• Joint Microbiome Facility (JMF)

    of the Medical University of Vienna and the University of Vienna

  • The Joint Microbiome Facility provides

    highly multiplexed gene amplicon sequencing

  • The Joint Microbiome Facility provides

    whole genome sequencing

  • The Joint Microbiome Facility provides

    metagenome and metatranscriptome sequencing

JMF News

Latest publications

Biomonitoring of Dietary Mycotoxin Exposure and Associated Impact on the Gut Microbiome in Nigerian Infants.

Mycotoxins are toxic chemicals that adversely affect human health. Here, we assessed the influence of mycotoxin exposure on the longitudinal development of early life intestinal microbiota of Nigerian neonates and infants (NIs). Human biomonitoring assays based on liquid chromatography tandem mass spectrometry were applied to quantify mycotoxins in breast milk ( = 68) consumed by the NIs, their stool ( = 82), and urine samples ( = 15), which were collected longitudinally from month 1-18 postdelivery. Microbial community composition was characterized by 16S rRNA gene amplicon sequencing of stool samples and was correlated to mycotoxin exposure patterns. Fumonisin B (FB), FB, and alternariol monomethyl ether (AME) were frequently quantified in stool samples between months 6 and 18. Aflatoxin M (AFM), AME, and citrinin were quantified in breast milk samples at low concentrations. AFM, FB, and ochratoxin A were quantified in urine samples at relatively high concentrations. and / were dominant in very early life stool samples (month 1), whereas was dominant between months 3 and 6. The total mycotoxin levels in stool were significantly associated with NIs' gut microbiome composition (PERMANOVA, < 0.05). However, no significant correlation was observed between specific microbiota and the detection of certain mycotoxins. Albeit a small cohort, this study demonstrates that mycotoxins may influence early life gut microbiome composition.

Ayeni KI, Seki D, Pjevac P, Hausmann B, Krausová M, Braun D, Wisgrill L, Berry D, Warth B, Ezekiel CN
2024 - Environ Sci Technol, in press

Fiber consumption stimulates the activity of microbial bile salt hydrolases


Previously we reported a microbiota-dependent caloric restriction (CR)-triggered increase in the levels of taurine and taurine-conjugated bile acids (BA) in the gut. Now, we show that restrictive diets, including intermittent fasting and fasting-mimicking diet, had a similar impact to CR. The type of cage bedding that CR mice were housed with affected the levels of BAs and taurine in the ileum. Removal of cage bedding neutralized CR phenotype in terms of taurine levels, BAs deconjugation, and fecal microbiota composition. Microbiota transplant from CR mice housed with bedding increased BAs deconjugation. Inhibition of bile salt hydrolase (BSH) prevented the increase in free taurine concentration while increasing taurine-conjugated BA levels. Ad libitum consumption of diets high in fiber increased the levels of taurine conjugates but did not elevate the levels of BAs. Dietary restriction is required to stimulate BAs secretion, while ingestion of fiber stimulates the capacity of microbiota to deconjugate BAs.

Gregor A, Auernigg-Haselmaier S, Malleier M, Bruckberger S, Séneca J, Pjevac P, Pignitter M, Duszka
2023 - Journal of Functional Foods, 107: in press

Microclimate shapes the phylosymbiosis of rodent gut microbiota in Jordan's Great Rift Valley.

Host phylogeny and the environment play vital roles in shaping animal microbiomes. However, the effects of these variables on the diversity and richness of the gut microbiome in different bioclimatic zones remain underexplored. In this study, we investigated the effects of host phylogeny and bioclimatic zone on the diversity and composition of the gut microbiota of two heterospecific rodent species, the spiny mouse and the house mouse , in three bioclimatic zones of the African Great Rift Valley (GRV). We confirmed host phylogeny using the sequencing method and analyzed the influence of host phylogeny and bioclimatic zone parameters on the rodent gut microbiome using high-throughput amplicon sequencing of 16S rRNA gene fragments. Phylogenetic analysis supported the morphological identification of the rodents and revealed a marked genetic difference between the two heterospecific species. We found that bioclimatic zone had a significant effect on the gut microbiota composition while host phylogeny did not. Microbial alpha diversity of heterospecific hosts was highest in the Mediterranean forest bioclimatic zone, followed by the Irano-Turanian shrubland, and was lowest in the Sudanian savanna tropical zone. The beta diversity of the two rodent species showed significant differences across the Mediterranean, Irano-Turanian, and Sudanian regions. The phyla and were highly abundant, and and were also prominent. Amplicon sequence variants (ASVs) were identified that were unique to the Sudanian bioclimatic zone. The core microbiota families recovered in this study were consistent among heterospecific hosts. However, diversity decreased in conspecific host populations found at lower altitudes in Sudanian bioclimatic zone. The composition of the gut microbiota is linked to the adaptation of the host to its environment, and this study underscores the importance of incorporating climatic factors such as elevation and ambient temperature, in empirical microbiome research and is the first to describe the rodent gut microbiome from the GRV.

Al-Khlifeh E, Khadem S, Hausmann B, Berry D
2023 - Front Microbiol, 1258775