The data presented here represent the first metagenomic characterization of the faecal microbiota of guinea pigs. The gene catalogue contains all of the prevalent gut microbial genes present in these animals.
It was a logical choice to compare our samples to the human gut microbiota, because this reference data set has been processed with the same sequencing and bioinformatic technologies developed during the European MetaHIT project (http://www.metahit.eu), which has given rise to several publications on the human metagenome [3, 4]. The guinea pig microbiota data presented in this study were thus obtained and processed in a way making them comparable to the human data analysed in the MetaHIT project. However, it should be noted that differences between methodologies for DNA extraction from faecal samples exist between the two studies.
The guinea pig and human gut microbiotas differed substantially on genus and lower taxonomic levels. Human samples as well as guinea pig samples had a fair amount of read matches to reference genes (66.7% and 60.2%, respectively) within the databases specifically created for each environment, however the fraction of assembled reads matching a cross-species database were minor at best (9.2% and 6.8% respectively, Additional file 1: Figure S1 b). This came as a surprise to us, as it shows that the range of strains within the human and guinea pig GI system is fairly restricted and specific to each of these two species. Given that the human samples were obtained from a heterogeneous population spanning two countries (Spain and Denmark), this selectivity of the gut environment across a wide geological range for specific commensal strains is notable. This was further confirmed on species level where we were able to assign 42% of human gut microbiota reads to a reference genome database, but could only assign 10% of guinea pig gut microbiota to genomes within this database. In fact, the human gut microbiota samples did not contain a single sample with as many unassigned reads as any guinea pig sample. While we expected a certain bias in our taxonomic reference database towards gut bacteria within human hosts due to the efforts of the Human Microbiome Project (HMP, http://www.hmpdacc.org/) and the targeted genome sequencing of several typical gut microbes from humans that were included in our reference database, we were surprised by a significant bias also on all functional levels. Not only were we unable to assign the same fraction of assembled guinea pig microbiome reads to KO’s, but these KO’s were more often also not assigned by general purpose functional pathway databases (KEGG, metacyc, SEED). This was also true for eggNOG’s and derived COG categories.
We speculate that the reason for the slightly lower proportion of guinea pig KO’s belonging to defined higher functional categories could be that the guinea pig gut harbors more bacteria that are not well described, than is the case for the human gut. Additionally, a higher amount of environmental bacteria (e.g. from soil) on the feed of the animals may cause a transient presence of soil bacteria encoding functions that are not essential to the gut microbial ecosystem, although this should not bias the general functions databases used. It thus appears that even the gut microbiome of a well-researched mammal living under human observation contains a wealth of undiscovered functionalities.
Herbivorous species (to which guinea pigs belong) typically harbour more phyla and have a higher richness on genus level than omnivores such as humans .
Consistently, on most taxonomic and functional levels the observed richness was higher in guinea pigs than in humans, while the diversity of human samples exceeded the diversity of guinea pig samples. Similarly, the lower diversity & higher richness in the KO and COG annotations points to a less specialized gut microbiota with redundant functionality present in many copies throughout the guinea pig microbiota. The guinea pig microbiota is probably more specialized in degrading a more homogenous type of food than the microbiota of the omnivore human host, thus a lower diversity is needed – e.g. the human microbiome may be more diverse because it meets more diverse types of nutrients. When looking at only the two highest level KEGG functional categories, we found that metabolism, but not information processing was overrepresented in the human samples, supporting that the two types of microbiotas differ with respect to the type of materials they metabolize.
Although most higher functional categories were most abundant in human samples, functions related to cell wall and DNA metabolism as well as carbohydrate biosynthesis (Figure4) are among the few functional categories significantly more abundant in guinea pigs. This might be because the fecal pellets from guinea pigs are much drier than human feces, which will likely require the bacteria to be more robust in sustaining continuous dehydration and rehydration, and thus to e.g. be able to re-synthesize bacterial cell wall components and polysaccharide structures of the outer membrane . Since guinea pigs practice coprophagy (re-ingestion of feces), the gut bacteria will have undergone repetitive cycles of dehydration/rehydration selecting for these traits, as well as for bacteria that can sustain the hostile environment of the stomach and digestive system. However, it should be noted that the SEED family containing traits directly related to desiccation stress was not overrepresented in guinea pigs.
We would have expected an increase in fermentation-related traits in the guinea pig hosts due to the plant polysaccharides in the diet and the increased abundance of H2 accepting bacteria (Methanobrevibacter, Desulfovibrio) in the guinea pig faeces, however in both MetaCyc database and SEED database, “fermentation” was significantly lower in guinea pigs. Given that guinea pigs as herbivorous hindgut fermenters extracts a significant part of their nutritional energy from coecal fermentation of otherwise indigestible carbohydrates, we speculate that this observation may be attributed to a bias within the databases towards omnivore/human fermentation pathways.
While the two most abundant phyla Firmicutes and Bacteriodetes constituted a relatively large part of the microbiota in humans compared to guinea pigs, the majority of other phyla were more abundant in guinea pigs. Specifically, guinea pig faecal samples contained a much higher fraction of bacteria belonging to the phylum Verrumicrobia, most of which (83%) were seen to be represented by Akkermansia. This genus is known to contain the species Akkermansia muciniphilia, which grows preferably on mucin, while only very few other carbohydrates supports its growth . Therefore, Akkermansia muciniphila has been suggested to be useful as a biomarker for mucin degradation, and the high amount of Akkermansia present in guinea pig faeces might indicate a high turnover of mucins in these animals, perhaps partly resulting from the ingestion of fecal pellets enveloped in mucus gel. If the mucus coating the epithelium is more abundant in guinea pigs, this is relevant in relation to the widespread use of guinea pigs as models for intestinal Listeria infections [26, 27], since the integrity and thickness of the intestinal mucus layer is known to affect the susceptibility to intestinal infection [28–30]. Additionally, it may be relevant for the design of such studies that Listeria were significantly more abundant in guinea pigs than in human samples (P = 1.4*10-7) due to an overrepresentation of the non-pathogenic L. innocua, probably originating from the commercially available feed given to these animals , which was primarily based on plant material likely to be containing L. innocua.
This study shows a substantial overlap in phyla inhabiting the human and guinea pig gut. However, on lower phylogenetic levels these environments become less similar. Similarly, the metabolic functions present in the guinea pig samples were different from those in the human samples, suggesting that food breakdown and nutrient extraction is fundamentally different between these two gut ecosystems.