The study focused on Nuclear Paraspeckle Assembly Transcript 1, or NEAT1, a mammalian long noncoding RNA involved in stress responses, metabolism, inflammation and transcriptional regulation. It produces two isoforms: the shorter NEAT1_1 and the longer NEAT1_2. NEAT1_2 has an important scaffolding role in paraspeckles, dynamic nuclear condensates associated with cellular stress, while NEAT1_1 has been linked to metabolic and inflammatory regulation. Most previous evidence has come from cultured cells, laboratory mice or human patients, leaving limited information about how Neat1 behaves in large farm animals exposed to social and psychological challenges.

For the pilot, investigators used 18 male and 18 female pigs that were 12 weeks old at the beginning of the experiment. These animals came from a larger study of 144 pigs housed in six mixed-sex groups and assigned to three environmental conditions for four weeks. The neutral condition represented conventional husbandry. The positive condition added regular stockperson interaction, new toys each week and fresh hay each day. The negative condition involved regularly changing pen mates, an approach intended to disrupt social relationships and create conflict and fear. At the end of this phase, half of the 36 sampled pigs were randomly selected for a five-minute snout-snare restraint; the others received no snare. The investigators then collected saliva and blood one hour later before euthanizing the pigs and dissecting the ventromedial hypothalamus, a brain region involved in emotional processing.

Because the pig genome did not then contain a fully annotated sequence for the gene, the team designed primers by aligning the human NEAT1 sequence with the pig genome and identifying a candidate region with approximately 60% similarity to human NEAT1. Conserved portions were used in reverse-transcription quantitative PCR, or RT-qPCR, assays for total Neat1 and the longer Neat1_2 isoform. Amplicon sequencing, melt-curve analysis and amplification efficiency helped select the final primers. Two reference genes were used for each sample type: Rpl4 and Gapdh for hypothalamus, Ppia and Gapdh for saliva, and Ppia and Rpl4 for blood. A later study annotated the pig ss_Neat1 gene and confirmed the region identified by the researchers, according to the paper.

Neat1 was readily detectable in all three biological materials. The ventromedial hypothalamus produced the greatest average RNA yield, 34.36 ± 14.35 micrograms, compared with 6.10 ± 2.39 micrograms from whole blood and 1.86 ± 0.84 micrograms from saliva. However, neither the four-week environmental treatment nor the acute snout snare significantly changed total Neat1 or Neat1_2 expression in the hypothalamus. The proportion of expression represented by Neat1_2 also did not differ by either type of treatment. These null results mean that the experiment found no evidence that its particular housing and restraint exposures altered the measured transcript in this brain region, rather than demonstrating that Neat1 is unrelated to stress.

Saliva produced the clearest acute-treatment signal, but only for total Neat1. Pigs subjected to the snout snare had significantly lower total Neat1 expression than pigs that did not receive the acute challenge, with a reported p value of 0.01. The four-week environmental treatment did not affect total Neat1 in saliva. Neither environmental nor acute treatment significantly altered Neat1_2 expression or the percentage of total expression attributable to that isoform. The finding is notable because saliva can be collected without invasive procedures, but it remains a single result from a small pilot and does not by itself show that salivary NEAT1 reports psychological stress.

Blood measurements revealed a difference between the first and final sampling points rather than a clear response to the experimental treatments. Neat1_2 expression was higher at the first sample, recorded when pigs were transferred to the experimental facility, than at the end of the four-week period. Average relative expression declined from 1.40 ± 1.09 to 0.32 ± 0.24, with a significant time effect at p = 0.023. The environmental and acute treatments did not significantly affect changes in total Neat1, Neat1_2 expression or the Neat1_2 percentage. Before treatment, females had higher blood Neat1_2 expression than males, and both sexes showed lower values at final sampling. The researchers could not rule out age-related change, although the four-week interval represented a modest developmental difference in pigs aged from 12 to 16 weeks and no age-related markers were measured.

Plasma cortisol, a conventional measure of endocrine stress, increased sharply by the final sampling. Its mean concentration rose from 21.4 ± 16.1 nanograms per milliliter at the first sample to 107.3 ± 33.0 nanograms per milliliter at the second. The acute snout snare itself did not significantly affect cortisol, and environmental treatment did not produce a significant difference at the end of the study. The researchers suggested that moving all pigs from communal pens, collecting blood and performing the subsequent procedures likely stressed every animal at the final sampling, potentially obscuring differences between the long-term environmental and acute snare groups. This uniform final stress response is a major limitation when interpreting the molecular results. Neat1 expression also did not correlate significantly with cortisol in blood, saliva or hypothalamus.

There were likewise no significant relationships between Neat1 measurements in the three sample types within individual pigs. Blood and hypothalamic total Neat1, Neat1_2 and the Neat1_2 percentage did not correlate significantly, nor did saliva measurements track those in the hypothalamus or blood. The cellular origins of the measured RNA were not established because the investigators did not isolate specific blood-cell populations. The paper notes that peripheral blood mononuclear cells are a plausible source in blood and can also occur in saliva, while earlier mouse work found especially high Neat1 expression in glia, including astrocytes and oligodendrocytes, rather than neurons. The absence of cross-tissue correlation may therefore reflect tissue-specific regulation, but the study cannot distinguish that explanation from other biological or methodological factors.

Overall, the research provides a technical proof of concept and a set of hypotheses rather than a practical stress test. The team argues that future work should separate acute and chronic challenges, control the intensity and context of stress, and collect samples at several times, including before and after restraint and during the weeks preceding final sampling. The one-hour post-restraint collection may also have been too early to capture a delayed Neat1 response: cell-culture studies cited by the authors detected increases in Neat1_2 roughly four to 12 hours after stress and sometimes as late as 24 hours. More potent, clearly characterized challenges, such as isolation, handling changes, auditory overstimulation or disruption of social bonds, could help determine whether Neat1 tracks specific emotional states. Additional brain regions, including the prefrontal cortex, would be needed to test whether central NEAT1 expression participates in stress processing. Until such evidence accumulates, the measurable decline in blood Neat1_2 across sampling times should not be described as a biomarker of negative welfare, and the absence of treatment effects should not be taken as proof that the transcript is insensitive to stress.

Subject of Research: Measurement of stress-associated Neat1 expression in blood, saliva and ventromedial hypothalamus of pigs exposed to psychosocial challenges

Article Title: Expression of the long noncoding RNA Neat1 in saliva, blood, and ventromedial hypothalamus of pigs exposed to psychosocial stressors

Article References: Webster, D., Ding, L., Zhang, S., D'Souza, D., Tilbrook, A., Tomas, K., Babington, S., Plush, K., Blache, D., & Fox, A. (2026). Expression of the long noncoding RNA Neat1 in saliva, blood, and ventromedial hypothalamus of pigs exposed to psychosocial stressors. Physiological Reports, 14(20), Article e71130. https://doi.org/10.14814/phy2.71130

Image Credits: AI Generated

DOI: 10.14814/phy2.71130

Keywords: pigs, psychosocial stress, Neat1 lncRNA, long noncoding RNA, saliva, blood biomarkers, hypothalamus, animal welfare, paraspeckles, cortisol, Expression, long

The researchers used genome-wide mapping to identify parental-origin effects affecting pig growth traits, then examined molecular variation using haplotype-resolved transcriptomes and epigenomes from reciprocal crosses. This approach distinguished parental alleles and allowed the investigators to compare their expression, epigenetic features and chromatin organization. The analysis also recapitulated established imprinting effects at loci such as IGF2 and KCNQ1, supporting the view that the method captured known genomic imprinting signals.

One group of signals involved rib length. The researchers linked distal POE loci for this trait with IGF2 through long-range chromatin interactions, indicating that physical contacts between distant genomic regions may contribute to the regulation of rib length. This is a genomic and chromatin association, not evidence that changing the interaction would necessarily alter the trait. The study therefore supports chromatin interactions as a possible contributor to parent-of-origin effects without establishing them as a proven causal mechanism.

