Genome-wide multi-omics analysis reveals the nutrient-dependent metabolic features of mucin-degrading gut bacteria

References

• Fan Y, Pedersen O. Gut microbiota in human metabolic health and disease. Nat Rev Microbiol. 2021;19(1):55–23. doi:10.1038/s41579-020-0433-9.
   PubMed Web of Science ®Google Scholar
• Hansson GC. Mucins and the microbiome. Ann Rev Biochem. 2020;89(1):769–793. doi:10.1146/annurev-biochem-011520-105053.
   PubMedGoogle Scholar
• Taherali F, Varum F, Basit AW. A slippery slope: on the origin, role and physiology of mucus. Adv Drug Deliv Rev. 2018;124:16–33. doi:10.1016/j.addr.2017.10.014.
   PubMed Web of Science ®Google Scholar
• Medzhitov R. Recognition of microorganisms and activation of the immune response. Nature. 2007;449(7164):819–826. doi:10.1038/nature06246.
   PubMed Web of Science ®Google Scholar
• Hall AB, Tolonen AC, Xavier RJ. Human genetic variation and the gut microbiome in disease. Nat Rev Genet. 2017;18(11):690–699. doi:10.1038/nrg.2017.63.
   PubMed Web of Science ®Google Scholar
• Moreira Lopes TC, Mosser DM, Goncalves R. Macrophage polarization in intestinal inflammation and gut homeostasis. Inflamm Res. 2020;69(12):1163–1172. doi:10.1007/s00011-020-01398-y.
   PubMed Web of Science ®Google Scholar
• Martino ME, Joncour P, Leenay R, Gervais H, Shah M, Hughes S, Gillet, B., Beisel, C, Leulier, F Bacterial adaptation to the host’s diet is a key evolutionary force shaping drosophila-Lactobacillus symbiosis. Cell Host & Microbe. 2018;24(1):109–19.e6. doi:10.1016/j.chom.2018.06.001.
   PubMed Web of Science ®Google Scholar
• Tramontano M, Andrejev S, Pruteanu M, Klünemann M, Kuhn M, Galardini M, Jouhten P, Zelezniak A, Zeller G, Bork P, et al. Nutritional preferences of human gut bacteria reveal their metabolic idiosyncrasies. Nature Microbiol. 2018;3(4):514–522. doi:10.1038/s41564-018-0123-9.
   PubMed Web of Science ®Google Scholar
• Desai MS, Seekatz AM, Koropatkin NM, Kamada N, Hickey CA, Wolter M, Pudlo NA, Kitamoto S, Terrapon N, Muller A, et al. A dietary fiber-deprived gut microbiota degrades the colonic mucus barrier and enhances pathogen susceptibility. Cell. 2016;167(5):1339–53 e21. doi:10.1016/j.cell.2016.10.043.
   PubMed Web of Science ®Google Scholar
• Camilleri M. Leaky gut: mechanisms, measurement and clinical implications in humans. Gut. 2019;68(8):1516–1526. doi:10.1136/gutjnl-2019-318427.
   PubMed Web of Science ®Google Scholar
• Litvak Y, Byndloss MX, Bäumler AJ. Colonocyte metabolism shapes the gut microbiota. Science. 2018;362(6418):eaat9076. doi:10.1126/science.aat9076.
   PubMed Web of Science ®Google Scholar
• Byndloss MX, Baumler AJ. The germ-organ theory of non-communicable diseases. Nat Rev Microbiol. 2018;16(2):103–110. doi:10.1038/nrmicro.2017.158.
   PubMed Web of Science ®Google Scholar
• Henao-Mejia J, Elinav E, Jin C, Hao L, Mehal WZ, Strowig T, Thaiss CA, Kau AL, Eisenbarth SC, Jurczak MJ, et al. Inflammasome-mediated dysbiosis regulates progression of NAFLD and obesity. Nature. 2012;482(7384):179–185. doi:10.1038/nature10809.
   PubMed Web of Science ®Google Scholar
• Cani PD, Bibiloni R, Knauf C, Waget A, Neyrinck AM, Delzenne NM, Burcelin R. Changes in gut microbiota control metabolic endotoxemia-induced inflammation in high-fat diet–induced obesity and diabetes in mice. Diabetes. 2008;57(6):1470–1481. doi:10.2337/db07-1403.
