Pectobacterium araliae sp. nov., a pathogen causing bacterial soft rot of Japanese angelica tree in Japan.

Phytopathogenic bacteria (MAFF 302110T and MAFF 302107) were isolated from lesions on Japanese angelica trees affected by bacterial soft rot in Yamanashi Prefecture, Japan. The strains were Gram-reaction-negative, facultatively anaerobic, motile with peritrichous flagella, rod-shaped, and non-spore-forming. The genomic DNA G+C content was 51.1 mol % and the predominant cellular fatty acids included summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C16 : 0, summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), summed feature 2 (comprising any combination of C12 : 0 aldehyde, an unknown fatty acid with an equivalent chain length of 10.928, C16 : 1 iso I, and C14 : 0 3OH), and C12 : 0. Phylogenetic analyses based on 16S rRNA and gyrB gene sequences, along with phylogenomic analysis utilizing whole-genome sequences, consistently placed these strains within the genus Pectobacterium. However, their phylogenetic positions did not align with any known species within the genus. Comparative studies involving average nucleotide identity and digital DNA-DNA hybridization with the closely related species indicated values below the thresholds employed for the prokaryotic species delineation (95-96 % and 70 %, respectively), with the highest values observed for Pectobacterium polonicum DPMP315T (92.10 and 47.1 %, respectively). Phenotypic characteristics, cellular fatty acid composition, and a repertoire of secretion systems could differentiate the strains from their closest relatives. The phenotypic, chemotaxonomic, and genotypic data obtained in this study show that MAFF 302110T/MAFF 302107 represent a novel species of the genus Pectobacterium, for which we propose the name Pectobacterium araliae sp. nov., designating MAFF 302110T (=ICMP 25161T) as the type strain.

Pseudomonas solani sp. nov. isolated from the rhizosphere of eggplant in Japan.

The search for bacteria that can be used as biocontrol agents to control crop diseases yielded a promising candidate, Sm006T, which was isolated from the rhizosphere of eggplant (Solanum melongena) growing in a field in Aichi Prefecture, Japan, in 2006. The cells were Gram-stain-negative, aerobic, non-spore-forming, rod-shaped and motile with one polar flagellum. The results of homology searches and phylogenetic analyses based on the 16S rRNA gene sequence indicated that Sm006T represents a member of the genus Pseudomonas. The genomic DNA G+C content was 66.3 mol% and the major cellular fatty acids (more than 5 % of the total fatty acids) were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C12 : 0. Phylogenetic analyses using the rpoD gene sequence and phylogenomic analysis of the whole genome sequence revealed that Sm006T represents a member of the Pseudomonas resinovorans group; however, its phylogenetic position does not match that of any known species of the genus Pseudomonas. The average nucleotide identity and digital DNA-DNA hybridisation values between the strain and closely related species were lower than the thresholds for prokaryotic species delineation (95-96 and 70 %, respectively), with the highest values observed for Pseudomonas tohonis TUM18999T (92.05 and 46.3 %, respectively). Phenotypic characteristics, cellular fatty acid composition and possession of 2,4-diacetylphloroglucinol biosynthetic gene cluster could be used to differentiate the strain from its closest relatives. The phenotypic, chemotaxonomic and genotypic data obtained during this study indicated that Sm006T represents a novel species of the genus Pseudomonas, for which we propose the name Pseudomonas solani sp. nov., with Sm006T (= MAFF 212523T = ICMP 24689T) as the type strain.

Clinical efficacy of Daikenchuto (DKT: TJ-100) for gastrointestinal symptoms in patients with a history of colon and rectosigmoid cancer surgery: a randomized crossover study.