The results further indicated that some POEs emerged from parent-specific three-dimensional chromatin architecture independently of allele-specific expression or histone marks. In these cases, parental differences appeared in the spatial organization of DNA even though the analyzed gene-expression and histone-based signals did not account for the effect. The authors identified chromatin topology as a plausible candidate mechanism of parental-origin regulation, while cross-species comparisons nominated additional candidate imprinted genes that require further validation. Together, the findings portray POEs as common and mechanistically diverse features of complex-trait inheritance in pigs.

Subject of Research: Genome-wide and haplotype-resolved analysis of parent-of-origin effects on growth traits in pigs

Article Title: Integrating genome-wide association study and haplotype-resolved epigenomes reveals complex parent-of-origin effects in pigs

Article References: Tao, L., Wang, L.-G., Li, J.-B., Zhang, S.-R., Zhang, L.-C., Deng, J.-K., Lin, J.-W., Hu, M., Adeola, A. C., Feng, X.-Y., Cen, D.-J., Huang, Z.-Q., Li, Q.-L., Liao, C.-Y., Yan, S.-S., Wang, L.-X., Xie, H.-B., & Zhang, Y.-P. (2026). Integrating genome-wide association study and haplotype-resolved epigenomes reveals complex parent-of-origin effects in pigs. BMC Genomics. https://doi.org/10.1186/s12864-026-13396-1

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DOI: 10.1186/s12864-026-13396-1

Keywords: parent-of-origin effects, pigs, genomic imprinting, growth traits, epigenomics, chromatin interactions, three-dimensional chromatin, IGF2, KCNQ1, complex trait inheritance, Integrating, genome-wide

Researchers collected 626 faecal samples representing multiple age groups from farms across Victoria. They used nested polymerase chain reaction assays targeting the small-subunit nuclear ribosomal RNA gene for Cryptosporidium and the tpi locus for G. duodenalis, then amplified the gp60 locus to characterise Cryptosporidium subtypes. Amplified products were analysed by Sanger sequencing. The cross-sectional survey estimated parasite prevalence and examined species composition and genetic diversity within the sampled pig population.

Cryptosporidium detections were dominated by two species. C. scrofarum accounted for 77.5% of Cryptosporidium-positive samples and C. suis for 18.4%. DNA from a third species, C. ubiquitum, was detected in three samples, all from a single farm. Subtyping identified the C. suis subtype XXVa-1 and the C. ubiquitum subtype XIIa; both have previously been identified in humans. This does not demonstrate transmission from pigs to people, but it shows that genotypes of public-health interest are present in the surveyed production environment.

By contrast, G. duodenalis was uncommon: seven of 626 samples were positive, corresponding to a prevalence of 1.1%. The infections occurred on three farms and comprised five samples with assemblage E and two with assemblage A. These findings describe low detected prevalence in this sample rather than establishing the parasite’s distribution throughout Victoria. Cryptosporidium prevalence, however, varied markedly among age groups and production systems, reaching 68.6% among weaners and 78.2% on semi-intensive farms, while it was absent from adult pigs.

The results show that Cryptosporidium is widespread across the Victorian pig farms included in the study, with detection in more than three-quarters of participating properties. The authors describe the work as the first molecular assessment of Cryptosporidium and G. duodenalis in pigs from Victoria and call for continued surveillance and targeted parasite management in Australian pig production. The geographic scope remains important: the estimates are based on 626 samples from 37 farms, and the absence of G. duodenalis outside three sampled farms should not be interpreted as proof that it is absent from other farms. Nevertheless, the baseline identifies frequent Cryptosporidium occurrence, limited detected G. duodenalis infection and zoonotically relevant Cryptosporidium genotypes in the state’s pig population.

Subject of Research: Molecular prevalence and genetic diversity of Cryptosporidium and Giardia duodenalis in pigs from Victoria, Australia

Article Title: First molecular survey of pigs in Victoria, Australia, reveals widespread Cryptosporidium infection, limited Giardia duodenalis occurrence and genotypes with zoonotic potential

Article References: Xu, J., Abbas, G., Gauci, C. G., Gasser, R. B., Jabbar, A., & Koehler, A. V. (2026). First molecular survey of pigs in Victoria, Australia, reveals widespread Cryptosporidium infection, limited Giardia duodenalis occurrence and genotypes with zoonotic potential. Parasites & Vectors. https://doi.org/10.1186/s13071-026-07739-w

Image Credits: AI Generated

DOI: 10.1186/s13071-026-07739-w

Keywords: Cryptosporidium, Giardia duodenalis, pig parasites, molecular epidemiology, zoonotic potential, Victorian agriculture, parasite surveillance, weaner pigs, First, molecular, survey, pigs

The numismatic evidence anchors the ritual activity firmly in time. The numerous coins recovered from the deposits range in date from the early second century AD to the late fourth century AD, with a clear peak in minting during the second half of the fourth century. That concentration matters, because it suggests the sanctuary flourished precisely during Late Antiquity, an era when traditional Roman religion was increasingly under pressure from Christianity and older cults were retreating into discreet, secluded spaces. A mine gallery, accessible only through a controlled entrance and plunged into permanent darkness, would have suited the Mithraic liturgy well. Mithraea across the Roman world were typically small, cave-like rooms without windows, and scholars have long noted that the cult’s reverence for the cave in which Mithras slew the bull made subterranean spaces especially attractive. Yet the Kropfsberg site holds a caveat: no direct depiction of Mithras, whether an altar, inscription, or metal plate, has so far come to light.

To test the ritual hypothesis, researchers turned to the animal bones. In total, 486 animal bones and teeth were recovered by hand from the Late Antiquity layers, of which 295 remains, weighing nearly 567 grams, could be identified to species. The analysis was carried out at the Natural History Museum Vienna, in its First Zoological Department and Archaeological-Zoological Collection, using the standard quantification methods of archaeozoology: the number of identified specimens, or NISP, and the weight of the material, the latter helping to estimate which species contributed most meat. The state of preservation was remarkably good, so good that fragile bones from birds and very young animals survived in high numbers, a fact that immediately hinted the assemblage was not an ordinary domestic refuse pile.

The species profile is dominated by domesticated animals, and the pattern is unusual. By fragment count, pig remains prevail at 47.5 percent of identified specimens, followed by chicken at 38.6 percent, sheep and goat at 12.9 percent, and cattle at a mere 1 percent. The weight analysis shifts the picture slightly, because heavier bones carry more mass: pigs still dominate at 50.5 percent, but sheep and goat follow at 20.7 percent, cattle at 15 percent, and chicken at 13.8 percent, indicating that after pigs the small ruminants were the most important meat suppliers at the site. Compare this with contemporary Late Antiquity settlements in northeastern Austria, such as Oberleiserberg, Drösing, Michelstetten, Zwingendorf, Potzneusiedl, and Podersdorf, where cattle typically make up 38 to 45 percent of identified remains and chicken rarely exceeds 5 percent. The Kropfsberg percentages fall entirely outside those ranges.

The age and sex structure of the animals sharpens the contrast further. Epiphyseal fusion of the bones shows that the overwhelming majority of pigs and sheep or goats were non-adult. Nearly 88 percent of the pig remains came from animals younger than two and a half to three years, with almost a third of them younger than one year. Tooth analysis confirmed the pattern: four of the five pig teeth recovered were milk fourth premolars from animals younger than six months, and the single permanent third molar belonged to an animal of roughly eighteen to twenty months. Sheep and goats tell the same story, with almost 89 percent of remains from individuals younger than three years and a third younger than one year. In ordinary settlements, animals were kept to adulthood because cattle, sheep, and goats had economic value beyond meat, in traction, wool, and milk. Slaughtering animals young is economically wasteful, unless the goal is a table of tender, succulent meat for a very specific occasion.

