So one of my projects for the last few months has been to try to create a collection of every peer-reviewed publication that resulted from the Alfred P. Sloan Foundation program of the Microbiology of the Built Environment. The program has been running for over 10 years and has funded over 100 grants. To generate this collection we tried many approaches, starting with basic searches for the funded labs and acknowledgement of Sloan funding. Next we contacted everyone who had ever received a grant through the program and asked them to check their publications… this approach almost doubled the number of publications in the collection. A last few gaps were filled by begging graduate students to check the lists for non-responsive PIs and a little bit of digging through grant reports at the Sloan Foundation. After some weeding, and manual addition of metadata we think we have a pretty good collection… but I’m sure we’re still missing publications!
With this collection we hope to do many things including a citation analysis, a network analysis, and other similar approaches that can shed light on the connectivity of labs in the field and the impact of the Sloan program.
We are looking for input on the list! If you work(ed) in a lab that received Sloan Funding, we would love it if you would ensure that all of your relevant publications are included. Relevant here meaning they resulted, directly or indirectly, from the Sloan MoBE program. Please post additions in the comments below. Thank you for any input!
Abarenkov, K., Adams, R.I., Laszlo, I., Agan, A., Ambrosio, E., Antonelli, A., Bahram, M., Bengtsson-Palme, J., Bok, G., Cangren, P., et al. (2016). Annotating public fungal ITS sequences from the built environment according to the MIxS-Built Environment standard – a report from a May 23-24, 2016 workshop (Gothenburg, Sweden). MycoKeys 16, 1–15.
Adams, R.I., Amend, A.S., Taylor, J.W., and Bruns, T.D. (2013a). A Unique Signal Distorts the Perception of Species Richness and Composition in High-Throughput Sequencing Surveys of Microbial Communities: a Case Study of Fungi in Indoor Dust. Microb Ecol 66, 735–741.
Adams, R.I., Miletto, M., Taylor, J.W., and Bruns, T.D. (2013b). Dispersal in microbes: fungi in indoor air are dominated by outdoor air and show dispersal limitation at short distances. ISME J 7, 1262–1273.
Adams, R.I., Miletto, M., Taylor, J.W., and Bruns, T.D. (2013c). The Diversity and Distribution of Fungi on Residential Surfaces. PLoS One 8.
Adams, R.I., Miletto, M., Lindow, S.E., Taylor, J.W., and Bruns, T.D. (2014). Airborne Bacterial Communities in Residences: Similarities and Differences with Fungi. PLoS One 9.
Adams, R.I., Bhangar, S., Pasut, W., Arens, E.A., Taylor, J.W., Lindow, S.E., Nazaroff, W.W., and Bruns, T.D. (2015a). Chamber Bioaerosol Study: Outdoor Air and Human Occupants as Sources of Indoor Airborne Microbes. PLoS One 10.
Adams, R.I., Bateman, A.C., Bik, H.M., and Meadow, J.F. (2015b). Microbiota of the indoor environment: a meta-analysis. Microbiome 3.
Adams, R.I., Tian, Y., Taylor, J.W., Bruns, T.D., Hyvärinen, A., and Täubel, M. (2015c). Passive dust collectors for assessing airborne microbial material. Microbiome 3.
Adams, R.I., Bhangar, S., Dannemiller, K.C., Eisen, J.A., Fierer, N., Gilbert, J.A., Green, J.L., Marr, L.C., Miller, S.L., Siegel, J.A., et al. (2016). Ten questions concerning the microbiomes of buildings. Building and Environment 109, 224–234.
Ahrendt, S.R., Medina, E.M., Chang, C.-E.A., and Stajich, J.E. (2017). Exploring the binding properties and structural stability of an opsin in the chytrid Spizellomyces punctatus using comparative and molecular modeling. PeerJ 5, e3206.
Alcaïs, A., Quintana-Murci, L., Thaler, D.S., Schurr, E., Abel, L., and Casanova, J.-L. (2010). Life-threatening infectious diseases of childhood: single-gene inborn errors of immunity?: Genetic architecture of infectious diseases. Annals of the New York Academy of Sciences 1214, 18–33.
Al-Hatmi, A.M.S., Van Den Ende, A.H.G.G., Stielow, J.B., Van Diepeningen, A.D., Seifert, K.A., McCormick, W., Assabgui, R., Gräfenhan, T., De Hoog, G.S., and Levesque, C.A. (2016). Evaluation of two novel barcodes for species recognition of opportunistic pathogens in Fusarium. Fungal Biol 120, 231–245.
Alivisatos, A.P., Blaser, M.J., Brodie, E.L., Chun, M., Dangl, J.L., Donohue, T.J., Dorrestein, P.C., Gilbert, J.A., Green, J.L., Jansson, J.K., et al. (2015). A unified initiative to harness Earth’s microbiomes. Science 350, 507–508.
Amend, A.S., Seifert, K.A., Samson, R., and Bruns, T.D. (2010a). Indoor fungal composition is geographically patterned and more diverse in temperate zones than in the tropics. Proc Natl Acad Sci U S A 107, 13748–13753.
Amend, A.S., Seifert, K.A., and Bruns, T.D. (2010b). Quantifying microbial communities with 454 pyrosequencing: does read abundance count? Mol. Ecol. 19, 5555–5565.
Amir, A., McDonald, D., Navas-Molina, J.A., Kopylova, E., Morton, J.T., Zech Xu, Z., Kightley, E.P., Thompson, L.R., Hyde, E.R., Gonzalez, A., et al. (2017). Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns. mSystems 2, e00191-16.
Bálint, M., Bahram, M., Eren, A.M., Faust, K., Fuhrman, J.A., Lindahl, B., O’Hara, R.B., Öpik, M., Sogin, M.L., Unterseher, M., et al. (2016). Millions of reads, thousands of taxa: microbial community structure and associations analyzed via marker genes. FEMS Microbiol. Rev.
Barberán, A., Ladau, J., Leff, J.W., Pollard, K.S., Menninger, H.L., Dunn, R.R., and Fierer, N. (2015a). Continental-scale distributions of dust-associated bacteria and fungi. Proc Natl Acad Sci U S A 112, 5756–5761.
Barberán, A., Dunn, R.R., Reich, B.J., Pacifici, K., Laber, E.B., Menninger, H.L., Morton, J.M., Henley, J.B., Leff, J.W., Miller, S.L., et al. (2015b). The ecology of microscopic life in household dust. Proc. Biol. Sci. 282.
Baron, J.L., Vikram, A., Duda, S., Stout, J.E., and Bibby, K. (2014). Shift in the Microbial Ecology of a Hospital Hot Water System following the Introduction of an On-Site Monochloramine Disinfection System. PLoS One 9.
Baron, J.L., Harris, J.K., Holinger, E.P., Duda, S., Stevens, M.J., Robertson, C.E., Ross, K.A., Pace, N.R., and Stout, J.E. (2015). Effect of monochloramine treatment on the microbial ecology of Legionella and associated bacterial populations in a hospital hot water system. Syst. Appl. Microbiol. 38, 198–205.
Bates, S.T., Ahrendt, S., Bik, H.M., Bruns, T.D., Caporaso, J.G., Cole, J., Dwan, M., Fierer, N., Gu, D., Houston, S., et al. (2013). Meeting Report: Fungal ITS Workshop (October 2012). Stand Genomic Sci 8, 118–123.
Benoit, J.B., Adelman, Z.N., Reinhardt, K., Dolan, A., Poelchau, M., Jennings, E.C., Szuter, E.M., Hagan, R.W., Gujar, H., Shukla, J.N., et al. (2016). Unique features of a global human ectoparasite identified through sequencing of the bed bug genome. Nat Commun 7.
Betts, M.N., Jospin, G., Eisen, J.A., and Coil, D.A. (2015). Draft Genome Sequence of Planomicrobium glaciei UCD-HAM (Phylum Firmicutes ). Genome Announcements 3, e01209-15.
Bhangar, S., Huffman, J.A., and Nazaroff, W.W. (2014). Size-resolved fluorescent biological aerosol particle concentrations and occupant emissions in a university classroom. Indoor Air 24, 604–617.
Bhangar, S., Adams, R.I., Pasut, W., Huffman, J.A., Arens, E.A., Taylor, J.W., Bruns, T.D., and Nazaroff, W.W. (2016a). Chamber bioaerosol study: human emissions of size-resolved fluorescent biological aerosol particles. Indoor Air 26, 193–206.
Bhangar, S., Brooks, B., Firek, B., Licina, D., Tang, X., Morowitz, M.J., Banfield, J.F., and Nazaroff, W.W. (2016b). Pilot study of sources and concentrations of size-resolved airborne particles in a neonatal intensive care unit. Building and Environment 106, 10–19.
Bik, H.M., Porazinska, D.L., Creer, S., Caporaso, J.G., Knight, R., and Thomas, W.K. (2012). Sequencing our way towards understanding global eukaryotic biodiversity. Trends Ecol Evol 27, 233–243.
Bik, H.M., Coil, D.A., and Eisen, J.A. (2014). microBEnet: Lessons Learned from Building an Interdisciplinary Scientific Community in the Online Sphere. PLoS Biol 12.
Blaser, M.J., Cardon, Z.G., Cho, M.K., Dangl, J.L., Donohue, T.J., Green, J.L., Knight, R., Maxon, M.E., Northen, T.R., Pollard, K.S., et al. (2016). Toward a Predictive Understanding of Earth’s Microbiomes to Address 21st Century Challenges. mBio 7.
Bokulich, N.A., Lewis, Z.T., Boundy-Mills, K., and Mills, D.A. (2016a). A new perspective on microbial landscapes within food production. Curr Opin Biotechnol 37, 182–189.
Bokulich, N.A., Rideout, J.R., Mercurio, W.G., Shiffer, A., Wolfe, B., Maurice, C.F., Dutton, R.J., Turnbaugh, P.J., Knight, R., and Caporaso, J.G. (2016b). mockrobiota: a Public Resource for Microbiome Bioinformatics Benchmarking. mSystems 1.
Borrowman, C.K., Zhou, S., Burrow, T.E., and Abbatt, J.P.D. (2015). Formation of environmentally persistent free radicals from the heterogeneous reaction of ozone and polycyclic aromatic compounds. Phys. Chem. Chem. Phys. 18, 205–212.
