Lack of in vivo mutagenicity of carbendazim in the liver and glandular stomach of MutaMice

BACKGROUND

Carbendazim (methyl 2-benzimidazolecarbamate, CASRN: 10605-21-7) exhibits spindle poisoning effects and is widely used as a fungicide. With respect to genotoxicity, carbendazim is deemed to be non-mutagenic in vitro, but it causes indicative DNA damage in vivo and chromosome aberrations in vitro and in vivo. In this study, we examined the mutagenicity of carbendazim in vivo.

RESULTS

MutaMice were treated with carbendazim orally at doses of 0 (corn oil), 250, 500, and 1,000 mg/kg/day once a day for 28 days. A lacZ assay was used to determine the mutant frequency (MF) in the liver and glandular stomach of mice. MutaMice were administered up to the maximum dose recommended by the Organization for Economic Co-operation and Development Test Guidelines for Chemicals No. 488 (OECD TG488). The lacZ MFs in the liver and glandular stomach of carbendazim-treated animals were not significantly different from those in the negative control animals. In contrast, positive control animals exhibited a significant increase in MFs in both the liver and glandular stomach.

CONCLUSIONS

Carbendazim is non-mutagenic in the liver and glandular stomach of MutaMice following oral treatment.

In vivo mutagenicity assessment of orally treated tert-butyl hydroperoxide in the liver and glandular stomach of MutaMouse

BACKGROUND

tert-Butyl hydroperoxide (TBHP; CAS 75-91-2), a hydroperoxide, is mainly used as a polymerization initiator to produce polyethylene, polyvinyl chloride, and unsaturated polyester. It is a high-production chemical, widely used in industrial countries, including Japan. TBHP is also used as an additive for the manufacturing of food utensils, containers, and packaging (UCP). Therefore, there could be consumer exposure through oral intake of TBHP eluted from UCPs. TBHP was investigated in various in vitro and in vivo genotoxicity assays. In Ames tests, some positive results were reported with and/or without metabolic activation. As for the mouse lymphoma assay, the positive result was reported, regardless of the presence or absence of metabolic activation enzymes. The results of some chromosomal aberrations test and comet assay in vitro also demonstrated the genotoxic positive results. On the other hand, in in vivo tests, there are negative results in the bone marrow micronucleus test of TBHP-administered mice by single intravenous injection and the bone marrow chromosomal aberration test using rats exposed to TBHP for 5 days by inhalation. Also, about dominant lethal tests, the genotoxic positive results appeared. In contrast, there is little information about in vivo mutagenicity and no information about carcinogenicity by oral exposure.

RESULTS

We conducted in vivo gene mutation assay using MutaMice according to the OECD Guidelines for the Testing of Chemicals No. 488 to investigate in vivo mutagenicity of TBHP through oral exposure. After repeated dosing for 28 days, there were no significant differences in the mutant frequencies (MFs) of the liver and glandular stomach up to 300 mg/kg/day (close to the maximum tolerable dose (MTD)). The positive and negative controls produced the expected responses.

CONCLUSIONS

These findings show that orally administrated TBHP is not mutagenic in the mouse liver and glandular stomach under these experimental conditions.

North-to-South diversity of lipomycetaceous yeasts in soils evaluated with a cultivation-based approach from 11 locations in Japan

To understand the species distribution, diversity, and density of lipomycetaceous yeasts in soil based on their north-to-south location in Japan, 1146 strains were isolated from soil samples at 11 locations from Hokkaido to Okinawa Prefecture and taxonomically characterized. Lipomycetaceous yeast strains were isolated efficiently from soil by selecting watery mucoid-like colonies on agar plates with nitrogen-depleted medium. Twenty-four (80%) of the 30 known species of the genus Lipomyces were isolated from the soil samples collected in Japan, including species recently proposed. Among the species isolated, L. starkeyi was the most predominant in Japan, except on Iriomote Island, Okinawa, and accounted for 60-98% of the isolated strains. Lipomyces yarrowii was the dominant species on Iriomote Island (64%). The second most dominant species were L. chichibuensis in Saitama Prefecture and L. doorenjongii from Yamaguchi to Okinawa Prefecture. The species diversity of lipomycetaceous yeasts was in Japan and the significant correlation with the latitude of the sampling sites was revealed.

Rapid Disappearance of Intraventricular Mobile Structures with Steroids in Eosinophilic Granulomatosis with Polyangiitis

Endomyocarditis in Eosinophilic granulomatosis with polyangiitis (EGPA) is a rare complication, commonly involving an apical mass compatible with a thrombus. However, no previous report has discussed mobile structures detected by echocardiography in a patient with EGPA. A 53-year-old man with asthma presented with low-grade fever, consciousness disturbance, and vomiting. Magnetic resonance imaging showed multiple acute infarctions in the bilateral cerebrum and cerebellum. Remarkable eosinophilia was observed, and transthoracic echocardiography showed multiple mobile structures originating from the left ventricular septum. The day after admission, he developed left partial hemianopia and intracranial hemorrhage was identified in his right occipital lobe. Skin biopsy showed infiltration of eosinophils in the arterial wall, and we diagnosed EGPA. Myocardial biopsy was performed from the right ventricular wall, and eosinophilic infiltration into the endocardium and myocardium was observed. Endomyocarditis secondary to EGPA was confirmed, and steroid therapy was immediately initiated. Ten days after steroid therapy, the mobile structures in the left ventricle disappeared completely. He suffered no recurrence of stroke with continued steroid therapy. Mobile structures in the left ventricle in patients with active EGPA could be treated conservatively with steroid therapy.

The Usefulness and Limitations of Point-of-care Cardiac Troponin Measurement in the Emergency Department

Objective This study was carried out to examine the usefulness of point-of-care (POC) cardiac troponin in diagnosing acute coronary syndrome (ACS) and to understand the limitations of a POC cardiac troponin I/T-based diagnoses. Methods Patients whose cardiac troponin levels were measured in the emergency department using a POC system (AQT System; Radiometer, Tokyo, Japan) between January and December 2016 were retrospectively examined (N=1,449). Patients who were < 20 years of age or who were admitted with cardiopulmonary arrest were excluded. The sensitivity and specificity of the POC cardiac troponin levels for the diagnosis of ACS were determined. Result One hundred and twenty of 1,449 total patients had ACS (acute myocardial infarction, n=88; unstable angina n=32). On comparing the receiver operating characteristic (ROC) curves, the area under the curve (AUC) values for POC cardiac troponin I and cardiac troponin T were 0.833 and 0.786, respectively. The sensitivity and specificity of POC cardiac troponin I when using the 99th percentile (0.023 ng/mL) as the diagnostic cut-off value were 69.0% and 88.1%, respectively. The sensitivity of POC cardiac troponin I (99th percentile) was higher in the patients sampled > 3 hours after symptom onset (83.3%) than in those sampled ≤ 3 hours after symptom onset (58.8%, p < 0.01). Conclusion When sampled > 3 hours after the onset of symptoms, the POC cardiac troponin I level is considered to be suitable for use in diagnosing ACS. However, when sampled ≤ 3 hours after the onset of symptoms, careful interpretation of POC cardiac troponins is therefore required to rule out ACS.