The chickens add a final, telling detail. Sex could not be determined for the mammals because too few adult bones were present, but the chicken bones could be sexed metrically. Comparing the Kropfsberg measurements, such as the greatest lengths of the coracoid, humerus, radius, ulna, carpometacarpus, and femur, with the large reference assemblage from the Avar-period cemetery of Vienna Csokorgasse, the researchers found that the values fall within the range of variation of male individuals. A dominance of male chickens, combined with the slaughter of juvenile pigs and sheep, matches precisely the faunal signature documented at Mithraea elsewhere in Europe, from older studies such as the classic mid-twentieth-century excavations to recent analyses of sanctuaries in Germany, Switzerland, Belgium, and France. Similar profiles have also been reported from the cult cave of Zillis in the Swiss canton of Graubünden, itself interpreted as a Mithraic site, and from sanctuaries of other deities, including the sanctuary of Jupiter Heliopolitanus at Carnuntum and the Apollo-Grannus sanctuary at Neuenstadt am Kocher, where chickens likewise play an outsized ritual role.

The bones also preserve the physical evidence of butchery and consumption. Chop marks far outnumber cut marks across all species. Pig crania were split in two, with additional chops removing the incisive bone, frontal bone, and maxillae, and severing the skull from the neck at the occipital condyles. Long bones were chopped diagonally at the joints, and one femur shows longitudinal blows for marrow extraction. Ribs were reduced to small portions, vertebrae were split mediansagittally or parasagittally, and sheep and goat carcasses were dismembered in comparable fashion, with cut marks above the teeth on the maxillae indicating careful separation of the head. Even the chicken bones carry oblique and transverse chops and cuts on the femur, tibiotarsus, furcula, coracoid, and radius. These marks demonstrate that the remains are food waste from meals eaten on site, while gnawing marks from scavengers show that at least some refuse lay exposed on the ground, or only partially buried, for a time. One pig rib bears new bone formation consistent with periostitis, the single pathological specimen in the assemblage.

Fire and sediment tell an even more intricate story. About 20 percent of the identified material, and many of the unidentified bones, show the black coloration characteristic of exposure to temperatures between roughly 300 and 600 degrees Celsius. Burning of animal remains is documented in numerous ritual practices across antiquity, including within the Mithras cult itself. Meanwhile, micromorphological analysis of soil thin sections revealed tiny bone splinters embedded in the matrix, mixed with charcoal and clods of sediment in a pit-like floor depression. A comparable phenomenon was first described at the Mithraea of Biesheim and Kempraten, where bone splinters embedded in floor layers were interpreted as evidence of multi-stage ritual activity. At Kropfsberg the splinters were not part of a renovated floor but were deposited in a deliberate depression, again suggesting ceremonies that unfolded in several phases, involving feasting, burning, and the working of bone fragments into the ground.

The teeth even offer a calendar. Age at death reconstructed from tooth eruption and wear, principally the milk fourth premolar and the unworn third molar of pigs, points to slaughtering around the summer season, though the researchers caution that the sample is small and the eruption timing of third molars in ancient pig populations may have been closer to that of wild boar, around 23 to 26 months, than to modern domestic pigs. Taken together, the evidence sketches a vivid scene: somewhere in the late fourth century, in the darkness of an old copper mine in the Alps, a small community slaughtered young pigs, sheep, and roosters, cooked and ate them in ritual meals, burned a fifth of the bones, and left the debris in a sealed underground chamber. Whether the Kropfsberg sanctuary ultimately belonged to Mithras cannot be proven without an image or inscription, and the authors acknowledge that comparable faunal profiles occur in other religious contexts. But the enclosed and lockable setting, the bench-like substructure, the votive sheets, the coins, and now an animal assemblage that mirrors known Mithraea north and south of the Alps make the Tyrolean mine one of the most intriguing new windows onto the secret religions of Rome’s fading frontier.

Subject of Research: Archaeozoological analysis of faunal remains from a possible Late Antique Mithraic sanctuary in an Austrian copper mine

Article Title: Faunal remains from the Late Antiquity ‘cave sanctuary’ (Mithraeum?) of Kropfsberg (Tyrol, Austria)

Article References: Saliari, K., Staudt, M., Cereda, S., & Goldenberg, G. (2026). Faunal remains from the Late Antiquity ‘cave sanctuary’ (Mithraeum?) of Kropfsberg (Tyrol, Austria). Annals of the Natural History Museum Vienna, 127, 95-104. https://doi.org/10.3897/anhmw.187321

Image Credits: AI Generated

DOI: 10.3897/anhmw.187321

Keywords: archaeozoology, Mithraism, Late Antiquity, Kropfsberg, Tyrol, Roman religion, faunal remains, ritual feasting, copper mining, chickens, pigs, Natural History Museum Vienna

The technical case for concern begins with the biology of the parasites themselves. A. suum undergoes a hepatotracheal migration, with larvae passing through the intestinal mucosa, the liver and the lungs before maturing in the jejunum, and this journey leaves characteristic white granulomas, so-called milk spots, on the liver that trigger condemnation at slaughter. Oesophagostomum spp. larvae embed in the submucosa of the caecum and colon, forming nodules before adults emerge into the lumen, while T. suis develops entirely within the large intestine, its whip-shaped anterior end threading into the mucosa of the caecum and colon. Each species follows a direct faecal-oral life cycle built around remarkably persistent eggs: A. suum and T. suis eggs can remain infective in the environment for at least four years, a durability that shapes virtually every management recommendation discussed in the review.

The productivity losses attributable to these infections are far from trivial, even when infections remain clinically silent. Depending on the parasite species and infection intensity, reductions in average daily weight gain range from one to thirty-one percent, corresponding to a daily loss of sixty to 128 grams of growth and roughly a four percent extension of the finishing period. Feed conversion ratios, the efficiency with which feed is converted into body mass, deteriorate by 14.9 to thirty-three percent. Carcass quality suffers in parallel, with infected pigs showing reduced carcass weight, backfat thickness reductions of 5.5 to 12.5 percent and lower lean meat percentage, changes that downgrade carcasses within the SEUROP classification system used across Europe to grade meat based on lean content. Historical estimates of the economic burden are striking: a European study calculated a 60.1 million euro increase in feeding costs attributable to worm infections in 2010 alone, and the same year an estimated 17.5 million euros were lost through liver condemnations.

Beyond productivity, the review highlights a growing body of evidence that gastrointestinal nematodes actively modulate the pig immune system in ways that worsen other diseases. Ascaris suum infection has been linked to increased lung pathology and reduced seroconversion following vaccination against Mycoplasma hyopneumoniae, one of the most economically important respiratory pathogens in swine. Migrating larvae impair pulmonary bacterial clearance, and experimentally infected pigs developed more severe disease after challenge with Bordetella bronchiseptica and Escherichia coli. Coinfection studies have associated A. suum with greater pulmonary consolidation in combination with M. hyopneumoniae, elevated mortality in piglets coinfected with Actinomyces pyogenes and Pasteurella multocida, higher Salmonella enterica burden, and more frequent detection of porcine circovirus type 2. The authors caution, however, that much of this mechanistic evidence derives from small experimental studies conducted in the 1990s, and its quantitative relevance to modern genetics, vaccination programmes and housing conditions remains untested.

There is also a zoonotic dimension that extends the significance of porcine worm control beyond the barn. Ascaris and Trichuris species infect humans, and molecular studies have documented hybridisation between human and pig Ascaris populations, indicating a bidirectional exchange between the two host species. People living near pigs show a 4.65-fold higher risk of ascariasis, and swine veterinarians are 1.5 times more likely to be seropositive for A. suum than their non-swine colleagues. Nematode eggs have been detected in wastewater and sludge used as fertiliser, with concentrations reaching up to 867 eggs per gram, and on fresh fruits and vegetables, raising food-safety concerns. The therapeutic use of Trichuris suis ova in experimental treatments for Crohn’s disease has even produced documented iatrogenic infections, a curious footnote that nonetheless illustrates how readily these parasites cross host boundaries.

