Neoadjuvant PARPi or chemotherapy in ovarian cancer informs targeting effector Treg cells for homologous-recombination-deficient tumors.

Homologous recombination deficiency (HRD) is prevalent in cancer, sensitizing tumor cells to poly (ADP-ribose) polymerase (PARP) inhibition. However, the impact of HRD and related therapies on the tumor microenvironment (TME) remains elusive. Our study generates single-cell gene expression and T cell receptor profiles, along with validatory multimodal datasets from >100 high-grade serous ovarian cancer (HGSOC) samples, primarily from a phase II clinical trial (NCT04507841). Neoadjuvant monotherapy with the PARP inhibitor (PARPi) niraparib achieves impressive 62.5% and 73.6% response rates per RECIST v.1.1 and GCIG CA125, respectively. We identify effector regulatory T cells (eTregs) as key responders to HRD and neoadjuvant therapies, co-occurring with other tumor-reactive T cells, particularly terminally exhausted CD8+ T cells (Tex). TME-wide interferon signaling correlates with cancer cells upregulating MHC class II and co-inhibitory ligands, potentially driving Treg and Tex fates. Depleting eTregs in HRD mouse models, with or without PARP inhibition, significantly suppresses tumor growth without observable toxicities, underscoring the potential of eTreg-focused therapeutics for HGSOC and other HRD-related tumors.

Leucine-tRNA-synthase-2-expressing B cells contribute to colorectal cancer immunoevasion.

Immunoregulatory B cells impede antitumor immunity through unknown features and mechanisms. We report the existence of leucine-tRNA-synthase-2 (LARS2)-expressing B cell (LARS B) subset with a transforming growth factor-ß1 (TGF-ß1)-dominant regulatory feature in both mouse and human progressive colorectal cancer (CRC). Of note, LARS B cells exhibited a leucine nutrient preference and displayed active mitochondrial aminoacyl-tRNA biosynthesis. They were located outside the tertiary lymphoid structure and correlated with colorectal hyperplasia and shortened survival in CRC patients. A leucine diet induced LARS B cell generation, whereas LARS B cell deletion by Lars2 gene ablation or leucine blockage repressed CRC immunoevasion. Mechanistically, LARS2 programmed mitochondrial nicotinamide adenine dinucleotide (NAD+) regeneration and oxidative metabolism, thus determining the regulatory feature of LARS B cells in which the NAD-dependent protein deacetylase sirtuin-1 (SIRT1) was involved. We propose a leucine-dieting scheme to inhibit LARS B cells, which is safe and useful for CRC therapy.

PCK2 maintains intestinal homeostasis and prevents colitis by protecting antibody-secreting cells from oxidative stress.

Maintaining intracellular redox balance is essential for the survival, antibody secretion, and mucosal immune homeostasis of immunoglobulin A (IgA) antibody-secreting cells (ASCs). However, the relationship between mitochondrial metabolic enzymes and the redox balance in ASCs has yet to be comprehensively studied. Our study unveils the pivotal role of mitochondrial enzyme PCK2 in regulating ASCs' redox balance and intestinal homeostasis. We discover that PCK2 loss, whether globally or in B cells, exacerbates dextran sodium sulphate (DSS)-induced colitis due to increased IgA ASC cell death and diminished antibody production. Mechanistically, the absence of PCK2 diverts glutamine into the TCA cycle, leading to heightened TCA flux and excessive mitochondrial reactive oxygen species (mtROS) production. In addition, PCK2 loss reduces glutamine availability for glutathione (GSH) synthesis, resulting in a decrease of total glutathione level. The elevated mtROS and reduced GSH expose ASCs to overwhelming oxidative stress, culminating in cell apoptosis. Crucially, we found that the mitochondria-targeted antioxidant Mitoquinone (Mito-Q) can mitigate the detrimental effects of PCK2 deficiency in IgA ASCs, thereby alleviating colitis in mice. Our findings highlight PCK2 as a key player in IgA ASC survival and provide a potential new target for colitis treatment.

Ten-eleven translocation-2 inactivation restrains IL-10-producing regulatory B cells to enable antitumor immunity in hepatocellular carcinoma.

