Type Strain Research Articles

Identification and characterisation of carbapenem-resistant Streptococcus nidrosiense sp. nov. isolated from blood culture

BackgroundThis study aimed to investigate a highly resistant strain of Streptococcus sp. isolated from a patient with bloodstream infection and determine its taxonomic classification. MethodsThe strain was isolated from blood culture from a 65-year-old male patient admitted to St. Olavs University hospital, Trondheim, Norway, in 2023. Antimicrobial susceptibility testing as well as phenotypic and biochemical characterization were performed. Whole genome sequencing was conducted and genomic comparison to Streptococcus type strains was carried out. ResultsThe strain was initially identified as Streptococcus mitis/oralis but showed significant genetic differences, suggesting that it belonged to an undescribed species within the Streptococcus genus. Phenotypic and biochemical characterization identified the strain as a non-motile, facultative anaerobic bacterium with α-hemolysis. Antimicrobial susceptibility testing showed resistance to all beta-lactams tested. Genomic analyses confirmed the classification of the strain as a novel species, which was designated Streptococcus nidrosiense. ConclusionThis study combines conventional phenotypic tests with whole genome sequencing for accurate taxonomic classification of a bacterial strain isolated from blood culture. The identification of a novel species within the Streptococcus genus contributes to the understanding of microbial diversity and antibiotic resistance of the Streptococcus genus in clinical settings.

Description of Aliirhizobium terrae sp. nov., A Plant Growth-Promoting Bacterium Isolated from a Maize-Rice Rotation Agriculture Field.

A polyphasic taxonomic approach was used to characterize a novel bacterium, designated strain CC-CFT758T, isolated from a maize-rice rotation agriculture field in Taiwan. The cells are aerobic, Gram-stain-negative, rod-shaped, positive for catalase and oxidase, and grow at 20-30°C (optimal 30℃), at pH 6.0-8.0 (optimal 8.0), and with 0-4% (w/v) NaCl (optimum, 2-3%). Phylogenetic analysis based on 16S rRNA gene sequencing, the strain CC-CFT758T belongs to the genus "Aliirhizobium" of the family Rhizobiaceae. The closest known relatives of this strain are "Aliirhizobium wenxiniae" 166T (with 98.7% similarity), "Aliirhizobium cellulosilyticum" SEMIA 448T (with 97.9% similarity), and "Aliirhizobium smilacinae" PTYR-5T (with 97.0% similarity). The genome size was 5.9 Mbp, with a G + C content of 60.6%. Values of digital DNA-DNA hybridization between the strain and closely related species were 29.5% for "Ali. cellulosilyticum", and 23.9% for "Ali. wenxiniae" and "Ali. smilacinae". Strain CC-CFT758T exhibited the highest orthologous average nucleotide identity (OrthoANI) values with members of the genus "Aliirhizobium", ranging from 80.4 to 81.6% (n = 3). Chemotaxonomical analysis indicated that strain CC-CFT758T contained C16:0, C16:0 3OH, C19:0 cyclo ω8c, C14:0 3OH/iso-C16:1 I, and C18:2 ω6,9c/ante C18:0 as dominant fatty acids, and the major polyamines were putrescine and spermidine. The polar lipids comprised diphosphatidylglycerol, phosphatidylcholin, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, seven unidentified aminolipids, three unidentified phospholipids, and two unidentified polar lipids. Strain CC-CFT758T exhibited distinct phylogenetic, phenotypic, and chemotaxonomic characteristics, as well as unique results in comparative analysis of 16S rRNA gene sequence, OrthoANI, AAI, dDDH, and phylogenomic placement. Therefore, this strain represents a new species of the genus "Aliirhizobium", for which the name Aliirhizobium terrae sp. nov. is proposed, with the type strain is CC-CFT758T (= BCRC 81364T = JCM 35482T).

Description and genome analysis of a novel archaeon isolated from a syntrophic pyrite-forming enrichment culture and reclassification of Methanospirillum hungatei strains GP1 and SK as Methanospirillum purgamenti sp. nov.

