A novel endophytic bacterium, designated strain SZ4R5S7T, was isolated from surface-sterilized root of an endangered medicinal plant (Ferula songorica Pall. ex Spreng) collected from Xinjiang, north-west China. The taxonomic position of the strain was investigated by using a polyphasic approach. The strain was found to be aerobic, Gram-stain-positive, oxidase-negative and catalase-positive, short rods and non-motile. Strain SZ4R5S7T grew at 4–37 °C (optimum, 28 °C), pH 5.0–9.0 (pH 6.0–8.0) and in the presence of 0–4 % (w/v) NaCl. The polar lipids detected for strain SZ4R5S7T were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol and two unidentified lipids. The predominant menaquinone of strain SZ4R5S7T was MK-8(H4), and the major fatty acids were iso-C16 : 0 and anteiso-C14 : 0. The DNA G+C content was determined to be 72.4 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain SZ4R5S7T belongs to the genus
and showed highest levels of 16S rRNA gene sequence similarity to members of the strain
KSL-2T (97.8 %). On the basis of phenotypic, genotypic and phylogenetic data, strain SZ4R5S7T represents a novel species in the genus Nocardioides, for which the name
ferulae sp. nov. is proposed and the type strain is SZ4R5S7T (=CGMCC 4.7456T=KCTC 39994T).
A novel Gram-negative, aerobic, rod-shaped, non-spore-forming bacterial strain, RYU5T, was isolated from a stool sample of an inpatient at a hospital in Okinawa, Japan. The optimal growth temperature of RYU5T was 30 °C. Phylogenetic analysis based on the sequences of housekeeping genes, including the 16S rRNA, rpoB, rpoD and gyrB genes, showed that RYU5T was a member of the
group and was located close to
. Whole-genome comparisons, using average nucleotide identity and digital DNA–DNA hybridization, confirmed that strain RYU5T should be classified as a novel species of
. Phenotypic characterization tests showed that utilization of d-mannose, d-serine, l-arabinose and d-fructose could distinguish this strain from other related species of the genus
. Based on genetic and phenotypic evidence, strain RYU5T should be classified as a novel species, for which the name
asiatica sp. nov. is proposed. The type strain is RYU5T (=DSM 107182T, =JCM 32716T), with a DNA G+C content of 62.25 mol%.
Recently a proposal was published to unify Rules 7, 8 and 9 of the International Code of Nomenclature of Prokaryotes. Based on this proposal, all names of taxa above the rank of genus must be in the feminine gender, the plural number. For the rank of class, this proposal contravenes Principle 3 of the Code, which states that the scientific names of all taxa are treated as Latin. The –ia ending of most names of classes belongs to nominative plural nouns of the neuter gender.
An extremely halophilic euryarchaeon, strain HArcel1T, was enriched and isolated in pure culture from the surface brines and sediments of hypersaline athalassic lakes in the Kulunda Steppe (Altai region, Russia) using amorphous cellulose as the growth substrate. The colonies of HArcel1T are pale-orange, and form large zones of cellulose hydrolysis around them. The cells are non-motile cocci of variable size with a thin monolayer cell wall. The isolate is an obligate aerobic heterotroph capable of growth with only three substrates: various forms of insoluble cellulose, xylan and cellobiose. Strain HArcel1T is an extremely halophilic neutrophile, growing within the salinity range from 2.5 to 5 M NaCl (optimum at 3.5–4 M). The core archaeal lipids are dominated by C20–C20 and C25–C20 dialkyl glycerol ethers, in approximately 6:1 proportion. The 16S rRNA and rpoB′ gene analysis indicated that HArcel1T forms a separate lineage within the family
, with the genera Halorhabdus and Halopricus as closest relatives. On the basis of the unique phenotypic properties and distinct phylogeny of the 16S rRNA and rpoB′ genes, it is suggested that strain HArcel1T is classified into a new genus and species Halococcoides cellulosivorans gen. nov., sp. nov. (JCM 31941T=UNIQEM U975T).
strains, i.e. 2020BT, 2028BT, 2033BT, 2034BT and 2036BT, were isolated from European beaver (Castor fiber), Goeldi's marmoset (Callimicogoeldii), black-capped squirrel monkey (Saimiriboliviensissubsp. peruviensis) and Patagonian mara (Dolichotispatagonum). All of these isolates were shown to be Gram-positive, facultative anaerobic, d-fructose 6-phosphate phosphoketolase-positive, non-motile and non-sporulating. Phylogenetic analyses based on 16S rRNA gene sequences, multilocus sequences (including hsp60, rpoB, dnaJ, dnaG and clpC genes) and the core genome revealed that bifidobacterial strains 2020BT, 2028BT, 2033BT, 2034BT and 2036BT exhibit close phylogenetic relatedness to
LMG 30187T and
LMG 30126T, respectively. Further genotyping based on the genome sequence of the isolated strains combined with phenotypic analyses, clearly show that these strains are distinct from each of the type strains of the so far recognized
castoris sp. nov. (2020BT=LMG 30937T=CCUG 72816T),
callimiconis sp. nov. (2028BT=LMG 30938T=CCUG 72814T),
samirii sp. nov. (2033BT=LMG 30940T=CCUG 72817T),
goeldii sp. nov. (2034BT=LMG 30939T=CCUG 72815T) and
dolichotidis sp. nov. (2036BT=LMG 30941T=CCUG 72818T) are proposed as novel
There are various ways in which the names of prokaryotes can be duplicated in the literature. An examination of the various ways that this may happen under the International Code of Nomenclature of Prokaryotes indicates that a concept is missing, namely the one that refers to the same name based on the same nomenclatural type published in the International Journal of Systematic Bacteriology/International Journal of Systematic and Evolutionary Microbiology, by the same or different authors in different manuscripts or in the Validation Lists. To cater for such instances it would be appropriate to introduce the concept of the isonym and to regulate how they are to be dealt with.