Predictors of oxygenation impairment in medical treatment for type B acute aortic dissection

Lung oxygenation impairment often occurs in patients with type B acute aortic dissection (AAD), necessitating mechanical ventilation. Patients receiving mechanical ventilation are at risk of complications, so a low-oxygen condition requiring mechanical ventilation should be avoided. We explored the predictors of oxygenation impairment. We enrolled 46 patients with type B AAD who had been medically treated and underwent computed tomography. Blood was sampled to measure markers of inflammation, such as the C-reactive protein (CRP) levels and white blood cell count. The arterial partial pressure of oxygen/fraction of inspired oxygen ratio (PaO₂/FiO₂) was calculated to quantify the severity of respiratory failure. Spearman's rank correlation analysis revealed that the minimum PaO₂/FiO₂ ratio was significantly correlated with gender, age, and current smoker, and the peak CRP, body temperature, and D-dimer values. A multivariate regression analysis revealed that younger age, male sex, and the peak CRP level were significant predictors of the minimum PaO₂/FiO₂ ratio (P = 0.01, 0.035 and 0.005, respectively). A covariance structure analysis showed that a younger age and the peak CRP level were significant predictors of oxygenation impairment in type B AAD. Oxygenation impairment in type B AAD is correlated with younger age and a higher peak CRP level. This will enable the identification of patients whose respiratory condition is susceptible to worsening and help prevent mechanical ventilation, leading to the provision of appropriate therapy.

Effects of pH on nano-bubble stability and transport in saturated porous media

An understanding of nano-scale bubble (NB) transport in porous media is important for potential application of NBs in soil/groundwater remediation. It is expected that the solution chemistry of NB water highly influences the surface characteristics of NBs and porous media and the interaction between them, thus affecting the stability and transport characteristics of NB. In this study, in addition to stability experiments, one-dimensional column transport experiments using glass beads were conducted to investigate the effects of pH on the NB transport behavior. The results showed that the NBs were more stable under higher pH. Column transport experiments revealed that entrapment of NBs, especially larger ones, was enhanced in lower-pH water, likely suggesting pH-dependent NB attachment and physical straining, both of which are also probably influenced by bubble size. Although relatively smaller NBs were released after switching the eluting fluid to one with lower ionic strength, most of the NBs in lower-pH water were still retained in the porous media even altering the chemical condition.

Propensity-Score Matched Comparison of Midterm Angiographic Outcomes of Sirolimus- Versus Everolimus- and Biolimus-Eluting Stents for De Novo Coronary Stenosis

We conducted propensity-score matched comparisons of midterm angiographic outcomes of sirolimus (SES) versus either everolimus- (EES) or biolimus- (BES) eluting stents after placements for coronary stenosis in a daily practice environment since previous randomized trials did not demonstrate the superiority of EES and BES over SES in terms of midterm angiographic outcomes.The present study was a non-randomized, retrospective, and lesion-based study, recruiting angiographically followed-up lesions within 550 days after successful and elective SES (n = 1793), EES (n = 1303), or BES (n = 324) placement for de novo native coronary stenosis during the period from August 2004 to January 2014 at 6 institutes. The endpoint, as an angiographic surrogate marker of clinical efficacy, was the distribution of in-stent follow-up percent diameter stenosis (%DS) which comprised the percentages of 1) follow-up %DS < 20 and 2) follow-up %DS > 50. Propensityscore matched analyses were conducted to adjust 21 baselines.In 1215 baseline adjusted lesions, the endpoints in the EES group [1) 74.1%, and 2) 4.6%] were significantly different from those in the SES group [57.9%; P < 0.001, 7.2%; P = 0.006, respectively). In 307 baseline adjusted lesions, the endpoints in the BES group [1) 80.5%, 2) 2.0%] were significantly different from those in the SES group [59.3%; P < 0.001, 2) 8.1%; P = 0.001, respectively].The present study is the first to confirm the superiority of midterm angiographic outcomes after the placement of EES and BES over SES for de novo coronary stenosis in a clinical setting.

Midterm angiographic outcomes with sirolimus- and everolimus-eluting stents for small vessels in diabetic patients: propensity-score-matched comparisons in three different vessel diameters

We conducted propensity-score-matched comparisons of midterm angiographic follow-up outcomes of sirolimus- versus everolimus-eluting stents (SES, EES) after elective placements for de novo coronary stenosis in small vessels (SV) in patients with diabetes mellitus (DM), because the angiographic efficacy of EES over SES for those cohorts remained unclear. The study was a non-randomized, retrospective, lesion-based, multicenter study, examining lesions followed up angiographically within 550 days, extracted from the unified database of 6 institutes. The endpoint (binary restenosis) was defined as the percentage of subjects having >50% diameter stenosis at follow-up. Propensity-score-matched analyses were conducted in 3 different vessel-size cohorts, defined by a preprocedural reference diameter (RD) <2.10, <2.35, and <2.60 mm, yielding group sizes of n = 107, 183, and 312 baseline-adjusted lesions in each of the 2 stent arms. The frequency of binary restenosis decreased significantly with increasing vessel size, at 16.8, 12.6, and 12.2%, in the SES group. However, it remained almost the same across vessel-size groups in the EES group (8.0, 6.0, and 7.5%). The p values for the significance of the differences in binary restenosis between EES and SES in each vessel size increased with the decrease in vessel size [p = 0.002, 0.040, and 0.063 (the last still nearly significant)]. Thus, in patients with DM, EES showed increasingly superior efficacy over SES for SV stenosis as the vessel size became smaller, i.e., the risk for binary restenosis became greater.

Complete genome sequencing of Dehalococcoides sp. strain UCH007 using a differential reads picking method

A novel Dehalococcoides sp. strain UCH007 was isolated from the groundwater polluted with chlorinated ethenes in Japan. This strain is capable of dechlorinating trichloroethene, cis-1,2-dichloroethene and vinyl chloride to ethene. Dehalococcoides bacteria are hardly cultivable, so genome sequencing has presented a challenge. In this study, we developed a differential reads picking method for mixed genomic DNA obtained from a co-culture, and applied it to the sequencing of strain UCH007. The genome of strain UCH007 consists of a 1,473,548-bp chromosome that encodes 1509 coding sequences including 29 putative reductive dehalogenase genes. Strain UCH007 is the first strain in the Victoria subgroup found to possess the pceA, tceA and vcrA genes.

Complete genome sequence of Lactobacillus acetotolerans RIB 9124 (NBRC 13120) isolated from putrefied (hiochi) Japanese sake

Lactobacillus acetotolerans RIB 9124 (NBRC 13120) was isolated from putrefied (hiochi) Japanese sake. Here we report the complete genome sequence of this organism. This paper is the first report demonstrating the fully sequenced and completely annotated genome of a L. acetotolerans strain.

Lactobacillus plajomi sp. nov. and Lactobacillus modestisalitolerans sp. nov., isolated from traditional fermented foods

Three Lactobacillus-like strains, NB53T, NB446T and NB702, were isolated from traditional fermented food in Thailand. Comparative 16S rRNA gene sequence analysis indicated that these strains belong to the Lactobacillus plantarum group. Phylogenetic analysis based on the dnaK, rpoA, pheS and recA gene sequences indicated that these three strains were distantly related to known species present in the L. plantarum group. DNA–DNA hybridization with closely related strains demonstrated that these strains represented two novel species; the novel strains could be differentiated based on chemotaxonomic and phenotypic characteristics. Therefore, two novel species of the genus Lactobacillus, Lactobacillus plajomi sp. nov. (NB53T) and Lactobacillus modestisalitolerans sp. nov. (NB446T and NB702), are proposed with the type strains NB53T ( = NBRC 107333T = BCC 38054T) and NB446T ( = NBRC 107235T = BCC 38191T), respectively.

