Codon usage bias analysis of mitochondrial protein-coding genes in 12 species of Candida.

The incidence of diseases that are caused by fungal infection is gradually increasing, together with antibiotic abuse and the number of patients with hypoimmunity. The many challenges in clinical anti-fungi treatment include serious adverse effects and drug resistance. The mitochondria of fungi have been found to be closely associated with pathopoiesia and drug resistance. Hence, we investigated patterns in Candida mitochondrial genes codon usage bias to provide new information to guide anti-fungal research. According to the nucleotide composition results, most mitochondrial genes of the analysed Candida tended to use A/T bases rather than G/C bases. The relative synonymous codon usage values demonstrated that UUA, AGU, CCU, GCU, UGA, AGA and GGU were the common preferential codons of mitochondrial genes in 12 Candida species. Codon adaptation index (CAI) analysis indicated that the ATP9 of Candida parapsilosis had the highest value, and the ND6 of C. auris had the lowest value. The CAI clearly correlated with the codon bias index, except in C. maltose and C. viswanathii, and was significantly positively correlated with the average GC content. Together, our results suggested that the codon usage pattern is affected by multiple factors, among which GC content is critical. Nucleotide composition, selection pressure and mutation pressure influence codon bias in Candida mitochondrial genes, with dominant status to mutation pressure. Codon usage bias analyses of Candida mitochondrial genes may provide new insight into its evolution.

Analysis of Pulmonary Microbial Diversity in Patients with Advanced Lung Cancer Based on High-throughput Sequencing Technology / 中国肺癌杂志

BACKGROUND@#The pulmonary microbiome is closely related to the occurrence of pulmonary diseases. The morbidity and mortality of lung cancer are relatively high in the world. It has been confirmed that lung microecology changes in lung cancer patients compared with healthy individuals. Furthermore, the abundance of some bacterial species shows obvious changes, suggesting their potential use as a microbial marker for the detection of lung cancer. The composition of the pulmonary microbiome in patients with different histological types of lung cancer has not been determined. We aim to study the correlation and difference of microbiome between different histological types of lung cancer.@*METHODS@#Illumina HiSeq high-throughput sequencing technology was used to sequenced the 16S rDNA V3-V4 region of bacterial in sputum samples of patients with advanced lung cancer.@*RESULTS@#It was found that Streptococcus, Neisseria and Prevotella were the main bacteria of lung cancer patients. Advantage bacterium group differ between different histological types of lung cancer. Adenocarcinoma (AD) group was dominated by Streptococcus and Neisseria, followed by Veillonella. Small cell lung cancer (SCLC) group was dominated by Neisseria, followed by Streptococcus. Squamous carcinoma (SCC) group was dominated by Streptococcus, followed by Veillonella. Combined small cell lung cancer (C-SCLC) group was dominated by Streptococcus, followed by Prevotella.@*CONCLUSIONS@#The pulmonary bacterial microbiome of lung cancer of different histological types is different. This experiment enrichs the pulmonary bacterial microbiome data of lung cancer and fills the gap of pulmonary microbiome of small cell lung cancer.