Complex indoor communities: bacterial life under extreme conditions in clean rooms and intensive care units.

Abstract

Indoor microbiomes are communities of microorganisms that inhabit the interior of built environments and are influenced by complex abiotic (e.g., climate, geographic location, building architecture, and maintenance) and biotic factors (human and animals/pets dynamics, greenery status, etc.).
Although microbes have often been recognized as pathogens, it is now well established that the majority of host-bacterial interactions are symbiotic (Blaser 2011). This partnership is based on molecular signaling to mediate beneficial outcomes for both microbes and their hosts. This relationship between microbial diversity and host health was shown not only for plants and soils but also for animals and humans (Keesing et al. 2010). Despite the fact that the majority of our lifetime is spent in indoor environments such as the home, workplace, or public buildings (Fig. 1, Table 1), our knowledge of
microbial diversity inside buildings is limited. We are not alone in these indoor environments: they provide new habitats and residence to numerous microbial communities comprising possibly hundreds of individual bacterial and fungal species. The most recent cultivation-based studies analyzed potential indoor pathogens with an emphasis on allergenic microorganisms (Yamamoto et al. 2011), yet little is known about the real microbial diversity indoors that has adapted to nutrient-poor, extreme conditions and communities that are composed of only a small fraction of cultivable microbes. The
indoor microbiome should be continuously explored with special focus on the beneficial microbial inhabitants.

Full text

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SpringerReference
MSc Lisa Oberauner, Mr. Alexander Mahnert, Dr. Anastasia Bragina and Dr. Gabriele Berg
Complex indoor bacterial communities
16 Jul 2014 04:11http://www.springerreference.com/index/chapterdbid/304188
© Springer-Verlag Berlin Heidelberg 2014
Complex indoor bacterial communities
Lisa Oberauner and Alexander Mahnert contributed equally
Synonyms
Microbiome of built environments
Definition
Indoor microbiomes are communities of microorganisms that inhabit the interior of built environments and are influenced
by complex abiotic (e.g., climate, geographic location, building architecture, and maintenance) and biotic factors (human
and animals/pets dynamics, greenery status, etc.).
Introduction to Indoor Microbiomes
Although microbes have often been recognized as pathogens, it is now well established that the majority of host-bacterial
interactions are symbiotic (Blaser ). This partnership is based on molecular signaling to mediate beneficial outcomes2011
for both microbes and their hosts. This relationship between microbial diversity and host health was shown not only for
plants and soils but also for animals and humans (Keesing et al. ). Despite the fact that the majority of our lifetime is2010
spent in indoor environments such as the home, workplace, or public buildings (Fig. 1, Table 1), our knowledge of
microbial diversity inside buildings is limited. We are not alone in these indoor environments: they provide new habitats
and residence to numerous microbial communities comprising possibly hundreds of individual bacterial and fungal
species. The most recent cultivation-based studies analyzed potential indoor pathogens with an emphasis on allergenic
microorganisms (Yamamoto et al. ), yet little is known about the real microbial diversity indoors that has adapted to2011
nutrient-poor, extreme conditions and communities that are composed of only a small fraction of cultivable microbes. The
indoor should be continuously explored with special focus on the beneficial microbial inhabitants.microbiome

2
SpringerReference
MSc Lisa Oberauner, Mr. Alexander Mahnert, Dr. Anastasia Bragina and Dr. Gabriele Berg
Complex indoor bacterial communities
16 Jul 2014 04:11http://www.springerreference.com/index/chapterdbid/304188
© Springer-Verlag Berlin Heidelberg 2014
Fig. 1
Illustrations of built environments. ( ) bedroom (private room), ( ) office (public room), ( ) intensive care unit , ( ) spacecrafta b c (ICU) d
assembly clean room
Table 1
Studies analyzing indoor environment microbiomes and parameters
Indoor
environment Classification Human
dynamic Maintenance Monitoring Materials References
Public
buildings Moderate
High (day),
moderate
(night)
Standard, mechanical ventilated Moderate
Polymers,
textiles,
wood
Flores et al. 2011
Hewitt et al. 2012
Qian et al. 2012
Private
buildings Spare
Moderate
(day), high
(night)
Diverse, window ventilated Low
Organic,
wood,
textiles,
polymers
Flores et al. 2013
Dunn et al. 2013
Intensive
care units
(ICUs)
Strict High (day
and night)
Standard, mechanical ventilated,
frequently cleaned, use of
disinfectants, very sanitary
Controlled
Polymers,
metals,
textiles
Hewitt et al. 2013
Oberauner et al. 2013
http://hospitalmicrobiome.com/
Minor (day
Cleaning with alkaline reagents;
controlling of particles, airflow, Polymer,
La Duc et al. 2007
Moissl et al. 2007