The archaeal isolate J.3.6.1-F.2.7.3T was obtained from an anaerobic enrichment culture, where it may play an important role in methane production during pyrite formation. The new isolate formed a species-level clade with Methanospirillum hungatei strains GP1 and SK, which is separate from the type strain JF-1T. Cultivation-independent surveys indicate the occurrence of this phylogenetic group in sediments and anaerobic digesters. The abundance of this clade appears to be negatively affected by high nitrogen loads, indicating a sensitivity to certain nitrogen compounds that is not known in M. hungatei JF-1T. The relatively large core genome of this Methanospirillum clade is indicative of niche specialization and efficient control of horizontal gene transfer. Genes for nitrogenase and F420-dependent secondary alcohol dehydrogenase contribute to the metabolic versatility of this lineage. Characteristics of the new isolate such as the ability to utilize 2-propanol as an electron donor or the requirement for acetate as a carbon source are found also in the strains GP1 and SK, but not in the type strain M. hungatei JF-1T. Based on the genomic differences to related species, a new species within the genus Methanospirillum is proposed with the name M. purgamenti sp. nov. The determined phenotypic characteristics support this proposal and indicate a metabolic adaptation to a separate ecological niche.

Identification of two novel B-cell epitopes located on the spike protein of swine acute diarrhea syndrome coronavirus

Swine acute diarrhea syndrome coronavirus (SADS-CoV) is an emerging alpha-coronavirus that causes diarrhea in piglets and results in serious economic losses. During SADS-CoV infection, the spike protein (S) serves as a crucial structural component of the virion, interacting with receptors and eliciting the production of neutralizing antibodies. Due to the potential risk of zoonotic transmission of SADS-CoV, the identification and screening of epitopes on the S glycoproteins will be crucial for development of sensitive and specific diagnostic tools. In this study, we immunized BALB/c mice with recombinant SADS-CoV S trimer protein and generated two S1-specific monoclonal antibodies (mAbs): 8D6 and 6E9, which recognized different linear B-cell epitopes. The minimal fragment recognized by mAb 8D6 was mapped to 311NPDQRD316, the minimal fragment recognized by mAb 6E9 was mapped to 492ARFVDRL498. Homology analysis of the regions corresponding to 13 typical strains of different SADS-CoV subtypes showed high conservation of these two epitopes. These findings contribute to a deeper understanding of the structure of the SADS-CoV S protein, which is valuable for vaccine design and holds potential for developing diagnostic methods to detect SADS-CoV.

Reliable delineation of Bacillus cytotoxicus from other members of the Bacillus cereus group by MALDI-TOF MS – An extensive validation study

Bacillus cytotoxicus is classified as a thermotolerant member of the Bacillus cereus group, producing the diarrhoea causing cytotoxin K1. This species came into the focus of food microbiologists when the type strain was isolated as the cause of a fatal food-borne outbreak. However, knowledge of the role of B. cytotoxicus as a food-borne microbe and data on its prevalence in food is still limited today. One reason for this is the lack of an easy to perform method of identification at the species level other than PCR, due to the highly similar phenotype of many B. cereus group representatives. Matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS) is widely used for the identification of microorganism species. This study describes the formal validation of a MALDI-TOF MS system for a reliable differentiation between B. cytotoxicus and other members of the B. cereus group. An extensive number of well-supported individual spectra from B. cytotoxicus, several other species of the B. cereus group, and 652 other microorganism species in a taxonomically wide range served as data sets. These were used to perform the validation for two database compilations: the commercial MALDI-Biotyper version K, and an extended compilation, including reference spectra from an open collection of spectra created by several users. Using both database combinations, the obtained values fulfil the formal criteria for the targeted identification of B. cytotoxicus in accordance with a national guideline for the validation of MALDI-TOF MS parameters in food analysis, with significant improvements due to the expanded database. By using 183 single spectra from 170 isolates, created in eleven different laboratories, the number of samples significantly exceeded the sample sizes for validation currently specified for ISO 16140–4:2020 for the validation of identification methods in food microbiology by single laboratories. Therefore, the method is suitable for routine application in an accredited laboratory context.

The Impact of the Major Endoribonucleases RNase E and RNase III and of the sRNA StsR on Photosynthesis Gene Expression in Rhodobacter sphaeroides Is Growth-Phase-Dependent.

Rhodobacter sphaeroides is a facultative phototrophic bacterium that performs aerobic respiration when oxygen is available. Only when oxygen is present at low concentrations or absent are pigment-protein complexes formed, and anoxygenic photosynthesis generates ATP. The regulation of photosynthesis genes in response to oxygen and light has been investigated for decades, with a focus on the regulation of transcription. However, many studies have also revealed the importance of regulated mRNA processing. This study analyzes the phenotypes of wild type and mutant strains and compares global RNA-seq datasets to elucidate the impact of ribonucleases and the small non-coding RNA StsR on photosynthesis gene expression in Rhodobacter. Most importantly, the results demonstrate that, in particular, the role of ribonuclease E in photosynthesis gene expression is strongly dependent on growth phase.

