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Background  Only a small fraction of bacteria and archaea that are identifiable by metagenomics can be grown on standard media. Recent efforts on deep metagenomics sequencing, single-cell genomics and the use of specialized culture conditions (culturomics) increasingly yield novel microbes some of which represent previously uncharacterized phyla and possess unusual biological traits.    Results  We report isolation and genome analysis of  Babela massiliensis , an obligate intracellular parasite of  Acanthamoeba castellanii. B. massiliensis  shows an unusual, fission mode of cell multiplication whereby large, polymorphic bodies accumulate in the cytoplasm of infected amoeba and then split into mature bacterial cells. This unique mechanism of cell division is associated with a deep degradation of the cell division machinery and delayed expression of the  ftsZ  gene. The genome of  B. massiliensis  consists of a circular chromosome approximately 1.12 megabase in size that encodes, 981 predicted proteins, 38 tRNAs and one typical rRNA operon. Phylogenetic analysis shows that  B. massiliensis  belongs to the putative bacterial phylum TM6 that so far was represented by the draft genome of the JCVI TM6SC1 bacterium obtained by single cell genomics and numerous environmental sequences.    Conclusions  Currently,  B. massiliensis  is the only cultivated member of the putative TM6 phylum. Phylogenomic analysis shows diverse taxonomic affinities for  B. massiliensis  genes, suggestive of multiple gene acquisitions via horizontal transfer from other bacteria and eukaryotes. Horizontal gene transfer is likely to be facilitated by the cohabitation of diverse parasites and symbionts inside amoeba.  B. massiliensis  encompasses many genes encoding proteins implicated in parasite-host interaction including the greatest number of ankyrin repeats among sequenced bacteria and diverse proteins related to the ubiquitin system. Characterization of  B. massiliensis , a representative of a distinct bacterial phylum, thanks to its ability to grow in amoeba, reaffirms the critical role of diverse culture approaches in microbiology.    Reviewers  This article was reviewed by Dr. Igor Zhulin, Dr. Jeremy Selengut, and Pr Martijn Huynen.    Electronic supplementary material  The online version of this article (doi:10.1186/s13062-015-0043-z) contains supplementary material, which is available to authorized users.

Babela massiliensis, a representative of a widespread bacterial phylum with unusual adaptations to parasitism in amoebae