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

Abstract

Background: 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.

Results: 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.

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

Figure 1

Distribution of Phyla present in humans and guinea pigs. Bacterial phyla found in the intestinal microbiota of humans (H. Sapiens) and guinea pigs (C. porcellus), by PhymmBL annotation excluding unassigned reads. The fraction marked unassigned could not be assigned to a specific phylum.

Figure 2

Most prevalent phyla. The 20 most prevalent bacterial phyla in guinea pigs (red) and humans (black). Asterisks denote significant differences in abundance, * : q-value < 0.1, ** : q-value < 0.05 and *** : q-value < 0.01. A complete list of the most abundant taxons is given in Table 1.

Figure 3

Bray-Curtis distances between samples. PCoA (Principle Coordinates Analysis) of Bray-Curtis distances between samples for (a) genus and (b) KO. A similar separation as shown for the genera was seen on all other taxonomic levels.

Figure 4

Functional categories. Normalized read counts of functional categories from a) COG categories b) KEGG subcategories and c) SEED families, respectively. Asterisks denote significant differences in abundance, * : q-value < 0.1, ** : q-value < 0.05 and *** : q-value < 0.01. COG categories are named as follows: A: RNA processing and modification, B: Chromatin Structure and dynamics, C: Energy production and conversion, D: Cell cycle control and mitosis, E: Amino Acid metabolism and transport, F: Nucleotide metabolism and transport, G: Carbohydrate metabolism and transport, H: Coenzyme metabolism, I: Lipid metabolism, J: Translation, K: Transcription, L: Replication and repair, M: Cell wall/membrane/envelop biogenesis, N: Cell motility, O: Post-translational modification, protein turnover, chaperone functions, P: Inorganic ion transport and metabolism, Q: Secondary Structure, T: Signal Transduction, U: Intracellular trafficking and secretion, Y: Nuclear structure, Z: Cytoskeleton, R: General Functional Prediction only, S: Function Unknown.