Racial/Ethnic Disparities in Post-acute Sequelae of SARS-CoV-2 Infection in New York: an EHR-Based Cohort Study from the RECOVER Program.

BACKGROUND: Compared to white individuals, Black and Hispanic individuals have higher rates of COVID-19 hospitalization and death. Less is known about racial/ethnic differences in post-acute sequelae of SARS-CoV-2 infection (PASC). OBJECTIVE: Examine racial/ethnic differences in potential PASC symptoms and conditions among hospitalized and non-hospitalized COVID-19 patients. DESIGN: Retrospective cohort study using data from electronic health records. PARTICIPANTS: 62,339 patients with COVID-19 and 247,881 patients without COVID-19 in New York City between March 2020 and October 2021. MAIN MEASURES: New symptoms and conditions 31-180 days after COVID-19 diagnosis. KEY RESULTS: The final study population included 29,331 white patients (47.1%), 12,638 Black patients (20.3%), and 20,370 Hispanic patients (32.7%) diagnosed with COVID-19. After adjusting for confounders, significant racial/ethnic differences in incident symptoms and conditions existed among both hospitalized and non-hospitalized patients. For example, 31-180 days after a positive SARS-CoV-2 test, hospitalized Black patients had higher odds of being diagnosed with diabetes (adjusted odds ratio [OR]: 1.96, 95% confidence interval [CI]: 1.50-2.56, q<0.001) and headaches (OR: 1.52, 95% CI: 1.11-2.08, q=0.02), compared to hospitalized white patients. Hospitalized Hispanic patients had higher odds of headaches (OR: 1.62, 95% CI: 1.21-2.17, q=0.003) and dyspnea (OR: 1.22, 95% CI: 1.05-1.42, q=0.02), compared to hospitalized white patients. Among non-hospitalized patients, Black patients had higher odds of being diagnosed with pulmonary embolism (OR: 1.68, 95% CI: 1.20-2.36, q=0.009) and diabetes (OR: 2.13, 95% CI: 1.75-2.58, q<0.001), but lower odds of encephalopathy (OR: 0.58, 95% CI: 0.45-0.75, q<0.001), compared to white patients. Hispanic patients had higher odds of being diagnosed with headaches (OR: 1.41, 95% CI: 1.24-1.60, q<0.001) and chest pain (OR: 1.50, 95% CI: 1.35-1.67, q < 0.001), but lower odds of encephalopathy (OR: 0.64, 95% CI: 0.51-0.80, q<0.001). CONCLUSIONS: Compared to white patients, patients from racial/ethnic minority groups had significantly different odds of developing potential PASC symptoms and conditions. Future research should examine the reasons for these differences.

Mesoterricola silvestris gen. nov., sp. nov., Mesoterricola sediminis sp. nov., Geothrix oryzae sp. nov., Geothrix edaphica sp. nov., Geothrix rubra sp. nov., and Geothrix limicola sp. nov., six novel members of Acidobacteriota isolated from soils.

Forty-eight Acidobacteriota strains were isolated from soils and sediments in Japan. Among them, six representative strains, designated W79T, W786T, Red222T, Red802T, Red803T, and Red804T, were subjected to the taxonomic classification. These six strains are Gram-stain-negative, non-spore-forming, rod-shaped, and facultative anaerobic bacterium that can reduce ferric iron. Phylogenetic and phylogenomic trees based on 16S rRNA genes and multiple single-copy gene sequences showed that strains Red222T, Red802T, Red803T, and Red804T formed a cluster with the type strains of Geothrix species, but strains W79T and W786T created an independent cluster from any other type strains. The former four strains shared 97.95-99.08% similarities of 16S rRNA gene sequence with the type strains of the genus Geothrix, whereas the latter two strains 94.86-95.49% similarities. The average amino acid identity of strains W79T and W786T were <63 % to any other type strains, which were below the genus delineation thresholds. Moreover, colonies of these two strains were white, while those of the other four isolated strains were reddish-yellow as well as the type strain Geothrix fermentans H-5T. Although the known type strains of Geothrix species have been reported to be non-motile, five strains (W79T, W786T, Red222T, Red803T, and Red804T) except for strain Red802T displayed motility. Furthermore, multiple genomic, phylogenetic, and phenotypic features supported the discrimination between these isolated strains. Based on the study evidence, we propose these six isolates as novel members within the Acidobacteriota/Holophagae/Holophagales/Holophagaceae, comprising two novel species of a novel genus, Mesoterricola silvestris gen. nov., sp. nov., and Mesoterricola sediminis sp. nov., and four novel species of the genus Geothrix: Geothrix oryzae sp. nov., Geothrix edaphica sp. nov., Geothrix rubra sp. nov., and Geothrix limicola sp. nov.

