Institut für Nutztierwissenschaften

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Nutrient utilisation and metabolic adaptation of broiler chickens to high levels of free amino acids in the diet
(2024) Ibrahim, Ahmad; Rodehutscord, Markus
Reducing dietary crude protein (CP) content in broiler chickens is a strategy used to reduce nitrogen excretion and its impact on the environment caused by the broiler industry. This requires an increased proportion of free amino acids (AA) in the diet to avoid insufficient AA supply. An upper limit of dietary free AA inclusion has often been suggested but could not be derived from the current literature. The overall objective of this dissertation was to determine the upper limit of free AA content in CP-reduced diets. Additionally, the aim was to investigate the effects of adding free AA on the acid-base status in the blood of broiler chickens. Furthermore, the physiological and metabolic responses to substituting peptide-bound AA with free AA were investigated. In a preliminary experiment of the first study, the precaecal AA digestibility of soya protein isolate (SPI) representing a peptide-bound AA source was determined. One diet with 80 g SPI per kg and another with the basal mix, including maize starch in substitution with SPI, were tested. The diets were offered from day 18–21 of age and tested in eight units with 15 animals each. On day 21, the birds were slaughtered and the content of the last distal ileum was sampled. The amount of precaecal digestible AA derived from SPI was calculated as the difference in AA digestibility between both diets. In the main trial of the first study, the amount of digestible AA derived from SPI was incrementally substituted with a free AA mixture, i.e. 0, 25, 50, 75, and 100 % to determine the maximum amount of peptide-bound AA that can be substituted by free AA without reducing growth performance. At each substitution level, the amounts of digestible aspartate (Asp) and glutamate (Glu), which, per analysis, also contained asparagine (Asn) and glutamine (Gln), were either substituted with free Asp and Glu or with a 50/50 mixture of Asp/Asn and Glu/Gln. Each diet was offered from day 7–21 of age and tested in 7 units of 10 animals each. Based on growth performance, there was a maximum limit of dietary free AA inclusion dependent on the inclusion of Asn and Gln. This indicates that Asn and/or Gln were limited in the diets including only Asp and Glu and high levels of free AA. Asn and Gln supply allowed for increased AA substitution from 10 to 19 % of CP in the diet and increased free AA concentration from about 37 to 54 g/kg without reducing growth. Additionally, as the AA substitution was done in 25 %-unit increments, the maximum amount of dietary free AA was estimated between 54–71 g/kg. The broken line linear regression estimated value of 57 g free AA/kg in the diets with Asn and Gln without impairing growth and 61 g free AA/kg without impairing feed intake. Blood data related to the acid-base balance indicated a compensated acidosis 14 days after the diet change, which was attenuated by including Asn and Gln in the diet. In the second study, three diets were selected based on the results of the first study. The first diet included SPI with 0 % AA substitution. The second diet included the maximum free AA level with 50 % AA substitution without negative effects on growth and nitrogen utilisation. The third diet with 100 % AA substitution had evidence of an acid-base shift. The second and third diets considered all 20 proteinogenic AA including Asn and Gln. The change to one of these three diets occurred on day 7 post-hatch and feeding continued until day 22. Excreta were collected on days 7–8, 8–9, 9–10, 11–12, 14–15, and 21–22. Repeated blood samples were withdrawn on days 7, 8, 9, 11, 14, and 21. There was no evidence of affected nitrogen utilisation by substituting peptide-bound with free AA, especially 3 days after the diet change. It was confirmed that up to 50 % AA substitution from SPI did not affect growth. The reduction in growth at 100 % AA substitution was mainly due to the reduced feed intake immediately after the diet change. Adaption of nitrogen utilisation and AA in blood plasma to high levels of dietary free AA occurred within 3 to 7 days after changing to 50 % and 100 % AA substitution diets, respectively. This was suggested by the data on feed intake, nitrogen accretion, nitrogen utilisation efficiency in the first 3 days and plasma free AA concentrations in the first 7 days after the diet change, which remained unaffected by the treatments thereafter. A significant increase in ammonia excretion was also observed with increasing levels of free AA at all points in time. The blood samples were also investigated for responses in the acid-base balance and plasma metabolites directly after the diet change. An acid-base shift was determined in the birds that received 100 % and 50 % AA substitution diets. An acute reaction of the acid-base balance was on days 4 to 7 and day 4 after a change to the 100 % and 50 % AA substitution diets, respectively. Thereafter, a compensated acid-base acidosis was determined on day 7 for 50 % AA substitution and on day 14 for 100 % AA substitution. This likely explained the increased ammonia excretion found for these diets as an adaptation to excrete acids after an acid-base shift. The untargeted metabolomics analysis effectively determined the reduction in the use of plant feed ingredients with increasing free AA inclusion. However, no changes in metabolic pathways by increasing free AA inclusion were detected. It can be concluded that there was a maximum limit to including free AA in diets for broiler chickens, which was dependent on the supply of Asn and Gln. A reduced feed intake was the primary response of the birds to this upper limit. One of the likely reasons for the reduced feed intake was the acid-base shift caused by the diets with AA substitution higher than 50 %. The dietary inclusion of Asn and Gln attenuated this acid-base shift. The knowledge gained from this dissertation can contribute to the targeted use of more free AA, representing a potential alternative to protein sources for the future and reducing the CP content of the feed. The free AA level used to date in practical feeding is below the limit identified in this dissertation. Nonetheless, such levels of free AA are often used in research to answer specific questions or to cover certain AA interactions for a more accurate estimation of the individual AA requirements for contemporary poultry breeds.
