Antibiotics are life-savers, but they're kryptonite to gut microbes.
An expensive test helped explain Sharon Walker’s “mutinous” gut, but it’s diet and supplements that really hold the key to rebooting our microbes.
A good gut is the holy grail of health. Barely a week goes by without a new study or expert singing the praises of a well-balanced microbiome.
Our gut microbes are the stars of our immune system, the secret ingredient needed for a happy heart and brain. Cognitive functioning and even performance in the bedroom, it seems, are at the mercy of billions if not trillions of microbes; the bacteria, fungi and viruses which have set up store in our colons. These little critters weren’t even on our radar until the last decade. Now we can’t move for them. As a health journalist, I have often wondered about the state of mine.
I have done my damnedest to make friends with my microbes, following the advice of experts like Professor Tim Spector – wooing them with fistfuls of fibre, studiously totting up my plant intake and quaffing kefir for breakfast. And yet I have long had the feeling that my microbes are not the happy campers they ought to be.
There were signs of mutiny: a belly like a space hopper, stabbing pains, erratic bowel habits. In the past year, things seemed to have calmed down a bit. But the ongoing issue has been my frequent intake of antibiotics. Antibiotics to knock out bugs in my lungs, to halt the yearly bronchitis which, left to fester, has a habit of turning into pneumonia; antibiotics to put the kibosh on UTIs; more antibiotics to deal with a scratch on my elbow that swelled like a balloon (cellulitis).
Antibiotics are life-savers and I’m grateful to have had them, but they are to good gut health what kryptonite is to Superman – a wrecking ball that smashes through the microbes, taking out the good with the bad.
Dr James Kinross is a gastrointestinal surgeon and senior lecturer in colorectal surgery at Imperial College London. He is an expert in gut health and the author of the book Dark Matter, The New Science of the Microbiome. He says: “If you take a broad-spectrum antibiotic you will probably see a decline in your gut microbes by 40,000 fold – you’ll have a decimation of that ecosystem.”
One study in Washington showed that a single dose of broad-spectrum antibiotics left healthy people with a microbiome similar to that of intensive care patients. Some never recovered.
Worryingly, some studies indicate that the way antibiotics can alter the gut microbiome may impact brain health and the risk of dementia. After watching my father die slowly and painfully of this condition, like most people, this is a fate I’m keen to do everything to avoid.
Fortunately, more targeted antibiotics are less devastating than broad-brush formulations. “You would see a dramatic change, with gradual recovery after about six weeks,” says Kinross. “But they will have a cumulative effect. And if you’ve had multiple courses over the years, it will 100% change your microbiome.”
I’ve had seven courses of antibiotics in the last two years alone. It’s no wonder my microbes are complaining.
Kinross says it’s not something the scientific community yet has a clear answer to. That hasn’t stopped numerous companies trying to answer the question.
The nutrition programme ZOE offers blue-dyed cookies to test “transit time”. The faster the cookies emerge, the better your gut is performing. The next step up from the blue poo test are the microbiome tests that examine the balance and diversity of the microbes. Given this is the best tech we have to date, I decided to give it a whirl.
The test I tried was from GutID, which has labs in the States. Reassuringly, these tests are also used by scientists from Imperial College and Yale.
GutID requires a stool sample which is then analysed in a lab. The box arrives with a paper contraption to catch the sample in the loo – I then remove a bit with a tiny spoon and send it back in a barcoded collection tube.
Four weeks later a report lands in my inbox – GutID’s top line on my microbiome. The report details the strains of bacteria, both good and bad, how many I have, and whether they are in balance, as shown by a kaleidoscope of colours representing hundreds of different species of microbes.
At first glance, things seem pretty good. GutID has awarded my microbes a not-too-shabby 72% which, given my recent antibiotic history, feels like a win. But there are also a few red flags. Fortunately, along with the printed report, I’m offered a consultation to explain my results with microbiome expert Elena Panzeri, who has an MSc in nutrition and genetics. “Your microbiome is not terrible at all,” she says. “You have some bacteria that are a bit off that may grow in future, so you need to keep those under control.”
So overall, not too bad, but what about those “off” bacteria? After all that kefir, I was shocked to learn I have zero probiotics. No Lactobacillus, nor any Bifidobacterium, both of which are “good” bacteria that aid digestion. Akkermansia, another probiotic that slows the development of obesity and restores the gut lining, is also conspicuous by its absence.
This is almost certainly down to my antibiotics-riddled past and most likely explains my temperamental belly. “You are clearly prone to IBS [irritable bowel syndrome],” Panzeri says.
When I show my report to Dr Kinross, he spots a few bad apples amongst my bacteria. “You’ve definitely got some players which are only there because you’ve been on antibiotics,” he says. “Your gut is dominated by four or five bacteria so you’ve got less diversity in your gut versus the rest of the population. But at the same time there are bits of your microbiome which are resilient, in what has been quite a big antibiotic insult.” So more a C+ than A–.
