Institut für Nutztierwissenschaften

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Predicting herbage biomass on small‐scale farms by combining sward height with different aggregations of weather data
(2024) Scheurer, Luca; Leukel, Joerg; Zimpel, Tobias; Werner, Jessica; Perdana‐Decker, Sari; Dickhoefer, Uta
Accurate predictions of herbage biomass are important for efficient grazing management. Small‐scale farms face challenges using remote sensing technologies due to insufficient resources. This limitation hinders their ability to develop machine learning‐based prediction models. An alternative is to adopt less expensive measurement methods and readily available data such as weather data. This study aimed to examine how different temporal aggregations of weather data combined with compressed sward height (CSH) affect the prediction performance. We considered weather features based on different numbers of weather variables, statistical functions, weather events, and periods. Between 2019 and 2021, data were collected from 11 organic dairy farms in Germany. Herbage biomass exhibited high variability (coefficient of variation [CV] = 0.65). Weather data were obtained from on‐farm and nearby public stations. Prediction models were learned on a training set ( n = 291) and evaluated on a test set ( n = 125). Random forest models performed better than models based on artificial neural networks and support vector regression. Representing weather data by a single feature for leaf wetness reduced the root mean square error (RMSE) by 12.1% (from 536 to 471 kg DM ha −1 , where DM is dry matter) and increased the R 2 by 0.109 (from 0.518 to 0.627). Adding features based on multiple variables, functions, events, and periods resulted in a further reduction in RMSE by 15.9% ( R 2 = 0.737). Overall, different aggregations of weather data enhanced the accuracy of CSH‐based models. These aggregations do not cause additional effort for data collection and, therefore, should be integrated into CSH‐based models for small‐scale farms.
Bacillus anthracis in South Africa, 1975–2013: are some lineages vanishing?
(2024) Lekota, Kgaugelo Edward; Hassim, Ayesha; Ledwaba, Maphuti Betty; Glover, Barbara A.; Dekker, Edgar. H.; van Schalkwyk, Louis Ockert; Rossouw, Jennifer; Beyer, Wolfgang; Vergnaud, Gilles; van Heerden, Henriette
The anthrax-causing bacterium Bacillus anthracis comprises the genetic clades A, B, and C. In the northernmost part (Pafuri) of Kruger National Park (KNP), South Africa, both the common A and rare B strains clades occur. The B clade strains were reported to be dominant in Pafuri before 1991, while A clade strains occurred towards the central parts of KNP. The prevalence of B clade strains is currently much lower as only A clade strains have been isolated from 1992 onwards in KNP. In this study 319 B. anthracis strains were characterized with 31-loci multiple-locus variable-number tandem repeat analysis (MLVA-31). B clade strains from soil ( n = 9) and a Tragelaphus strepsiceros carcass ( n = 1) were further characterised by whole genome sequencing and compared to publicly available genomes. The KNP strains clustered in the B clade before 1991 into two dominant genotypes. South African strains cluster into a dominant genotype A.Br.005/006 consisting of KNP as well as the other anthrax endemic region, Northern Cape Province (NCP), South Africa. A few A.Br.001/002 strains from both endemic areas were also identified. Subclade A.Br.101 belonging to the A.Br.Aust94 lineage was reported in the NCP. The B-clade strains seems to be vanishing, while outbreaks in South Africa are caused mainly by the A.Br.005/006 genotypes as well as a few minor clades such as A.Br.001/002 and A.Br.101 present in NCP. This work confirmed the existence of the rare and vanishing B-clade strains that group in B.Br.001 branch with KrugerB and A0991 KNP strains.
Phylogenetic analysis and public health implications of Salmonella Strains in southwestern states of Nigeria using InvA gene sequences
(2025) Fadipe, Emmanuel O.; Hölzle, Ludwig E.; Hölzle, Ludwig E.; Department of Livestock Infectiology and Environmental Hygiene, Institute of Animal Sciences, Faculty of Agriculture, University of Hohenheim, 70599 Stuttgart, Germany; Da Silveira, Júlia Angélica Gonçalves; Department of Livestock Infectiology and Environmental Hygiene, Institute of Animal Sciences, Faculty of Agriculture, University of Hohenheim, 70599 Stuttgart, Germany; Salvarani, Felipe M.; Department of Livestock Infectiology and Environmental Hygiene, Institute of Animal Sciences, Faculty of Agriculture, University of Hohenheim, 70599 Stuttgart, Germany; Domingues, Sheyla Farhayldes Souza; Department of Livestock Infectiology and Environmental Hygiene, Institute of Animal Sciences, Faculty of Agriculture, University of Hohenheim, 70599 Stuttgart, Germany; Da Silveira, Júlia Angélica Gonçalves; Salvarani, Felipe M.; Domingues, Sheyla Farhayldes Souza
Salmonella is a significant public health concern in Nigeria causing foodborne illnesses. Genetic diversity and prevalence of Salmonella is poorly understood in Nigeria. This study assessed the occurrence of Salmonella in various poultry houses in Nigeria and explored the evolutionary relationships among the isolates by analysis on invA gene. A total number of 314 samples (feces, feed, dust, waters, and palm swab) were collected from 49 farms in Abeokuta (18), Ibadan (20) and Oshogbo (11). Salmonella was detected with a prevalence of 2.75% in Ogun, 6.0% in Osun and 5.71%, in Oyo States, respectively. The overall prevalence of Salmonella in poultry farms sampled was 15/314 (4.78%). Sequence analysis revealed two sequences 01 and 02 to have 99.59% and 89.04 homologies with sequence of Paratyphi serovar (LC320032) and Enteritidis serovar (LC318423) in GenBank, respectively. Sequence 01 clustered with S. serovar Enteritidis from the USA, whereas Sequence 02 formed a distinct clade near S. serovar Typhimurium from Egypt. These findings underscore the public health significance of S. enterica in Nigeria, particularly in relation to food animals. The study highlights the need for improved farm management practices, stringent food safety regulations, and robust surveillance systems to mitigate the risk of Salmonella outbreaks.
