Open Access Highly Accessed Research article

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

Dong Jin1, Chen Chen1, Lianqing Li2, Shan Lu1, Zhenjun Li1, Zhemin Zhou3, Huaiqi Jing1, Yanmei Xu1, Pengcheng Du1, Haiyin Wang1, Yanwen Xiong1, Han Zheng1, Xuemei Bai1, Hui Sun1, Lei Wang3, Changyun Ye1, Marcelo Gottschalk4 and Jianguo Xu1*

Author Affiliations

1 State Key Laboratory for Infectious Disease Prevention and Control, and National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China

2 Molecular Microbiology Laboratory, ShanXi Children’s Hospital, TaiYuan, 030013, China

3 College of Life Sciences, Nankai University, Tianjin, China

4 Groupe de Recherche sur les Maladies Infectieuses du Porc, Faculté de médecine vétérinaire, Université de Montréal, Québec, Canada

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BMC Microbiology 2013, 13:141  doi:10.1186/1471-2180-13-141

Published: 19 June 2013



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.


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.


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.

Microbial communities; 16S rRNA gene analysis; Streptococcus lutetiensis; Genome analysis; Pathogenic island