Antoni van Leeuwenhoek’s discovery of microbes, or as he called them, animalcules:

 Leeuwenhoek Scott Chimileski animalcule bacteria
“And the motion of most of these animalcules in the water was so swift, and so various, upwards, downwards, and round about, that ’twas wonderful to see: and I judge that some of these little creatures were above a thousand times smaller than the smallest ones I have ever yet seen, upon the rind of cheese, in wheaten flour, mould, and the like.”        


Any biologist can put themselves in the position of Antonie van Leeuwenhoek or Robert Hooke and wonder at the thought of seeing an entire dimension of life invisible to every person that ever lived on Earth.

Scott Chimileski Robert Hooke Micrographia

Robert Hooke’s Micrographia (1665).

Leeuwenhoek and Hooke were also the first to observe microbes as multicellular forms. Leeuwenhoek found microbes living together in biofilms when he used his handmade microscope to look at the “scruff” collected from the surface of his own teeth and Hooke included drawings of fungal fruiting bodies in his major work Micrographia

Robert Hooke microscope Scott Chimileski

Robert Hooke’s 17th century microscope.

A historical perspective provides a context for modern science. Leeuwenhoek’s letters to the Royal Society from just a few hundred years ago represent a massive leap forward in what would become the field of microbiology. While the word animalcule seems crude today, what else would he have called these microscopic creatures? He could only compare them to what humans could see up until that point: the animals. Ironically, microbiology is in a sense coming full circle. The more we learn of the diversity, complexity and interactivity of microbes, the more we realize they really are like little animals.

This story should remind scientists of the power of observation. It also gives us a sense for how confident we should be in the prevailing hypotheses of today.


The concept of biofilms

While the 17th century pioneers of microscopy observed microbes as they exist naturally–together with other microbes—modern microbiology went through a sort of awkward adolescence between now and then. For the longest time, individual species were pulled from the microbial jungles they were found in and grown mostly on their own in liquid culture.

Like our our human adolescence it was a necessary period of learning and maturation. In order to develop the field and understand microbes, it was essential to isolate them. We could study their morphology and physiology and reveal phylogenetic patterns–see what they look like, find out what they do and figure out how they are related to each other and to other forms of life. This was a great reductionist period of microbiology, an era largely dominated by the discovery of microorganisms that cause disease. And it still is and always will be necessary to study single species in many cases.


Biofilms, City of Microbes. Watnick and Kolter, 2000.     Journal of Bacteriology vol. 182, no. 10: 2675-2679.

But beginning with the concept of biofilms that has emerged in the past few decades, and with the realization that most microbes in nature live and interact in diverse communities, a new era of microbiology has begun.


An era of synthesis  


“All science grows to maturity by repetitive cycles of reduction and synthesis.”                                                                                                                     – E.O. Wilson


It is time to look at all we have learned about microbes and begin putting it together. This is a time when we have realized that biodiversity itself exists at several size scales. The human body and all animals are superorganisms: a combination of trillions of our own cells, and trillions of microbial cells. Look in any direction and despite what your eyes perceive, the majority of the genetic information in that scene is microbial. Just as every type of climate and geological landscape attracts certain animal and plant species that come to define a macroscopic ecosystem, individual sites on and within animals or plants, and all other microhabitats, are unique microbial ecosystems.


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