Imperial College London
Alternate

DrJonathanSwann

Faculty of Medicine, Department of Metabolism, Digestion and Reproduction

Visiting Professor
 
 
 
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Contact

 

+44 (0)20 7594 0728j.swann

 
 
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Location

 

660Sir Alexander Fleming BuildingSouth Kensington Campus

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Summary

 

Publications

Citation

BibTex format

@article{Randall:2019:10.1186/s40168-019-0738-y,
author = {Randall, DW and Kieswich, J and Swann, J and McCafferty, K and Thiemermann, C and Curtis, M and Hoyles, L and Yaqoob, MM},
doi = {10.1186/s40168-019-0738-y},
journal = {Microbiome},
pages = {1--10},
title = {Batch effect exerts a bigger influence on the rat urinary metabolome and gut microbiota than uraemia: a cautionary tale},
url = {http://dx.doi.org/10.1186/s40168-019-0738-y},
volume = {7},
year = {2019}
}
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RIS format (EndNote, RefMan)

TY  - JOUR
AB  - BackgroundRodent models are invaluable for studying biological processes in the context of whole organisms. The reproducibility of such research is based on an assumption of metabolic similarity between experimental animals, controlled for by breeding and housing strategies that minimise genetic and environmental variation. Here, we set out to demonstrate the effect of experimental uraemia on the rat urinary metabolome and gut microbiome but found instead that the effect of vendor shipment batch was larger in both areas than that of uraemia.ResultsTwenty four Wistar rats obtained from the same commercial supplier in two separate shipment batches underwent either subtotal nephrectomy or sham procedures. All animals undergoing subtotal nephrectomy developed an expected uraemic phenotype. The urinary metabolome was studied using 1H-NMR spectroscopy and found to vary significantly between animals from different batches, with substantial differences in concentrations of a broad range of substances including lactate, acetate, glucose, amino acids, amines and benzoate derivatives. In animals from one batch, there was a complete absence of the microbiome-associated urinary metabolite hippurate, which was present in significant concentrations in animals from the other batch. These differences were so prominent that we would have drawn quite different conclusions about the effect of uraemia on urinary phenotype depending on which batch of animals we had used. Corresponding differences were seen in the gut microbiota between animals in different batches when assessed by the sequencing of 16S rRNA gene amplicons, with higher alpha diversity and different distributions of Proteobacteria subtaxa and short-chain fatty acid producing bacteria in the second batch compared to the first. Whilst we also demonstrated differences in both the urinary metabolome and gut microbiota associated with uraemia, these effects were smaller in size than those associated with shipment batch.Conclusi
AU  - Randall,DW
AU  - Kieswich,J
AU  - Swann,J
AU  - McCafferty,K
AU  - Thiemermann,C
AU  - Curtis,M
AU  - Hoyles,L
AU  - Yaqoob,MM
DO  - 10.1186/s40168-019-0738-y
EP  - 10
PY  - 2019///
SN  - 2049-2618
SP  - 1
TI  - Batch effect exerts a bigger influence on the rat urinary metabolome and gut microbiota than uraemia: a cautionary tale
T2  - Microbiome
UR  - http://dx.doi.org/10.1186/s40168-019-0738-y
UR  - http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000483509300001&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=1ba7043ffcc86c417c072aa74d649202
UR  - https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-019-0738-y
UR  - http://hdl.handle.net/10044/1/73553
VL  - 7
ER  -
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