BACKGROUND
periodontitis is a chronic inflammatory disorder mediated by host and bacteria interactions and manifested by damage to the periodontal tissues that may progress to tooth loss.
the host inflammatory responses stimulated by periodontal pathogens intend to eliminate the invaded bacteria and attribute to the destruction of tooth supporting tissues and tooth loss  <cit> .
moreover, the local periodontal environment may change the gene expression profile of periodontal pathogens .
to a certain extent, the variation of bacterial gene expression may alter the pathogenic ability of bacteria.
porphyromonas gingivalis  is an opportunistic pathogen of the oral mucosa and a prominent member of the oral biofilms.
it is well known that p.gingivalis is implicated in the onset and progression of chronic periodontitis.
p.gingivalis can induce immune cells to secrete cytokines when they invade into hosts.
these cytokines are present in inflamed gingiva and aggravate the destruction of oral gingival tissues and alveolar bone  <cit> .
in the meantime, the expression of p.gingivalis genes varies under different conditions, such as iron or hemin  <cit> , polyphosphate  <cit> , rhein  <cit> .
p.gingivalis may up-regulate or downregulate gene expression to adapt environment and survive  <cit> .
the development of chronic periodontitis was not only due to periodontal pathogens, but also the interaction between periodontal pathogens and host.
most researches focus on periodontal pathogens acting on hosts, but ignore the action of host on p.gingivalis.
actually, the changes in p.gingivalis gene expression may affect the progression of chronic periodontitis.
in the present study, the differential gene expression in p.gingivalis w <dig> inoculated in rat oral cavity and wild strain was analyzed.
methods
ethical statement
all rats were manipulated in accordance with animal research reporting in vivo experiments  guidelines.
the experimental protocols were approved by the ethical committee of china medical university.
bacteria and animals
this study was carried out with 6-week-old spf rats  provided by department of experimental animals, china medical university, and maintained in a temperature-controlled room .
p.gingivalis w <dig> was obtained from the american type culture collection  and grown anaerobically  in enriched brain-heart infusion  broth containing 5 % fiber-free sheep blood, 1 % vitamin k and hemin, at 37 °c.
p.gingivalis w <dig> inoculation
<dig> rats were given azithromycin  ad libitum for 4 days to reduce the original oral flora.
this was followed by a 7-day antibiotic-free period.
<dig> rats were then orally challenged with p. gingivalis w <dig>  by gavage into the esophagus and oral cavity five times every other day  <cit> .
the other  <dig> rats  were only challenged with bhi broth.
all  <dig> rats received steel wire ligature in cervical part in two sides of first molars and an 8-week high sugar feeding.
alveolar bone loss analysis
horizontal bone loss was assessed morphometrically by measuring the distance between the cement − enamel junction and the alveolar bone crest of the first, the second and the third molar.
the alveolar bone destruction was detected by morphological and macroscopic observation, radiographic  and stereomicroscope  fitted with a digimed viewer imaging measurement system evaluation at  <dig> sites per molars.
alveolar bone loss of every molar was presented in the figures as mean ± sd.
independent samples t-test was used to calculate the significance among the groups .
p-value <  <dig>  was considered statistically significant.
isolating culture and acquiring plaque
after p.gingivalis w <dig> inoculation in rat oral cavity for 8 weeks, plaques were acquired from periodontal pockets of first molar using toothpicks and put into  <dig>  ml transfer tube.
the plaques were dispersed by oscillator.
100 μl ten-fold serial dilutions were inoculated on bhi culture medium anaerobically at 37 °c for 5– <dig> days.
the morphology of colonies was observed in primary cultures.
p.gingivalisw <dig> colonies were identified by their black pigmentation, gram staining and pcr.
the single clone was purified in bhi medium for subcultures in order to detect the differences in the gene of p.gingivalisw <dig>
microarray hybridization
<dig> samples were picked up from wild strain p.gingivalis w <dig> and inoculated p.gingivalis w <dig>  respectively.
the total rna was extracted and labeled with klenow, and then hybridism with p.gingivalis w <dig> chip.
the commercial genechip p.gingivalis w <dig> genome array used here was provided by capitalbio corporation , a service provider authorized by roche nimblegen .
