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Microbiology of the Built Environment

Guest edited by Jack A Gilbert and Brent Stephens

This collection of research and reviews from Microbiome explores the microbiology of Built Environments (BE), the buildings, cities, and towns where we live and work. Over the last 80 years they have become our most intimate ecosystem. Yet our ignorance of this ecosystem is profound, despite its significant impact on humanity. The bacteria, fungi, and viruses that colonize these environments help shape the human microbiome, and can fundamentally alter the trajectory of our health. Designing our buildings and city spaces with the microbiome in mind may help to improve energy efficiency, health, sustainability, and consequently, worker performance and economic productivity. By mapping the microbiome of our built environments we may track biothreats and diseases, develop sophisticated early warning systems, and understand how a changing climate and increasing population density will shape this world.

The indoor microbiome may impact the immunological, physiological and neurological development of children. Infants can spend 98% of their first year of life indoors, with a highly depauperate exposure to a complex microbiome that would normally train a healthy immune system and stimulate healthy physiology and neurology. The indoor ecosystem, and the urban environment in particular, are hotspots for reduced microbial diversity, with this reduction having untold consequences for our health and wellbeing. 

This collection of articles has not been sponsored and articles have undergone the journal’s standard peer-review process. The Guest Editors declare no competing interests.

View all collections published in Microbiome.

  1. Content type: Research

    The microbiome of the built environment has important implications for human health and wellbeing; however, bidirectional exchange of microbes between occupants and surfaces can be confounded by lifestyle, arc...

    Authors: Anukriti Sharma, Miles Richardson, Lauren Cralle, Christopher E. Stamper, Juan P. Maestre, Kelly A. Stearns-Yoder, Teodor T. Postolache, Katherine L. Bates, Kerry A. Kinney, Lisa A. Brenner, Christopher A. Lowry, Jack A. Gilbert and Andrew J. Hoisington

    Citation: Microbiome 2019 7:70

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  2. Content type: Research

    The International Space Station (ISS) is a closed system inhabited by microorganisms originating from life support systems, cargo, and crew that are exposed to unique selective pressures such as microgravity. ...

    Authors: Aleksandra Checinska Sielaff, Camilla Urbaniak, Ganesh Babu Malli Mohan, Victor G. Stepanov, Quyen Tran, Jason M. Wood, Jeremiah Minich, Daniel McDonald, Teresa Mayer, Rob Knight, Fathi Karouia, George E. Fox and Kasthuri Venkateswaran

    Citation: Microbiome 2019 7:50

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  3. Content type: Research

    Microbial communities present in environmental waters constitute a reservoir for antibiotic-resistant pathogens that impact human health. For this reason, a diverse variety of water environments are being anal...

    Authors: Pablo Fresia, Verónica Antelo, Cecilia Salazar, Matías Giménez, Bruno D’Alessandro, Ebrahim Afshinnekoo, Christopher Mason, Gastón H. Gonnet and Gregorio Iraola

    Citation: Microbiome 2019 7:35

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  4. Content type: Research

    The International Space Station (ISS) is an ideal test bed for studying the effects of microbial persistence and succession on a closed system during long space flight. Culture-based analyses, targeted gene-ba...

    Authors: Nitin Kumar Singh, Jason M. Wood, Fathi Karouia and Kasthuri Venkateswaran

    Citation: Microbiome 2018 6:204

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    The Correction to this article has been published in Microbiome 2018 6:214

  5. Content type: Research

    The neonatal intensive care unit (NICU) contains a unique cohort of patients with underdeveloped immune systems and nascent microbiome communities. Patients often spend several months in the same room, and it ...

    Authors: Brandon Brooks, Matthew R. Olm, Brian A. Firek, Robyn Baker, David Geller-McGrath, Sophia R. Reimer, Karina R. Soenjoyo, Jennifer S. Yip, Dylan Dahan, Brian C. Thomas, Michael J. Morowitz and Jillian F. Banfield

    Citation: Microbiome 2018 6:112

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  6. Content type: Research

    A majority of indoor residential microbes originate from humans, pets, and outdoor air and are not adapted to the built environment (BE). Consequently, a large portion of the microbes identified by DNA-based m...

    Authors: Cinta Gomez-Silvan, Marcus H. Y. Leung, Katherine A. Grue, Randeep Kaur, Xinzhao Tong, Patrick K. H. Lee and Gary L. Andersen

    Citation: Microbiome 2018 6:71

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  7. Content type: Research

    Numerous studies have thus far characterized the temporal dynamics of the skin microbiota of healthy individuals. However, there is no information regarding the dynamics of different microbial association netw...

    Authors: Marcus H. Y. Leung, Xinzhao Tong, David Wilkins, Hedwig H. L. Cheung and Patrick K. H. Lee

    Citation: Microbiome 2018 6:26

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  8. Content type: Research

    Establishing reliable methods for assessing the microbiome within the built environment is critical for understanding the impact of biological exposures on human health. High-throughput DNA sequencing of dust ...

