You treated the SIBO, and for a few weeks your belly felt like your own again. Then the bloating crept back, along with the urgent trips to the bathroom, the constipation, or a swing between both, and the list of safe foods got shorter. Maybe you have worked through a low FODMAP diet, an antimicrobial course, a round of antibiotics and a few probiotics, and you still catch yourself thinking, “What did I eat wrong this time?”
I know that loop from the inside out. IBS and SIBO were both on my own list of diagnoses, and at my worst I was down to five foods (and formula for a time!) and still reacting. What I eventually understood is that the gut never works alone. The gut has its own network of nerves, and that network stays in conversation with the brain all day, in both directions. On this page I explain what the gut-brain axis is, why IBS and SIBO so often come back when only the gut gets treated, and how I use all five phases of the 5R Histamine Modulation Protocol™ with clients who have IBS or SIBO.
Does any of this sound like your IBS or SIBO?
- A SIBO treatment that helped for a while, and then the symptoms came back
- Bloating, pain, constipation or diarrhoea that flare after meals you thought were safe
- A low FODMAP or elimination diet that keeps getting stricter
- Gut symptoms that get louder during stressful weeks or after poor sleep
- Feeling anxious or tense around eating, before the gut even starts to react
- Anxiety, low mood or brain fog showing up alongside the gut symptoms
- A breath test or stool test that did not match how unwell you feel
- A growing sense that you have run out of protocols to try
If you nodded at several of these signs, you have not failed the protocols, and nothing is wrong with you. IBS and SIBO are complicated, and the gut is one half of a two-way conversation. When only one half of the conversation gets attention, symptoms can drift back.
What is the gut-brain axis in IBS and SIBO?
The gut-brain axis is the two-way communication line between the gut and the brain. The line runs through the vagus nerve, through hormones, through the immune system and through the gut microbiome. Irritable bowel syndrome affects an estimated 10 to 20 percent of people, and researchers have not found one consistent cause. A review of brain-gut interactions in IBS lists infection, inflammation, anxiety, depression and major negative life events as possible contributors, and describes disturbances in the autonomic nervous system, with less parasympathetic (rest and digest) activity and more sympathetic (fight or flight) activity (Fichna and Storr, Frontiers in Pharmacology, 2012).
Here’s why the nervous system matters so much for the gut. Digestion is designed to happen in rest and digest, so when the nervous system is stuck in a stress response, digestion gets pushed to the back of the queue. The gut keeps sending signals up to the brain, and the brain keeps sending signals back down. A direct count of the human enteric nervous system, the gut’s own network of nerves, reported about 168 million neurons, a number comparable to the neurons in the spinal cord (Michel et al., 2022). Tap each part of the diagram below to see its role.
Interactive guide
The gut-brain axis, one part at a time
Tap the brain, the vagus nerve, the gut, the gut microbiome or the HPA axis to see the role of each part. Watch the signals travel along the vagus nerve in both directions.
Signals stream along the vagus nerve, and most travel from the gut to the brain.
Tap a part of the axis
The gut and the brain are in constant two-way conversation, through the vagus nerve, hormones, the immune system and the gut microbiome. When the gut is struggling, the brain and the nervous system usually feel the effects too.
Tap any labelled part of the diagram to begin.
The core idea: make, carry, feel
How a gut signal becomes a feeling
The gut and the gut microbes make the messengers, the vagus nerve carries the messengers, and the brain feels the result.
Gut and microbes
The makers
Gut bacteria and the cells of the gut wall make messengers, including serotonin and short-chain fatty acids.
Vagus nerve
The messenger
The vagus nerve carries signals both ways. Most of the signals travel upward, from the gut to the brain.
The brain
The receiver
Mood, stress, focus, appetite and sleep can all respond to what the gut is signalling.
Thriving Practitioners · Gut-Brain Axis Visual Aid, a practitioner-led patient education tool
Sources: Furness et al., 2014; Michel et al., 2022; Yano et al., 2015; Bonaz et al., 2018; Fichna and Storr, 2012. Figures are approximate estimates, and full references are at the bottom of this page. This interactive guide is education and not a diagnosis, and the guide does not replace advice from your doctor.