array hybridization, washing, scanning and data analysis were performed at the capitalbio corporation, beijing, china and carried out according to the nimblegen’s expression user’s guide.
real-time quantitative pcr
to independently confirm the expression data generated by the microarray experiments, we performed real-time quantitative pcr analyses for  <dig> genes differentially regulated.
total rna was extracted.
quality and concentration of the rna were determined by measuring its absorbance at  <dig> and 280 nm using a microplate reader .
total bacterial rna was subsequently reverse-transcribed using the m-mlv rtase cdna synthesis kit  following the manufacturer’s protocol.
real-time quantitative pcr analysis was conducted in an abi prism  <dig> sequence detection system  in combination with the sybr® premix ex taqtm ii pcr master mix reagents kit , as recommended by the manufacturer of the wall clear pcr strip tubes .
the primers for the real-time quantitative pcr analysis were designed using primer <dig>  .
p.gingivalis w <dig> 16 s dna was used as the internal reference.
real-time quantitative pcr was performed three times for each sample.
the data were analyzed according to relative gene expression by the 2-ΔΔct method.table  <dig> sequences for real-time pcr
statistics
significantly differentially expressed genes between the inoculated periodontitis and wild strains were identified using two class unpaired method in the significant analysis of microarray software .
genes were determined to be significantly differentially expressed with a selection threshold of false discovery rate, fdr < 5 % and fold change >  <dig>  in the sam output result.
RESULTS
pathogenic effects of p.gingivalis w <dig> on rat oral cavity
after p.gingivalis w <dig> inoculation in rat oral cavity for 8 weeks, the gingival tissues were inflammatory and bleeding .
severe alveolar bone losses were found in rats with p.gingivalis w <dig> inoculation .
the distance between cementoenamel junction and alveolar bone crest  was measured at proximal, middle and distal sites of buccal and palatal per molar, respectively.
in first molars, second molars, third molars, the distances were significantly increased, which were  <dig>  ±  <dig>  μm,  <dig>  ±  <dig>  μm,  <dig>  ±  <dig>  μm, compared with normal rats, which were  <dig>  ±  <dig>  μm,  <dig>  ±  <dig>  μm,  <dig>  ±  <dig>  μm.fig.
<dig> pathogenic effects of p.gingivalis w <dig> on rat oral cavity.
the gingival tissues were inflammatory and bleeding after p.gingivalis w <dig> inoculation in rat oral cavity for 8 weeks.
severe alveolar bone losses were found in rats with p.gingivalis w <dig> inoculation.
left: control groups.
right: rats inoculated with p.gingivalis w <dig> intraorally for 8 weeks
identification of the inoculated p.gingivalis w <dig> in rat with periodontitis
suspicious gram-negative bacilli were taken from plaque culture.
after pure subculture, gram staining and polymerase chain reaction  proved that the bacteria were p.gingivalis w <dig>  pcr fragment length of the product was 857 bp, as shown in fig.
<dig> fig.
<dig> isolation and identification of inoculated p.gingivalis w <dig>   some suspicious black colonies were found from plaque mixture.
suspious black colonies were pure cultured.
gram staining proved the pure culture as gram-negative brevibacterium .
agarose gel electrophoresis proved that pcr fragment length was 857 bp.
<dig> and 2: wild type p.gingivalis w83; 3–8: three inoculated p.gingivalis w <dig> samples for microarray analysis
genes upregulated in the inoculated p.gingivalis w83
we determined the expression of  <dig> genes by microarray analysis in p.gingivalis wild strain and p.gingivalis inoculated in oral cavity.
the complete list of gene expression values has been deposited in ncbi’s gene expression omnibus .
the detection showed that  <dig> genes were up-regulated in the inoculated p.gingivalis w <dig> compared with wild strain  .
in these upregulated genes,  <dig> expressed hypothetical proteins.
among other  <dig> genes, pg <dig>  pg <dig>  pg <dig>  pg <dig> and pg <dig> function as transposons.
pg <dig>  pg <dig>  pg <dig> and pg <dig> encode ispg <dig> transposases; and pg <dig> encodes an int protein as a mobilizable transposon.table  <dig> genes upregulated in the inoculated p.gingivalis w83
αlocus number, identification and functional classification according to jcvi p.gingivalis genome database
fig.
