Genome-based taxonomic classification of the genus Sulfitobacter along with the proposal of a new genus Parasulfitobacter gen. nov. and exploring the gene clusters associated with sulfur oxidation.

BACKGROUND: The genus Sulfitobacter, a member of the family Roseobacteraceae, is widely distributed in the ocean and is believed to play crucial roles in the global sulfur cycle. However, gene clusters associated with sulfur oxidation in genomes of the type strains of this genus have been poorly studied. Furthermore, taxonomic errors have been identified in this genus, potentially leading to significant confusion in ecological and evolutionary interpretations in subsequent studies of the genus Sulfitobacter. This study aims to investigate the taxonomic status of this genus and explore the metabolism associated with sulfur oxidation. RESULTS: This study suggests that Sulfitobacter algicola does not belong to Sulfitobacter and should be reclassified into a novel genus, for which we propose the name Parasulfitobacter gen. nov., with Parasulfitobacter algicola comb. nov. as the type species. Additionally, enzymes involved in the sulfur oxidation process, such as the sulfur oxidization (Sox) system, the disulfide reductase protein family, and the sulfite dehydrogenase (SoeABC), were identified in almost all Sulfitobacter species. This finding implies that the majority of Sulfitobacter species can oxidize reduced sulfur compounds. Differences in the modular organization of sox gene clusters among Sulfitobacter species were identified, along with the presence of five genes with unknown function located in some of the sox gene clusters. Lastly, this study revealed the presence of the demethylation pathway and the cleavage pathway used by many Sulfitobacter species to degrade dimethylsulfoniopropionate (DMSP). These pathways enable these bacteria to utilize DMSP as important source of sulfur and carbon or as a defence strategy. CONCLUSIONS: Our findings contribute to interpreting the mechanism by which Sulfitobacter species participate in the global sulfur cycle. The taxonomic rearrangement of S. algicola into the novel genus Parasulfitobacter will prevent confusion in ecological and evolutionary interpretations in future studies of the genus Sulfitobacter.

An experimental study on the visual identification of Fritillaria ussuriensis based on LAMP and nucleic acid colloidal gold technique.

Fritillaria ussuriensis Maxim is one of the traditional Chinese valuable herbs, which is the dried bulb of Fritillaria, a plant of the lily family. The identification of authenticity about F. ussuriensis is still technically challenging. In this study, visual identification was performed by ring-mediated isothermal amplification and nucleic acid colloidal gold techniques. Firstly, multiple sequence comparative analysis was performed by DNAMAN to find the differential sites of F. ussuriensis and its mixed pseudo-products, and the specific identification primers of F. ussuriensis were designed. Genomic DNA was extracted by the modified CTAB method, and the reaction system and reaction conditions were optimized to construct LAMP for the visual detection of F. ussuriensis, meanwhile, the genuine product was cloned and the extracted plasmid was sequenced. The specificity and sensitivity were detected, and also verified by nucleic acid colloidal gold method, and 20 commercially available samples were tested. The extracted DNA met the requirements of the experiment, and the genuine F. ussuriensis PCR product titrated on a test strip showed two bands on the T and C lines, while the counterfeit and negative control showed only one band on the C line, which matched the LAMP results. The specificity was 100 %, and the sensitivity of LAMP assay was up to 0.01 ng µL-1, while that of colloidal gold assay was 0.1 ng µL-1, thus the LAMP assay had high sensitivity. 14 out of 20 commercially available samples of F. ussuriensis were qualified, and 6 were unqualified, and the results of the two methods of identification were consistent. In this study, the combined detection method of LAMP and colloidal gold for nucleic acid was established to be specific, rapid, precise and visualized, which can provide a new technical idea for the detection of F. ussuriensis.

Parasedimentitalea denitrificans sp. nov., a novel denitrifying bacteria isolated from the Yellow Sea and transfer of Zongyanglinia huanghaiensis and Zongyanglinia marina to the genus Parasedimentitalea as Parasedimentitalea huanghaiensis comb. nov. and Parasedimentitalea maritima nom. nov.