PURPOSE: This randomized crossover trial investigated the effects of Daikenchuto (DKT: TJ-100) on gastrointestinal symptoms of patients after colon and rectosigmoid cancer surgery. METHODS: Among patients who had completed surgery for colon cancer, including rectosigmoid cancer, over 6 months ago, 20 who complained of gastrointestinal symptoms were enrolled. Subjects were randomly assigned to two sequences: sequences: A and B. In period 1, sequence A subjects were orally administered DKT, whereas sequence B subjects were untreated for 28 days. After a 5-day interval, in period 2, sequences A and B were reversed. Quality-of-life markers (GSRS and VAS), the Sitzmark transit study, the orocecal transit time (lactulose hydrogen breath test) and Gas volume score were evaluated before and after each period with findings compared between the presence of absence of DKT administration. RESULTS: Between sequences, there were no significant differences in clinicopathological characters or any evaluations before randomization. There was no carryover effect in this crossover trial. The administration of DKT significantly ameliorated the GSRS in total, indigestion, and diarrhea, although the planned number of subjects for inclusion in this trial was not reached. CONCLUSIONS: DKT may ameliorate subjective symptoms for postoperative patients who complain of gastrointestinal symptoms.

A novel species of lactic acid bacteria, Ligilactobacillus pabuli sp. nov., isolated from alfalfa silage.

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 duodenal gastrointestinal stromal tumor mimicking a pancreatic neuroendocrine tumor: a case report.

BACKGROUND: Duodenal gastrointestinal stromal tumors are rare. If tumor growth is extraluminal and involves the head of the pancreas, the diagnosis of a duodenal gastrointestinal stromal tumor is difficult. CASE PRESENTATION: A 44-year-old Japanese woman was referred to our hospital with anemia. An enhanced computed tomography scan showed a hypervascular mass 30 mm in diameter, but the origin of the tumor, either the duodenum or the head of the pancreas, was unclear. Upper gastrointestinal endoscopy revealed bulging accompanied by erosion and redness in part of the duodenal bulb. Mucosal biopsy was not diagnostic. Endoscopic ultrasound fine-needle aspiration was difficult to perform because a pulsating blood vessel was present in the region to be punctured. These findings led to a diagnosis of pancreatic neuroendocrine tumor invasion to the duodenum. The patient underwent pancreaticoduodenectomy. Histologically, the tumor was made up of spindle-shaped cells immunohistochemically positive for c-Kit and CD34. The tumor was ultimately diagnosed as a duodenal gastrointestinal stromal tumor. CONCLUSION: Extraluminal duodenal gastrointestinal stromal tumors are rare and mimic pancreatic neuroendocrine tumors. Endoscopic ultrasound fine-needle aspiration is useful for preoperative diagnosis, but it is not possible in some cases. Intraoperative diagnosis based on a completely resected specimen of the tumor may be useful for modifying the surgical technique.

High-Output Stoma Leading to the Diagnosis of Antiphospholipid Syndrome.

Diverting stoma (DS) is widely created in colorectal surgery. High-output stoma (HOS) is a major complication of DS, which can lead to dehydration and thrombosis. Additionally, antiphospholipid syndrome (APS) is a risk factor for thrombosis, and it rarely occurs in men. Herein, we describe a case of multiple thromboses caused by chronic dehydration after HOS. A 48-year-old man visited our hospital with fever and lower abdominal pain; he was diagnosed with sigmoid diverticulitis. He underwent laparoscopic high anterior resection for relapsing diverticulitis and diverting ileostomy during the same operation. On postoperative day 1, an output of 3,000 mL/day was observed from the ileostomy. The stoma output exceeded 2,000 mL/day, which was diagnosed as HOS, and chronic dehydration persisted despite supplementation and restriction of oral water intake. Three months postoperatively, a computed tomography scan before ileostomy closure showed multiple thrombi in the inferior vena cava, right common iliac vein, and pulmonary artery. After antithrombotic therapy, ileostomy closure was performed. As lupus anticoagulant was positive twice and APS was diagnosed, antithrombotic therapy was changed from warfarin to direct oral anticoagulants. Thrombosis did not recur 6 months postoperatively. This is the first report of a case wherein APS was present in the background of thrombosis caused by HOS or chronic dehydration. It is important to be cautious about APS when there is thrombosis after HOS to select appropriate therapeutic agents.