<dig> genes analyzed by microarray in the inoculated p.gingivalis w <dig>  fluorescence signal strength values in x axes and y axes represent control groups and experimental groups, respectively.
each data point was behalf of a gene chip hybridization signal.
red marking data points were t/c value ≥ <dig>  representing upregulated genes, and green marking data points were t/c value ≤ <dig> , representing downregulated genes
genes downregulated in the inoculated p.gingivalis w83
compared with wild strain,  <dig> genes were down-regulated in the inoculated strain  .
among these genes, pg <dig>  pg <dig>  pg <dig>  pg <dig> and pg <dig> encode abc transporters.
products of pg <dig>  pg <dig> and pg <dig> are putative permease proteins; and products of pg <dig> and pg <dig> are atp-binding proteins.
in addition, pg <dig> and pg <dig> also encode transport and binding proteins.
all these proteins are involved in cell transmembrane transportation.
some downregulated genes encode proteins related to protein and nucleic acid metabolism, including pg <dig>  pg <dig>  pg <dig> and pg <dig>  products of other genes are related to energy metabolism , cell division ,bacterial pathogenicity , and so on.table  <dig> genes downregulated in the inoculated p.gingivalis w83
αlocus number, identification and functional classification according to jcvi p.gingivalis genome database
microarray result confirmation by real-time quantitative pcr
among the upregulated and downregulated genes, we picked up  <dig> genes to detect the expression by real-time quantitative pcr.
consistent with microarray hybridization, real-time quantitative pcr detection showed similar expression trends in these genes .table  <dig> microarray result confirmation by real-time pcr
discussion
chronic periodontitis is initiated by periodontal pathogens, including p.gingivalis.
our study showed that p.gingivalis w <dig> induced rat gingival tissue inflammation, and alveolar bone loss, which is the key feature of periodontitis.
therefore, our study demonstrates that p.gingivalis w <dig> has pathogenic effects on rat oral cavity.
after inoculation in rat oral cavity for 8 weeks, p.gingivalis w <dig> were isolated, and analyzed by microarray.
in the detected  <dig> genes,  <dig> genes were upregulated, whereas  <dig> genes were downregulated, indicating that the local periodontal environment can change the gene expression profile of p.gingivalis w <dig>
in the  <dig> upregulated genes,  <dig> expressed hypothetical proteins.
among other  <dig> genes, pg <dig>  pg <dig>  pg <dig>  pg <dig> and pg <dig> are in the same class in jcvi cell function classification.
they all function as mobile extrachromosomal factor: transposon.
transposon is a removable genome dna sequence, which can “jump” in genome from one location to another through the process of cutting and integration.
transposition is generally known to be triggered by cellular stress , therefore upregulation of these transposons suggests that p.gingivalis w <dig> inoculated in rat oral cavity may adapt local environment for its own survival, which is consistent with some other studies  <cit> .
in the  <dig> downregulated genes,  <dig> genes encode transport and binding proteins.
all these proteins are involved in cell transmembrane transportation.
they can transport many substrates, such as metabolites, ion, sugar, amino acids, lipids, cholesterol and drugs  <cit> .
pg <dig> encodes a tonb dependent receptor protein, responsible for iron transmembrane transportation  <cit> .
as iron ion is necessary for the breeding and spreading of p.gingivalis w <dig>  downregulation of pg <dig> suggests the subdued iron transferring and proliferation of p.gingivalis w <dig>  there are  <dig> downregulated genes encoding proteins related to nucleic acid and protein metabolism.
pg <dig> encodes a nucleotide reductase, which is related to purine, pyrimidine, nucleotide and dna metabolism, and plays a regulating role in cell proliferation.
products of pg <dig> and pg <dig> are related to the metabolism of dna, such as copy, restructuring and repair.
therefore, downregulation of these genes means that the proliferation of inoculated p.gingivalis w <dig> is in certain obstacles.
pg <dig> encodes a putative glycogen synthase, involved in biosynthesis and degradation of polysaccharides.
downregulation of pg <dig> suggests a disturbed energy metabolism.
pg <dig> encodes a spooj protein related to cell division, and pg <dig> encodes hemagglutinin hagc related to pathogenicity of p.gingivalis w <dig>  in addition, pg <dig> encodes a crispr protein related to cas <dig> family.