First report of Erwinia pyrifoliae causing flower blight and fruit rot on greenhouse-grown Fragaria × ananassa in the United States.

Erwinia pyrifoliae causes disease of pear (Pyrus spp.), apple (Malus spp.), and strawberry (Fragaria × ananassa) (Wenneker and Bergsma-Vlami 2015), which are economically important commodities in the US. Disease symptoms on pear and apple are indistinguishable from those caused by the non-quarantine fire blight pathogen, E. amylovora (Kim et al. 1999), which also causes disease on strawberries (Atanasova et al. 2005). Samples of greenhouse-grown strawberry 'Albion' from Ohio were submitted to the Purdue Plant and Pest Diagnostic Lab in December 2023. Fruits were stunted with brown lesions, while sepals and pedicels had brown-black water-soaked lesions. Cut fruit exuded bacterial ooze from the main vascular bundle. Bacterial streaming was observed microscopically from symptomatic tissue which tested positive with the E. amylovora ImmunoStrip® (Agdia Inc., Elkhart, IN); reported by the manufacturer to cross-react with E. pyrifoliae. Isolation from symptomatic tissue produced pure cultures on sucrose peptone agar and Kings medium B after incubation at 27°C for 48 hr, and colonies appeared circular and white/opaque. Crude DNA extractions were prepared by boiling colony suspensions in Tris-EDTA buffer. Two independent real-time PCR tests specific for E. pyrifoliae (Lehman et al. 2008; Yasuhara-Bell et al. 2024) produced positive results. Conventional PCR using an E. pyrifoliae-specific primer set targeting a divergent region between pstS and glmS genes (Wensing et al. 2011) also produced positive results. The amplicon was Sanger-sequenced and deposited into NCBI GenBank (Accession PP757383). BLASTn analysis using the Nucleotide collection and Whole-genome shotgun contigs revealed top matches (100% query coverage; 97.5% identity to type strain DSM 12163) with E. pyrifoliae only; next closest match was E. amylovora (53% query coverage). To confirm Koch's postulates, immature fruit of six healthy strawberry 'Albion' plants were wounded with a sterile pipette tip and then submersed in a bacterial suspension in sterile deionized water (DI H2O) (3.1×107 cells/ml). Fruit of six additional plants were mock inoculated using sterile DI H2O. Plants were placed in plastic bags for 48 hr at room temperature with a 12-hr photoperiod. Symptoms were first observed on inoculated plants 1.5 days post-inoculation (DPI). Brown discoloration was observed within fruit and as spreading lesions on fruit pedicels by 4 DPI; mock-inoculated plants remained asymptomatic. Bacterial streaming from symptomatic tissue allowed successful re-isolation of the bacterium. Molecular testing confirmed isolates to be E. pyrifoliae, thus completing Koch's postulates. Following initial confirmation, additional samples of infected strawberry ('Albion' and 'GB96') from the same greenhouse were confirmed positive for E. pyrifoliae by molecular testing and sequencing. To our knowledge this is the first time Erwinia pyrifoliae was detected in the US. There are many known pathways of introduction from Asia and Europe; however, pstS-glmS sequence comparison with strawberry isolates from the Netherlands (sequences provided by M.J.C. Pel) suggests this US strawberry strain is unique, but most closely related to Japanese strains (98.5% identity). Potential origin of this strain is unknown, but comparative genomics studies to investigate relatedness among strains are planned.

Salinicola avicenniae sp. nov., a Novel Gammaproteobacterium Isolated from Mangrove Plant, Avicennia marina, in Beibu Gulf, China.

