Research

The Crofts' microbiology lab studies the biochemical and genetic factors that underly interactions between emerging contaminants – such as antibiotics and pharmaceuticals – and organisms in microbial communities

These interactions impact human health and industry, encompassing antimicrobial resistance and antibiotic degradation as well as changes in the efficacy and toxicity of pharmaceuticals. We develop and use functional metagenomic assays to mine microbiomes for the determinants of these interactions. By studying these functions in isolation and in their native context it is possible to gain greater insight into their evolutionary origins and biochemical niche, as well as to access the great genetic diversity found in microbiomes.

Description

Soil and host-associated microbiomes are well-known reservoirs for antimicrobial resistance genes including genes that confer resistance to clinical antibiotics. While many of these genes are well characterized, the tremendous diversity of microbiomes means that many novel and clinically important resistance mechanisms remain to be identified. We have identified several novel variants of streptothricin resistance genes as well as a new mechanism of resistance to this class of antibiotic from the soil microbiome, novel tetracycline and colistin resistance genes in the gut microbiome of wild geese, and have characterized new examples of chloramphenicol reductase enzymes from human pathogens. Discovery and characterization of these mechanisms and their evolvution and regulation can teach us about the ecology of antibiotics in the environment and suggest ways to future-proof new antimicrobials.

We have also previously discovered and characterized a pathway in multiple soil bacteria to use penicillin as a sole carbon source. The pathway consists of β-lactamase inactivation of the antibiotic, amide hydrolysis of the product to release phenylacetic acid, and breakdown of phenylacetic acid into products that enter central metabolism. We are now investigating catabolism pathways for other antimicrobials besides penicillin. Discovery of enzymes and pathways involved in antibiotic catabolism could lead to new opportunities for semi-synthesis of novel compounds and new approaches to remediating antibiotic pollution in the environment.

Publications
Press
Description

The human microbiome, and especially the large intestinal microbial community, is an important actor in the efficacy/toxicity of many pharmaceuticals, but the vast majority of these interactions lack description at the enzymatic level. The Crofts lab is approaching this field by using a combination of next-generation sequencing and functional metagenomic techniques to identify and capture genes encoding enzymes with activity against pharmaceuticals. We are investigating the xenobiotic metabolism of nitro-pharmaceuticals by the human microbiome using the antibiotic chloramphenicol as a model compound. We have structurally and functionally characterized enzymes from host-associated bacteria that modify chloramphenicol at the nitro position and are looking to expand this research further. Other important lines of research into microbiome-pharmaceutical interactions are how microbiome-immune system interactions alter the efficacy of immunotherapeutics, and how early-life antibiotic therapy might also alter the developing infant microbiome.

Publications
Description

The Crofts lab is also involved in the development of high-throughput methods for studying microbiomes at the genetic and biochemical level. One powerful tool for this is functional metagenomic libraries which allow sequence-naïve and cultivation-independent gene discovery. Functional metagenomic libraries can be used to discover novel genes for antimicrobial resistance or pharmaceutical modification (among other functions) from microbiomes. We have invented and applied a new method for creating functional metagenomic libraries that consistently produces significantly larger libraries using a fraction of the quantity of input DNA needed by current methods. We are in the process of expanding and applying this method further. The ability to use less DNA more efficiently will allow functional metagenomic libraries to be prepared from rare and low biomass microbiomes that were previously out of reach of this method.

Publications