Sampling of agricultural and natural environments in two US states (Colorado and Florida) yielded 18 Listeria-like isolates that could not be assigned to previously described species using traditional methods. Using whole-genome sequencing and traditional phenotypic methods, we identified five novel species, each with a genome-wide average blast nucleotide identity (ANIb) of less than 85 % to currently described species. Phylogenetic analysis based on 16S rRNA gene sequences and amino acid sequences of 31 conserved loci showed the existence of four well-supported clades within the genus Listeria ; (i) a clade representing Listeria monocytogenes , L. marthii , L. innocua , L. welshimeri , L. seeligeri and L. ivanovii , which we refer to as Listeria sensu stricto, (ii) a clade consisting of Listeria fleischmannii and two newly described species, Listeria aquatica sp. nov. (type strain FSL S10-1188T = DSM 26686T = LMG 28120T = BEI NR-42633T) and Listeria floridensis sp. nov. (type strain FSL S10-1187T = DSM 26687T = LMG 28121T = BEI NR-42632T), (iii) a clade consisting of Listeria rocourtiae , L. weihenstephanensis and three novel species, Listeria cornellensis sp. nov. (type strain TTU A1-0210T = FSL F6-0969T = DSM 26689T = LMG 28123T = BEI NR-42630T), Listeria grandensis sp. nov. (type strain TTU A1-0212T = FSL F6-0971T = DSM 26688T = LMG 28122T = BEI NR-42631T) and Listeria riparia sp. nov. (type strain FSL S10-1204T = DSM 26685T = LMG 28119T = BEI NR- 42634T) and (iv) a clade containing Listeria grayi . Genomic and phenotypic data suggest that the novel species are non-pathogenic.
In this study, the taxonomic position and group classification of the phytoplasma associated with a lethal yellowing-type disease (LYD) of coconut (Cocos nucifera L.) in Mozambique were addressed. Pairwise similarity values based on alignment of nearly full-length 16S rRNA gene sequences (1530 bp) revealed that the Mozambique coconut phytoplasma (LYDM) shared 100 % identity with a comparable sequence derived from a phytoplasma strain (LDN) responsible for Awka wilt disease of coconut in Nigeria, and shared 99.0–99.6 % identity with 16S rRNA gene sequences from strains associated with Cape St Paul wilt (CSPW) disease of coconut in Ghana and Côte d’Ivoire. Similarity scores further determined that the 16S rRNA gene of the LYDM phytoplasma shared <97.5 % sequence identity with all previously described members of ‘Candidatus Phytoplasma ’. The presence of unique regions in the 16S rRNA gene sequence distinguished the LYDM phytoplasma from all currently described members of ‘Candidatus Phytoplasma ’, justifying its recognition as the reference strain of a novel taxon, ‘Candidatus Phytoplasma palmicola’. Virtual RFLP profiles of the F2n/R2 portion (1251 bp) of the 16S rRNA gene and pattern similarity coefficients delineated coconut LYDM phytoplasma strains from Mozambique as novel members of established group 16SrXXII, subgroup A (16SrXXII-A). Similarity coefficients of 0.97 were obtained for comparisons between subgroup 16SrXXII-A strains and CSPW phytoplasmas from Ghana and Côte d’Ivoire. On this basis, the CSPW phytoplasma strains were designated members of a novel subgroup, 16SrXXII-B.
A novel Gram-staining-positive, moderately halophilic bacterium, designated strain A76T, was isolated from a brine sample of the hypersaline lake Aran-Bidgol in Iran. Cells were strictly aerobic, coccus-shaped, non-motile, non-sporulating, and catalase- and oxidase-positive. Strain A76T grew between pH 7.0 and 10.0 (optimal growth at pH 8.0), between 20 and 45 °C (optimal growth at 35 °C) and at salinities of 0.5 to 12.5 % (w/v) NaCl (optimal growth at 7.5 %, w/v, NaCl). On the basis of 16S rRNA gene sequence analysis, strain A76T was shown to belong to the phylum Firmicutes with sequence similarities of 94.1, 93.1 and 91.1 %, to the type species of the genera Jeotgalicoccus , Salinicoccus and Nosocomiicoccus , respectively. The DNA G+C content of this new isolate was 38.8 mol%. The major cellular fatty acids of strain A76T were anteiso-C15 : 0 and iso-C15 : 0, and its polar lipid pattern consisted of diphosphatidylglycerol, phosphatidylglycerol, a glycolipid, an unknown lipid and two unknown phospholipids. The isoprenoid quinones were MK-6 (94 %), MK-5 (3 %) and MK-7 (3 %). The amino acid constituents of the cell wall were Lys, Asp, Gly, Glu and Ala. The physiological, biochemical and phylogenetic differences between strain A76T and type strains of taxa with validly published names suggest that this strain represents a novel species in a novel genus within the family Staphylococcaceae , for which the name Aliicoccus persicus gen. nov., sp. nov. is proposed. The type strain of Aliicoccus persicus is strain A76T ( = CECT 8508T = DSM 28306T = IBRC-M 10081T).