Prevalence data across Europe, the review finds, are frustratingly inconsistent. Reported farm-level prevalence for A. suum spans from one to one hundred percent, for Oesophagostomum spp. from two to twenty-seven percent and for T. suis from 0.3 to seventy-five percent. The discrepancy reflects genuine differences between production systems, outdoor, organic and small-scale farms consistently report higher infection levels, but also profound methodological heterogeneity. Faecal egg counting methods such as the McMaster and FLOTAC techniques dominate surveillance for Oesophagostomum and T. suis, while A. suum assessment increasingly employs serological assays including the Ascaris haemoglobin ELISA and L3-larva ELISA, alongside slaughterhouse milk-spot inspection. Serological studies report farm-level seroprevalences of 91 to one hundred percent for A. suum, whereas faecal-based surveys frequently record individual-level prevalence below eight percent, a gap that likely reflects differences in test sensitivity, infection biology and sampling design rather than true epidemiological variation.

Slaughterhouse data provide one of the few large-scale, ongoing indicators. Recent German statistics from 2024 recorded 3,621,397 livers discarded from fattening pigs due to hepatitis parasitaria, the formal designation of milk-spot lesions, out of 43,511,330 pigs subjected to official meat inspection, implying at least an 8.3 percent liver condemnation rate, down slightly from approximately 9.8 percent in 2023. But even this figure demands careful interpretation: German inspection practice historically classified only livers with more than five milk spots as affected, and European regulations, while mandating liver inspection, do not define standardised criteria for recording or quantifying parasitic lesions, undermining cross-country comparability. Denmark reported milk-spot prevalence of up to 96 percent in a survey of organic farms, while Austria and Italy reported rates near 19 and 30 percent respectively, figures that almost certainly reflect both husbandry differences and inspection standards.

On the control side, the review delivers a sober assessment. Under EU Regulation 37/2010, only four chemical classes are authorised for deworming food-producing pigs: benzimidazoles, macrocyclic lactones, piperazine and imidazothiazoles. Prophylactic, blanket deworming without prior diagnostics remains the dominant practice in Europe, a strategy the authors identify as a key driver of anthelmintic resistance. Reduced efficacy and outright resistance have already been documented for Oesophagostomum spp. against both flubendazole and ivermectin, although comparable resistance has not yet been reported for A. suum or T. suis. Intriguingly, treatment efficacy appears to depend on dietary fibre content, with high-fibre rations potentiating drug activity. Management measures offer complementary leverage: all-in/all-out production, easy-to-clean housing surfaces, adequate drying periods between batches and pre-farrowing treatment of sows all reduce transmission, while slatted floors lower liver condemnation risk compared to littered systems. The welfare-driven move away from fully slatted flooring, however, threatens to reverse these gains by returning pigs to bedding systems where eggs persist.

The review’s forward agenda is unambiguous. The authors call for standardised, EU-wide surveillance integrating abattoir monitoring with serological testing, a shift from prophylactic to diagnostic-guided anthelmintic treatment modelled on equine parasite control programmes, routine tracking of emerging resistance, and long-overdue field-based intervention studies evaluating integrated control under commercial conditions. They also identify promising but immature alternatives, including dietary interventions with fermentable carbohydrates such as inulin and chicory-derived fibres, which reduce worm burdens in the large intestine through short-chain fatty acid production, probiotics that moderately decrease milk-spot risk, and selective breeding, since Danish hybrid studies revealed strong heritability of resistance to both A. suum and T. suis. Vaccine development remains a research priority but, given the substantial biological barriers and the absence of a market-ready product, is positioned as a future component of integrated control rather than an imminent replacement for diagnostics, management and targeted drug use. As organic production expands under the European Green Deal and welfare regulations reshape housing, the conditions favouring nematode transmission are set to intensify, making the review’s message increasingly urgent: Europe’s pig sector must modernise its approach to parasite control before the worms, and their resistance genes, outpace it.

Subject of Research: Control strategies and surveillance gaps for gastrointestinal nematode infections in European pig production

Article Title: Current strategies for controlling gastrointestinal nematodes of pigs in Europe

Article References: Hohensee, L., Oser, L., Laubschat, A., Schlosser-Brandenburg, J., & Ebner, F. (2026). Current strategies for controlling gastrointestinal nematodes of pigs in Europe. Parasites & Vectors, 19(1), Article 448. https://doi.org/10.1186/s13071-026-07715-4

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DOI: 10.1186/s13071-026-07715-4

Keywords: Ascaris suum, Oesophagostomum, Trichuris suis, gastrointestinal nematodes, pigs, anthelmintic resistance, Europe, pig production, zoonosis, surveillance, animal welfare, organic farming

The stakes of this research extend well beyond animal welfare, although that alone would justify the effort. Stress at slaughter is a well-established driver of pale, soft and exudative meat, a quality defect that costs the pork industry dearly. When pigs experience acute stress, muscle glycogen is depleted, lactic acid accumulates, pH drops rapidly and proteins denature, degrading color, tenderness and moisture retention. Because pork is the most consumed meat in the world, even modest improvements in slaughter handling could translate into substantial gains in quality and consumer trust, particularly as welfare-certified products gain market share in countries such as South Korea, which introduced a pig farm welfare certification system in 2013.

Electrical stunning, the most common method in commercial slaughterhouses, works by passing a current through the brain to render the animal instantly unconscious. In Korea, the recommended protocol applies at least 1.25 amps at 240 volts to the brain for two to four seconds. Yet the method has known drawbacks: high voltage can induce PSE meat and rupture capillaries, and the sudden muscular force can cause fractures, including pelvic fractures. Carbon dioxide stunning takes a different route, exposing pigs to 80 to 90 percent CO2 for roughly three minutes. As CO2 dissolves into the blood, breathing quickens, blood pH falls, cerebrospinal fluid acidifies and consciousness is lost. Previous studies have linked gas stunning to a lower incidence of PSE meat and a reduced likelihood of animals regaining consciousness during exsanguination.

What remained largely unknown, however, was what happens at the molecular level. To find out, the researchers, led by Seok-Won Lim and corresponding authors Jung Hwan Jeon and Jun-Mo Kim, studied twenty crossbred finishing pigs of about 106 kilograms raised on a farm in the Chungnam region. Ten pigs received electrical stunning and ten received CO2 stunning, with all pre-stunning conditions matched so that the stunning method was the only major variable. Whole blood was collected in RNA-stabilizing tubes before and after stunning, and high-quality RNA was sequenced on an Illumina NovaSeq6000 platform using 151-base-pair paired-end reads, with globin depletion to improve detection of the transcriptome.

The sequencing produced an average of roughly 20.9 million raw reads per sample, with more than 95 percent of trimmed reads mapping to the pig reference genome. After quality control and removal of one outlier sample, the team identified 104 differentially expressed genes in the electrical stunning group, 67 upregulated and 37 downregulated, and 56 in the CO2 group, 39 upregulated and 17 downregulated. Thirteen genes were upregulated under both methods, including FASLG, PRF1, KLRK1, IL12RB2, CCL4, GZMA and IFNG, a shared core pointing to a universal cytotoxic immune response to acute tissue stress regardless of how consciousness is lost.

Functional annotation and gene set enrichment analysis showed that both methods activated natural killer cell-mediated cytotoxicity, cytokine-cytokine receptor interactions and pathways associated with graft-versus-host disease, allograft rejection and type I diabetes, all driven by genes such as IFNG, PRF1 and FASLG that mobilize cytotoxic T cells and NK cells to remove damaged cells. But the similarities ended there. Under electrical stunning, the chemokines CXCL10, CX3CR1 and CCL5 were recruited, suggesting a broader influx of immune cells into tissues, while the gene DCN, which encodes decorin, a proteoglycan that stabilizes the extracellular matrix, was sharply downregulated. The authors interpret this as evidence of extracellular matrix destabilization and potential inflammatory reactions triggered by the abrupt sympathetic-adrenal surge that electrical stimulation provokes.

