Institut für Nutztierwissenschaften

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The active core microbiota of two high-yielding laying hen breeds fed with different levels of calcium and phosphorus
(2022) Roth, Christoph; Sims, Tanja; Rodehutscord, Markus; Seifert, Jana; Camarinha-Silva, Amélia
The nutrient availability and supplementation of dietary phosphorus (P) and calcium (Ca) in avian feed, especially in laying hens, plays a vital role in phytase degradation and mineral utilization during the laying phase. The required concentration of P and Ca peaks during the laying phase, and the direct interaction between Ca and P concentration shrinks the availability of both supplements in the feed. Our goal was to characterize the active microbiota of the entire gastrointestinal tract (GIT) (crop, gizzard, duodenum, ileum, caeca), including digesta- and mucosa-associated communities of two contrasting high-yielding breeds of laying hens (Lohmann Brown Classic, LB; Lohmann LSL-Classic, LSL) under different P and Ca supplementation levels. Statistical significances were observed for breed, GIT section, Ca, and the interaction of GIT section x breed, P x Ca, Ca x breed and P x Ca x breed (p < 0.05). A core microbiota of five species was detected in more than 97% of all samples. They were represented by an uncl. Lactobacillus (average relative abundance (av. abu.) 12.1%), Lactobacillus helveticus (av. abu. 10.8%), Megamonas funiformis (av. abu. 6.8%), Ligilactobacillus salivarius (av. abu. 4.5%), and an uncl. Fusicatenibacter (av. abu. 1.1%). Our findings indicated that Ca and P supplementation levels 20% below the recommendation have a minor effect on the microbiota compared to the strong impact of the bird’s genetic background. Moreover, a core active microbiota across the GIT of two high-yielding laying hen breeds was revealed for the first time.
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/ .
Anoxic cell rupture of Prevotella bryantii by high-pressure homogenization protects the Na+-translocating NADH:quinone oxidoreductase from oxidative damage
(2020) Schleicher, Lena; Fritz, Günter; Seifert, Jana; Steuber, Julia
Respiratory NADH oxidation in the rumen bacterium Prevotella bryantii is catalyzed by the Na+-translocating NADH:quinone oxidoreductase (NQR). A method for cell disruption and membrane isolation of P. bryantii under anoxic conditions using the EmulisFlex-C3 homogenizer is described. We compared NQR activity and protein yield after oxic and anoxic cell disruption by the EmulsiFlex, by ultrasonication, and by glass beads treatment. With an overall membrane protein yield of 50 mg L–1 culture and a NADH oxidation activity of 0.8 µmol min−1 mg−1, the EmulsiFlex was the most efficient method. Anoxic preparation yielded fourfold higher NQR activity compared to oxic preparation. P. bryantii lacks genes coding for superoxide dismutases and cell extracts do not exhibit superoxide dismutase activity. We propose that inactivation of NQR during oxic cell rupture is caused by superoxide, which accumulates in P. bryantii extracts exposed to air. Anoxic cell rupture is indispensable for the preparation of redox-active proteins and enzymes such as NQR from P. bryantii.
Assessing functional properties of diet protein hydrolysate and oil from fish waste on canine immune parameters, cardiac biomarkers, and fecal microbiota
(2024) Cabrita, Ana R. J.; Barroso, Carolina; Fontes-Sousa, Ana Patrícia; Correia, Alexandra; Teixeira, Luzia; Maia, Margarida R. G.; Vilanova, Manuel; Yergaliyev, Timur; Camarinha-Silva, Amélia; Fonseca, António J. M.
Locally produced fish hydrolysate and oil from the agrifood sector comprises a sustainable solution both to the problem of fish waste disposal and to the petfood sector with potential benefits for the animal’s health. This study evaluated the effects of the dietary replacement of mainly imported shrimp hydrolysate (5%) and salmon oil (3%; control diet) with locally produced fish hydrolysate (5%) and oil (3.2%) obtained from fish waste (experimental diet) on systemic inflammation markers, adipokines levels, cardiac function and fecal microbiota of adult dogs. Samples and measurements were taken from a feeding trial conducted according to a crossover design with two diets (control and experimental diets), six adult Beagle dogs per diet and two periods of 6 weeks each. The experimental diet, with higher docosahexaenoic (DHA) and eicosapentaenoic (EPA) acids contents, decreased plasmatic triglycerides and the activity of angiotensin converting enzyme, also tending to decrease total cholesterol. No effects of diet were observed on serum levels of the pro-inflammatory cytokines interleukin (IL)-1β, IL-8, and IL-12/IL-23 p40, and of the serum levels of the anti-inflammatory adipokine adiponectin. Blood pressure, heart rate and echocardiographic measurements were similar between diets with the only exception of left atrial to aorta diameter ratio that was higher in dogs fed the experimental diet, but without clinical relevance. Diet did not significantly affect fecal immunoglobulin A concentration. Regarding fecal microbiome, Megasphaera was the most abundant genus, followed by Bifidobacterium , Fusobacterium , and Prevotella , being the relative abundances of Fusobacterium and Ileibacterium genera positively affected by the experimental diet. Overall, results from the performed short term trial suggest that shrimp hydrolysate and salmon oil can be replaced by protein hydrolysate and oil from fish by-products without affecting systemic inflammatory markers, cardiac structure and function, but potentially benefiting bacterial genera associated with healthy microbiome. Considering the high DHA and EPA contents and the antioxidant properties of fish oil and hydrolysate, it would be worthwhile in the future to assess their long-term effects on inflammatory markers and their role in spontaneous canine cardiac diseases and to perform metabolomic and metagenomics analysis to elucidate the relevance of microbiota changes in the gut.
