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Table 1 Summary of cystic fibrosis microbiota studies; type of sample, technique used and genus identified

From: The microbiome of the upper airways: focus on chronic rhinosinusitis

Author

Year

n

Sample

Techinque

Achromobacter

Actinomyces

Atopobium

Bacteroidetes

Burkholderia

Campylobacter

Capnocytophaga

Craurococcus

Fusobacterium

Granulicatella

Haemophilus

Lactobacillus

Leptotrichia

Ochrobactrum

Peptostreptococcus

Porphyromonas

Prevotella

Pseudomonas

Rhizobium

Rothia

Staphylococcus

Stenotrophomonas

Streptococcus

Veillonella

Ref.

Salipante SJ *

2013

60 CF

Sputum

16 s rRNA pyrosequencing

          

x

      

x

   

x

x

 

[49]

Zemanick ET

2013

37 CF

Sputum

Conventional culture 16S rRNA pyrosequencing

 

x

x

  

x

x

 

x

x

 

x

x

  

x

x

x

 

x

x

 

x

x

[35]

Delhaes L

2012

8 CF

Sputum

Conventional culture 16S rRNA pyrosequencing

        

x

 

x

    

x

x

x

    

x

x

[39]

Fodor AA

2012

23 CF

Sputum

16S rRNA pyrosequencing

    

x

           

x

x

 

x

  

x

x

[37]

Stressmann FA **

2012

14 CF

Sputum

Conventional culture analysis T-RFLP

                 

x

  

x

x

x

 

[44]

Zhao J

2012

6 CF

Sputum

16 s rRNA pyrosequencing

        

x

       

x

x

 

x

  

x

x

[41]

Guss AM

2011

4 CF

Sputum

16 s rRNA pyrosequencing

 

x

 

x

    

x

      

x

x

  

x

  

x

x

[50]

Sibley CD

2011

6 CF

Sputum

Conventional culture T-RFLP 16S rRNA pyrosequencing

x

x

 

x

x

     

x

     

x

x

  

x

x

x

x

[51]

Cox MJ***

2010

63 CF

Sputum Throat swab

Microarray

                 

x

  

x

   

[52]

J Harris JK ****

2007

28 CF 14 healthy

Bronchoalveolar lavage fluid

DGGE/TGGE

          

x

      

x

  

x

 

x

 

[53]

Rogers GB *****

2004

34 CF

Sputum

T-RFLP

       

x

     

x

x

x

x

x

x

     

[54]

  1. *Stenotrophomonas maltophilia, Streptococcus agalactiae, Haemophilus influenzae, Pseudomonas aeruginosa.
  2. **P. aeruginosa, Stenotrophomonas maltophili’, Staphylococcus aureus, Streptococcus Group F.
  3. ***S. aureus, P. aeruginosa.
  4. ****S. aureus, S. maltophilia, P. aeruginosa, Streptococcus mitis, H. influenza.
  5. *****P. aeruginosa, Porphyromonas endodontalis, P. gingivalis, Prevotella denticola, P. melaninogenica, P. nigrescens, P. veroralis, P. intermedia, P. loescheii, P. salivae, P. buccae, P. oris, Craurococcus roseus, Rhizobium loti, Ochrobactrum anthropi, Peptostreptococcus anaerobius.
  6. Asterisks indicate studies in which mentioned species were identified.