Table 1.
Studies included in this 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 |
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
aIncluded kit controls
bStudy also used in Open-reference OTU picking
cShared habitats study