A prospective exploratory study on potential systemic causes and risk factors for subconjunctival bleeding in neonatal calves
(2025) Steffl, Martin; Euchner, Katharina; Nautscher, Nadine; Euchner, Katharina; Institute of Animal Science, University of Hohenheim, 70593 Stuttgart, Germany; (K.E.); (N.N.); Nautscher, Nadine; Institute of Animal Science, University of Hohenheim, 70593 Stuttgart, Germany; (K.E.); (N.N.); Benoit-Biancamano, Marie-Odile; Institute of Animal Science, University of Hohenheim, 70593 Stuttgart, Germany; (K.E.); (N.N.); Vanore, Maria; Institute of Animal Science, University of Hohenheim, 70593 Stuttgart, Germany; (K.E.); (N.N.); Benoit-Biancamano, Marie-Odile; Vanore, Maria
Subconjunctival bleeding in neonatal calves is most commonly seen in association with birth trauma. There are currently no investigations available that examine the systemic causes of this phenomenon. In this prospective and exploratory case–control study, seven out of eighty neonatal calves examined over a two-year period were born with subconjunctival bleeding. The anatomical location of the subconjunctival bleeding and details related to the cow’s and calf’s parturitional and gestational history were recorded. Blood samples from cases and controls ( n = 7) were analyzed hematologically, and the serum lysyl oxidase-like enzyme 4 (LOXL4) concentration was determined through an ELISA to establish evidence for possible structural, copper-dependent vascular abnormalities. We found no significant difference in the clinical data of both groups. Hematological examinations revealed no evidence of anemia or thrombocytopenia. Additionally, no significant differences in differential leukocyte counts were observed between the different groups. However, the neutrophil–lymphocyte ratio (NLR) demonstrated a significant difference between the calves with subconjunctival bleeding and controls. The serum LOXL4 protein concentration was not significantly different in calves with subconjunctival bleeding compared to controls. In conclusion, our clinical, hematological, and biochemical data provided no evidence for potential systemic causes of subconjunctival bleeding. However, these results must be considered in light of this study’s small sample size and thus low statistical power.
Intestinal dysbiosis associated with non-nutritive sweeteners intake: an effect without a cause?
(2025) Marongiu, Luigi; Brzozowska, Ewa; Hetjens, Svetlana; Hoelzle, Ludwig E.; Venturelli, Sascha; Brzozowska, Ewa; Laboratory of Medical Microbiology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland; Hetjens, Svetlana; Department of Medical Statistics, Biomathematics and Information Processing, University Clinic Mannheim, Mannheim, Germany; Hoelzle, Ludwig E.; Department of Food Microbiology and Hygiene, Institute of Food Science and Biotechnology, University of Hohenheim, Stuttgart, Germany; Venturelli, Sascha; Department of Nutritional Biochemistry, University of Hohenheim, Stuttgart, Germany
Non-nutritive sweeteners (NNS) are present in various commercial articles, from foodstuffs to oral hygiene products. Despite their alleged safety, mounting evidence indicates that NNS intake is associated with an alteration of intestinal bacterial populations (dysbiosis) in animals and humans. Since NNS are commercialized based on the assumption that they are not metabolized by human cells and negligible effect on bacterial, the insurgence of dysbiosis associated with NNS intake remains unexplained. The current review aims to assess the effect of selected NNS (acesulfame potassium, advantame, aspartame, neotame, saccharin, stevia, and sucralose) on the human intestinal microbiota. Findings from this review suggests that NNS intake is linked not only to alterations in human physiology but also to modifications of bacterial biochemistry, including the hindrance of quorum sensing pathways, in a species-specific manner. Moreover, there were suggestions that NNS could also affect the biology of phages, namely by binding to the active sites of proteins involved in the infection process and altering the induction rate of prophages. The studies gathered in the present review provide a framework for understanding how NNS might be connected to dysbiosis, both directly through alterations in bacterial biochemistry and indirectly through impaired phage activity.
