Choclo virus (CHOV) recovered from deep metatranscriptomics of archived frozen tissues in natural history biorepositories.

BACKGROUND: Hantaviruses are negative-stranded RNA viruses that can sometimes cause severe disease in humans; however, they are maintained in mammalian host populations without causing harm. In Panama, sigmodontine rodents serve as hosts to transmissible hantaviruses. Due to natural and anthropogenic forces, these rodent populations are having increased contact with humans. METHODS: We extracted RNA and performed Illumina deep metatranscriptomic sequencing on Orthohantavirus seropositive museum tissues from rodents. We acquired sequence reads mapping to Choclo virus (CHOV, Orthohantavirus chocloense) from heart and kidney tissue of a two-decade old frozen museum sample from a Costa Rican pygmy rice rat (Oligoryzomys costaricensis) collected in Panama. Reads mapped to the CHOV reference were assembled and then validated by visualization of the mapped reads against the assembly. RESULTS: We recovered a 91% complete consensus sequence from a reference-guided assembly to CHOV with an average of 16X coverage. The S and M segments used in our phylogenetic analyses were nearly complete (98% and 99%, respectively). There were 1,199 ambiguous base calls of which 93% were present in the L segment. Our assembled genome varied 1.1% from the CHOV reference sequence resulting in eight nonsynonymous mutations. Further analysis of all publicly available partial S segment sequences support a clear relationship between CHOV clinical cases and O. costaricensis acquired strains. CONCLUSIONS: Viruses occurring at extremely low abundances can be recovered from deep metatranscriptomics of archival tissues housed in research natural history museum biorepositories. Our efforts resulted in the second CHOV genome publicly available. This genomic data is important for future surveillance and diagnostic tools as well as understanding the evolution and pathogenicity of CHOV.

Great diversity of KSα sequences from bat-associated microbiota suggests novel sources of uncharacterized natural products.

Polyketide synthases (PKSs) are multidomain enzymes in microorganisms that synthesize complex, bioactive molecules. PKS II systems are iterative, containing only a single representative of each domain: ketosynthase alpha (KS[Formula: see text]), ketosynthase beta and the acyl carrier protein. Any gene encoding for one of these domains is representative of an entire PKS II biosynthetic gene cluster (BGC). Bat skin surfaces represent an extreme environment prolific in Actinobacteria that may constitute a source for bioactive molecule discovery. KS[Formula: see text] sequences were obtained from culturable bacteria from bats in the southwestern United States. From 467 bat bacterial isolates, we detected 215 (46%) had KS[Formula: see text] sequences. Sequencing yielded 210 operational taxonomic units, and phylogenetic placement found 45 (21%) shared <85% homology to characterized metabolites. Additionally, 16 Actinobacteria genomes from the bat microbiome were analyzed for biosynthetic capacity. A range of 69-93% of the BGCs were novel suggesting the bat microbiome may contain valuable uncharacterized natural products. Documenting and characterizing these are important in understanding the susceptibility of bats to emerging infectious diseases, such as white-nose syndrome. Also noteworthy was the relationship between KS [Formula: see text] homology and total BGC novelty within each fully sequenced strain. We propose amplification and detection of KS[Formula: see text] could predict a strain's global biosynthetic capacity.

Breathing can be dangerous: Opportunistic fungal pathogens and the diverse community of the small mammal lung mycobiome.

Human lung mycobiome studies typically sample bronchoalveolar lavage or sputum, potentially overlooking fungi embedded in tissues. Employing ultra-frozen lung tissues from biorepositories, we obtained fungal ribosomal RNA ITS2 sequences from 199 small mammals across 39 species. We documented diverse fungi, including common environmental fungi such as Penicillium and Aspergillus, associates of the human mycobiome such as Malassezia and Candida, and others specifically adapted for lungs (Coccidioides, Blastomyces, and Pneumocystis). Pneumocystis sequences were detected in 83% of the samples and generally exhibited phylogenetic congruence with hosts. Among sequences from diverse opportunistic pathogens in the Onygenales, species of Coccidioides occurred in 12% of samples and species of Blastomyces in 85% of samples. Coccidioides sequences occurred in 14 mammalian species. The presence of neither Coccidioides nor Aspergillus fumigatus correlated with substantial shifts in the overall mycobiome, although there was some indication that fungal communities might be influenced by high levels of A. fumigatus. Although members of the Onygenales were common in lung samples (92%), they are not common in environmental surveys. Our results indicate that Pneumocystis and certain Onygenales are common commensal members of the lung mycobiome. These results provide new insights into the biology of lung-inhabiting fungi and flag small mammals as potential reservoirs for emerging fungal pathogens.