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In order to select halophilic microorganisms as a source of compounds with cytotoxic activities, a total of 135 bacterial strains were isolated from water and sediment samples collected from the Zipaquirá salt mine in the Colombian Andes. We determined the cytotoxic effects of 100 crude extracts from 54 selected organisms on the adherent murine mammary cell carcinoma 4T1 and human mammary adenocarcinoma MCF-7 cell lines. These extracts were obtained from strains of  Isoptericola, Ornithinimicrobium, Janibacter, Nesterenkonia, Alkalibacterium, Bacillus, Halomonas, Chromohalobacter, Shewanella, Salipiger, Martellela, Oceanibaculum, Caenispirillum  and  Labrenzia . The extracts of 23 strains showed an IC 50  of less than 100 μg mL −1 . They were subsequently analyzed by LC/MS allowing dereplication of 20 compounds. The cytotoxic effect was related to a complex mixture of diketopiperazines present in many of the extracts analyzed. The greatest cytotoxic activity against both of the evaluated cell lines was obtained from the chloroform extract of  Labrenzia aggregata  USBA 371 which had an IC 50  < 6 μg mL −1 . Other extracts with high levels of cytotoxic activity were obtained from  Bacillus  sp. (IC 50  < 50 μg mL −1 ) which contained several compounds such as macrolactin L and A, 7- O -succinoylmacrolactin F and iturin.  Shewanella chilikensis  USBA 344 also showed high levels of cytotoxic activity against both cell lines in the crude extract: an IC 50  < 15 μg mL −1  against the 4T1 cell line and an IC 50  < 68 μg mL −1  against the MCF-7 cell line.  Nesterenkonia sandarakina  CG 35, which has an IC 50  of 118 µg mL −1  against 4T1, is a producer of diketopiperazines and 1-acetyl-β-carboline. Also,  Ornithinimicrobium kibberense  CG 24, which has IC 50  < 50 μg mL −1 , was a producer of diketopiperazines and lagunamycin. Our study demonstrates that these saline environments are habitats of halophilic and halotolerant bacteria that have previously unreported cytotoxic activity.   Electronic supplementary material  The online version of this article (10.1186/s13568-017-0527-6) contains supplementary material, which is available to authorized users.

Microbial diversity of saline environments: searching for cytotoxic activities