Most of the traffic runs from the gut to the brain
The vagus nerve is the main physical line of the gut-brain axis. The vagus nerve is commonly described as about 80% afferent, meaning the fibres carry signals up to the brain, and about 20% efferent, meaning the fibres carry signals down to the gut (Bonaz, Bazin and Pellissier, Frontiers in Neuroscience, 2018). The ratio varies between species and nerve segments, so I use 80% as a guide and not as an exact human measurement. The same review notes that a low vagal tone has been described in people with IBS. Vagal tone describes how well the vagus nerve helps the body settle into rest and digest.
Because most signals travel up from the gut, an unsettled gut can keep sending the brain messages of alarm, and the brain and the nervous system respond to those messages. The nervous system and the gut keep influencing each other, so I work on both at the same time.
“Supporting the gut so often lifts how a patient feels.”
Luanne Hopkinson, Clinical Nutritionist and Nervous System Coach
Why IBS and SIBO come back when only the gut is treated
SIBO stands for small intestinal bacterial overgrowth, a larger than expected number of bacteria in the small intestine. The research on SIBO in IBS is more mixed than most online guides suggest. A systematic review and meta-analysis of 12 studies and 1,921 adults with IBS found that the share testing positive for SIBO depended heavily on the test used: 4% on jejunal aspirate culture, 31% on a glucose breath test and 54% on a lactulose breath test. The authors wrote that the role of SIBO testing in people with suspected IBS remains unclear (Ford et al., Clinical Gastroenterology and Hepatology, 2009).
I hold a SIBO result loosely for that reason. A positive breath test tells us that something is happening in the small intestine, and a negative breath test does not mean your symptoms are imagined. Antibiotics and antimicrobials have a place. But there is a gentler way to approach IBS and SIBO: restoring the whole gut microbiome. What I see is that treating the overgrowth on its own leaves out fully restoring the gut microbiome and ignores the nervous system half of the conversation, and for some people the symptoms come back.
“When someone has tried every protocol for IBS or SIBO and feels they've hit a dead end, I find the nervous system connection through the gut-brain axis is the missing piece. Once we work on that nervous system connection alongside restoring the gut microbiome (rather than using strong antibiotics that they may have tried in the past), we can get a better and more sustainable result.”
Luanne Hopkinson, Clinical Nutritionist and Nervous System Coach
Not all strains of bacteria we see on a gut test have good research behind them. For that reason I pair gut testing with the nervous system work, and I do not treat one result as the whole answer.
What working on the gut and the nervous system together looks like
I work on the gut and the nervous system at the same time, because the gut, the brain and the nervous system are in constant communication with each other. The nervous system gives the gut enough calm to respond to gut care, and gut care gives the nervous system fewer alarm signals to answer. I use the 5R Histamine Modulation Protocol™ with clients who have IBS or SIBO, and all five phases get used, in a fixed order: Relieve, Regulate, Repair, Restore and Reintroduce.
Within the 5R Histamine Modulation Protocol™, the Regulate phase carries the gut-brain axis, and the Restore phase carries the gut microbiome, while the Relieve, Repair and Reintroduce phases support the same plan. I think of the gut microbiome as a forest. A forest needs the trees, the plants, the birds, the little animals, the mushrooms and the fungi to flourish, so the aim is a fuller forest and not a shorter list of organisms. Antimicrobials can have a place, and the aim is to restore the forest afterwards and not leave the ground bare.
My framework
The 5R Histamine Modulation Protocol™ for IBS and SIBO: all five phases
I use all five phases with clients who have IBS or SIBO, in this order, because sequence matters more than any single treatment or approach.
Relieve
A personalised dietary starting point, tailored to your symptoms and condition, that calms the system and stabilises symptoms.
Food foundationsRegulate
Nervous system regulation creates the space the gut needs in order to heal.
Nervous systemRepair
Soothing and repairing the gut lining, with enzyme support and nutrient repletion.
Gut repairRestore
Rebalancing the gut microbiome, targeted to what testing shows is actually there.
Gut repairReintroduce
Food and activity freedom: expanding the diet and activities, and getting back into life with confidence.
Food foundationsNervous system regulation runs underneath all five phases, so the gut and the diet have a calm system to work with.
Who this is for
This page is for you if you have a diagnosis of IBS or SIBO, or you recognise the pattern, and you want gut care and nervous system care in the same plan.