The CO2-stunned pigs told a different molecular story. Albumin, the most abundant plasma protein, was the most strongly upregulated gene in this group, consistent with a systemic defense against the oxidative and hypoxic stress that CO2 exposure creates. At the same time, the matrix metalloproteinases MMP1 and MMP9 were downregulated, pointing to preserved extracellular matrix integrity and limited immune cell infiltration. Crucially, the CO2 group also engaged inhibitory receptors: KLRD1, which recognizes MHC class I molecules and restrains NK cells from attacking the body’s own tissues, and CD244, which dampens cytotoxic responses to prevent immune overactivation. Together with selective activation of the MHC class I recognition pathway, these findings suggest that gas stunning coaxes the immune system into a more balanced, tissue-protective mode rather than an all-out inflammatory assault.

Perhaps the most intriguing signals emerged from the pathway networks unique to the CO2 group. One network linked oxidative phosphorylation and proteasome activity with neurodegenerative disease pathways, indicating that cells were clearing damaged proteins and restoring mitochondrial ATP production while regulating reactive oxygen species. Another network comprised DNA replication, nucleotide excision repair and mismatch repair, implying that cells were actively repairing oxidative DNA damage rather than succumbing to apoptosis. Meanwhile, the phospholipase C and PI3K-AKT signaling axes were broadly suppressed, a metabolic downshift that the authors suggest may reduce intracellular calcium release, slow the onset of rigor mortis, cut energy consumption and limit ROS generation, an adaptive response that could help explain why CO2 stunning is associated with a lower incidence of PSE meat.

The study is not without limitations. It focused on a single CO2-based protocol, and the authors themselves call for work on alternative gas mixtures such as nitrogen and argon, as well as studies that integrate blood transcriptomics with physiological stress indicators and meat quality traits. Sample sizes were modest, and blood transcriptomes reflect a blend of stunning effects and individual responses to handling and sampling. Still, the research opens a genuinely new window on slaughter stress, demonstrating that the choice of stunning method is written into the transcriptome within minutes. If validated further, the gene signatures identified here, from decorin suppression to albumin induction and inhibitory receptor engagement, could serve as biomarkers for objective welfare assessment, guiding the industry toward methods that minimize suffering while delivering better meat to consumers.

Subject of Research: Comparative blood transcriptome analysis of electrical versus CO2 controlled atmosphere stunning in finishing pigs

Article Title: Comparative transcriptome profiling of electrical and controlled atmosphere stunning in finishing pigs

Article References: Lim, S.-W., Lee, S.-H., Lim, B., Lim, C., Jang, M.-J., Lim, S. J., Cheon, S. N., Jeon, J. H., & Kim, J.-M. (2026). Comparative transcriptome profiling of electrical and controlled atmosphere stunning in finishing pigs. Food Science of Animal Resources, 46(1), Article 53. https://doi.org/10.1007/s44463-026-00058-9

Image Credits: AI Generated

DOI: 10.1007/s44463-026-00058-9

Keywords: pigs, RNA-Seq, transcriptomics, electrical stunning, CO2 stunning, animal welfare, meat quality, stress response, immune response, gene expression, PSE meat, slaughter

The study, led by Chang Huang, Zhiyuan Ren, and Nengshui Ding of Jiangxi Agricultural University together with colleagues at Aonong Group and Jiangxi Science and Technology Normal University, focused on runs of homozygosity, or ROH. These are continuous segments of the genome in which an animal carries two identical copies of the same ancestral DNA sequence, one from each parent. When two parents share recent common ancestors, their offspring are likely to inherit matching segments on both sides, producing these long homozygous tracts. Because their length reflects how far back in the pedigree the shared ancestor lived, ROH provide a genome-wide, DNA-level measure of inbreeding that is often more accurate and more informative than traditional pedigree-based estimates, which depend on complete and accurate record keeping that commercial herds rarely have.

To capture this signal, the team analyzed genotypes from 5,859 pigs after stringent quality control, drawn from the three American breed populations. They defined ROH as segments of at least one megabase, one million DNA letters, and restricted their search to autosomes 1 through 18, excluding the sex chromosomes to keep the analysis comparable across males and females. Across all animals they detected a remarkable 416,225 individual ROH segments. That sheer number illustrates how pervasive autozygosity is in commercial breeding populations, where decades of selection for lean growth, litter size, and carcass quality have reshaped the genome through both deliberate selection and the unavoidable relatedness that accumulates in closed breeding lines.

One of the clearest findings was that the three breeds differ in their overall ROH burden. American Duroc pigs showed the highest individual-level ROH of the three populations. This pattern is consistent with the breeding structure of terminal sire lines, which are often maintained in relatively small nucleus herds under intense selection for growth and meat quality, conditions that tend to concentrate ancestral haplotypes. Landrace and Yorkshire, maternal breeds selected primarily for reproductive performance, showed different ROH architectures. The differences among breeds matter because they suggest that the historical sources of inbreeding, whether from small effective population sizes, founder effects, or selection sweeps, have acted with different intensities in each genetic line.

The heart of the study, however, lay in asking whether this autozygosity has consequences that can be measured in the barn. The researchers computed for each animal a genomic inbreeding coefficient, FROH, defined as the proportion of the autosomal genome covered by ROH. They then tested whether FROH was associated with a panel of production-related traits, using mixed statistical models that included a genomic relationship matrix. This matrix accounts for the ordinary kinship among all animals in the dataset, a crucial control, because relatives resemble each other both genetically and phenotypically for reasons that have nothing to do with inbreeding per se. Without this correction, any association between FROH and a trait could simply reflect family structure rather than the specific effect of homozygous segments.

Across 51 population-by-trait tests, the team identified 19 nominally significant associations between FROH and production traits at a probability threshold of 0.05. Thirteen of these survived correction for the false discovery rate using the Benjamini-Hochberg procedure, a statistical safeguard that limits the expected proportion of false positives among the declared findings. The pattern of surviving associations was strikingly uneven. American Landrace showed the broadest set of FDR-supported associations, Duroc had fewer, and in Yorkshire the nominal associations were restricted to body length and body height, with only the body height association holding up after correction. This breed-by-breed heterogeneity is the study’s central message: the genomic consequences of inbreeding are not a universal constant but depend on which population is being examined and which trait is being measured.

Why should different breeds show different inbreeding effects? The likely explanation lies in the concept of inbreeding load. Recessive deleterious variants are scattered across every genome, but their identity and genomic location differ among populations, shaped by each breed’s unique history of selection and drift. When autozygous segments arise, they expose whatever recessive variants happen to lie within them. If a breed’s deleterious burden happens to overlap regions influencing, say, body length or backfat, inbreeding will depress those particular traits. If the burden lies elsewhere, different traits will suffer. The population-specific associations observed here are exactly what this model predicts, and they argue strongly against a one-size-fits-all approach to managing inbreeding in multi-breed breeding programs.

The study also probed two more subtle questions. First, the researchers asked whether the effect of FROH differed between males and females, testing FROH-by-sex interactions. They found 45 estimable interaction tests, with some nominally significant results in Duroc, but none of these survived false discovery rate correction, meaning the evidence for sex-specific inbreeding effects remains tentative at best. Second, they used segmented regression models to look for thresholds, points beyond which additional autozygosity might cause a disproportionate decline in performance. Here they detected 25 nominally significant threshold responses, but again none survived FDR correction, with the smallest corrected value reaching 0.118. Importantly, the candidate breakpoints suggested by these exploratory analyses differed by population, trait, and ROH length class, hinting that if true thresholds exist, they are not universal values but properties of each population’s genome.

The distinction between ROH length classes deserves attention because it carries biological meaning. Short ROH reflect ancient shared ancestors, often reaching back many generations or even to the founding of the breed, while long ROH flag recent inbreeding, typically within the last few generations. Long ROH are therefore the ones most responsive to current mating decisions. The observation that associations and candidate thresholds varied across length classes suggests that old and new inbreeding may contribute differently to trait variation, a finding that could eventually help breeders distinguish the inbreeding they can control through mating plans from the legacy burden embedded in the breed’s history.