A Gram-stain-negative and rod-shaped bacterium, designated strain CY04T, was isolated from a sediment sample collected from the Yellow Sea. CY04T exhibited the highest 16S rRNA gene sequence similarity of 98.7 % to Zongyanglinia huanghaiensis CY05T, followed by the similarities of 98.6 %, 98.0 and 98.0 % to Zongyanglinia marina DSW4-44T, Parasedimentitalea marina W43T and Parasedimentitalea psychrophila QS115T respectively. Phylogenetic analysis based on 16S rRNA gene and phylogenomic analysis based on genome sequences revealed that CY04T formed a robust cluster with Z. huanghaiensis CY05T, Z. marina DSW4-44T, P. marina W43T and P. psychrophila QS115T. Calculated digital DNA-DNA hybridisation and average nucleotide identity values between CY04T and its closely related species were 22.2-23.7 % and 79.0-81.2 % respectively. Cells of CY04T were strictly aerobic, non-motile and positive for catalase, oxidase and denitrification. CY04T harboured a set of genes encoding the enzymes involved in denitrification. Growth occurred at 10-30 °C (optimum, 20 °C), at pH 6.5-9.5 (optimum, pH 8.0) and with 1-6 % (w/v) (optimum, 2.5 %,) NaCl. The major component of the fatty acids was summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The isoprenoid quinone was Q-10. Results of the phenotypic, chemotaxonomic and molecular study indicate that strain CY04T represents a novel species of the genus Parasedimentitalea, for which the name Parasedimentitalea denitrificans sp. nov. is proposed. The type strain is CY04T (=MCCC 1K08635T=KCTC 62199T). It is also proposed that Zongyanglinia huanghaiensis and Zongyanglinia marina should be reclassified as Parasedimentitalea huanghaiensis comb. nov. and Parasedimentitalea maritima nom. nov. An emended description of the genus Parasedimentitalea is also proposed.

The Analgesic Effect of Ultrasound-guided Erector Spinae Plane Block in Median Sternotomy Cardiac Surgery in Adults: A Systematic Review and Meta-analysis of Randomized Controlled Trials.

OBJECTIVES: To assess the analgesic effect of erector spinae plane block in adults undergoing median sternotomy cardiac surgery. DESIGN AND SETTING: The Cochrane, Embase, and PubMed databases from inception to January 2024 were searched. The study has been registered in the International Prospective Register of Systematic Reviews (CRD42023470375). PARTICIPANTS: Eight randomized controlled trials involving 543 patients, comparing with no block or sham block, were included, whether it was a single injection or continuous. MEASUREMENTS AND MAIN RESULTS: The primary outcomes were pain scores and opioid consumption. Erector spinae plane block reduced pain scores immediately after extubation (mean difference [MD], -1.19; 95% confidence interval [CI], -1.67 to -0.71; p for heterogeneity = 0.10), at 6 hours after extubation (MD, -1.96; 95% CI, -2.85 to -1.08; p for heterogeneity < 0.0001), and at 12 hours after extubation (MD, -0.98; 95% CI, -1.55 to -0.40; p for heterogeneity < 0.00001). The decrease in pain scores reached the minimal clinically important difference within 6 hours. Opioid consumption 24 hours after surgery decreased by 35.72 mg of oral morphine equivalents (95% CI, -50.88 to -20.57; p for heterogeneity < 0.0001). Sensitivity analysis confirmed the stability of results. The quality of primary outcomes was rated as very low to moderate. CONCLUSIONS: Erector spinae plane block decreased pain scores within 12 hours after extubation, reached the minimal clinically important difference within 6 hours, and decreased opioid consumption 24 hours after surgery, based on data of very low to moderate quality. However, high-quality randomized controlled trials are necessary to validate these findings.

Effect of basal metabolic rate on rheumatoid arthritis: a Mendelian randomization study.

