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The variety and makeup of the gut microbiome are frequently regarded as the primary determinants of health and production performances in domestic animals. High-throughput DNA/RNA sequencing techniques (NGS) have recently gained popularity and permitted previously unheard-of advancements in the study of gut microbiota, particularly for determining the taxonomic composition of such complex communities. Here, we summarize the existing body of knowledge on livestock gut microbiome, discuss the state-of-the-art in sequencing techniques, and offer predictions for next research. We found that the enormous volumes of available data are biased toward a small number of globally distributed and carefully chosen varieties, while local breeds (or populations) are frequently overlooked despite their demonstrated resistance to harsh environmental circumstances. Furthermore, the bulk of this research has mostly focused on bacteria, whereas other microbial components such as protists, fungi, and viruses have received far less attention. The majority of these data were gathered utilizing traditional metabarcoding techniques that taxonomically identify the gut microbiota by analyzing small portions of their genome (less than 1000 base pairs). However, to extend the coverage of microbial genomes for a more precise and thorough characterization of microbial communities, a variety of increasingly practical and economical shotgun techniques are currently available.

Background: The genus Orthobornavirus comprises RNA viruses infecting humans, mammals, birds and reptiles, where parrot bornavirus 1 to 8 causes fatal neurological and/or gastrointestinal syndromes in psittacines. There is, to the best of our knowledge, no publication describing avian bornaviruses in pet parrots in Sweden. We aimed to identify and to produce epidemiologic knowledge about the etiologic agent associated with a history of severe weight loss and death of a Primolius maracana.Methods and results: The results of histopathology, immunohistochemistry and real-time RT-PCR were compatible with avian bornavirus infection. Sequencing indicated infection by parrot bornavirus 4 (PaBV-4). The genotype reported shared high identity with PaBV-4 identified from pet psittacines and from wild birds in several countries. The N gene and X protein showed genotype clusters formation. P protein revealed to be more conserved within and between species of bornaviruses. Findings suggest horizontal transmission within and between avian orders and species.Conclusion: There seems to be a worldwide trading without biosafety measures, hence, further disease transmission could be avoided. For screening purposes, the P gene is a good candidate as a universal target in molecular diagnostics. Wild birds may be key pieces in the puzzle of bornavirus epidemiology.

Background: The genus Orthobornavirus comprises non-segmented, negative-stranded RNA viruses able to infect humans, mammals, reptiles and various birds. Parrot bornavirus 1 to 8 (PaBV-1 to 8) causes neurological and/or gastrointestinal syndromes and death on psittacines. We aimed to identify and to produce epidemiologic knowledge about the etiologic agent associated with a death of two female Psittacus erithacus (grey parrot). Methods and Results: Both parrots were submitted for a complete standardised necropsy. Tissue samples were analysed by PCR. The findings in necropsy were compatible with bornavirus infection. Analysis revealed PaBV-4 related with genotypes detected in captive and in wild birds. The N and X proteins of PaBV-4 were more related to avian bornaviruses, while phosphoprotein was more related to variegated squirrel bornavirus 1 (VSBV-1). Within the P gene/phosphoprotein a highly conserved region between and within bornavirus species was found. Conclusions: Portugal is on the routes of the intensive world trade of psittacines. Broad screening studies are required to help understanding the role of wild birds in the emergence and spread of pathogenic bornaviruses. PaBV-4 phosphoprotein is closer to VSBV-1 associated with lethal encephalitis in humans than with some of the avian bornaviruses. The highly conserved P gene/phosphoprotein region is a good target for molecular diagnostics screenings.

