Differentiating the Microbiome From a Biofilm

Entities we refer to as biofilms and microbiomes are intrinsically intertwined with one another, however it is important to recognise that they are two distinct things. In this blog ‘Differentiating the Microbiome From a Biofilm’, we explain the differences between biofilms and microbiomes and why their relationship matters more than ever in science.

A microbiome is the entire microbial community that associates with a specific environment. They are highly diverse and complex microscopic ecosystems, composed of microorganisms such as bacteria and fungi, and their structural elements (e.g. sugars and proteins). Microbiomes are extremely dynamic, constantly changing spatially and temporally in response to environmental conditions [1-2]. Whilst each microorganism has a particular role to play within a microbiome [1], these microorganisms are constantly communicating and interacting with one another using signalling molecules –  this is an essential process for facilitating microbiome functioning [2]. Microbiomes are found in almost every environment throughout the world, in oceans and soils, and even our own bodies. 

Biofilms share many of the features of microbiomes – they are also complex, dynamic, and interactive microbial systems. However, biofilms are structured communities of microorganisms that aggregate and stick to one another within a ‘glue’ like substance referred to as the matrix. Made from proteins, sugars and genetic material, the matrix that surrounds the microorganisms within a biofilm protects them from environmental stressors. Biofilms therefore play an important role in increasing the resilience of microbial communities.  

© 2025 National Biofilms Innovation Centre. Depiction of biofilms within the microbiome. Image not to scale.

Biofilms can be made from a single microbial species, or a collection of many different microbes. These microbes live close to one another within a biofilm, which encourages them to work together to thrive in their environment. 

Biofilms are the predominant lifestyle of microbial life, with 80% of cells on Earth estimated to live within biofilms [3].

What connects these two microbial entities, is the fact that biofilms are contained within microbiomes; meaning that both microbial communities can have a direct influence on one another.  

Let’s take for example the gut microbiome. It is estimated that 100 trillion microorganisms reside within our gut and form our gut microbiome [4]. Many of the bacteria which inhabit our gut live in biofilms [5], with our large intestine specifically possessing thick, dense biofilms [6]. Our gut microbiome and the biofilms that reside within it are essential for maintaining our health, promoting nutrient exchange, regulating the immune system and preventing harmful microorganisms establishing within our gut [5].  

However, if the gut microbiome experiences disruption, the biofilms residing within it can be directly impacted as a result. If the gut microbiome is infiltrated with harmful microbes, the diversity and amount of microbial species within biofilms can change [7]. Disruption to the microbiome can also alter the structure of biofilms and trigger them to disperse, thereby releasing harmful microorganisms back into the gut microbiome [6-7].  

It is important to stress that microbiomes and biofilms are not just significant in human health but also play an important role throughout environments. They are essential for ecosystems to function properly, performing processes such as nutrient cycling and water filtration [8]. Without them, life on Earth would not exist.  

Over the last few decades microbiomes and biofilms have received more attention in research. Between 2009-2019 it was estimated that US$1.7 billion was invested into human microbiome research alone [9]. The gut microbiome in particular is receiving much of this attention as more studies are revealing its importance in influencing our overall physical and mental health [10].  

Despite the link between these two microbial communities, scientists have highlighted that previous research into microbiomes and biofilms has remained fairly separate [11]. Additionally, researchers have highlighted that we still have much more to learn about these microbial entities to truly understand how they not only shape us as humans, but the world around us to. It is important that we continue to fuel the momentum that microbiomes and biofilms are receiving in research to accurately grasp and comprehend their impacts.  

References 

[1] Microbiology Society. Unlocking the Microbiome. London, UK. Microbiology Society. 2017. Available at: https://microbiologysociety.org/static/uploaded/39528033-cee2-4359-984085e439fb5825.pdf 

[2] Berg, G. Rybakova, D. Fischer, D. Cernava, T. Champomier Vergès, M-C. Charles, T et al. Microbiome definition re-visited: old concepts and new challenges. Microbiome. 2020. 8. https://doi.org/10.1186/s40168-020-00875-0  

[3] Flemming, H-C. Wuertz, S. Bacteria and archaea on Earth and their abundance in biofilms. Nature Reviews Microbiology. 2019. 17: 247-260. https://doi.org/10.1038/s41579-019-0158-9 

[4] Guinane, CM. Cotter, PD. Role of the gut microbiota in health and chronic gastrointestinal disease: understanding a hidden metabolic organ. Therapeutic Advances in Gastroenterology. 2013. 6(4): 295-308. https://doi.org/10.1177/1756283X13482996  

[5] Miller, AL. Bessho, S. Grando, K. Tükel, Ç. Microbiome or Infections: Amyloid-Containing Biofilms as a Trigger for Complex Human Diseases. Frontiers in Microbiology. 2021. 12. DOI: 10.3389/fimmu.2021.638867 

[6] Buret, AG. Allain, T. Gut microbiota biofilms: From regulatory mechanisms to therapeutic targets. Journal of Experimental Medicine. 2023. 220(3). https://doi.org/10.1084/jem.20221743 

[7] Buret, AG. Motta, J-P. Allain, T. Ferraz, J. Wallace, JL. Pathobiont release from dysbiotic gut microbiota biofilms in intestinal inflammatory diseases: a role for iron? Journal of Biomedical Science. 2019. 26. https://doi.org/10.1186/s12929-018-0495-4 

[8] Sessitsch, A. Wakelin, S. Schloter, M. Maguin, E. Cernava, T. Champomier-Verges, M-C. Microbiome Interconnectedness throughout Environments with Major Consequences for Healthy People and a Healthy Planet. Microbiology and Molecular Biology Reviews. 2023. 87(3). https://doi.org/10.1128/mmbr.00212-22 

[9] Proctor, L. Priorities for the next 10 years of human microbiome research. Nature. 2019. 569: 623-625. https://doi.org/10.1038/d41586-019-01654-0 

[10] Brody, H. The gut microbiome. Nature. 2020. 577: S5. https://doi.org/10.1038/d41586-020-00194-2 

[11] Brandwein, M. Steinberg, D. Meshner, S. Microbial biofilms and the human skin microbiome. Npj Biofilms and Microbiomes. 2016. 2. https://doi.org/10.1038/s41522-016-0004-z