Culturomics and metagenomics: In understanding of environmental resistome

doi:10.1007/s11783-019-1121-8

Front. Environ. Sci. Eng.

2019, Vol. 13

Issue (3) : 40 https://doi.org/10.1007/s11783-019-1121-8

REVIEW ARTICLE

Culturomics and metagenomics: In understanding of environmental resistome

Monika Nowrotek¹, Łukasz Jałowiecki¹, Monika Harnisz², Grażyna Anna Płaza³(

)

¹. Microbiology Unit, Institute for Ecology of Industrial Areas, Kossutha 6 Str., 40-844 Katowice, Poland
². Department of Environmental Microbiology, Faculty of Environmental Sciences, University of Warmia and Mazury, Prawocheńskiego 1 Str., 10-720 Olsztyn, Poland
³. Silesian University of Technology, Faculty of Organization and Management, Institute of Engineering Production, Roosevelta 26 Str., 41-800 Zabrze, Poland

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Abstract

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.

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.

Keywords Culturomics Metagenomics Antibiotic resistance Resistome

Corresponding Author(s): Grażyna Anna Płaza

Issue Date: 11 June 2019

Cite this article:

Monika Nowrotek,Łukasz Jałowiecki,Monika Harnisz, et al. Culturomics and metagenomics: In understanding of environmental resistome[J]. Front. Environ. Sci. Eng., 2019, 13(3): 40.

URL:

https://academic.hep.com.cn/fese/EN/10.1007/s11783-019-1121-8
https://academic.hep.com.cn/fese/EN/Y2019/V13/I3/40

Fig.1 The history of culturomics approach in clinical microbiology and possible its applications in environmental microbiology (adopted from ^{Lagier et al. (2018)}).

Tab.1 Comparison between metagenomics and culturomics (according to ^{Greub (2012)})

Fig.2 The methodology of culturomics approach.

Fig.3 Number of articles published on culturomics in the past 4 years (Kambouris et al., 2017).

Tab.2 Timeline of the major stages in metagenomics research (modified from ^{Escobar-Zepeda et al. (2015)}; ^{Alves et al. (2018)})

Fig.4 Overview of metagenomic approaches used in antibiotic resistomes study (adopted from ^{Monier et al. (2011)}; Schmieder and Edwards (2012)).

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