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

Hildebrand F, Ebersbach T, Nielsen HB, Li X, Sonne SB, Bertalan M, Dimitrov P, Madsen L, Qin J, Wang J, Raes J, Kristiansen K, Licht TR - BMC Genomics (2012)

Bottom Line: 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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: National Food Institute, Technical University of Denmark, Denmark.

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.

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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.
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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.

Mentions: The observed differences on genus level are summarized in a PCoA plot (Figure3`). A similar clear separation between human and guinea pig samples was observed on all phylogenetic levels (data not shown). In total we found 320 of 376 genera to be significantly different between human and guinea pig microbiota (Additional file 4: Table S1). Of these, 225 were more abundant in guinea pig, including genera such as Methanobrevibacter, Desulfovibrio, while some of the genera known to be important for butyrate formation in the human gut [19] including e.g. Roseburia and Faecalibacterium were less abundant in guinea pigs. Additionally, many of the genera known to contain human pathogens (Salmonella, Klebsiella, Treponema, Yersinia, Haemophilus) were also overrepresented in guinea pigs, although low in abundance. This was true also for Listeria, mainly due to an overrepresentation of L. innocua (data not shown).


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

Hildebrand F, Ebersbach T, Nielsen HB, Li X, Sonne SB, Bertalan M, Dimitrov P, Madsen L, Qin J, Wang J, Raes J, Kristiansen K, Licht TR - BMC Genomics (2012)

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.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3472315&req=5

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.
Mentions: The observed differences on genus level are summarized in a PCoA plot (Figure3`). A similar clear separation between human and guinea pig samples was observed on all phylogenetic levels (data not shown). In total we found 320 of 376 genera to be significantly different between human and guinea pig microbiota (Additional file 4: Table S1). Of these, 225 were more abundant in guinea pig, including genera such as Methanobrevibacter, Desulfovibrio, while some of the genera known to be important for butyrate formation in the human gut [19] including e.g. Roseburia and Faecalibacterium were less abundant in guinea pigs. Additionally, many of the genera known to contain human pathogens (Salmonella, Klebsiella, Treponema, Yersinia, Haemophilus) were also overrepresented in guinea pigs, although low in abundance. This was true also for Listeria, mainly due to an overrepresentation of L. innocua (data not shown).

Bottom Line: 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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: National Food Institute, Technical University of Denmark, Denmark.

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.

Show MeSH
Related in: MedlinePlus