Journal of Applied Biological Chemistry

The Korean Society for Applied Biological Chemistry (한국응용생명화학회)
권호 표지
DOI QR코드

DOI QR Code

Mucin modifies microbial composition and improves metabolic functional potential of a synthetic gut microbial ecosystem

  • Mabwi, Humphrey A. (Natural Product Informatics Research Center, KIST Gangneung Institute of Natural Products) ;
  • Komba, Erick V.G. (Department of Microbiology, Parasitology, and Biotechnology, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture) ;
  • Mwaikono, Kilaza Samson (Department of Science and Laboratory Technology, Dar es Salaam Institute of Technology) ;
  • Hitayezu, Emmanuel (Natural Product Informatics Research Center, KIST Gangneung Institute of Natural Products) ;
  • Mauliasari, Intan Rizki (Natural Product Informatics Research Center, KIST Gangneung Institute of Natural Products) ;
  • Jin, Jong Beom (Natural Product Informatics Research Center, KIST Gangneung Institute of Natural Products) ;
  • Pan, Cheol-Ho (Natural Product Informatics Research Center, KIST Gangneung Institute of Natural Products) ;
  • Cha, Kwang Hyun (Natural Product Informatics Research Center, KIST Gangneung Institute of Natural Products)
  • Received : 2022.02.05
  • Accepted : 2022.03.11
  • Published : 2022.03.31
Download PDF
⟨ Previous Next ⟩

Abstract

Microbial dysbiosis in the gut is associated with human diseases, and variations in mucus alter gut microbiota. Therefore, we explored the effects of mucin on the gut microbiota using a community of 19 synthetic gut microbial species. Cultivation of these species in modified Gifu anaerobic medium (GAM) supplemented with mucin before synthetic community assembly facilitated substantial growth of the Bacteroides, Akkermansia, and Clostridium genera. The results of 16S rRNA microbial relative abundance profiling revealed more of the beneficial microbes Collinsella, Bifidobacterium, Ruminococcus, and Lactobacillus. This increased acetate levels in the community cultivated with, rather than without (control), mucin. We identified differences in predicted cell function and metabolism between microbes cultivated in GAM with and without mucin. Mucin not only changed the composition of the gut microbial community, but also modulated metabolic functions, indicating that it could help to modulate microbial changes associated with human diseases.

Keywords

Acknowledgement

This work was supported by the National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT) (No. 2021R1C1C1007945) and an intramural grant (2Z06662) from the Korea Institute of Science and Technology (KIST), in collaboration with the Partnership for Skills in Applied Sciences, Engineering and Technology-Regional Scholarship and Innovation Fund (PASET-RSIF). The fellowship was hosted by the SACIDS foundation of one health at Sokoine University of Agriculture in Tanzania.

