Downloaded from www.microbiologyresearch.org by IP: 54.70.40.11 On: Sat, 09 Mar 2019 02:36:32 Lactobacillus rodentium sp. nov., from the digestive tract of wild rodents J. Killer, 1,2 J. Havlı ´k, 2 E. Vlkova ´, 2 V. Rada, 2 R. Pechar, 2 O. Benada, 3,4 J. Kopec ˇny ´, 1 O. Kofron ˇ ova ´ 3 and H. Sechovcova ´ 1 Correspondence J. Killer Killer.Jiri@seznam.cz or killer@ iapg.cas.cz 1 Institute of Animal Physiology and Genetics v.v.i., Academy of Sciences of the Czech Republic, Vı ´den ˇ ska ´ 1083, Prague 4 – Krc ˇ 142 20, Czech Republic 2 Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Department of Microbiology, Nutrition and Dietetics, Kamy ´cka ´ 129, Prague 6 – Suchdol 165 21, Czech Republic 3 Laboratory of Molecular Structure Characterization, Institute of Microbiology, Institute of Microbiology, v.v.i., Academy of Sciences of the Czech Republic, Vı ´den ˇ ska ´ 1083, Prague 4 – Krc ˇ 142 20, Czech Republic 4 Department of Biology, Faculty of Science, J. E. Purkyne ˇ University in Ustı ´ nad Labem, Za Va ´ lcovnou 1000/8, 400 96 U ´ stı ´ nad Labem, Czech Republic Three strains of regular, long, Gram-stain-positive bacterial rods were isolated using TPY, M.R.S. and Rogosa agar under anaerobic conditions from the digestive tract of wild mice (Mus musculus). All 16S rRNA gene sequences of these isolates were most similar to sequences of Lactobacillus gasseri ATCC 33323 T and Lactobacillus johnsonii ATCC 33200 T (97.3 % and 97.2 % sequence similarities, respectively). The novel strains shared 99.2–99.6 % 16S rRNA gene sequence similarities. Type strains of L. gasseri and L. johnsonii were also most related to the newly isolated strains according to rpoA (83.9–84.0 % similarities), pheS (84.6–87.8 %), atpA (86.2–87.7 %), hsp60 (89.4–90.4 %) and tuf (92.7–93.6 %) gene sequence similarities. Phylogenetic studies based on 16S rRNA, hsp60, rpoA, atpA and pheS gene sequences, other genotypic and many phenotypic characteristics (results of API 50 CHL, Rapid ID 32A and API ZYM biochemical tests; cellular fatty acid profiles; cellular polar lipid profiles; end products of glucose fermentation) showed that these bacterial strains represent a novel species within the genus Lactobacillus. The name Lactobacillus rodentium sp. nov. is proposed to accommodate this group of new isolates. The type strain is MYMRS/TLU1 T (5DSM 24759 T 5CCM 7945 T ). Representatives of the genus Lactobacillus are phylogeneti- cally classified into the bacterial phylum Firmicutes, class Bacilli, order Lactobacillales and family Lactobacillaceae. Various species of lactobacilli have been isolated from different environments rich in complex organic substrates. They are found on plant surfaces, and in plant-origin fermented products, milk, dairy and meat products, fish and marinated fish, oral cavities of mammals, urogenital tracts of mammals and gastrointestinal tract of vertebrates and insects (Hammes & Hertel, 2009; Forsgren et al., 2010). More than 90 different species of the genus Lactobacillus have been described (Hammes & Hertel, 2009). However, the List of Prokaryotic names with Standing in Nomencla- ture (available at http://www.bacterio.net/lactobacillus.html) includes one hundred and seventy species and subspecies of the genus Lactobacillus at the time of writing. Many bacterial species that were assigned to the genus Lactobacillus have recently been reclassified into new genera within the family Lactobacillaceae (Mora et al., 2003; Endo & Okada, 2008; Salvetti et al., 2011). Lactobacilli are generally considered as safe, non-pathogenic bacteria. In addition, many species of lactobacilli are used as probiotics in human and veterinary Abbreviations: ITS, intergenic transcribed spacer; MLST, multilocus sequence typing. The GenBank/EMBL/DDBJ accession numbers for the partial 16S rRNA gene sequences of strains MYMRS/TLU1 T , MYTPY/TEN3 and MYMRS/TEN2 are HQ851022, HQ851020 and HQ851021, respect- ively. The accession numbers for the partial hsp60, pheS, rpoA and atpA gene sequences of strains MYMRS/TLU1 T , MYTPY/TEN3 and MYMRS/TEN2 are JQ363678, JQ363679 and KF841362; JQ363687, JQ363688 and KF841360; JQ363696, KF841355 and KF841356; and JQ363703, KF841367 and KF841368, respectively. The accession numbers for the partial Tuf gene sequences of strains MYMRS/TLU1 T and MYTPY/TEN3 are JQ363713 and JQ363714, respectively. The accession number for the partial ITS of strain MYMRS/ TLU1 T is JQ363710. Six supplementary figures and one supplementary table are available with the online version of this paper. International Journal of Systematic and Evolutionary Microbiology (2014), 64, 1526–1533 DOI 10.1099/ijs.0.054924-0 1526 054924 G 2014 IUMS Printed in Great Britain