Distribution of Genes Encoding the Trypsin-Dependent Lantibiotic Ruminococcin A among Bacteria Isolated from Human Fecal Microbiota

ABSTRACT Fourteen bacterial strains capable of producing a trypsin-dependent antimicrobial substance active against Clostridium perfringens were isolated from human fecal samples of various origins (from healthy adults and children, as well as from adults with chronic pouchitis). Identification of these strains showed that they belonged to Ruminococcus gnavus, Clostridium nexile, and Ruminococcus hansenii species or to new operational taxonomic units, all from the Clostridium coccoides phylogenetic group. In hybridization experiments with a probe specific for the structural gene encoding the trypsin-dependent lantibiotic ruminococcin A (RumA) produced by R. gnavus, seven strains gave a positive response. All of them harbored three highly conserved copies of rumA-like genes. The deduced peptide sequence was identical to or showed one amino acid difference from the hypothetical precursor of RumA. Our results indicate that the rumA-like genes have been disseminated among R. gnavus and phylogenetically related strains that can make up a significant part of the human fecal microbiota.

[1]  F. Sanger,et al.  DNA sequencing with chain-terminating inhibitors. , 1977, Proceedings of the National Academy of Sciences of the United States of America.

[2]  M. Riley,et al.  The ecological role of bacteriocins in bacterial competition. , 1999, Trends in microbiology.

[3]  A. Braude,et al.  The influence of bacteriocins on resistance to infection by gram-negative bacteria. II. Colicin action, transfer of colicinogeny, and transfer of antibiotic resistance in urinary infections. , 1968, The Journal of clinical investigation.

[4]  W. M. Vos,et al.  Comparison of lantibiotic gene clusters and encoded proteins , 1996, Antonie van Leeuwenhoek.

[5]  James R. Cole,et al.  A new version of the RDP (Ribosomal Database Project) , 1999, Nucleic Acids Res..

[6]  F. Blattner,et al.  DNA Sequencing and Analysis of the Low-Ca2+-Response Plasmid pCD1 of Yersinia pestis KIM5 , 1998, Infection and Immunity.

[7]  D. Crothers,et al.  Improved estimation of secondary structure in ribonucleic acids. , 1973, Nature: New biology.

[8]  G. Siragusa.  Production of bacteriocin inhibitory to Listeria species by Enterococcus hirae , 1992, Applied and environmental microbiology.

[9]  L. Dicks,et al.  Characterization and Cloning of the Genes Encoding Enterocin 1071A and Enterocin 1071B, Two Antimicrobial Peptides Produced by Enterococcus faecalis BFE 1071 , 2000, Applied and Environmental Microbiology.

[10]  M. Fons,et al.  Ruminococcin A, a New Lantibiotic Produced by aRuminococcus gnavus Strain Isolated from Human Feces , 2001, Applied and Environmental Microbiology.

[11]  M. Riley,et al.  Temporal changes in the frequency of colicinogeny in Escherichia coli from house mice. , 1998, Microbiology.

[12]  I. Hautefort.  Adhesion to the digestive mucosa is not sufficient for durable persistence of different Lactobacillus fermentum strains in the digestive tract of mice , 2000 .

[13]  P. A. Vandenbergh.  Lactic acid bacteria, their metabolic products and interference with microbial growth , 1993 .

[14]  J. Hillman,et al.  Colonization of the Human Oral Cavity by a Streptococcus mutans Mutant Producing Increased Bacteriocin , 1987, Journal of dental research.

[15]  E. Bergogne-Bérézin.  Microbial ecology and intestinal infections , 1989 .

[16]  J. Ferretti,et al.  Duplication of the lantibiotic structural gene in M-type 49 group A streptococcus strains producing streptococcin A-M49 , 1994, Applied and environmental microbiology.

[17]  R. Ducluzeau.  Role of experimental microbial ecology in gastroenterology , 1989 .

