title: A five-species transcriptome array for oral mixed-biofilm studies.
abstract: BACKGROUND
  Oral polymicrobial interactions and biofilm formation are associated with initiation and progression of caries, gingivitis, and periodontitis. Transcriptome studies of such interactions, allowing a first mechanistic insight, are hampered by current single-species array designs.
  
  
  RESULTS
  In this study we used 385 K NimbleGene™ technology for design and evaluation of an array covering the full genomes of 5 important physiological-, cariogenic-, and periodontitis-associated microorganisms (Streptococcus sanguinis, Streptococcus mutans, Fusobacterium nucleatum, Aggregatibacter actinomycetemcomitans, and Porphyromonas gingivalis). Array hybridization was done with cDNA from cultures grown for 24 h anaerobically. Single species experiments identified cross-species hybridizing array probes. These probes could be neglected in a mixed-species experimental setting without the need to exclude the whole genes from the analysis. Between 69% and almost 99% of the genomes were actively transcribed under the mono-species planktonic, monolayer, and biofilm conditions. The influence of Streptococcus mitis (not represented on the array) on S. mutans gene transcription was determined as a test for a dual-species mixed biofilm setup. Phenotypically, under the influence of S. mitis an increase in S. mutans biofilm mass and a decrease in media pH-value were noticed, thereby confirming previously published data. Employing a stringent cut-off (2-fold, p<0.05), 19 S. mutans transcripts were identified with increased abundance, and 11 with decreased abundance compared to a S. mutans mono-species biofilm. Several of these genes have previously been found differentially regulated under general and acid stress, thereby confirming the value of this array.
  
  
  CONCLUSIONS
  This new array allows transcriptome studies on multi-species oral biofilm interactions. It may become an important asset in future oral biofilm and inhibitor/therapy studies.
authors.affiliation: Institute of Medical Microbiology, Virology and Hygiene, University Hospital Rostock, Rostock, Germany.
authors.forename: Sylvio
authors.initials: S
authors.lastname: Redanz
authors.forename: Kerstin
authors.initials: K
authors.lastname: Standar
authors.forename: Andreas
authors.initials: A
authors.lastname: Podbielski
authors.forename: Bernd
authors.initials: B
authors.lastname: Kreikemeyer
mesh_terms: D018441:Biofilms; D015342:DNA Probes / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial; D005798:Genes, Bacterial / Q000235:genetics; D006801:Humans; D009055:Mouth / Q000382:microbiology*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D060888:Real-Time Polymerase Chain Reaction; D015203:Reproducibility of Results; D013045:Species Specificity; D034361:Streptococcus mitis / Q000235:genetics; D013295:Streptococcus mutans / Q000235:genetics; D059467:Transcriptome / Q000235:genetics*
chemical_list: D015342:DNA Probes; D012333:RNA, Messenger