Browsing by Subject "Metabolome"

Now showing 1 - 4 of 4
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    Analysis of aging-related changes and influencing factors on the metabolome of beef
    (2023) Bischof, Greta; Gibis, Monika
    Aging of beef is necessary to improve its flavor and tenderness. There are two most common aging types, dry-aging and wet-aging. Dry-aged beef is often associated with a higher eating quality than wet-aged beef. The term “dry-aged beef” is not legally defined, so authentication methods are needed to protect the consumers from food fraud. During beef aging, the metabolome of beef changes due to the postmortem metabolism. This dissertation focuses on the aging method as a postmortem process and the resulting changes in the metabolome. As a hypothesis of this study, it was postulated that the detection of these metabolic changes due to aging of beef is feasible by 1H NMR spectroscopy and based on these measurements the evaluation of an authentication model for the aging method of beef is possible. In order to test this hypothesis, a sample preparation and measurement method was developed and based on this, potential influencing factors such as sampling position in muscle, breed and sex were investigated on the metabolome of fresh and aged beef. In the first part of this thesis, the sample preparation and the 1H NMR measurement method were developed. In the sample preparation, the polar fraction of the metabolome was extracted from 200 mg of beef, allowing 24 samples to be prepared in parallel. The sample preparation and the measurement method were validated, and the first aged beef samples were analyzed to check if the aging-related changes in the metabolome could be detected by this method. In the second part of this thesis, the sampling position in the muscle were analyzed for changes or differences in the metabolome due to its location in the muscle. The results showed that the metabolome changes along the length of the M. longissimus thoracis et lumborum, but the influence of the aging type and aging time was more pronounced in the metabolome of beef. The comparison of the surface and the inner part of wet-aged and dry-aged beef showed that the metabolome of dry-aged beef differed greatly between the surface and the inner part, despite the exclusion of the moisture content by freeze-drying and the low microbial load. There were only slight differences between the surface and the inner part for wet-aged beef, which could be due to the influence of microbiota and their metabolites. Therefore, the sampling location in the M. longissimus thoracis et lumborum was determined as precisely as possible for the further studies. The muscles were cut into ten pieces from cranial to caudal and dry-aged or wet-aged for 0, 7, 14, 21, and 28 days, in duplicates. The third part of this thesis focuses on the potential influencing factors such as breed and sex of the animals. Fresh and aged beef samples from three cattle types (heifer, cow, and young bull) and two different breeds (‘Fleckvieh’ and ‘Schwarzbunt’) were analyzed by targeted and non-targeted 1H NMR spectroscopy. Both factors were shown to influence the metabolome of fresh and aged beef. Therefore, these factors had to be included in the authentication model based on both targeted and non-targeted model. The calculation of the authentication model was the main part of this thesis and showed a good prediction of cattle type, breed, aging time and aging type of beef. The authentication model was based on the combination of multiple models of PLS-R and PLS-DA. The model for predicting the cattle type showed an accuracy of 99 %, and the models for predicting the breed depending on the cattle type showed an accuracy of 100 %. Aging time could be predicted with an error of 2.28 days. The statistical models for aging type were separated by aging time based on the determination of aging time. The model for predicting the aging type of 28-day aged samples had an accuracy of 99 %. The other statistical models for predicting aging type were additionally separated by cattle type and breed, and their accuracy ranged from 90 % to 100 %. In conclusion, an authentication model to determine the cattle type, breed, aging time and aging type of beef was developed in this dissertation. Therefore, it is possible to authenticate beef samples using a single 1H NMR spectrum. In future studies, it would be useful to extend this authentication model to other samples of other breeds and influencing factors.
