Assessing biochemical activity and metagenomic codes to a “T”

We’re recruiting a student/postdoc for this project! If it sounds interesting, please contact the Huttenhower Lab!

We were happy to hear that we’ve been funded by the Sloan Foundation to continue our study of microbes on the Boston subway. Our original study involved 1) identifying which microbes were resident in this built environment, 2) understanding their functional potential, and 3) quantifying gene families of interest, including antibiotic resistance and virulence factors. In brief, we found that it’s not so bad – even (and perhaps especially) on a crowded subway, you’re surrounded mainly by harmless microbes largely from human skin.

However, this still leaves many open questions in terms of public health. Although we now know what microbes are present, the built-environment is chemically unique, and we have yet to characterize which microbes are biochemically active, persistent, or dead. Metagenomic surveys reveal which metabolic pathways are present, but this may include DNA from inactive cells. It also does not identify which pathways are transcriptionally active, driving the cells that do persist in the built environment. Finally, since we collected all train samples at one time point and all touchscreen samples at another time point, we have limited knowledge on how stable different locations’ microbial activities are over time.

Project OverviewTo determine which microbes are active, we will use a combination of ‘omics approaches on newly collected samples that include metagenomics, metatranscriptomics, and metabolomics. From this, we can identify live bacteria (DNA) based on those that are transcriptionally active (RNA). We can further determine which metabolites are being produced by 1) associating taxonomic profiles with metabolites, 2) identifying genes within taxa that correspond to these metabolic pathways, and 3) confirming pathway activation through transcriptomic data. Cases in which interacting genes, transcripts, and metabolites covary (or are co-absent) provide “guilt-by-association” evidence of new functional annotations, novel biochemical pathways, or metabolite contributions from non-microbial sources.

To construct microbial signatures for different built environments, we will use the hitting set algorithm generated by Eric Franzosa, a research associate in the lab. This was developed to identify human hosts by their persistent microbial strain combinations, and in this study, we will test how these “codes” may identify individual built-environments as well. In brief, we will determine sets of features (taxa, genes, functions) that are unique to train lines and stations. We can then evaluate how stable these microbial codes are between our previous and new collections. Together, these features may provide a strategy for characterizing recently-visited environments using microbes newly acquired by an individual.

Generally, it is believed that microbes in the built environment originate from their human inhabitants and surrounding environments. This was the case in our last study, e.g. contrasting the presence of environmental taxa on indoor versus outdoor touchscreens, the prevalence of skin microbes on trains, and the presence of vaginal microbes on seats but not seatbacks. In terms of macroecology, urbanization frequently reduces biodiversity,1 though there are select animals such as pigeons and sparrows that thrive in (or more typically near) the built environment.2 Analogously, there may also be specific microbes that thrive and contribute to the built environment, which will be increasingly important to understand as more people move to cities. Overall, this study will help identify these microbes and the mechanisms they use to survive, as well as determine how stably they inhabit built environments across time.


1. Sol, D., Lapiedra, O., Gonzalez-Lagos, C. (2013). Behavioural adjustments for a life in the city. Animal Behaviour, 85, 1101-1112.
2. Kark, S., Iwaniuk, A., Schalimtzek, A. and Banker, E. (2007), Living in the city: can anyone become an ‘urban exploiter’?. Journal of Biogeography, 34: 638–651. doi:10.1111/j.1365-2699.2006.01638.x

Reports from #LAMG16 Lake Arrowhead Microbial Genomes

Collecting together here some reports from the Lake Arrowhead Microbial Genomes Meeting

David Coil’s summaries

From me



Emily Anthes on “Can science build the perfect workspace? ” #BuiltEnvironment #microbiomes

Windows, desks and employees are being wired up in a quest to create healthy, evidence-based environments.

