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Table 1 Studies included in this meta-analysis

From: Microbiota of the indoor environment: a meta-analysis

Study Total no. Target PCR Sequencing DNA extraction Avg. sequence Avg % assignment Sampling Geolocation Sampling Sourcetracker Citation Data
name of samples region primers platform method length (bp) of sequences method   sites assignment   source
  per study       per sample       
California 59 V1–V2 8f_357r 454 GS Phenol:Chloroform 314 58.67 % (+/ − 13.79 %) Air (settle Albany, CA, Rooms in apartment Sink/source [14] Contributed
residence     FLX plus MoBio PowerSoil    plate) USA building (living room,    by author
air (Berk) a      DNA isolation kit      balcony, bedroom,    
           bathroom)    
California 86 V4 515f_806r Illumina ZR96 Fecal DNA 252 67.73 % (+/ − 14.76 %) Surface Davis, CA, Rooms in industrial Sink [23] Qiime
dairy b     MiSeq extraction kit    (cotton USA cheese processing    database
         swab)   building (wagon wheel    
           room, scooping room,    
           production room,    
           brine_main room,    
           bloomy_rind room,    
           drying room, aging    
           room, packaging room)    
California 147 V4 515f_806r Illumina ZR96 Fecal DNA 252 53.94 % (+/ − 10.22 %) Surface Sacramento, Hospital (neonatal Sink [3] Qiime
NICU (Sac) b     MiSeq extraction kit    (cotton CA, USA intensive care    database
         swab)   units) surfaces    
           and devices    
Colorado 285 V4 515f_806r Illumina MoBio PowerSoil 89 67.9 % (+/ − 27.1) Surface Boulder, Kitchens in family Sink [12] Qiime
kitchen     HiSeq2000 DNA isolation kit    (cotton CO, USA homes    database
surfaces a,b,c         swab)      
Colorado 126 V1–V2 27f_338r 454 GS MoBio PowerSoil 232 91.6 % (+/ − 7.46 %) Surface Boulder, Public restrooms Sink [1] Qiime
restroom     Junior DNA isolation kit    (cotton CO, USA     database
surfaces a,b,c         swab)      
France 3 V2–V3 535f_789r 454 GS QiaAmp 228 92.23 % (+/ − 1.86 %) Air Paris, Hospital, Sink [5] Contributed
building air     FLX     (filter) France museum,    by author
     Titanium       office building    
South Korea 28 V1–V3 9f_541r 454 GS FastDNA SPIN 120 60.8 % (+/ − 17.68 %) Surfaces Seoul, Rooms in Sink [11] Qiime
homes c     Junior extraction kit    (Easy Korea family homes    database
         Swab Kit)   (kitchen,    
           bathroom)    
California 30 V1–V2 27f_338r 454 GS DNeasy 221 94.22 % (+/– 4.67 %) Surface San Diego, Hospital (neonatal Sink [7] Qiime
NICU (SD)     FLX Tissue Kit    (cotton CA, USA intensive care units)    database
         swabs)      
California 55 V1–V2 27f_338r 454 GS DNeasy 227 93.95 % (+/ − 4.07 %) Surface San Francisco, Office building Sink [22] Qiime
office     FLX Tissue Kit    (cotton CA; New York, objects    database
         swabs) NY; Tucson, AZ     
Oregon 173 V4 515f_806r Illumina MO BIO 130 85.67 % (+/ − 7.83 %) Dust Eugene, OR, University building Sink [47] Contributed
university     MiSeq PowerWater    (vacuum USA (office, storage,    by author
dust      DNA Isolation    filter)   classroom, food    
      Kit      service)    
North 384 V4 515f_806r Illumina directPCR 109 86.37 % (+/ − 15.91) Surface (Rayon- Raleigh- Homes Sink/source [9] Qiime
Carolina     HiSeq     tipped swab) Durham Area, (condominium,    database
homes c     2000;      NC, USA low-rise apartment,    
     Illumina       family homes)    
