The goal of this clinical trial is to investigate the differences in microbiota, height and weight between infants born by cesarean section and randomized to receive fecal microbiota transplant after birth. The main questions it aims to answer are:

• Could micobiota transplant be used improve gut microbiota and prevent overweight or obesity.
• Is the source of colonization a modifiable factor and can it be changed by using an early fecal microbiota transplant.

1. BACKGROUND

   In recent decades, the prevalence of obesity in children has increased dramatically worldwide. Obese children and adolescents are around five times more likely to be obese in adulthood than those who are not obese. Although childhood obesity is a complex and multifactorial outcome, it seems that obese children have different gut microbiome already at birth. Many of the previous studies highlight maternal risk factors such as higher maternal BMI before pregnancy, excess gestational weight gain, gestational diabetes (GDM) and C-section as a risk factor for childhood overweight or obesity. Perinatal factors, in particular the birth by Cesarean section as well as perinatal antibiotics, have also been identified as a critical determinant of early-life microbiota composition and development. However, the mechanisms are not clear.

   Mothers with obesity and/or gestational diabetes have been reported to have obesity-associated gut microbiota. The changes in microbiota could be transmitted to child during vaginal birth. Previously, metagenome sequencing has been succesfully used for comparing the main source of colonization in infants and vertical transmission of gut microbiota and shown that >70% of microbiota is vertically transmitted from the mother to the newborn infant during vaginal delivery.

   In Finland, the rate of C-section has increased from 16-17% to 19.6% of all births. The estimated global average rates are similar, but the C-section rate are expected to increase from the current 21.1% to 28.5%. It is hypnotized that C-section disrupts the vertical transmission of beneficial microbes from the mother to the infant during a critical developmental window. In addition to risk of obesity, C-section increases risk of infectious and chronic diseases such as autoimmune diseases, asthma, and even some cancers.

   Different therapeutic approaches have been proposed and tested for neonatal microbiome restoration in C-section in infants. Intestinal microbes and maternal intestinal strains contribute the most persistent proportion of the neonatal intestinal microbiota after birth, whereas vaginal bacteria and maternal vaginal strains constitute only a small and transient fraction. In two studies, fecal microbiota compositions in infants born by C-section, have succeeded to restore disrupted transmission of intestinal Bacteroides strains by vaginal seeding, while oral administration of the maternal vaginal microbiota to C-section infants had no discernible effect on microbiota composition. In a previous study, fecal transplant from the mother, with a published protocol has been shown to modify the development of infants' gut microbiota successfully and safely.

   As there are evidence, that is possible to modify infants gut microbiota during a critical developmental window, the metabolic consequences and clinical significance of these interventions are unknown. In addition, it is not known what kind of microbiota and from whom would be best for the health of the child in long term.

   The investigators hypothesize that obesity may be a vertically transmitted disease as a newborn child receives obesity-related microbiota from the mother. Furthermore, the source of colonization is a modifiable factor and can be changed by using an early fecal microbiota transplant.

2. STUDY DESIGN AND METHODS

2.1. Recruitment and screening fecal and vaginal samples from the mother

The midwifes and doctors inform potentially participating mothers of the study at the visit and those who are interested to participate are contacted by the study nurse. After informed consent, the mothers are tested for potential contagious diseases as explained below, at the latest 10-14 days before scheduled CS. A fecal sample of 100 g and a blood sample of 15 mL are collected from the mother. The mother divides the feces into the administered sample tubes according to written instructions. Feces for the transplant is collected into an empty tube using a spoon in the cap. The mother informs the research nurse, who delivers the tubes taken for screening to the laboratory as soon as possible, where the transplant is prepared from the fresh sample - this process is completed with a 6 h time frame.

The fresh fecal sample is screened for the presence of parasites and pathogenic viruses and bacteria. An aliquot (0.125 g) of the fresh fecal sample is used to determine the bacterial composition of the sample. Vaginal samples will be obtained during a visit for the assessment of mode of delivery if not already obtained at maternal welfare clinic as a part of routine follow-up.

Blood tests: Complete Blood Count, Erythrocyte sedimentation rate, C-reactive protein, Alanine transaminase, Alkaline phosphatase, Gamma-glutamyl transferase, Albumin, Creatinine, HIV, Hepatitis B, C and E, Treponema pallidum, Human T-cell leukemia virus, CMV ja EBV

Vaginal and perineal screening: Group B Streptococcus, Methicillin-resistant Staphylococcus aureus (MRSA), Extended Spectrum Beta Lactamase (ESBL)

Fecal screening: Salmonella spp., Shigella sp., Campylobacter coli/jejuni, Yersinia enterocolitica, Enterohemorragic E. coli (EHEC), Enteroinvasive E. coli (EIEC), Enterotoxigenic E. coli (ETEC), Vibrio sp., Plesiomonas shigelloides, Clostridium difficile, Cryptosporidium spp., Entamoeba histolytica, Giardia lamblia, Norovirus, Multi drug resistant gram negative bacteria (MDRGN), Vancomycin Resistant Enterococcus (VRE), Listeria monocytogenes, Helicobacter pylori, Sars-CoV-2.

2.2 Fecal micrbiota transplant

Another part of the fresh fecal sample from mother is used as the transplant and for that purpose 1 g of feces is dissolved in 15 mL of isotonic saline and 10% glycerol, homogenized, and the 0.5 mL aliquots of the transplant are immediately frozen and stored at -80 °C.

Fecal transplant from normal weight, healthy female donor (18 to 35 years) from Turku Microbiome Biobank (University of Turku and Turku University Hospital). Donor is tested for potential contagious diseases simultaneously as mother.