   PubMed Web of Science ®Google Scholar
• Trompette A, Gollwitzer ES, Yadava K, Sichelstiel AK, Sprenger N, Ngom-Bru C, Blanchard C, Junt T, Nicod LP, Harris NL, et al. Gut microbiota metabolism of dietary fiber influences allergic airway disease and hematopoiesis. Nat Med. 2014;20(2):159–166. doi:10.1038/nm.3444.
   PubMed Web of Science ®Google Scholar
• Lee MJ, Kang MJ, Lee SY, Lee E, Kim K, Won S, Suh DI, Kim KW, Sheen YH, Ahn K, et al. Perturbations of gut microbiome genes in infants with atopic dermatitis according to feeding type. J Allergy Clin Immunol. 2018;141(4):1310–1319. doi:10.1016/j.jaci.2017.11.045.
   PubMed Web of Science ®Google Scholar
• Yoshimoto S, Loo TM, Atarashi K, Kanda H, Sato S, Oyadomari S, Iwakura Y, Oshima K, Morita H, Hattori M, et al. Obesity-induced gut microbial metabolite promotes liver cancer through senescence secretome. Nature. 2013;499(7456):97–101. doi:10.1038/nature12347.
   PubMed Web of Science ®Google Scholar
• Lloyd-Price J, Abu-Ali G, Huttenhower C. The healthy human microbiome. Genome Med. 2016;8(1):51. doi:10.1186/s13073-016-0307-y.
   PubMed Web of Science ®Google Scholar
• Zmora N, Suez J, Elinav E. You are what you eat: diet, health and the gut microbiota. Nat Rev Gastroenterol Hepatol. 2019;16(1):35–56. doi:10.1038/s41575-018-0061-2.
   PubMed Web of Science ®Google Scholar
• Pruss KM, Marcobal A, Southwick AM, Dahan D, Smits SA, Ferreyra JA, Higginbottom SK, Sonnenburg ED, Kashyap PC, Choudhury B, et al. Mucin-derived O-glycans supplemented to diet mitigate diverse microbiota perturbations. Isme J. 2021;15(2):577–591. doi:10.1038/s41396-020-00798-6.
   PubMed Web of Science ®Google Scholar
• Lee J-E, Kim KS, Koh H, Lee D-W, Kang NJ. Diet-induced host–microbe interactions: personalized diet strategies for improving inflammatory bowel Disease. Curr Dev Nutr. 2022;6(8):nzac110. doi:10.1093/cdn/nzac110.
   PubMed Web of Science ®Google Scholar
• Belzer C, Chia LW, Aalvink S, Chamlagain B, Piironen V, Knol J, de Vos WM. Microbial metabolic networks at the mucus layer lead to diet-independent butyrate and vitamin B12 production by intestinal symbionts. mBio. 2017;8(5). doi:10.1128/mBio.00770-17.
   PubMed Web of Science ®Google Scholar
• Ranjbar R, Vahdati SN, Tavakoli S, Khodaie R, Behboudi H. Immunomodulatory roles of microbiota-derived short-chain fatty acids in bacterial infections. Biomed Pharmacother. 2021;141:111817. doi:10.1016/j.biopha.2021.111817.
   PubMed Web of Science ®Google Scholar
• Derrien M, Veiga P. Rethinking diet to aid human–microbe symbiosis. Trends Microbiol. 2017;25(2):100–112. doi:10.1016/j.tim.2016.09.011.
   PubMed Web of Science ®Google Scholar
• Trastoy B, Naegeli A, Anso I, Sjogren J, Guerin ME. Structural basis of mammalian mucin processing by the human gut O-glycopeptidase OgpA from Akkermansia muciniphila. Nat Commun. 2020;11(1):4844. doi:10.1038/s41467-020-18696-y.
   PubMed Web of Science ®Google Scholar
• Collado MC, Derrien M, Isolauri E, de Vos WM, Salminen S, de Vos WM. Intestinal integrity and Akkermansia muciniphila, a mucin-degrading member of the intestinal microbiota present in infants, adults, and the elderly. Appl Environ Microbiol. 2007;73(23):7767–7770. doi:10.1128/AEM.01477-07.
   PubMed Web of Science ®Google Scholar
• Depommier C, Van Hul M, Everard A, Delzenne NM, De Vos WM, Cani PD. Pasteurized Akkermansia muciniphila increases whole-body energy expenditure and fecal energy excretion in diet-induced obese mice. Gut Microbes. 2020;11(5):1231–1245. doi:10.1080/19490976.2020.1737307.
