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The study of coronaviruses has undergone unprecedented acceleration over recent years, driven largely by the global impact of SARS-CoV-2 and growing recognition of the extraordinary diversity and zoonotic potential of coronaviruses across species [...]

Methane (CH 4 ) is an important greenhouse gas (GHG). Enteric methane emissions from farmed ruminant livestock account for approximately 15% of global GHG emissions, with approximately 44% of livestock emissions in the form of methane. The purpose of the research is to study the influence of feeding types and regional characteristics of Kazakhstan on the microbiota of feces and the number of methane-forming archaea of beef and meat-and-dairy cattle productivity. For this purpose, fecal samples were taken rectally from 37 cattle heads from four regions of Kazakhstan (Western, Southern, Northern and Southeast). The taxonomic composition of the community in all samples was determined by 16S metabarcoding; additionally alpha and beta diversities were calculated. The dominant phyla were: Firmicutes (57.30%), Bacteroidetes (17.00%), Verrucomicrobia (6.88%), Euryarchaeota (6.49%), Actinobacteria (4.77%) and Patescibacteria (3.38%). Significant differences with regard to methanogens bacteria were found: Euryarchaeota were less present in animals from Western Kazakhstan (2.40%), while Methanobacteriales and Methanobrevibacter were prevalent in Southeast, and less abundant in Western region. Western Kazakhstan differs from the other regions likely because animals are mainly grazed in the pasture. Thus, grazing animals has an impact on their microbiota thus leading to a decrease in methane emissions.

The correct identification of mosquito vectors is often hampered by the presence of morphologically indiscernible sibling species. The Maculipennis complex is one of these groups that include both malaria vectors of primary importance and species of low/negligible epidemiological relevance, of which distribution data in Italy are outdated. Our study was aimed at providing an updated distribution of Maculipennis complex in Northern Italy through the sampling and morphological/molecular identification of specimens from five regions. The most abundant species was Anopheles messeae (2032), followed by Anopheles maculipennis s.s. (418), Anopheles atroparvus (28) and Anopheles melanoon (13). Taking advantage of ITS2 barcoding, we were able to finely characterize tested mosquitoes, classifying all the Anopheles messeae specimens as Anopheles daciae , a taxon with debated rank to which we referred as species inquirenda ( sp. inq. ). The distribution of species was characterized by Ecological Niche Models (ENMs), fed by recorded points of presence. ENMs provided clues on the ecological preferences of the detected species, with An. daciae sp. inq. linked to stable breeding sites and An. maculipennis s.s. more associated to ephemeral breeding sites. We demonstrate that historical Anopheles malaria vectors are still present in Northern Italy.

Dolphin morbillivirus (DMV) is considered an emerging threat having caused several epidemics worldwide. Only few DMV genomes are publicly available. Here, we report the use of target enrichment directly from cetacean tissues to obtain novel DMV genome sequences, with sequence comparison and phylodynamic analysis. RNA from 15 tissue samples of cetaceans stranded along the Italian and French coasts (2008–2017) was purified and processed using custom probes (by bait hybridization) for target enrichment and sequenced on Illumina MiSeq. Data were mapped against the reference genome, and the novel sequences were aligned to the available genome sequences. The alignment was then used for phylogenetic and phylogeographic analysis using MrBayes and BEAST. We herein report that target enrichment by specific capture may be a successful strategy for whole-genome sequencing of DMV directly from field samples. By this strategy, 14 complete and one partially complete genomes were obtained, with reads mapping to the virus up to 98% and coverage up to 7800X. The phylogenetic tree well discriminated the Mediterranean and the NE-Atlantic strains, circulating in the Mediterranean Sea and causing two different epidemics (2008–2015 and 2014–2017, respectively), with a limited time overlap of the two strains, sharing a common ancestor approximately in 1998.