BACKGROUND AND AIMS: IL-10-producing regulatory B cells (IL-10 + B cells), a dominant regulatory B cell (Breg) subset, foster tumor progression. However, the mechanisms underlying their generation in HCC are poorly understood. Ten-eleven translocation-2 (TET2), a predominant epigenetic regulatory enzyme in B cells, regulates gene expression by catalyzing demethylation of 5-methylcytosine into 5-hydroxymethyl cytosine (5hmC). In this study, we investigated the role of TET2 in IL-10 + B cell generation in HCC and its prospects for clinical application. APPROACH AND RESULTS: TET2 activation in B cells triggered by oxidative stress from the HCC microenvironment promoted IL-10 expression, whereas adoptive transfer of Tet2 -deficient B cells suppressed HCC progression. The aryl hydrocarbon receptor is required for TET2 to hydroxylate Il10 . In addition, high levels of IL-10, TET2, and 5hmc in B cells indicate poor prognosis in patients with HCC. Moreover, we determined TET2 activity using 5hmc in B cells to evaluate the efficacy of anti-programmed death 1 (anti-PD-1) therapy. Notably, TET2 inhibition in B cells facilitates antitumor immunity to improve anti-PD-1 therapy for HCC. CONCLUSIONS: Our findings propose a TET2-dependent epigenetic intervention targeting IL-10 + B cell generation during HCC progression and identify the inhibition of TET2 activity as a promising combination therapy with immune checkpoint inhibitors for HCC.

Systematic evaluation of the efficacy of treatments for cesarean scar pregnancy.

STUDY OBJECTIVE: Cesarean scar pregnancy (CSP) is a type of ectopic pregnancy associated with severe complications, including significant hemorrhage, the potential need for hysterectomy, and life-threatening risks. Currently, two classification methods exist for CSP: Vial (type Ia and IIa) and Chinese Expert's Consensus (type Ib, type IIb, and type IIIb). However, these methods have limitations in guiding the selection of appropriate treatment plans for CSP. The purpose of this study was to systematically evaluate the effectiveness of various treatments for CSP within our clinic. METHOD: Our study included 906 patients with CSP from January 2013 to December 2018. The chi-squared test and logistic analysis were used to compare the clinical characteristics. The median and interquartile range (IQR) was calculated. We also analyzed whether preoperative application of methotrexate (MTX) could improve surgical outcomes and the relevant characteristics of misdiagnosed CSP patients. RESULTS: There was a significant difference in gestational age, gestational sac diameter, gestational sac width, gestational sac area, remnant myometrial thickness, vaginal bleeding and preoperative hemoglobin levels (p < 0.001) but not in the incidence of residual tissue (p = 0.053). The other factors (intraoperative blood loss, hemoglobin decline, first hemoglobin after operation, total hospital stay, hospital stay after operation, transfusion and duration of catheter drain) were significantly different (p < 0.001). For type Ia and type Ib CSP, 39.3% and 40.2% of patients were treated with dilatation and curettage (D&E) under ultrasound, respectively. For type IIa and type IIIb CSP, 29.9% and 62.7% of patients were treated with laparotomy, respectively. There were no differences in surgical methods, residual tissue and reoperation between the MTX and non-MTX groups (p = 0.20), but liver damage, hospital stay and pain perception were more remarkable in the MTX group. It is noteworthy that 14% of the patients were misdiagnosed with an intrauterine pregnancy. The incidence of misdiagnosis in type IIa CSP patients was higher than that in type Ia CSP patients (p < 0.001). CONCLUSION: For type I CSP patients, D&E under ultrasound or D&E under hysteroscopy should be recommended. For type IIIb CSP patients, operative resection should be used. It is currently difficult to choose the appropriate treatment methods for type IIa or type IIb CSP patients.

Molecular Dynamics Simulation of the Adsorption and Diffusion of C8 Aromatic Isomers in MIL-47(V).

