Paper of possible interest: Microbial analysis of Heating systems’ surfaces 

Just a quick post – this may be of interest to some:

An analysis of experimental investigation focused on microbial pollution of heated was carried out for heating systems installed in different types of buildings as residential houses and civil buildings. The results point on importance of maintenance and cleaning the heating systems for quality of indoor air and occupants’ comfort.

Source: Microbial analysis of Heating systems’ surfaces – AD Publications


Humans as collectors and emitters of environmental microbes

As part of the Healthy Buildings 2015 America Conference, there was a technical session on Indoor Microbiome Research where we discussed strategies on, among other things, how to sample and analyze bioaerosols using modern high throughput sequencing techniques. In that workshop, we did a small exercise highlighting the potential for humans to transport microbes into different settings. Prior to the session, one of the panelists (names protected) left the room and handled a fruiting body of a puffball known as Pisolithus tinctorius. Attendees of the workshop were invited to swab those of us on the panel and our possessions in explore if we could later identify which panelist handled the specimen. We used this is a springboard to talk about potential issues in microbiome sampling – spatial variation in microbial communities, do we need duplicate samples, how much pressure to apply and what size area to swab?

Pisolithus tinctorius, also known as the dog turn fungus.

The fungal sequences from those dozen swabs from that workshop were pretty clear: the dog turd fungus appeared on swabs from the targeted panelist’s hands, computer, and chair. In fact, it was second most abundant fungus in those samples and not present at all from swabs of other panelists.

I think about these results in the context of different routes of microbial transmission. Occupants and their activities are a large determinant of the bioaerosols in indoor spaces, and there are thought to be three routes of “occupant emissions”:

  1. Direct shedding from the human envelope (shedding, spitting, etc)
  2. Resuspension of microbes that have settled in the indoor environment (“reservoir” microbes)
  3. A transport vector of microbes collected in other spaces, as in our session

It’s always been a concern in occupational settings for workers not to bring harmful substances on their clothing to the home setting, where in this case it would be workers transporting microbes into their home and creating an opportunity for direct transmission or subsequent resuspension from surfaces in the home.

For a more comprehensive understanding of indoor bioaerosols, it’s important to know the strengths of these three different transmission routes. Teasing apart the relative contributions of these three processes which sum to create a Snoopy-inspired Pig-Pen model of aerosol generation can be challenging.

Some research is tackling this challenge by using environmental chambers. For example, (bio)aerosol particle emissions were approximately 6 times greater when occupants walked around a chamber, compared to when they were sitting. While some of the increased particles were associated increased vigor of upper body movements, most was attributable to release of particles from the floor. In another study, the air in a small chamber with an occupant sitting and wearing minimal clothing can show a unique microbial signature as to identify the individual occupant, showing that direct shedding is detectable when other sources are sufficiently removed. Recently, a study focusing on particles shed from the human envelopment and aiming to minimize resuspsension from the floor linked aerosol release from different activities with personal exposure. For questions about cross-contamination in indoor environments, these kinds of studies can help us better understand the nature of occupant emissions.

Paper of interest: Environmental Viral Metagenomics Analyses in Aquaculture

Just a quick post here.  Studies of the microbiology of built environments that house animals (e.g., aquaria, farms, animal shelters, zoos, etc) are of growing interest for multiple reasons.  In that regard this paper might be of interest to some – because it covers some topics that are sometimes neglected in this general area – viral diversity and aquaculture.  Here is a link to the paper

Source: Environmental Viral Metagenomics Analyses in Aquaculture: Applications in Epidemiology and Disease Control

Microbial Anthropology: the convergence of microbiomes and their modern impacts, through the lens of evolution and ecology

Figure 1 from Maria Gloria Dominguez-Bello 2016. The fieldwork team leaving a community in the jungle. Image courtesy of Oscar Noya.


In a recent story published in Cell this week, I walk through my own life and career, to deliver the message that humans are changing their own microbial communities as well as those in animals and in the environment, and that health research needs a substantial dose of an evolutionary, ecological and anthropological perspective to understand the etiology of modern diseases. After all, humans have coevolved with bacteria, and modern lifestyles are impacting not only the human microbiome itself, but also the environmental microbes we need to be exposed to in childhood, to be healthy the rest of our lives. This attains the microbes of the built environment.

