Collier, F. | Search bioRxiv

bioRxiv2021

Developmental and Intergenerational Landscape of Human Circulatory Lipidome and its Association with Obesity Risk

Lipids play a vital role in human health and development, but changes to their circulatory levels during gestation and in early life are poorly understood. Here we present the first developmental and intergenerational landscape of the human circulatory lipidome, derived by profiling of 480 lipid species representing 25 lipid classes, in mothers and their offspring (n=2491). Levels of 66% of the profiled lipids increased in maternal circulation during gestation, while cord blood had higher concentrations of acylcarnitines and lysophospholipids. The offspring lipidome at age six years revealed striking similarities with postnatal maternal lipidome (adult) in its lipid composition and concentrations. Comparison of lipids associated with child and maternal adiposity identified a 92% overlap, implying intergenerational similarities in the lipid signatures of obesity risk. We also catalogued lipid signatures linked with maternal adiposity during gestation and offspring birthweight, and validated (>70% overlap) the findings in an independent birth-cohort (n=1935).

systems biology↗

bioRxiv2020

A preliminary investigation of major bacterial antibiotic resistance genes present in Australian fecal samples using shotgun metagenomics and targeted sequencing.

The gut microbiota is an immense reservoir of antimicrobial resistance genes (ARGs); however, in Australia the profile of the gut resistome, or ensemble of ARGs, has not been investigated. This study provides a first preliminary mapping of the major bacterial ARGs present in human, domestic dog and wild duck fecal samples collected from south-eastern Victoria, Australia; and evaluates the use of shotgun metagenomics sequencing (SMS) and targeted amplification of ARGs. We analysed SMS data using an in-house method and web-based bioinformatics tools: ResFinder and KmerResistance. We examined targeted sequences using One Codex or the PanBacterialAnalysis Torrent Suite plugin. All methods detected ARGs in all samples, with resistance to up to 13 classes of antibiotics detected overall. ARGs were more abundant in the human and dog samples than the duck samples. They mostly conferred resistance to three classes of antibiotics that are the most frequently prescribed in Australia: tetracycline, {beta}-lactams and MLSB (macrolide, lincosamide, streptogramin B). Targeted sequencing significantly improved sensitivity for detection of ARGs included in the panel; however, SMS provided quantitative information and allowed tentative identification of the host bacteria. For SMS, web-based and in-house methods gave comparable results, with discrepancies mostly due to different reference databases. The in-house method allowed manually checking results and potential errors, while web-based methods were user-friendlier and less time-consuming. More samples need to be investigated to fully describe the resistome in humans and animals in Australia.

genomics↗