The separation of C8 aromatic isomers (oX: o-xylene, pX: p-xylene, mX: m-xylene, and EB: ethylbenzene) remains an enormous challenge in industrial production due to their similar molecular structures and physical properties. Porous materials with suitable pore structures and selective recognition sites to discriminate the slight structural differences of isomers are imminently needed. In this paper, MIL-47(V) with a three-dimensional (3D) grid structure of 10.5 × 10.5 Å2 and a one-dimensional (1D) diamond channel was selected as the adsorbent. However, the mechanism of the adsorption and separation of C8 aromatic isomers in porous materials still needs to be understood. Given the importance of C8 aromatic isomers' confinement in MIL-47(V) for adsorption and diffusion applications, it is important to understand C8 aromatic isomers' behavior in MIL-47(V). Here, we demonstrated from a simulation perspective that metal-organic frameworks MIL-47(V) with one-dimensional (1D) diamond channels can identify C8 aromatic isomers. Molecular dynamics (MD) simulations have shown that organic ligands with guest response sites of MIL-47(V) can effectively distinguish between C8 aromatic isomers by adaptation to the shape of a specific isomer. MIL-47(V) has high adsorption and an excellent separation sequence between C8 aromatic isomers: oX > pX ≈ mX > EB. Significant differences exist in π-π superposition interactions between C8 aromatic isomers and between C8 aromatic isomers and the skeletons. This phenomenon is mainly caused by the unique pore structure and guest response characteristics of MIL-47(V). This work is identified as a supplementary instruction to experimental research and is expected to provide profound insights into research on developing C8 aromatic isomers' adsorption and separation and theoretical support.

Photobacterium pectinilyticum sp. nov., a novel bacterium isolated from surface seawater of Qingdao offshore.

A Gram-staining-negative, facultative aerobic, motile strain, designated strain ZSDE20T, was isolated from the surface seawater of Qingdao offshore. Phylogenetic analysis of the 16S rRNA gene of strain ZSDE20T, affiliated it to the genus Photobacterium. It was closely related to Photobacterium lutimaris DF-42 T (98.92% 16S rRNA gene sequence similarity). Growth occurred at 4-28ºC (optimum 28ºC), pH 1.0-7.0 (optimum 7.0) and in the presence of 1-7% (w/v) NaCl (optimum 3%). The dominant fatty acids were summed feature 3 (C16:1 ω7c or/and C16:1 ω6c, 34.23%), summed feature 8 (C18:1 ω7c and C18:1 ω6c, 10.36%) and C16:0 (20.05%). The polar lipids of strain ZSDE20T comprised phosphatidylethanolamine, phosphatidylcholine, lyso-phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol dimannoside, phosphatidylinositol mannosides and two unknown lipids. The major respiratory quinone was ubiquinone-8 (Q-8). The DNA G + C content of strain ZSDE20T was 45.6 mol%. Average nucleotide identity (ANI) values between ZSDE20T and its reference species were lower than the threshold for species delineation (95-96%); in silico DNA-DNA hybridization further showed that strain ZSDE20T had less than 70% similarity to its relatives. Based on the polyphasic evidences, strain ZSDE20T is proposed as representing a novel species of the genus Photobacterium, for which the name Photobacterium pectinilyticum sp. nov. is proposed. The type strain is ZSDE20T (= MCCC 1K06283T = KCTC 82885 T).

Observation and Characterization of Multiple Resonance Modes in a Chiral Helimagnet CrNb3S6.

The chiral helimagnet CrNb3S6 hosts various temperature- and magnetic-field-stabilized chiral soliton lattices (CSLs) and corresponding exotic collective spin resonance modes, which make it an ideal candidate for future magnetic storage/memory and magnon-based information processing. While most studies have focused on characterizing various static spin textures in this chiral helimagnet, its corresponding collective dynamics have rarely been explored. This study systematically investigates the temperature- and magnetic-field-dependent magnetic dynamics of a single crystal of CrNb3S6 using broadband microwave spectroscopy. We observe an optical mode with a temperature-independent mode number in addition to Kittel-like ferromagnetic resonance (FMR) modes in the CSL phase, consistent with the temperature-independent normalized CSL period L(H)/L(0) based on the 1D chiral sine-Gordon model. Furthermore, combining theoretical model fitting and micromagnetic simulation, we provide a detailed phase diagram and temporal-spatial resolution of dynamic modes, which may help to develop high-frequency exchange-coupling-based spintronic devices.

[Microcirculatory visualization and metabolomics of Dalbergia cochinchinensis in ameliorating coronary microvascular dysfunction in rats].

