The objective of this study was to evaluate the effect of the subcutaneous injection of a trace mineral preparation (ITM: Zinc (60 mg/ml), Copper (15 mg/ml), Manganese (10 mg/ml) and Selenium (5 mg/ml)) at dry-off and pre-calving on the occurrence of clinical mastitis and high somatic cell count during the first 30 days post-partum in dairy cows. A randomized field trial was conducted in 2 commercial dairy farms located in Northern Italy, with 280 and 160 Holstein cows respectively with bulk tank SCC greater than 300,000 scc/ml for all year. Cows treated with ITM had lower clinical mastitis occurrence during the first 30 DIM (3.13%) compared to control (CON 12.37%; p = 0.03). New infections during the dry period (ITM 7.50%, CON 20.51%; p = 0.09) and subclinical mastitis at first test day occurrence (ITM 10.99%, CON 17.2% p = 0.22). were numerically lower for ITM, but did not significantly differ.

Unmanned aerial vehicles (UAVs) have become indispensable tools in precision agriculture and plant phenotyping, enabling the rapid, non-destructive assessment of crop traits across space and time. Equipped with RGB, multispectral, thermal, and other sensors, UAVs provide detailed information on canopy structure, physiology, and stress responses that can guide management decisions and accelerate breeding programs. Despite these advances, the downstream processing of UAV imagery remains technically demanding. Converting orthomosaics into standardized, biologically meaningful data often requires a combination of photogrammetry, geospatial analysis, and custom scripting, which can limit reproducibility and accessibility across research groups. We present drone2report, an open-source python-based software that processes orthomosaics from UAV flights to generate vegetation indices, summary statistics, derived subimages, and text (html) reports, supporting both research and applied crop breeding needs. Alongside the basic structure and functioning of drone2report, we also present five case studies that illustrate practical applications common in UAV-/drone-phenotyping of plants: (i) thresholding to remove background noise and highlight regions of interest; (ii) monitoring plant phenotypes over time; (iii) extracting information on plant height to detect events like lodging or the falling over of spikes; (iv) integrating multiple sensors (cameras) to construct and optimize new synthetic indices; (v) integrate a trained deep learning network to implement a classification task. These examples demonstrate the tool’s ability to automate analysis, integrate heterogeneous data and models, and support reproducible computation of agronomically relevant traits. drone2report streamlines orthorectified UAV-image processing for precision agriculture by linking orthomosaics to standardized, plot-level outputs. Its modular, configuration-driven design allows transparent workflows, easy customization, and integration of multiple sensors within a unified analytical framework. By facilitating reproducible, multi-modal image analysis, drone2report lowers technical barriers to UAV-based phenotyping and opens the way to robust, data-driven crop monitoring and breeding applications.

Over centuries, dogs have accompanied human populations during seasonal livestock movements associated with transhumance, contributing to the development of specialized pastoral dog populations. This study focuses on a population of heeling dogs distributed across the Italian Apennines, here referred to as Apennine heeling dogs, traditionally selected by shepherds based on homogeneous morphological and behavioral traits. The aim of the present study was to provide a genome-wide characterization of this population and to investigate its genetic relationships with other shepherd and herding breeds. A total of 16 individuals with documented pastoral ancestry (AppHeelDog) and 6 morphologically similar dogs with uncertain ancestry (AppMorph) were genotyped using a medium-density SNP array and analyzed together with publicly available datasets. The results indicate that the Apennine heeling dog forms a genetically coherent and distinct cluster across all analyses. ADMIXTURE revealed a characteristic ancestry component largely absent in other breeds, while TreeMix indicated a predominantly tree-like evolutionary history with no evidence of recent gene flow. A genomic affinity with continental European herding breeds, particularly German and Belgian Shepherd lineages, was also observed. Despite moderate genetic diversity, the population exhibited substantial genomic inbreeding and a reduced effective population size. The AppMorph group showed partial genetic overlap with the core AppHeelDog population but also evidence of heterogeneity, highlighting the importance of integrating genomic and phenotypic data when defining population boundaries. Overall, this study provides the first genomic evidence supporting the distinctiveness of the Apennine heeling dog and establishes a foundation for its recognition and conservation.

