Institut für Nutztierwissenschaften

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Effects of dietary phosphorus and myo-inositol supplementation on NaPi-IIb and TRPV6 protein expression in duodenal apical membranes of laying hens from two strains
(2026) Shomina, Nataliia; Sommerfeld, Vera; Hanauska, Anna; Oster, Michael; Rodehutscord, Markus; Huber, Korinna
Phosphorus (P) and calcium (Ca) absorption in the intestine is mediated by apical brush border membrane (BBM) transporters, including the sodium-dependent phosphate (Pi) transporter NaPi-IIb and the Ca²⁺-selective channel TRPV6. Both are highly expressed in the duodenum and exhibit dietary adaptability; yet little is known about how this adaptability varies with strain and age in laying hens. The present study examined the effects of dietary mineral P renunciation and myo-inositol (MI) supplementation on NaPi-IIb and TRPV6 protein expression in the duodenal BBM of Lohmann Brown-Classic (LB) and Lohmann LSL-Classic (LSL) hens. Two independent feeding trials were conducted: hens received diets either with or without mineral P supplementation (wk 15 - 19 and 20 – 24), or with graded MI levels (0 - 3 g/kg; wk 26 – 30). At the end of each period, hens were euthanized and protein expression of NaPi-IIb and TRPV6 in duodenal BBM was studied by western blotting. Statistical correlation with additional traits of mineral metabolism was analyzed. An immunoreactive NaPi-IIb band was detected at ∼ 45 kDa; therefore, all results reported here refer to this NaPi-IIb fragment. Mineral P renunciation did not affect NaPi-IIb fragment or TRPV6 expression in either hen strain. In LSL hens NaPi-IIb fragment expression increased from wk 19 to wk 24, whereas in LB hens it remained unchanged. NaPi-IIb fragment expression was positively associated with duodenal phosphatase activity and plasma estradiol. TRPV6 expression tended to reduce in LB hens from wk 19 to wk 24, but remained stable in LSL hens. TRPV6 expression was positively associated with duodeno-jejunal P content. MI supplementation upregulated NaPi-IIb fragment expression in LB, but downregulated it in LSL hens with high dietary MI levels, without affecting TRPV6. These findings demonstrate strain-dependent regulatory patterns of duodenal expression of NaPi-IIb fragment and TRPV6 in response to physiological stage and MI supply, indicating that mineral feeding strategies may benefit from genotype-specific consideration, whereas the mechanisms underlying MI-related effects require further clarification.
Nutrient–response modeling with a single and interpretable artificial neuron
(2025) Rodehutscord, Markus; Ahmadi, Hamed
Precise estimation of nutrient requirements and utilization efficiency is fundamental to nutritional sciences, yet it is mainly performed using classical nonlinear regression models. These models are interpretable but require careful selection of the functional form and initial parameter values. Flexible machine learning (ML) methods are seemingly disliked due to their perceived “black box” nature, which can obscure biological insight. A minimal and interpretable ML framework addresses this gap in nutrient–response modeling. The proposed approach uses a single artificial neuron with a hyperbolic tangent activation. Mathematically, this resembles a four-parameter sigmoidal function but with greater flexibility and distinct parameter definitions, allowing capture of the monotonic, saturating dynamics typical of essential nutrient responses. The method is enhanced with modern ML best practices, including data augmentation, Bayesian regularization, and bootstrap resampling, providing robust, uncertainty-quantified estimates of key nutritional metrics—such as asymptotic response, inflection point, and nutrient requirements—even from small datasets. Evaluations across 12 diverse datasets from poultry and fish studies, including amino acids and phosphorus, demonstrated that the single artificial neuron matches or exceeds the performance of classical models while providing full analytical transparency. The framework is implemented as a no-code graphical application, ‘NutriCurvist’, offering an easy-to-use alternative tool for nutrient-response modeling to support data-driven, precision nutrition.
The chicken gut microbiome in conventional and alternative production systems
(2025) Cheng, Yu-Chieh; Krieger, Margret; Korves, Anna-Maria; Camarinha‑Silva, Amélia
The poultry gut microbiome plays a key role in nutrient digestion, immune function, and overall health. Differences among various farming systems, including conventional, antibiotic-free, free-range, and organic systems, influence microbial composition and function through variations in diet, genetic selection, environmental exposure, and antibiotic use. Conventional systems typically rely on formulated diets and controlled housing conditions, often with routine antimicrobial use. In contrast, organic systems emphasize natural feed ingredients, including roughage, outdoor access, and strict limitations on the use of antibiotics. These divergent practices shape the gut microbiota differently, with organic systems generally associated with greater exposure to environmental microbes and, consequently, greater microbial diversity. However, the implications of this increased diversity for poultry health and performance are complex, as organic systems may also carry a higher risk of pathogen exposure. This review summarizes current findings on the chicken gut microbiome across conventional and alternative production systems (antibiotic-free, free-range, and organic), focusing on microbial diversity, functional potential, and disease resilience. The need for standardized methodologies and consistent nomenclature in microbiome research is also discussed to improve comparability across studies. Understanding how production systems influence the gut microbiota is essential for improving poultry health and productivity while addressing challenges related to antimicrobial resistance and sustainable farming practices.
