Viruses contribute to microbial diversification in the rumen ecosystem and are associated with certain animal production traits.

BACKGROUND: The rumen microbiome enables ruminants to digest otherwise indigestible feedstuffs, thereby facilitating the production of high-quality protein, albeit with suboptimal efficiency and producing methane. Despite extensive research delineating associations between the rumen microbiome and ruminant production traits, the functional roles of the pervasive and diverse rumen virome remain to be determined. RESULTS: Leveraging a recent comprehensive rumen virome database, this study analyzes virus-microbe linkages, at both species and strain levels, across 551 rumen metagenomes, elucidating patterns of microbial and viral diversity, co-occurrence, and virus-microbe interactions. Additionally, this study assesses the potential role of rumen viruses in microbial diversification by analyzing prophages found in rumen metagenome-assembled genomes. Employing CRISPR-Cas spacer-based matching and virus-microbe co-occurrence network analysis, this study suggests that the viruses in the rumen may regulate microbes at strain and community levels through both antagonistic and mutualistic interactions. Moreover, this study establishes that the rumen virome demonstrates responsiveness to dietary shifts and associations with key animal production traits, including feed efficiency, lactation performance, weight gain, and methane emissions. CONCLUSIONS: These findings provide a substantive framework for further investigations to unravel the functional roles of the virome in the rumen in shaping the microbiome and influencing overall animal production performance. Video Abstract.

Potential use of seaweed as a dietary supplement to mitigate enteric methane emission in ruminants.

Seaweeds or marine algae exhibit diverse morphologies, sizes, colors, and chemical compositions, encompassing various species, including red, green, and brown seaweeds. Several seaweeds have received increased research attention and application in animal feeding investigations, particularly in ruminant livestock, due to their higher yield and convenient harvestability at present. Recent endeavors encompassing both in vitro and in vivo experiments have indicated that many seaweeds, particularly red seaweed (Asparagopsis taxiformis and Asparagopsis armata), contain plant secondary compounds, such as halogenated compounds and phlorotannins, with the potential to reduce enteric ruminal methane (CH4) emissions by up to 99 % when integrated into ruminant diets. This review provides an encompassing exploration of the existing body of knowledge concerning seaweeds and their impact on rumen fermentation, the toxicity of ruminal microbes, the health of animals, animal performance, and enteric ruminal CH4 emissions in both in vitro and in vivo settings among ruminants. By attaining a deeper comprehension of the implications of seaweed supplementation on rumen fermentation, animal productivity, and ruminal CH4 emissions, we could lay the groundwork for devising innovative strategies. These strategies aim to simultaneously achieve environmental benefits, reduce greenhouse gas emissions, enhance animal efficiency, and develop aquaculture and seaweed production systems, ensuring a high-quality and consistent supply chain. Nevertheless, future research is essential to elucidate the extent of the effect and gain insight into the mode of action.

Characterization of intestinal mononuclear phagocyte subsets in young ruminants at homeostasis and during Cryptosporidium parvum infection.

Introduction: Cryptosporidiosis is a poorly controlled zoonosis caused by an intestinal parasite, Cryptosporidium parvum, with a high prevalence in livestock (cattle, sheep, and goats). Young animals are particularly susceptible to this infection due to the immaturity of their intestinal immune system. In a neonatal mouse model, we previously demonstrated the importance of the innate immunity and particularly of type 1 conventional dendritic cells (cDC1) among mononuclear phagocytes (MPs) in controlling the acute phase of C. parvum infection. These immune populations are well described in mice and humans, but their fine characterization in the intestine of young ruminants remained to be further explored. Methods: Immune cells of the small intestinal Peyer's patches and of the distal jejunum were isolated from naive lambs and calves at different ages. This was followed by their fine characterization by flow cytometry and transcriptomic analyses (q-RT-PCR and single cell RNAseq (lamb cells)). Newborn animals were infected with C. parvum, clinical signs and parasite burden were quantified, and isolated MP cells were characterized by flow cytometry in comparison with age matched control animals. Results: Here, we identified one population of macrophages and three subsets of cDC (cDC1, cDC2, and a minor cDC subset with migratory properties) in the intestine of lamb and calf by phenotypic and targeted gene expression analyses. Unsupervised single-cell transcriptomic analysis confirmed the identification of these four intestinal MP subpopulations in lamb, while highlighting a deeper diversity of cell subsets among monocytic and dendritic cells. We demonstrated a weak proportion of cDC1 in the intestine of highly susceptible newborn lambs together with an increase of these cells within the first days of life and in response to the infection. Discussion: Considering cDC1 importance for efficient parasite control in the mouse model, one may speculate that the cDC1/cDC2 ratio plays also a key role for the efficient control of C. parvum in young ruminants. In this study, we established the first fine characterization of intestinal MP subsets in young lambs and calves providing new insights for comparative immunology of the intestinal MP system across species and for future investigations on host-Cryptosporidium interactions in target species.

