Swine Research Articles

Domestic pig husbandry strategy during the Shuangdun Culture period (ca. 7300–6800 BP) from the stable isotopic perspective: A case study of the Yuhuicun site in Anhui Province, China

Shuangdun Culture, spanning from about 7300 to 6800 BP, was primarily distributed along the middle Huai River valley. This study aimed to elucidate the domestic pig husbandry strategy of Shuangdun Culture using stable carbon and nitrogen isotopes on animal bones from the Yuhuicun site. The results revealed that most of the Sus, displaying δ13C values from −20.5 to −17.1‰, had diets based on C3 plants, comparable to the diets of large and middle-sized deer whose δ13C values ranged from −20.7 to −18.1‰. Previous zooarchaeological investigations have suggested that domestic pigs were predominant among the faunal assemblage of the Yuhuicun site, with few wild boars and feral pigs present. However, the present study found no significant differences regarding the diet among the Sus population. Domestic pigs at Yuhuicun were inferred to be reared loosely and fed with wild plants, given that the human inhabitants primarily relied on gathering, with rice cultivation being small in scale. A comparison of pig husbandry strategies among the Yuhuicun, Houjiazhai, and Shuangdun sites revealed that most Sus from these three archaeological sites had similar diets. However, three Sus individuals with mixed diets of C3 and C4 plants were identified from the Shuangdun site, which may have been introduced from an outside area where millets were widely planted. The Shuangdun site is a central settlement in the middle Huai River valley, and its inhabitants likely had access to introduced food sources. This differentiation in the diet of domestic pigs is indicative of varying settlement patterns during this time period.

Brincidofovir Effectively Inhibits Proliferation of Pseudorabies Virus by Disrupting Viral Replication.

Pseudorabies is an acute and febrile infectious disease caused by pseudorabies virus (PRV), a member of the family Herpesviridae. Currently, PRV is predominantly endemoepidemic and has caused significant economic losses among domestic pigs. Other animals have been proven to be susceptible to PRV, with a mortality rate of 100%. In addition, 30 human cases of PRV infection have been reported in China since 2017, and all patients have shown severe neurological symptoms and eventually died or developed various neurological sequelae. In these cases, broad-spectrum anti-herpesvirus drugs and integrated treatments were mostly applied. However, the inhibitory effect of the commonly used anti-herpesvirus drugs (e.g., acyclovir, etc.) against PRV were evaluated and found to be limited in this study. It is therefore urgent and important to develop drugs that are clinically effective against PRV infection. Here, we constructed a high-throughput method for screening antiviral drugs based on fluorescence-tagged PRV strains and multi-modal microplate readers that detect fluorescence intensity to account for virus proliferation. A total of 2104 small molecule drugs approved by the U.S. Food and Drug Administration (FDA) were studied and validated by applying this screening model, and 104 drugs providing more than 75% inhibition of fluorescence intensity were selected. Furthermore, 10 drugs that could significantly inhibit PRV proliferation in vitro were strictly identified based on their cytopathic effects, virus titer, and viral gene expression, etc. Based on the determined 50% cytotoxic concentration (CC50) and 50% inhibitory concentration (IC50), the selectivity index (SI) was calculated to be 26.3-3937.2 for these 10 drugs, indicating excellent drugability. The antiviral effects of the 10 drugs were then assessed in a mouse model. It was found that 10 mg/kg brincidofovir administered continuously for 5 days provided 100% protection in mice challenged with lethal doses of the human-origin PRV strain hSD-1/2019. Brincidofovir significantly attenuated symptoms and pathological changes in infected mice. Additionally, time-of-addition experiments confirmed that brincidofovir inhibited the proliferation of PRV mainly by interfering with the viral replication stage. Therefore, this study confirms that brincidofovir can significantly inhibit PRV both in vitro and in vivo and is expected to be an effective drug candidate for the clinical treatment of PRV infections.

