Describing a new bacterial species: mixing biology and history

Kirrobacter mercurialis
Kirrobacter mercurialis

After way more work than I imagined when we embarked on this project, we are almost ready to submit our first description of a new bacterial species, Kirrobacter mercurialis.   Not exactly earth-shattering, given that about 40 bacterial species descriptions come out every month in the International Journal of Systematic and Evolutionary Microbiology (IJSEM).  However, our lab tends to focus on the grand-scale of biology (metagenomics, 16S surveys, population biology) or on bioinformatics (phylogenomics, genome assembly, software development).   We’re not really a “microbiology” lab in any sort of classical sense.  In fact when I joined the lab I had to order petri dishes and microscope slides since the only wet lab work was DNA extractions and library preparations.   However, I always wanted to describe a new species and the opportunity arose through Project MERCCURI (a.k.a space microbes) where one of the isolates we grew up only showed 95% 16S identity to any cultured bacterial species.  With the help of a series of undergraduates in the lab (Jennifer Flanagan, Andrew Stump, and Alex Alexiev) we began to try to figure out what this process would entail.

I started off by reading a number of existing species descriptions, and in my naivety was struck by several things:

DNA-DNA hybridization is still considered a gold standard to measure the relatedness of a new species to close relatives.   IMHO this is insane, given the fact that this is a technically difficult, expensive (you usually have to buy DNA for comparison from culture collections) technique that is, at best, a fairly gross measure of relatedness.  In our case the very first thing we did was to sequence the genome… we could compare that to other genomes at a fraction of the cost and effort.  Fortunately,  our bug was distant enough from close relatives that it would have been pointless to even try the DNA-DNA hybridization.

Speaking of having the genome, there are a number of aspects to classical microbiology that can benefit enormously from having this kind of data.   For example, members of the family where Kirrobacter is located contain carotenoids, so measuring these is a standard part of a species description.   This process entails a methanol extraction of cell lysate, followed by analysis of absorption peaks on a spectrophotometer.   Or in our case, I spent 30 seconds looking up the carotenoids in the RAST annotation of the genome.  Done.  Another interesting case for us was with flagella.  We performed motility tests (negative) and examined the bug using both light and electron microscopy during both exponential and stationary phase.   Never once did we observe flagella, yet the genome contains 30 flagella genes (compared to 0 for another non-motile close relative).  This suggests that the picture is more complicated than just saying “no flagella”.

Kirrobacter mercurialis
Kirrobacter mercurialis

Just to be clear, I think there is very significant value in doing species-level classical microbiology!   That’s partly why I started this… I think I looked at one too many lists of taxa in QIIME and wondered “but what are they *doing*?”.   There are many aspects to the biology of a species that can’t (yet) be determined from the sequence.   For example; morphology, temperature range, salt tolerance, etc.   Many of these are important in understanding what niche a species might occupy, or what it might be actually doing in a community.   I think far more work on cultured microbes is needed before we can start to paint complete pictures of complex microbial communities in the real world.

That being said, I don’t get the impression that that the requirements to describe a new species reflect what’s really important, given access to modern tools like cheap genome sequencing and good sequence-based taxonomy.   For example, all bacterial species descriptions devote a lot of space and either pain/$$$ to characterizing the fatty acids in the membrane.   Historically, this was an important part of determining taxonomy.  Nowadays there are important arguments between various schools of thought as to whether a determinative taxonomy should come from 16S, a collection of housekeeping genes, or whole genomes… but no one (that I’m aware of) is discussing fatty acid profiles.  And functionally, I’m not sure there’s much value in knowing that Kirrobacter mercurialis has a normal amount of C18:1ω7cis compared to other members of the family, but has more C16:0.

For this, my first involvement in a species description, I wanted to do it “right” and use the appropriate classical tools.  The only exceptions to this were the DNA-DNA hybridization as mentioned above and publishing in the closed-access IJSEM (fortunately you can petition for the name to be mentioned in IJSEM, which still qualifies for official standing in nomenclature).   I’d like to do another species description sometime that focuses on information from the genome, and those characteristics likely to be most useful to someone who either wanted to culture the organisms or understand something about it’s biology.   Sadly, lacking the classical measures would probably mean that the species would never have official standing in nomenclature.

Read More

Antibiotic resistance genes in goat and lamb slaughterhouse surfaces

The spread of antibiotic resistance traits is an ongoing and important issue that is poorly studied. This PLoS One study by Lerma et al. is the first to use a culture independent approach to characterize antibiotic resistance traits in the total microbiota present in a goat and lamb slaughterhouse. Lerma et al. found that tetracycline resistance genes (tetA and tetB) and Sulfonamide resistance genes were widely distributed throughout the slaughterhouse and in meat products (Figure 1). The authors suggest that adequate disinfection could help to reduce the risk of transmission of these antibiotic resistant traits into the food supply.