Intra- and interspecies variation and population dynamics of Fasciola gigantica among ruminants in Sudan.

Fasciola gigantica is a widespread parasite that causes neglected disease in livestock worldwide. Its high transmissibility and dispersion are attributed to its ability to infect intermediate snail hosts and adapt to various mammalian definitive hosts. This study investigated the variation and population dynamics of F. gigantica in cattle, sheep, and goats from three states in Sudan. Mitochondrial cytochrome c oxidase subunit I (COI) and NADH dehydrogenase subunit 1 (ND1) genes were sequenced successfully to examine intra and interspecific differences. ND1 exhibited higher diversity than COI, with 15 haplotypes and 10 haplotypes, respectively. Both genes had high haplotype diversity but low nucleotide diversity, with 21 and 11 polymorphic sites for ND1 and COI, respectively. Mismatch distribution analysis and neutrality tests revealed that F. gigantica from different host species was in a state of population expansion. Maximum likelihood phylogenetic trees and median networks revealed that F. gigantica in Sudan and other African countries had host-specific and country-specific lineages for both genes. The study also indicated that F. gigantica-infected small ruminants were evolutionarily distant, suggesting deep and historical interspecies adaptation.

Trematode infection in ruminants and diversity of snail hosts across three agro-ecological zones in Ethiopia.

The occurrence of trematodes among ruminants and their snail vectors is a major concern across various agro-ecological regions of Ethiopia. Trematodes pose significant threats to animals, causing considerable economic losses and impacting public health. In this study, we have investigated 784 ruminant fecal samples, and 520 abattoir samples, alongside the collection and identification of snail vectors from various agro-ecological regions. Fecal examinations revealed Fasciola, Paramphistomum and Schistosoma species infected 20.5% (95% CI: 17.6, 23.8), 11.7% (95% CI: 9.6, 14.2), and 6.3% (95% CI: 4.1, 9.1) of the animals, respectively. The overall prevalence of trematodes among ruminants was 28.8% (95% CI: 25.7, 32.1%), with 6.0% (95% CI: 4.3, 7.7) showing mixed infections. Fasciola was more prevalent in Asela (26%) compared to Batu (19%) and Hawassa (11.5%), while a higher proportion of animals in Batu were infected with Paramphistomum. Schistosoma eggs were detected only in Batu (12.5%), but not in other areas. Sheep and cattle exhibited higher infection rates with Fasciola, Paramphistoma, and Schistosoma compared to goats. Significant associations were observed between trematode infections and risk factors including agro-ecology, animal species, body condition score, and deworming practices. About 20.8% and 22.7% of the slaughtered animals harbored Fasciola and Paramphistomum flukes, respectively, with a higher prevalence in Asela and Hawassa abattoirs compared to Batu abattoir. Additionally, a total of 278 snails were collected from the study areas and identified as lymnae natalensis, lymnae trancatula, Biomphalaria pffiferi, Biomphlaria sudanica, and Bulinus globosus. In conclusion, the study highlights the widespread occurrence of trematode infections, emphasizing the need for feasible control measures to mitigate their economic and public health impacts.

Goat flock abortion: a retrospective study at Abergelle Agricultural Research Center, Tigray, Ethiopia.

