Culturomics and metagenomics: In understanding of environmental resistome

Abstract

Pharmaceutical residues, mainly antibiotics, have been called “emerging contaminants” in the environment because of their increasing frequency of detection in aquatic and terrestrial systems and their sublethal ecological effects. Most of them are undiscovered. Both human and veterinary pharmaceuticals, including antibiotics, are introduced into the environment via many different routes, including discharges from municipal wastewater treatment plants and land application of animal manure and biosolids to fertilize croplands. To gain a comprehensive understanding of the widespread problem of antibiotic resistance, modern and scientific approaches have been developed to gain knowledge of the entire antibiotic-resistant microbiota of various ecosystems, which is called the resistome. In this review, two omics methods, i.e. culturomics, a new approach, and metagenomics, used to study antibiotic resistance in environmental samples, are described. Moreover, we discuss how both omics methods have become core scientific tools to characterize microbiomes or resistomes, study natural communities and discover new microbes and new antibiotic resistance genes from environments. The combination of the method for get better outcome of both culturomics and metagenomics will significantly advance our understanding of the role of microbes and their specific properties in the environment.

References

  1. Abdallah R A, Beye M, Diop A, Bakour S, Raoult D, Fournier P E (2017). The impact of culturomics on taxonomy in clinical microbiology. Antonie van Leeuwenhoek, 110(10): 1327–1337

    Article  Google Scholar 

  2. Akiyama T, Savin M C (2010). Populations of antibiotic-resistant coliform bacteria change rapidly in a wastewater effluent dominated stream. The Science of the total environment, 408(24): 6192–6201

    CAS  Article  Google Scholar 

  3. Allan E (2014). Metagenomics: unrestricted access to microbial communities. Virulence, 5(3): 397–398

    Article  Google Scholar 

  4. Alves L F, Westmann C A, Lovate G L, de Siqueira G M V, Borelli T C, Guazzaroni M E (2018). Metagenomic approaches for understanding new concepts in microbial science. International Journal of Genomics, 2018: 1

    Article  CAS  Google Scholar 

  5. Amos G C A, Zhang L, Hawkey P M, Gaze W H, Wellington E M (2014). Functional metagenomic analysis reveals rivers are a reservoir for diverse antibiotic resistance genes. Veterinary Microbiology, 171(3–4): 441–447

    CAS  Article  Google Scholar 

  6. Amrane S, Lagier J C (2018). Metagenomic and clinical microbiology. Human Microbiome Journal, 9(1): 1–6

    Article  Google Scholar 

  7. Anjum M F (2015). Screening methods for the detection of antimicrobial resistance genes present in bacterial isolates and the microbiota. Future Microbiology, 10(3): 317–320

    CAS  Article  Google Scholar 

  8. Bilen M, Dufour J C, Lagier J C, Cadoret F, Daoud Z, Dubourg G, Raoult D (2018). The contribution of culturomics to the repertoire of isolated human bacterial and archaeal species. Microbiome, 6(1): 94

    Article  Google Scholar 

  9. Chen B, Yang Y, Liang X, Yu K, Zhang T, Li X (2013). Metagenomic profiles of antibiotic resistance genes (ARGs) between human impacted estuary and deep ocean sediments. Environmental Science & Technology, 47(22): 12753–12760

    CAS  Article  Google Scholar 

  10. Chistoserdova L (2010). Functional metagenomics: recent advances and future challenges. Biotechnology & Genetic Engineering Reviews, 26(1): 335–352

    CAS  Article  Google Scholar 

  11. Christgen B, Yang Y, Ahammad S Z, Li B, Rodriquez D C, Zhang T, Graham D W (2015). Metagenomics shows that low-energy anaerobic-aerobic treatment reactors reduce antibiotic resistance gene levels from domestic wastewater. Environmental Science & Technology, 49(4): 2577–2584

    CAS  Article  Google Scholar 

  12. Chu B T T, Petrovich M L, Chaudhary A, Wright D, Murphy B, Wells G, Poretsky R (2018). Metagenomics reveals the impact of wastewater treatment plants on the dispersal of microorganisms and genes in aquatic sediments. Applied and Environmental Microbiology, 84(5): e02168–e17