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MSc Lisa Oberauner, Mr. Alexander Mahnert, Dr. Anastasia Bragina and Dr. Gabriele Berg
Complex indoor bacterial communities
16 Jul 2014 04:11http://www.springerreference.com/index/chapterdbid/304188
© Springer-Verlag Berlin Heidelberg 2014
Clean rooms Strict and night) humidity, temperature; mechanical
ventilated
Strict metals Moissl-Eichinger 2011
Vaishampayan et al. 2013
Recently, the application of next-generation sequencing (NGS) techniques has provided new insights into indoor microbial
communities (Fig. 2). In general, they are characterized by a high prokaryotic diversity and comprise diverse bacterial and
archaeal phyla (Flores et al. , ; Moissl-Eichinger ; Hewitt et al. , ; Kembel et al. ; Kelley and2011 2013 2011 2012 2013 2012
Gilbert ). Indoor environments are also characterized by a specifically adapted fungal microbiome with an atypical2013
building composition unlike those shown for bacteria (Pitkäranta et al. ). In addition, fungi are able to grow indoors2008
when water is available (Zalar et al. ). Indoor microbiomes originate mainly from human skin, pets, or outside air and2011
are even known to include extremophiles. Furthermore, all of them can contain potential human pathogens in addition to
beneficial bacteria that are characterized by a positive interaction with their host (Flores et al. ; Kembel et al. ).2011 2012
Kembel et al. ( ) were the first to analyze patient rooms and find a strong impact from both architecture and2012
ventilation. Similarly, other the indoor diversity are of geographic and climatic origin (Hewitt et al. factors influencing 2012
). Two different types of microbial communities live indoors: airborne and surface-associated organisms. Airborne
microbes - bacteria, fungi, or microscopic algae - are scattered and can travel long distances such as in the wind or in
clouds before returning to the ground. Surface-associated microbes, however, tend to form biofilms. Despite the studies
concerning indoor microbial communities published within the last 2 years in which molecular microbial ecology methods
were applied, the majority of microbial coinhabitants in our built environments and their dynamics are still unknown.
Fig. 2
Overview of typical and dominant bacterial groups in the built environments. Schematic chart represents occurrence of the bacterial
inhabitants indoors. Bacterial families and genera ( ) are arranged according to their phylum ( ) and areblack ellipses affiliation bold
connected to certain types of the built environments ( ). This image was compiled from the information in Table 1 andcolored squares
is not a holistic representation
The Impact of Indoor Microbiome on Human Health
Indoor microbial communities are an important component of everyday human health. They are partially composed of
human-associated bacteria (Fierer et al. ) due to the high emission rate of up to 10 bacteria per person per hour, as2008 6