BACKGROUND: Small ruminants are the principal component of livestock production in Tigray region, Ethiopia. But their productivity is affected by various factors. According to farmers and expert observation, goat abortion is among the leading causes of production losses in Tanqua-Abergelle district. However, study findings that examine the extent of distribution and economic impact of abortion cases in goats in the district are scarce. This retrospective study investigated the occurrence of abortion and its associated risk factors in three goat breed types at Abergelle Agricultural Research Center goat breeding site over a seven year period. The study included a total of does above one year old, and data were collected from a casebook that was specifically prepared for abortion cases. A thorough follow up was conducted to identify abortion cases. Additionally, a community survey was conducted in selected villages where the research center is located. RESULTS: The overall abortion proportion was 29.8% in the goat farm. Begait goat breeds had the highest abortion proportion (50.9%, CI 0.36-0.64) in 2015/16. Multivariate logistic regression analysis identified year, season, age and breed as major risk factors of abortion occurrence at flock level. Accordingly, the likelihood of goats experiencing abortion during the dry season (proportion = 34) was 1.87 times higher compared to those in the wet season (proportion = 22.8). Begait breeds had a higher incidence of abortion (proportion 37.5%, OR 4.87, CI 2.49-10.35) compared to other breeds. Age was negatively associated with abortion, suggesting that older goats (OR = 0.67) had a higher relative risk than younger goats (OR = 0.57). Moreover, the study noted a high incidence of abortion during the years 2014/15 to 2016/17 (proportion = 35.7-39.7). Within-breed analysis revealed that age and season were significant risk factors for Abergelle and Begait breeds, respectively by using a multivariate logistic regression analysis. A community survey indicated that 89.7% households responded their goats experienced abortion. CONCLUSIONS: This study highlighted the high prevalence of goat abortion at Abergelle and identifies important risk factors associated with its occurrence. The findings can inform targeted interventions to reduce abortion rates and improve goat productivity in the district.

Review: Mechanism, effectiveness, and the prospects of medicinal plants and their bioactive compounds in lowering ruminants' enteric methane emission.

Animal nutritionists continue to investigate new strategies to combat the challenge of methane emissions from ruminants. Medicinal plants (MPs) are known to be beneficial to animal health and exert functional roles in livestock due to their phytogenic compounds with antimicrobial, immunostimulatory, antioxidative, and anti-inflammatory activities. Some MP has been reported to be anti-methanogenic and can effectively lower ruminants' enteric methane emissions. This review overviews trends in MP utilization in ruminants, their bioactivity and their effectiveness in lowering enteric methane production. It highlights the MP regulatory mechanism and the gaps that must be critically addressed to improve its efficacy. MP could reduce enteric methane production by up to 8-50% by regulating the rumen fermentation pathway, directing hydrogen toward propionogenesis, and modifying rumen diversity, structure, and population of the methanogens and protozoa. Yet, factors such as palatability, extraction techniques, and economic implications must be further considered to exploit their potential fully.

Understanding the Diversity and Roles of the Ruminal Microbiome.

The importance of ruminal microbiota in ruminants is emphasized, not only as a special symbiotic relationship with ruminants but also as an interactive and dynamic ecosystem established by the metabolites of various rumen microorganisms. Rumen microbial community is essential for life maintenance and production as they help decompose and utilize fiber that is difficult to digest, supplying about 70% of the energy needed by the host and 60-85% of the amino acids that reach the small intestine. Bacteria are the most abundant in the rumen, but protozoa, which are relatively large, account for 40-50% of the total microorganisms. However, the composition of these ruminal microbiota is not conserved or constant throughout life and is greatly influenced by the host. It is known that the initial colonization of calves immediately after birth is mainly influenced by the mother, and later changes depending on various factors such as diet, age, gender and breed. The initial rumen microbial community contains aerobic and facultative anaerobic bacteria due to the presence of oxygen, but as age increases, a hypoxic environment is created inside the rumen, and anaerobic bacteria become dominant in the rumen microbial community. As calves grow, taxonomic diversity increases, especially as they begin to consume solid food. Understanding the factors affecting the rumen microbial community and their effects and changes can lead to the early development and stabilization of the microbial community through the control of rumen microorganisms, and is expected to ultimately help improve host productivity and efficiency.

A compendium of ruminant gastrointestinal phage genomes revealed a higher proportion of lytic phages than in any other environments.

BACKGROUND: Ruminants are important livestock animals that have a unique digestive system comprising multiple stomach compartments. Despite significant progress in the study of microbiome in the gastrointestinal tract (GIT) sites of ruminants, we still lack an understanding of the viral community of ruminants. Here, we surveyed its viral ecology using 2333 samples from 10 sites along the GIT of 8 ruminant species. RESULTS: We present the Unified Ruminant Phage Catalogue (URPC), a comprehensive survey of phages in the GITs of ruminants including 64,922 non-redundant phage genomes. We characterized the distributions of the phage genomes in different ruminants and GIT sites and found that most phages were organism-specific. We revealed that ~ 60% of the ruminant phages were lytic, which was the highest as compared with those in all other environments and certainly will facilitate their applications in microbial interventions. To further facilitate the future applications of the phages, we also constructed a comprehensive virus-bacteria/archaea interaction network and identified dozens of phages that may have lytic effects on methanogenic archaea. CONCLUSIONS: The URPC dataset represents a useful resource for future microbial interventions to improve ruminant production and ecological environmental qualities. Phages have great potential for controlling pathogenic bacterial/archaeal species and reducing methane emissions. Our findings provide insights into the virome ecology research of the ruminant GIT and offer a starting point for future research on phage therapy in ruminants. Video Abstract.