Modulation of hepatic insulin and glucagon signaling by nutritional factors in broiler chicken
(2022) Petrilla, Janka; Mátis, Gábor; Mackei, Máté; Kulcsár, Anna; Sebők, Csilla; Papp, Márton; Gálfi, Péter; Fébel, Hedvig; Huber, Korinna; Neogrády, Zsuzsanna
Influencing the endocrine metabolic regulation of chickens by nutritional factors might provide novel possibilities for improving animal health and productivity. This study was designed to evaluate the impact of dietary cereal type (wheat-based (WB) vs. maize-based (MB) diets), crude protein level (normal (NP) vs. lowered (LP)), and sodium (n-)butyrate (1.5 g/kg diet) supplementation (vs. no butyrate) on the responsiveness of hepatic glucagon receptor (GCGR), insulin receptor beta (IRβ) and mammalian target of rapamycin (mTOR) in the phase of intensive growth of chickens. Liver samples of Ross 308 broiler chickens (Gallus gallus domesticus) were collected on day 21 for quantitative real-time polymerase chain reaction and Western blot analyses. Hepatic GCGR and mTOR gene expressions were up-regulated by WB and LP diet. GCGR and IRβ protein level decreased in groups with butyrate supplementation; however, the quantity of IRβ and mTOR protein increased in WB groups. Based on these data, the applied dietary strategies may be useful tools to modulate hepatic insulin and glucagon signaling of chickens in the period of intensive growth. The obtained results might contribute to the better understanding of glycemic control of birds and increase the opportunity of ameliorating insulin sensitivity, hence, improving the production parameters and the welfare of broilers.
Dietary L-carnitine affects leukocyte count and function in dairy cows around parturition
(2022) Kononov, Susanne Ursula; Meyer, Jennifer; Frahm, Jana; Kersten, Susanne; Kluess, Jeannette; Bühler, Susanne; Wegerich, Anja; Rehage, Jürgen; Meyer, Ulrich; Huber, Korinna; Dänicke, Sven
In early lactation, an energy deficit leading to a negative energy balance (NEB) is associated with increased susceptibility to disease and has been shown to be an important factor during transition in dairy cows. L-carnitine as a key factor in the mitochondrial transport of fatty acids and subsequently for β-oxidation and energy release is known to modulate mitochondrial biogenesis and thus influence metabolism and immune system. In the current study, we characterized hematological changes around parturition and investigated the potential effects of dietary L-carnitine supplementation on immune cell functions. For this approach, dairy cows were assigned either to a control (CON, n = 30) or an L-carnitine group [CAR, n = 29, 25 g rumen-protected L-carnitine per cow and day (d)]. Blood samples were taken from d 42 ante partum (ap) until d 110 post-partum (pp), with special focus and frequent sampling from 0.5 to72 h post-calving to clarify the impact of L-carnitine supplementation on leukocyte count, formation of reactive oxygen species (ROS) in polymorphonuclear cells (PMN) and peripheral mononuclear cells (PBMC) and their phagocytosis activity. Blood cortisol concentration and the capacity of PBMC proliferation was also investigated. All populations of leukocytes were changed during the peripartal period, especially granulocytes showed a characteristic increase up to 4 h pp. L-carnitine supplementation resulted in increased levels of eosinophils which was particularly pronounced one day before to 4 h pp, indicating a possible enhanced support for tissue repair and recovery. Non-supplemented cows showed a higher phagocytic activity in PBMC as well as a higher phagocytic capacity of PMN during the most demanding period around parturition, which may relate to a decrease in plasma levels of non-esterified fatty acids reported previously. L-carnitine, on the other hand, led to an increased efficiency to form ROS in stimulated PMN. Finally, a short period around calving proved to be a sensitive period in which L-carnitine administration was effective.
