This study aimed to isolate and characterize treponemes present in the bovine gastrointestinal (GI) tract and compare them with bovine digital dermatitis (BDD) treponemes. Seven spirochete isolates were obtained from the bovine GI tract, which, on the basis of 16S rRNA gene comparisons, clustered within the genus Treponema as four novel phylotypes. One phylotype was isolated from several different GI tract regions, including the omasum, colon, rumen, and rectum. These four phylotypes could be divided into two phylotype pairs that clustered closest with each other and then with different, previously reported rumen treponemes. The treponemes displayed great genotypic and phenotypic diversity between phylotypes and differed considerably from named treponeme species and those recently reported by metagenomic studies of the bovine GI tract. Phylogenetic inference, based on comparisons of 16S rRNA sequences from only bovine treponemes, suggested a marked divergence between two important groups. The dendrogram formed two major clusters, with one cluster containing GI tract treponemes and the other containing BDD treponemes. This division among the bovine treponemes is likely the result of adaptation to different niches. To further differentiate the bovine GI and BDD strains, we designed a degenerate PCR for a gene encoding a putative virulence factor, tlyC, which gave a positive reaction only for treponemes from the BDD cluster.Treponema species are typically anaerobic, fastidious, highly motile, spiral microorganisms and may be found in the oral cavity, digestive tract, and genital areas of humans, animals, and insects (20, 32). Several treponeme taxa are associated with disease, such as the human syphilis infectious agent Treponema pallidum (30), various Treponema species associated with human periodontal infections (10), and several treponeme phylotypes involved in bovine digital dermatitis (BDD) (4). In contrast, several treponemes have been reported to be commensal, living as symbionts in the gastrointestinal (GI) tracts of animals and insects. The spirochetes Treponema bryantii and Treponema saccharophilum have been isolated from the rumen of cows (26,36), and another three novel treponeme taxa have been isolated from GI material of pigs (6, 23). In insects, Treponema azotonutricium and Treponema primitia were isolated from the guts of termites (15).The relative paucity of data regarding treponemes and their locations in animal tissues is primarily the result of difficulties associated with their isolation, cultivation, and purification. More frequently, molecular techniques such as 16S rRNA gene clone libraries have been used to identify treponemes within animal samples but without subsequent culture. While no targeted studies of bovine GI tract treponeme 16S rRNA genes have been reported, several global bacterial studies showed that there are several phylotypes of treponemes in the bovine GI tract (11,29,38,44). Although only two bovine GI tract treponemes have been proposed as novel taxa (26, 36), considerable...