Contrasting PRRSV temporal lineage patterns at the individual farm, production system, and regional levels in Ohio and neighboring states from 2017 to 2021

Porcine reproductive and respiratory virus (PRRSV), one of the most significant viruses in the swine industry, has been challenging to control due to its high mutation and recombination rates and complexity. This retrospective study aimed to describe and compare the distribution of PRRSV lineages obtained at the individual farm, production system, and regional levels. PRRSV-2 (type 2) sequences (n = 482) identified between 2017 – 2021 were provided by a regional state laboratory (Ohio Department of Agriculture, Animal Disease Diagnostic Center (ODA-ADDL)) collected from swine farms in Ohio and neighboring states, including Indiana, Michigan, Pennsylvania, and West Virginia. Additional sequences (n = 138) were provided by one collaborating swine production system. The MUSCLE algorithm on Geneious Prime® was used to align the ORF5 region of PRRSV-2 sequences along with PRRSV live attenuated vaccine strains (n = 6) and lineage anchors (n = 169). Sequenced PRRSV-2 were assigned to the most identical lineage anchors/vaccine strains. Among all sequences (n = 620), 29.8% (185/620) were ≥ 98.0% identity with the vaccine strains, where 93.5% (173/185) and 6.5% (12/185) were identical with the L5 Ingelvac PRRS® MLV and L8 Fostera® PRRS vaccine strains, respectively, and excluded from the analysis. At the regional level across five years, the top five most identified lineages included L1A, L5, L1H, L1C, and L8. Among non-vaccine sequences with production system known, L1A sequences were mostly identified (64.3% – 100.0%) in five systems, followed by L1H (0.0% - 28.6%), L1C (0.0% – 10.5%), L5 (0.0% – 14.4%), L8 (0.0% – 1.3%), and L1F (0.0% – 0.5%). Furthermore, among non-vaccine sequences with the premise identification available (n = 262), the majority of sequences from five individual farms were either classified into L1A or L5. L1A and L5 sequences coexisted in three farms, while samples submitted by one farm contained L1A, L1H, and L5 sequences. Additionally, the lineage classification results of non-vaccine sequences were associated with their restriction fragment length polymorphism (RFLP) patterns (Fisher’s exact test, p < 0.05). Overall, our results show that individual farm and production system-level PRRSV-2 lineage patterns do not necessarily correspond to regional-level patterns, highlighting the influence of individual farms and systems in shaping PRRSV occurrence within those levels, and highlighting the crucial goal of within-farm and system monitoring and early detection for accurate knowledge on PRRSV-2 lineage occurrence and emergence.

Risk factors for African swine fever spread in wild boar in the Russian Federation

The analysis and assessment of risk factors associated with the occurrence, spread and persistence of African swine fever (ASF) virus in wild boar population are an important tool in determining the strategic measures aimed at eradicating epizootics and mitigating their consequences. A thorough examination of foreign and domestic literature revealed that wild boar population management factors, socio-economic and environmental ones, that mainly account for the density and number of animals were the most significant and associated with the risk of ASF outbreak occurrence in wild animals. In order to identify risk factors for the spread of the disease in wild boar in the Russian Federation Subjects, a regression model was built to examine the relationship between the annual number of ASF outbreaks in wild boar at the municipal raion level, wild boar population density and some other factors for the period between 2007 and 2022. Based on the Subject-level regression modelling results, a positive association between the intensity of the disease outbreaks and wild boar population density was identified in 42.5% of the model regions of the Russian Federation. Other significant factors were the length of roads, the presence of forest cover and outbreaks in domestic pigs. However, on the whole, for all the infected Subjects, the regression model demonstrated the failure of the wild boar population density factor to explain the observed ASF outbreak distribution, and this may be indicative of the existence of other epizootic drivers of the disease spread in the wild. One of such mechanisms may be the persistence of infectious potential in the external environment and in the formed stationary local foci of African swine fever, despite the anti-epizootic measures taken, including the measures aimed at regulating the number of susceptible population – depopulation.

Strategies for Transboundary Swine Disease Management in Asian Islands: Foot and Mouth Disease, Classical Swine Fever, and African Swine Fever in Taiwan, Japan, and the Philippines.

Swine transboundary diseases pose significant challenges in East and Southeast Asia, affecting Taiwan, Japan, and the Philippines. This review delves into strategies employed by these islands over the past two decades to prevent or manage foot and mouth disease (FMD), classical swine fever (CSF), and African swine fever (ASF) in domestic pigs and wild boars. Despite socio-economic differences, these islands share geographical and climatic commonalities, influencing their thriving swine industries. Focusing on FMD eradication, this study unveils Taiwan's success through mass vaccination, Japan's post-eradication surveillance, and the Philippines' zoning strategy. Insights into CSF in Japan emphasize the importance of wild boar control, whereas the ASF section highlights the multifaceted approach implemented through the Philippine National ASF Prevention and Control Program. This review underscores lessons learned from gained experiences, contributing to a comprehensive understanding of swine disease management in the region.