Consistent with their long evolutionary history and with their omnipresence in our planet, the study of microbes and their functions deserves to be approached from many angles, by multidisciplinary teams, to get some light out of the intrincate complexity of the habitats microbes colonize.

Maria Gloria Dominguez-Bello


The hot new 10 questions concerning the microbiomes of buildings will surprise you

Ok so I made this into Clickbait.  But you really should read this and that has nothing to do with me being a co-author.

The paper is “Ten questions concerning the microbiomes of buildings” and it is in “Building and Environment” a journal that I am becoming more and more appreciative of every month.  The paper is to be #openaccess but still in the processing at the journal for that.  So until then, here is a PDF of the paper.

The full reference is:

Adams RI, Bhangar S, Dannemiller KC, Eisen JA, Fierer N, Gilbert JA, Green JL, Marr LC, Miller SL, Siegel JA, Stephens B, Waring MS, Bibby K, Ten questions concerning the microbiomes of buildings, Building and Environment (2016), doi: 10.1016/j.buildenv.2016.09.001.


Fig. 1. The absolute number of citations that are flagged in Google Scholar by the keywords: ‘microbiology OR microbiome OR bioaerosol AND indoor’ (left axis), and that number of citations normalized by ‘microbiology OR microbiome OR bioaerosol’ (right axis).

In the paper, this group of authors basically asked and then answered a series of questions about microbiomes of the built environment.

The questions are:

  • Q1) What does the microbiome of a typical indoor environment look like?
  • Q2) How do building characteristics, including occupants and their behaviors, influence the indoor microbiome?
  • Q3) How do moisture problems alter typical indoor microbiomes?
  • Q4) How does the microbiome affect indoor chemistry, and how do chemical processes and the composition of building materials influence the indoor microbiome?
  • Q5) What do DNA sequencing and modern analytical techniques tell us about the indoor environment?
  • Q6) What are appropriate sampling methods and constraints for studies of the microbiology of the built environment?
  • Q7) What technological developments will enhance our understanding of the microbiology of the built environment?
  • Q8) What are the connections between indoor microbiomes and occupant health?
  • Q9) What are the implications of recent work for building design and maintenance?
  • Q10) What do all these recent studies NOT tell us?

Lots and lots of information in here for people who want to learn about this field and related topics.

Maybe some people can even use it to edit the relatively new Wikipedia page on “Microbiomes of the Built Environment


Journal Club: Factors Influencing Early Life Gut Microbial Communities

A new paper by Levin, A. et al was published open access in Scientific Reports entitled, “Joint effects of pregnancy, sociocultural, and environmental factors on early life gut microbiome structure and diversity.” The paper confirmed a lot of what we already now about what factors influence infant gut microbiomes (ex. breastfeeding, mode of delivery, pets, etc). However, there were two unique aspects to this paper: (1) they included race and socioeconomics into the analysis (made possible by the fact they actually sampled a diverse cohort in the first place compared to other studies) and (2) are apparently the first research group to take a multi-factor approach.

I’ll be honest – I found the multi-factor approach a bit confusing. The authors mention this means they used a “backwards variable selection” procedure/approach, which I understand as an iterative process where you fit the data to a model (by variable), drop the least significant variables, and re-fit to the model until all variables are significant. What surprised me is how much this approach changed the data (see attached figure comparison): different variables were significant in the multi-factor analysis compared to the single factor analysis and vice versa.

Significant differences were correlated to demographics (eg marital status and ethnicity), but very few confounding variables were considered in the discussion or analysis that could also explain these differences. This is not to say the authors lacked attention to detail; capturing the whole picture would be nearly impossible. There were fascinating details included that I would never even think of, such as the type of C-section (planned vs unplanned) was correlated to significant differences in the gut microbial community composition of infants.