Improving the accuracy of multi-breed prediction in admixed populations by accounting for the breed origin of haplotype segments
(2022) Schmid, Markus; Stock, Joana; Bennewitz, Jörn; Wellmann, Robin
Numerically small breeds have often been upgraded with mainstream breeds. This historic introgression predisposes the breeds for joint genomic evaluations with mainstream breeds. The linkage disequilibrium structure differs between breeds. The marker effects of a haplotype segment may, therefore, depend on the breed from which the haplotype segment originates. An appropriate method for genomic evaluation would account for this dependency. This study proposes a method for the computation of genomic breeding values for small admixed breeds that incorporate phenotypic and genomic information from large introgressed breeds by considering the breed origin of alleles (BOA) in the evaluation. The proposed BOA model classifies haplotype segments according to their origins and assumes different but correlated SNP effects for the different origins. The BOA model was compared in a simulation study to conventional within-breed genomic best linear unbiased prediction (GBLUP) and conventional multi-breed GBLUP models. The BOA model outperformed within-breed GBLUP as well as multi-breed GBLUP in most cases.
Multi-omics reveals different strategies in the immune and metabolic systems of high-yielding strains of laying hens
(2022) Iqbal, Muhammad Arsalan; Reyer, Henry; Oster, Michael; Hadlich, Frieder; Trakooljul, Nares; Perdomo-Sabogal, Alvaro; Schmucker, Sonja; Stefanski, Volker; Roth, Christoph; Camarinha Silva, Amélia; Huber, Korinna; Sommerfeld, Vera; Rodehutscord, Markus; Wimmers, Klaus; Ponsuksili, Siriluck
Lohmann Brown (LB) and Lohmann Selected Leghorn (LSL) are two commercially important laying hen strains due to their high egg production and excellent commercial suitability. The present study integrated multiple data sets along the genotype-phenotype map to better understand how the genetic background of the two strains influences their molecular pathways. In total, 71 individuals were analyzed (LB, n = 36; LSL, n = 35). Data sets include gut miRNA and mRNA transcriptome data, microbiota composition, immune cells, inositol phosphate metabolites, minerals, and hormones from different organs of the two hen strains. All complex data sets were pre-processed, normalized, and compatible with the mixOmics platform. The most discriminant features between two laying strains included 20 miRNAs, 20 mRNAs, 16 immune cells, 10 microbes, 11 phenotypic traits, and 16 metabolites. The expression of specific miRNAs and the abundance of immune cell types were related to the enrichment of immune pathways in the LSL strain. In contrast, more microbial taxa specific to the LB strain were identified, and the abundance of certain microbes strongly correlated with host gut transcripts enriched in immunological and metabolic pathways. Our findings indicate that both strains employ distinct inherent strategies to acquire and maintain their immune and metabolic systems under high-performance conditions. In addition, the study provides a new perspective on a view of the functional biodiversity that emerges during strain selection and contributes to the understanding of the role of host–gut interaction, including immune phenotype, microbiota, gut transcriptome, and metabolome.
Does carrying a rider change motor and sensory laterality in horses?
(2022) Schwarz, Sophie; Marr, Isabell; Farmer, Kate; Graf, Katja; Stefanski, Volker; Krueger, Konstanze
Laterality in horses has been studied in recent decades. Although most horses are kept for riding purposes, there has been almost no research on how laterality may be affected by carrying a rider. In this study, 23 horses were tested for lateral preferences, both with and without a rider, in three different experiments. The rider gave minimal aids and rode on a long rein to allow the horse free choice. Firstly, motor laterality was assessed by observing forelimb preference when stepping over a pole. Secondly, sensory laterality was assessed by observing perceptual side preferences when the horse was confronted with (a) an unfamiliar person or (b) a novel object. After applying a generalised linear model, this preliminary study found that a rider increased the strength of motor laterality (p = 0.01) but did not affect sensory laterality (p = 0.8). This suggests that carrying a rider who is as passive as possible does not have an adverse effect on a horse’s stress levels and mental state.
Central carbon metabolism, sodium-motive electron ransfer, and ammonium formation by the vaginal pathogen Prevotella bivia
(2021) Schleicher, Lena; Herdan, Sebastian; Fritz, Günter; Trautmann, Andrej; Seifert, Jana; Steuber, Julia
Replacement of the Lactobacillus dominated vaginal microbiome by a mixed bacterial population including Prevotella bivia is associated with bacterial vaginosis (BV). To understand the impact of P. bivia on this microbiome, its growth requirements and mode of energy production were studied. Anoxic growth with glucose depended on CO2 and resulted in succinate formation, indicating phosphoenolpyruvate carboxylation and fumarate reduction as critical steps. The reductive branch of fermentation relied on two highly active, membrane-bound enzymes, namely the quinol:fumarate reductase (QFR) and Na+-translocating NADH:quinone oxidoreductase (NQR). Both enzymes were characterized by activity measurements, in-gel fluorography, and VIS difference spectroscopy, and the Na+-dependent build-up of a transmembrane voltage was demonstrated. NQR is a potential drug target for BV treatment since it is neither found in humans nor in Lactobacillus. In P. bivia, the highly active enzymes L-asparaginase and aspartate ammonia lyase catalyze the conversion of asparagine to the electron acceptor fumarate. However, the by-product ammonium is highly toxic. It has been proposed that P. bivia depends on ammonium-utilizing Gardnerella vaginalis, another typical pathogen associated with BV, and provides key nutrients to it. The product pattern of P. bivia growing on glucose in the presence of mixed amino acids substantiates this notion.