Pseudomonas petroselini sp. nov., a pathogen causing bacterial rot of parsley in Japan.

Phytopathogenic bacterial strains (MAFF 311094T, MAFF 311095, MAFF 311096 and MAFF 311097), which were isolated from rot lesions of parsley (Petroselinum crispum) sampled in Miyagi, Japan, were subjected to polyphasic characterization to determine their taxonomic position. The cells were Gram-reaction-negative, aerobic, non-spore-forming, motile with one or two polar flagella and rod-shaped. The 16S rRNA gene sequences analyses revealed that the strains belong to the genus Pseudomonas, exhibiting the highest sequence similarity to Pseudomonas sivasensis P7T (99.93% sequence similarity), Pseudomonas cyclaminis MAFF 301449T (99.93 %), Pseudomonas extremaustralis 14-3T (99.86 %), Pseudomonas kitaguniensis MAFF 212408T (99.86 %) and Pseudomonas antarctica CMS 35T (99.79 %). The genomic DNA G+C content was 60.1 mol%, and the major cellular fatty acids (>5 % of the total fatty acids) were C16:0, summed feature 3 (C16:1 ω7c/C16:1 ω6c), summed feature 8 (C18:1 ω7c/C18:1 ω6c) and C17:0 cyclo. The rpoD sequence-based phylogenetic and whole genome-based phylogenomic analyses demonstrated that the strains are a member of the Pseudomonas fluorescens subgroup, but their phylogenetic position does not match those of any members of this subgroup. The average nucleotide identity and digital DNA-DNA hybridization values between the strains and their closely related species were ≤90.64% and ≤41.9 %, respectively, which were below the thresholds for prokaryotic species delineation (95-96 and 70%, respectively). Phenotypic characteristics, pathogenicity toward parsley and cellular fatty acid composition could differentiate the strains from their closest relatives. The phenotypic, chemotaxonomic and genotypic data presented in this study revealed that the strains constitute a novel Pseudomonas species, for which we propose the name Pseudomonas petroselini sp. nov., with MAFF 311094T (=ICMP 24279T) being the type strain.

Foot Trajectory Features in Gait of Parkinson's Disease Patients.

Parkinson's disease (PD) is a progressive neurological disorder characterized by movement disorders, such as gait instability. This study investigated whether certain spatial features of foot trajectory are characteristic of patients with PD. The foot trajectory of patients with mild and advanced PD in on-state and healthy older and young individuals was estimated from acceleration and angular velocity measured by inertial measurement units placed on the subject's shanks, just above the ankles. We selected six spatial variables in the foot trajectory: forward and vertical displacements from heel strike to toe-off, maximum clearance, and change in supporting leg (F1 to F3 and V1 to V3, respectively). Healthy young individuals had the greatest F2 and F3 values, followed by healthy older individuals, and then mild PD patients. Conversely, the vertical displacements of mild PD patients were larger than the healthy older individuals. Still, those of healthy older individuals were smaller than the healthy young individuals except for V3. All six displacements of the advanced PD patients were smaller than the mild PD patients. To investigate features in foot trajectories in detail, a principal components analysis and soft-margin kernel support vector machine was used in machine learning. The accuracy in distinguishing between mild PD patients and healthy older individuals and between mild and advanced PD patients was 96.3 and 84.2%, respectively. The vertical and forward displacements in the foot trajectory was the main contributor. These results reveal that large vertical displacements and small forward ones characterize mild and advanced PD patients, respectively.

Locally advanced gallbladder cancer treated with effective chemotherapy and subsequent curative resection: a case report.