Anaeromyxobacter oryzae sp. nov., Anaeromyxobacter diazotrophicus sp. nov. and Anaeromyxobacter paludicola sp. nov., isolated from paddy soils.

Three bacterial strains (Red232T, Red267T and Red630T) were isolated from paddy soils sampled in Japan. Cells of these strains were Gram-stain-negative, facultative anaerobic, long rod-shaped with monotrichous flagella or pilus-like structures for motility, and formed red colonies on agar plates. Phylogenetic trees based on 16S rRNA gene and multiple single-copy gene sequences showed that the three strains formed a cluster with the type strains of Anaeromyxobacter species, independent from any other strain genera. Similarity values of the 16S rRNA gene sequences and genomes among the three isolated strains and the type strain of Anaeromyxobacter, Anaeromyxobacter dehalogenans 2CP-1T, were 95.4-97.4% for 16S rRNA gene sequence, 75.3-79.5% for average nucleotide identity, 19.6-21.7% for digital DNA-DNA hybridization and 64.1-72.6% for average amino acid identity, all of which are below the species delineation thresholds. Nitrogenase genes were observed in the genomes of the three novel strains, but not in A. dehalogenans 2CP-1T. Moreover, multiple genomic, physiological and chemotaxonomic features supported the discrimination between these three strains. Based on the evidence in this study, the three isolates represent three novel independent species for which the following names are proposed: Anaeromyxobacter oryzae sp. nov., Anaeromyxobacter diazotrophicus sp. nov. and Anaeromyxobacter paludicola sp. nov. The type strains are Red232T (=NBRC 114074T=MCCC 1K03954T), Red267T (=NBRC 114075T=MCCC 1K04211T), and Red630T (=NBRC 114076T=MCCC 1K03957T), respectively.

Sepsis subphenotyping based on organ dysfunction trajectory.

BACKGROUND: Sepsis is a heterogeneous syndrome, and the identification of clinical subphenotypes is essential. Although organ dysfunction is a defining element of sepsis, subphenotypes of differential trajectory are not well studied. We sought to identify distinct Sequential Organ Failure Assessment (SOFA) score trajectory-based subphenotypes in sepsis. METHODS: We created 72-h SOFA score trajectories in patients with sepsis from four diverse intensive care unit (ICU) cohorts. We then used dynamic time warping (DTW) to compute heterogeneous SOFA trajectory similarities and hierarchical agglomerative clustering (HAC) to identify trajectory-based subphenotypes. Patient characteristics were compared between subphenotypes and a random forest model was developed to predict subphenotype membership at 6 and 24 h after being admitted to the ICU. The model was tested on three validation cohorts. Sensitivity analyses were performed with alternative clustering methodologies. RESULTS: A total of 4678, 3665, 12,282, and 4804 unique sepsis patients were included in development and three validation cohorts, respectively. Four subphenotypes were identified in the development cohort: Rapidly Worsening (n = 612, 13.1%), Delayed Worsening (n = 960, 20.5%), Rapidly Improving (n = 1932, 41.3%), and Delayed Improving (n = 1174, 25.1%). Baseline characteristics, including the pattern of organ dysfunction, varied between subphenotypes. Rapidly Worsening was defined by a higher comorbidity burden, acidosis, and visceral organ dysfunction. Rapidly Improving was defined by vasopressor use without acidosis. Outcomes differed across the subphenotypes, Rapidly Worsening had the highest in-hospital mortality (28.3%, P-value < 0.001), despite a lower SOFA (mean: 4.5) at ICU admission compared to Rapidly Improving (mortality:5.5%, mean SOFA: 5.5). An overall prediction accuracy of 0.78 (95% CI, [0.77, 0.8]) was obtained at 6 h after ICU admission, which increased to 0.87 (95% CI, [0.86, 0.88]) at 24 h. Similar subphenotypes were replicated in three validation cohorts. The majority of patients with sepsis have an improving phenotype with a lower mortality risk; however, they make up over 20% of all deaths due to their larger numbers. CONCLUSIONS: Four novel, clinically-defined, trajectory-based sepsis subphenotypes were identified and validated. Identifying trajectory-based subphenotypes has immediate implications for the powering and predictive enrichment of clinical trials. Understanding the pathophysiology of these differential trajectories may reveal unanticipated therapeutic targets and identify more precise populations and endpoints for clinical trials.

Geomonas silvestris sp. nov., Geomonas paludis sp. nov. and Geomonas limicola sp. nov., isolated from terrestrial environments, and emended description of the genus Geomonas.

