Blame biology. That's what we do when lifestyle interventions such as diet or exercise don't lead to weight loss, and so we'll say things like “It's my slow metabolism!” or “It's in my genes!”
But while genetics does affect the metabolic reactions that let us lose weight, it's not only our biology we should consider. The human body is also home to an estimated 39 trillion individual bacteria (that’s at least equal to our cells) and their metabolism matters too.
The vast majority of our collection of microorganisms (our ‘microbiota’) inhabit the gastrointestinal tract, where their products and interactions create a community: the microbiome.
So how can you harness their abilities to help you lose weight? Bacteria and the other members of your gut microbiome can help – if you feed them right. Here are five steps you can follow.
1. Personalise your diet...or pop a poo pill
Losing weight reduces your risk of multiple medical conditions, including diabetes and heart disease. These are connected through physiology and metabolism so they often coincide to form cardiometabolic syndrome, a cluster of conditions affecting both your cardiovascular and metabolic systems.
But losing weight is really tough. That’s partly because modern Western diets include cheap and convenient foods that are also highly processed and unhealthy – and human evolution hasn't kept up.
“Our biology hasn't evolved at the same pace as the food landscape,” says Prof Sarah Berry, a nutritional scientist at King's College London, who studies how diet influences the risk of cardiometabolic diseases.
Berry leads the Personalised Responses to Dietary Composition Trial (PREDICT), a project funded by ZOE, a company whose customers form a large cohort in research and provide data from their at-home health tests.
Microbiome tests identify bacteria from a stool sample using what’s called ‘metagenomics’ – reading DNA fragments instead of sequencing the full genome of every bacteria species.
In a 2021 study, PREDICT tested 1,098 people then ranked bacteria species as 'favourable' or 'unfavourable' for health, based on their correlations with markers of cardiometabolic risk (including a person’s amount of belly fat) and everyday diet.
That led to an 18-week intervention trial, in which 347 American participants were prescribed diets based on their health data. Compared to a control group (given standard, one-size-fits-all dietary advice), those who followed a personalised diet ended up with improved blood sugar, waist circumference and body weight.
“We believe that if you can manipulate the microbiome through diet, it will have direct impacts on health outcomes,” says Berry.
ZOE’s studies suggest that a personalised diet could help you lose weight. The research also shows a correlation between obesity and dysbiosis – a dysfunctional microbiome.
What about evidence that manipulating your microbiome could actually cause weight loss?
Well, that causal link comes from pioneering mouse experiments in the US. In 2004, biologists at Washington University in St Louis, in the US, showed that mice raised in sterile conditions, without microbiota, gained less weight than regular rodents – even though they ate more.
Later, when those 'germ-free' mice received microbes in faeces from lean mice, they gained less fat compared to when the faecal transplant came from obese animals.
Outside an artificial lab, humans and other animals can’t escape all the microbes in their natural surroundings. Nonetheless, the mouse experiments imply that you could swallow a capsule full of faeces to help you lose weight.
Yep, that’s right. Poo pills. If you can stomach that, a word of warning: faecal microbiota transplantation (FMT) is a brute-force approach that not only introduces microbes good for your gut, but also disease-causing pathogens – bad bacteria such as E. coli.
Besides, there are other, more palatable, ways to upgrade your microbiome.
Read more:
- Here's the only science-backed way to lose belly fat
- How to boost your metabolism: 5 simple ways to speed up fat loss
2. Expand your social circle
Where do our microbes come from? As babies, we inherit some from our mothers – mainly in breast milk. But surprisingly, only three per cent originate from food, and when they do reach us, the microbes fail to colonise our guts because established residents keep the status quo. So what about the rest?
Whether you like it or not, most microbiota are introduced via unintended faecal transplants: in other words, you inhale or ingest other people’s poo particles. This typically happens after your hands have touched contaminated surfaces, and then your face (infectious pathogens also invade through this faecal-oral route).
Given that FMT can cause obesity, it's possible that another person’s poo can influence your body weight. So the next question is: Who are we getting microbes from?
The answer comes from a 2023 study of person-to-person transmission that compared microbiome profiles from 9,715 people and measured the proportion of bacterial strains they had in common.
By cross-referencing the identity of strains against data like whether their human hosts were related or lived together, the study found that you share a third of strains with your mother until age three, after which other social contacts make a larger contribution to your microbiome’s composition.
Adults and children aged four or older in the same household share 12 per cent of strains on average. Twins (with almost identical genomes) share a third of strains as cohabiting kids, dropping to 10 per cent after 30 years living apart.
By contrast, if you pick any two people at random, they share less than one per cent of strains (though their genomes are over 99.9 per cent similar).
These results suggest that spending extensive time with an overweight person raises the risk of receiving donations from their 'obese microbiota'. It could also mean obesity isn't always a non-communicable disease caused by our biology or environment, but instead can spread via microbes.