On the upside, the report shows I have a very low level of bacteria associated with dementia. It doesn’t rule it out, but it’s reassuring all the same. GutID has also flagged potential pathogens (bad bacteria), commonly associated with colon cancer, as well as bacteria associated with other intestinal issues like SIBO (small intestinal bacterial overgrowth) and IBD, along with some linked to heart health and antibiotic resistance – a growing problem due to the skyrocketing use of antibiotics. On these, somewhat surprisingly, I pass with flying colours.
Panzeri sends me away with a long list of foods to include in my diet. I need more fibre to feed my good bacteria – no surprise there. Many are foods I already eat, but I must double down on onions, leeks and bananas to feed my Akkermansia bacteria, along with polyphenol-rich berries, red grapes, black coffee and wholegrains.
However, she does not think I can address my lack of probiotics with diet alone, and for that I will need supplements. She also suggests that I check my vitamin D, as this can encourage the good bacteria in our gut.
I will repeat the GutID test in three months to see if these dietary tweaks have made a difference. You can buy a single test for £349 (about NZ$780), or a TriCare pack (£899), which includes three tests, to check your microbiome over time and check whether interventions are having the desired effect.
Given that our microbiomes are as individual as a fingerprint, Kinross says it’s a good idea to take the test when you’re healthy – in my case, before the antibiotic onslaught.
“If I’d known where your gut was three years ago, it would inform me in getting your gut back to where it needs to be. So I encourage people to take these tests when they’re well rather than when they get sick.”
Microbiome tests are often criticised as unreliable because the microbiome frequently changes in response to diet and lifestyle, so a single snapshot might not be representative. Then there are the issues with the varying methods used in analysing the data, which can lead to inconsistent results, even when taken from the same sample. So are my test results even worth the paper they are written on?
Paul Denslow, CEO of Intus Bio, creator of GutID, says his test is more reliable than most. It uses new technology and AI to analyse “a slice of the genome – a small perfect piece of data”, enough to identify all the bacteria in your gut.
Kinross uses the GutID test in his clinical practice. He says: “It gives you that precision, and it’s reproducible. If used in the right way it’s extremely helpful.”
But the results need to be considered within a wider context, along with symptoms and lifestyle.
So what should I do in the future to keep my microbes happy?
Kinross isn’t against antibiotics: “If you need them, for God’s sake take them.”
But what he would like to see is more “microbiome conservationism” amongst the medical profession. In his clinic, where he deals with patients suffering from gut-wrenching problems, he frequently sees those dealing with post-antibiotic scarring. “They get inflammatory bowel disease symptoms and the doctor sees microbial overgrowth and prescribes more antibiotics – it’s a vicious cycle.”
When things get really bad, he suggests faecal transplants (don’t try this at home, folks), where microbes are transplanted from a healthy donor.
But usually what their microbiomes need is simply “rest and space and room to grow back”.
My own microbiome clearly needs a well-earned break, but just before I’m due to take my second GutID test, I’m felled by a tooth infection. I hold out for a week, but the swelling in my gum won’t go away on its own. I’m back on the antibiotic bandwagon.
Beyond the common-sense advice on diet and lifestyle that Panzeri has provided, is there anything else I need to know to keep my gut health on track?
When you’re taking an antibiotic, there are a couple of things you should do, Kinross says.
“The first is to have a discussion with your physician. Ask them: ‘Am I taking the narrowest spectrum of antibiotics that I possibly can for this particular problem that I have?’
“That means they should be culturing what they think is infecting you and trying to identify that bug, to make sure you are on precisely the right [dose of] antibiotic you need.” (From looking at my microbiome data, he strongly suspected that I have not always been on the correct antibiotics and that this had led to “leaky gut”.)
The second thing is to make sure that the antibiotic you’re taking is working as effectively as possible, so you need to watch your diet. “No ultra-processed foods please, no refined sugars, no booze. A high fibre plant-based diet helps antibiotics to work better. And you can supplement that with a prebiotic or probiotic.”
So that’s a hard no to the Lucozade that accompanied every antibiotic-fuelled illness of my childhood, and back to working on my fibre intake.
So was the test useful? I have to admit that before I took the test, I’d hoped for a near-perfect score. But my generally healthy diet (bar the odd glass of wine) had been no match for all those antibiotics. I need to persist with a diverse diet to encourage more diversity in my microbes. No surprise there – I probably didn’t need a microbiome test to tell me that.
Where the test excelled, however, was in pinpointing particular microbes that were out of whack. Without the test or Elena Panzeri’s input, I wouldn’t have taken the probiotic supplements, which seem to have helped. She also suggested I have my estrogen levels checked, as a drop in estrogen after menopause can result in decreased microbial diversity. This tip alone proved potentially transformative after an NHS blood test revealed I was barely absorbing any estrogen from HRT patches (I’ve since switched to estrogen gel).
Was the test worth it? For me, with my health issues, it was definitely useful. But if you’re in good health, with zero gut issues, is it worth shelling out over £300 to take a peak inside your microbiome? Probably not.
I’m hopeful that a test in six months will prove my microbes are back on track. “It isn’t a quick process,” Kinross warns. If that doesn’t work, the next step could be a faecal transplant. Am I prepared to ingest a “crapsule” (freeze-dried stools) for the sake of my future health? To be frank, the thought fills me with horror. For now, I’ll stick with the kefir.
'I’m only still here because it was found early.'