Bern Birth Cohort / Trajectory of Microbiota Maturation in Healthy Bern Infants - a Network Approach

Background: Intestinal microbiota composition is fundamental to human health and undergoes critical changes within the first two years of life. Factors probably influencing the microbiota are the maternal microbiota and the general environment in Switzerland. However, the development of the intestinal microbiota is incompletely understood. Gaining knowledge of the trajectory of microbiota maturation is likely key to the understanding of the pathogenesis of many pathologies in childhood.

Aims: The investigators aim for a deep understanding of the maturation of the healthy infant intestinal microbiota regarding composition, diversity and metabolic activities. The investigators aim for identifying parameters affecting microbiota maturation and effects of the microbiota on infant outcome.

Methods: The investigators will recruit 250 pregnant mothers who will be followed as mother-baby pairs until 10 years of age. Infants will be followed clinically to determine adequate growth and development as well as pathology including abdominal pain. Epidemiological parameter and infant nutrition will be assessed. The investigators will collect biological samples such as stool, maternal milk, vaginal swaps and skin swaps.

Species composition and diversity will be assessed by 16S sequencing. Metagenomic shotgun sequencing and bacterial messenger ribonucleic acid (mRNA) analysis will inform about metabolic potential and metabolic activity of the microbiota. Mass spectrometry will assess the small molecule content of stool and maternal milk samples. Network analysis will be used to assess the complex relationships between bacteria metabolic activities and small molecular content.

Expected results: The investigators expect an increase in complexity and metabolic potential and activity with age. Microbiota parameters will differ according to nutrition and might predict infant outcomes such as growth and abdominal pain. Systematic analysis of sequential maternal and infant bacteria samples from stool, skin and maternal milk will help characterizing bacterial transfer from mother to infant Conclusion: The investigators propose an observational study of healthy Bern mother baby pairs with clinical characterisation and biological sampling. Advanced analysis tools will be used to characterise the microbiota and address mechanistic questions.

Methods for sample analysis:

For the primary objective and outcome/ endpoint of the study, bacterial content of infant stool will be analyzed by:

* Mass spectrometry to assess intestinal content (metabolome). Techniques have been established in the laboratory of Prof. U. Sauer who already collaborated with the investigators' group in previous studies.
* 16S ribosomal ribonucleic acid (rRNA) sequencing for bacterial species composition as well as microbial diversity.
* Bacterial full genome metagenomics shotgun sequencing to identify bacterial genes present (metabolic potential of the microbiota).
* Bacterial mRNA sequencing to assess transcription and a functional role of the microbiota (metabolic activity of microbiota).
* Analysis of the intestinal virome and eukaryotic intestinal populations by appropriate sequencing or culturing techniques.
* Analysis of IgA antibodies in human milk and stool and the interaction of antibodies with intestinal bacteria.

For the secondary endpoints identical analyses will be performed in skin swabs, maternal milk, maternal vaginal swabs and maternal stool. Parameters for infant growth, neurodevelopment, immune maturation and potential occurrence of pathology will be assessed at every visit. Maternal and infant nutrition, hygiene, socioeconomic status and clinical history will be assessed by questionnaires at every visit. Milk samples will further be analyzed for their cellular contents by flow cytometry and single cell RNA-sequencing, as well as for cytokines and exosome-based miRNAs. All biosamples will be analyzed by mass spectrometry to assess impact of the environment on infant metabolism and physiology.

Further follow-up experiments with the acquired samples are possible. Specifically, individual bacteria strains can be isolated and cultured in vitro and also tested alone or in combination in experimental animals.

Bacterial sequencing by the methods described above will also inevitably identify maternal or infant DNA sequences, since metagenomic shotgun sequencing cannot differentiate between bacterial and human DNA. These human DNA sequences will not be analyzed within the scope of this project. However, these sequences might be the subject of future studies. Study participants will therefore be asked for permission to analyze human DNA from mother and/ or child at the page for "further analyses" within the consent form. An option to "opt out" for human DNA analysis will be provided and refusal will not lead to exclusion from the study.

Any findings of clear relevance to the health of the participant (i.e. mother or child) will be reported to the participant in collaboration with their treating pediatrician. Participants will need to inform the study team if they do not wish to be informed.

Eligibility Criteria:
Inclusion Criteria:

* Signed informed consent.
* Ability to understand and follow study procedures and understand informed consent
* From week 20 of pregnancy until birth
* General good health, i.e. absence of major severe medical/ surgical/ psychiatric condition requiring ongoing management. Minor well controlled conditions (e.g. medically controlled arterial hypertension, occupational asthma, gestational diabetes mellitus) may be present.
* Absence of known severe embryonal pathology, expected normal pregnancy (e.g. minor conditions including twin/ triplet pregnancy, final pelvic position may be present)
* Age 18-45 years.

Exclusion Criteria:

• Participation in another clinical study interfering with study procedures.