While the human microbiota is a hot area of research and has captured the attention of lay press, it has also brought misconceptions that could distort the public’s perception and expectations on its applications.

The explosion of microbiome research have brought with it “hype and entrenched misconceptions that have become ‘facts’ through constant repetition”, caution microbiologists Alan Walker and Lesley Hoyles in a new perspective article published in the journal Nature Microbiology. They highlight that: “Given the potential significance of human microbiomes on human health, it is crucial that claims be based on evidence”.


Here are some of the main myths about the microbiome:

The field of microbiome is in its infancy ❌

While microbiome research has accelerated over the past 15 years, “there has been much research in the field of human-associated microorganisms since at least the late nineteenth century. Similarly, concepts such as the gut-brain have been researched for centuries”.

Nor is it true, as is often read in many sources, that Joshua Lederberg coined the term ‘microbiome’ in 2011, as it had been in use in the field for at least a decade before that.


Our bacteria weigh 1 to 2 kg ❌

The origin of this information is poorly documented. The authors state that: “The majority of the human microbiota resides in the colon, and these microorganisms typically account for less than half of the weight of fecal stools”.

It is more likely that the total human microbiota weighs less than 500 grams, and the gut microbiota about 200 grams, which is the equivalent of a mango.

It is also important to acknowledge that most studies published so far on the human gut microbiota are based on fecal samples. However, fecal stools do not provide an accurate ‘photo’ of what happens inside our gut.


The bacteria in a human body outnumber human cells ❌

The myth that our bodies have a 10:1 bacteria-cell (and other microbes) ratio persists since the estimate conducted in 1972 by microbiologist Thomas Luckey.

“More detailed analyses indicate that the true figure, albeit still impressive, is probably closer to a ratio of 1:1”, state the authors. This ratio can also vary from person to person as it is influenced by gender, age and obesity. In addition, current estimates are mostly based on adult individuals living in urbanized high-income countries, while it is not known if they also apply to people from rural settings and other ages.

Previous data also estimated the number of bacteria in the colon in about 1014. The fact is that there are between 1010 and 1011 bacterial cells per gram of fecal stools.


Most diseases are characterized by an altered microbiota or ‘dysbiosis’ ❌

It is common to read in the scientific literature and commercial microbiome test kits that most diseases are caused by an altered microbiota. For example, an imbalance in the Firmicutes: Bacteroidetes ratio, which comprises the two largest phyla making up the human gut microbiome, has been repeatedly claimed as a hallmark of obesity. Yet, the reproducibility of these studies in human is poor. Authors also ask whether comparisons at such broad taxonomic level are useful at all. As an example they state that, despite hugely different physiologies, lifestyles etc., humans, birds, fish, reptiles and sea squirts all belong to the same phylum of Chordata.

As such, the terms ‘dysbiosis’ and ‘pathobiome’ have been coined to define a ‘bad’ microbiota profile in terms of composition and/or functions that needs to be reversed by diet and other interventions in order to improve one’s health.

The authors acknowledge that the term ‘dysbiosis’ is “vague with limited clinical applicability” and the term “pathobiome” “overly simplistic and inherently flawed”.  The reality is that “microorganisms and their metabolites are neither ‘good’ nor ‘bad’, they merely exist”, explain the authors. While almost all conditions have been associated with a ‘dysbiosis’, it is difficult to know which came first, the chicken (an altered microbiota) or the egg (the disease or condition).

The behavior of a particular microorganism from the microbiota depends on the context and location. For example, healthy individuals carry Clostridioides difficile in their gut throughout life. This bacterium usually only causes problems in older adults in the hospital setting, particularly if they have a weak immune system or are treated with antibiotics.


The microbiota is mostly inherited from the mother at birth ❌

“Although some microorganisms are directly transferred from mother to baby during birth, proportionally few microbiota species are truly ‘heritable’ and persist from birth to adulthood in the offspring”, note the authors.

The environment, diet, antibiotics, and genes have a more relevant influence in shaping your microbiota than the mother’s microorganisms.


Gut microbiota composition is different between people, while its functions are similar ❌

Scientists infer microbiota functions by comparing microorganisms’ genomes to reference databases. The caveat is that this analysis leaves out the big amount of genomic data that do not map to reference databases, so it fails to explore less well characterized functions of the microbiota.

The truth is that some functions are maintained across different human microbiota species (e. g., short-chain fatty acid production), while other functions are only carried out by a small number of microorganisms (e.g., digestion of resistant starch). Almost 20% of bacterial gene sequences have not been identified and the function of 40% of the estimated 10 million total of bacterial genes remains unknown, which highlights that the known unknowns of the microbiome are astonishing.

Overall, it is becoming evident that the microorganisms that live in and on us are important for our health and represent a potentially different way of addressing different conditions and diseases. However, it is difficult to stay up to date with the vast number of scientific studies in the field. Most important, the perspective paper published by Walker and Hoyles shows that interpreting microbiome science requires a healthy dose of curiosity and skepticism.


*In this article, the word ‘microbiota’ refers to the community of microorganisms that inhabit a particular environment, while the term ‘microbiome’ refers to the entire habitat, including the microorganisms, their genomes, and the surrounding environment.



Walker AW, Hoyles L. Human microbiome myths and misconceptions. Nat Microbiol. 2023; 8(8):1392-1396. doi: 10.1038/s41564-023-01426-7.