Brooks B, Olm MR, Firek BA, Baker R, Thomas BC, Morowitz MJ, et al. Strain-resolved analysis of hospital rooms and infants reveals overlap between the human and room microbiome. Nat Commun. 1814;2017:8.
Google Scholar
Raveh-Sadka T, Firek B, Sharon I, Baker R, Brown CT, Thomas BC, et al. Evidence for persistent and shared bacterial strains against a background of largely unique gut colonization in hospitalized premature infants. Isme J. 2016;10:2817–30.
Article
PubMed
PubMed Central
Google Scholar
Lax S, Smith DP, Hampton-Marcell J, Owens SM, Handley KM, Scott NM, et al. Longitudinal analysis of microbial interaction between humans and the indoor environment. Science. 2014;345:1048.
Article
CAS
PubMed
PubMed Central
Google Scholar
Vickery K, Deva A, Jacombs A, Allan J, Valente P, Gosbell IB. Presence of biofilm containing viable multiresistant organisms despite terminal cleaning on clinical surfaces in an intensive care unit. J Hosp Infect. 2012;80:52–5.
Article
CAS
PubMed
Google Scholar
Constantinides B, Chau KK, Quan TP, Rodger G, Andersson MI, Jeffery K, Lipworth S, Gweon HS, Peniket A, Pike G, Millo J, Byukusenge M, Holdaway M, Gibbons C, Mathers AJ, Crook DW, Peto TEA, Walker AS, Stoesser N. Genomic surveillance of Escherichia coli and Klebsiella spp. in hospital sink drains and patients. Microb Genom. 2020;6(7). https://doi.org/10.1099/mgen.0.000391.
Martineau C, Li X, Lalancette C, Perreault T, Fournier E, Tremblay J, et al. Serratia marcescens outbreak in a neonatal intensive care unit: new insights from next-generation sequencing applications. J Clin Microbiol. 2018;56:e00235–18.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hu H, Johani K, Gosbell IB, Jacombs AS, Almatroudi A, Whiteley GS, et al. Intensive care unit environmental surfaces are contaminated by multidrug-resistant bacteria in biofilms: combined results of conventional culture, pyrosequencing, scanning electron microscopy, and confocal laser microscopy. J Hosp Infect. 2015;91:35–44.
Article
CAS
PubMed
Google Scholar
Burgos-Garay M, Ganim C, de Man TJB, Davy T, Mathers AJ, Kotay S, et al. Colonization of carbapenem-resistant Klebsiella pneumoniae in a sink-drain model biofilm system. Infect Control Hosp Epidemiol. 2021;42:722–30.
Article
PubMed
Google Scholar
Kotay S, Chai W, Guilford W, Barry K, Mathers AJ. Spread from the Sink to the patient: in situ study using green fluorescent protein (GFP)-expressing Escherichia coli to model bacterial dispersion from hand-washing sink-trap reservoirs. Appl Environ Microbiol. 2017;83:e03327–16.
Article
CAS
PubMed
PubMed Central
Google Scholar
D'Souza AW, Potter RF, Wallace M, Shupe A, Patel S, Sun X, et al. Spatiotemporal dynamics of multidrug resistant bacteria on intensive care unit surfaces. Nat Commun. 2019;10:4569.
Article
PubMed
PubMed Central
Google Scholar
Ben Maamar S, Glawe AJ, Brown TK, Hellgeth N, Hu J, Wang JP, et al. Mobilizable antibiotic resistance genes are present in dust microbial communities. PLoS Pathog. 2020;16:e1008211.
Article
CAS
PubMed
PubMed Central
Google Scholar
Selway CA, Eisenhofer R, Weyrich LS. Microbiome applications for pathology: challenges of low microbial biomass samples during diagnostic testing. J Pathol Clin Res. 2020;6:97–106.
Article
CAS
PubMed
PubMed Central
Google Scholar
Shen J, McFarland AG, Young VB, Hayden MK, Hartmann EM. Toward accurate and robust environmental surveillance using metagenomics. Front Genet. 2021:12.
Nayfach S, Pollard KS. Toward accurate and quantitative comparative metagenomics. Cell. 2016;166:1103–16.
Article
CAS
PubMed
PubMed Central
Google Scholar
Eisenhofer R, Minich JJ, Marotz C, Cooper A, Knight R, Weyrich LS. Contamination in low microbial biomass microbiome studies: issues and recommendations. Trends Microbiol. 2019;27:105–17.
Article
CAS
PubMed
Google Scholar
McLaren MR, Willis AD, Callahan BJ. Consistent and correctable bias in metagenomic sequencing experiments. eLife. 2019;8:e46923.
