The Human Microbiome - what’s the latest?
Over the past year, research into the human microbiome—the trillions of tiny organisms living mostly in our gut—has continued to reveal just how much influence these microbes have on our health. From digestion and immunity to mental wellbeing and even skin health, the gut microbiome is proving to be one of the body’s most important partners.
This blog post shares some of the latest discoveries from 2024, based on the Gut Microbiota for Health Year at a Glance report. Whether you’re wondering what the signs of a healthy gut are or already sipping kefir and growing your ginger, or fermenting foods for gut health, there’s something here for you.
Rather than focusing on specific “good” or “bad” species, what is important is cooperative microbial behaviours and competition between groups. The implication is that long-term health may depend more on maintaining balance between these microbial guilds than on targeting individual species.
This research marks a significant turning point in microbiome science: moving from identifying microbes to learning what they do and how they interact.
This article covers:
What Defines a Healthy Gut Microbiome?
Your Gut Talks to Your Brain—And It Matters in IBS & SIBO
Natural Ways to Support the Gut in IBS
The Gut Talks to Other Organs Too
The Microbiome’s Role in Metabolism, Immunity and Reproduction
Phage Therapy - Fighting Superbugs With... Viruses?
What Defines a Healthy Gut Microbiome?
It turns out, we still don’t really know - there’s no one-size-fits-all answer. Scientists still haven’t agreed on a single definition of what makes a gut microbiome “healthy.” But new research last year brought us a little closer.
Rather than focusing on which microbes are present, researchers are now looking more closely at what those microbes do. They’ve identified three key traits that tend to be seen in healthier guts:
Richness: Having a wide variety of microbial species, just like any ecosystem; the more and different microbes, the better and more stable it is.
Redundancy: Having several microbes that can do the same jobs, which helps the system stay stable even if some are lost. This is particularly important when looking at the molecules (metabolites) they produce.
Stability: A gut that can bounce back after illness, antibiotics or stress is usually in better shape long term.
Excitingly, researchers also identified two competing “microbial guilds” in the gut: one group supports good health, while the other is more common in people with chronic illnesses. It’s the balance between these communities, rather than any one species, that may matter most.
Scientists are now using tools like the Gut Microbiome Wellness Index 2, which uses stool samples to help spot signs of illness before symptoms appear, and to monitor recovery after illness or treatment.
In simple terms: A healthy gut isn’t just about what’s living there—it’s about how well those microbes work together to support you.
Health in the gut is on a spectrum
Your Gut Talks to Your Brain—And It Matters in IBS & SIBO
The connection between the gut and the brain is getting more attention, especially in conditions like Irritable Bowel Syndrome (IBS) and small intestinal bacterial overgrowth (SIBO). If you’ve ever had a gut feeling or felt sick from stress, you’ve experienced this link in action.
IBS and SIBO are described as disorders of the gut-brain interaction (DGBI). New research showed that people with IBS are much more likely to experience anxiety or depression. Sometimes the gut symptoms come first, sometimes the mood issues do—but they’re often connected.
Here’s what the science says:
The microbes in your gut can produce chemicals that affect your mood, appetite, and stress response.
Inflammation in the gut may influence the nervous system and how your brain responds to pain.
Treating the gut—through diet, stress reduction, or microbiome support—may also help improve mental wellbeing.
This growing area of research is even giving rise to a new term: psychobiotics, which refers to probiotics and other interventions that support mental health by acting on the gut microbiome.
The bottom line: Our gut and brain are constantly talking. Supporting your gut health may also support your emotional wellbeing, especially if you have IBS or SIBO.
Natural Ways to Support the Gut in IBS
Many people living with IBS are turning to non-prescription treatments, and the evidence is building that some of these options can help.
According to this year’s findings:
Probiotics: Specific strains of Lactobacillus, Bifidobacterium, Saccharomyces, and others may ease bloating, improve bowel regularity, and reduce pain in some people with IBS. It is important, however, to choose the right strains depending on what needs to be altered. Just any old probiotic isn’t necessarily going to help - seeing a gut-focused practitioner will help identify what your body needs.
Prebiotics: These are plant fibres that feed beneficial microbes. Using them in small, controlled amounts may be gentler than strict diets like low FODMAP. The FODMAP diet is no longer viewed as a healthy ‘long-term’ strategy, as these fibres are necessary for some important microbes’ survival, and can lead to nutritional deficiencies.
Fecal Microbiota Transplantation (FMT): While still experimental, this approach involves transferring healthy microbes from one person to another. In IBS, it may help when delivered to the small intestine, although more research is needed, as the results haven’t been entirely what was expected.
Other options: Peppermint oil (which may relax gut muscles), glutamine (to support the gut lining), and plant-derived melatonin or phytomelatonin (for gut-brain regulation) are also being explored.
Fresh Ginger in food or as a tea can give relief for nausea and bloating
Slippery elm bark powder can help relieve reflux, or heartburn
What to keep in mind: These approaches won’t work for everyone, and the evidence is still emerging. But they offer real potential—especially when part of a personalised plan that considers diet, stress, sleep, and gut function.
Digestion is complex, and this is why it’s important to seek the help of a practitioner skilled to help identify the root cause, and treat accordingly - there is no ‘one size fits all’ approach to gut health!
The Gut Talks to Other Organs Too
The gut doesn’t just talk to the brain—it has conversations with your liver, lungs, heart, skin, and reproductive organs too. This is called the organ-gut-microbiota axis, and 2024 research helped us better understand how it works.