Three bacterial strains, designated Red330T, Red736T and Red745T, were isolated from forest and paddy soils in Japan. Strains Red330T, Red736T and Red745T are flagella-harbouring and strictly anaerobic bacteria forming red colonies. A 16S rRNA gene sequence-based phylogenetic tree showed that all three strains were located in a cluster, including the type strains of Geomonas species, which were recently separated from the genus Geobacter within the family Geobacteraceae. Similarities of the 16S rRNA gene sequences among the three strains and Geomonas oryzae S43T, the type species of the genus Geomonas, were 96.3-98.5 %. The genome-related indexes, average nucleotide identity, digital DNA-DNA hybridization, and average amino acid identity, among the three strains and G. oryzae S43T were 74.7-86.8 %, 21.2-33.3 % and 70.4-89.8 %, respectively, which were lower than the species delineation thresholds. Regarding the phylogenetic relationships based on genome sequences, the three strains clustered with the type strains of Geomonas species, which were independent from the type strains of Geobacter species. The distinguishableness of the three isolated strains was supported by physiological and chemotaxonomic properties, with the profile of availability of electron donors and cellular fatty acids composition being particularly different among them. Based on genetic, phylogenetic and phenotypic properties, the three isolates represent three novel independent species in the genus Geomonas, for which the names Geomonas silvestris sp. nov., Geomonas paludis sp. nov. and Geomonas limicola sp. nov. are proposed. The type strains are Red330T (=NBRC 114028T=MCCC 1K03949T), Red736T (=NBRC 114029T=MCCC 1K03950T) and Red745T (=NBRC 114030T=MCCC 1K03951T), respectively.

Diazotrophic Anaeromyxobacter Isolates from Soils.

Biological nitrogen fixation is an essential reaction in a major pathway for supplying nitrogen to terrestrial environments. Previous culture-independent analyses based on soil DNA/RNA/protein sequencing could globally detect the nitrogenase genes/proteins of Anaeromyxobacter (in the class Deltaproteobacteria), commonly distributed in soil environments and predominant in paddy soils; this suggests the importance of Anaeromyxobacter in nitrogen fixation in soil environments. However, direct experimental evidence is lacking; there has been no research on the genetic background and ability of Anaeromyxobacter to fix nitrogen. Therefore, we verified the diazotrophy of Anaeromyxobacter based on both genomic and culture-dependent analyses using Anaeromyxobacter sp. strains PSR-1 and Red267 isolated from soils. Based on the comparison of nif gene clusters, strains PSR-1 and Red267 as well as strains Fw109-5, K, and diazotrophic Geobacter and Pelobacter in the class Deltaproteobacteria contain the minimum set of genes for nitrogenase (nifBHDKEN). These results imply that Anaeromyxobacter species have the ability to fix nitrogen. In fact, Anaeromyxobacter PSR-1 and Red267 exhibited N2-dependent growth and acetylene reduction activity (ARA) in vitro Transcriptional activity of the nif gene was also detected when both strains were cultured with N2 gas as a sole nitrogen source, indicating that Anaeromyxobacter can fix and assimilate N2 gas by nitrogenase. In addition, PSR-1- or Red267-inoculated soil showed ARA activity and the growth of the inoculated strains on the basis of RNA-based analysis, demonstrating that Anaeromyxobacter can fix nitrogen in the paddy soil environment. Our study provides novel insights into the pivotal environmental function, i.e., nitrogen fixation, of Anaeromyxobacter, which is a common soil bacterium.IMPORTANCEAnaeromyxobacter is globally distributed in soil environments, especially predominant in paddy soils. Current studies based on environmental DNA/RNA analyses frequently detect gene fragments encoding nitrogenase of Anaeromyxobacter from various soil environments. Although the importance of Anaeromyxobacter as a diazotroph in nature has been suggested by culture-independent studies, there has been no solid evidence and validation from genomic and culture-based analyses that Anaeromyxobacter fixes nitrogen. This study demonstrates that Anaeromyxobacter harboring nitrogenase genes exhibits diazotrophic ability; moreover, N2-dependent growth was demonstrated in vitro and in the soil environment. Our findings indicate that nitrogen fixation is important for Anaeromyxobacter to survive under nitrogen-deficient environments and provide a novel insight into the environmental function of Anaeromyxobacter, which is a common bacterium in soils.

Identifying sub-phenotypes of acute kidney injury using structured and unstructured electronic health record data with memory networks.