Assessing the combination efficiency of some unconventional feed resources with concentrates and Chloris gayana grass in mitigating ruminal methane production in vitro
(2024) Melesse, Aberra; Steingass, Herbert; Holstein, Julia; Titze, Natascha; Rodehutscord, Markus
In a preliminary in vitro study, leaves of Acacia nilotica, Prosopis juliflora, Cajanus cajan, Leucaena leucocephala and seed kernel of Mangifera indica were identified as potential candidates in mitigating ruminal methane (CH4) production. The objective of the current study was to investigate the combination efficiency of these unconventional feeds with concentrate mix (CM) or Chloris gayana grass in CH4 reduction. Two feed combinations in different proportions were incubated in vitro with buffered rumen fluid at Hohenheim Gas test. In combination 1, C. gayana and CM were included as basal substrates, while in combination 2, A. nilotica, P. juliflora, C. cajan, L. leucocephala or M. indica seed kernel were included as CH4 reducing supplements at different proportions. The CH4 reducing potentials of feed combinations were presented as the ratio of CH4 to net gas production and expressed as percentage (pCH4). The pCH4 for CM and C. gayana was 16.7% and 16.9%, respectively, while it ranged from 3.18% in A. nilotica to 13.1% in C. cajan. The pCH4 was reduced (p < 0.05) from 14.6% to 9.39% when A. nilotica was combined with CM. In combination of L. leucocephala or C. cajan with CM, the pCH4 (p < 0.05) was reduced from 16.5% and 16.6% with the lowest proportion to 15.1% and 15.2% with the highest inclusion rate respectively. The combination of C. gayana with L. leucocephala or C. cajan reduced (p < 0.05) the pCH4 from 16.3% and 16.4% to 15.1% and 14.9% respectively. The pCH4 was reduced (p < 0.05) from 13.4% to 7.60% when A. nilotica was combined with C. gayana. Estimated digestible organic matter (dOM) and metabolizable energy (ME) increased (p < 0.05) with increasing proportions of M. indica seed kernel with CM or C. gayana. In conclusion, the combination of the basal substrates with unconventional supplements resulted in CH4 reduction without affecting the dOM and ME at lower inclusion rates. Animal‐based experiments await to validate in vitro findings.
Changes of microorganism composition in fresh and stored bee pollen from Southern Germany
(2021) Friedle, Carolin; D’Alvise, Paul; Schweikert, Karsten; Wallner, Klaus; Hasselmann, Martin
Analysis of plant pollen can provide valuable insights into the existing spectrum of microorganisms in the environment. When harvesting bee-collected pollen as a dietary supplement for human consumption, timely preservation of the freshly collected pollen is fundamental for product quality. Environmental microorganisms contained in freshly collected pollen can lead to spoilage by degradation of pollen components. In this study, freshly collected bee pollen was sampled at different locations and stored under various storage conditions to examine the hypothesis that storage conditions may have an effect on the composition of microorganisms in pollen samples. The samples were analyzed using 16S and 18S amplicon sequencing and characterized by palynological analysis. Interestingly, the bacterial communities between pollen samples from different locations varied only slightly, whereas for fungal community compositions, this effect was substantially increased. Further, we noticed that fungal communities in pollen are particularly sensitive to storage conditions. The fungal genera proportion Cladosporium and Mycosphaerella decreased, while Zygosaccharomyces and Aspergillus increased during storage. Aspergillus and Zygosaccharomyces fractions increased during storage at 30 °C, which could negatively impact the pollen quality if it is used as a dietary supplement.
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.
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.