Epiberberine: a potential rumen microbial urease inhibitor to reduce ammonia release screened by targeting UreG.

Rumen microbial urease inhibitors have been proposed for regulating nitrogen emission and improving nitrogen utilization efficiency in ruminant livestock industry. However, studies on plant-derived natural inhibitors of rumen microbial urease are limited. Urease accessory protein UreG, plays a crucial role in facilitating urease maturation, is a new target for design of urease inhibitor. The objective of this study was to select the potential effective inhibitor of rumen microbial urease from major protoberberine alkaloids in Rhizoma Coptidis by targeting UreG. Our results showed that berberine chloride and epiberberine exerted superior inhibition potential than other alkaloids based on GTPase activity study of UreG. Berberine chloride inhibition of UreG was mixed type, while inhibition kinetics type of epiberberine was uncompetitive. Furthermore, epiberberine was found to be more effective than berberine chloride in inhibiting the combination of nickel towards UreG and inducing changes in the second structure of UreG. Molecular modeling provided the rational structural basis for the higher inhibition potential of epiberberine, amino acid residues in G1 motif and G3 motif of UreG formed interactions with D ring of berberine chloride, while interacted with A ring and D ring of epiberberine. We further demonstrated the efficacy of epiberberine in the ruminal microbial fermentation with low ammonia release and urea degradation. In conclusion, our study clearly indicates that epiberberine is a promising candidate as a safe and effective inhibitor of rumen microbial urease and provides an optimal strategy and suitable feed additive for regulating nitrogen excretion in ruminants in the future. KEY POINTS: • Epiberberine is the most effective inhibitor of rumen urease from Rhizoma Coptidis. • Urease accessory protein UreG is an effective target for design of urease inhibitor. • Epiberberine may be used as natural feed additive to reducing NH3 release in ruminants.

Gastrointestinal anthelmintic plants used on small ruminants in Benin: Traditional use and scientific results - Review.

In Benin, livestock breeders frequently use medicinal plants to treat gastrointestinal diseases in small ruminants. The aim of this review is to list the plants traditionally used in this context and to present the scientific findings on the efficacy of these plants. An extensive search was carried out using PubMed, Scopus, ScienceDirect, Biomed Central and Google Scholar databases to collect data, with combinations of relevant french and english keywords such as "ethnobotanical survey", "anthelmintic properties", "medicinal plants", "gastrointestinal parasites", "digestive strongyles", "Haemonchus", "Trichostrongylus", "small ruminants", "sheep", "goats" and "Benin". A total of 45 published articles met the eligibility criteria. This review listed 123 plants used by breeders to treat gastrointestinal ailments in small ruminants. The most commonly used parts are leaves and barks, and the most common forms are decoction, maceration and powder. Scientific studies have demonstrated the anthelmintic properties of 18 plants, including Zanthoxylum zanthoxyloides, Newbouldia laevis, Mitragyna inermis and Combretum glutinosum. The powders or leaf extracts of these plants showed in vivo significant reductions of over 50% in egg excretion, larval establishment, viability and fertility of gastrointestinal strongyles in small ruminants. Extracts of these plants also revealed in vitro inhibitory activity of over 50% on egg hatching, larval migration and motility of gastrointestinal strongyles. This manuscript highlights the traditional use of anthelmintic plants in small ruminants in Benin and provides scientific results supporting the efficacy of these plants.

Emergence of epizootic hemorrhagic disease in red deer (Cervus elaphus), Spain, 2022.