Jatrophihabitans soli sp. nov., isolated from soil

One bacterial strain, designated KIS75-12T, isolated from a soil sample collected from Wonsando island located in Boryeong city, Republic of Korea, was characterized as aerobic, Gram-stain-positive, non-flagellated and a short rod. It grew between temperatures of 15–37 °C, pH 4–9 and 0–3.0 % (w/v) NaCl. The 16S rRNA gene analysis showed the strain was moderately related to Jatrophihabitans endophyticus S9-650T (97.7 %) and revealed low sequence similarity (≤94.7 %) with all the other species with validly published names. Its major fatty acid was iso-C16 : 0. The predominant menaquinone of strain KIS75-12T was MK-9(H4). The polar lipids consisted of diphosphatidylglycerol and several small amounts of phosphatidylinositol, aminolipids and glycolipid. The peptidoglycan contained meso-A2pm as diagnostic diamino acid and the peptidoglycan type is A4γ. The genomic DNA G+C content of the type strain was 72.1 mol%. The combined phenotypic, chemotaxonomic and phylogenetic data showed that strain KIS75-12T could be clearly distinguished from the only member of the genus Jatrophihabitans , J. endophyticus . Therefore, the results of this study indicate the existence of a representative of a novel species of the genus Jatrophihabitans , for which we propose the name Jatrophihabitans soli sp. nov., with strain KIS75-12T ( = KACC 17298T = DSM 45908T  =  NBRC 109658T) as the type strain. An emended description of the genus Jatrophihabitans is also given.

Serinibacter tropicus sp. nov., an actinobacterium isolated from the rhizosphere of a mangrove, and emended description of the genus Serinibacter

A novel Gram-stain-positive actinobacterium, designated PS-14-7T, was isolated from the rhizosphere of a mangrove on Pramuka Island, Indonesia, and its taxonomic position was investigated using a polyphasic approach. The peptidoglycan type of strain PS-14-7T was A4α and lysine was the diagnostic diamino acid of the peptidoglycan. The predominant menaquinone was MK-8(H4) and the major fatty acids were anteiso-C15 : 0, C16 : 0 and iso-C16 : 0. The DNA G+C content was 72.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain PS-14-7T was closely related to Serinibacter salmoneus Kis4-28T (99.6 %). However, DNA–DNA hybridization and phenotypic characteristics revealed that strain PS-14-7T differed from Serinibacter salmoneus . Therefore, strain PS-14-7T represents a novel species of the genus Serinibacter , for which the name Serinibacter tropicus sp. nov. is proposed. The type strain is PS-14-7T ( = NBRC 110108T = InaCC A 515T). An emended description of the genus Serinibacter is also proposed.

Tropicihabitans flavus gen. nov., sp. nov., a new member of the family Cellulomonadaceae

Two novel Gram-stain positive actinobacteria, designated PS-14-16(T) and RS-7-1, were isolated from the rhizosphere of a mangrove and sea sediment, respectively, and their taxonomic positions were investigated by a polyphasic approach. Both strains were observed to form vegetative hyphae in the early phase of growth but the hyphae eventually fragment into short rods to coccoid cells. The peptidoglycan type of both strains was found to be A4α. Their predominant menaquinone was identified as MK-9(H4) and the major fatty acid as anteiso-C(15:0). The DNA G+C content was determined to be 68.4-68.5 mol%. 16S rRNA gene sequencing revealed that strains PS-14-16(T) and RS-7-1 were related to members of the family Cellulomonadaceae. Their nearest phylogenetic neighbour was found to be Sediminihabitans luteus, which is currently the only species of the genus Sediminihabitans, with a similarity of 97.94%. However, strains PS-14-16(T) and RS-7-1 were distinguishable from the members of the genus Sediminihabitans and the other genera within the family Cellulomonadaceae in terms of chemotaxonomic characteristics and phylogenetic relationship. The results of DNA-DNA hybridization experiments indicated that strains PS-14-16(T) and RS-7-1 belong to the same species. Strains PS-14-16(T) and RS-7-1 are concluded to represent a novel genus and species of the family Cellulomonadaceae, for which the name Tropicihabitans flavus gen. nov., sp. nov. is proposed. The type strain of T. flavus is PS-14-16(T) (=NBRC 110109(T) = IanCC A 516(T)). [corrected].

The Optimal Cut-off Value of Plasma BNP to Differentiate Heart Failure in the Emergency Department in Japanese Patients with Dyspnea

OBJECTIVE

In the emergency department, it is sometimes difficult to differentiate heart failure (HF) from other diseases (e.g., respiratory diseases) in patients who develop dyspnea. The plasma B-type natriuretic peptide (BNP) levels increase in patients with HF, and various levels are associated with specific New York Heart Association classes. Although the diagnosis of HF should not be made based only on the plasma BNP levels, the identification of a cut-off value for BNP to diagnose HF would be helpful.

METHODS

Patients admitted to the emergency department of our hospital with dyspnea between January 2010 and December 2011 were retrospectively reviewed. The patients whose estimated glomerular filtration rate was less than 30 mL/min/1.73 m(2) were excluded. Patients were divided into two groups: those with HF (n=131) and those without HF (n=138). The cut-off value for BNP was determined by the receiver-operating characteristic curve.

RESULTS

The area under the curve of this curve was 0.934. The optimal cut-off point for detection of HF was 234 pg/mL. The sensitivity and specificity were 87.0% and 85.5%, respectively. The fifth and 95th percentiles of the HF group were 132.2 and 2,420.8 pg/mL, respectively. Those of the non-HF group were 9.7 and 430.2 pg/mL, respectively.

CONCLUSION

Our study suggests that a plasma BNP level cut-off value of 234 pg/mL can be used to detect HF in the emergency department.

Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains

This manuscript calls for an international effort to generate a comprehensive catalog from genome sequences of all the archaeal and bacterial type strains.

Microbes hold the key to life. They hold the secrets to our past (as the descendants of the earliest forms of life) and the prospects for our future (as we mine their genes for solutions to some of the planet's most pressing problems, from global warming to antibiotic resistance). However, the piecemeal approach that has defined efforts to study microbial genetic diversity for over 20 years and in over 30,000 genome projects risks squandering that promise. These efforts have covered less than 20% of the diversity of the cultured archaeal and bacterial species, which represent just 15% of the overall known prokaryotic diversity. Here we call for the funding of a systematic effort to produce a comprehensive genomic catalog of all cultured Bacteria and Archaea by sequencing, where available, the type strain of each species with a validly published name (currently∼11,000). This effort will provide an unprecedented level of coverage of our planet's genetic diversity, allow for the large-scale discovery of novel genes and functions, and lead to an improved understanding of microbial evolution and function in the environment.