Lastly, there is a cool network analysis in this paper that represents a bold attempt to connect variables associated with pregnancy (mode of delivery, previous pregnancies, etc), sociocultural (race, income, etc), and environmental (tobacco smoke, air filter, etc) factors.

Overall, a well-done study and cool analysis tools/visualization – worth the read!

Figures 3 and 4 from Levin et al. A: Sing-factor gut microbiome compositional analyses for both neonates and infants. B: Multi-factor gut microbiome compositional analyses for both neonates and infants
Figures 3 and 4 from Levin et al. A: Sing-factor gut microbiome compositional analyses for both neonates and infants. B: Multi-factor gut microbiome compositional analyses for both neonates and infants

Green space influences human health and airborne microbial communities

A recent open access paper from the BioBE Center at University of Oregon explored the differences between airborne bacteria collected in parks and parking lots. Entitled “Urban greenness influences airborne bacterial community composition” and published in Science of the Total Environment, this interdisciplinary study combined research methods from microbiology and landscape architecture to answer the question: are airborne microbes a plausible mechanism through which health benefits from green space may accrue?

View from sampling site in Alton Baker Park, Eugene, OR.

The authors hope that answering this question and identifying how vegetation affects the nearby airborne microbial communities will help landscape architects and urban planners to better design urban green space in future cities. This work follows in the footsteps of Frederick Law Olmsted, designer of Central Park and proponent of public health in early 20th century industrializing cities, and is bolstered by other recent work on vegetation and airborne microbes, notably “Contribution of vegetation to the microbial composition of nearby outdoor air” by Lymperopoulou et al.

Student theses on microbiology of the built environment of interest

I have some automated Google Scholar searches for MoBE related topics and recently a few theses came up in the searches and I thought Iwould post about them here

Here is one: Indoor biological exposures : what can HVAC filter dust tell us?

Author: Jennings, Wiley Charles from Kerry Kinney’s lab.


Because people in the US spend an estimated 80-90% of their time indoors, much of it at home, understanding the potential health impacts of biological exposures that occur in the home is crucial. Recently, rapid advances in high-throughput DNA sequencing technology have spurred increased study of the relationships between the human and built environment microbiomes. HVAC filters hold promise as long-term, spatially integrated, high volume samplers to characterize the airborne home microbiome. In order to optimize HVAC sampling protocols and improve comparability between studies employing HVAC filters for bacterial community analysis, three HVAC filter dust sampling methods were compared. These three methods, vacuuming the filter surface, swabbing the filter surface, and eluting filter dust in a buffer, were selected as representative of previously published methods. Our findings suggest that vacuum and swab samples produced more repeatable and representative bacterial communities than did elution. Furthermore, given the reduced labor and cost of vacuum and swab methods, and the additional advantage that these two methods may also be applied to sampling dust from other home surfaces, vacuum and swab sampling of HVAC filter dust are found to be superior to elution.
It is estimated that on average people spend more than 90 percent of their time indoors. And yet, when we think about our health and how the environment affects it, most are unaware that indoor environments may have a larger impact on our health and well-being than even the outdoor environment. Given the amount of time we spend indoors, what are we exposed to indoors? Can we design indoor environments that are not only not harmful to us, but actually good for us? And can we do this in an energy efficient manner? What does a “healthy building” look like?

To start answering these questions, we focused on studying how various building characteristics and interventions affected indoor air microbiology and energy efficiency, two qualities that are critical when designing a healthy building. This work is split into three parts: (1) Investigating a healthy building intervention: cooling coil ultraviolet germicidal irradiation (UVG-CC), (2) investigating the microbiology of indoor air quality in a university dormitory and its effect on student health, and (3) a review of the role of mechanical ventilation in the airborne transmission of infectious agents in buildings.

