The gene coding for the flageliw protein of Roseburia cecicola, an oxygen-intolerant, gram-negative, anaerobic bacterium indigenous to the murine cecum, has been cloned and sequenced. NH2-terminal amino acid sequence data from the flagellin protein were used as a basis for the synthesis of two mixed-sequence deoxyoligonucleotides. The oligonucleotides were used to identify and clone the flagellin structural gene. DNA sequence analysis of M13mp8 and mp9 subclones revealed a protein with a length of 293 amino acids and a molecular weight of 31,370. Comparisons with the sequences of flagellins of other species revealed conserved regions and suggested that although R. cecicola has structural characteristics of a gram-negative bacterium, it may be most closely related to the gram-positive bacteria.Motility and chemotaxis may be ecologically important for many species of microorganisms colonizing specific habitats on mammalian cell surfaces (2, 19). In the oxygen-free environment of the murine gastrointestinal tract, especially in the cecum and colon, many species of bacteria are motile (6,17,23). Motility for some of these organisms is a propitious and possibly essential trait (25).One such bacterium is Roseburia cecicola, a motile, anaerobic, gram-negative rod in the Bacteroidaceae family that was originally isolated from cecal scrapings from a conventional laboratory mouse (24). This. organism has an unusual flagellar arrangement composed of a fascicle of 20 to 35 flagella anchored in the polar to subpolar region at one end of the cell (24). Even though motility is a metabolically expensive trait, it is essential for this strict anaerobe to be able to colonize the cecum and colon in animals with a competing indigenous microflora (25). We are using R. cecicola as a model organism to investigate the influence of motility and chemotaxis on the ability of motile bacteria to colonize the gastrointestinal tract.Despite considerable information on the flagellins of facultative anaerobes, little is known about these proteins in the many motile anaerobic species colonizing habitats in gastrointestinal ecosystems. In this report we describe the use of families of synthetic oligonucleotides to clone the R. cecicola flagellin structural gene.