For the pork industry, the practical implications are concrete. Genomic inbreeding coefficients computed from routine SNP chip data could be incorporated into selection indices and mate allocation algorithms, allowing breeding companies to balance genetic gain against the accumulation of autozygosity on a population-specific basis. Rather than imposing a generic inbreeding ceiling, programs could weight the traits that are demonstrably sensitive to FROH in each line. The authors note that their findings provide a basis for population-specific evaluation of inbreeding load and for improving genomic management strategies in commercial pig breeding. As genomic selection accelerates the rate of genetic change, it also accelerates the loss of genetic diversity, making tools that measure and manage autozygosity directly from DNA increasingly essential. This study demonstrates both the promise of that approach and the statistical caution needed to interpret it: the strongest signals are real and breed-specific, while the more tantalizing patterns of sex effects and inbreeding thresholds remain, for now, hypotheses for larger datasets to test.

Subject of Research: Associations between runs of homozygosity-based genomic inbreeding and production traits in three commercial pig populations

Article Title: Runs of homozygosity reveal associations between autozygosity and production traits in three commercial pig populations

Article References: Huang, C., Ren, Z., Yang, W., Meng, Q., Wu, G., Chen, H., & Ding, N. (2026). Runs of homozygosity reveal associations between autozygosity and production traits in three commercial pig populations. BMC Genomics. https://doi.org/10.1186/s12864-026-13326-1

Image Credits: AI Generated

DOI: 10.1186/s12864-026-13326-1

Keywords: runs of homozygosity, autozygosity, genomic inbreeding, pigs, Duroc, Landrace, Yorkshire, production traits, FROH, genomic selection, animal breeding, quantitative genetics

The choice of the pig as the experimental recipient was central to the study’s design. Pigs share striking anatomical and molecular similarities with humans, including comparable ratios of small intestine length to body weight, well-developed submucosal glands and villus structures, similar cell populations, and a high degree of genomic homology. Previous comparative work has also shown that mature human donor microbiota establish more efficiently and persistently in piglets than in mice under matched conditions. That makes the porcine intestine a valuable translational bridge between reductionist rodent experiments and human intestinal biology, particularly for a question that hinges on how an intact human microbial community behaves in a mammalian gut.

To carry out the experiment, the team worked with eighteen two-month-old Bama miniature pigs, divided into a control group and two groups receiving fecal microbiota from either young donors aged 22 to 29 years or elderly donors aged 70 to 85 years. Five donors contributed to each age group, with two fecal samples per donor. The researchers first depleted the pigs’ resident microbes with a three-day course of oral antibiotics, then administered human fecal suspensions on alternate days over eight days. After a week of colonization, they collected blood, intestinal tissues, and gut contents for analysis. The antibiotic pretreatment sharply reduced microbial diversity, and transplantation restored overall richness to baseline levels, but the compositional structure of the community was substantially reshaped by the transplanted human microbiota, with clear separation between FMT recipients and control animals.

Microbial profiling revealed how profoundly donor age shaped the reconstituted communities. Although pigs receiving young and elderly donor microbiota showed no significant differences in alpha diversity, meaning overall richness and evenness, their community structures differed significantly. Pigs colonized with elderly donor microbiota exhibited a reduced gut microbiome health index and an elevated microbial dysbiosis index, exploratory measures originally derived from human datasets. The two age groups also produced distinct core communities: 986 amplicon sequence variants were unique to the young donor group and 797 to the elderly donor group, with only 611 shared. Notably, pigs receiving young donor microbiota harbored higher proportions of transient microbial variants, suggesting greater environmental sensitivity, while communities from elderly donors contained fewer such variants, implying reduced responsiveness to environmental fluctuations. At the species level, Phocea massiliensis was enriched in pigs receiving young donor microbiota, whereas Blautia obeum emerged as a signature species in those receiving elderly donor microbiota.

These microbial differences translated into structural and functional consequences for the gut. Histological examination showed that ileal villus height was significantly reduced in pigs transplanted with elderly donor microbiota, while the duodenum, jejunum, and colon were largely spared, pointing to a region-specific impact of donor age on intestinal architecture. Reduced villus height is significant because it may partly account for the impaired nutrient absorption frequently reported in older adults, and the accompanying transcriptomic data reinforced this connection, with differential gene expression enriched in pathways related to lipid digestion and absorption. More striking still were the barrier findings: serum diamine oxidase, a marker of mucosal disruption and intestinal permeability, was significantly elevated in pigs receiving elderly donor microbiota, and levels of the tight junction proteins ZO-1, Claudin-1, and Occludin were markedly reduced across the jejunum, ileum, and colon.

Correlation analysis linked specific bacterial species to these barrier changes. The abundance of P. massiliensis was positively correlated with ileal Claudin-1 expression, while B. obeum abundance was negatively associated with tight junction protein expression across multiple intestinal segments. This pattern is intriguing given what is known about the two organisms. P. massiliensis, a strict anaerobic Gram-negative bacillus found in the intestines of humans and animals, has shown age-associated decline in mouse models, and murine studies have reported a negative correlation between frailty and its abundance. B. obeum, by contrast, has been implicated as a potential risk factor in several diseases, including the exacerbation of colitis in mice, and its increased abundance has been associated with altered markers of diabetes risk. The enrichment of B. obeum in the elderly gut may therefore predispose individuals to age-related disease susceptibility, although the authors caution that these relationships remain correlative.

The metabolomic analysis added another layer to the story. Plasma metabolic signatures separated clearly between the two FMT groups, and five metabolites differed significantly: 3-methyloxindole, prostaglandin E3, and 2-hydroxybutanoic acid were elevated in pigs receiving elderly donor microbiota, while 2-hydroxyoctadecanoic acid and the dipeptide Tyr-Phe were diminished. The three elevated metabolites were inversely correlated with tight junction protein expression across intestinal segments, whereas the two reduced metabolites showed positive correlations with selected barrier proteins. To probe function directly, the researchers tested these metabolites on porcine intestinal epithelial cells in vitro. Tyr-Phe increased both cell viability and transepithelial electrical resistance, a measure of barrier tightness, providing evidence for a protective role. 2-Hydroxyoctadecanoic acid promoted cell viability but did not alter resistance under the tested conditions. Prostaglandin E3, meanwhile, left viability unchanged but reduced transepithelial electrical resistance, consistent with earlier work showing that prostaglandin E3 increases paracellular permeability in human intestinal cell monolayers through EP1- and EP4-mediated signaling.

Transcriptomic profiling of the ileal mucosa revealed 108 genes significantly upregulated and 109 downregulated in pigs receiving elderly donor microbiota, with enrichment in pathways including steroid hormone biosynthesis, retinol metabolism, PPAR signaling, and bile secretion. Each of these pathways has plausible relevance to intestinal aging: retinoid metabolism is closely tied to epithelial homeostasis and mucosal immune regulation, PPAR signaling governs energy metabolism and oxidative stress responses, and bile acids are microbiota-modified signaling molecules that regulate epithelial renewal and permeability. The most striking finding, however, emerged from hub gene analysis. The top seven genes identified by network analysis, MX2, ISG15, IFI6, IFIT1, OAS1, DHX58, and ISG12(A), were all significantly downregulated in pigs receiving elderly donor microbiota, and all belong to a coherent module of interferon-stimulated genes that form the intestine’s baseline antiviral defense.

This coordinated suppression of the interferon-stimulated gene module carries particular weight because tonic interferon signaling in the gut is not merely a response to infection but contributes to basal mucosal preparedness. Commensal bacteria can stimulate localized interferon-lambda-dependent expression of these genes in intestinal epithelial cells, establishing preemptive antiviral defense. The downregulated genes span multiple levels of the antiviral cascade: MX2 blocks viral replication after entry, IFIT1 recognizes non-self viral RNA, OAS1 activates an RNA-degrading antiviral pathway, and DHX58 modulates viral RNA sensing. Several of these genes, including ISG15, IFI6, and ISG12(A), also positively correlated with ileal tight junction protein expression, suggesting a mechanistic link between the suppression of epithelial interferon responsiveness and impaired barrier integrity. Elderly donor microbiota may either provide weaker microbial cues for maintaining this homeostatic antiviral tone or generate signals that dampen epithelial interferon responsiveness.