Systematic selection of best performing mathematical models for in vitro gas production using machine learning across diverse feeds
(2025) Ahmadi, Hamed; Titze, Natascha; Wild, Katharina; Rodehutscord, Markus
In vitro gas production (GP) is commonly used to evaluate ruminant feed, yet its accurate interpretation requires robust mathematical modeling. This study systematically explores a wide array of nonlinear models to explain GP dynamics across various feed types, addressing the question: how can efficient and versatile models that accurately represent GP profiles be identified? We hypothesized that distinct feed types exhibit unique GP characteristics, effectively captured by specific models, and that statistical and machine learning methodologies can streamline model selection. Utilizing a comprehensive dataset derived from 849 unique GP profiles across concentrate feed categories—including cereal and leguminous grains and processed protein feeds—21 candidate models were rigorously evaluated based on their goodness-of-fit metrics, with a particular emphasis on Bayesian Information Criterion (BIC) for model selection. A group of three models—namely Burr XII, Inverse paralogistic, and Log-logistic—consistently emerged as top performers, demonstrating high generalizability and predictive power across feed types. Notably, our analysis indicated that model type significantly influenced GP predictions, surpassing the impact of feed type characteristics. This research establishes a decision-making framework for model selection and sets the stage for further investigations linking in vitro GP parameters to in vivo digestibility, ultimately enhancing ruminant nutrition strategies.
Effects of Prosopis juliflora pods on sheep performance and carcass traits, and their methane mitigation potential as assessed in vitro
(2025) Tadesse, Assefa; Titze, Natascha; Rodehutscord, Markus; Melesse, Aberra
This study aimed to assess the effect of partial substitution of concentrate mix (CM) with Prosopis juliflora pod (PJP) on growth performance and carcass traits in sheep, and its potential to reduce methane (CH4) production in vitro. A total of 25 yearling rams with an initial body weight of 15.8±1.53 kg was randomly assigned to five treatment diets. The diets were a control diet (JP0) and JP0 replaced with PJP at the level of 5% (JP5), 10% (JP10), 15% (JP15), and 20% (JP20). Data were collected on feed intake, body weight, and carcass characteristics. Methane production was determined from 24 h in vitro gas production. The substitution of CM with PJP did not affect feed intake, body weight, weight gain, feed efficiency, and carcass traits (p>0.05). The in vitro CH4 production was reduced (p<0.001) in diets containing increased levels of PJP. The metabolizable energy for JP10, JP15 and JP20 diets was 11.9, 11.6 and 11.5 MJ/kg DM, respectively (p>0.05). In conclusion, replacing CM with PJP did not negatively affect growth performance and carcass characteristics and could be used as potential supplement to mitigate methane emissions. Further in vivo studies involving respiration chambers are recommended to investigate the CH4 reduction potential of PJP.
Genomic dissection of the correlation between milk yield and various health traits using functional and evolutionary information about imputed sequence variants of 34,497 German Holstein cows
(2024) Schneider, Helen; Krizanac, Ana-Marija; Falker-Gieske, Clemens; Heise, Johannes; Tetens, Jens; Thaller, Georg; Bennewitz, Jörn
Background: Over the last decades, it was subject of many studies to investigate the genomic connection of milk production and health traits in dairy cattle. Thereby, incorporating functional information in genomic analyses has been shown to improve the understanding of biological and molecular mechanisms shaping complex traits and the accuracies of genomic prediction, especially in small populations and across-breed settings. Still, little is known about the contribution of different functional and evolutionary genome partitioning subsets to milk production and dairy health. Thus, we performed a uni- and a bivariate analysis of milk yield (MY) and eight health traits using a set of ~34,497 German Holstein cows with 50K chip genotypes and ~17 million imputed sequence variants divided into 27 subsets depending on their functional and evolutionary annotation. In the bivariate analysis, eight trait-combinations were observed that contrasted MY with each health trait. Two genomic relationship matrices (GRM) were included, one consisting of the 50K chip variants and one consisting of each set of subset variants, to obtain subset heritabilities and genetic correlations. In addition, 50K chip heritabilities and genetic correlations were estimated applying merely the 50K GRM. Results: In general, 50K chip heritabilities were larger than the subset heritabilities. The largest heritabilities were found for MY, which was 0.4358 for the 50K and 0.2757 for the subset heritabilities. Whereas all 50K genetic correlations were negative, subset genetic correlations were both, positive and negative (ranging from -0.9324 between MY and mastitis to 0.6662 between MY and digital dermatitis). The subsets containing variants which were annotated as noncoding related, splice sites, untranslated regions, metabolic quantitative trait loci, and young variants ranked highest in terms of their contribution to the traits’ genetic variance. We were able to show that linkage disequilibrium between subset variants and adjacent variants did not cause these subsets’ high effect. Conclusion: Our results confirm the connection of milk production and health traits in dairy cattle via the animals’ metabolic state. In addition, they highlight the potential of including functional information in genomic analyses, which helps to dissect the extent and direction of the observed traits’ connection in more detail.