Acute Kidney Injury (AKI) is a common clinical syndrome characterized by the rapid loss of kidney excretory function, which aggravates the clinical severity of other diseases in a large number of hospitalized patients. Accurate early prediction of AKI can enable in-time interventions and treatments. However, AKI is highly heterogeneous, thus identification of AKI sub-phenotypes can lead to an improved understanding of the disease pathophysiology and development of more targeted clinical interventions. This study used a memory network-based deep learning approach to discover AKI sub-phenotypes using structured and unstructured electronic health record (EHR) data of patients before AKI diagnosis. We leveraged a real world critical care EHR corpus including 37,486 ICU stays. Our approach identified three distinct sub-phenotypes: sub-phenotype I is with an average age of 63.03±17.25 years, and is characterized by mild loss of kidney excretory function (Serum Creatinine (SCr) 1.55±0.34 mg/dL, estimated Glomerular Filtration Rate Test (eGFR) 107.65±54.98 mL/min/1.73 m2). These patients are more likely to develop stage I AKI. Sub-phenotype II is with average age 66.81±10.43 years, and was characterized by severe loss of kidney excretory function (SCr 1.96±0.49 mg/dL, eGFR 82.19±55.92 mL/min/1.73 m2). These patients are more likely to develop stage III AKI. Sub-phenotype III is with average age 65.07±11.32 years, and was characterized moderate loss of kidney excretory function and thus more likely to develop stage II AKI (SCr 1.69±0.32 mg/dL, eGFR 93.97±56.53 mL/min/1.73 m2). Both SCr and eGFR are significantly different across the three sub-phenotypes with statistical testing plus postdoc analysis, and the conclusion still holds after age adjustment.

Inducible expression of agar-degrading genes in a marine bacterium Catenovulum maritimus Q1T and characterization of a ß-agarase.

Agar-degrading bacteria are crucial drivers for the carbon cycle in the marine environments due to their ability that use algae as a carbon source. Although numerous agar-degrading bacteria and agarases have been reported, little is known about expression levels of agar-degrading genes in wild strains. Here, the genome of an agar-hydrolyzing marine bacterium, Catenovulum maritimus Q1T, was sequenced and annotated with 11 agarase and 2 neoagarooligosaccharide hydrolase genes. Quantitative PCR revealed that all the annotated agar-degrading genes were expressed consistently that initially upregulated and then gradually downregulated under agarose induction. Moreover, the presence of glucose inhibited the agar-degrading ability, in terms of both gene expression and enzymatic activity. These facts indicated the agar-degrading ability of wild bacteria was mainly induced by agarose and repressed by the available carbon source. Additionally, a ß-agarase, AgaQ1, belonging to the GH16 family, with high expression in strain Q1T, was cloned and characterized. Biochemical analysis showed that the recombinant AgaQ1 was substrate-specific, yielding neoagarotetraose and neoagarohexaose as the main products. It exhibited optimal activity at 40 °C, pH 8.0, and an agarose concentration of 1.6% (w/v). Besides, AgaQ1 showed a high-specific activity (757.7 U/mg) and stable enzymatic activity under different ion or agent treatments; thus, AgaQ1 has great potential in industrial applications. KEY POINTS: • The genome of C. maritimus Q1T was sequenced and annotated with 11 agarases and 2 Nabh genes. • The expression of agar-degrading genes in the strain C. maritimus Q1T was induced by agarose. • Glucose was the carbon source utilized prior to agarose for bacterial growth. • A ß-agarase, AgaQ1, with high expression and activity was identified.

Deep learning control model for adaptive optics systems.

To correct wavefront aberrations, commonly employing proportional-integral control in adaptive optics (AO) systems, the control process depends strictly on the response matrix of the deformable mirror. The alignment error between the Hartmann-Shack wavefront sensor and the deformable mirror is caused by various factors in AO systems. In the conventional control method, the response matrix can be recalibrated to reduce the impact of alignment error, but the impact cannot be eliminated. This paper proposes a control method based on a deep learning control model (DLCM) to compensate for wavefront aberrations, eliminating the dependence on the deformable mirror response matrix. Based on the wavefront slope data, the cost functions of the model network and the actor network are defined, and the gradient optimization algorithm improves the efficiency of the network training. The model network guarantees the stability and convergence speed, while the actor network improves the control accuracy, realizing an online identification and self-adaptive control of the system. A parameter-sharing mechanism is adopted between the model network and the actor network to control the system gain. Simulation results show that the DLCM has good adaptability and stability. Through self-learning, it improves the convergence accuracy and iterations, as well as the adjustment tolerance of the system.

Salegentibacter sediminis sp. nov., a marine bacterium of the family Flavobacteriaceae isolated from coastal sediment.