Electronic nose for the rapid detection of deoxynivalenol in wheat using classification and regression trees
(2022) Camardo Leggieri, Marco; Mazzoni, Marco; Bertuzzi, Terenzio; Moschini, Maurizio; Prandini, Aldo; Battilani, Paola
Mycotoxin represents a significant concern for the safety of food and feed products, and wheat represents one of the most susceptible crops. To manage this issue, fast, reliable, and low-cost test methods are needed for regulated mycotoxins. This study aimed to assess the potential use of the electronic nose for the early identification of wheat samples contaminated with deoxynivalenol (DON) above a fixed threshold. A total of 214 wheat samples were collected from commercial fields in northern Italy during the periods 2014–2015 and 2017–2018 and analyzed for DON contamination with a conventional method (GC-MS) and using a portable e-nose “AIR PEN 3” (Airsense Analytics GmbH, Schwerin, Germany), equipped with 10 metal oxide sensors for different categories of volatile substances. The Machine Learning approach “Classification and regression trees” (CART) was used to categorize samples according to four DON contamination thresholds (1750, 1250, 750, and 500 μg/kg). Overall, this process yielded an accuracy of >83% (correct prediction of DON levels in wheat samples). These findings suggest that the e-nose combined with CART can be an effective quick method to distinguish between compliant and DON-contaminated wheat lots. Further validation including more samples above the legal limits is desirable before concluding the validity of the method.
Feed clusters according to In Situ and In Vitro ruminal crude protein degradation
(2023) Okon, Paul; Bachmann, Martin; Wensch-Dorendorf, Monika; Titze, Natascha; Rodehutscord, Markus; Rupp, Christiane; Susenbeth, Andreas; Greef, Jörg Michael; Zeyner, Annette
Effective degradation (ED) of crude protein (CP) was estimated in vitro at 0.02, 0.05 and 0.08 h−1 assumed ruminal passage rates for a total of 40 feedstuffs, for which in situ ED was available and used as reference degradation values. For this, the Streptomyces griseus protease test was used. The differences between in vitro CP degradation and the in situ CP degradation values were lowest in legume grains and highest in cereal by-products and barley. The differences between in situ and in vitro ED were expressed using a degradation quotient (degQ), where degQ = (EDin vitro − EDin situ)/EDin situ. Among the tested feedstuffs, eight specific clusters were identified according to degQ for the assumed passage rates. The feedstuffs clustered in an unspecific way, i.e., feedstuffs of different nutrient composition, origin or treatment did not necessarily group together. Formaldehyde–treated rapeseed meal, soybean meal, wheat, a treated lupin, sunflower meal and barley could not be assigned to any of the clusters. Groupwise degradation (range of degQ for assumed passage rates are given in brackets) was detected in grass silages (−0.17, −0.11), cereal by-products together with sugar beet pulp (−0.47, −0.35) and partly in legume grains (−0.14, 0.14). The clustering probably based on different specific nutrient composition and matrix effects that influence the solubility of feed protein and limit the performance of the protease. The matrix can be affected by treatment (chemically, thermally or mechanically), changing the chemical and physical structure of the protein within the plant. The S. griseus protease test had reliable sensitivity to reflect differences between native feedstuffs and treatments (thermally or chemically) that were found in situ. The in situ results, however, are mostly underestimated. The clustering results do not allow a clear conclusion on the groupwise or feed-specific use of carbohydrate-degrading enzymes as pre- or co-inoculants as part of the S. griseus protease test and need to be tested for its potential to make this test more conform with in situ data.
Bi-objective optimization of nutrient intake and performance of broiler chickens using Gaussian process regression and genetic algorithm
(2023) Ahmadi, Hamed; Rodehutscord, Markus; Siegert, Wolfgang
This study investigated whether quantifying the trade-off between the maxima of two response traits increases the accuracy of diet formulation. To achieve this, average daily weight gain (ADG) and gain:feed ratio (G:F) responses of 7–21-day-old broiler chickens to the dietary supply of three nutrients (intake of digestible glycine equivalents, digestible threonine, and total choline) were modeled using a newly developed hybrid machine learning-based method of Gaussian process regression and genetic algorithm. The dataset comprised 90 data lines. Model-fit-criteria indicated a high model adjustment and no prediction bias of the models. The bi-objective optimization scenarios through Pareto front revealed the trade-off between maximized ADG and maximized G:F and provided information on the needed input of the three nutrients that interact with each other to achieve the trade-off scenarios. The trade-off scenarios followed a nonlinear pattern. This indicated that choosing target values intermediate to maximized ADG and G:F after single-objective optimization is less accurate than feed formulation after quantifying the trade-off. In conclusion, knowledge of the trade-off between maximized ADG and maximized G:F and the needed nutrient inputs will help feed formulators to optimize their feed with a more holistic approach.