Epizootic hemorrhagic disease (EHD) virus serotype 8 (EHDV-8) emerged in Spain in autumn 2022. In this study, we aimed to (1) characterize the clinical and lesional presentation of EHDV infection in European red deer (Cervus elaphus), and (2) study the spatial spread of the virus in wild ruminants in Spain after its introduction, in 2022/2023. We confirmed EHDV infection in two clinically compatible sick red deer by PCR and detection of anti-EHDV specific antibodies. EHDV infection occurred in red deer with hyperacute to acute clinical signs and lesions associated to vascular changes leading to death of the animals. Partial sequences of variable segment 2 (VP2) and segment 5 (NS1) genes of the detected viruses had >99% nucleotide identity with EHDV-8 sequences from Tunisia and Italy. In a cross-sectional serological study of EHDV in 592 wild ruminants, mainly red deer (n=578), in southwestern Spain, we detected anti-EHDV antibodies in 37 of 592 samples (6.3%; 95% confidence interval: 4.3-8.2), all from red deer and from the localities where clinical cases of EHD were confirmed in red deer. We conclude that EHDV-8 infection causes severe EHD in European red deer. The serosurvey revealed a limited spread of EHDV-8 in Spanish wild ruminant populations in the first year of virus detection in Spain.

Nucleic acid-extracted torula yeast from the paper industry as a protein feed for ruminants: A comparison with soybean meal.

We compared nucleic acid-extracted torula yeast (NTY) with soybean meal (SBM) to evaluate NTY as a potential protein feed for ruminants in a metabolic trial using four castrated male goats. NTY was replaced isonitrogenously with SBM at a 25% crude protein (CP) level on a dry matter (DM) basis. NTY has 55% CP and 74% total digestive nutrients on DM. Absorbed N was lower on the NTY diet, but since the urinary N excretion was lower on the NTY diet, no significant between-diet difference in retained N was observed. The efficiency of N utilization (retained N/absorbed N) was significantly higher on the NTY diet. The Lys and Met contents (presumed limiting amino acids for dairy cattle) were higher in NTY than SBM, which may be why N utilization efficiency was higher for the NTY diet. Ruminal ammonia-N and blood serum N were lower on the NTY diet, suggesting that NTY has more rumen undegradable protein than SBM. There was no significant between-diet difference in the visceral disorder indicators or antioxidant activities. Our results indicate that NTY is a safe protein feed with a high CP ratio and high-quality amino acid profile for ruminants that is equivalent to SBM.

Validation of deep amplicon sequencing of Dicrocoelium in small ruminants from Northern regions of Pakistan.

Dicrocoelium lancet flukes cause significant production loss in ruminant livestock. Although co-infection with multiple Dicrocoelium species within a host is common, techniques for studying the composition of these complex parasite communities are lacking. The pathogenicity, epidemiology, and therapeutic susceptibility of different helminth species vary, and little is known about the interactions that take place between co-infecting species and their hosts. Here, we describe the first applicationof metabarcoding deep amplicon sequencing method to studythe Dicrocoelium species in sheep and goats. First, rDNA ITS-2 sequences of four Dicrocoelium species (Dicrocoelium dendriticum, Dicrocoelium hospes, Dicrocoelium orientalis, and Dicrocoelium chinensis) were extracted from the NCBI public database. Phylogenetic analysis revealed separate clades of Dicrocoelium species; hence, molecular differentiation between each species is possible in co-infections. Second, 202 flukes belonging to seventeen host populations (morphologically verified as belonging to the Dicrocoelium genus) were evaluated to determine the deep amplicon sequencing read threshold of an individual fluke for each of the four species. The accuracy of the method in proportional quantification of samples collected from single hosts was further assessed. Overall, 198 (98.01%) flukes were confirmed as D. dendriticum and 1.98% produced no reads. The comparison of genetic distances between rDNA ITS-2 revealed 86% to 98% identity between the Dicrocoelium species. Phylogenetic analysis demonstrated a distinct clustering of species, apart from D. orientalis and D. chinensis, which sit very close to each other in a single large clade whereas D. hospes and D. dendriticum are separated into their own clade. In conclusion each sample was identified as D. dendriticum based on the proportion of MiSeq reads and validated the presence of this group of parasites in the Gilgit Baltistan and Khyber Pakhtunkhwa provinces of Pakistan. The metabarcoding deep amplicon sequencing technology and bioinformatics pathway have several potential applications, including species interactions during co-infections, identifying the host and geographical distribution of Dicrocoelium in livestock, drug therapy response evaluation and understanding of the emergence and spread of drug resistance.

Snow avalanches are a primary climate-linked driver of mountain ungulate populations.