PURPOSE: Basal metabolic rate (BMR) as one of the most basic and significant indicators of metabolism has been associated with human health. Previous studies showed that the development of rheumatoid arthritis (RA) is linked to BMR; however, the causal relationship between BMR and RA is unknown. Thus, we aimed to explore the causal relationship between BMR and RA as well as RA-related factors. METHODS: Mendelian randomization (MR) analysis was performed on collected genome-wide association studies information. The effect of horizontal pleiotropy was detected by MR-PRESSO and MR-Radial. Five MR analysis methods were applied, including inverse variance weighted, MR-Egger, weighted median, weighted mode, and simple mode. Four sensitivity analysis methods were used for the validation of the significant MR analysis results. A two-component mixture of regressions method was additionally used to validate single nucleotide polymorphisms and to verify results. RESULTS: Genetically, there is a causal effect of BMR on overall RA (odds ratio = 1.25, 95% confidence interval: 1.07-1.47, PIVW = .006), seropositive RA (odds ratio = 1.20, 95% confidence interval: 1.01-1.44, PIVW = .035), and seronegative RA (odds ratio = 1.36, 95% confidence interval: 1.04-1.78, PIVW = .023). Sensitivity analyses validated the robustness of the above associations. No evidence supported the effect of RA on BMR. Moreover, BMR showed no causal relationship with rheumatoid factor, C-reactive protein, erythrocyte sedimentation rate, interleukin-1ß, tumor necrosis factor-α, and matrix metallopeptidase 3. CONCLUSION: MR results implied the causal effect of BMR on RA and raised our attention to the importance of BMR in RA's pathology.

Clinical and genomic features in patients with second primary glioblastoma following first primary renal cell carcinoma.

PURPOSE: To explore the potential pathogenesis and clinical features of second primary glioblastoma (spGBM) following first primary renal cell carcinoma (fpRCC). METHODS: Patients with spGBM after fpRCC were enrolled from our institution and the SEER dataset. Sanger sequencing, whole genome sequencing, and immunehistochemistry were used to detect molecular biomarkers. RESULTS: Four and 122 cases from our institution and the SEER dataset, respectively, were collected with an overall median age of 69 years at spGBM diagnosis following fpRCC. The median interval time between fpRCC and spGBM was 50.7 months and 4 years, for the four and 122 cases respectively. The median overall survival time was 11.2 and 6.0 months for the two datasets. In addition, spGBM patients of younger age (< 75 years) or shorter interval time (< 1 year) had favorable prognosis (p = 0.081 and 0.05, respectively). Moreover, the spGBM cases were molecularly classified as TERT only paired with TP53 mutation, PIK3CA mutation, EGFR alteration, low tumor mutation burden, and stable microsatellite status. CONCLUSIONS: This is the first study to investigate the pathogenesis and clinical features of spGBM following spRCC. We found that spGBMs are old-age related, highly malignant, and have short survival time. Moreover, they might be misdiagnosed and treated as brain metastases from RCC. Thus, the incidence of spGBMs after fpRCC is underestimated. Further studies are needed to investigate the underlying molecular mechanisms and clinical biomarkers for the development of spGBM following fpRCC.

Spermidine protects cartilage from IL-1ß-mediated ferroptosis.

Rheumatoid arthritis is characterized by a burst of inflammation, the destruction of cartilage and the abundant release of inflammatory factors such as IL-1ß. Thus, the effect of IL-1ß on cartilage was examined in this study. IL-1ß could cause lipid peroxidation and disturbances in iron metabolism by increasing the expression of NCOA4 and decreasing the expression of FTH, which also induced ferritinophagy. In addition, the expression of the key antioxidant proteins SLC7A11 and GPX4 was inhibited by IL-1ß, resulting in ferroptosis in chondrocytes. Spermidine (SPD), a low-molecular-weight aliphatic nitrogen-containing compound that widely exists in animals, has been reported to be an antioxidant. In our study, we found that SPD could inhibit ferritinophagy and reverse the decrease in the expression of SLC7A11 and GPX4. Therefore, we uncovered one of the molecular mechanisms of cartilage destruction and inflammation and provide a potential polyamine for the treatment of RA.

Reclassification of Sabulilitoribacter multivorans and Sabulilitoribacter arenilitoris as Flaviramulus multivorans comb. nov. and Wocania arenilitoris comb. nov., respectively, based on genome sequence analysis.

