We examined the abundance, diversity and community composition of airborne fungi in swine houses during winter and summer seasons by using quantitative PCR and Illumina HiSeq sequencing of ITS1 region. The abundance of airborne fungi varied significantly only between seasons, while fungal diversity varied significantly both within and between seasons, with both abundance and diversity peaked in winter. The fungal OTU composition was largely structured by the swine house unit and season as well as by their interactions. Of the measured microclimate variables, relative humidity, particulate matters (PMs), ammonia, and stocking density were significantly correlated with fungal OTU composition. The variation in beta diversity was higher within swine houses during summer, which indicates that the airborne fungal community composition was more heterogeneous in summer compared to winter. We also identified several potential allergen/pathogen related fungal genera in swine houses. The total relative abundance of potential allergen/pathogen related fungal genera varied between swine houses in both seasons, and showed positive correlation with PM2.5. Overall, our findings show that the abundance, diversity and composition of airborne fungi are highly variable in swine houses and to a large extent structured by indoor microclimate variables of swine houses.

The Eurasian otter (Lutra lutra) is an endangered species for which diet analyses are needed as part of its conservation efforts. Eurasian otters feed on vertebrates, such as fishes, and invertebrates, such as crustaceans, but their detailed taxonomies are not fully understood in part due to limited resolving power of traditional morphological identification methods. Here, we used high-throughput sequencing (HTS)-based DNA metabarcoding approaches to analyze diet profiles of Eurasian otters inhabiting a marshy estuary area in Korea. We investigated their diet profiles based on spraint sampling followed by DNA metabarcoding analyses targeting 12S rRNA gene region for vertebrates, 16S rRNA gene region for invertebrates, and cytochrome c oxidase 1 (COI) gene region for fishes. For the vertebrate analysis, a blocking oligonucleotide (OBS1) was designed to suppress amplification of DNA fragments derived from the otters. The 12S rRNA gene sequencing assay detected species belonging to fishes (95%) and amphibians (3.3%). Fishes detected by 12S rRNA gene sequencing included crucian carp (Carassius auratus), mullets (Mugil spp.), bluegill (Lepomis macrochirus), and northern snakehead (Channa argus), which were also detected by COI gene sequencing. Among invertebrates, mud flat crabs (Helicana spp.) and shrimps (Palaemon spp.) were abundant. The designed blocking oligonucleotide OBS1 effectively inhibited amplification of the otter’s DNA, with only up to 0.21% of vertebrate sequence reads assigned to the otter. This study demonstrated that HTS-based DNA metabarcoding methods were useful to provide in-depth information regarding diet profiles of the otters at our sampling site. By using HTS-based DNA metabarcoding approaches, future research will explore detailed taxonomies of their diets across locations and seasons.

Little is known about the seasonal dynamics of biotic contaminants in swine confinement buildings (SCBs). The biotic contaminants of seven SCBs were monitored during one visit in the winter and one during the summer. Paired-end Illumina sequencing of the 16S rRNA gene, V3 region, was used to examine seasonal shifts in bacterial community composition and diversity. The abundances of 16S rRNA genes and six tetracycline resistance genes (tetB, tetH, tetZ, tetO, tetQ, and tetW) were also quantified using real-time PCR. Bacterial abundances, community composition and diversity all showed strong seasonal patterns defined by winter peaks in abundance and diversity. Microclimatic variables of SCBs, particularly air speed, PM2.5 and total suspended particles (TSP) were found significantly correlated to abundances, community composition, and diversity of bacterial bioaerosols. Seasonal fluctuations were also observed for four tetracycline resistance genes, tetH, tetO, tetQ, and tetW. The frequency of occurrences of these resistance genes were significantly higher in samples collected during winter and was also significantly correlated with air speed, PM2.5 and TSP. Overall, our results indicate that biotic contaminants in SCBs exhibit seasonal trends, and these could be associated with the microclimatic variables of SCBs. The correlations established in the current study could be helpful in establishing better management strategies to minimize the potential health impacts on both livestock and humans working in this environment.

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Little is known about the factors influencing the abundance and community composition of airborne biotic contaminants in swine confinement buildings (SCBs). Microbial air samples were collected from three different SCBs equipped with three different types of manure removal systems (deep-pit manure removal with slats, scraper removal system, and deep-litter bed system). The abundance and composition of airborne biotic contaminants of all the collected air samples were analyzed using cultivation-independent methods. The V1-V3 region of the 16S rRNA gene was amplified from the extracted DNA and sequenced using 454-pyrosequencing. The abundances of 16S rRNA genes and six tetracycline resistance genes (tetB, tetH, tetZ, tetO, tetQ, and tetW) were quantified using real-time PCR. The abundance of 16S rRNA gene and tetracycline resistance genes were significantly higher in SCBs equipped with a deep-pit manure removal system with slats, except for tetB gene. This contrasts with the opposite trend found previously by culture-based studies. The aerial bacterial community composition, as measured by pairwise Bray-Curtis distances, varied significantly according to the manure removal system. 16S rRNA-based pyrosequencing revealed Firmicutes (72.4%) as the dominant group with Lactobacillus as the major genus, while Actinobacteria constituted 10.7% of the detectable bacteria. Firmicutes were more abundant in SCBs with deep pit with slats, whereas Actinobacteria were highly abundant in SCBs with a deep-litter bed system. Overall, the results of this study suggest that the manure removal system plays a key role in structuring the abundance and composition of airborne biotic contaminants in SCBs.