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    Impact of age and weaning time on the gut microbiome and the potential host-microbe interactions in calves
    (2021) Amin, Nida; Seifert, Jana
    The period from birth until the end of weaning is critical for calves as they undergo extreme stress caused by maternal separation, transportation, and weaning related dietary shifts, that can cause long-lasting effects on animal behaviour, health as well as future production parameters. Monitoring the development of microbial ecosystem throughout the gastrointestinal tract of calves and host-microbe interactions during the challenging life periods such as perinatal and weaning is essential for sustainable ruminant production. The present thesis provided new insight on the suitability of buccal swabs as an alternative to complex stomach tubing method for predictive analysis of rumen microbial communities. The changes in oral, rumen and faecal microbial community structure of female German Holstein calves from 8-days to 5-months of age as well as during early- and late-weaning event were identified. The oral microbiota plays a crucial role in animal health. A high dominance of oral pathogens was observed during the first 11-weeks of calves’ life. Similar to the oral microbiota, faeces of 8-day-old calves also showed high abundances of certain opportunistic pathogenic bacteria. Both oral and faecal pathogens showed a decrease in abundance with age and after weaning event in the earlyC group, indicating the age and weaning-dependent maturation of the host immune system. The establishment of dense microbial communities in the faeces of 8-day-old (experimental day 1) pooled herd milk and milk replacer fed Holstein calves was shown and it was dominated by phyla Firmicutes and Actinobacteria and potential lactose- and starch-degrading bacterial species, but as the calves aged and became more mature (5-months of age), their rumen and faecal bacterial communities were dominated by potential fibre-utilizing bacterial genera. The weaning related dietary transitions are critical for calves as their gastrointestinal tract undergoes several modifications, enabling them to digest plant-based diet during the postweaning period. Thus, it was proposed that the age at which animals should be weaned must be carefully considered as it clearly impacted the gastrointestinal tract microbial communities and plasma metabolic profiles of calves in the present study. Early introduction of roughages in the diet of 7-week-old calves increased the abundances of plant fiber degrading bacteria and decreased the abundances of potential lactose- and starch-degrading bacteria in the buccal cavity, rumen and faeces, indicating the weaning-related increase in fiber ingestion and the decrease in milk consumption of the early-weaned group. However, when roughages were introduced in the diet of late-weaned calves at 17-weeks of age, no significant modifications in the structure of gastrointestinal tract microbial communities were observed. Similar to the microbiome, plasma metabolic profiles of early-weaned calves during days 42–112, showed lower concentrations of most of the amino acids, few biogenic amines, and sphingomyelins as compared to the late-weaned calves, suggesting that the liquid diet could provide certain metabolites that can be transported into the bloodstream through gastrointestinal tract. Similarly, the weaning-dependent changes in the quantity of dietary protein, fat and carbohydrates resulted in substantial changes in amino acid metabolism of the early-weaned group. The early-weaning event not only impacted the host microbiome and metabolome but also the host-microbe metabolic interactions as the abundances of potential lactose- and starch degrading bacteria and plasma concentrations of amino acid, biogenic amines and sphingomyelins were strongly positively correlated, both were negatively impacted by the early-weaning event. Thus, it can be concluded that late-weaning was beneficial as it allowed better adaptability of microbes to weaning-related dietary shifts, perhaps due to the greater maturation of their gastrointestinal tract with age as compared to the early-weaning group.
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    A shift towards succinate‐producing Prevotella in the ruminal microbiome challenged with monensin
    (2022) Trautmann, Andrej; Schleicher, Lena; Koch, Ariane; Günther, Johannes; Steuber, Julia; Seifert, Jana
    The time‐resolved impact of monensin on the active rumen microbiome was studied in a rumen‐simulating technique (Rusitec) with metaproteomic and metabolomic approaches. Monensin treatment caused a decreased fibre degradation potential that was observed by the reduced abundance of proteins assigned to fibrolytic bacteria and glycoside hydrolases, sugar transporters and carbohydrate metabolism. Decreased proteolytic activities resulted in reduced amounts of ammonium as well as branched‐chain fatty acids. The family Prevotellaceae exhibited increased resilience in the presence of monensin, with a switch of the metabolism from acetate to succinate production. Prevotella species harbour a membrane‐bound electron transfer complex, which drives the reduction of fumarate to succinate, which is the substrate for propionate production in the rumen habitat. Besides the increased succinate production, a concomitant depletion of methane concentration was observed upon monensin exposure. Our study demonstrates that Prevotella sp. shifts its metabolism successfully in response to monensin exposure and Prevotellaceae represents the key bacterial family stabilizing the rumen microbiota during exposure to monensin.
