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A comparative analysis of the intestinal metagenomes present in guinea pigs (Cavia porcellus) and humans (Homo sapiens)

Falk Hildebrand12, Tine Ebersbach3, Henrik Bjørn Nielsen4, Xiaoping Li5, Si Brask Sonne6, Marcelo Bertalan4, Peter Dimitrov4, Lise Madsen67, Junjie Qin5, Jun Wang568, Jeroen Raes12, Karsten Kristiansen6 and Tine Rask Licht3*

Author Affiliations

1 Department of Structural Biology, VIB, Pleinlaan 2, Brussels, 1050, Belgium

2 Microbiology Unit (MICR), Department of Applied Biological Sciences (DBIT), Vrije Universiteit Brussel, Pleinlaan 2, Brussels, 1050, Belgium

3 National Food Institute, Technical University of Denmark, Moerkhoj Bygade 19, Soeborg 2860, Denmark

4 Department of Systems Biology, Technical University of Denmark, Lyngby, 2800, Denmark

5 BGI-Shenzhen, Shenzhen, 518083, China

6 Department of Biology, University of Copenhagen, Copenhagen, 2200, Denmark

7 National Institute of Nutrition and Seafood Research, Bergen, Norway

8 The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark

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BMC Genomics 2012, 13:514  doi:10.1186/1471-2164-13-514

Published: 28 September 2012



Guinea pig (Cavia porcellus) is an important model for human intestinal research. We have characterized the faecal microbiota of 60 guinea pigs using Illumina shotgun metagenomics, and used this data to compile a gene catalogue of its prevalent microbiota. Subsequently, we compared the guinea pig microbiome to existing human gut metagenome data from the MetaHIT project.


We found that the bacterial richness obtained for human samples was lower than for guinea pig samples. The intestinal microbiotas of both species were dominated by the two phyla Bacteroidetes and Firmicutes, but at genus level, the majority of identified genera (320 of 376) were differently abundant in the two hosts. For example, the guinea pig contained considerably more of the mucin-degrading Akkermansia, as well as of the methanogenic archaea Methanobrevibacter than found in humans. Most microbiome functional categories were less abundant in guinea pigs than in humans. Exceptions included functional categories possibly reflecting dehydration/rehydration stress in the guinea pig intestine. Finally, we showed that microbiological databases have serious anthropocentric biases, which impacts model organism research.


The results lay the foundation for future gastrointestinal research applying guinea pigs as models for humans.