   PubMed Web of Science ®Google Scholar
• Grander C, Grabherr F, Spadoni I, Enrich B, Oberhuber G, Rescigno M, Tilg H. The role of gut vascular barrier in experimental alcoholic liver disease and A. muciniphila supplementation. Gut Microbes. 2020;12(1):1851986. doi:10.1080/19490976.2020.1851986.
   PubMed Web of Science ®Google Scholar
• Everard A, Belzer C, Geurts L, Ouwerkerk JP, Druart C, Bindels LB, Guiot Y, Derrien M, Muccioli GG, Delzenne NM, et al. Cross-talk between Akkermansia muciniphila and intestinal epithelium controls diet-induced obesity. Proc Natl Acad Sci U S A. 2013;110(22):9066–9071. doi:10.1073/pnas.1219451110.
   PubMed Web of Science ®Google Scholar
• Roshanravan N, Mahdavi R, Alizadeh E, Ghavami A, Rahbar Saadat Y, Mesri Alamdari N, Alipour S, Dastouri MR, Ostadrahimi A. The effects of sodium butyrate and inulin supplementation on angiotensin signaling pathway via promotion of Akkermansia muciniphila abundance in type 2 diabetes; a randomized, double-blind, placebo-controlled trial. J Cardiovasc Thorac Res. 2017;9(4):183–190. doi:10.15171/jcvtr.2017.32.
   PubMed Web of Science ®Google Scholar
• Lloyd-Price J, Arze C, Ananthakrishnan AN, Schirmer M, Avila-Pacheco J, Poon TW, Andrews E, Ajami NJ, Bonham KS, Brislawn CJ, et al. Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases. Nature. 2019;569(7758):655–662. doi:10.1038/s41586-019-1237-9.
   PubMed Web of Science ®Google Scholar
• Wang F, Cai K, Xiao Q, He L, Xie L, Liu Z. Akkermansia muciniphila administration exacerbated the development of colitis-associated colorectal cancer in mice. J Cancer. 2022;13(1):124–133. doi:10.7150/jca.63578.
   PubMed Web of Science ®Google Scholar
• Osman MA, Neoh HM, Ab Mutalib NS, Chin SF, Mazlan L, Raja Ali RA, Zakaria AD, Ngiu CS, Ang MY, Jamal R. Parvimonas micra, Peptostreptococcus stomatis, Fusobacterium nucleatum and Akkermansia muciniphila as a four-bacteria biomarker panel of colorectal cancer. Sci Rep. 2021;11(1):2925. doi:10.1038/s41598-021-82465-0.
   PubMed Web of Science ®Google Scholar
• Khedr EM, Omeran N, Karam-Allah Ramadan H, Ahmed GK, Abdelwarith AM. Alteration of gut microbiota in Alzheimer’s disease and their relation to the cognitive impairment. J Alzheimer’s Disease: JAD. 2022;88(3):1103–1114. doi:10.3233/JAD-220176.
   PubMed Web of Science ®Google Scholar
• Png CW, Linden SK, Gilshenan KS, Zoetendal EG, McSweeney CS, Sly LI, McGuckin MA, Florin THJ. Mucolytic bacteria with increased prevalence in IBD mucosa augment in vitro utilization of mucin by other bacteria. Am J Gastroenterol. 2010;105(11):2420–2428. doi:10.1038/ajg.2010.281.
   PubMed Web of Science ®Google Scholar
• Henke MT, Kenny DJ, Cassilly CD, Vlamakis H, Xavier RJ, Clardy J. Ruminococcus gnavus, a member of the human gut microbiome associated with Crohn’s disease, produces an inflammatory polysaccharide. Proc Natl Acad Sci U S A. 2019;116(26):12672–12677. doi:10.1073/pnas.1904099116.
   PubMed Web of Science ®Google Scholar
• Gren C, Spiegelhauer MR, Rotbain EC, Ehmsen BK, Kampmann P, Andersen LP. Ruminococcus gnavus bacteraemia in a patient with multiple haematological malignancies. Access Microbiol. 2019;1(8):e000048. doi:10.1099/acmi.0.000048.
   PubMedGoogle Scholar
• Hall AB, Yassour M, Sauk J, Garner A, Jiang X, Arthur T, Lagoudas GK, Vatanen T, Fornelos N, Wilson R, et al. A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients. Genome Med. 2017;9(1):103. doi:10.1186/s13073-017-0490-5.
   PubMedGoogle Scholar
• Dabard J, Bridonneau C, Phillipe C, Anglade P, Molle D, Nardi M, Ladiré M, Girardin H, Marcille F, Gomez A, et al. Ruminococcin A, a new lantibiotic produced by a Ruminococcus gnavus strain isolated from human feces. Appl Environ Microbiol. 2001;67(9):4111–4118. doi:10.1128/AEM.67.9.4111-4118.2001.
