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Viruses are the most abundant biological entity on earth. Despite this, viral diversity in current reference databases is poorly described. With limited number of studies investigating environmental viromes, our understanding of the virosphere composition and diversity is limited. Improvement in metagenomic sequencing methodologies has allowed for identification of novel genomic sequences, especially for new and emerging viral taxa, and improvement in existing ambiguous viral phylogenetic groupings. Here we describe a viral discovery-based study that evaluated viral metagenomes collected from the hands and scalps of 42 human subjects (n = 642) for identification of environmentally contracted DNA viruses. Due to direct interaction between humans and animals either through owning pets or through vocation, it is hypothesized that surveillance of the human skin virome will contain animal associated viruses contracted through environmental contact that can then potentially become zoonotic pathogens. To investigate this, viral genome assemblies from the metagenomes were bioinformatically predicted using model and reference-based tools. A gene and protein sequence variation and binning approach was then employed to resolve viral dark matter. Evaluation of animal associated viruses resulted in the identification of a feline papillomavirus from a subject who reportedly owned a cat. Phylogenetic analysis suggests this isolate is related to feline papillomavirus type 2 sharing approximately 75% sequence synteny thus making it a novel papillomavirus isolate. Additionally, a new grouping of porcine associated Cressdnaviricota viruses were identified through protein sequence similarity network clustering of conserved Rep genes and all other NCBI reported Rep gene sequences. This grouping contained both novel viral genomes collected from the human skin virome dataset and unclassified Cressdnaviruses all collected from porcine samples obtained from NCBI. Further phylogenetic analysis showed similarity to this novel cluster to that of porcine circovirus (PCV). This discovery and phylogenetic based investigation of novel viral genome assemblies demonstrates that animal associated viruses can be identified from the skin of humans and thus studying human viromes can provide information into the spread and emergence of novel viruses.

Additional file 10: Figure S10. Heatmap of differential KOs associated with each sampling timepoint of collection. Only KOs that are significantly different at p

Additional file 5: Figure S5. Distribution of opportunistic pathogens Moraxella spp. and Mycoplasma spp. across the 4 sampling time points. Moraxella spp. and Mycoplasma spp. are considered as opportunistic pathogens that predispose animals to IBK infection.

Additional file 4: Figure S4. Differential ASVs found among time sampling comparison. (Key- * denotes taxa at family level, ** denotes taxa at order level, and *** denotes taxa at class level.).

Additional file 8: Figure S8. Observed ASVs (A) and Chao1 estimates (B) indicating alpha-diversity differences between sampling time points. Significant differences in predicted functional gene alpha-diversity was identified between all sampling periods. After initial swabbing for baseline community, the diversity significantly decreased and recovered over time in subsequent samplings. The initial swabbing, would be deemed as the first perturbation or disruption to the ocular microbiota.

Additional file 3: Figure S3. Distribution of “Core” ASVs across sampling time-points demonstrating predominance of opportunistic pathogens in the bovine ocular microbiota. Perturbations, or disruptions, to the ocular microbiota occurred by taking ocular swabs. Core bacterial ASVs were identified based on the presence of an ASV in at least 80% of all samples. Only 3 core ASVs were identified that fell into this criteria. The core ASVs include; Pasteurellaceae spp. (Blue), Mycoplasma spp. (Orange) and Weeksellacea spp. (Grey).

Additional file 7: Figure S7. Prevalence of Moraxella spp. in total (7a), as well as individually for Moraxella bovis (7b) and Moraxella bovoculi (7c) obtained from the eyes of calves at different time points. Letters denote statistically different groups (p

Additional file 11: Figure S11. List of CMM ASV with relative abundance at each time sampling. (Key- * denotes taxa at family level, ** denotes taxa at order level, and *** denotes taxa at class level.).

Additional file 9: Figure S9. Principal Coordinate analysis (PCoA) demonstrating between sample variations in predicted functional genes. PCoA plot was generated using a Bray-Curtis distance matrix. Day 0 and day 139 demonstrated similar gene structure that was different from 21 days and 41 days. Color scheme; Red – time point 1, Green - time point 2, Teal – time point 3, and Purple – time point 4.

Additional file 2: Figure S2. Principal Coordinate analysis (PCoA) demonstrating between individual cohort sample variations in beta-diversity. PCoA plot was generated using a weighted UniFrac distance matrix. A) Cohort A B) Cohort B and C) Cohort C. PERMANOVA revealed there was no significant difference between the eyes sampled at day 17 (p = 0.37, p = 0.245, and p = 0.659; respectively).

Additional file 13: Table S1. Scores of ulcers from cattle infected with IBK during the study.

Additional file 12: Figure S12. Distribution of the calves age throughout the duration of the trial.

