DOME

Univ.-Prof. Dr. Alexander Loy

Professor at the Division of Microbial Ecology

☎ +43 1 4277 91205
✉ alexander.loy(at)univie.ac.at

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CeMESS\Thomas Suchanek

Our research covers a diverse spectrum of topics in microbial ecology and symbiosis, from the role of intestinal microbiota in health and disease, to the ecology and evolution of sulfur-compounds-utilising microorganisms. We develop and apply various stable isotope-labelling, imaging, and molecular biology methods for in situ analysis of complex host-associated and environmental microbiota.

We explore how physiological interactions among microbiome members impacts their environment or host. This includes how environmental microbes impact sulfur and carbon cycling, as well as how symbionts and pathogens affect the health and nutrition of their animal and human hosts. This knowledge could ultimately translate to development of microbiome-based health interventions. Our current projects focus on microbial sulfur metabolism in soils, sediments, and the intestinal tract, impact of emerging pollutants on human and environmental microbiomes, as well as exploring production of new secondary metabolites, such as antibiotics, by complex microbiome members.

Research Topics

Cycling of Sulfur and other Nutrients

Microorganisms are key drivers of global nutrient cycles and tightly couple sulfur transformations to the cycling of other elements such as carbon, nitrogen, and iron. Our research investigates the evolution of sulfur-metabolizing microorganisms and their still largely unexplored diversity, distribution, and ecological functions across natural environments. We focus on how physiological interactions among individual members of complex microbiomes control major biogeochemical processes, including organic matter degradation and greenhouse gas emissions. Our work has revealed previously unrecognized sulfur-metabolizing microorganisms in wetlands that can substantially mitigate methane emissions (Hausmann et al., 2018, ISME Journal; Gwak et al., 2022, PNAS) and demonstrated that rare microbial taxa can exert disproportionate functional impacts on ecosystem processes (Hausmann et al., 2016, ISME Journal; Hausmann et al., 2019, mBio). In marine sediments, we have characterized microorganisms involved in the degradation of diverse necromass macromolecules (Müller et al., 2018, Environmental Microbiology; Pelikan et al., 2021, ISME Journal), including novel bacteria specialized in extracellular DNA metabolism (Wasmund et al., 2021, Nature Microbiology). A major recent breakthrough was the discovery of microbial iron oxide respiration coupled to sulfide oxidation (MISO), revealing a previously unknown and environmentally relevant microbial energy metabolism with broad implications for marine and terrestrial biogeochemistry (Chen et al., 2025, Nature).

Intestinal Microbiome

The intestinal microbiome performs essential functions for animal and human hosts, including the breakdown of complex nutrients, modulation of the immune system, and protection against enteric pathogens. Our research investigates the ecophysiology of gut microbiota members, with a focus on how specific diet- and host-derived compounds, as well as microbial interactions, shape intestinal homeostasis and disease outcomes. A central emphasis is placed on the metabolism of sulfur-containing compounds in the gut. We characterized the first taurine-respiring murine gut bacterium and demonstrated its protective role against enteropathogens such as Salmonella (Ye et al., 2023, Nature Communications). In addition, we showed that the green-diet-derived sugar sulfoquinovose is a selective nutrient and potential prebiotic for distinct gut bacteria and constitutes a previously unrecognized source of hydrogen sulfide in the human gut (Hanson et al., 2021, ISME Journal; Krasenbrink et al., 2025, Microbiome).

Functional microbiome methods

A central pillar of our research is the development and synergistic application of molecular, microscopy-based, and isotope-labeling approaches that enable functional analyses of microbiomes in environmental and biomedical systems. We have pioneered single-cell methods that allow quantitative imaging of substrate uptake by individual microorganisms directly in their natural environment or within their host (Berry et al., 2013, PNAS; Wasmund et al., 2021, Nature Microbiology). These approaches provide unprecedented insights into microbial niche partitioning, metabolic interactions, and microbe-host relationships. In parallel, we establish and curate functional gene resources, particularly for dissimilatory sulfur metabolism, which underpin the development of molecular and bioinformatic tools for large-scale ecological and biogeochemical studies (Müller et al., 2015, ISME Journal; Pelikan et al., 2016, Environmental Microbiology; Chen et al., 2025, Nature).

Public Outreach

Our research and professional activities have been covered in over hundred newspapers, magazines or online articles and in several features on Austrian and German radio and in reports and documentaries on Austrian TV. I was a lecturer at the annual children university in Vienna KinderUni. I am an expert for Open Science, a non-profit association committed to life science communication, and involved in diverse outreach activities such as microbiome quizzes, developing teaching material on the human microbiome for Austrian school kids, and educating biology teachers. Additionally, I serve as executive committee member of the Austrian Microbiome Initiative AMICI and I am a faculty member of the Austrian Polar Research Institute APRI.

Educational seminar on 'The human microbiome' for high school biology teacher, Pädagogische Hochschule Wien, accompanied by information on microorganisms and the problem of antibiotic resistance and an online quiz on antibiotics and antibiotic resistance in the DerStandard (2024)

Educational seminar on ‘The human microbiome’ for high school biology teacher, Pädagogische Hochschule Burgenland (2021)

Bayern 2 Radio - IQ - Wissenschaft und Forschung Der Meeresboden - Mikroorganismen am Grund des Ozeans (2025)

Profil Chronische Schmerzen: Liegt die Ursache in den Darmbakterien? (2025)

Ö1 Radio - Wissen Aktuell: Artenvielfalt, Mikrobiom, Künstliche Intelligenz (2022)

Group Members

Dr. Marc Mußmann

Senior Scientist

Dr. Claire Lamb

Postdoc

Dr. Tomohisa Sebastian Tanabe

Postdoc

Natalia Solntseva

PhD Student

Guoqing Guan

PhD Student

Julia Krasenbrink

PhD Student

Mathias Flieder

PhD Student

Lea Arneth

Master's Student

Aleksandra Stevanovic

Master's Student

Theresa Villunger

Master's Student

Publications

Loy A, Horn M, Wagner M. probeBase: An online resource for rRNA-targeted oligonucleotide probes. Nucleic Acids Research. 2003;31(1):514-516.

Loy A, Daims H, Wagner M. Activated sludge: Molecular techniques for determining community composition. In Bitton G, editor, The Encyclopedia of Environmental Microbiology. New York: John Wiley & Sons, Inc. 2002. p. 26-43

Wagner M, Loy A. Bacterial community composition and function in sewage treatment systems. Current Opinion in Biotechnology. 2002;13:218-227.

Wagner M, Loy A, Nogueira R, Purkhold U, Daims H. Microbial community composition and function in wastewater treatment plants. Antonie van Leeuwenhoek: international journal of general and molecular microbiology. 2002;81:665-680.

Loy A, Lehner A, Adamczyk J, Meier H, Ernst J, Schleifer KH et al. Oligonucleotide microarray for 16S rRNA gene-based detection of all recognized lineages of sulfate-reducing prokaryotes in the environment. Applied and Environmental Microbiology. 2002;68(10):5064-5081.

Juretschko S, Loy A, Lehner A, Wagner M. The microbial community composition of a nitrifying-denitrifying activated sludge from an industrial sewage treatment plant analyzed by the full-cycle rRNA approach. Systematic and Applied Microbiology. 2002;25(1):84-99. doi: 10.1078/0723-2020-00093

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Microbiomes Drive Planetary Health

Alexander Loy is part of the FWF-funded Cluster of Excellence (CoE)

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