Table 1 Studies included in this meta-analysis

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