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Background  The sequences of the 16S rRNA genes extracted from fecal samples provide insights into the dynamics of fecal microflora. This potentially gives valuable etiological information for patients whose conditions have been ascribed to unknown pathogens, which cannot be accomplished using routine culture methods. We studied 33 children with diarrhea who were admitted to the Children’s Hospital in Shanxi Province during 2006.    Results  Nineteen of 33 children with diarrhea could not be etiologically diagnosed by routine culture and polymerase chain reaction methods. Eleven of 19 children with diarrhea of unknown etiology had  Streptococcus  as the most dominant fecal bacterial genus at admission. Eight of nine children whom three consecutive fecal samples were collected had  Streptococcus  as the dominant fecal bacterial genus, including three in the  Streptococcus bovis  group and three  Streptococcus  sp . , which was reduced during and after recovery. We isolated strains that were possibly from the  S. bovis  group from feces sampled at admission, which were then identified as  Streptococcus lutetiensis  from one child and  Streptococcus gallolyticus  subsp.  pasteurianus  from two children. We sequenced the genome of  S. lutetiensis  and identified five antibiotic islands, two pathogenicity islands, and five unique genomic islands. The identified virulence genes included hemolytic toxin  cylZ  of  Streptococcus agalactiae  and sortase associated with colonization of pathogenic streptococci.    Conclusions  We identified  S. lutetiensis  and  S .  gallolyticus  subsp.  pasteurianus  from children with diarrhea of unknown etiology, and found pathogenic islands and virulence genes in the genome of  S. lutetiensis.

Dynamics of fecal microbial communities in children with diarrhea of unknown etiology and genomic analysis of associated Streptococcus lutetiensis