PhD thesis

Methane emissions and microbial dynamics in ruminants

PhD student: Rajan Dhakal
Thesis defended: 11 March 2024

Ruminants are commonly associated with the production of enteric methane (CH4) emissions due to the anerobic fermentation that occurs in the rumen. Ruminant agriculture has contributed to global warming, which is a growing concern in society. In recent years, ruminants and the rumen microbiome have emerged as the main focus of scientific research to reduce CH4 emissions. To effectively screen and evaluate potential mitigation strategies for CH4 emissions from ruminants, a rapid, accurate, and precise scientific technique is necessary.


The intimate interactions between bacteriophages and bacteria

PhD student: Veronika Theresa Lutz
Thesis defended: 20 March 2024

Bacteriophages are possible alternatives to antibiotics since they specifically infect and kill bacteria. Elucidating how phages selectively target their host bacteria by binding to the bacterial surface is particularly important for developing phages for therapy.

Learn MORE about the project's  Straboviridae phages.

Immunologic effects of probiotics against respiratory viral infections

PhD student: Katrine Damgaard Winther

The overall aim of this thesis was to investigate if and how specific probiotic strains can modulate responses in immune cells, and whether they will have beneficial effects against respiratory viruses through stimulation of local and/or systemic immune responses when administered in vivo to mice and pigs.
Read more about the project

Exploration of Genetic Factors Influencing Gut Health in Pigs

PhD Student: Emil Ibragimov
Theses defended: 3 November 2023

Post-weaning diarrhea (PWD) poses a significant challenge in pig farming leading to diminished animal well-being, decreased meat yield and often necessitating antimicrobial intervention. LEARN MORE about this project,

Field Methods for the Identification of Emerging Viruses

PhD Student: Anna Signe Fomsgaard
Thesis defended: 2 November 2023

Viruses are major contributors to novel emerging infectious diseases. Due to the versatile nature of viruses, human activities, contact with animals and environmental factors, the world is increasingly experiencing viral disease outbreaks. Learn more about the project.

Genomic epidemiology of Acinetobacter baumannii from patients and wastewater at hospitals in southwestern Nigeria

PhD Student: Erkison Ewomazino Odih
Thesis defended: 23 October 2023

This project was conducted to determine the epidemiology of A. baumannii infections in Nigeria and characterize the clinically relevant lineages and burden of carbapenem resistance using whole genome sequencing. Learn MORE about this project.

Effect of intramuscular Lawsonia intracellularis vaccination on production parameters, antimicrobial consumption and mixed-pathogen intestinal infections in grower pigs

PhD Student: Susanne Leth Musse
Thesis defended: 16 June 2023

Effect of intramuscular Lawsonia intracellularis vaccination on production parameters, antimicrobial consumption and mixed-pathogen intestinal infections in grower pigs. Learn MORE about this project.

Causes and Bacteriological Findings in Carcasses Condemned at a Danish Broiler Abattoir

PhD Student: Ahmed Eassa H Alfifi
Thesis defended: 13 December 2022

Causes and Bacteriological Findings in Carcasses Condemned at a Danish Broiler Abattoir - LEARN more about this project. 

Insulin-induced hypoglycaemia in healthy and streptozotocin-induced diabetic Göttingen Minipigs

PhD Student: Mille Kronborg Lyhne
Thesis defended: 5 January 2023

Insulin-induced hypoglycaemia in healthy and streptozotocin-induced diabetic Göttingen Minipigs. LEARN more about this project.

Investigations of NASH and hepatic fibrosis in the guinea pig model

PhD Student: Josephine Skat-Rørdam
Thesis defended: 24 November 2022

Investigations of NASH and hepatic fibrosis in the guinea pig model.
LEARN more about this project.

Colibacillosis in poultry – Aetiology, pathogenesis, diagnosis, and control

PhD Student: Sofie Kromann
Thesis defended: 7 October 2022

Infections with Escherichia coli, collectively referred to as colibacillosis, constitute a major health challenge in poultry. LEARN more about this project. 

Towards an evidence-based welfare assessment protocol for polar bears (Ursus maritimus) in Zoos

PhD Student: Cecilie Ravn Skovlund
Thesis defended: 14 November 2022

The purpose of the present PhD project was to begin the development of a welfare assessment protocol for polar bears in zoos, based on an adaptation of the Welfare Quality® and 24/7 Approach framework, with focus on behavioural welfare indicators.
LEARN MORE about this project.

Modulation of mucosal immunity and enteric pathogens by dietary compounds

PhD Student: Ling Zhu
Thesis defended: 7 November 2022

Enteric pathogens infect more than one billion people, as well as livestock all over the world, and cause diarrhea, chronic inflammation and ill health, even death.
LEARN MORE about the project.

