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.
Adipose tissue gene expression of entire male, immunocastrated and surgically castrated pigs
(2021) Poklukar, Klavdija; Čandek-Potokar, Marjeta; Vrecl, Milka; Batorek-Lukač, Nina; Fazarinc, Gregor; Kress, Kevin; Stefanski, Volker; Škrlep, Martin
Differences in adipose tissue deposition and properties between pig male sex categories, i.e., entire males (EM), immunocastrates (IC) and surgical castrates (SC) are relatively well-characterized, whereas the underlying molecular mechanisms are still not fully understood. To gain knowledge about the genetic regulation of the differences in adipose tissue deposition, two different approaches were used: RNA-sequencing and candidate gene expression by quantitative PCR. A total of 83 differentially expressed genes were identified between EM and IC, 15 between IC and SC and 48 between EM and SC by RNA-sequencing of the subcutaneous adipose tissue. Comparing EM with IC or SC, upregulated genes related to extracellular matrix dynamics and adipogenesis, and downregulated genes involved in the control of lipid and carbohydrate metabolism were detected. Differential gene expression generally indicated high similarity between IC and SC as opposed to EM, except for several heat shock protein genes that were upregulated in EM and IC compared with SC. The candidate gene expression approach showed that genes involved in lipogenesis were downregulated in EM compared with IC pigs, further confirming RNA-sequencing results.
Amino acid digestibility and metabolisable energy of spring and winter faba beans grown on two sites and effects of dehulling in caecectomised laying hens
(2021) Siegert, Wolfgang; Ibrahim, Ahmad; Link, Wolfgang; Lux, Guido; Schmidtke, Knut; Hartung, Jens; Nautscher, Nadine; Rodehutscord, Markus
BACKGROUND: The variation in amino acid (AA) digestibility and metabolisable energy (MEN) in four spring and four winter faba bean genotypes differing in vicine/convicine (V/C) concentrations grown on two sites was investigated in caecectomised LSL-Classic laying hens. Effects of dehulling one faba bean genotype were also examined. Diets containing one out of 17 faba bean variants each and a basal diet were fed to ten caecectomised laying hens in a row-column design to achieve five replicates per diet. RESULTS: Ranges and levels of digestibility of the hulled variants differed widely among AA with the lowest and highest range determined for Arg (90–93%) and Cys (−12–65%), respectively. MEN ranged between 10.3 and 12.3 MJ kg−1 dry matter. Lower MEN and digestibility of Cys, Glx, Phe, Pro, Tyr, and Val (P < 0.050) was determined for the winter genotypes grown in Nimtitz compared to the other variants. Digestibility of Ser was lower for the spring than for the winter genotypes (P < 0.050). Negative correlations with AA digestibility were determined for phytate, but not for tannin and V/C concentrations (P < 0.050). Negative correlations between tannin fractions and MEN were weak (P = 0.082–0.099). Dehulling increased MEN by 1.8 MJ kg−1 dry matter and raised the digestibility of Pro, His, and Glx (P < 0.050). CONCLUSIONS: The results indicated that the digestible AA and MEN supply of laying hens was increased by using low phytate faba beans while breeding for low V/C genotypes did not affect AA digestibility or MEN. Dehulling increased MEN and the digestibility of some AA.
An evaluation of the lineage of Brucella isolates in turkey by a whole-genome single-nucleotide polymorphism analysis
(2024) Akar, Kadir; Holzer, Katharina; Hoelzle, Ludwig E.; Yıldız Öz, Gülseren; Abdelmegid, Shaimaa; Baklan, Emin Ayhan; Eroğlu, Buket; Atıl, Eray; Moustafa, Shawky A.; Wareth, Gamal; Elkhayat, Manar; Pedersen, Karl
Brucellosis is a disease caused by the Brucella ( B. ) species. It is a zoonotic disease that affects farm animals and causes economic losses in many countries worldwide. Brucella has the ability to persist in the environment and infect the host at low doses. Thus, it is more important to trace brucellosis outbreaks, identify their sources of infection, and interrupt their transmission. Some countries already have initial data, but most of these data are based on a Multiple-Locus Variable-Number Tandem-Repeat Analysis (MLVA), which is completely unsuitable for studying the Brucella genome. Since brucellosis is an endemic disease in Turkey, this study aimed to examine the genome of Turkish Brucella isolates collected between 2018 and 2020, except for one isolate, which was from 2012. A total of 28 strains of B. melitensis ( n = 15) and B. abortus ( n = 13) were analyzed using a core-genome single-nucleotide polymorphism (cgSNP) analysis. A potential connection between the Turkish isolates and entries from Sweden, Israel, Syria, Austria, and India for B. melitensis was detected. For B. abortus , there may be potential associations with entries from China. This explains the tight ties found between Brucella strains from neighboring countries and isolates from Turkey. Therefore, it is recommended that strict measures be taken and the possible effects of uncontrolled animal introduction are emphasized.