Part (1) (Chapter 2) investigates the effect of ultraviolet germicidal coil cleaning (UVG-CC) technology on building energy efficiency and indoor air microbiology. Cooling coil surfaces within building ventilation systems are ideal sites for biofilm formation due to the presence of adequate nutrients (i.e. deposited particles) and moisture (i.e. condensate). Biofouling of cooling coils can contribute to decreased heat transfer efficiency and possible contamination of indoor air by releasing toxins or allergens into the air entering the building. We found that, in mild condensing conditions, UVG-CC increased heat transfer effectiveness by 3—6.4%, with an uncertainty of ± 2.7% resulting from the accuracy of our instrumentation. Microbial results showed increased airborne cell counts downstream of the coil one month after UVG-CC installation. This increase coincided with drastic (80—90%) decreases in surface cell counts, which suggests that UVGI inactivated biofilms from the surface of the coil and these clusters were then re-entrained into the airstream. Overall this study suggests that UVG-CC is most effective at reducing microbial contamination and increasing heat transfer effectiveness in humid climates with high latent loads but care must be taken one month after installation, especially in the case of retrofits, as inactive biological material may re-entrain into the air. Installation of this technology should be carefully considered depending on the climatic region, and may not need to be operated during non-condensing states. Future studies of UVG-CC should pay careful attention to the sensitivity and detection limits of their instrumentation, and would benefit from studying environments prone to excessive biological fouling so that differences between UV and non-UV coils are more pronounced.

Part (2) (Chapter 3) of this dissertation investigates the microbiota in indoor air in a student dormitory. We have long known that human occupants are a major source of microbes in the built environment. What remains undetermined is what, if anything, we can learn about the occupants of a building by analyzing the microbial communities found in indoor air. We investigated bacterial and fungal diversity found in settled dust samples and dust collected onto HVAC air filters from 91 rooms within a university dormitory in Boulder, CO. The sex of the room occupants had the most significant effect on the bacterial communities found in both the settled dust and air filter samples, while the room occupants had no significant effect on fungal communities. By examining the abundances of taxa at the genus level, we can predict the sex of room occupants with 79% accuracy, a finding that demonstrates the potential forensic applications of studying indoor air microbiology. We also identified which taxa at the OTU level were most different in abundance and frequency of occurrence between female and male rooms, and found that taxa often identified as members of the vaginal microbiome were more common in female-occupied rooms while taxa associated with human skin or the male urogenital microbiota were more common in male-occupied rooms. Measurement methods used to characterize the dormitory HVAC system and methods of health data collection are also described.

Part (3) (Chapter 4) is a comprehensive literature review of the role of mechanical ventilation in the transmission of infectious agents in buildings. Infectious disease outbreaks and epidemics such as those due to SARS, influenza, measles, or tuberculosis have raised concern about the airborne transmission of pathogens in indoor environments. There are insufficient data to quantify how various parameters controlled by HVAC systems may affect the airborne transmission of infectious agents. To improve our understanding and design of HVAC systems to promote better infection control, our review reveals a strong need for more epidemiologic studies and meta-analyses. Specifically, we call for well designed prospective observational or intervention studies in buildings to establish causal relationships between airborne exposures and outcomes and between building factors and exposures. Future studies will benefit greatly from improved experimental design, standardized measurement methods, and better collaboration between epidemiologists and HVAC engineers.

The work presented here provides a glimpse into the complex and interdisciplinary nature of indoor air and building science and makes connections across building energy systems, HVAC science, and microbiology to demonstrate the nuances of how building characteristics or design decisions can affect indoor exposures.

Science Friday on New Superbugs

As posted in this blog last week, an article was published in the ASM Journal Antimicrobial Agents and Chemotherapy on May 26 that describes the first discovery in the United States of mcr-1 gene, responsible for colistin resistance, in E. coli in a patient with a urinary tract infection. Colistin is considered an antibiotic of last resort because, while it causes kidney damage, it has been used to successfully treat infections resistant to standard treatments. This announcement was met with a flurry of reports in the media, including many with wild inaccuracies, announcing that this was the ultimate multiple drug resistant superbug, which is isn’t. The patient was successfully treated using other standard antibiotics. The significance of this finding is that a bacterial isolate containing the mcr-1 gene on a plasmid was isolated from a patient here in the US (not just in China, where a similar case was reported in an article in the Lancet in November). Because the gene is on a plasmid, it can be easily passed to other bacteria that have additional genes for antimicrobial resistance, and the concern is that this will happen in the not too distant future. Even the author of this article on antimicrobial resistance in last week’s issue of the Economist was confused about the difference between plastids and plasmids. (Plastids are organelles with double-membranes found in the cells of plants and algae and plasmids are small circular strands of DNA found in the cytoplasm of a bacterium.) Rather than posting links to the many examples of weak science journalism that last week’s news generated, instead I want recommend this week’s episode of Science Friday, where they provide (as usual) a careful and thoughtful discussion of the significance of the finding in the context of potential solutions for a post-antibiotic future. You can listen to it here. And I recommend this nice blog post called Apocalypse Pig: The Last Antibiotic Begins to Fail that explores the role that the agricultural use of colistin (to promote the growth of livestock) may have played in the evolution and dispersal of the mcr-1 gene in China.

