Institut für Nutztierwissenschaften

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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; Haeussermann, Iris; Institute of Animal Science, Department of Livestock Population Genomics, Centre for Biodiversity and Integrative Taxonomy (KomBioTa), University of Hohenheim, Stuttgart, Germany; Hasselmann, Martin; Institute of Animal Science, Department of Livestock Population Genomics, Centre for Biodiversity and Integrative Taxonomy (KomBioTa), University of Hohenheim, Stuttgart, Germany
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; Gebremedhn, Haftom; Ghent University, Ghent, Belgium; Gebrewahid, Yikunoamlak; Tigray Agricultural Research Institute, Mekelle, Ethiopia; Haile, Gebremedhin Gebremeskel; Department of Earth and Environmental Sciences, Wesleyan University, Middletown, USA; Hadgu, Gebre; Tigray Agricultural Research Institute, Mekelle, Ethiopia; Atsbha, Tesfay; Tigray Agricultural Research Institute, Mekelle, Ethiopia; Hailu, Teweldemedhn Gebretinsae; Institute of Animal Science, University of Hohenheim, Stuttgart, Germany; Bezabih, Gebreamlak; Tigray Agricultural Research Institute, Mekelle, Ethiopia
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; Keßler, Franziska; Institute of Animal Science, University of Hohenheim, Garbenstr. 17, 70599, Stuttgart, Germany; Zölch, Maximilian; Institute of Animal Science, University of Hohenheim, Garbenstr. 17, 70599, Stuttgart, Germany; Wellman, Robin; Institute of Animal Science, University of Hohenheim, Garbenstr. 17, 70599, Stuttgart, Germany; Bennewitz, Jörn; Institute of Animal Science, University of Hohenheim, Garbenstr. 17, 70599, Stuttgart, Germany
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.
Occurrence and quantification of porcine hemotrophic mycoplasmas in blood-sucking Stomoxys calcitrans
(2025) Arendt, Mareike; Hoelzle, Katharina; Stadler, Julia; Ritzmann, Mathias; Ade, Julia; Hoelzle, Ludwig E.; Schwarz, Lukas; Rossi, Franca
Hemotrophic mycoplasmas (HMs) are cell wall-less, small and uncultivable pathogens, which can cause infections in pigs with no to severe clinical signs and can contribute to significant economic losses in the pig industry. In addition to the known mechanical transmission routes of HMs (e.g., via blood-contaminated instruments or lesions from ranking fights), transmission to pigs by arthropod vectors such as Stomoxys calcitrans is being discussed. To date, there is scant available data concerning the transmission of HMs by stable flies. The objective of this study is to gain more data concerning the occurrence of HMs in Stomoxys calcitrans . Therefore, quantitative real-time PCR was conducted on different stable fly samples (surface washings and whole flies). We found Mycoplasma ( M. ) suis in 5.2% of crushed flies and 4.2% of fly wash solutions, and M. parvum was detected in 5.2% of flies and 9.4% of fly wash solutions. ‘ Candidatus ( Ca .) M. haemosuis’ was not detected in any sample. The mean bacterial loads were 2.0 × 10 2 M. suis /fly, 9.3 × 10 2 M. suis /fly wash solution and, for M. parvum , 2.4 × 10 3 M. parvum /fly and 2.1 × 10 3 M. parvum /fly wash solution. This molecular occurrence of porcine HMs in blood-sucking flies and reasonable bacterial loads in the two- to three-digit range demonstrate that these flies serve as mechanical vectors in stables and are, therefore, of epidemiological importance.