Bowers, R.M., Kyrpides, N.C., Stepanauskas, R., Harmon-Smith, M., Doud, D., Reddy, T.B.K., Schulz, F., Jarett, J., Rivers, A.R., Eloe-Fadrosh, E.A., et al. (2017). Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nat. Biotechnol. 35, 725–731.
Brooks, B., Firek, B.A., Miller, C.S., Sharon, I., Thomas, B.C., Baker, R., Morowitz, M.J., and Banfield, J.F. (2014). Microbes in the neonatal intensive care unit resemble those found in the gut of premature infants. Microbiome 2, 1.
Brown, G.Z., Kline, J., Mhuireach, G., Northcutt, D., and Stenson, J. (2016). Making microbiology of the built environment relevant to design. Microbiome 4.
Busby, P.E., Soman, C., Wagner, M.R., Friesen, M.L., Kremer, J., Bennett, A., Morsy, M., Eisen, J.A., Leach, J.E., and Dangl, J.L. (2017). Research priorities for harnessing plant microbiomes in sustainable agriculture. PLOS Biology 15, e2001793.
Buse, H.Y., Ji, P., Gomez-Alvarez, V., Pruden, A., Edwards, M.A., and Ashbolt, N.J. (2016). Effect of temperature and colonization of Legionella pneumophila and Vermamoeba vermiformis on bacterial community composition of copper drinking water biofilms. Microbial Biotechnology.
Caporaso, J.G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F.D., Costello, E.K., Fierer, N., Peña, A.G., Goodrich, J.K., Gordon, J.I., et al. (2010). QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 7, 335–336.
Caverly, L.J., Carmody, L.A., Haig, S.-J., Kotlarz, N., Kalikin, L.M., Raskin, L., and LiPuma, J.J. (2016). Culture-Independent Identification of Nontuberculous Mycobacteria in Cystic Fibrosis Respiratory Samples. PLoS One 11.
Chamberlain, A.T., Lehnert, J.D., and Berkelman, R.L. (2017). The 2015 New York City Legionnaires’ Disease Outbreak: A Case Study on a History-Making Outbreak. J Public Health Manag Pract 23, 410–416.
Chase, J., Fouquier, J., Zare, M., Sonderegger, D.L., Knight, R., Kelley, S.T., Siegel, J., and Caporaso, J.G. (2016a). Geography and Location Are the Primary Drivers of Office Microbiome Composition. mSystems 1, e00022-16.
Chase, J.H., Bolyen, E., Rideout, J.R., and Caporaso, J.G. (2016b). cual-id: Globally Unique, Correctable, and Human-Friendly Sample Identifiers for Comparative Omics Studies. mSystems 1.
Chen, A.J., Frisvad, J.C., Sun, B.D., Varga, J., Kocsub?, S., Dijksterhuis, J., Kim, D.H., Hong, S.-B., Houbraken, J., and Samson, R.A. (2016a). Aspergillus section Nidulantes (formerly Emericella): Polyphasic taxonomy, chemistry and biology. Studies in Mycology 84, 1–118.
Chen, A.J., Sun, B.D., Houbraken, J., Frisvad, J.C., Yilmaz, N., Zhou, Y.G., and Samson, R.A. (2016b). New Talaromyces species from indoor environments in China. Studies in Mycology 84, 119–144.
Chitsaz, H., Yee-Greenbaum, J.L., Tesler, G., Lombardo, M.-J., Dupont, C.L., Badger, J.H., Novotny, M., Rusch, D.B., Fraser, L.J., Gormley, N.A., et al. (2011). Efficient de novo assembly of single-cell bacterial genomes from short-read data sets. Nature Biotechnology 29, 915–921.
Coil, D.A. Citizen Microbiology: A Case Study in Space. In The Rightful Place of Science: Citizen Science, (Consortium for Science, Policy & Outcomes), p.
Coil, D.A., and Eisen, J.A. (2015). Draft Genome Sequence of Porphyrobacter mercurialis (sp. nov.) Strain Coronado. Genome Announcements 3, e00856-15.
Coil, D., Jospin, G., and Darling, A.E. (2015a). A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data. Bioinformatics 31, 587–589.
Coil, D.A., Doctor, J.I., Lang, J.M., Darling, A.E., and Eisen, J.A. (2013). Draft Genome Sequence of Kocuria sp. Strain UCD-OTCP (Phylum Actinobacteria). Genome Announcements 1, e00172-13-e00172-13.
Coil, D.A., Flanagan, J.C., Stump, A., Alexiev, A., Lang, J.M., and Eisen, J.A. (2015b). Porphyrobacter mercurialis sp. nov., isolated from a stadium seat and emended description of the genus Porphyrobacter. PeerJ 3, e1400.
Coil, D.A., Benardini, J.N., and Eisen, J.A. (2015c). Draft Genome Sequence of Bacillus safensis JPL-MERTA-8-2, Isolated from a Mars-Bound Spacecraft. Genome Announcements 3, e01360-15.
Coil, D.A., Neches, R.Y., Lang, J.M., Brown, W.E., Severance, M., Cavalier, D., and Eisen, J.A. (2016). Growth of 48 built environment bacterial isolates on board the International Space Station (ISS). PeerJ 4, e1842.
Coil, D.A., Ettinger, C.L., and Eisen, J.A. (2017). Gut Check: The evolution of an educational board game. PLOS Biology 15, e2001984.
Collins, R.A., Stajich, J.E., Field, D.J., Olive, J.E., and DeAbreu, D.M. (2015). The low information content of Neurospora splicing signals: implications for RNA splicing and intron origin. RNA 21, 997–1004.
Committee on Microbiomes of the Built Environment: From Research to Application, Board on Life Sciences, Board on Environmental Studies and Toxicology, Division on Earth and Life Studies, Health and Medicine Division, Board on Infrastructure and the Constructed Environment, Division on Engineering and Physical Sciences, National Academy of Engineering, and National Academies of Sciences, Engineering, and Medicine (2017). Microbiomes of the Built Environment: A Research Agenda for Indoor Microbiology, Human Health, and Buildings (Washington, D.C.: National Academies Press).
Corsi, R.L., Kinney, K.A., and Levin, H. (2012). Microbiomes of built environments: 2011 symposium highlights and workgroup recommendations. Indoor Air 22, 171–172.
Craine, J.M., Barberán, A., Lynch, R.C., Menninger, H.L., Dunn, R.R., and Fierer, N. (2017). Molecular analysis of environmental plant DNA in house dust across the United States. Aerobiologia 33, 71–86.
Crous, P.W., Wingfield, M.J., Burgess, T.I., Hardy, G.E.S.J., Crane, C., Barrett, S., Cano-Lira, J.F., Leroux, J.J., Thangavel, R., Guarro, J., et al. (2016). Fungal Planet description sheets: 469?557. Persoonia – Molecular Phylogeny and Evolution of Fungi 37, 218–403.
Dahlhausen, K., Krebs, B.L., Watters, J.V., and Ganz, H.H. (2016). Crowdfunding Campaigns Help Researchers Launch Projects and Generate Outreach. Journal of Microbiology & Biology Education 17, 32–37.
Dahms, P.A., Martin, A.L., Ganz, H.H., Eisen, J.A., and Coil, D.A. (2017). Draft Genome Sequence of Propionibacterium avidum Strain UCD-PD2 Isolated from a Feline Anal Sac. Genome Announcements 5, e00034-17.
Dai, D., Prussin, A.J., Marr, L.C., Vikesland, P.J., Edwards, M.A., and Pruden, A. (2017). Factors Shaping the Human Exposome in the Built Environment: Opportunities for Engineering Control. Environmental Science & Technology 51, 7759–7774.
Dannemiller, K.C., Lang-Yona, N., Yamamoto, N., Rudich, Y., and Peccia, J. (2014a). Combining real-time PCR and next-generation DNA sequencing to provide quantitative comparisons of fungal aerosol populations. Atmospheric Environment 84, 113–121.
Dannemiller, K.C., Reeves, D., Bibby, K., Yamamoto, N., and Peccia, J. (2014b). Fungal high-throughput taxonomic identification tool for use with next-generation sequencing (FHiTINGS). J. Basic Microbiol. 54, 315–321.
Dannemiller, K.C., Mendell, M.J., Macher, J.M., Kumagai, K., Bradman, A., Holland, N., Harley, K., Eskenazi, B., and Peccia, J. (2014c). Next-generation DNA sequencing reveals that low fungal diversity in house dust is associated with childhood asthma development. Indoor Air 24, 236–247.
Dannemiller, K.C., Weschler, C.J., and Peccia, J. (2016a). Fungal and bacterial growth in floor dust at elevated relative humidity levels. Indoor Air.
Dannemiller, K.C., Gent, J.F., Leaderer, B.P., and Peccia, J. (2016b). Indoor microbial communities: Influence on asthma severity in atopic and nonatopic children. J. Allergy Clin. Immunol. 138, 76–83.e1.
Dannemiller, K.C., Gent, J.F., Leaderer, B.P., and Peccia, J. (2016c). Influence of housing characteristics on bacterial and fungal communities in homes of asthmatic children. Indoor Air 26, 179–192.
Davis, J.C.C., Totten, S.M., Huang, J.O., Nagshbandi, S., Kirmiz, N., Garrido, D.A., Lewis, Z.T., Wu, L.D., Smilowitz, J.T., German, J.B., et al. (2016). Identification of Oligosaccharides in Feces of Breast-fed Infants and Their Correlation with the Gut Microbial Community. Mol. Cell Proteomics 15, 2987–3002.
Davis, J.C.C., Lewis, Z.T., Krishnan, S., Bernstein, R.M., Moore, S.E., Prentice, A.M., Mills, D.A., Lebrilla, C.B., and Zivkovic, A.M. (2017). Growth and Morbidity of Gambian Infants are Influenced by Maternal Milk Oligosaccharides and Infant Gut Microbiota. Scientific Reports 7, 40466.
De Filippis, F., Genovese, A., Ferranti, P., Gilbert, J.A., and Ercolini, D. (2016). Metatranscriptomics reveals temperature-driven functional changes in microbiome impacting cheese maturation rate. Sci Rep 6.
De Vries, D.R., Martin, A.L., Ganz, H.H., Eisen, J.A., and Coil, D.A. (2016). Draft Genome Sequence of Enterococcus faecalis Strain UCD-PD3. Genome Announcements 4, e01386-16.
Dedesko, S., and Siegel, J.A. (2015). Moisture parameters and fungal communities associated with gypsum drywall in buildings. Microbiome 3.