The authors are careful to frame their findings as association-based rather than definitively causal, noting that the study’s comparative design, moderate sample size, and short observation period leave open questions about the specific contributions of individual taxa, metabolites, and host genes. Future work, they suggest, should test whether aged microbiota directly suppress epithelial interferon signaling, whether supplementation with young donor microbiota or defined metabolites restores antiviral gene expression, and whether manipulating the interferon axis can rescue barrier function. Even with those caveats, the study delivers a compelling demonstration that the chronological age of a gut microbial community can reprogram the biology of its host, from villus architecture to plasma metabolites to mucosal gene expression. As populations worldwide age, the prospect of microbiota-targeted nutritional or therapeutic strategies designed to preserve intestinal integrity in the elderly looks increasingly grounded in mechanism rather than mere correlation.

Subject of Research: Effects of age-specific human gut microbiota transplantation on intestinal barrier function, metabolism, and mucosal gene expression in pigs

Article Title: Transplantation of Elderly Human Gut Microbiota Into Pigs Reprograms Intestinal Barrier Function, Plasma Metabolome, and Gut Mucosal Transcriptomic Landscape

Article References: Wang, J., Li, L., Mei, L., Tang, Z., Liao, B., Zhao, Q., Wang, Y., Fu, Q., Ren, L., Zhai, Z., Xu, Y., Yang, A., Duan, S., Zhai, Z., Hao, Y., Zhou, Y., Xu, Y., Yang, Y., Wu, Z., & Ji, Y. (2026). Transplantation of Elderly Human Gut Microbiota Into Pigs Reprograms Intestinal Barrier Function, Plasma Metabolome, and Gut Mucosal Transcriptomic Landscape. Aging Cell, 25(10), Article e70725. https://doi.org/10.1111/acel.70725

Image Credits: AI Generated

DOI: 10.1111/acel.70725

Keywords: gut microbiota, fecal microbiota transplantation, aging, intestinal barrier, tight junctions, pigs, metabolomics, transcriptomics, interferon-stimulated genes, Blautia obeum, Phocea massiliensis, intestinal permeability

The team, led by Jie Gao and colleagues at the State Key Laboratory of Animal Nutrition and Feeding within the Chinese Academy of Agricultural Sciences, worked with eighteen castrated male Large White pigs weighing around seventy kilograms. The animals were split into three groups: an untreated control, a group injected with diquat, and a group fed a diet containing 800 milligrams of lipoic acid per kilogram before receiving the same diquat challenge. Diquat is a bipyridine herbicide widely used in research to trigger oxidative stress; inside cells it hijacks molecular oxygen to generate superoxide radicals and hydrogen peroxide, mimicking the damage that modern farming stressors, from early weaning to poor diets, can inflict on porcine liver. Fourteen days after the injection, the researchers collected liver samples to examine tissue in its recovery phase, a window that most previous studies overlooked.

The technical scale of the analysis is impressive. Using tandem mass tag labeling combined with liquid chromatography-tandem mass spectrometry, the team identified 7,271 hepatic proteins and accurately quantified 5,326 of them. A parallel label-free ubiquitylome analysis detected 1,651 ubiquitination sites across 594 proteins, with 1,208 sites quantified. Ubiquitination is a post-translational modification in which a small regulatory protein is attached to lysine residues on target proteins, often marking them for degradation by the proteasome but sometimes altering their activity or location. Because the ubiquitin system is increasingly recognized as a master switch for ferroptosis, cataloguing these tags provided a direct readout of how stressed liver cells reorganize their survival machinery.

Ferroptosis itself is a relatively recently characterized form of regulated cell death, driven by iron-dependent lipid peroxidation. Unlike apoptosis, it culminates in the catastrophic oxidation of cellular membranes. The liver, as the body’s principal iron storage organ, is especially vulnerable. When free ferrous iron accumulates in the cytoplasm, it catalyzes the Fenton reaction, converting hydrogen peroxide into highly destructive hydroxyl radicals. Prior work has already tied ferroptosis to liver injury in pigs and in models of metabolic and ischemic liver disease, but the upstream regulation of the pathway, particularly through ubiquitination, remained murky.

Two proteins emerged from the molecular fog as the study’s central characters. The first is ferritin heavy chain 1, or FTH1, the functional core of ferritin, the cell’s iron vault. FTH1 possesses ferroxidase activity, converting dangerous ferrous iron into its safer ferric form and sequestering it within the ferritin shell, thereby preventing the Fenton reaction from running unchecked. The researchers found that lipoic acid supplementation increased FTH1 abundance in recovering livers, a trend confirmed by parallel reaction monitoring, an independent mass spectrometry method, and by Western blotting, though the Western blot difference reached only marginal statistical significance with a p-value of 0.054.

The second protagonist is poly(rC)-binding protein 1, known as PCBP1, a cytosolic iron chaperone that grabs ferrous iron through conserved cysteine residues and delivers it to ferritin for safe storage. The ubiquitylome data revealed that lipoic acid promoted ubiquitination of PCBP1 at lysine 314, a residue the authors showed is highly conserved across species, hinting at an evolutionarily important function. Co-immunoprecipitation experiments on liver tissue confirmed that total PCBP1 ubiquitination was significantly higher in lipoic acid-fed pigs than in the diquat-only group. What this ubiquitination does to PCBP1’s iron-binding activity is not yet resolved, and the authors are explicit that functional verification of the K314 site will be a centerpiece of their future work.

The cellular story was reinforced by experiments in THLE-2 cells, an immortalized human liver epithelial line. When the cells were stressed with hydrogen peroxide, lipoic acid treatment at 200, 400, and 800 micromolar concentrations significantly blunted the stress-induced drop in FTH1 and the surge in intracellular ferrous iron, in a dose-dependent fashion. The treatment also preserved cell viability, reduced malondialdehyde, a lipid peroxidation byproduct, and restored the activities of total and copper-zinc superoxide dismutase. The authors acknowledge that cross-species differences between human cells and the porcine model are a limitation and plan to validate the findings in primary pig hepatocytes.

One of the more counterintuitive results came from the antioxidant measurements. Fifteen days after the diquat challenge, livers of the stressed pigs showed elevated, not depressed, activity of catalase, superoxide dismutase, and glutathione peroxidase, along with higher total antioxidant capacity. Rather than contradicting earlier reports of diquat toxicity, the authors interpret this as a compensatory overshoot: after acute oxidative shock subsides, the body’s Nrf2-driven antioxidant program remains cranked up, pumping out protective enzymes to mop up lingering peroxides. Histological sections supported the idea of a recovery phase, showing mild microvacuoles, some binucleated hepatocytes, and slight sinusoidal congestion but no outright necrosis. Lipoic acid-fed pigs generally landed between the controls and the stressed animals on most indices, suggesting the supplement gently steered the overactivated antioxidant system back toward balance rather than flipping it abruptly.

At the pathway level, the enrichment analyses added further texture. Differentially expressed proteins in lipoic acid-supplemented pigs were significantly enriched in mineral absorption and, notably, in the ferroptosis pathway itself, while gene ontology terms for iron ion transport, ferric iron binding, and iron homeostasis appeared repeatedly at both the protein and ubiquitination levels. The ubiquitinome also lit up the AMPK and FoxO signaling pathways, which the authors speculate may act as upstream hubs governing the E3 ubiquitin ligases, such as Parkin and HUWE1, that in other contexts have been shown to degrade ferroptosis regulators like ACSL4 and the transferrin receptor. Which specific ligases or deubiquitinases modify PCBP1 in response to lipoic acid remains an open question the team is chasing next.

The practical implications extend beyond the laboratory. Heat stress, weaning, mycotoxins, and transport all impose oxidative burdens on swine, costing the industry real money in growth performance and welfare. By establishing that a dietary additive can tune the ubiquitination of iron-handling proteins and thereby suppress ferroptosis, the study offers a mechanistic rationale for lipoic acid as a functional feed additive, not merely a generic antioxidant. It also demonstrates, more broadly, that post-translational modifications deserve a seat at the table when nutritionists evaluate how supplements actually work. Whether the same iron-sequestration strategy can be exploited in human liver disease, where ferroptosis is implicated in conditions from steatohepatitis to acute liver failure, is an enticing question, and one that this porcine ubiquitylome has now made considerably easier to ask.