Evaluation of fresh and preserved sheep faeces as an inoculum source in in vitro gas production assays
(2025) Rippstein, Lena; Rodehutscord, Markus
In order to meet the animals’ requirements of energy and nutrients, knowledge of the feed value of individual feed components is essential. In this context, information on ruminal degradability of feeds is crucial for formulating rations for ruminants. Information of this kind can be obtained using in vitro methods, such as the Hohenheim gas test (HGT). This method allows for the estimation of the organic matter digestibility and the energy value, as well as the protein value of ruminant feeds when applying the extended HGT (eHGT). In vitro methods provide a cost-efficient, rapid, and standardisable alternative to in situ and in vivo approaches, while contributing to reducing animal burden and the number of experimental animals. However, the HGT currently depends on using rumen fluid, which is commonly obtained from rumen-cannulated animals. Due to ethical concerns related to animal welfare and practical considerations, there is growing interest in replacing rumen-cannulated animals for the in vitro feed evaluation in the HGT and eHGT systems. However, the use of individual enzymes or enzyme mixtures for in vitro evaluation of feeds has not yet proven suitable for adequately representing the complex microbial activity of a rumen fluid inoculum (RI). In contrast, several findings in the literature indicate the potential of faeces as an alternative inoculum source to rumen fluid. However, to date, this approach has not been established in the routine analysis of ruminant feeds. The overarching aim of the present thesis was to systematically evaluate the suitability of sheep faeces as an alternative inoculum source to rumen fluid in the HGT. To this end, in vitro gas production (GP) was compared between faecal inoculum (FI) and RI. Additionally, the potential of using preserved faeces as an alternative inoculum source to fresh faeces, as well as the application of FI in the eHGT system, was evaluated. To compare faeces and rumen fluid as inoculum sources in the HGT and eHGT, RI was prepared according to the standard procedure using rumen fluid obtained from two rumen-cannulated lactating dairy cows and FI was prepared from rectally collected faeces of three adult wether sheep. The objective of Manuscript 1 was to examine whether FI and RI generally follow similar GP kinetics and to assess whether feed-specific variation could be observed. Furthermore, there was considerable interest in determining whether FI-GP and RI-GP are related to each other, as this could provide the basis for the future applicability of FI. A total of 90 currently relevant ruminant feeds from various categories and differing nutrient compositions were incubated in vitro with both FI and RI for 72 h, with multiple readings in the HGT. By using FI, lower GP kinetics were observed across all feed categories compared to RI. On average of all feeds, the potential GP was 9 mL/200 mg dry matter (DM) lower and the GP rate was 3.1%/h lower with FI than RI. Additionally, a lag phase of 1.51 h was estimated with FI, whereas no lag phase was observed for RI. The results indicate an overall lower fermentation activity of FI compared to RI. Despite these differences, the GP kinetic curves of the two inocula exhibited a very similar progression. Moreover, strong linear relationships were found between RI-GP at 24 h, the common incubation time of RI in the HGT, and FI-GP at both 24 h (Slope = 1.02, R² = 0.97) and 48 h (Slope = 1.1, R² = 0.97). Additionally, within the scope of this thesis, linear regression analyses were conducted based on a combined dataset from Manuscript 1 and previous studies. By using data from more than 400 different feeds in these analyses, the strong linear relationships between RI-GP at 24 h and FI-GP at 24 h (Slope = 0.98, R² = 0.93) as well as 48 h (Slope = 1.02, R² = 0.96) were confirmed. Dividing the dataset into the feed categories roughages and concentrates for the calculation of separate regression equations did not provide a clear advantage over using a single equation for all feeds. Despite the lower GP observed with FI, a consistent relationship was evident between the GP of both inocula across the different feeds, enabling a reliable estimation of RI-GP from FI-GP in the HGT. The use of preserved instead of fresh faeces would allow for a centralised housing of donor sheep, thereby reducing the number of animals required and improving standardisation. The aim of Manuscript 2 was to investigate the effect of differently preserved sheep faeces on the in vitro GP of nine different feeds and the microbiome in the HGT, intending to maintain a high level of microbial activity during incubations. Seven different freezing and freeze-drying treatments were applied. On average across all feeds, the potential GP of the frozen treatments (61 mL/200 mg DM) was comparable to that of the fresh faeces (62 mL/200 mg DM), whereas the freeze-dried treatments accounted for only 71-85% of the fresh faecal value. The results were confirmed by metaproteome analyses, as the microbiomes of the fresh and frozen treatments were significantly different from that of the freeze-dried treatments based on the relative abundance of the core proteins (p < 0.001). This demonstrated that stress factors associated with the freeze-drying process significantly impaired the microbiome, consequently affecting fermentation activity and GP. By contrast, the freezing process appeared more gentle on the microbiome, preserving a high microbial activity. Furthermore, strong relationships were found between RI-GP at 24 h and GP of the frozen treatments at 48 h of incubation (Slope = 1.27, R² = 0.96). Additionally, the effect of storage on freeze-dried and frozen treatments was investigated, revealing a considerable negative impact on GP and its relationship with RI-GP for both treatments. This limits the high potential for estimating RI-GP, which was particularly demonstrated with frozen faeces, and therefore requires further research. Manuscript 3 aimed to investigate the potential suitability of FI in the eHGT for estimating the protein value of ruminant feeds. The eHGT is used to estimate ruminally undegradable crude protein (RUP) and microbial crude protein. Ammonia-nitrogen (NH3-N) is a key parameter in this context, as it is released during microbial crude protein degradation and provides a nitrogen source for the microbes. FI and RI were therefore compared based on NH3-N and calculated microbially bound nitrogen (mN) following in vitro incubation of six different feeds for 8, 24, and 48 h. The NH3 N content was 17 and 23% lower with FI than with RI after 24 and 48 h, respectively. With RI, mN values decreased over the incubation time for most feeds, whereas with FI, mN initially increased before declining at later incubation times. This suggests that crude protein degradation and microbial binding of nitrogen occur more slowly and to a lesser extent with FI. However, both inocula demonstrated a comparable response to an additional energy source and showed strong linear relationships for NH3-N, particularly after 24 h (Slope = 1.39, R² = 0.98), indicating similar microbial mechanisms in faeces and rumen fluid. The RUP was also estimated for both inocula in this thesis, and the results showed an inconsistent ratio between FI and RI incubations across the six feeds. Similarly, an inconsistent ratio between the two inocula was observed for the mN data. Therefore, further studies involving a larger number of feeds, as well as the testing of mathematical approaches, are necessary to better evaluate the suitability of FI for estimating the protein value of ruminant feeds with the eHGT. In conclusion, the use of sheep faeces as an inoculum source for the in vitro analysis of ruminant feeds can be considered suitable for replacing rumen fluid and thus rumen-cannulated animals in the HGT. By reliably predicting the RI-GP from FI-GP, the predicted RI-GP can be used in the official and validated equations to estimate organic matter digestibility and metabolisable energy of ruminant feeds. The methodological approach applied in this thesis, including sheep feeding, faeces collection, and inoculum preparation, appeared appropriate in achieving a high and consistent microbial activity in the FI. Furthermore, a high potential was demonstrated for using preserved, particularly frozen, sheep faeces for application in the HGT, as well as the use of FI for estimating the protein value of feeds in the eHGT. However, further investigations are required for the two application fields to assess the suitability of FI comprehensively.