Rapid advancements in DNA sequencing technologies are providing new approaches for bacterial taxonomy. The genus Sabulilitoribacter is a member of the family Flavobacteriaceae, which consists of more than 150 genera. In this study, genome sequence analysis was conducted to revisit the taxonomic status of Sabulilitoribacter arenilitoris and Sabulilitoribacter multivorans, the only two species of this genus. Genome sequence based phylogeny analysis showed that the genus Sabulilitoribacter was non-monophyletic: S. multivorans, the type species of genus Sabulilitoribacter, was clustered with the type species of the genus Flaviramulus, whereas S. arenilitoris formed a robust cluster with the only two species of the genus Wocania. The values of average amino acid identity, genome-wide average nucleotide identity, alignment fractions and some phenotypic features showed that S. multivorans was more closely related with the type species of the genus Flaviramulus than with S. arenilitoris, and S. arenilitoris was more closely related with the only two species of the genus Wocania than with S. multivorans. Based on these results, we consequently propose that S. multivorans and S. arenilitoris should be reclassified as Flaviramulus multivorans comb. nov. and Wocania arenilitoris comb. nov. respectively.

Rhizosphere environmental factors regulated the cadmium adsorption by vermicompost: Influence of pH and low-molecular-weight organic acids.

Vermicompost is a promising amendment for immobilization of cadmium (Cd) in soils; however, its effectiveness can be influenced by rhizosphere environment conditions, such as pH and the presence of low-molecular-weight organic acids (LMWOAs). In this study, a batch experiment was conducted to examine the characteristics of Cd adsorption by vermicompost at different pH (pH = 3, 5, and 7) and after the addition of different LMWOAs (oxalic acid; citric acid; malic acid). Furthermore, a series of morphology and structural analyses were conducted to elucidate the mechanisms of observed effects. The results showed that the adsorption capacity of vermicompost for Cd increased as pH increased, and chemisorption dominated the adsorption process. Changes in pH altered adsorption performance by affecting the -OH groups of alcohol/phenol and the -CH2 groups of aliphatics. Further, the addition of oxalic acid promoted Cd adsorption, and the effect was concentration dependent. Modifying the verimicompost surface with more adsorption sites might be the main reason. Conversely, citric acid and malic acid showed the ability to inhibit Cd adsorption by vermicompost. Citric acid caused a blocking effect by covering flocculent substances on the vermicompost surface while reducing surface adsorption sites by dissolving mineral components such as iron oxides. However, the action of malic acid did not appear to be related to changes in morphology or the structure of vermicompost. Overall, the results of this study partially explain the limited effectiveness of Cd immobilization within the rhizosphere by vermicompost, and provide theoretical support for regulating rhizosphere environments to improve the effectiveness of vermicompost immobilization of Cd.

A Secure Scheme Based on a Hybrid of Classical-Quantum Communications Protocols for Managing Classical Blockchains.

Blockchain technology affords data integrity protection and building trust mechanisms in transactions for distributed networks, and, therefore, is seen as a promising revolutionary information technology. At the same time, the ongoing breakthrough in quantum computation technology contributes toward large-scale quantum computers, which might attack classic cryptography, seriously threatening the classic cryptography security currently employed in the blockchain. As a better alternative, a quantum blockchain has high expectations of being immune to quantum computing attacks perpetrated by quantum adversaries. Although several works have been presented, the problems of impracticality and inefficiency in quantum blockchain systems remain prominent and need to be addressed. First, this paper develops a quantum-secure blockchain (QSB) scheme by introducing a consensus mechanism-quantum proof of authority (QPoA) and an identity-based quantum signature (IQS)-wherein QPoA is used for new block generation and IQS is used for transaction signing and verification. Second, QPoA is developed by adopting a quantum voting protocol to achieve secure and efficient decentralization for the blockchain system, and a quantum random number generator (QRNG) is deployed for randomized leader node election to protect the blockchain system from centralized attacks like distributed denial of service (DDoS). Compared to previous work, our scheme is more practical and efficient without sacrificing security, greatly contributing to better addressing the challenges in the quantum era. Extensive security analysis demonstrates that our scheme provides better protection against quantum computing attacks than classic blockchains. Overall, our scheme presents a feasible solution for blockchain systems against quantum computing attacks through a quantum strategy, contributing toward quantum-secured blockchain in the quantum era.