     MiSeq          
France 3 V2–V3 Custom 454 GS Custom 263 87.42 % (+/ − 0.58 %) Air Paris, France Art museum Sink [26] Contributed
museum     FLX     (cyclone      by author
air     Titanium     sampler)      
Oregon 321 V4 515f_806r Illumina MO BIO 127 85.77 % (+/ − 5.54 %) Air Eugene, OR, University Sink/source [19] Contributed
classroom     MiSeq PowerWater    (filter) USA classroom    by author
air b      DNA Isolation         
      Kit         
Oregon 62 V4 515f_806r Illumina MO BIO 127 91.41 % (+/ − 4.00 %) Surfaces Eugene, OR, USA University Sink [19] Contributed
classroom     MiSeq PowerWater      classroom    by author
surfaces b      DNA Isolation         
      Kit         
Austria 24 V1–V2– 27f_1492r; 454 GS Custom XS 236 94.66 % (+/ − 3.72 %) Surfaces (BiSKits Austria Hopital Sink [6] Contributed
ICU   V3–V4– 515f_927r FLX PC    and nylon-   (intensive    by author
   V6–V9; V4   plus     flocked swabs)   care unit)    
Connecticut 15 V3–V4 331f_797r 454 GS FLX MoBio PowerMax 508 68.34 % (+/ − 3.52 %) Vacuum (dust New Haven, University N/A [20] Contributed
classroom air     Titanium Soil DNA    and air), HVAC (air) CT, USA classroom    by author
      Extraction Kit         
Colorado 9 V1–V2 27f_338r 454 GS MoBio UltraClean 225 83.38 % (+/ − 20.64 %) Air (filter) Steamboat Aerial source Source [52] Qiime
mountaintop air     FLX PlantDNA     Springs, CO, USA of biota    database
     Titanium Isolation Kit      (atmosphere)    
Ireland 168 V4 520f_802r 454 GS FLX QIAGEN kit 221 93.83 % (+/ − 3.16 %) Surface Cork, Ireland Human gut (source) Source [53] Qiime
elderly gut     Titanium     (feces sample)      database
Colorado 602 V1–V2 27f_338r 454 GS MoBio PowerSoil 229 92.76 % (+/ − 4.56 %) Surface Boulder, Human body Source [36] Qiime
body sites     FLX DNA isolation kit    (cotton CO, USA sites (source)    database
     Titanium     swab)      
Europe/Africa 29 V4–V5 784f_1061r 454 GS FLX Custom 247 93.24 % (+/ − 3.17 %) Surface Boulpon, Burkina Human gut Source [54] Qiime
children gut     Titanium proteinaseK    (feces Sample) Faso; Florence, Italy (source)    database
      phenolchloroform         
Colorado 182 V1–V2 27f_338r 454 GS FLX MoBio UltraClean 228 94.78 % (+/ − 3.5 %) Surface Boulder, CO, USA Human palms Source [43] Qiime
undergraduate      PlantDNA Isolation Kit    (cotton swab)   (source)    database
palms a              
N + S America 89 V1–V2 27f_338r 454 GS FLX MoBio PowerSoil 231 47.4 % (+/ − 5.96 %) Soil USA, Puerto Rico, Outdoor source Source [55] Qiime
soils     Titanium DNA isolation kit     Peru, Argentina, of biota (soil)    database
          Canada     
Colorado 1071 V1–V2 27f_338r Illumina GAIIx MoBio PowerSoil 128 87.00 % (+/ − 15.42 %) Surface Boulder, CO, USA Human and dog Source [56] Qiime
family      DNA isolation kit    (cotton swab)   body sites (source)    database
  1. We combined high-throughput sequence data from 23 published, publicly available studies characterizing the built environment (sink) or studies that characterize potential sources of microbial dispersal into the built environment habitat (source). The Sourcetracker method requires a priori assignment of the samples in each of the studies as either an ecological source or sink, as indicated in the Sourcetracker Assignment column; three studies included source samples in their study design
  2. aIncluded kit controls
  3. bStudy also used in Open-reference OTU picking
  4. cShared habitats study