Fecal metatranscriptomics of macaques with idiopathic chronic diarrhea reveals altered mucin degradation and fucose utilization
Tóm tắt
Idiopathic chronic diarrhea (ICD) is a common cause of morbidity and mortality among juvenile rhesus macaques. Characterized by chronic inflammation of the colon and repeated bouts of diarrhea, ICD is largely unresponsive to medical interventions, including corticosteroid, antiparasitic, and antibiotic treatments. Although ICD is accompanied by large disruptions in the composition of the commensal gut microbiome, no single pathogen has been concretely identified as responsible for the onset and continuation of the disease. Fecal samples were collected from 12 ICD-diagnosed macaques and 12 age- and sex-matched controls. RNA was extracted for metatranscriptomic analysis of organisms and functional annotations associated with the gut microbiome. Bacterial, fungal, archaeal, protozoan, and macaque (host) transcripts were simultaneously assessed. ICD-afflicted animals were characterized by increased expression of host-derived genes involved in inflammation and increased transcripts from bacterial pathogens such as Campylobacter and Helicobacter and the protozoan Trichomonas. Transcripts associated with known mucin-degrading organisms and mucin-degrading enzymes were elevated in the fecal microbiomes of ICD-afflicted animals. Assessment of colon sections using immunohistochemistry and of the host transcriptome suggests differential fucosylation of mucins between control and ICD-afflicted animals. Interrogation of the metatranscriptome for fucose utilization genes reveals possible mechanisms by which opportunists persist in ICD. Bacteroides sp. potentially cross-fed fucose to Haemophilus whereas Campylobacter expressed a mucosa-associated transcriptome with increased expression of adherence genes. The simultaneous profiling of bacterial, fungal, archaeal, protozoan, and macaque transcripts from stool samples reveals that ICD of rhesus macaques is associated with increased gene expression by pathogens, increased mucin degradation, and altered fucose utilization. The data suggest that the ICD-afflicted host produces fucosylated mucins that are leveraged by potentially pathogenic microbes as a carbon source or as adhesion sites.
Tài liệu tham khảo
Vallender EJ, Miller GM. Nonhuman primate models in the genomic era: a paradigm shift. ILAR J. 2013;54(2):154–65.
Ardeshir A, Oslund KL, Ventimiglia F, Yee J, Lerche NW, Hyde DM. Idiopathic microscopic colitis of rhesus macaques: quantitative assessment of colonic mucosa. Anat Rec (Hoboken). 2013;296(8):1169–79.
Broadhurst MJ, Ardeshir A, Kanwar B, Mirpuri J, Gundra UM, Leung JM, Wiens KE, Vujkovic-Cvijin I, Kim CC, Yarovinsky F, et al. Therapeutic helminth infection of macaques with idiopathic chronic diarrhea alters the inflammatory signature and mucosal microbiota of the colon. PLoS Pathog. 2012;8(11):e1003000.
Fox JG, Handt L, Xu S, Shen Z, DeWhirst FE, Paster BJ, Dangler CA, Lodge K, Motzel S, Klein H. Novel Helicobacter species isolated from rhesus monkeys with chronic idiopathic colitis. J Med Microbiol. 2001;50:8.
Farkas T, Falkenstein KP, Bohm RP, Pecotte J, Sestak K. High incidence of rhesus enteric calicivirus infections and diarrhea in captive juvenile macaques: a likely association. J Med Primatol. 2012;41(5):325–8.
Blackwood RS, Tarara RP, Christe KL, Spinner A, Lerche NW. Effects of the macrolide drug tylosin on chronic diarrhea in rhesus macaques (Macaca mulatta). Comparative medicine. 2008;58(1):81–7.
McKenna P, Hoffmann C, Minkah N, Aye PP, Lackner A, Liu Z, Lozupone CA, Hamady M, Knight R, Bushman FD. The macaque gut microbiome in health, lentiviral infection, and chronic enterocolitis. PLoS Pathog. 2008;4(2):e20.
