Microbiome and Microbiota - Defintion & History

Written by
Fathalla Ali, Bsc MSc, MPH and PHD student UNSW

Advancement the in the DNA/RNA analysis and computing technologies has transformed the field of microbial community analysis. This advancement has accompanied by rapid increase in the number of researches describing the composition, structure and function of microbial communities that inhabiting our bodies. Consequently, this led to a confusion between the definition of microbiome and microbiota by scientific researchers and general public (1). Therefore, it’s very important to differentiate between the two terms.

Microbiota: “refers to microorganisms that present in defined environment” (1).
Microbiome: “refers to the entire habitat, including the microorganism (bacteria, archaea, eukaryotes and viruses), their genes and the surrounding environment” (1).

It has been continuously claimed that the term microbiome was coined by Nobel laureate-microbiologist Joshua Lederberg in 2001. However, it’s believed that the underlying concept and importance of microbiome research dated back to the very beginning of microbial ecology and to Sergei Winogradsky in the 1800’s (2). Winogradsky was born in Russia in 1856 and was to become a founder of modern microbiology (3). Additionally, in 1988 the University of Warwick (UK) professor Johun M. Whipps and colleagues provided a specific definition that directly in line with its current use in microbiology: ‘‘A convenient ecological framework in which to examine biocontrol systems is that of the microbiome. This may be defined as a characteristic microbial community occupying a reasonably well defined habitat which has distinct physio-chemical properties. The term thus not only refers to the microorganisms involved but also encompasses their theatre of activity” (4).


  1. Marchesi, J.R., Ravel, J., 2015, The vocabulary of microbiome research: a proposal. Microbiome 331. Click here
  2. Prescott, S. L,. 2017. History of Medicine: Origin of the Term Microbiome and Why it Matters. Human Microbiome Journal. 4: 24-25. Click here.
  3. Dworkin, M., Gutnik, D., 2012. Sergei Winogradsky: a Founder of Modern Microbiology and the First Microbial Ecologist. FEMS Microbiology Reviews. 36: 364-379. Click here
  4. Eisen, J., 2015. What does the term microbiome mean? And where did it come from? A bit of a surprise. Microbiology of the Built Environment Network. Click here