NaMeco - Nanopore full-length 16S rRNA gene reads clustering and annotation
(2026) Yergaliyev, Timur; Rios-Galicia, Bibiana; Camarinha-Silva, Amélia; Yergaliyev, Timur; Institute of Animal Science, University of Hohenheim, Stuttgart, Germany; Rios-Galicia, Bibiana; Institute of Animal Science, University of Hohenheim, Stuttgart, Germany; Camarinha-Silva, Amélia; Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
Background: Nanopore sequencing is currently one of the leading third-generation sequencing technologies on the market and is gaining popularity among researchers. Due to its long-read capabilities, full-length 16S rRNA gene metabarcoding using Oxford Nanopore Technologies (ONT) offers great potential for metataxonomic studies. However, the relatively high error rate poses a significant challenge for bioinformatic processing, often limiting taxonomy resolution to the genus level despite the longer read length. Results: This study presents NaMeco, a novel tool specifically developed to efficiently process long 16S rRNA gene reads sequenced using Oxford Nanopore Technologies, requiring minimal user input. Our tool performs read quality control, primer-specific extraction of sequences and their clustering, followed by taxonomic annotation with percent identity thresholds that minimize the amount of false-positive annotations. It produces several outputs: a table of cluster counts, taxonomic annotations of clusters, their representative sequences in fasta format and taxa counts at each taxonomy rank. Output files are compatible with the Qiime2 pipeline and can be imported into the required format for downstream analyses. Conclusions: NaMeco, in combination with the full SSU GTDB database, outperforms existing tools such as NanoCLUST and EPI2ME, while delivering taxonomy accuracy and detection rates comparable to Emu.
Simulation of dual-purpose chicken breeding programs implementing gene editing
(2024) Chuang, Edward Y. S.; Wellmann, Robin; Meijboom, Franck L. B.; Tetens, Jens; Bennewitz, Jörn
Background: In spite of being controversial and raising ethical concerns, the application of gene editing is more likely to be accepted when it contributes to improving animal welfare. One of the animal welfare and ethical issues in chicken breeding is chick culling, the killing of the male layer chicks after hatching due to the poor fattening performance. Although establishing dual-purpose chicken lines could solve this problem, unfavorable genetic correlations between egg and meat production traits hindered their competitiveness. Although it is also controversial in ethical terms, gene editing may accelerate genetic progress in dual-purpose chicken and alleviate the ethical concerns from chick culling. Results: The simulation compared the utility improvement in dual-purpose use under two breeding schemes: one consisting in the improvement of the laying hens, and the second in the improvement of a synthetic line obtained from a layer broiler cross. In each breeding scheme, the breeding programs were simulated with and without gene editing. Polygenic breeding values and 500 simulated quantitative trait loci (QTL) with different levels of pleiotropy caused negative correlations between egg production, meat production, and overall health. The results of the simulation demonstrated that genetic gain could be accelerated by at most 81% for several generations if gene editing was used. The actual increase in genetic gain depended on the number of single nucleotide polymorphisms (SNPs) being edited per animal. The rate of genetic improvement became equal in scenarios with and without gene editing after 20 generations. This is because the remaining segregating QTL had small effects and their edition would have negative overall health effects from potential off-target edits. Although gene editing can improve genetic gain in quantitative traits, it can only be recommended as long as QTL with reasonable effect sizes are segregating and detectable. Conclusions: This simulation demonstrates the potential of gene editing to accelerate the simultaneous improvement of negatively correlated traits. When the risk of negative consequences from gene editing persists, the number of SNPs to be edited should be chosen carefully to obtain the optimal genetic gain.
Genomic landscape of high‐altitude adaptation in East African mountain honey bees (Apis mellifera)
(2025) Mazzoni, Marco; Loidolt, Florian; Kersten, Sonja; Amulen, Deborah Ruth; Vudriko, Patrick; Meyer, Philipp; Scharnhorst, Victor Sebastian; Scheiner, Ricarda; Hasselmann, Martin
Understanding the evolutionary processes leading to differentiation within species is a central goal in population biology. A key process is local adaptation, for which organisms evolve traits enhancing the survival and reproduction in specific environments. Honey bees ( Apis mellifera ) in East Africa are well adapted to highland environments, showing different phenotypes, including behavior, compared to lowland bees. Despite these differences, highland and lowland honey bees show very low genetic differentiation, with the exception of two segments on chromosome 7 (r7) and chromosome 9 (r9), which were previously identified as chromosomal inversions. These inversions are rare in lowland populations, suggesting a key role in adaptation to high‐elevation habitats. In this study, we obtained 24 whole genomes from honey bees of Western Uganda and compared these with existing data from Kenya. We show that the chromosomal inversions play a pivotal role in local adaptation in both regions but with substantial differentiation. Genome‐wide analysis of polymorphism revealed additional genomic regions potentially involved in high‐altitude adaptation. The acquisition of transcriptome data from highland and lowland honey bees in Uganda has enabled the first insights into the differential expression of genes between these bees. Our findings elucidate the involvement of genes in behavioral and oxygen consumption processes. This paves the way to clarify the interplay of r7 and r9 with gene expression and to unravel the regulatory network underlying A. mellifera adaptation to high‐elevation habitats. Our study will contribute to a better understanding of the evolutionary processes in honey bee populations driven by environmental conditions.
