Human Gut Metagenomics: Success and Limits of the Activity-Based Approaches

  • Alexandra S. Tauzin
  • Elisabeth Laville
  • Davide Cecchini
  • Hervé M. Blottière
  • Marion Leclerc
  • Joël Doré
  • Gabrielle Potocki-Veronese
Chapter
First Online:

Abstract

The symbiotic relationship between the host and its gut microbiota has evolved to benefit both parties, especially by maintaining the host health and providing nutrients to the microbiota. Until recently, the study of this complex relationship was limited to culture-based studies. For this purpose, functional metagenomics has proved to be a powerful technique for exploring the diversity of the microbiota, discovering new functions and signaling pathways and extending our knowledge in the cross talk between the host and its gut microbiota. By assigning functions to proteins without any a priori knowledge of their sequences, the activity-based metagenomic approach allows to rationalize the sequencing efforts, to boost enzyme discovery, and to obtain knowledge on their mode of action, from the molecular to the ecosystem scales. This review offers an overview of the recent results obtained by activity-based metagenomic approach on the exploration of the human gut microbiota and gives insights on future developments and promising discoveries in the field.

This is a preview of subscription content, log in to check access.

References

  1. Abrahamsson TR, Jakobsson HE, Andersson AF et al (2014) Low gut microbiota diversity in early infancy precedes asthma at school age. Clin Exp Allergy 44:842–850. doi: 10.1111/cea.12253 CrossRefPubMedGoogle Scholar
  2. Anderson KL, Salyers AA (1989a) Genetic evidence that outer membrane binding of starch is required for starch utilization by Bacteroides thetaiotaomicron. J Bacteriol 171:3199–3204CrossRefPubMedPubMedCentralGoogle Scholar
  3. Anderson KL, Salyers AA (1989b) Biochemical evidence that starch breakdown by Bacteroides thetaiotaomicron involves outer membrane starch-binding sites and periplasmic starch-degrading enzymes. J Bacteriol 171:3192–3198CrossRefPubMedPubMedCentralGoogle Scholar
  4. Cecchini DA, Laville E, Laguerre S et al (2013) Functional metagenomics reveals novel pathways of prebiotic breakdown by human gut bacteria. PLoS One 8:e72766. doi: 10.1371/journal.pone.0072766 CrossRefPubMedPubMedCentralGoogle Scholar
  5. Cheng G, Hu Y, Yin Y et al (2012) Functional screening of antibiotic resistance genes from human gut microbiota reveals a novel gene fusion. FEMS Microbiol Lett 336:11–16. doi: 10.1111/j.1574-6968.2012.02647.x CrossRefPubMedGoogle Scholar
  6. Cohen LJ, Kang H-S, Chu J et al (2015) Functional metagenomic discovery of bacterial effectors in the human microbiome and isolation of commendamide, a GPCR G2A/132 agonist. Proc Natl Acad Sci 112:E4825–E4834. doi: 10.1073/pnas.1508737112 CrossRefPubMedPubMedCentralGoogle Scholar
  7. Crost EH, Tailford LE, Le Gall G et al (2013) Utilisation of mucin glycans by the human gut symbiont Ruminococcus gnavus is strain-dependent. PLoS One 8:e76341. doi: 10.1371/journal.pone.0076341 CrossRefPubMedPubMedCentralGoogle Scholar
  8. Culligan EP, Marchesi JR, Hill C, Sleator RD (2014a) Combined metagenomic and phenomic approaches identify a novel salt tolerance gene from the human gut microbiome. Front Microbiol 5:189. doi: 10.3389/fmicb.2014.00189 CrossRefPubMedPubMedCentralGoogle Scholar
