Call for Papers MoBE 2017 Microbiome Special Issue

Call for Papers: MoBE 2017 Special Issue of BioMed Central’s Microbiome Journal  (Submission Guidelines)

We invite submissions of MoBE papers highlighting recent research and emerging hot topics along the theme of “MoBE Research to Applications” for our peer-reviewed MoBE special issue.

Publishing charges are sponsored by the MoBE meeting and BioMed Central’s Microbiome Journal. This special issue will be available by October 1st, 2017.

Please share this announcement among your MoBE colleagues !! 

Timeline:

March 1: paper topic submission (2-3 sentence outline).

These can be submitted via the MoBE 2017 contact form.

June 1:        full paper submission deadline

July 30:      reviews complete, notice to submitters

August 30: revisions due to BioMed Central’s Microbiome Journal

Wanted – examples of excellent #microbiology reporting

A few years ago I wrote a post where I tried to compile a list of names of reporters who did a good job on stories on microbiology related topics.

Source: The Tree of Life: Compiling a list of reporters who cover #microbiology stories well; suggestions wanted

Well, I would like to revisit that. So here goes.

I am compiling a list of examples of excellent microbiology reporting. This would include reporting in any format or system or site (e.g., long reads, short reads, Tweets, etc) and any type of microbiology topic.

What I would love to get from people are answers to the following:

  • Who do you think is doing excellent microbiology reporting? Self nominations welcome.
  • Can you give examples of some excellent of their work that you like?
  • Are there any sites / sources that you think are particularly good at covering microbiology related topics?

Thanks.  I will compile the answers and report back.


The concept of hygiene and the human microbiome.

(This post was written by Roo Vandegrift at the University of Oregon)

I was recently asked to spearhead the writing of a review centered around the interaction between the concept of hygiene and our increasingly nuanced understanding of the human skin microbiome for the Biology and the Built Environment (BioBE) Center at the University of Oregon.

This review began with an invitation from Dyson to conduct an impartial review of hand drying studies, which have been mired in competing interests and faulty methods. We saw an opportunity to not only provide an unbiased review of the literature, but also to ask a more fundamental question: how should hygiene be defined in light of our evolving perspective of the human and indoor microbiome?  We delivered a brief summary to Dyson (here) and then built upon that work to develop this question.  

As we started digging into the body of literature on hand hygiene, two things struck us as peculiar: the first was that in the hundreds of studies explicitly examining hygiene, the concept was never explicitly defined; the second was that there seemed to be a clear division between skin microbiological investigations coming from clinically and ecologically informed perspectives, with clinical research generally relying on older cultivation-dependent techniques. These two issues became the drivers for our review, and our goal was to provide an explicit definition of hygiene that would help to bridge the gap between the clinical skin microbiology literature and the newer human-associated microbial ecology literature. We were then able to use the body of literature on hand drying as a case-study to examine the implications of using a microbial ecology-based approach to defining hygiene.

You can read the full review as a preprint on bioRxiv now: http://biorxiv.org/content/early/2016/12/20/0957450

You can read the shorter, white page summary of the review on the BioBE blog: https://biobe.uoregon.edu/2016/11/04/cleanliness-in-context

Our review is broadly split into three sections: one section summarizing previous work on hygiene, one section briefly outlining previous work on human-associated microbial communities (including those found on the skin and in the built environment), and one section attempting to synthesize the two.

In the first section, we start seeing some of the limitations of cultivation-dependent methods, and how those limitations combine with implicit assumptions about the concept of hygiene. One thing that stands out to me from a thorough reading of clinical literature on hand hygiene is how often the idea of sterilization is used as a stand-in for the idea of hygiene — one result of the complete adoption of the germ theory of disease is the common misconception that “all microbes are germs”. This is apparent in the majority of studies of hygiene, particularly reflected in the focus on bulk reduction in microbial load, regardless of the identities of those microbes. I would, however, like to acknowledge Allison Aiello and Elaine Larson’s careful 2002 review, “What is the evidence for a causal link between hygiene and infections?“, which goes considerably beyond thinking of all microbes as germs and examines hundreds of studies, pulling out those that actually examine health outcomes as a dependent variable. Their review lays the conceptual foundations for what we are trying to do in our review.

