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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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Related in: MedlinePlus

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 Table1.
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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 Table1.

Mentions: As in humans, two bacterial phyla, Bacteroidetes and Firmicutes, dominated the faecal microbiota of guinea pigs (Figure1). However the distribution of the phyla was quite different in the two hosts, as most of the less abundant phyla were more abundant in guinea pigs than in humans. Only 4 of the 26 significantly different phyla were more abundant in the human gut microbiota than in the guinea pigs (Figure2). These included the two most abundant phyla, Bacteroidetes (q = 0.00018) and Firmicutes (q = 0.02). Actinobacteria were also more abundant in humans, although this was only suggestive (P = 0.052, q = 0.062). This phylum includes the genus Bifidobacterium, that was also most abundant in humans (q = 0.000213) and believed to be important for human health [18]. A complete list of phyla with significantly different abundances in the two hosts is given in Table1. Thus, in guinea pigs most phyla were more abundant, while in humans the gut microbiota is dominated by fewer phyla. Specifically, the fraction of the total population constituted by Verrucomicrobia was five times more abundant in guinea pigs (2.0%) than in humans (0.37%). Furthermore, of the Verrucomicrobia found in guinea pigs, 83% were identified as bacteria belonging to the genus Akkermansia, while this was true only for 2% of the Verrucomicrobia in humans, thus the guinea pig microbiota contains considerably more Akkermansia than the microbiota of humans.


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)

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 Table1.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

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 Table1.
Mentions: As in humans, two bacterial phyla, Bacteroidetes and Firmicutes, dominated the faecal microbiota of guinea pigs (Figure1). However the distribution of the phyla was quite different in the two hosts, as most of the less abundant phyla were more abundant in guinea pigs than in humans. Only 4 of the 26 significantly different phyla were more abundant in the human gut microbiota than in the guinea pigs (Figure2). These included the two most abundant phyla, Bacteroidetes (q = 0.00018) and Firmicutes (q = 0.02). Actinobacteria were also more abundant in humans, although this was only suggestive (P = 0.052, q = 0.062). This phylum includes the genus Bifidobacterium, that was also most abundant in humans (q = 0.000213) and believed to be important for human health [18]. A complete list of phyla with significantly different abundances in the two hosts is given in Table1. Thus, in guinea pigs most phyla were more abundant, while in humans the gut microbiota is dominated by fewer phyla. Specifically, the fraction of the total population constituted by Verrucomicrobia was five times more abundant in guinea pigs (2.0%) than in humans (0.37%). Furthermore, of the Verrucomicrobia found in guinea pigs, 83% were identified as bacteria belonging to the genus Akkermansia, while this was true only for 2% of the Verrucomicrobia in humans, thus the guinea pig microbiota contains considerably more Akkermansia than the microbiota of humans.

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