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    The intestinal microbiome and metabolome of dairy cows under challenging conditions
    (2022) Tröscher-Mußotter, Johanna; Seifert, Jana
    The modern dairy cow is confronted with a multitude of stressors throughout live. Especially calving, transition, and microbial infections are strong challenges that can have long-lasting impacts on the cow’s health and performance. Yet, individuals can differ in their response towards these challenges, raising the question which characteristics in the dairy cow contribute to a more or less robust animal. Apart from genetics, the gut microbiome and the entailed metabolome is assumed to play an important role in buffering or promoting host stress. This is also due to the fact that the gut microbiome is strongly involved in the hosts energy metabolism and immune system. As dairy cows often show performance impairments during high energy demanding periods, it could be suggested that improving energy metabolism in these specific phases might reduce the negative phenotypic outcomes. This was tested using dietary L-carnitine, a metabolite inevitably necessary for energy metabolism. However, no supplement effects on the intestinal microbiome or metabolome have been found in the present work. Supplementation was continued throughout the complete trial. Calving functioned as an individual stimulus, and an intra-venous LPS injection induced a standardized inflammatory challenge, as a specific amount of LPS per kg of bodyweight was applied per cow. Supplemented animals were compared to a control group. In total, the animals were studied across 168 days and sampled extensively at several sites. The focus of this thesis was to analyze the bacterial consortia and metabolites of both, host and bacteria, in rumen, duodenum, and feces throughout the given period. This was to elucidate the metabolic reactions and bacterial shifts during the mentioned challenging periods and their response to the L-carnitine supplementation. First, the ruminal and duodenal fluid microbiome of eight double cannulated animals during the two respective challenges was analysed. Before calving and feed change, rumen and duodenal fluid bacterial consortia were significantly different, thereafter very alike. Strong microbial community shifts were observed throughout the complete trial irrespectively of the matrix. Both matrices varied in their metabolite patterns indicating functional variation among sites. Also, a strong increase of Bifidobacterium at three days after calving was observed in almost all animals pointing towards a strong biological purpose. This needs to be investigated in upcoming studies. The study could show increasing ketogenic activities in the animals after calving and proposes a possible protective host-microbial interaction, against a ruminal collapse induced by LPS challenge, here described as "microbial airbag". The second part included fecal samples of the same animals, which were analyzed for their bacterial consortia and targeted metabolites. Different dynamics and diversities of microbial communities amongst the individuals were observed, according to which animals could be grouped into three microbiome clusters. These showed in part fundamentally different metabolic, health, and performance parameters, indicating strong host-microbiome-metabolite interactions. The study demonstrated that microbiome clustering may contribute to identifying different metabo- and production types. Again, the study observed a strong increase of Bifidobacterium at three days after calving and even during the LPS challenge supporting the findings of the former study. This strengthens the hypothesis that also for the cow Bifidobacterium may have protective effects, as this genus is largely involved in health promoting activities. The power of this project lies in the massive sampling of different body sites in dairy cows across a very long period of time and finally, merging of the collected data. This, however, requires high computational efforts as numerous time points, matrices, animals, measurements, treatments, feeding regimen, and challenges resulted into a large bandwidth of parameters and metadata. Yet, it bears the potential to better elucidate and understand actions and reactions of the host, its microbiome and metabolism, as well as organ-axes in dairy cows and thereby gaining a more holistic picture of these complex animals. The aim of analyzing the host, its microbiome and metabolome throughout challenging periods resulted into the following main findings. Time, calving, and feed change remarkably change the microbial communities and to a lesser extent the metabolomes in all three matrices. Rumen and proximal duodenal fluid samples significantly differ in their metabolomes but not in their microbiome. In all matrices, an increase of Bifidobacterium is seen within three days after calving, which has to be further researched. Across the herd, three distinct microbiome clusters are found, which significantly differ in their production and health parameters.