In bridging into the second section, which outlines human-associated microbial ecology, we wanted to clearly illustrate the advances in techniques that the field utilizes. We put together this simple, but hopefully informative, conceptual figure to help:

Figure 1: Cultivation-dependent methods (A) are commonly used to study aspects of hand hygiene; many microbes are not detectable using this methodology (represented in grey). Handwashing reduces bulk microbial load, and cultivation yields data showing changes in the numbers of colony-forming units (counts); some studies identify colonies using morphological or molecular methods, yielding limited taxonomic information. Cultivation-independent methods (B), including high-throughput DNA sequencing, are commonly used to study the microbial ecology of the skin. Using these methods, it is possible to quantify alterations in relative abundance of bacterial populations with treatment (such as handwashing), obtain deep, comprehensive taxonomic diversity estimates; depending on technique, it may be possible to also obtain information on functional metabolic pathways (using metagenomics), assessment of proportion of the community that is active (using rRNA / rDNA comparisons, or live/dead cell assays), among other things.

It is clear that hygienic practices may interact significantly with human-associated microbial ecology. We highlight and summarize some of the important ecological factors that may interact with hygienic practice in a second conceptual figure:

Figure 2: Conceptual illustration of important ecological factors impacted by hygienic practice. Dispersal (a) is the movement of organisms across space; a patch of habitat is continuously sampling the pool of available colonists, which vary across a variety of traits (dispersal efficiency, rate of establishment, ex host survivability, etc.) (Vellend 2010); high dispersal rates due to human behaviors (e.g., microbial resuspension due to drying hands with an air dryer) have the potential to disperse both beneficial and harmful bacteria alike. Protective mutualisms (b) function through the occupation of niche space; harmful microorganisms are excluded from colonization via saturation of available habitat by benign, non-harmful microbes (Poisot et al. 2014). Host/microbe feedbacks (c) occur via the microbiota’s ability to activate host immune response, and the host immune system’s ability to modulate the skin microbiota (Chehoud et al, 2013; Garcia-Garcera et al, 2012; Oh et al, 2013) — multiple pathways, including IL-1 signalling (Naik et al 2012) and differential T-cell activation (Seneschal et al 2012), are involved — such feedbacks between host immune response and the skin microbiota are thought to be important to the maintenance of a healthy microbiota and the exclusion of invasive pathogenic microbes (Zhang et al 2015). Environmental filtering (d) works on the traits of dispersed colonists — microbes that can survive in a given set of environmental conditions are filtered from the pool of potential colonists (Vellend 2010): the resources and conditions found there permit the survival/growth of some organisms but not others. The importance of diversity of the microbiota to each of these ecological factors should not be underestimated; interactions between taxa may modulate their ecological roles, and community variation across a range of ecological traits may be altered by changes in community membership or structure (HMPC, 2012).

Coming to the third and final section, it should be clear to the reader that future work on hygiene would benefit from integrating modern techniques and an ecological perspective from recent human microbiome research. To facilitate that, we believe that it would be helpful to have a clear, concise definition of hygiene from which to work. This is probably the most important moment from our paper:

The evidence that microbes are essential for maintaining a healthy skin microbiota supports the idea that hygienic practices aimed at the simple removal of microbes may not be the best approach. Rather, hygienic practices should aim to reduce pathogenic microorganisms and simultaneously increase and maintain the presence of beneficial microorganisms essential for host protection. It is clear that microbial colonization of the skin is not deleterious, per se. Humans are covered in an imperceptible skim of microbial life at all times, with which we interact constantly. We posit that the conception of hygiene as a unilateral reduction or removal of microbial load has outlived its usefulness and that a definition of hygiene that is quantitative, uses modern molecular biology tools, and is focused on disease reduction is needed. As such, we explicitly define hygiene as ‘those actions and practices that reduce the spread or transmission of pathogenic microorganisms, and thus reduce the incidence of disease’.