    Google Scholar 

  13. Crofts T S, Gasparrini A J, Dantas G (2017). Next-generation approaches to understand and combat the antibiotic resistome. Nature Reviews. Microbiology, 15(7): 422–434

    CAS  Google Scholar 

  14. Davies J, Davies D (2010). Origins and evolution ofantibiotic resistance. Microbiology Molecular Reports, 74(3): 417–433

    CAS  Article  Google Scholar 

  15. Di Bella J M, Bao Y, Gloor G B, Burton J P, Reid G (2013). High throughput sequencing methods and analysis for microbiome research. Journal of Microbiological Methods, 95(3): 401–414

    CAS  Article  Google Scholar 

  16. Elbehery A H A, Aziz R K, Siam R (2016). Antibiotic resistome: Improving detection and quantification accuracy for comparative metagenomics. OMICS: A Journal of Integrative Biology, 20(4): 229–238

    CAS  Article  Google Scholar 

  17. Escobar-Zepeda A, Vera-Ponce de Leon A, Sanchez-Flores A (2015). The road to metagenomics: From microbiology to DNA sequencing technologies and bioinformatics. Froniers in Genetics, 6: 348

    Google Scholar 

  18. Fitzpatrick D, Walsh F (2016). Antibiotic resistance genes across a wide variety of metagenomes. FEMS Microbiology Ecology, 92(2): 11–21

    Article  CAS  Google Scholar 

  19. Gatica J, Tripathi V, Green S, Manaia C M, Berendonk T, Cacace D, Merlin C, Kreuzinger N, Schwartz T, Fatta-Kassinos D, Rizzo L, Schwermer C U, Garelick H, Jurkevitch E, Cytryn E (2016). High throughput analysis of integrin gene cassettes in wastewater environments. Environmental Science & Technology, 50(21): 11825–11836

    CAS  Article  Google Scholar 

  20. Greub G (2012). Culturomics: A new approach to study the human microbiome. Clinical Microbiology and Infection, 18(12): 1157–1159

    CAS  Article  Google Scholar 

  21. Guo J, Li J, Chen H, Bond P L, Yuan Z (2017). Metagenomic analysis reveals wastewater treatment plants as hotspots of antibiotic resistance genes and mobile genetic elements. Water Research, 123(3): 468–478

    CAS  Article  Google Scholar 

  22. Gupta S K, Shin H, Han D, Hur H G, Unno T (2018). Metagenomic analysis reveals the prevalence and persistence of antibiotic- and heavy metal-resistance genes in wastewater treatment plant. Journal of Microbiology (Seoul, Korea), 56(6): 408–415

    CAS  Google Scholar 

  23. Hamad I, Ranque S, Azhar E I, Yasir M, Jiman-Fatani A A, Tissot-Dupont H, Raoult D, Bittar F, Bittar F (2017). Culturomics and Amplicon-based Metagenomic Approaches for the Study of Fungal Population in Human Gut Microbiota. Scientific Reports, 7(1): 16788

    Article  CAS  Google Scholar 

  24. Handelsman J, Rondon M R, Brady S F, Clardy J, Goodman R M (1998). Molecular biological access to the chemistry of unknown soil microbes: A new frontier for natural products. Chemistry & Biology, 5(10): R245–R249

    CAS  Article  Google Scholar 

  25. Hu Q, Zhang X X, Jia S, Huang K, Tang J, Shi P, Ye L, Ren H (2016). Metagenomic insights into ultraviolet disinfection effects on antibiotic resistome in biologically treated wastewater. Water Research, 101(3): 309–317

    CAS  Article  Google Scholar 

  26. Hugon P, Dufour J C, Colson P, Fournier P E, Sallah K, Raoult D (2015). A comprehensive repertoire of prokaryotic species identified in human beings. The Lancet. Infectious Diseases, 15(10): 1211–1219