Figure 1. Detection of different antibiotic resistance genes (tetracycline, sulfonamide and beta-lactam genes) in different slaughterhouse zones and meat products. doi:10.1371/journal.pone.0114252.g001

This study makes a useful contribution towards understanding the distribution of antibiotic resistance genes in a slaughterhouse.

In recent years, we have become increasingly aware of the misuse of antibiotics in conventional agricultural practices, particularly where antibiotics are used to promote animal growth rather than to treat sick individuals. In an annual report posted in October 2014, the FDA reported that the quantity of antibiotics sold for livestock use increased by 16% from 2009 to 2012. Although antibiotics do promote growth, the use of antibiotics to promote growth is risky because it may spread of antibiotic resistance traits into both livestock and human populations. In December 2013, one year ago, the FDA implemented a new policy (to be phased in over three years) that makes it illegal for farmers and ranchers to use antibiotics to make animals grow bigger. Fortunately (as we reported here last week), there are other strategies that seem to work like the one taken by a national chicken producer who is using probiotics instead of antibiotics for animal growth promotion. And lest we go overboard and ban the use of antibiotics in livestock altogether, it bears mentioning that that denying care to sick animals raised for human purposes is inhumane (even if that is what may be required to sell meat as organic).


Read More

Healthcare Design discusses design issues relating to hospital acquired infections

Just a quick post here pointing people to an article of possible interest: Healthcare-associated Infections Keep Industry On High Alert.  In the article Sara Marberry discusses some issues relating to microbes and the built environment in hospital design.  Among the topics covered are hydrogen peroxide vapor systems, UV irradiation devices, and copper as possible antimicrobials.  Also discusses are facility guidelines and factors such as filters, coiling coils, room sizes and more.  Definitely worth a look.  I hope they start to consider more the microbial ecology and not just what to do about possible pathogens.

Read More

Preliminary Analysis of Project MERCURRI… a.k.a. #spacemicrobes

Analysis of the growth data from space is ongoing but we have some preliminary results to share:

-Firstly, 47 of the 48 bacteria grew at least a little bit in space, the only exception was the sample collected from the Philadelphia Phillies dugout.  Sorry guys!

-A number of the bacteria grew quite well in fact, filling up the entire well on the plate.   We’ll have pictures of this once the next Dragon spacecraft returns with our plates, hopefully sometime in January.

-We had hoped to be able to announce the winners of the microbial playoffs by today, but it’s such a close race in each category that we’re going to have to do some more detailed analysis over the next couple of days.   Instead we’re announcing the finalists in each category, from which the winner will be decided.  Rumor has it that a special prize is in order for each of the winners.   So here are the categories:

Wikipedia Commons

“Best Tip-Off”.   This is for the bacteria that starts growing right out of the gate.  We measured this by the percentage increase in growth between time 0 and our first growth measurement 24 hours later.   These bacteria all spent 9 months in the deep freeze, going around the earth every 90 minutes, but as soon as they thawed out they took off as if nothing had happened.


-Pantoea eucrina, collected from the Mercury Space Capsule at the Smithsonian Museum of Air and Space in Washington D.C.

-Macrococcus brunensis, collected from the central keyboard at WHYY radio in Philadelphia, PA.

-Leucobacter chironomi, collected from a residential toilet in Davis, CA.

-Exiguobacterium acetylicum, collected from the 50-yard line at Candlestick Park, home of the San Francisco 49ers.

-Paenibacillus elgii, collected from the Mars Exploration Rover before launch at the Jet Propulsion Laboratory (JPL-NASA) in Pasadena, CA.

-Microbacterium oleivorans, collected from the mascot head at St. Joseph’s Preparatory School in Philadelphia, PA.


“Best Sprint”.  This category was for the bacteria who really hit their longer-term stride quickly.   We defined this roughly as the shortest time to reach halfway to the maximum growth observed… this is much later than the time for the best tip-off as described above.


Public Domain
Public Domain

-Bacillus megaterium, collected from an antique pressure vessel at the Chemical Heritage Foundation in Philadelphia, PA.

-Arthrobacter nitroguajacolicus, collected on the 50-yard line of McCulloch Stadium in Salem OR, by Chapman Hill Elementary School students.

-Kocuria kristinae, collected on the court after a San Antonio Spurs game in San Antonio TX.

-Streptomyces kanamyceticus, collected in the kitchen on the set of Kare11 Morning News, Minneapolis/St. Paul, MN.