Novel Phytogenics’ Impact on Weaned Pigs’ Growth Performance, Heamatology and Serum Biochemical Indicators

This experiment was carried out to investigate a novel phytogenics’ (PCCPR) an acronym for (peppermint, celery, coriander, parsley and rosemary leaf meal mixture) impact on weaned pigs’ performance, heamato-biochemical indicators. A total of forty cross bred weaned male pigs (Large white × Landrace) with an initial body weight of 7.33 ± 0.38 weaned at 28 days of age were individually housed in an open sided pen were randomly divided into four treatment group of six pigs each. Basal diet were adequate in all nutrients (NRC, 2012). The animals were fed as follows; basal diet with antibiotics (neomycin – 1.5 g/kg) in treatment one, treatment two, three and four were fed basal diet supplemented with PCCPR at 5 g, 10 g and 15 g/kg respectively. The experiment lasted for two months and all necessary management practices were observed. Average daily weight gain and average daily feed intake were similar in diet three and four compared to the other groups (P˂0.05). Dietary supplementation of PCCPR resulted in a numerical increase in pack cell volume, haemoglobin and red blood cell, white blood cell and its differentials (monocytes, eosinophils, basophils and leucocytes) and a remarkable improvement in mean corpuscular volume mean corpuscular haemoglobin and mean corpuscular haemoglobin concentrations. All the serum biochemical parameters were significantly affected by the treatments (P˂0.05). However, all values were within the normal physiological range for healthy pigs. It was concluded that the use of PCCPR up to 15 g/kg could boost swine productivity at weaned stage without causing any negative impact on the health status of animals.

Simultaneous Detection of Antigen and Antibodies of African Swine Fever in a Novel Combo Lateral Flow Assay.

African swine fever (ASF) is a contagious disease of wild boar and domestic pigs notifiable to the World Organisation for Animal Health due to its high socio-economic impact. ASF is caused by the complex ASF virus (ASFV), and it can present different clinical manifestations that can be confused with other diseases; for this reason, laboratory testing is necessary for the proper diagnosis of clinically suspected animals. Despite the efforts put into it over decades, no treatment or safe vaccine is globally available, and disease control is based on early diagnosis and the implementation of strict biosecurity measures. In this context, rapid tests have the potential to accelerate and facilitate the identification of infected animals by giving fast on-site results. In this work, we improved the available point-of-care assays for the diagnosis of the disease by the development of a more specific antigen test and a more sensitive antibody test. This antibody detection test allowed for the earlier detection of infected animals than two commercial indirect ELISAs (statistically significant). Moreover, we developed a combined dual rapid test, unifying, in the same cassette, an antigen detection strip and an antibody detection strip. In this study, we confirmed that this combo approach is a useful tool for implementing rapid tests in the field since it increases the percentage of positive samples detected, even when PCR turns negative, while maintaining a good specificity.

Near-complete genome sequences of multiple genotype 1 African swine fever virus isolates from 2016 to 2018 in Cameroon.

African swine fever virus has been endemic in Cameroon since 1982. Here, we announce the sequences of Cameroon/2016/C1, Cameroon/2016/C5, Cameroon/2017/C-A2, Cameroon/2018/C02, and Cameroon/2018/CF3, five genotype 1 African swine fever virus genomes collected from domestic pigs between 2016 and 2018.

Approaching the complexity of Crimean-Congo hemorrhagic fever virus serology: A study in swine

Crimean-Congo hemorrhagic fever virus (CCHFV) is a tick-borne zoonotic orthonairovirus of public health concern and widespread geographic distribution. Several animal species are known to seroconvert after infection with CCHFV without showing clinical symptoms. The commercial availability of a multi-species ELISA has led to an increase in recent serosurveillance studies as well as in the range of species reported to be exposed to CCHFV in the field, including wild boar (Sus scrofa). However, development and validation of confirmatory serological tests for swine based on different CCHFV antigens or test principles are hampered by the lack of defined control sera from infected and non-infected animals. For the detection of anti-CCHFV antibodies in swine, we established a swine-specific in-house ELISA using a panel of swine sera from CCHFV-free regions and regions with reported CCHFV circulation. We initially screened more than 700 serum samples from wild boar and domestic pigs and observed a correlation of ≃67% between the commercial and the in-house test. From these sera, we selected a panel of 60 samples that were further analyzed in a newly established indirect immunofluorescence assay (iIFA) and virus neutralization test. ELISA-non-reactive samples tested negative. Interestingly, only a subset of samples reactive in both ELISA and iIFA displayed CCHFV-neutralizing antibodies. The observed partial discrepancy between the tests may be explained by different test sensitivities, antibody cross-reactivities or suggests that the immune response to CCHFV in swine is not necessarily associated with eliciting neutralizing antibodies. Overall, this study highlights that meaningful CCHFV serology in swine, and possibly other species, should involve the performance of multiple tests and careful interpretation of the results.