    Google Scholar 

  27. Jackson R W, Vinatzer B, Arnold D L, Dorus S, Murillo J (2011). The influence of the accessory genome on bacterial pathogen evolution. Mobile Genetic Elements, 1(1): 55–65

    Article  Google Scholar 

  28. Jalowiecki L, Chojniak J, Dorgeloh E, Hegedusova B, Ejhed H, Magnér J, Plaza G (2017). Using phenotype microarrays in the assessment of the antibiotic susceptibility profile of bacteria isolated from waste-water in on-site treatment facilities. Folia Microbiologica, 62(6): 453–461

    CAS  Article  Google Scholar 

  29. Kambouris M E, Pavlidis C, Skoufas E, Arabatzis M, Kantzanou M, Velegraki A, Patrinos G P (2018). Culturomics: A new kid on the block of OMICS to enable personalized medicine. OMICS: A Journal of Integrative Biology, 22(2), 234–245

    Article  CAS  Google Scholar 

  30. Khelaifia S, Lagier J Ch, Bibi F, Azhar E I, Croce O, Padmanabhan R, Jiman-Fatani A A, Yasir M, Robert C, Andrieu C, Fournier P E, Raoult D (2016). Microbial culturomics to map halophilic bacterium in human gut: genome sequence and description of Oceanobacillus jeddahense sp. nov. Journal of Integrative Biolology, 20(4): 248–258

    CAS  Google Scholar 

  31. Lagier J C, Armougom F, Million M, Hugon P, Pagnier I, Robert C, Bittar F, Fournous G, Gimenez G, Maraninchi M, Trape J F, Koonin E V, La Scola B, Raoult D (2012). Microbial culturomics: paradigm shift in the human gut microbiome study. Clinical Microbiology and Infection, 18(12): 1185–1193

    CAS  Article  Google Scholar 

  32. Lagier J C, Dubourg G, Million M, Cadoret F, Bilen M, Fenollar F, Levasseur A, Rolain J M, Fournier P E, Raoult D (2018). Culturing the human microbiota and culturomics. Nature Reviews. Microbiology, 16(9): 540–550

    CAS  Google Scholar 

  33. Lagier J C, Hugon P, Khelaifia S, Fournier P E, La Scola B, Raoult D (2015). The rebirth of culture in microbiology through the example of culturomics to study human gut microbiota. Clinical Microbiology Reviews, 28(1): 237–264

    CAS  Article  Google Scholar 

  34. Lagier J C, Khelaifia S, Alou M T, Ndongo S, Dione N, Hugon P, Caputo A, Cadoret F, Traore S I, Seck E H, Dubourg G, Durand G, Mourembou G, Guilhot E, Togo A, Bellali S, Bachar D, Cassir N, Bittar F, Delerce J, Mailhe M, Ricaboni D, Bilen M, Dangui Nieko N P, Dia Badiane N M, Valles C, Mouelhi D, Diop K, Million M, Musso D, Abrahão J, Azhar E I, Bibi F, Yasir M, Diallo A, Sokhna C, Djossou F, Vitton V, Robert C, Rolain J M, La Scola B, Fournier P E, Levasseur A, Raoult D (2016). Culture of previously uncultured members of the human gut microbiota by culturomics. Nature Microbiology, 1(2): 16203

    CAS  Article  Google Scholar 

  35. Lam K N, Cheng J, Engel K, Neufeld J D, Charles T C (2015). Current and future resources for functional metagenomics. Frontiers in Microbiology, 6: article1196

    Article  Google Scholar 

  36. Lanza V F, Baquero F, Martínez J L, Ramos-Ruíz R, González-Zorn B, Andremont A, Sánchez-Valenzuela A, Ehrlich S D, Kennedy S, Ruppé E, van Schaik W, Willems R J, de la Cruz F, Coque T M (2018). In-depth resistome analysis by targeted metagenomics. Microbiome, 6(1): 11