crispr/cas system can protect bacteria against the encroachment by phage, and resist other chromosome genetic material and prevent from the expression of their genes .
downregulation of pg <dig> suggests a decrease in the defense capability of p.gingivalis w <dig>
it should be noted that gene expression observed in this study was in mrna level.
as we have known, alterations in mrna expression are not always consistent with those in protein expression.
therefore, observations in protein level of gene expression will be more convincing.
however, it is impracticable to analyze the protein expression of all  <dig> genes with rna expression alteration.
moreover, some products of these genes are still hypothetical proteins.
because the inoculated p.gingivalis was cultured outside the rat oral cavity for some days before rna extraction, the rna samples cannot exactly reflect the changes in gene expression after inoculation, although the results can still indicate which genes are upregulated or downregulated.
CONCLUSIONS
our study shows that p.gingivalis w <dig> has pathogenic effects on host, and local inflammatory oral environment alters the gene expression profile of p.gingivalis w <dig>  products of these upregulated and downregulated genes are mainly related to transposon functions, cell transmembrane transportation, protein and nucleic acid metabolism, energy metabolism, cell division and bacterial pathogenicity.
these changes may lead to decreased proliferation and pathogenicity of p.gingivalis w <dig>  and favor themselves to adapt local environment for survival.
abbreviations
p.gingivalisporphyromonas gingivalis
pcrpolymerase chain reaction
spfspecific pathogen free
atccamerican type culture collection
cfucolony forming unit
cejcementoenamel junction
abcalveolar bone crest
crisprclustered regularly interspaced short palindromic repeats
cascrispr associated genes
competing interests
the authors declare that they have no competing interests.
authors’ contributions
jz carried out microarray analysis,analyzed and interpreted the data, and drafted the manuscript.
ql performed p.gingivalis w <dig> culture and inoculation.
clp performed real-time pcr analysis.
jcl and hyw were responsible for the isolation and identification of the strain.
lst performed alveolar bone loss analysis.
ypp designed the study and drafted the manuscript.
all authors read and approved the final manuscript.
this work was supported by national natural science foundation of china .

 periodontitis is a chronic inflammatory disorder mediated by host and bacteria interactions and manifested by damage to the periodontal tissues that may progress to tooth loss. the host inflammatory responses stimulated by periodontal pathogens intend to eliminate the invaded bacteria and attribute to the destruction of tooth supporting tissues and tooth loss. moreover, the local periodontal environment may change the gene expression profile of periodontal pathogens. to a certain extent, the variation of bacterial gene expression may alter the pathogenic ability of bacteria. porphyromonas gingivalis is an opportunistic pathogen of the oral mucosa and a prominent member of the oral biofilms. it is well known that p.gingivalis is implicated in the onset and progression of chronic periodontitis. p.gingivalis can induce immune cells to secrete cytokines when they invade into hosts. these cytokines are present in inflamed gingiva and aggravate the destruction of oral gingival tissues and alveolar bone. in the meantime, the expression of p.gingivalis genes varies under different conditions, such as iron or hemin, polyphosphate, rhein. p.gingivalis may up-regulate or downregulate gene expression to adapt environment and survive. the development of chronic periodontitis was not only due to periodontal pathogens, but also the interaction between periodontal pathogens and host. most researches focus on periodontal pathogens acting on hosts, but ignore the action of host on p.gingivalis. actually, the changes in p.gingivalis gene expression may affect the progression of chronic periodontitis. in the present study, the differential gene expression in p.gingivalis w inoculated in rat oral cavity and wild strain was analyzed. methods ethical statement all rats were manipulated in accordance with animal research reporting in vivo experiments guidelines. the experimental protocols were approved by the ethical committee of china medical university. bacteria and animals this study was carried out with 6-week-old spf rats provided by department of experimental animals, china medical university, and maintained in a temperature-controlled room. p.gingivalis w was obtained from the american type culture collection and grown anaerobically in enriched brain-heart infusion broth containing 5 % fiber-free sheep blood, 1 % vitamin k and hemin, at 37 °c. p.gingivalis w inoculation rats were given azithromycin ad libitum for 4 days to reduce the original oral flora. this was followed by a 7-day antibiotic-free period. rats were then orally challenged with p. gingivalis w