Article
PubMed
PubMed Central
Google Scholar
Martí JM. Recentrifuge: robust comparative analysis and contamination removal for metagenomics. PLoS Comput Biol. 2019;15:e1006967.
Article
PubMed
PubMed Central
Google Scholar
Davis NM, Proctor DM, Holmes SP, Relman DA, Callahan BJ. Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data. Microbiome. 2018;6:226.
Article
PubMed
PubMed Central
Google Scholar
Bowers RM, Clum A, Tice H, Lim J, Singh K, Ciobanu D, et al. Impact of library preparation protocols and template quantity on the metagenomic reconstruction of a mock microbial community. BMC Genomics. 2015;16:856.
Article
PubMed
PubMed Central
Google Scholar
Mahnert A, Moissl-Eichinger C, Zojer M, Bogumil D, Mizrahi I, Rattei T, et al. Man-made microbial resistances in built environments. Nat Commun. 2019;10:968.
Article
PubMed
PubMed Central
Google Scholar
Minich JJ, Zhu Q, Janssen S, Hendrickson R, Amir A, Vetter R, et al. KatharoSeq enables high-throughput microbiome analysis from low-biomass samples. mSystems. 2018;3:e00218–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Nocker A, Cheung CY, Camper AK. Comparison of propidium monoazide with ethidium monoazide for differentiation of live vs. dead bacteria by selective removal of DNA from dead cells. J Microbiol Methods. 2006;67:310–20.
Article
CAS
PubMed
Google Scholar
Wang Y, Yan Y, Thompson KN, Bae S, Accorsi EK, Zhang Y, et al. Whole microbial community viability is not quantitatively reflected by propidium monoazide sequencing approach. Microbiome. 2021;9:17.
Article
CAS
PubMed
PubMed Central
Google Scholar
Elizaquivel P, Aznar R, Sanchez G. Recent developments in the use of viability dyes and quantitative PCR in the food microbiology field. J Appl Microbiol. 2014;116:1–13.
Article
CAS
PubMed
Google Scholar
Fittipaldi M, Nocker A, Codony F. Progress in understanding preferential detection of live cells using viability dyes in combination with DNA amplification. J Microbiol Methods. 2012;91:276–89.
Article
CAS
PubMed
Google Scholar
Morton JT, Marotz C, Washburne A, Silverman J, Zaramela LS, Edlund A, et al. Establishing microbial composition measurement standards with reference frames. Nat Commun. 2019;10:2719.
Article
PubMed
PubMed Central
Google Scholar
Liwinski T, Leshem A, Elinav E. Breakthroughs and bottlenecks in microbiome research. Trends Mol Med. 2021;27:298–301.
Article
PubMed
Google Scholar
Vandeputte D, Kathagen G, D'Hoe K, Vieira-Silva S, Valles-Colomer M, Sabino J, et al. Quantitative microbiome profiling links gut community variation to microbial load. Nature. 2017;551:507–11.
Article
CAS
PubMed
Google Scholar
Hingamp P, Grimsley N, Acinas SG, Clerissi C, Subirana L, Poulain J, et al. Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes. ISME J. 2013;7:1678–95.
Article
CAS
PubMed
PubMed Central
Google Scholar
Satinsky BM, Gifford SM, Crump BC, Moran MA. Chapter Twelve - Use of internal standards for quantitative metatranscriptome and metagenome analysis. In: DeLong EF, editor. Methods in Enzymology. Volume 531: Academic Press; 2013. p. 237–50.
Google Scholar
Yamamoto N, Hospodsky D, Dannemiller KC, Nazaroff WW, Peccia J. Indoor emissions as a primary source of airborne allergenic fungal particles in classrooms. Environ Sci Technol. 2015;49:5098–106.
Article
CAS
PubMed
Google Scholar
Satinsky BM, Zielinski BL, Doherty M, Smith CB, Sharma S, Paul JH, et al. The Amazon continuum dataset: quantitative metagenomic and metatranscriptomic inventories of the Amazon River plume, June 2010. Microbiome. 2014;2:17.
Article
PubMed
PubMed Central
Google Scholar
Tkacz A, Hortala M, Poole PS. Absolute quantitation of microbiota abundance in environmental samples. Microbiome. 2018;6:110.
Article
PubMed
PubMed Central
Google Scholar
Stammler F, Glasner J, Hiergeist A, Holler E, Weber D, Oefner PJ, et al. Adjusting microbiome profiles for differences in microbial load by spike-in bacteria. Microbiome. 2016;4:28.