This study employed microcirculation visualization and metabolomics methods to explore the effect and possible mechanism of Dalbergia cochinchinensis in ameliorating coronary microvascular dysfunction(CMD) induced by microsphere embolization in rats. Sixty SPF-grade male SD rats were randomized into sham, model, and low-, medium-, and high-dose [1.5, 3.0, and 6.0 g·kg~(-1)·d~(-1), respectively] D. cochinchinensis water extract groups. The rats in sham and model groups were administrated with equal volume of normal saline by gavage once a day for 7 consecutive days. The rat model of CMD was prepared by injecting polyethylene microspheres into the left ventricle, while the sham group was injected with an equal amount of normal saline. A blood flow meter was used to measure blood flow, and a blood rheometer to measure blood viscosity and fibrinogen content. An automatic biochemical analyzer and reagent kits were used to measure the serum levels of myocardial enzymes, glucose, and nitric oxide(NO). Hematoxylin-eosin(HE) staining was used to observe the pathological changes of myocardial tissue. DiI C12/C18 perfusion was used to infuse coronary microvessels, and the structural and morphological changes were observed using a confocal laser scanning microscope. AngioTool was used to analyze the vascular area, density, radius, and mean E lacunarity in the microsphere embolization area, and vascular blood flow resistance was calculated based on Poiseuille's law. Non-targeted metabolomics based on high performance liquid chromatography-quadrupole-time-of-flight mass spectrometry(UPLC-Q-TOF-MS) was employed screen potential biomarkers and differential metabolites regulated by D. cochinchinensis and the involved metabolic pathways were enriched. The pharmacodynamic results showed that compared with the model group, D. cochinchinensis significantly increased mean blood flow, reduced plasma fibrinogen content, lowered the levels of myocardial enzymes such as creatine kinase(CK), creatine kinase-MB(CK-MB), and lactate dehydrogenase(LDH), alleviate myocardial injury, and protect damaged myocardium. In addition, D. cochinchinensis significantly increased serum NO content, promoted vascular smooth muscle relaxation, dilated blood vessels, lowered serum glucose(GLU) level, improved myocardial energy metabolism, and alleviated pathological changes in myocardial fibrosis and inflammatory cell infiltration. The results of coronary microcirculation perfusion showed that D. cochinchinensis improved the vascular morphology, increased the vascular area, density, and radius, reduced vascular mean E lacunarity and blood flow resistance, and alleviated vascular endothelial damage in CMD rats. The results of metabolomics identified 45 differential metabolites between sham and model groups, and D. cochinchinensis recovered the levels 25 differential metabolites, which were involved in 8 pathways including arachidonic acid metabolism, arginine biosynthesis, and sphingolipids metabolism. D. cochinchinensis can ameliorate coronary microcirculation dysfunction caused by microsphere embolization in rats, and it may alleviate the pathological changes of CMD rats by regulating inflammatory reaction, endothelial damage, and phospholipid metabolism.

Single-cell landscape and clinical outcomes of infiltrating B cells in colorectal cancer.

B cells constitute a major component of infiltrating immune cells in colorectal cancer (CRC). However, the characteristics of B cells and their clinical significance remain unclear. In this study, using single-cell RNA sequencing and multicolour immunofluorescence staining experiments, we identified five distinct subtypes of B cells with their marker genes, distribution patterns and functional properties in the CRC tumour microenvironment. Meanwhile, we found a higher proportion of IgG plasma cells in tumour sites than that in adjacent normal mucosal tissues. In addition, the CXCL13-producing CD8+ T cells in the tumour tissues could promote the formation of tertiary lymphoid structure (TLS) B cells, and the CCL28-CCR10 axis is pivotal for IgG plasma cell migration from the periphery of TLSs to the tumour stroma. Finally, we identified four distinct colon immune classes (CICs: A-D) and found that CD20+ B cells within TLSs were enriched in one immune-inflamed or hot tumour group (CIC D). This B cell-rich group, which was characterized by strong antigen presentation, IgG plasma cells accumulation, microsatellite instability-high (MSI-H) and high tumour mutation burden (TMB-H), as well as immunosuppressive property in particular, might become a potential predictive biomarker for future immunotherapy. Additionally, in an immunotherapy cohort, patients with the enrichment of B cells and TLSs were demonstrated to obtain significant therapeutic advantages. Together, our findings provide the detailed landscape of infiltrating B cells and their potential clinical significance in CRC.

Exosomal lncRNA HOTAIR induces PDL1+ B cells to impede anti-tumor immunity in colorectal cancer.