Arabidopsis PAP17 is a dual-localized purple acid phosphatase up-regulated during phosphate deprivation, senescence, and oxidative stress.

A 35 kDa monomeric purple acid phosphatase (APase) was purified from cell wall extracts of Pi starved (-Pi) Arabidopsis thaliana suspension cells and identified as AtPAP17 (At3g17790) by mass spectrometry and N-terminal microsequencing. AtPAP17 was de novo synthesized and dual-localized to the secretome and/or intracellular fraction of -Pi or salt-stressed plants, or senescing leaves. Transiently expressed AtPAP17-green fluorescent protein localized to lytic vacuoles of the Arabidopsis suspension cells. No significant biochemical or phenotypical changes associated with AtPAP17 loss of function were observed in an atpap17 mutant during Pi deprivation, leaf senescence, or salinity stress. Nevertheless, AtPAP17 is hypothesized to contribute to Pi metabolism owing to its marked up-regulation during Pi starvation and leaf senescence, broad APase substrate selectivity and pH activity profile, and rapid repression and turnover following Pi resupply to -Pi plants. While AtPAP17 also catalyzed the peroxidation of luminol, which was optimal at pH 9.2, it exhibited a low Vmax and affinity for hydrogen peroxide relative to horseradish peroxidase. These results, coupled with absence of a phenotype in the salt-stressed or -Pi atpap17 mutant, do not support proposals that the peroxidase activity of AtPAP17 contributes to the detoxification of reactive oxygen species during stresses that trigger AtPAP17 up-regulation.

Moisture Retention and Multi-mechanistic Transport Behavior in Nanoporous Coal.

Coal-water interactions induced by water retention in coals control the performance of coalbed methane reservoirs and coal utilizations. Experimental measurements on Illinois coal samples using X-ray diffraction, X-ray photoelectron spectroscopy, Fourier transform infrared spectroscopy, low-temperature N2 adsorption, low-pressure CO2 adsorption, and dynamic water vapor sorption were carried out. A mechanism-based isothermal model of water vapor sorption was proposed to estimate the water adsorption capacity at varied relative humidity, which implicitly considered both monolayer and multilayer adsorptions and capillary condensation. The analytical models for quantifying the stage-based diffusion coefficients as well as the apparent diffusion coefficients at different relative humidities were proposed and well validated. The contributions of different diffusion regimes to the total mass flow were discussed. At the first stage, both free water vapor diffusion and surface diffusion of adsorbed water molecules contribute to the total mass flow whereas the apparent diffusion at this stage is dominated by latter flow regime; during the second stage, the contribution of free water vapor flow to the apparent flow can be neglected and the mass transfer at this stage is still dominated by the surface diffusion flow; upon reaching the critical relative humidity, the flow in capillary condensation will dominate the total mass flow.

The inhibitory effect of rBCG on EB virus-positive tumours using an EB virus fusion gene.

At present, studies have found that latent Epstein-Barr virus (EBV) infection is associated with a variety of human tumours, and a vaccine is not available in this field. In this research, RT-PCR was used to obtain BZLF1 (immediately expressed early antigen Z) and LMP2 (latent membrane protein 2) cDNA from EBV. A ZLP2 fusion gene containing a linker sequence that encoded the polypeptide (Gly4Ser)3 was obtained using the sequence splicing overlap extension method. Then, ZLP2 was inserted into pMV261 cells, and the recombinant plasmid pMV-ZLP2 was transformed into BCG competent cells. After EB virus-positive tumour cell (NPRC18) cancer models were established with C57BL/6 J mice, tumour weight, tumour formation time and mouse survival conditions were analyzed, and flow cytometry was used to analyze the quantities of CD8 + and CD4 + T cells. HE staining was used to detect and analyze lymphocyte infiltration, and statistical analysis was used to analyze the immunological effect of recombinant BCG (rBCG). Compared with the control group, rBCG could significantly prolong the survival time of mice, slow tumour growth and delay tumour formation time. Recombinant BCG exhibits an obvious immune effect in mice and an inhibitory effect on EBV-positive cancer.Key points• AZLP2 fusion gene with BZLF1 and LMP2 of EB virus was constructed.• ZLP2 fusion gene was expressed with rBCG.• rBCG with ZLP2 has an obvious effect on EBV-positive cancer.