Composition of the ileum microbiota is a mediator between the host genome and phosphorus utilization and other efficiency traits in Japanese quail (Coturnix japonica)
(2022) Haas, Valentin; Vollmar, Solveig; Preuß, Siegfried; Rodehutscord, Markus; Camarinha-Silva, Amélia; Bennewitz, Jörn
Background: Phosphorus is an essential nutrient in all living organisms and, currently, it is the focus of much attention due to its global scarcity, the environmental impact of phosphorus from excreta, and its low digestibility due to its storage in the form of phytates in plants. In poultry, phosphorus utilization is influenced by composition of the ileum microbiota and host genetics. In our study, we analyzed the impact of host genetics on composition of the ileum microbiota and the relationship of the relative abundance of ileal bacterial genera with phosphorus utilization and related quantitative traits in Japanese quail. An F2 cross of 758 quails was genotyped with 4k genome-wide single nucleotide polymorphisms (SNPs) and composition of the ileum microbiota was characterized using target amplicon sequencing. Heritabilities of the relative abundance of bacterial genera were estimated and quantitative trait locus (QTL) linkage mapping for the host was conducted for the heritable genera. Phenotypic and genetic correlations and recursive relationships between bacterial genera and quantitative traits were estimated using structural equation models. A genomic best linear unbiased prediction (GBLUP) and microbial (M)BLUP hologenomic selection approach was applied to assess the feasibility of breeding for improved phosphorus utilization based on the host genome and the heritable part of composition of the ileum microbiota. Results: Among the 59 bacterial genera examined, 24 showed a significant heritability (nominal p ≤ 0.05), ranging from 0.04 to 0.17. For these genera, six genome-wide significant QTL were mapped. Significant recursive effects were found, which support the indirect host genetic effects on the host’s quantitative traits via microbiota composition in the ileum of quail. Cross-validated microbial and genomic prediction accuracies confirmed the strong impact of microbial composition and host genetics on the host’s quantitative traits, as the GBLUP accuracies based on the heritable microbiota-mediated components of the traits were similar to the accuracies of conventional GBLUP based on genome-wide SNPs. Conclusions: Our results revealed a significant effect of host genetics on composition of the ileal microbiota and confirmed that host genetics and composition of the ileum microbiota have an impact on the host’s quantitative traits. This offers the possibility to breed for improved phosphorus utilization based on the host genome and the heritable part of composition of the ileum microbiota.
Cow’s microbiome from antepartum to postpartum: a long-term study covering two physiological challenges
(2022) Tröscher-Mußotter, Johanna; Deusch, Simon; Borda-Molina, Daniel; Frahm, Jana; Dänicke, Sven; Camarinha-Silva, Amélia; Huber, Korinna; Seifert, Jana
Little is known about the interplay between the ruminant microbiome and the host during challenging events. This long-term study investigated the ruminal and duodenal microbiome and metabolites during calving as an individual challenge and a lipopolysaccharide-induced systemic inflammation as a standardized challenge. Strong inter- and intra-individual microbiome changes were noted during the entire trial period of 168 days and between the 12 sampling time points. Bifidobacterium increased significantly at 3 days after calving. Both challenges increased the intestinal abundance of fiber-associated taxa, e.g., Butyrivibrio and unclassified Ruminococcaceae. NMR analyses of rumen and duodenum samples identified up to 60 metabolites out of which fatty and amino acids, amines, and urea varied in concentrations triggered by the two challenges. Correlation analyses between these parameters indicated a close connection and dependency of the microbiome with its host. It turns out that the combination of phylogenetic with metabolite information supports the understanding of the true scenario in the forestomach system. The individual stages of the production cycle in dairy cows reveal specific criteria for the interaction pattern between microbial functions and host responses.
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.