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MSc Lisa Oberauner, Mr. Alexander Mahnert, Dr. Anastasia Bragina and Dr. Gabriele Berg
Complex indoor bacterial communities
16 Jul 2014 04:11http://www.springerreference.com/index/chapterdbid/304188
© Springer-Verlag Berlin Heidelberg 2014
reported from genome copies measured in the air from individual persons (Qian et al. ). In hospitals and especially in2012
intensive care units (ICUs), microbial spread can result in hospital-acquired "nosocomial infections" that compound
underlying severe disease (Plowman ). remain among the leading causes of death in2000 Nosocomial infections
hospitals of developed countries, as the risk for nosocomial infections for patients in European ICUs, for example, was
reported as 45 % (Plowman ). Hospital surfaces are often overlooked reservoirs for these bacteria (Kramer et al. 2000
). Therefore, new sanitation standards are needed to drastically reduce the risk for these hospital-acquired2006
infections. Indoor microorganisms also affect human health as allergenic agents (Hanski et al. ). They are also2012
involved in the development of the , which causes symptoms such as sensory irritation ofsick building syndrome (SBS)
the eyes, nose, and throat; neurotoxic or general health problems; skin irritation; nonspecific ;hypersensitivity reactions
and odor and taste sensations.
Bacterial Communities in Intensive Care Units
In contrast to the majority of indoor environments, rooms in hospitals and especially in intensive care units (ICUs) are
routinely monitored for the presence of microbes (Fig. 1, Table 1) (Hewitt et al. ). However, this monitoring is based2013
on microbial cultivation and not . In a recent study, 16S gene was usedDNA sequencing rRNA amplicon pyrosequencing
to study the in comparison with the currently used standard cultivation technique (Oberauner et al. ).ICU microbiome 2013
Only 2.5 % of the total bacterial diversity was detected using cultivation; however, all sequences were represented in the
sequencing libraries. The phylogenetic spectrum comprised 7 phyla and 76 genera and included species associated with
the outside environment, taxa closely related to potential human pathogens, and others belonging to beneficial
organisms. Specifically, , , and were identified as important sources ofPropionibacterium Pseudomonas Burkholderia
infection (Fig. 2). Despite significantly different bacterial area profiles for floors, , and workplaces, networkmedical devices
analysis and molecular fingerprints were used to show similarities and evidence for the transmission of strains. This
information allows for a new assessment of public health risks in ICUs and will help to create new sanitation protocols to
better understand the development of hospital-acquired infections.
Bacterial Communities in Clean Rooms
Clean rooms are established facilities that have been involved in various industrial processes since the 1940s (Fig. 1).
Whereas clean rooms were first applied in the areas of microtechnology and optics, today they are used for the
production of semiconductors and in medical, pharmaceutical, and food production, as well as in spacecraft assembly.
Clean rooms are classified by the numbers and sizes of particles allowed within them. For the EN-ISO 14644-1DIN
classification, the classes 1-6 correspond to the number of particles (10-10 ) per m with 0.1-0.2 μm in size. TheISO 6 3
amount of these particles is controlled via filters, airflow rate, pressure, humidity, and temperature. Despite stringent
cleaning and maintenance, clean rooms used for spacecraft assembly are not devoid of microorganisms, and many hardy
extremophiles can survive in these oligotrophic conditions (Table 1) (La Duc et al. ; Moissl et al. ;2007 2007
Moissl-Eichinger ). Due to regulations, a peculiar monitoring of biological contaminants 2011 planetary protection
and characterization of the microbial populations in the well maintained, extremely low-biomass environment(bioburden)
must be followed at each step of the assembly process. Most of the standard assays are based on cultivation-dependent
methods; however, there has been a recent trend to also include cultivation-independent methods that include genomic
approaches (Vaishampayan et al. ).2013
Bacterial communities in the spacecraft assembly clean rooms at the EADS facility in Friedrichshafen (Germany) and at
the ( , CA, ) were investigated in a joint project. Floor samples were studiedNASA Jet Propulsion Laboratory JPL USA
using cultivation-dependent (mesophiles/oligotrophs, alkaliphiles/alkalitolerants, and ) andfacultative anaerobes
cultivation-independent assays [ATP assays and propidium monoazide pretreatment PCRs] to measure microbial(PMA)
burden (Vaishampayan et al. ). When samples were pretreated with PMA prior to , the chemical2013 DNA extraction
intercalated into from dead microbes, thus disabling PCR amplification (Wagner et al. ). The PMA-pretreatedDNA 2008
(viable microbes) and untreated (total microbes) portions were analyzed using (qPCR) and 16S quantitative PCR rRNA
gene to estimate bioburden and to measure viable microbial diversity, respectively. Overall,amplicon deep sequencing
the floors contained less total and viable microbial burden when measured by any assay than the adjacentclean room
servicing area locations. Hence, stringent maintenance and cleaning reduced the viable microbial population in the clean
room by 1-2 orders of magnitude. This reiterates the fact that the proper maintenance of the NASA JPL spacecraft

