• We seek to understand

    the role of microorganisms in Earth's nutrient cycles

    and as symbionts of other organisms

  • Cycling of carbon, nitrogen and sulfur

    affect the health of our planet

  • Ancient invaders -

    Bacterial symbionts of amoebae

    and the evolution of the intracellular lifestyle

  • The human microbiome -

    Our own social network of microbial friends

  • Marine symbioses:

    Listening in on conversations

    between animals and the microbes they can't live without

  • Single cell techniques offer new insights

    into the ecology of microbes

  • Apply for the DOME International PhD/PostDoc program

Dome News

Latest publications

Genome-guided design of a novel defined mouse microbiota that confers colonization resistance against Salmonella enterica serovar Typhimurium

Protection against enteric infections, also termed colonization resistance, results from mutualistic interactions of the host and its indigenous microbes. The gut microbiota of humans and mice is highly diverse and it is therefore challenging to assign specific properties to its individual members. Here, we have used a collection of murine bacterial strains and a modular design approach to create a minimal bacterial community that, once established in germ-free mice, provided colonization resistance against the human enteric pathogen Salmonella enterica serovar Typhimurium (S. Tm). Initially, a community of 12 strains, termed Oligo-Mouse Microbiota (Oligo-MM12), representing members of the major bacterial phyla in the murine gut, was selected. This community was stable over consecutive mouse generations and provided colonization resistance against S. Tm infection, albeit not to the degree of a conventional complex microbiota. Comparative (meta)genome analyses identified functions represented in a conventional microbiome but absent from the Oligo-MM12. By genome-informed design, we created an improved version of the Oligo-MM community harbouring three facultative anaerobic bacteria from the Mouse Intestinal Bacterial Collection (miBC) that provided conventional-like colonization resistance. In conclusion, we have established a highly versatile experimental system that showed efficacy in an enteric infection model. Thus, in combination with exhaustive bacterial strain collections and systems-based approaches, genomeguided design can be used to generate insights into microbe–microbe and microbe–host interactions for the investigation of ecological and disease-relevant mechanisms in the intestine.

Brugiroux S, Beutler M, Pfann C, Garzetti D, Ruscheweyh H-J, Ring D, Diehl M, Herp S, Lötscher Y, Hussain S, Bunk B, Pukall R, Huson DH, Münch PC, McHardy AC, McCoy KD, Macpherson AJ, Loy A, Clavel T, Berry D, Stecher B
2016 - Nature Microbiol, In press

Cultivation and characterization of Candidatus Nitrosocosmicus exaquare, an ammonia-oxidizing archaeon from a municipal wastewater treatment system

Thaumarchaeota have been detected in several industrial and municipal wastewater treatment plants (WWTPs), despite the fact that ammonia-oxidizing archaea (AOA) are thought to be adapted to low ammonia conditions. The activity, physiology, and metabolism of WWTP-associated AOA remains poorly understood. We report here the cultivation and complete genome sequence of Candidatus Nitrosocosmicus exaquare, a novel AOA representative from a municipal WWTP in Guelph, Ontario (Canada). In enrichment culture, Ca. N. exaquare oxidizes ammonia to nitrite stoichiometrically, is mesophilic, and tolerates at least 15 mM of ammonium chloride or sodium nitrite. Microautoradiography (MAR) for enrichment cultures demonstrates that Ca. N. exaquare assimilates bicarbonate in association with ammonia oxidation. However, despite using inorganic carbon, the ammonia-oxidizing activity of Ca. N. exaquare is greatly stimulated in enrichment culture by the addition of organic compounds, especially malate and succinate. Ca. N. exaquare cells are coccoid with a diameter of approximately 1-2 µm. Phylogenetically, Ca. N. exaquare belongs to the Nitrososphaera sister cluster within the Group 1.Ib Thaumarchaeota, a lineage which includes most other reported AOA sequences from municipal and industrial WWTPs. The 2.99 Mbp genome of Ca. N. exaquare encodes pathways for ammonia oxidation, bicarbonate fixation, and urea transport and breakdown. In addition, this genome encodes several key genes for dealing with oxidative stress, including peroxidase and catalase. Incubations of WWTP biofilm demonstrate partial inhibition of ammonia-oxidizing activity by 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide (PTIO), suggesting that Ca. N. exaquare-like AOA might contribute to nitrification in situ. However, CARD-FISH-microautoradiography showed no incorporation of bicarbonate by detected Thaumarchaeaota, suggesting that detected AOA may incorporate non-bicarbonate carbon sources or rely on an alternative, yet unknown metabolism.


Sauder LA, Albertsen M, Engel K, Schwarz J, Nielsen PH, Wagner M, Neufeld JD
2016 - ISME J, in press

Environmental enteric dysfunction and growth failure/stunting in global child health

Approximately 25% of the world’s children under age 5 years have stunted growth, which is associated with increased mortality, cognitive dysfunction, and loss of productivity. Reducing by 40% the number of stunted children is a global target for 2030. The pathogenesis of stunting is poorly understood. Pre- and post-natal nutritional deficits and enteric and systemic infections clearly contribute, but recent findings implicate a central role for environmental enteric dysfunction (EED), a generalized disturbance of small intestinal structure and function found at high prevalence in children living under unsanitary conditions. Mechanisms contributing to growth failure in EED include intestinal leakiness and heightened permeability, gut inflammation, dysbiosis and bacterial translocation, systemic inflammation, and nutrient malabsorption. Since EED has multiple causal pathways, approaches to manage it need to be multi-faceted. Potential interventions to tackle EED include: a) reduction of exposure to feces and contact with animals through programs like improved water, sanitation and hygiene (WASH); b) breastfeeding and enhanced dietary diversity; c) probiotics and prebiotics; d) nutrient supplements including zinc, polyunsaturated fatty acids, and amino acids; e) anti-inflammatory agents such as 5-aminosalicyclic acid; and f) antibiotics in the context of acute malnutrition and infection. Better understanding of the underlying causes of EED, and development of non-invasive, practical, simple, and affordable point of care diagnostic tools remain key gaps. ‘Omics’ technologies (genomics, epigenomics, transcriptomics, proteomics, and metabolomics) and stable isotope techniques (e.g., 13Carbon breath tests) targeted at children and their intestinal microbiota will enhance our ability to successfully identify, manage, and prevent the disorder.

Owino V, Ahmed T, Freemark M, Kelly P, Loy A, Manary M, Loechl C
2016 - Pediatrics, 138: e20160641

Lecture series

The tale of the rumen microbiome – from interaction with the host to plasmid mediated gene mobility

Itzhak Mizrahi
Ben-Gurion University of the Negev, Israel
12:00 h
Hörsaal 2. (UZA I)

Importance of chemosymbiotic lucinid bivalves in seagrass community functioning

Matthijs van der Geest
Université de Montpellier
11:00 h
Seminar room DoME (2.309), UZA 1

The contribution of phage-mediated gene transfer to microbial genome evolution

Tal Dagan
Christian-Albrechts-Universität zu Kiel
13:30 h
Seminar room DoME (2.309)