Dietary phosphorus and calcium in feed affects miRNA profiles and their mRNA targets in jejunum of two strains of laying hens
(2021) Iqbal, Muhammad Arsalan; Ali, Asghar; Hadlich, Frieder; Oster, Michael; Reyer, Henry; Trakooljul, Nares; Sommerfeld, Vera; Rodehutscord, Markus; Wimmers, Klaus; Ponsuksili, Siriluck
Phosphorus (P) and calcium (Ca) are critical for egg production in laying hens. Most of P in plant-based poultry diet is bound as phytic acid and needs to be hydrolysed before absorption. To increase P bioavailability, exogenous phytases or bioavailable rock phosphate is added in feed. There is growing evidence of the importance of miRNAs as the epicentre of intestinal homeostasis and functional properties. Therefore, we demonstrated the expression of miRNA profiles and the corresponding target genes due to the different levels of P (recommended vs. 20% reduction) and/or Ca (recommended vs. 15% reduction) in feed. Jejunal miRNA profiles of Lohmann Selected Leghorn (LSL) and Lohmann Brown (LB) laying hens strains were used (n = 80). A total of 34 and 76 miRNAs were differentially expressed (DE) in the different diet groups within LSL and LB strains respectively. In LSL, the DE miRNAs and their targets were involved in calcium signaling pathway, inositol phosphate metabolism, and mitochondrial dysfunction. Similarly, in LB miRNAs targets were enriched in metabolic pathways such as glutathione metabolism, phosphonate metabolism and vitamin B6 metabolism. Our results suggest that both strains employ different intrinsic strategies to cope with modulated P and Ca supply and maintain mineral homeostasis.
The genome reduction excludes the ribosomal rescue system in acholeplasmataceae
(2022) Zübert, Christina; Ilic, Anna-Marie; Duduk, Bojan; Kube, Michael
The trans-translation process is a ribosomal rescue system for stalled ribosomes processing truncated mRNA. The genes ssrA and smpB fulfil the key functions in most bacteria, but some species have either lost these genes or the function of the ribosomal rescue system is taken over by other genes. To date, the ribosomal rescue system has not been analysed in detail for the Acholeplasmataceae. This family, in the Mollicutes class, comprises the genus Acholeplasma and the provisional taxon “Candidatus Phytoplasma”. Despite their monophyletic origin, the two clades can be separated by traits such as not representing primary pathogens for acholeplasmas versus being phytopathogenic for the majority of phytoplasmas. Both taxa share reduced genomes, but only phytoplasma genomes are characterised by a remarkable level of instability and reduction. Despite the general relevance of the ribosomal rescue system, information is lacking on coding, the genomic context and pseudogenisation of smpB and ssrA and their possible application as a phylogenetic marker. Herein, we provide a comprehensive analysis of the ribosomal rescue system in members of Acholeplasmataceae. The examined Acholeplasmataceae genomes encode a ribosomal rescue system, which depends on tmRNA encoded by ssrA acting in combination with its binding protein SmpB. Conserved gene synteny is evident for smpB, while ssrA shows a less conserved genomic context. Analysis of the tmRNA sequences highlights the variability of proteolysis tag sequences and short conserved sites at the 5′- and 3′-ends. Analyses of smpB provided no hints regarding the coding of pseudogenes, but they did suggest its application as a phylogenetic marker of Acholeplasmataceae – in accordance with 16S rDNA topology. Sequence variability of smpB provides sufficient information for species assignment and phylogenetic analysis.
Microbial incubations of 8‐phenyloctanoic acid and furan fatty acids in rumen fluid
(2022) Wiedmaier‐Czerny, Nina; Blumberg, Olga; Schulz, Tobias; Kemmler, Franziska; Titze, Natascha; Wild, Katharina; Vetter, Walter
Aims: The digestive tract of ruminants is specialized in the digestion of various plant components. One of the largest parts of the stomach is the so-called rumen, which contains a large number of micro-organisms that may degrade or modify fatty acids, for example by β-oxidation, chain elongation and/or hydrogenation. Methods and Results: Here we performed incubation experiments with less com- mon fatty acids by in vitro incubations with rumen fluid of fistulated cows for 24 h. Sample extracts were analysed by gas chromatography with mass spectrometry. As substrates, we selected one phenyl fatty acid and four furan fatty acids (FuFAs). All studied fatty acids were degraded by β-oxidation (two or three chain-shortening steps) while chain elongation or saturation of the aromatic part (terminal phenyl or central furan moiety) was not observed in any case. Conclusions: The percentage of β-oxidation products was low, especially in the case of the FuFAs. This could be due to the rather long carbon number of FuFAs (19–22 carbon atoms). In addition, compound-specific differences in the degradation rates were observed in our experiments. Significance and Impact of the Study: Our results produce evidence that FuFAs, which are valuable antioxidants that are known to be present in various feed items of the cow, can be effectively passed on the rumen into the milk.