  9. Culligan EP, Sleator RD, Marchesi JR, Hill C (2012) Functional metagenomics reveals novel salt tolerance loci from the human gut microbiome. ISME J 6:1916–1925. doi: 10.1038/ismej.2012.38 CrossRefPubMedPubMedCentralGoogle Scholar
  10. Culligan EP, Sleator RD, Marchesi JR, Hill C (2014b) Metagenomic identification of a novel salt tolerance gene from the human gut microbiome which encodes a membrane protein with homology to a brp/blh-family β-carotene 15,15′-monooxygenase. PLoS One 9:e103318. doi: 10.1371/journal.pone.0103318 CrossRefPubMedPubMedCentralGoogle Scholar
  11. Culligan EP, Sleator RD, Marchesi JR, Hill C (2013) Functional environmental screening of a metagenomic library identifies stlA; a unique salt tolerance locus from the human gut microbiome. PLoS One 8:e82985. doi: 10.1371/journal.pone.0082985 CrossRefPubMedPubMedCentralGoogle Scholar
  12. Cuskin F, Lowe E, Temple M, Zhu Y (2015) Human gut Bacteroidetes can utilize yeast mannan through a selfish mechanism. Nature 517(7533):165–169. doi: 10.1038/nature13995 CrossRefPubMedPubMedCentralGoogle Scholar
  13. D’Costa VM, McGrann KM, Hughes DW, Wright GD (2006) Sampling the antibiotic resistome. Science 311:374–377. doi: 10.1126/science.1120800 CrossRefPubMedGoogle Scholar
  14. Dague E, Le DTL, Zanna S et al (2010) Probing in vitro interactions between Lactococcus lactis and mucins using AFM. Langmuir 26:11010–11017. doi: 10.1021/la101862n CrossRefPubMedGoogle Scholar
  15. David LA, Maurice CF, Carmody RN et al (2014) Diet rapidly and reproducibly alters the human gut microbiome. Nature 505:559–563. doi: 10.1038/nature12820 CrossRefPubMedGoogle Scholar
  16. Davidson AL, Dassa E, Orelle C, Chen J (2008) Structure, function, and evolution of bacterial ATP-binding cassette systems. Microbiol Mol Biol Rev 72:317–364. doi: 10.1128/MMBR.00031-07 CrossRefPubMedPubMedCentralGoogle Scholar
  17. de Wouters T, Ledue F, Nepelska M et al (2014) A robust and adaptable high throughput screening method to study host-microbiota interactions in the human intestine. PLoS One 9:e105598. doi: 10.1371/journal.pone.0105598 CrossRefPubMedPubMedCentralGoogle Scholar
  18. 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 CrossRefPubMedGoogle Scholar
  19. Dobrijevic D, Di Liberto G, Tanaka K et al (2013) High-throughput system for the presentation of secreted and surface-exposed proteins from Gram-positive bacteria in functional metagenomics studies. PLoS One 8:e65956. doi: 10.1371/journal.pone.0065956 CrossRefPubMedPubMedCentralGoogle Scholar
  20. El Kaoutari A, Armougom F, Gordon JI et al (2013) The abundance and variety of carbohydrate-active enzymes in the human gut microbiota. Nat Rev Microbiol 11:497–504. doi: 10.1038/nrmicro3050 CrossRefPubMedGoogle Scholar
  21. Ferrer M, Beloqui A, Vieites JM et al (2009) Interplay of metagenomics and in vitro compartmentalization. Microb Biotechnol 2:31–39. doi: 10.1111/j.1751-7915.2008.00057.x CrossRefPubMedGoogle Scholar
  22. Findley SD, Mormile MR, Sommer-Hurley A et al (2011) Activity-based metagenomic screening and biochemical characterization of bovine ruminal protozoan glycoside hydrolases. Appl Environ Microbiol 77:8106–8113. doi: 10.1128/AEM.05925-11 CrossRefPubMedPubMedCentralGoogle Scholar
