By Jie Jiang
Principal supervisor: Professor Jakob Stokholm, COPSAC
Co-supervisors: Associate Professor Jonathan Thorsen and Senior Researcher Casper Sahl Poulsen, COPSAC
Chairperson: Bekzod Khakimov, Associate Professor, University of Copenhagen
Opponent: John Penders, PhD, Professor, Maastricht University Medical Centre, Netherlands
Opponent: Carsten Eriksen, PhD, Tenure-track scientist, Technical University of Denmark
Summary
Early life represents a critical window for immune development, during which the gut microbiome plays a central role in shaping long-term health. Delivery by cesarean section (CS) profoundly alters the initial establishment of the infant gut microbiota and has been consistently associated with increased risks of immune-mediated diseases, including asthma. However, the mechanisms linking early microbial perturbations to later disease remain incompletely understood, and potential modifiable factors supporting microbiome restoration have not been clearly identified. This PhD thesis aimed to characterize the development of the infant gut microbiome following CS delivery, identify key ecological and environmental drivers of its restoration, and elucidate the microbial and metabolic pathways that may mediate the association between CS delivery and asthma risk.
The PhD thesis is based on data from the Copenhagen Prospective Studies on Asthma in Childhood 2010 (COPSAC2010) cohort of 700 mother-child pairs, recruited during pregnancy week 24 and monitored through childhood with frequent detailed clinical visits to the COPSAC study clinic. A validation and replication study was based on data from a Canadian birth cohort (the CHILD study), which enrolled 3,405 subjects since pregnancy from 4 largely urban study centers across Canada (Vancouver, Edmonton, Winnipeg, and Toronto) from 2008 to 2012. The primary endpoints for both cohorts are the development of asthma, which was prospectively diagnosed using pre-defined quantitative criteria in both cohorts.
The thesis contains three scientific papers.
In paper I, we investigated the ecological and environmental factors that facilitate the restoration of the gut microbiome in CS-born infants. Based on a 1-year restoration score defined in our previous work, we quantified how closely the 1-year microbial community of each infant resembled that of vaginally delivered infants. Through 16S rRNA gene sequencing at 1 week and 1 month in the COPSAC cohort, we found that the abundance of Bifidobacterium longum, Bacteroides fragilis, and Bacteroides vulgatus at 1 week predicted a higher degree of restoration at 1 year. The presence of older siblings emerged as a strong environmental factor promoting microbiome restoration, mediated through increased colonization with restoration- associated bacteria and inhibition of Clostridium perfringens. The restoration score, its determinants, and its relationship with later asthma were successfully replicated in the independent CHILD cohort (16S rRNA), highlighting the robustness of these findings. Together, this work identifies specific microbial and environmental targets for early interventions to mitigate the long-term health risks associated with CS delivery.
In paper II, we expanded our previous findings based on 16S rRNA data to metagenomics data in the COPSAC2010 cohort. We profiled not only the taxonomic composition but also the functional development of the gut microbiome at 1 month and 1 year of age using metagenomics sequencing, and investigated how CS affects the gut microbiome composition and its pathways. At 1 month, CS-born infants showed very distinct taxonomic and functional compositions. By 1 year, taxonomic profiles remained distinguishable by delivery mode, 8whereas pathway profiles largely converged. An increased asthma risk was only associated with 1-year CS microbial scores but not with CS pathway scores (1-year CS microbial score: Generalized Estimating Equation (GEE) Odds ratio (OR) per SD=1.21, 95% confidence interval [1.01,1.45], P=0.03; Adjusted GEE OR=1.23, [1.02,1.48], P=0.03). In conclusion, we confirmed the association between the persistent perturbed microbial composition and asthma risk, but we found no association between the CS-altered pathways and asthma risk, expanding our understanding of the influence of CS delivery on the gut microbiome.
In paper III, we leveraged metagenomic and gut metabolomic data from the CHILD cohort to identify metabolic alterations following CS. We characterized the CS microbial signatures at 3 months and 1 year of age using machine learning models. The association between CS and the gut microbiota composition was more pronounced at 3 months (area under the curve (AUC)=0.78) and attenuated to age 1 year (AUC=0.60). An increased asthma risk was only associated with 1-year CS microbial scores (Odds ratio 1.41[1.12,1.80], P<0.01; adjusted Odds ratio 1.30[1.03,1.68], P=0.03), which is in line with previous work. Extending this, we identified metabolic imbalances associated with 1-year cesarean section microbial scores, marked by elevated tryptophan metabolites in the stool metabolome at 1 year of age. Our results replicate the mediating role of the 1-year cesarean section microbial signature in the association between cesarean section and asthma risk, and provide new insight into possible underlying mechanisms of host-microbe interaction following cesarean section. Collectively, these findings shed light on the relevance of the gut microbiome for asthma in childhood based on different birth cohorts and data layers. In the future, strategies for restoring the gut microbiota may help prevent and alleviate asthma in childhood.