Dynamic development of viral and bacterial diversity during grass silage preservation
(2023) Sáenz, Johan S.; Rios-Galicia, Bibiana; Rehkugler, Bianca; Seifert, Jana
Ensilaging is one of the most common feed preservation processes using lactic acid bacteria to stabilize feed and save feed quality. The silage bacterial community is well known but the role of the virome and its relationship with the bacterial community is scarce. In the present study, metagenomics and amplicon sequencing were used to describe the composition of the bacterial and viral community during a 40-day grass silage preservation. During the first two days, we observed a rapid decrease in the pH and a shift in the bacterial and viral composition. The diversity of the dominant virus operational taxonomic units (vOTUs) decreased throughout the preservation. The changes in the bacterial community resembled the predicted putative host of the recovered vOTUs during each sampling time. Only 10% of the total recovered vOTUs clustered with a reference genome. Different antiviral defense mechanisms were found across the recovered metagenome-assembled genomes (MAGs); however, only a history of bacteriophage infection with Lentilactobacillus and Levilactobacillus was observed. In addition, vOTUs harbored potential auxiliary metabolic genes related to carbohydrate metabolism, organic nitrogen, stress tolerance, and transport. Our data suggest that vOTUs are enriched during grass silage preservation, and they could have a role in the establishment of the bacterial community.
Male reproductive organ weight: Criteria for detection of androstenone-positive carcasses in immunocastrated and entire male pigs
(2023) Fazarinc, Gregor; Batorek-Lukač, Nina; Škrlep, Martin; Poklukar, Klavdija; Van den Broeke, Alice; Kress, Kevin; Labussière, Etienne; Stefanski, Volker; Vrecl, Milka; Čandek-Potokar, Marjeta
Immunocastration and rearing of entire males (EMs) are sustainable alternatives to surgical castration. However, these animal carcasses have variable risk of boar taint and should be identified at the slaughter line. We aimed to identify a simple and reliable indicator of androstenone-related boar taint by evaluating pelvic urogenital tract weight as a marker of boar-taint animals at the slaughter line. The pelvic urogenital tract, testes, and accessory sex glands of EMs and immunocastrates (ICs) were collected, dissected, and weighed, before colorimetric measurements of testicular tissue. Additionally, GnRH antibody titers and testosterone, androstenone, and skatole levels were determined. Our results showed that 81.8% of EMs had androstenone levels above the risk threshold (>0.5 µg/g fat; EM/Ahigh subgroup), whereas in ICs, the C/Ahigh subgroup with androstenone >0.5 µg/g fat accounted for only 4.3%. Androstenone levels correlated negatively with GnRH antibody titers and positively with testosterone levels and reproductive organ weights. Identification of ICs with androstenone levels above the threshold (IC/Ahigh subgroup) may be achieved via testes or pelvic urogenital tract weight measurements. However, in EMs, the latter is a more reliable parameter. A principal component analysis based on these variables and hierarchical clustering also distinguished the Ahigh from the Alow subgroup, irrespective of IC/EM. The findings highlight the possible use of pelvic urogenital tract weight along with testes weight as a simple, reliable, and efficient morphometric indicator for identifying androstenone-positive carcasses of different sex categories.
Cognitive alterations in old mice are associated with intestinal barrier dysfunction and induced toll-like receptor 2 and 4 signaling in different brain regions
(2023) Brandt, Annette; Kromm, Franziska; Hernández-Arriaga, Angélica; Martínez Sánchez, Inés; Bozkir, Haktan Övül; Staltner, Raphaela; Baumann, Anja; Camarinha-Silva, Amélia; Heijtz, Rochellys Diaz; Bergheim, Ina
Emerging evidence implicate the ‘microbiota–gut–brain axis’ in cognitive aging and neuroinflammation; however, underlying mechanisms still remain to be elucidated. Here, we assessed if potential alterations in intestinal barrier function and microbiota composition as well as levels of two key pattern-recognition receptors namely Toll-like receptor (TLR) 2 and TLR4, in blood and different brain regions, and depending signaling cascades are paralleling aging associated alterations of cognition in healthy aging mice. Cognitive function was assessed in the Y-maze and intestinal and brain tissue and blood were collected in young (4 months old) and old (24 months old) male C57BL/6 mice to determine intestinal microbiota composition by Illumina amplicon sequencing, the concentration of TLR2 and TLR4 ligands in plasma and brain tissue as well as to determine markers of intestinal barrier function, senescence and TLR2 and TLR4 signaling. Cognitive function was significantly impaired in old mice. Also, in old mice, intestinal microbiota composition was significantly altered, while the relative abundance of Gram-negative or Gram-positive bacteria in the small and large intestines at different ages was not altered. Moreover, intestinal barrier function was impaired in small intestine of old mice, and the levels of TLR2 and TLR4 ligands were also significantly higher in both portal and peripheral blood. Furthermore, levels of TLR2 and TLR4 ligands, and downstream markers of TLR signaling were higher in the hippocampal and prefrontal cortex of old mice compared to young animals. Taken together, our results suggest that even in ‘healthy’ aging, cognitive function is impaired in mice going along with an increased intestinal translocation of TLR ligands and alterations of TLR signaling in several brain regions.