Effects of herbal feed additives and processing methods on the concentration of skatole in the adipose tissue of pigs
(2024) Marro, Philipp; Stefanski, Volker
Die betäubungslose Kastration männlicher Ferkel ist seit 2021 verboten; Alternativen wie die Ebermast bergen jedoch das Risiko von Ebergeruch, der hauptsächlich durch Androstenon und Skatol verursacht wird. Da ein ausreichender Schutz der Verbraucher vor geruchsbelastetem Fleisch bislang nicht gewährleistet ist, werden sowohl fütterungsbasierte Maßnahmen zur Reduktion der Skatolbildung als auch verarbeitungstechnische Ansätze diskutiert. Ziel der Arbeit war es daher, den Einfluss verschiedener Pflanzenextrakte und ätherischer Öle aus Oregano, Schisandra chinensis und Knoblauch auf die Bildung und den Abbau von Skatol zu untersuchen und gleichzeitig die Wirksamkeit der Fleischverarbeitung zur Reduktion von Skatol und Androstenon zu bewerten. Die Untersuchungen zum Skatolstoffwechsel bei kastrierten männlichen Schweinen zeigten, dass die Supplementierung der Zusätze in die Aktivität des Cytochrom-P450-Enzymkomplexes (CYP2E1 und CYP2A) eingreifen kann. Knoblauchöl senkte die Aktivität von CYP2A und führte zu erhöhten Skatolkonzentrationen in Plasma und Fettgewebe. Oregano und Schisandra chinensis hatten dagegen keinen Einfluss auf die enzymatische Aktivität oder die Skatolkonzentrationen. Die Analyse des Darminhalts entlang des Dickdarms zeigte ebenfalls keine reduzierende Wirkung der Zusätze; zudem gab es keine Unterschiede in der Skatolproduktion zwischen Caecum, Colon und Rektum. Eine Korrelationsanalyse machte deutlich, dass bei Zugabe von Knoblauch und Schisandra chinensis positive Zusammenhänge zwischen den Skatolkonzentrationen in Plasma, Fett und Darminhalt bestehen. Insgesamt konnten die eingesetzten Zusätze unter den verwendeten Bedingungen – einschließlich Konzentration, Darreichungsform und Anwendungsdauer – die Skatolkonzentration nicht senken, während Knoblauch sie sogar erhöhte. Die Untersuchung der Fleischverarbeitung anhand von Salami, Wiener Würstchen und Leberwurst ergab, dass Androstenon durch Hitzeeinwirkung reduziert werden kann, während Skatol insbesondere durch Räucherung verringert wurde. Eine Kombination beider Verfahren erscheint somit als geeignetes Mittel, um stark geruchsbelastetes Fleisch weiterzuverarbeiten und verbrauchertaugliche Produkte herzustellen. Insgesamt zeigt die Arbeit, dass die getesteten ätherischen Öle und Pflanzenextrakte unter den untersuchten Bedingungen nicht zur Senkung der Skatolkonzentration beitragen. Gleichzeitig wird deutlich, dass spezifische Verarbeitungsschritte ein wirkungsvolles Instrument darstellen, um die Geruchsbelastung von Fleisch mit erhöhtem Androstenon- und Skatolgehalt zu reduzieren.
Complex European invasion history of Anoplophora glabripennis (Motschulsky): new insights in its population genomic differentiation using genotype-by-sequencing
(2024) Haeussermann, Iris; Hasselmann, Martin
Anthropogenic activities like trade facilitate increasing rates of biological invasions. Asian long-horned beetle (ALB), which is naturally distributed in eastern Asia (China, Korean peninsula), was introduced via wood packing materials (WPM) used in trade to North America (1996) and Europe (2001). We used 7810 single nucleotide polymorphisms (SNPs) derived by a genotype-by-sequencing (GBS) approach to decipher the introduction patterns into Europe. This is applied for the first time on European ALB outbreaks from Germany, Switzerland, and Italy, both from still active and already eradicated infestations. The genome-wide SNPs detected signs of small and highly structured populations within Europe, showing clear founder effects. The very high population differentiation is presumably derived from multiple independent introductions to Europe, which are spatially restricted in mating. By admixture and phylogenetic analyses, some cases of secondary dispersal were observed. Furthermore, some populations suggest admixture, which might have been originated by either multiple introductions from different sources into the new sites or recurrent introductions from an admixed source population. Our results confirmed a complex invasion history of the ALB into Europe and the usability of GBS obtained SNPs in invasion science even without source populations.