Methionine supplementation during the suckling period of ewe lambs may modify DNA methylation in the germline (F0) during this critical window period for the neonate. This circumstance may promote the intergenerational transmission of epigenetic marks to the offspring (F1), thus altering the expression of specific genes and physiological traits throughout F1 life. To test this hypothesis, 27 newborn ewe lambs (F1) born from either ewes being supplemented 0.1 % methionine (dry matter basis) during the suckling period (F0-MET) or not supplemented (F0-CTRL) were assigned to two different groups (F1-CTRL, n = 13 and F1-MET, n = 14), being the dietary treatment of their mothers (F0) the only source of variation. Thus, all the F1 animals (both groups) were raised exactly in the same way along the whole life (including lactation). In this study, we determined differences in the global blood methylation patterns, biochemical profile, and metabolome of female offspring (F1). Our data showed that functional categories such as those related to developmental process and anatomical structure development were significantly enriched in the F1-MET ewe lambs due to differentially methylated regions of genes in these categories. These F1-MET ewes also presented lower live body weight (P < 0.05) and reduced lipomobilization and milk yield (P = 0.099) during the lactation period, together with increased PUFAs content (P = 0.075) in the milk fatty acid profile when compared to F1-CTRL. Increased levels of insulin (P = 0.031) and beta-hydroxybutyrate (P = 0.043), along with certain features of the metabolome profiles, revealed altered lipid metabolism when compared to F1-CTRL animals. As far as fecal microbiota is concerned, no significant differences were found in alpha and beta diversity between the two groups. However, DESeq2 analysis performed on OTU-filtered data revealed that Treponema (genus) and Spirochaetaceae (family), both from the Spirochaetes phylum, were reduced in the F1-MET group compared to the F1-CTRL group (log2FC=-3.96, p(adj) < 0.05). The results suggest that early methionine supplementation in F0 ewe lambs has an intergenerational impact on their F1 female offspring, with negative consequences on lipomobilization and milk production during F1 lactation.

Milk microbiota is a complex microbial ecosystem with implications for product quality, safety, and animal health. However, limited data exist on goat milk microbiota, particularly in local breeds. This study provides the first detailed characterization of the milk microbiota of Girgentana goats, a resilient Sicilian breed valued for high-quality dairy products. Illumina NovaSeq sequencing was used to analyze the 16S rRNA V3–V4 regions of 44 individual and 3 bulk milk samples. Briefly, 16S rRNA-gene sequencing produced a total of 8,135,944 high-quality reads, identifying 1134 operational taxonomic units (OTUs) across all individual samples. On average, each sample showed 864 OTUs with counts > 0. Alpha diversity metrics, based on richness estimators (Chao1: 948.1; ACE: 936.3) and diversity indices (Shannon: 4.06; Simpson: 0.95; Fisher: 118.5), indicated a heterogeneous community with both common and low-abundance taxa. Firmicutes (51%) and Proteobacteria (27%) were the predominant phyla, with Lactobacillaceae (54%) and Bifidobacteriaceae (22%) dominating at the family level. Notably, farm bulk milk profiles closely mirrored individual samples. These results establish a milk microbiota baseline for the Girgentana breed and offer valuable insights into microbial ecology in traditional dairy systems, supporting future comparisons across breeds and farming practices.

This study investigated the effects of yeast-derived nucleotides (YN) supplementation via drinking water on growth performance, intestinal morphology, barrier function, and cecal microbiota in broiler chickens. A total of 480 one-day-old male Ross 308 broilers were randomly assigned to three groups: control (CTR), and two treatment groups receiving YN at 90 g/100 kg (T1) or 180 g/100 kg (T2) in drinking water for 42 days. Growth performance parameters were recorded throughout the trial, and intestinal samples were collected on days 21 and 42 for histomorphological evaluation, gene expression analysis, and microbiota profiling using 16S rRNA gene sequencing.YN supplementation significantly improved body weight on day 21 and average daily gain during the grower phase in the T2 group. Carcass weight was also significantly increased in T2 at day 21. Intestinal morphology analysis revealed improved villus-to-crypt ratio on day 21 in both treatment groups, and gene expression analysis demonstrated upregulation of tight junction-related genes (ZO-1, OCLN, CLDN3) in T2, indicating enhanced intestinal barrier integrity. No differences were observed in mucous layer thickness or MUC2 expression.Microbiota analysis showed a significant increase in alpha diversity indices over time, consistent with normal microbial maturation. While T1 increased Shannon and Simpson indices compared to CTR, no significant changes were observed for T2. Beta diversity was not affected by treatment, although a clear temporal shift in microbial community composition was evident between days 21 and 42.In conclusion, administering yeast-derived nucleotides via drinking water improved early growth performance and intestinal health in broilers, particularly at higher inclusion levels. This mode of administration offers a practical, flexible alternative to feed-based supplementation, allowing targeted use during critical growth periods or under stress conditions. These findings support the functional role of YN as a dietary strategy to promote gut health and performance in poultry production.