Two endophytic bacterial strains, designated S1-1-2T and S1-1-8, were isolated from the leaves of a mangrove plant, Avicennia marina. The isolates were Gram-stain-negative, motile, rod-shaped bacteria with lateral flagella. Growth occurred at 4-41°C, pH 4.0-11.0, and 0.5-25.0% NaCl. The predominant fatty acids of the novel strains were C18:1 ω6c/ω7c, C19:0 cyclo ω8c, and C16:0. The predominant respiratory quinone was Q-9. The DNA G + C contents of strains S1-1-2T and S1-1-8 analyzed by genome sequences were 63.8%. Phylogenetic analysis based on 16S rRNA gene sequences obtained using sanger sequencing and whole-genome phylogenetic analysis revealed an affiliation between the two strains and the genus Salinicola in the class Gammaproteobacteria. Detailed genotypic, chemotaxonomic, and phenotypic data support the conclusion that these two strains should be described as a novel species in the genus Salinicola. Here, Salinicola avicenniae sp. nov. (type strain S1-1-2T = LMG 32655T = MCCC 1A19027T) is proposed.

Dolosigranulum savutiense sp. nov., isolated from human upper respiratory samples collected in Botswana.

Four strains (MSK211, MSK294T, MSK312, MSK433) of a novel Dolosigranulum species were cultured from nasopharyngeal swabs collected from mother-infant dyads in southern Botswana. These strains grew optimally on tryptic soy agar with 5% sheep blood solid medium and in fastidious bacteria broth. Colonies on tryptic soy agar with 5% sheep blood agar appeared grey or white with a flat, smooth surface and variable alpha haemolysis. Cells were Gram-positive, non-spore-forming, non-motile cocci that lacked catalase or oxidase activity. Major fatty acids were C16 : 0 (palmitic acid), C18 : 1 ω9c (oleic acid), and C18 : 0 (stearic acid). Analyses of 16S rRNA gene sequences identified these strains as belonging to the genus Dolosigranulum (family Carnobacteriaceae), which currently contains only a single validly published species (Dolosigranulum pigrum). Whole-genome sequencing revealed that the genomes of these strains are 1.98-2.07 Mbp in size and have a G+C content of 39.6-39.9 mol%. Comparisons of these genomes to publicly available genomes of D. pigrum yielded average nucleotide identities and in silico DNA-DNA hybridization values of 92.3-92.9% and 49.1-51.4%, respectively. These results indicate that these strains represent a novel species of Dolosigranulum, for which we propose the name Dolosigranulum savutiense sp. nov., with the type strain MSK294T (=DSM 117171T=JCM 36673T).

Mechanistic insights into antifungal potential of Alexidine dihydrochloride and hexachlorophene in Candida albicans: a drug repurposing approach.

Candida albicans has been listed in the critical priority group by the WHO in 2022 depending upon its contribution in invasive candidiasis and increased resistance to conventional drugs. Drug repurposing offers an efficient, rapid, and cost-effective solution to develop alternative therapeutics against pathogenic microbes. Alexidine dihydrochloride (AXD) and hexachlorophene (HCP) are FDA approved anti-cancer and anti-septic drugs, respectively. In this study, we have shown antifungal properties of AXD and HCP against the wild type (reference strain) and clinical isolates of C. albicans. The minimum inhibitory concentrations (MIC50) of AXD and HCP against C. albicans ranged between 0.34 and 0.69 µM and 19.66-24.58 µM, respectively. The biofilm inhibitory and eradication concentration of AXD was reported comparatively lower than that of HCP for the strains used in the study. Further investigations were performed to understand the antifungal mode of action of AXD and HCP by studying virulence features like cell surface hydrophobicity, adhesion, and yeast to hyphae transition, were also reduced upon exposure to both the drugs. Ergosterol content in cell membrane of the wild type strain was upregulated on exposure to AXD and HCP both. Biochemical analyses of the exposed biofilm indicated reduced contents of carbohydrate, protein, and e-DNA in the extracellular matrix of the biofilm when compared to the untreated control biofilm. AXD exposure downregulated activity of tissue invading enzyme, phospholipase in the reference strain. In wild type strain, ROS level, and activities of antioxidant enzymes were found elevated upon exposure to both drugs. FESEM analysis of the drug treated biofilms revealed degraded biofilm. This study has indicated mode of action of antifungal potential of alexidine dihydrochloride and hexachlorophene in C. albicans.

Rufibacter psychrotolerans sp. nov., a Cold-Tolerating Novel Species Isolated from Desert Soil.