Microbiota responses to feed particle size, calcium concentration, and phytase supplementation in broiler chickens
(2026) Rubio-Cervantes, Ismael; Wolfrum, Stephanie; Siegert, Wolfgang; Rodehutscord, Markus; Camarinha-Silva, Amélia
This research aimed to investigate the modulation of broiler-chickens gut microbiota by dietary particle size (PS), exogenous phytase, and calcium (Ca) concentration. Eight experimental diets varied in PS (fine 222 µm (PF) and coarse 309 µm (PC)), Ca concentration (4.9 and 7.2 g/kg), and exogenous phytase (0 and 1000 FTU/kg). A total of 560 Ross 308 broiler chickens were allocated to 56 metabolism units at 7 days of age and randomly assigned to each diet (7 replicates per treatment). On days 22 and 23, the birds were slaughtered, and the digesta from the gizzard, ileum, and ceca were sampled and pooled on a metabolism unit basis. DNA extraction was followed by 16S rRNA gene amplicon sequencing. Thirteen amplicon sequence variants (ASV) were present across the gizzard, ileum, and ceca, most of which were assigned to Limosilactobacillus and represented a substantial share of the total relative abundance in each section, 86 % in the gizzard, 88 % in the ileum, and 30 % in the ceca. Six of these L. reuteri ASVs were significantly enriched by coarse particle feeding, suggesting strain-specific adaptation to enhanced phosphorus availability. In the ileum, Candidatus arthromitus (p < 0.001) and Rombustia (p < 0.05) showed a significant increase in relative abundance in PC compared to PF. Phytase supplementation reduced the relative abundance of Lactobacillus and Streptococcus (p < 0.05), while higher Ca concentration decreased that of C. arthromitus (p < 0.05). In the ceca, increases in the relative abundance of Anaerostipes (p < 0.05) and Clostridia vadin BB60 were found for PC diets compared to PF (p < 0.001). The addition of phytase and Ca also significantly affected several genera, albeit the variations were less than 1 %. Dietary PS, exogenous phytase, and Ca concentration modulated the gut microbiota, specifically influencing the abundance of key microorganisms like Candidatus arthromitus, Anaerostipes, and Clostridia vadin BB60, involved in phosphorus metabolism and overall broiler chickens' health.
Breeding for resilient cows
(2025) Keßler, Franziska; Bennewitz, Jörn
Dairy cows are an indispensable part of modern livestock farming and make a significant contribution to human nutrition with producing a high-quality protein. At the same time, they are influenced by environmental factors and must maintain their performance, stay healthy, and remain fertile under given environmental conditions. In recent decades, we have faced an increasing number of new or suddenly emerging environmental stressors: extreme weather events, heatwaves, invasive species, and constantly changing requirements for housing conditions are just a few examples. This demands a high level of robustness and resilience from our dairy cows. While comprehensive research has been conducted on adaptation to changing environmental conditions, there is still a lack of knowledge about coping with short-term disturbances. Resilience is the ability of an individual to respond to these disturbances, recover from them, and return to its previous physiological equilibrium while maintaining the same level of performance. This study examines the concept of resilience in German dairy cattle breeds, analyzes genetic parameters, and discusses possibilities for future breeding strategies. The first chapter describes interactions between organisms and the environment, as well as statistical approaches to assessing the influence of environmental gradients on livestock. The concepts of resilience and robustness were distinguished, and methods for measuring and phenotyping resilience were explored. A promising approach is the analysis of variance and autocorrelation of daily milk yields during lactation. Under the assumption that resilient animals maintain a stable performance level along a natural lactation curve, low variance and an autocorrelation close to zero indicate high resilience. The genetic parameters of these resilience indicator traits were studied in the second chapter for the three most important German dairy breeds: German Holstein, German Fleckvieh, and German Brown Swiss. Within each breed and across breeds, low to moderate heritabilities were observed, along with desirable phenotypic and genetic correlations with performance traits. A comparison between breeds revealed only minimal differences, with no clear trend across all resilience indicator traits studied. Next, correlations between resilience indicator traits and functional as well as health traits were analyzed. While hardly any significant correlations were found for autocorrelation, the variance of daily milk yield correlated in a desirable direction with these traits. Resilient animals appear to be healthier and more long-lived. Chapter three also discusses the design of a selection index for resilience. This requires economic weighting factors, which cannot yet be determined. Therefore, optimizing the selection index resilience by maximizing breeding response in the selection index health was proposed. It was shown that breeding for resilience would lead to genetic progress in overall health. In the German Holstein breed, which was exclusively considered in this context, a selection index consisting of two different variance-based resilience indicator traits was recommended. The adaptation of the methodology to optimize a selection index to the German Fleckvieh and German Brown Swiss breeds was subsequently addressed in the general discussion and considered feasible. The fourth chapter analyzes the genetic architecture of resilience using genome-wide association studies within the three dairy breeds. The results indicated that the resilience indicator traits are polygenic traits. SNPs that significantly influence resilience are located near to QTLs known to affect performance, fertility, or health. Additionally, population structure was examined using linkage disequilibrium analysis. The final general discussion applied the methods from chapter three to the German Fleckvieh and German Brown Swiss breeds. Significant negative, undesirable correlations between autocorrelation and functional and health traits were found in German Fleckvieh. In contrast, variance-based resilience indicator traits correlated positively with most known traits, which is desirable. A selection index resilience was proposed for both breeds, consisting of two to three individual indicator traits, similar to the German Holstein breed. To better understand resilience, differences in breeding values were translated into milk loss per lactation, the number of disturbances an individual suffered from, and the impact on test-day results for milk ingredients. Finally, an outlook was provided on potential future research directions for resilience in livestock.