Assessment of antimicrobial susceptibility, intrinsic resistance, and virulence in industrially relevant bacteria

PhD Student: Katrine Nøhr-Meldgaard
Thesis defended: 14 October 2022

When a bacteria is used for industrial purposes, it needs to be ensured that it is safe for the consumer and worker. Thus, bacterial strains used for food, feed and probiotic production should not encode acquired antibiotic resistance genes.
LEARN more about this project

Bacterial factors affecting macrophage survival and induction of immune responses in avian host-specific serovar S. Pullorum

PhD Student: Xiao Fei
Thesis defended: 24 August 2022

Salmonella enterica is an important pathogen infecting humans and warm blooded animals. 
LEARN more about this project.

In vitro characterization of Actinobacillus pleuropneumoniae outer membrane vesicles

PhD student: Zhuang Zhu
Thesis defended: 16 August 2022

Outer membrane vesicles (OMVs) open up a new avenue different from any other strategies used before in vaccine research. OMVs are non-replicative sphere structures originating from the outer membrane of Gram-negative bacteria. 
Read more about this project

Avian Schistosomes and Cercarial Dermatitis in Denmark

PhD student: Azmi Al-Jubury
Thesis defended: June 2022

During the last decades human infections with avian schistosome larvae have been observed in Denmark with increasing frequency. The infection in human is termed cercarial dermatitis or swimmer’s itch, which is a skin disorder caused by penetrating avian schistosome cercariae.

Read more about this project

Disease prevention against Gallibacterium anatis with special emphasis on outer membrane vesicles

PhD student: Toloe Allahghadry
Thesis defended: 20 May 2022

The global emergence and spread of antimicrobial-resistant pathogens have become an increasing concern to public health. Besides affecting human healthcare, antimicrobial-resistant bacteria have also affected the livestock industry worldwide, which led to increased mortality and economic loss over the last decades.
Read more about this project

Anti-parasitic activity of seaweed extracts and effects of dietary seaweed supplementation on nematode infections and gut health in pigs

PhD student: Charlotte Smith Bonde
Thesis defended: 31 March 2022

Infections with parasitic worms are common in livestock causing substantial economic losses and posing health risks to infected animals. Parasitic worms of pigs include species such as the large roundworm (Ascaris suum) and nodular worm (Oesophagostomum spp.). The nodular worm is a smaller worm up to 1.5 cm long, located in the large intestine of pigs. The large roundworm is located in the small intestine of the pigs and females can grow up to 40 cm long. This parasite can also infect humans. LEARN MORE

Antimicrobial use in dairy cattle explored through mixed methods. Focusing on the farmer-veterinarian collaboration

PhD student: Nanna Krogh Skjølstrup
Thesis defended: 28 March 2022

Farmers and veterinarians are the primary responsible actors for refining or reducing antimicrobial use (AMU) within dairy cattle. Their collaborative framework of veterinary herd health consultancy (VHHC) comprises an obvious setting to explicitly work towards this task. Research shows that changing AMU is a complex issue for the individual farmer or veterinarian, involving many influential barriers and motivators. 
Read more about this project.

Trematodes in Danish freshwater systems

PhD student: Yajiao Duan
Thesis defended: 1 March 2022

Digenean trematodes belong to the phylum Platyhelminthes. They have a complex life cycle and require at least two hosts, one of which is usually a mollusc. Other invertebrates and vertebrates may serve as second and/or definitive hosts. The free-living stage (termed cercariae), which is released from the mollusk, to the aquatic system becomes exposed to a range of abiotic and biotic factors.
Read more about this project.

In vitro and in vivo pharmacodynamics of tulathromycin against Actinobacillus pleuropneumoniae

PhD student: Astrid Katarina Larberg
Thesis defended: 21 January 2022

Actinobacillus pleuropneumoniae is an important lung pathogen in pig production which is commonly treated and prevented with antimicrobials. 

Tulathromycin is a long-acting macrolide antimicrobial, frequently used in the treatment and prevention of A. pleuropneumoniae. One single injection of tulathromycin creates a sufficient antimicrobial exposure for effect, which is beneficial for the user.

Read MORE about the project. 

Co-infection of wounds with Arcanobacterium phocae and Streptococcus halichoeri in farm mink - Disease mechanisms and diagnostic

PhD student: Oliver Legarth Honoré
Thesis defended: 6 January 2022

In 1996 a new disease was observed within fur animals in Canada. The disease was characterized as rapid forming necrotizing wounds.