The purpose of this study was to estimate the growth curve parameters and carcass traits yields of three Portuguese autochthonous chicken breeds, Amarela (AM), Preta Lusitânica (PL) and Pedrês Portuguesa (PP). Birds (198) were individually weighed at pre-established time intervals (6682 records) and the study period lasted 30 months. The growth data were fitted to a mixed nonlinear model based on the Gompertz growth function. Fixed effects were breed, sex, lot, temperature and photoperiod. The adult weight estimated for males (females) were 2851.3 (1951.6) g for AM, 3047.5 (2147.7) g for PL, and 3243.7 (2344.0) g for PP, respectively. The males (females) estimated maximum daily growth were 22.7 (18.1) g at 77 (69) days for AM, 20.7 (17.5) g at 79 (72) days for PL, and 18.1 (16.3) g at 82 (74) days for PP, respectively. Within breed the males were heavier than females at 365 days but with lower maturity rates. Yields of carcass and noble meat pieces were evaluated on data collected from 10 males of each breed, sacrificed at 240 days. Traditionally, these breeds are commercialised whole and again the PP had the heaviest carcass with the highest yield. Growth of these autochthonous breeds after 240 days was minimal and may justify the decrease of the traditional slaughter age of approximately one year, in order to increase profitability. Establishing special market niches will also be a valuable complement for the rural economy of Portugal and an important contribution to the conservation of this genetic heritage.

Endogenous retroviruses, non-retroviral RNA viruses and DNA viruses have been found in the mammalian genomes. The origin of Hepatitis C virus (HCV), the major cause of chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma in humans, remains unclear since its discovery. Here we show that fragments homologous to HCV structural and non-structural (NS) proteins present in the European rabbit (Oryctolagus cuniculus) and hare (Lepus europaeus) genomes replicate in bovine cell cultures. The HCV genomic homolog fragments were demonstrated by RT-PCR, PCR, mass spectrometry, and replication in bovine cell cultures by immunofluorescence assay (IFA) and immunogold electron microscopy (IEM) using specific MAbs for HCV NS3, NS4A, and NS5 proteins. These findings may lead to novel research approaches on the HCV origin, genesis, evolution and diversity.

The search for molecular markers in the feline mammary gland, namely, the adhesion molecules belonging to the cadherin family, is useful in the understanding of the development of mammary carcinomas in felines and humans. To study P-cadherin expression in the feline mammary gland, 61 samples of normal (n=4), hyperplastic (n=12), and neoplastic (n=45) feline mammary tissues were examined. In both normal and hyperplastic mammary tissues as well as in benign tumours, P-cadherin immunolabelling was restricted to myoepithelial cells. In malignant tumours, however, there was an aberrant epithelial P-cadherin immunoexpression in 64.1% (n=25) of cases, with a membranous and/or cytoplasmic pattern of distribution. A statistically significant relationship was seen between epithelial P-cadherin expression and malignant mammary lesions (P=0.0001). In malignant mammary tumours, there was likewise a statistically significant relationship between aberrant P-cadherin immunoexpression and histological grade (P=0.0132). Aberrant epithelial P-cadherin expression seems to be related to malignancy in the feline mammary gland. To confirm the results of this investigation, further studies with larger samples and follow-up studies are warranted.

Abstract Background Pseudomonas aeruginosa may cause venereal disease and infertility in horses. A Pseudomonas aeruginosa - carrier stallion, often unresponsive to artificial vagina collection, was used to naturally breed mares. Semen collected from the same stallion was also used to perform artificial inseminations. Pregnancy rates, embryo quality and incidence of uterine infection were compared between inseminated or naturally-bred mares. Methods P. aeruginosa was isolated from swabbing of the penis, prepuce and distal urethra of the stallion. Before being bred or inseminated, clitoral/vestibular samples were collected from all mares, and cultured for isolation of P. aeruginosa. At the first observed estrus, endometrial swabs were also collected. All mares subjected to natural mating (NS) were re-evaluated for P.aeruginosa by culture of clitoral and endometrial swabs. Artificial inseminations (AI) were performed either with fresh-extended semen (11 AI/7 mares) or frozen semen (10 AI/7 mares). The stallion was also used to breed 3 mares (4 services). For embryo collection, 2 mares were inseminated with fresh-extended semen (1 AI/mare), and 2 additional mares were inseminated with frozen semen (2 AI/mare). Two mares were naturally-bred with a total of 9 services, for embryo collection. All mares were examined after AI or natural service (NS), for uterine pathologies. Embryo recoveries were attempted passing a catheter with inflatable cuff connected to a sterile flexible 2-way flushing catheter, through the cervix. Flushed media was recovered into an Em-Con filter, and embryos searched using a stereoscope. Embryos were graded from 1 (excellent) to 4 (degenerated/dead). Results Pregnancy rates obtained after NS was 50% per cycle. However, more than half of the NS resulted in uterine disease, while uterine pathology was seen only in 22% of the time following AI. Half of the mares bred by NS got positive to P. aeruginosa. Percentage of embryo recovery rates was identical after AI or NS (66.7%). The 4 embryos recovered after AI were classified as Grade 1, while after NS only 2 out of the 6 recovered embryos were Grade 1. Conclusion a) there was no evidence of reduced fertilization after AI or NS, b) a numerically higher incidence of uterine disease was noticed after NS, c) venereal transmission of P. aeruginosa after NS was confirmed, d) a lower percentage of G1 embryos may be obtained after NS. Overall, the data supports the indication for P. aeruginosa-carrier stallions to be bred by AI rather than by NS, and raises the possibility that P. aeruginosa may affect embryo quality.