References

  1. Lloyd-Price J, Abu-Ali G, Huttenhower C (2016) The healthy human microbiome. Genome Med 8: 51. doi: 10.1186/s13073-016-0307-y
  2. Xiao L, Feng Q, Liang S, Sonne SB, Xia Z, Qiu X, Li X, Long H, Zhang J, Zhang D, Liu C, Fang Z, Chou J, Glanville J, Hao Q, Kotowska D, Colding C, Licht TR, Wu D, Yu J, Sung JJ, Liang Q, Li J, Jia H, Lan Z, Tremaroli V, Dworzynski P, Nielsen HB, Backhed F, Dore J, Le Chatelier E, Ehrlich SD, Lin JC, Arumugam M, Wang J, Madsen L, Kristiansen K (2015) A catalog of the mouse gut metagenome. Nat Biotechnol 33: 1103-1108. doi: 10.1038/nbt.3353
  3. Ridaura VK, Faith JJ, Rey FE, Cheng J, Duncan AE, Kau AL, Griffin NW, Lombard V, Henrissat B, Bain JR, Muehlbauer MJ, Ilkayeva O, Semenkovich CF, Funai K, Hayashi DK, Lyle BJ, Martini MC, Ursell LK, Clemente JC, Van Treuren W, Walters WA, Knight R, Newgard CB, Heath AC, Gordon JI (2013) Gut microbiota from twins discordant for obesity modulate metabolism in mice. Science 341: 1241214. doi: 10.1126/science.1241214
  4. Tilg H, Moschen AR (2014) Microbiota and diabetes: an evolving relationship. Gut 63: 1513-1521. doi: 10.1136/gutjnl-2014-306928
  5. Shaw KA, Bertha M, Hofmekler T, Chopra P, Vatanen T, Srivatsa A, Prince J, Kumar A, Sauer C, Zwick ME, Satten GA, Kostic AD, Mulle JG, Xavier RJ, Kugathasan S (2016) Dysbiosis, inflammation, and response to treatment: a longitudinal study of pediatric subjects with newly diagnosed inflammatory bowel disease. Genome Med 8: 75 https://doi.org/10.1186/s13073-016-0331-y
  6. Schmidt TSB, Raes J, Bork P (2018) The human gut microbiome: from association to modulation. Cell 172: 1198-1215. doi: 10.1186/s13073-016-0331-y
  7. Rajilic-Stojanovic M, De Vos WM (2014) The first 1000 cultured species of the human gastrointestinal microbiota. FEMS microbiology reviews 38: 996-1047. doi: 10.1111/1574-6976.12075
  8. Mabwi HA, Kim E, Song DG, Yoon HS, Pan CH, Komba EVG, Ko G, Cha KH (2021) Synthetic gut microbiome: Advances and challenges. Comput Struct Biotechnol J 19: 363-371. doi: 10.1016/j.csbj.2020.12.029
  9. Koropatkin NM, Cameron EA, Martens EC (2012) How glycan metabolism shapes the human gut microbiota. Nat Rev Microbiol 10: 323-335. doi: 10.1038/nrmicro2746. doi: 10.1038/nrmicro2746
  10. Etienne-Mesmin L, Chassaing B, Desvaux M, De Paepe K, Gresse R, Sauvaitre T, Forano E, de Wiele TV, Schuller S, Juge N, Blanquet-Diot S (2019) Experimental models to study intestinal microbes-mucus interactions in health and disease. FEMS Microbiol Rev 43: 457-489. doi: 10.1093/femsre/fuz013
  11. Li L, Zhang X, Ning Z, Mayne J, Moore JI, Butcher J, Chiang C-K, Mack D, Stintzi A, Figeys D (2018) Evaluating in vitro culture medium of gut microbiome with orthogonal experimental design and a metaproteomics approach. J Proteome Res 17: 154-163. doi: 10.1021/acs.jproteome.7b00461
  12. Yang K, Xu M, Zhu J (2020) Evaluating the impact of four major nutrients on gut microbial metabolism by a targeted metabolomics approach. J Proteome Res 19: 1991-1998. doi: 10.1021/acs.jproteome.9b00806
  13. Tramontano M, Andrejev S, Pruteanu M, Klunemann M, Kuhn M, Galardini M, Jouhten P, Zelezniak A, Zeller G, Bork P, Typas A, Patil KR (2018) Nutritional preferences of human gut bacteria reveal their metabolic idiosyncrasies. Nat Microbiol 3: 514-522. doi: 10.1038/s41564-018-0123-9
  14. Morrison DJ, Preston T (2016) Formation of short chain fatty acids by the gut microbiota and their impact on human metabolism. Gut Microbes 7: 189-200. doi: 10.1080/19490976.2015.1134082