Strain SYSU D00308T, a short-rod-shaped bacterium, was isolated from a sandy soil collected from the Gurbantunggut Desert, Xinjiang, PR China. Strain SYSU D00308T was Gram-stain-negative, aerobic, pink-pigmented, non-motile, catalase- and oxidase-positive. The strain grew at 4-37 ℃, pH 5.0-8.0 and 0-1.5% (w/v) NaCl. 16S rRNA gene sequencing analyses demonstrated that strain SYSU D00308T belonged to the genus Rufibacter and exhibited the highest sequence similarity (97.4%) to Rufibacter glacialis MDT1-10-3T. Summed features 3, 4, and iso-C15:0 were the major fatty acids, and menaquinone 7 (MK-7) was the sole respiratory menaquinone. The polar lipid profiles comprised phosphatidylethanolamine, an unidentified glycolipid, an unidentified phospholipid, two unidentified aminophospholipids, and two unidentified lipids. The genome size and DNA G + C content of strain SYSU D00308T were 5,176,683 bp and 54.8%, respectively. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between SYSU D00308T and members of the genus Rufibacter were 77.7-81.8% and 20.4-23.4% respectively, which were less than the corresponding thresholds (ANI: 95-96%; dDDH: 70%) for prokaryotic species definition. According to the genotypic, phenotypic and phylogenetic characteristics, strain SYSU D00308T represents a novel species of the genus Rufibacter. We propose the name, Rufibacter psychrotolerans sp. nov., with SYSU D00308T (= CGMCC 1.18621T = KCTC 82275T = MCCC 1K04970T) as the type strain.

Description of Pseudomarimonas salicorniae sp. nov., Isolated from Salicornia herbacea L. in the Tidal Flat of the Yellow Sea.

A Gram-stain-negative, strictly aerobic, non-motile, rod-shaped, designated strain CAU 1642T, was isolated from a Salicornia herbacea collected from a tidal flat in the Yellow Sea. Strain CAU 1642T grew optimally at pH 8.0 and 30°C. The highest 16S rRNA gene sequence similarity was 97.25%, with Pseudomarinomonas arenosa CAU 1598T, and phylogenetic analysis indicated that strain CAU 1642T belongs to the genus Pseudomarinomonas. The major cellular fatty acids were iso-C15:0, iso-C16:0, and summed feature 9 (iso-C17:1ω9c and/or 10-methyl C16:0). Ubiquinone-8 was the major respiratory quinone. The draft genome of strain CAU 1642T was 4.5Mb, with 68.7mol% of G + C content. The phylogenetic, phenotypic, and chemotaxonomic analysis data reveal strain CAU 1642T to be of a novel genus in the family Lysobacteraceae, with the proposed name Pseudomarinomonas salicorniae sp. nov. with type strain CAU 1642T (= KCTC 92084T = MCCC 1K07085T).

First Report of Mango Stem-end Rot Caused by Pestalotiopsis kenyana in Yunnan Province, China.

Stem End Rot (SER) is a devastating post-harvest disease of mango fruits causing severe losses during storage. In 22 July 2023, 31 out of 50 intact mangoes (cv. Sensation) collected from five orchards in Huaping county (26°37'N 101°15') showed typical symptoms of SER after stored for 9 d in room temperature (24-28℃). Initially, small dark brown to black spots appeared around the fruit peduncle, which rapidly expanded through the pulp tissues. The symptomatic mangoes were surface disinfected by 3% NaClO for 30 s after soaking in 75% alcohol for 3 min, and cleaned by sterile water for 3 times. Tissues were cut from the edge of lesions, dried by sterile filter paper, transferred to PDA and cultured at 28 ℃ for 5 d (Tovar-Pedraza et al., 2020). The single-spore isolation method was used to obtain pure culture. Thirty eight isolates presented four distinct kind of morphology on PDA medium. Among them, 11 isolates with same morphology were significantly distinct from common pathogens of SER. The colonies were white and pale yellow on reverse side. Mycelia grew fast and reached the edge of 90 mm Petri dish after cultured for 5d. Pycnidia were black and scattered on the mycelial mats after 15-20 d. Conidia were fusoid, straight to slightly curved, four septa, and brown. Pigmented median cells doliiform, 14.97 - 18.62(16.11 ±0.89)×5.61- 7.28 (6.61±0.51) μm. Apical cell hyaline, subcylindrical; 1-3 tubular transparent apical appendages 12.27 - 16.68 (13.65±3.78)×1.14 - 1.99 (1.59±0.36) μm. Basal cell conical with a truncate base, hyaline, and 1-2 tubulose basal appendages with 2.85 - 7.97 (5.18±1.88)×0.99 - 1.85 (1.38±0.29) μm (n=50). These fungi were described as Pestalotiopsis kenyana. based on morphological characters (Maharachchikumbura et al., 2014) which were different from isolates characterized as other common SER pathogens (Botryosphaeria, Neofusicoccum). Based on morphology, HPSX-4 was selected for further identification. ITS region, tef1-α, β-tub of HPSX-4 were amplified and sequenced (Xun et al., 2023). The sequences were deposited in GenBank (ITS:OR889126, tef1-α:OR913431, β-tub: OR913432). The ITS, tef1-α, β-tub sequence of HPSX-4 showed 100% (525/525)，99.59% (241/242), and 100% (742/742) identity to the P. kenyana CBS442.67 sequences (ITS: NR147549，tef1-α: KM199502, β-tub: KM199395), respectively. HPSX-4 clustered with P. kenyana CBS 442.67 (type strain) based on maximum likelihood method by MEGA 7.0.21(Minh et al., 2013). Pathogenicity test was performed on 12 healthy mangoes (cv. Golek) by placing mycelial plugs around the peduncle and the middle of the fruit by pin-prick method according to Feng et al.(2023). Sterile PDA were used as control (three mangoes). Every inoculated fruit was incubated at 28°C, 95% ± 3% humidity with three replicates for each treatment. The experiment was repeated three times. Typical symptoms of SER were observed. There were no symptoms in the control group. The strain was reisolated and identified as P. kenyana with the method mentioned above which fulfilled Koch's postulates. This is the first report of P. kenyana causing SER disease on Mangifera indica L.. This study expands our understanding of the pathogen range of mango SER which conducive to prevent and control the SER caused by P. kenyana.