Mendelian randomization analysis of 34,497 German Holstein cows to infer causal associations between milk production and health traits
(2024) Schneider, Helen; Haas, Valentin; Krizanac, Ana-Marija; Falker-Gieske, Clemens; Heise, Johannes; Tetens, Jens; Thaller, Georg; Bennewitz, Jörn
Background: Claw diseases and mastitis represent the most important health issues in dairy cattle with a frequently mentioned connection to milk production. Although many studies have aimed at investigating this connection in more detail by estimating genetic correlations, they do not provide information about causality. An alternative is to carry out Mendelian randomization (MR) studies using genetic variants to investigate the effect of an exposure on an outcome trait mediated by genetic variants. No study has yet investigated the causal association of milk yield (MY) with health traits in dairy cattle. Hence, we performed a MR analysis of MY and seven health traits using imputed whole-genome sequence data from 34,497 German Holstein cows. We applied a method that uses summary statistics and removes horizontal pleiotropic variants (having an effect on both traits), which improves the power and unbiasedness of MR studies. In addition, genetic correlations between MY and each health trait were estimated to compare them with the estimates of causal effects that we expected. Results: All genetic correlations between MY and each health trait were negative, ranging from − 0.303 (mastitis) to − 0.019 (digital dermatitis), which indicates a reduced health status as MY increases. The only non-significant correlation was between MY and digital dermatitis. In addition, each causal association was negative, ranging from − 0.131 (mastitis) to − 0.034 (laminitis), but the number of significant associations was reduced to five nominal and two experiment-wide significant results. The latter were between MY and mastitis and between MY and digital phlegmon. Horizontal pleiotropic variants were identified for mastitis, digital dermatitis and digital phlegmon. They were located within or nearby variants that were previously reported to have a horizontal pleiotropic effect, e.g., on milk production and somatic cell count. Conclusions: Our results confirm the known negative genetic connection between health traits and MY in dairy cattle. In addition, they provide new information about causality, which for example points to the negative energy balance mediating the connection between these traits. This knowledge helps to better understand whether the negative genetic correlation is based on pleiotropy, linkage between causal variants for both trait complexes, or indeed on a causal association.
Projecting the impact of climate change on honey bee plant habitat distribution in Northern Ethiopia
(2024) Gebremedhn, Haftom; Gebrewahid, Yikunoamlak; Haile, Gebremedhin Gebremeskel; Hadgu, Gebre; Atsbha, Tesfay; Hailu, Teweldemedhn Gebretinsae; Bezabih, Gebreamlak
Climate change significantly affects the diversity, growth, and survival of indigenous plant species thereby influencing the nutrition, health and productivity of honey bees ( Apis mellifera ). Hypoestes forskaolii (Vahl) is one of the major honey bee plant species in Ethiopia’s Tigray region. It is rich in pollen and nectar that typically provides white honey, which fetches a premium price in both local and inter-national markets. Despite its socio-economic and apicultural significance, the distribution of H. forskaolii has been declining, raising concerns regarding its conservation efforts. However, there is limited knowledge on how environmental and climatic factors affect its current distribution and response to future climate change. The study investigates the current and projected (the 2030s, 2050s, 2070s, and 2090s) habitat distributions of H. forskaolii under three future climate change scenarios (ssp126, ssp245, and ssp585) using the Maximum Entropy Model (MaxEnt). The results show that land use (50.1%), agro-ecology (28%), precipitation during the Driest Quarter (11.2%) and soil texture (6.1%) predominantly influence the distribution of H. forskaolii, collectively explaining 95.4% of the model's predictive power. Habitats rich in evergreen trees and mosaic herbaceous with good vegetation cover are identified as the most suitable for H. forskaolii . The spatial distribution of H. forskaolii is concentrated in the highlands and mid-highlands of the eastern and southern parts of Tigray, characterized by a colder temperature. Across the three climate change scenarios, the size of suitable habitat for H. forskaolii is projected to decrease over the four time periods studied. Predictions under the ssp585 scenario reveal alarming results, indicating a substantial decrease in the suitable habitat for H. forskaolii from 4.26% in the 2030s to 19.09% in the 2090s. Therefore, given the challenges posed by climate change, research efforts should focus on identifying and evaluating new technologies that can help the H. forskaolii species in adapting and mitigating the effects of climate change.
Expression of fibroblast growth factor 23 (FGF23) and αKlotho in two commercial laying hen strains fed with and without dietary mineral P supplements before and after the onset of the laying phase
(2025) Meier, Leonie; Wallauch, Nadine; Feger, Martina; Oster, Michael; Sommerfeld, Vera; Schmucker, Sonja; Wimmers, Klaus; Huber, Korinna; Stefanski, Volker; Rodehutscord, Markus; Föller, Michael
Maintenance of phosphate homeostasis is particularly critical in laying hens for bone formation and calcium mobilization. The supplementation of their feed with mineral phosphate is common although recent research questions the usual levels of supplementation. Phosphate homeostasis is classically regulated by active vitamin D (calcitriol) and parathyroid hormone, whereas fibroblast growth factor 23 (FGF23) and its co-receptor αKlotho are novel factors. FGF23 has emerged as an important disease biomarker and αKlotho as an anti-aging factor in mammals, however, little is known about their role in poultry. Here, we studied FGF23 and αKlotho expression in two commercial laying hen strains under conditions of dietary mineral phosphorus renunciation and sufficient phosphorus supply. Fifteen- and 20-week-old Lohmann Brown-Classic (LB) or LSL-Classic (LSL) hens were fed a standard maize-soybean-based diet containing 0 or 1 g/kg additional mineral phosphorus for 4 weeks. The animals were sacrificed, and gene expression studied in different organs by quantitative real-time PCR and protein expression by western blotting. Statistical correlation with further parameters of mineral metabolism was analyzed by Pearson’s correlation coefficient or Spearman’s Rho. As a result, FGF23 bone expression was significantly lower and hepatic FGF23 expression higher in 24-week-old than in 19-week-old hens. Bone, hepatic, and renal αKlotho expression was significantly higher in older than younger animals. Compared to LB hens, LSL hens exhibited higher hepatic αKlotho irrespective of diet and age. Dietary phosphorus content did not significantly affect FGF23 and αKlotho expression. Bone FGF23 expression was positively and hepatic FGF23 negatively associated with plasma phosphate concentration whereas bone FGF23 expression was negatively and hepatic FGF23 positively associated with plasma calcitriol concentration. To conclude, we uncovered a strong impact of age and strain on FGF23 and αKlotho expression in two high performance laying hen strains, effects possibly associated with initiation of the egg-laying phase. Moreover, the regulation of hepatic FGF23 expression differed from the regulation of bone FGF23 expression. Further studies are needed to elucidate the physiological relevance.