  15. Venturelli OS, Carr AC, Fisher G, Hsu RH, Lau R, Bowen BP, Hromada S, Northen T, Arkin AP (2018) Deciphering microbial interactions in synthetic human gut microbiome communities. Mol Syst Biol 14: e8157. doi: 10.15252/msb.20178157
  16. Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, Bisanz JE, Bittinger K, Brejnrod A, Brislawn CJ, Brown CT, Callahan BJ, Caraballo-Rodriguez AM, Chase J, Cope EK, Da Silva R, Diener C, Dorrestein PC, Douglas GM, Durall DM, Duvallet C, Edwardson CF, Ernst M, Estaki M, Fouquier J, Gauglitz JM, Gibbons SM, Gibson DL, Gonzalez A, Gorlick K, Guo J, Hillmann B, Holmes S, Holste H, Huttenhower C, Huttley GA, Janssen S, Jarmusch AK, Jiang L, Kaehler BD, Kang KB, Keefe CR, Keim P, Kelley ST, Knights D, Koester I, Kosciolek T, Kreps J, Langille MGI, Lee J, Ley R, Liu YX, Loftfield E, Lozupone C, Maher M, Marotz C, Martin BD, McDonald D, McIver LJ, Melnik AV, Metcalf JL, Morgan SC, Morton JT, Naimey AT, NavasMolina JA, Nothias LF, Orchanian SB, Pearson T, Peoples SL, Petras D, Preuss ML, Pruesse E, Rasmussen LB, Rivers A, Robeson MS, 2nd, Rosenthal P, Segata N, Shaffer M, Shiffer A, Sinha R, Song SJ, Spear JR, Swafford AD, Thompson LR, Torres PJ, Trinh P, Tripathi A, Turnbaugh PJ, Ul-Hasan S, van der Hooft JJJ, Vargas F, Vazquez-Baeza Y, Vogtmann E, von Hippel M, Walters W, Wan Y, Wang M, Warren J, Weber KC, Williamson CHD, Willis AD, Xu ZZ, Zaneveld JR, Zhang Y, Zhu Q, Knight R, Caporaso JG (2019) Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol 37: 852-857. doi: 10.1038/s41587-019-0209-9
  17. Dhariwal A, Chong J, Habib S, King IL, Agellon LB, Xia J (2017) MicrobiomeAnalyst: a web-based tool for comprehensive statistical, visual and meta-analysis of microbiome data. Nucleic Acids Res 45: W180-W188. doi: 10.1093/nar/gkx295
  18. Knights D, Costello EK, Knight R (2011) Supervised classification of human microbiota. FEMS Microbiol Rev 35: 343-359. doi: 10.1111/j.1574-6976.2010.00251.x
  19. David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE, Wolfe BE, Ling AV, Devlin AS, Varma Y, Fischbach MA, Biddinger SB, Dutton RJ, Turnbaugh PJ (2014) Diet rapidly and reproducibly alters the human gut microbiome. Nature 505: 559-563. doi: 10.1038/nature12820
  20. Langille MG, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes JA, Clemente JC, Burkepile DE, Vega Thurber RL, Knight R, Beiko RG, Huttenhower C (2013) Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol 31: 814-821. doi: 10.1038/nbt.2676
  21. Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett WS, Huttenhower C (2011) Metagenomic biomarker discovery and explanation. Genome Biol 12: R60. doi: 10.1186/gb-2011-12-6-r60
  22. Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018) MEGA X: Molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35: 1547-1549. doi: 10.1093/molbev/msy096
  23. Roager HM, Hansen LB, Bahl MI, Frandsen HL, Carvalho V, Gobel RJ, Dalgaard MD, Plichta DR, Sparholt MH, Vestergaard H, Hansen T, Sicheritz-Ponten T, Nielsen HB, Pedersen O, Lauritzen L, Kristensen M, Gupta R, Licht TR (2016) Colonic transit time is related to bacterial metabolism and mucosal turnover in the gut. Nat Microbiol 1: 16093 https://doi.org/10.1038/nmicrobiol.2016.93
  24. Vandeputte D, Falony G, Vieira-Silva S, Tito RY, Joossens M, Raes J (2016) Stool consistency is strongly associated with gut microbiota richness and composition, enterotypes and bacterial growth rates. Gut 65: 57-62. doi: 10.1136/gutjnl-2015-309618