A Succinct Method for Non-Line-of-Sight Mitigation for Ultra-Wideband Indoor Positioning System.

Ultra-wideband (UWB) is a promising indoor position technology with centimetre-level positioning accuracy in line-of-sight (LOS) situations. However, walls and other obstacles are common in an indoor environment, which can introduce non-line-of-sight (NLOS) and deteriorate UWB positioning accuracy to the meter level. This paper proposed a succinct method to identify NLOS induced by walls and mitigate the error for improved UWB positioning with NLOS. First, NLOS is detected by a sliding window method, which can identify approximately 90% of NLOS cases in a harsh indoor environment. Then, a delay model is designed to mitigate the error of the UWB signal propagating through a wall. Finally, all the distance measurements, including LOS and NLOS, are used to calculate the mobile UWB tag position with ordinary least squares (OLS) or weighted least squares (WLS). Experiment results show that with correct NLOS indentation and delay model, the proposed method can achieve positioning accuracy in NLOS environments close to the level of LOS. Compared with OLS, WLS can further optimise the positioning results. Correct NLOS indentation, accurate delay model and proper weights in the WLS are the keys to accurate UWB positioning in NLOS environments.

Pontixanthobacter rizhaonensis sp. nov., a marine bacterium isolated from surface seawater of the Yellow Sea, and proposal of Pseudopontixanthobacter gen. nov., Pseudopontixanthobacter confluentis comb. nov. and Pseudopontixanthobacter sediminis comb. nov.

A bacterial strain designated RZ02T was isolated from surface seawater collected from the Yellow Sea in PR China and characterized by polyphasic taxonomy. Cells of strain RZ02T were Gram-stain-negative, aerobic, non-motile, catalase- and oxidase-positive rods forming ochre-pigmented colonies. Growth occurred at 7-36 °C (optimum, 30 °C), at pH 6.0-9.0 (optimum, pH 7.0) and with 1-5 % (optimum, 2 %) NaCl. The major cellular fatty acids (>10 %) of strain RZ02T were summed feature 8 (C18 : 1 ω6c and/or C18 : 1 ω7c), summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) and C16 : 0. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol and sphingoglycolipid. The genome size of strain RZ02T was 2.79 Mbp with a G+C content of 55.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain RZ02T was mostly related to Pontixanthobacter luteolus SW-109T and Pontixanthobacter aestiaquae HDW-31T (97.3 and 97.1% sequence similarity, respectively), and formed a phyletic lineage with members of the genus Pontixanthobacter. The phylogenetic analysis based on the up-to-date bacterial core gene sequences confirmed that strain RZ02T clustered within the genus Pontixanthobacter. The average nucleotide identity and in silico DNA-DNA hybridization values between strain RZ02T and P. luteolus SW-109T and P. aestiaquae HDW-31T were 72.8 and 72.9 % and 18.7 and 18.5%, respectively. Based on these evidences, strain RZ02T is proposed to represent a novel species of the genus Pontixanthobacter under the name Pontixanthobacter rizhaonensis sp. nov. The type strain is RZ02T (=KCTC 62828T=MCCC 1K04521T). In addition, based on the results of whole genome analyses, proposals of Pseudopontixanthobacter gen. nov., Pseudopontixanthobacter confluentis comb. nov. and Pseudopontixanthobacter sediminis comb. nov. are also included.

Zongyanglinia huanghaiensis gen. nov., sp. nov., a novel denitrifying bacterium isolated from the yellow sea, and transfer of Pelagicola marinus to Zongyanglinia gen. nov. as Zongyanglinia marinus comb. nov.