Later in 2007, the first cases emerged in Finland. In 2015, the first confirmed cases of FNP were recorded on five Danish mink farms. It remains unknown how many farms are affected by the disease.
Read more about the project

Seroepidemiology of Toxoplasma gondii in Danish pigs & the zoonotic potential from pork consumed in Denmark

PhD student: Abbey Olsen
Thesis defended: 5 November 2021

Among various sources of human toxoplasmosis, infection from consuming undercooked meat is an important one, as the meat may contain viable Toxoplasma gondii parasites. Acquired toxoplasmosis is rarely reported in healthy humans because the symptoms are either mild or absent. But toxoplasmosis in immunocompromised individuals like those with HIV, infection can be life-threatening. In pregnant women, infection may lead to abortions or infection may be passed on to the fetus resulting in brain damage or blindness from congenital toxoplasmosis.

For a summary of the thesis.  

An intracellular perspective of the metabolism of uropathogenic Escherichia coli

PhD Student: Sisse Mortensen
Thesis defended: 28 October 2021

Extraintestinal pathogenic E. coli (ExPEC) are able to cause infections outside the intestines. Uropathogenic (UPEC) and Avian Pathogenic (APEC) E. coli are two ExPEC variants. They cause infection in the urinary tract system of human (UPEC) and in the salpinx and airways of birds (APEC), respectively. Genetically, these two ExPECs cannot be distinguished from one another. Previous studies have shown that APEC strains are able to infect in vivo models of human urinary tract infection (UTI), suggesting that they may be zoonotic. But no studies have shown that UPEC can infect in adult immonucompetent bird and examined a potential anthrozoonotic potential of UPEC.

Learn more about the project.

Immuno-modulatory Properties of Proanthocyanidins and Implications during Helminth-induced Inflammation in the Gut

PhD Student: Audrey Inge Schytz Andersen-Civil
Thesis defended: 6 September 2021

Proanthocyanidins (PAC) are specialized plant metabolites, more commonly known as a type of anti-oxidant, and they are part of the larger phytochemical group of polyphenols. Interestingly, several studies have demonstrated important anti-oxidant and anti-inflammatory properties of PAC both in cellular and animal models.

Read MORE about the project.

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Annotation and Transcriptomic Analysis of Bacillus subtilis with Application in Biotechnology

PhD Student: Adrian Geissler
Thesis defended: 17 September 2021

Enzymes are crucial to biotechnology and consumer goods. These enzymes are produced by micro-organisms, which are also referred to as cell-factories (in contrast to concrete buildings). One such specific cell-factory organism is the bacterium Bacillus subtilis.

Read MORE about the project. 

Transcriptome profiling of neurodegenerative disorders modelled with IPSCs and computational methods for CRISPR/Cas9 editing

PhD Student: Giulia Corsi
Thesis defended: 3th September 2021
The primary goal of the project was to better understand the cellular mechanisms related to two neurodegenerative disorders, namely Alzheimer’s disease (AD) and frontotemporal dementia linked to chromosome 3 (FTD3).
READ MORE about the project

Casualty or carrier? Understanding the pathogenesis of elephant endotheliotropic herpesvirus haemorrhagic-disease in Asian elephants (Elephas maximus)

PhD Student: Kathryn Louise Perrin, BVetMed, PhD, Dipl ACZM, Dipl ECZM (ZHM), Zoo Veterinarian
Thesis defended: 4th June 2021
Elephant endotheliotropic herpesvirus (EEHV) infection is endemic within the worldwide Asian elephant (Elephas maximus) population. An acute and often fatal haemorrhagic syndrome, EEHV-haemorrhagic disease (EEHV-HD), is associated with EEHV infection and is reported to be the most common cause of death of young Asian elephants. READ MORE about the project

Transduction in Staphylococcus aureus

PhD Student: Ahlam Alsaadi
Thesis defended: 18 May 2021

In Staphylococcus aureus is a pathogenic bacterium that able to infect humans and animals. Third of healthy human population carries Staphylococcus aureus in their interior nares, while the rest are intermittent carriers. READ MORE about the project

The ClpX Chaperone and Super-Resolution Imaging – a promising toolbox to explore Staphylococcus aureus cell division and the killing mechanism of β-lactam antibiotics

PhD Student: Camilla Jensen
Thesis defended: 27 April 2021

You have probably taken penicillin to cure tonsillitis or other bacterial infections - but have you ever wondered how penicillin actually works? Read more about the CIpX Chaperone and Super-resolution imaging

Development of new tools for veterinary practice in relation to cystitis and urolithiasis in mink - optimization of prevention and treatment

PhD Student: Karin Mundbjerg
Thesis defended: 9 July 2021

Mink urinary tract disease (MUTD) is a disease complex characterized by stones in the urinary tract and infection in of the urinary bladder and kidneys. The disease often leads to fatal urethral obstruction, especially in males and is a common cause of mortality in growing mink kits. Urinary tract stones in mink are reported to be composed of the mineral struvite which forms in alkaline urine. 
READ MORE about the new tools