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 e1321.
Chen T, Long W, Zhang C, Liu S, Zhao L, Hamaker BR. Fiber-utilizing capacity varies in Prevotella- versus Bacteroides-dominated gut microbiota. Sci Rep. 2017;7(1):2594.
Sonnenburg ED, Sonnenburg JL. Starving our microbial self: the deleterious consequences of a diet deficient in microbiota-accessible carbohydrates. Cell Metab. 2014;20(5):779–86.
Zhernakova A, Kurilshikov A, Bonder MJ, Tigchelaar EF, Schirmer M, Vatanen T, Mujagic Z, Vila AV, Falony G, Vieira-Silva S, et al. Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity. Science. 2016;352(6285):565–9.
Sonnenburg ED, Smits SA, Tikhonov M, Higginbottom SK, Wingreen NS, Sonnenburg JL. Diet-induced extinctions in the gut microbiota compound over generations. Nature. 2016;529(7585):212–5.
Parthasarathy G, Chen J, Chen X, Chia N, O'Connor HM, Wolf PG, Gaskins HR, Bharucha AE. Relationship between microbiota of the colonic mucosa vs feces and symptoms, colonic transit, and methane production in female patients with chronic constipation. Gastroenterology. 2016;150(2):367–79 e361.
El Kaoutari A, Armougom F, Gordon JI, Raoult D, Henrissat B. The abundance and variety of carbohydrate-active enzymes in the human gut microbiota. Nat Rev Microbiol. 2013;11(7):497–504.
Engevik MA, Yacyshyn MB, Engevik KA, Wang J, Darien B, Hassett DJ, Yacyshyn BR, Worrell RT. Human Clostridium difficile infection: altered mucus production and composition. Am J Physiol Gastrointest Liver Physiol. 2015;308(6):G510–24.
Conway T, Cohen PS. Commensal and pathogenic Escherichia coli metabolism in the gut. Microbiol Spectr. 2015;3(3).
Levy M, Kolodziejczyk AA, Thaiss CA, Elinav E. Dysbiosis and the immune system. Nat Rev Immunol. 2017;17(4):219–32.
Pereira FC, Berry D. Microbial nutrient niches in the gut. Environ Microbiol. 2017;19(4):1366–78.
Marini RP, Muthupalani S, Shen Z, Buckley EM, Alvarado C, Taylor NS, Dewhirst FE, Whary MT, Patterson MM, Fox JG. Persistent infection of rhesus monkeys with ‘Helicobacter macacae’ and its isolation from an animal with intestinal adenocarcinoma. J Med Microbiol. 2010;59(Pt 8):961–9.
Sonnenberg A, Melton SD, Genta RM, Lewis AD. Absence of focally enhanced gastritis in macaques with idiopathic colitis. Inflamm Bowel Dis. 2011;17(12):2456–61.
Westreich ST, Korf I, Mills DA, Lemay DG. SAMSA: a comprehensive metatranscriptome analysis pipeline. BMC Bioinformatics. 2016;17(1):399.
Loktionov A. Cell exfoliation in the human colon: myth, reality and implications for colorectal cancer screening. Int J Cancer. 2007;120(11):2281–9.
Mersich AT, Miller MR, Chkourko H, Blystone SD. The formin FRL1 (FMNL1) is an essential component of macrophage podosomes. Cytoskeleton (Hoboken). 2010;67(9):573–85.
Moein S, Qujeq D, Vaghari Tabari M, Kashifard M, Hajian-Tilaki K. Diagnostic accuracy of fecal calprotectin in assessing the severity of inflammatory bowel disease: from laboratory to clinic. Caspian J Intern Med. 2017;8(3):178–82.
Sipponen T, Kolho KL. Fecal calprotectin in diagnosis and clinical assessment of inflammatory bowel disease. Scand J Gastroenterol. 2015;50(1):74–80.
