The gut mycobiome is shaped by interactions with the bacterial community in twins

Konrad Lehr; Ramiro Vilchez-Vargas; Jurgita Skieceviciene; Noam Mathias Hipler; Greta Gedgaudienė; Indre Gustaityte; Laimutis Kucinskas; Mindaugas Urba; Cosima Thon; Denny Schanze; Martin Zenker; Juozas Kupcinskas; Alexander Link

doi:10.1016/j.isci.2026.115786

The gut mycobiome is shaped by interactions with the bacterial community in twins

iScience. 2026 Apr 16;29(6):115786. doi: 10.1016/j.isci.2026.115786. eCollection 2026 Jun 19.

Authors

Konrad Lehr^{1

2}, Ramiro Vilchez-Vargas¹, Jurgita Skieceviciene³, Noam Mathias Hipler¹, Greta Gedgaudienė³, Indre Gustaityte⁴, Laimutis Kucinskas⁵, Mindaugas Urba⁴, Cosima Thon¹, Denny Schanze⁶, Martin Zenker⁶, Juozas Kupcinskas^{3

4}, Alexander Link^{1

2

7}

Affiliations

¹ Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke University, 39120 Magdeburg, Germany.
² Molecular Gastroenterology and Microbiome Research Unit, Institute for University Teaching and Research Medical Campus Upper Franconia, Friedrich-Alexander University Erlangen-Nürnberg, 95445 Bayreuth, Germany.
³ Institute for Digestive Research, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania.
⁴ Department of Gastroenterology, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania.
⁵ Institute of Biology Systems and Genetic Research, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania.
⁶ Institute of Human Genetics, Otto-von-Guericke University, 39120 Magdeburg, Germany.
⁷ Department of Gastroenterology, Friedrich-Alexander University Erlangen-Nürnberg, Medical Campus Upper Franconia, Klinikum Bayreuth, 95445 Bayreuth, Germany.

Abstract

The human gut microbiome comprises bacteria, viruses, and fungi, yet the fungal component (mycobiome) remains poorly characterized. Here, we investigated gut fungal composition and fungal-bacterial interactions in healthy monozygotic and dizygotic twins. Fungal communities showed substantially higher inter-individual variability than bacterial communities. Zygosity, age, and shared environment had no major influence on fungal abundance, similarity, or dominant genera. Candida was the most abundant genus (mean 5.2% in 161 individuals), followed by Geotrichum (3.7% in 132), whereas Saccharomyces was detected less frequently (0.8% in 92). Most bacterial genera were negatively correlated with Candida and Geotrichum, with stronger negative associations observed at higher bacterial abundances (up to rho = -0.6 for Alistipes). Network analysis revealed complex negative correlations among Bacteroides, Prevotella, and Candida. Overall, our findings reveal a highly variable gut mycobiome independent of host zygosity, pointing to a competitive bacterial-fungal interplay as a key regulator of fungal homeostasis in humans.

Keywords: microbiome.