Interesting article by Emily Anthes in Nature: The office experiment: Can science build the perfect workspace? : Nature News & Comment

It focuses on a collaboration between the Mayo Clinic and a design firm – Delos to create something called the “Well Living Lab”.  Basically it is a high tech facility to study the interaction between people and the built environment.  And it even has some microbial work going on or that will be happening:

The complexity will also grow as the team begins to layer studies on top of one another. Nicholas Clements, a director at Delos Labs, is collecting samples of the office microbiome: bacteria, fungi and more that live in the office’s nooks and crannies, and on the surfaces that people touch every day. Scientists think that it may be possible to actively shape the indoor microbiome to improve human health, but research into this idea is in its infancy.

“We’d like to push that science further and hopefully we can accomplish that here,” says Clements, who plans to test whether certain environmental interventions, such as changing flooring and surface materials or installing a ‘green wall’ of living plants, can alter the office’s microbes–or the health of its human occupants. (He will also track participants’ exposure to indoor air pollutants, such as the volatile organic compounds emitted by paint and furniture.)

Now, I wish the article and/or some of the people interviewer placed more of this in context of the rich and growing body of literature of the human-built environment interaction (e.g., this facility seems really fancy and nice and all but I wish the article had spent a bit more time on other facilities that are being used in the same or similar ways some of which were mentioned briefly).

Anyway – the concept is worth considering and some of the aspects of this facility are quite interesting.  Overall, I think the article is worth checking out.  We need more and more efforts like this (well, maybe not at this cost) to start to get a better handle on the complexities of built environment – human interactions (and of course, on the microbiome aspects of such interactions).

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


The Jefferson Memorialome? The Jeffersonome? The Jefferson Microbiome? A biofilm by any other name …

Who wants a new project?  Seems like they could use some microbiology of the built environment experts to provide additional help on this one: 

Officials fret as fungi, algae and bacteria leave growing stains on hallowed stone.

Source: A grimy, black biofilm is starting to cover the Jefferson Memorial, and it can’t be killed – The Washington Post


Guest post from Dr. Koh Tse Hsien on “Clinical microbiology and Social Media”

This is a guest post from  Dr. Koh Tse Hsien who maintains the blog Microcosm and also is in the Pathology Department at Singapore General Hospital.

Clinical microbiology and social media

We are a diagnostic laboratory that provides bacteriology services to a busy 1600-bedded tertiary care hospital in Singapore ( We receive about 360,000 specimens a year.

Towards the end of 2014, inspired by other microbiology blogs on the web (like microBEnet), we decided to develop a strategy to explore the possibilities of social media.

The initial purpose for setting up a blog was to showcase some of the work that goes on in a diagnostic laboratory. Since the lab is off limits to most of our hospital colleagues, the amount of thought and effort that goes into generating a microbiology result is usually unappreciated (e.g. We also feel that some of the micro-organisms we encounter are pretty cool and would like to share them with a wider audience (e.g. So the blog offers a “window into the laboratory, (and) a glimpse of a world in miniature”.

The advantage of the blog over a corporate website is that it can be more dynamic and we have control over the content. For example, last year Singapore experienced a large outbreak of serious Group B Streptoccus infection that was related to raw fish consumption. This is probably the first time something like this has been described in the world. While the ‘proper’ scientific manuscripts are still being written up, we have already documented ‘the human interest story behind the paper’ on the blog ( Even after the scientific manuscript is published, the blog post will remain more accessible and readable for the general public. Increasing public awareness of microbiology can only be a good thing.

We also have a Facebook page ( This is where we post lab/hospital activities, but can also be useful for disseminating news like new guidelines or interesting publications. In our experience, the Facebook page is also good for lab esprit de corps and presenting a ‘lab face’ to our customers.

Lastly, we also have a Twitter account ( We find Twitter very useful for keeping up to date with developments in bioinformatics, infection control, and outbreaks like Ebola, MERS-COV and Zika. You can get a sense of what we think is interesting, or is an important trend, based on what we retweet.

Finally, all three social media platforms are integrated. Whatever we blog gets reflected on Facebook, which also automatically posts to our Twitter feed.

Dr Koh Tse Hsien (left) maintains the blog and twitter account. Dr James Sim (right) updates the Facebook page.

