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.

Bioprospecting of Novel Extremozymes From Prokaryotes—The Advent of Culture-Independent Methods

“…Historically, these methods have been used in microbiology, including selective or differential media, microscopy, Gram-staining, and biochemical tests. These methods are sensitive, reliable, inexpensive, and provide qualitative and quantitative results on the bacterial populations ( Nowrotek et al, 2019 ). However, only a small fraction of all microbes can be grown in a laboratory setting.…”

“…Based on this legacy, microbial culturomics has emerged as a tool that complements metagenomics data and gives another way to determine composition of microbial populations. Several studies have shown that culture-dependent and culture-independent methods often deliver different results ( Steven et al, 2007 ; Carraro et al, 2011 ; Stefani et al, 2015 ; Nowrotek et al, 2019 ; Rego et al, 2019 ). For example, using 212 different culture conditions, such as temperature, various oxygen levels, and selective media, many researchers have isolated 340 different bacterial species ( Lagier et al, 2012 ).…”

“…Interestingly, the metagenomics approach could identify only 51 species out of 340 cultured species in this study. Therefore, it is crucial to combine both culture-dependent and culture-independent ways to study a given microbiome ( Steven et al, 2007 ; Lagier et al, 2016 ; Nowrotek et al, 2019 ; Sarhan et al, 2019 ).…”

Exploring the Potential of Micrococcus luteus Culture Supernatant With Resuscitation-Promoting Factor for Enhancing the Culturability of Soil Bacteria

“…While novel culturing methods can be very diverse ( Pham and Kim, 2012 ; Overmann et al, 2017 ), several still rely on the use of the petri dish. Because of its versatility, the petri dish is still a central tool for the recent field of culturomics, the “extensive assessment of microbial composition by high-throughput culture” ( Greub, 2012 ; Nowrotek et al, 2019 ). Richard Petri’s development of a simple device for culturing bacteria has thus withstood the test of time and remains a protean tool for research, even in the genomic era.…”

Culture-Dependent and Amplicon Sequencing Approaches Reveal Diversity and Distribution of Black Fungi in Antarctic Cryptoendolithic Communities

“…Despite lower sensitivity, cultivation may allow detection of species that are overlooked with molecular tools and offers the opportunity to develop biological resources for functional and genetic studies. Moreover, the integration of cultivation and HTS has allowed a complete survey of microbial diversity, uncovering species that were previously neglected or unknown to science, when applied in samples from different extreme environments (e.g., [ 25 , 26 ]).…”