    Authors: Juan P. Maestre, Wiley Jennings, Dennis Wylie, Sharon D. Horner, Jeffrey Siegel and Kerry A. Kinney

    Citation: Microbiome 2018 6:22

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  9. Content type: Research

    The ExoMars 2016 mission, consisting of the Trace Gas Orbiter and the Schiaparelli lander, was launched on March 14 2016 from Baikonur, Kazakhstan and reached its destination in October 2016. The Schiaparelli ...

    Authors: Kaisa Koskinen, Petra Rettberg, Rüdiger Pukall, Anna Auerbach, Lisa Wink, Simon Barczyk, Alexandra Perras, Alexander Mahnert, Diana Margheritis, Gerhard Kminek and Christine Moissl-Eichinger

    Citation: Microbiome 2017 5:143

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  10. Content type: Research

    The limited understanding of microbial characteristics in moisture-damaged buildings impedes efforts to clarify which adverse health effects in the occupants are associated with the damage and to develop effec...

    Authors: Balamuralikrishna Jayaprakash, Rachel I. Adams, Pirkka Kirjavainen, Anne Karvonen, Asko Vepsäläinen, Maria Valkonen, Kati Järvi, Michael Sulyok, Juha Pekkanen, Anne Hyvärinen and Martin Täubel

    Citation: Microbiome 2017 5:138

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  11. Content type: Commentary

    The public commonly associates microorganisms with pathogens. This suspicion of microorganisms is understandable, as historically microorganisms have killed more humans than any other agent while remaining lar...

    Authors: Daria Shamarina, Iana Stoyantcheva, Christopher E. Mason, Kyle Bibby and Eran Elhaik

    Citation: Microbiome 2017 5:132

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  12. Content type: Research

    Several biotic and abiotic factors have been reported to influence the proliferation of microbes, including Legionella pneumophila, in hot water premise plumbing systems, but their combined effects have not been ...

    Authors: Caitlin R. Proctor, Dongjuan Dai, Marc A. Edwards and Amy Pruden

    Citation: Microbiome 2017 5:130

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  13. Content type: Research

    Microorganisms influence the chemical milieu of their environment, and chemical metabolites can affect ecological processes. In built environments, where people spend the majority of their time, very little is...

    Authors: Rachel I. Adams, Despoina S. Lymperopoulou, Pawel K. Misztal, Rita De Cassia Pessotti, Scott W. Behie, Yilin Tian, Allen H. Goldstein, Steven E. Lindow, William W. Nazaroff, John W. Taylor, Matt F. Traxler and Thomas D. Bruns

    Citation: Microbiome 2017 5:128

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  14. Content type: Research

    Microbial communities in our built environments have great influence on human health and disease. A variety of built environments have been characterized using a metagenomics-based approach, including some hea...

    Authors: Niamh B. O’Hara, Harry J. Reed, Ebrahim Afshinnekoo, Donell Harvin, Nora Caplan, Gail Rosen, Brook Frye, Stephen Woloszynek, Rachid Ounit, Shawn Levy, Erin Butler and Christopher E. Mason

    Citation: Microbiome 2017 5:125

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  15. Content type: Meeting Report

    The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium is a novel, interdisciplinary initiative comprised of experts across many fields, including genomics, data ana...


    Citation: Microbiome 2016 4:24

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    The Erratum to this article has been published in Microbiome 2016 4:45

  16. Content type: Research

    For potential future human missions to the Moon or Mars and sustained presence in the International Space Station, a safe enclosed habitat environment for astronauts is required. Potential microbial contaminat...

    Authors: Teresa Mayer, Adriana Blachowicz, Alexander J. Probst, Parag Vaishampayan, Aleksandra Checinska, Tiffany Swarmer, Pablo de Leon and Kasthuri Venkateswaran

    Citation: Microbiome 2016 4:22

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  17. Content type: Review

    The Neolithic revolution—the transition of our species from hunter and gatherer to cultivator—began approximately 14,000 years ago and is essentially complete for macroscopic food. Humans remain largely pre-Ne...

    Authors: David S. Thaler

    Citation: Microbiome 2016 4:14

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  18. Content type: Software

    Fungi play critical roles in many ecosystems, cause serious diseases in plants and animals, and pose significant threats to human health and structural integrity problems in built environments. While most fung...

    Authors: Jennifer Fouquier, Jai Ram Rideout, Evan Bolyen, John Chase, Arron Shiffer, Daniel McDonald, Rob Knight, J Gregory Caporaso and Scott T. Kelley

    Citation: Microbiome 2016 4:11

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  19. Content type: Commentary

    Architects are enthusiastic about “bioinformed design” as occupant well-being is a primary measure of architectural success. However, architects are also under mounting pressure to create more sustainable buil...

    Authors: G. Z. Brown, Jeff Kline, Gwynne Mhuireach, Dale Northcutt and Jason Stenson

    Citation: Microbiome 2016 4:6

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  20. Content type: Methodology

    A variety of different sampling devices are currently available to acquire air samples for the study of the microbiome of the air. All have a degree of technical complexity that limits deployment. Here, we eva...