Intrinsic resistance mechanisms and CRISPR-Cas immunity of the opportunistic pathogen, Staphylococcus aureus

PhD Student: Kasper Mikkelsen, email:
Thesis defended: 23 April 2021

Staphylococcus aureus is a serious human pathogen with a remarkable ability to adapt to challenging conditions and cause life-threatening infections. The most important class of antimicrobials for the treatment of S. aureus infections is the β-lactams. By the acquisition of the staphylococcal chromosome cassette (SCCmec), some S. aureus isolates have evolved methicillin-resistance (MRSAs) that are resistant to nearly every β-lactam antibiotic, why additional measures are needed to combat this pathogen. READ MORE 

Decoding the lamination, cytoarchitecture and cellular composition of the entorhinal cortex

PhD Student: Tobias Borgtoft Bergmann, email:, 
Thesis defended: 21 April 2021.  

The entorhinal cortex, as part of the parahippocampal region, is involved in unique functions related to spatial navigation and consolidating episodic memory. The entorhinal cortex and the entorhinal cells that are responsible for its unique tasks have mainly been investigated by electrophysiological and histological studies. READ MORE

Contracaecum osculatum larvae in Baltic cod (Gadus morhua): Effects on growth and immune response

PhD student: Huria Marnis, e-mail:

The eastern Baltic cod has experienced a marked increase in infection caused by third-stage larvae of the nematode Contracaecum osculatum. The cod acts as transport host with the third-stage larvae located in the liver. The PhD project produced three published papers. READ MORE

Biofluid proteome profiling of perinatal infectious diseases in preterm neonates

PhD student: Tik Muk, e-mail:
Department of Veterinary and Animal Sciences, Comparative Pediatrics and Nutrition
Thesis defended: February 2020

Perinatal infectious diseases, such as chorioamnionitis (CA) and neonatal sepsis, remain a major cause of neonatal morbidity and mortality, especially for the preterm infant population. Read more

Gut and systemic immune responses to prenatal inflammation in preterm neonates

PhD student: Shuqiang Ren, e-mail:
Department of Veterinary and Animal Sciences, Comparative Pediatrics and Nutrition
Status: Defended February 2020

The immature functions of the organs and immune system of preterm infants predispose them to gut and immune disorders. Growth and developmental delays in preterm neonates may affect various organ systems differently at the term-corrected age. Read more

Genomic Epidemiology and Aquatic Reservoirs of the Seventh Pandemic Vibrio cholerae in Tanzania
PhD student: Yaovi Mahuton Gildas Hounmanou, e-mail:
Department of Veterinary and Animal Sciences, Section of Food Safety and Zoonosis
Status: Defended 19 December 2019

With the currently available scientific knowledge and tools to guide prevention and treatment, every death due to cholera can be avoided. Cholera, however, continues to take a heavy toll in developing countries especially in Sub-Saharan Africa, where it has become recurrent for the past forty years favored by poverty, poor hygiene and the vulnerability of populations living around lakes and those affected by conflicts or natural disasters.
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Antimicrobial-induced plasmid-transfer in Escherichia coli

PhD student: Gang Liu, e-mail:,
Department of Veterinary and Animal Sciences, Section for Veterinary Clinical Microbiology
Status: Defended 18 December 2019

Antimicrobial resistance (AMR) is a serious threat to human and animal health, and it is projected that by the year 2050 more people will die due to infections with AMR bacteria than cancer, if we do not find ways to prevent development and spread of AMR.
Read more 

Genetic diversity and antimicrobial resistance in commensal Escherichia coli from pigs and broiler chickens
PhD student: Shahana Ahmed, e-mail:
Department of Veterinary and Animal Sciences, Section of Veterinary Clinical Microbiology
Status: Defended 28 November 2019

Escherichia coli is an important part of the gut flora of all warm-blooded vertebrates. So far research has focused on the few types of E. coli that cause disease, while the large group of harmless, commensal E. coli has been neglected.
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Fasciolosis in Danish dairy cattle: epidemiology, diagnostics, impact and aspects of control (Fasciolose hos dansk malkekvæg: epidemiologi, diagnostik, betydning og kontrol)
Ph.d.-student: Nao Takeuchi-Storm, e-mail:
Status: Forsvaret 22. marts 2019

Den store leverikte, på latin Fasciola hepatica, er en parasitisk fladorm (ikte), som inficerer drøvtyggere og flere andre pattedyr, inklusive mennesket.
Læs mere om fasciolosis.