RESULTS:

In this study we isolated a novel strain of lactic acid bacteria AF129T from alfalfa silage prepared locally in Morioka Iwate Japan. Polyphasic taxonomy was used to characterize the bacterial strain. The bacterium was rod-shaped Gram-stain-positive non-spore-forming and catalase-negative. The strain grew at various temperatures (15–40°C) and pH levels (4.0–8.0). The optimum growth conditions were a temperature of 30°C and a pH of 6.0. AF129T exhibited growth at salt (NaCl) concentrations of up to 6.5 % (w/v). The G+C content of the strain’s genomic DNA was 41.5 %. The major fatty acids were C16 : 0 C18 : 1ω9c C19 : 0cyclo ω8c and summed feature 8. 16S rRNA gene sequencing revealed that AF129T represents a member of the genus Ligilactobacillus and it has higher sequence similarities with Ligilactobacillus pobuzihii (98.4 %) Ligilactobacillus acidipiscis (97.5 %) and Ligilactobacillus salitolerans (97.4 %). The digital DNA–DNA hybridization values for AF129T and phylogenetically related species of the genus Ligilactobacillus ranged from 19.8% to 24.1%. The average nucleotide identity of the strain with its closely related taxa was lower than the threshold (95 %–96 %) used for species differentiation. In the light of the above-mentioned physiological genotypic chemotaxonomic and phylogenetic evidence we confirm that AF129T represents a member of the genus Ligilactobacillus and constitutes a novel species; we propose the name Ligilactobacillus pabuli sp. nov. for this species. The type strain is AF129T =MAFF 518002T =JCM 34518T=BCRC 81335T.

A corrigendum of this article has been published full details can be found at 10.1099/ijsem.0.006564

Seven novel lactic acid bacterial strains (BF125T BF186 TKL145 YK3 YK6 YK10 and NSK) were isolated from the fresh faeces of Japanese black beef cattle and weanling piglets spent mushroom substrates or steeping water of a corn starch production plant. These strains are rod-shaped Gram-stain-positive non-motile non-spore-forming catalase-negative cytochrome oxidase-negative facultatively anaerobic and homofermentative. Strain BF125T did not produce any gas from glucose; both d- and l-lactate were produced as end-products of glucose (D/L 40 : 60). Growth occurred at 30–45 °C (optimum 37 °C) pH 5.0–8.0 (optimum pH 6.0) and with NaCl concentration of 1.0–3.0% (w/v). The G+C content of genomic DNA of strain BF125T was 37.8 mol% (whole-genome analysis). The major fatty acids were C16 : 0 C18 : 1 ω9c C19 cyclopropane 9 10 and summed feature 10. The 16S rRNA gene in strain BF125T showed high similarity to that of the type strain of Lactobacillus amylovorus (99.93%) and the other isolates were also identified as L. amylovorus based on these similarities. A phylogenetic tree based on the core genomes of L. amylovorus strains (n=54) including the seven isolates showed that they could be divided into two clusters. Strains YK3 YK6 YK10 and NSK were in the first cluster along with the type strain DSM 20531T while the second cluster included isolates BF125T BF186 TKL145 and other strains isolated from various animal origins. Phenotypic differences in fermentability were observed for lactose salicin and gentiobiose between these two groups. The intergroup digital DNA–DNA hybridization values (72.9–78.6%) and intergroup average nucleotide identity values (95.64–96.92%) were comparable to values calculated using datasets of other valid subspecies of the genus (ex-) Lactobacillus. In light of the physiological genotypic and phylogenetic evidence we propose a novel subspecies of L. amylovorus named Lactobacillus amylovorus subsp. animalis subsp. nov. (type strain BF125T=MAFF 212522T=DSM 115528T). Our findings also led to the automatic creation of Lactobacillus amylovorus subsp. amylovorus subsp. nov. and an emended description of the species L. amylovorus.

Two Gram-stain-negative terminal endospore-forming rod-shaped and aerotolerant bacterial strains designated D1-1T and B3 were isolated from soil samples of an organic paddy in Japan. Strain D1-1T grew at 15–37 °C pH 5.0–7.3 and with up to 0.5 % (w/v) NaCl. Phylogenetic analysis of the 16S rRNA gene revealed that strain D1-1T belonged to the genus Clostridium and was closely related to Clostridium zeae CSC2T (99.7 % sequence similarity) Clostridium fungisolvens TW1T (99.7 %) and Clostridium manihotivorum CT4T (99.3 %). Strains D1-1T and B3 were whole-genome sequenced and indistinguishable with an average nucleotide identity value of 99.7 %. The average nucleotide identity (below 91.1 %) and digital DNA–DNA hybridization (below 43.6 %) values between the two novel isolates and their corresponding relatives showed that strains D1-1T and B3 could be readily distinguished from their closely related species. A novel Clostridium species Clostridium folliculivorans sp. nov. with type strain D1-1T (=MAFF 212477T=DSM 113523T) is proposed based on genotypic and phenotypic data.