by gavage into the esophagus and oral cavity five times every other day. the other rats were only challenged with bhi broth. all rats received steel wire ligature in cervical part in two sides of first molars and an 8-week high sugar feeding. alveolar bone loss analysis horizontal bone loss was assessed morphometrically by measuring the distance between the cement − enamel junction and the alveolar bone crest of the first, the second and the third molar. the alveolar bone destruction was detected by morphological and macroscopic observation, radiographic and stereomicroscope fitted with a digimed viewer imaging measurement system evaluation at sites per molars. alveolar bone loss of every molar was presented in the figures as mean ± sd. independent samples t-test was used to calculate the significance among the groups. p-value <  was considered statistically significant. isolating culture and acquiring plaque after p.gingivalis w inoculation in rat oral cavity for 8 weeks, plaques were acquired from periodontal pockets of first molar using toothpicks and put into  ml transfer tube. the plaques were dispersed by oscillator. 100 μl ten-fold serial dilutions were inoculated on bhi culture medium anaerobically at 37 °c for 5– days. the morphology of colonies was observed in primary cultures. p.gingivalisw colonies were identified by their black pigmentation, gram staining and pcr. the single clone was purified in bhi medium for subcultures in order to detect the differences in the gene of p.gingivalisw microarray hybridization samples were picked up from wild strain p.gingivalis w and inoculated p.gingivalis w respectively. the total rna was extracted and labeled with klenow, and then hybridism with p.gingivalis w chip. the commercial genechip p.gingivalis w genome array used here was provided by capitalbio corporation, a service provider authorized by roche nimblegen. array hybridization, washing, scanning and data analysis were performed at the capitalbio corporation, beijing, china and carried out according to the nimblegen’s expression user’s guide. real-time quantitative pcr to independently confirm the expression data generated by the microarray experiments, we performed real-time quantitative pcr analyses for genes differentially regulated. total rna was extracted. quality and concentration of the rna were determined by measuring its absorbance at and 280 nm using a microplate reader. total bacterial rna was subsequently reverse-transcribed using the m-mlv rtase cdna synthesis kit following the manufacturer’s protocol. real-time quantitative pcr analysis was conducted in an abi prism sequence detection system in combination with the sybr® premix ex taqtm ii pcr master mix reagents kit, as recommended by the manufacturer of the wall clear pcr strip tubes. the primers for the real-time quantitative pcr analysis were designed using primer. p.gingivalis w 16 s dna was used as the internal reference. real-time quantitative pcr was performed three times for each sample. the data were analyzed according to relative gene expression by the 2-ΔΔct method.table sequences for real-time pcr statistics significantly differentially expressed genes between the inoculated periodontitis and wild strains were identified using two class unpaired method in the significant analysis of microarray software. genes were determined to be significantly differentially expressed with a selection threshold of false discovery rate, fdr < 5 % and fold change >  in the sam output result.  pathogenic effects of p.gingivalis w on rat oral cavity after p.gingivalis w inoculation in rat oral cavity for 8 weeks, the gingival tissues were inflammatory and bleeding. severe alveolar bone losses were found in rats with p.gingivalis w inoculation. the distance between cementoenamel junction and alveolar bone crest was measured at proximal, middle and distal sites of buccal and palatal per molar, respectively. in first molars, second molars, third molars, the distances were significantly increased, which were  ±   μm,  ±   μm,  ±   μm, compared with normal rats, which were  ±   μm,  ±   μm,  ±   μm.fig. pathogenic effects of p.gingivalis w on rat oral cavity. the gingival tissues were inflammatory and bleeding after p.gingivalis w inoculation in rat oral cavity for 8 weeks. severe alveolar bone losses were found in rats with p.gingivalis w inoculation. left: control groups. right: rats inoculated with p.gingivalis w intraorally for 8 weeks identification of the inoculated p.gingivalis w in rat with periodontitis suspicious gram-negative bacilli were taken from plaque culture. after pure subculture, gram staining and polymerase chain reaction proved that the bacteria were p.gingivalis w pcr fragment length of the product was 857 bp, as shown in fig.  fig. isolation and identification of inoculated p.gingivalis w some suspicious black colonies were found from plaque mixture. suspious black colonies were pure cultured. gram staining proved the pure culture as gram-negative brevibacterium. agarose gel electrophoresis proved that pcr