Background The microbiota of the bovine upper respiratory tract has been recently characterized, but no data for the lower respiratory tract are available. A major health problem in bovine medicine is infectious bronchopneumonia, the most common respiratory syndrome affecting cattle. With this study, we used 16S rRNA gene sequencing to characterize and compare the microbial community composition of the upper and lower respiratory tracts in calves. Results The microbiota of the upper (nasal swab [NS]) and the lower (trans-tracheal aspiration [TTA]) respiratory tracts of 19 post-weaned Piedmontese calves with (8/19) and without (11/19) clinical signs of respiratory disease, coming from six different farms, was characterized by 16S rRNA gene metabarcoding. A total of 29 phyla (29 in NS, 21 in TTA) and 305 genera (289 in NS, 182 in TTA) were identified. Mycoplasma (60.8%) was the most abundant genus identified in both the NS (27.3%) and TTA (76.7%) samples, followed by Moraxella (16.6%) in the NS and Pasteurella (7.3%) in the TTA samples. Pasteurella multocida (7.3% of total operational taxonomic units [OTUs]) was the most abundant species in the TTA and Psychrobacter sanguinis (1.1% of total OTUs) in the NS samples. Statistically significant differences between the NS and the TTA samples were found for both alpha (Shannon index, observed species, Chao1 index, and Simpson index; P  = 0.001) and beta (Adonis; P  = 0.001) diversity. Comparison of the NS and TTA samples by farm origin and clinical signs revealed no statistical difference ( P  > 0.05), except for farm origin for the NS samples when compared by the unweighted UniFrac metric ( P  = 0.05). Conclusions Using 16S rRNA gene sequencing, we characterized the microbiota of the upper and lower respiratory tracts of calves, both healthy individuals and those with clinical signs of respiratory disease. Our results suggest that environmental factors may influence the composition of the upper airway microbiota in cattle. While the two microbial communities (upper and lower airways) differed in microbial composition, they shared several OTUs, suggesting that the lung microbiota may be a self-sustaining, more homogeneous ecosystem, influenced by the upper respiratory tract microbiota.

Antimicrobial resistance (AMR) is a growing global concern, exacerbated by the overuse of antibiotics in livestock farming. Honey bees (Apis mellifera), widely used as bioindicators of environmental contamination, may also serve as sentinels for monitoring the environmental spread of antibiotic resistance genes (ARGs). This study investigated the presence of ARGs and the gut microbiota composition of honey bees sampled from 11 apiaries located in a region of Northwestern Italy characterized by intensive livestock farming. PCR and Sanger sequencing analyses revealed a widespread presence of tetracycline resistance genes—particularly tetB and tetC—as well as occasional detection of blaTEM, qnrB, and int1 genes. tetB and tetC were also identified in three bacterial colonies isolated from bee guts, notably in Hafnia spp. 16S rRNA gene sequencing of the gut microbiota revealed dominance of genera such as Bartonella, Snodgrassella, Gilliamella, Bombilactobacillus, and Lactobacillus. Some samples showed shifts in the microbial diversity. The findings confirm the potential of honey bees as bioindicators for environmental AMR surveillance and underscore the need for further research to elucidate correlations between ARG presence and microbial community structure in honey bees from various ecological contexts.

Currently food fraud and authenticity of products composition are topics of great concern; ingredients quantification could allow to identify small amounts of contaminats or voluntary addition of improper components. Many molecular methods are available for species identification in foodstuffs but, for a better application, they should not be affected by the interference of other ingredients. The main purpose of this work was to verify the Real Time PCR and the Digital PCR (dPCR) quantification performances on baby food samples, specifically selected for their high miscibility to limit variability; chicken was selected as target to verify the performance of quantification of methods after having spiked the same quantity in different baby foods. The other aims were: (1) to verify a constant genome copies ratio existence between mammalian and avian species (2) to verify the dPCR performance, set up on housekeeping, to quantify mammalian and avian species in commercial products. Digital PCR showed fewer differences respect to Real Time PCR, at the same 15% w/w chicken spiking level. Despite the constant difference between mammalian and avian genome copies, in samples with the same spiking weight, the confidence intervals increasing towards the extreme values, made impossible to use genome copies ratio as a sort of correction factor between species. Finally, the dPCR system using the myostatin housekeeping gene to determine the chicken content seemed reliable to verify the labelling compliance in meat-based commercial products.

