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/ .
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.
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 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.
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.
Genetic variation, phylogenetic relationship and spatial distribution of ‘Candidatus Phytoplasma ulmi’ strains in Germany
(2020) Schneider, B.; Hüttel, B.; Zübert, C.; Kube, M.
A recent survey in Germany revealed the wide presence of ‘Candidatus Phytoplasma ulmi’ in native elm stands. Accessions were studied for their genetic variability and phylogenetic relationship based on the conserved groEL and the variable imp gene. While the groEL sequences revealed a high intraspecific homology of more than 99%, the homology of the imp gene dropped to 71% between distantly related sequences. Twenty-nine groEL and 74 imp genotypes were distinguished based on polymorphic sites. Phylogenetic analysis of the groEL gene clustered all ‘Ca. P. ulmi’ strains and separated them from related phytoplasmas of the 16SrV group. The inferred phylogeny of the imp gene resulted in a different tree topology and separated the ‘Ca. P. ulmi’ genotypes into two clusters, one closely related to the flavescence dorée phytoplasma strain FD-D (16SrV-D), the other affiliated with the flavescence dorée phytoplasma strains FD-C and FD70 and the alder yellows phytoplasma (16SrV-C). In both phylograms, ‘Ca. P. ulmi’ genotypes from Scots elm trees formed a coherent cluster, while genotypes from European white elms and field elms grouped less strictly. The regional distribution pattern was congruent for some of the groEL and imp genotypes, but a strict linkage for all genotypes was not apparent.
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.
Insights into Ethiopian honey bee diversity based on wing geomorphometric and mitochondrial DNA analyses
(2020) Hailu, Teweldemedhn Gebretinsae; D’Alvise, Paul; Tofilski, Adam; Fuchs, Stefan; Greiling, Juergen; Rosenkranz, Peter; Hasselmann, Martin
Traditional beekeeping has been playing important socio-economic roles in Ethiopia for millennia. The country is situated in northeast Africa, where ranges of major evolutionary lineages of Apis mellifera adjoin. However, studies on the classification and distribution of subspecies and lineages of honey bees in the country are partly inconsistent, either proposing multiple subspecies and lineages or a unique A. m. simensis. This study was conducted with the aim of elucidating Ethiopian honey bees in reference to African subspecies and major global lineages using wing geometric morphometrics and COI-COII mitochondrial DNA analyses. For this purpose, 660 worker bees were collected from 66 colonies representing highland, midland, and lowland zones in different locations. Both methods indicated that the samples from this study form a distinct cluster together with A. m. simensis reference. In addition, forewing venation patterns showed that most of the Ethiopian samples are separate from all reference subspecies, except A. m. simensis. Analysis of COI-COII sequences revealed five DraI haplotypes (Y2, Y1, A1, and O5’), of which one was new denoted as Y3. Moreover, centroid size strongly associated with elevation. In conclusion, the results supported that Ethiopian honey bees are distinct both at lineage and subspecies levels; however, there is an indication of lineage O in the north.
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.
Projecting the impact of climate change on honey bee plant habitat distribution in Northern Ethiopia
(2024) Gebremedhn, Haftom; Gebrewahid, Yikunoamlak; Haile, Gebremedhin Gebremeskel; Hadgu, Gebre; Atsbha, Tesfay; Hailu, Teweldemedhn Gebretinsae; Bezabih, Gebreamlak
Climate change significantly affects the diversity, growth, and survival of indigenous plant species thereby influencing the nutrition, health and productivity of honey bees ( Apis mellifera ). Hypoestes forskaolii (Vahl) is one of the major honey bee plant species in Ethiopia’s Tigray region. It is rich in pollen and nectar that typically provides white honey, which fetches a premium price in both local and inter-national markets. Despite its socio-economic and apicultural significance, the distribution of H. forskaolii has been declining, raising concerns regarding its conservation efforts. However, there is limited knowledge on how environmental and climatic factors affect its current distribution and response to future climate change. The study investigates the current and projected (the 2030s, 2050s, 2070s, and 2090s) habitat distributions of H. forskaolii under three future climate change scenarios (ssp126, ssp245, and ssp585) using the Maximum Entropy Model (MaxEnt). The results show that land use (50.1%), agro-ecology (28%), precipitation during the Driest Quarter (11.2%) and soil texture (6.1%) predominantly influence the distribution of H. forskaolii, collectively explaining 95.4% of the model's predictive power. Habitats rich in evergreen trees and mosaic herbaceous with good vegetation cover are identified as the most suitable for H. forskaolii . The spatial distribution of H. forskaolii is concentrated in the highlands and mid-highlands of the eastern and southern parts of Tigray, characterized by a colder temperature. Across the three climate change scenarios, the size of suitable habitat for H. forskaolii is projected to decrease over the four time periods studied. Predictions under the ssp585 scenario reveal alarming results, indicating a substantial decrease in the suitable habitat for H. forskaolii from 4.26% in the 2030s to 19.09% in the 2090s. Therefore, given the challenges posed by climate change, research efforts should focus on identifying and evaluating new technologies that can help the H. forskaolii species in adapting and mitigating the effects of climate change.