Bovine mastitis is a major challenge in dairy farms. Since the agents commonly used for pre- and post-dipping can affect the udder health by modifying milk microbiota, alternative products are needed. This study aimed to evaluate the effect of the use of pre- and post-dipping formulations containing the fermented broth of Nisin A-producing Lactococcus cremoris FT27 strain (treated group, TR) on the abundance and biodiversity of milk microbiota as compared to iodine-based commercial disinfectants (control group, CTR) during a three-month trial. The experiment was conducted on 20 dairy cows, divided into two groups (CTR and TR) of 10 lactating cows each. Milk samples were collected from two selected healthy quarters of each cow at 3 time-points. Microbial communities were investigated by cultural and sequence-based methods, and analyzed through bioinformatic and statistical approaches. Clear differences in bacterial community composition were observed among groups, with higher species richness in TR, especially of Staphylococcus, Enterococcus, Lactococcus, and Streptococcus genera. The microbiota was dominated by Firmicutes, followed by Actinobacteriota, Proteobacteria, and Bacteroidota. Staphylococcaceae family was significantly higher in TR (p < 0.009), whereas Carnobacteriaceae, Mycobacteriaceae, and Pseudomonadaceae were significantly lower (p = 0.005, p = 0.001, and p = 0.040, respectively). CTR had considerably higher abundances of the genera Alkalibacterium (p = 0.011), Pseudomonas_E (p = 0.045), Corynebacterium (p = 0.004), and Alloiococcus (p = 0.004), and lower abundances of Staphylococcus (p < 0.009). Milk microbiota changed noticeably during the experimental period, regardless of treatment. A significant decrease was observed in both groups for Firmicutes_A phylum, with an increment in Actinobacteriota phylum, Propionibacteriaceae family, and Cutibacterium genus. Streptococcaceae significantly decreased in CTR (p = 0.013) and rose in TR (p = 0.001). Several differences were observed between the two groups during the experimental period. Streptococcus genus almost disappeared in CTR (p = 0.013), whereas it significantly increased in TR (p = 0.001). Three and twelve enriched groups were significantly identified respectively in CTR and TR using LEfSe. The use of Nisin A-based teat dip formulations could be linked to greater microbial diversity compared to commercial products. Despite the influence of seasonality, the experimental formulations maintained higher milk biodiversity, suggesting that lactic acid bacteria metabolites prevent alterations in the milk microbiota.

BACKGROUND:Genetically modified soybean is largely used in animal feed and its massive cultivation affects the environmental sustainability of livestock and the dependency for the import in the European market. OBJECTIVES:The aim of this study was to evaluate the partial substitution of soybean meal with an innovative common bean genotype (Phaseolus vulgaris lec-lpa) with reduced content of anti-nutritional factors on zootechnical performance, gut microbiota modulation and faecal minerals in post-weaning piglets. METHODS:Fourteen piglets were divided into a control group fed with a basal diet and a treatment group fed with a commercial diet in which 7.3% of soybean meal and 0.8% of soybean oil were replaced with 10% of P. vulgaris lec- lpa for 28 days. BW, ADG, ADFI and FCR were evaluated, and diarrhoea incidence was recorded. Evaluation of pH, nitrogen content, protein digestibility and mineral content was performed on faecal samples. Microbiota was analysed by rectal swabs samples. Blood serum metabolic profile was evaluated. RESULTS:The treatment group showed lower BW and ADG during the trial (p < 0.05), but the health status of the animals was preserved. The treatment group released lower levels of minerals in faeces when compared with the control group after 28 days (p < 0.05) suggesting a lower dispersion of faecal minerals in the environment. Significant Beta diversity index was observed at 14 and 28 days (p < 0.05). Roseburia and Butyricicoccus increased in treatment group at day 28 (p < 0.05). These genera are associated with SCFA production, contributing to the maintenance of intestinal integrity, promoting positive bacterial populations and limiting inflammatory phenomena. CONCLUSIONS:In conclusion, P. vulgaris lec- lpa could be a viable and sustainable alternative protein source to reduce the European protein gap, playing a potential role in microbiota modulation and faecal minerals release.