BACKGROUND: Surgical resection of gallbladder cancer with negative margins is the only potentially curative therapy. Most patients with gallbladder cancer are diagnosed in an advanced stage and, despite the availability of several chemotherapies, the prognosis remains dismal. We report a case of locally advanced gallbladder cancer that was successfully treated with effective cisplatin plus gemcitabine, followed by curative resection. CASE PRESENTATION: A 55-year-old Japanese female was hospitalized with right hypochondrial pain. Enhanced computed tomography revealed a 49 × 47 mm mass at the neck of the gallbladder, with suspected invasion of the liver and right hepatic artery. Endoscopic retrograde cholangiopancreatography demonstrated displacement of the upper bile duct. Intraductal ultrasonography showed irregular wall thickening and disappearance of the wall structure in bile ducts from the B4 branch to distal B2 and B3. Percutaneous transhepatic biliary biopsy revealed a poorly differentiated carcinoma. The patient was diagnosed with unresectable gallbladder cancer (T4N0M0 stage IVA). Cisplatin plus gemcitabine chemotherapy was initiated. After six courses of chemotherapy, enhanced computed tomography showed that the mass in the neck of the gallbladder had shrunk to 30 mm, Endoscopic retrograde cholangiopancreatography showed improvement of the hilar duct stenosis. A biopsy of the bile duct mucosa showed no malignant cells in the branch of the left and right hepatic ducts, the left hepatic duct, or the intrapancreatic ducts. The patient underwent conversion surgery with right and segment 4a liver resection, extrahepatic duct resection, and cholangiojejunostomy. The histopathologic diagnosis showed that the tumor cells had shrunk to 2 × 1 mm, and that R0 resection of the T2aN0M0 stage IIA tumor was successful. CONCLUSION: Although conversion surgery for gallbladder cancer is rarely possible, curative resection may offer a better prognosis, and it is important to regularly pursue possibilities for surgical resection even during chemotherapy.

[Clinical Outcome of Robot-Assisted Distal Pancreatectomy in Our Institutional Introduction].

We evaluated the clinical outcome and assessed the safety of robot-assisted distal pancreatectomy(RADP)of early 5 cases in our institutional introduction. We followed the guidelines for introduction of robot-assisted pancreatectomy proposed by Japanese Society of Endoscopic Surgery. Patients' characteristics were 2 men and 3 women, 45-79(median 52) years old, and 3 patients with neuroendocrine neoplasm, 1 with intraductal papillary neoplasm and 1 with mucinous cystic neoplasm. Spleen-preserving RADP was performed in 2 cases. Clinical outcomes of 5 cases underwent RADP were, operation time was 308-437(median 330)minutes, blood loss was 5-270(median 100)mL and none received transfusion. Postoperative pancreatic fistula and postoperative complication more than Grade Ⅲa(Clavien-Dindo classification)were none. Postoperative hospital stay was 7-11(median 8)days. RADP in our institution was safely introduced by following the proposal of guidelines.

Synchronous gastric cancer and carcinoma in situ of the pancreas.

Abnormal findings in the pancreatic duct without a mass may require serial pancreatic juice aspiration cytological examination. In cases of synchronous gastric cancer and stage 0 pancreatic cancer, spleen-preserving pancreatectomy may have advantage.

Anal Atresia in a Patient Who Had Undergone Hartmann Procedure.