Thermotoga profunda sp. nov. and Thermotoga caldifontis sp. nov., anaerobic thermophilic bacteria isolated from terrestrial hot springs

Two thermophilic, strictly anaerobic, Gram-negative bacteria, designated strains AZM34c06T and AZM44c09T, were isolated from terrestrial hot springs in Japan. The optimum growth conditions for strain AZM34c06T were 60 °C, pH 7.4 and 0 % additional NaCl, and those for strain AZM44c09T were 70 °C, pH 7.4 and 0 % additional NaCl. Complete genome sequencing was performed for both strains, revealing genome sizes of 2.19 Mbp (AZM34c06T) and 2.01 Mbp (AZM44c09T). Phylogenetic analyses based on 16S rRNA gene sequences and the concatenated predicted amino acid sequences of 33 ribosomal proteins showed that both strains belonged to the genus Thermotoga . The closest relatives of strains AZM34c06T and AZM44c09T were the type strains of Thermotoga lettingae (96.0 % similarity based on the 16S rRNA gene and 84.1 % similarity based on ribosomal proteins) and Thermotoga hypogea (98.6 and 92.7 % similarity), respectively. Using blast, the average nucleotide identity was 70.4–70.5 % when comparing strain AZM34c06T and T. lettingae TMOT and 76.6 % when comparing strain AZM44c09T and T. hypogea NBRC 106472T. Both values are far below the 95 % threshold value for species delineation. In view of these data, we propose the inclusion of the two isolates in the genus Thermotoga within two novel species, Thermotoga profunda sp. nov. (type strain AZM34c06T = NBRC 106115T = DSM 23275T) and Thermotoga caldifontis sp. nov. (type strain AZM44c09T = NBRC 106116T = DSM 23272T).

Genome based analysis of type-I polyketide synthase and nonribosomal peptide synthetase gene clusters in seven strains of five representative Nocardia species

BACKGROUND

Actinobacteria of the genus Nocardia usually live in soil or water and play saprophytic roles, but they also opportunistically infect the respiratory system, skin, and other organs of humans and animals. Primarily because of the clinical importance of the strains, some Nocardia genomes have been sequenced, and genome sequences have accumulated. Genome sizes of Nocardia strains are similar to those of Streptomyces strains, the producers of most antibiotics. In the present work, we compared secondary metabolite biosynthesis gene clusters of type-I polyketide synthase (PKS-I) and nonribosomal peptide synthetase (NRPS) among genomes of representative Nocardia species/strains based on domain organization and amino acid sequence homology.

RESULTS

Draft genome sequences of Nocardia asteroides NBRC 15531(T), Nocardia otitidiscaviarum IFM 11049, Nocardia brasiliensis NBRC 14402(T), and N. brasiliensis IFM 10847 were read and compared with published complete genome sequences of Nocardia farcinica IFM 10152, Nocardia cyriacigeorgica GUH-2, and N. brasiliensis HUJEG-1. Genome sizes are as follows: N. farcinica, 6.0 Mb; N. cyriacigeorgica, 6.2 Mb; N. asteroides, 7.0 Mb; N. otitidiscaviarum, 7.8 Mb; and N. brasiliensis, 8.9 - 9.4 Mb. Predicted numbers of PKS-I, NRPS, and PKS-I/NRPS hybrid clusters ranged between 4-11, 7-13, and 1-6, respectively, depending on strains, and tended to increase with increasing genome size. Domain and module structures of representative or unique clusters are discussed in the text.

CONCLUSION

We conclude the following: 1) genomes of Nocardia strains carry as many PKS-I and NRPS gene clusters as those of Streptomyces strains, 2) the number of PKS-I and NRPS gene clusters in Nocardia strains varies substantially depending on species, and N. brasiliensis strains carry the largest numbers of clusters among the species studied, 3) the seven Nocardia strains studied in the present work have seven common PKS-I and/or NRPS clusters, some of whose products are yet to be studied, and 4) different N. brasiliensis strains have some different gene clusters of PKS-I/NRPS, although the rest of the clusters are common within the N. brasiliensis strains. Genome sequencing suggested that Nocardia strains are highly promising resources in the search of novel secondary metabolites.

Agromyces iriomotensis sp. nov. and Agromyces subtropicus sp. nov., isolated from soil

Three novel Gram-stain-positive bacteria, designated IY07-20T, IY07-56T and IY07-113, were isolated from soil samples from Iriomote Island, Okinawa, Japan, and their taxonomic positions were investigated by a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that the three isolates were closely related to the members of the genus Agromyces , with similarity range of 95.6–98.7 %. The isolates contained l-2,4-diaminobutylic acid, d-alanine, d-glutamic acid and glycine in their peptidoglycans. The predominant menaquinone was MK-12 and the major fatty acids were anteiso-C15 : 0 and anteiso-C17 : 0. The DNA G+C contents were 70.9–72.9 mol%. The chemotaxonomic characteristics of the isolates matched those described for members of the genus Agromyces . The results of phylogenetic analysis and DNA–DNA hybridization, along with differences in phenotypic characteristics between strains IY07-20T, IY07-56T and IY07-113 and the species of the genus Agromyces with validly published names, indicate that the three isolates merit classification as representatives of two novel species of the genus Agromyces , for which the names Agromyces iriomotensis sp. nov. and Agromyces subtropica sp. nov. are proposed; the type strains are IY07-20T ( = NBRC 106452T = DSM 26155T) and IY07-56T ( = NBRC 106454T = DSM 26153T), respectively.

Diaminobutyricibacter tongyongensis gen. nov., sp. nov. and Homoserinibacter gongjuensis gen. nov., sp. nov. belong to the family Microbacteriaceae

Two bacterial strains, KIS66-7(T) and 5GH26-15(T), were isolated from soil samples collected in the South Korean cities of Tongyong and Gongju, respectively. Both strains were aerobic, Gram-stain-positive, mesophilic, flagellated, and rodshaped. A phylogenetic analysis revealed that both strains belonged to the family Microbacteriaceae of the phylum Actinobacteria. The 16S rRNA gene sequence of strain KIS66-7(T) had the highest similarities with those of Labedella gwakjiensis KSW2-17(T) (97.3%), Cryobacterium psychrophilum DSM 4854T (97.2%), Leifsonia lichenia 2Sb(T) (97.2%), Leifsonia naganoensis JCM 10592(T) (97.0%), and Cryobacterium mesophilum MSL-15(T) (97.0%). Strain 5GH26-15(T) showed the highest sequence similarities with Leifsonia psychrotolerans LI1T (97.4%) and Schumannella luteola KHIAT (97.1%). The 16S rRNA gene sequence from KIS66-7(T) exhibited 96.4% similarity with that from 5GH26-15(T). Strain KIS66-7(T) contained a B2γ type peptidoglycan structure with D-DAB as the diamino acid; MK-13, MK-12, and MK-14 as the respiratory quinones; ai-C15:0, ai-C17:0, and i-C16:0 as the major cellular fatty acids; and diphosphatidylglycerol, phatidylglycerol, and glycolipids as the predominant polar lipids. Strain 5GH26-15T had a B2β type peptidoglycan structure with D-DAB as the diamino acid; MK-14 and MK-13 as the respiratory quinones; ai-C15:0, i-C16:0, and ai-C{vn17:0} as the major cellular fatty acids; and diphosphatidylglycerol, phatidylglycerol, and glycolipids as the predominant polar lipids. Both strains had low DNA-DNA hybridization values (<40%) with closely related taxa. Based on our polyphasic taxonomic characterization, we propose that strains KIS66-7(T) and 5GH26-15(T) represent novel genera and species, for which we propose the names Diaminobutyricibacter tongyongensis gen. nov., sp. nov. (type strain KIS66-7(T)=KACC 15515(T)=NBRC 108724(T)) and Homoserinibacter gongjuensis gen. nov., sp. nov. (type strain 5GH26-15(T)=KACC 15524(T)=NBRC 108755(T)) within the family Microbacteriaceae.

