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Writer's pictureKatrin Peo

Understanding the Microbiome, Microbiota, Microflora, and Metagenome: Key Differences & Why Gut Health Really Matters

Our understanding of the human body is continuously evolving decade by decade, especially in terms of the communities of microorganisms living within us- it's truly a rainforest. I attended yesterday a seminar on 'Fermented vegetables impact on human health' at TFTAK (Center of Food and Fermentation Technologies), where they gave an overview of the research study they conducted with a selected group of people, to determine how the consumption of fermented vegetables impact human gut. I am not going to go into sharing any details of this study as TFTAK will publish the scientific research summary themselves in the near future, but the results shared proved yet again that by regularly (daily) consuming fermented foods, you can definitely impact your gut and therefore your overall health positively. This seminar inspired me to cover the topic of gut health in my blog again, but bringing some more insights.


Microbiome, microbiota, microflora- what's the difference and why gut health matters?


Firstly, I use this opportunity and explain what are the differences between the terms like microbiome, microbiota, microflora, and metagenome, frequently used in health and wellness discussions, as they can be confusing as well as highlight again why supporting our gut health with probiotics and prebiotics is crucial.


What is the Microbiome?

The microbiome refers to the complete ecosystem of microorganisms—including bacteria, fungi, viruses, and their genetic material—living in a particular environment, like your gut (but can also be on your skin- learn more about skin microbiome here). It includes not just the microbes but also the genes they contain and the environmental conditions they thrive in. Think of the microbiome as the "neighbourhood," where all the various organisms live, interact, and influence each other.


What is Microbiota?

While the microbiome represents the full habitat, microbiota refers specifically to the community of microorganisms (bacteria, archaea, fungi) living in that environment. For example, your gut microbiota is the collection of microbes in your digestive tract. It plays an essential role in digestion, immune function, and even mental health.


Key difference: If the microbiome is the entire ecosystem, the microbiota are the organisms within it. It’s like comparing a forest (microbiome) to the trees, plants, and animals (microbiota) living inside it.


What is Microflora?

The term microflora is older and was originally used to describe microscopic plants. Over time, it has come to include bacteria and other microorganisms, particularly in popular literature. However, it is now largely replaced by microbiota in scientific contexts, as it’s less precise. If you hear "gut flora," it generally refers to the bacteria in your intestines, but microbiota is the preferred term in medical literature today.


What is the Metagenome?

The metagenome is all the genetic material present within a specific microbiota. By extracting DNA from the microbiota (a process called metagenomics), scientists can analyse the genes of all the organisms living in a particular environment, helping us understand how they function and influence our health.


More Bacterial Cells Than Human Cells?

One of the most fascinating facts about the human body is that we have more bacterial cells than human cells. It’s estimated that our bodies are made up of about 39 trillion bacterial cells compared to 30 trillion human cells. This staggering number illustrates the importance of the microbiome and the need to maintain its balance for our overall health.


Why Supporting Gut Health is Important

Your gut microbiome is crucial for digesting food, absorbing nutrients, and regulating your immune system. However, modern diets, stress, and certain medications (like antibiotics, proton pump inhibitors, metmorfin, laxatives, nonsteroidal anti-inflammatory drugs (ibuprofin, paracetamol) can disrupt the balance of your gut microbiota, leading to a variety of health problems such as digestive issues, weakened immunity, and even mood disorders. You can read more about the gut microbiome, what affects it, what are the consequences of imbalanced gut microbiome and what can you do to support it from this article.


Probiotics and Prebiotics: Key Players in Gut Health


To maintain a healthy gut, from a dietary point of view it’s essential to support your microbiome daily with fermented foods and drinks and prebiotic foods.



Why Regular Consumption Matters

Different bacteria have different lifespan in the gut. To insure that the good bacteria gets into the gut and colonises, you need to consume both fermented foods and drinks and prebiotic foods regularly. It’s not a one-time fix (consuming for 2 weeks and then stoping); making these foods a consistent part of your diet is key to long-term health.


Aim to consume 3 servings of fermented foods a day, which is for example 1-2 tbsp of kimchi, 1-2 tbsp of sauerkraut, 1 cup of kefir or 1 cup of yoghurt (look for on the package specific bacteria- for example LGG (lactic acid bacterium Lactobacillus rhamnosus GG) or Lactobacillus fermentum ME-3. Aim to consume 25-35g of fibre a day- in this article I share example menus to get to the adequate fibre consumption. If you are someone who has never consumed fermented foods, then start slowly, maybe 1tbsp of kimchi a day so you avoid unnecessary stomach discomfort.


Also, when you purchase fermented foods (kimchi, sauerkraut, yoghurt) or drinks (kefir, kombucha) from the grocery store, make sure you purchase them from the fridge section of the areas in the store, where these products are sold as these are living foods (live bacteria within the products). There are kimchis and kombuchas sold in the inside store isles as well, but then you know that these are pasteurised therefore bacteria within the products is dead.


Understanding the differences between the microbiome, microbiota, microflora, and metagenome is the first step to appreciating the complexity of your body’s microbial ecosystem. By supporting your gut with probiotic and prebiotic foods, you can promote a healthy microbiome and reap numerous health benefits. A healthy gut can enhance digestion, improve mental clarity, boost immune function, and even reduce inflammation in the body. The science is clear: caring for your gut is an investment in your well-being.


If you are looking to improve your diet, but don't know where to start, how to change it, so it's healthy, diverse and sustainable, don't hesitate to reach out to me for nutrition counseling at info@katrinpeo.com.

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