This research aimed to analyze and compare bacterial diversity in bulk tank milk (BTM) samples from five Brazilian regions using 16 S rRNA gene sequencing, while correlating this diversity with Somatic Cell Count (SCC) values. A total of 57 samples from Santa Catarina, São Paulo, Minas Gerais, Goiás, Maranhão, Pará, and Tocantins were sequenced through Next Generation Sequencing (NGS). The analysis revealed one kingdom, four phyla, six classes, 14 orders, 28 families, and 43 genera, with Moraxellaceae (22.3

Sixty Alpine dairy goats were classified as healthy (HEAL, n = 30) or infected (INFE, n = 30) based on bacteriological culture of udder-half samples collected 7 d before dry-off. At -61 d from kidding (DFK), goats were dried off and randomly allocated to 2 homogeneous groups either receiving no treatment (15 HEAL, 15 INFE) or being treated intramammarily with 250 mg of cefazolin per half-udder (15 HEAL, 15 INFE). Milk yield, composition, and SCC were monitored at -82, 17, 45, and 80 DFK, and blood samples were collected at -66, -56, -7, and 8 DFK to assess plasma analytes. Antibiotic administration at dry-off did not affect productive performances in the new lactation or plasma analyte trends. Regardless of udder health status, lactose decreased in late lactation despite stable yield, likely due to increased SCC and mammary permeability during involution. The INFE goats had higher SCC before dry-off and higher SCS at 45 DFK. Following dry-off, plasma urea decreased across all groups, reflecting dietary changes aimed at easing milk cessation. Glucose and nonesterified fatty acids (NEFA) remained stable during the dry period. The INFE goats showed elevated plasma cholesterol at -57 DFK, suggesting transient dyslipidemia due to IMI. After kidding, all goats showed peaks in NEFA, NEFA/albumin ratio, BHB, bilirubin, and glutamate oxaloacetate transaminase, indicating body reserve mobilization and hepatic stress. Concurrently, increases in haptoglobin and ceruloplasmin, and decreases in albumin/globulin ratio and paraoxonase, reflect an acute phase response. The INFE goats showed higher reactive oxygen metabolites and thiol concentrations between -57 and 8 DFK, and elevated ceruloplasmin at -7 and 8 DFK, indicating sustained systemic inflammation. Plasma analytes could serve as effective diagnostic tools to improve the detection of subclinical mastitis in dairy goats.

Intramammary dry-off treatment is widely considered an effective method for preventing and curing intramammary infection (IMI) in lactating cows; however, it is not commonly used in small ruminants like goats. Therefore, this study was designed to evaluate the effect of an approved cefazolin-based intramammary treatment on the milk microbiota of Alpine dairy goats during the dry and early lactation periods. Sixty goats were randomly selected based on bacteriological results and randomly allocated into the control group (CG) or the treatment group (TG). Cefazolin 250 mg (Cefovet A, Dopharma, Firenze, Italy) was administered to the TG group at dry-off, whereas the CG received no treatment. Pooled milk samples were collected at dry-off (T1; 52 samples), colostrum (T2; 46 samples), and 5-10 days in milk (T3; 55 samples) for bacteriological analysis, somatic cell count (SCC), and 16 S rRNA gene sequencing. SCC levels were initially high in both groups at T1 (TG: 1,588,000 cells/mL; CG: 1,629,000 cells/mL), which significantly decreased at T3 (TG: 148,000 cells/mL; CG: 153,000 cells/mL). Notably, the TG had fewer infected mammary glands than the CG at T3 (p = 0.0248), while no differences were found at T1 or T2. Despite the reduction in SCC and infection rates, cefazolin-based treatment did not significantly affect the alpha- and beta-diversity between the TG and CG. On the other hand, shifts in microbial composition, including fluctuations in Firmicutes, Proteobacteria, and Actinobacteria, were primarily due to the lactation stage rather than the treatment. Differential abundance analyses identified non-pathogenic genera, such as Acinetobacter, Bacteroides, and Paracoccus, that varied between groups at different timepoints. The study provided insights into the effects of cefazolin-based dry goat treatment on goat milk microbiota and its changes during the lactation cycle, demonstrating its potential to reduce SCC and mammary gland infections without significant alterations to the milk microbiota.

