Open Access Highly Accessed Research article

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

Additional files

Additional file 1:

Figure S1.a) Gene rarefaction curve showing that the number of new genes decreases with each sample added. b) Comparative assignment of human and guine pig samples to their respective gene catalogue (H-H, G-G) and cross species assignment fractions (G-H, H-G).

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Additional file 2:

Figure S2. Sample-wise rarefaction curves for guinea pig and human samples on a) genus and b) COG data. On these two data levels, differences in richness are significantly different on the highest rarefaction depth (3.5*106).

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Additional file 3:

Figure S3. Phylogenetic assignment of guinea pig and human metagenomic reads using Blast with an identity cutoff of 95% against bacterial database. Question marks designates reads that were not assignable to a bacterial genome.

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Additional file 4:

Table S1. Significantly different genera (q < 0.1, p < 0.05) between human and guinea pig gut microbiome. The depth taxonomic of taxonomic classification is not consistent (due to the PhymmBL algorithm) and this is marked by “?” if the phylogenetic level could not be determined with high confidence.

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Additional file 5:

Table S2. Significant functional differences (q < 0.1) between guinea pig and human gut microbiome. These were summarized in five Worksheets: COG categories, KEGG module subsubcategories, SEED categories, SEED families and MetaCyc.

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Additional file 6:

Table S3. Assembly statistics for the 8 guinea pig metagenomes, each based on samples from 7 or 8 individual animals. ‘Matched Reads’ designates the number of reads that could be matched to the non-redundant contig set. These were used for subsequent results on functional or phylogenetic characteristics.

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