Wednesday, February 11, 2015

Study - Bacterial Diversity in a City Environment - No Reason to Fear

A recent study looked at the human and bacterial diversity that exists on NYC subways.  The study, Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics, (Afshinnekoo, et al. 2015) finds that the subway is teaming with a great diversity of microbes and the cells of humans.  Pathogenic organisms are found, but with no cases of reported illnesses in this area, it is surmised that this is just part of the normal urban microbial environment.   Bacterial species associated with the skin are present in higher proportions compared to bacterial species associated with the intestinal tract (poop bacteria).

Of course to read the headlines (NY Times, New Republic), it can be unsettling to some that so much 'contamination' present....whether it is human cells, bacteria, or viruses.  Heck, there are bacterial species that have not yet been determined.

But as this is life on earth.  It is not sterile.  We coexist with a lot of microorganisms.  For the most part, they are under control.  However, there are certain instances, when our immune system is off or we encounter a large dose of a given microorganism (such as when we temperature abuse our food), we get sick.  But encountering a diversity of microorganisms is important for our immune systems to develop.  So don't worry about the myriad of microorganisms on the subway, embrace the fact that that 'what doesn't kill me, makes me stronger".  And wash your hands before dinner.

A few passages from the study:

Thus, when calculating the enrichment of expected versus observed bacteria, based upon these normalized proportions, we found that the subway is most strongly associated with skin bacteria (8 expected versus 18 observed, a 2.3- fold enrichment). Thus, the subway’s microbiome is most highly enriched for skin (Figure 5B), including species like Staphylococcus aureus (Figure 5). Other enrichments included the airways (1.7-fold) and the urogenital tract (1.2-fold), whereas the under-represented categories were the GI-tract ( 1.6-fold) and the oral cavity ( 3.5-fold). This means that although some classes of bacteria, such as the GI-tract and Enterococcus faecium, may be abundant across the subway, these are actually lower than expected from known annotations, whereas the skin bacteria represent a strong enrichment from the baseline HMP data.  
Our data indicate that densely populated, highly trafficked areas of human transit show strong evidence of bacteria that are resistant to antibiotics and some presence of potentially pathogenic organisms. But, most importantly, these potentially infectious agents are not creating widespread sickness or disease. Instead, they likely represent normal co-habitants of a shared urban infrastructure, and they may even be essential to maintaining such an environment (Gilbert and Neufeld, 2014) and likely represent a normal, ‘‘healthy’’ metagenome profile of a city. 
Indeed, these data indicate that the subway, in general, is primarily a safe surface. Although evidence of B. anthracis, Y. pestis, MRSA, and other CDC infectious agents was found on the subway system in multiple stations, the results do not suggest that the plague or anthrax is prevalent, nor do they suggest that NYC residents are at risk.
The rapid bacterial dynamics of Penn Station suggest that, even on an hourly basis, there is a vast bacterial ecology that is constantly shifting around commuters, which likely represents the diverse ecology of human urban populations (Gonzalez et al., 2012; Tyakht et al., 2013; Be et al., 2014). This diversity is confounded with the thousands of passengers traveling through the subway system, their personal microbial histories, station air flow, subway-cleaning frequencies, surface composition, and
the particulars of this one site. 
One notable result from these data was the conclusion that half of our high-quality sequence reads do not match any known organism, which is similar to the range reported in other studies (Yooseph et al., 2013) and demonstrates the large, unknown catalog of life directly beneath our fingertips that remains to be discovered and characterized. Because the majority of the DNA left on surfaces is bacterial, many of these unknown DNA fragments likely represent un-culturable species and strains of bacteria.

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