fragment length was 857 bp. and 2: wild type p.gingivalis w83; 3–8: three inoculated p.gingivalis w samples for microarray analysis genes upregulated in the inoculated p.gingivalis w83 we determined the expression of genes by microarray analysis in p.gingivalis wild strain and p.gingivalis inoculated in oral cavity. the complete list of gene expression values has been deposited in ncbi’s gene expression omnibus. the detection showed that genes were up-regulated in the inoculated p.gingivalis w compared with wild strain. in these upregulated genes, expressed hypothetical proteins. among other genes, pg pg pg pg and pg function as transposons. pg pg pg and pg encode ispg transposases; and pg encodes an int protein as a mobilizable transposon.table genes upregulated in the inoculated p.gingivalis w83 αlocus number, identification and functional classification according to jcvi p.gingivalis genome database fig. genes analyzed by microarray in the inoculated p.gingivalis w fluorescence signal strength values in x axes and y axes represent control groups and experimental groups, respectively. each data point was behalf of a gene chip hybridization signal. red marking data points were t/c value ≥ representing upregulated genes, and green marking data points were t/c value ≤, representing downregulated genes genes downregulated in the inoculated p.gingivalis w83 compared with wild strain, genes were down-regulated in the inoculated strain. among these genes, pg pg pg pg and pg encode abc transporters. products of pg pg and pg are putative permease proteins; and products of pg and pg are atp-binding proteins. in addition, pg and pg also encode transport and binding proteins. all these proteins are involved in cell transmembrane transportation. some downregulated genes encode proteins related to protein and nucleic acid metabolism, including pg pg pg and pg products of other genes are related to energy metabolism, cell division,bacterial pathogenicity, and so on.table genes downregulated in the inoculated p.gingivalis w83 αlocus number, identification and functional classification according to jcvi p.gingivalis genome database microarray result confirmation by real-time quantitative pcr among the upregulated and downregulated genes, we picked up genes to detect the expression by real-time quantitative pcr. consistent with microarray hybridization, real-time quantitative pcr detection showed similar expression trends in these genes.table microarray result confirmation by real-time pcr discussion chronic periodontitis is initiated by periodontal pathogens, including p.gingivalis. our study showed that p.gingivalis w induced rat gingival tissue inflammation, and alveolar bone loss, which is the key feature of periodontitis. therefore, our study demonstrates that p.gingivalis w has pathogenic effects on rat oral cavity. after inoculation in rat oral cavity for 8 weeks, p.gingivalis w were isolated, and analyzed by microarray. in the detected genes, genes were upregulated, whereas genes were downregulated, indicating that the local periodontal environment can change the gene expression profile of p.gingivalis w in the upregulated genes, expressed hypothetical proteins. among other genes, pg pg pg pg and pg are in the same class in jcvi cell function classification. they all function as mobile extrachromosomal factor: transposon. transposon is a removable genome dna sequence, which can “jump” in genome from one location to another through the process of cutting and integration. transposition is generally known to be triggered by cellular stress, therefore upregulation of these transposons suggests that p.gingivalis w inoculated in rat oral cavity may adapt local environment for its own survival, which is consistent with some other studies. in the downregulated genes, genes encode transport and binding proteins. all these proteins are involved in cell transmembrane transportation. they can transport many substrates, such as metabolites, ion, sugar, amino acids, lipids, cholesterol and drugs. pg encodes a tonb dependent receptor protein, responsible for iron transmembrane transportation. as iron ion is necessary for the breeding and spreading of p.gingivalis w downregulation of pg suggests the subdued iron transferring and proliferation of p.gingivalis w there are downregulated genes encoding proteins related to nucleic acid and protein metabolism. pg encodes a nucleotide reductase, which is related to purine, pyrimidine, nucleotide and dna metabolism, and plays a regulating role in cell proliferation. products of pg and pg are related to the metabolism of dna, such as copy, restructuring and repair. therefore, downregulation of these genes means that the proliferation of inoculated p.gingivalis w is in certain obstacles. pg encodes a putative glycogen synthase, involved in biosynthesis and degradation of polysaccharides. downregulation of pg suggests a disturbed energy metabolism. pg encodes a spooj protein related to cell division, and pg encodes hemagglutinin hagc related to pathogenicity of p.gingivalis w