Imperial College London

Emeritus ProfessorJeremyNicholson

Faculty of MedicineDepartment of Metabolism, Digestion and Reproduction

Emeritus Professor of Biological Chemistry



+44 (0)20 7594 3195j.nicholson Website




Ms Wendy Torto +44 (0)20 7594 3225




Office no. 665Sir Alexander Fleming BuildingSouth Kensington Campus






BibTex format

author = {Lees, H and Swann, J and Poucher, SM and Nicholson, JK and Holmes, E and Wilson, ID and Marchesi, JR},
doi = {10.1371/journal.pone.0100916},
journal = {PLOS One},
title = {Age and Microenvironment Outweigh Genetic Influence on the Zucker Rat Microbiome},
url = {},
volume = {9},
year = {2014}

RIS format (EndNote, RefMan)

AB - ArticleAuthorsMetricsCommentsRelated ContentAbstractIntroductionMethodsResultsDiscussionConclusionsSupporting InformationAuthor ContributionsReferencesReader Comments (0)Media Coverage (0)FiguresAbstractAnimal models are invaluable tools which allow us to investigate the microbiome-host dialogue. However, experimental design introduces biases in the data that we collect, also potentially leading to biased conclusions. With obesity at pandemic levels animal models of this disease have been developed; we investigated the role of experimental design on one such rodent model. We used 454 pyrosequencing to profile the faecal bacteria of obese (n=6) and lean (homozygous n=6; heterozygous n=6) Zucker rats over a 10 week period, maintained in mixed-genotype cages, to further understand the relationships between the composition of the intestinal bacteria and age, obesity progression, genetic background and cage environment. Phylogenetic and taxon-based univariate and multivariate analyses (non-metric multidimensional scaling, principal component analysis) showed that age was the most significant source of variation in the composition of the faecal microbiota. Second to this, cage environment was found to clearly impact the composition of the faecal microbiota, with samples from animals from within the same cage showing high community structure concordance, but large differences seen between cages. Importantly, the genetically induced obese phenotype was not found to impact the faecal bacterial profiles. These findings demonstrate that the age and local environmental cage variables were driving the composition of the faecal bacteria and were more deterministically important than the host genotype. These findings have major implications for understanding the significance of functional metagenomic data in experimental studies and beg the question; what is being measured in animal experiments in which different strains are housed separately, nature or nurture?
AU - Lees,H
AU - Swann,J
AU - Poucher,SM
AU - Nicholson,JK
AU - Holmes,E
AU - Wilson,ID
AU - Marchesi,JR
DO - 10.1371/journal.pone.0100916
PY - 2014///
SN - 1932-6203
TI - Age and Microenvironment Outweigh Genetic Influence on the Zucker Rat Microbiome
T2 - PLOS One
UR -
UR -
VL - 9
ER -