Lignocellulose digestion by wood-feeding termites depends on the mutualistic interaction of unusual, flagellate protists located in their hindgut. Most of the flagellates harbor numerous prokaryotic endosymbionts of so-far-unknown identity and function. Using a full-cycle molecular approach, we show here that the endosymbionts of the larger gut flagellates of Reticulitermes santonensis belong to the so-called termite group 1 (TG-1) bacteria, a group of clones previously obtained exclusively from gut homogenates of Reticulitermes speratus that are only distantly related to other bacteria and are considered a novel bacterial phylum based on their 16S rRNA gene sequences. Fluorescence in situ hybridization with specifically designed oligonucleotide probes confirmed that TG-1 bacteria are indeed located within the flagellate cells and demonstrated that Trichonympha agilis (Hypermastigida) and Pyrsonympha vertens (Oxymonadida) harbor phylogenetically distinct populations of symbionts (<95% sequence similarity). Transmission electron microscopy revealed that the symbionts are small, spindle-shaped cells (0.6 m in length and 0.3 m in diameter) surrounded by two membranes and located within the cytoplasm of their hosts. The symbionts of the two flagellates are described as candidate species in the candidate genus "Endomicrobium." Moreover, we provide evidence that the members of the TG-1 phylum, for which we propose the candidate name "Endomicrobia," are phylogenetically extremely diverse and are present in and also restricted to the guts of all lower termites and wood-feeding cockroaches of the genus Cryptocercus, the only insects that are in an exclusive, obligately mutualistic association with such unique cellulose-fermenting protists.Digestive symbioses are most common among insects feeding on wood or other lignified plant materials. The most prominent example is that of wood-feeding termites (order Isoptera), where the symbiotic digestion of lignocellulose is a complex series of events involving both the host and its gut microbiota. While the events in foregut and midgut are due mainly to host activities, the digestive processes in the hindgut are largely controlled by the symbiotic gut microbiota (5, 7).In the evolutionarily lower termites, the bulk of the hindgut volume is occupied by unicellular eukaryotes which belong to several flagellate taxa that are unique to termites (14, 37). These oxygen-sensitive protozoa, which can make up more than one-third of the body weight of their host, are essential for wood digestion and represent the major source of cellulolytic and xylanolytic activities in the hindgut (14, 16).The gut flagellates are regularly colonized by prokaryotic epibionts attached to the surface and by endosymbionts located in the cytoplasm or in the nucleus (see, e.g., references 1, 8, and 18). Although up to 85% of the total prokaryotes in the termite gut are associated with the gut flagellates (2), only a few of the epibiotic bacteria have been identified by using molecular techniques (23,35,36). Wh...