A Gram-stain-negative, aerobic, non-motile, rod-shaped (0.2-0.3×0.8-1.4 µm) and yellow-pigmented bacterium, designated K5023T, was isolated from marine sediment obtained off the coast of Weihai, China. Strain K5023T was found to grow at 16-37 °C (optimum, 33 °C), at pH 6.5-8.0 (optimum, 7.0-7.5) and in the presence of 1-10 % (w/v) NaCl (optimum, 5 %). Cells were oxidase-positive and catalase-negative. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain K5023T is a member of the genus Salegentibacter and exhibited the hightest sequence similarity to Salegentibacter flavus DSM 22702T (97.0 %). Menaquinone-6 (MK-6) was detected as the major respiratory quinone. The dominant cellular fatty acids were iso-C15 : 0 and anteiso-C15 : 0. The DNA G+C content of strain K5023T was 40.1 mol%. The polar lipids included one phosphatidylethanolamine, three phospholipids and four unidentified lipids. Based on the phylogenetic and phenotypic characteristics, strain K5023T is considered to represent a novel species of the genus Salegentibacter, for which the name Salegentibacter sediminis sp. nov. is proposed. The type strain is K5023T (=KCTC 52477T=MCCC 1H00173T).

Jeotgalibacillus proteolyticus sp. nov., a protease-producing bacterium isolated from ocean sediments.

A Gram-stain-positive, rod-shaped bacterial strain, 22-7T, was isolated from ocean sediment of Laizhou Bay, China, and was characterized by using a polyphasic approach. Optimal growth was observed at 33 °C on a 2216E agar plate of pH 7.5 and with 2 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences identified it as a member of the genus Jeotgalibacillus, most similar to Jeotgalibacillus campisalis SF-57T (98.7 % similarity), Jeotgalibacillus marinus DSM 1297T (98.2 %) and Jeotgalibacillus soli P9T (97.1 %). Average nucleotide identity values and digital DNA-DNA hybridization values were less than 74.2 and 18.1 %, respectively, between strain 22-7T and the type strains of closely related species. The major polar lipids were aminophospholipid, phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol; the major fatty acids (>10 %) were anteiso-C15 : 0 and iso-C15 : 0; and the major menaquinone was MK-7. The peptidoglycan type of the cell wall was A1α linked through l-lysine as the diamino acid. Combined data from phenotypic, chemotaxonomic and genotypic characterizations demonstrated that strain 22-7T represents a novel Jeotgalibacillus species, for which the name Jeotgalibacillus proteolyticus sp. nov. is proposed. The type strain is 22-7T(=MCCC 1H00228T=KCTC 33930T).

Geofilum rhodophaeum sp. nov., isolated from coastal sediment.

A novel Gram-stain-negative, facultatively anaerobic, filamentous and rose-brown pigmented bacterium, designated strain HF401T, was isolated from marine sediment off the coast of Weihai, China. The isolate grew at temperatures between 4 and 45 °C (optimal growth at 33 °C), at pH 6.5-8.5 (optimal growth at pH 7.5) and with 0.5-6.0 % (w/v) NaCl (optimal growth at 3.0 %). The predominant menaquinone was menaquinone 7 (MK-7). The G+C content of the genomic DNA was 50.8 mol% (from high-performance liquid chromatography). The major fatty acids were iso-C15 : 0, C16:0, anteiso-C15 : 0 and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2OH). The major polar lipids were phosphatidylethanolamine, phospholipid and an unidentified lipid. Phylogenetic analysis of 16S rRNA gene sequences indicated that strain HF401T formed a distinct branch with Geofilum rubicundum JCM 15548T in the family Marinilabiliaceae. The most closely related strains of strain HF401T were Natronoflexuspectinivorans AP1T (96.2 % 16S rRNA gene sequence similarity), G. rubicundum JCM 15548T (96.2 %) and Alkalitaleasaponilacus SC/BZ-SP2T (96.0 %). Average nucleotide identity (ANI) values between strain HF401T and G. rubicundum JCM 15548T showed a relatedness of 71.3 % (ANIb) and 86.0 % (ANIm). The percentage of conserved proteins (POCP) value between strain HF401T and G. rubicundum JCM 15548T was 61.2 %. Based on polyphasic analysis, especially the phylogenetic relationships and the higher POCP value, strain HF401T is considered to represent a novel species in the genus Geofilum, for which the name Geofilum rhodophaeum sp. nov. is proposed. The type strain of Geofilum rhodophaeum is HF401T (KCTC 42595T=MCCC 1H00119T).

Tenacibaculum agarivorans sp. nov., an agar-degrading bacterium isolated from marine alga Porphyra yezoensis Ueda.