  23. Foerstner KU, Doerks T, Creevey CJ et al (2008) A computational screen for type I polyketide synthases in metagenomics shotgun data. PLoS One 3:e3515. doi: 10.1371/journal.pone.0003515 CrossRefPubMedPubMedCentralGoogle Scholar
  24. Forsberg KJ, Reyes A, Wang B et al (2012) The shared antibiotic resistome of soil bacteria and human pathogens. Science 337:1107–1111. doi: 10.1126/science.1220761 CrossRefPubMedPubMedCentralGoogle Scholar
  25. Forslund K, Sunagawa S, Kultima JR et al (2013) Country-specific antibiotic use practices impact the human gut resistome. Genome Res 23:1163–1169. doi: 10.1101/gr.155465.113 CrossRefPubMedPubMedCentralGoogle Scholar
  26. Frank D, Amand A (2007) Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc Natl Acad Sci 104:13780–13785. doi: 10.1073/pnas.0706625104 CrossRefPubMedPubMedCentralGoogle Scholar
  27. Gibson MK, Forsberg KJ, Dantas G (2015) Improved annotation of antibiotic resistance determinants reveals microbial resistomes cluster by ecology. ISME J 9:207–216. doi: 10.1038/ismej.2014.106 CrossRefPubMedGoogle Scholar
  28. Gildersleeve JC, Wang B, Achilefu S et al (2012) Glycan array analysis of the antigen repertoire targeted by tumor-binding antibodies. Bioorg Med Chem Lett 22:6839–6843. doi: 10.1016/j.bmcl.2012.09.055 CrossRefPubMedPubMedCentralGoogle Scholar
  29. Gill SR, Pop M, Deboy RT et al (2006) Metagenomic analysis of the human distal gut microbiome. Science 312:1355–1359. doi: 10.1126/science.1124234 CrossRefPubMedPubMedCentralGoogle Scholar
  30. Gloux K, Berteau O, El Oumami H et al (2011) A metagenomic β-glucuronidase uncovers a core adaptive function of the human intestinal microbiome. Proc Natl Acad Sci U S A 108:4539–4546. doi: 10.1073/pnas.1000066107 CrossRefPubMedGoogle Scholar
  31. Gloux K, Leclerc M, Iliozer H et al (2007) Development of high-throughput phenotyping of metagenomic clones from the human gut microbiome for modulation of eukaryotic cell growth. Appl Environ Microbiol 73:3734–3737. doi: 10.1128/AEM.02204-06 CrossRefPubMedPubMedCentralGoogle Scholar
  32. Gueimonde M, Salminen S, Isolauri E (2006) Presence of specific antibiotic (tet) resistance genes in infant faecal microbiota. FEMS Immunol Med Microbiol 48:21–25. doi: 10.1111/j.1574-695X.2006.00112.x CrossRefPubMedGoogle Scholar
  33. Handelsman J (2004) Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev 68:669–685. doi: 10.1128/MMBR.68.4.669-685.2004 CrossRefPubMedPubMedCentralGoogle Scholar
  34. Hehemann J-H, Correc G, Barbeyron T et al (2010) Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota. Nature 464:908–912. doi: 10.1038/nature08937 CrossRefPubMedGoogle Scholar
  35. Högberg LD, Heddini A, Cars O (2010) The global need for effective antibiotics: challenges and recent advances. Trends Pharmacol Sci 31:509–515. doi: 10.1016/j.tips.2010.08.002 CrossRefPubMedGoogle Scholar
  36. Hu Y, Yang X, Qin J et al (2013) Metagenome-wide analysis of antibiotic resistance genes in a large cohort of human gut microbiota. Nat Commun 4:2151. doi: 10.1038/ncomms3151 PubMedGoogle Scholar
  37. Jones BV (2010) The human gut mobile metagenome: a metazoan perspective. Gut Microbes 1:415–431. doi: 10.4161/gmic.1.6.14087 CrossRefPubMedPubMedCentralGoogle Scholar
  38. Jones BV, Begley M, Hill C et al (2008) Functional and comparative metagenomic analysis of bile salt hydrolase activity in the human gut microbiome. Proc Natl Acad Sci U S A 105(36):13580–13585. doi: 10.1073/pnas.0804437105 CrossRefPubMedPubMedCentralGoogle Scholar
