Analyzing Gut Microbiome Changes in Weight Loss

Stool samples will be collected at pre-baseline and 2 weeks before the end of the weight loss and weight maintenance phases using OMNIgene GUT DNA Stabilization Kits (DNA Genotek). DNA extraction will be performed using MoBio Powerlyzer Powersoil DNA Isolation Kit (MoBio Laboratories, Carlsbad, California, USA) as described previously.96 (link) DNA concentration will be quantified fluorometrically with a Qubit dsDNA HS Assay kit (Life Technologies). Faecal microbial composition will be assessed by 16S rRNA amplicon sequencing.97 (link) This analysis will include determination of Firmicutes:Bacteroidetes ratios and quantification of Akkermansia muciniphila abundance. A subsample of highest responders (n=10) and lowest responders (n=10) (based on weight regain) will also undergo more detailed analysis of samples from pre-baseline, end of weight loss and end of weight maintenance. Samples will be assessed for identification of responder/non-responder phylogenetic and functional traits using shotgun metagenomic sequencing.98 (link)

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Carter S., Hill A.M., Yandell C., Buckley J.D., Tan S.Y., Rogers G.B., Childs J., Matheson M., Lamb K., Ward S., Stanton T.R., Fraysse F., Hills A.P, & Coates A.M. (2020). Study protocol for a 9-month randomised controlled trial assessing the effects of almonds versus carbohydrate-rich snack foods on weight loss and weight maintenance. BMJ Open, 10(7), e036542.

Publication 2020

MoBio Powerlyzer Powersoil DNA Isolation Kit Qubit dsDNA HS Assay kit

16s rrna Akkermansia muciniphila Assay Bacteroidetes Dsdna Faecal Firmicutes Isolation Metagenomic

Corresponding Organization : University of South Australia

Other organizations : Deakin University, Flinders University, South Australian Health and Medical Research Institute, Neuroscience Research Australia, University of Tasmania

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Variable analysis

independent variables

Weight loss and weight maintenance phases

dependent variables

Faecal microbial composition assessed by 16S rRNA amplicon sequencing
Firmicutes:Bacteroidetes ratios
Akkermansia muciniphila abundance
Responder/non-responder phylogenetic and functional traits using shotgun metagenomic sequencing

control variables

Stool samples collected at pre-baseline and 2 weeks before the end of the weight loss and weight maintenance phases
DNA extraction performed using MoBio Powerlyzer Powersoil DNA Isolation Kit
DNA concentration quantified fluorometrically with a Qubit dsDNA HS Assay kit

controls

Positive control: Not specified
Negative control: Not specified

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