Subject of Research: The role of ubiquitination in alpha-lipoic acid-mediated suppression of ferroptosis during hepatic oxidative stress recovery in finishing pigs

Article Title: Ubiquitylome analysis reveals the protective effect of α-lipoic acid via the ferroptosis pathway during recovery after hepatic oxidative stress in finishing pigs

Article References: Gao, J., Cui, Y., Li, C., Bao, W., Hao, Y., Piao, X., Meng, Q., & Gu, X. (2026). Ubiquitylome analysis reveals the protective effect of α-lipoic acid via the ferroptosis pathway during recovery after hepatic oxidative stress in finishing pigs. Stress Biology, 6(1), Article 68. https://doi.org/10.1007/s44154-026-00341-1

Image Credits: AI Generated

DOI: 10.1007/s44154-026-00341-1

Keywords: alpha-lipoic acid, ferroptosis, ubiquitination, oxidative stress, liver, FTH1, PCBP1, iron homeostasis, pigs, proteomics, diquat, feed additive

Why does this matter? Proteins almost never work alone. They form intricate interaction networks that govern everything from immune responses to reproduction, growth, and product quality. Understanding these networks at a systems level is essential for improving traits such as disease resistance, fertility, and meat or egg quality—the cornerstones of food security and sustainable farming. Yet existing interaction databases like STRING, BioGRID, IntAct, and MINT offer only sparse coverage of agricultural species, and they typically lack the structural annotations needed to identify binding interfaces, functional hotspots, or the molecular consequences of mutations. Without such detail, linking a genetic variant to a measurable trait—an essential step in molecular breeding—remains a matter of guesswork.

The new database was built through an ambitious integrative pipeline that combines three complementary prediction strategies. The first, interolog mapping, exploits evolutionary conservation: if two proteins in a model organism are known to interact, their homologs in a farm animal are likely to interact as well. The team assembled a rigorously filtered library of experimentally supported interactions from seven model organisms, including human, mouse, fly, worm, yeast, E. coli, and Arabidopsis, retaining only high-confidence interactions scored by the HIPPIE scheme. The second strategy, domain–domain interaction inference, predicts interactions based on conserved protein domain pairings drawn from the 3did catalog and expanded with an expectation–maximization algorithm applied to curated interaction data.

The third and most modern component is a deep learning model. The researchers retrained PPITrans, a transformer-based architecture built on the ProtT5 protein language model, using a curated set of 44,035 high-confidence human interactions as positive samples and 430,370 negative pairs. Training on an NVIDIA A30 GPU with the AdamW optimizer, the model learned sequence-derived interaction patterns that generalize across species. The scores from all three methods were then fused through a logistic regression model trained on a mouse benchmark dataset, producing a single interaction probability for every protein pair. On independent testing, the integrated model achieved an area under the ROC curve of 0.914 and an area under the precision–recall curve of 0.679, outperforming each individual component. Interactions were classified as high-confidence only above a stringent threshold calibrated at a 0.1 percent false positive rate.

The resulting species-specific networks are striking in scale. Cattle lead the pack with 173,331 predicted interactions covering 34.0 percent of the proteome, followed by pig with 90,987 interactions, chicken with 61,593, duck with 43,886, and sheep with 40,624. In total, these interactomes span proteomes at coverage rates ranging from 19.5 to 34.0 percent—a dramatic expansion of molecular data for organisms that have historically been interaction-data deserts. Cross-validation against independent resources lent credibility to the predictions: the cattle network shared 8,127 interactions with a D-SCRIPT-based dataset and captured 207 of 632 experimentally solved cattle complex structures in Interactome3D, both overlaps highly significant by Fisher’s exact test.

What truly distinguishes AASIA, however, is its structural dimension. The team used ESMFold, a cutting-edge structure prediction system powered by the ESM-2 protein language model, to generate three-dimensional models for every protein monomer across the five proteomes and, in multimer mode, for all 410,000-plus interacting pairs. Unlike earlier approaches requiring multiple sequence alignments or structural templates, ESMFold predicts structures directly from amino acid sequences, enabling proteome-scale modeling at unprecedented speed. Most monomer models showed high confidence, with pLDDT scores predominantly above 70. Each complex was then annotated with interface residues defined by geometric contact and hotspot residues identified through computational alanine scanning with the FoldX force field, which flags positions whose mutation would destabilize the interface by at least 0.5 kilocalories per mole.

To demonstrate the database’s power, the researchers dove deep into the chicken interactome. Its network topology follows classic small-world, scale-free architecture, with an average of 24 interactions per protein, a mean shortest path length of 3.3, and a clustering coefficient of 0.63—far higher than randomized networks of the same size. Fifty predicted chicken interactions overlapped significantly with experimentally supported ones, and predicted pairs showed Gene Ontology semantic similarity comparable to known interactions and far above random pairs. A flagship case study examined the actin-capping protein assembly: the predicted CAPZA1–CAPZB heterodimer aligned with the experimentally solved crystal structure with a root-mean-square deviation of just 1.6 angstroms, and the predicted binding interfaces for both subunits with ACTIN matched mutagenesis-verified actin-binding motifs at the C-termini of the CapZ subunits.

Perhaps the most compelling illustration of AASIA’s practical value involves a predicted interaction between XRCC5, a DNA repair factor, and H2AC39, a histone variant, in chicken. The interaction was independently supported by all three prediction methods and scored 0.94 overall. Remarkably, the predicted interface overlaps a known quantitative trait locus associated with eggshell strength. A residue at that locus, arginine 10 of XRCC5, sits directly at the interaction interface and was flagged as a putative hotspot: FoldX predicted that mutating it to alanine would destabilize the complex by 1.09 kilocalories per mole, and the database’s variant effect module predicted a corresponding drop in the interaction score. This offers a testable, structure-based hypothesis that genetic variation at this position could alter chromatin dynamics during eggshell mineralization—precisely the kind of genotype-to-phenotype bridge molecular breeders have long sought.

The platform itself is designed for broad usability, built on a Vue.js frontend, Express.js backend, and MySQL metadata management, with Cytoscape.js for network visualization and Mol* and NGL Viewer for interactive 3D structure exploration. Users can search by UniProt, Ensembl, or Entrez identifiers, gene names, or keywords; browse protein and interaction pages with functional annotations from Gene Ontology and KEGG; and, crucially, submit their own protein sequences to the Predict module for de novo interaction inference or quantitative assessment of mutation effects on interaction scores. This last capability turns AASIA from a static repository into an active hypothesis-generating engine.

The authors acknowledge limitations: public databases mix direct binary interactions with association-level evidence, and ESMFold does not explicitly model intrinsically disordered regions that mediate many interactions. Still, performance on a stricter binary-only test subset was even stronger, with an AUROC of 0.928. Looking forward, the team plans to expand AASIA with host–pathogen interaction data—potentially illuminating conserved interfaces exploited by avian influenza and African swine fever viruses—and to integrate transcriptomic, epigenomic, and genome-wide variant data. By transforming raw omics information into spatially resolved, residue-level insight, AASIA positions itself as a foundational tool for the next generation of livestock genomics and biotech breeding.

Subject of Research: A structure-informed protein–protein interactome database for five agricultural animal species

Article Title: AASIA: A comprehensive protein structural interactome database for agricultural animals

Article References: Li, J., Yuan, M., Jiang, L., Li, D., Yin, Z., Zhu, F., Shi, W., Hou, Z., & Zhang, Z. (2026). AASIA: A comprehensive protein structural interactome database for agricultural animals. Journal of Advanced Research. https://doi.org/10.1016/j.jare.2026.09.015

Image Credits: AI Generated

DOI: 10.1016/j.jare.2026.09.015

Keywords: AASIA, protein-protein interactions, agricultural animals, structural biology, ESMFold, deep learning, interolog mapping, molecular breeding, livestock genomics, variant effect prediction, disease resistance, food security