2.3 Follow-up in the mother and baby unit

During hospital stay, fecal samples are collected from the first stool of the life and at the age of two to three days. After the first feeding the newborn is followed-up according to the hospital protocols at the rooming-in ward. In previous studies fever has been reported rarely in newborns who have received fecal transplant. Possible adverse events, such as increased peristalsis, diarrhea, vomiting, fever, and rash, are reported to the electronic database of patient records and collected from there by the researchers. Before discharge, the child is weighted and discharge examination is performed by pediatrician or doctor specializing in pediatrics, typically on postnatal day 2.

At the age of 2 days, simultaneously to the screening samples for SCID and metabolic diseases, peripheral blood mononuclear cells (PBMCs) are isolated from capillary blood samples (100µl) drawn from the heel and stored at -140℃. Serum is separated and stored at -80℃. Cells are subjected to analyses, including single cell mRNA sequencing to examine gene expression levels and immunophenotyping by flow cytometry to examine distribution of immune cell types as well as functional properties, including activation and surface receptors. The inflammatory, immunity and obesity related serum components are examined from serum samples (10µl) by high-multiplex Olink or other immunoassays.

2.4 Follow-up after discharge

From the first postnatal week on, the infant is followed in the well-baby clinic according to normal national protocols. As a part of the study, the parents can be in contact with the pediatric emergency department of Oulu University Hospital.

At 3 and 12 months postnatally, parents are asked to fulfill an online questionnaire about child's health and collect and send the fecal samples of the infant and mother to the XXOMNIgeneGUT (DNA genotek, Ontario, Canada) tubes for microbiota analysis and to OMNImetGUT tubes for metabolites and temporarily stored at room temperature before transfer to Turku Microbiome Biobank by mail. At 3 months postnatally, the fecal sample is collected before the second orally given rota virus vaccination, if possible. Fecal samples are not collected during the acute gastrointestinal infection.

DNA from the microbiota samples will be isolated using Chemagic 360 machines and Chemagic Stool 200 H96 kit (PerkinElmer, Turku, Finland). The samples will be sequenced either at the Turku University Hospital, Clinical Microbiology on an Illumina Nextseq 2000 machine or at the Finnish Functional Genomics Centre on an Illumina Novaseq 6000 machine.

Microbiome outcomes:

• 16S next generations sequencing
• Metagenome sequencing and source of colonization
• Microbiome-derived extracellular vesicles: proteome, bacterial 16S
• Microbiota produced metabolites
• Antimicrobial resistance genes

Advanced bioinformatics will be used for microbiome analysis. Source of colonization using metagenome sequencing will be determined as reported earlier.

2.5 Questionnaires

Data are collected on the families' lifestyle, environmental exposures and the health of the study infants and their parents using online questionnaires, enabling monitoring and data query during data collection. Questionnaires are filled by the parents before the birth of the infant and subsequently. Parents are requested to fill in questionnaires on child's nutrition, gastrointestinal function, and care practices in the 3 months, and in the 12 months of age. The questions change as the child grows. Illnesses, medication and use of probiotics and other dietary supplements are reported in the questionnaires. The questionnaires related to nutrition, health and background are mainly similar as in the ongoing HELMi study and Secflor study. To enhance compliance of response rates to the questionnaire, parents receive automatic reminders via email and SMS-messages.

2.6 Patient records

The perinatal data will be obtained from electronic delivery record data concerning newborn's hypoglycemia, follow-up of glucose levels, need for intravenous glucose infusion before discharge from hospital, age at discharge, symptoms of infection, levels of infection parameters and use of antibiotics during hospital stay, will be collected from hospitals patient records. Growth data up to age of three years measured during normal visits to well-baby clinic and vaccination data will be gathered from parents or from well-baby clinics. Use of antibiotics and other medication up to age of three years will be collected via questionnaires and confirmed from Kanta-service with written permission of the parents.

2.7 Power analysis

Resulting from the screening process, a 40% exclusion rate is expected because of group B streptococci (GBS) carrier state 24% of pregnant women in our region and other positive findings in the screening samples. The trial is designed with a planned sample of 150 mothers, allowing the final number of the subjects with an estimated 40% drop-out rate due to screening positivity to be 90 (30 in each intervention group) taking into consideration that it is likely to have drop-outs during the follow-up period. Microbiome data are multidimensional and binary outcomes are not suitable for power analysis.

Inclusion Criteria:

• Pregnant women age 18-49 years who are scheduled for elective CS at term, are recruited at 36 weeks of gestation during a visit for the assessment of mode of delivery at Oulu university Hospital, Oulu, Finland.

Exclusion Criteria:

• Use of regular immunosuppressive biological medication; inflammatory bowel disease in the mother; immunodeficiency disorder of the mother or any first-degree family member of the unborn baby; known or suspected major fetal congenital abnormality; travel outside Europe, the United States, Canada, Japan, Australia, or New Zealand within the last three months; and antibiotic treatment within three months of delivery (excluding prophylactic cefuroxime - or an alternative in case of allergy - administered prior to the elective cesarean section).
• Infant exclusion criteria are preterm birth (birth before 37 weeks of gestation), birth weight below 2500 g, admission to neonatal intensive care unit, need for respiratory support or antibiotic treatment of the newborn before discharge. In case of a suspected infection or newborn screening result for severe combined immunodeficiency (SCID) is out of the normal range, of the newborn the randomization code can be opened.

Pregnant women.

IPD will not be shared with other researchers.

The research statistician performs the computer-generated randomization. The study nurse prepares the fecal transplant according to the randomization. Study participants or investigators are not aware of study group.