Taking advantage of the fact that this week marks World Microbiome Day, we couldn’t resist talking about this topic. And it’s impossible to deny that the role of the microbiome—also known as the microbiota—in health is a growing trend.
I must admit that writing this article was a challenge for me, because the first thing I did was visit PubMed, the main database specialised in health sciences, and search for the term “microbiome”. Filtering by the last year alone, no fewer than 5,963 scientific publications appeared, and over the last five years, 23,882. That’s insane! But don’t worry—I’ll try to convey the information in the clearest and most objective way possible.
To dive into the world of the human microbiome, we first need to understand some basic concepts.
Are there differences between the microbiome and the microbiota?
You’ve probably heard these concepts used interchangeably, and although they’re closely related, they’re not exactly the same.
The human microbiota refers to the collection of microorganisms (bacteria, parasites, viruses, fungi, etc.) that live in our body, and can be found in the gut, skin, mouth, genitourinary tract, respiratory tract, and more.
The term microbiome, on the other hand, refers not only to the microorganisms themselves, but to the entire habitat—specifically their genes, metabolites and the environmental conditions surrounding them. Like the microbiota, its composition depends on the body site.
It’s worth highlighting that the microbiome is considered a “new organ” essential for life, complementing functions missing in the human body—not only because microbial genes outnumber human genes by a factor of 100, but also because of the constant interaction and “conversation” with our organism, from which both benefit. This is known as symbiotic and mutualistic behaviour.
When discussing this topic, the term microbiota is often easier for the general public to understand; however, from a scientific standpoint, microbiome is the more commonly used term due to its broader scope.
Dynamics of the microbiota and factors influencing its composition
We must bear in mind that the microbiome is not a static organ that remains unchanged over time, but rather one that varies due to multiple factors, which also depend on its location. The factors that influence the vaginal microbiome are not necessarily the same as those affecting the gut microbiome, for example.
The microbiome changes throughout life due to both intrinsic factors—such as genetics and the immune system—and extrinsic factors, such as diet, medication, antimicrobial exposure, or interactions with other microbiomes.
These variations should not always be classified as “negative alterations”, as in many cases they can be positive. A good example is the change in the gut microbiome induced by physical training, which promotes the growth of butyrate-producing microorganisms, such as Clostridial bacteria or Firmicutes. These create a natural intestinal barrier that prevents pathogenic (harmful) bacteria from entering the body.
However, in other cases, changes can be detrimental, such as intestinal dysbiosis, characterised by an increase in Proteobacteria (20–30%), including species like Escherichia coli and Klebsiella. Triggering factors described in the literature include genetic defects, stress, diet, alcohol consumption, infection, and exposure to medications, including antibiotics and non-antibiotics.
At this point, we can begin to appreciate the impact our lifestyle habits have on the different types of microbiomes in our body.
“Healthy” microbiome
Since the launch of the Human Microbiome Project in 2008, there is still debate around what defines a healthy microbiome. In this project, researchers analysed the microbiome of 300 healthy volunteers and found that despite being “healthy”, their microbiomes were very different. They also discovered several key points:
- The human microbiota contains a greater number of genes responsible for human survival than the individual’s own genes.
- Microbial metabolic activities, such as fat digestion, are not always carried out by the same bacterial species—making routine microbiota analysis difficult to interpret.
- The microbiome changes over time due to medication use and disease, but can return to equilibrium despite changes in microbial composition.
These findings complicate what once seemed like a simple question: What is a healthy microbiome? To date, microbiome research suggests that there is no single state of health—health has many faces.
Microbiota as a multimodal and omics data source in personalised approaches
A large proportion of scientific studies on the microbiome adopt four main approaches aimed at improving quality of life through personalised strategies that account for individual differences:
- The impact of consuming/applying/transferring beneficial bacterial strains on human health. A notable example is faecal microbiota transplantation (FMT), approved in the EU to treat Clostridium difficile infection (CDI). FMT from healthy donors has shown a 93% cure rate in recurrent CDI.
- Comparing the microbiome of patients with various diseases to that of healthy controls. For example, in psoriasis, Fahlén et al. observed changes in bacterial populations compared to healthy individuals, with higher levels of Proteobacteria on the trunk and increased Streptococcus and Propionibacterium in lesions.
- Searching for risk biomarkers by analysing the microbiome in specific diseases. For instance, Faecalibacterium prausnitzii is elevated in the gut microbiota of patients with type 2 diabetes, while Akkermansia muciniphila is found at lower levels.
As we can see, science in this area is advancing rapidly. Many microbiota tests are already available on the market, although they still face several challenges.
Current and future challenges
Healthcare professionals are increasingly aware of the importance of the microbiome and its potential applications in patient care. However, significant challenges remain.
One of the most important challenges is defining what a “healthy” microbiome looks like in order to establish a reference for comparison.
Another challenge lies in sample collection. In the case of gut microbiota, samples are obtained from stool, assuming that faecal microbiota represents the colon—but what about the small intestine, which also hosts large bacterial populations?
Time is another challenge. The microbiome is dynamic, like a snapshot taken at a specific moment. Could it be that by the time results are delivered, the microbiome has already changed?
That said, microbiota tests can be extremely useful in certain cases, such as detecting intestinal dysbiosis. If you’re considering a microbiota test, consult your healthcare professional or contact us—we’ll be happy to help.
References
Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature. 2012;486(7402):207–214.
Mańkowska K et al. Microbiota in sports. Arch Microbiol. 2022;204(8):485.
Bidell MR et al. Gut microbiome health and dysbiosis: A clinical primer. Pharmacotherapy. 2022;42(11):849–857.
Fahlén A et al. Comparison of bacterial microbiota in normal and psoriatic skin. Arch Dermatol Res. 2012;304(1):15–22.
Fujimoto K, Uematsu S. Phage therapy for Clostridioides difficile infection. Front Immunol. 2022;13:1057892.