While antimicrobial therapies have conferred immense benefits in both animal and human health, agricultural use of antibiotics has largely contributed to antimicrobial resistance, affecting both agricultural and nonagricultural use. It is estimated that approximately 40% of all antibiotics produced are used in livestock as feed additives. Current explorations of Antimicrobial Resistance (AMR) genes and their abundance have utilized real-time or conventional PCR-based analyses of AMR genes. However, such approaches fail to identify variants within AMR genes and whether certain variants are transmitted faster or are fixed in a given environment. As such, to identify AMR gene diversity within most abundant AMR genes, we have developed and utilized an amplicon-based sequencing strategy to evaluate AMR genes and their hosts. Such AMR gene variants can be correlated with 16S rDNA-based community profiling to understand what bacterial species may be associated with different AMR gene variants, as well as to identify functional variants of the AMR genes that show resistance. This sequence-based AMR gene analysis approach provides information into the diversity and ecology of AMR genes.

We have characterized the molecular and genomic diversity of the microbiota of the starlet sea anemone Nematostella vectensis, a cnidarian model for comparative developmental and functional biology and a year-round inhabitant of temperate salt marshes. Molecular phylogenetic analysis of 16S rRNA gene clone libraries revealed four ribotypes associated with N. vectensis at multiple locations and times. These associates include two novel ribotypes within the ε-Proteobacterial order Campylobacterales and the Spirochetes, respectively, each sharing 99% 16S rRNA identity with Endozoicomonas elysicola and Pseudomonas oleovorans, respectively. Species-specific PCR revealed that these populations persisted in N. vectensis asexually propagated under laboratory conditions. cDNA indicated expression of the Campylobacterales and Endozoicomonas 16S rRNA in anemones from Sippewissett Marsh, MA. A collection of bacteria from laboratory raised N. vectensis was dominated by isolates from P. oleovorans and Rhizobium radiobacter. Isolates from field-collected anemones revealed an association with Limnobacter and Stappia isolates. Genomic DNA sequencing was carried out on 10 cultured bacterial isolates representing field- and laboratory-associates, i.e., Limnobacter spp., Stappia spp., P. oleovorans and R. radiobacter. Genomes contained multiple genes identified as virulence (host-association) factors while S. stellulata and L. thiooxidans genomes revealed pathways for mixotrophic sulfur oxidation. A pilot metatranscriptome of laboratory-raised N. vectensis was compared to the isolate genomes and indicated expression of ORFs from L. thiooxidans with predicted functions of motility, nutrient scavenging (Fe and P), polyhydroxyalkanoate synthesis for carbon storage, and selective permeability (porins). We hypothesize that such activities may mediate acclimation and persistence of bacteria in a N. vectensis holobiont defined by both internal and external gradients of chemicals and nutrients in a dynamic coastal habitat., Massachusetts Institute of Technology. Department of Civil and Environmental Engineering, National Science Foundation (U.S.). Graduate Research Fellowship, National Research Foundation of Korea (Fellowship)

Cyanobacterial harmful algal blooms (cyanoHABs) appear to be increasing in frequency on a global scale. The Cyanobacteria in blooms can produce toxic secondary metabolites that make freshwater dangerous for drinking and recreation. To characterize microbial activities in a cyanoHAB, transcripts from a eutrophic freshwater reservoir in Singapore were sequenced for six samples collected over one day-night period. Transcripts from the Cyanobacterium Microcystis dominated all samples and were accompanied by at least 533 genera primarily from the Cyanobacteria, Proteobacteria, Bacteroidetes and Actinobacteria. Within the Microcystis population, abundant transcripts were from genes for buoyancy, photosynthesis and synthesis of the toxin microviridin, suggesting that these are necessary for competitive dominance in the Reservoir. During the day, Microcystis transcripts were enriched in photosynthesis and energy metabolism while at night enriched pathways included DNA replication and repair and toxin biosynthesis. Microcystis was the dominant source of transcripts from polyketide and non-ribosomal peptide synthase (PKS and NRPS, respectively) gene clusters. Unexpectedly, expression of all PKS/NRPS gene clusters, including for the toxins microcystin and aeruginosin, occurred throughout the day-night cycle. The most highly expressed PKS/NRPS gene cluster from Microcystis is not associated with any known product. The four most abundant phyla in the reservoir were enriched in different functions, including photosynthesis (Cyanobacteria), breakdown of complex organic molecules (Proteobacteria), glycan metabolism (Bacteroidetes) and breakdown of plant carbohydrates, such as cellobiose (Actinobacteria). These results provide the first estimate of secondary metabolite gene expression, functional partitioning and functional interplay in a freshwater cyanoHAB., Singapore. National Research Foundation (Singapore MIT Alliance for Research and Technology (SMART), Center for Environmental Sensing and Modeling (CENSAM) research program), National Science Foundation (U.S.) (Postdoctoral Research Fellowship in Biology, Grant No. DBI-1202865), National Institute of Environmental Health Sciences (NIEHS Grant P30-ES002109 to the MIT Center for Environmental Health Sciences), MIT International Science and Technology Initiatives (MISTI-Hayashi fund)