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Proper identification of strain is essential in understanding the ecology of a bacteria species. The classification of Pseudomonas nitroreducens is still being questioned and revised until now. The novel P. nitroreducens strains FY43 and FY47 used in this study have been reported to show a high level of tolerance to glyphosate. In this study, next-generation sequencing (NGS) and whole genome analysis were used to clarify the delineation of the species. Whole genome analysis showed that P. nitroreducens strains FY43 and FY47 shared high homology to five reference genomes of P. nitroreducens: strain B, Aramco J, NBRC 12694, DF05, and TX01. Phylogenomic and phylogenetic analysis (average nucleotide identity based on BLAST (ANIb), genome-to-genome distance (GGDC) analysis) showed that both P. nitroreducens strains FY43 and FY47 are Pseudomonas nitroreducens members. However, strains DF05 and TX01 were not correctly assigned at the species level for all the analyses. The P. nitroreducens strain DF05 and TX01 should be further investigated for their classification as the correct species classification is the prerequisite for future diversity studies.

A novel glufosinate-tolerant Pseudomonas sp. LA21, was isolated from soil samples of an oil palm plantation with a long history of glufosinate application. The genome of Pseudomonas sp. LA21 was sequenced with 150 bp paired-end conducted using Illumina sequencing technology. De novo genome assembly was performed using SPAdes, ABySS, and Velvet assemblers. Phylogenetic analysis using 16S rRNA gene sequence showed that Pseudomonas sp. LA21 was closely related to Pseudomonas nitroreducens ATCC 33634. Multilocus sequence analysis (MLSA) based on four bacterial housekeeping genes (16S rRNA, gyrB, rpoB, and rpoD) was conducted together with 138 reference genomes of Pseudomonas species. The phylogenetic tree derived from MLSA analysis using concatenated 16S rRNA-gryB-rpoD-rpoB sequences grouped Pseudomonas sp. LA21 under Pseudomonas aeruginosa group and Pseudomonas nitroreducens subgroup. Detailed phylogenomic analysis using average nucleotide identity (ANI) and genome-to-genome distance calculator (GGDC) approaches showed that Pseudomonas sp. LA21 could be classified as a novel Pseudomonas species. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-022-03185-4.

Background: The current study analyzed resected stage I–IIIA pulmonary lymphoepithelioma-like carcinoma (LELC) cases to define the clinical characteristics, prognosis and long-term outcomes of resected LELC, with the purpose of guiding clinical management for this rare tumor.Methods: Resected stage I–IIIA LELC, adenocarcinoma (ADC) and squamous cell carcinoma (SCC) cases from our center were enrolled. Propensity score matching (PSM) was applied to minimize the selection bias. Overall survival (OS) and disease-free survival (DFS) were compared between groups. Multivariate analyses were performed to identify the prognostic factors, and a nomogram was developed.Results: A total of 159 LELCs, 2,757 ADCs, and 1,331 SCCs were included. LELC, dominated among younger patients and non-smokers. LELC was a poorly differentiated disease that lacked driver gene mutations and was positive for immunohistochemistry indicators of squamous cell lineage. Survival analyses revealed that OS was significantly better for LELC than for other common non-small cell lung cancers (NSCLCs) both before PSM (all P < 0.001) and after PSM (all P < 0.05). Further analyses revealed that early pathological node stage and preoperative albumin level ≥35 were identified as independent prognostic factors favoring OS and DFS.Conclusions: LELC, dominated among younger and non-smoking populations, lacked driver gene mutations and was positive for immunohistochemistry indicators of squamous cell lineage. The survival outcome of LELC was better than other common NSCLCs.

Background The current study analyzed resected stage I-IIIA pulmonary lymphoepithelioma-like carcinoma (LELC) cases to define the clinical characteristics, prognosis and long-term outcomes of LELC, with the purpose of guiding clinical management for this rare tumor.Methods Resected stage I-IIIA LELC, adenocarcinoma (ADC), squamous cell carcinoma (SCC) and adenosquamous carcinoma (ASC) cases from our center were enrolled. Propensity score matching (PSM) was applied to minimize the selection bias. Overall survival (OS) and disease-free survival (DFS) were compared between groups. Multivariate analyses were performed to identify the prognostic factors, and a nomogram was developed.Results A total of 159 LELCs, 2,757 ADCs, 1,331 SCCs and 155 ASCs were included. LELC, dominated among younger patients and nonsmokers, always presented without typical imaging manifestations of lung cancer. LELC was a poorly differentiated disease that lacked driver gene mutations and was positive for immunohistochemistry indicators of squamous cell lineage. Survival analyses revealed that OS was significantly better for LELC than for other common non-small cell lung cancer (NSCLC) both before PSM (all P < 0.001) and after PSM (all P < 0.05). Further analyses revealed that early pathological node stage and preoperative albumin level ≥35 were identified as independent prognostic factors favoring OS and DFS.Conclusions LELC, dominated among younger and nonsmoking populations, showed a lower extent of malignancy regarding CT characteristics. It lacked driver gene mutations and was positive for immunohistochemistry indicators of squamous cell lineage. The survival outcome of PSC was better than other common NSCLCs.

5-Enolpyruvylshikimate 3-phosphate synthase (EPSPS) is the primary target for the broad-spectrum herbicide, glyphosate. Improvement of EPSPS gene for high level of glyphosate tolerance is important to generate glyphosate-tolerant crops. In this study, we report the isolation and characterization of EPSPS genes of glyphosate-tolerant Pseudomonas nitroreducens strains FY43 and FY47. Both P. nitroreducens strains FY43 and FY47, which showed glyphosate tolerance up to 8.768% (518.4 mM, 32 × higher than field application), were isolated from soil samples collected from oil palm plantation with a long history of glyphosate application. The glyphosate tolerance property of EPSPS genes of strains FY43 and FY47 was functionally characterized by expressing the genes in Escherichia coli strain BL21(DE3). Error-prone PCR was performed to mutagenize native EPSPS gene of strains FY43 and FY47. Ten mutagenized EPSPS with amino acid changes (R21C, N265S, A329T, P71L, T258A, L184F, G292C, G292S, L35F and A242V) were generated through error-prone PCR. Both native and mutated EPSPS genes of strains FY43 and FY47 were introduced into Escherichia coli strain BL21(DE3) and transformants were selected on basal salt medium supplemented with 8.768% (518.4 mM) glyphosate. Mutants with mutations (R21C, N265S, A329T, P71L, T258A, L35F, A242V, L184F and G292C) showed sensitivity to 8.768% glyphosate, whereas glyphosate tolerance for mutant with G292S mutation was not affected by the mutation. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s13205-020-02176-7) contains supplementary material, which is available to authorized users.