  39. Karlsson FH, Tremaroli V, Nookaew I et al (2013) Gut metagenome in European women with normal, impaired and diabetic glucose control. Nature 498:99–103. doi: 10.1038/nature12198 CrossRefPubMedGoogle Scholar
  40. Kazimierczak KA, Rincon MT, Patterson AJ et al (2008) A new tetracycline efflux gene, tet(40), is located in tandem with tet(O/32/O) in a human gut firmicute bacterium and in metagenomic library clones. Antimicrob Agents Chemother 52:4001–4009. doi: 10.1128/AAC.00308-08 CrossRefPubMedPubMedCentralGoogle Scholar
  41. Ladevèze S, Cioci G, Roblin P et al (2015) Structural bases for N-glycan processing by mannoside phosphorylase. Acta Crystallogr D Biol Crystallogr 71:1335–1346. doi: 10.1107/S1399004715006604 CrossRefPubMedPubMedCentralGoogle Scholar
  42. Ladevèze S, Tarquis L, Cecchini DA et al (2013) Role of glycoside phosphorylases in mannose foraging by human gut bacteria. J Biol Chem 288:32370–32383. doi: 10.1074/jbc.M113.483628 CrossRefPubMedPubMedCentralGoogle Scholar
  43. Lakhdari O, Cultrone A, Tap J et al (2010) Functional metagenomics: a high throughput screening method to decipher microbiota-driven NF-κB modulation in the human gut. PLoS One 5:1–10. doi: 10.1371/journal.pone.0013092 CrossRefGoogle Scholar
  44. Larsbrink J, Rogers TE, Hemsworth GR et al (2014) A discrete genetic locus confers xyloglucan metabolism in select human gut Bacteroidetes. Nature 506:498–502. doi: 10.1038/nature12907 CrossRefPubMedPubMedCentralGoogle Scholar
  45. Le Chatelier E, Nielsen T, Qin J et al (2013) Richness of human gut microbiome correlates with metabolic markers. Nature 500:541–546. doi: 10.1038/nature12506 CrossRefPubMedGoogle Scholar
  46. Li J, Jia H, Cai X et al (2014) An integrated catalog of reference genes in the human gut microbiome. Nat Biotechnol 32:834–841. doi: 10.1038/nbt.2942 CrossRefPubMedGoogle Scholar
  47. Moore AM, Patel S, Forsberg KJ et al (2013) Pediatric fecal microbiota harbor diverse and novel antibiotic resistance genes. PLoS One 8:e78822. doi: 10.1371/journal.pone.0078822 CrossRefPubMedPubMedCentralGoogle Scholar
  48. Ouwerkerk JP, de Vos WM, Belzer C (2013) Glycobiome: bacteria and mucus at the epithelial interface. Best Pract Res Clin Gastroenterol 27:25–38. doi: 10.1016/j.bpg.2013.03.001 CrossRefPubMedGoogle Scholar
  49. Park AJ, Collins J, Blennerhassett PA et al (2013) Altered colonic function and microbiota profile in a mouse model of chronic depression. Neurogastroenterol Motil 25:733–e575. doi: 10.1111/nmo.12153 CrossRefPubMedPubMedCentralGoogle Scholar
  50. Qin J, Li R, Raes J et al (2010) A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464:59–65. doi: 10.1038/nature08821 CrossRefPubMedPubMedCentralGoogle Scholar
  51. Rampelli S, Schnorr SL, Consolandi C et al (2015) Metagenome sequencing of the Hadza hunter-gatherer gut microbiota. Curr Biol 25(13):1682–1693. doi: 10.1016/j.cub.2015.04.055 CrossRefPubMedGoogle Scholar
  52. Roberfroid M (2007) Prebiotics: the concept revisited. J Nutr 137:830S–837SPubMedGoogle Scholar
  53. Sommer MOA, Dantas G, Church GM (2009) Functional characterization of the antibiotic resistance reservoir in the human microflora. Science 325:1128–1131. doi: 10.1126/science.1176950 CrossRefPubMedPubMedCentralGoogle Scholar