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/ .
Antiviral defense systems in the rumen microbiome
(2025) Sáenz, Johan S.; Rios-Galicia, Bibiana; Seifert, Jana
The continuous interaction between phages and their respective hosts has resulted in the evolution of multiple bacterial immune mechanisms. However, the diversity and prevalence of antiviral defense systems in complex communities are still unknown. We therefore investigated the diversity and abundance of viral defense systems in 3,038 high-quality bacterial and archaeal genomes from the rumen. In total, 14,241 defense systems and 31,948 antiviral-related genes were identified. Those genes represented 114 unique system types grouped into 49 families. We observed a high prevalence of defense systems in the genomes. However, the number of defense systems, defense system families, and system density varied widely from genome to genome. Additionally, the number of defense system per genome correlated positively with the number of defense system families and the genome size. Restriction modification, Abi, and cas system families were the most common, but many rare systems were present in only 1% of the genomes. Antiviral defense systems are prevalent and diverse in the rumen, but only a few are dominant, indicating that most systems are rarely present. However, the collection of systems throughout the rumen may represent a pool of mechanisms that can be shared by different members of the community and modulate the phage–host interaction.
Assessing functional properties of diet protein hydrolysate and oil from fish waste on canine immune parameters, cardiac biomarkers, and fecal microbiota
(2024) Cabrita, Ana R. J.; Barroso, Carolina; Fontes-Sousa, Ana Patrícia; Correia, Alexandra; Teixeira, Luzia; Maia, Margarida R. G.; Vilanova, Manuel; Yergaliyev, Timur; Camarinha-Silva, Amélia; Fonseca, António J. M.
Locally produced fish hydrolysate and oil from the agrifood sector comprises a sustainable solution both to the problem of fish waste disposal and to the petfood sector with potential benefits for the animal’s health. This study evaluated the effects of the dietary replacement of mainly imported shrimp hydrolysate (5%) and salmon oil (3%; control diet) with locally produced fish hydrolysate (5%) and oil (3.2%) obtained from fish waste (experimental diet) on systemic inflammation markers, adipokines levels, cardiac function and fecal microbiota of adult dogs. Samples and measurements were taken from a feeding trial conducted according to a crossover design with two diets (control and experimental diets), six adult Beagle dogs per diet and two periods of 6 weeks each. The experimental diet, with higher docosahexaenoic (DHA) and eicosapentaenoic (EPA) acids contents, decreased plasmatic triglycerides and the activity of angiotensin converting enzyme, also tending to decrease total cholesterol. No effects of diet were observed on serum levels of the pro-inflammatory cytokines interleukin (IL)-1β, IL-8, and IL-12/IL-23 p40, and of the serum levels of the anti-inflammatory adipokine adiponectin. Blood pressure, heart rate and echocardiographic measurements were similar between diets with the only exception of left atrial to aorta diameter ratio that was higher in dogs fed the experimental diet, but without clinical relevance. Diet did not significantly affect fecal immunoglobulin A concentration. Regarding fecal microbiome, Megasphaera was the most abundant genus, followed by Bifidobacterium , Fusobacterium , and Prevotella , being the relative abundances of Fusobacterium and Ileibacterium genera positively affected by the experimental diet. Overall, results from the performed short term trial suggest that shrimp hydrolysate and salmon oil can be replaced by protein hydrolysate and oil from fish by-products without affecting systemic inflammatory markers, cardiac structure and function, but potentially benefiting bacterial genera associated with healthy microbiome. Considering the high DHA and EPA contents and the antioxidant properties of fish oil and hydrolysate, it would be worthwhile in the future to assess their long-term effects on inflammatory markers and their role in spontaneous canine cardiac diseases and to perform metabolomic and metagenomics analysis to elucidate the relevance of microbiota changes in the gut.