Article
PubMed
PubMed Central
Google Scholar
Rodriguez RL, Konstantinidis KT. Nonpareil: a redundancy-based approach to assess the level of coverage in metagenomic datasets. Bioinformatics. 2014;30:629–35.
Article
Google Scholar
Rodriguez RL, Konstantinidis KT. Estimating coverage in metagenomic data sets and why it matters. ISME J. 2014;8:2349–51.
Article
Google Scholar
Rodriguez-R LM, Gunturu S, Tiedje JM, Cole JR, Konstantinidis KT. Nonpareil 3: fast estimation of metagenomic coverage and sequence diversity. mSystems. 2018;3:e00039–18.
Article
PubMed
PubMed Central
Google Scholar
Leung MH, Wilkins D, Li EK, Kong FK, Lee PK. Indoor-air microbiome in an urban subway network: diversity and dynamics. Appl Environ Microbiol. 2014;80:6760–70.
Article
PubMed
PubMed Central
Google Scholar
Davis A, Kohler C, Alsallaq R, Hayden R, Maron G, Margolis E. Improved yield and accuracy for DNA extraction in microbiome studies with variation in microbial biomass. BioTechniques. 2019;66:285–9.
Article
CAS
PubMed
Google Scholar
Hu J, Ben Maamar S, Glawe AJ, Gottel N, Gilbert JA, Hartmann EM. Impacts of indoor surface finishes on bacterial viability. Indoor Air. 2019;29:551–62.
Article
PubMed
PubMed Central
Google Scholar
Mo Y, Zhang W, Yang J, Lin Y, Yu Z, Lin S. Biogeographic patterns of abundant and rare bacterioplankton in three subtropical bays resulting from selective and neutral processes. ISME J. 2018;12:2198–210.
Article
PubMed
PubMed Central
Google Scholar
Nyirabuhoro P, Liu M, Xiao P, Liu L, Yu Z, Wang L, et al. Seasonal variability of conditionally rare taxa in the water column bacterioplankton community of subtropical reservoirs in China. Microb Ecol. 2020;80:14–26.
Article
CAS
PubMed
Google Scholar
Ji BW, Sheth RU, Dixit PD, Huang Y, Kaufman A, Wang HH, et al. Quantifying spatiotemporal variability and noise in absolute microbiota abundances using replicate sampling. Nat Methods. 2019;16:731–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Barbau-Piednoir E, Mahillon J, Pillyser J, Coucke W, Roosens NH, Botteldoorn N. Evaluation of viability-qPCR detection system on viable and dead Salmonella serovar Enteritidis. J Microbiol Methods. 2014;103:131–7.
Article
CAS
PubMed
Google Scholar
Bengtsson-Palme J, Richardson RT, Meola M, Wurzbacher C, Tremblay ED, Thorell K, et al. Metaxa2 Database Builder: enabling taxonomic identification from metagenomic or metabarcoding data using any genetic marker. Bioinformatics. 2018;34:4027–33.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bengtsson-Palme J, Thorell K, Wurzbacher C, Sjöling Å, Nilsson RH. Metaxa2 Diversity Tools: easing microbial community analysis with Metaxa2. Ecol Inform. 2016;33:45–50.
Article
Google Scholar
Bengtsson-Palme J, Hartmann M, Eriksson KM, Pal C, Thorell K, Larsson DG, et al. METAXA2: improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data. Mol Ecol Resour. 2015;15:1403–14.
Article
CAS
PubMed
Google Scholar
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013;41:D590–6.
Article
CAS
PubMed
Google Scholar
Yilmaz P, Parfrey LW, Yarza P, Gerken J, Pruesse E, Quast C, et al. The SILVA and "All-species Living Tree Project (LTP)" taxonomic frameworks. Nucleic Acids Res. 2014;42:D643–8.
Article
CAS
PubMed
Google Scholar
Beghini F, McIver LJ, Blanco-Míguez A, Dubois L, Asnicar F, Maharjan S, et al. Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3. eLife. 2021;10:e65088.
Article
CAS
PubMed
PubMed Central
Google Scholar
Truong DT, Tett A, Pasolli E, Huttenhower C, Segata N. Microbial strain-level population structure and genetic diversity from metagenomes. Genome Res. 2017;27:626–38.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lax S, Sangwan N, Smith D, Larsen P, Handley KM, Richardson M, et al. Bacterial colonization and succession in a newly opened hospital. Sci Transl Med. 2017;9:eaah6500.
Article
PubMed
PubMed Central
Google Scholar
O'Hara NB, Reed HJ, Afshinnekoo E, Harvin D, Caplan N, Rosen G, et al. Metagenomic characterization of ambulances across the USA. Microbiome. 2017;5:125.
