• CUBE - Computational Systems Biology

  • DOME - Microbial Ecology

  • TER - Terrestrial Ecosystem Research

DMES News

  • TER excursion: Canoeing the Danube river

    22.06.17
    Event
    TER discovered the UNESCO World Heritage Site Wachau, a stretch of the Danube valley north of Vienna, by canoe on the hottest days of the year so far. 
    We paddled about 30 km from Emmersbach to Unterloiben and had a good swim and ...
  • DOC fellowship awarded to Sarah Zauner

    20.06.17
    News

    DoME congratulates Sarah Zauner on her DOC fellowship from the Austrian Academy of Sciences (ÖAW)! In her project "From Bacteria to Birds: Inter-kingdom Interactions in a Marine Symbiosis", Sarah will work together with Jill Petersen.

     

  • Michael Wagner EMBO Member

    Michael Wagner elected as EMBO Member

    16.06.17
    People

    Michael is one among the 65 researchers from across the world to be honoured with election to the European Molecular Biology Organisation (EMBO). Election to EMBO Membership is recognition of research excellence and EMBO Members are actively involved in the execution ...

  • FIRST RELEASE OF 45 PICA MODELS READY FOR DOWNLOAD

    12.06.17
    News

    The first release of 45 PICA models is available on this site in the Download area of our new website PhenDB. Brief instructions on the download page will enable you to install the PICA software and the models on a ...

Latest publications

Evaluating the Detection of Hydrocarbon-Degrading Bacteria in 16S rRNA Gene Sequencing Surveys.

Hydrocarbonoclastic bacteria (HCB) play a key role in the biodegradation of oil hydrocarbons in marine and other environments. A small number of taxa have been identified as obligate HCB, notably the Gammaproteobacterial genera Alcanivorax, Cycloclasticus, Marinobacter, Neptumonas, Oleiphilus, Oleispira, and Thalassolituus, as well as the Alphaproteobacterial genus Thalassospira. Detection of HCB in amplicon-based sequencing surveys relies on high coverage by PCR primers and accurate taxonomic classification. In this study, we performed a phylogenetic analysis to identify 16S rRNA gene sequence regions that represent the breadth of sequence diversity within these taxa. Using validated sequences, we evaluated 449 universal 16S rRNA gene-targeted bacterial PCR primer pairs for their coverage of these taxa. The results of this analysis provide a practical framework for selection of suitable primer sets for optimal detection of HCB in sequencing surveys.

Berry D, Gutierrez T
2017 - Front Microbiol, 8: 2460

Vibrational Spectroscopy for Imaging Single Microbial Cells in Complex Biological Samples.

Vibrational spectroscopy is increasingly used for the rapid and non-destructive imaging of environmental and medical samples. Both Raman and Fourier-transform infrared (FT-IR) imaging have been applied to obtain detailed information on the chemical composition of biological materials, ranging from single microbial cells to tissues. Due to its compatibility with methods such as stable isotope labeling for the monitoring of cellular activities, vibrational spectroscopy also holds considerable power as a tool in microbial ecology. Chemical imaging of undisturbed biological systems (such as live cells in their native habitats) presents unique challenges due to the physical and chemical complexity of the samples, potential for spectral interference, and frequent need for real-time measurements. This Mini Review provides a critical synthesis of recent applications of Raman and FT-IR spectroscopy for characterizing complex biological samples, with a focus on developments in single-cell imaging. We also discuss how new spectroscopic methods could be used to overcome current limitations of single-cell analyses. Given the inherent complementarity of Raman and FT-IR spectroscopic methods, we discuss how combining these approaches could enable us to obtain new insights into biological activities either in situ or under conditions that simulate selected properties of the natural environment.

Harrison JP, Berry D
2017 - Front Microbiol, 675

Members of the Oral Microbiota Are Associated with IL-8 Release by Gingival Epithelial Cells in Healthy Individuals.

The triggers for the onset of oral diseases are still poorly understood. The aim of this study was to characterize the oral bacterial community in healthy humans and its association with nutrition, oral hygiene habits, and the release of the inflammatory marker IL-8 from gingival epithelial cells (GECs) with and without stimulation by bacterial endotoxins to identify possible indicator operational taxonomic units (OTUs) associated with inflammatory marker status. GECs from 21 healthy participants (13 females, 8 males) were incubated with or without addition of bacterial lipopolysaccharides (LPSs), and the oral microbiota was profiled using 16S rRNA gene-targeted sequencing. The basal IL-8 release after 6 h was between 9.9 and 98.2 pg/ml, and bacterial communities were characteristic for healthy oral microbiota. The composition of the oral microbiota was associated with basal IL-8 levels, the intake of meat, tea, white wine, sweets and the use of chewing gum, as well as flossing habits, allergies, gender and body mass index. Additionally, eight OTUs were associated with high basal levels of IL-8 and GEC response to LPS, with high basal levels of IL-8, and 1 with low basal levels of IL8. The identification of indicator bacteria in healthy subjects with high levels of IL-8 release is of importance as they may be promising early warning indicators for the possible onset of oral diseases.

Schueller K, Riva A, Pfeiffer S, Berry D, Somoza V
2017 - Front Microbiol, 8: 416