    Authors: Julian Gordon, Prasanthi Gandhi, Gajendra Shekhawat, Angel Frazier, Jarrad Hampton-Marcell and Jack A. Gilbert

    Citation: Microbiome 2015 3:79

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  21. Content type: Review

    Each day people are exposed to millions of bioaerosols, including whole microorganisms, which can have both beneficial and detrimental effects. The next chapter in understanding the airborne microbiome of the ...

    Authors: Aaron J. Prussin II and Linsey C. Marr

    Citation: Microbiome 2015 3:78

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  22. Content type: Research

    Westernized lifestyle and hygienic behavior have contributed to dramatic changes in the human-associated microbiota. This particularly relates to indoor activities such as house cleaning. We therefore investig...

    Authors: Ekaterina Avershina, Anuradha Ravi, Ola Storrø, Torbjørn Øien, Roar Johnsen and Knut Rudi

    Citation: Microbiome 2015 3:65

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  23. Content type: Review

    The microbiome of the built environment (MoBE) is a relatively new area of study. While some knowledge has been gained regarding impacts of the MoBE on the human microbiome and disease vulnerability, there is ...

    Authors: Andrew J. Hoisington, Lisa A. Brenner, Kerry A. Kinney, Teodor T. Postolache and Christopher A. Lowry

    Citation: Microbiome 2015 3:60

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  24. Content type: Research

    A wide variety of specialty textiles are used in health care settings for bedding, clothing, and privacy. The ability of textiles to host or otherwise sequester microbes has been well documented; however, thei...

    Authors: Alina Handorean, Charles E. Robertson, J. Kirk Harris, Daniel Frank, Natalie Hull, Cassandra Kotter, Mark J. Stevens, Darrel Baumgardner, Norman R. Pace and Mark Hernandez

    Citation: Microbiome 2015 3:72

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  25. Content type: Research

    Recent studies posit a reciprocal dependency between the microbiomes associated with humans and indoor environments. However, none of these metagenome surveys has considered the viability of constituent microo...

    Authors: Thomas Weinmaier, Alexander J. Probst, Myron T. La Duc, Doina Ciobanu, Jan-Fang Cheng, Natalia Ivanova, Thomas Rattei and Parag Vaishampayan

    Citation: Microbiome 2015 3:62

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  26. Content type: Meeting Report

    The Sloan Symposium, “Microbiology of the Indoor Environment,” was held to facilitate dialog on biological research between scientists and practitioners in the field which was complementary to the adjoining ac...

    Authors: Hal Levin, Martin Täubel and Mark Hernandez

    Citation: Microbiome 2015 3:68

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  27. Content type: Research

    Lowering water heater temperature set points and using less drinking water are common approaches to conserving water and energy; yet, there are discrepancies in past literature regarding the effects of water h...

    Authors: William J. Rhoads, Pan Ji, Amy Pruden and Marc A. Edwards

    Citation: Microbiome 2015 3:67

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  28. Content type: Research

    Microorganisms are distributed on surfaces within homes, workplaces, and schools, with the potential to impact human health and disease. University campuses represent a unique opportunity to explore the distri...

    Authors: Ashley A. Ross and Josh D. Neufeld

    Citation: Microbiome 2015 3:66

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  29. Content type: Research

    Newborns delivered by C-section acquire human skin microbes just after birth, but the sources remain unknown. We hypothesized that the operating room (OR) environment contains human skin bacteria that could be...

    Authors: Hakdong Shin, Zhiheng Pei, Keith A. Martinez II, Juana I. Rivera-Vinas, Keimari Mendez, Humberto Cavallin and Maria G. Dominguez-Bello

    Citation: Microbiome 2015 3:59

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    The Erratum to this article has been published in Microbiome 2016 4:4

  30. Content type: Research

    The International Space Station (ISS) is a unique built environment due to the effects of microgravity, space radiation, elevated carbon dioxide levels, and especially continuous human habitation. Understandin...

    Authors: Aleksandra Checinska, Alexander J. Probst, Parag Vaishampayan, James R. White, Deepika Kumar, Victor G. Stepanov, George E. Fox, Henrik R. Nilsson, Duane L. Pierson, Jay Perry and Kasthuri Venkateswaran

    Citation: Microbiome 2015 3:50

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  31. Content type: Research

    As modern humans, we spend the majority of our time in indoor environments. Consequently, environmental exposure to microorganisms has important implications for human health, and a better understanding of the...

    Authors: Rachel I. Adams, Ashley C. Bateman, Holly M. Bik and James F. Meadow

    Citation: Microbiome 2015 3:49

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  32. Content type: Research

    Settled airborne dust is used as a surrogate for airborne exposure in studies that explore indoor microbes. In order to determine whether detecting differences in dust environments would depend on the sampler ...

    Authors: Rachel I. Adams, Yilin Tian, John W. Taylor, Thomas D. Bruns, Anne Hyvärinen and Martin Täubel

    Citation: Microbiome 2015 3:46

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