Francisella sciaenopsi sp. nov. isolated from diseased red drum Sciaenops ocellatus in Florida, USA.

Piscine francisellosis is one of the most important bacterial diseases affecting various fish species worldwide. Francisella orientalis, F. noatunensis, and F. salimarina (F. marina) have been reported as etiological agents of disease in fish. A Francisella sp. was isolated from several diseased red drum Sciaenops ocellatus experiencing morbidity in Florida, USA, in 2008. In this study, molecular and phenotypic characterization of the recovered isolate was conducted. Phenotypically, the isolate showed a biochemical reaction profile distinct from that of F. orientalis and F. salimarina. Although the 16S rRNA sequence of this isolate shared 99.61% identity to the type strain of F. philomiragia O#319LT, whole genome analysis (average nucleotide identity <95%; digital DNA-DNA hybridization <70%) and a multilocus sequence analysis of 8 concatenated housekeeping genes in comparison with other Francisella spp. indicated that this isolate was a novel Francisella species, more closely related to F. orientalis. Immersion, intracoelomic injection, and co-habitation challenges using a Nile tilapia Oreochromis niloticus fingerling model of infection were done to investigate virulence in a piscine model. Variably pigmented granulomas and pigmented macrophage aggregates were observed in the kidneys and spleens of the challenged fish, but no mortality was recorded during the 15 d challenge period, suggesting that this novel Francisella sp. might be an opportunistic pathogen of fish. Based on the phenotypic and genotypic differences from other Francisella spp. observed in this study, we propose the name Francisella sciaenopsi sp. nov. for this novel isolate.

Auxetic kirigami structure-based self-powered strain sensor with customizable performance using machine learning

Recently, soft material based wearable sensors have discovered numerous applications in healthcare, sports monitoring, and virtual reality/augmented reality (VR/AR) systems. For these sensors, fulfilling user-specified requirements rather than just improving the sensor performance has become an important issue. In this study, a self-powered piezo-transmittance type strain sensor based on auxetic structures was optimized for configurable and user-specified characteristics using a machine-learning surrogate model. The sensor mechanism is based on the optical transmittance change induced by the gap opening of the auxetic kirigami structure. The sensor performance was analyzed according to the geometric design variables, and the optimal design was determined using Bayesian and Gaussian process to maximize the sensor performance for different purposes. The optimally designed geometries were used for self-powered sensors on a structural health monitoring (SHM) system, a human motion monitoring (HMM) system for monitoring sports performance and incorporated into an AR system.

Pseudomonas fragariae sp. nov., a novel bacterial species causing leaf spots on strawberry (Fragaria×ananassa).