Dedesko, S., Stephens, B., Gilbert, J.A., and Siegel, J.A. (2015). Methods to assess human occupancy and occupant activity in hospital patient rooms. Building and Environment 90, 136–145.
DeVries, Z.C., Mick, R., and Schal, C. (2016). Feel the heat: Activation, orientation, and feeding responses of bed bugs to targets at different temperatures. J. Exp. Biol.
Diep, A.L., Lang, J.M., Darling, A.E., Eisen, J.A., and Coil, D.A. (2013). Draft Genome Sequence of Dietzia sp. Strain UCD-THP (Phylum Actinobacteria). Genome Announcements 1, e00197-13-e00197-13.
Duda, S., Kandiah, S., Stout, J.E., Baron, J.L., Yassin, M., Fabrizio, M., Ferrelli, J., Hariri, R., Wagener, M.M., Goepfert, J., et al. (2014). Evaluation of a new monochloramine generation system for controlling Legionella in building hot water systems. Infect Control Hosp Epidemiol 35, 1356–1363.
Dunitz, M.I., Lang, J.M., Jospin, G., Darling, A.E., Eisen, J.A., and Coil, D.A. (2015). Swabs to genomes: a comprehensive workflow. PeerJ 3, e960.
Dunn, R.R., Fierer, N., Henley, J.B., Leff, J.W., and Menninger, H.L. (2013). Home Life: Factors Structuring the Bacterial Diversity Found within and between Homes. PLoS One 8.
Eisen, J. (2015). What does the term microbiome mean? And where did it come from? A bit of a surprise .. The Winnower.
Emerson, J.B., Keady, P.B., Brewer, T.E., Clements, N., Morgan, E.E., Awerbuch, J., Miller, S.L., and Fierer, N. (2015). Impacts of flood damage on airborne bacteria and fungi in homes after the 2013 Colorado Front Range flood. Environ. Sci. Technol. 49, 2675–2684.
Emerson, J.B., Keady, P.B., Clements, N., Morgan, E.E., Awerbuch, J., Miller, S.L., and Fierer, N. (2017a). High temporal variability in airborne bacterial diversity and abundance inside single-family residences. Indoor Air 27, 576–586.
Emerson, J.B., Adams, R.I., Román, C.M.B., Brooks, B., Coil, D.A., Dahlhausen, K., Ganz, H.H., Hartmann, E.M., Hsu, T., Justice, N.B., et al. (2017b). Schrödinger’s microbes: Tools for distinguishing the living from the dead in microbial ecosystems. Microbiome 5, 86.
Emerson, J.B., Adams, R.I., Román, C.M.B., Brooks, B., Coil, D.A., Dahlhausen, K., Ganz, H.H., Hartmann, E.M., Hsu, T., Justice, N.B., et al. (2017c). Schrödinger’s microbes: Tools for distinguishing the living from the dead in microbial ecosystems. Microbiome 5.
Eren, A.M., Vineis, J.H., Morrison, H.G., and Sogin, M.L. (2013a). A Filtering Method to Generate High Quality Short Reads Using Illumina Paired-End Technology. PLoS One 8.
Eren, A.M., Maignien, L., Sul, W.J., Murphy, L.G., Grim, S.L., Morrison, H.G., Sogin, M.L., and Freckleton, R. (2013b). Oligotyping: differentiating between closely related microbial taxa using 16S rRNA gene data. Methods Ecol Evol 4, 1111–1119.
Eren, A.M., Morrison, H.G., Lescault, P.J., Reveillaud, J., Vineis, J.H., and Sogin, M.L. (2015). Minimum entropy decomposition: Unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences. ISME J 9, 968–979.
Falkinham, J.O., Pruden, A., and Edwards, M. (2015). Opportunistic Premise Plumbing Pathogens: Increasingly Important Pathogens in Drinking Water. Pathogens 4, 373–386.
Feazel, L.M., Baumgartner, L.K., Peterson, K.L., Frank, D.N., Harris, J.K., and Pace, N.R. (2009). Opportunistic pathogens enriched in showerhead biofilms. Proc Natl Acad Sci U S A 106, 16393–16399.
Fitzsimons, M.S., Novotny, M., Lo, C.-C., Dichosa, A.E.K., Yee-Greenbaum, J.L., Snook, J.P., Gu, W., Chertkov, O., Davenport, K.W., McMurry, K., et al. (2013). Nearly finished genomes produced using gel microdroplet culturing reveal substantial intraspecies genomic diversity within the human microbiome. Genome Research 23, 878–888.
Flanagan, J.C., Lang, J.M., Darling, A.E., Eisen, J.A., and Coil, D.A. (2013). Draft Genome Sequence of Curtobacterium flaccumfaciens Strain UCD-AKU (Phylum Actinobacteria). Genome Announcements 1, e00244-13-e00244-13.
Flores, G.E., Bates, S.T., Knights, D., Lauber, C.L., Stombaugh, J., Knight, R., and Fierer, N. (2011). Microbial Biogeography of Public Restroom Surfaces. PLoS One 6.
Flores, G.E., Bates, S.T., Caporaso, J.G., Lauber, C.L., Leff, J.W., Knight, R., and Fierer, N. (2013). Diversity, distribution and sources of bacteria in residential kitchens. Environ. Microbiol. 15, 588–596.
Fouquier, J., Schwartz, T., and Kelley, S.T. (2015). Rapid assemblage of diverse environmental fungal communities on public restroom floors. Indoor Air.
Fouquier, J., Rideout, J.R., Bolyen, E., Chase, J., Shiffer, A., McDonald, D., Knight, R., Caporaso, J.G., and Kelley, S.T. (2016). ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses. Microbiome 4.
Fox, K., Fox, A., Elssner, T., Feigley, C., and Salzberg, D. (2010). MALDI-TOF mass spectrometry speciation of staphylococci and their discrimination from micrococci isolated from indoor air of schoolrooms. J Environ Monit 12, 917–923.
Fox, K., Fox, A., Rose, J., and Walla, M. (2011). Speciation of coagulase negative staphylococci, isolated from indoor air, using SDS PAGE gel bands of expressed proteins followed by MALDI TOF MS and MALDI TOF-TOF MS-MS analysis of tryptic peptides. J. Microbiol. Methods 84, 243–250.
Fujimura, K.E., Demoor, T., Rauch, M., Faruqi, A.A., Jang, S., Johnson, C.C., Boushey, H.A., Zoratti, E., Ownby, D., Lukacs, N.W., et al. (2014). House dust exposure mediates gut microbiome Lactobacillus enrichment and airway immune defense against allergens and virus infection. Proceedings of the National Academy of Sciences 111, 805–810.
Fujimura, K.E., Sitarik, A.R., Havstad, S., Lin, D.L., Levan, S., Fadrosh, D., Panzer, A.R., LaMere, B., Rackaityte, E., Lukacs, N.W., et al. (2016). Neonatal gut microbiota associates with childhood multisensitized atopy and T cell differentiation. Nature Medicine 22, 1187–1191.
Ganz, H.H., Doroud, L., Firl, A.J., Hird, S.M., Eisen, J.A., and Boyce, W.M. (2017). Community-Level Differences in the Microbiome of Healthy Wild Mallards and Those Infected by Influenza A Viruses. mSystems 2, e00188-16.
Garbarino, J., and Mason, C.E. (2016). The Power of Engaging Citizen Scientists for Scientific Progress. J Microbiol Biol Educ 17, 7–12.
Garner, E., Zhu, N., Strom, L., Edwards, M., and Pruden, A. (2016). A human exposome framework for guiding risk management and holistic assessment of recycled water quality. Environ. Sci.: Water Res. Technol. 2, 580–598.
Gibbons, S.M., Schwartz, T., Fouquier, J., Mitchell, M., Sangwan, N., Gilbert, J.A., and Kelley, S.T. (2015a). Ecological Succession and Viability of Human-Associated Microbiota on Restroom Surfaces. Appl Environ Microbiol 81, 765–773.
Gibbons, S.M., Schwartz, T., Fouquier, J., Mitchell, M., Sangwan, N., Gilbert, J.A., and Kelley, S.T. (2015b). Ecological Succession and Viability of Human-Associated Microbiota on Restroom Surfaces. Appl Environ Microbiol 81, 765–773.
Gilbert, J.A. (2016). How do we make indoor environments and healthcare settings healthier? Microb Biotechnol.
Glass, E.M., Dribinsky, Y., Yilmaz, P., Levin, H., Van Pelt, R., Wendel, D., Wilke, A., Eisen, J.A., Huse, S., Shipanova, A., et al. (2014). MIxS-BE: a MIxS extension defining a minimum information standard for sequence data from the built environment. ISME J 8, 1–3.
Gobet, A., Böer, S.I., Huse, S.M., van Beusekom, J.E.E., Quince, C., Sogin, M.L., Boetius, A., and Ramette, A. (2012). Diversity and dynamics of rare and of resident bacterial populations in coastal sands. ISME J 6, 542–553.
Gordon, J., Gandhi, P., Shekhawat, G., Frazier, A., Hampton-Marcell, J., and Gilbert, J.A. (2015). A simple novel device for air sampling by electrokinetic capture. Microbiome 3.
Grantham, N.S., Reich, B.J., Pacifici, K., Laber, E.B., Menninger, H.L., Henley, J.B., Barberán, A., Leff, J.W., Fierer, N., and Dunn, R.R. (2015). Fungi Identify the Geographic Origin of Dust Samples. PLoS One 10.
Green, J.L. (2014). Can bioinformed design promote healthy indoor ecosystems? Indoor Air 24, 113–115.
Gu, H., Chen, A., Song, X., Brasch, M.E., Henderson, J.H., and Ren, D. (2016a). How Escherichia coli lands and forms cell clusters on a surface: a new role of surface topography. Sci Rep 6.
Gu, H., Lee, S.W., Buffington, S.L., Henderson, J.H., and Ren, D. (2016b). On-Demand Removal of Bacterial Biofilms via Shape Memory Activation. ACS Appl Mater Interfaces 8, 21140–21144.
Gu, H., Kolewe, K.W., and Ren, D. (2017). Conjugation in Escherichia coli Biofilms on Poly(dimethylsiloxane) Surfaces with Microtopographic Patterns. Langmuir 33, 3142–3150.
Hara, T., Desmet, G., Baron, G.V., Minakuchi, H., and Eeltink, S. (2016). Effect of polyethylene glycol on pore structure and separation efficiency of silica-based monolithic capillary columns. J Chromatogr A.
