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Background  The environmental gliding bacteria  Lysobacter  are emerging as a new group of biocontrol agents due to their prolific production of lytic enzymes and potent antibiotic natural products. These bacteria are intrinsically resistant to many antibiotics, but the mechanisms behind the antibiotic resistance have not been investigated.    Results  Previously, we have used chloramphenicol acetyltransferase gene ( cat ) as a selection marker in genetic manipulation of natural product biosynthetic genes in  Lysobacter , because chloramphenicol is one of the two common antibiotics that  Lysobacter  are susceptible to. Here, we found  L. enzymogenes , the most studied species of this genus, could still grow in the presence of a low concentration of chloramphenicol. Three chloramphenicol derivatives ( 1 – 3 ) with an unusual acylation pattern were identified in a  cat -containing mutant of  L. enzymogenes  and in the wild type. The compounds included chloramphenicol 3'-isobutyrate ( 1 ), a new compound chloramphenicol 1'-isobutyrate ( 2 ), and a rare chloramphenicol 3'-isovalerate ( 3 ). Furthermore, a mutation of a global regulator gene ( clp ) or a Gcn5-related  N -acetyltransferase (GNAT) gene in  L. enzymogenes  led to nearly no growth in media containing chloramphenicol, whereas a complementation of  clp  restored the chloramphenicol acylation as well as antibiotic HSAF production in the  clp  mutant.    Conclusions  The results indicated that  L. enzymogenes  contains a pool of unusual acyl donors for enzymatic modification of chloramphenicol that confers the resistance, which may involve the Clp-GNAT regulatory system. Because  Lysobacter  are ubiquitous inhabitants of soil and water, the finding may have important implications in understanding microbial competitions and bioactive natural product regulation.    Electronic supplementary material  The online version of this article (doi:10.1186/s12896-017-0377-y) contains supplementary material, which is available to authorized users.

Unusual acylation of chloramphenicol in Lysobacter enzymogenes, a biocontrol agent with intrinsic resistance to multiple antibiotics