  25. Kraal L, Abubucker S, Kota K, Fischbach MA, Mitreva M (2014) The prevalence of species and strains in the human microbiome: a resource for experimental efforts. PloS one 9: e97279. doi: 10.1371/journal.pone.0097279
  26. Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, Mende DR, Li J, Xu J, Li S, Li D, Cao J, Wang B, Liang H, Zheng H, Xie Y, Tap J, Lepage P, Bertalan M, Batto JM, Hansen T, Le Paslier D, Linneberg A, Nielsen HB, Pelletier E, Renault P, Sicheritz-Ponten T, Turner K, Zhu H, Yu C, Li S, Jian M, Zhou Y, Li Y, Zhang X, Li S, Qin N, Yang H, Wang J, Brunak S, Dore J, Guarner F, Kristiansen K, Pedersen O, Parkhill J, Weissenbach J, MetaHIT Consortium, Bork P, Ehrlich SD, Wang J (2010) A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464: 59-65. doi: 10.1038/nature08821
  27. Forster SC, Kumar N, Anonye BO, Almeida A, Viciani E, Stares MD, Dunn M, Mkandawire TT, Zhu A, Shao Y (2019) A human gut bacterial genome and culture collection for improved metagenomic analyses. Nat Biotechnol. 37: 186-192. doi: 10.1038/s41587-018-0009-7
  28. Maier L, Pruteanu M, Kuhn M, Zeller G, Telzerow A, Anderson EE, Brochado AR, Fernandez KC, Dose H, Mori H, Patil KR, Bork P, Typas A (2018) Extensive impact of non-antibiotic drugs on human gut bacteria. Nature 555: 623-628. doi: 10.1038/nature25979
  29. Gotoh A, Nara M, Sugiyama Y, Sakanaka M, Yachi H, Kitakata A, Nakagawa A, Minami H, Okuda S, Katoh T, Katayama T, Kurihara S (2017) Use of Gifu Anaerobic Medium for culturing 32 dominant species of human gut microbes and its evaluation based on short-chain fatty acids fermentation profiles. Biosci Biotechnol Biochem 81: 2009-2017. doi: 10.1080/09168451.2017.1359486
  30. Marcobal A, Barboza M, Sonnenburg ED, Pudlo N, Martens EC, Desai P, Lebrilla CB, Weimer BC, Mills DA, German JB (2011) Bacteroides in the infant gut consume milk oligosaccharides via mucus-utilization pathways. Cell Host Microbe 10: 507-514. doi: 10.1016/j.chom.2011.10.007
  31. Xu J, Bjursell MK, Himrod J, Deng S, Carmichael LK, Chiang HC, Hooper LV, Gordon JI (2003) A genomic view of the human-Bacteroides thetaiotaomicron symbiosis. Science 299: 2074-2076. doi: 10.1126/science.1080029
  32. Comstock LE (2009) Importance of glycans to the host-bacteroides mutualism in the mammalian intestine. Cell Host Microbe 5: 522-526. doi: 10.1016/j.chom.2009.05.010
  33. Tailford LE, Crost EH, Kavanaugh D, Juge N (2015) Mucin glycan foraging in the human gut microbiome. Front Genet 6: 81. doi: 10.3389/fgene.2015.00081
  34. Berry D, Stecher B, Schintlmeister A, Reichert J, Brugiroux S, Wild B, Wanek W, Richter A, Rauch I, Decker T (2013) Host-compound foraging by intestinal microbiota revealed by single-cell stable isotope probing. Proc Natl Acad Sci USA 110: 4720-4725. doi: 10.1073/pnas.1219247110
  35. Marcobal A, Sonnenburg J (2012) Human milk oligosaccharide consumption by intestinal microbiota. Clin Microbiol Infect 18: 12--15. doi: 10.1111/j.1469-0691.2012.03863.x
  36. Ruas-Madiedo P, Gueimonde M, Fernandez-Garcia M, de los ReyesGavilan CG, Margolles A (2008) Mucin degradation by Bifidobacterium strains isolated from the human intestinal microbiota. Appl Environ Microbiol 74: 1936-1940. doi: 10.1128/AEM.02509-07
  37. Edgar R (2018) Taxonomy annotation and guide tree errors in 16S rRNA databases. PeerJ 6: e5030. doi: 10.7717/peerj.5030