Background Brucellosis is the most common zoonotic disease in Oman. Studies about genetic diversity of Brucella are limited in the country. This study aimed to genotype Brucella melitensis in human isolates and milk samples using multi-locus variable number tandem repeats analysis (MLVA-14) in Oman. Methods MLVA-14 was employed for forty-nine B. melitensis recovered from human isolates (n = 21), one goat isolate, and milk samples (n = 27). Results Clustering analysis separated the 49 B. melitensis strains into two main clusters including 31 genotypes. In Dhofar Governorate, shared genotypes among different animal species were identified; the same genotypes were found also in human isolates. Moreover, there was a close genetic relationship between human and milk sample strains from Dhofar and AD Dakhiliya Governorates. Phylogeography investigated by Minimum Spanning Tree analysis showed that Omani strains belonged to the East Mediterranean lineage and formed a distinct branch with a close relationship with two strains from the United Arab Emirates. Moreover, eight Omani strains genotyped from milk shared the same MLVA profile as strains from Spain, Portugal, China, India, and Turkey. The caprine isolate was an outlier correlated with a big cluster mostly formed by isolates from China with other strains from Portugal, Kazakhstan, Turkey, Mongolia, Marocco, France and Spain. Conclusions This study highlights the zoonotic nature of B. melitensis transmission from infected livestock to humans and also its circulation among different animal species. The One Health approach is the way to develop policies and programs for disease surveillance and control.

Arthropod vectors are responsible for the transmission of human pathogens worldwide. Several arthropod species are bird ectoparasites, however, no study to date has characterized their microbiota as a whole. We sampled hematophagous ectoparasites that feed on migratory birds and performed 16S rRNA gene metabarcoding to characterize their microbial community. A total of 194 ectoparasites were collected from 115 avian hosts and classified into three groups: a) Hippoboscidae diptera; b) ticks; c) other arthropods. Metabarcoding showed that endosymbionts were the most abundant genera of the microbial community, including Wolbachia for Hippoboscidae diptera, Candidatus Midichloria for ticks, Wolbachia and Arsenophonus for the other arthropod group. Genera including pathogenic species were: Rickettsia, Borrelia, Coxiella, Francisella, Bartonella, Anaplasma. Co-infection with Borrelia-Rickettsia and Anaplasma-Rickettsia was also observed. A global overview of the microbiota of ectoparasites sampled from migratory birds was obtained with the use of 16S rRNA gene metabarcoding. A novel finding is the first identification of Rickettsia in the common swift louse fly, Crataerina pallida. Given their possible interaction with pathogenic viruses and bacteria, the presence of endosymbionts in arthropods merits attention. Finally, molecular characterization of genera, including both pathogenic and symbiont species, plays a pivotal role in the design of targeted molecular diagnostics.

The Coronaviridae family represents a broad group of RNA-containing viruses that infect humans and animals. This family belongs to the order Nidovirales and is divided into four main genera: α-CoV, β-CoV, γ-CoV and δ-CoV. It is particularly noteworthy that representatives of β-CoV have caused serious epidemics in humans, such as the outbreaks of SARS-CoV, MERS-CoV, and COVID-19 caused by SARS-CoV-2. Although the clinical manifestations of CoVs can range from mild cold-like symptoms to severe respiratory diseases, they share common features in their structure, modes of transmission, and natural reservoirs. Identifying natural reservoirs, as well as establishing intermediate hosts, is crucial for understanding the mechanisms of interspecies transmission of CoVs. These processes are often mediated by molecular interactions between viral spike (S) proteins and cellular receptors of different species, which contribute to zoonotic outbreaks. Thus, the interaction of various species and the study of these processes of viral spread, cross-species transmission, and pathogen evolution play a key role in ensuring global biological safety. Therefore, we conducted this review to summarize the data from existing studies focused on the taxonomy of CoVs, their main types, natural reservoirs, intermediate hosts, pathways of interspecies transmission, and the significance of the One Health concept as an interdisciplinary approach to monitoring, prevention and control of CoV infections at the intersection of human, animal, and environmental health. We examined databases such as PubMed, Science Direct, Web of Science, and Google Scholar to identify relevant scientific articles in English available for such a review. The aim of this work is to study the taxonomy and classification of coronaviruses, as well as to identify their natural reservoirs, intermediate hosts, and applicable control measures. A review of human and animal coronaviruses has revealed their evolutionary diversity, their main natural reservoirs, their intermediate hosts, and their interactions with cellular receptors. This information allows for a better understanding of the mechanisms by which the viruses are transmitted from animals to humans. The concept of One Health demonstrated the interconnections between human, animal and environmental factors.