• 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

Pediatric obesity is associated with an altered gut microbiota and discordant shifts in Firmicutes populations

An altered gut microbiota has been linked to obesity in adulty, though little is known about childhood obesity. The aim of this study was to characterize the composition of the gut microbiota in obese (n=42) and normal-weight (n=36) children aged 6 to 16. Using 16S rRNA gene-targeted sequencing, we evaluated taxa with differential abundance according to age- and sex-normalized body mass index (BMI z-score). Obesity was associated with an altered gut microbiota characterized by elevated levels of Firmicutes and depleted levels of Bacteroidetes. Correlation network analysis revealed that the gut microbiota of obese children also had increased correlation density and clustering of operational taxonomic units (OTUs). Members of the Bacteroidetes were generally better predictors of BMI z-score and obesity than Firmicutes, which was likely due to discordant responses of Firmicutes OTUs. In accordance with these observations, the main metabolites produced by gut bacteria, short chain fatty acids (SCFAs), were higher in obese children, suggesting elevated substrate utilization. Multiple taxa were correlated with SCFA levels, reinforcing the tight link between the microbiota, SCFAs, and obesity. Our results suggest that gut microbiota dysbiosis and elevated fermentation activity may be involved in the etiology of childhood obesity.

Riva A, Borgo F, Lassandro C, Verduci E, Morace G, Borghi E, Berry D
2016 - Environmental Microbiology, in press

The root-associated microbial community of the world's highest growing vascular plants

Upward migration of plants to barren subnival areas is occurring worldwide due to raising ambient temperatures and glacial recession. In summer 2012, the presence of six vascular plants, growing in a single patch, was recorded at an unprecedented elevation of 6150 m.a.s.l. close to the summit of Mount Shukule II in the Western Himalayas (Ladakh, India). Whilst showing multiple signs of stress, all plants have managed to establish stable growth and persist for several years. To learn about the role of microbes in the process of plant upward migration, we analysed the root-associated microbial community of the plants (three individuals from each) using microscopy and tagged amplicon sequencing. No mycorrhizae were found on the roots, implying they are of little importance to the establishment and early growth of the plants. However, all roots were associated with a complex bacterial community, with richness and diversity estimates similar or even higher than the surrounding bare soil. Both soil and root-associated communities were dominated by members of the orders Sphingomonadales and Sphingobacteriales, which are typical for hot desert soils, but were different from communities of temperate subnival soils and typical rhizosphere communities. Despite taxonomic similarity on the order level, the plants harboured a unique set of highly dominant operational taxonomic units which were not found in the bare soil. These bacteria have been likely transported with the dispersing seeds and became part of the root-associated community following germination. The results indicate that developing soils act not only as a source of inoculation to plant roots but also possibly as a sink for plant-associated bacteria.

Angel R, Conrad R, Dvorsky M, Kopecky M, Kotilínek M, Hiiesalu I, Schweingruber F, Doležal J
2016 - Microbial Ecology, 72: 394-406

Stable isotope techniques for the assessment of host and microbiota response during gastrointestinal dysfunction

The International Atomic Energy Agency convened a technical meeting on environmental enteric dysfunction (EED) in Vienna (28th – 30th October 2015; https://nucleus.iaea.org/HHW/Nutrition/EED_Technical_Meeting/index.html) to bring together international experts in the fields of EED, nutrition and stable isotope technologies. Advances in stable isotope labelling techniques open up new possibilities to improve our understanding of gastrointestinal dysfunction and the role of the microbiota in host health. In the context of EED, little is known about the role gut dysfunction may play in macro- and micronutrient bioavailability and requirements and what the consequences may be for nutritional status and linear growth. Stable isotope labelling techniques have been used to assess intestinal mucosal injury and barrier function, carbohydrate digestion and fermentation, protein derived amino acid bioavailability and requirements, micronutrient bioavailability and to track microbe-microbe and microbe-host interactions at the single cell level. The non-invasive nature of stable isotope technologies potentially allows for low-hazard, field deployable tests of gut dysfunction that are applicable across all age-groups. The purpose of this review is to assess the state-of-the-art in the use of stable isotope technologies and to provide a perspective on where these technologies can be exploited to further our understanding of gut dysfunction in EED.

Butler RN, Kosek M, Krebs N, Loechl C, Loy A, Owino V, Zimmermann M, and Morrison DJ
2016 - Journal of Pediatric Gastroenterology & Nutrition, In press

Lecture series

Importance of chemosymbiotic lucinid bivalves in seagrass community functioning

Matthijs van der Geest
Université de Montpellier
20.01.2016
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
23.10.2015
13:30 h
Seminar room DoME (2.309)

Cool microbes: Assessing the role of acidobacteria communities in carbon and nitrogen cycling processes in arctic tundra soils

Max Häggblom
Department of Biochemistry and Microbiology School of Environmental and Biological Sciences Rutgers, The State University of New Jersey
11.09.2015
11:00 h
Seminar Room DOME (2.309)