Kucharzik T, Hudson JT 3rd, Lugering A, Abbas JA, Bettini M, Lake JG, Evans ME, Ziegler TR, Merlin D, Madara JL, et al. Acute induction of human IL-8 production by intestinal epithelium triggers neutrophil infiltration without mucosal injury. Gut. 2005;54(11):1565–72.
Grennan AK. Genevestigator. Facilitating web-based gene-expression analysis. Plant Physiol. 2006;141(4):1164–6.
Jarry A, Vallette G, Cassagnau E, Moreau A, Bou-Hanna C, Lemarre P, Letessier E, Le Neel J-C, Galmiche J-P, Laboisse CL. Interleukin 1 and interleukin 1β converting enzyme (caspase 1) expression in the human colonic epithelial barrier. Caspase 1 downregulation in colon cancer. Gut. 1999;45:246–51.
Ciorba MA. Indoleamine 2,3 dioxygenase in intestinal disease. Curr Opin Gastroenterol. 2013;29(2):146–52.
Ferdinande L, Demetter P, Perez-Novo C, Waeytens A, Taildeman J, Rottiers I, Rottiers P, De Vos M, Cuvelier CA. Inflamed intestinal mucosa features a specific epithelial expression pattern of Indoleamine 2,3-dioxygenase. Int J Immunopathol Pharmacol. 2008;21(2):289–95.
Gombart AF, Krug U, O'Kelly J, An E, Vegesna V, Koeffler HP. Aberrant expression of neutrophil and macrophage-related genes in a murine model for human neutrophil-specific granule deficiency. J Leukoc Biol. 2005;78(5):1153–65.
Peeters PM, Wouters EF, Reynaert NL. Immune homeostasis in epithelial cells: evidence and role of inflammasome signaling reviewed. J Immunol Res. 2015;2015:828264.
Kumar A, Yu FS. Toll-like receptors and corneal innate immunity. Curr Mol Med. 2006;6(3):327–37.
Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, Edwards RA, Gerdes S, Parrello B, Shukla M, et al. The SEED and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res. 2014;42(Database issue):D206–14.
Chatzidaki-Livanis M, Comstock Laurie E. Friend turned foe: a role for bacterial sulfatases in colitis. Cell Host Microbe. 2015;17(5):540–1.
Roager HM, Hansen LB, Bahl MI, Frandsen HL, Carvalho V, Gobel RJ, Dalgaard MD, Plichta DR, Sparholt MH, Vestergaard H, et al. Colonic transit time is related to bacterial metabolism and mucosal turnover in the gut. Nat Microbiol. 2016;1(9):16093.
Donaldson GP, Lee SM, Mazmanian SK. Gut biogeography of the bacterial microbiota. Nat Rev Microbiol. 2016;14(1):20–32.
Vandeputte D, Falony G, Vieira-Silva S, Tito RY, Joossens M, Raes J. Stool consistency is strongly associated with gut microbiota richness and composition, enterotypes and bacterial growth rates. Gut. 2016;65(1):57–62.
Bremer H, Dennis PP. Modulation of chemical composition and other parameters of the cell at different exponential growth rates. EcoSal Plus. 2008;3(1).
Newcombe G, Campbell J, Griffith D, Baynes M, Launchbaugh K, Pendleton R. Revisiting the life cycle of dung fungi, including Sordaria fimicola. PLoS One. 2016;11(2):e0147425.
Li J, Dong H, Wang R, Yu F, Wu Y, Chang Y, Wang C, Qi M, Zhang L. An investigation of parasitic infections and review of molecular characterization of the intestinal protozoa in nonhuman primates in China from 2009 to 2015. Int J Parasitol Parasites Wildl. 2017;6(1):8–15.
Pimentel M, Lin HC, Enayati P, van den Burg B, Lee HR, Chen JH, Park S, Kong Y, Conklin J. Methane, a gas produced by enteric bacteria, slows intestinal transit and augments small intestinal contractile activity. Am J Physiol Gastrointest Liver Physiol. 2006;290(6):G1089–95.
