Genome-wide overview of Trichosporon akiyoshidainum HP-2023, new insights into its mechanism of dye discoloration

Comprehensive genome analysis of Lentzea reveals repertoire of polymer-degrading enzymes and bioactive compounds with clinical relevance

The genus Lentzea is a rare group of actinobacteria having potential for the exploration of bioactive compounds. Despite its proven ability to produce compounds with medical relevance, Lentzea genome analysis remains unexplored. Here we show a detailed understanding of the genetic features, biosynthetic gene clusters (BGCs), and genetic clusters for carbohydrate-active enzymes present in the Lentzea genome. Our analysis determines the genes for core proteins, non-ribosomal peptide synthetase condensation domain, and polyketide synthases-ketide synthase domain. The antiSMASH-based sequence analysis identifies 692 BGCs among which 8% are identical to the BGCs that produce geosmin, citrulassin, achromosin (lassopeptide), vancosamine, anabaenopeptin NZ857/nostamide A, alkylresorcinol, BE-54017, and bezastatin. The remaining BGCs code for advanced category antimicrobials like calcium-dependent, glycosylated, terpenoids, lipopeptides, thiopeptide, lanthipeptide, lassopeptide, lingual antimicrobial peptide and lantibiotics together with antiviral, antibacterial, antifungal, antiparasitic, anticancer agents. About 28% of the BGCs, that codes for bioactive secondary metabolites, are exclusive in Lentzea and could lead to new compound discoveries. We also find 7121 genes that code for carbohydrate-degrading enzymes which could essentially convert a wide range of polymeric carbohydrates. Genome mining of such genus is very much useful to give scientific leads for experimental validation in the discovery of new-generation bioactive molecules of biotechnological importance.

Complete Genome Sequencing and Comparative Analysis of the Clinically-Derived Apiotrichum mycotoxinivorans Strain GMU1709

Over the past decade, Apiotrichum mycotoxinivorans has been recognized globally as a source of opportunistic infections. It is a yeast-like fungus, and its association as an uncommon pulmonary pathogen with cystic fibrosis patients has been previously reported. Immunocompromised patients are at the highest risk of A. mycotoxinivorans infections. Therefore, to investigate the genetic basis for the pathogenicity of A. mycotoxinivorans, we performed whole-genome sequencing and comparative genomic analysis of A. mycotoxinivorans GMU1709 that was isolated from sputum specimens of a pneumonia patient receiving cardiac repair surgery. The assembly of Oxford Nanopore reads from the GMU1709 strain and its subsequent correction using Illumina paired-end reads yielded a high-quality complete genome with a genome size of 30.5 Mb in length, which comprised six chromosomes and one mitochondrion. Subsequently, 8,066 protein-coding genes were predicted based on multiple pieces of evidence, including transcriptomes. Phylogenomic analysis indicated that A. mycotoxinivorans exhibited the closest evolutionary affinity to A. veenhuisii, and both the A. mycotoxinivorans strains and the formerly Trichosporon cutaneum ACCC 20271 strain occupied the same phylogenetic position. Further comparative analysis supported that the ACCC 20271 strain belonged to A. mycotoxinivorans. Comparisons of three A. mycotoxinivorans strains indicated that the differences between clinical and non-clinical strains in pathogenicity and drug resistance may be little or none. Based on the comparisons with strains of other species in the Trichosporonaceae family, we identified potential key genetic factors associated with A. mycotoxinivorans infection or pathogenicity. In addition, we also deduced that A. mycotoxinivorans had great potential to inactivate some antibiotics (e.g., tetracycline), which may affect the efficacy of these drugs in co-infection. In general, our analyses provide a better understanding of the classification and phylogeny of the Trichosporonaceae family, uncover the underlying genetic basis of A. mycotoxinivorans infections and associated drug resistance, and provide clues into potential targets for further research and the therapeutic intervention of infections.

Genome analysis to decipher syntrophy in the bacterial consortium 'SCP' for azo dye degradation

Background

A bacterial consortium SCP comprising three bacterial members, viz. Stenotrophomonas acidaminiphila APG1, Pseudomonas stutzeri APG2 and Cellulomonas sp. APG4 was developed for degradation of the mono-azo dye, Reactive Blue 28. The genomic analysis of each member of the SCP consortium was done to elucidate the catabolic potential and role of the individual organism in dye degradation.

Results

The genes for glycerol utilization were detected in the genomes of APG2 and APG4, which corroborated with their ability to grow on a minimal medium containing glycerol as the sole co-substrate. The genes for azoreductase were identified in the genomes of APG2 and APG4, while no such trait could be determined in APG1. In addition to co-substrate oxidation and dye reduction, several other cellular functions like chemotaxis, signal transduction, stress-tolerance, repair mechanisms, aromatic degradation, and copper tolerance associated with dye degradation were also annotated. A model for azo dye degradation is postulated, representing the predominant role of APG4 and APG2 in dye metabolism while suggesting an accessory role of APG1.

Conclusions

This exploratory study is the first-ever attempt to divulge the genetic basis of azo-dye co-metabolism by cross-genome comparisons and can be harnessed as an example for demonstrating microbial syntrophy.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-021-02236-9.

Multidrug-resistant Trichosporon species: underestimated fungal pathogens posing imminent threats in clinical settings

Species of Trichosporon and related genera are widely used in biotechnology and, hence, many species have their genome sequenced. Importantly, yeasts of the genus Trichosporon have been increasingly identified as a cause of life-threatening invasive trichosporonosis (IT) in humans and are associated with an exceptionally high mortality rate. Trichosporon spp. are intrinsically resistant to frontline antifungal agents, which accounts for numerous reports of therapeutic failure when echinocandins are used to treat IT. Moreover, these fungi have low sensitivity to polyenes and azoles and, therefore, are potentially regarded as multidrug-resistant pathogens. However, despite the clinical importance of Trichosporon spp., our understanding of their antifungal resistance mechanisms is quite limited. Furthermore, antifungal susceptibility testing is not standardized, and there is a lack of interpretive epidemiological cut-off values for minimal inhibitory concentrations to distinguish non-wild type Trichosporon isolates. The route of infection remains obscure and detailed clinical and environmental studies are required to determine whether the Trichosporon infections are endogenous or exogenous in nature. Although our knowledge on effective IT treatments is rather limited and future randomized clinical trials are required to identify the best antifungal agent, the current paradigm advocates the use of voriconazole, removal of central venous catheters and recovery from neutropenia.