in addition, pg encodes a crispr protein related to cas family. crispr/cas system can protect bacteria against the encroachment by phage, and resist other chromosome genetic material and prevent from the expression of their genes. downregulation of pg suggests a decrease in the defense capability of p.gingivalis w it should be noted that gene expression observed in this study was in mrna level. as we have known, alterations in mrna expression are not always consistent with those in protein expression. therefore, observations in protein level of gene expression will be more convincing. however, it is impracticable to analyze the protein expression of all genes with rna expression alteration. moreover, some products of these genes are still hypothetical proteins. because the inoculated p.gingivalis was cultured outside the rat oral cavity for some days before rna extraction, the rna samples cannot exactly reflect the changes in gene expression after inoculation, although the results can still indicate which genes are upregulated or downregulated.  our study shows that p.gingivalis w has pathogenic effects on host, and local inflammatory oral environment alters the gene expression profile of p.gingivalis w products of these upregulated and downregulated genes are mainly related to transposon functions, cell transmembrane transportation, protein and nucleic acid metabolism, energy metabolism, cell division and bacterial pathogenicity. these changes may lead to decreased proliferation and pathogenicity of p.gingivalis w and favor themselves to adapt local environment for survival. abbreviations p.gingivalisporphyromonas gingivalis pcrpolymerase chain reaction spfspecific pathogen free atccamerican type culture collection cfucolony forming unit cejcementoenamel junction abcalveolar bone crest crisprclustered regularly interspaced short palindromic repeats cascrispr associated genes competing interests the authors declare that they have no competing interests. authors’ contributions jz carried out microarray analysis,analyzed and interpreted the data, and drafted the manuscript. ql performed p.gingivalis w culture and inoculation. clp performed real-time pcr analysis. jcl and hyw were responsible for the isolation and identification of the strain. lst performed alveolar bone loss analysis. ypp designed the study and drafted the manuscript. all authors read and approved the final manuscript. this work was supported by national natural science foundation of china.
products of these upregulated and downregulated genes are mainly related to transposon functions, cell transmembrane transportation, protein and nucleic acid metabolism, energy metabolism, cell division and bacterial pathogenicity. the aim of this study is to investigate the alterations in gene expression in porphyromonas gingivalis w after inoculation in rat oral cavity. p.gingivalis w inoculation in rat oral cavity caused inflammatory responses in gingival tissues and destroyed host alveolar bone. the development of chronic periodontitis was due to not only periodontal pathogens, but also the interaction between periodontal pathogens and host. microarray analysis revealed that genes were upregulated, and genes were downregulated in the detected genes in the inoculated p.gingivalis w real-time quantitative pcr detection confirmed the expression alterations in some selected genes. these changes in gene expression may limit the proliferation and weaken the pathogenicity of p.gingivalis w and favor themselves to adapt local environment for survival. meanwhile, inflammatory oral environment alters p.gingivalis w gene expression profile. porphyromonas gingivalisperiodontitismicroarraygene expressionissue-copyright-statement© the author 2015
 the development of chronic periodontitis was due to not only periodontal pathogens, but also the interaction between periodontal pathogens and host. the aim of this study is to investigate the alterations in gene expression in porphyromonas gingivalis w after inoculation in rat oral cavity.  p.gingivalis w inoculation in rat oral cavity caused inflammatory responses in gingival tissues and destroyed host alveolar bone. microarray analysis revealed that genes were upregulated, and genes were downregulated in the detected genes in the inoculated p.gingivalis w real-time quantitative pcr detection confirmed the expression alterations in some selected genes. products of these upregulated and downregulated genes are mainly related to transposon functions, cell transmembrane transportation, protein and nucleic acid metabolism, energy metabolism, cell division and bacterial pathogenicity.  p.gingivalis w has a pathogenic effect on host oral cavity. meanwhile, inflammatory oral environment alters p.gingivalis w gene expression profile. these changes in gene expression may limit the proliferation and weaken the pathogenicity of p.gingivalis w and favor themselves to adapt local environment for survival. keywords porphyromonas gingivalisperiodontitismicroarraygene expressionissue-copyright-statement© the author 2015 