Hartmann, E.M., Hickey, R., Hsu, T., Betancourt Román, C.M., Chen, J., Schwager, R., Kline, J., Brown, G.Z., Halden, R.U., Huttenhower, C., et al. (2016). Antimicrobial Chemicals Are Associated with Elevated Antibiotic Resistance Genes in the Indoor Dust Microbiome. Environ Sci Technol 50, 9807–9815.
He, Y., Caporaso, J.G., Jiang, X.-T., Sheng, H.-F., Huse, S.M., Rideout, J.R., Edgar, R.C., Kopylova, E., Walters, W.A., Knight, R., et al. (2015). Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversity. Microbiome 3, 20.
Hewitt, K.M., Gerba, C.P., Maxwell, S.L., and Kelley, S.T. (2012). Office Space Bacterial Abundance and Diversity in Three Metropolitan Areas. PLoS One 7.
Hewitt, K.M., Mannino, F.L., Gonzalez, A., Chase, J.H., Caporaso, J.G., Knight, R., and Kelley, S.T. (2013). Bacterial Diversity in Two Neonatal Intensive Care Units (NICUs). PLoS One 8.
Hinde, K., and Lewis, Z.T. (2015). Mother’s littlest helpers. Science 348, 1427–1428.
Hirooka, Y., Tanney, J.B., Nguyen, H.D.T., and Seifert, K.A. (2016). Xerotolerant fungi in house dust: taxonomy of Spiromastix, Pseudospiromastix and Sigleria gen. nov. in Spiromastigaceae (Onygenales, Eurotiomycetes). Mycologia 108, 135–156.
Hoisington, A., Maestre, J.P., Siegel, J.A., and Kinney, K.A. (2014a). Exploring the microbiome of the built environment: A primer on four biological methods available to building professionals. HVAC&R Research 20, 167–175.
Hoisington, A., Maestre, J.P., Kinney, K.A., and Siegel, J.A. (2016). Characterizing the bacterial communities in retail stores in the United States. Indoor Air 26, 857–868.
Hoisington, A.J., Maestre, J.P., King, M.D., Siegel, J.A., and Kinney, K.A. (2014b). Impact of sampler selection on the characterization of the indoor microbiome via high-throughput sequencing. Building and Environment 80, 274–282.
Holinger, E.P., Ross, K.A., Robertson, C.E., Stevens, M.J., Harris, J.K., and Pace, N.R. (2014). Molecular analysis of point-of-use municipal drinking water microbiology. Water Res. 49, 225–235.
Holland-Moritz, H.E., Bevans, D.R., Lang, J.M., Darling, A.E., Eisen, J.A., and Coil, D.A. (2013). Draft Genome Sequence of Leucobacter sp. Strain UCD-THU (Phylum Actinobacteria). Genome Announcements 1, e00325-13-e00325-13.
Hospodsky, D., Yamamoto, N., and Peccia, J. (2010). Accuracy, Precision, and Method Detection Limits of Quantitative PCR for Airborne Bacteria and Fungi. Appl Environ Microbiol 76, 7004–7012.
Hospodsky, D., Qian, J., Nazaroff, W.W., Yamamoto, N., Bibby, K., Rismani-Yazdi, H., and Peccia, J. (2012). Human Occupancy as a Source of Indoor Airborne Bacteria. PLoS One 7.
Hospodsky, D., Pickering, A.J., Julian, T.R., Miller, D., Gorthala, S., Boehm, A.B., and Peccia, J. (2014). Hand bacterial communities vary across two different human populations. Microbiology (Reading, Engl.) 160, 1144–1152.
Hospodsky, D., Yamamoto, N., Nazaroff, W.W., Miller, D., Gorthala, S., and Peccia, J. (2015). Characterizing airborne fungal and bacterial concentrations and emission rates in six occupied children’s classrooms. Indoor Air 25, 641–652.
Houbraken, J., Visagie, C.M., Meijer, M., Frisvad, J.C., Busby, P.E., Pitt, J.I., Seifert, K.A., Louis-Seize, G., Demirel, R., Yilmaz, N., et al. (2014). A taxonomic and phylogenetic revision of Penicillium section Aspergilloides. Studies in Mycology 78, 373–451.
Hsu, T., Joice, R., Vallarino, J., Abu-Ali, G., Hartmann, E.M., Shafquat, A., DuLong, C., Baranowski, C., Gevers, D., Green, J.L., et al. (2016). Urban Transit System Microbial Communities Differ by Surface Type and Interaction with Humans and the Environment. mSystems 1, e00018-16.
Huber, J.A., Cantin, H.V., Huse, S.M., Welch, D.B.M., Sogin, M.L., and Butterfield, D.A. (2010). Isolated communities of Epsilonproteobacteria in hydrothermal vent fluids of the Mariana Arc seamounts. FEMS Microbiology Ecology 73, 538–549.
Hull, N.M., Reens, A.L., Robertson, C.E., Stanish, L.F., Harris, J.K., Stevens, M.J., Frank, D.N., Kotter, C., and Pace, N.R. (2015). Molecular analysis of single room humidifier bacteriology. Water Res. 69, 318–327.
Huse, S.M., Welch, D.M., Morrison, H.G., and Sogin, M.L. (2010). Ironing out the wrinkles in the rare biosphere through improved OTU clustering. Environ Microbiol 12, 1889–1898.
Huse, S.M., Mark Welch, D.B., Voorhis, A., Shipunova, A., Morrison, H.G., Eren, A.M., and Sogin, M.L. (2014). VAMPS: a website for visualization and analysis of microbial population structures. BMC Bioinformatics 15, 41.
Hyde, E.R., Navas-Molina, J.A., Song, S.J., Kueneman, J.G., Ackermann, G., Cardona, C., Humphrey, G., Boyer, D., Weaver, T., Mendelson, J.R., et al. (2016). The Oral and Skin Microbiomes of Captive Komodo Dragons Are Significantly Shared with Their Habitat. mSystems 1, e00046-16.
Inglis, D.O., Skrzypek, M.S., Liaw, E., Moktali, V., Sherlock, G., and Stajich, J.E. (2014). Literature-based gene curation and proposed genetic nomenclature for cryptococcus. Eukaryotic Cell 13, 878–883.
Jain, P., Hsu, T., Arai, M., Biermann, K., Thaler, D.S., Nguyen, A., González, P.A., Tufariello, J.M., Kriakov, J., Chen, B., et al. (2014). Specialized Transduction Designed for Precise High-Throughput Unmarked Deletions in Mycobacterium tuberculosis. mBio 5.
James, T.Y., Pelin, A., Bonen, L., Ahrendt, S., Sain, D., Corradi, N., and Stajich, J.E. (2013). Shared signatures of parasitism and phylogenomics unite Cryptomycota and microsporidia. Curr. Biol. 23, 1548–1553.
Jančič, S., Nguyen, H.D.T., Frisvad, J.C., Zalar, P., Schroers, H.-J., Seifert, K.A., and Gunde-Cimerman, N. (2015). A Taxonomic Revision of the Wallemia sebi Species Complex. PLoS One 10.
Jeffries, T.C., Ostrowski, M., Williams, R.B., Xie, C., Jensen, R.M., Grzymski, J.J., Senstius, S.J., Givskov, M., Hoeke, R., Philip, G.K., et al. (2015). Spatially extensive microbial biogeography of the Indian Ocean provides insights into the unique community structure of a pristine coral atoll. Scientific Reports 5, 15383.
Jensen, K., Ko, A.E., Schal, C., and Silverman, J. (2016). Insecticide resistance and nutrition interactively shape life-history parameters in German cockroaches. Sci Rep 6.
Ji, P., Parks, J., Edwards, M.A., and Pruden, A. (2015). Impact of Water Chemistry, Pipe Material and Stagnation on the Building Plumbing Microbiome. PLoS One 10.
Ji, P., Rhoads, W.J., Edwards, M.A., and Pruden, A. (2017). Impact of water heater temperature setting and water use frequency on the building plumbing microbiome. The ISME Journal 11, 1318–1330.
Kelley, S.T. Your Office Has a Distinct Microbiome.
Kelley, S.T., and Gilbert, J.A. (2013). Studying the microbiology of the indoor environment. Genome Biol 14, 202.
Kembel, S.W., Jones, E., Kline, J., Northcutt, D., Stenson, J., Womack, A.M., Bohannan, B.J., Brown, G.Z., and Green, J.L. (2012). Architectural design influences the diversity and structure of the built environment microbiome. ISME J 6, 1469–1479.
Kembel, S.W., Meadow, J.F., O’Connor, T.K., Mhuireach, G., Northcutt, D., Kline, J., Moriyama, M., Brown, G.Z., Bohannan, B.J.M., and Green, J.L. (2014). Architectural Design Drives the Biogeography of Indoor Bacterial Communities. PLoS One 9.
Kincheloe, G.N., Eisen, J.A., and Coil, D.A. (2017). Draft Genome Sequence of Arthrobacter sp. Strain UCD-GKA (Phylum Actinobacteria ). Genome Announcements 5, e01599-16.
Klein, A.M., Bohannan, B.J.M., Jaffe, D.A., Levin, D.A., and Green, J.L. (2016a). Molecular Evidence for Metabolically Active Bacteria in the Atmosphere. Front Microbiol 7.
Klein, B.A., Lemon, K.P., Faller, L.L., Jospin, G., Eisen, J.A., and Coil, D.A. (2016b). Draft Genome Sequence of Curtobacterium sp. Strain UCD-KPL2560 (Phylum Actinobacteria ). Genome Announcements 4, e01040-16.
Klein, B.A., Lemon, K.P., Gajare, P., Jospin, G., Eisen, J.A., and Coil, D.A. (2017). Draft Genome Sequences of Dermacoccus nishinomiyaensis Strains UCD-KPL2534 and UCD-KPL2528 Isolated from an Indoor Track Facility. Genome Announcements 5, e01652-16.
Kleindienst, S., Grim, S., Sogin, M., Bracco, A., Crespo-Medina, M., and Joye, S.B. (2016). Diverse, rare microbial taxa responded to the Deepwater Horizon deep-sea hydrocarbon plume. ISME J 10, 400–415.
Knight, R., Callewaert, C., Marotz, C., Hyde, E.R., Debelius, J.W., McDonald, D., and Sogin, M.L. (2017). The Microbiome and Human Biology. Annual Review of Genomics and Human Genetics 18.
