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 |