Cryptosporidium parvum infection alters the intestinal mucosa transcriptome in neonatal calves: impacts on epithelial barriers and transcellular transport systems
(2024) Veshkini, Arash; Kühn, Christa; Dengler, Franziska; Bachmann, Lisa; Liermann, Wendy; Helm, Christiane; Ulrich, Reiner; Delling, Cora; Hammon, Harald M.
Introduction: Cryptosporidium parvum (C. parvum) is the most prevalent enteric protozoan parasite causing infectious diarrhea in neonatal calves worldwide with a direct negative impact on their health and welfare. This study utilized next-generation sequencing (NGS) to deepen our understanding of intestinal epithelial barriers and transport mechanisms in the pathophysiology of infectious diarrhea in neonatal calves, which could potentially unveil novel solutions for treatment. Methods: At day 1 of life, male Holstein-Friesian calves were either orally infected (n = 5) or not (control group, n = 5) with C. parvum oocysts (in-house strain LE-01-Cp-15). On day 8 after infection, calves were slaughtered and jejunum mucosa samples were taken. The RNA was extracted from collected samples and subjected to sequencing. Differentially expressed genes (DEG) between the infected and CTRL groups were assessed using DESeq2 at a false discovery rate < 0.05 and used for gene ontology (GO) and pathway enrichment analysis in Cytoscape (v3.9.1). Results and discussion: To study the pathophysiology of infectious diarrhea on intestinal permeability, 459 genes related to epithelial cell barrier integrity and paracellular and transmembrane transport systems were selected from 12,908 identified genes in mucus. Among, there were 61 increased and 109 decreased gene transcripts belonged to adhesion molecules (e.g. ADGRD1 and VCAM1), ATP-binding cassette (ABC, e.g. ABCC2 and ABCD1) and solute carrier (SLC, e.g. SLC28A2 and SLC38A3) transporters, and ion channels (e.g. KCNJ15). Our results suggest deregulation of cellular junctions and thus a possibly increased intestinal permeability, whereas deregulation of ABC and SLC transporters and ion channels may influence the absorption/secretion of amino acids, carbohydrates, fats, and organic compounds, as well as acid-based balance and osmotic hemostasis. Besides pathogen-induced gene expression alterations, part of the DEG may have been triggered or consequently affected by inflammatory mechanisms. The study provided a deeper understanding of the pathophysiology of infectious diarrhea in neonatal calves and the host-pathogen interactions at the transcript level. For further studies with a particular focus on the transport system, these results could lead to a new approach to elucidating pathophysiological regulatory mechanisms.
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.
Effects of different dietary energy and essential amino acid levels on growing turkeys under organic farming conditions
(2025) Kirn, Anna Isabella; Rodehutscord, Markus
An adequate supply of dietary apparent metabolizable energy (AMEN) and essential amino acids (EAA) is crucial for turkeys to reach their genetic growth potential. However, optimizing diets in organic turkey production is challenging due to regulatory restrictions under EU Regulation 2018/848, which often lead to increased crude protein levels, potentially compromising animal health and environmental sustainability. To address this, targeted feeding strategies can be applied, leveraging compensatory growth through an initial qualitative feed restriction followed by a re-alimentation phase. Previous research showed that a consistent 10% reduction in AMEN combined with an initial EAA reduction of up to 20% (relative to commercial breeder guidelines), gradually restored to 90-100% during refeeding, effectively triggered compensatory growth, resulting in full catch-up growth. Nevertheless, as nutrient intake also affects welfare indicators such as plumage condition and injury prevalence, a balance between growth and welfare is essential. The present thesis aimed to evaluate whether dietary EAA levels could be further reduced by up to 30%, maintaining a constant 10% AMEN reduction, in male and female turkeys of two genotypes (slow-growing Auburn and fast-growing B.U.T. 6) across various housing systems (indoor, indoor with silage, and mobile housing with free-range). The study focused on evaluating growth, slaughter performance, and welfare indicators. Additionally, the potential of a newly introduced scoring system for wing feather structure and depigmentation was examined as a sensitive indicator of dietary EAA supply status. In the first study, 600 male day-old chicks from two genotypes (B.U.T. 6 and Auburn) were allocated to three feeding strategies differing in EAA levels across five 4-week phases: F1 (80/90/90/90/90%), F2 (80/80/90/100/90%), and F3 (70/80/90/100/90%). After rearing in indoor housing until week 8, the turkeys were transferred to one of three housing systems (indoor, indoor with silage, and mobile with free-range; weeks 9–20). Results showed that up to 30% initial EAA reduction followed by gradual re-alimentation triggered compensatory growth without affecting final body weight, total feed intake, or valuable cuts. No genotype by feeding interaction was observed. However, compensatory feed intake increased the feed conversion ratio and nutrient intake per kilogram of weight gain. While there was no housing by feeding interaction, housing significantly affected