.1128/MMBR.00033-06. PMID: 17347520
   Google Scholar
• Valentine DL. 2007. Adaptations to energy stress dictate the ecology and evolution of the archaea. Nat Rev Microbiol. 5(4):316–323. doi:10.1038/nrmicro1619. PMID: 17334387
   Google Scholar
• Borrel G, McCann A, Deane J, Neto MC, Lynch DB, Brugere JF,O'Toole PW. 2017. Genomics and metagenomics of trimethylamine-utilizing archaea in the human gut microbiome. ISME J. 11(9):2059–2074. PMID: 28585938. doi:10.1038/ismej.2017.72.
   Google Scholar
• Dridi B, Henry M, El Khechine A, Raoult D, Drancourt M, Dobrindt U. 2009. High prevalence of methanobrevibacter smithii and methanosphaera stadtmanae detected in the human gut using an improved DNA detection protocol. PLoS One. 4(9):e7063. doi:10.1371/journal.pone.0007063. PMID: 19759898
   Google Scholar
• Horz HP, Conrads G. 2010. The discussion goes on: what is the role of Euryarchaeota in humans? Archaea. 2010:967271. PMID: 21253553. doi:10.1155/2010/967271.
   Google Scholar
• Hajishengallis G, Darveau RP, Curtis MA. 2012. The keystone-pathogen hypothesis. Nat Rev Microbiol. 10(10):717–725. doi:10.1038/nrmicro2873. PMID: 22941505
   Google Scholar
• Gaci N, Borrel G, Tottey W, O’Toole PW, Brugere JF. 2014. Archaea and the human gut: new beginning of an old story. World J Gastroenterol. 20(43):16062–16078. doi:10.3748/wjg.v20.i43.16062. PMID: 25473158
   Google Scholar
• Borrel G, Brugere JF, Gribaldo S, Schmitz RA, Moissl-Eichinger C. 2020. The host-associated archaeome. Nat Rev Microbiol. 18(11):622–636. doi:10.1038/s41579-020-0407-y. PMID: 32690877
   Google Scholar
• Bang C, Schmitz RA, Robinson NP. 2018. Archaea: forgotten players in the microbiome. Emerg Top Life Sci. 2(4):459–468. doi:10.1042/ETLS20180035. PMID: 33525830
   Google Scholar
• Pausan MR, Csorba C, Singer G, Till H, Schopf V, Santigli E, Klug B, Högenauer C, Blohs M, Moissl-Eichinger C, et al. 2019. Exploring the archaeome: detection of archaeal signatures in the human body. Front Microbiol. 10:2796. PMID: 31866971. doi:10.3389/fmicb.2019.02796.
   Google Scholar
• Grine G, Lotte R, Chirio D, Chevalier A, Raoult D, Drancourt M, Ruimy R. 2019. Co-culture of Methanobrevibacter smithii with enterobacteria during urinary infection. EBioMedicine. 43:333–337. PMID: 31072770. doi:10.1016/j.ebiom.2019.04.037.
   Google Scholar
• Lepp PW, Brinig MM, Ouverney CC, Palm K, Armitage GC, Relman DA. 2004. Methanogenic archaea and human periodontal disease. Proc Natl Acad Sci U S A. 101(16):6176–6181. doi:10.1073/pnas.0308766101. PMID: 15067114
   Google Scholar
• Blais Lecours P, Marsolais D, Cormier Y, Berberi M, Hache C, Bourdages R, Duchaine C. 2014. Increased prevalence of methanosphaera stadtmanae in inflammatory bowel diseases. PLoS One. 9(2):e87734. doi:10.1371/journal.pone.0087734. PMID: 24498365
   Google Scholar
• Pimentel M, Lin HC, Enayati P, van den Burg B, Lee HR, Chen JH, Park S, Kong Y, Conklin J. 2006. Methane, a gas produced by enteric bacteria, slows intestinal transit and augments small intestinal contractile activity. Am J Physiol Gastrointest Liver Physiol. 290(6):G1089–95. doi:10.1152/ajpgi.00574.2004. PMID: 16293652
   Google Scholar
• Triantafyllou K, Chang C, Pimentel M. 2014. Methanogens, methane and gastrointestinal motility. J Neurogastroenterol Motil. 20(1):31–40. doi:10.5056/jnm.2014.20.1.31. PMID: 24466443
   Google Scholar
• Bang C, Weidenbach K, Gutsmann T, Heine H, Schmitz RA, Foligne B. 2014. The intestinal archaea methanosphaera stadtmanae and methanobrevibacter smithii activate human dendritic cells. PLoS One. 9(6):e99411. doi:10.1371/journal.pone.0099411. PMID: 24915454
   Google Scholar
• Blais Lecours P, Duchaine C, Taillefer M, Tremblay C, Veillette M, Cormier Y, Marsolais D. 2011. Immunogenic properties of archaeal species found in bioaerosols. PLoS One. 6(8):e23326. doi:10.1371/journal.pone.0023326. PMID: 21858070
   Google Scholar
• Vierbuchen T, Bang C, Rosigkeit H, Schmitz RA, Heine H. 2017. The human-associated archaeon methanosphaera stadtmanae is recognized through its RNA and induces TLR8-Dependent NLRP3 inflammasome activation. Front Immunol. 8:1535. PMID: 29181003. doi:10.3389/fimmu.2017.01535.
   Google Scholar
• Bang C, Vierbuchen T, Gutsmann T, Heine H, Schmitz RA, Proost P. 2017. Immunogenic properties of the human gut-associated archaeon methanomassiliicoccus luminyensis and its susceptibility to antimicrobial peptides. PLoS One. 12(10):e0185919. doi:10.1371/journal.pone.0185919. PMID: 28982164
   Google Scholar
• Samuel BS, Hansen EE, Manchester JK, Coutinho PM, Henrissat B, Fulton R, Latreille P, Kim K, Wilson RK, Gordon JI, et al. 2007. Genomic and metabolic adaptations of Methanobrevibacter smithii to the human gut. Proc Natl Acad Sci U S A. 104(25):10643–10648. PMID: 17563350. doi:10.1073/pnas.0704189104.
   Google Scholar
• Gao B, Zhang X, Schnabl B. 2021. Fungi-bacteria correlation in alcoholic hepatitis patients. Toxins (Basel). 13(2):143. doi:10.3390/toxins13020143. PMID: 33672887
   Google Scholar
• Gilbert JA, Quinn RA, Debelius J, Xu ZZ, Morton J, Garg N, Jansson JK, Dorrestein PC, Knight R. 2016. Microbiome-wide association studies link dynamic microbial consortia to disease. Nature. 535(7610):94–103. doi:10.1038/nature18850. PMID: 27383984
   Google Scholar
• Wu X, Xia Y, He F, Zhu C, Ren W. 2021. Intestinal mycobiota in health and diseases: from a disrupted equilibrium to clinical opportunities. Microbiome. 9(1):60. doi:10.1186/s40168-021-01024-x. PMID: 33715629
   Google Scholar
• Townsend EM, Kelly L, Muscatt G, Box JD, Hargraves N, Lilley D, Jameson E.  2021. The human gut phageome: origins and roles in the human gut microbiome. Front Cell Infect Microbiol. 11:643214. PMID: 34150671. doi:10.3389/fcimb.2021.643214.
   Google Scholar