Mapping genes for resilient dairy cows by means of across-breed genome-wide association analysis
(2025) Keßler, Franziska; Zölch, Maximilian; Wellman, Robin; Bennewitz, Jörn
Background: Indicator traits based on variance and autocorrelation of longitudinal data are increasingly used to measure resilience in animal breeding. While these traits show promising heritability and can be routinely collected, their genetic architecture remains poorly understood. We conducted GWAS for three resilience indicators across German Holstein ( n = 2,300), Fleckvieh ( n = 2,330), and Brown Swiss ( n = 1,073) dairy cattle ( Bos Taurus ) populations. The indicators included variance ( ) and autocorrelation ( ) of deviations of observed from predicted daily milk yield and variance of relative daily milk yield ( ). Additionally, we analysed a selection index combining these traits. Prior to GWAS, we examined population structure through multi-dimensional scaling (MDS) and LD patterns, revealing distinct genetic clusters for each breed and similar LD decay patterns. Results: The GWAS results confirmed the polygenic nature of resilience, with multiple genomic regions showing significant associations. Notable signals were detected on BTA5 ( ), BTA14 ( ), BTA2 and BTA8 ( ) for single indicator traits. For selection index resilience, strong suggestive SNPs are located on BTA4 , BTA16 , BTA21 , and BTA27 . Detected regions overlapped with previously reported QTLs for performance, reproduction, longevity and health, providing new insights into the biological pathways underlying dairy cattle resilience. Conclusions: Our findings demonstrate that resilience indicators have a complex genetic architecture with both breed-specific and shared components, supporting their potential use in selective breeding programs while highlighting the importance of careful trait definition.
Microbiota and nutrient portraits of European roe deer (Capreolus capreolus) rumen contents in characteristic Southern German habitats
(2023) Dahl, Sarah-Alica; Seifert, Jana; Camarinha-Silva, Amélia; Cheng, Yu-Chieh; Hernández-Arriaga, Angélica; Hudler, Martina; Windisch, Wilhelm; König, Andreas
Roe deer ( Capreolus capreolus ) are found in various habitats, from pure forest cultures to agricultural areas and mountains. In adapting to the geographically and seasonally differentiating food supply, they depend, above all, on an adapted microbiome. However, knowledge about the microbiome of wild ruminants still needs to be improved. There are only a few publications for individual species with a low number of samples. This study aims to identify a core microbiota for Bavarian roe deer and present nutrient and microbiota portraits of the individual habitat types. This study investigated the roe deer’s rumen (reticulorumen) content from seven different characteristic Bavarian habitat types. The focus was on the composition of nutrients, fermentation products, and the rumen bacterial community. A total of 311 roe deer samples were analysed, with the most even possible distribution per habitat, season, age class, and gender. Significant differences in nutrient concentrations and microbial composition were identified for the factors habitat, season, and age class. The highest crude protein content (plant protein and microbial) in the rumen was determined in the purely agricultural habitat (AG), the highest value of non-fibre carbohydrates in the alpine mountain forest, and the highest fibre content (neutral detergent fibre, NDF) in the pine forest habitat. Maximum values for fibre content go up to 70% NDF. The proportion of metabolites (ammonia, lactate, total volatile fatty acids) was highest in the Agriculture-Beech-Forest habitat (ABF). Correlations can be identified between adaptations in the microbiota and specific nutrient concentrations, as well as in strong fluctuations in ingested forage. In addition, a core bacterial community comprising five genera could be identified across all habitats, up to 44% of total relative abundance. As with all wild ruminants, many microbial genera remain largely unclassified at various taxonomic levels. This study provides a more in-depth insight into the diversity and complexity of the roe deer rumen microbiota. It highlights the key microorganisms responsible for converting naturally available nutrients of different botanical origins.
The AnimalAssociatedMetagenomeDB reveals a bias towards livestock and developed countries and blind spots in functional-potential studies of animal-associated microbiomes
(2023) Avila Santos, Anderson Paulo; Kabiru Nata’ala, Muhammad; Kasmanas, Jonas Coelho; Bartholomäus, Alexander; Keller-Costa, Tina; Jurburg, Stephanie D.; Tal, Tamara; Camarinha-Silva, Amélia; Saraiva, João Pedro; Ponce de Leon Ferreira de Carvalho, André Carlos; Stadler, Peter F.; Sipoli Sanches, Danilo; Rocha, Ulisses
Background: Metagenomic data can shed light on animal-microbiome relationships and the functional potential of these communities. Over the past years, the generation of metagenomics data has increased exponentially, and so has the availability and reusability of data present in public repositories. However, identifying which datasets and associated metadata are available is not straightforward. We created the Animal-Associated Metagenome Metadata Database (AnimalAssociatedMetagenomeDB - AAMDB) to facilitate the identification and reuse of publicly available non-human, animal-associated metagenomic data, and metadata. Further, we used the AAMDB to (i) annotate common and scientific names of the species; (ii) determine the fraction of vertebrates and invertebrates; (iii) study their biogeography; and (iv) specify whether the animals were wild, pets, livestock or used for medical research. Results: We manually selected metagenomes associated with non-human animals from SRA and MG-RAST. Next, we standardized and curated 51 metadata attributes (e.g., host, compartment, geographic coordinates, and country). The AAMDB version 1.0 contains 10,885 metagenomes associated with 165 different species from 65 different countries. From the collected metagenomes, 51.1% were recovered from animals associated with medical research or grown for human consumption (i.e., mice, rats, cattle, pigs, and poultry). Further, we observed an over-representation of animals collected in temperate regions (89.2%) and a lower representation of samples from the polar zones, with only 11 samples in total. The most common genus among invertebrate animals was Trichocerca (rotifers). Conclusion: Our work may guide host species selection in novel animal-associated metagenome research, especially in biodiversity and conservation studies. The data available in our database will allow scientists to perform meta-analyses and test new hypotheses (e.g., host-specificity, strain heterogeneity, and biogeography of animal-associated metagenomes), leveraging existing data. The AAMDB WebApp is a user-friendly interface that is publicly available at https://webapp.ufz.de/aamdb/ .