Dynamics of bone mineralization in primiparous sows as a function of dietary phosphorus and calcium during lactation

To maximize the efficiency of dietary P utilization in swine production, understanding the mechanisms of P utilization in lactating sows is relevant due to their high P requirement and the resulting high inorganic P intake. Gaining a better knowledge of the Ca and P quantities that can be mobilized from bones during lactation, and subsequently replenished during the following gestation, would enable the development of more accurate P requirements incorporating this process of bone dynamics. The objective was to measure the amount of body mineral reserves mobilized during lactation, depending on dietary digestible P and phytase addition and to measure the amount recovered during the following gestation. Body composition of 24 primiparous sows was measured by dual-energy x-ray absorptiometry 2, 14, 26, 70 and 110 days after farrowing. Four lactation diets were formulated to cover nutritional requirements, with the exception of Ca and digestible P: 100% (Lact100; 9.9 g Ca and 3.0 g digestible P/kg), 75% (Lact75), 50% without added phytase (Lact50) and 50% with added phytase (Lact50 + FTU). The gestation diet was formulated to cover the nutritional requirements of Ca and digestible P (8.2 g Ca and 2.6 g digestible P/kg). During the 26 days of lactation, each sow mobilized body mineral reserves. The mean amount of mobilized bone mineral content (BMC) was 664 g, representing 240 g Ca and 113 g P. At weaning, the BMC (g/kg of BW) of Lact50 sows tended to be lower than Lact100 sows (−12.8%, linear Ca and P effect × quadratic time effect) while the BMC of Lact50 + FTU sows remained similar to that of Lact100 sows. During the following gestation, BMC returned to similar values among treatments. Therefore, the sows fed Lact50 could recover from the higher bone mineral mobilization that occurred during lactation. The P excretion was reduced by 40 and 43% in sows fed Lact50 and Lact50 + FTU, respectively, relative to sows fed Lact100. In conclusion, the quantified changes in body composition during the lactation and following gestation of primiparous sows show that bone mineral reserves were mobilized and recovered and that its degree was dependent on the dietary P content and from phytase supplementation during lactation. In the future, considering this potential of the sows’ bone mineralization dynamics within the factorial assessment of P requirement and considering the digestible P equivalency of microbial phytase could greatly limit the dietary use of inorganic phosphates and, thus, reduce P excretion.

Wild boar (Sus scrofa) carcasses as an attraction for scavengers and a potential source for soil contamination with the African swine fever virus.

The wild boar (Sus scrofa) is a social animal species native to Eurasia. During the last decade, the wild boar population in Estonia has been severely affected by the African swine fever virus (ASFV), which has also affected domestic pig farming. The potential transmission routes of ASFV remain unclear and are currently under intensive investigation. This pilot study aimed to clarify the frequency and characteristics of contacts between living wild boars and the carcasses of their conspecifics, which could play a role in the transmission of ASFV. Wild animals' contact and scavenging behavior on wild boar carcasses were studied using trail cameras in an experimental setting on Hiiumaa, Western Estonia. Four legally hunted carcasses were used in the present study. This study aimed to determine whether intraspecies scavenging occurs in wild boars. The persistence of ASFV DNA in soil contaminated with infected wild boar carcasses was investigated separately. Among the 17 identified wildlife species that visited wild boar carcasses, the common raven (Corvus corax) was the most frequent one (37.26%), followed by raccoon dogs (Nyctereutes procyonoides; 4.25%), carcass conspecific/wild boars (3.16%), and red foxes (Vulpes vulpes; 2.14%). Regarding the direct contact with the carcass, the same species ranking was detected: common raven (74.95%), raccoon dogs (9.94%), wild boars (4.21%), and red foxes (4.21%). No clear signs of cannibalism were noted among the wild boars, although brief physical contact with the carcasses was evident. The persistence of ASFV DNA in soil contaminated by infected wild boar carcasses was investigated separately. This study revealed that ASFV DNA from infected carcasses could be detected in forest soil for prolonged periods, even after removing the carcasses. Hence, the carcasses of infected wild boars may play an important role in spreading the African swine fever virus in wild boar populations; thus, prompt removal and disinfection of the soil could be considered necessary to limit the spread of the infection.