BACKGROUND Hartmann procedure can be necessary for the treatment of rectal cancer and colonic perforation. The distal diverted intestinal tract is usually disregarded, while the proximal colon is diverted with a stoma. Most of the reported complications related to a diverted intestinal tract following Hartmann procedure include inflammation and intestinal tumors; however, there are only a few reports about postoperative anal complications. Herein, we report a rare case of anal atresia following Hartmann procedure. Anal atresia is generally considered as a congenital malformation; therefore, this was an extremely rare case, as there are no previous reports about anal atresia following Hartmann procedure. CASE REPORT An 84-year-old woman presented to our hospital with a persistent feeling of incomplete evacuation. She had undergone Hartmann procedure for diverticular disease of the sigmoid colon, with perforation, 5 years ago and had no major complications after the surgery. She had no history of anal disorders such as hemorrhoids or anal fissures. On examination, her anus was found to be closed by a thin skin, and computed tomography revealed stool retention in the diverted rectum. The anus was surgically opened to remove the stool, after which the feeling of incomplete evacuation resolved with no subsequent recurrence. CONCLUSIONS This is the first report of anal atresia in a patient following Hartmann procedure. The surgical intervention was effective in resolving the blockage and relieving the patient's feeling of incomplete evacuation.

Pseudomonas lactucae sp. nov., a pathogen causing bacterial rot of lettuce in Japan.

Two phytopathogenic bacteria, MAFF 301380T and MAFF 301381, isolated from rot lesions of lettuce (Lactuca sativa L. var. capitata L.) in Japan, were characterized using a polyphasic approach. The cells were Gram-reaction-negative, aerobic, non-spore-forming, rod-shaped and motile with one to three polar flagella. Analysis of the 16S rRNA gene sequences showed that the strains belong to the genus Pseudomonas and are closely related to Pseudomonas cedrina subsp. cedrina CFML 96-198T (99.72 %), Pseudomonas cedrina subsp. fulgida P515/12T (99.65 %), Pseudomonas gessardii DSM 17152T (99.51 %), Pseudomonas synxantha DSM 18928T (99.44 %), Pseudomonas libanensis CIP 105460T (99.44 %) and Pseudomonas lactis DSM 29167T (99.44 %). The genomic DNA G+C content was 60.4 mol% and the major fatty acids consisted of summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c), C16 : 0 and summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c). Phylogenetic analysis using the rpoD gene sequences and phylogenomic analyses based on the whole genome sequences demonstrated that the strains are members of the Pseudomonas fluorescens subgroup but formed a monophyletic and robust clade separated from their closest relatives. The average nucleotide identity and digital DNA-DNA hybridization values between the strains and their closely related species were 88.65 % or less and 36.3 % or less, respectively. The strains could be distinguished from their closest relatives by phenotypic characteristics, pathogenicity towards lettuce and whole-cell MALDI-TOF MS profiles. The evidence presented in this study supports the classification of the strains as representing a novel Pseudomonas species, for which we propose the name Pseudomonas lactucae sp. nov., with the type strain MAFF 301380T (=ICMP 23838T).

A Case of Stage II Ascending Colon Cancer with Cardiac Tamponade Due to Pericardial Metastasis.

BACKGROUND Malignant tumors, such as lung and breast cancers, can metastasize to the heart. However, cardiac metastasis rarely occurs in colorectal cancer. Cardiac metastasis cases are typically asymptomatic and rarely cause cardiac tamponade. Heart failure due to systemic metastasis is a terminal symptom; therefore, cardiac metastasis is rarely diagnosed when a patient is alive. We report a case of stage II ascending colon cancer with cardiac tamponade due to pericardial metastasis. CASE REPORT The patient was a 63-year-old woman who underwent laparoscopic ileocecal resection for ascending colon cancer. The final pathological diagnosis was stage IIB cancer. At the time of surgery, computed tomography scans revealed no metastases to the regional lymph nodes, liver, lungs, and other organs. The patient was then referred for dyspnea 5 months after the surgery. Computed tomography revealed large quantities of pericardial effusion, and the patient was diagnosed with cardiac tamponade. The symptoms were alleviated after pericardiocentesis. Cytological examination of the pericardial fluid confirmed the diagnosis of adenocarcinoma, and by extension, cardiac metastasis of the ascending colon cancer. Anticancer agents were recommended, but the patient opted for palliative treatment. CONCLUSIONS We report a rare case of ascending colon cancer with pericardial metastasis. The advancements in chemotherapy have made the prognosis of colorectal cancer more favorable. The prevalence of pericardial metastasis is expected to increase as well. As such, it is necessary to discuss similar case encounters and establish appropriate treatment.

