FFoQSI – Feed and Food Quality, Safety and Innovation


Tracing microbial contamination sources in the meat production chain:

Bacterial spoilage of meat is a global public health and economic challenge. Especially pork, which accounts for half of the annual meat production in the European Union, is one of the main causative agents of food-borne disease outbreaks. Approximately 1/3 of bacteria in pork are not pig associated and are presumably transmitted during cutting via personal, from the equipment or from the machine and slaughter environment. However, little is known about the actual microbial diversity in meat cutting plants. In this project, we will elucidate the abundances as well as the types of microorganisms present at different stages along the meat processing chain using state of the art molecular techniques and next generation sequencing technologies.  As a result, we will be able to construct a high-resolution transmission map of bacterial flows during the cutting of pork, and foremost, define critical carrier points of bacterial contamination. Our goal is to optimize cutting processes to systematically avoid contamination of microbes throughout meat processing.

Improved understanding of fermentation to raise the safety and quality of raw meat sausage:

Raw fermented sausages have been produced for centuries and are highly valued as traditional foods, yet traditional manufacturing processes do not warrant microbiologically safe products. Indeed, recent surveys have shown the presence of a number of different pathogenic bacteria in raw meat sausages. Usually, starter cultures are applied to these sausages to ensure a dominant microbiome of commensals, but the effectiveness of different starter cultures in terms of an efficient competitive exclusion against pathogens is largely unknown. Our objective is to monitor microbial changes during ripening of raw meat sausages and to define effective fermenters which might suppress the growth of food pathogens like Listeria monocytogenes and Verotoxin-producing Escherichia coli (VTEC).

Safety of durable heat treated meat products:

Most processed meat products are heat treated during manufacture to improve food safety and to extend their shelf life. Although heat treatment significantly reduces the microbial load, some microorganisms still persist, potentially causing spoilage of the product. Microbes that survive pasteurization might have upregulated genetic transcription patterns which explain their survival. Particularly, genes for stress response, SOS, stringent- and heat-shock genes are upregulated. First, we will evaluate the microbiological status of heat treated meat products of different facilities, thus tracking facility specific microbes which survived the pasteurization process. Then, a strain of interest will be examined in more detail in a comparative RNA sequencing experiment to identify specific upregulated genes after thermal treatment.

Each project is performed in collaboration with the Austrian Competence Centre for Feed and Food Quality, Safety and Innovation

More Information 2 


Microbes in the gastrointestinal tract of farm animals

Metabolic activity of highly abundant Campylobacter phylotypes at the rumen wall: The bovine epimural bacterial microbiome (BEBM) in the rumen is suggested to fulfill a multitude of physiologically important functions. This bacterial community is at the interface between the rumen content and the host and is distinct from the bacterial community in rumen fluid and mat. Recent data from our working group suggest Campylobacter phylotypes to be highly abundant in the BEBM of the rumen and to have a stabile abundance during acidotic insults (Wetzels et al., 2015, Wetzels et al., 2016). The aim of this project is to i) develop and optimize an isolation method for Campylobacter phylotypes from rumen wall, suitable for studying, ii) the influence of stress conditions on growth of Campylobacter isolates and, iii) to determine whether and how those responses affect gene expression.  This project was founded by the Bright-Sparks-Award 2016 (Vetmeduni Vienna, Austria).


K-project ADDA (Advancing of Dairying in Austria)

Developing innovative health-promoting feeding concepts for high-producing dairy cattle: Despite the significant progress made in studies of the rumen microbiome, there are still deficits in our understanding of how rumen disorders affect the microbiome (Brulc et al., 2009) – in particular the epimural microbiome (the microbiome attached to rumen epithelium) - and how this microbiome interacts with the host to modulate rumen health. Our knowledge regarding the effects of rumen disorders on fiber digestion, and the potential means of stimulation through efficient and natural dietary strategies is limited as well. Disorders have consequences for fiber degradation in the rumen and on the productivity of cattle. Development of prophylactic strategies against rumen disorders and the stimulation of the rumen microbiome by dietary means require system-wide knowledge starting at the level of the rumen microbiome and its interaction with the host and extending to the molecular regulation of the metabolic and barrier functions of the rumen epithelium. The more we know about metabolic adaptive capacity and the regulation of the barrier functions of the rumen at the molecular level, the better we can tailor feeding strategies towards the goal of more efficient production of healthy ruminants - thus leading to higher product quality. Project leader: Prof. Zebeli, project partner: BIOMIN GmbH.