performance. Mobile housing with free-range and silage supplementation improved the feed conversion ratio and reduced abdominal fat. Additionally, mobile housing increased breast meat yield. Notably, a significant genotype by housing interaction suggested that B.U.T. 6 may demonstrate superior adaptability to the nutritional and environmental variability of the housing systems compared to Auburn. Building on this, the second study tested a similar approach in 432 female turkeys across three feeding strategies (F1: 80/90/90/90%, F2: 80/80/90/90%, F3: 70/80/90/90%) over four four-week phases. After being reared indoors until week 8, birds were assigned to indoor or mobile housing with free-range access (weeks 9-16). While a 20% EAA reduction maintained growth and slaughter performance, a 30% reduction led to significant decreases in final body weight, slaughter weight, and dressing percentage. A significant genotype by feeding interaction suggested that B.U.T. 6 was more sensitive to the 30% reduction than Auburn. Mobile housing improved breast meat yield and reduced abdominal fat but increased feed conversion ratio, likely due to winter fattening conditions. The third study examined the effects of dietary AMEN and EAA reductions on injuries, plumage damage, and the potential of a newly introduced scoring system for wing feather structure and depigmentation as an indicator of dietary EAA supply status. A total of 216 non-beak-trimmed female turkeys from the second study, housed indoors and subjected to the same feeding strategies, were evaluated. The most restrictive feeding strategy (30% EAA reduction) increased the prevalence of skin injuries, plumage damage, alterations in feather structure, and depigmentation. In contrast, the 20% EAA reduction preserved welfare and performance outcomes. Importantly, wing feather structure and pigmentation showed graded responses to varying EAA levels, supporting their potential as sensitive indicators of dietary EAA status in turkeys. In conclusion, this thesis demonstrated that reducing EAA levels by 20%, followed by a re-alimentation phase, alongside a 10% AMEN reduction, can be successfully applied in organic turkey production. This approach maintained final growth performance, slaughter performance, and welfare in male and female Auburn and B.U.T. 6 turkeys by effectively leveraging compensatory growth. Wing feather structure and pigmentation scoring proved to be a sensitive indicator of EAA supply status. External feed sources such as silage and free-range foraging contributed nutritionally, while mobile housing enhanced breast muscle yield and reduced abdominal fat. Overall, turkey growth and performance under organic conditions resulted from complex interactions between endogenous factors (sex, genotype, age) and exogenous factors (housing, environment, feeding), highlighting the need for integrated and adaptive management approaches.
Risk factors for omphalitis in neonatal dairy calves
(2024) Meier, Kim K.; Stock, Annegret; Merle, Roswitha; Arndt, Heidi; Dachrodt, Linda; Hoedemaker, Martina; Kellermann, Laura; Knubben-Schweizer, Gabriela; Volkmann, Maria; Müller, Kerstin-Elisabeth
Knowledge about potential risk factors for animal health is crucial to achieve animal welfare. The aim of this study was to provide practical guidance for farmers to improve the health status of their youngstock by identifying and eliminating risk factors for omphalitis in neonatal calves. A cross-sectional study including 3,445 dairy calves from 567 farms located in three structurally different regions of Germany was performed from December 2016 to July 2019. On each farm calves aged five to 21 days underwent clinical examinations with special consideration of the umbilicus for signs of inflammation. Information regarding animal health, hygiene, and management was obtained via interviews with the farmers. Rearing conditions were recorded following visual inspection using written standard operating procedures. Multifactorial statistical analyses were performed to identify potential risk factors for omphalitis on animal and farm level. The overall omphalitis prevalence in calves aged five to 21 days was 30.9%. Across all regions and farms, every fourth calf per farm exhibited signs of omphalitis (median farm prevalence: 25.0%, interquartile range: 0.0–50.0%). According to the farmers, however, only 4.5% of the calves had been treated for omphalitis in the preceding 12 months. Risk factors for omphalitis identified included the dampness of the lying area in the first 2 weeks of life, a body condition score of the dam after calving outside the optimal range, and the time that calves spent with their dam after birth. Calves on farms providing dry lying areas in the first 2 weeks of life had 0.77 times the risk of omphalitis compared to calves on farms with predominantly damp bedding. When the dams were judged under- or over-conditioned after calving, their offspring had a 1.4 times higher omphalitis risk, respectively, compared to calves from dams optimal conditioned. Calves from farms separating calf and dam beyond 12 h after birth were 0.75 times as likely to develop omphalitis than calves from farms performing immediate separation. These results highlight the complexity of multifactorial diseases such as umbilical infection. The evidence presented can help to establish guidelines for dairy farmers to improve the umbilical health of their calves.
