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Frontiers of Environmental Science & Engineering

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     
This article is part of themed collection: Environmental Antibiotics and Antibiotic Resistance (Xin Yu, Hui Li & Virender K. Sharma)
Corresponding Authors: 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.
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http://journal.hep.com.cn/fese/EN/10.1007/s11783-019-1121-8
http://journal.hep.com.cn/fese/EN/Y2019/V13/I3/40
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Monika Nowrotek
Łukasz Jałowiecki
Monika Harnisz
Grażyna Anna Płaza
Fig.1  The  history of culturomics approach in clinical microbiology and possible its applications in environmental microbiology (adopted from Lagier et al. (2018)).
Features Metagenomics Culturomics
Definition Method allowing the description of microbial composition by high-throughput sequencing Method allowing the description of the microbial composition by high-throughput culture
Methodology Pyrosequencing of 16S rRNA amplicons Use of various selective and/or enrichment culture conditions coupled to MALDI-TOF MS identification
Limitations Does not provide a strain for further studies.
Not complete population (depth bias)a.
Only detects eubacteria.
Does not provide information on enzymatic abilities and specific metabolitesb.
Detects “non-cultivable” microbes
Misses so-called “non-cultivable” microbes.
Does not directly provide information on enzymatic abilities.
Major workload
Advantages Detects “non-cultivable” microbes Detect not complete populations.
Open approach.
Detects only viable bacteriac
Rate of success Approximately 200 bacterial species/sampled Approximately 100 bacterial species/sampled
Possible future development Increased deph of sequencing because of new technology. Coupling pyroseqencing with direct metagenomics Automated detection of microbial growthe.
Automated identificationf. Miniaturization.
Other innovative culture conditions
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).
Time Milestones
1676 Leeuwenhoek, his observations on oral microbiota
1888 Koch R., isolation of microbes on solid media
1931 Winogradsky, microbial ecology experiments
1953 J.D. Watson and F. Crick published “a radically different structure” for DNA
1977 Sanger et al. develop DNA sequencing; rRNA was proposed by Woese C. as marker for taxonomy
1980 Mullis K. develops PCR
1986 Pace et al. perform cloning DNA directly from the environmental samples
1990 Giovannoni et al. perform the first microbial community study by 16S rRNA libraries
1991 Schimdt et al. generate metagenomic library from marine plankton
1995 Healy et al. construct metagenomic libraries from a gene of interest-related environment to mining cellulases
1996 Stein et al. Describ genomic sequence bearing a 16S rRNA gene of an uncultured archaeon
1998 Handelsman et al. introduce the term “metagenomics”
2004 Sequencing of the sargasso sea by Venter et al.
2005 First next-generation sequencing machine released by Roche
2006 GA sequencer from Solexa is released
2008 Human microbiome project publication
2010 MetaHIT consortium releases the human gut microbial gene catalog
2011 PacBio RS sequencer is released
2016 MetaSUB consortium is created
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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