Metabolomics and Microbial Metabolism: Toward a Systematic Understanding

Over the past decades, our understanding of microbial metabolism has increased dramatically. Metabolomics, a family of techniques that are used to measure the quantities of small molecules in biological samples, has been central to these efforts. Advances in analytical chemistry have made it possible to measure the relative and absolute concentrations of more and more compounds with increasing levels of certainty. In this review, we highlight how metabolomics has contributed to understanding microbial metabolism and in what ways it can still be deployed to expand our systematic understanding of metabolism. To that end, we explain how metabolomics was used to (a) characterize network topologies of metabolism and its regulation networks, (b) elucidate the control of metabolic function, and (c) understand the molecular basis of higher-order phenomena. We also discuss areas of inquiry where technological advances should continue to increase the impact of metabolomics, as well as areas where our understanding is bottlenecked by other factors such as the availability of statistical and modeling frameworks that can extract biological meaning from metabolomics data.

MOB rules: Antibiotic Exposure Reprograms Metabolism to Mobilize Bacillus subtilis in Competitive Interactions

Antibiotics have dose-dependent effects on exposed bacteria. The medicinal use of antibiotics relies on their growth-inhibitory activities at sufficient concentrations. At subinhibitory concentrations, exposure effects vary widely among different antibiotics and bacteria. Bacillus subtilis responds to bacteriostatic translation inhibitors by mobilizing a population of cells (MOB-Mobilized Bacillus) to spread across a surface. How B. subtilis regulates the antibiotic-induced mobilization is not known. In this study, we used chloramphenicol to identify regulatory functions that B. subtilis requires to coordinate cell mobilization following subinhibitory exposure. We measured changes in gene expression and metabolism and mapped the results to a network of regulatory proteins that direct the mobile response. Our data reveal that several transcriptional regulators coordinately control the reprogramming of metabolism to support mobilization. The network regulates changes in glycolysis, nucleotide metabolism, and amino acid metabolism that are signature features of the mobilized population. Among the hundreds of genes with changing expression, we identified two, pdhA and pucA, where the magnitudes of their changes in expression, and in the abundance of associated metabolites, reveal hallmark metabolic features of the mobilized population. Using reporters of pdhA and pucA expression, we visualized the separation of major branches of metabolism in different regions of the mobilized population. Our results reveal a regulated response to chloramphenicol exposure that enables a population of bacteria in different metabolic states to mount a coordinated mobile response.

Tracking Uptake and Metabolism of Xenometallomycins Using a Multi-Isotope Tagging Strategy

Synthetic and naturally occurring siderophores and their conjugates provide access to the bacterial cytoplasm via active membrane transport. Previously, we displaced iron with the radioactive isotope ⁶⁷Ga to quantify and track in vitro and in vivo uptake and distribution of siderophore Trojan Horse antibiotic conjugates. Here, we introduce a multi-isotope tagging strategy to individually elucidate the fate of metal cargo and the ligand construct with radioisotopes ⁶⁷Ga and ¹²⁴I. We synthesized gallium(III) model complexes of a ciprofloxacin-functionalized linear desferrichrome (Ga-D6) and deferoxamine (Ga-D7) incorporating an iodo-tyrosine linker to enable radiolabeling using the metal-binding (⁶⁷Ga) and the cargo-conjugation site (¹²⁴I). Radiochemical experiments with Escherichia coli, Staphylococcus aureus, and Pseudomonas aeruginosa wt strains show that ⁶⁷Ga-D6/D7 and Ga-D6-¹²⁴I/D7-¹²⁴I have comparable uptake, indicating intact complex import and siderophore-mediated uptake. In naive mice, ⁶⁷Ga-D6/D7 and Ga-D6-¹²⁴I/D7-¹²⁴I demonstrate predominantly renal clearance; urine metabolite analysis indicates in vivo dissociation of Ga(III) is a likely mechanism of degradation for ⁶⁷Ga-D6/D7 when compared to ligand radiolabeled compounds, Ga-D6-¹²⁴I/D7-¹²⁴I, which remain >60% intact in urine. Cumulatively, this work demonstrates that a multi-isotope tagging strategy effectively elucidates the in vitro uptake, pharmacokinetics, and in vivo stability of xenometallomycins with modular chemical structures.

Understanding the fundamentals of microbial remediation with emphasize on metabolomics

The post-genomic tool metabolomics is a great advancement in science and technology which acquires novel strategies and pathways to analyze various biological compounds. Metabolomics aids in retrieving the qualitative and quantitative data from the various biological system. The current review is focused on the application of metabolomics in bioremediation and helps to focus on the xenobiotic compounds which are discharged into the environment and have long term impact. The microbial based biodegradation can be effectively used along with the combination of metabolomic approach for a better understanding of the breakdown of certain recalcitrant. Additionally, this review also discusses the candidate gene approach which helps to comprehend the functional analysis of microbial genes in response to different contaminants. Therefore, this review intends to discuss the metabolomics in bioremediation by studying the complete set of metabolites involved during the process of degradation and their interaction with the environment.