Ko, A.E., Bieman, D.N., Schal, C., and Silverman, J. (2015). Insecticide resistance and diminished secondary kill performance of bait formulations against German cockroaches (Dictyoptera: Blattellidae). Pest Manag. Sci.
Ko, A.E., Schal, C., and Silverman, J. (2016). Diet quality affects bait performance in German cockroaches (Dictyoptera: Blattellidae). Pest Manag. Sci. 72, 1826–1836.
Kõljalg, U., Tedersoo, L., Nilsson, R.H., and Abarenkov, K. (2016). Digital identifiers for fungal species. Science 352, 1182–1183.
Konya, T., and Scott, J.A. (2014). Recent Advances in the Microbiology of the Built Environment. Curr Sustainable Renewable Energy Rep 1, 35–42.
Kooken, J.M., Fox, K.F., and Fox, A. (2012). Characterization of Micrococcus strains isolated from indoor air. Molecular and Cellular Probes 26, 1–5.
Kopylova, E., Navas-Molina, J.A., Mercier, C., Xu, Z.Z., Mahé, F., He, Y., Zhou, H.-W., Rognes, T., Caporaso, J.G., and Knight, R. (2016). Open-Source Sequence Clustering Methods Improve the State Of the Art. mSystems 1.
Kuczynski, J., Stombaugh, J., Walters, W.A., González, A., Caporaso, J.G., and Knight, R. (2012). Using QIIME to Analyze 16S rRNA Gene Sequences from Microbial Communities. Curr Protoc Microbiol 0 1, Unit-1E.5.
Kunkel, S.A., Azimi, P., Zhao, H., Stark, B.C., and Stephens, B. (2017). Quantifying the size-resolved dynamics of indoor bioaerosol transport and control. Indoor Air.
Langar, S., and Pearce, A.R. Implementation Trends for Rainwater-Harvesting Technologies and Strategies and Their Relationship with Building Information Modeling. Journal of Architectural Engineering 0, 04016016.
Langille, M.G.I., Zaneveld, J., Caporaso, J.G., McDonald, D., Knights, D., Reyes, J.A., Clemente, J.C., Burkepile, D.E., Vega Thurber, R.L., Knight, R., et al. (2013). Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol 31, 814–821.
Lax, S., and Gilbert, J.A. (2015). Hospital-associated microbiota and implications for nosocomial infections. Trends Mol Med 21, 427–432.
Lax, S., and Gilbert, J.A. (2017). Forensic microbiology in built environments. In Forensic Microbiology, D.O. Carter, J.K. Tomberlin, M.E. Benbow, and J.L. Metcalf, eds. (Chichester, UK: John Wiley & Sons, Ltd), pp. 328–338.
Lax, S., Smith, D.P., Hampton-Marcell, J., Owens, S.M., Handley, K.M., Scott, N.M., Gibbons, S.M., Larsen, P., Shogan, B.D., Weiss, S., et al. (2014). Longitudinal analysis of microbial interaction between humans and the indoor environment. Science 345, 1048–1052.
Lax, S., Hampton-Marcell, J.T., Gibbons, S.M., Colares, G.B., Smith, D., Eisen, J.A., and Gilbert, J.A. (2015a). Forensic analysis of the microbiome of phones and shoes. Microbiome 3.
Lax, S., Nagler, C.R., and Gilbert, J.A. (2015b). Our interface with the built environment: immunity and the indoor microbiota. Trends Immunol 36, 121–123.
Lax, S., Sangwan, N., Smith, D., Larsen, P., Handley, K.M., Richardson, M., Guyton, K., Krezalek, M., Shogan, B.D., Defazio, J., et al. (2017). Bacterial colonization and succession in a newly opened hospital. Science Translational Medicine 9, eaah6500.
Leff, J.W., and Fierer, N. (2013). Bacterial Communities Associated with the Surfaces of Fresh Fruits and Vegetables. PLoS One 8.
Levin, H., Täubel, M., and Hernandez, M. (2015a). Summary of Sloan symposium: healthy buildings 2015-Europe. Microbiome 3.
Levin, H., Täubel, M., and Hernandez, M. (2015b). Summary of Sloan symposium: healthy buildings 2015-Europe. Microbiome 3.
Lewis, C.T. (2011). Identification of Fungal DNA Barcode Targets and PCR Primers Based on Pfam Protein Families and Taxonomic Hierarchy. The Open Applied Informatics Journal 5, 30–44.
Lewis, Z.T., and Mills, D.A. (2017). Differential Establishment of Bifidobacteria in the Breastfed Infant Gut. In Nestlé Nutrition Institute Workshop Series, E. Isolauri, P.M. Sherman, and W.A. Walker, eds. (S. Karger AG), pp. 149–159.
Lewis, Z.T., Davis, J.C.C., Smilowitz, J.T., German, J.B., Lebrilla, C.B., and Mills, D.A. (2016a). The impact of freeze-drying infant fecal samples on measures of their bacterial community profiles and milk-derived oligosaccharide content. PeerJ 4.
Lewis, Z.T., Shani, G., Masarweh, C.F., Popovic, M., Frese, S.A., Sela, D.A., Underwood, M.A., and Mills, D.A. (2016b). Validating bifidobacterial species and subspecies identity in commercial probiotic products. Pediatric Research 79, 445–452.
Lewis, Z.T., Sidamonidze, K., Tsaturyan, V., Tsereteli, D., Khachidze, N., Pepoyan, A., Zhgenti, E., Tevzadze, L., Manvelyan, A., Balayan, M., et al. (2017). The Fecal Microbial Community of Breast-fed Infants from Armenia and Georgia. Scientific Reports 7, 40932.
Licina, D., Bhangar, S., Brooks, B., Baker, R., Firek, B., Tang, X., Morowitz, M.J., Banfield, J.F., and Nazaroff, W.W. (2016). Concentrations and Sources of Airborne Particles in a Neonatal Intensive Care Unit. PLoS One 11.
Licina, D., Tian, Y., and Nazaroff, W.W. (2017a). Emission rates and the personal cloud effect associated with particle release from the perihuman environment. Indoor Air.
Licina, D., Tian, Y., and Nazaroff, W.W. (2017b). Inhalation intake fraction of particulate matter from localized indoor emissions. Building and Environment 123, 14–22.
Ling, A.L., Pace, N.R., Hernandez, M.T., and LaPara, T.M. (2013). Tetracycline resistance and Class 1 integron genes associated with indoor and outdoor aerosols. Environ. Sci. Technol. 47, 4046–4052.
Ling, A.L., Robertson, C.E., Harris, J.K., Frank, D.N., Kotter, C.V., Stevens, M.J., Pace, N.R., and Hernandez, M.T. (2014). Carbon dioxide and hydrogen sulfide associations with regional bacterial diversity patterns in microbially induced concrete corrosion. Environ. Sci. Technol. 48, 7357–7364.
Ling, A.L., Robertson, C.E., Harris, J.K., Frank, D.N., Kotter, C.V., Stevens, M.J., Pace, N.R., and Hernandez, M.T. (2015). High-Resolution Microbial Community Succession of Microbially Induced Concrete Corrosion in Working Sanitary Manholes. PLoS One 10.
Liu, P., and Stajich, J.E. (2015). Characterization of the Carbohydrate Binding Module 18 gene family in the amphibian pathogen Batrachochytrium dendrobatidis. Fungal Genet. Biol. 77, 31–39.
Liu, S., Li, R., Wild, R.J., Warneke, C., de Gouw, J.A., Brown, S.S., Miller, S.L., Luongo, J.C., Jimenez, J.L., and Ziemann, P.J. (2016). Contribution of human-related sources to indoor volatile organic compounds in a university classroom. Indoor Air 26, 925–938.
Lujan, K.M., Eisen, J.A., and Coil, D.A. (2017). Draft Genome Sequences of Pseudomonas moraviensis UCD-KL30, Vibrio ostreicida UCD-KL16, Colwellia sp. Strain UCD-KL20, Shewanella sp. Strain UCD-KL12, and Shewanella sp. Strain UCD-KL21, Isolated from Seagrass. Genome Announcements 5, e00023-17.
Luongo, J.C., Barberán, A., Hacker-Cary, R., Morgan, E.E., Miller, S.L., and Fierer, N. (2017). Microbial analyses of airborne dust collected from dormitory rooms predict the sex of occupants. Indoor Air 27, 338–344.
Lymperopoulou, D.S., Adams, R.I., and Lindow, S.E. (2016). Contribution of vegetation to the microbial composition of nearby outdoor air. Appl. Environ. Microbiol.
Lymperopoulou, D.S., Coil, D.A., Schichnes, D., Lindow, S.E., Jospin, G., Eisen, J.A., and Adams, R.I. (2017). Draft genome sequences of eight bacteria isolated from the indoor environment: Staphylococcus capitis strain H36, S. capitis strain H65, S. cohnii strain H62, S. hominis strain H69, Microbacterium sp. strain H83, Mycobacterium iranicum strain H39, Plantibacter sp. strain H53, and Pseudomonas oryzihabitans strain H72. Standards in Genomic Sciences 12.
Ma, X., Baron, J.L., Vikram, A., Stout, J.E., and Bibby, K. (2015). Fungal diversity and presence of potentially pathogenic fungi in a hospital hot water system treated with on-site monochloramine. Water Res. 71, 197–206.
Madden, A.A., Barberán, A., Bertone, M.A., Menninger, H.L., Dunn, R.R., and Fierer, N. (2016). The diversity of arthropods in homes across the United States as determined by environmental DNA analyses. Molecular Ecology 25, 6214–6224.
Madrid, N., Boulton, R., and Knoesen, A. (2017). Remote monitoring of winery and creamery environments with a wireless sensor system. Building and Environment 119, 128–139.
Marchesi, I., Ferranti, G., Bargellini, A., Marchegiano, P., Predieri, G., Stout, J.E., and Borella, P. (2013). Monochloramine and chlorine dioxide for controlling Legionella pneumophila contamination: biocide levels and disinfection by-product formation in hospital water networks. J Water Health 11, 738–747.
Marsh, A. (2016). FAQ: Microbiology of Built Environments. Report on an American Academy of Microbiology Colloquium held in Washington, DC, in September 2015.
