title: 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.
authors.affiliation: National Food Institute, Technical University of Denmark, Denmark.
authors.forename: Falk
authors.initials: F
authors.lastname: Hildebrand
authors.forename: Tine
authors.initials: T
authors.lastname: Ebersbach
authors.forename: Henrik Bjørn
authors.initials: HB
authors.lastname: Nielsen
authors.forename: Xiaoping
authors.initials: X
authors.lastname: Li
authors.forename: Si Brask
authors.initials: SB
authors.lastname: Sonne
authors.forename: Marcelo
authors.initials: M
authors.lastname: Bertalan
authors.forename: Peter
authors.initials: P
authors.lastname: Dimitrov
authors.forename: Lise
authors.initials: L
authors.lastname: Madsen
authors.forename: Junjie
authors.initials: J
authors.lastname: Qin
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.forename: Jeroen
authors.initials: J
authors.lastname: Raes
authors.forename: Karsten
authors.initials: K
authors.lastname: Kristiansen
authors.forename: Tine Rask
authors.initials: TR
authors.lastname: Licht
mesh_terms: D000818:Animals; D041963:Bacteroidetes / Q000235:genetics* / Q000302:isolation & purification; D006168:Guinea Pigs; D006801:Humans; D007422:Intestines / Q000382:microbiology*; D056186:Metagenomics / Q000379:methods*