Disease Course of Korean African Swine Fever Virus in Domestic Pigs Exposed Intraorally, Intranasally, Intramuscularly, and by Direct Contact with Infected Pigs.

African swine fever (ASF) is a fatal contagious disease affecting swine. The first Korean ASF virus (ASFV) isolate (Korea/Pig/Paju1/2019) was used to compare the disease course of ASFV in pigs inoculated via the four routes. In the challenge experiment, domestic pigs were infected via the intraoral (IO) and intranasal (IN) routes with a 106 50% hemadsorbing dose (HAD50) and an intramuscular (IM) injection of 103 HAD50. In the direct contact (DC) group, five naïve pigs were brought into direct contact with two IM-ASFV-infected pigs. IO-, IN-, and IM-inoculated pigs showed similar disease courses, whereas DC pigs had comparable ASF syndrome after a 7-day latent period. The disease course in the DC route, one of the most common routes of infection, was not significantly different from that in the IO and IN routes. IM and DC groups differed in terms of the severity of fever and hemorrhagic lesions in the lymph nodes and spleen, indicating that the IM route, suitable for early vaccine development trials, is not appropriate for studying the ASFV infection mechanism, including early stage of infection, and IO and IN challenges with a designated dose can be alternatives in trials for assessing ASFV pathogenicity and vaccine efficacy investigations.

Biosecurity measures for the prevention of African swine fever on German pig farms: comparison of farmers’ own appraisals and external veterinary experts’ evaluations

BackgroundSince its first introduction into the German wild boar population in 2020, African swine fever (ASF) has been spreading slowly from the eastern border westwards and has been introduced into eight domestic pig farms thus far. The European Food Safety Authority has named deficits in farm biosecurity and increased human activity as major risk factors for the introduction of the ASF virus into pig farms. Studies have shown that pig farms in Germany generally have a high level of biosecurity. However, veterinary practitioners and policy-makers have expressed concerns that not all pig farmers are appropriately prepared to deal with the threat of ASF. This study aimed to evaluate the level of biosecurity on pig farms in Lower Saxony and explore the reasons for deficits in the implementation of biosecurity measures. For this purpose, pig farmers were interviewed in open structured face-to-face interviews about their perception of ASF and biosecurity, and the implemented measures on their farms were assessed with a checklist. In the data analysis, the farmers’ answers and the results of the biosecurity check were compared to gain further insights into the factors influencing the implementation of biosecurity measures on the farms.ResultsThe biosecurity check showed that on most farms, a high level of biosecurity had been implemented. Nevertheless, deficits were found concerning the fences and the delimitation of clean and dirty areas on farm grounds and in the anteroom. Overall, the farmers were well informed about ASF and had a realistic perception of their own biosecurity. They considered the farm layout, financial means and practicality of hygiene measures to be the main barriers to implementing biosecurity measures against ASF. However, the results also suggested that farmers’ attitudes and legal regulations were major influencing factors.ConclusionThe results indicated a high level of biosecurity against ASF on most pig farms and a realistic perception of their own biosecurity by the farmers. Current knowledge transfer and information should focus on building upon the farmers’ own motivation and expertise and supporting them to put existing knowledge into practice.

The horizontal ladder test (HLT) protocol: a novel, optimized, and reliable means of assessing motor coordination in Sus scrofa domesticus.