Martin, L.J., Adams, R.I., Bateman, A., Bik, H.M., Hawks, J., Hird, S.M., Hughes, D., Kembel, S.W., Kinney, K., Kolokotronis, S.-O., et al. (2015). Evolution of the indoor biome. Trends in Ecology & Evolution 30, 223–232.
Matos, Y.K., and Schal, C. (2016). Laboratory and Field Evaluation of Zyrox Fly Granular Bait Against Asian and German Cockroaches (Dictyoptera: Blattellidae). J. Econ. Entomol. 109, 1807–1812.
McDonald, D., Price, M.N., Goodrich, J., Nawrocki, E.P., DeSantis, T.Z., Probst, A., Andersen, G.L., Knight, R., and Hugenholtz, P. (2012a). An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J 6, 610–618.
McDonald, D., Clemente, J.C., Kuczynski, J., Rideout, J.R., Stombaugh, J., Wendel, D., Wilke, A., Huse, S., Hufnagle, J., Meyer, F., et al. (2012b). The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome. Gigascience 1, 7.
McLean, J.S., Lombardo, M.-J., Badger, J.H., Edlund, A., Novotny, M., Yee-Greenbaum, J., Vyahhi, N., Hall, A.P., Yang, Y., Dupont, C.L., et al. (2013a). Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum. Proceedings of the National Academy of Sciences 110, E2390–E2399.
McLean, J.S., Lombardo, M.-J., Ziegler, M.G., Novotny, M., Yee-Greenbaum, J., Badger, J.H., Tesler, G., Nurk, S., Lesin, V., Brami, D., et al. (2013b). Genome of the pathogen Porphyromonas gingivalis recovered from a biofilm in a hospital sink using a high-throughput single-cell genomics platform. Genome Research 23, 867–877.
Meadow, J.F., Bateman, A.C., Herkert, K.M., O’Connor, T.K., and Green, J.L. (2013). Significant changes in the skin microbiome mediated by the sport of roller derby. Peerj 1.
Meadow, J.F., Altrichter, A.E., Kembel, S.W., Moriyama, M., O’Connor, T.K., Womack, A.M., Brown, G.Z., Green, J.L., and Bohannan, B.J.M. (2014a). Bacterial communities on classroom surfaces vary with human contact. Microbiome 2, 7.
Meadow, J.F., Altrichter, A.E., Kembel, S.W., Kline, J., Mhuireach, G., Moriyama, M., Northcutt, D., O’Connor, T.K., Womack, A.M., Brown, G.Z., et al. (2014b). Indoor airborne bacterial communities are influenced by ventilation, occupancy, and outdoor air source. Indoor Air 24, 41–48.
Meadow, J.F., Altrichter, A.E., and Green, J.L. (2014c). Mobile phones carry the personal microbiome of their owners. PeerJ 2.
Meadow, J.F., Altrichter, A.E., Bateman, A.C., Stenson, J., Brown, G., Green, J.L., and Bohannan, B.J.M. (2015). Humans differ in their personal microbial cloud. PeerJ 3.
Mélida, H., Sain, D., Stajich, J.E., and Bulone, V. (2015). Deciphering the uniqueness of Mucoromycotina cell walls by combining biochemical and phylogenomic approaches. Environ. Microbiol. 17, 1649–1662.
Mensah-Attipoe, J., Täubel, M., Hernandez, M., Pitkäranta, M., and Reponen, T. (2017). An emerging paradox: Toward a better understanding of the potential benefits and adversity of microbe exposures in the indoor environment. Indoor Air 27, 3–5.
Mhuireach, G., Johnson, B.R., Altrichter, A.E., Ladau, J., Meadow, J.F., Pollard, K.S., and Green, J.L. (2016). Urban greenness influences airborne bacterial community composition. Science of The Total Environment 571, 680–687.
Nackerdien, Z.E., Keynan, A., Bassler, B.L., Lederberg, J., and Thaler, D.S. (2008). Quorum Sensing Influences Vibrio harveyi Growth Rates in a Manner Not Fully Accounted For by the Marker Effect of Bioluminescence. PLoS ONE 3, e1671.
Nazaroff, W.W. (2016). Indoor bioaerosol dynamics. Indoor Air 26, 61–78.
Nazaroff, W.W., and Goldstein, A.H. (2015). Indoor chemistry: research opportunities and challenges. Indoor Air 25, 357–361.
Neches, R.Y., Flynn, K.J., Zaman, L., Tung, E., and Pudlo, N. (2016). On the intrinsic sterility of 3D printing. PeerJ 4, e2661.
Newton, R.J., Huse, S.M., Morrison, H.G., Peake, C.S., Sogin, M.L., and McLellan, S.L. (2013). Shifts in the Microbial Community Composition of Gulf Coast Beaches Following Beach Oiling. PLoS One 8.
Nguyen, H.D.T., Jančič, S., Meijer, M., Tanney, J.B., Zalar, P., Gunde-Cimerman, N., and Seifert, K.A. (2015). Application of the Phylogenetic Species Concept to Wallemia sebi from House Dust and Indoor Air Revealed by Multi-Locus Genealogical Concordance. PLoS One 10.
Nguyen, T.A., Cissé, O.H., Yun Wong, J., Zheng, P., Hewitt, D., Nowrousian, M., Stajich, J.E., and Jedd, G. (2017). Innovation and constraint leading to complex multicellularity in the Ascomycota. Nat Commun 8, 14444.
O’Dwyer, J.P., Kembel, S.W., and Green, J.L. (2012). Phylogenetic Diversity Theory Sheds Light on the Structure of Microbial Communities. PLoS Comput Biol 8.
Olm, M.R., Brown, C.T., Brooks, B., Firek, B., Baker, R., Burstein, D., Soenjoyo, K., Thomas, B.C., Morowitz, M., and Banfield, J. (2017). Identical bacterial populations colonize premature infant gut, skin, and oral microbiomes and exhibit different in situ growth rates. Genome Res. gr.213256.116.
Peccia, J., and Kwan, S.E. (2016). Buildings, Beneficial Microbes, and Health. Trends in Microbiology 24, 595–597.
Petras, D., Nothias, L.-F., Quinn, R.A., Alexandrov, T., Bandeira, N., Bouslimani, A., Castro-Falcón, G., Chen, L., Dang, T., Floros, D.J., et al. (2016). Mass Spectrometry-Based Visualization of Molecules Associated with Human Habitats. Analytical Chemistry 88, 10775–10784.
Pruden, A. (2014). Balancing water sustainability and public health goals in the face of growing concerns about antibiotic resistance. Environ. Sci. Technol. 48, 5–14.
Prussin, A.J., and Marr, L.C. (2015). Sources of airborne microorganisms in the built environment. Microbiome 3.
Prussin, A.J., Marr, L.C., and Bibby, K.J. (2014). Challenges of studying viral aerosol metagenomics and communities in comparison with bacterial and fungal aerosols. FEMS Microbiol. Lett. 357, 1–9.
Prussin, A.J., Garcia, E.B., and Marr, L.C. (2015). Total Virus and Bacteria Concentrations in Indoor and Outdoor Air. Environ Sci Technol Lett 2, 84–88.
Prussin, A.J., Vikram, A., Bibby, K.J., and Marr, L.C. (2016). Seasonal Dynamics of the Airborne Bacterial Community and Selected Viruses in a Children’s Daycare Center. PLoS One 11.
Qian, J., Hospodsky, D., Yamamoto, N., Nazaroff, W.W., and Peccia, J. (2012). Size-resolved emission rates of airborne bacteria and fungi in an occupied classroom: Size-resolved bioaerosol emission rates. Indoor Air 22, 339–351.
Qian, J., Peccia, J., and Ferro, A.R. (2014). Walking-induced particle resuspension in indoor environments. Atmospheric Environment 89, 464–481.
Ramos, T., Dedesko, S., Siegel, J.A., Gilbert, J.A., and Stephens, B. (2015). Spatial and Temporal Variations in Indoor Environmental Conditions, Human Occupancy, and Operational Characteristics in a New Hospital Building. PLoS One 10.
Raveh-Sadka, T., Firek, B., Sharon, I., Baker, R., Brown, C.T., Thomas, B.C., Morowitz, M.J., and Banfield, J.F. (2016). Evidence for persistent and shared bacterial strains against a background of largely unique gut colonization in hospitalized premature infants. The ISME Journal 10, 2817–2830.
Raveh-Sadka, T., Thomas, B.C., Singh, A., Firek, B., Brooks, B., Castelle, C.J., Sharon, I., Baker, R., Good, M., Morowitz, M.J., et al. Gut bacteria are rarely shared by co-hospitalized premature infants, regardless of necrotizing enterocolitis development. eLife 4.
Rhoads, W.J., Pruden, A., and Edwards, M.A. (2014). Anticipating challenges with in-building disinfection for control of opportunistic pathogens. Water Environ. Res. 86, 540–549.
Rhoads, W.J., Ji, P., Pruden, A., and Edwards, M.A. (2015). Water heater temperature set point and water use patterns influence Legionella pneumophila and associated microorganisms at the tap. Microbiome 3.
Rhoads, W.J., Pruden, A., and Edwards, M.A. (2016). Convective Mixing in Distal Pipes Exacerbates Legionella pneumophila Growth in Hot Water Plumbing. Pathogens 5.
Rhoads, W.J., Pruden, A., and Edwards, M.A. (2017). Interactive Effects of Corrosion, Copper, and Chloramines on Legionella and Mycobacteria in Hot Water Plumbing. Environmental Science & Technology.
Rideout, J.R., He, Y., Navas-Molina, J.A., Walters, W.A., Ursell, L.K., Gibbons, S.M., Chase, J., McDonald, D., Gonzalez, A., Robbins-Pianka, A., et al. (2014). Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences. PeerJ 2, e545.
Rideout, J.R., Chase, J.H., Bolyen, E., Ackermann, G., González, A., Knight, R., and Caporaso, J.G. (2016). Keemei: cloud-based validation of tabular bioinformatics file formats in Google Sheets. Gigascience 5, 27.
Robertson, C.E., Baumgartner, L.K., Harris, J.K., Peterson, K.L., Stevens, M.J., Frank, D.N., and Pace, N.R. (2013). Culture-Independent Analysis of Aerosol Microbiology in a Metropolitan Subway System. Appl Environ Microbiol 79, 3485–3493.
Rosenfeld, J.A., Reeves, D., Brugler, M.R., Narechania, A., Simon, S., Durrett, R., Foox, J., Shianna, K., Schatz, M.C., Gandara, J., et al. (2016). Genome assembly and geospatial phylogenomics of the bed bug Cimex lectularius. Nat Commun 7.