Genome comparison of ‘Candidatus Phytoplasma rubi’ with genomes of other 16SrV phytoplasmas highlights special group features
(2023) Böhm, Jan Werner; Duckeck, Dominik; Duduk, Bojan; Schneider, Bernd; Kube, Michael
Phytoplasmas are associated with important bacterial diseases, causing severe symptoms in agricultural and ornamental crops. ‘Candidatus Phytoplasma rubi’, associated with the Rubus stunt in raspberries (Rubus idaeus) and blackberries (Rubus subgenus Rubus), causes shortened internodes, elongated sepals, proliferation, phyllody, and virescence. The recently published genome of ‘Ca. P. rubi’ RS enabled a comprehensive genomic comparison to the complete genomes of 16SrV phytoplasmas, comprising strains of the flavescence dorée-associated phytoplasma CH and two ‘Candidatus Phytoplasma ziziphi’ strains. Besides the typical transporters and metabolic features of phytoplasmas, the phosphorolysis of sucrose and the utilization of the carboxylic acid L-lactate became apparent for the 16SrV-group. With respect to the effector repertoire and the encoded immunodominant membrane proteins involved in host colonization, the group revealed conserved features that comprise the variable membrane proteins A and B. However, SAP11- and SAP54 orthologs were limited to ‘Ca. P. rubi’ RS and ‘Ca. P. ziziphi’. Genome-sequence-based phylogenetic analysis supports the close relationship of these genomes relative to alder yellows phytoplasmas. The analyses supported the impact of the mobilome on phytoplasma evolution but also highlighted that there is the possibility of identifying phytoplasmas with a larger metabolic repertoire in the future.
Reduced parasite burden in feral honeybee colonies
(2023) Kohl, Patrick L.; D'Alvise, Paul; Rutschmann, Benjamin; Roth, Sebastian; Remter, Felix; Steffan‐Dewenter, Ingolf; Hasselmann, Martin
Bee parasites are the main threat to apiculture and since many parasite taxa can spill over from honeybees (Apis mellifera) to other bee species, honeybee disease management is important for pollinator conservation in general. It is unknown whether honeybees that escaped from apiaries (i.e. feral colonies) benefit from natural parasite‐reducing mechanisms like swarming or suffer from high parasite pressure due to the lack of medical treatment. In the latter case, they could function as parasite reservoirs and pose a risk to the health of managed honeybees (spillback) and wild bees (spillover). We compared the occurrence of 18 microparasites among managed (N = 74) and feral (N = 64) honeybee colony samples from four regions in Germany using qPCR. We distinguished five colony types representing differences in colony age and management histories, two variables potentially modulating parasite prevalence. Besides strong regional variation in parasite communities, parasite burden was consistently lower in feral than in managed colonies. The overall number of detected parasite taxa per colony was 15% lower and Trypanosomatidae, chronic bee paralysis virus, and deformed wing viruses A and B were less prevalent and abundant in feral colonies than in managed colonies. Parasite burden was lowest in newly founded feral colonies, intermediate in overwintered feral colonies and managed nucleus colonies, and highest in overwintered managed colonies and hived swarms. Our study confirms the hypothesis that the natural mode of colony reproduction and dispersal by swarming temporally reduces parasite pressure in honeybees. We conclude that feral colonies are unlikely to contribute significantly to the spread of bee diseases. There is no conflict between the conservation of wild‐living honeybees and the management of diseases in apiculture.
Optimization strategies to adapt sheep breeding programs to pasture-based production environments: A simulation study
(2023) Martin, Rebecca; Pook, Torsten; Bennewitz, Jörn; Schmid, Markus
Strong differences between the selection (indoor fattening) and production environment (pasture fattening) are expected to reduce genetic gain due to possible genotype-by-environment interactions (G × E). To investigate how to adapt a sheep breeding program to a pasture-based production environment, different scenarios were simulated for the German Merino sheep population using the R package Modular Breeding Program Simulator (MoBPS). All relevant selection steps and a multivariate pedigree-based BLUP breeding value estimation were included. The reference scenario included progeny testing at stations to evaluate the fattening performance and carcass traits. It was compared to alternative scenarios varying in the progeny testing scheme for fattening traits (station and/or field). The total merit index (TMI) set pasture-based lamb fattening as a breeding goal, i.e., field fattening traits were weighted. Regarding the TMI, the scenario with progeny testing both in the field and on station led to a significant increase in genetic gain compared with the reference scenario. Regarding fattening traits, genetic gain was significantly increased in the alternative scenarios in which field progeny testing was performed. In the presence of G × E, the study showed that the selection environment should match the production environment (pasture) to avoid losses in genetic gain. As most breeding goals also contain traits not recordable in field testing, the combination of both field and station testing is required to maximize genetic gain.