Pigs can be an important model for preclinical biological research, including neurological diseases such as Alcohol Use Disorder. Such research often involves longitudinal assessment of changes in motor coordination as the disease or disorder progresses. Current motor coordination tests in pigs are derived from behavioral assessments in rodents and lack critical aspects of face and construct validity. While such tests may permit for the comparison of experimental results to rodents, a lack of validation studies of such tests in the pig itself may preclude the drawing of meaningful conclusions. To address this knowledge gap, an apparatus modeled after a horizontally placed ladder and where the height of the rungs could be adjusted was developed. The protocol that was employed within the apparatus mimicked the walk and turn test of the human standardized field sobriety test. Here, five Sinclair miniature pigs were trained to cross the horizontally placed ladder, starting at a rung height of six inches and decreasing to three inches in one-inch increments. It was demonstrated that pigs can reliably learn to cross the ladder, with few errors, under baseline/unimpaired conditions. These animals were then involved in a voluntary consumption of ethanol study where animals were longitudinally evaluated for motor coordination changes at baseline, 2.5, 5, 7.5, and 10% ethanol concentrations subsequently to consuming ethanol. Consistent with our predictions, relative to baseline performance, motor incoordination increased as voluntary consumption of escalating concentrations of ethanol increased. Together these data highlight that the horizontal ladder test (HLT) test protocol is a novel, optimized and reliable test for evaluating motor coordination as well as changes in motor coordination in pigs.

Performance evaluation and application of host-specific Bacteroidales and mitochondrial DNA markers to identify sources of fecal contamination in river water in Japan

Microbial source tracking (MST) using host-specific Bacteroidales and mitochondrial DNA (mtDNA) markers is an efficient tool to identify the sources of fecal contamination in environmental water. This study evaluated and updated the previously reported performances of seven host-specific Bacteroidales markers (three human-, two cattle-, and two pig-specific). Additionally, the performance of a cattle-specific Bovine mtDNA and a pig-specific Swine mtDNA marker were evaluated and then applied to MST of river water samples collected in Yamanashi Prefecture, Japan. We collected 48 fecal-source samples, including raw sewage, secondary-treated sewage, an effluent of a domestic wastewater treatment tank, pig feces, pig wastewater, and cattle feces, which were quantitatively analyzed using host-specific Bacteroidales and mtDNA markers. BacHum and gyrB markers (human-specific), BacR and Bovine mtDNA markers (cattle-specific), and Pig2Bac and Swine mtDNA markers (pig-specific) were judged the best-performing markers. Then, these selected markers were applied to MST to identify the sources of fecal contamination in 59 river water samples collected at 21 sites. Of them, 20 (95%), 21 (100%), and 16 (76%) sites were positive for at least one human, cattle, and pig marker, respectively, indicating the need for immediate action and monitoring to control fecal pollution.

The role of vehicle movement in swine disease dissemination: Novel method accounting for pathogen stability and vehicle cleaning effectiveness uncertainties

SummarySeveral propagation routes drive animal disease dissemination, and among these routes, contaminated vehicles traveling between farms have been associated with indirect disease transmission. In this study, we used near-real-time vehicle movement data and vehicle cleaning efficacy to reconstruct the between-farm dissemination of the African swine fever virus (ASFV). We collected one year of Global Positioning System data of 823 vehicles transporting feed, pigs, and people to 6363 swine production farms in two regions in the U.S. Without cleaning, vehicles connected up to 2157 farms in region one and 437 farms in region two. Individually, in region one vehicles transporting feed connected 2151 farms, pigs to farms 2089 farms, pigs to market 1507 farms, undefined vehicles 1760 farm, and personnel three farms. The simulation results indicated that the contact networks were reduced the most for crew transport vehicles with a 66% reduction, followed by vehicles carrying pigs to market and farms, with reductions of 43% and 26%, respectively, when 100% cleaning efficacy was achieved. The results of this study showed that even when vehicle cleaning and disinfection are 100% effective, vehicles are still connected to numerous farms. This emphasizes the importance of better understanding transmission risks posed by vehicles to the swine industry and regulatory agencies.

Genomics-based analysis of four porcine-derived lactic acid bacteria strains and their evaluation as potential probiotics.