Ruiz-Calderon, J.F., Cavallin, H., Song, S.J., Novoselac, A., Pericchi, L.R., Hernandez, J.N., Rios, R., Branch, O.H., Pereira, H., Paulino, L.C., et al. (2016). Walls talk: Microbial biogeography of homes spanning urbanization. Sci Adv 2.
Sachs, J.L., Skophammer, R.G., Bansal, N., and Stajich, J.E. (2014). Evolutionary origins and diversification of proteobacterial mutualists. Proc. Biol. Sci. 281, 20132146.
Samson, R.A., Visagie, C.M., Houbraken, J., Hong, S.-B., Hubka, V., Klaassen, C.H.W., Perrone, G., Seifert, K.A., Susca, A., Tanney, J.B., et al. (2014). Phylogeny, identification and nomenclature of the genus Aspergillus. Studies in Mycology 78, 141–173.
Schoch, C.L., and Seifert, K.A. (2012). Reply to Kiss: Internal transcribed spacer (ITS) remains the best candidate as a universal DNA barcode marker for Fungi despite imperfections. Proceedings of the National Academy of Sciences 109, E1812–E1812.
Schoch, C.L., Seifert, K.A., Huhndorf, S., Robert, V., Spouge, J.L., Levesque, C.A., Chen, W., Bolchacova, E., Voigt, K., Crous, P.W., et al. (2012). Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proc Natl Acad Sci U S A 109, 6241–6246.
Schoch, C.L., Robbertse, B., Robert, V., Vu, D., Cardinali, G., Irinyi, L., Meyer, W., Nilsson, R.H., Hughes, K., Miller, A.N., et al. (2014). Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi. Database 2014, bau061-bau061.
Schwake, D.O., Garner, E., Strom, O.R., Pruden, A., and Edwards, M.A. (2016). Legionella DNA Markers in Tap Water Coincident with a Spike in Legionnaires’ Disease in Flint, MI. Environ. Sci. Technol. Lett. 3, 311–315.
Segers, F.J.J., Meijer, M., Houbraken, J., Samson, R.A., Wösten, H.A.B., and Dijksterhuis, J. (2015). Xerotolerant Cladosporium sphaerospermum Are Predominant on Indoor Surfaces Compared to Other Cladosporium Species. PLoS One 10.
Shin, H., Pei, Z., Martinez, K.A., Rivera-Vinas, J.I., Mendez, K., Cavallin, H., and Dominguez-Bello, M.G. (2015). The first microbial environment of infants born by C-section: the operating room microbes. Microbiome 3.
Shogan, B.D., Smith, D.P., Packman, A.I., Kelley, S.T., Landon, E.M., Bhangar, S., Vora, G.J., Jones, R.M., Keegan, K., Stephens, B., et al. (2013). The Hospital Microbiome Project: Meeting report for the 2nd Hospital Microbiome Project, Chicago, USA, January 15th, 2013. Stand Genomic Sci 8, 571–579.
Sinha, R., Abnet, C.C., White, O., Knight, R., and Huttenhower, C. (2015). The microbiome quality control project: baseline study design and future directions. Genome Biol 16.
Smith, D., Alverdy, J., An, G., Coleman, M., Garcia-Houchins, S., Green, J., Keegan, K., Kelley, S.T., Kirkup, B.C., Kociolek, L., et al. (2013). The Hospital Microbiome Project: Meeting Report for the 1st Hospital Microbiome Project Workshop on sampling design and building science measurements, Chicago, USA, June 7th-8th 2012. Stand Genomic Sci 8, 112–117.
Spangler, R., Goddard, N.L., and Thaler, D.S. (2009a). Optimizing Taq Polymerase Concentration for Improved Signal-to-Noise in the Broad Range Detection of Low Abundance Bacteria. PLoS One 4.
Spangler, R., Goddard, N.L., Spangler, D.N., and Thaler, D.S. (2009b). Tests of the Single-hit DNA Damage Model. Journal of Molecular Biology 392, 283–300.
Stajich, J.E., Harris, T., Brunk, B.P., Brestelli, J., Fischer, S., Harb, O.S., Kissinger, J.C., Li, W., Nayak, V., Pinney, D.F., et al. (2012). FungiDB: an integrated functional genomics database for fungi. Nucleic Acids Res. 40, D675-681.
Stamper, C.E., Hoisington, A.J., Gomez, O.M., Halweg-Edwards, A.L., Smith, D.G., Bates, K.L., Kinney, K.A., Postolache, T.T., Brenner, L.A., Rook, G. a. W., et al. (2016). The Microbiome of the Built Environment and Human Behavior: Implications for Emotional Health and Well-Being in Postmodern Western Societies. Int. Rev. Neurobiol. 131, 289–323.
Stein, M.M., Hrusch, C.L., Gozdz, J., Igartua, C., Pivniouk, V., Murray, S.E., Ledford, J.G., Marques dos Santos, M., Anderson, R.L., Metwali, N., et al. (2016). Innate Immunity and Asthma Risk in Amish and Hutterite Farm Children. N. Engl. J. Med. 375, 411–421.
Stephens, B. (2016). What Have We Learned about the Microbiomes of Indoor Environments? mSystems 1, e00083-16.
Stephens, B., Adams, R.I., Bhangar, S., Bibby, K., and Waring, M.S. (2015). From commensalism to mutualism: integrating the microbial ecology, building science, and indoor air communities to advance research on the indoor microbiome. Indoor Air 25, 1–3.
Stielow, J.B., L?vesque, C.A., Seifert, K.A., Meyer, W., Irinyi, L., Smits, D., Renfurm, R., Verkley, G.J.M., Groenewald, M., Chaduli, D., et al. (2015). One fungus, which genes? Development and assessment of universal primers for potential secondary fungal DNA barcodes. Persoonia – Molecular Phylogeny and Evolution of Fungi 35, 242–263.
Stoeckle, M.Y., and Thaler, D.S. (2014). DNA Barcoding Works in Practice but Not in (Neutral) Theory. PLoS One 9.
Sun, Y., Cai, Y., Huse, S.M., Knight, R., Farmerie, W.G., Wang, X., and Mai, V. (2012). A large-scale benchmark study of existing algorithms for taxonomy-independent microbial community analysis. Brief Bioinform 13, 107–121.
Tanney, J.B., and Seifert, K.A. (2013). Rasamsonia pulvericola sp. nov., isolated from house dust. IMA Fungus 4, 205–212.
Taylor, D.L., Walters, W.A., Lennon, N.J., Bochicchio, J., Krohn, A., Caporaso, J.G., and Pennanen, T. (2016). Accurate Estimation of Fungal Diversity and Abundance through Improved Lineage-Specific Primers Optimized for Illumina Amplicon Sequencing. Appl. Environ. Microbiol. 82, 7217–7226.
Thaler, D.S. (2009). The cytoplasmic structure hypothesis for ribosome assembly, vertical inheritance, and phylogeny. BioEssays 31, 774–783.
Thaler, D.S. (2016). Toward a microbial Neolithic revolution in buildings. Microbiome 4.
Thaler, D.S., and Stoeckle, M.Y. (2016). Bridging two scholarly islands enriches both: COI DNA barcodes for species identification versus human mitochondrial variation for the study of migrations and pathologies. Ecology and Evolution 6, 6824–6835.
Uejio, C.K., Tamerius, J.D., Vredenburg, J., Asaeda, G., Isaacs, D.A., Braun, J., Quinn, A., and Freese, J.P. (2016). Summer indoor heat exposure and respiratory and cardiovascular distress calls in New York City, NY, U.S. Indoor Air 26, 594–604.
Valm, A.M., Welch, J.L.M., Rieken, C.W., Hasegawa, Y., Sogin, M.L., Oldenbourg, R., Dewhirst, F.E., and Borisy, G.G. (2011). Systems-level analysis of microbial community organization through combinatorial labeling and spectral imaging. Proc Natl Acad Sci U S A 108, 4152–4157.
Valm, A.M., Welch, J.L.M., and Borisy, G.G. (2012). CLASI-FISH: Principles of Combinatorial Labeling and Spectral Imaging. Syst Appl Microbiol 35, 496–502.
Valm, A.M., Oldenbourg, R., and Borisy, G.G. (2016). Multiplexed Spectral Imaging of 120 Different Fluorescent Labels. PLOS ONE 11, e0158495.
Vandegrift, R., Bateman, A.C., Siemens, K.N., Nguyen, M., Wilson, H.E., Green, J.L., Van Den Wymelenberg, K.G., and Hickey, R.J. (2017). Cleanliness in context: reconciling hygiene with a modern microbial perspective. Microbiome 5, 76.
Vázquez-Baeza, Y., Pirrung, M., Gonzalez, A., and Knight, R. (2013). EMPeror: a tool for visualizing high-throughput microbial community data. Gigascience 2, 16.
Vincent Robert, L., Sz?ke, S., Eberhardt, U., Cardinali, G., Meyer, W., Seifert, K.A., L?vesque, C.A., and Lewis, C.T. (2011). The Quest for a General and Reliable Fungal DNA Barcode. The Open Applied Informatics Journal 5, 45–61.
Visagie, C.M., Houbraken, J., Rodriques, C., Pereira, C.S., Dijksterhuis, J., Seifert, K.A., Jacobs, K., and Samson, R.A. (2013). Five new <I>Penicillium</I> species in section <I>Sclerotiora</I>: a tribute to the Dutch Royal family. Persoonia – Molecular Phylogeny and Evolution of Fungi 31, 42–62.
Visagie, C.M., Hirooka, Y., Tanney, J.B., Whitfield, E., Mwange, K., Meijer, M., Amend, A.S., Seifert, K.A., and Samson, R.A. (2014a). Aspergillus, Penicillium and Talaromyces isolated from house dust samples collected around the world. Studies in Mycology 78, 63–139.
Visagie, C.M., Seifert, K.A., Houbraken, J., Samson, R.A., and Jacobs, K. (2014b). Diversity of Penicillium section Citrina within the fynbos biome of South Africa, including a new species from a Protea repens infructescence. Mycologia 106, 537–552.
Visagie, C.M., Houbraken, J., Frisvad, J.C., Hong, S.-B., Klaassen, C.H.W., Perrone, G., Seifert, K.A., Varga, J., Yaguchi, T., and Samson, R.A. (2014c). Identification and nomenclature of the genus Penicillium. Studies in Mycology 78, 343–371.