   PubMed Web of Science ®Google Scholar
• Lee JY, Jin HS, Kim KS, Baek JH, Kim BS, Lee DW. Nutrient-specific proteomic analysis of the mucin degrading bacterium Akkermansia muciniphila. Proteomics. 2022;22(3):e2100125. doi:10.1002/pmic.202100125.
   PubMed Web of Science ®Google Scholar
• Brown AJ, Goldsworthy SM, Barnes AA, Eilert MM, Tcheang L, Daniels D, Muir AI, Wigglesworth MJ, Kinghorn I, Fraser NJ, et al. The orphan G protein-coupled receptors GPR41 and GPR43 are activated by propionate and other short chain carboxylic acids. J Biol Chem. 2003;278(13):11312–11319. doi:10.1074/jbc.M211609200.
   PubMed Web of Science ®Google Scholar
• Littlewood-Evans A, Sarret S, Apfel V, Loesle P, Dawson J, Zhang J, Muller A, Tigani B, Kneuer R, Patel S, et al. GPR91 senses extracellular succinate released from inflammatory macrophages and exacerbates rheumatoid arthritis. J Exp Med. 2016;213(9):1655–1662. doi:10.1084/jem.20160061.
   PubMed Web of Science ®Google Scholar
• Liu Q, Sikand P, Ma C, Tang Z, Han L, Li Z, Sun S, LaMotte RH, Dong X. Mechanisms of Itch Evoked by β-Alanine. J Neurosci. 2012;32(42):14532. doi:10.1523/JNEUROSCI.3509-12.2012.
   PubMed Web of Science ®Google Scholar
• Lockridge A, Gustafson E, Wong A, Miller RF, Alejandro EU. Acute D-serine co-agonism of β-cell NMDA receptors potentiates glucose-stimulated insulin secretion and excitatory β-cell membrane activity. Cells. 2021;10(1):10. doi:10.3390/cells10010093.
   Web of Science ®Google Scholar
• Roager HM, Licht TR. Microbial tryptophan catabolites in health and disease. Nat Commun. 2018;9(1). doi:10.1038/s41467-018-05470-4.
   Google Scholar
• Ehrlich AM, Pacheco AR, Henrick BM, Taft D, Xu G, Huda MN, Mishchuk D, Goodson ML, Slupsky C, Barile D, et al. Indole-3-lactic acid associated with Bifidobacterium-dominated microbiota significantly decreases inflammation in intestinal epithelial cells. BMC Microbiol. 2020;20(1):357. doi:10.1186/s12866-020-02023-y.
   PubMed Web of Science ®Google Scholar
• Diener C, Gibbons SM, Resendis-Antonio O, Chia N. MICOM: metagenome-scale modeling to infer metabolic interactions in the gut microbiota. mSystems. 2020;5(1). doi:10.1128/mSystems.00606-19.
   PubMed Web of Science ®Google Scholar
• Liu Q, Lu W, Tian F, Zhao J, Zhang H, Hong K, Yu, L. Akkermansia muciniphila exerts strain-specific effects on DSS-induced ulcerative colitis in mice. Front Cell Infect Microbiol. 2021;11:698914. doi:10.3389/fcimb.2021.698914.
   PubMed Web of Science ®Google Scholar
• Seregin SS, Golovchenko N, Schaf B, Chen J, Pudlo NA, Mitchell J, Baxter NT, Zhao L, Schloss PD, Martens EC, et al. NLRP6 protects Il10 mice from colitis by limiting colonization of Akkermansia muciniphila. Cell Rep. 2017;19(4):733–745. doi:10.1016/j.celrep.2017.03.080.
   PubMed Web of Science ®Google Scholar
• Willdigg JR, Helmann JD. Bacterial membrane composition and its modulation in response to stress. Front Mol Biosci. 2021;8:634438. doi:10.3389/fmolb.2021.634438.
   PubMed Web of Science ®Google Scholar
• Van Teeseling MCF, de Pedro MA, Cava F, van Teeseling MCF, de Pedro MA. Determinants of bacterial morphology: from fundamentals to possibilities for antimicrobial targeting. Front Microbiol. 2017;8:1264. doi:10.3389/fmicb.2017.01264.
