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, 1388 (1), 42-58

Genomic and Functional Techniques to Mine the Microbiome for Novel Antimicrobials and Antimicrobial Resistance Genes


Genomic and Functional Techniques to Mine the Microbiome for Novel Antimicrobials and Antimicrobial Resistance Genes

Boahemaa Adu-Oppong et al. Ann N Y Acad Sci.


Microbial communities contain diverse bacteria that play important roles in every environment. Advances in sequencing and computational methodologies over the past decades have illuminated the phylogenetic and functional diversity of microbial communities from diverse habitats. Among the activities encoded in microbiomes are the abilities to synthesize and resist small molecules, yielding antimicrobial activity. These functions are of particular interest when viewed in light of the public health emergency posed by the increase in clinical antimicrobial resistance and the dwindling antimicrobial discovery and approval pipeline, and given the intimate ecological and evolutionary relationship between antimicrobial biosynthesis and resistance. Here, we review genomic and functional methods that have been developed for accessing the antimicrobial biosynthesis and resistance capacity of microbiomes and highlight outstanding examples of their applications.

Keywords: antimicrobial resistance; antimicrobials; metagenomics; microbiome.

Conflict of interest statement

The authors declare no conflicts of interest.


Figure 1
Figure 1
The introduction of an antimicrobial to the clinic (green) is rapidly followed by the first observation of resistance to that antimicrobial (red).,
Figure 2
Figure 2
An overview of function- and sequence-based methods for the discovery of antimicrobials and antimicrobial resistance from microbiomes. DNA is isolated from source material (center), which can then be mined for antimicrobial resistance genes (left) or antimicrobial biosynthetic pathways (right). Functional metagenomic methods (top) typically entail shotgun cloning metagenomic DNA into an expression vector and selecting for a desired phenotype (e.g., antimicrobial resistance or antimicrobial activity). Sequence-based methods (bottom) customarily involve sequencing metagenomic DNA and annotating sequences using general or function-specific databases.

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