title: Comparative genomics analysis of Streptococcus isolates from the human small intestine reveals their adaptation to a highly dynamic ecosystem.
abstract: The human small-intestinal microbiota is characterised by relatively large and dynamic Streptococcus populations. In this study, genome sequences of small-intestinal streptococci from S. mitis, S. bovis, and S. salivarius species-groups were determined and compared with those from 58 Streptococcus strains in public databases. The Streptococcus pangenome consists of 12,403 orthologous groups of which 574 are shared among all sequenced streptococci and are defined as the Streptococcus core genome. Genome mining of the small-intestinal streptococci focused on functions playing an important role in the interaction of these streptococci in the small-intestinal ecosystem, including natural competence and nutrient-transport and metabolism. Analysis of the small-intestinal Streptococcus genomes predicts a high capacity to synthesize amino acids and various vitamins as well as substantial divergence in their carbohydrate transport and metabolic capacities, which is in agreement with observed physiological differences between these Streptococcus strains. Gene-specific PCR-strategies enabled evaluation of conservation of Streptococcus populations in intestinal samples from different human individuals, revealing that the S. salivarius strains were frequently detected in the small-intestine microbiota, supporting the representative value of the genomes provided in this study. Finally, the Streptococcus genomes allow prediction of the effect of dietary substances on Streptococcus population dynamics in the human small-intestine.
authors.affiliation: Top Institute Food and Nutrition (TIFN), Wageningen, The Netherlands ; Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands.
authors.forename: Bartholomeus
authors.initials: B
authors.lastname: Van den Bogert
authors.affiliation: Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, The Netherlands ; NIZO Food Research B.V., Ede, The Netherlands.
authors.forename: Jos
authors.initials: J
authors.lastname: Boekhorst
authors.affiliation: Top Institute Food and Nutrition (TIFN), Wageningen, The Netherlands ; Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands.
authors.forename: Ruth
authors.initials: R
authors.lastname: Herrmann
authors.affiliation: Top Institute Food and Nutrition (TIFN), Wageningen, The Netherlands ; Laboratory of Food Microbiology, Wageningen University, Wageningen, The Netherlands.
authors.forename: Eddy J
authors.initials: EJ
authors.lastname: Smid
authors.affiliation: Top Institute Food and Nutrition (TIFN), Wageningen, The Netherlands ; Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands.
authors.forename: Erwin G
authors.initials: EG
authors.lastname: Zoetendal
authors.affiliation: Top Institute Food and Nutrition (TIFN), Wageningen, The Netherlands ; Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands ; NIZO Food Research B.V., Ede, The Netherlands ; Host-Microbe Interactomics Group, Wageningen University, Wageningen, The Netherlands.
authors.forename: Michiel
authors.initials: M
authors.lastname: Kleerebezem
mesh_terms: D000222:Adaptation, Physiological; D000596:Amino Acids / Q000378:metabolism; D050260:Carbohydrate Metabolism; D002244:Carbon / Q000378:metabolism; D059647:Gene-Environment Interaction; D016680:Genome, Bacterial; D006801:Humans; D007421:Intestine, Small / Q000382:microbiology* / Q000502:physiology*; D056186:Metagenomics; D010802:Phylogeny; D019289:Pyruvic Acid / Q000378:metabolism; D017422:Sequence Analysis, DNA; D013291:Streptococcus / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification / Q000378:metabolism; D014815:Vitamins / Q000378:metabolism
chemical_list: D000596:Amino Acids; D014815:Vitamins; D002244:Carbon; D019289:Pyruvic Acid