Regulatory B cells (Bregs) contribute to tumor immunosuppression. However, how B cells acquire their regulatory features in tumors remain unclear. Exosomes are important messengers that transmit tumor information to remodel tumor immunity. Here we revealed that tumor-derived exosomes drive Bregs to suppress anti-tumor immunity by delivering long non-coding RNAs (lncRNAs). HOTAIR was screened by lncRNA profiling in both colorectal cancer (CRC)-derived exosomes and infiltrating B cells. Tumor-derived HOTAIR polarized B cells toward a regulatory feature marked by programmed cell death-ligand 1 (PDL1) in CRC, and induced PDL1+ B cells to suppress CD8+ T cell activity. Exosomal HOTAIR bound to and protected pyruvate kinase M2 (PKM2) against ubiquitination degradation, resulting in STAT3 activation and PDL1 expression. Results from CRC patients showed a positive correlation between exosomal HOTAIR and tumor-infiltrating PDL1+ B cells. These findings reveal how B cells acquire PDL1-dominant regulatory feature in CRC, implying the clinical significance of exosomal therapy targeting HOTAIR.

Microbial Dimethylsulfoniopropionate Cycling in Deep Sediment of the Mariana Trench.

Dimethylsulfoniopropionate (DMSP) and related organic sulfur compounds play key roles in global sulfur cycling. Bacteria have been found to be important DMSP producers in seawater and surface sediments of the aphotic Mariana Trench (MT). However, detailed bacterial DMSP cycling in the Mariana Trench subseafloor remains largely unknown. Here, the bacterial DMSP-cycling potential in a Mariana Trench sediment core (7.5 m in length) obtained at a 10,816-m water depth was investigated using culture-dependent and -independent methods. The DMSP content fluctuated along the sediment depth and reached the highest concentration at 15 to 18 cm below the seafloor (cmbsf). dsyB was the dominant known DMSP synthetic gene, existing in 0.36 to 1.19% of the bacteria, and was identified in the metagenome-assembled genomes (MAGs) of previously unknown bacterial DMSP synthetic groups such as Acidimicrobiia, Phycisphaerae, and Hydrogenedentia. dddP, dmdA, and dddX were the major DMSP catabolic genes. The DMSP catabolic activities of DddP and DddX retrieved from Anaerolineales MAGs were confirmed by heterologous expression, indicating that such anaerobic bacteria might participate in DMSP catabolism. Moreover, genes involved in methanethiol (MeSH) production from methylmercaptopropionate (MMPA) and dimethyl sulfide (DMS), MeSH oxidation, and DMS production were highly abundant, suggesting active conversions between different organic sulfur compounds. Finally, most culturable DMSP synthetic and catabolic isolates possessed no known DMSP synthetic and catabolic genes, and actinomycetes could be important groups involved in both DMSP synthesis and catabolism in Mariana Trench sediment. This study extends the current understanding of DMSP cycling in Mariana Trench sediment and highlights the need to uncover novel DMSP metabolic genes/pathways in extreme environments. IMPORTANCE Dimethylsulfoniopropionate (DMSP) is an abundant organosulfur molecule in the ocean and is the precursor for the climate-active volatile gas dimethyl sulfide. Previous studies focused mainly on bacterial DMSP cycling in seawater, coastal sediment, and surface trench sediment samples, but DMSP metabolism in the Mariana Trench (MT) subseafloor sediments remains unknown. Here, we describe the DMSP content and metabolic bacterial groups in the subseafloor of the MT sediment. We found that the tendency for vertical variation of the DMSP content in the MT was distinct from that of the continent shelf sediment. Although dsyB and dddP were the dominant DMSP synthetic and catabolic genes in the MT sediment, respectively, both metagenomic and culture methods revealed multiple previously unknown DMSP metabolic bacterial groups, especially anaerobic bacteria and actinomycetes. The active conversion of DMSP, DMS, and methanethiol may also occur in the MT sediments. These results provide novel insights for understanding DMSP cycling in the MT.

Iron Vacancy Tunable Superconductor-Insulator Transition in FeSe/SrTiO_{3} Monolayer.