The search for probiotics and exploration of their functions are crucial for livestock farming. Recently, porcine-derived lactic acid bacteria (LAB) have shown great potential as probiotics. However, research on the evaluation of porcine-derived LAB as potential probiotics through genomics-based analysis is relatively limited. The present study analyzed four porcine-derived LAB strains (Lactobacillus johnsonii L16, Latilactobacillus curvatus ZHA1, Ligilactobacillus salivarius ZSA5 and Ligilactobacillus animalis ZSB1) using genomic techniques and combined with in vitro tests to evaluate their potential as probiotics. The genome sizes of the four strains ranged from 1,897,301bp to 2,318,470bp with the GC contents from 33.03 to 41.97%. Pan-genomic analysis and collinearity analysis indicated differences among the genomes of four strains. Carbohydrate active enzymes analysis revealed that L. johnsonii L16 encoded more carbohydrate active enzymes than other strains. KEGG pathway analysis and in vitro tests confirmed that L. johnsonii L16 could utilize a wide range of carbohydrates and had good utilization capacity for each carbohydrate. The four strains had genes related to acid tolerance and were tolerant to low pH, with L. johnsonii L16 showing the greatest tolerance. The four strains contained genes related to bile salt tolerance and were able to tolerate 0.1% bile salt. Four strains had antioxidant related genes and exhibited antioxidant activity in in vitro tests. They contained the genes linked with organic acid biosynthesis and exhibited antibacterial activity against enterotoxigenic Escherichia coli K88 (ETEC K88) and Salmonella 6,7:c:1,5, wherein, L. johnsonii L16 and L. salivarius ZSA5 had gene clusters encoding bacteriocin. Results suggest that genome analysis combined with in vitro tests is an effective approach for evaluating different strains as probiotics. The findings of this study indicate that L. johnsonii L16 has the potential as a probiotic strain among the four strains and provide theoretical basis for the development of probiotics in swine production.

Copy number variants selected during pig domestication inferred from whole genome resequencing.

Over extended periods of natural and artificial selection, China has developed numerous exceptional pig breeds. Deciphering the germplasm characteristics of these breeds is crucial for their preservation and utilization. While many studies have employed single nucleotide polymorphism (SNP) analysis to investigate the local pig germplasm characteristics, copy number variation (CNV), another significant type of genetic variation, has been less explored in understanding pig resources. In this study, we examined the CNVs of 18 Wanbei pigs (WBP) using whole genome resequencing data with an average depth of 12.61. We identified a total of 8,783 CNVs (~30.07 Mb, 1.20% of the pig genome) in WBP, including 8,427 deletions and 356 duplications. Utilizing fixation index (Fst), we determined that 164 CNVs were within the top 1% of the Fst value and defined as under selection. Functional enrichment analyses of the genes associated with these selected CNVs revealed genes linked to reproduction (SPATA6, CFAP43, CFTR, BPTF), growth and development (NR6A1, SMYD3, VIPR2), and immunity (PARD3, FYB2). This study enhances our understanding of the genomic characteristics of the Wanbei pig and offers a theoretical foundation for the future breeding of this breed.

Genomic diversity of group A rotaviruses from wild boars and domestic pigs in Japan: wide prevalence of NSP5 carrying the H2 genotype.

Group A rotavirus (RVA) sequences were detected in 10.8% (23/212) and 20.7% (87/421) of fecal samples collected in 2017-2022 from wild boars and domestic pigs, using next-generation sequencing. Complete genome sequence analysis of one wild boar and 13 domestic pig RVAs revealed that six of them carried the rare H2 NSP5 genotype. Out of the 39 samples for which the NSP5 genotype could be determined, 23 (59.0%) were of genotype H2. H2 porcine RVAs consist exclusively of Japanese porcine RVAs and exhibit sequence diversity in each segment, suggesting that H2 porcine RVAs may have evolved through reassortment within the Japanese pig population.

Tuberculosis in Wild Pigs from Argentina.

Mycobacterium bovis, a member of the Mycobacterium tuberculosis complex (MTC) and non-tuberculous Mycobacteria (NTM), may infect wild and domestic mammals, including humans. Although cattle are the main hosts and spreaders of M. bovis, many wildlife hosts play an important role worldwide. In Argentina, wild boar and domestic pigs are considered important links in mammalian tuberculosis (mTB) transmission. The aim of this work was to investigate the presence of M. bovis in wild pigs from different regions of Argentina, to characterize isolates of M. bovis obtained, and to compare those with other previously found in vertebrate hosts. A total of 311 samples from wild pigs were obtained, and bacteriological culture, molecular identification and genotyping were performed, obtaining 63 isolates (34 MTC and 29 NTM). Twelve M. bovis spoligotypes were detected. Our findings suggest that wild pigs have a prominent role as reservoirs of mTB in Argentina, based on an estimated prevalence of 11.2 ± 1.8% (95% CI 8.0-14.8) for MTC and the frequency distribution of spoligotypes shared by cattle (75%), domestic pigs (58%) and wildlife (50%). Argentina has a typical scenario where cattle and pigs are farm-raised extensively, sharing the environment with wildlife, creating conditions for effective transmission of mTB in the wildlife-livestock-human interface.