Essential oils (EO) are known for their antibacterial and anti-inflammatory properties and can be used as an alternative to reduce the reliance on antimicrobials in dairy cattle. While many studies have explored the beneficial properties of EO in vitro, their effects on milk quality and milk microbiota, when applied directly to the udder skin, remain relatively unknown. This study aimed to investigate the impact of Thymus capitatus essential oil (TCEO), known for its high antibacterial and antioxidant properties, on milk microbiota using 16S rRNA sequencing, the lipidomic profile via liquid chromatography-quadrupole time-of-flight mass spectrometry, udder skin microbiota, and inflammatory biomarkers of dairy cows at the end of lactation. Sixteen-quarters of 12 Holstein cows were selected, and TCEO was topically applied to the udder skin twice a day for 7 days. Milk was collected aseptically on days 0, 7, 21, and 28 before morning farm milking. The results showed no significant changes in microbiota composition after the EO treatment in alpha and beta diversity or taxonomical composition at the phylum and genus levels. TCEO induced limited changes in the milk lipidome, primarily affecting diacylglycerols at T21. The treatment did not affect inflammatory biomarkers, milk sensory properties, or quality. Our study is the first to demonstrate that a local application of 10% TCEO on cow’s quarters does not significantly alter milk quality or microbiota composition in milk and skin. More studies should be conducted to ensure the safe use of TCEO in dairy cows and explore its potential benefits on antibiotic-resistant bacteria as an alternative or support for antibiotic therapy.

Background/Objectives: In the Aosta Valley, the alpine grazing system integrates livestock production and land management. Valdostana breeding has adapted to this mountainous region, but the spread of Staphylococcus aureus within pastures may impact animal health. The aim of this study was to provide an overview of S. aureus genotypes associated with antimicrobial resistance (AMR) and virulence profiles in four dairy herds in the Aosta Valley from July 2022 to August 2023. Methods: A total of 468 composite milk samples were collected at three timepoints: T1 (pasture-livestock system), T2 (farm-livestock system), and T3 (pasture-livestock system). S. aureus isolates were characterized by antimicrobial susceptibility testing, ribosomal spacer (RS)-PCR, multilocus sequence typing (MLST), PCR analysis for 28 virulence genes and 6 AMR genes, and adlb-targeted real-time PCR. Results: RS-PCR analysis of 82 S. aureus strains revealed 12 genotypes (GT) in eight clusters (CL). The most prevalent variant was GTRI (61%), followed by GTB (15%). Resistance to penicillin was high (69%), with CLR strains showing 88% resistance, and 51% resistance to amoxicillin plus clavulanate. All strains were susceptible to cephalosporins and oxacillin. Macrolide resistance was low (4%), and multi-drug resistance was 6%. AMR gene presence corresponded with susceptibility, with blaZ detected in 94% of CLR strains. CLR strains also possessed genes for biofilm formation and virulence factors. Conclusions: This study highlights the presence of AMR and virulence factors in S. aureus strains from alpine grazing systems, underscoring the need for ongoing monitoring to mitigate risks to animal health.

Nutritional strategies that supply methyl donors, such as methionine in the early post-natal period of lambs could program feed efficiency, milk production and metabolism along the whole life due to persistent changes in epigenetic marks. To test this hypothesis, 34 newborn ewe lambs from the same flock were stratified and distributed into two groups with equal body weight distribution. The control group (F0-CTRL, n = 17) was fed ad libitum with a milk replacer. In contrast, the second group (F0-MET, n = 17) received the same milk replacer supplemented with 1 g methionine/kg DM. After weaning, all animals were raised the same way and fed ad libitum with a complete pelleted diet formulated according to nutrient requirements. At 45 days of age, blood was collected from the jugular vein for DNA isolation, and DNA methylation was analyzed by Reduced Representation Bisulfite Sequencing (RRBS) in ten animals [5 ewe lambs (F0-MET) vs. 5 ewe lambs (F0-CTRL), corresponding to 5 twin births, of which one lamb was assigned to each group]. The main results show that CPT1B, a gene involved in fatty acid catabolism, was differentially methylated in F0-MET lambs (45 days of life). In addition, these animals presented increased insulin and non-esterified fatty acid concentrations while cholesterol levels were reduced, most of these changes being persistent along the whole life. No differences were observed in milk production and feed efficiency during lactation. Still, the milk's fatty acid (FA)

