The bacteriome, mycobiome and extracellular vesicles of the neonatal and infant gut microbiota

Thesis event information

Date and time of the thesis defence

Place of the thesis defence

Leena Palotie auditorium (101A), Aapistie 5A

Topic of the dissertation

The bacteriome, mycobiome and extracellular vesicles of the neonatal and infant gut microbiota

Doctoral candidate

Master of Science Jenni Turunen

Faculty and unit

University of Oulu Graduate School, Faculty of Medicine, Research Unit of Clinical Medicine

Subject of study



Assistant Professor Samuli Rautava, University of Helsinki and Helsinki University Hospital


Professor Terhi Tapiainen, University of Oulu and Oulu University Hospital

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The microbiota of the first stool of life includes bacteria, fungi and bacteria-derived vesicles

According to the study, the gut microbiota develops during delivery and birth events affect the gut microbiota development later in childhood.

The gut microbiota is a collection of microbes living in the gut, such as bacteria and fungi. Its composition and effects on health have been widely studied for the past ten years but its origin and development are not yet known. Furthermore, microbes secrete small cargo-carriers, extracellular vesicles, the effects of which in the microbiome development have not been researched yet. The gut microbiota has been assumed to develop after birth when the child is exposed to microbes outside the womb because the womb has been assumed to be a sterile environment for the fetus. Nowadays the sterility of the womb is a controversial topic because microbes have been found in the newborn’s first stool of life known as first-pass meconium, which develops during pregnancy.

The aim of the study was to characterize the microbiota of the first stool and bacteria-derived extracellular vesicles, as well as explore the pregnancy and birth events that affect the microbiota composition. Next-generation sequencing methods were used to identify the collection of bacteria known as the bacteriome in the first stool as well as the potential origins of the microbiota of the first stool, placenta and amniotic fluid. Furthermore, the collection of fungi, known as the mycobiome, was characterized in the first and later stool samples of infants.

The study showed that the first stool of life harbors a detectable bacteriome and mycobiome, while placenta and amniotic fluid do not harbor a microbiota. Therefore, placenta and amniotic fluid are likely not the origin of the gut microbiota. Birth events, including the mode of delivery and use of antibiotics during delivery, strongly affected the microbiota composition of the first stool. These effects were noticeable in the infant gut mycobiome up to 18 months of age. Furthermore, bacteria-derived extracellular vesicles were present in the first stool.

The study results imply that microbiota of the first stool may be able to predict gut microbiota development and the health of the child at an older age. The presence of bacteria-derived extracellular vesicles is a new finding and their role in the newborn gut is unknown. Vesicles are known to have a role in communication between cells and they work as good biomarkers for many diseases, which is why their functions in the first stool require more research.
Last updated: 23.1.2024