    Article  Google Scholar 

  37. Lee J, Jeon J H, Shin J, Jang H M, Kim S, Song M S, Kim Y M (2017). Quantitative and qualitative changes in antibiotic resistance genes after passing through treatment processes in municipal wastewater treatment plants. Science of the Total Environment, 605–606: 906–914

    Article  CAS  Google Scholar 

  38. Lefkowitz J R, Duran M (2009). Changes in antibiotic resistance patterns of Escherichia coli during domestic wastewater treatment. Water Environment Research, 81(9): 878–885

    CAS  Article  Google Scholar 

  39. Luby E, Ibekwe A M, Zilles J, Pruden A (2016). Molecular methods for assessment of antibiotic resistance in agricultural ecosystems: prospects and challenges. Journal of Environmental Quality, 45(2): 441–453

    CAS  Article  Google Scholar 

  40. Ma Y, Metch JW, Yang Y, Pruden A, Zhang T (2016). Shift in antibiotic resistance gene profiles associated with nanosilver during wastewater treatment. FEMS Microbiology Ecology, 92(3): pii: fiw022

    Article  CAS  Google Scholar 

  41. March-Rosselló G A (2017). Rapid methods for detection of bacterial resistance to antibiotics. Enfermedades Infecciosas y Microbiologia Clinica, 35(3): 182–188

    Article  Google Scholar 

  42. Martínez J L, Coque T M, Lanza V F, de la Cruz F, Baquero F (2017). Genomic and metagenomic technologies to explore the antibiotic resistance mobilome. Annals of the New York Academy of Sciences, 1388(1): 26–41

    Article  CAS  Google Scholar 

  43. Masucci L, Quaranta G, Nagel D, Primus S, Romano L, Graffeo R, Ianiro G, Gasbarrini A, Cammarota G, Sanguinetti M (2017). Culturomics: Bacterial species isolated in 3 healthy donors for faecal microbiota transplantation in Clostridium difficile infection. Microbiologia Medica, 32: 6510

    Article  Google Scholar 

  44. McLain J E, Cytryn E, Durso L M, Young S (2016). Culture-based methods for detection of antibiotic resistance in agroecosystems: Advantages, challenges, and gaps in knowledge. Journal of Environmental Quality, 45(2): 432–440

    CAS  Article  Google Scholar 

  45. Miller R R, Montoya V, Gardy J L, Patrick D M, Tang P (2013). Metagenomics for pathogen detection in public health. Genome Medicine, 5(9): No article: 81

    Article  CAS  Google Scholar 

  46. Mohammadali M, Davies J (2018). Antimicrobial resistance genes and wastewater treatment. In: Keen P L, Fugère R, eds. Antimicrobial Resistance in Wastewater Treatment Processes. 1st ed. Hoboken: John Wiley & Sons, Inc., 1–14

    Google Scholar 

  47. Monier J M, Demanèche S, Delmont T O, Mathieu A, Vogel T M, Simonet P (2011). Metagenomic exploration of antibiotic resistance in soil. Current Opinion in Microbiology, 14(3): 229–235

    CAS  Article  Google Scholar 

  48. Mullany P (2014). Functional metagenomics for the investigation of antibiotic resistance. Virulence, 5(3): 443–447

    Article  Google Scholar 

  49. Nagarajan M. (2018). Metagenomics. Perspectives, Methods, and Applications. 1st ed. London: Academic Press, Elsevier, 1–10

    Google Scholar 

  50. Pärnänen K, Karkman A, Tamminen M, Lyra C, Hultman J, Paulin L, Virta M (2016). Evaluating the mobility potential of antibiotic resistance genes in environmental resistomes without metagenomics. Scientific Reports, 6(1): 35790

    Article  CAS  Google Scholar 

  51. Perry J A, Westman E L, Wright G D (2014). The antibiotic resistome: What’s new? Current Opinion in Microbiology, 21: 45–50

    CAS  Article  Google Scholar 

  52. Płaza G, Turek A, Szczygłowska R (2013). Characterization of E. coli strains obtained from wastewater effluent. International Journal of Environmental of Research, 2(1): 67–74

