title: Inter-individual differences in the gene content of human gut bacterial species.
abstract: BACKGROUND
  Gene content differences in human gut microbes can lead to inter-individual phenotypic variations such as digestive capacity. It is unclear whether gene content variation is caused by differences in microbial species composition or by the presence of different strains of the same species; the extent of gene content variation in the latter is unknown. Unlike pan-genome studies of cultivable strains, the use of metagenomic data can provide an unbiased view of structural variation of gut bacterial strains by measuring them in their natural habitats, the gut of each individual in this case, representing native boundaries between gut bacterial populations. We analyzed publicly available metagenomic data from fecal samples to characterize inter-individual variation in gut bacterial species.
  
  
  RESULTS
  A comparison of 11 abundant gut bacterial species showed that the gene content of strains from the same species differed, on average, by 13% between individuals. This number is based on gene deletions only and represents a lower limit, yet the variation is already in a similar range as observed between completely sequenced strains of cultivable species. We show that accessory genes that differ considerably between individuals can encode important functions, such as polysaccharide utilization and capsular polysaccharide synthesis loci.
  
  
  CONCLUSIONS
  Metagenomics can yield insights into gene content variation of strains in complex communities, which cannot be predicted by phylogenetic marker genes alone. The large degree of inter-individual variability in gene content implies that strain resolution must be considered in order to fully assess the functional potential of an individual's human gut microbiome.
authors.affiliation: European Molecular Biology Laboratory, Meyerhofstr. 1, 69117, Heidelberg, Germany. azhu@embl.de.
authors.forename: Ana
authors.initials: A
authors.lastname: Zhu
authors.affiliation: European Molecular Biology Laboratory, Meyerhofstr. 1, 69117, Heidelberg, Germany. sunagawa@embl.de.
authors.forename: Shinichi
authors.initials: S
authors.lastname: Sunagawa
authors.affiliation: European Molecular Biology Laboratory, Meyerhofstr. 1, 69117, Heidelberg, Germany. mende@embl.de.|Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawaii, 1950 East-West Road, Honolulu, HI, 96822, USA. mende@embl.de.
authors.forename: Daniel R
authors.initials: DR
authors.lastname: Mende
authors.affiliation: European Molecular Biology Laboratory, Meyerhofstr. 1, 69117, Heidelberg, Germany. bork@embl.de.
authors.forename: Peer
authors.initials: P
authors.lastname: Bork
mesh_terms: D002874:Chromosome Mapping; D030541:Databases, Genetic; D005243:Feces / Q000382:microbiology; D000069196:Gastrointestinal Microbiome / Q000235:genetics*; D041981:Gastrointestinal Tract / Q000382:microbiology*; D017353:Gene Deletion; D056426:Genetic Loci; D014644:Genetic Variation; D059646:Genome Size; D016680:Genome, Bacterial; D006801:Humans; D054892:Metagenome; D010802:Phylogeny; D011134:Polysaccharides / Q000378:metabolism; D012641:Selection, Genetic
chemical_list: D011134:Polysaccharides