Let me repeat that last part: we explicitly define hygiene as ‘those actions and practices that reduce the spread or transmission of pathogenic microorganisms, and thus reduce the incidence of disease’. We feel that it is incredibly important to define hygiene in terms of health outcomes, not just in terms of reduction in number of microbes. This allows for research (consider, for example, probiotics research) to address the root of hygienic practice: cleanliness in pursuit of improved health.

From the hand drying example, it is clear that a standard definition of hygiene would be helpful: it turns out the vast majority of research on the hygienic aspects of hand drying has been funded by either the paper towel industry or the blow drier industry as advertising tools. There appears to be something of a feud going on between these two competing industries. Sadly, there is much about the current state of hand drying literature that is clearly partisan, and it is difficult to evaluate claims from either side because they define hygiene differently.

The hand drying literature can be separated into two opposing divisions: one attempting to demonstrate that the newer air dryers are as hygienically efficacious as paper towels, and the other attempting to discredit the newer technology in favor of paper towels. While both divisions utilize bulk reduction in microbial load as a proxy for hand hygiene, research from the first division largely focuses on the potential of wet hands to transfer microbes and the ability of air dryers (whether warm or jet) to effectively dry hands: the hypothesis in this case is drying is hygienically efficacious if hands are dry and new microbes are not acquired through the process. Research from the second division tends to focus on the risk of air dryers to spread microbes throughout the environment by aerosolizing moisture from the hands: the hypothesis in this case is drying is hygienically efficacious if new microbes are not acquired through the process and if production of aerosols are minimized. It is difficult to compare the two divisions because many of these studies include methodological issues (e.g., variation in protocols, lack of appropriate controls or statistical analyses) that make it difficult to compare results across studies.

Despite there being an obvious interplay between these two divisions, many of the concerns on either side remain unaddressed. Utilizing a definition of hygiene that explicitly relies on reduction in disease spread would address concerns on both sides of the debate: there is currently no evidence linking aerosolization of residual moisture (and associated microbes) with the actual spread of disease. Likewise, despite demonstrations that wet hands allow for increased bacterial transmission, there does not seem to be evidence linking wet hands after washing to deleterious health outcomes. The complex ecological context of the hand microbiota may modulate effects of both aerosolization and prolonged moistening. Additionally, the majority of hand drying research largely ignores the relative hygienic contribution of the hand washing step; understanding the relative contribution of washing to hygienic efficacy is necessary to put the hand drying literature in proper context.

The experience of working on this review has been incredibly positive: I’ve gotten to read deeply in corners of the scientific literature that I would not have expected I would be delving into even six months ago, I’ve learned a number of beautiful and startling things, and I believe that we have been able to contribute something necessary and worthwhile to the scientific discussion of hygiene. There is a gradual paradigm shift occurring right now in the clinical sciences, with germ theory being gently replaced by a more nuanced theory of disease that takes into account the beneficial role that our symbiotic microbiome plays; this review, I hope, will be a helpful building block for that new paradigm.

Experimenting with a “microbiology of the built environment” Flipboard

We are always looking to recruit more people to contribute to microBEnet on topics related to microbiology of the built environment. And if you have something to say about this topic, by all means, we want you to blog here. Tell us your stories about your work about your projects about your outreach and papers and grants and such. Email me if you do not have an account and want to write something.

But another activity we are interested in for which writing blog posts may be too cumbersome, is just sharing interesting links one discovers – to news stories, or papers, or new software, or talks, or videos, etc. I have been experimenting with different options for this and one that has promise is Flipboard. So I have made a microBEnet Flipboard site. It is embedded below. If you have any interest in contributing to this, let me know.

View my Flipboard Magazine.

June 21 was International Swab Day for MetaSUB

June 21 was International Swab Day for the MetaSUB project. MetaSUB stands for “Metagenomics and Metadesign of the Subways and Urban Biomes”, an initiative in which experts together with citizens will study the microbial ecosystems of public transportation systems from all over the world. From the MetaSUB website:

Screen Shot 2016-06-25 at 12.03.55 AMBy developing and testing standards for the field and optimizing methods for urban sample collection, DNA/RNA isolation, taxa characterization, and data visualization, the MetaSUB consortium is pioneering an unprecedented study of urban mass-transit systems and cities around the world. These data will benefit city planners, public health officials, and designers, as well as discovery new species, biological systems, and biosynthetic gene clusters (BGCs), thus enabling an era of more quantified, responsive, and “smarter cities.”