Snow is a major, climate-sensitive feature of the Earth's surface and catalyst of fundamentally important ecosystem processes. Understanding how snow influences sentinel species in rapidly changing mountain ecosystems is particularly critical. Whereas effects of snow on food availability, energy expenditure, and predation are well documented, we report how avalanches exert major impacts on an ecologically significant mountain ungulate - the coastal Alaskan mountain goat (Oreamnos americanus). Using long-term GPS data and field observations across four populations (421 individuals over 17 years), we show that avalanches caused 23-65% of all mortality, depending on area. Deaths varied seasonally and were directly linked to spatial movement patterns and avalanche terrain use. Population-level avalanche mortality, 61% of which comprised reproductively important prime-aged individuals, averaged 8% annually and exceeded 22% when avalanche conditions were severe. Our findings reveal a widespread but previously undescribed pathway by which snow can elicit major population-level impacts and shape demographic characteristics of slow-growing populations of mountain-adapted animals.

Global and regional seroprevalence of coxiellosis in small ruminants: A systematic review and meta-analysis.

BACKGROUND: Coxiellosis is a neglected zoonosis for occupationally exposed people in many parts of the world. Sheep and goats are two important small ruminants that act as reservoirs for human contamination; however, there is a lack of comprehensive data on the epidemiological aspects of coxiellosis in sheep and goats at regional and global levels. The aim of this study was to systematically review the available articles on seroprevalence of coxiellosis in sheep and goats and estimate the overall seroprevalence in different regions. METHODS: A systematic search strategy was performed in five electronic repositories for articles published until December 2021. Relevant data were extracted from the selected articles based on the inclusion criteria. A random effect meta-analysis model was used to analyse the data. Results are presented as the prevalence of seropositivity as a percentage and 95% confidence intervals. RESULTS: The global pooled seroprevalence of coxiellosis in sheep was 17.38% (95% confidence interval [CI]: 15.59%-19.17%). Overall, the regional level pooled prevalence estimates in sheep ranged from 15.04% (95% CI: 7.68%-22.40%) to 19.14% (95% CI: 15.51%-22.77%), depending on region. The global pooled seroprevalence of coxiellosis in goats was 22.60% (95% CI: 19.54%-25.66%). Overall, the regional level pooled prevalence estimates in goats ranged from 6.33% (95% CI: 2.96%-9.71%) to 55.13% (95% CI: 49.61%-60.65%), depending on the region. The prevalence estimates also varied significantly in both sheep and goats depending on age, sex, and rearing systems of the animals (p < 0.001). CONCLUSION: Seroprevalence of coxiellosis in both sheep and goats is considerable. Routine monitoring of the sheep and goat populations is needed to prevent spillover infection in other livestock and humans.

Animal Exposure Model for Mapping Crimean-Congo Hemorrhagic Fever Virus Emergence Risk.

To estimate the determinants of spatial variation in Crimean-Congo hemorrhagic fever virus (CCHFV) transmission and to create a risk map as a preventive public health tool, we designed a survey of small domestic ruminants in Andalusia, Spain. To assess CCHFV exposure spatial distribution, we analyzed serum from 2,440 sheep and goats by using a double-antigen ELISA and modeled exposure probability with environmental predictors by using generalized linear mixed models. CCHFV antibodies detected in 84 samples confirmed low CCHFV prevalence in small domestic ruminants in the region. The best-fitted statistical model indicated that the most significant predictors of virus exposure risk were cattle/horse density and the normalized difference vegetation index. Model validation showed 99.7% specificity and 10.2% sensitivity for identifying CCHFV circulation areas. To map CCHFV exposure risk, we projected the model at a 1 × 1-km spatial resolution. Our study provides insight into CCHFV ecology that is useful for preventing virus transmission.

Future prediction of biogas potential and CH4 emission with boosting algorithms: the case of cattle, small ruminant, and poultry manure from Turkey.

