The study of the human microbiome has changed the way we think of ourselves in health and disease. From fecal transplants to pre- and probiotics, popular, basic, and applied sciences, including human medicine are beginning to acknowledge the role of bacteria and other microbes in eukaryotic health. The term” microbiome” was coined in 2001 by J. Lederberg [1]. The first studies to change our perception of what it is to be human, probably started with the first releases of papers from the National Institutes of Health funded Human Microbiome Project (NIH HMP) in 2010 [2] and 2012 [3]. However, the true recorded origins of microbiology and first recorded studies of the human microbiome began with a cloth merchant at the beginnings of the organized study of science in Europe.

Past perspectives on the human microbiome

In 1677 Antony van Leewenhoeck – a citizen scientist – first described “animalcula” in letters conveyed by a physician friend to the newly formed Royal Society of London [4]. Leewenhoeck’s meticulous and detailed descriptions and measurements of the microscopic world were made through simple microscopes he made out of glass lenses and metal plates. His most powerful microscope magnified an object 266 times!

Replica of one of van Leewenhoeck's microscopes. Jeroen Rouwkema [CC BY-SA 3.0 or GFDL], via Wikimedia Commons
Replica of one of van Leewenhoeck’s microscopes. Jeroen Rouwkema [CC BY-SA 3.0 or GFDL], via Wikimedia Commons
Initially, his findings were met with skepticism, but eventually another early microscopist – Robert Hooke– demonstrated the presence of these “animalcules” to the members of the Royal Society. This acceptance of Leewenhoeck’s findings led to him publishing many articles in the society’s Philosophical Transactions of the Royal Society and becoming a full member of this fledgling, but foundational scientific society.

Leewenhoeck did not limit his discoveries of the microscopic world to rain and pond water [4], but included the first human microbiome project! In examining his own skin, saliva, mouth, teeth, gums, tongue coating, mucus, and diarrhea Leewenhoeck found these curious “animalcules” everywhere [5]. He did comparisons of himself when sick and healthy. Next Leewenhoeck compared scrapings from the tooth surface, between the “scurf” of the teeth, and the saliva of himself (he emphasizes that he cleans his teeth), two women, an 8 year old, a sober old man who had never cleaned his teeth [6]. In them all he finds “many very little living animalcules, very prettily a-moving”.

van Leewenhoeck's drawings of the bacteria he found in dental plaque.
van Leewenhoeck’s drawings of the bacteria he found in dental plaque or “scurf” 1684. Philosophical Transactions. 14:568-574.

He then examined the influence of different substances on the animalcules when he examined the teeth of another non-tooth-brushing man who drank brandy and wine and smoked tobacco. Leewenhoeck seemed surprised that all the “continual” alcohol and tobacco didn’t kill the small, living animals in the mouth. Instead there was “..such enormous numbers, that all the water…seemed to be alive”.

Leewenhoeck tries to unsuccessfully sterilize his own mouth using vinegar. He could kill “only those animals on the outside of the scurf” but not those within it. With each of these people, he finds the animals living in the “scurf”[6]. This scurf, we now know is plaque, which is a biofilm formed by these bacteria that allows them to attach to the tooth’s surface. The citizen scientist, Antony van Leewenhoeck, went on to make many more observations, discoveries, and describe both micro- and macro-organisms, especially insects. Clearly, the fascination with microscopes, microbes, and insects indicates that Leewenhoeck and I are cut from the same cloth! (har-de-har) Leewenhoeck’s findings changed the way the scientists of that day, and perhaps the neighbors he sampled from, thought about the world. So today are studies of the human microbiome changing the way we think of ourselves in this microbial world.

Present perspectives on the human microbiome

In the 21st century, our microscopes are much powerful and we’ve learned that describing morphology will only get us so far with bacteria. Bacteria, viruses, and fungi are more often identified by their DNA sequence. Even when using microscopy, bacteria can be visualized using fluorescent probes that bind to specific sequences of DNA. With FISH (fluorescent in situ hybridization), scientists can see where specific bacteria are located within plaque or a tissue. They can see how bacterial community composition changes when different chemicals are consumed, oxygen levels change, the presence of specific beneficial or pathogenic organisms, or a wide variety of other conditions.