A novel Gram-stain-positive, motile, catalase- and oxidase-positive, aerobic, endospore-forming, peritrichous, rod-shaped bacterium, designated YIM M13235T, was isolated from a marine sediment sample collected from the South China Sea. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM M13235T belonged to the genus Bacillus . The strain grew optimally at 30 °C, pH 7.0 and in the presence of 2–4 % (w/v) NaCl. meso-Diaminopimelic acid was present in the cell-wall peptidoglycan. Strain YIM M13235T exhibited a menaquinone system with MK-7, and the major polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, four unknown phospholipids and one unknown glycolipid. The major fatty acids (>5 %) were iso-C15 : 0, anteiso-C15 : 0, anteiso-C17 : 0, iso-C17 : 1ω10c and summed feature 4 (anteiso-C17 : 1 and/or iso-C17 : 1). The genomic DNA G+C content was 42.1 mol%. The DNA–DNA relatedness values between strain YIM M13235T and its close relatives (16S rRNA gene sequence similarities >97 %) including Bacillus halmapalus DSM 8723T, Bacillus horikoshii DSM 8719T and Bacillus zhanjiangensis JSM 099021T were 41 %, 44 % and 44 %, respectively. On the basis of genotypic, phenotypic and DNA–DNA relatedness data, it is apparent that strain YIM M13235T represents a novel species of the genus Bacillus , for which the name Bacillus tianshenii sp. nov. is proposed. The type strain is YIM M13235T ( = DSM 25879T = KCTC 33044T).
Four Gram-staining-positive, catalase-negative, coccoid isolates, designated NTUH_1465T, NTUH_2196, NTUH_4957 and NTUH_5572T, were isolated from human specimens. The four isolates displayed more than 99.6 % 16S rRNA gene sequence similarity with Gemella haemolysans ATCC 10379T, and 96.7 to 98.6 % similarity with Gemella sanguinis ATCC 700632T, Gemella morbillorum ATCC 27824T or Gemella cuniculi CCUG 42726T. However, phylogenetic analysis of concatenated sequences of three housekeeping genes, groEL, rpoB and recA, suggested that the four isolates were distinct from G. haemolysans ATCC 10379T and other species. Isolates NTUH_2196, NTUH_4957 and NTUH_5572T clustered together and formed a stable monophyletic clade. DNA–DNA hybridization values among strains NTUH_1465T and NTUH_5572T and their phylogenetically related neighbours were all lower than 49 %. The four isolates could be distinguished from G. haemolysans and other species by phenotypic characteristics. Based on the phylogenetic and phenotypic results, two novel species Gemella parahaemolysans sp. nov. (type strain NTUH_1465T = BCRC 80365T = JCM 18067T) and Gemella taiwanensis sp. nov. (type strain NTUH_5572T = BCRC 80366T = JCM 18066T) are proposed.
A halophilic, Gram-staining-positive, non-motile, endospore forming rod-shaped bacterial strain, S1LM8T, was isolated from a sediment sample collected from an inland solar saltern located in La Malahá, Granada (Spain). Growth was observed in media containing 7.5–30 % total salts (optimum 15 % total salts), at pH 7–10 (optimum pH 8) and at 15–50 °C (optimum 35–38 °C). The predominant isoprenoid quinone was MK-7. It contained A1γ-type peptidoglycan with meso-diaminopimelic acid as the diagnostic diamino acid. The major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The G+C content of its genomic DNA was 38.2 mol%. The affiliation of strain S1LM8T with the species of the genus Alkalibacillus was determined by 16S rRNA gene sequence comparison. The most closely related species were Alkalibacillus halophilus YIM 012T with 99.8 % similarity, Alkalibacillus salilacus BH163T with 99.8 % similarity and Alkalibacillus flavidus ISL-17T with 98.1 % similarity between their 16S rRNA gene sequences. However, DNA–DNA relatedness between the novel isolate and the related species of the genus Alkalibacillus was less than 34 %. Based on the phylogenetic, phenotypic and chemotaxonomic features, a novel species, Alkalibacillus almallahensis sp. nov. is proposed. The type strain is S1LM8T ( = CECT 8373T = DSM 27545T).