Janibacter cremeus sp. nov., an actinobacterium isolated from sea sediment

A novel Gram-stain-positive actinobacterium, designated HR08-44T, was isolated from a sea-sediment sample collected from the foreshore of Rishiri Island, Japan, and its taxonomic position was investigated by a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain HR08-44T was closely related to the members of the genus Janibacter , with pairwise sequence similarities of 97.3–98.8 %. Strain HR08-44T had peptidoglycan type A1γ, with meso-diaminopimelic acid as the diagnostic diamino acid. The predominant menaquinone was MK-8(H4) and the major fatty acids were iso-C16 : 0, C17 : 1ω8c, C17 : 0 and C18 : 1ω9c. These data supported the affiliation of the novel strain to the genus Janibacter . Meanwhile, the results of DNA–DNA hybridization and physiological and biochemical tests indicated that strain HR08-44T can be distinguished from recognized species of the genus Janibacter . Therefore, strain HR08-44T represents a novel species of the genus Janibacter , for which the name Janibacter cremeus sp. nov. is proposed; the type strain is HR08-44T ( = NBRC 107693T = DSM 26154T).

Simple and rapid characterization of mycolic acids from Dietzia strains by using MALDI spiral-TOFMS with ultra high mass-resolving power

Mycolic acids have been used as important chemotaxonomic markers. In this study, a newly developed matrix-assisted laser desorption/ionization time-of-flight mass spectrometer with a spiral ion trajectory (MALDI spiral-TOFMS) was applied to the characterization of mycolic acids of three type strains of validated species belonging to the genus Dietzia (D. papillomatosis 105045(T), D. kunjamensis NBRC 105042(T) and D. timorensis NBRC 104184(T)), by analysis of total fatty acid methyl ester fractions. In addition, owing to the high mass-resolving power of MALDI spiral-TOFMS, adjacent peaks (0.036 Da mass differences) were successfully separated, and weak peaks corresponding to oxygenated mycolic acids were detected. For all samples, the distributions of carbon-chain lengths were mainly in the range of C30-C42 and the average number of carbon-chain lengths was about 37, which agreed reasonably well with reported results for the genus Dietzia. The number of double bonds and/or cyclopropane rings was 0-2. Relative peak intensities of each mycolic acid methyl ester were used to compare the mycolic acids of the three strains. The mycolic acids of D. papillomatosis and D. kunjamensis were characterized by a high content of mycolic acids with 0-1 double bond or cyclopropane ring and an almost equal content of mycolic acids with odd- and even-numbered carbon-chain lengths. In contrast, mycolic acids of D. timorensis were characterized by a high content of mycolic acids with 1-2 double bonds and/or cyclopropane rings with an even-numbered carbon-chain length. By using MALDI spiral-TOFMS, mycolic acids from three type strains of the genus Dietzia were characterized easily and rapidly.

Paraoerskovia sediminicola sp. nov., an actinobacterium isolated from sea sediment, and emended description of the genus Paraoerskovia

A novel Gram-stain-positive actinobacterium, designated H25-14T, was isolated from a sea sediment sample, and its taxonomic position was investigated by a polyphasic approach. The peptidoglycan type of strain H25-14T was A4α and lysine was the diagnostic diamino acid of the peptidoglycan. The predominant menaquinone was MK-9(H4) and the major fatty acids were anteiso-C15 : 0 and iso-C15 : 0. The DNA G+C content was 73.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain H25-14T was closely related to Paraoerskovia marina NBRC 104352T (98.3 %). However, DNA–DNA hybridization data and phenotypic characteristics revealed that strain H25-14T differed from P. marina NBRC 104352T. Therefore, strain H25-14T represents a novel species of the genus Paraoerskovia , for which the name Paraoerskovia sediminicola sp. nov. is proposed. The type strain is H25-14T ( = NBRC 108565T = DSM 25477T). An emended description of the genus Paraoerskovia is also proposed.

Lysinibacillus chungkukjangi sp. nov., isolated from Chungkukjang, Korean fermented soybean food

One bacterial strain 2RL3-2(T) was isolated from Chungkukjang, a traditional Korean fermented food made from soybeans, and determined to be a Gram-positive, aerobic, spore-forming rod. Growth of the novel strain was optimal at 30°C and pH 7.0. The 16S rRNA gene of strain 2RL3-2(T) showed the highest level of sequence similarity to Lysinibacillus sinduriensis BLB-1(T) (99.0%), Lysinibacillus massiliensis 4400831(T) (97.1%), Lysinibacillus xylanilyticus XDB9(T) (97.0%), and Lysinibacillus odysseyi 34hs-1(T) (96.8%). Phylogenetic analysis showed that strain 2RL3-2(T) formed a robust cluster with L. sinduriensis BLB-1(T), L. massiliensis 4400831(T), and L. odyssey 34hs-1(T). The major fatty acids were anteiso-C15:0 (47.3%), iso-C16:0 (16.3%), and anteiso-C17:0 (11.3%), and the only menaquinone was MK-7. Diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine were the major polar lipids, along with an unknown phospholipid and two unknown lipids. The peptidoglycan type was A4α, with an interpeptide bridge of l-Lys-d-Asp. DNA-DNA hybridization values between strain 2RL3-2(T) and closely related Lysinibacillus species were below 43±4%. Therefore, based on phenotypic, chemotaxonomic, and phylogenetic characteristics, it was determined that strain 2RL3-2(T) represents a novel species of the genus Lysinibacillus, for which the name Lysinibacillus chungkukjangi sp. nov. is proposed. The type strain is 2RL3-2(T) (=KACC 16626(T) =NBRC 108948(T)).

Lysinimonas soli gen. nov., sp. nov., isolated from soil, and reclassification of Leifsonia kribbensis Dastager et al. 2009 as Lysinimonas kribbensis sp. nov., comb. nov

A Gram-stain-positive, non-motile rod, designated strain SGM3-12T, was isolated from paddy soil in Suwon, Republic of Korea. 16S rRNA gene sequence analysis revealed that the strain represented a novel member of the family Microbacteriaceae . The nearest phylogenetic neighbour was Leifsonia kribbensis MSL-13T (97.4 % 16S rRNA gene sequence similarity). Strain SGM3-12T and Leifsonia kribbensis MSL-13T formed a distinct cluster within the family Microbacteriaceae . Strain SGM3-12T contained MK-12(H2) and MK-11(H2) as the predominant menaquinones with moderate amounts of MK-12 and MK-11; anteiso-C15 : 0 and iso-C16 : 0 as the major cellular fatty acids (>10 % of total); and diphosphatidylglycerol, phosphatidylglycerol and unidentified glycolipids as the polar lipids. The peptidoglycan type of the isolate was B1δ with l-Lys as the diagnostic cell-wall diamino acid. On the basis of these results, strain SGM3-12T represents a novel species within a new genus, for which the name Lysinimonas soli gen. nov., sp. nov. is proposed (the type strain of the type species is SGM3-12T = KACC 13362T = NBRC 107106T). It is also proposed that Leifsonia kribbensis be transferred to this genus as Lysinimonas kribbensis comb. nov. (the type strain is MSL-13T = DSM 19272T = JCM 16015T = KACC 21108T = KCTC 19267T).