Abstract The aim of this study was to evaluate different dietary level of Zinc (Zn) and Copper (Cu) supplementation according to European and non-European levels on the health and performance of pigs 14 d after weaning. A total of 120 piglets [initial body weight = 7.14 ± 0.92 kg] were divided into 4 experimental treatments: positive control (PC, 2,500 ppm of Zn, ZnO) and 3 treatments in which Zn and Cu were added through potentiated ZnO and Cu2O according to different European and non-European levels of inclusion: EU (120 ppm of Zn; 140 ppm of Cu), non-EU+ (300 ppm of Zn; 200 ppm of Cu) and non-EU- (300 ppm of Zn; 140 ppm of Cu). Growth performance, serum Zn and Cu concentrations, fecal score, blood biomarkers of intestinal integrity, and fecal microbial composition were examined and analyzed using GLM and MIXED procedures of SAS. Fecal samples at 14 d were collected and the V3–V4 hypervariable regions of the bacterial 16S gene were sequenced in one Illumina MiSeq run. Body weight (BW), average daily gain (ADG), average daily feed intake (ADFI), feed conversion ratio (FCR) and (feed efficiency (FE) were not affected by the experimental treatments. The fecal score suggests that during the first 14d, the consistency of the feces tended (P < 0.10) to be less in the three treatment groups while in PC, the greatest concentration of Zn favored a better fecal consistency. The initial serum Zn and Cu concentrations were similar for all dietary treatment groups. After 14 d, serum Zn concentration was significantly greater in PC (15.71 ± 6.25 µg/L, P < 0.05). No differences were highlighted in serum Zn concentration among the other 3 treatment groups. Serum Cu concentrations revealed statistically significant results (P < 0.05) on 14 d after weaning in EU, non-EU+ and non-EU- groups, showing greater concentrations of Cu (17.65 ± 5.49 µmol/L, 17.73± 3.46 µmol/L 18.33 ± 4.13 µmol/L, respectively) compared with PC (11.87 ± 3.60 µmol/L). These results suggested that the EU level of inclusion of both potentiated Zn and monovalent Cu is enough to reach the same Cu and Zn plasma concentrations of non-EU treatments. Plasma DAO was negatively (P < 0.05) affected in non-EU-. Firmicutes and Bacteroidetes were the most abundant phyla in fecal microbiome. Non-EU- contributed to a significant decrease in biodiversity in fecal microbiota as depicted with Shannon for diversity and Simpson for evenness indexes (P < 0.05). In fecal samples, the presence of genera linked to a greater disruption of the gut barrier (Escherichia-Shigella) was depicted in non-EU- group, indicating significant modifications of the microbial community. These results suggest the need for a balanced supplementation of Cu and Zn through more bioavailable sources. The use of potentiated ZnO and Cu2O according to European levels could represent a valid strategy to enhance weanling piglets gut health and to reduce the environmental impact.

Non-aureus staphylococci and mammaliicocci (NASM) are the most frequently isolated bacterial group from bovine milk samples. Most studies focus on subclinical mastitis caused by NASM; however, NASM can cause clinical mastitis (CM) as well. We evaluated retrospective data from 6 years (2017-2022) to determine the species and frequency of NASM isolated from quarter bovine CM. The data was comprised of microbiological results from quarter CM samples routinely submitted to Quality Milk Production Services at Cornell University for microbial identification by MALDI-TOF mass spectrometry. A total of 9,909 microbiological results from 410 dairy herds were evaluated. Our results showed that 29 distinct NASM species were identified, with the 8 most prevalent NASM species being Staphylococcus chromogenes, Staphylococcus haemolyticus, Staphylococcus simulans, Staphylococcus epidermidis, Staphylococcus sciuri (now Mammaliicoccus sciuri), Staphylococcus agnetis/Staphylococcus hyicus, Staphylococcus borealis, and Staphylococcus xylosus. The NASM distribution remained similar among seasons, but the frequency of NASM CM cases was higher during the summer. Our results showed different patterns of variations in the isolation frequency over time, depending on the bacterial species: increasing or decreasing trends, cyclic fluctuations, and, except for Staphylococcus borealis, a significant seasonality effect for our study's most prevalent NASM. This study showed that Staphylococcus chromogenes remains the most frequent (43%) NASM species identified from bovine CM, followed by Staphylococcus haemolyticus (18%), and Staphylococcus simulans (12%).