Animal waste can be converted into a renewable energy source using biogas technology. This process has an impact on greenhouse gas emissions and is a sustainable source of energy for countries. It can reduce the effects of climate change and protect the planet for future generations. Tier1 and tier2 approaches are commonly used in the literature to calculate emissions factors. With boosting algorithms, this study estimated each animal category's biogas potential and CH4 emissions (tier1 and tier2 approach) for 2004-2021 in all of Turkey's provinces. Two different scenarios were created in the study. For scenario-1, the years 2020-2021 were predicted using data from 2004 to 2019, while for scenario-2, the years 2022-2024 were predicted using data from 2004 to 2021. According to the scenario-1 analysis, the eXtreme Gradient Boosting Regressor (XGBR) algorithm was the most successful algorithm with an R2 of 0.9883 for animal-based biogas prediction and 0.9835 and 0.9773 for animal-based CH4 emission predictions (tier1 and tier2 approaches) for the years 2020-2021. When the mean absolute percentage error was evaluated, it was found to be relatively low at 0.46%, 1.07%, and 2.78%, respectively. According to the scenario-2 analysis, the XGBR algorithm predicted the log10 values of the animal-based biogas potential of five major cities in Turkey for the year 2024, with 11.279 for Istanbul, 12.055 for Ankara, 12.309 for Izmir, 11.869 for Bursa, and 12.866 for Antalya. In the estimation of log10 values of CH4 emission, the tier1 approach yielded estimates of 3.080, 3.652, 3.929, 3.411, and 3.321, respectively, while the tier2 approach yielded estimates of 1.810, 2.806, 2.757, 2.552 and 2.122, respectively.

Initial diet shapes resistance-gene composition and fecal microbiome dynamics in young ruminants during nursing.

This study was conducted to examine how colostrum pasteurization affects resistance genes and microbial communities in calf feces. Forty female Holstein calves were randomly assigned to either the control (CON) group, which received unheated colostrum, or the pasteurized colostrum (PAT) group. The calves body weight was measured weekly before morning feeding. Calf starter intake were measured and recorded daily before morning feeding. Samples of colostrum were collected before feeding. Blood was collected on d 1 and 70 before morning feeding. Ten calves were randomly selected from each group (n = 20 calves total) for fecal sampling on d 3, 28, 56 and 70 for subsequent DNA extraction and metagenomic sequencing. Total bacterial counts in the colostrum were markedly higher in the CON group than in the PAT group. Pasteurized colostrum administration substantially reduced the ARO diversity and diminishes the abundance of Enterobacteriaceae, thereby decreasing their contribution to resistance genes. Pasteurization also reduced glucoside hydrolase-66 activity in 3-day-old calves which led to an increase in the activity of aminoglycoside antibiotics, resulting in 52.63 % of PAT-enriched bacteria acquiring aminoglycoside resistance genes. However, from the perspective of overall microbial community, the proportion of aminoglycoside, beta-lactam and tetracycline resistance genes carried by microbial community in PAT group was lower than CON group (P < 0.05). Fecal samples from the PAT group contained greater abundances of Subdoligranulum (P < 0.05) and Lachnospiraceae_NK4A136_group (P < 0.05) on days 28 and 70 compared to CON. Network analysis and abundance variations of the different bacteria obtained by linear discriminant analysis effect size analysis showed that pasteurized colostrum feeding reduced the interactions among related bacteria and maintained stability of the hind-gut microbiome. In conclusion, these findings underscore the intricate interactions between early diet, calf resistance-gene transmission and microbial dynamics, which should be carefully considered in calf-rearing practices.

Epidemiological Analyses of the First Incursion of the Epizootic Hemorrhagic Disease Virus Serotype 8 in Tunisia, 2021-2022.

Epizootic hemorrhagic disease (EHD) is a non-contagious arthropod-transmitted viral disease and a World Organization for Animal Health (WOAH)-listed disease of domestic and wild ruminants since 2008. EHDV is transmitted among susceptible animals by a few species of midges of genus Culicoides. During the fall of 2021, a large outbreak caused by the epizootic hemorrhagic disease virus (EHDV), identified as serotype 8, was reported in Tunisian dairy and beef farms with Bluetongue virus (BTV)-like clinical signs. The disease was detected later in the south of Italy, in Spain, in Portugal and, more recently, in France, where it caused severe infections in cattle. This was the first evidence of EHDV-8 circulation outside Australia since 1982. In this study, we analyzed the epidemiological situation of the 2021-2022 EHDV outbreaks reported in Tunisia, providing a detailed description of the spatiotemporal evolution of the disease. We attempted to identify the eco-climatic factors associated with infected areas using generalized linear models (GLMs). Our results demonstrated that environmental factors mostly associated with the presence of C. imicola, such as digital elevation model (DEM), slope, normalized difference vegetation index (NDVI), and night-time land surface temperature (NLST)) were by far the most explanatory variables for EHD repartition cases in Tunisia that may have consequences in neighboring countries, both in Africa and Europe through the spread of infected vectors. The risk maps elaborated could be useful for disease control and prevention strategies.