    Google Scholar 

  53. Rizzo L, Manaia C, Merlin C, Schwartz T, Dagot C, Ploy M C, Michael I, Fatta-Kassinos D (2013). Urban wastewater treatment plants as hotspots for antibiotic resistant bacteria and genes spread into the environment: A review. The Science of the total environment, 447: 345–360

    CAS  Article  Google Scholar 

  54. Rosso G E, Muday J A, Curran J F (2018). Tools for Metagenomic Analysis at Wastewater Treatment Plants: Application to a Foaming Episode. Water environment research: A research publication of the Water Environment Federation, 90(3): 258–268

    CAS  Article  Google Scholar 

  55. Schmidt T M, DeLong E F, Pace N R (1991). Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing. Journal of Bacteriology, 173(14): 4371–4378

    CAS  Article  Google Scholar 

  56. Schmieder R, Edwards R (2012). Insights into antibiotic resistance through metagenomic approaches. Future Microbiology, 7(1): 73–89

    CAS  Article  Google Scholar 

  57. Seck E H, Diop A, Armstrong N, Delerce J, Fournier P E, Raoult D, Khelaifia S (2018). Microbial culturomics to isolate halophilic bacteria from table salt: genome sequence and description of the moderately halophilic bacterium Bacillus salis sp. nov. New Microbes and New Infections, 23(1): 28–38

    CAS  Article  Google Scholar 

  58. Tang J, Bu Y, Zhang X X, Huang K, He X, Ye L, Shan Z, Ren H (2016). Metagenomic analysis of bacterial community composition and antibiotic resistance genes in a wastewater treatment plant and its receiving surface water. Ecotoxicology and Environmental Safety, 132(2): 260–269

    CAS  Article  Google Scholar 

  59. Venter J C, Remington K, Heidelberg J F, Halpern A L, Rusch D, Eisen J A, Wu D, Paulsen I, Nelson K E, Nelson W, Fouts D E, Levy S, Knap A H, Lomas M W, Nealson K, White O, Peterson J, Hoffman J, Parsons R, Baden-Tillson H, Pfannkoch C, Rogers Y H, Smith H O (2004). Environmental genome shotgun sequencing of the Sargasso Sea. Science, 304(5667): 66–74

    CAS  Article  Google Scholar 

  60. Wang Z, Zhang X X, Huang K, Miao Y, Shi P, Liu B, Long C, Li A (2013). Metagenomic profiling of antibiotic resistance genes and mobile genetic elements in a tannery wastewater treatment plant. PLoS One, 8(10): e76079

    CAS  Article  Google Scholar 

  61. Xiao K Q, Li B, Ma L, Bao P, Xue Zhou X, Zhang T, Zhu Y G (2016). Metagenomic profiles of antibiotic resistance genes in paddy soils from South China. FEMS Microbiology Ecology, 92: fiw023

    Article  CAS  Google Scholar 

  62. Yang Y, Li B, Ju F, Zhang T (2013). Exploring variation of antibiotic resistance genes in activated sludge over a four-year period through a metagenomic approach. Environmental Science & Technology, 47(18): 10197–10205

    CAS  Article  Google Scholar 

Download references

Acknowledgements

This paper was prepared in connection with the work done under the project No. 2017/26/M/NZ9/00071 funded by the National Science Center (Poland).

Author information

Affiliations

Authors

Corresponding author

Correspondence to Grażyna Anna Płaza.

Additional information

Highlights

• State of the art of culturomics and metagenomics to study resistome was presented.

• The combination of culturomics and metagenomics approaches was proposed.

• The research directions of antibiotic resistance study has been suggested.

Rights and permissions

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit https://doi.org/creativecommons.org/licenses/by/4.0/.

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Nowrotek, M., Jałowiecki, Ł., Harnisz, M. et al. Culturomics and metagenomics: In understanding of environmental resistome. Front. Environ. Sci. Eng. 13, 40 (2019). https://doi.org/10.1007/s11783-019-1121-8

Download citation

Keywords

  • Culturomics
  • Metagenomics
  • Antibiotic resistance
  • Resistome