Milk microbiomes significantly influence the pathophysiology of bovine mastitis. To assess the association between microbiome diversity and bovine mastitis, we compared the microbiome of clinical mastitis (CM, n = 14) and healthy (H, n = 7) milk samples through deep whole metagenome sequencing (WMS). A total of 483.38 million reads generated from both metagenomes were analyzed through PathoScope (PS) and MG-RAST (MR), and mapped to 380 bacterial, 56 archaeal, and 39 viral genomes. We observed distinct shifts and differences in abundance between the microbiome of CM and H milk in phyla Proteobacteria, Bacteroidetes, Firmicutes and Actinobacteria with an inclusion of 68.04% previously unreported and/or opportunistic strains in CM milk. PS identified 363 and 146 bacterial strains in CM and H milk samples respectively, and MR detected 356 and 251 bacterial genera respectively. Of the identified taxa, 29.51% of strains and 63.80% of genera were shared between both metagenomes. Additionally, 14 archaeal and 14 viral genera were found to be solely associated with CM. Functional annotation of metagenomic sequences identified several metabolic pathways related to bacterial colonization, proliferation, chemotaxis and invasion, immune-diseases, oxidative stress, regulation and cell signaling, phage and prophases, antibiotic and heavy metal resistance that might be associated with CM. Our WMS study provides conclusive data on milk microbiome diversity associated with bovine cM and its role in udder health. Mastitis is one of the most prevalent diseases in the dairy industry with the highest clinical and economic significance worldwide 1. The condition usually happens when pathogenic microbes enter the mammary gland, mostly by the disruption of the physical barriers of the mammary quarters, requiring prompt and appropriate host defenses to prevent colonization and subsequent disease pathology 2. Diverse groups of microbes are known to colonize the mammary quarters of cows and have evolved novel mechanisms that facilitate their proliferation, leading to clinical mastitis (CM). Despite knowledge of a few of these invading microbial groups, the etiology of bovine mastitis is continuously changing, with new microbial species identified as causing disease frequently. Additionally, although bacteria are the main cause of mastitis 3 , other microbes like archaea, viruses, and fungi might be associated with the disease process 4 and should therefore be investigated as well. During the progression of the mastitis, dysbiosis of the milk microbiome can occur with the increase of opportunistic pathogenic bacteria and reduction of healthy commensal bacteria 5. Until recently, investigations of the microbiome associated with bovine mastitis have been mostly restricted to individual pathogen isolation and characterization. The disease is caused by epidemiologically diverse groups of microorganisms and categorized into

Bovine clinical mastitis (CM) is one of the most prevalent diseases caused by a wide range of resident microbes. The emergence of antimicrobial resistance in CM bacteria is well-known, however, the genomic resistance composition (the resistome) at the microbiome-level is not well characterized. In this study, we applied whole metagenome sequencing (WMS) to characterize the resistome of the CM microbiome, focusing on antibiotics and metals resistance, biofilm formation (BF), and quorum sensing (QS) along with in vitro resistance assays of six selected pathogens isolated from the same CM samples. The WMS generated an average of 21.13 million reads (post-processing) from 25 CM samples that mapped to 519 bacterial strains, of which 30.06% were previously unreported. We found a significant (P = 0.001) association between the resistomes and microbiome composition with no association with cattle breed, despite significant differences in microbiome diversity among breeds. The in vitro investigation determined that 76.2% of six selected pathogens considered "biofilm formers" actually formed biofilms and were also highly resistant to tetracycline, doxycycline, nalidixic acid, ampicillin, and chloramphenicol and remained sensitive to metals (Cr, Co, Ni, Cu, Zn) at varying concentrations. We also found bacterial flagellar movement and chemotaxis, regulation and cell signaling, and oxidative stress to be significantly associated with the pathophysiology of CM. Thus, identifying CM microbiomes, and analyzing their resistomes and genomic potentials will help improve the optimization of therapeutic schemes involving antibiotics and/or metals usage in the prevention and control of bovine CM.