The Fe_{4}Se_{5} with a sqrt[5]×sqrt[5] Fe vacancy order is suggested to be a Mott insulator and the parent state of bulk FeSe superconductor. The iron vacancy ordered state has been considered as a Mott insulator and the parent compound of bulk FeSe-based superconductors. However, for the superconducting FeSe/SrTiO_{3} monolayer (FeSe/STO) with an interface-enhanced high transition temperature (T_{c}), the electronic evolution from its Fe vacancy ordered parent phase to the superconducting state, has not been explored due to the challenge to realize an Fe vacancy order in the FeSe/STO monolayer, even though important to the understanding of superconductivity mechanism. In this study, we developed a new method to generate Fe vacancies within the FeSe/STO monolayer in a tunable fashion, with the assistance of atomic hydrogen. As a consequence, an insulating sqrt[5]×sqrt[5] Fe vacancy ordered monolayer is realized as the parent state. By using scanning tunneling microscopy and scanning tunneling spectroscopy, the spectral evolution from superconductivity to insulator is fully characterized. Surprisingly, a prominent spectral weight transfer occurs, thus implying a strong electron correlation effect. Moreover, the Fe vacancy induced insulating gap exhibits no Mott gap-like features. This work provides new insights in understanding the high-T_{c} superconductivity in FeSe/STO monolayer.

Vibrio amylolyticus sp. nov. and Vibrio gelatinilyticus sp. nov., two marine bacteria isolated from surface seawater of Qingdao.

Two Gram-stain-negative, oxidase-positive, facultative anaerobic and rod-shaped motile bacteria, designated strains ZSDZ34 and ZSDE26, were isolated from offshore surface seawater collected near Qingdao. Phylogenetic analysis based on 16S rRNA gene sequences placed ZSDE26T and ZSDZ34T within the genus Vibrio, family Vibrionaceae, class Gammaproteobacteria. Strain ZSDE26T was most closely related to Vibrio gallaecicus VB 8.9T with 97.3 % sequence similarity, whereas ZSDZ34T was most closely related to Vibrio aestuarianus subsp. cardii DSM 109723T with 97.8 % sequence similarity. Strain ZSDE26T grew with 1-5 % (w/v) NaCl (optimum, 4 %), at 16-28 °C (optimum, 28 °C) and at pH 6.0-9.0 (optimum, pH 7.0). Growth of strain ZSDZ34T occurred with 1-6 % (w/v) NaCl (optimum, 3 %), at 16-37 °C (optimum, 28 °C) and at pH 6.0-9.0 (optimum, pH 7.0). Both strains shared the same major fatty acid components (more than 10 % of total fatty acids) of summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) and C16 : 0. Additionally, strain ZSDZ34T contained a higher proportion of iso-C16 : 0. The DNA G+C contents of strains ZSDE26T and ZSDZ34T were 42.8 and 44.5 mol%, respectively. On the basis of the results of polyphasic analysis, ZSDE26T and ZSDZ34T are considered to represent novel species within the genus Vibrio, for which the names Vibrio amylolyticus sp. nov. (type strain, ZSDE26T=KCTC 82890T=MCCC 1K06290T) and Vibrio gelatinilyticus sp. nov. (type strain, ZSDZ34T=KCTC 82888T=MCCC 1K06292T) are proposed, respectively.

Profundirhabdus halotolerans gen. nov., sp. nov., an haloalkaliphilic actinobacterium isolated from seawater of the Mariana Trench.