Effects of a transient lack of dietary mineral phosphorus on renal gene expression and plasma metabolites in two high-yielding laying hen strains
(2025) Qasir, Hiba; Reyer, Henry; Oster, Michael; Ponsuksili, Siriluck; Trakooljul, Nares; Sommerfeld, Vera; Rodehutscord, Markus; Wimmers, Klaus
Background: There is an emerging body of evidence that current poultry feed is formulated in excess for phosphorus (P), which results in unnecessarily high P excretions. Sustainable concepts for agricultural P flows should trigger animal-intrinsic mechanisms for efficient P utilization. In the current study, Lohmann Brown (LB) and Lohmann Selected Leghorn (LSL) laying hens were fed either a high P diet (P+) with 1 g/kg mineral P supplement or a low P diet (P-) with 0 g/kg mineral P supplement for a period of 4 weeks prior to sampling. Before and after onset of laying, i.e., at 19 and 24 weeks of life, kidney and plasma samples were collected to investigate the endogenous P utilization in response to restricted dietary P, laying hen strain, and sexual maturation. Results: Plasma analyses of minerals and metabolites confirmed the response to a low P diet, which was characterized by a significant reduction in plasma P levels at week 19 in both strains. The plasma calcium (Ca) levels were tightly regulated throughout the entire experimental period. Notably, there was a numerical trend of increased plasma calcitriol levels in P- fed birds of both strains compared to the P + group, which might have mediated a substantial role regarding the adaptive responses to low P supply. At week 19, RNA sequencing of kidney identified 1,114 and 556 differentially expressed genes (DEGs) unique to the LB and LSL strains, respectively. The number of DEGs declined with increasing maturity of the hens culminating in 90 and 146 DEGs for LB and LSL strains at week 24. Analyses revealed an enrichment of pathways related to energy metabolism and cell cycle, particularly at week 19 in both strains. The diet-specific expression of target genes involved in P homeostasis highlighted transcripts related to active ( SLC34A1 , SLC20A2 ) and passive mineral transport ( CLDN14 , CLDN16 ), Ca utilization ( STC1 , CALB1 ), and acid-base balance ( CA2 , SLC4A1 ). Conclusions: Results suggest that both laying hen strains adapted to the lack of mineral P supplements and achieved a physiological Ca: P-ratio in body compartments through endogenous regulation as evidenced via the endocrine profile.
Investigating the interplay of stressors and health in horses through fecal cortisol metabolite analysis
(2025) Nowak, Aurelia C.; Macho-Maschler, Sabine; Biermann, Nora M.; Palme, Rupert; Dengler, Franziska
Introduction: Horses are highly sensitive to stress, which can affect their wellbeing and lead to various health issues. Effective and objective stress assessment is therefore crucial for improving their care and management. The production of the glucocorticoid cortisol is increased in response to stressful stimuli and its metabolites can be measured non-invasively in feces. Therefore, this study aimed to explore the impact of different environmental and physiological stressors on fecal cortisol metabolite (FCM) concentrations in horses, with a particular focus on the relationship between stress, health, and welfare. We hypothesized that increased FCM levels may be indicative of disease and thus improve early detection and subsequent intervention. Methods: Fresh fecal samples of N = 41 horses (20 geldings and 21 mares) from the same herd were collected once weekly for 1 year. Horses had been housed in the same stable for at least a month and were accustomed to the habitat, daily routine, and social groups. Environmental conditions, health data, and potentially stressful events were recorded. Fecal concentrations of 11,17-dioxoandrostanes were measured via 11-oxoetiocholanolone enzyme immunoassay. Results: We showed stable baseline FCM concentrations of 6.3 ng/g feces (range 0.6–28.1 ng/g feces). During the summer months, median FCM concentrations increased significantly ( p < 0.05; One Way RM ANOVA), and this increase correlated with higher ambient temperatures ( p < 0.0001, adj r 2 = 0.669, Pearson Product Moment correlation). Additionally, other factors such as breed, coat color, and housing conditions influenced the FCM concentrations. Stressful events, such as riding exams and some painful conditions, also resulted in elevated FCM levels, although the magnitude of these responses varied across individual horses. However, not all diseases were associated with increased FCMs. Discussion: Our findings emphasize the complexity of the hypothalamic-pituitary-adrenal axis in horses, suggesting that while high FCM levels can indicate stress, they may not be reliable biomarkers for early disease detection. Particularly in the light of climate change, the impact of heat stress in the summer months should not be neglected and measures to improve the housing conditions accordingly should become an essential part of equine health management.
Host metabolome and faecal microbiome shows potential interactions impacted by age and weaning times in calves
(2023) Amin, Nida; Schwarzkopf, Sarah; Tröscher-Mußotter, Johanna; Camarinha-Silva, Amélia; Dänicke, Sven; Huber, Korinna; Frahm, Jana; Seifert, Jana
Background: Calves undergo nutritional, metabolic, and behavioural changes from birth to the entire weaning period. An appropriate selection of weaning age is essential to reduce the negative effects caused by weaning-related dietary transitions. This study monitored the faecal microbiome and plasma metabolome of 59 female Holstein calves during different developmental stages and weaning times (early vs. late) and identified the potential associations of the measured parameters over an experimental period of 140 days. Results: A progressive development of the microbiome and metabolome was observed with significant differences according to the weaning groups (weaned at 7 or 17 weeks of age). Faecal samples of young calves were dominated by bifidobacterial and lactobacilli species, while their respective plasma samples showed high concentrations of amino acids (AAs) and biogenic amines (BAs). However, as the calves matured, the abundances of potential fiber-degrading bacteria and the plasma concentrations of sphingomyelins (SMs), few BAs and acylcarnitines (ACs) were increased. Early-weaning at 7 weeks significantly restructured the microbiome towards potential fiber-degrading bacteria and decreased plasma concentrations of most of the AAs and SMs, few BAs and ACs compared to the late-weaning event. Strong associations between faecal microbes, plasma metabolites and calf growth parameters were observed during days 42–98, where the abundances of Bacteroides, Parabacteroides , and Blautia were positively correlated with the plasma concentrations of AAs, BAs and SMs as well as the live weight gain or average daily gain in calves. Conclusion: The present study reported that weaning at 17 weeks of age was beneficial due to higher growth rate of late-weaned calves during days 42–98 and a quick adaptability of microbiota to weaning-related dietary changes during day 112, suggesting an age-dependent maturation of the gastrointestinal tract. However, the respective plasma samples of late-weaned calves contained several metabolites with differential concentrations to the early-weaned group, suggesting a less abrupt but more-persistent effect of dietary changes on host metabolome compared to the microbiome.