The project is a continuation from the New York Subway Microbiome project, but on a much larger scale. It will collect and analyze samples from 54 major cities all over the world. Read more about MetaSUB in this paper:

The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium inaugural meeting report – The MetaSUB International Consortium – Microbiome (OA)

June 21 was Global City Sampling Day, the official start of the sampling phase project, where many samples were collected with the aid of “citizen scientists”.  Here is a selection of news articles:

‘Global City Sampling Day’ to Launch Weill Cornell Medicine-Led Study of Antimicrobial Resistance Across 54 International Cities – Weill Cornell Medical College

Screen Shot 2016-06-25 at 12.09.10 AMWeill Cornell Medicine is kicking off its groundbreaking international study of antimicrobial resistance with an event called Global City Sampling Day. Spanning six continents, 32 countries and 54 cities, this synchronized event brings together more than 400 people, who are expected to collect about 12,000 samples of DNA, RNA and microbes from surfaces in subways, buses, airports and other well-traveled public meeting spaces.

Global Microbiome Initiative Explores Subways for Drug-Resistance Markers – GenEngNews

Screen Shot 2016-06-24 at 11.42.22 PMMetaSUB Consortium will collect DNA and RNA samples from high-traffic areas in subway systems, buses, and parks in 54 cities worldwide (…) The study seeks insights on the prevalence of pathogens, including antimicrobial resistance, in urban environments–and expands on a 2015 metagenomic portrait of microbes in the New York City subways.

VideoBiologists Study What Kind Of Bacteria Is On New York City Subways – CBS New York

Screen Shot 2016-06-24 at 11.44.58 PMA team of biologists want to know what sort of bacteria is riding on the subways with straphangers. CBS2’s Christine Sloan reported the Weill Cornell Medicine biologists, led by Dr. Chris Mason, took nylon swabs of benches, turnstiles, railings and seats on trains. “The place we got the most bacteria and division of organisms was on wooden seats,” Mason said. “We actually see less on steel surfaces.” The swabbing is part of a global anti-microbial resistance study as 54 cities in 32 countries are collecting DNA and microbes simultaneously. The study is funded by the Gates Foundation.

Scientific study wants to identify all the microbes in subways around the world – Dan Rivoli – NY Daily News

Screen Shot 2016-06-25 at 12.13.08 AMThere are creepy creatures lurking in the subway – and they’re not just rats and insects. Christopher Mason, a geneticist at Weill Cornell Medicine, has been studying the microscopic ecosystem in the subway, already identifying more than 600 varieties of microbes. And on Tuesday he descended below ground again. Equipped with nylon swabs and latex gloves, Mason and his team were back in the subway to swab wooden benches, handrails and train seats to collect microbial material as part of an international expansion of his project, called MetaSub.

Mapping the subway’s microbiome: Barcelona – EurekAlert

Screen Shot 2016-06-24 at 11.37.52 PMBarcelona takes part in the international research project Metasub, which aims to map the microbiome of public transit systems in 54 cities worldwide, including New York, Hong Kong, Paris or Sydney. Scientists at the Centre for Genomic Regulation (CRG) are contributing to this project by providing, processing, and sequencing samples from the Barcelona subway and also by leading the sampling processing working group.

Global Project Uses GIS Cloud for Mapping Pathogens in Public Transit Systems – Directions Magazine

Screen Shot 2016-06-25 at 12.16.35 AMEvery day, hundreds of millions of people around the world use public transit systems without noticing a complex microbiome that is invisible to the naked eye. In more than 50 cities around the world, scientists are working on building a molecular and genetic atlas of these transportation systems in order to establish a worldwide “DNA map” of their microbiomes. Researchers studying these microbiomes as part of the MetaSUB project will use the GIS Cloud Mobile Data Collection app, highlighting the importance of its geospatial component.