Demequina flava sp. nov. and Demequina sediminicola sp. nov., isolated from sea sediment

Two novel Gram-stain-positive bacteria, designated HR08-7T and HR08-43T, were isolated from a sea sediment sample from Rishiri Island, Hokkaido, Japan, and their taxonomic positions were investigated by a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strains HR08-7T and HR08-43T and the members of the genus Demequina formed a monophyletic cluster with similarity range of 95.5–99.0 %. The peptidoglycan type of strains HR08-7T and HR08-43T was A4β. The predominant menaquinone of both strains was demethylmenaquinone DMK-9(H4) and the major fatty acid was anteiso-C15 : 0. The DNA G+C contents of strains HR08-7T and HR08-43T were 64.5 and 62.4 mol%, respectively. The results of phylogenetic analysis and DNA–DNA hybridization, along with differences of strains HR08-7T and HR08-43T from the recognized Demequina species in phenotypic characteristics, indicate that the two strains merit classification as representatives of two novel species of the genus Demequina , for which the names Demequina flava sp. nov. and Demequina sediminicola sp. nov. are proposed; the type strains are HR08-7T ( = NBRC 105854T = DSM 24865T) and HR08-43T ( = NBRC 105855T = DSM 24867T), respectively.

Compostimonas suwonensis gen. nov., sp. nov., isolated from spent mushroom compost

A Gram-positive, aerobic, non-motile, short rod, designated SMC46T, was isolated from a spent mushroom compost sample collected in the Suwon region, South Korea. 16S rRNA gene sequence analysis revealed that strain SMC46T was a member of the family Microbacteriaceae ; however, the isolate formed a branch separate from other genera within the family. Sequence similarity between strain SMC46T and other members of the family Microbacteriaceae was ≤97 %, the highest sequence similarity being with Frigoribacterium faeni 801T and Frondihabitans australicus E1HC-02T (both 97.0 %). Some chemotaxonomic properties of strain SMC46T were consistent with those of the family Microbacteriaceae : MK-11 and MK-12 as the predominant menaquinones, anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0 as the major cellular fatty acids and diphosphatidylglycerol, phosphatidylglycerol and an unidentified glycolipid as the polar lipids. However, strain SMC46T contained a B-type peptidoglycan not previously found in the family Microbacteriaceae . The DNA G+C content was 68 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic distinctiveness, strain SMC46T was considered to represent a novel genus and species in the family Microbacteriaceae , for which the name Compostimonas suwonensis gen. nov., sp. nov. is proposed. The type strain of the type species is SMC46T ( = KACC 13354T  = NBRC 106304T).

Salinirepens amamiensis gen. nov., sp. nov., a member of the family Cryomorphaceae isolated from seawater, and emended descriptions of the genera Fluviicola and Wandonia

The taxonomic position of bacterial strain AM11-6T, isolated from seawater in Japan, was determined by using a polyphasic taxonomic approach. The strain was a strictly aerobic and Gram-staining-negative slender rod, motile by gliding. The major respiratory quinone was menaquinone-6 and the predominant cellular fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, C14 : 0 and iso-C15 : 1 G. The polar lipid pattern indicated the presence of an unidentified phospholipid, several glycolipids and an unidentified polar lipid. The G+C content of the genomic DNA was 36.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain AM11-6T clustered with members of the genera Wandonia and Fluviicola in the family Cryomorphaceae of the phylum Bacteroidetes . The strain required NaCl and MgCl2 for growth and could be differentiated from members of other genera in the family Cryomorphaceae by fatty acid composition and other phenotypic characters. On the basis of these results, we describe the novel genus and species, Salinirepens amamiensis gen. nov., sp. nov. The type strain of Salinirepens amamiensis is AM11-6T ( = NBRC 101268T = NCIMB 14607T). Emended descriptions of the genera Fluviicola and Wandonia are also proposed.

Lysinimicrobium mangrovi gen. nov., sp. nov., an actinobacterium isolated from the rhizosphere of a mangrove

A novel strain of Gram-staining-positive bacterium, designated HI08-69T, was isolated from the rhizosphere of a mangrove on Iriomote Island, Japan, and its taxonomic position was investigated by a polyphasic approach. The strain had peptidoglycan of the A4α type, with lysine as the diagnostic diamino acid. The predominant menaquinone was demethylmenaquinone DMK-9(H4) and the major fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and C16 : 0. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and an unidentified polar lipid but minor amounts of other polar lipids were also detected. The genomic DNA G+C content of strain HI08-69T was 71.7 mol%. In phylogenetic analyses based on 16S rRNA gene sequences, the novel strain and members of the genus Demequina formed a monophyletic cluster, with pairwise sequence similarities of 95.6–96.8 %. However, strain HI08-69T was clearly distinguishable from all established members of the genus Demequina in terms of several chemotaxonomic characteristics. On the basis of the phenotypic and genotypic characteristics, strain HI08-69T represents a novel species in a new genus for which the name Lysinimicrobium mangrovi gen. nov., sp. nov. is proposed. The type strain of the type species is HI08-69T ( = NBRC 105856T = DSM 24868T).

Trichoderma matsushimae and T. aeroaquaticum: two aero-aquatic species with Pseudaegerita-like propagules

Four isolates tentatively identified as Pseudaegerita matsushimae on the basis of the morphology of bulbil-like propagules were collected from substrates submerged in water in Thailand and Japan. In culture studies the two Thai isolates were found to produce phialoconidia on conidiogenous cells and phialoconidiophores whose morphology was similar to that of Trichoderma. Phylogenetic analysis based on D1/D2 regions of LSU rDNA sequences showed that the four isolates were nested in Hypocrea/Trichoderma (Hypocreales) while P. corticalis, the type species of Pseudaegerita, belongs to Hyaloscypha (Helotiales). Preliminary analysis by ISTH Web tools based on 5.8S-ITS rDNA and phylogenetic analysis based on rpb2 and tef1-int4 genes showed that the isolates have specific sequences of Trichoderma (anchors 1-5) and belong to the Hamatum clade but they grouped apart from any known species of Trichoderma. The sequences of the tef1-int4 gene, which were amplified from the authentic specimen of P. matsushimae (IMI 266915), also showed that it belongs to the Hamatum clade closely clustering with T. yunnanense but separate from our four isolates. The morphology of P. matsushimae (IMI 266915), especially the sizes of phialides and phialoconidia, were different from T. yunnanense. Thus, we conclude that IMI 266915 and our isolates are to be assigned to two different species in the Hamatum clade of Trichoderma, although both species have similar morphology of bulbils and phialoconidia. Morphology and molecular data revealed that P. matsushimae should be assigned to the genus Trichoderma as T. matsushimae and the Thai and Japanese isolates are placed in T. aeroaquaticum sp. nov. This finding supports the interpretation that aero-aquatic fungi have evolved from terrestrial fungi. We assume that these fungi probably were derived from typically soil-inhabiting species of Trichoderma; an adaptation to aquatic environments is shown by formation of bulbil-like propagules floating on water.