Two Gram-stain-negative, oxidase- and catalase-positive, aerobic strains (CY05T and H18S-6) were isolated from sediment samples of the Yellow Sea, China. The strains were positive for denitrification. Optimum growth was observed at 20 °C, pH 7.5-8.0 and with 2.0%-3.0% NaCl. The predominant cellular fatty acids (> 10%) were summed feature 8 (C18:1 ω7c and/or C18:1 ω6c), major respiratory quinone was ubiquinone-10 and main polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, one unidentified phospholipid and one unidentified aminolipid. The approximate genome size of strains CY05T and H18S-6 were 4.86 and 5.04 Mbp, the genomic G + C content of them were 54.2 and 54.5%, respectively. Both of the phylogenetic analysis based on 16S rRNA gene sequences and the up-to-date bacterial core gene (UBCG) sequences revealed that strains CY05T, H18S-6 and Pelagicola marinus DSW4-44T formed a distinct monophyletic clade within the family Rhodobacteraceae. The ANI and isDDH values between strains CY05T and H18S-6 were 94.0% and 56.5%, between CY05T and Pelagicola marinus DSW4-44T were 94.1% and 59.8%, respectively, all below the accepted threshold value for species delineation. But the ANI and isDDH values between strains H18S-6 and Pelagicola marinus DSW4-44T were 96.8% and 76.7% respectively, indicating that strains H18S-6 and Pelagicola marinus DSW4-44T belong to the same species. Based on the distinctive polyphasic evidence, CY05T represent a novel species of a novel genus of the family Rhodobacteraceae, for which the name Zongyanglinia huanghaiensis gen. nov., sp. nov. is proposed. The type strain is CY05T (= MCCC 1K04409T = KCTC 62200T). Moreover, the reclassification of Pelagicola marinus Choi et al. 2019 as Zongyanglinia marinus comb. nov. (type strain DSW4-44T = KCTC 62762T = KCCM 43261T = JCM 33637T) is proposed based on the polyphasic taxonomic data obtained in this study.

Melatonin alleviates titanium nanoparticles induced osteolysis via activation of butyrate/GPR109A signaling pathway.

BACKGROUND: Inflammatory osteolysis after total joint replacement (TJR) may cause implant failure, periprosthetic fractures, and be a severe threat to global public health. Our previous studies demonstrated that melatonin had a therapeutic effect on wear-particles induced osteolysis. Gut microbiota is closely related to bone homeostasis, and has been proven to be affected by melatonin. However, whether melatonin could play its anti-osteolysis effects through reprogramming gut microbiota remains elusive. RESULTS: Here, we demonstrated that melatonin could alleviate Ti-particles induced osteolysis, while this therapeutic effect was blocked by antibiotic cocktail treatment. Interestingly, transplantation of fecal microbiota from mice treated with melatonin reappeared the same beneficial effect. Analysis of the 16S rRNA revealed that melatonin could reverse dysbacteriosis triggered by osteolysis, and elevate the relative abundance of some short chain fatty acid (SCFA) producing bacteria. Moreover, butyrate was enriched by exogenous melatonin administration, while acetate and propionate did not show an evident difference. This was consistent with the results of the metagenomic approach (PICRUSt2) analysis, which revealed a general increase in the synthetic enzymes of butyrate. More importantly, direct supplementation of butyrate could also recapitulate the anti-osteolysis effect of melatonin. Further analysis identified that butyrate alleviated osteolysis via activating its receptor GPR109A, and thus to suppress the activation of NLRP3 inflammasome triggered by Ti-particles. CONCLUSIONS: Taken together, our results suggested that the benefits of melatonin mainly depend on the ability of modulating gut microbiota and regulating butyrate production.

Reclassification of Algibacter wandonensis as a Later Heterotypic Synonym of Algibacter lectus Based on Whole-Genome Sequence Analysis.

