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Background  Most lactobacilli found in animal intestines are generally non-motile, but there are few exceptions. Our previous work showed that  Lactobacillus agilis  BKN88, which is a highly motile strain originating from a chicken, takes advantage of motility in gut colonization in murine models, and thus motile lactobacilli likely have unique ecological characteristics conferred by motility. However, the ecology and habitat of gut-derived motile lactobacilli are still rarely understood. In addition, the limited availability of motile  Lactobacillus  isolates is one of the major obstacles for further studies. To gain insight into the ecology and habitat of the motile lactobacilli, we established a routinely applicable detection method for motile lactobacilli using PCR and subsequent selective isolation in semi-solid MRS medium for the collection of additional motile lactobacilli from animal feces.    Results  We applied the PCR detection using motile lactobacilli-specific primers, based on the motor switch protein gene ( fliG ) of flagella, to 120 animal feces, followed by selective isolation performed using 45 animal feces. As a result, motile lactobacilli were detected in 44 animal feces. In the selective isolation, 29 isolates of  L. agilis  and 2 isolates of  L. ruminis  were obtained from 8 animal species.    Conclusions  These results indicated that motile lactobacilli are distributed in different animal species. Moreover, phylogenetic analysis of the  L. agilis  isolates suggests co-evolution with the host, and adaptation to a particular environmental niche.

PCR-based screening, isolation, and partial characterization of motile lactobacilli from various animal feces