Reproduction of Varroa destructor does not elicit varroa sensitive hygiene (VSH) or recapping behaviour in honey bee colonies (Apis mellifera)
(2021) Sprau, Lina; Hasselmann, Martin; Rosenkranz, Peter
Suppressed mite reproduction (SMR) is an important trait for the selection of Varroa resistant honey bee colonies. It has repeatedly been assumed that SMR is an effect of varroa sensitive hygiene (VSH) when hygienic bees preferably remove those brood cells where the mite has reproduced. We here compare the VSH behaviour of honey bees toward brood cells artificial infested with a varroa mite. By infesting half of the brood cells directly after the cell capping and the other half only 24 h later, we established two groups with high (> 75%) and low (< 2%) mite reproduction. After 8 days, about 40% of the infested brood cells were removed, however without any difference between both groups. Likewise, no group differences were recorded in the percentage of recapped brood cells. This strongly indicates that the presence of mite offspring is not a crucial trigger for the VSH behaviour. SMR data like the percentage of non-reproducing mites are therefore not the optimal measure for the selection of colonies with high VSH.
Transcriptional responses in jejunum of two layer chicken strains following variations in dietary calcium and phosphorus levels
(2021) Reyer, Henry; Oster, Michael; Ponsuksili, Siriluck; Trakooljul, Nares; Omotoso, Adewunmi O.; Iqbal, Muhammad A.; Muráni, Eduard; Sommerfeld, Vera; Rodehutscord, Markus; Wimmers, Klaus
Background: Calcium (Ca) and phosphorus (P) are essential nutrients that are linked to a large array of biological processes. Disturbances in Ca and P homeostasis in chickens are associated with a decline in growth and egg laying performance and environmental burden due to excessive P excretion rates. Improved utilization of minerals in particular of P sources contributes to healthy growth while preserving the finite resource of mineral P and mitigating environmental pollution. In the current study, high performance Lohmann Selected Leghorn (LSL) and Lohmann Brown (LB) hens at peak laying performance were examined to approximate the consequences of variable dietary Ca and P supply. The experimental design comprised four dietary groups with standard or reduced levels of either Ca or P or both (n = 10 birds per treatment group and strain) in order to stimulate intrinsic mechanisms to maintain homeostasis. Jejunal transcriptome profiles and the systemic endocrine regulation of mineral homeostasis were assessed (n = 80). Results: Endogenous mechanisms to maintain mineral homeostasis in response to variations in the supply of Ca and P were effective in both laying hen strains. However, the LSL and LB appeared to adopt different molecular pathways, as shown by circulating vitamin D levels and strain-specific transcriptome patterns. Responses in LSL indicated altered proliferation rates of intestinal cells as well as adaptive responses at the level of paracellular transport and immunocompetence. Endogenous mechanisms in LB appeared to involve a restructuring of the epithelium, which may allow adaptation of absorption capacity via improved micro-anatomical characteristics. Conclusions: The results suggest that LSL and LB hens may exhibit different Ca, P, and vitamin D requirements, which have so far been neglected in the supply recommendations. There is a demand for trial data showing the mechanisms of endogenous factors of Ca and P homeostasis, such as vitamin D, at local and systemic levels in laying hens.

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