Visagie, C.M., Varga, J., Houbraken, J., Meijer, M., Kocsubé, S., Yilmaz, N., Fotedar, R., Seifert, K.A., Frisvad, J.C., and Samson, R.A. (2014d). Ochratoxin production and taxonomy of the yellow aspergilli (Aspergillus section Circumdati). Studies in Mycology 78, 1–61.
Visagie, C.M., Yilmaz, N., Renaud, J.B., Sumarah, M.W., Hubka, V., Frisvad, J.C., Chen, A.J., Meijer, M., and Seifert, K.A. (2017). A survey of xerophilic Aspergillus from indoor environment, including descriptions of two new section Aspergillus species producing eurotium-like sexual states. MycoKeys 19, 1–30.
Wada-Katsumata, A., Zurek, L., Nalyanya, G., Roelofs, W.L., Zhang, A., and Schal, C. (2015). Gut bacteria mediate aggregation in the German cockroach. Proc Natl Acad Sci U S A 112, 15678–15683.
Walters, W., Hyde, E.R., Berg-Lyons, D., Ackermann, G., Humphrey, G., Parada, A., Gilbert, J.A., Jansson, J.K., Caporaso, J.G., Fuhrman, J.A., et al. (2016). Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys. mSystems 1, e00009-15.
Wang, H., Pryor, M.A., Edwards, M.A., Falkinham, J.O., and Pruden, A. (2013a). Effect of GAC pre-treatment and disinfectant on microbial community structure and opportunistic pathogen occurrence. Water Res. 47, 5760–5772.
Wang, H., Edwards, M.A., Falkinham, J.O., and Pruden, A. (2013b). Probiotic approach to pathogen control in premise plumbing systems? A review. Environ. Sci. Technol. 47, 10117–10128.
Wang, H., Masters, S., Edwards, M.A., Falkinham, J.O., and Pruden, A. (2014a). Effect of disinfectant, water age, and pipe materials on bacterial and eukaryotic community structure in drinking water biofilm. Environ. Sci. Technol. 48, 1426–1435.
Wang, H., Proctor, C.R., Edwards, M.A., Pryor, M., Santo Domingo, J.W., Ryu, H., Camper, A.K., Olson, A., and Pruden, A. (2014b). Microbial community response to chlorine conversion in a chloraminated drinking water distribution system. Environ. Sci. Technol. 48, 10624–10633.
Wang, H., Masters, S., Falkinham, J.O., Edwards, M.A., and Pruden, A. (2015). Distribution System Water Quality Affects Responses of Opportunistic Pathogen Gene Markers in Household Water Heaters. Environ. Sci. Technol. 49, 8416–8424.
Wang, H., Bédard, E., Prévost, M., Camper, A.K., Hill, V.R., and Pruden, A. (2017). Methodological approaches for monitoring opportunistic pathogens in premise plumbing: A review. Water Research 117, 68–86.
Wang, M., Carver, J.J., Phelan, V.V., Sanchez, L.M., Garg, N., Peng, Y., Nguyen, D.D., Watrous, J., Kapono, C.A., Luzzatto-Knaan, T., et al. (2016a). Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. Nature Biotechnology 34, 828–837.
Wang, X.W., Houbraken, J., Groenewald, J.Z., Meijer, M., Andersen, B., Nielsen, K.F., Crous, P.W., and Samson, R.A. (2016b). Diversity and taxonomy of Chaetomium and chaetomium-like fungi from indoor environments. Studies in Mycology 84, 145–224.
Wilke, A., Glass, E.M., Bartels, D., Bischof, J., Braithwaite, D., D’Souza, M., Gerlach, W., Harrison, T., Keegan, K., Matthews, H., et al. (2013). A metagenomics portal for a democratized sequencing world. Meth. Enzymol. 531, 487–523.
Willger, S.D., Grim, S.L., Dolben, E.L., Shipunova, A., Hampton, T.H., Morrison, H.G., Filkins, L.M., O‘Toole, G.A., Moulton, L.A., Ashare, A., et al. (2014). Characterization and quantification of the fungal microbiome in serial samples from individuals with cystic fibrosis. Microbiome 2, 40.
Williams, K., Pruden, A., Falkinham, J., Edwards, M., Williams, K., Pruden, A., Iii, J., and Edwards, M. (2015). Relationship between Organic Carbon and Opportunistic Pathogens in Simulated Glass Water Heaters. Pathogens 4, 355–372.
Womack, A.M., Bohannan, B.J.M., and Green, J.L. (2010). Biodiversity and biogeography of the atmosphere. Philos Trans R Soc Lond B Biol Sci 365, 3645–3653.
Womack, A.M., Artaxo, P.E., Ishida, F.Y., Mueller, R.C., Saleska, S.R., Wiedemann, K.T., Bohannan, B.J.M., and Green, J.L. (2015). Characterization of active and total fungal communities in the atmosphere over the Amazon rainforest. Biogeosciences 12, 6337–6349.
Wood, M., Gibbons, S.M., Lax, S., Eshoo-Anton, T.W., Owens, S.M., Kennedy, S., Gilbert, J.A., and Hampton-Marcell, J.T. (2015). Athletic equipment microbiota are shaped by interactions with human skin. Microbiome 3.
Woudenberg, J.H.C., Meijer, M., Houbraken, J., and Samson, R.A. (2017). Scopulariopsis and scopulariopsis-like species from indoor environments. Studies in Mycology 88, 1–35.
Yamamoto, N., Shendell, D.G., and Peccia, J. (2011). Assessing allergenic fungi in house dust by floor wipe sampling and quantitative PCR: Assessing house dust fungi by wipe sampling and qPCR. Indoor Air 21, 521–530.
Yamamoto, N., Bibby, K., Qian, J., Hospodsky, D., Rismani-Yazdi, H., Nazaroff, W.W., and Peccia, J. (2012). Particle-size distributions and seasonal diversity of allergenic and pathogenic fungi in outdoor air. ISME J 6, 1801–1811.
Yamamoto, N., Nazaroff, W.W., and Peccia, J. (2014a). Assessing the aerodynamic diameters of taxon-specific fungal bioaerosols by quantitative PCR and next-generation DNA sequencing. Journal of Aerosol Science 78, 1–10.
Yamamoto, N., Dannemiller, K.C., Bibby, K., and Peccia, J. (2014b). Identification accuracy and diversity reproducibility associated with internal transcribed spacer-based fungal taxonomic library preparation. Environ. Microbiol. 16, 2764–2776.
Yamamoto, N., Hospodsky, D., Dannemiller, K.C., Nazaroff, W.W., and Peccia, J. (2015). Indoor emissions as a primary source of airborne allergenic fungal particles in classrooms. Environ. Sci. Technol. 49, 5098–5106.
Yilmaz, N., Visagie, C.M., Houbraken, J., Frisvad, J.C., and Samson, R.A. (2014). Polyphasic taxonomy of the genus Talaromyces. Studies in Mycology 78, 175–341.
Ying, S., Zeng, D.-N., Chi, L., Tan, Y., Galzote, C., Cardona, C., Lax, S., Gilbert, J., and Quan, Z.-X. (2015). The Influence of Age and Gender on Skin-Associated Microbial Communities in Urban and Rural Human Populations. PLOS ONE 10, e0141842.
Yooseph, S., Andrews-Pfannkoch, C., Tenney, A., McQuaid, J., Williamson, S., Thiagarajan, M., Brami, D., Zeigler-Allen, L., Hoffman, J., Goll, J.B., et al. (2013). A Metagenomic Framework for the Study of Airborne Microbial Communities. PLOS ONE 8, e81862.
Yu, H., Guo, S., Zhu, Y., Ishida, M., and Zhou, H. (2014). Novel titanium-based O3-type NaTi 0.5 Ni 0.5 O 2 as a cathode material for sodium ion batteries. Chem. Commun. 50, 457–459.
Zinger, L., Amaral-Zettler, L.A., Fuhrman, J.A., Horner-Devine, M.C., Huse, S.M., Welch, D.B.M., Martiny, J.B.H., Sogin, M., Boetius, A., and Ramette, A. (2011). Global Patterns of Bacterial Beta-Diversity in Seafloor and Seawater Ecosystems. PLoS One 6.
Zook, J.M., Catoe, D., McDaniel, J., Vang, L., Spies, N., Sidow, A., Weng, Z., Liu, Y., Mason, C.E., Alexander, N., et al. (2016). Extensive sequencing of seven human genomes to characterize benchmark reference materials. Sci Data 3.
(2016a). Erratum to: The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium Inaugural Meeting Report. Microbiome 4, 45.
(2016b). The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium inaugural meeting report. Microbiome 4, 24.
Miletto, M., & Lindow, S. E. (2015). Relative and contextual contribution of different sources to the composition and abundance of indoor air bacteria in residences. Microbiome, 3(1), 61.
These did not explicitly acknowledge Sloan funding but were synergistic with our Sloan projects. Prussin was a Sloan post-doc.
Prussin II, A.J., Schwake, D.O., Marr, L.C., (2017). Ten questions concerning the aerosolization and transmission of Legionella in the built environment, Building and Environment, 123, 684-695.
Lin, K., Marr, L.C., (2017). Aerosolization of Ebola virus surrogates in wastewater systems, Environmental Science and Technology, 51, 2669–2675.
Khare, P., Marr, L.C., (2015). Simulation of vertical concentration gradient of influenza viruses in dust resuspended by walking, Indoor Air, 25(4), 428-440.
Hull NM, Holinger EP, Ross KA, Robertson CE, Harris JK, Stevens MJ, and Pace NR (2017). Longitudinal and Source-to-Tap New Orleans, LA, USA Drinking Water Microbiology. ES&T 51(8):4220-4229.
Stanish LF, Hull NM, Robertson CE, Harris JK, Stevens JK, Spear JR, and Pace NR (2016). Factors Influencing Bacterial Diversity and Composition in Municipal Drinking Waters in the Ohio River Basin, USA. PLoS One 11 (6): e0157966.
Handorean A, Robertson CE, Harris JK, Frank DN, Hull NM, Kotter C, Stevens MJ, Baumgardner D, Pace NR, and Hernandez MT (2015). Microbial aerosol liberation from soiled textiles isolated during routine residuals handling in a modern health care setting. Microbiome 3:72.
Thank you Despina, Linsey, and Natalie! I will add all of these.