FISH of a subgingival biofilm from a periodontitis patient. The overview (left) shows the complex multispecies biofilm stained with a genus-specific probe for streptococci (orange) combined with EUB338 (green), which detects most bacteria, and the nucleic acid stain DAPI (blue). At higher resolution (inset, right), the streptococci appear to grow along the orientation of the rods. Images courtesy of Annette Moter in: Haussler S , and Fuqua C J. Bacteriol. 2013;195:2947-2958
FISH of a subgingival biofilm from a periodontitis patient. The overview (left) shows the complex multispecies biofilm stained with a genus-specific probe for streptococci (orange) combined with EUB338 (green), which detects most bacteria, and the nucleic acid stain DAPI (blue). At higher resolution (inset, right), the streptococci appear to grow along the orientation of the rods. Images courtesy of Annette Moter. In Haussler and Fuqua. J. Bacteriol. 2013;195:2947-2958

In the 21st century, citizen scientists still have a valuable role in exploring the microbial world. From American Gut to µBiome –people can submit their own samples of tooth scrapings or diarrhea, stool samples of their whole family, including pets, or monitor their own microbiomes over time, during diet changes, medicine use, illness, etc… You submit your sample(s), a small fee for the service, and answer a questionnaire. The sample is analyzed, your data is compared to that of others, and your analyzed data is returned to you. The scientists are providing a fee-for-service, but they also can mine through these samples from thousands of people and the answers (metadata) that people provide with the samples and see what interesting correlations pop up. This is an exciting new way to approach the natural history of microbes (bacteria in this case). In doing this, the American Gut project found a correlation between high microbiome diversity and several factors: 1) eating a diversity of plants [7], 2) not having taken antibiotics in the last year, 3) sleeping more and exercising outside, and 4) drinking alcohol [8] (bet Leeuwenhoek would be interested in that!).


Of course, all of this is in its early stages and scientists are still trying to figure out what “healthy” and “disease” states are for humans in general. There are some data that suggest that what is normal and healthy for some populations is not for others. At this point scientists look for correlations, the presence of particular microbial assemblages and a specific condition like diabetes, obesity, anxiety, and so on. If those particular microbes can be cultured, experiments can be done on gnotobiotic mice, mice that are born and reared without bacteria. Such mice can be colonized by the bacteria in question and then the correlations tested. For example, when bacterium x is present, do the mice gain weight faster than mice that don’t have bacterium x. Of course, many people are conducting their own experiments on themselves and their microbiome and sharing it with the world. A few such examples are the Human Food Project, a family science starch project, and Hacking Sleep. I’m sure there are many more out there and more in the works and if the Father of Microbiology – Antony van Leeuwenhoek – were around, I have no doubt he would be submitting samples and learning about his “animicules”.


  1. Lederberg, J., and A. McCray. 2001. Ome sweet ‘omics: — A genealogical treasury of words, p. 8. The Scientist, vol. 15.
  2. Caporaso, J. G., C. L. Lauber, E. K. Costello, D. Berg-Lyons, A. Gonzalez, J. Stombaugh, D. Knights, P. Gajer, J. Ravel, N. Fierer, et al. 2011. Moving pictures of the human microbiome. Genome Biol 12:R50.
  3. The Human Microbiome Project Consortium. 2012. Structure, function and diversity of the healthy human microbiome. Nature 486:207-214.
  4. van Leewenhoeck, A. 1677. Observations, Communicated to the Publisher by Mr. Antony van Leewenhoeck, in a Dutch Letter of the 9th of Octob. 1676. Here English’d: concerning Little Animals by Him Observed in Rain-Well-Sea. and Snow Water; as Also in Water Wherein Pepper Had Lain Infused. Philosophical Transactions 12:821-831.
  5. van Leewenhoeck, A. 1708. A Letter from Mr. Anthony van Leeuwenhoek, F. R. S. Containing His Observations upon the White Matter on the Tongues of Feverish Persons, &c. Philosophical Transactions 26:210-214.
  6. van Leewenhoeck, A. 1684. An Abstract of a Letter from Mr. Anthony Leewenhoeck at Delft, Dated Sep. 17. 1683. Containing Some Microscopical Observations, about Animals in the Scurf of the Teeth, the Substance Call’d Worms in the Nose, the Cuticula Consisting of Scales. Philosophical Transactions 14:568-574.
  7. Knight, R. 2014. Recent findings from the American Gut Project. 5th Annual Beneficial Microbes Meeting, American Society for Microbiology.
  8. Leach, J. 2014, posting date. American Gut releases latest results and pipeline. [Online.]

Here’s a small sampling of media stories on the American Gut Project:

NPR Health Blog

Michael Pollan in NYT

Carl Zimmer – Tending the Body’s Microbial Garden

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