Article
PubMed
PubMed Central
Google Scholar
Chng KR, Li C, Bertrand D, Ng AHQ, Kwah JS, Low HM, et al. Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment. Nat Med. 2020;26:941–51.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mishra P, Pandey CM, Singh U, Gupta A, Sahu C, Keshri A. Descriptive statistics and normality tests for statistical data. Ann Card Anaesth. 2019;22:67–72.
Article
PubMed
PubMed Central
Google Scholar
Blaustein RA, Michelitsch LM, Glawe AJ, Lee H, Huttelmaier S, Hellgeth N, et al. Toothbrush microbiomes feature a meeting ground for human oral and environmental microbiota. Microbiome. 2021;9:32.
Article
CAS
PubMed
PubMed Central
Google Scholar
Glass EM, Dribinsky Y, Yilmaz P, Levin H, Van Pelt R, Wendel D, et al. MIxS-BE: a MIxS extension defining a minimum information standard for sequence data from the built environment. ISME J. 2014;8:1–3.
Article
CAS
PubMed
Google Scholar
Adams RI, Bateman AC, Bik HM, Meadow JF. Microbiota of the indoor environment: a meta-analysis. Microbiome. 2015;3:49.
Article
PubMed
PubMed Central
Google Scholar
El Khouli RH, Macura KJ, Barker PB, Habba MR, Jacobs MA, Bluemke DA. Relationship of temporal resolution to diagnostic performance for dynamic contrast enhanced MRI of the breast. J Magn Reson Imaging. 2009;30:999–1004.
Article
PubMed
PubMed Central
Google Scholar
Escobar-Zepeda A, Godoy-Lozano EE, Raggi L, Segovia L, Merino E, Gutierrez-Rios RM, et al. Analysis of sequencing strategies and tools for taxonomic annotation: defining standards for progressive metagenomics. Sci Rep. 2018;8:12034.
Article
PubMed
PubMed Central
Google Scholar
Wang Y, Thompson KN, Yan Y, Short MI, Zhang Y, Franzosa EA, Shen J, Hartmann EM, Huttenhower C. Characterizing microbial community viability with RNA-based high-throughput sequencing [PREPRINT]. Res Sq. 2022. https://doi.org/10.21203/rs.3.rs-1870950/v1.
Joseph TA, Chlenski P, Litman A, Korem T, Pe'er I. Accurate and robust inference of microbial growth dynamics from metagenomic sequencing reveals personalized growth rates. Genome Res. 2022;32:558–68.
Article
PubMed
PubMed Central
Google Scholar
Emiola A, Oh J. High throughput in situ metagenomic measurement of bacterial replication at ultra-low sequencing coverage. Nat Commun. 2018;9:4956.
Article
PubMed
PubMed Central
Google Scholar
Gao Y, Li H. Quantifying and comparing bacterial growth dynamics in multiple metagenomic samples. Nat Methods. 2018;15:1041–4.
Article
CAS
PubMed
PubMed Central
Google Scholar
Korem T, Zeevi D, Suez J, Weinberger A, Avnit-Sagi T, Pompan-Lotan M, et al. Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samples. Science. 2015;349:1101–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Long AM, Hou S, Ignacio-Espinoza JC, Fuhrman JA. Benchmarking microbial growth rate predictions from metagenomes. ISME J. 2021;15:183–95.
Article
CAS
PubMed
Google Scholar
Marotz CA, Sanders JG, Zuniga C, Zaramela LS, Knight R, Zengler K. Improving saliva shotgun metagenomics by chemical host DNA depletion. Microbiome. 2018;6:42.
Article
PubMed
PubMed Central
Google Scholar
Nelson MT, Pope CE, Marsh RL, Wolter DJ, Weiss EJ, Hager KR, et al. Human and extracellular DNA depletion for metagenomic analysis of complex clinical infection samples yields optimized viable microbiome profiles. Cell Rep. 2019;26(2227-2240):e2225.
Google Scholar
Amar Y, Lagkouvardos I, Silva RL, Ishola OA, Foesel BU, Kublik S, et al. Pre-digest of unprotected DNA by benzonase improves the representation of living skin bacteria and efficiently depletes host DNA. Microbiome. 2021;9:123.
Article
CAS
PubMed
PubMed Central
Google Scholar
Barlow JT, Bogatyrev SR, Ismagilov RF. A quantitative sequencing framework for absolute abundance measurements of mucosal and lumenal microbial communities. Nat Commun. 2020;11:2590.
Article
CAS
PubMed
PubMed Central
Google Scholar
Costea PI, Zeller G, Sunagawa S, Pelletier E, Alberti A, Levenez F, et al. Towards standards for human fecal sample processing in metagenomic studies. Nat Biotechnol. 2017;35:1069–76.