Dr Koh Tse Hsien (left) maintains the blog and twitter account. Dr James Sim (right) updates the Facebook page.
Dr Koh Tse Hsien (left) maintains the blog and twitter account. Dr James Sim (right) updates the Facebook page.

Don’t Cry. Don’t Raise Your Eye. It’s Only Microbe Wasteland

These will almost certainly be of interest to the MoBE community.  There is a new paper in mSystems “Geography and Location Are the Primary Drivers of Office Microbiome Composition” by John Chase, Jennifer Fouquier, Mahnaz Zare, Derek L. Sonderegger, Rob Knight, Scott T. Kelley, Jeffrey Siegel, J. Gregory Caporaso.  I found out about the paper via Jack Gilbert sharing a link to a commentary about the paper by Sean Gibbons:  The Built Environment Is a Microbial Wasteland  (Love the title, though I am not sure I would go so far as to say wasteland as I love deserts and such places. And I am happy the Title made me think of The Who).

Lots of interesting material in the paper.  Check it out and check out the commentary.  Also, the commentary has a great figure which I think I will probably use for many purposes:

Microbial diversity in outdoor environments and BEs. On the left is the silhouette of a cowboy brushing past a pine tree while riding a horse. On the right is the silhouette of a person sitting in an office chair and working on a laptop. Blue microbes are human associated, while other colors represent nonhuman microbial diversity.
Microbial diversity in outdoor environments and BEs. On the left is the silhouette of a cowboy brushing past a pine tree while riding a horse. On the right is the silhouette of a person sitting in an office chair and working on a laptop. Blue microbes are human associated, while other colors represent nonhuman microbial diversity. (Note in the Acknowledgements there is this text about the Figure: I gratefully acknowledge Cache Gibbons and Samantha Veysey for the original artwork in Fig. 1)

A true must read: amazing essay by Tal Addaby “Less Disinfectant, More Rioja”

There is a wonderfully essay by Tal Abbady coming out in tomorrow’s New York Times (and available online now).

A few years in Spain, and my mother’s last days, helped me see the futility of a sterilized life.

Source: Less Disinfectant, More Rioja 

The essay is about many things, including differences between cultures (pun intended by me), her mother, her life, fear and freedom.  The fear part includes a focus on fear of germs.  She includes discussion of people who try to sterilize the world around them – their hands – surfaces – and every bit of their lives.  I don’t want to spoil the essay, but just want to really suggest that everyone reads it.  And I love the ending

When fears of a contaminated-armrest death creep up, just contemplate the many millions of microbes that sheathe any human body. Most, but not all, are quite friendly.



For a related (though nowhere near as well written) post I wrote about how germophobia has gone crazy see Studying — not wantonly killing — the microbes around us and the rise of the “microbiology of the built environment”

A microbiology of the built environment April Fools’ joke

Well I am sad I missed this yesterday but there was an April Fools’ joke published in the Western University Gazette that had a microbiology of the built environment angle.

“We’re holding Ivey business classes in there to decontaminate the premises,” Chakma said.

Source: English Department relocated to broom closets | Spoof |

“There were trace sources of freeloadica poverticanus found in the building,” says President Chakma in a press release. “It’s a bacteria found most often in flakey, unprofitable liberal arts institutions. We’re holding Ivey business classes in there to decontaminate the premises.”

The discovery of this bacterium (I do wish they capitalized the genus name) led to the English Department to be moved to broom closet’s.  I think they labelled this as “spoof” because it was in fact too believable.  Anyway – it is the only microbiology of the built environment April Fools’ joke I saw from yesterday. 

Use of Copper in Structures and the Growing Resistant Bacteria

Interesting article addressing the risks of using copper in human structures for its antimicrobial qualities.  Copper resistant bacteria could prove to be a risk for human health, as certain parts of the human immune system (notably macrophages) utilize it to dispatch potentially dangerous microbes.  While many places use copper as a safety measure against harmful bacterial growth, over-use may lead to more resistant and possibly pathogenic bacteria.  Link to the full article is here: Copper Resistant Bacteria