TY - JOUR
T1 - Microbial community patterns associated with automated teller machine keypads in New York City
AU - Bik, Holly M.
AU - Maritz, Julia M.
AU - Luong, Albert
AU - Shin, Hakdong
AU - Dominguez-Bello, Maria Gloria
AU - Carlton, Jane M.
N1 - Funding Information:
We thank Steven Sullivan for providing comments and edits on a draft of the manuscript. We thank the personnel of the NYU Center for Genomics and Systems Biology GenCore for their sequencing services. J.M.C. and M.G.D.-B. designed the study. A.L. collected swab samples from ATM keypads, performed DNA extractions, and carried out PCR and sequencing of 16S rRNA genes. J.M.M. carried out PCR and sequencing of 18S rRNA. H.M.B., J.M.M., and H.S. performed computational analyses of 16S and 18S rRNA data. J.M.C. and M.G.D.-B. provided support during sequencing and data analysis. H.M.B., J.M.M., and J.M.C. wrote the manuscript. J.M.M. is supported by the MacCracken Program in the Graduate School of Arts and Science at New York University. This study was partially funded by a New York University Grand Challenge project, "Microbes, Sewage, Health and Disease: Mapping the New York City Metagenome" (J.M.C.). We thank the Sloan Foundation for their support to pioneer studies, including ours, on the microbiology of the built environment. The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication
Publisher Copyright:
© 2016 Bik et al.
PY - 2016/11/1
Y1 - 2016/11/1
N2 - In densely populated urban environments, the distribution of microbes and the drivers of microbial community assemblages are not well understood. In sprawling metropolitan habitats, the "urban microbiome" may represent a mix of human-associated and environmental taxa. Here we carried out a baseline study of automated teller machine (ATM) keypads in New York City (NYC). Our goal was to describe the biodiversity and biogeography of both prokaryotic and eukaryotic microbes in an urban setting while assessing the potential source of microbial assemblages on ATM keypads. Microbial swab samples were collected from three boroughs (Manhattan, Queens, and Brooklyn) during June and July 2014, followed by generation of Illumina MiSeq datasets for bacterial (16S rRNA) and eukaryotic (18S rRNA) marker genes. Downstream analysis was carried out in the QIIME pipeline, in conjunction with neighborhood metadata (ethnicity, population, age groups) from the NYC Open Data portal. Neither the 16S nor 18S rRNA datasets showed any clustering patterns related to geography or neighborhood demographics. Bacterial assemblages on ATM keypads were dominated by taxonomic groups known to be associated with human skin communities (Actinobacteria, Bacteroides, Firmicutes, and Proteobacteria), although SourceTracker analysis was unable to identify the source habitat for the majority of taxa. Eukaryotic assemblages were dominated by fungal taxa as well as by a low-diversity protist community containing both free-living and potentially pathogenic taxa (Toxoplasma, Trichomonas). Our results suggest that ATM keypads amalgamate microbial assemblages from different sources, including the human microbiome, eukaryotic food species, and potentially novel extremophilic taxa adapted to air or surfaces in the built environment. DNA obtained from ATM keypads may thus provide a record of both human behavior and environmental sources of microbes.
AB - In densely populated urban environments, the distribution of microbes and the drivers of microbial community assemblages are not well understood. In sprawling metropolitan habitats, the "urban microbiome" may represent a mix of human-associated and environmental taxa. Here we carried out a baseline study of automated teller machine (ATM) keypads in New York City (NYC). Our goal was to describe the biodiversity and biogeography of both prokaryotic and eukaryotic microbes in an urban setting while assessing the potential source of microbial assemblages on ATM keypads. Microbial swab samples were collected from three boroughs (Manhattan, Queens, and Brooklyn) during June and July 2014, followed by generation of Illumina MiSeq datasets for bacterial (16S rRNA) and eukaryotic (18S rRNA) marker genes. Downstream analysis was carried out in the QIIME pipeline, in conjunction with neighborhood metadata (ethnicity, population, age groups) from the NYC Open Data portal. Neither the 16S nor 18S rRNA datasets showed any clustering patterns related to geography or neighborhood demographics. Bacterial assemblages on ATM keypads were dominated by taxonomic groups known to be associated with human skin communities (Actinobacteria, Bacteroides, Firmicutes, and Proteobacteria), although SourceTracker analysis was unable to identify the source habitat for the majority of taxa. Eukaryotic assemblages were dominated by fungal taxa as well as by a low-diversity protist community containing both free-living and potentially pathogenic taxa (Toxoplasma, Trichomonas). Our results suggest that ATM keypads amalgamate microbial assemblages from different sources, including the human microbiome, eukaryotic food species, and potentially novel extremophilic taxa adapted to air or surfaces in the built environment. DNA obtained from ATM keypads may thus provide a record of both human behavior and environmental sources of microbes.
KW - 16S rRNA
KW - 18S rRNA
KW - Automated teller machine
KW - Environmental sequencing
KW - New York City
KW - Urban microbiome
UR - http://www.scopus.com/inward/record.url?scp=85017132229&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85017132229&partnerID=8YFLogxK
U2 - 10.1128/mSphere.00226-16
DO - 10.1128/mSphere.00226-16
M3 - Article
AN - SCOPUS:85017132229
VL - 1
JO - mSphere
JF - mSphere
SN - 2379-5042
IS - 6
M1 - e00226-16
ER -