We all emit our own 'microbial cloud'

Every individual has a microbiome compiled of millions of bacteria, fungi, viruses, and other microorganisms that is unique for each one of us. Whenever we travel to a new location and sit down or touch something, we are spreading our microbiome to that new location. A lot of research has gone into this phenomenon and is called the microbiome of the built environment. A new study out of the University of Oregon has expanded on this understanding and has described what they call a “microbial cloud”.

The scientists found that individuals not only spread their microbiome to new locations through direct contact but the microorganisms on our body are also dispersed into the air making up this microbial cloud. To better understand this, the scientists had 11 individuals sit in an enclosed room for 4 hours and they analyzed the DNA from the bacteria in the air. They found that when each individual sat in the room, there were thousands of bacteria in the room and everyone’s was distinct. They were able to identify specific characteristics of the people such as if it was a man or a woman.

The bacterial combinations found in the room could be linked back to specific individuals even after the person inhabited the room for only 4 hours. There were specific groups of bacteria like Streptococcus, often found in the mouth, as well as Propionibacterium and Corynebacterium, often found on the skin, that were most useful in identifying the individuals. While these bacteria were found around all the study participants it was the combination of bacteria that was key to identifying the individuals.

This finding could have several important applications. One often-discussed application of the microbiome is its use in forensic applications. It may be possible to use this ability to identify people and know if they were in a room or not to see if someone committed a crime, though it is not clear if it will be possible to identify people in a crowd of other individuals. Other applications include understanding the spread of infectious disease between individuals and within buildings. This is an exciting new development and I am certain we will see more research looking at our microbial clouds in the future.

What bacteria live in the gym?

A lot of research goes into understanding the complexity and dynamics of the human microbiome in the GI tract or the mouth, to name a few locations. In an article published by Microbiome, researchers at Northwestern University took a different perspective in that they looked at how the human microbiome affects the environments around us. A very interesting point raised by the article is that Americans spend most of their time in so-called “built environments,” which are indoors. The microbes of these indoor environments are mainly affected by the humans that interact with them, so the scientists at Northwestern University took to studying how the bacterial composition of indoor athletic equipment and facilities are affected. This specific environment was chosen mainly because of the numerous different human encounters it experiences.

For 2 days, the researchers collected swab samples in 3 athletic facilities. Samples were collected every 2 hours from the floor, mats, elliptical handles, free weights, and benches from 8 am to 6 pm, and a total of 356 samples were collected.  After sequencing and analysis, the researchers concluded that, consistent with all three facilities, the bacteria found on the equipment was most likely to be from the human skin, with Pseudomonas and Acinetobacter showing up in the most samples. Besides microbiota from the skin, other bacteria were found to be abundant such as Bacteroides from the human intestinal tract on elliptical handles and Finegoldia, also from the GI tract, on benches.

As for which sampled location had the most stable bacterial community, it was found that the floor and mats showed the least change in structure. This is most likely because elliptical handles, free weights, and benches come in more direct contact with human skin. Across the board, the only genera which were found in all samples from every surface type were Staphylococcus and Pseudomonas. It is important to remember that none of this means athletic facilities are blooming with harmful bacteria, and we should stay far away. In fact, the environment is not very conducive to the thriving of bacteria, because it lacks a lot of resources. What we should take away from this study is that any surface that comes in contact with human skin is likely to reflect the microbiome of that person. 

What does NYC's microbiome look like?

Grand Central Station

Every week we talk about the human microbiome that makes up each and every one of us, but what about the environmental microbiome, particularly in urban areas?  Cities are just like people (kind of), and they have a microbiome too! A very cool study published yesterday in Cell Systems describes New York City's microbiome.  A large team of scientists, led by a group at Weill Cornell Medical College investigated the DNA profile of the city’s public transit system, several public spaces, and the Gowanus Canal.

They collected samples from every open NYC subway station (466 of them), the Staten Island Railway, 12 locations along the Gowanus Canal in Brooklyn, four public parks, as well as the South Ferry Station that was closed at the time of sampling due to flooding from Hurricane Sandy. At the subway stations, they sampled inside the trains, kiosks, benches, turnstiles, garbage cans, and railings. The results were fascinating. 

Almost half of all the reads could not be matched to any known organism.  They found that South Ferry Station, the only station in NYC that was completely submerged in Hurricane Sandy, represented a marine environment.  They discovered that some known pathogenic bacteria, such as Yersinia pestis, the cause of the bubonic plague, and Bacillus anthracis, anthrax, were present in a few subway stations.

Not surprisingly, the scientists found that the most common bacteria in these locations were those that are abundant on humans' skin.  This makes sense as thousands of people pass through each one of the subway stations every day.  In addition, stations with the greatest levels of traffic on a daily basis, like Grand Central and Times Square, had the greatest diversity of bacteria.

What about all these unknown organisms that couldn’t be identified? These exemplify the huge amount of life right in front of us that has yet to be characterized.  What about all the pathogenic bacteria and antibiotic resistant bacteria like MRSA that were identified? Should we be worried that these? The authors state that the subways generally contain safe surfaces for the following reasons. First, they note that it is impossible to tell if the sequenced organisms are dead or alive. Second, even more importantly, these bacteria help make up a dynamic and shared urban infrastructure, and they may even help maintain its equilibrium. Finally, the bacteria that were connected to the plague, anthrax, and other diseases were found in very small traces, not enough to colonize our bodies. (Did you know that people in the United States, almost exclusively on the West Coast, are still getting the bubonic plague today?)

It will be very interesting to see what comes from this study. I, for one, would like to know what the South Ferry Station microbiome looks like now compared to when the scientists initially sampled, because the sampling was performed when it was still closed due to Hurricane Sandy.  Now that it is back up and running with thousands of people passing through it every day, how has the ecosystem of the station changed?. 

The authors suggest that a study like this could help facilitate forensic investigations. For example, the bottom of one’s shoe could represent where that person traveled over the past day or week. They also suggest that faster, or maybe even real-time analysis, of the microbiome of the city’s transit system could be used to protect the city from bioterrorism and other public health threats like our recent scare with Ebola. 

If you want to see what bacteria were found at your favorite station, The Wall Street Journal put together a very easy-to-use interactive map. Check it out here.

What microbes are living in public bathrooms?

Do you ever wonder how clean our bathrooms are, or question what kinds of bacterial communities are lurking in the public bathrooms you use? Well lucky for you and I, a team of scientists wondered the same exact thing. Published in Applied and Environmental Microbiology, the scientists sampled the microbial communities of four public restrooms at San Diego State University to better understand how they shifted over time.

At the beginning of the study, the restrooms were sterilized using a bleach solution.  Just one-hour post sterilization, the bathrooms were already filled with microbes again and as you can imagine, a significant portion of the microbes were of fecal origin.  They found that despite varying frequency of use and sampling bathrooms of both sexes, the four bathrooms all eventually had microbial communities that were very similar to one another.

The scientists found one specific bacterium, Staphylococcus, was prevalent in all the restrooms. One kind of staph can be very pathogenic, specifically when it is resistant to antibiotics (MRSA), however Staphylococcus does often live harmless in our bodies.  They did not find any Staphylococcus that was resistant to antibiotics in any of the restrooms. The restrooms were cleaned regularly using soap and water over the course of this study, yet the microbial communities remained largely stable.

You may read this and be grossed out about bacteria being prevalent in public restrooms even after regular cleaning, but they are most likely harmless, or even beneficial. Perhaps bleaching a bathroom may be like taking antibiotics - it leaves open the possibility for harmful bacteria to colonize, like what Clostridium difficile does in the gut.