Characterization of host and bacterial proteins in crossbred grower pigs at marginal lysine concentration
(2025) Kurz, Alina; Seifert, Jana
The current pork production strategies still result in high nitrogen emissions and thus harmful effects on the environment. The animals excrete about two-thirds of the protein in the diet unused, which increases nitrogen emissions and makes feeding the animals according to their needs expensive and inefficient. To minimize the negative aspects of pork production, it is important to reduce the use of proteins in feed while improving the protein efficiency of pigs. Improving protein efficiency requires a comprehensive understanding of physiological processes, particularly enzymatic activities, amino acid transporter capacities, the proteome, the metabolome and the microbiome. The aim of this work was therefore to identify animal- specific and quantitatively expressed proteins, enzymes, amino acid transporters and metabolites and to correlate these findings with protein turnover data. The study also examined whether the efficiency of protein utilization is influenced by these variables. A total of 48 male crossbred animals (German Landrace x Pietrain) were slaughtered in the 21st week of life for the present experiment. The animals were kept individually under the same conditions from the 75th day of life until the day of slaughter. A two-phase ad libitum feeding was carried out, with the change from phase 1 to phase 2 taking place in the 14th week of life. Since the genetic potential of protein utilization efficiency was to be estimated, the content of the first limiting amino acid lysine was 90 %, just below the GfE (2006) requirement limit in order to ensure a limiting factor for the protein approach. Thus, lysine was the limiting factor for protein retention and allowed animals to exploit their full genetic potential for protein utilization. After euthanizing, the animals were opened, and the stomach, small intestine and large intestine removed. Mucosal samples were taken from the sections of the pars nonglandularis, cardiac gland zone and pars pylorica, as well as digesta samples from the stomach. In addition, digesta and mucosal samples were collected from the duodenum, jejunum, ileum, colon, and cecum. The proteome in all samples was analyzed. The metabolome and enzyme activities were determined in all digesta samples. In addition, amino acid transporter expression was examined in all small intestinal mucosal samples. The activity of the enzymes trypsin, chymotrypsin, carboxypeptidase A and carboxypeptidase B were examined in the digesta samples from all sections. The highest activities were found in the small intestine, the lowest activities in the stomach and large intestine. The trypsin and chymotrypsin activity was highest in the jejunum, whereas the activities of the carboxypeptidases were highest in the duodenum. In addition, individual animal differences in enzyme activities could be identified. In addition, the expression rate of various amino acid transporters was examined in the present work. In the duodenum the transporter SLC1A5 showed the highest expression rate, in the jejunum the transporters SLC5A1 and SLC6A19. In the ileum, the rates of the transporters SLC1A1, SLC7A1 and SLC7A9 were at the highest level. The identification of the host proteome revealed different protein patterns in the examined sections of the gastrointestinal tract. In particular, host proteins were identified in the mucosa samples, with the exception of those from the ileum and cecum. The high number of host proteins in the mucosa samples, which are associated with cellular processes and metabolism, underlines its role in physiological digestive processes. In addition, the examined host proteins could be assigned to numerous KEGG pathways, thus creating a deeper understanding of physiological and metabolic pathways. The study of the bacterial proteome allowed not only categorization into different metabolic pathways, but also identification of the active microbiome in the different sections. For example, it was shown that Firmicutes dominate in the stomach and small intestine, whereas Bacteroidetes are mainly found in the large intestine. This highlights the different roles of the sections examined, with Firmicutes being primarily responsible for breaking down proteins and carbohydrates and Bacteroidetes playing a central role in the fermentation of undigested proteins and carbohydrates in the large intestine. Additionally, the increased presence of Tenericutes in the mucosal samples indicated a possible specialization of this family to the conditions in the mucosal environment, where they interact with host cells and contribute to metabolic processes. The identification of numerous unclassified bacterial groups also shows how complex the composition of the microbiome is and that further research must be carried out in order to be able to fully identify connections. The examination of the various metabolites in the digesta samples from the gastrointestinal tract showed clear differences in the detection rate. While the fatty acids acetate, butyrate, valerate, isobutyrate and propionate were found primarily in the sections of the large intestine, lactate, isovalerate and the amino acids showed a higher occurrence in the sections of the small intestine. This is in line with the scientific knowledge that fatty acids are primarily formed during microbial fermentation in the large intestine and should therefore occur in higher quantities here. Overall, the results of the present work showed that, in addition to physiological differences between the sections of the gastrointestinal tract, there also appear to be significant animal- specific differences in all parameters examined. These differences can have an influence on the efficiency of the animals, but it is still important to find out which factors cause these differences. Since the feeding, husbandry concept and experimental design were chosen in such a way that there is as little variation and discrepancy between the animals as possible, a genetic influence on the efficiency of the animals cannot be ruled out. If the animals' genetic potential to use nitrogen efficiently becomes apparent, a further foundation stone has been laid for making pork production tailored to needs and conserving resources and the environment.