Association between alterations in plasma metabolome profiles and laminitis in intensively finished Holstein bulls in a randomized controlled study
(2021) Bäßler, Sonja Christiane; Kenéz, Ákos; Scheu, Theresa; Koch, Christian; Meyer, Ulrich; Dänicke, Sven; Huber, Korinna
Metabolic consequences of an energy and protein rich diet can compromise metabolic health of cattle by promoting a pro-inflammatory phenotype. Laminitis is a common clinical sign, but affected metabolic pathways, underlying pathophysiology and causative relationships of a systemic pro-inflammatory phenotype are unclear. Therefore, the aim of this study was to elucidate changes in metabolome profiles of 20 months old Holstein bulls fed a high energy and protein diet and to identify novel metabolites and affected pathways, associated with diet-related laminitis. In a randomized controlled feeding trial using bulls fed a high energy and protein diet (HEP; metabolizable energy [ME] intake 169.0 ± 1.4 MJ/day; crude protein [CP] intake 2.3 ± 0.02 kg/day; calculated means ± SEM; n = 15) versus a low energy and protein diet (LEP; ME intake 92.9 ± 1.3 MJ/day; CP intake 1.0 ± 0.01 kg/day; n = 15), wide ranging effects of HEP diet on metabolism were demonstrated with a targeted metabolomics approach using the AbsoluteIDQ p180 kit (Biocrates Life Sciences). Multivariate statistics revealed that lower concentrations of phosphatidylcholines and sphingomyelins and higher concentrations of lyso-phosphatidylcholines, branched chain amino acids and aromatic amino acids were associated with an inflammatory state of diet-related laminitis in Holstein bulls fed a HEP diet. The latter two metabolites share similarities with changes in metabolism of obese humans, indicating a conserved pathophysiological role. The observed alterations in the metabolome provide further explanation on the underlying metabolic consequences of excessive dietary nutrient intake.
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.
Bulbus destruction by choroidal melanocytoma in a dog: a 3-year history
(2022) Nautscher, Nadine; Steffl, Martin; Schmon, Katharina; Ludwig, Eva
A 3-year-old male Slovak Hound with retinal detachment was presented. The causative intraocular mass was detected by ultrasonography, and the course of the disease was monitored over a 3-year period. Enucleation was performed due to secondary glaucoma. A benign choroidal melanocytoma was diagnosed by histopathology. To our knowledge, this is the first report that describes the disease over such a long period of time. The mild course of the disease questions enucleation of eyes with no or minor symptoms. Conventional treatment may be a suitable alternative to surgery for dogs with high anesthesia risks.
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.
Ceramide metabolism associated with chronic dietary nutrient surplus and diminished insulin sensitivity in the liver, muscle, and adipose tissue of cattle
(2022) Kenéz, Ákos; Bäßler, Sonja Christiane; Jorge-Smeding, Ezequiel; Huber, Korinna
High dietary energy and protein supply is common practice in livestock nutrition, aiming to maximize growth and production performance. However, a chronic nutritional surplus induces obesity, promotes insulin insensitivity, and triggers low-grade inflammation. Thirty Holstein bulls were randomly assigned to two groups, low energy and protein (LEP), and high energy and protein (HEP) intake, provided from the 13th to the 20th month of life. Body weight, carcass composition, laminitis score, and circulating insulin and glucose concentrations were assessed. The expression and extent of phosphorylation of insulin signaling proteins were measured in the liver, muscle, and adipose tissue. The sphingolipid metabolome was quantified by a targeted liquid chromatography-mass spectrometry based metabolomics approach. The HEP bulls were obese, had hyperinsulinemia with euglycemia, and expressed clinical signs of chronic laminitis. In the liver, protein kinase B (PKB) phosphorylation was decreased and this was associated with a higher tissue concentration of ceramide 16:0, a sphingolipid that diminishes insulin action by dephosphorylating PKB. In the adipose tissue, insulin receptor expression was lower in HEP bulls, associated with higher concentration of hexosylceramide, which reduces the abundance of functional insulin receptors. Our findings confirm that diet-induced metabolic inflammation triggers ceramide accumulation and disturbs insulin signaling. As insulin insensitivity exacerbates metabolic inflammation, this self-reinforcing cycle could explain the deterioration of metabolic health apparent as chronic laminitis. By demonstrating molecular relationships between insulin signaling and sphingolipid metabolism in three major tissues, our data extend our mechanistic understanding of the role of ceramides in diet-induced metabolic inflammation.