Meiothermus hypogaeus sp. nov., a moderately thermophilic bacterium isolated from a hot spring

A novel moderately thermophilic, red-pigmented bacterium, designated strain AZM34c11T, was isolated from the bottom of a 1000 m-deep drilled well located in a Japanese hot spring. Cells were Gram-negative and grew optimally at 50 °C, at pH 7.6 and with 0–0.3 % (w/v) NaCl. Analysis of the 16S rRNA gene sequence revealed that the isolate belonged to the genus Meiothermus. Levels of 16S rRNA gene sequence similarity between strain AZM34c11T and the type strains of recognized Meiothermus species were 88.2–94.8 %. Strain AZM34c11T was distinguished from recognized Meiothermus species by its cellular fatty acid profile: iso-C16 : 0 was one of the predominant components and hydroxy fatty acids were present only in trace amounts. The strain could also be differentiated based on its growth substrate preferences and characteristic enzyme reactions. On the basis of these results, strain AZM34c11T is considered to represent a novel species of the genus Meiothermus, for which the name Meiothermus hypogaeus sp. nov. is proposed. The type strain is AZM34c11T ( = NBRC 106114T  = DSM 23238T).

Descriptions of Actinoplanes ianthinogenes nom. rev. and Actinoplanes octamycinicus corrig. comb. nov., nom. rev

Phylogenetic analysis of ‘Actinoplanes ianthinogenes’ Coronelli et al. 1974 and ‘Actinoplanes ianthinogenes subsp. octamycini’ Gauze et al. 1979 based on 16S rRNA gene sequencing data revealed that these organisms form a clade in the family Micromonosporaceae. Morphological and chemotaxonomic characteristics of strains of these species were consistent with those of members of the genus Actinoplanes. Morphological, DNA–DNA hybridization, physiological, biochemical and chemotaxonomic data showed that ‘A. ianthinogenes’ and ‘A. ianthinogenes subsp. octamycini’ can be easily differentiated from each other and that they merit separate species status. On the basis of morphological, physiological, biochemical, chemotaxonomic and DNA–DNA hybridization data, it is concluded that ‘A. ianthinogenes’ and ‘A. ianthinogenes subsp. octamycini’ should be assigned the status of two novel species: Actinoplanes ianthinogenes nom. rev. (type strain NBRC 13996T = A/1668T = ATCC 21884T = BCRC 13611T = DSM 43864T = IMSNU 20032T = JCM 3249T = KCTC 9347T = KCTC 9592T = NCIMB 12639T = NRRL B-16720T) and Actinoplanes octamycinicus corrig. comb. nov., nom. rev. (type strain NBRC 14524T = INA 4041T = ATCC 43632T = JCM 9649T = KCTC 9593T), respectively.

Phylogenetic study of the species within the family Streptomycetaceae

Species of the genus Streptomyces, which constitute the vast majority of taxa within the family Streptomycetaceae, are a predominant component of the microbial population in soils throughout the world and have been the subject of extensive isolation and screening efforts over the years because they are a major source of commercially and medically important secondary metabolites. Taxonomic characterization of Streptomyces strains has been a challenge due to the large number of described species, greater than any other microbial genus, resulting from academic and industrial activities. The methods used for characterization have evolved through several phases over the years from those based largely on morphological observations, to subsequent classifications based on numerical taxonomic analyses of standardized sets of phenotypic characters and, most recently, to the use of molecular phylogenetic analyses of gene sequences. The present phylogenetic study examines almost all described species (615 taxa) within the family Streptomycetaceae based on 16S rRNA gene sequences and illustrates the species diversity within this family, which is observed to contain 130 statistically supported clades, as well as many unsupported and single member clusters. Many of the observed clades are consistent with earlier morphological and numerical taxonomic studies, but it is apparent that insufficient variation is present in the 16S rRNA gene sequence within the species of this family to permit bootstrap-supported resolution of relationships between many of the individual clusters.

Thioprofundum hispidum sp. nov., an obligately chemolithoautotrophic sulfur-oxidizing gammaproteobacterium isolated from the hydrothermal field on Suiyo Seamount, and proposal of Thioalkalispiraceae fam. nov. in the order Chromatiales

A novel mesophilic, facultatively anaerobic, sulfur-oxidizing bacterial strain, designated gps61T, was isolated from a surface rock sample collected from the hydrothermal field of Suiyo Seamount on the Izu-Bonin Arc in the Western Pacific Ocean. Cells of the isolate were rod-shaped with a single sheathed polar flagellum. Neither extensive internal membranes nor storage materials were present in the cells. In a 20 % CO2 atmosphere, strain gps61T grew using thiosulfate, sulfur or tetrathionate as electron donors and oxygen or nitrate as electron acceptors. Other substrates, including organic acids and sugars, did not support growth, indicating that strain gps61T was an obligate chemolithoautotroph. 16S rRNA gene sequence analysis revealed that strain gps61T was closely related to Thioprofundum lithotrophicum 106T (98.5 % sequence similarity) in the order Chromatiales. Phylogenetic trees grouped strain gps61T and Thioprofundum lithotrophicum in the same cluster along with Thioalkalispira microaerophila and Thiohalophilus thiocyanoxidans, but it was apparent from the analysis that the novel strain had definitely departed from the family lineage. On the basis of its phylogenetic position along with its morphological and physiological characteristics, strain gps61T ( = NBRC 101261T  = DSM 18546T) represents a novel species of the genus Thioprofundum, for which the name Thioprofundum hispidum sp. nov. is proposed. In addition, we propose a novel family name, Thioalkalispiraceae, in the order Chromatiales, to accommodate the genera Thioalkalispira, Thiohalophilus and Thioprofundum.

Mobilicoccus pelagius gen. nov., sp. nov. and Piscicoccus intestinalis gen. nov., sp. nov., two new members of the family Dermatophilaceae, and reclassification of Dermatophilus chelonae (Masters et al. 1995) as Austwickia chelonae gen. nov., comb. nov

Two Gram-positive bacteria, designated strains Aji5-31(T) and Ngc37-23(T), were isolated from the intestinal tracts of fishes. 16S rRNA gene sequence analysis indicated that both strains were related to the members of the family Dermatophilaceae, with 95.6-96.9% 16S rRNA gene sequence similarities. The family Dermatophilaceae contains 2 genera and 3 species: Dermatophilus congolensis, Dermatophilus chelonae and Kineosphaera limosa. However, it has been suggested that the taxonomic position of D. chelonae should be reinvestigated using a polyphasic approach, because the chemotaxonomic characteristics are not known (Stackebrandt, 2006; Stackebrandt and Schumann, 2000). Our present study revealed that strains Aji5-31(T), Ngc37-23(T) and D. chelonae NBRC 105200(T) should be separated from the other members of the family Dermatophilaceae on the basis of the following characteristics: the predominant menaquinone of strain Aji5-31(T) is MK-8(H(2)), strain Ngc37-23(T) possesses iso- branched fatty acids as major components, and the menaquinone composition of D. chelonae is MK-8(H(4)), MK-8 and MK-8(H(2)) (5 : 3 : 2, respectively). On the basis of these distinctive phenotypic characteristics and phylogenetic analysis results, it is proposed that strains Aji5-31(T) and Ngc37-23(T) be classified as two novel genera and species of the family Dermatophilaceae. The names are Mobilicoccus pelagius gen. nov., sp. nov. and Piscicoccus intestinalis gen. nov., sp. nov., and the type strains are Aji5-31(T) (=NBRC 104925(T) =DSM 22762(T)) and Ngc37-23(T) (=NBRC 104926(T) =DSM 22761(T)), respectively. In addition, D. chelonae should be reassigned to a new genus of the family Dermatophilaceae with the name Austwickia chelonae gen. nov., comb. nov.