Although several studies have investigated the factors affecting imputation accuracy, most of these studies involved a large number of genotyped animals. Thus, results from these studies cannot be directly applied to small populations, since the population structure affects imputation accuracy. In addition, factors affecting imputation accuracy may also be intensified in small populations. Therefore, we aimed to compare different imputation strategies for the Portuguese Holstein cattle population considering several commercially available single nucleotide polymorphism (SNP) panels in a relatively small number of genotyped animals. Data from 1359 genotyped animals were used to evaluate imputation in 7 different scenarios. In the S1 to S6 scenarios, imputations were performed from LDv1, 50Kv1, 57K, 77K, HDv3 and Ax58K panels to 50Kv2 panel. In these scenarios, the bulls in 50Kv2 were divided into reference (352) and validation (101) populations based on the year of birth. In the S7 scenario, the validation population consisted of 566 cows genotyped with the Ax58K panel with their genotypes masked to LDv1. In general, all sample imputation accuracies were high with correlations ranging from 0.94 to 0.99 and concordance rate ranging from 92.59 to 98.18%. SNP-specific accuracy was consistent with that of sample imputation. S4 (40.32% of SNPs imputed) had higher accuracy than S2 and S3, both with less than 7.59% of SNPs imputed. Most probably, this was due to the high number of imputed SNPs with minor allele frequency (MAF) < 0.05 in S2 and S3 (by 18.43% and 16.06% higher than in S4, respectively). Therefore, for these two scenarios, MAF was more relevant than the panel density. These results suggest that genotype imputation using several commercially available SNP panels is feasible for the Portuguese national genomic evaluation.

The objectives of this study were to estimate linkage disequilibrium (LD), describe and scan a haplotype block for the presence of genes that may affect milk production traits in Portuguese Holstein cattle. Totally 526 animals were genotyped using the Illumina BovineSNP50 BeadChip, which contained a total of 52 890 single nucleotide polymorphisms (SNPs). The final set of markers remaining after considering quality control standards consisted of 37 031 SNPs located on 29 autosomes. The LD parameters historical recombinations through allelic association (D') and squared correlation coefficient between locus alleles frequencies ( r2) were estimated and haplotype block analyses were performed using the Haploview software. The averages of D' and r2 values were 0.628 and 0.122, respectively. The LD value decreased with increasing physical distance. The D' and r2 values decreased respectively from 0.815 and 0.283 at the distance of 0-30 kb to 0.578 and 0.090 at the distance of 401-500 kb. The identified total number of blocks was 969 and consisted of 4259 SNPs that covered 159.06 Mb (6.24% of the total genome) on 29 autosomes. Several genes inside the haplotype blocks were detected; CSN1S2 gene in haplotype block 51 on BTA 6, IL6 and B4GALT1 genes in haplotype blocks 6 and 33 on BTA 8, IL1B and ID2 genes in haplotype blocks 19 and 29 on BTA 11, and DGAT1 gene in haplotype block 1 on BTA 14. The extension of LD using BovineSNP50 BeadChip did not exceed 500 kb and its parameters r2 and D' were less than 0.2 and 0.70, respectively, after 70-100 kb. Consequently, the 50K BeadChip would have a poor power in genome wide association studies at distances between adjacent markers lower than 70 kb.