A novel Gram-stain-negative, aerobic, rod-shaped, non-flagellated and agar-digesting marine bacterium, designated as HZ1T, was isolated from the marine alga Porphyra yezoensis Ueda (AST58-103) collected from the coastal area of Weihai, PR China. Phylogenetic analysis based on 16S rRNA gene sequences placed HZ1T in the genus Tenacibaculum, and it formed a distinct clade in the phylogenetic tree with the type strains of Tenacibaculum amylolyticum and Tenacibaculum skagerrakense, with 97.0 % and 96.7 % 16S rRNA gene sequence similarities, respectively. The DNA G+C content of the isolate was 31.8 mol%. HZ1T contained MK-6 as the predominant menaquinone and iso-C15 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), iso-C17 : 0 3-OH and iso-C15 : 1G as the major fatty acids. The major polar lipids were phosphatidylethanolamine, four unidentified lipids and five unidentified aminolipids. On the basis of the results of the phylogenetic analysis and phenotypic properties, it is concluded that HZ1T represents a novel species of the genus Tenacibaculum, for which the name Tenacibaculumagarivorans sp. nov. is proposed. The type strain is HZ1T (=MCCC 1H00174T=KCTC 52476T).

Colwellia agarivorans sp. nov., an agar-digesting marine bacterium isolated from coastal seawater.

A novel Gram-stain-negative, facultatively anaerobic, yellowish and agar-digesting marine bacterium, designated strain QM50T, was isolated from coastal seawater in an aquaculture site near Qingdao, China. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolate represented a member of the genus Colwellia and exhibited the highest sequence similarity (97.4 %) to Colwellia aestuarii SMK-10T. Average nucleotide identity (ANI) values based on draft genome sequences between strain QM50T and C. aestuarii KCTC 12480T showed a relatedness of 72.0 % (ANIb) and 85.1 % (ANIm). Cells of strain QM50T were approximately 0.3-0.6×0.8-2.5 µm in size and motile by means of a polar flagellum. Growth occurred in the presence of 1.0-6.0 % (w/v) NaCl (optimum, 2.0-3.0 %), at pH 6.5-8.5 (optimum, pH 7.0) and at 4-37 °C (optimum, 28-30 °C). Strain QM50T was found to contain ubiquinone 8 (Q-8) as the predominant ubiquinone and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), C16 : 0 and C17 : 1ω8c as the main cellular fatty acids. Phosphatidylethanolamine and phosphatidylglycerol were found to be major polar lipids. The DNA G+C content of strain QM50T was determined to be 35.7 mol%. On the basis of phylogenetic and phenotypic data, strain QM50T represents a novel species of the genus Colwellia, for which the name Colwellia agarivorans sp. nov. is proposed. The type strain is QM50T (=KCTC 52273T=MCCC 1H00143T).

[Effects of Huatan Tongluo Recipe on IL-1ß-induced Proliferation of Rheumatoid Arthritis Synovial Fibroblasts and the Production of TNF-α and aFGF].

Objective To observe the effects of Huatan Tongluo Recipe (HTTLR) on the proliferation of IL-ß p induced rheumatoid arthritis synovial fibroblast ( RASFB) and secretion of necrosis factor α (TNF-α) and acidic fibroblast growth factor (aFGF) in vitro. Methods RASFB cell line was cultured in vitro and stimulated by IL-1ß. The proliferation of RASFB was detected using WST-1 after adding IL-1ß with final concentrations of 1 , 5, 10, 20 µg/L for 24 and 48 h respectively. Then 20 µg/L IL-1ß recruited as induction dose was set up as IL-1ß group. High, middle, low dose HTTLR groups were set up by adding HT- TLR decoction with final concentration of 5%, 2%, 1% (V/V) , respectively for 24 and 48 h. A blank con- trol group was also set up. The proliferation rates were compared. Contents of TNF-α and aFGF were detected in each group using ELISA. mRNA expressions of TNF-α and aFGF were detected using RT-PCR. Results The proliferation rates of RASFB at 24 h and 48 h were lower at 1 µg/L IL-1 ß than at 5, 10, 20 µg/L IL-1ß (P <0. 01). The proliferation rate of RASFB was higher at 10 and 20 µg/L IL-1ß than at 5 µg/L IL-1ß (P <0. 01). Besides, the proliferation rate of RASFB was higher at 20 µg/L IL-1ß than at 10 µg/L IL-1 ß (P <0. 01). The proliferation rate of RASFB was higher at 48 h than at 24 h (P <0. 01). Com- pared with the high dose HTTLR group, the proliferation rate of RASFB was lowered in middle and low dose HTTLR groups (P <0. 01). Besides, IL-1ß induced proliferation rate of RASFB was obviously reduced in the middle dose HTTLR group (P <0. 01). Compared with the blank control group, mRNA ex- pressions of TNF-α and aFGF and their contents were elevated in the IL-1ß group at 24 and 48 h (P < 0. 05). Compared with the IL-1 ß group, mRNA expressions of TNF-α- and aFGF and their contents, except TNF-α- mRNA expression in the low dose HTTLR group at 24 h, were all obviously lowered in 3 dose HTTLR groups at 24 h and 48 h (P <0. 05). Compared with the high dose HTTLR group, mRNA expressions of TNF-(α and aFGF increased in middle and low dose HTTLR groups at 24 h and 48 h; TNF-α content in the low dose HTTLR group at 24 h; contents of TNF-α and aFGF in middle and low dose HTTLR groups at 24 h and 48 h all increased (P <0. 05). Conclusion The mechanism of HTTLR treatment for RA might be related to inhibiting RASFB proliferation, and decreasing mRNA expressions of TNF-α and aFGF as well as their protein secretion.

