• Our new home

    since summer 2021.

  • Hunting for microbes since 2003

  • 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

  • The human microbiome -

    Our own social network of microbial friends

  • Ancient invaders -

    Bacterial symbionts of amoebae

    and the evolution of the intracellular lifestyle

  • 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

  • Doctoral School in Microbiology and Environmental Sciences

  • PhD program in Microbial Symbioses

    A special FWF funded track in our doctoral school

Dome News

Latest publications

Human follicular mites: Ectoparasites becoming symbionts

Most humans carry mites in the hair follicles of their skin for their entire lives. Follicular mites are the only metazoans that continuously live on humans. We propose that Demodex folliculorum (Acari) represents a transitional stage from a host-injuring obligate parasite to an obligate symbiont. Here, we describe the profound impact of this transition on the genome and physiology of the mite. Genome sequencing revealed that the permanent host association of D. folliculorum led to an extensive genome reduction through relaxed selection and genetic drift, resulting in the smallest number of protein-coding genes yet identified among panarthropods. Confocal microscopy revealed that this gene loss coincided with an extreme reduction in the number of cells. Single uninucleate muscle cells are sufficient to operate each of the three segments that form each walking leg. While it has been assumed that the reduction of the cell number in parasites starts early in development, we identified a greater total number of cells in the last developmental stage (nymph) than in the terminal adult stage, suggesting that reduction starts at the adult or ultimate stage of development. This is the first evolutionary step in an arthropod species adopting a reductive, parasitic, or endosymbiotic lifestyle. Somatic nuclei show under-replication at the diploid stage. Novel eye structures or photoreceptors as well as a unique human host melatonin-guided day/night rhythm are proposed for the first time. The loss of DNA repair genes coupled with extreme endogamy might have set this mite species on an evolutionary dead-end trajectory.

Smith G, Manzano-Marín A, Reyes-Prieto M, Ribeiro Antunes CS, Ashworth V, Goselle ON, Jan AAA, Moya A, Latorre A, Perotti MA, Braig HR
2022 - Mol Biol Evol, 39: msac125

SRS-FISH: A high-throughput platform linking microbiome metabolism to identity at the single-cell level

One of the biggest challenges in microbiome research in environmental and medicalsamples is to better understand functional properties of microbial community membersat a single-cell level. Single-cell isotope probing has become a key tool for this purpose,but the current detection methods for determination of isotope incorporation into singlecells do not allow high-throughput analyses. Here, we report on the development of animaging-based approach termed stimulated Raman scattering–two-photon fluorescencein situ hybridization (SRS-FISH) for high-throughput metabolism and identity analysesof microbial communities with single-cell resolution. SRS-FISH offers an imaging speedof 10 to 100 ms per cell, which is two to three orders of magnitude faster than achievableby state-of-the-art methods. Using this technique, we delineated metabolic responses of 30,000 individual cells to various mucosal sugars in the human gut microbiome viaincorporation of deuterium from heavy water as an activity marker. Application of SRS-FISH to investigate the utilization of host-derived nutrients by two major human gutmicrobiome taxa revealed that response to mucosal sugars tends to be dominated byBacteroidales, with an unexpected finding that Clostridia can outperform Bacteroidalesat foraging fucose. With high sensitivity and speed, SRS-FISH will enable researchers toprobe the fine-scale temporal, spatial, and individual activity patterns of microbial cellsin complex communities with unprecedented detail.

Gea X, Pereira FC, Mitteregger M, Berry D, Zhanga M, Hausmann B, Zhange J, Schintlmeister A, Wagner M, Cheng J-X
2022 - Proc Natl Acad Sci U S A, 119: e2203519119

CT295 Is Chlamydia trachomatis’ phosphoglucomutase and a type 3 secretion substrate

The obligate intracellular bacteria Chlamydia trachomatis store glycogen in the lumen of the vacuoles in which they grow. Glycogen catabolism generates glucose-1-phosphate (Glc1P), while the bacteria can take up only glucose-6-phosphate (Glc6P). We tested whether the conversion of Glc1P into Glc6P could be catalyzed by a phosphoglucomutase (PGM) of host or bacterial origin. We found no evidence for the presence of the host PGM in the vacuole. Two C. trachomatis proteins, CT295 and CT815, are potential PGMs. By reconstituting the reaction using purified proteins, and by complementing PGM deficient fibroblasts, we demonstrated that only CT295 displayed robust PGM activity. Intriguingly, we showed that glycogen accumulation in the lumen of the vacuole of a subset of Chlamydia species (C. trachomatis, C. muridarum, C. suis) correlated with the presence, in CT295 orthologs, of a secretion signal recognized by the type three secretion (T3S) machinery of Shigella. C. caviae and C. pneumoniae do not accumulate glycogen, and their CT295 orthologs lack T3S signals. In conclusion, we established that the conversion of Glc1P into Glc6P was accomplished by a bacterial PGM, through the acquisition of a T3S signal in a “housekeeping” protein. Acquisition of this signal likely contributed to shaping glycogen metabolism within Chlamydiaceae.

Triboulet A, N’Gadjaga MD, Niragire B, Köstlbacher S, Horn M, Aimanianda V, Subtil A
2022 - Front Cell Infect Microbiol, 12: 866729

Lecture series

DOME Lecture: “'Dark oxygen' - an electron acceptor for productive and diverse microbial communities in ancient groundwaters"

Emil Ruff
Marine Biological Laboratory, Massachusetts, USA
12:00 h
hybrid, UBB HS 2

DOME Lecture: "Creating a “niche” and making the most of it: Bacteria – insect interactions in a mutualistic endosymbiosis"

Anna Zaidman-Remy
Institut National des Sciences Appliquées, Lyon, France
12:00 h
hybrid, UBB HS 2

DOME Lecture: "A physical niche regulates a complex microbiome in the Drosophila gut"

William Ludington
Department of Embryology, Carnegie Institution of Science, Maryland, USA
14:00 h