A Gram-stain-negative, obligate aerobic, non-motile and rod-shaped bacterium, designated MME-070T, was isolated from a tidal flat near Muui-do, Incheon, Republic of Korea. This bacterium belonged to the
clade within the family
. The isolate grew at 20–40 °C, pH 7.0–9.0 with 1–5 % (w/v) NaCl. Optimal growth required 2–3 % (w/v) NaCl at 25–30 °C and pH 8.0. The 16S rRNA gene sequence of strain MME-070T was most closely related to
SMK-122T (96.9 %). Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain MME-070T clustered with the genus
. The sole respiratory quinone was Q-10. Polar lipids were phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol, unidentified aminolipid and some unidentified lipids. Major cellular fatty acids were summed feature 8 (C18 : 1
ω7c and/or C18 : 1
ω6c), 11-methyl C18 : 1
ω7c and C16 : 0. The genomic DNA G+C content of the type strain was 63.6 mol%. Based on polyphasic taxonomic analysis, strain MME-070T is proposed to represent a novel species of the genus
, for which the name
faecimaris sp. nov. is proposed. The type strain is MME-070T (=KCCM 43142T=JCM 30757T).
A Gram-stain-negative, facultative aerobic, motile by a polar flagellum, rod-shaped strain, designated BEI247T, was isolated from seawater at the bottom of the East China Sea. Phylogenetic analysis of the 16S rRNA gene and whole genome data affiliated it with the genus
. It was most closely related to
P03D4T (97.36 % 16S rRNA gene similarity). Multi-locus sequence analysis (MLSA) revealed a distinct lineage with
P03D4T as its closest relative. Strain BEI247T was found to have lower than 86.0 % similarities to the type strains of its most closely related species in MLSA, less than 82.3 % using genome average nucleotide identities, and less than 25.3 % in DNA–DNA relatedness studies. Growth occurred at 10–37 °C (optimum, 24 °C), pH 5.0–8.0 (pH 7.0) and in the presence of 1–5 % (w/v) NaCl (3 %). The dominant fatty acids were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. The polar lipids of strain BEI247T comprised phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, two phospholipids and one unknown lipid. The major respiratory quinone was ubiquinone-8 (Q-8). The DNA G+C content of strain BEI247T was 46.45 mol%. On the basis of the polyphasic evidence, strain BEI247T is proposed as representing a novel species of the genus
, for which the name
chitinilyticum sp. nov. is proposed. The type strain is BEI247T (=JCM 32689T=MCCC 1K03517T=KCTC 62619T).
A novel Gram-negative, aerobic, rod-shaped bacterium, designated NS26T, was isolated from a sediment sample collected from Taihu Lake in China. Colonies were orange, circular, smooth and neat-edged on Reasoner’s 2A agar. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain NS26T belonged to the genus
and had the closest relationship with
DSM 24448T (96.9 %). It grew at 20–37 °C (optimum, 28 °C), pH 5.5–10.5 (pH 7.0) and without NaCl. The major isoprenoid quinone was Q-10. The dominant cellular fatty acids were C18 : 1ω7c, C16 : 0 and C18 : 1ω7c 11-methyl. The polar lipid profile comprised 1,2-diacyl-3-O-(6-phosphatidyl-α-d-glucopyranosyl) glycerol, 1,2-di-O-acyl-3-O-α-d-glycopyranuronosyl glycerol, sulfoquinovosyl diacylglycerol, 1,2-di-O-acyl-3-O-[d-glycopyranosyl-(1→4)-α-d-glucopyranuronosyl] glycerol and phosphatidylglycerol. The G+C content of genomic DNA was 68.4 mol%. The average nucleotide identity value between strain NS26T and
DSM 24448T was 75.6 %. Based on the polyphasic taxonomic study, strain NS26T is suggested to be a novel species, for which the name
lutea sp. nov. is proposed. The type strain is NS26T (=CGMCC 1.13680T=NBRC 113554T).
A Gram-stain-negative, facultative anaerobic, non-motile and rod-shaped bacterial strain, designated LX32T, was isolated from arsenic and cadmium contaminated farmland soil. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain LX32T was closely related to
HKS-05T (97.7 % sequence similarity),
CCTCC AB 2013085T (97.4 %) and
CCTCC AB 2016297T (97.1 %). The average nucleotide identity values of the whole genome sequences of LX32T/P.
CCTCC AB 2013085T and LX32T/P.
CCTCC AB 2016297T were 79.8, 77.9 and 77.5 %, respectively. Its genome size was 4.02 Mb, comprising 3998 predicted genes with a DNA G+C content of 70.1 mol%. The major fatty acids were C15 : 0, C16 : 0 and summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c). The polar lipid profiles consisted of phosphatidylglycerol, aminophospholipid, seven glycolipids and two unidentified polar lipids. The predominantly respiratory quinone was ubiquinone-10. Based on polyphasic analyses, the isolate is considered to represent a novel species of the genus
, for which the name
soli sp. nov. is proposed. The type strain is LX32T (=KCTC 62522=CCTCC AB 2018055).