Biotropical Resources (GHTM/IHMT NOVA biobank): Biobanking African Pediatric Upper Respiratory and Gut Microbiomes

The main mission of Biotropical Resources (BIOTROP) is to provide high quality biological material to support research on infectious diseases, following good laboratory practices and standard operating procedures (SOP), in strict compliance with ethical and legal frameworks.
Biobanking human microbiome is a valuable resource to investigate the role of microbiota in human health. Preservation of complex microorganism communities is challenging and requires the support of specialized infrastructures, since preservation techniques remain an unsolved challenge, especially when samples are collected in low-resource countries. Few studies on human microbiome have been done in Africa and barely none in African children. To fill this gap, a collaborative project was designed in 2018 with Bandim Health Project (Pilot Study Ref Micro-OPV, Guinea-Bissau) in partnership with BIOTROP, following the Human Microbiome best practices and Good Clinical Practice guidelines. BIOTROP developed SOPs for collection, preservation, transportation, DNA extraction and sample biobank integration together with researchers from Micro-OPV project. The Micro-OPV project was approved by the National Health Research Ethics Committee of Guinea-Bissau (Ref 038/CNES/INASA/2018).
After explaining the study objectives and obtaining the informed consent, researchers collected epidemiological data, and nasopharyngeal and rectal swabs from participating infants. Samples were immediately preserved in DNA/RNA ShieldTM (ZymoResearch), maintained at 4ºC/24 hours and -20 °C until biobank storage at −80 °C. DNA was extracted using DNA Kit ZymoBIOMICS™ (ZymoResearch) with a bead beating step optimized through a bacterial mock community. DNA quantification and purity indicators were analyzed on a Nanodrop spectrophotometer (ThermoFisher).
A total of 215 nasopharyngeal and 215 rectal swabs, the respective bacterial DNA, and associated data, were systematically deposited in the BIOTROP, under access restriction level defined by researchers.
Average of DNA yields and A260/280 ratio of 30.3 ng/uL and 1.88 from nasopharyngeal samples, and 61.4 ng/uL and 1.92 from faecal samples were obtained, respectiv ely. Despite the harsh field conditions, excellent microbiome quality indicators were achieved. As a result of this collaboration, well characterized African pediatric upper respiratory and gut microbiome collections were integrated in BIOTROP. Together w ith associated clinical and epidemiological data, these collections constitute a valuable resource to support future research projects.