The Secret World Inside You at the AMNH runs through August 14

In the past, we have lamented the poor representation of microbes in natural history museums. And so I must mention that there’s a wonderful microbiome exhibit currently on exhibit at the American Museum of Natural History in New York City. The Secret World Inside You, is a microbe related exhibit co-curated by Susan Perkins and Rob DeSalle, curators at the AMNH. The exhibition opened last fall and will remain on view until August 14, 2016. I had the opportunity to visit the exhibit last week and I highly recommend it if you find yourself in the area. Then the exhibit moves to the North Carolina Museum of Natural History in Raleigh, NC next, so if you don’t make it to NYC, you may also be able to catch it there.

We loved the giant, glowing bacteria!

Help they are taking over!
Help they are taking over!

Another highlight was the classroom area where an expert answers questions and passes around a replica of Antonie van Leeuwenhoek‘s original microscope.

Replica of Leewenhoek's microscope, photo by Jeroen Rouwkema on Wikipedia
Replica of Leewenhoek’s microscope, photo by Jeroen Rouwkema on Wikipedia

And they even talk about data showing that we share bacteria with dogs.

IMG_4040

There’s a video featuring some prominent members of MoBE community that’s almost as good as kittybiome‘s.

IMG_4049 IMG_4048

Towards the end, we got to share some sticker microbes with dogs and skateboarders.

Of course we shared our microbes with the dog.
Of course we shared our microbes with the dog.
The bookstore has wonderful microbe related books and games and of course stuffed microbes.
The bookstore has wonderful microbe related books and games and of course stuffed microbes.

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.

Built mycobiome sequence metadata annotation workshop, Gothenburg, May 23-24, 2016

workshopIn the context of an Alfred P. Sloan Foundation grant to the UNITE database to improve the support for fungi in the built environment, a workshop centered on public fungal ITS (barcode) sequences from the built environment was organized in Gothenburg, Sweden on May 23-24, 2016. Specifically, the ~40 physical and remote workshop participants sought to annotate these sequences according to the MIxS-BE standard to enable more precise query of the built mycobiome.

 

DNA sequences tend to be submitted to public sequence databases with very little metadata. Many sequences come with little extra information than the name of the sequence author and the tentative name of the study. Thus, anyone interested in retrieving all fungal sequences from, e.g., bathrooms or tiles will be hard put to assemble such a dataset.

 

There is, of course, every reason to think that analysis of all sequences recovered from bathrooms, or indeed any other substrate or locality, will prove to be a worthwhile scientific endeavor. The inability to pursue such research questions hampers progress both in the context of the built environment and of mycology itself.

 

The workshop participants went through and annotated all built-environment fungal ITS sequences from the international nucleotide sequence databases (INSDC) according to the MIxS-BE standard. The workshop participants noted a marked difference between the level of detail provided in the database entries — typically low — compared to the level provided in the underlying scientific publications — typically much higher. Although the final results have yet to be assembled, more than 10,000 new data points were recovered. The results will be implemented in the UNITE database and shared with other initiatives and online resources.

 

The workshop raised several pressing questions: is it scientifically defensible to release DNA sequences with virtually no metadata at all, when indeed those metadata are available to the sequence authors? When metadata are provided with sequence entries, shouldn’t we try to provide them in a homogenous, standardized way? And the fact that metadata are available in print-only journals or non-open access electronic journals, does that really make them “available”?

 

The workshop participants were, furthermore, surprised by the diversity of research efforts targeting the built environment. Expected substrates and localities such as dust, indoor air, and offices were common. Less expectedly, however, spacecraft, prehistoric buildings such as tumuli and man-made caves, and tombs and crypts (and even mummies) were also found to be fairly frequent targets for mycological research efforts. These exotic research efforts stretched the MIxS-BE standard to its limits.

 

The workshop participants also covered outdoor sequences that were found to belong to UNITE species hypotheses featuring sequences from the built environment. These outdoor sequences were annotated with country and host of origin in recognition of the fact that they, too, are in a position to inform us of the nature of indoor fungal communities.