Spore-forming bacteria as a major source for spoilage in dairying: Spore-formers are able to survive the heat treatment in the processing of the milk, and can cause spoilage of the product and food-borne diseases - like food poisoning - in humans. Psychrotrophic strains are able to germinate and grow during refrigerated storage of pasteurized and extended shelf life (ELS) milk. Therefore, one of the goals for a further improvement of milk quality is a reduction of the spore load. If a routine procedure for the assessment of aerobic spore-formers would be available, it would make possible the routine monitoring of the milk processing chain. In this project, spore-formers will be isolated from milk and characterized in terms of toxin production. Subsequently a rapid test for the enumeration of presumptive Bacillus cereus will be developed, which reduces the time to result, is simple to perform and can be automated to a high degree. Molecular tools will enable species identification, as well as the presence of toxin related genes. All analytical technologies will be validated based on statistical principles and ISO procedures. Project leader: Dr. Konrad Domig (BOKU), project partner: SY-LAB Geräte GmbH.

More information  ADDA  3


Characterization and prevention of diet-induced metabolic disorders in dairy cows


This project will address a key issue of high-producing dairy cattle microbiology and nutrition of the rumen: How the enhanced plane of nutrition, needed to support high milk yields, can induce rumen wall–attached (epimural) microbiota shifts and subacute rumen acidosis (SARA). More specifically, we will evaluate how the changes in rumen conditions due to SARA can modulate epimural microbiota structure. The exact relation between SARA and microbial changes at the rumen wall during a long-term feeding experiment is not completely understood yet. Two models of elevated plane of nutrition will be evaluated in rumen-cannulated cows to induce SARA-like conditions, including a persistent (feeding model 1) and transient (feeding model 2) SARA challenge, in order to understand the resultant disruptions of the ecological balance in the bacterial epimural community. The characterization of the bacterial epimural community will be done using next generation sequencing of 16S rRNA gene amplicons. This project will provide important information on the adaption of the rumen associated microbiota of cows in response to an enhanced plane of nutrition. This will help to optimize the feeding of high-producing dairy cows and will enhance the rumen health in these animals as well as finding a compromise between healthy nutrition and economic use of lifestock. This project is a collaboration of the institute of animal nutrition and functional plant compounds and the institute of milk hygiene, milk technology and food science. Funding for this project is provided by the project “D-I.INFLACOW, LS12-010” of Vienna Science and Technology fund (WWTF) lead by Prof. Qendrim Zebeli.


Mechanisms of cytoplasmic incompatibility caused by Cardinium in parasitoid wasps

Photo credits Suzanne Kelly

Cytoplasmic incompatibility (CI) is a symbiont associated reproductive manipulation that has long intrigued biologists for its subtlety. At its simplest, female hosts fail to produce viable offspring when infected males mate with uninfected females, a phenomenon that favors the survival of symbiont-infected insects. CI-inducing symbionts are strictly maternally inherited. CI-inducing symbionts thus decrease the fitness of uninfected females (Werren and O‘Neill 1997). Consequently, infected females have an advantage in reproduction. CI infections can spread rapidly and have a significant impact on host population. CI is associated primarily with Wolbachia (alpha-Proteobacteria), but concerted efforts have failed to reveal the molecular mechanism that allows bacteria-modified sperm to effectively recognize whether the egg cytoplasm is infected with related symbionts. Cardinium (phylum: Bacteroidetes) is the only bacterial lineage besides Wolbachia known to cause CI (Hunter et al., 2003). One natural host of Cardinium is the wasp Encarsia, which lays its eggs in nymphs of a whitefly (Bemisia tabaci). The larva totally consumes the whitefly, pupates and finally the wasp emerges from the whitefly cuticle. Cardinium endosymbionts cause variable phenotypes (CI-inducing, parthenogenesis or asymptomatic) in different Encarsia species. We are adopting a comparative framework for examining CI in Cardinium, drawing on the recently published Cardinium genome. The Cardinium hertigii strain cEper1 of Encarsia was published recently (Penz et al., 2012). The genome lacks all major biosynthetic pathways except the biotin pathway. Comparative genomics to Wolbachia suggests an independent CI evolution in Cardinium.We aim to identify genes involved with CI and host interactions by transcriptional profiling of a CI-inducing Cardinium in male and female parasitiod wasps (Encarsia pergandiella) and genome sequencing of four Cardinium strains causing different phenotypes. We will compare expression of Cardinium genes in male and female Encarsia, and analyze the expression of candidate genes in more detail in a panel of male and female Cardinium-infected Encarsia species, including CI and non-CI strains. We expect that the results of transcriptome sequencing and comparison of Cardinium genomes causing different phenotypes will reveal first deep insights into the mechanisms of reproductive manipulation in Cardinium. We expect that the tractability of this experimental system and the comparative insights it can provide will ultimately enhance understanding of CI in Wolbachia as well as Cardinium. This project is led by Prof. Martha Hunter (University of Arizona, USA) and Dr. Stephan Schmitz-Esser and funded by the FWF and the NSF.
Link to Prof. Martha Hunter’s Homepage  7