A Gram-stain-positive, strictly aerobic, rod-shaped actinobacterium, designated strain ZYF776T, was isolated from seawater of the Mariana Trench collected at a depth of 4000 m. Results of 16S rRNA gene sequence analysis indicated that strain ZYF776T was a member of the class Nitriliruptoria and closely related to Nitriliruptor alkaliphilus DSM 45188T (member of the order Nitriliruptorales, 94.94 % sequence similarity) and Egicoccus halophilus KCTC 33612T (member of the order Egicoccales, 94.46 %). Strain ZYF776T was catalase-positive and oxidase-negative. Growth occurred at 16-37 °C (optimum, 28 °C), in the presence of 0-13 % NaCl (w/v; optimum, 4 %) and at pH 7.0-10.0 (optimum, pH 8.0). Cell-wall hydrolysates of strain ZYF776T contained meso-diaminopimelic (peptidoglycan type A1γ), with ribose, rhamnose and a smaller amount of xylose as the cell-wall sugars. The major menaquinone was MK-10. The predominant fatty acids (>10 %) were C16:0, C17:1 ω8c and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c). The polar lipid profile mainly contained diphosphatidylglycerol, phosphatidylglycerol and phosphoglycolipid. The genomic DNA G+C content of strain ZYF776T was 68.7 mol%. The genome of strain ZYF776T was about 5.61 Mbp in size, which was larger than those of the reference strains N. alkaliphilus DSM45188T (5.56 Mbp) and E. halophilus KCTC 33612T (3.98 Mbp). The average nucleotide identity and digital DNA-DNA hybridization values between ZYF776T and the related strains N. alkaliphilus DSM 45188T and E. halophilus KCTC 33612T were 76.7 and 20.3 % and 75.8 and 20.0 %, respectively. Based on the polyphasic evidence, a novel genus and species with the name Profundirhabdus halotolerans gen. nov., sp. nov. is proposed. The type strain is ZYF776T (=JCM 33008T=MCCC 1K03555T).

Photobacterium obscurum sp. nov., a marine bacterium isolated from the coast of Qingdao.

A Gram-stain-negative, facultative anaerobic, rod-shaped strain, named SDRW27T, was isolated from offshore seawater collected near Qingdao. Strain SDRW27T was able to grow at 16-37 °C (optimum, 28 °C), pH 6.0-9.0 (optimum, pH 6.0) and in the presence of 1-7 % (w/v) NaCl (optimum, 3 %). Phylogenetic analysis using 16S rRNA gene sequences indicated that strain SDRW27T was most closely related to Photobacterium toruni H01100410BT (97.89 % sequence similarity), Photobacterium andalusiense H01100409BT (97.89 %) and Photobacterium leiognathi ATCC 25521T (97.82 %). The predominant fatty acids were summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH), summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) and C16 : 0. The polar lipids of strain SDRW27T comprised phosphatidylglycerol, phosphatidylinositol dimannoside, phosphatidylcholine, phosphatidylethanolamine and three unidentified lipids. The major respiratory quinone was ubiquinone-8. The G+C content was 47.71 mol%. The genome size was 5.84 Mbp, including 85 contigs with an N50 value of 223 542. The average nucleotide identity (ANI) values of SDRW27T with its three most similar strains, P. toruni H01100410BT, P. andalusiense H01100409BT and P. leiognathi ATCC 25521T, were 71.36, 71.58 and 72.23 %, respectively (all lower than the 95-96 % ANI threshold), and the DNA-DNA hybridization (DDH) values were 20.4, 20.8 and 20.4 % (all lower than the 70 % DDH threshold). The obtained results of polyphasic analysis demonstrate that strain SDRW27T represents a novel species, for which the name Photobacterium obscurum sp. nov. is proposed. The type strain is SDRW27T (=MCCC 1K06286T=KCTC 82892T).

Vibrio paucivorans sp. nov. and Vibrio qingdaonensis sp. nov., two marine bacteria.

Two Gram-stain-negative, facultatively anaerobic, motile, rod-shaped and flagellated marine bacteria, designated strains DBSS07T and ZSDZ65T, were isolated from the surface sediments of the Bohai sea and Qingdao coastal seawater, respectively. Phylogenetic analysis based on 16S rRNA genes, multilocus sequence analysis (MLSA), phylogenomic analysis of single-copy gene families and whole-genome data placed DBSS07T and ZSDZ65T within the genus Vibrio. DBSS07T was most closely related to Vibrio aestivus M22T, with 97.51 % sequence similarity, whereas ZSDZ65T was most closely related to Vibrio variabilis R-40492T with 97.58 % sequence similarity. DBSS07T grew with 1-7 % (w/v) NaCl (optimum 3 %), at 16-37 °C (optimum 28 °C) and at pH 6.0-9.0 (optimum pH 7.0); whereas ZSDZ65T grew with 1-5 % (w/v) NaCl (optimum 2 %), at 16-32 °C (optimum 28 °C) and at pH 6.0-9.0 (optimum pH 8.0). Both strains shared the same major fatty acid components (more than 10 % of total fatty acids) of summed feature 3 (C16 : 1ω7c or/and C16 : 1ω6c), with different proportions. The DNA G+C contents of DBSS07T and ZSDZ65T were 44.7 and 44.3 %, respectively. On the basis of the results of polyphasic analysis, DBSS07T and ZSDZ65T are considered to represent novel species within the genus Vibrio, for which the names V. paucivorans sp. nov. (type strain, DBSS07T = KCTC 82896T= MCCC 1K06284T) and V. qingdaonensis sp. nov. (type strain, ZSDZ65T = KCTC 82893T = MCCC 1K06289T) are proposed, respectively.