 

We intend to publish the outcome of the workshop, and all data assembled during the workshop, in a scientific outlet later in 2016. In the meanwhile, the data will gradually be released in UNITE and in resources relying on UNITE for molecular identification of fungi.

Concentrations and Sources of Airborne Particles in a NICU

Hello everyone! I’d like to draw your attention to our just published year-long study focusing on little investigated topic titled: “Concentrations and sources of airborne particles in a neonatal intensive care unit”. The main outcomes of the study are the following:

  • The contribution of outdoor particles to indoor particle mass concentrations was particularly low owing to the effectiveness of the ventilation system including HEPA filtration. Although the mass concentration of particles from outdoor air was small, the contribution of ventilation to small particles as assessed by total particle number concentration was highly sensitive to the influence of outdoor air, which highlights the importance of maintaining efficient particle filtration and limiting air infiltration through the building envelope.
  • This work has also demonstrated a strong temporal and spatial association between the indoor particle mass concentration and human occupancy, both considering the temporal pattern in the hospital overall and focusing on infant rooms in particular. The detected particle peaks tied to occupancy were substantially more discernible among larger particles, as would be expected for shedding and resuspension. Conversely, room occupancy contributed little to submicron particle generation.
  • Within-room emissions made the highest relative source contribution to baby room coarse particle concentrations. Near-room emissions also contributed substantially to baby room coarse particle loads, especially in relation to the small contribution from outdoor air, indicating a possibility to reduce infants’ exposure by further isolating the air in their room from nearby air outside the room.
  • That the occupancy-associated emissions within the room are dominant contributors to airborne particulate concentrations in NICU environments suggests that they may also be an environmental factor influencing infant health. Further evidence supporting this view emerged from our pilot study, revealing that the particle concentrations inside an infant incubator were a substantial proportion of those in room air.
  • Emerging evidence supports a view that occupancy is an important source of indoor airborne bacteria and fungi. It seems worthwhile to consider whether improved nosocomial infection control can be achieved by further limiting bioaerosol emissions associated with occupancy.

It’s also worth noting we have amassed several thousand swab and wipe samples from around this NICU. While the data is still being generated, early results point to an environment largely dominated by skin associated microorganisms. In tracking biomass across time, our data echoes that of the indoor “wasteland” recently reported, but we do find some reservoirs of active growth. More details on microbes in the NICU will be presented during an oral presentation in a couple of weeks at the Sloan MoBE conference in Boulder.

Built environment microbiome design charrette

During the winter term at University of Oregon, I led a design-oriented microbiome course for graduate and undergraduate students from a variety of disciplines (Architecture, Environmental Studies, Landscape Architecture, and Planning). Just for the record, these design students were VERY enthusiastic to learn about microbiome science, although they were somewhat disconcerted to find out how nascent the field is. For the final exam, students in the course were tasked to do a design charrette (i.e. a brief but intense design exercise) focused on solving specific design problems related to creating “healthier” built environment microbiomes.

Below is an example of what one Landscape Architecture undergraduate student came up with to improve typical apartment units, which are frequently closed off from the outdoors and are likely to have a very “human-looking” indoor microbiome. This particular student inverted the relationship between the apartment units and their garden/yard, using ancient Roman courtyard homes as a precedent. The idea was to create a safe, sheltered, and unpolluted interior green space that would entice residents to open up their doors and windows for natural ventilation, while also increasing social interaction. This is in contrast to the design of most apartment complexes, where there is often an unused sward of mown grass exterior to the buildings. In terms of microbes, her concept was supported by studies like Hanski et al. (2012), which showed that species richness of native flowering plants around the home was negatively correlated with atopy and that atopy was negatively correlated with diversity of Gammaproteobacteria on residents’ skin. Another linkage in her design proposal was using natural ventilation to make the indoor microbiome more similar to the immediate outdoor microbiome (e.g., Meadow et al., 2013).

Now, if we only knew enough to specify exactly which plant species and how many of them to put in that courtyard garden, I could really get those Landscape Architecture students motivated!

1_courtyardsketch_sm
Quick sketch done during the final design charrette

 

Design concept/parti: “third place”

 

1_courtyardprec
Precedent study: Roman courtyard home