The genus Algibacter belongs to the family Flavobacteriaceae of the Bacteroidetes, and all members of this genus were isolated from marine environments. Among the Algibacter species, two members, Algibacter lectus KMM 3902T and Algibacter wandonensis WS-MY22T, were isolated from green algae and sediment around a brown algae respectively. The 16S rRNA gene sequences of these two type strains possess 99.4% sequence similarity. In this study, further studies were undertaken to clarify the taxonomic assignments of the two species. Whole-genome sequence analysis showed that the similarities for other phylogenetic markers are also very high (i.e. 99.9% for gyrB, 99.6% for recA and 99.9% for rpoD). Average nucleotide identity, average amino acids identity and digital DNA-DNA hybridization value between A. lectus KMM 3902T and A. wandonensis WS-MY22T are 98.3%, 98.6% and 89.4% respectively, all clearly exceed suggested species delineation thresholds. Furthermore, phylogenetic trees based on sequences of 16S rRNA gene and up-to-date bacterial core gene set (UBCG) consisting of 92 genes provided additional evidence that A. lectus KMM 3902T and A. wandonensis WS-MY22T are very closely related. In addition, a review of their profiles indicated that A. lectus KMM 3902T and A. wandonensis WS-MY22T did not present pronounced differences at phenotypic and chemotaxonomic levels. Based on these evidence, we propose that A. wandonensis should be reclassified as later heterotypic synonyms of A. lectus.

Phylogenomic Analyses of a Clade Within the Family Flavobacteriaceae Suggest Taxonomic Reassignments of Species of the Genera Algibacter, Hyunsoonleella, Jejuia, and Flavivirga, and the Proposal of Pseudalgibacter gen. nov. and Pseudalgibacter alginicilyticus comb. nov.

The family Flavobacteriaceae forms a major branch within the phylum Bacteroidetes. Whole-genome sequence-based analysis could significantly improve the accuracy of taxonomic assignments. In this study, phylogenomic analyses were carried out to revisit the taxonomic status of a clade of the family Flavobacteriaceae. Taking genome-based phylogeny as the primary guideline and average amino acid identity and phenotypic information as supplements, the following taxonomic proposals were put forward: Arenitalea lutea should be reclassified into the genus Algibacter; Algibacter aquaticus should be reclassified into the genus Flavivirga; Jejuia pallidilutea and Algibacter aestuarii should be reclassified into the genus Hyunsoonleella; Algibacter alginicilyticus should be reclassified into the novel genus Pseudalgibacter gen. nov. This study builds up a solid framework for taxonomic decisions of a clade of the family Flavobacteriaceae and will contribute to further insights into the evolution of this family.

Maribacter luteus sp. nov., a marine bacterium isolated from intertidal sand of the Yellow Sea.

A novel rod-shaped and Gram-stain-negative bacterium, designated strain RZ05T, was isolated from a sand sample collected from the intertidal zone of the Yellow Sea, PR China. Results of phylogenetic analysis based on 16S rRNA gene sequences revealed that strain RZ05T clusters within the genus Maribacter, a member of the family Flavobacteriaceae, and has the highest sequence similarity to Maribacter polysiphoniae KCTC 22021T (97.8 %), followed by Maribacter arenosus KCTC 52191T (97.2 %). Cells of this strain were observed to be aerobic, oxidase- and catalase-positive, motile by gliding and formed yellow colonies. Growth occurred at 7-40 °C (optimum, 30 °C), at pH 6.5-9.5 (optimum, pH 7.0) and with 0.5-6 % (optimum, 2 %) NaCl. Its polar lipid profile included phosphatidylethanolamine, two unidentified glycolipids, one unidentified aminolipid and four unidentified lipids. The major cellular fatty acids were iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 3-OH, iso-C16 : 0 3-OH, iso-C15 : 0 3-OH, summed feature 9 (10-methyl C16 : 0/iso-C17 : 1 ω9c) and summed feature 3 (iso-C15 : 0 2-OH/C16 : 1 ω7c/C16 : 1 ω6c). The only respiratory quinone was menaquinone 6 (MK-6). The genome of strain RZ05T was 4.65 Mbp with a G+C content of 38.9 mol%. The average nucleotide identity and in silico DNA-DNA hybridization values between strain RZ05T and its most closely related type strain M. polysiphoniae KCTC 22021T were 80.3 and 26.3  %, respectively. The results of phylogenetic, phenotypic and chemotaxonomic analyses indicated that strain RZ05T represents a novel species of the genus Maribacter, for which the name Maribacter luteus sp. nov. is proposed. The type strain is RZ05T (=KCTC 62834T=MCCC 1K03617T).