A liver metastasis 7 years after resection of a low-risk duodenal gastrointestinal stromal tumor.

Duodenal gastrointestinal stromal tumors (dGISTs) are rare, and a lack of consensus exists regarding their treatment, particularly for recurrent disease. We herein report a rare case of liver metastasis 7 years after resection of a low-risk duodenal gastrointestinal stromal tumor. A 45-year-old woman revealed positive fecal occult blood. Upper gastrointestinal endoscopy revealed a submucosal duodenal tumor with ulceration and oozing on the apex. Endoscopic ultrasound showed a hypoechoic mass originating in the submucosa. Contrast-enhanced abdominal computed tomography (CT) revealed a 30-mm hyper-vascular tumor in the duodenal bulb. The patient underwent partial resection of the duodenal bulb with distal gastrectomy, followed by Roux-en-Y reconstruction. Histopathological evaluation revealed a tumor comprised of spindle-shaped cells including 5 mitotic figures per 50 high-power fields. Immunohistochemical evaluation indicated that the tumor cells were positive for c-Kit and CD34 expression. The tumor was diagnosed as low-risk dGIST. Postoperative follow-up was continued, and 7 years later, CT revealed a 39-mm enhanced tumor in liver segment 4. The tumor was diagnosed as a metastatic liver tumor, and the patient underwent S4 partial hepatectomy. As a result of histological and immunohistochemical analysis, the tumor was diagnosed as a liver metastasis from dGIST. The patient has been receiving oral imatinib 400 mg daily and remains free of disease 5 years after her last surgery. Low-risk dGIST can metastasize relatively long after surgery. However, an excellent long-term prognosis may be achieved by combining complete resection and imatinib therapy in patients with recurrent liver metastases.

Peritoneal lavage with hydrogen-rich saline can be an effective and practical procedure for acute peritonitis.

PURPOSE: Acute peritonitis has remained a fatal disease despite of recent advances in care and treatment, including antibiotic and anticoagulant treatments. The cause of death is mostly sepsis-induced multiple organ failure. Oxidative stress can play an important role in this situation, but antioxidant therapy to capture any excessive reactive oxygen species has not yet been fully established. METHODS: Two experiments were performed. In the first experiment, we confirmed the effects of peritoneal lavage with hydrogen-rich saline (HRS) after a cecal ligation and puncture (CLP) operation in rats. In the second experiment, the changes in the hemodynamic state following this procedure were observed in a porcine model of abdominal sepsis to evaluate its safety and utility. RESULTS: Peritoneal lavage with HRS significantly improved the survival after CLP in rats, and it ameliorated the levels of sepsis-induced organ failure. Moreover, it showed anti-inflammatory and anti-apoptosis as well as antioxidant effects. The second experiment demonstrated the potential safety and feasibility of this procedure in a large animal model. CONCLUSION: This procedure can improve survival after sepsis through mitigating the sepsis-induced organ failure by inhibiting oxidative stress, apoptosis, and inflammatory pathways. Peritoneal lavage with HRS may therefore be an effective, safe, and practical therapy for patients with acute peritonitis.

Pseudomonas allii sp. nov., a pathogen causing soft rot of onion in Japan.

