Microbial colonization of marine invertebrate guts is widespread, but in general the roles that these bacteria play in the nutrition of their hosts are unknown. To examine the diversity and potential nutritional roles of hindgut microbiota in a deposit feeder, PCR-amplified 16S rRNA genes were cloned from the bacterial community attached to the hindguts of the thalassinid shrimp Neotrypaea californiensis exposed to different feeding treatments. Partial 16S rDNA sequences were analyzed for 30 clones for three shrimp per treatment for a total of 270 clones. No effects of host starvation or high-protein diets were apparent on hindgut bacterial community composition. Diversity analyses indicated high variability between bacterial communities in individual shrimp hindguts, but partial 16S rDNA sequences revealed remarkable species-level similarity (>98%) within clusters of sequences from the different shrimp hindguts, and many sequences from different shrimp hindguts were identical. Sequences belonged to three main groups of bacteria: Cytophaga-Flavobacteria-Bacteroides (CFB), proteobacteria, and gram-positives. Of the 270 sequences, 40% belonged to the alpha-proteobacteria, > or = 5% each to the gamma- and epsilon -proteobacteria, and > or =20% each to the gram-positive and CFB groups. All except one sequence are novel with < or = 95% sequence similarity to known genes. Despite weak similarity to known taxa,about 75% of the sequences were most closely related to known symbiotic and sedimentary bacteria. The bacteria in shrimp hindguts represent new species that have not yet been en-countered in other environments, and gut environments may be a rich source of the difficult-to-culture and novel components of marine bacterial diversity.