Termites are important ecosystem engineers in tropical habitats, with different feeding groups able to decompose wood, grass, litter, and soil organic matter. In most tropical regions, termite abundance and species diversity are assumed to increase with rainfall, with highest levels found in rainforests. However, in the Australian tropics, this pattern is thought to be reversed, with lower species richness and termite abundance found in rainforest than drier habitats. The potential mechanisms underlying this pattern remain unclear. We compared termite assemblages (abundance, activity, diversity, and feeding group composition) across five sites along a precipitation gradient (ranging from ∼800 to 4,000 mm annual rainfall), spanning dry and wet savanna habitats, wet sclerophyll, and lowland and upland rainforests in tropical North Queensland. Moving from dry to wet habitats, we observed dramatic decreases in termite abundance in both mounds and dead wood occupancy, with greater abundance and activity at savanna sites (low precipitation) compared with rainforest or sclerophyll sites (high precipitation). We also observed a turnover in termite species and feeding group diversity across sites that were close together, but in different habitats. Termite species and feeding group richness were highest in savanna sites, with 13 termite species from wood-, litter-, grass-, dung-, and soil-feeding groups, while only five termite species were encountered in rainforest and wet sclerophyll sites—all wood feeders. These results suggest that the Australian termite diversity anomaly may be partly driven by how specific feeding groups colonized habitats across Australia. Consequently, termites in Australian rainforests may be less important in ecosystem processes, such as carbon and nutrient cycling during decomposition, compared with termites in other tropical rainforests.

Variation in decay rates across woody species is a key uncertainty in predicting the fate of carbon stored in deadwood, especially in the tropics. Quantifying the relative contributions of biotic decay agents, particularly microbes and termites, under different climates and across species with diverse wood traits could help explain this variation. To fill this knowledge gap, we deployed woody stems from 16 plant species native to either rainforest (n = 10) or savanna (n = 6) in northeast Australia, with and without termite access. For comparison, we also deployed standardized, non‐native pine blocks at both sites. We hypothesized that termites would increase rates of deadwood decay under conditions that limit microbial activity. Specifically, termite contributions to wood decay should be greater under dry conditions and in wood species with traits that constrain microbial decomposers. Termite discovery of stems was surprisingly low with only 17.6% and 22.6% of accessible native stems discovered in the rainforest and savanna respectively. Contrary to our hypothesis, stems discovered by termites decomposed faster only in the rainforest. Termites discovered and decayed pine blocks at higher rates than native stems in both the rainforest and savanna. We found significant variation in termite discovery and microbial decay rates across native wood species within the same site. Although wood traits explained 85% of the variation in microbial decay, they did not explain termite‐driven decay. For stems undiscovered by termites, decay rates were greater in species with higher wood nutrient concentrations and syringyl:guiacyl lignin ratios but lower carbon concentrations and wood densities. Synthesis. Ecosystem‐scale predictions of deadwood turnover and carbon storage should account for the impact of wood traits on decomposer communities. In tropical Australia, termite‐driven decay was lower than expected for native wood on the ground. Even if termites are present, they may not always increase decomposition rates of fallen native wood in tropical forests. Our study shows how the drivers of wood decay differ between Australian tropical rainforest and savanna; further research should test whether such differences apply world‐wide.

The damselflies Hetaerininae, a subfamily of Calopterygidae, comprise four genera distributed from North to South America: Hetaerina, Mnesarete, Ormenophlebia and Bryoplathanon. While several studies have focused on the intriguing behavioral and morphological modifications within Hetaerina, little of the evolutionary history of the group is well understood. Understanding the biogeographical history of Hetaerininae is further complicated by uncertainty in important geological events, such as the closure of the Central American Seaway (CAS). We generated a phylogenetic hypothesis to test the relationships and divergence times within Hetaerininae using IQtree and BEAST2 and found that Mnesarete and Ormenophlebia render Hetaerina paraphyletic. Reclassification of the genera within Hetaerininae is necessary based on our results. We also tested the fit to our dataset of two different hypotheses for the closure of CAS. Our results supported a gradual closure, starting in the Oligocene and ending in the Pliocene. Using Ancestral Character State Reconstruction, we found that the rubyspot, which is associated with higher fecundity in several species, was ancestral for Hetaerininae and subsequently lost four times. Estimates of diversification in association with the rubyspot are needed to understand the plasticity of this important character. Forest habitat was the ancestral state for Hetaerininae, with transitions to generalist species of Hetaerina found primarily in the Mesoamerican region. These results add to our understanding of the relationship between morphology, biogeography and habitat in a charismatic group of damselflies.

SARS-CoV-2 (CoV) is the etiological agent of the COVID-19 pandemic and evolves to evade both host immune systems and intervention strategies. We divided the CoV genome into 29 constituent regions and applied novel analytical approaches to identify associations between CoV genomic features and epidemiological metadata. Our results show that nonstructural protein 3 (nsp3) and Spike protein (S) have the highest variation and greatest correlation with the viral whole-genome variation. S protein variation is correlated with nsp3, nsp6, and 3′-to-5′ exonuclease variation. Country of origin and time since the start of the pandemic were the most influential metadata associated with genomic variation, while host sex and age were the least influential. We define a novel statistic—coherence—and show its utility in identifying geographic regions (populations) with unusually high (many new variants) or low (isolated) viral phylogenetic diversity. Interestingly, at both global and regional scales, we identify geographic locations with high coherence neighboring regions of low coherence; this emphasizes the utility of this metric to inform public health measures for disease spread. Our results provide a direction to prioritize genes associated with outcome predictors (e.g., health, therapeutic, and vaccine outcomes) and to improve DNA tests for predicting disease status.