Genome interpretation (GI) encompasses the computational attempts to model the relationship between genotype and phenotype with the goal of understanding how the first leads to the second. While traditional approaches have focused on sub-problems such as predicting the effect of single nucleotide variants or finding genetic associations, recent advances in neural networks (NNs) have made it possible to develop end-to-end GI models that take genomic data as input and predict phenotypes as output. However, technical and modeling issues still need to be fixed for these models to be effective, including the widespread underdetermination of genomic datasets, making them unsuitable for training large, overfitting-prone, NNs. Here we propose novel GI models to address this issue, exploring the use of two types of transfer learning approaches and proposing a novel Biologically Meaningful Sparse NN layer specifically designed for end-to-end GI. Our models predict the leaf and seed ionome in A.thaliana, obtaining comparable results to our previous over-parameterized model while reducing the number of parameters by 8.8 folds. We also investigate how the effect of population stratification influences the evaluation of the performances, highlighting how it leads to (1) an instance of the Simpson's Paradox, and (2) model generalization limitations.

In the context of the RABOLA project, which aimed to identify operational practices that lead to the reduction of antibiotic use in dairy cattle farming, lyophilised Aloe arborescens was administered orally to cows during the dry-off and peripartum periods. In this specific paper we wanted to examine whether oral administration of Aloe arborescens, in combination with the topical application of a teat sealant could exert an effect on the microbial populations of three cow microbiomes (rumen, milk, rectum), between dry-off and peripartum. Dry-off and peripartum are critical physiological phases of the cow’s life, where both the mammary gland and the gastrointestinal tract undergo dramatic modifications, hence the relevance of evaluating the effects of dietary treatments. Thirty multiparous dairy cows were randomly allocated to three groups: Control (antibiotic treatment and internal teat sealant), Sealant (only internal teat sealant) and Aloe (internal teat sealant and Aloe arborescens homogenate administered orally). For 16S rRNA gene sequencing, rumen, rectum and milk samples were collected, not synchronously, at the most critical timepoints around dry-off and calving, considering the physiological activity of each biological site. The rumen microbiome was predominantly characterized by Bacteroidetes and Firmicutes followed by Proteobacteria, while the rectum exhibited a prevalence of Firmicutes and Bacteroidetes. The milk microbiome mainly comprised Firmicutes, Proteobacteria, Actinobacteria and Bacteroidetes. Alistipes spp., Ruminococcaceae UCG-10 group, Prevotellaceae UCG-001 group, and Bacteroides spp., involved in cellulose and hemicellulose degradation, enhancement of energy metabolism, and peptide breakdown, showed increment in the rectum microbiome with Aloe supplementation. The rectum microbiome in the Aloe group exhibited a significant increase in the Firmicutes to Bacteroidetes ratio and alpha-diversity at seven days after dry-off period. Beta-diversity showed a significant separation between treatments for the rectum and milk microbiomes. Aloe supplementation seemed to enrich milk microbial composition, whereas the Sealant group showed greater diversity compared to the Control group, albeit this included an increase in microorganisms frequently associated with mastitis. Aloe arborescens administration during the dry-off period did not demonstrate any observable impact on the microbial composition of the rumen, a finding further supported by volatilome analysis. Instead, the oral Aloe supplementation at dry-off appears to significantly influence the composition of the dairy cow rectum and milk microbiomes in the following lactation.

High-throughput genotyping offers great potential to increase our understanding of the genomic basis of canid variation. Braque Français Type Pyrénées (BRA) are smart, agile, and friendly dogs originally developed for tracking, hunting, and retrieving feathered game. On a population of 44 unrelated BRA dogs, single nucleotide polymorphism (SNP) genotype data from the CanineHD Whole-Genome Genotyping BeadChip and evaluation scores for 12 traits related to morphology and hunting performance were available. After quality filtering, 95,859 SNPs on the 38 dog autosomes (CFA) were retained. Phenotypic scores were expressed on a scale from 1 (worst) to 6 (best) and were mostly poorly to moderately correlated except for some morphological traits (e.g. r = 0.81 between the conformation of the head and that of the eye). From GWAS, a total of 378 SNP-phenotype associations with posterior odds of association > 1 have been detected. The strongest associations were found for the eye conformation, for the skull/muzzle ratio, and for connection to the hunter. These included both new and previously identified markers and genes potentially involved with type and behavior traits in BRA. Six of the significant markers mapped within SETDB2, a gene known to be related to pointing behavior in dogs. These results advance our understanding of the genetic basis for morphology and hunting behavior in dogs and identify new variants which are potential targets for further research.