General aim
To collect data on – and analyze associations between microbial, behavioral and sociocultural factors in relation to oral and metabolic health of children during the first 1000 days of life, particularly in those from families (to be) in vulnerable conditions.
Objectives related to the oral and gut microbiome
Objectives related to oral and metabolic health outcomes
To collect information on oral and metabolic health in children in the first 1000 days, to assess if / how they are related, and how microbial, behavioral and sociodemographic factors are associated with both oral and metabolic health outcomes.
Objectives related to sociocultural factors and practices
Active period
Year 1-8
ACTA, AUMC, UvA-FMG, VU, Inholland, UPorto, TNO Microbiology & Systems Biology, TNO Child Health.
GGD, Sarphati Amsterdam, NVvK, JTV Amsterdam, Bètapartners, PANEL, NCJ, Food4Smiles, PHAROS, Gezonde en Kansrijke start, NIBI, BaseClear.
Research in WP 2 focused on three components: 1) the inclusion of participants and collection of data in the three cohort studies: the Amsterdam Infant Microbiome Study (AIMS), the OralBioBorn study and the Sarphati Ethnography study, 2) first analysis of the oral and gut microbiome from samples of mother-child pairs from AIMS, and 3) collection and analysis of qualitative data on health practices within Sarphati Ethnography.
AIMS is a prospective birth cohort study, led by the GGD Amsterdam, following 500 children from Amsterdam and their family members from pregnancy until three years of age, to study the development of the microbiome and its effect on child development and growth. The second-year reporting period of the MetaHealth project focussed on inclusion of families and the collection of biological samples, questionnaire data and anthropometric and oral health measurements in partnership with the GGD, ACTA and JTV Amsterdam.
In 2024, 200 new families were recruited via pregnancy centering groups of the GGD and via the vaccination walk-in hours of the baby well clinics. By November 2024, recruitment of families was completed, with 500 children and their parents being included. In March 2025, 150 of the 500 families have completed the three-year study protocol, and 2800 biosamples of these families have been sequenced by BaseClear and are ready to be analysed. The research within WP2 using AIMS data is conducted by PhD student Nicholas Pucci and postdoc Susanne Pinto and the supervision team.
Results from AIMS data:
Across the last year, we have finalized the analysis of the AIMS gut pilot study and published the results (Pucci et al., PeerJ, 2025, see below under Results. In this study, we analyzed newly sequenced gut microbiome samples of mother-infant pairs from the Amsterdam Infant Microbiome Study (AIMS) and four publicly available datasets to identify important environmental and bifidobacterial features associated with the colonization success and succession outcomes of B. longum subspecies.
Analyses have been done on the associated dataset on the oral microbiome from the same mother-infant pairs. In this study, we performed shotgun metagenomics on a time series of the infant oral microbiome and identified novel, interacting species using a meta-pangenomics approach. Using meta- and pangenomic approaches, we identified significant co-occurrences between two previously undescribed Streptococcus and Rothia species, found to be among the most abundant and prevalent bacteria in the oral microbiome of weaning children. Manuscript is in preparation.
OralBioBorn is a birth cohort study led by the University of Porto, in collaboration with MetaHealth, following mother-child pairs up to the child’s third year of life. It follows a similar protocol of AIMS. The study aims to better understand the longitudinal evolution of the microbiome in mother-child dyads and to investigate the impact of maternal cardiometabolic disease on early-life microbiome dynamics. By March 2025, the OralBioBorn cohort has recruited 300 pregnant women, of whom 50% have cardiometabolic conditions, specifically obesity, hypertension, and/or gestational diabetes. Biological samples, including oral swabs and faeces, are being collected alongside comprehensive clinical metadata, covering chronic and acute oral and cardiovascular conditions, obstetric and perinatal history, medication use, diet, and health-related behaviors. Up to March 2025, 800 biosamples have been sequenced by BaseClear. This research is being conducted by PhD student Inês Magalhães and assistant Manuel Baptista and the research and supervision team, with funding from MetaHealth, in collaboration with the OralBioBorn/Perimyr team.
Sarphati Ethnography Cohort follows 20 households in Amsterdam from pregnancy until the first child turns four, and studies how diverse everyday parenting practices and child behaviors develop over the years and how they are influenced by social factors (Sarphati Amsterdam 2021). Currently, there are 20 active families, along with four new contacts who may soon join the panel (we aim for 25 families). Data are being collected using interviews and participant observations and families are being contacted three to four times a year. The interviews and observations explore how child practices, such as eating, sleeping, physical activity and hygiene, develop and how parents relate to microbes through hygiene and cleaning practices. In parallel, we are also working on a side project to interview families concluding their participation in AIMS cohort, aiming to explore potential research participation effects on their health (and microbiome-related) practices.
The research is being conducted by postdoc Carla Ferreira Rodrigues and the research and supervision team. In the past year, the Sarphati Ethnography team has been slightly reconfigured, and we now have two junior social science researchers – Zana Chadud Cosac and Lola Kurpershoek – collaborating with us on recruitment, as well as on data collection, management and analysis.
The initial colonization of the infant gut is a complex process that defines the foundation for a healthy microbiome development. Bifidobacterium longum is one of the first colonizers of newborns’ gut, playing a crucial role in the healthy development of both the host and its microbiome. However, B. longum exhibits significant genomic diversity, with subspecies (e.g., Bifidobacterium longum subsp. infantis and subsp. longum) displaying distinct ecological and metabolic strategies including differential capabilities to break down human milk glycans (HMGs). To promote healthy infant microbiome development, a good understanding of the factors governing infant microbiome dynamics is required.
We analyzed newly sequenced gut microbiome samples of mother-infant pairs from the Amsterdam Infant Microbiome Study (AIMS) and four publicly available datasets to identify important environmental and bifidobacterial features associated with the colonization success and succession outcomes of B. longum subspecies. Metagenome-assembled genomes (MAGs) were generated and assessed to identify characteristics of B. longum subspecies in relation to early-life gut colonization. We further implemented machine learning tools to identify significant features associated with B. longum subspecies abundance.
B. longum subsp. longum was the most abundant and prevalent gut Bifidobacterium at one month, being replaced by B. longum subsp. infantisat six months of age. By utilizing metagenome-assembled genomes (MAGs), we reveal significant differences between and within B. longumsubspecies in their potential to break down HMGs. We further combined strain-tracking, meta-pangenomics and machine learning to understand these abundance dynamics and found an interplay of priority effects, milk-feeding type and HMG-utilization potential to govern them across the first six months of life. We find higher abundances of B. longum subsp. longumin the maternal gut microbiome, vertical transmission, breast milk and a broader range of HMG-utilizing genes to promote its abundance at one month of age. Eventually, we find B. longum subsp. longum to be replaced by B. longum subsp. infantis at six months of age due to a combination of nutritional intake, HMG-utilization potential and a diminishment of priority effects.
Our results establish a strain-level ecological framework explaining early-life abundance dynamics of B. longum subspecies. We highlight the role of priority effects, nutrition and significant variability in HMG-utilization potential in determining the predictable colonization and succession trajectories of B. longum subspecies, with potential implications for promoting infant health and well-being.
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