Table 6.

Laboratory analyses

Sample type	Assay	Method	Location of work	Study subjects	Time-points
Plasma	I-FABP, CRP, AGP, TNFα, LBP, sCD14, IGF-1	ELISA	Zvitambo	All	Baseline, endline
Peripheral blood leucocytes	Innate immune cell phenotype*	Flow cytometry	Zvitambo	All	Baseline, endline
Whole blood	Whole Blood Culture with and without LPS	Cell culture, flow cytometry and ELISA	Zvitambo	All	Baseline, endline
Whole blood	Bacterial binding Assay	Cell culture, flow cytometry	Zvitambo	All	Baseline, endline
Stool	Myeloperoxidase, neopterin, alpha-1 antitrypsin	ELISA	Zvitambo	All	Baseline, endline
Urine	Global untargeted metabolomic phenotyping	1H NMR spectroscopy	Southampton, UK	All	Baseline, endline
Plasma	Global untargeted metabolomic phenotyping	1H NMR spectroscopy	Southampton, UK	All	Baseline, endline
Plasma	Kynurenine:tryptophan ratio, citrulline, essential amino acids, choline	Ultrahigh-performance liquid chromatography tandem mass spectrometry with electrospray ionisation	Southampton, UK	All	Baseline, endline
Stool	Whole metagenome shotgun sequencing	Illumina HiSeq	Blizard Institute, UK	All	Baseline, endline
Stool	Metabolic phenotyping of faecal water	1H NMR spectroscopy	Southampton, UK	All	Baseline, endline
Urine	Aflatoxin M1 and creatinine	ELISA	Zvitambo	All	Baseline, endline

*Expression of surface activation markers HLA-DR, CD64 and CD16 on monocytes and HLA-DR, CD64, CD16 and CD62L on neutrophils.

AGP, alpha-1 acid glycoprotein; CRP, C reactive protein; I-FABP, intestinal fatty acid binding protein; IGF-1, insulin like growth factor 1; LBP, lipopolysaccharide binding protein; LPS, lipopolysaccharide; NMR, nuclear MR.