Some highlights:
Skin health: Links have been found between gut microbes and skin conditions like rosacea and eczema. In fact, this link is so strong that naturopaths treat gut health first in order to resolve skin conditions (actually, we’ve always done this, but the science is now catching up and we’re learning why those strategies have been so successful!)
Liver health: In people with liver disease, combinations of specific probiotics, amino acid supplements, and gentle home exercise may reduce frailty and support better outcomes.
Mood and memory: Diets high in fibre and polyphenols (plant molecules) and low in highly processed foods and alcohol may support better emotional balance and brain function throughout life.
These discoveries reinforce the idea that gut health is whole-body health.
A useful perspective: If an organ has a blood supply, it is probably affected by your gut microbes. Supporting one supports the other.
The Microbiome’s Role in Metabolism, Immunity and Reproduction
New research offered further evidence that microbes in the gut play a role in many chronic health conditions, including metabolic and hormonal issues.
Key findings:
Obesity and blood sugar regulation: Certain gut bacteria appear to support a healthier metabolism. Two in particular—Dysosmobacter welbionis and Adlercreutzia equolifaciens—were lower in people with metabolic issues, and dropped further as conditions worsened.
Immune and inflammatory conditions: In IBS and other gut disorders, immune cells called eosinophils may become overactive, contributing to inflammation and symptoms. Gut microbes seem to influence this response.
Women’s health: Researchers are exploring how gut and vaginal microbes might influence endometriosis, urinary tract infections, and bacterial vaginosis. While it’s still early days, this line of research could open up future probiotic therapies for these conditions.
Why it matters: Your gut health doesn’t just affect digestion. It may influence your hormones, metabolism, and even your risk of chronic inflammation.
Phage Therapy - Fighting Superbugs With... Viruses?
Antibiotic resistance is one of the world’s biggest health threats. As bacteria become resistant to antibiotics, scientists are looking for new tools—and one surprising candidate is an old one: phage therapy.
Phages are viruses that infect and kill bacteria. They were studied in the early 20th century but fell out of use once antibiotics became widely available. Now they are making a comeback, particularly for treating infections that don’t respond to regular medications.
The World Health Organisation (WHO) recently updated its priority list of antibiotic-resistant bacteria, and phage therapy is being considered as a possible alternative for hard-to-treat infections.
Challenges include scaling up production, creating personalised treatments, and getting regulatory approval. But the potential is enormous.
In essence: The future of medicine may include precision treatments that support your microbiome, rather than wipe it out.
Final Thoughts
The science from 2024 confirms what many in the natural health world have long suspected: a healthy gut is essential for overall wellbeing. But the details are becoming clearer—and more exciting.
We now know that the gut microbiome affects far more than digestion. It influences mood, immune balance, skin health, hormone regulation, and resilience to illness. Tools for measuring gut health are becoming more precise, and new interventions—both natural and clinical—are gaining traction.
Whether you’re a practitioner or simply someone who wants to feel better in your body, understanding your gut is one of the smartest health investments you can make.
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It’s a little hard to define if you poop every day, around the same time with an easy-to-pass medium-dark brown soft, sausage-like stool, with no signs of nausea, bloating, abdominal pain, no undigested food in your stool, no excess or super smelly flatulence, no signs of urgency, no blood, mucus or pus in the stool - then, it’s probably pretty good. However, if you can say yes to all of those questions and you have an autoimmune condition, skin condition, chronic health condition of any kind, then it’s possible that something is still going on in the gut.
The more its researched, the more we understand that the gut microbiome is key to all aspects of health.
It might be easier to answer ‘what are the signs of an unhealthy gut?! -
That depends on what is wrong with the gut. Our digestive system is incredibly complex, it’s an interaction between trillions of microbes, our mucosal linings, the health of the linings themselves, the types of foods we eat, what we are exposed to, how well hydrated we are and our mental state. Any one of those things can change the balance.
Generally, eating a diet of fresh, whole, predominantly plant-based and ideally organic foods will support good gut health. The more fibre, the better! Having said that, if your gut is out of balance, sometimes fibre can make you feel the worst - that’s when you need the help of a gut-focused naturopath to help get to the ‘bottom’ of your problems.
Julie Forrester is a Melbourne naturopath, who has helped many, many people to achieve healthy guts and balanced microbiomes. -
A question I’m asked from time to time is ‘do I need a detox’, and the answer is usually ‘probably not’. The body has some really great ways of detoxifying the body - in fact, it’s the liver’s main job!
If you are constipated, though, it’s like keeping the garbage inside the house and wondering why the bin (liver) is still full!
If you are not drinking at least 2 L of water each day, then it’s like the plumbing is blocked.
The liver, and the gut both need water to properly detoxify. The best detox starts with eating lots of fresh, whole foods, home-cooked, mostly plant-based and eliminating all the highly processed foods & drinks, and alcohol - every day!
As a gut-focused naturopath specialist in Melbourne, I can help you to optimise your health and your detoxification pathways. -
Eat food, not too much, mostly plants - Michael Pollen.
Probably, the most succinct way of putting it, but it’s essentially true. Aside from food intolerances and allergies (many of which come from gut imbalances), eating a whole-food, home-cooked diet, rich in high quality proteins whether they are plant or animal (grass fed, organic, wild-caught, free-range) is the best way to health.
Seeing a great naturopath in Melbourne can help you decide what is the best diet for you, sort out any microbiome imbalances, and optimise your health.