Effects of dietary phosphorus and myo-inositol supplementation on NaPi-IIb and TRPV6 protein expression in duodenal apical membranes of laying hens from two strains
(2026) Shomina, Nataliia; Sommerfeld, Vera; Hanauska, Anna; Oster, Michael; Rodehutscord, Markus; Huber, Korinna
Phosphorus (P) and calcium (Ca) absorption in the intestine is mediated by apical brush border membrane (BBM) transporters, including the sodium-dependent phosphate (Pi) transporter NaPi-IIb and the Ca²⁺-selective channel TRPV6. Both are highly expressed in the duodenum and exhibit dietary adaptability; yet little is known about how this adaptability varies with strain and age in laying hens. The present study examined the effects of dietary mineral P renunciation and myo-inositol (MI) supplementation on NaPi-IIb and TRPV6 protein expression in the duodenal BBM of Lohmann Brown-Classic (LB) and Lohmann LSL-Classic (LSL) hens. Two independent feeding trials were conducted: hens received diets either with or without mineral P supplementation (wk 15 - 19 and 20 – 24), or with graded MI levels (0 - 3 g/kg; wk 26 – 30). At the end of each period, hens were euthanized and protein expression of NaPi-IIb and TRPV6 in duodenal BBM was studied by western blotting. Statistical correlation with additional traits of mineral metabolism was analyzed. An immunoreactive NaPi-IIb band was detected at ∼ 45 kDa; therefore, all results reported here refer to this NaPi-IIb fragment. Mineral P renunciation did not affect NaPi-IIb fragment or TRPV6 expression in either hen strain. In LSL hens NaPi-IIb fragment expression increased from wk 19 to wk 24, whereas in LB hens it remained unchanged. NaPi-IIb fragment expression was positively associated with duodenal phosphatase activity and plasma estradiol. TRPV6 expression tended to reduce in LB hens from wk 19 to wk 24, but remained stable in LSL hens. TRPV6 expression was positively associated with duodeno-jejunal P content. MI supplementation upregulated NaPi-IIb fragment expression in LB, but downregulated it in LSL hens with high dietary MI levels, without affecting TRPV6. These findings demonstrate strain-dependent regulatory patterns of duodenal expression of NaPi-IIb fragment and TRPV6 in response to physiological stage and MI supply, indicating that mineral feeding strategies may benefit from genotype-specific consideration, whereas the mechanisms underlying MI-related effects require further clarification.
Nutrient–response modeling with a single and interpretable artificial neuron
(2025) Rodehutscord, Markus; Ahmadi, Hamed
Precise estimation of nutrient requirements and utilization efficiency is fundamental to nutritional sciences, yet it is mainly performed using classical nonlinear regression models. These models are interpretable but require careful selection of the functional form and initial parameter values. Flexible machine learning (ML) methods are seemingly disliked due to their perceived “black box” nature, which can obscure biological insight. A minimal and interpretable ML framework addresses this gap in nutrient–response modeling. The proposed approach uses a single artificial neuron with a hyperbolic tangent activation. Mathematically, this resembles a four-parameter sigmoidal function but with greater flexibility and distinct parameter definitions, allowing capture of the monotonic, saturating dynamics typical of essential nutrient responses. The method is enhanced with modern ML best practices, including data augmentation, Bayesian regularization, and bootstrap resampling, providing robust, uncertainty-quantified estimates of key nutritional metrics—such as asymptotic response, inflection point, and nutrient requirements—even from small datasets. Evaluations across 12 diverse datasets from poultry and fish studies, including amino acids and phosphorus, demonstrated that the single artificial neuron matches or exceeds the performance of classical models while providing full analytical transparency. The framework is implemented as a no-code graphical application, ‘NutriCurvist’, offering an easy-to-use alternative tool for nutrient-response modeling to support data-driven, precision nutrition.
The chicken gut microbiome in conventional and alternative production systems
(2025) Cheng, Yu-Chieh; Krieger, Margret; Korves, Anna-Maria; Camarinha‑Silva, Amélia
The poultry gut microbiome plays a key role in nutrient digestion, immune function, and overall health. Differences among various farming systems, including conventional, antibiotic-free, free-range, and organic systems, influence microbial composition and function through variations in diet, genetic selection, environmental exposure, and antibiotic use. Conventional systems typically rely on formulated diets and controlled housing conditions, often with routine antimicrobial use. In contrast, organic systems emphasize natural feed ingredients, including roughage, outdoor access, and strict limitations on the use of antibiotics. These divergent practices shape the gut microbiota differently, with organic systems generally associated with greater exposure to environmental microbes and, consequently, greater microbial diversity. However, the implications of this increased diversity for poultry health and performance are complex, as organic systems may also carry a higher risk of pathogen exposure. This review summarizes current findings on the chicken gut microbiome across conventional and alternative production systems (antibiotic-free, free-range, and organic), focusing on microbial diversity, functional potential, and disease resilience. The need for standardized methodologies and consistent nomenclature in microbiome research is also discussed to improve comparability across studies. Understanding how production systems influence the gut microbiota is essential for improving poultry health and productivity while addressing challenges related to antimicrobial resistance and sustainable farming practices.