Six phytopathogenic bacterial strains, MAFF 301512, MAFF 301513, MAFF 301514T, MAFF 301515, MAFF 301516 and MAFF 301517, were isolated from soft rot lesions of onion (Allium cepa L.) in Japan. The cells were Gram-reaction-negative, aerobic, non-spore-forming, motile with one or two polar flagella and rod-shaped. Analysis of their 16S rRNA gene sequences showed that they belong to the genus Pseudomonas, with the highest similarities to Pseudomonas poae DSM 14936T (99.86 %), Pseudomonas simiae OLiT (99.85 %), Pseudomonas trivialis DSM 14937T (99.79 %) and Pseudomonas extremorientalis KMM 3447T (99.79 %). Their genomic DNA G+C content was 60.9 mol% and the major fatty acids (>5 % of the total fatty acids) present were C16 : 0, summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c), summed feature 8 (C18 : 1 ω7c /C18 : 1 ω6c) and C17 : 0 cyclo. Phylogenetic and phylogenomic analyses based on the rpoD gene and whole genome sequences, respectively, demonstrated that the strains belong to the Pseudomonas fluorescens subgroup, but form a monophyletic and robust clade, with Pseudomonas azotoformans as their neighbour. Between the strains and P. azotoformans, the average nucleotide identity scores were 95.63-95.70 %, whereas the digital DNA-DNA hybridization scores of the strains against their closest relatives, including P. azotoformans, were 65.4 % or less, which are lower than the 70 % cut-off for prokaryotic species delineation. The strains were differentiated from their closest relatives by phenotypic characteristics, pathogenicity in onion and cellular fatty acid composition. The phenotypic, chemotaxonomic and genotypic data showed that the strains represent a novel Pseudomonas species, proposed to be named Pseudomonas allii sp. nov., with MAFF 301514T (=ICMP 23680T) being the type strain.

Draft Genome Sequences of Nine Japanese Strains of the Kiwifruit Bacterial Canker Pathogen Pseudomonas syringae pv. actinidiae Biovar 3.

Pseudomonas syringae pv. actinidiae is the pathogen that causes kiwifruit bacterial canker and is categorized into several groups (biovars). In Japan, biovar 3, known as the pandemic group, was first discovered in 2014. Here, we sequenced the genomes of nine Japanese biovar 3 strains.

Pseudomonas brassicae sp. nov., a pathogen causing head rot of broccoli in Japan.

Phytopathogenic bacteria, MAFF 212426, MAFF 212427T, MAFF 212428 and MAFF 212429, were isolated from head rot lesions of broccoli (Brassica oleracea L. var. italica Plenck) in Hokkaido, Japan, and subjected to polyphasic taxonomic characterization. The cells were Gram-reaction-negative, aerobic, non-spore-forming, motile with one or two polar flagella, rod-shaped and formed pale yellow colonies. Results of 16S rRNA gene sequence analysis showed that they belong to the genus Pseudomonas with the highest similarity to 'Pseudomonas qingdaonensis' JJ3T (99.86 %), Pseudomonas laurentiana GSL-010T (99.22 %), Pseudomonas huaxiensis WCHPs060044T (99.01 %), Pseudomonas japonica NBRC 103040T (98.87 %) and Pseudomonas alkylphenolica KL28T (98.73 %). The genomic DNA G+C content was 63.4 mol% and the major fatty acids (>5 % of the total fatty acids) were summed feature 3 (C16 : 1 ω7c / C16 : 1 ω6c), C16 : 0, summed feature 8 (C18 : 1 ω7c / C18 : 1 ω6c) and C17 : 0 cyclo. Multilocus sequence analysis using the partial rpoD, gyrB and rpoB gene sequences and phylogenomic analyses based on the whole genome sequences demonstrated that the strains are members of the Pseudomonas putida group, but form a monophyletic, robust clade separated from their closest relatives. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values corroborated their novel species status, with 88.39 % (ANI) and 35.8 % (dDDH) as the highest scores with 'P. qingdaonensis' JJ3T. The strains were differentiated from their closest relatives by phenotypic characteristics, pathogenicity on broccoli, and whole-cell MALDI-TOF mass spectrometry profiles. The phenotypic, chemotaxonomic and genotypic data showed that the strains represent a novel Pseudomonas species, for which the name Pseudomonas brassicae sp. nov. is proposed. The type strain is MAFF 212427T (=ICMP 23635T).