In Florida, angular leaf spot, caused by Xanthomonas fragariae, was the only known bacterial disease in strawberry, which is sporadic and affects the foliage and calyx. However, from the 2019-2020 to 2023-2024 Florida strawberry seasons, unusual bacterial-like symptoms were observed in commercial farms, with reports of up to 30 % disease incidence. Typical lesions were water-soaked and angular in early stages that later became necrotic with a circular-ellipsoidal purple halo, and consistently yielded colonies resembling Pseudomonas on culture media. Strains were pathogenic on strawberry, fluorescent, oxidase- and arginine-dihydrolase-negative, elicited a hypersensitive reaction on tobacco, and lacked pectolytic activity. Although phenotypic assays, such as fatty acid methyl profiles and Biolog protocols, placed the strains into the Pseudomonas group, there was a low similarity at the species level. Further analysis using 16S rRNA genes, housekeeping genes, and whole genome sequencing showed that the strains cluster into the Pseudomonas group but do not share more than 95 % average nucleotide identity compared to representative members. Therefore, the genomic and phenotypic analysis confirm that the strains causing bacterial spot in strawberry represent a new plant pathogenic bacterial species for which we propose the name Pseudomonas fragariae sp. nov. with 20-417T (17T=LMG 32456T=DSM 113340 T) as the type strain, in relation to Fragaria×ananassa, the plant species from which the pathogen was first isolated. Future work is needed to assess the epidemiology, cultivar susceptibility, chemical sensitivity, and disease management of this possible new emerging strawberry pathogen.

Two new members of the genus Sphingobacterium: Sphingobacterium zhuxiongii sp. nov. and Sphingobacterium luzhongxinii sp. nov.

Four strains, designated dk4302T, dk4209, xlx-73T, and xlx-183, were isolated from Tibetan gazelle and red swamp crawfish collected from the Qinghai-Tibet Plateau and Jiangxi Province, PR China. The strains were Gram-stain-negative, aerobic, rod-shaped, non-motile, mucoid, and yellow-pigmented. Strains dk4302T and dk4209 grew at 10-40 °C and pH 6.0-9.0, while strains xlx-73T/xlx-183 grew at 15-40 °C and pH 6.0-10.0. Both strains exhibited growth in the presence of up to 3.5 % (w/v) NaCl. Phylogenetic and phylogenomic analyses based on the 16S rRNA gene sequences and 652 core genes, respectively, revealed that the four strains formed two distinct clusters in the genus Sphingobacterium. Strains dk4302T and dk4209 formed a distinct clade with Sphingobacterium hotanense XH4T and Sphingobacterium humi D1T. The most closely related strains to xlx-73T and xlx-183 were Sphingobacterium nematocida M-SX103T. The DNA G+C contents were 38.9 and 39.8 mol%. The digital DNA-DNA hybridization (dDDH) values between dk4302T and S. humi D1T and S. hotanense XH4T were 19.2 and 21.8 % (19.0 and 21.6 % for strain dk4209), respectively. The corresponding average nucleotide identity (ANI) values were 74.3 and 78.1 % (74.4 and 78.3 % for strain dk4209), respectively. The dDDH values between xlx-73T (xlx-183) and S. nematocida M-SX103T was 24.6 % (25.7 %). The corresponding ANI value was 85.7 % (85.5 % for strain xlx-183). The major fatty acid and respiratory quinone of dk4302T and xlx-73T were iso-C15:0 and MK7. The polar lipids identified in all of the novel strains were phosphatidylethanolamine, phosphoglycolipids, aminophospholipids, and phospholipids. A total of 61/190 (32.1 %) and 82/190 (43.2 %) carbon substrates were metabolized by strains dk4302T and xlx-73T in the Biolog MicroPlates, respectively. Based on the results from this polyphasic taxonomic study, two novel species in the genus Sphingobacteruim are proposed, namely Sphingobacteruim zhuxiongii sp. nov. (type strain dk4302T=CGMCC 1.16795T=JCM 33600T) and Sphingobacteruimluzhongxinii sp. nov. (type strain xlx-73T=GDMCC 1.1712T=JCM 33886T).

Psychrosphaera algicola sp. nov. and Paraglaciecola algarum sp. nov., and reclassification of Pseudoalteromonas elyakovii, Pseudoalteromonas flavipulchra, and Pseudoalteromonas profundi as later heterotypic synonyms of P. distincta, P. maricaloris, and P. gelatinilytica.

