Deciphering chloramphenicol biotransformation mechanisms and microbial interactions via integrated multi-omics and cultivation-dependent approaches

Abstract

Background As a widely used broad-spectrum antibiotic, chloramphenicol is prone to be released into environments, thus resulting in the disturbance of ecosystem stability as well as the emergence of antibiotic resistance genes. Microbes play a vital role in the decomposition of chloramphenicol in the environment, and the biotransformation processes are especially dependent on synergistic interactions and metabolite exchanges among microbes. Herein, the comprehensive chloramphenicol biotransformation pathway, key metabolic enzymes, and interspecies interactions in an activated sludge-enriched consortium were elucidated using integrated multi-omics and cultivation-based approaches. Results The initial biotransformation steps were the oxidization at the C1-OH and C3-OH groups, the isomerization at C2, and the acetylation at C3-OH of chloramphenicol. Among them, the isomerization is an entirely new biotransformation pathway of chloramphenicol discovered for the first time. Furthermore, we identified a novel glucose-methanol-choline oxidoreductase responsible for the oxidization of the C3-OH group in Sphingomonas sp. and Caballeronia sp. Moreover, the subsequent biotransformation steps, corresponding catalyzing enzymes, and the microbial players responsible for each step were deciphered. Synergistic interactions between Sphingomonas sp. and Caballeronia sp. or Cupriavidus sp. significantly promoted chloramphenicol mineralization, and the substrate exchange interaction network occurred actively among key microbes. Conclusion This study provides desirable strain and enzyme resources for enhanced bioremediation of chloramphenicol-contaminated hotspot sites such as pharmaceutical wastewater and livestock and poultry wastewater. The in-depth understanding of the chloramphenicol biotransformation mechanisms and microbial interactions will not only guide the bioremediation of organic pollutants but also provide valuable knowledge for environmental microbiology and biotechnological exploitation.

Establishment of microbial model communities capable of removing trace organic chemicals for biotransformation mechanisms research

“…They can be mutant-based communities, the multispecies synthetic communities and the (semi-) natural communities as Bengtsson-Palme [ 14 ] suggested. Compared with those reported model communities [ 47 – 49 ], our workflow (Fig. 1 ) has the strong advantages of, firstly, high-throughput cultivation under highly controlled and well-understood conditions which allows large numbers of varying diversity communities providing a more reliable reflection of natural microbial ecosystems.…”

“…To our best knowledge, this is the first study that investigated a wide range of TOrC biotransformation based on different model communities derived from varying natural microbial systems. Although there have been previous attempts addressing TOrC biotransformation mechanisms [ 18 , 49 ], they have limitations that either the systems themselves are too complex (e.g., soil and sludge) to characterize the key players and microbial functions, or too simplified (e.g., isolates degrading specific compound) to be applicable under environment conditions. Our method with reduced richness model communities serves as a compromise, which scales down the complex microbial interactions but their diverse combinations are still reflective of the actual environmental communities.…”

A panoramic view of the virosphere in three wastewater treatment plants by integrating viral‐like particle‐concentrated and traditional non‐concentrated metagenomic approaches

“…MAGs were recovered from NC metagenomes through a strategy established in our previous study [ 58 , 59 ]. As outlined in Figure 1 , the raw Illumina reads were filtered by fastp (v0.23.2) [ 60 ].…”

Profiling trace organic chemical biotransformation genes, enzymes and associated bacteria in microbial model communities

“…Biotransformation is considered as the primary removal process for most TOrCs in wastewater treatment plants, which is mainly attributed to oxidative reactions and ammonia oxidizing bacteria 11,12 . There have been many studies focusing on pure cultures or synthetic microbial consortium that attempted to decipher the metabolic mechanisms including biotransformation byproducts and pathways, key metabolic enzymes, and interspecies interactions 13,14,15 . Nevertheless, our current knowledge about biotransformation at the level of gene/enzyme-chemical interactions is still limited especially for refractory TOrCs.…”