Effects of calcium level and source, formic acid, and phytase on phytate degradation and the microbiota in the digestive tract of broiler chickens
(2021) Krieg, Jochen; Borda-Molina, Daniel; Siegert, Wolfgang; Sommerfeld, Vera; Chi, Yung Ping; Taheri, Hamid Reza; Feuerstein, Dieter; Camarinha-Silva, Amélia; Rodehutscord, Markus
Background: Diet acidification, dietary calcium (Ca) level, and phytase supplementation are known influences on the microbial community in the digestive tract and on phosphorus (P) utilization of broiler chickens. Effects of dietary factors and microbiota on P utilization may be linked because microorganisms produce enzymes that release P from phytate (InsP6), the main source of P in plant feedstuffs. This study aimed to detect linkages between microbiota and InsP6 degradation by acidifying diets (i.e., replacing Ca carbonate (CaCO3) by Ca formate or adding formic acid to CaCO3-containing diets), varying Ca levels, and supplementing phytase in a three-factorial design. We investigated i) the microbial community and pH in the digestive tract, ii) prececal (pc) P and Ca digestibility, and iii) InsP6 degradation. Results: All factors under investigation influenced digesta pH and the microbiota composition. Predicted functionality and relative abundance of microorganisms indicated that diets influenced the potential contribution of the microbiota on InsP degradation. Values of InsP6 degradation and relative abundance of the strains Lactobacillus johnsonii and Lactobacillus reuteri were correlated. Phytase supplementation increased pc InsP6 disappearance, with differences between Ca levels, and influenced concentrations of lower inositol phosphate isomers in the digestive tract. Formic acid supplementation increased pc InsP6 degradation to myo-inositol. Replacing CaCO3 by Ca-formate and the high level of these Ca sources reduced pc InsP6 disappearance, except when the combination of CaCO3 + formic acid was used. Supplementing phytase to CaCO3 + formic acid led to the highest InsP6 disappearance (52%) in the crop and increased myo-inositol concentration in the ileum digesta. Supplementing phytase leveled the effect of high Ca content on pc InsP6 disappearance. Conclusions: The results point towards a contribution of changing microbial community on InsP6 degradation in the crop and up to the terminal ileum. This is indicated by relationships between InsP6 degradation and relative abundance of phosphatase-producing strains. Functional predictions supported influences of microbiota on InsP6 degradation. The extent of such effects remains to be clarified. InsP6 degradation may also be influenced by variation of pH caused by dietary concentration and solubility of the Ca in the feed.
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.
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.
Fecal cortisol metabolites indicate increased stress levels in horses during breaking-in: a pilot study
(2025) Krieber, Julia; Nowak, Aurelia C.; Geissberger, Jakob; Illichmann, Oliver; Macho-Maschler, Sabine; Palme, Rupert; Dengler, Franziska; Madigan, John
Sport horses are frequently exposed to situations that were identified as stressors, indicated by an increased cortisol release, which might impair animal welfare. However, while many studies deal with the impact of exercise, transport, and competition on stress in horses, little is known about the early phase of a horse’s sports career and studies investigating the stress level of young horses during breaking-in are limited. To compare stress levels in unridden horses, horses during breaking-in, and horses in training we collected fecal samples of young, unridden horses ( n = 28) and of horses in different training stages ( n = 13) and measured fecal cortisol metabolite (FCM) concentrations. Our preliminary results showed that FCM concentrations of unridden horses were significantly lower than those of horses in training (Mann–Whitney rank sum test, p < 0.001). Particularly in the first year under the saddle FCMs were significantly higher than in unridden horses (one way ANOVA + post hoc Holm–Sidak test, p < 0.05), with a tendency for FCM levels to decrease with time in training. Furthermore, we observed that within the group of ridden horses there was a larger range of variability in FCM levels, suggesting individual variations regarding their ability to deal with (training-induced) stress. These results indicate that breaking-in is a stressful time for young horses, underlining the importance of carrying out the initial training as carefully as possible.
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.
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.
Identification of the key molecular drivers of phosphorus utilization based on host miRNA-mRNA and gut microbiome interactions
(2020) Ponsuksili, Siriluck; Reyer, Henry; Hadlich, Frieder; Weber, Frank; Trakooljul, Nares; Oster, Michael; Siengdee, Puntita; Muráni, Eduard; Rodehutscord, Markus; Camarinha-Silva, Amélia; Bennewitz, Jörn; Wimmers, Klaus
Phosphorus is an essential mineral for all living organisms and a limited resource worldwide. Variation and heritability of phosphorus utilization (PU) traits were observed, indicating the general possibility of improvement. Molecular mechanisms of PU, including host and microbial effects, are still poorly understood. The most promising molecules that interact between the microbiome and host are microRNAs. Japanese quail representing extremes for PU were selected from an F2 population for miRNA profiling of the ileal tissue and subsequent association with mRNA and microbial data of the same animals. Sixty-nine differentially expressed miRNAs were found, including 21 novel and 48 known miRNAs. Combining miRNAs and mRNAs based on correlated expression and target prediction revealed enrichment of transcripts in functional pathways involved in phosphate or bone metabolism such as RAN, estrogen receptor and Wnt signaling, and immune pathways. Out of 55 genera of microbiota, seven were found to be differentially abundant between PU groups. The study reveals molecular interactions occurring in the gut of quail which represent extremes for PU including miRNA-16-5p, miR-142b-5p, miR-148a-3p, CTDSP1, SMAD3, IGSF10, Bacteroides, and Alistipes as key indicators due to their trait-dependent differential expression and occurrence as hub-members of the network of molecular drivers of PU.
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.
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.

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