[18]  J. Tagg,et al.  Copyright � 1995, American Society for Microbiology Bacteriocins of Gram-Positive Bacteria , 1995 .

[19]  H. Sahl,et al.  The genetics of lantibiotic biosynthesis , 1995, BioEssays : news and reviews in molecular, cellular and developmental biology.

[20]  R. Moletta,et al.  Molecular microbial diversity of an anaerobic digestor as determined by small-subunit rDNA sequence analysis , 1997, Applied and environmental microbiology.

[21]  B L Maidak,et al.  The RDP-II (Ribosomal Database Project) , 2001, Nucleic Acids Res..

[22]  Bruce A. Roe,et al.  Complete genome sequence of an M1 strain of Streptococcus pyogenes , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[23]  S. Ehrlich,et al.  Molecular diversity and relationship within Lactococcus lactis, as revealed by randomly amplified polymorphic DNA (RAPD). , 1998, Systematic and applied microbiology.

[24]  T. Klaenhammer,et al.  Genetics of bacteriocins produced by lactic acid bacteria. , 1993, FEMS microbiology reviews.

[25]  M. Kalmokoff,et al.  Isolation and characterization of a bacteriocin (Butyrivibriocin AR10) from the ruminal anaerobe Butyrivibrio fibrisolvens AR10: evidence in support of the widespread occurrence of bacteriocin-like activity among ruminal isolates of B. fibrisolvens , 1997, Applied and environmental microbiology.

[26]  Ian Rowland,et al.  Metabolic Activities of the Gut Microflora in Relation to Cancer , 2000 .

[27]  J. Nicoli,et al.  Trypsin-dependent production of an antibacterial substance by a human Peptostreptococcus strain in gnotobiotic rats and in vitro , 1993, Applied and environmental microbiology.

[28]  M. Riley,et al.  Molecular mechanisms of bacteriocin evolution. , 1998, Annual review of genetics.

[29]  M. Fons,et al.  Trypsin Mediates Growth Phase-Dependent Transcriptional Regulation of Genes Involved in Biosynthesis of Ruminococcin A, a Lantibiotic Produced by a Ruminococcus gnavus Strain from a Human Intestinal Microbiota , 2002, Journal of bacteriology.

[30]  P. Doty,et al.  Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature. , 1962, Journal of molecular biology.

[31]  M. Kalmokoff,et al.  Evidence for Production of a New Lantibiotic (Butyrivibriocin OR79A) by the Ruminal Anaerobe Butyrivibrio fibrisolvensOR79: Characterization of the Structural Gene Encoding Butyrivibriocin OR79A , 1999, Applied and Environmental Microbiology.

[32]  G R Gibson,et al.  Dietary modulation of the human colonic microbiota: introducing the concept of prebiotics. , 1995, The Journal of nutrition.

[33]  J. Sambrook,et al.  Molecular Cloning: A Laboratory Manual , 2001 .

[34]  H. Harmsen,et al.  Analysis of the Fecal Microflora of Human Subjects Consuming a Probiotic Product Containing Lactobacillus rhamnosusDR20 , 2000, Applied and Environmental Microbiology.

[35]  J. Lipuma,et al.  Haemocin, the bacteriocin produced by Haemophilus influenzae: species distribution and role in colonization , 1990, Infection and immunity.

[36]  J. Ley,et al.  The quantitative measurement of DNA hybridization from renaturation rates. , 1970, European journal of biochemistry.

[37]  S. Salzberg,et al.  Complete Genome Sequence of a Virulent Isolate of Streptococcus pneumoniae , 2001, Science.

[38]  J. Doré,et al.  Direct Analysis of Genes Encoding 16S rRNA from Complex Communities Reveals Many Novel Molecular Species within the Human Gut , 1999, Applied and Environmental Microbiology.

[39]  N. W. Davis,et al.  Genome sequence of enterohaemorrhagic Escherichia coli O157:H7 , 2001, Nature.