Detection of Anti-Hepatitis B Virus Drug Resistance Mutations Based on Multicolor Melting Curve Analysis.

Detection of anti-hepatitis B virus (HBV) drug resistance mutations is critical for therapeutic decisions for chronic hepatitis B virus infection. We describe a real-time PCR-based assay using multicolor melting curve analysis (MMCA) that could accurately detect 24 HBV nucleotide mutations at 10 amino acid positions in the reverse transcriptase region of the HBV polymerase gene. The two-reaction assay had a limit of detection of 5 copies per reaction and could detect a minor mutant population (5% of the total population) with the reverse transcriptase M204V amino acid mutation in the presence of the major wild-type population when the overall concentration was 104 copies/µl. The assay could be finished within 3 h, and the cost of materials for each sample was less than $10. Clinical validation studies using three groups of samples from both nucleos(t)ide analog-treated and -untreated patients showed that the results for 99.3% (840/846) of the samples and 99.9% (8,454/8,460) of the amino acids were concordant with those of Sanger sequencing of the PCR amplicon from the HBV reverse transcriptase region (PCR Sanger sequencing). HBV DNA in six samples with mixed infections consisting of minor mutant subpopulations was undetected by the PCR Sanger sequencing method but was detected by MMCA, and the results were confirmed by coamplification at a lower denaturation temperature-PCR Sanger sequencing. Among the treated patients, 48.6% (103/212) harbored viruses that displayed lamivudine monoresistance, adefovir monoresistance, entecavir resistance, or lamivudine and adefovir resistance. Among the untreated patients, the Chinese group had more mutation-containing samples than did the Pakistani group (3.3% versus 0.56%). Because of its accuracy, rapidness, wide-range coverage, and cost-effectiveness, the real-time PCR assay could be a robust tool for the detection if anti-HBV drug resistance mutations in resource-limited countries.

Marinifilum albidiflavum sp. nov., isolated from coastal sediment.

A novel Gram-stain-negative, facultatively anaerobic, filamentous, and yellowish-white-pigmented marine bacterium, designated strain FB208T, was isolated from marine sediment obtained off the coastal area of Weihai, China. Cells of strain FB208T were filamentous during exponential growth, fragmented to rods in the stationary growth phase and became spherical in aged cultures. It grew optimally at 33 °C, at pH 7.0-7.5 and in the presence of 2.0-3.0 % (w/v) NaCl. Based on the 16S rRNA gene sequence, strain FB208T was found to be closely related to Marinifilum flexuosum DSM 21950T (96.9 % similarity) and Marinifilum fragile JCM 15579T (96.4 %), with less than 90.0 % sequence similarity to other genera of the class Bacteroidia. Phylogenetic analysis, also based on 16S rRNA gene sequences, placed strain FB208T in the genus Marinifilum, family Marinifilaceae. The predominant isoprenoid quinone of strain FB208T was identified as menaquinone MK-7. The main cellular fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and iso-C17 : 1ω9c, and the major polar lipids were an unidentified lipid and aminophospholipid. The G+C content of the genomic DNA was 43.8 mol%. Based on these phylogenetic and phenotypic data, strain FB208T represents a novel species of the genus Marinifilum, for which the name Marinifilum albidiflavum sp. nov. is proposed. The type strain is FB208T (=KCTC 42591T=MCCC 1H00113T).

Nocardioides gilvus sp. nov., isolated from Namtso Lake.