Before you jump to conclusions, note that catching bugs has only a small effect on your weight, says Prof Nicola Segata, head of the laboratory of computational metagenomics at the University of Trento, Italy, who analysed the bacterial strains: “Our microbiome is much more generally influenced by overall diet than by specific organisms.”
There’s also a more optimistic perspective. “We shouldn't be afraid of living with someone who's obese,” says Dr Mireia Valles-Colomer of Pompeu Fabra University in Barcelona, Spain, who led the study.
She points out that the link with bacteria could have a positive impact on those with obesity. “Maybe social contacts will be beneficial for their microbiomes.”
In other words, if you're overweight and don't meet many people, expanding your social circle could give you a healthier microbiome.
3. Boost your gut diversity
While cutting down on body fat can be difficult, weight loss can change the composition of your microbiome – making losing further pounds easier.
This was shown by a 2022 meta-analysis that pooled data from almost 2,000 participants in 47 trials and uncovered some clear patterns. “We found that the more weight people lost, the more the diversity of their gut microbiome improved,” says Dr Dimitrios Koutoukidis, a dietitian at Oxford University.
Scientists aren't sure why higher diversity is good for the gut. One hypothesis is that it allows redundancy: if you lose a specific bacterium that plays a starring role in performing beneficial functions, you may be carrying a capable understudy.
The meta-analysis also revealed a mechanism to explain why a diverse microbiome is better for the body: a less leaky gut.
“Higher diversity might reduce the permeability of the gut,” says Koutoukidis. “This means bacteria from the gut are less likely to go into the bloodstream and to the liver, and that might reduce inflammation.”
While we don’t yet know exactly why this happens, one particular bacterium’s role stands out: Akkermansia muciniphila.
A. muciniphila feeds on mucin, a sugary protein that forms the protective layer of mucus lining the gut. It produces sugars for other species, boosting diversity, and prompts our cells to create a thicker mucus barrier so toxic molecules are less able to pass through the gut wall.
Such toxic molecules include lipopolysaccharide (LPS) – and if these reach the liver they can interfere with the organ’s functions, such as metabolising food and filtering out toxins. That’s when inflammation happens, which can lead to chronic bowel disease.
So how can you stop that from happening? Losing a few kilos through a calorie-controlled diet helps: weight loss improved gut permeability in patients with fatty liver disease, and temporarily increased their microbe diversity.
Boosting your microbiome diversity seems to increase your chances of carrying specific bacteria that plug your leaky gut.
In the meta-analysis, A. muciniphila was shown to reduce several markers of obesity when given to overweight people as supplements in clinical trials led by researchers at the University of Louvain, Belgium.
These beneficial functions make A. muciniphila a probiotic. According to the International Scientific Association for Probiotics and Prebiotics (ISAPP), probiotics are “live microorganisms that, when administered in adequate amounts, confer a health benefit on the host.”
No doubt you've seen TV ads for yoghurt drinks containing 'friendly bacteria' that promise to increase your gut microbes. But, while a meta-analysis did find that, in general, probiotics may be helpful for reducing weight, it's unclear which foods are most effective.
Interestingly, while living A. muciniphila are beneficial, the dead bacterium works even better: its purified proteins improve fat and glucose metabolism in mice. This means inanimate, pasteurised microbes – or just their parts – can be consumed as ‘postbiotics’.
4. Feed your brain
Bacteria like A. muciniphila use their own metabolism to harvest energy from our leftovers. Notably, some species can break down undigested carbohydrates through fermentation to produce short-chain fatty acids (SCFAs). While these are mostly waste products for our microbes, they are extremely useful to us.
Through these molecules, bacteria can alter our brain and behaviour by binding to receptors on gut cells and prompting them to release hormones that control our appetites.
“They can stimulate our body to make gut hormones that make us feel full or hungry,” says Dr Harriët Schellekens, nutritional neuroscientist at University College Cork, Ireland.
One of them, acetate, can even cross the blood-brain barrier (your brain’s protective wall against harmful toxins and pathogens) to directly activate the hypothalamus, the region that regulates feeding. Others can stimulate metabolism in organs such as adipose tissue, which burns fat.
These connections form the microbiome-gut-brain axis, a communications network that even allows microbes to control the mind, and even which foods we eat: in mice, bacteria suppress a host’s sugar consumption for a healthier diet.
The microbiome-gut-brain axis carries signals in both directions – meaning we could, potentially, manipulate bacteria to stimulate gut cells into releasing hormones. These hormones include glucagon-like peptide 1 (GLP1), which weight-loss drugs like Ozempic interact with to rebalance energy in people with diabetes or obesity.
“Microbiota modulate the appetite and reward centres in our brain to prefer foods that they thrive on,” says Schellekens. “It's like we're the restaurant.”
Schellekens’ team has discovered a probiotic that has an effect on obesity via glucose metabolism. When given as supplements, Bifidobacterium longum APC1472 led to lower fat and weight in mice, and healthy blood sugar levels in humans.
This is partly because the strain is particularly good at producing acetate, the molecule that stops signals from the 'hunger hormone' ghrelin reaching the brain.