  54. Steele HL, Jaeger K-E, Daniel R, Streit WR (2009) Advances in recovery of novel biocatalysts from metagenomes. J Mol Microbiol Biotechnol 16:25–37. doi: 10.1159/000142892 CrossRefPubMedGoogle Scholar
  55. Tasse L, Bercovici J, Pizzut-Serin S et al (2010) Functional metagenomics to mine the human gut microbiome for dietary fiber catabolic enzymes. Genome Res 20:1605–1612. doi: 10.1101/gr.108332.110 CrossRefPubMedPubMedCentralGoogle Scholar
  56. Thomas F, Hehemann J-H, Rebuffet E et al (2011) Environmental and gut bacteroidetes: the food connection. Front Microbiol 2:93. doi: 10.3389/fmicb.2011.00093 CrossRefPubMedPubMedCentralGoogle Scholar
  57. Turnbaugh PJ, Bäckhed F, Fulton L, Gordon JI (2008) Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome. Cell Host Microbe 3:213–223. doi: 10.1016/j.chom.2008.02.015 CrossRefPubMedPubMedCentralGoogle Scholar
  58. Turnbaugh PJ, Quince C, Faith JJ et al (2010) Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins. Proc Natl Acad Sci U S A 107:7503–7508. doi: 10.1073/pnas.1002355107 CrossRefPubMedPubMedCentralGoogle Scholar
  59. Turnbaugh PJ, Ridaura VK, Faith JJ et al (2009) The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice. Sci Transl Med 1:6ra14. doi: 10.1126/scitranslmed.3000322 CrossRefPubMedPubMedCentralGoogle Scholar
  60. Ufarté L, Potocki-Veronese G, Laville É (2015) Discovery of new protein families and functions: new challenges in functional metagenomics for biotechnologies and microbial ecology. Front Microbiol 6:563. doi: 10.3389/fmicb.2015.00563 PubMedPubMedCentralGoogle Scholar
  61. Van den Abbeele P, Grootaert C, Possemiers S et al (2009) In vitro model to study the modulation of the mucin-adhered bacterial community. Appl Microbiol Biotechnol 83:349–359. doi: 10.1007/s00253-009-1947-2 CrossRefPubMedGoogle Scholar
  62. Wang Y, Antonopoulos DA, Zhu X et al (2010) Laser capture microdissection and metagenomic analysis of intact mucosa-associated microbial communities of human colon. Appl Microbiol Biotechnol 88:1333–1342. doi: 10.1007/s00253-010-2921-8 CrossRefPubMedGoogle Scholar
  63. Wilkens S (2015) Structure and mechanism of ABC transporters. F1000Prime Rep 7:14. doi: 10.12703/P7-14 CrossRefPubMedPubMedCentralGoogle Scholar
  64. Wu GD, Chen J, Hoffmann C et al (2011) Linking long-term dietary patterns with gut microbial enterotypes. Science 334:105–108. doi: 10.1126/science.1208344 CrossRefPubMedPubMedCentralGoogle Scholar
  65. Yoon MY, Lee KM, Yoon Y et al (2013) Functional screening of a metagenomic library reveals operons responsible for enhanced intestinal colonization by gut commensal microbes. Appl Environ Microbiol 79(12):3829–3838. doi: 10.1128/AEM.00581-13 CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer International Publishing AG 2017

Authors and Affiliations

  • Alexandra S. Tauzin
    • 1
  • Elisabeth Laville
    • 1
  • Davide Cecchini
    • 1
  • Hervé M. Blottière
    • 2
    • 3
  • Marion Leclerc
    • 2
  • Joël Doré
    • 2
    • 3
  • Gabrielle Potocki-Veronese
    • 1
  1. 1.LISBP, Université de Toulouse, CNRS, INRA, INSAToulouseFrance
  2. 2.Micalis Institute, INRA, AgroParisTech, Université Paris-SaclayJouy-en-JosasFrance
  3. 3.MGP MetaGenoPolis, INRA, Univsersité Paris-SaclayJouy en JosasFrance

Personalised recommendations