Cohort Profile: The LoewenKIDS Study - life-course perspective on infections, the microbiome and the development of the immune system in early childhood

The Relationship between Gut Microbiota and Respiratory Tract Infections in Childhood: A Narrative Review

Respiratory tract infections (RTIs) are common in childhood and represent one of the main causes of hospitalization in this population. In recent years, many studies have described the association between gut microbiota (GM) composition and RTIs in animal models. In particular, the “inter-talk” between GM and the immune system has recently been unveiled. However, the role of GM in human, and especially infantile, RTIs has not yet been fully established. In this narrative review we provide an up-to-date overview of the physiological pathways that explain how the GM shapes the immune system, potentially influencing the response to common childhood respiratory viral infections and compare studies analysing the relationship between GM composition and RTIs in children. Most studies provide evidence of GM dysbiosis, but it is not yet possible to identify a distinct bacterial signature associated with RTI predisposition. A better understanding of GM involvement in RTIs could lead to innovative integrated GM-based strategies for the prevention and treatment of RTIs in the paediatric population.

Birth cohort studies using symptom diaries for assessing respiratory diseases–a scoping review

Background

Respiratory infections are the most frequent health problem in childhood leading to morbidity and socioeconomic burden. Studying symptoms of respiratory infections in home based settings requires dedicated prospective cohort studies using diaries. However, no information is available on which birth cohort studies using symptom diary data. A review of birth cohort studies with available symptom diary data, follow-up data, and bio samples is needed to support research collaborations and create potential synergies.

Methods

We conducted a scoping review of birth cohort studies using diaries for the collection of respiratory symptoms. The scoping review was conducted in accordance with the PRISMA Extension. We searched the electronic databases PubMed, Embase, Web of science and CINAHL (last search November 2020) resulting in 5872 records (based on title and abstract screening) eligible for further screening.

Results

We examined 735 records as full text articles and finally included 57 according to predefined inclusion criteria. We identified 22 birth cohort studies that collect(ed) data on respiratory symptoms using a symptom diary starting at birth. Numbers of participants ranged from 129 to 8677. Eight studies collected symptom diary information only for the first year of life, nine for the first two years or less and six between three and six years. Most of the cohorts collected biosamples (n = 18) and information on environmental exposures (n = 19).

Conclusion

Information on respiratory symptoms with daily resolution was collected in several birth cohorts, often including related biosamples, and these data and samples can be used to study full spectrum of infections, particularly including those which did not require medical treatment.

Feasibility and Comparison Study of Fecal Sample Collection Methods in Healthy Volunteers and Solid Organ Transplant Recipients Using 16S rRNA and Metagenomics Approaches

The human microbiome encompasses a variety of microorganisms that change dynamically and are in close contact with the body. The microbiome influences health and homeostasis, as well as the immune system, and any significant change in this equilibrium (dysbiosis) triggers both acute and chronic health conditions. Microbiome research has surged, in part, due to advanced sequencing technologies enabling rapid, accurate, and cost-effective identification of the microbiome. A major prerequisite for stool sample collection to study the gut microbiome in longitudinal prospective studies requires standardized protocols that can be easily replicated. However, there are still significant bottlenecks to stool specimen collection that contribute to low patient retention rates in microbiome studies. These barriers are further exacerbated in solid organ transplant recipients where diarrhea is estimated to occur in up to half the patient population. We sought to test two relatively easy sample collection methods (fecal swab and wipes) and compare them to the more cumbersome "gold" standard collection method (scoop) using two different sequencing technologies (16S ribosomal RNA sequencing and shotgun metagenomics). Our comparison of the collection methods shows that both the swabs and the wipes are comparable to the scoop method in terms of bacterial abundance and diversity. The swabs, however, were closer in representation to the scoop and were easier to collect and process compared to the wipes. Potential contamination of the swab and the wipe samples by abundant skin commensals was low in our analysis. Comparison of the two sequencing technologies showed that they were complementary, and that 16S sequencing provided enough coverage to detect and differentiate between bacterial species identified in the collected samples. Our pilot study demonstrates that alternative collection methods for stool sampling are a viable option in clinical applications, such as organ transplant studies. The use of these methods may result in better patient retention recruitment rates in serial microbiome studies.