Methanospirillum lacunae sp. nov., a methane-producing archaeon isolated from a puddly soil, and emended descriptions of the genus Methanospirillum and Methanospirillum hungatei

A mesophilic, hydrogenotrophic methanogen, designated strain Ki8-1T, was isolated from soil. Cells were strictly anaerobic, Gram-stain-negative, non-sporulating, motile by means of a single flagellum or tufted flagella, and curved or wavy rod-shaped (11–25 μm long). The temperature and pH for optimum growth were 30 °C and 7.5. The strain grew best in basal medium without the addition of NaCl. Methane was produced from H2 and formate. Acetate or yeast extract was required for growth. The G+C content of the genomic DNA of strain Ki8-1T was 45.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain Ki8-1T was a member of the genus Methanospirillum and showed 95.1 % sequence similarity to Methanospirillum hungatei NBRC 100397T. On the basis of its phenotypic characteristics and phylogenetic position, strain Ki8-1T is considered to represent a novel species of the genus Methanospirillum, for which the name Methanospirillum lacunae sp. nov. is proposed. The type strain is Ki8-1T (NBRC 104920T =JCM 16384T =DSM 22751T). Emended descriptions of the genus Methanospirillum and of Methanospirillum hungatei are also provided.

Persicobacter psychrovividus sp. nov., isolated from shellfish, and emended descriptions of the genus Persicobacter and Persicobacter diffluens

The taxonomic position of three bacterial strains, Asr22-19T, NBRC 101035 and NBRC 101041, isolated from shellfish in Japan, was determined by using a polyphasic taxonomic approach. The strains were facultatively anaerobic, motile by gliding and Gram-staining-negative slender rods. Their major respiratory quinone was menaquinone-7 and their predominant cellular fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, iso-C15 : 0 3-OH, C16 : 0 3-OH, and C16 : 0. The G+C content of the genomic DNA was 42.0–42.7 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that the strains clustered with the genus Persicobacter in the family ‘Flammeovirgaceae’. DNA–DNA relatedness values were higher than 68 % among strains Asr22-19T, NBRC 101035 and NBRC 101041, and were lower than 28 % between strain Asr22-19T and Persicobacter diffluens NBRC 15940T. The three novel strains could be differentiated from Persicobacter diffluens by several phenotypic characteristics. On the basis of these results, the novel species Persicobacter psychrovividus sp. nov. (type strain Asr22-19T=NBRC 101262T=CIP 109100T) is proposed and emended descriptions are given for the genus Persicobacter and for Persicobacter diffluens.

Ignavibacterium album gen. nov., sp. nov., a moderately thermophilic anaerobic bacterium isolated from microbial mats at a terrestrial hot spring and proposal of Ignavibacteria classis nov., for a novel lineage at the periphery of green sulfur bacteria

A moderately thermophilic chemoheterotrophic bacterium, strain Mat9-16T, was isolated from microbial mats developed in hot spring water streams from Yumata, Nagano, Japan. Cells of strain Mat9-16T were strictly anaerobic, Gram-stain-negative, non-sporulating, non-motile and short to long rods (2.0–15.5 μm in length). Strain Mat9-16T grew fermentatively with optimum growth at 45 °C, pH 7.0–7.5 and 1 % NaCl (w/v). Phylogenetic analysis based on the 16S rRNA gene revealed that strain Mat9-16T was affiliated with an uncultivated lineage, and the nearest cultivated neighbours were green sulfur bacteria belonging to the class Chlorobea with 77–83 % sequence similarity. However, strain Mat9-16T could not grow phototrophically and did not possess light-harvesting structures, morphologically and genetically, such as the chlorosomes of green sulfur bacteria. On the basis of phenotypic features and phylogenetic position, a novel genus and species are proposed for strain Mat9-16T, to be named Ignavibacterium album gen. nov., sp. nov. (=NBRC 101810T =DSM 19864T). We also propose to place the cultivated bacterial lineage accommodating the sole representative Mat9-16T in a novel class, Ignavibacteria classis nov. In addition, we present a formal description of the phylum-level taxon ‘Chlorobi’ as Chlorobi phyl. nov.

Luteimicrobium subarcticum gen. nov., sp. nov., a new member of the suborder Micrococcineae

A novel Gram-stain-positive bacterium, designated R19-04T, was isolated from a soil sample from Rishiri Island, Japan, and its taxonomic position was investigated by a polyphasic approach. Cells of strain R19-04T exhibited a rod–coccus cycle. The peptidoglycan type of the isolate was A4α; lysine was the diagnostic diamino acid. The predominant menaquinone was MK-8(H2) and the major fatty acid was anteiso-C15 : 0. The polar lipids were diphosphatidylglycerol and phosphatidylglycerol. The DNA G+C content was 72.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain R19-04T represented a novel member of the suborder Micrococcineae. Its nearest phylogenetic neighbours were the members of the genus Oerskovia, with 16S rRNA gene sequence similarity of 97.0–97.1 %. However, strain R19-04T was clearly distinguishable from members of the genus Oerskovia and phylogenetically related genera in terms of chemotaxonomic characteristics. On the basis of the chemotaxonomic and phylogenetic characteristics, a novel genus and species are proposed, Luteimicrobium subarcticum gen. nov., sp. nov. The type strain of Luteimicrobium subarcticum is R19-04T (=NBRC 105647T =DSM 22413T).

Acidocella aluminiidurans sp. nov., an aluminium-tolerant bacterium isolated from Panicum repens grown in a highly acidic swamp in actual acid sulfate soil area of Vietnam

An aluminium-tolerant bacterium, strain AL46T, was isolated from a waterweed, Panicum repens, grown in a highly acidic swamp (pH 3) at an actual acid sulfate soil area of Vietnam. Cells were Gram-negative, aerobic, non-spore-forming, non-motile rods (0.3 μm wide and 1.2–1.6 μm long). 16S rRNA gene sequence analysis indicated that strain AL46T belongs to the genus Acidocella, class Alphaproteobacteria. Strain AL46T was related most closely to the type strains of Acidocella facilis and Acidocella aminolytica (99.4 and 97.8 % 16S rRNA gene sequence similarity, respectively). Levels of DNA–DNA relatedness between strain AL46T and the above type strains were 40 %. The results of physiological and biochemical tests allowed the novel strain to be differentiated phenotypically from the two recognized Acidocella species. Data for predominant cellular fatty acids (cyclopropyl C19 : 0 and C18 : 1), major isoprenoid quinone (Q-10) and DNA G+C content (65.6 mol%) were in accordance with those reported for the genus Acidocella. Therefore, strain AL46T is considered to represent a novel species of the genus Acidocella, for which the name Acidocella aluminiidurans sp. nov. is proposed. The type strain is AL46T (=NBRC 104303T =VTCC-D9-1T).