Two Gram-negative, obligately aerobic, rod-shaped bacteria, strains G1-22T and G1-23T, were isolated from the phycosphere of a marine brown alga. Both strains exhibited catalase- and oxidase-positive activities. Strain G1-22T displayed optimal growth at 25 °C, pH 8.0, and 2.0-3.0% (w/v) NaCl, while strain G1-23T exhibited optimal growth at 25 °C, pH 8.0, and 4.0% NaCl. Ubiquinone-8 was identified as the sole isoprenoid quinone in both strains. As major fatty acids (> 5%), strain G1-22T contained C16 : 0, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), C12 : 1 3-OH, and C10 : 0 3-OH, while strain G1-23T contained C16 : 0, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), and C14 : 0. Phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol were major polar lipids in both strains. Strains G1-22T and G1-23T had DNA G+C contents of 40.2 and 38.9 mol%, respectively. Phylogenetic analyses based on 16S rRNA and genome sequences revealed that strains G1-22T and G1-23T formed distinct phylogenetic lineages within the genera Psychrosphaera and Paraglaciecola, respectively. Strain G1-22T showed closest relatedness to Psychrosphaera ytuae MTZ26T with 97.8% 16S rRNA gene sequence similarity, 70.2% average nucleotide identity (ANI), and a 21.5% digital DNA-DNA hybridization (dDDH) value, while strain G1-23T was most closely related to Paraglaciecola aquimarina KCTC 32108T with 95.6% 16S rRNA gene sequence similarity, 74.6% ANI, and a 20.1% dDDH value. Based on phenotypic and molecular characteristics, strains G1-22T and G1-23T are proposed to represent two novel species, namely Psychrosphaera algicola sp. nov. (type strain G1-22T=KACC 22486T=JCM 34971T) and Paraglaciecola algarum sp. nov. (type strain G1-23T=KACC 22490T=JCM 34972T), respectively. Additionally, based on the comparison of whole genome sequences, it is proposed that Pseudoalteromonas elyakovii, Pseudoalteromonas flavipulchra, and Pseudoalteromonas profundi are reclassified as later heterotypic synonyms of Pseudoalteromonas distincta, Pseudoalteromonas maricaloris, and Pseudoalteromonas gelatinilytica, respectively.

Salmonirosea aquatica gen. nov., sp. nov., a Novel Genus within the Family Spirosomaceae, Was Isolated from Brackish Water in the Republic of Korea.

A Gram-stain-negative, obligately aerobic, non-motile, rod-shaped bacterial strain designated SJW1-29T was isolated from brackish water samples collected from the Seomjin River, Republic of Korea. The purpose of this study was to characterize strain SJW1-29T and determine its taxonomic position as a potential new genus within the family Spirosomaceae. The strain grew within the range of 10-30 °C (optimum, 25 °C), pH 5.0-10.0 (optimum, 7.0), and 1-4% NaCl (optimum, 3%). Phylogenetic analysis based on the 16S rRNA gene revealed that strain SJW1-29T belongs to the family Spirosomaceae and is closely related to Persicitalea jodogahamensis Shu-9-SY12-35CT (91.3% similarity), Rhabdobacter roseus R491T (90.6%), and Arundinibacter roseus DMA-K-7aT (90.0%), while the similarities to strains within the order Cytophagales were lower than 90.0%. The genome is 7.1 Mbp with a G+C content of 50.7 mol%. The use of genome-relatedness indices confirmed that this strain belongs to a new genus. The major polar lipid profile consisted of phosphatidylethanolamine, and MK-7 was the predominant menaquinone. The predominant fatty acids were summed feature 3 (C16:1ω7c and/or C16:1ω6c), iso-C15:0, iso-C17:0 3-OH, and C16:0, representing more than 80% of the total fatty acids. The phenotypic, chemotaxonomic, genetic, and phylogenetic properties suggest that strain SJW1-29T represents a novel species within a new genus in the family Spirosomaceae, for which the name Salmonirosea aquatica gen. nov., sp. nov., is proposed. The type strain of Salmonirosea aquatica is SJW1-29T (=KCTC 72493T = NBRC 114061T = FBCC-B16924T).

Complete genome sequences of Thermus thermophilus strains isolated from Shirahama Hot Spring in Japan.

We isolated six Thermus thermophilus strains from Shirahama Hot Spring in Japan. Complete genome sequences, determined by combining Oxford Nanopore long-read and Illumina short-read sequence data, revealed that they showed >99.9% average nucleotide identities with each other and approximately 97% to the genome of the type strain HB8T.