Univ.-Prof. Dr. Alexander Loy






Deputy Head of the Department of Microbiology and Ecosystem Science
Deputy Head of the Division of Microbial Ecology

☎ +43 1 4277 91205


Alexander Loy’s 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. He has long-standing expertise in developing and applying stable isotope-labelling and molecular biology methods for in situ analysis of complex host-associated and environmental microbiota.

Alexander’s group explores 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 hosts. This knowledge could ultimately translate to development of microbiome-based health interventions. Their current projects focus on microbial sulfur metabolism in wetlands and the intestinal tract, impact of emerging pollutants on human and environmental microbiomes, as well as the development of defined microbial communities for production of new secondary metabolites, such as antibiotics.

Research Topics

Sulfur Microorganisms

It is mainly through microbial activities that the sulfur cycle is intimately intertwined with the cycling of other elements such as carbon or nitrogen. My group is interested in the evolution of sulfur microorganisms, their yet largely unexplored diversity, distribution, and ecological function in various environments, and their roles as symbionts of animals and humans.

We are investigating the evolution of sulfur microorganisms by comparative phylogenetic analysis of key genes such as dsrAB, encoding dissimilatory (bi)sulfite reductase and by phylogenomics. We specifically aim to reveal the ecology and biogeography of sulfur-cycling microorganisms (e.g. sulfate reducers) in globally relevant anoxic ecosystems such as the ocean floor (Wasmund et al. 2017. Environ Microbiol Rep) and terrestrial wetlands (Pester et al. 2012 Front Microbiol).

Isotope-labeling techniques allow us to show how the physiological interactions of individual members of complex microbial communities influence important processes in the global carbon and sulfur cycles such as degradation of organic matter and greenhouse gas emissions. We further use genomics and targeted genome-centric gmetagenomic/-transcriptomic approaches to get insights into the genome evolution and metabolism of ecologically important sulfur microorganisms such as rare but cosmopolitan sulfate-reducing Desulfosporosinus species in wetlands (Hausmann et al. 2019. mBio). 

Join the Team

If you are interested in joining our team, explore our open positions and learn more about available PhD and postdoc stipends here.


To view Alexander Loy's teaching activities at the University of Vienna, visit u:find.

Intestinal Microbiota

The symbiotic intestinal microbiota provides important benefits to its animal and human host such as breakdown of complex nutritional substrates and protection against pathogens. Changes in the intestinal microbiota are, however, associated with many diseases. We are interested in the ecophysiology of the gut microbiota in health and disease. In the context of various diseases such as inflammatory bowel disease, cancer or intestinal infections, we specifically aim to answer how nutrition impacts the gut microbiota and which/how individual community members influence physiology and health of their host.

Individual cells of the intestinal microbiota either compete for substrates due to functional overlap or cooperate in syntrophic substrate degradation, resulting in a dynamic network of synergistic and antagonistic physiological interactions that are reciprocally influenced by the fluctuating physical and chemical environment of the gut. Here, in particular single cell isotope labeling tools promise yet unavailable detailed insights into host- or diet-derived substrate partitioning and niche competition among individual intestinal microbiota members, including incoming pathogens (Loy and Berry, 2018. Trends MicrobiolStecher, Berry, and Loy. 2013. FEMS Microbiol Rev).

One focus of our work is the evolution and function of sulfur compounds-utilizing and hydrogen sulfide-producing gut microorganisms because a balanced sulfur metabolism is crucial for intestinal homeostasis and host health. Furthermore, some pathogens such as Salmonella influence the intestinal sulfur metabolism to selectively support their outgrowth and fitness, but the role of the indigenous sulfur microbiota during these intestinal infections is unknown.

Active Projects

If all microbial life disappeared from Earth, our world would change dramatically. Microorganisms are essential for nutrient recycling, decomposing...

The discovery of antibiotics is one of the greatest achievements in human medicine. However, the introduction and overuse of antibiotics led towards...

Many bacterial species produce secondary metabolites that are not essential for their growth but provide advantages in environmental adaptation, e.g....

Past Projects

The human gut is a complex microbial bioreactor which protects the host from enteropathogens, facilitates the harvesting of nutrients and energy from...

The sediments underlying our oceans are inhabited by massive numbers of microbes that contribute substantially to global cycles of elements such as...

Protection against bacterial pathogens is one of the most important symbiotic functions that the diverse intestinal microbiota confers to its host....


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Loy, A. (2024). Biodiversität in Moorböden: Neue Mikroorganismen und kryptische Redoxprozesse im Schwefelkreislauf. Verlag Dr. Friedrich Pfeil. Rundgespräche Forum Ökologie Vol. 50

Ye, H., Borusak, S., Eberl, C., Krasenbrink, J., Weiss, A. S., Chen, S., Hanson, B. T., Hausmann, B., Herbold, C. W., Pristner, M., Zwirzitz, B., Warth, B., Pjevac, P., Schleheck, D., Stecher, B., & Loy, A. (2023). Ecophysiology and interactions of a taurine-respiring bacterium in the mouse gut. Nature Communications, 14(1), [5533]. https://doi.org/10.1038/s41467-023-41008-z

Gwak, J-H., Awala, S. I., Nguyen, N-L., Yu, W-J., Yang, H-Y., von Bergen, M., Jehmlich, N., Kits, K. D., Loy, A., Dunfield, P. F., Dahl, C., Hyun, J-H., & Rhee, S-K. (2022). Sulfur and methane oxidation by a single microorganism. Proceedings of the National Academy of Sciences of the United States of America, 119(32), [e2114799119]. https://doi.org/10.1073/pnas.2114799119