Preference and possible consumption of provided enrichment and bedding materials and disinfectant powder by growing pigs
(2022) Koch, Felicitas; Kowalczyk, Janine; Mielke, Hans; Schenkel, Hans; Bachmann, Martin; Zeyner, Annette; Leinweber, Peter; Pieper, Robert
Background: Domestic pigs have an evolutionary conserved exploratory behaviour. To comply with this requirement, the European Union aims at setting standards for appropriate enrichment materials for pigs (Council Directive 2008/120/EC). As recommended characteristics include ‘chewable’ and ‘edible’, pigs might also consume these materials (Commission Recommendation (EU) 2016/336), which are often additionally advertised to enhance lying comfort and hygienic conditions in stables. To date, a wide range of bedding, enrichment and disinfectant materials is available on the market to ensure environmental enrichment, a dry, hygienic environment or lying comfort. Previous studies revealed considerable amounts of undesirable substances in some of these materials possibly being a risk for food safety considering oral uptake by the animal. To determine interest and indicators for consumption of different types of materials by pigs during exploratory behaviour, a camera-assisted observational study with 12 female pigs (German Landrace) was conducted. We tested their preference for a disinfectant powder, peat, biochar and straw as reference material in a 4 × 6 factorial arrangement. Results: Pigs manipulated and consumed all offered materials. However, longest manipulation time per pig was observed for biochar (63 min/day) and peat (50 min/day) (p < 0.05). Analyses of the bulk molecular-chemical composition and n-alkanes and acid insoluble ash as markers in the materials and in faeces clearly revealed the consumption of these materials by pigs. Conclusions: Whether the consumption of considerable amounts together with certain levels of undesirable substances represents a risk for pig and consumer health could yet not be established. Future studies will address the quantitative contribution of undesirable substances by oral ingestion of bedding and enrichment materials and disinfectant powders to the daily feed ration.
Defining valid breeding goals for animal breeds
(2023) Wellmann, Robin; Gengler, Nicolas; Bennewitz, Jörn; Tetens, Jens
Background: The objective of any valid breeding program is to increase the suitability of a breed for its future purposes. The approach most often followed in animal breeding for optimizing breeding goals assumes that the sole desire of the owners is profit maximization. As this assumption is often violated, a generalized approach is needed that does not rely on this assumption. Results: The generalized approach is based on the niche concept. The niche of a breed is a set of environments in which a small population of the breed would have a positive population growth rate. Its growth rate depends on demand from prospective consumers and supply from producers. The approach involves defining the niche that is envisaged for the breed and identifying the trait optima that maximize the breed’s adaptation to its envisaged niche within the set of permissible breeding goals. The set of permissible breeding goals is the set of all potential breeding goals that are compatible with animal welfare and could be reached within the planning horizon of the breeding program. In general, the breed’s adaptation depends on the satisfaction of the producers with the animals and on the satisfaction of the consumers with the products produced by the animals. When consumers buy live animals, then the breed needs to adapt to both the environments provided by the producers, and the environments provided by the consumers. The profit function is replaced by a more general adaptedness function that measures the breed’s adaptation to its envisaged niche. Conclusions: The proposed approach coincides with the traditional approach if the producers have the sole desire to maximize their income, and if consumer preferences are well reflected by the product prices. If these assumptions are not met, then the traditional approach to breeding goal optimization is unlikely to result in a valid breeding goal. Using the example of companion breeds, this paper shows that the proposed approach has the potential to fill the gap.
Food fermentation: an essential unit operation towards secure, sustainable, safe, and sustaining food systems
(2025) Gänzle, Michael G.; Seifert, Jana; Weiss, Jochen; Zijlstra, Ruurd T.
Lactic acid fermentation inactivates Salmonella Typhimurium in contaminated cattle manure at moderate and low temperatures
(2025) Halm, Hannah; Woelke, Sören; Lehnert, Ines; Schilling, Thorben; Meissner, Thorsten; Schröder, Charlotte; Hoelzle, Ludwig E.; Scheinemann, Hendrik A.; Britz, Margaret L.
In the case of a notifiable animal disease like salmonellosis, manure is contaminated and must be disinfected. This can be performed using heat measures, chemical disinfectants, or long-term storage. All these measures bring along severe economic, ecological, and logistical problems. The aim of this study was to evaluate lactic acid fermentation (LAF) as an alternative disinfection method. Fermentation was started by adding a carbohydrate source to the manure and creating anaerobic conditions. For testing, cattle manure was enriched with different carbohydrate (CHO) sources and spiked with Salmonella Typhimurium ( S. Ty.). The samples were incubated at 10 °C and 21 °C for 111 days (Exp1) and at 21 °C for 50 days (Exp2). The microbial shift was determined using cultural methods and MALDI-TOF. Both the change in pH and Enterococcus spp. were tested as suitable indicators. The results showed the different suitability of the selected CHO for hygienization by LAF. Using squeezed oat as an additive, S. Ty was reduced to below the detection limit under both temperature conditions within 21 days and 14 days. Additional saccharose decreased the reduction time. This study showed that LAF is a valuable alternative for disinfecting cattle manure in the case of bovine salmonellosis. Using this method, both manure and feed residues can be treated in one approach and afterwards be used as fertilizer.

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