UPCOMING EVENTS: GENETIC TESTS AND GUT MICROBIOME – 9 SEPTEMBER 2024
Why is ‘gut flora’ no longer correct?
Microbiota and microbiome explained
For many years, terms such as ‘bacterial flora’ or ‘gut flora’ have been widely used to describe the community of micro-organisms inhabiting the human intestinal tract. However, with scientific advances in molecular biology these terms have become obsolete and conceptually incorrect.
Origin of the term "flora" and its inappropriate use
The term ‘flora’ has its origins in botany and refers to the set of plants growing in a region or ecosystem. It was historically adopted in microbiology because, in the early days of the study of microorganisms, bacteria were thought to be similar to plants due to their structural characteristics and their ability to grow in specific media, such as solid cultures. At that time, knowledge about the diversity of micro-organisms was limited, and their nature was not fully understood.
With scientific progress it became clear that bacteria, along with other micro-organisms such as viruses, fungi and archaea, have no evolutionary relationship with plants. Using the term ‘flora’ to describe microbial communities perpetuates a conceptual error that is no longer consistent with our modern understanding of the microbiota.
Differences between microbiota and microbiome
Today, the terms microbiota and microbiome are used. Although they are related, there are differences: :
- Microbiota: refers to the community of living micro-organisms that inhabit a specific ecosystem, such as the gut, skin or mouth. It includes bacteria, fungi, archaea and viruses.
- Microbiome: refers to the set of genes of the microbiota and their metabolic products, i.e. the genetic material of micro-organisms together with their functional environment.
These definitions reflect the diversity and complexity of the micro-organisms that inhabit the human body, something that the term ‘flora’ does not encompass.
Microbial diversity beyond bacteria
One of the main reasons for abandoning the term “bacterial flora” is that the gut microbiome includes much more than just bacteria. This ecosystem includes:
- Archaea
- Fungi: Although in smaller numbers, fungi such as Candida are part of the microbiome and play specific roles in health and disease.
- Viruses and bacteriophages
- Protozoa
The use of the term “bacterial flora” excludes these microbes.
Impact of terminology change on scientific research
The shift towards terms such as ‘microbiota’ and ‘microbiome’ has clinical implications:
- To more accurately reflect the complexity and diversity of gut microorganisms.
- Promote a more detailed understanding of the interactions between these organisms and their human host.
- To recognise the functional role of the microbiome in aspects such as digestion, the immune system, metabolism and mental health.
The persistent use of ‘gut flora’ in non-scientific contexts, such as education and the media, reflects a lack of up-to-date terminology. This outdated language can hinder public understanding of modern microbiology and perpetuate misconceptions about the microbiome.
The term ‘bacterial flora’ or ‘gut flora’ is no longer appropriate in the current context of modern microbiology. The gut microbiota and microbiome are more precise concepts that reflect the diversity and complexity of the microorganisms that inhabit the human gut. This change in terminology not only aligns language with scientific advances, but also improves our ability to communicate and understand the fundamental role of these microorganisms in human health. It is time to adopt this accurate terminology and abandon outdated terms that no longer adequately represent current knowledge.
Marchesi, J. R., & Ravel, J. (2015). The vocabulary of microbiome research: a proposal. Microbiome, 3, 31. https://doi.org/10.1186/s40168-015-0094-5
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