Pavlovskis OR, Rollins DM, Haberberger RL, Green AE, Habash L, Strocko S, Walker RI. Significance of flagella in colonization resistance of rabbits immunized with Campylobacter spp. Infect Immun. 1991;59(7):2259–64.
Grant CC, Konkel ME, Cieplak W Jr, Tompkins LS. Role of flagella in adherence, internalization, and translocation of Campylobacter jejuni in nonpolarized and polarized epithelial cell cultures. Infect Immun. 1993;61(5):1764–71.
Wassenaar TM, Bleumink-Pluym NM, van der Zeijst BA. Inactivation of Campylobacter jejuni flagellin genes by homologous recombination demonstrates that flaA but not flaB is required for invasion. EMBO J. 1991;10(8):2055–61.
Yao R, Burr DH, Doig P, Trust TJ, Niu H, Guerry P. Isolation of motile and non-motile insertional mutants of Campylobacter jejuni: the role of motility in adherence and invasion of eukaryotic cells. Mol Microbiol. 1994;14(5):883–93.
Gaynor EC, Wells DH, MacKichan JK, Falkow S. The Campylobacter jejuni stringent response controls specific stress survival and virulence-associated phenotypes. Mol Microbiol. 2005;56(1):8–27.
Bacon DJ, Alm RA, Hu L, Hickey TE, Ewing CP, Batchelor RA, Trust TJ, Guerry P. DNA sequence and mutational analyses of the pVir plasmid of Campylobacter jejuni 81-176. Infect Immun. 2002;70(11):6242–50.
Tailford LE, Crost EH, Kavanaugh D, Juge N. Mucin glycan foraging in the human gut microbiome. Front Genet. 2015;6:81.
Lepage P, Häsler R, Spehlmann ME, Rehman A, Zvirbliene A, Begun A, Ott S, Kupcinskas L, Doré J, Raedler A, et al. Twin study indicates loss of interaction between microbiota and mucosa of patients with ulcerative colitis. Gastroenterology. 2011;141(1):227–36.
Maloy KJ, Powrie F. Intestinal homeostasis and its breakdown in inflammatory bowel disease. Nature. 2011;474(7351):298–306.
Kelly RJ, Rouquier S, Giorgi D, Lennon GG, Lowe JB. Sequence and expression of a candidate for the human secretor blood group alpha(1,2)fucosyltransferase gene (FUT2). Homozygosity for an enzyme-inactivating nonsense mutation commonly correlates with the non-secretor phenotype. J Biol Chem. 1995;270(9):4640–9.
Xu J, Bjursell MK, Himrod J, Deng S, Carmichael LK, Chiang HC, Hooper LV, Gordon JI. A genomic view of the human-Bacteroides thetaiotaomicron symbiosis. Science. 2003;299(5615):2074–6.
Hooper LV, Xu J, Falk PG, Midtvedt T, Gordon JI. A molecular sensor that allows a gut commensal to control its nutrient foundation in a competitive ecosystem. Proc Natl Acad Sci U S A. 1999;96(17):9833–8.
Shin NR, Whon TW, Bae JW. Proteobacteria: microbial signature of dysbiosis in gut microbiota. Trends Biotechnol. 2015;33(9):496–503.
Zoetendal EG, Raes J, van den Bogert B, Arumugam M, Booijink CC, Troost FJ, Bork P, Wels M, de Vos WM, Kleerebezem M. The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates. Isme j. 2012;6(7):1415–26.
Noguera-Julian M, Rocafort M, Guillen Y, Rivera J, Casadella M, Nowak P, Hildebrand F, Zeller G, Parera M, Bellido R, et al. Gut microbiota linked to sexual preference and HIV infection. EBioMedicine. 2016;5:135–46.