Selection index theory for populations under directional and stabilizing selection
(2023) Wellmann, Robin
Background: The purpose of a selection index is that its use to select animals for breeding maximizes the profit of a breed in future generations. The profit of a breed is in general a quantity that predicts the satisfaction of future owners with their breed, and the satisfaction of the consumers with the products that are produced by the breed. Many traits, such as conformation traits and product quality traits have intermediate optima. Traditional selection index theory applies only to directional selection and cannot achieve any further improvement once the trait means have reached their optima. A well-founded theory is needed that extends the established selection index theory to cover directional as well as stabilizing selection as limiting cases, and that can be applied to maximize the profit of a breed in both situations. Results: The optimum selection index shifts the trait means towards the optima and, in the case of stabilizing selection, decreases the phenotypic variance, which causes the phenotypes to be closer to the optimum. The optimum index depends not only on the breeding values, but also on the squared breeding values, the allele contents of major quantitative trait loci (QTL), the QTL heterozygosities, the inbreeding coefficient of the animal, and the kinship of the animal with the population. Conclusion: The optimum selection index drives the alleles of major QTL to fixation when the trait mean approaches the optimum because decreasing the phenotypic variance shifts the trait values closer to the optimum, which increases the profit of the breed. The index weight on the kinship coefficient balances the increased genetic gain that can be achieved in future generations by outcrossing, and the increased genetic gain that can be achieved under stabilizing selection by reducing the phenotypic variance. In a model with dominance variance, it can also account for the effect of inbreeding depression. The combining ability between potential mating partners, which predicts the total merit of their offspring, could become an important parameter for mate allocation that could be used to further shift the phenotypes towards their optimum values.
Transcriptional responses to diets without mineral phosphorus supplementation in the jejunum of two high-yielding laying hen strains
(2024) Abitew, Yosef A.; Reyer, Henry; Hadlich, Frieder; Oster, Michael; Trakooljul, Nares; Sommerfeld, Vera; Rodehutscord, Markus; Wimmers, Klaus; Ponsuksili, Siriluck
Phosphorus (P) is an essential mineral for all forms of life including laying hens, playing a crucial role in growth and efficient egg production. Recent studies suggest that current P recommendations might exceed the physiological demand, leading to unnecessarily high P excretions. This study on Lohmann Brown (LB) and Lohmann Selected Leghorn (LSL) laying hens (n=80; 10 replicates per strain, production period, and dietary group) investigates transcriptional changes in the jejunum, a critical intestinal segment for mineral absorption, in response to a diet either without (P-) or with (P+) a mineral supplement from monocalcium phosphate, administered over a 4-week period during the transition (15–19 weeks) or onset of laying (20–24 weeks). DESeq2 analysis of RNA sequencing data revealed that most differentially expressed genes (DEGs) varied between strains and age groups, with less pronounced effects from dietary mineral P content. The 19-week-old LB hens showed a stronger response to dietary mineral P removal, with transcripts affiliated with increased adaptation of the metabolism and decreased immune pathway activation. The identified pathways such as folate biosynthesis and p53 signaling, potentially link altered energy and amino acid metabolism (2-oxocarboxylic acid and arginine). Interestingly, genes involved in calcium transport (CALB1) and cellular signaling (PRKCA, STEAP4) along with tight junctions (CLDN2) were affected by complete removal of mineral P supplements, suggesting a promoted intestinal mineral uptake. Transcriptional regulation in the jejunum in response to low dietary mineral content is strain-specific when the laying phase begins, which may contribute to a physiological Ca:P ratio.

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