Article
CAS
PubMed
Google Scholar
Pacholewicz E, Buhler C, Wulsten IF, Kraushaar B, Luu HQ, Iwobi AN, et al. Internal sample process control improves cultivation-independent quantification of thermotolerant Campylobacter. Food Microbiol. 2019;78:53–61.
Article
PubMed
Google Scholar
Hardwick SA, Chen WY, Wong T, Kanakamedala BS, Deveson IW, Ongley SE, et al. Synthetic microbe communities provide internal reference standards for metagenome sequencing and analysis. Nat Commun. 2018;9:3096.
Article
PubMed
PubMed Central
Google Scholar
Tourlousse DM, Yoshiike S, Ohashi A, Matsukura S, Noda N, Sekiguchi Y. Synthetic spike-in standards for high-throughput 16S rRNA gene amplicon sequencing. Nucleic Acids Res. 2017;45:e23.
PubMed
Google Scholar
Shen J, Hartmann EM. Collect, extract, pool, and cultivate surface swab samples from built environments. Protocol Exchange. 2022. https://doi.org/10.21203/rs.3.pex-1656/v1.
Gomez-Silvan C, Leung MHY, Grue KA, Kaur R, Tong X, Lee PKH, et al. A comparison of methods used to unveil the genetic and metabolic pool in the built environment. Microbiome. 2018;6:71.
Article
PubMed
PubMed Central
Google Scholar
Shen J, Hartmann EM. Snap freezing of environmental microbial samples in liquid. Protocol Exchange. 2022. https://doi.org/10.21203/rs.3.pex-1657/v1.
Wang X, Howe S, Deng F, Zhao J. Current applications of absolute bacterial quantification in microbiome studies and decision-making regarding different biological questions. Microorganisms. 2021;9:1797.
Article
CAS
PubMed
PubMed Central
Google Scholar
Fahimipour AK, Hartmann EM, Siemens A, Kline J, Levin DA, Wilson H, et al. Daylight exposure modulates bacterial communities associated with household dust. Microbiome. 2018;6:175.
Article
PubMed
PubMed Central
Google Scholar
Shen J, Rose LJ, Perry-Dow KA, Hartmann EM. An optimized protocol for propidium monoazide treatment. Protocol Exchange. 2022. https://doi.org/10.21203/rs.3.pex-1659/v1.
Leung MHY, Tong X, Boifot KO, Bezdan D, Butler DJ, Danko DC, et al. Characterization of the public transit air microbiome and resistome reveals geographical specificity. Microbiome. 2021;9:112.
Article
CAS
PubMed
PubMed Central
Google Scholar
Shen J, Hartmann EM. DNA extraction protocol for low-biomass environmental samples: adapted from the Lucigen MasterPure Complete DNA and RNA Purification Kit manual. Protocol Exchange. 2022. https://doi.org/10.21203/rs.3.pex-1658/v1.
Singer VL, Jones LJ, Yue ST, Haugland RP. Characterization of PicoGreen reagent and development of a fluorescence-based solution assay for double-stranded DNA quantitation. Anal Biochem. 1997;249:228–38.
Article
CAS
PubMed
Google Scholar
Klindworth A, Pruesse E, Schweer T, Peplies J, Quast C, Horn M, et al. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res. 2013;41:e1.
Article
CAS
PubMed
Google Scholar
Segata N, Waldron L, Ballarini A, Narasimhan V, Jousson O, Huttenhower C. Metagenomic microbial community profiling using unique clade-specific marker genes. Nat Methods. 2012;9:811–4.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li D, Liu C-M, Luo R, Sadakane K, Lam T-W. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics. 2015;31:1674–6.
Article
CAS
PubMed
Google Scholar
Nurk S, Meleshko D, Korobeynikov A, Pevzner PA. metaSPAdes: a new versatile metagenomic assembler. Genome Res. 2017;27:824–34.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics. 2013;29:1072–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kang DD, Li F, Kirton E, Thomas A, Egan R, An H, et al. MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies. PeerJ. 2019;7:e7359.
Article
PubMed
PubMed Central
Google Scholar
Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015;25:1043–55.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chaumeil P-A, Mussig AJ, Hugenholtz P, Parks DH. GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics. 2019;36:1925–7.
PubMed
PubMed Central
Google Scholar
Team RC: R: a language and environment for statistical computing. 2013.
Google Scholar
Wickham H. ggplot2: Elegant Graphics for Data Analysis. New York: Springer-Verlag; 2016.
Book
Google Scholar