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Background  A restricted set of aerobic bacteria dominated by the  Acinetobacter  genus was identified in murine intestinal colonic crypts. The vicinity of such bacteria with intestinal stem cells could indicate that they protect the crypt against cytotoxic and genotoxic signals. Genome analyses of these bacteria were performed to better appreciate their biodegradative capacities.    Results  Two taxonomically different clusters of  Acinetobacter  were isolated from murine proximal colonic crypts, one was identified as  A. modestus  and the other as  A. radioresistens . Their identification was performed through biochemical parameters and housekeeping gene sequencing. After selection of one strain of each cluster ( A. modestus  CM11G and  A. radioresistens  CM38.2), comparative genomic analysis was performed on whole-genome sequencing data. The antibiotic resistance pattern of these two strains is different, in line with the many genes involved in resistance to heavy metals identified in both genomes. Moreover whereas the operon  benABCDE  involved in benzoate metabolism is encoded by the two genomes, the operon  antABC  encoding the anthranilate dioxygenase, and the phenol hydroxylase gene cluster are absent in the  A. modestus  genomic sequence, indicating that the two strains have different capacities to metabolize xenobiotics. A common feature of the two strains is the presence of a type IV pili system, and the presence of genes encoding proteins pertaining to secretion systems such as Type I and Type II secretion systems.    Conclusions  Our comparative genomic analysis revealed that different  Acinetobacter  isolated from the same biological niche, even if they share a large majority of genes, possess unique features that could play a specific role in the protection of the intestinal crypt.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-017-3925-x) contains supplementary material, which is available to authorized users.

Comparative genomic analysis of Acinetobacter strains isolated from murine colonic crypts