26Milk microbiomes impose a significant influence on the pathophysiology of bovine mastitis. To 27 assess the association, we compared the microbiome of clinical mastitis (CM) and healthy (H) 28 milk samples through whole metagenomic deep sequencing. A total of 483.38 million reads 29 generated from both metagenomes were analyzed through PathoScope and MG-RAST, and 30 mapped to 380 bacterial, 56 archaeal, and 39 viral genomes. We observed distinct shifts and 31 differences in abundance between the microbiome of CM and H milk in phyla Proteobacteria, 32Bacteroidetes, Firmicutes and Actinobacteria with an inclusion of 68.04% unreported and/or 33 opportunistic species in CM milk. Additionally, 14 archaeal and 14 viral genera were found to be 34 solely associated with CM. The functional metagenomics identified several pathways related to 35 bacterial proliferation and colonization such as metabolism, chemotaxis and invasion, immune-36 diseases, oxidative stress, regulation and cell signaling, phage and prophases, antibiotic and 37 heavy metal resistance to be associated with CM. Therefore, the present study provides 38 conclusive data on milk microbiome diversity associated with bovine CM and its role in udder 39 health. 40 41 42 43 Keywords: Bovine Clinical and Healthy milk, Microbiome, Whole metagenome sequencing 44 (WMS), Taxonomic and Functional diversity. 45 46 47 48 65The disease is caused by epidemiologically diverse groups of microorganisms and categorized 66 into contagious and environmental mastitis 6 . The udder of the dairy cows is the primary reservoir 67 of contagious pathogens including Staphylococcus aureus, Streptococcus agalactiae, 68Streptococcus dysgalactiae, Mycoplasma spp. and Corynebacterium bovis 1,6 . The involvement of 69 the bovine mammary gland microbiota in the host-pathogen interaction has little investigated 70 except during the infectious episode 7 . Environmental pathogens such as Escherichia coli, 71 Klebsiella pneumoniae, Klebsiella oxytoca, Enterobacter aerogenes, Streptococcus dysgalactiae 72and Streptococcus uberis 1,6 can also be implicated in disease. Rapid advances in high-throughput 73 NGS technology and bioinformatics tools 8 during the last decade have initiated a transition from 74 clinical microbiology to genomic characterization of the microbiome associated with infection, 75including mastitis in lactating women 5 and animals 9 . Shotgun whole metagenome sequencing 76 (WMS) produces a metagenome reflecting the total microbial makeup of a sample (pathogenic, 77 environmental, bacterial, fungal, viral) and has been used successfully to gain insights into the 78 phylogenetic composition and species diversity of a variety of microbiomes 10 , including profiling 79 of their functional attributes 11 . Thus, data can be generated regarding the identity and abundance 80 of genes related to microbial metabolism, virulence and antibiotic resistance enabling 81 identification of unknown etiological agents that play a role in mammary gland pathogenesis. 82Overexpression of putative ...

Members of the insect order Diptera respond differentially to environmental changes and may play an important role in understanding the effects that livestock grazing disturbances have on biodiversity. Here we examine how increasing grazing pressures on the Mongolian steppe affect Diptera diversity and abundance. Using 2334 yellow pan traps, we sampled a total of 132 sites over four years to collect 17,348 flies. We compared fly diversity and abundance at five levels of livestock grazing. We observed that fly family diversity decreased in heavily grazed sites and that diptera communities at sites with intense grazing have proportionally higher prevalence of taxa from the families Muscidae, Sepsidae, Ephydridae, Chloropidae, and Tachinidae, two of which are often associated with animal waste. Chironomidae, Ceratopogonidae, Sarcophagidae, and Sciaridae are most prevalent at sites with very little or no grazing, and Anthomyiidae, Calliphoridae, Carnidae, Cecidomyiidae, Dolichopodidae, Empididae, Scatopsidae and Sphaeroceridae are most often encountered at sites with intermediate amounts of grazing. Observing changes in a few guilds of fly families at different grazing levels is beneficial in understanding human effects on fly diversity.