Clinical, haematological and pathomorphological findings in Mycoplasma suis infected pigs
(2021) Stadler, Julia; Ade, Julia; Hermanns, Walter; Ritzmann, Mathias; Wentzel, Sarah; Hoelzle, Katharina; Hoelzle, Ludwig E.
Background: Mycoplasma suis (M. suis) belongs to the group of haemotrophic mycoplasmas and is known as the causative agent of infectious anaemia in pigs. In the last few years valuable insights into the mechanism of adhesion and invasion, shedding patterns and cell tropism of M. suis were gained by the use of new molecular techniques. However, details on M. suis induced lesions as well as the distribution of M. suis in different organs are still lacking. Therefore, seven splenectomised pigs were experimentally infected and clinical and laboratory investigations as well as a detailed histopathological examination were performed. Detection and quantification of M. suis DNA in blood and various tissue samples was done using a quantitative real-time PCR. Results: During the course of experimental infection, periodically occurring signs of infectious anaemia of pigs including severe icteroanaemia, fever, apathy and anorexia were observed. In addition, dermatological manifestations such as haemorrhagic diathesis presenting as petechiae occurred. The most important haematological alterations were normochromic, normocytic anaemia, hypoglycaemia as well as increased bilirubin and urea concentrations. Necropsy revealed predominant evidence of haemolysis with consecutive anaemia, as well as disseminated intravascular coagulation. M. suis was found in all investigated tissues with the highest copy numbers found in the kidneys. In Giemsa stained sections M. suis was only detected red blood cell (RBC)-associated. Conclusion: In the present study, no RBC independent sequestration of M. suis was detected in organs of experimentally infected pigs. Pathological findings are most likely resulting from haemolysis, consecutive anaemia as well as from disseminated intravascular coagulation and subsequent organ impairments.
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.
Composition of the ileum microbiota is a mediator between the host genome and phosphorus utilization and other efficiency traits in Japanese quail (Coturnix japonica)
(2022) Haas, Valentin; Vollmar, Solveig; Preuß, Siegfried; Rodehutscord, Markus; Camarinha-Silva, Amélia; Bennewitz, Jörn
Background: Phosphorus is an essential nutrient in all living organisms and, currently, it is the focus of much attention due to its global scarcity, the environmental impact of phosphorus from excreta, and its low digestibility due to its storage in the form of phytates in plants. In poultry, phosphorus utilization is influenced by composition of the ileum microbiota and host genetics. In our study, we analyzed the impact of host genetics on composition of the ileum microbiota and the relationship of the relative abundance of ileal bacterial genera with phosphorus utilization and related quantitative traits in Japanese quail. An F2 cross of 758 quails was genotyped with 4k genome-wide single nucleotide polymorphisms (SNPs) and composition of the ileum microbiota was characterized using target amplicon sequencing. Heritabilities of the relative abundance of bacterial genera were estimated and quantitative trait locus (QTL) linkage mapping for the host was conducted for the heritable genera. Phenotypic and genetic correlations and recursive relationships between bacterial genera and quantitative traits were estimated using structural equation models. A genomic best linear unbiased prediction (GBLUP) and microbial (M)BLUP hologenomic selection approach was applied to assess the feasibility of breeding for improved phosphorus utilization based on the host genome and the heritable part of composition of the ileum microbiota. Results: Among the 59 bacterial genera examined, 24 showed a significant heritability (nominal p ≤ 0.05), ranging from 0.04 to 0.17. For these genera, six genome-wide significant QTL were mapped. Significant recursive effects were found, which support the indirect host genetic effects on the host’s quantitative traits via microbiota composition in the ileum of quail. Cross-validated microbial and genomic prediction accuracies confirmed the strong impact of microbial composition and host genetics on the host’s quantitative traits, as the GBLUP accuracies based on the heritable microbiota-mediated components of the traits were similar to the accuracies of conventional GBLUP based on genome-wide SNPs. Conclusions: Our results revealed a significant effect of host genetics on composition of the ileal microbiota and confirmed that host genetics and composition of the ileum microbiota have an impact on the host’s quantitative traits. This offers the possibility to breed for improved phosphorus utilization based on the host genome and the heritable part of composition of the ileum microbiota.