Stakelama marina sp. nov., isolated from seawater of the Tangyin hydrothermal field in the Okinawa Trough.

A Gram-stain-negative, strictly aerobic, rod-shaped and non-flagellated marine bacterium, designated strain LXI357T, was isolated from deep-sea water sampled at the Tangyin hydrothermal field in the Okinawa Trough. The growth temperature range was 20-45 °C (optimum, 28 °C). Strain LXI357T was also able to grow at pH 5.0-7.5 (optimum, pH 6.0-7.0) and in the presence of 0.5-11 % (optimum, 7%, w/v) NaCl. Strain LXI357T was oxidase-negative and catalase-positive. The predominant fatty acids were C18 : 1 ω7c and C16 : 0. The major polar lipids of strain LXI357T contained phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, phospholipid, sphingoglycolipid, diphosphatidylglycero and an unidentified aminolipid. Based on the results of 16S rRNA gene sequence analysis, strain LXI357T belonged to the genus Stakelama and was most closely related to Stakelama flava CBK3Z-3T (96.28%, 16S rRNA gene sequence similarity), followed by Stakelama algicida Yeonmyeong 1-13T (95.67%), Stakelama pacifica JLT832T (95.46%) and Sphingosinicella vermicomposti YC7378T (95.43%). Genome relatedness between strain LXI357T and Stakelama flava CBK3Z-3T was computed using average nucleotide identity, digital DNA-DNA hybridization and average amino acid identity, with values of 76.02, 20.9 and 71.1 %, respectively. The genomic DNA G+C content of strain LXI357T is 64.1 mol%. In addition, strain LXI357T has multiple genes related to sulphur metabolism, including genes encoding for the Sox system. The morphological, physiological, chemotaxonomic and phylogenetic analyses clearly distinguished strain LXI357T from its closest phylogenetic neighbours. According to the results of polyphasic analyses, strain LXI357T is considered to represent a novel species of the genus Stakelama, for which the name Stakelama marina sp. nov. is proposed. The type strain is LXI357T (=MCCC 1K06076T=KCTC 82726T).

Vibrio sinus sp. nov., a marine bacterium isolated from coastal seawater.

A Gram-straining-negative, facultatively anaerobic, motile by means of a polar flagellum and rod-shaped marine bacterium, designated S4M6T, was isolated from surface seawater collected in Dongshan Bay (Fujian, PR China). Phylogenetic analysis based on 16S rRNA genes, phylogenomic analysis of single-copy gene families and whole genome data indicated that S4M6T represented a member of the genus Vibrio. The closest phylogenetic relatives of S4M6T were Vibrio marisflavi CGMCC 1.8994T (97.8 % 16S rRNA gene sequence pairwise similarity), Vibrio variabilis LMG 25438T (96.9 %), Vibrio gangliei SZDIS-1T (96.2 %) and Vibrio aestivus M22T (96.1 %). The growth of S4M6T occurred at 15-35 °C (optimum 28 °C), pH 4.0-9.0 (optimum 5.0-7.0) and in the presence of 2-5 % (w/v) NaCl (optimum 3 %). The predominant fatty acids (>10 %) are C16 : 0, summed feature 3 (C16 : 1ω7c and/or C16 :  1ω6c) and summed feature 8 (C18 : 1ω7c and/or C18 :  1ω6c). The DNA G+C content of the assembled genomic sequences was 43.4 % for S4M6T. Average nucleotide identity (ANI) values between S4M6T and the reference species were lower than the threshold for species delineation (95-96 %); in silico DNA-DNA hybridization further indicated that S4M6T had less than 70 % similarity to its relatives. On the basis of the polyphasic evidence, strain S4M6T is proposed to represent a novel species of the genus Vibrio, for which the name Vibrio sinus sp. nov. is proposed. The type strain is S4M6T (= KCTC 92312T= MCCC 1K06167T).