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SpringerReference
MSc Lisa Oberauner, Mr. Alexander Mahnert, Dr. Anastasia Bragina and Dr. Gabriele Berg
Complex indoor bacterial communities
16 Jul 2014 04:11http://www.springerreference.com/index/chapterdbid/304188
© Springer-Verlag Berlin Heidelberg 2014
assembly clean room floors removed substantial numbers of microbial cells, but some selective microbial populations
were able to survive under these clean conditions. ATP assays and PMA-qPCRs are both suitable to target the viable
microbial population. However, the deep sequencing analysis in combination with a prior PMA treatment showed that
viable microbial diversity also exists in the clean room and not only in the servicing area as expected. While
Proteobacteria and were the dominant bacterial phyla (Fig. 2), Archaea and fungi were also detected. MostFirmicutes
microbes seem to be introduced by humans. In addition, a metagenomic approach targeting various genes is planned at
JPL to reveal the presence of active functional . Results of this study will enable scientists to accuratelymicrobial species
track the true viable microbial population and perform accurate risk assessment of microbial contamination to the
assembled products in the clean room environment.
Summary and Conclusions
Indoor microbiomes are complex microbial ecosystems influenced by diverse abiotic and biotic factors. Indoor microbes
originate from humans, pets, indoor and outdoor plants, dust, and soil; altogether every individual leaves a significant
signature within his or her as a result of unique microbiomes and activities. Advances driven by novelbuilt environment
high-throughput technologies (e.g., next-generation sequencing) have completely altered our perspective on the
microbiology of built environments. Therefore, these techniques should also be used not only for the evaluation of
standard maintenance in clean rooms and validation of clean room products but also for the evaluation of our hygiene
standards in hospitals. Overall, the indoor plays an important role for human health and includes bothmicrobiome
pathogens and a substantial proportion of , which should be ultimately maintained.beneficials
Cross-References
Air, Metagenomics of (id, 304452)
Approaches in Metagenomic Research - Progress and Challenges (id, 363415)
Bacteria and Archaea, Definition, Features and Classification Schemes (id, 304217)
Fungus in the Human Microbiome, Definition and Examples (id, 303269)
Human Microbiome (id, 303365)
Methanogenic Archaea in the Human Microbiome (id, 349968)
Methods and Ecological Applications of Metagenomic Research (id, 350646)
Microbial Diversity, Barcoding Approaches (id, 309118)
Microbial Ecology in the Age of Metagenomics: An Introduction (350418)
Microbiome, Definition (304438)
Microbiome, Overview (304017)
Molecular Ecological Network of Microbial Communities (id, 349973)
New Tools for Understanding, Composition and Dynamics of Microbial Communities, Project (id, 304414)
Tag-Encoded FLX Amplicon Pyrosequencing (id 303989)
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MSc Lisa Oberauner, Mr. Alexander Mahnert, Dr. Anastasia Bragina and Dr. Gabriele Berg
Complex indoor bacterial communities
16 Jul 2014 04:11http://www.springerreference.com/index/chapterdbid/304188
© Springer-Verlag Berlin Heidelberg 2014
Complex indoor bacterial communities
MSc Lisa
Oberauner Institute of Environmental Biotechnology, Graz University of Technology,
Graz, Austria
Mr. Alexander
Mahnert Institute of Environmental Biotechnology, Graz University of Technology,
Graz, Austria
Dr. Anastasia
Bragina Insitute of Environmental Biotechnology, Graz University of Technology,
Graz, Austria
Dr. Gabriele Berg Institute of Environmental Biotechnology (Head), Graz University of
Technology, Graz, AUSTRIA
DOI: 10.1007/SpringerReference_304188
URL: http://www.springerreference.com/index/chapterdbid/304188
Part of: Encyclopedia of Metagenomics
Editor: Dr. Karen E. Nelson
PDF created on: July, 16, 2014 04:11
© Springer-Verlag Berlin Heidelberg 2014