Detailed genomic analysis of correlation and causality between milk production and health traits in German Holstein cattle using high-dimensional genomic data and novel statistical methods
(2024) Schneider, Helen Hiam; Bennewitz, Jörn
Adverse side effects of high milk production on animal health have been mentioned frequently. They are compromising animal welfare, the farmers` economy, and the ecological footprint as well as the social acceptance of milk production. Consequently, many countries started to include functional traits into their breeding goal a few decades ago. The intention is thereby to avoid putative undesirable side effects of high production and to improve the cows` health in the long term through genetic gain. Indeed, positive genetic trends for various functional and health traits have been described in the literature. At the same time, the genetic trend of milk production traits remained positive. In general, sustainable genetic gain requires an appropriate weight of the individual traits in the selection index and a comprehensive understanding of the traits` genetic architecture and their interrelationship. This can be facilitated by recent innovations that enable the widespread availability of whole genome sequence (WGS) data. WGS data contains genomic information about millions of SNPs, derived either from sequencing or from imputing lower density SNP chip data to sequence level. Using external information about these sequence variants in genomic analyses, e.g., concerning their function during transcription and translation, has been shown to reveal additional knowledge about biological and molecular mechanisms shaping complex traits. Hence, applying external information to estimate genetic correlations might help to dissect the traits` interrelationship in more detail. Additionally, going beyond global genetic correlations, this is, reflecting the shared genetic effect throughout the genome, to the local scale, this is, the genetic sharing in specific genomic regions, would be an alternative to provide novel knowledge about the extent and direction of the shared genetic effect and its localization in the genome. The expected information is desired to understand and to avoid potential detrimental effects of selection decisions on animal health. Moreover, moving away from correlation towards causation would enable to predict the impact of management decisions and external interventions. The aim of this thesis was to scrutinize the genetic connection between health and milk production traits in dairy cattle using a large sample of 34,497 German Holstein cows with pedigree, 50K SNP chip, and imputed WGS data consisting of ~17 million variants. To this end, standard quantitative genetic analyses were augmented by a set of novel approaches to detect genomic regions with a substantial genetic effect on several traits and to investigate causal associations. Chapter one applied the 50K chip data to estimate additive genetic and dominance variance components for the milk production and health traits. This was done since substantial nonadditive genetic effects for functional traits have been mentioned in the literature, whereas little is known about these effects for the health traits examined in this thesis. It was demonstrated that the contribution of the dominance variance to the phenotypic variance was rather small for all traits. However, regarding the health traits, the contribution of the dominance variance to the genetic variance was almost as high as, and sometimes even higher than the contribution of the additive genetic variance. In addition, significant inbreeding depression was found for the milk production traits. Chapter two consisted of three steps. First, pedigree-based heritabilities of and global genetic correlations between milk production and health traits were estimated. Most heritabilities of the health traits and their genetic correlations with the milk production traits were low, whereby the genetic correlations were in an unfavorable direction. Next, genome-wide association studies (GWAS) were performed for each trait utilizing the 50K chip data to generate summary statistics. The summary statistics are required as input data for the last step that applied a tool to detect shared genomic regions. Genomic regions simultaneously affecting milk production and health traits were identified for each trait combination, of which some also had a sign in the favorable direction. This chapter confirmed the advantage of scrutinizing global genetic correlations down to the local scale. Chapter three utilized the 50K chip as well as the imputed WGS data. The latter was thereby divided into 27 subsets depending on the variants` functional and evolutionary annotation, e.g., as gene expression quantitative trait loci or selection signature. Heritabilities of and genetic correlations between milk yield and several health traits were estimated for the 50K chip and each of the 27 subsets. The results indicate that the 50K chip appears to be sufficient to explain the genetic variance of the investigated traits, whereas it seems to underestimate their genetic covariance. Furthermore, the importance of alternative splicing for the (co-)variation of quantitative traits and the important role of the negative energy balance causing the unfavorable side effects of high production on animal health has been confirmed. Chapter four was a Mendelian randomization (MR) analysis. Here, the causal effect of milk yield on a set of health traits was examined using a method that is based on summary statistics. In this chapter, the summary statistics were generated using the imputed WGS data. Unfavorable causal effects of milk yield on most health traits were identified that were strongest for mastitis and digital phlegmon. This indicates potential detrimental consequences for these traits with increasing milk yields, owed to selection decisions or inappropriately chosen weights in the selection index. The general discussion is addressing the negative side effects of high production on animal health with special focus on the negative energy balance. Moreover, including feed efficiency and resilience indicator traits into the breeding goal is discussed with respect to the results reported in the previous chapters. Besides, additional information about the methodology of MR analyses and the results of a MR analysis investigating the causal effect of protein and fat yield on the health traits are presented and debated. The general discussion ends with practical implications of the results regarding hologenomic selection strategies and strategies including functional information in genomic prediction.

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