Systematic selection of best performing mathematical models for in vitro gas production using machine learning across diverse feeds
(2025) Ahmadi, Hamed; Titze, Natascha; Wild, Katharina; Rodehutscord, Markus
In vitro gas production (GP) is commonly used to evaluate ruminant feed, yet its accurate interpretation requires robust mathematical modeling. This study systematically explores a wide array of nonlinear models to explain GP dynamics across various feed types, addressing the question: how can efficient and versatile models that accurately represent GP profiles be identified? We hypothesized that distinct feed types exhibit unique GP characteristics, effectively captured by specific models, and that statistical and machine learning methodologies can streamline model selection. Utilizing a comprehensive dataset derived from 849 unique GP profiles across concentrate feed categories—including cereal and leguminous grains and processed protein feeds—21 candidate models were rigorously evaluated based on their goodness-of-fit metrics, with a particular emphasis on Bayesian Information Criterion (BIC) for model selection. A group of three models—namely Burr XII, Inverse paralogistic, and Log-logistic—consistently emerged as top performers, demonstrating high generalizability and predictive power across feed types. Notably, our analysis indicated that model type significantly influenced GP predictions, surpassing the impact of feed type characteristics. This research establishes a decision-making framework for model selection and sets the stage for further investigations linking in vitro GP parameters to in vivo digestibility, ultimately enhancing ruminant nutrition strategies.
Effects of Prosopis juliflora pods on sheep performance and carcass traits, and their methane mitigation potential as assessed in vitro
(2025) Tadesse, Assefa; Titze, Natascha; Rodehutscord, Markus; Melesse, Aberra
This study aimed to assess the effect of partial substitution of concentrate mix (CM) with Prosopis juliflora pod (PJP) on growth performance and carcass traits in sheep, and its potential to reduce methane (CH4) production in vitro. A total of 25 yearling rams with an initial body weight of 15.8±1.53 kg was randomly assigned to five treatment diets. The diets were a control diet (JP0) and JP0 replaced with PJP at the level of 5% (JP5), 10% (JP10), 15% (JP15), and 20% (JP20). Data were collected on feed intake, body weight, and carcass characteristics. Methane production was determined from 24 h in vitro gas production. The substitution of CM with PJP did not affect feed intake, body weight, weight gain, feed efficiency, and carcass traits (p>0.05). The in vitro CH4 production was reduced (p<0.001) in diets containing increased levels of PJP. The metabolizable energy for JP10, JP15 and JP20 diets was 11.9, 11.6 and 11.5 MJ/kg DM, respectively (p>0.05). In conclusion, replacing CM with PJP did not negatively affect growth performance and carcass characteristics and could be used as potential supplement to mitigate methane emissions. Further in vivo studies involving respiration chambers are recommended to investigate the CH4 reduction potential of PJP.
Genomic dissection of the correlation between milk yield and various health traits using functional and evolutionary information about imputed sequence variants of 34,497 German Holstein cows
(2024) Schneider, Helen; Krizanac, Ana-Marija; Falker-Gieske, Clemens; Heise, Johannes; Tetens, Jens; Thaller, Georg; Bennewitz, Jörn
Background: Over the last decades, it was subject of many studies to investigate the genomic connection of milk production and health traits in dairy cattle. Thereby, incorporating functional information in genomic analyses has been shown to improve the understanding of biological and molecular mechanisms shaping complex traits and the accuracies of genomic prediction, especially in small populations and across-breed settings. Still, little is known about the contribution of different functional and evolutionary genome partitioning subsets to milk production and dairy health. Thus, we performed a uni- and a bivariate analysis of milk yield (MY) and eight health traits using a set of ~34,497 German Holstein cows with 50K chip genotypes and ~17 million imputed sequence variants divided into 27 subsets depending on their functional and evolutionary annotation. In the bivariate analysis, eight trait-combinations were observed that contrasted MY with each health trait. Two genomic relationship matrices (GRM) were included, one consisting of the 50K chip variants and one consisting of each set of subset variants, to obtain subset heritabilities and genetic correlations. In addition, 50K chip heritabilities and genetic correlations were estimated applying merely the 50K GRM. Results: In general, 50K chip heritabilities were larger than the subset heritabilities. The largest heritabilities were found for MY, which was 0.4358 for the 50K and 0.2757 for the subset heritabilities. Whereas all 50K genetic correlations were negative, subset genetic correlations were both, positive and negative (ranging from -0.9324 between MY and mastitis to 0.6662 between MY and digital dermatitis). The subsets containing variants which were annotated as noncoding related, splice sites, untranslated regions, metabolic quantitative trait loci, and young variants ranked highest in terms of their contribution to the traits’ genetic variance. We were able to show that linkage disequilibrium between subset variants and adjacent variants did not cause these subsets’ high effect. Conclusion: Our results confirm the connection of milk production and health traits in dairy cattle via the animals’ metabolic state. In addition, they highlight the potential of including functional information in genomic analyses, which helps to dissect the extent and direction of the observed traits’ connection in more detail.

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