   PubMed Web of Science ®Google Scholar
• Lapujade P, Cocaign-Bousquet M, Loubiere P. Glutamate biosynthesis in Lactococcus lactis subsp. lactis NCDO 2118. Appl Environ Microbiol. 1998;64(7):2485–2489. doi:10.1128/AEM.64.7.2485-2489.1998.
   PubMed Web of Science ®Google Scholar
• Huang L, Huang L, Zhao L, Qin Y, Su Y, Yan Q. The regulation of oxidative phosphorylation pathway on Vibrio alginolyticus adhesion under adversities. Microbiologyopen. 2019;8(8):e00805. doi:10.1002/mbo3.805.
   PubMed Web of Science ®Google Scholar
• Meng D, Sommella E, Salviati E, Campiglia P, Ganguli K, Djebali K, Zhu W, Walker WA. Indole-3-lactic acid, a metabolite of tryptophan, secreted by Bifidobacterium longum subspecies infantis is anti-inflammatory in the immature intestine. Pediatr Res. 2020;88(2):209–217. doi:10.1038/s41390-019-0740-x.
   PubMed Web of Science ®Google Scholar
• Mitchell MK, Ellermann M. Long chain fatty acids and virulence repression in intestinal bacterial pathogens. Front Cell Infect Microbiol. 2022;12:928503. doi:10.3389/fcimb.2022.928503.
   PubMed Web of Science ®Google Scholar
• Crouch LI, Liberato MV, Urbanowicz PA, Baslé A, Lamb CA, Stewart CJ, Cooke K, Doona M, Needham S, Brady RR, et al. Prominent members of the human gut microbiota express endo-acting O-glycanases to initiate mucin breakdown. Nat Commun. 2020;11(1):4017. doi:10.1038/s41467-020-17847-5.
   PubMed Web of Science ®Google Scholar
• Ang Z, Ding JL. GPR41 and GPR43 in obesity and inflammation -protective or causative? Front Immunol. 2016;7:28–. doi:10.3389/fimmu.2016.00028.
   PubMed Web of Science ®Google Scholar
• Mills E, O’Neill LA. Succinate: a metabolic signal in inflammation. Trends Cell Biol. 2014;24(5):313–320. doi:10.1016/j.tcb.2013.11.008.
   PubMed Web of Science ®Google Scholar
• Murty VL, Piotrowski J, Czajkowski A, Slomiany A, Slomiany BL. Inhibition of Helicobacter pylori glycosulfatase activity towards human gastric sulfomucin by a gastroprotective agent, sulglycotide. Gen Pharmacol. 1993;24(6):1463–1466. doi:10.1016/0306-3623(93)90436-2.
   PubMedGoogle Scholar
• Bian X, Wu W, Yang L, Lv L, Wang Q, Li Y, Ye J, Fang D, Wu J, Jiang X, et al. Administration of Akkermansia muciniphila ameliorates dextran sulfate sodium-induced ulcerative colitis in mice. Front Microbiol. 2019;10:2259. doi:10.3389/fmicb.2019.02259.
   PubMed Web of Science ®Google Scholar
• Zhou Q, Zhang Y, Wang X, Yang R, Zhu X, Zhang Y, Chen C, Yuan H, Yang Z, Sun L, et al. Gut bacteria Akkermansia is associated with reduced risk of obesity: evidence from the American Gut Project. Nutr Metab (Lond). 2020;17(1):90. doi:10.1186/s12986-020-00516-1.
   PubMedGoogle Scholar
• Gu Z, Pei W, Shen Y, Wang L, Zhu J, Zhang Y, Fan S, Wu Q, Li L, Zhang Z, et al. Akkermansia muciniphila and its outer protein Amuc_1100 regulates tryptophan metabolism in colitis. Food Funct. 2021;12(20):10184–10195. doi:10.1039/D1FO02172A.
   PubMed Web of Science ®Google Scholar
• Powell DN, Swimm A, Sonowal R, Bretin A, Gewirtz AT, Jones RM, Kalman D. Indoles from the commensal microbiota act via the AHR and IL-10 to tune the cellular composition of the colonic epithelium during aging. Proc Natl Acad Sci USA. 2020;117(35):21519–21526. doi:10.1073/pnas.2003004117.
   PubMed Web of Science ®Google Scholar
• Ganesh BP, Klopfleisch R, Loh G, Blaut M, Ryffel B. Commensal Akkermansia muciniphila exacerbates gut inflammation in Salmonella Typhimurium-infected gnotobiotic mice. PLos One. 2013;8(9):e74963. doi:10.1371/journal.pone.0074963.
