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Bacterial Signature

November 12, 2015

Upstate New York, where I spent the early years of my life, is a vast forest occasionally punctuated by a small town or city. The larger cities of Upstate developed along the Erie Canal, a 584 kilometer waterway that links the Hudson River at Albany to Lake Erie at Buffalo. The only way such a waterway can function is by a system of locks that controls the flow of water through a differential elevation of about 172 meters. The canal opened in 1825.

A 1912 engraving of Lock No. 11 of the New York Barge (née Erie) Canal.

A 1912 engraving of Lock No. 11, at Amsterdam, New York, of the Barge (née Erie) Canal.

(Via Wikimedia Commons.)

The Erie canal was an innovation and an engineering marvel at its time. Just as today, when the automobile has inspired many useful technologies, waterway transportation did the same in its era. American engineer, Robert Fulton (1765-1815), was inspired by the Watt steam engine of the late 18th century to construct the first commercially successful steam-powered boat in 1807. I wrote about steam power in a previous article (Steam Power, January 28, 2011).

This boat, the Clermont, carried passengers between New York City and Albany. Although it was a success, it was initially called "Fulton's Folly." This characterization was apt for steam engines of the time, which had a likelihood of exploding. As recalled in a recent story in the Pittsburgh Post-Gazette, Charles Dickens and his wife were uneasy about steam travel during their 1842 visit to Pittsburgh, but they were advised that steamboats fitted with a pressure relief valve were considered safe.[1]

During my childhood, I lived in Utica, New York, one of the cities along the Erie Canal. A trip of just a few miles in any direction would lead off into the wilderness. One wilderness adventure for our family was a trip to the Catskill Game Farm, which, despite the name, was actually a zoo. What do I remember most about this zoo? It's the odor.

It's not the the staff was negligent in its responsibilities. It's just that bacteria feed from both the input and output streams of animal life, and there are multiple sources for bacterial infiltration in a zoo, such as food, feces, and urine. Perhaps I exaggerate, but you could turn off your GPS within a mile of a zoo and still find your way. This is much more of a problem with industrial farming, such as pig and poultry farms.

An article in Modern Farmer magazine states that there are more than 200 chemical compounds in swine odor, which includes such notables as ammonia, hydrogen sulfide, and a mixture of organic compounds that smells like rotting flesh.[2] Poultry farms emit 60-150 odoriferous compounds, such as "volatile fatty acids, mercaptans, esters, carbonyls, aldehydes, alcohols, ammonia, and amines."[3]

American Gothic (1930) by Grant Wood

American Gothic (oil on beaver board, 1930) by Grant Wood (1891-1942)

The number of farms in the US peaked at 7 million in 1935. There are just 1.9 million remaining, but with nearly the same total acreage as at the peak.

(From the Friends of American Art Collection of the Art Institute of Chicago, via Wikimedia Commons.)

Humans are animals, too, and a quick look around a supermarket or pharmacy will show that we're very concerned about our odor. Some odors are beneficial, like the sex-attractant pheromones,[4] and there are a variety of perfumes and colognes that attempt to mimic their attractive properties. For the unpleasant odors, we at first resort to soap, and then to things like antiperspirants, and aptly named "deodorants."

Antiperspirants contain chemical compounds, notably aluminum chlorohydrate, that slow the rate of perspiration. This has a beneficial effect, since underarm odor comes from bacterial action on human sweat, with the armpit area being a nice warm environment for bacterial growth. The chemical, trans-3-Methyl-2-hexenoic acid, is the principal component of body odor.

Trans-3-Methyl-2-hexenoic acid

Trans-3-Methyl-2-hexenoic acid

(Wikimedia Commons image.)

Not all body odor is bad. In fact, there are subtle differences in the scent of a person; and, as shown by experiment, individuals can be identified by their scent. In one study, 100% of women tested were able to identify their newborn babies by scent after an hour or more exposure to the infants.[5]

While most odors are a second-order effect caused by bacteria, today's technology makes it possible to analyze small quantities of bacteria themselves. This leads to the possibility that individuals might have a traceable bacterial "signature." That's the idea tested by scientists at the University of Oregon (Eugene, Oregon) and the Santa Fe Institute (Santa Fe, New Mexico). They found that occupied spaces have a microbial signature distinct from unoccupied spaces, and that individuals have a personalized microbial aura.[6-7]

Says lead author, James F. Meadow, who conducted this research while a postdoctoral researcher at the University of Oregon,
"We expected that we would be able to detect the human microbiome in the air around a person, but we were surprised to find that we could identify most of the occupants just by sampling their microbial cloud."[7]

Bacteria associated with individuals are dispersed into the environment through direct contact and by bioaerosol particle emission from breath, clothes, skin and hair.[6] Humans shed about a million particles of size less than 0.5 micrometer every hour, many of which would contain bacteria.[6]

In their experiments, the University of Oregon researchers sampled microbes from the air space of a single person sitting in a sanitized environmental chamber, and they compared that to air sampled in an adjacent, identical, unoccupied chamber.[6] They used high-throughput DNA sequencing methods to characterize the airborne bacteria.[6] In subsequent, higher resolution, experiments they sampled 8 different people for 90 min each with air flowing through a collection filter at on and three air change per hour.[6]

Individuals could be distinguished through their airborne emissions in the chamber within 1.5-4 hours.[6] They authors comment that their experiments might help to understand the mechanisms involved in infectious disease transmission in buildings.[7] At this point, considerable time is involved in detection, but there might be potential forensic applications.[7] Perhaps the surveillance society might be worse than we imagined.


  1. Len Barcousky, "Eyewitness 1842: Dickens finds Pittsburgh full of smoke and fires," Pittsburgh Post-Gazette, August 30, 2015.
  2. Christopher Weber, "Stink Wars: When a Foul Wind Wafts From a Farm, Is it a Problem?" Modern Farmer, January 27, 2014.
  3. John P. Chastain, "Odor Control From Poultry Facilities," Chapter 9 of Poultry Training Manual, Clemson Cooperative Extension.
  4. Napoleon supposedly wrote in a letter to Josephine, Ne te lave pas. Je reviens. (Don't bathe. I'm coming home.)
  5. M. Kaitz, A. Good, A. M. Rokem, and A. I. Eidelman, "Mothers' recognition of their newborns by olfactory cues," Developmental Psychobiology, vol. 20, no. 6 (November, 1987), pp. 587-591.
  6. James F. Meadow​, Adam E. Altrichter, Ashley C. Bateman, Jason Stenson, GZ Brown, Jessica L. Green, Brendan, and J.M. Bohannan, "Humans differ in their personal microbial cloud," Peerj, vol. 3, Document No. e1258 (September 22, 2015), DOI: 10.7717/peerj.1258.
  7. New research finds that people emit their own personal microbial cloud, Peerj PressRelease, September 22, 2015.

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