A Gram-stain positive, facultatively anaerobic, non-motile and rod to coccoid-shaped bacterium, designated XZ17(T), was isolated from Namtso Lake of Tibet, China. Strain XZ17(T) grew optimally at pH 8.0-9.0, at 30-33 °C and in the presence of 0-1.0 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences demonstrated that strain XZ17(T) belongs to the genus Nocardioides in the family Nocardioidaceae. Strain XZ17(T) shared pairwise 16S rRNA gene sequence similarities of 97.2, 96.8, 96.5, 96.4 and <96.0 % to Nocardioides solisilvae KCTC 39528(T), Nocardioides daejeonensis JCM 16922(T), Nocardioides jensenii NCIB 9770(T), Nocardioides dubius KCTC 9992(T) and other Nocardioides species, respectively. It contained MK-8 (H4) as the predominant menaquinone and C17:1 ω8c, C15:0, C17:0 and C18:1 ω9c as the major fatty acid. The strain had cell wall peptidoglycan based on LL-2,6-diaminopimelic acid. The polar lipids of strain XZ17(T) comprised diphosphatidylglycerol, phosphatidylglycerol, three unidentified phospholipids, three unidentified glycolipids and two unidentified lipids. The DNA G+C content of strain XZ17(T) was 68.9 mol%. Based on distinctive phenotypic characteristics, phylogenetic analysis and chemotaxonomic data, it can be concluded that strain XZ17(T) represents a novel species within the genus Nocardioides, for which the name Nocardioides gilvus sp. nov. is proposed. The type strain is strain XZ17(T) (=KCTC 39561(T) = MCCC 1H00114(T)).

Pistricoccus aurantiacus gen. nov., sp. nov., a moderately halophilic bacterium isolated from a shark.

A novel Gram-stain negative, non-motile, moderately halophilic, facultatively anaerobic and spherical bacterium designated strain SS9T was isolated from the gill homogenate of a shark. Cells of SS9T were observed to be 0.8-1.2 µm in diameter. The strain was found to grow optimally at 33 °C, pH 7.0-8.0 and in the presence of 6.0 % (w/v) NaCl. On the basis of 16S rRNA gene phylogeny, strain SS9T can be affiliated with the family Halomonadaceae and is closely related to Chromohalobacter marismortui NBRC 103155T (95.6 % sequence similarity), Halomonas ilicicola SP8T (95.6 %) and Chromohalobacter salexigens DSM 3043T (95.5 %). Multilocus sequence analysis of strain SS9T using the housekeeping genes 16S rRNA, 23S rRNA, gyrB, rpoD and secA revealed the strain's distinct phylogenetic position, separate from other known genera of the family Halomonadaceae. Strain SS9T was found to contain ubiquinone-9 (Q-9) as the predominant ubiquinone and C18:1 ω7c, C16:0 and summed feature 3 (C16:1 ω7c and/or iso-C15:0 2-OH) as the major fatty acids. The major polar lipids of strain SS9T were identified as phosphatidylglycerol and phosphatidylethanolamine. The DNA G + C content of strain SS9T was determined to be 60.4 mol%. It is evident from phylogenetic, genotypic, phenotypic and chemotaxonomic results that strain SS9T represents a novel species in a new genus, for which the name Pistricoccus aurantiacus gen. nov., sp. nov. is proposed. The type strain is SS9T (=KCTC 42586T = MCCC 1H00111T).

Thalassotalea sediminis sp. nov., isolated from coastal sediment.

A novel Gram-stain negative, facultatively anaerobic, rod-shaped and yellowish-white-pigmented marine bacterium, designated strain N211(T), was isolated from marine sediment obtained off the coastal area of Weihai, China. The cells are approximately 0.4-0.9 × 1.8-3.5 µm in size and motile by means of a polar flagellum. The strain grows optimally at 33 °C, pH 7.5-8.5 and in the presence of 3.0 % (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences indicated that strain N211(T) fell within the clade comprising the type strains of species of the genus Thalassotalea. Strain N211(T) was most closely related to Thalassotalea ganghwensis DSM 15355(T) (96.4 %) based on the 16S rRNA gene sequence, and shared 94.4-96.4 % similarity with type strains of all members of the genus Thalassotalea. The predominant isoprenoid quinone of strain N211(T) was identified as ubiquinone-8 (Q-8). The major polar lipids were found to be phosphatidylethanolamine, phosphatidylglycerol and an unidentified lipid. C17:1 w8c, summed feature 3 (C16:1 w7c and/or iso-C 15:0 2-OH) and C16:0 were found to be main cellular fatty acids. The G+C content of the genomic DNA is 39.1 mol%. It is evident from phenotypic data and phylogenetic inference that strain N211(T) represents a novel species of the genus Thalassotalea, for which the name T. sediminis sp. nov. is proposed. The type strain is N211(T) (=KCTC 42588(T) = MCCC 1H00116(T)).