   PubMed Web of Science ®Google Scholar
• McCormick DA, Horton LW, Mee AS. Mucin depletion in inflammatory bowel disease. J Clin Pathol. 1990;43(2):143–146. doi:10.1136/jcp.43.2.143.
   PubMed Web of Science ®Google Scholar
• Zou J, Chassaing B, Singh V, Pellizzon M, Ricci M, Fythe MD, Kumar MV, Gewirtz AT. Fiber-mediated nourishment of gut microbiota protects against diet-induced obesity by restoring IL-22-mediated colonic health. Cell Host & Microbe. 2018;23(1):41–53 e4. doi:10.1016/j.chom.2017.11.003.
   PubMed Web of Science ®Google Scholar
• Gilbert JA, Blaser MJ, Caporaso JG, Jansson JK, Lynch SV, Knight R. Current understanding of the human microbiome. Nat Med. 2018;24(4):392–400. doi:10.1038/nm.4517.
   PubMed Web of Science ®Google Scholar
• Eckmann L, Karin M. NOD2 and Crohn’s disease: loss or gain of function? Immunity. 2005;22(6):661–667. doi:10.1016/j.immuni.2005.06.004.
   PubMed Web of Science ®Google Scholar
• Hattori M, Taylor TD. The human intestinal microbiome: a new frontier of human biology. DNA Res. 2009;16(1):1–12. doi:10.1093/dnares/dsn033.
   PubMed Web of Science ®Google Scholar
• Schroeder BO, Birchenough GMH, Stahlman M, Arike L, Johansson MEV, Hansson GC, Bäckhed F. Bifidobacteria or fiber protects against diet-induced microbiota-mediated colonic mucus deterioration. Cell Host & Microbe. 2018;23(1):27–40 e7. doi:10.1016/j.chom.2017.11.004.
   PubMed Web of Science ®Google Scholar
• Sugihara K, Kitamoto S, Saraithong P, Nagao-Kitamoto H, Hoostal M, McCarthy C, Rosevelt A, Muraleedharan CK, Gillilland MG, Imai J, et al. Mucolytic bacteria license pathobionts to acquire host-derived nutrients during dietary nutrient restriction. Cell Rep. 2022;40(3):111093. doi:10.1016/j.celrep.2022.111093.
   PubMed Web of Science ®Google Scholar
• Grabinger T, Glaus Garzon JF, Hausmann M, Geirnaert A, Lacroix C, Hennet T. Alleviation of intestinal inflammation by oral supplementation with 2-fucosyllactose in mice. Front Microbiol. 2019;10:1385. doi:10.3389/fmicb.2019.01385.
   PubMed Web of Science ®Google Scholar
• Kim HJ, Hou BK, Lee SG, Kim JS, Lee DW, Lee SJ. Genome-wide analysis of redox reactions reveals metabolic engineering targets for D-lactate overproduction in Escherichia coli. Metab Eng. 2013;18:44–52. doi:10.1016/j.ymben.2013.03.004.
   PubMed Web of Science ®Google Scholar
• Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA. 2005;102(43):15545–15550. doi:10.1073/pnas.0506580102.
   PubMed Web of Science ®Google Scholar
• Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. Newark, DE, USA: MIDI Technical Note 101. MIDI Inc; 1990.
   Google Scholar
• Chen S, Zhou Y, Chen Y, Gu J. Fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018;34(17):i884–i90. doi:10.1093/bioinformatics/bty560.
   PubMed Web of Science ®Google Scholar
• Liu T, Chen CY, Chen-Deng A, Chen YL, Wang JY, Hou YI, Lin M-C. Joining Illumina paired-end reads for classifying phylogenetic marker sequences. BMC Bioinform. 2020;21(1):105. doi:10.1186/s12859-020-3445-6.
   PubMed Web of Science ®Google Scholar
• Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJ, Holmes SP. DADA2: high-resolution sample inference from Illumina amplicon data. Nat Methods. 2016;13(7):581–583. doi:10.1038/nmeth.3869.
   PubMed Web of Science ®Google Scholar
• Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol. 2019;37(8):852–857. doi:10.1038/s41587-019-0209-9.
   PubMed Web of Science ®Google Scholar
• Magnusdottir S, Heinken A, Kutt L, Ravcheev DA, Bauer E, Noronha A, Greenhalgh K, Jäger C, Baginska J, Wilmes P, et al. Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota. Nat Biotechnol. 2017;35(1):81–89. doi:10.1038/nbt.3703.
   PubMed Web of Science ®Google Scholar