A bias in the codon utilization pattern of members of the ciliate family Ophryoscolecidae is described. A pattern of preferential use of AGA to encode arginine, and a bias against the occurrence of G in position three of codons for lysine, glutamine and glutamic acid, are described. Evidence is provided primarily for species of the Ophryoscolecidae family which are found in the rumen, but the general principle extends to a species found in non-rumen environments. Within those species found in the rumen, it appears to have the potential for use as a discriminatory tool for the identification of sequences against a background of possible contamination. The origin of such sequence contamination may be the host organism, plant material eaten by the host, and fungal material present in the host. Comparisons with other organisms possessing a similarly low GC content suggests that much of this codon bias is not solely attributable to the low GC content, but that a more complex phenomenon, such as strand bias, is in operation. (C) 2000 Academic Press.