- Your SIBO symptoms came back after one or more rounds of treatment
- Your safe food list keeps getting shorter, and eating feels more stressful every week
- Your gut symptoms rise and fall with stress, sleep and busy weeks
- You live with histamine intolerance, MCAS or anxiety alongside the gut symptoms
- You want to understand the why before you decide on a next step
Frequently asked questions about IBS, SIBO and the gut-brain axis
Does the gut-brain axis cause IBS?
The gut-brain axis does not cause IBS on its own, and researchers have not found one cause of IBS. A review of brain-gut interactions in IBS lists stress, anxiety, infection and inflammation as possible contributors, and describes disturbances in the autonomic nervous system, the part of the nervous system that runs digestion without conscious thought (Fichna and Storr, 2012). I see the gut-brain axis as a reason to support the nervous system alongside the gut, and not as the single cause.
Why does my SIBO keep coming back?
SIBO can come back for more than one reason, and the nervous system is a reason I find is often left out of treatment. The gut has its own network of nerves that runs reflex circuits in the small intestine and colon, and that network stays connected to the brain through the vagus nerve and other nerve pathways (Furness et al., 2014). When SIBO treatment targets the bacteria and leaves the nervous system out, some people find that the symptoms return. Working on both together, alongside restoring the gut microbiome, is the approach I use.
Is IBS a gut problem or a mental health problem?
IBS is a real gut condition, and the brain and the nervous system are part of how the gut works, so a nervous system component does not mean your symptoms are in your head. The gut and the brain communicate through nerves, hormones and the immune system (Fichna and Storr, 2012), and a low vagal tone has been described in people with IBS (Bonaz et al., 2018).
How do you use the 5R protocol for IBS and SIBO?
I use all five phases of the 5R Histamine Modulation Protocol™ with clients who have IBS or SIBO, in a fixed order: Relieve, Regulate, Repair, Restore and Reintroduce. Relieve starts with a personalised dietary starting point, tailored to your symptoms and condition, Regulate supports the nervous system, Repair supports the gut lining, Restore works on the gut microbiome, and Reintroduce widens food and activity again.
How does stress affect IBS and SIBO symptoms?
Stress can change how the gut works, because the gut and the brain communicate through the vagus nerve, hormones and the immune system. Stress and disturbances in the autonomic nervous system, with less rest and digest activity and more fight or flight activity, are both described in IBS research (Fichna and Storr, 2012). Stress does not explain every symptom, and gut care still has its place alongside nervous system care.
Ready to look at the gut and the nervous system together?
My gut microbiome restoration page explains how I work on the gut microbiome and the nervous system at the same time.
See gut microbiome restorationReferences
- Bonaz B, Bazin T, Pellissier S. The vagus nerve at the interface of the microbiota-gut-brain axis. Frontiers in Neuroscience. 2018;12:49. doi:10.3389/fnins.2018.00049
- Fichna J, Storr MA. Brain-gut interactions in IBS. Frontiers in Pharmacology. 2012;3:127. doi:10.3389/fphar.2012.00127
- Ford AC, Spiegel BMR, Talley NJ, Moayyedi P. Small intestinal bacterial overgrowth in irritable bowel syndrome: systematic review and meta-analysis. Clinical Gastroenterology and Hepatology. 2009;7(12):1279-1286. doi:10.1016/j.cgh.2009.06.031
- Furness JB, Callaghan BP, Rivera LR, Cho H-J. The enteric nervous system and gastrointestinal innervation: integrated local and central control. In: Lyte M, Cryan JF, editors. Microbial Endocrinology: The Microbiota-Gut-Brain Axis in Health and Disease. Advances in Experimental Medicine and Biology. 2014. doi:10.1007/978-1-4939-0897-4_3
- Michel K, Kuch B, Dengler S, Demir IE, Zeller F, Schemann M. How big is the little brain in the gut? Neuronal numbers in the enteric nervous system of mice, guinea pig, and human. Neurogastroenterology and Motility. 2022;34(12):e14440. doi:10.1111/nmo.14440
- Yano JM, Yu K, Donaldson GP, et al. Indigenous bacteria from the gut microbiota regulate host serotonin biosynthesis. Cell. 2015;161(2):264-276. doi:10.1016/j.cell.2015.02.047
This page is general education. The figures are approximate estimates from the sources above, and nothing on this page replaces advice from your doctor.