You can encourage probiotics that produce useful metabolites (such as SCFAs) to grow by giving them prebiotics. According to ISAPP's definition, prebiotics are nutrients “selectively utilised” by beneficial microbes. Simply put, you target a select group or organism already in your gut by supplying its favourite food.
It's also possible to combine a probiotic and prebiotic to create a ‘synbiotic’. Mixing APC1472 with the sweetener oligofructose, which feeds species like APC1472 and causes weight loss, is what Schellekens calls “the ultimate treatment”.
While specific prebiotics aren’t yet available to buy in shops, you can try targeting them through diet. Fatty acids (such as omega-3 from fish), phenols and phytochemicals (found in plants) and oligosaccharides (sugar chains, in fruit and vegetables) are all prebiotics.
The Mediterranean diet is rich in these prebiotic molecules, so eating these foods not only supplies 'brain food' for better cognitive function, it could also help you lose weight by feeding your microbiome.
5. Harness your dark matter
Bacteria dominate the gut microbiome in terms of species diversity. But like the dark matter that makes up most of the Universe, our microbial communities contain hidden yet important members.
One such group is fungi. While bacteria constitute over 99 per cent of individual microbial cells, the fungal community – the mycobiome – could have a greater influence on the gut ecosystem because its members are bigger in size.
“Although fungi are smaller in terms of number, they form a sizeable proportion of the biomass,” says Prof Siew Ng, who leads the inflammatory bowel disease team at the Chinese University of Hong Kong.
Ng has studied how geography and diet affect mycobiome composition, by comparing Kunming, a city in a rural area where local diets are more plant-based and mushroom-rich, and Hong Kong, an urban metropolis where Western food is easy to access.
This comparison revealed that fungal signatures of lean and obese people were distinct. They discovered that a potential probiotic, Schizosaccharomyces pombe, is less abundant in overweight humans. Obese mice on high-fat diets lost weight when supplemented with the fungus.
The study also found that ecological interactions among fungi – and with bacteria – were disrupted in obese people. ”We think that may be one of the reasons to explain why they can't maintain a good or steady weight,” says Ng.
Another group with a disproportionate influence is viruses. The parasites, which replicate by invading cells, outnumber human gut bacteria by at least 10-to-1 – and almost all of them have bacterial hosts.
According to the old proverb, ‘the enemy of my enemy is my friend.’ So could we recruit these phages (viruses that hunt and kill bacteria) to fight our bad microbes?
So far, transferring a viral community (via a faecal virome transplantation) from lean donors to obese mice has reduced weight gain and improved growth of the good bacterium A. muciniphila.
Scientists don't yet know which viruses are our allies, however. “There are no clear clues as to which phages can reduce body weight,” says Prof Tao Zuo, who leads the microbiome research lab at Sun Yat-Sen University in Guangzhou, China.
Zuo believes that harnessing a whole virome will be more effective. “Our microbiome has to work together – a cocktail is better than a single species.”
Dark matter highlights the hidden influence of your microbiome on metabolism within your body. In fact, some biologists believe that humans can’t really survive without their microbes – that microbiota and the host are a single biological unit. That makes you a meta-organism, or ‘holobiont’.
Ultimately, our microbes can cause or cure obesity, and can act as friends or foes in the fight for weight loss. They eat our food, but they also cook up healthy metabolites. And if we’re going to serve as restaurants for microbes, we need to employ the best chefs.
Read more:
- Your microbiome holds the key to stress resilience, study shows
- New microbiome breakthrough could be key to fighting obesity
- Why your gut microbiome is the key to better health, explained by a doctor
About our experts
Professor Sarah Berry is a nutritional scientist at King's College London, where she leads randomised control trials on diet and cardiometabolic health. She is chief scientist of the personalised nutrition company ZOE.
Dr Mireia Valles-Colomer is a group leader at Pompeu Fabra University in Barcelona, where she studies the role of the human microbiome in mental health. Her work on social transmission was published in the journal Nature.
Professor Nicola Segata is a computational biologist at the University of Trento, where he studies the diversity and diseases of the human microbiome. His work has been published in journals such as Nature Medicine and Cell.
Dr Dimitrios Koutoukidis is a dietitian and senior research fellow at the University of Oxford, where he studies mechanisms of weight loss and the use of behavioural science to improve outcomes for patients with obesity.
Dr Harriët Schellekens is a senior lecturer at University College Cork and investigator with APC Microbiome and Food for Health Ireland. She studies the microbiome-gut-brain axis in nutritional neuroscience and psychiatry.
Professor Siew Ng is a clinical scientist at the Chinese University of Hong Kong, where she developed the first faecal microbiota transplantation programme in Asia. Her work has been published in journals like Nature Genetics and Gut.
Professor Tao Zuo is a microbiologist at Sun Yat-Sen University and the associate director of the Guangdong Institute of Gastroenterology. He has a special interest in the 'dark matter' of the gut microbiome.