Outdoors, occupants, and the pan-microbiome: a review

Our group here at the City University of Hong Kong is interested in looking at microbial communities in built environments (BEs) of various sorts, including subways and residences. We have recently come up with a review article describing how outdoor and indoor occupants help shape a potential global BE “pan-microbiome,” the microbiome that encompasses BEs around the globe, which is likely to be larger than that of any single BE.

Before I summarise what the review talks about, I just want to say that, where our group is in terms of location puts us in a very unique position to work on this emerging field of indoor microbiology. Let the photo below speak for us:


This is a photo taken minutes from where I live in Hong Kong, and a couple of things pop into my mind. 1) You get a great variation in the types of BEs, from skyscrapers to street-level retail shops and residential units (all with different building and interior designs), positioned in close proximity, 2) this type of urban/city design is very different from those in most other places in the world.

Scientists conducting research works in indoor microbiology know clearly that adjacent outdoor environments and indoor occupants play fundamental roles in shaping the microbiome of the BE (specifically, they act as microbiome sources for the BE). In addition, ventilation and other building design may help facilitate how microbes from the outdoors are introduced into the BE, and occupant activities and lifestyles govern how human-associated microbes are released into their indoor habitats . While their roles are likely to be universal, the nature of the microbiomes in these sources will be different depending on geographical location, due to differences in local terrains, environmental characteristics, and occupant/population lifestyles. For example, microbial communities in the outdoors in the picture above will be different from, say, what is out there in the picture below, taken from my trip a few years ago in Norway.


As a result, it is possible that the BEs from these two pictures will also present much-varied indoor microbiomes, due to its relationship with the immediate outdoor environments:

Comparative analyses from our work as well as others also reveal that the microbiomes on various human sites (skin, gut) also differ by global populations, potentially attributed to variations in physiology, life practices and activities. Therefore, indoor occupants of different areas around the world will release different microbes into their respective BEs.

Taken together, the combined effects of the outdoors, occupants, and how microbiomes of these two sources differ by geographical locations, will contribute to varying microbiomes in BEs of different areas. Therefore, the conglomeration of microbiomes of different BEs around the world will contribute to a global BE pan-microbiome. Therefore, the focus of the review is to describe how universal and location/population-specific factors help shape the BE pan-microbiome. Also, the article also introduces indoor microbiology research before the era of high-throughput sequencing, and potential future outlooks, such as dedication to assessing the viability of detected organisms, and emergence of novel building types (green buildings) around the world, that will help appreciate the magnitude and importance of the pan-microbiome size.

As building design and other factors influence our exposure to microorganisms in BEs, determining a global BE pan-microbiome is important to understand whether our current knowledge is continentally representative. We believe that both universal (e.g. how building designs fundamentally shape BE microbiomes), as well as local factors (local outdoor and occupant microbiome variations, mediated by environmental and anthropogenic properties) govern the microbial communities that are present in a given BE. However, current BE microbiology research works are heavily focused on locations in the western world (with a particular set of outdoor environmental and population/lifestyle characteristics), with much less representation elsewhere. We hope that, through this article, additional BE microbiome research will be focused in other parts of the world, as a more global appreciation of this concept is required to improve the health, comfort, and productivity of indoor occupants on a continental scale.