  38. Koropatkin NM, Cameron EA, Martens EC (2012) How glycan metabolism shapes the human gut microbiota. Nature Reviews Microbiology 10: 323-335 https://doi.org/10.1038/nrmicro2746
  39. Ibrahim M, Anishetty S (2012) A meta-metabolome network of carbohydrate metabolism: Interactions between gut microbiota and host. Biochem Biophys Res Commun 428: 278-284. doi: 10.1016/j.bbrc.2012.10.045
  40. Rodriguez-Diaz J, Rubio-del-Campo A, Yebra MJ (2012) Lactobacillus casei ferments the N-acetylglucosamine moiety of fucosyl-α-1, 3-N-acetylglucosamine and excretes l-fucose. Appl Environ Microbiol. 78: 4613-4619. doi: 10.1128/AEM.00474-12
  41. Ravcheev DA, Thiele I (2017) Comparative genomic analysis of the human gut microbiome reveals a broad distribution of metabolic pathways for the degradation of host-synthetized mucin glycans and utilization of mucin-derived monosaccharides. Front Genet 8: 111. doi: 10.3389/fgene.2017.00111.
  42. Rizzatti G, Lopetuso LR, Gibiino G, Binda C, Gasbarrini A (2017) Proteobacteria: A common factor in human diseases. Biomed Res Int 2017: 9351507. doi: 10.1155/2017/9351507
  43. Hibbing ME, Fuqua C, Parsek MR, Peterson SB (2010) Bacterial competition: Surviving and thriving in the microbial jungle. Nat Rev Microbiol. 8: 15-25. doi: 10.1038/nrmicro2259
  44. Louis P, Flint HJ (2017) Formation of propionate and butyrate by the human colonic microbiota. Environ Microbiol 19: 29-41. doi: 10.1111/1462-2920.13589
  45. Brody LP, Sahuri-Arisoylu M, Parkinson JR, Parkes HG, So PW, Hajji N, Thomas EL, Frost GS, Miller AD, Bell JD (2017) Cationic lipid-based nanoparticles mediate functional delivery of acetate to tumor cells in vivo leading to significant anticancer effects. Int J Nanomedicine 12: 6677-6685. doi: 10.2147/IJN.S135968
  46. Hague A, Elder DJ, Hicks DJ, Paraskeva C (1995) Apoptosis in colorectal tumour cells: induction by the short chain fatty acids butyrate, propionate and acetate and by the bile salt deoxycholate. Int J Cancer 60: 400-406. doi: 10.1002/ijc.2910600322
  47. Jan G, Belzacq A, Haouzi D, Rouault A, Metivier D, Kroemer G, Brenner C (2002) Propionibacteria induce apoptosis of colorectal carcinoma cells via short-chain fatty acids acting on mitochondria. Cell Death Differ 9: 179-188. doi: 10.1038/sj.cdd.4400935
  48. Bindels LB, Porporato P, Dewulf E, Verrax J, Neyrinck AM, Martin J, Scott K, Calderon PB, Feron O, Muccioli G (2012) Gut microbiotaderived propionate reduces cancer cell proliferation in the liver. Br J Cancer 107: 1337-1344. doi: 10.1038/bjc.2012.409
  49. Bunesova V, Lacroix C, Schwab C (2018) Mucin cross-feeding of infant Bifidobacteria and Eubacterium hallii. Microb Ecol 75: 228-238. doi: 10.1007/s00248-017-1037-4
  50. Mabwi HA, Hitayezu E, Mauliasari IR, Mwaikono KS, Yoon HS, Komba EVG, Pan C-H, Cha KH (2021) Simulation of the mucosal environment in the re-construction of the synthetic gut microbial ecosystem. J Microbiol Methods 191: 106351. doi: 10.1016/j.mimet.2021.106351
  51. Derrien M, Vaughan EE, Plugge CM, de Vos WM (2004) Akkermansia muciniphila gen. nov., sp. nov., a human intestinal mucin-degrading bacterium. Int J Syst Evol Microbiol. 54: 1469-1476. doi: 10.1099/ijs.0.02873-0
  52. den Besten G, van Eunen K, Groen AK, Venema K, Reijngoud DJ, Bakker BM (2013) The role of short-chain fatty acids in the interplay between diet, gut microbiota, and host energy metabolism. J Lipid Res 54: 2325-2340. doi : 10.1194/jlr.R036012.