Correction: Schwarzkopf et al. Weaning Holstein calves at 17 weeks of age enables smooth transition from liquid to solid feed. Animals 2019, 9, 1132
(2021) Schwarzkopf, Sarah; Kinoshita, Asako; Kluess, Jeannette; Kersten, Susanne; Meyer, Ulrich; Huber, Korinna; Dänicke, Sven; Frahm, Jana
Cow’s microbiome from antepartum to postpartum: a long-term study covering two physiological challenges
(2022) Tröscher-Mußotter, Johanna; Deusch, Simon; Borda-Molina, Daniel; Frahm, Jana; Dänicke, Sven; Camarinha-Silva, Amélia; Huber, Korinna; Seifert, Jana
Little is known about the interplay between the ruminant microbiome and the host during challenging events. This long-term study investigated the ruminal and duodenal microbiome and metabolites during calving as an individual challenge and a lipopolysaccharide-induced systemic inflammation as a standardized challenge. Strong inter- and intra-individual microbiome changes were noted during the entire trial period of 168 days and between the 12 sampling time points. Bifidobacterium increased significantly at 3 days after calving. Both challenges increased the intestinal abundance of fiber-associated taxa, e.g., Butyrivibrio and unclassified Ruminococcaceae. NMR analyses of rumen and duodenum samples identified up to 60 metabolites out of which fatty and amino acids, amines, and urea varied in concentrations triggered by the two challenges. Correlation analyses between these parameters indicated a close connection and dependency of the microbiome with its host. It turns out that the combination of phylogenetic with metabolite information supports the understanding of the true scenario in the forestomach system. The individual stages of the production cycle in dairy cows reveal specific criteria for the interaction pattern between microbial functions and host responses.
Defining valid breeding goals for animal breeds
(2023) Wellmann, Robin; Gengler, Nicolas; Bennewitz, Jörn; Tetens, Jens
Background: The objective of any valid breeding program is to increase the suitability of a breed for its future purposes. The approach most often followed in animal breeding for optimizing breeding goals assumes that the sole desire of the owners is profit maximization. As this assumption is often violated, a generalized approach is needed that does not rely on this assumption. Results: The generalized approach is based on the niche concept. The niche of a breed is a set of environments in which a small population of the breed would have a positive population growth rate. Its growth rate depends on demand from prospective consumers and supply from producers. The approach involves defining the niche that is envisaged for the breed and identifying the trait optima that maximize the breed’s adaptation to its envisaged niche within the set of permissible breeding goals. The set of permissible breeding goals is the set of all potential breeding goals that are compatible with animal welfare and could be reached within the planning horizon of the breeding program. In general, the breed’s adaptation depends on the satisfaction of the producers with the animals and on the satisfaction of the consumers with the products produced by the animals. When consumers buy live animals, then the breed needs to adapt to both the environments provided by the producers, and the environments provided by the consumers. The profit function is replaced by a more general adaptedness function that measures the breed’s adaptation to its envisaged niche. Conclusions: The proposed approach coincides with the traditional approach if the producers have the sole desire to maximize their income, and if consumer preferences are well reflected by the product prices. If these assumptions are not met, then the traditional approach to breeding goal optimization is unlikely to result in a valid breeding goal. Using the example of companion breeds, this paper shows that the proposed approach has the potential to fill the gap.
Determination of optimal phage load and administration time for antibacterial treatment
(2024) Plunder, Steffen; Burkard, Markus; Helling, Thomas; Lauer, Ulrich M.; Hoelzle, Ludwig E.; Marongiu, Luigi
Using phages as antibacterials is becoming a customary practice in Western countries. Nonetheless, successful treatments must consider the growth rate of the bacterial host and the degradation of the virions. Therefore, successful treatments require administering the right amount of phage (viral load, Vφ) at the right moment (administration time, Tφ). The present protocols implement a machine learning approach to determine the best combination of Vφ and Tφ to obtain the elimination of the target bacterium from a system. Basic Protocol 1: One bacterium, one phage. Alternate Protocol 1: One bacterium, one phage (wrapping function). Alternate Protocol 2: One bacterium, one phage (wrapping function, alternative growing model). Basic Protocol 2: Two bacteria, one phage. Alternate Protocol 3: Two bacteria, one phage (launch from terminal).
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.

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