Interrelations between feed, host and rumen microbiota in dairy cows
von Melanie Schären
Datum der mündl. Prüfung:2017-11-16
Erschienen:2019-04-25
Betreuer:Prof. Dr. Jürgen Hummel
Gutachter:Prof. Dr. Sven Dänicke
Gutachter:Prof. Dr. Gerhard Breves
Dateien
Name:thesis.PAG.draft.20.11.2017 PRINT_SUB.pdf
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Zusammenfassung
Englisch
The adaptability of the rumen microbiome to new nutritional situations is a key feature in ruminant survival strategy. Different studies and reviews describe the high redundancy and resilience of the rumen microbiome allowing the fermentation and nutrient extraction from a wide range of feedstuffs. They further highlight the strong host effect and that many questions concerning the temporal, spatial and microbial dynamics involved are still unanswered. The aim of this thesis was therefore to investigate different factors influencing the rumen microbiome and their interrelations. Three different studies were performed, each examining a different aspect in the rumen host-microbiome interplay: the adaptation to a new diet, the influence of anti-ketogenic feed additives, and the interrelations with phenotypic characteristics of the host. The database for the three studies was formed by rumen microbiota samples which were analyzed by a DNA-fingerpriting technique (single-strand conformation polymorphism, SSCP) and next generation sequencing (16S rRNA gene amplicon sequencing using the Illumina MiSeq platform). For the first study samples were collected from three different sites in the rumen (liquid, fiber mat and epithelium) at three points in time, in a trial involving the transition from a silage- and concentrate-based ration to pasture in spring. To investigate the influence of anti-ketogenic feed additives on the rumen microbiome, rumen liquid samples were collected during a trial performed to investigate the influence of monensin and essential oils on health, production and rumen fermentation of transition dairy cows. For the third study, a large dataset of 36 healthy dairy cows in the first weeks of their lactation was analyzed for interrelations concerning the rumen microbiome, production, behavior, rumen fermentation, metabolic, and immunological variables. The first study confirmed that the concept of a “core and variable microbiome” accounts for all three locations in the rumen and that the ration fed has the largest influence on the rumen microbiome compilation. The first trial further illustrated that a ration change from a concentrate- and silage-based ration to pasture influences the microbiome at all three locations, opposite the generally acknowledged hypothesis that the epithelium-associated prokaryotes remain more consistent throughout dietary changes. The data also suggests that the alterations observed in the rumen microbiome across a ration change cannot solely be accounted to the time needed for the different microbial species to adapt to the new substrate, but also to temporal aspects in behavioral and physiological alterations of and in the host. In the second study, we show that the feed additive monensin alters the “core microbiome” and confirm that the reason for the ineffectiveness of essential oils can most likely be attributed to the adaptability of the rumen microbiome. Different aspects of the mode of action and the prokaryotes affected are discussed. In the first study, we were able to statistically proof the concept of the “variable or individual microbiome” for different prokaryotes. In the final study, it was hypothesized that the feed intake behavior of the host could be responsible for this “individual microbiome” through induction of alterations in the rumen fermentation profile. This hypothesis was however not confirmed. Nevertheless, several previously described interrelations between the abundance of certain rumen prokaryotes and production traits were confirmed. Throughout the three studies different methodological aspects are discussed in detail, possible bottlenecks and key-influencing factors are identified, and it is illustrated that caution needs to be taken when interpreting and comparing microbiome sequencing data. A major finding of the presented studies is that prokaryotes which are phylogenetically close do not necessarily exhibit functional communality. This aspect has been largely ignored in previous studies and stresses the importance of functional characterization aside taxonomic classification. It is concluded that future studies should not only involve more sophisticated methods to characterize the rumen microbiome as well as phenotypic attributes of its host, but also focus on an array of previously insufficiently investigated aspects, such as the interrelations between the microbiota and its hosts metabolism, the role of the low abundant microbial species and the rumen wall associated microbiota, the interrelations between the different rumen microorganisms and the role of the lower-gut microbiota.
Keywords: rumen; microbiota; dairy cow; pasture; monensin