-Kocuria marina, collected on a water fountain at a Yuri’s Night party in the Museum of Life and Science, Durham, NC.

-Bacillus stratosphericus, collected by St. Peter’s School students in a butterfly water dish at the Academy of Natural Sciences in Philadelphia, PA.


“Best Huddle”.   This is for the microbes that grew to the highest density… really packing those cells into the space allowed.  It might have been fast, it might have been slow, but these bacteria crammed into their wells.


Wikipedia Commons.
Wikipedia Commons.

-Exiguobacterium indicum, collected on the center field logo at FedEx Field (home of the Washington NFL team) in Maryland

-Bacillus amyloliquefaciens, collected on the statue of Benjamin Franklin at the Franklin Institute in Philadelphia, PA

-Kocuria kristinae, collected on the court after a San Antonio Spurs game in San Antonio TX.

-Kocuria rhizophila, collected on a camera at a Yuri’s Night Party with Buzz Aldrin in Los Angeles, CA.

-Bacillus megaterium, collected from the Liberty Bell in Philadelphia, PA.

-Bacillus aryabhattai, collected from a practice football field used by the Oakland Raiders in Oakland, CA.






Read More

Update on Project MERCCURI a.k.a. #spacemicrobes

10014531_10102230365591373_8633462824931932305_nAfter 9 months of technical delays, during which time our collection of frozen built environment microbes went around the earth every 90 minutes, we are finally getting growth data from the International Space Station (ISS)!   Astronaut Terry Virts has been taking daily growth readings of our collection of 48 microbes and today (Friday) is the last day of data collection.   Meanwhile here on earth, I’ve been collecting data from the control plates.   Hopefully within the next week we’ll have an idea of which microbes survived the delay and more excitingly if any of them behave differently in microgravity than on earth.   Updates and data will be posted here.    For more information on Project MERCCURI, check out our website.

For a little teaser, here’s a short video piece that NASA released today which talks about the project on the ISS.  For more media coverage of the project, check out our “Press” page.


Read More

C. difficile on the rise outside the hospital

Just a quick post here about the spreading of C. difficile among patients who visited healthcare settings but didn’t take antiobiotics.   Traditionally C. difficile is thought to infect people whose normal microbiota was disturbed by antibiotics.  It’s also the target of most experiments on fecal transplants since those have been shown to be very effective against this disease.

They key point of this story is that some recent cases have been observed that don’t appear to be hospital-acquired, or have occurred in patients that didn’t even have antibiotics.   Worth keeping an eye on this one…

Read More

Congrats to Jack Gilbert, one of the “40 under 40″ in Chicago

I generally try to avoid any type of discussion of the age of researchers and I also generally never ask people about their age.  But this time it is in a story so I think it is OK to mention: Jack Gilbert of Argonne National Laboratory is on Crain’s Chicago 40 Under 40 2014 list.  This 40 under 40 list is from Crain’s and focuses on people in Chicago and it is good to see them select a microbial ecologist as one of the honorees.  Congrats Jack.

Read More

Chicken Probiotics?

Just a quick post here on an NPR story that caught my attention “Giving Chickens Bacteria … To Keep Them Antibiotic-Free”.  Unlike with humans where determining the effect of probiotics is complicated by a lot of variation in the population (genetic, cultural, diet, etc.), with a whole bunch of chickens it’s easier to measure the effects.  And, according to this story, they do have a beneficial effect and can significantly reduce antibiotic usuage by the farmer which is pretty much a win for everybody.   Would love to see more of this kind of work… as well as some hard data.

Read More

Humans living underground – doesn’t look like fun, but interesting topic for #microbiome work

Heard this story on NPR yesterday:  ‘A Universe Beneath Our Feet': Life In Beijing’s Underground : NPR.  It discusses the growing trend in Beijing for people to be living in apartments / basements comlpetely underground.  This is happening for multiple reasons and it clearly has some potential big consequences.  It does seem like a possible important area for “microbiology of the built environment” studies as these apartments seems be on the extreme edge of certain building parameters (e.g., no windows, unusual air flow, lack of natural light, very damp, etc).  Could make an interesting comparison to other studies of built environments and their microbiology.

Read More

Congrats to Gwynne Mhuireach on new grant to study people, plants, microbes in urban settings

Just a quick post here.  Found this news story (from Nov 18) doing some Google Searchers: UO student gets EPA grant to study health link between plants, people – Portland Business Journal.  It discusses a new grant on “Relationships Among Airborne Microbial Communities, Urban Land Uses and Vegetation Cover: Implications for Urban Planning and Human Health.” to Gwynne Mhuireach from the University of Oregon and the BioBE Center.  Sounds like a neat project .

Read More