Dillon SM, Lee EJ, Kotter CV, Austin GL, Gianella S, Siewe B, Smith DM, Landay AL, McManus MC, Robertson CE, et al. Gut dendritic cell activation links an altered colonic microbiome to mucosal and systemic T-cell activation in untreated HIV-1 infection. Mucosal Immunol. 2016;9(1):24–37.
Scher JU, Sczesnak A, Longman RS, Segata N, Ubeda C, Bielski C, Rostron T, Cerundolo V, Pamer EG, Abramson SB, et al. Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis. Elife. 2013;2:e01202.
Wu GD, Chen J, Hoffmann C, Bittinger K, Chen YY, Keilbaugh SA, Bewtra M, Knights D, Walters WA, Knight R, et al. Linking long-term dietary patterns with gut microbial enterotypes. Science. 2011;334(6052):105–8.
Ley RE. Gut microbiota in 2015: Prevotella in the gut: choose carefully. Nat Rev Gastroenterol Hepatol. 2016;13(2):69–70.
Marcobal A, Barboza M, Sonnenburg ED, Pudlo N, Martens EC, Desai P, Lebrilla CB, Weimer BC, Mills DA, German JB, et al. Bacteroides in the infant gut consume milk oligosaccharides via mucus-utilization pathways. Cell Host Microbe. 2011;10(5):507–14.
Ohkawara S, Furuya H, Nagashima K, Asanuma N, Hino T. Effect of oral administration of Butyrivibrio fibrisolvens MDT-1 on experimental enterocolitis in mice. Clin Vaccine Immunol. 2006;13(11):1231–6.
Sestak K, Merritt CK, Borda J, Saylor E, Schwamberger SR, Cogswell F, Didier ES, Didier PJ, Plauche G, Bohm RP, et al. Infectious agent and immune response characteristics of chronic enterocolitis in captive rhesus macaques. Infect Immun. 2003;71(7):4079–86.
Rivera-Chavez F, Lopez CA, Baumler AJ. Oxygen as a driver of gut dysbiosis. Free Radic Biol Med. 2017;105:93–101.
Johansson ME, Gustafsson JK, Holmen-Larsson J, Jabbar KS, Xia L, Xu H, Ghishan FK, Carvalho FA, Gewirtz AT, Sjovall H, et al. Bacteria penetrate the normally impenetrable inner colon mucus layer in both murine colitis models and patients with ulcerative colitis. Gut. 2014;63(2):281–91.
Pickard JM, Chervonsky AV. Intestinal fucose as a mediator of host-microbe symbiosis. J Immunol. 2015;194(12):5588–93.
Tropini C, Earle KA, Huang KC, Sonnenburg JL. The gut microbiome: connecting spatial organization to function. Cell Host Microbe. 2017;21(4):433–42.
Westreich ST, Treiber ML, Mills DA, Korf I, Lemay DG. SAMSA2: a standalone metatranscriptome analysis pipeline. BMC Bioinformatics. 2018;19(1):175.
Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30(15):2114–20.
Zhang J, Kobert K, Flouri T, Stamatakis A. PEAR: a fast and accurate Illumina Paired-End reAd mergeR. Bioinformatics. 2014;30(5):614–20.
Meyer F, Paarmann D, D'Souza M, Olson R, Glass EM, Kubal M, Paczian T, Rodriguez A, Stevens R, Wilke A, et al. The metagenomics RAST server-a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics. 2008;9:386.
Tatusova T, Ciufo S, Fedorov B, O’Neill K, Tolstoy I. RefSeq microbial genomes database: new representation and annotation strategy. Nucleic Acids Res. 2014;42(Database issue):D553–9.
Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15(12):550.
Huang da W, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009;4(1):44–57.
Kramer A, Green J, Pollard J Jr, Tugendreich S. Causal analysis approaches in Ingenuity Pathway Analysis. Bioinformatics. 2014;30(4):523–30.