Faecalibacterium: What It Is, Why Your Levels Matter, and How to Raise Them

Key takeaways

• Faecalibacterium is one of the most common ‘good bugs’ in a healthy gut. In most healthy adults, it makes up about 5 out of every 100 bacteria in a stool sample (Martín et al., 2018).
• Its job is to feed your gut lining. It turns the fibre you eat into a fuel called butyrate. Your gut lining runs on that fuel — about 70% of its energy comes from it (Hodgkinson et al., 2023).
• When levels drop, the gut lining gets less fuel. Low levels show up again and again in people with gut pain, bloating and bowel problems (Sokol et al., 2008).
• You can’t buy it in a probiotic. This bug dies the moment it touches air.
• You raise it by feeding it, not by swallowing it. In one study, people ate a bit more of a fibre called inulin for just over two weeks, and their levels went up from about 10% to 14.5% (Ramirez-Farias et al., 2009).
• Low levels are a clue, not a diagnosis. They tell you your gut is under strain. They don’t tell you what’s causing it.
• Gut microbiome testing and targeted health plans, like those from our team of certified Nutritional Therapists, can help learn where you’re levels are at, and how to improve it.

Why you’re probably here

Maybe your day looks a bit like this.

You wake up and the first thing you check is your stomach. Is today a good day or a bad day? You get dressed and pick the loose trousers, because by 3pm you’ll look four months pregnant and you know it. You’re always researching your commutes to work for toilets. You turn down lunch with friends, again, because you don’t know how your body will behave. You’re tired in a way that sleep doesn’t fix. You feel foggy. And you’re slowly running out of foods you trust.

That’s not “just a sensitive tummy.” That’s a real thing that is shrinking your life. And if you’ve had a gut test come back with low Faecalibacterium, this article explains what that actually means — in plain English, without the jargon.

What is Faecalibacterium?

Faecalibacterium is a type of good bacteria that lives in your large bowel. It’s one of the most common bugs in a healthy gut. In a healthy adult, it makes up around 5 out of every 100 bacteria in a stool sample (Martín et al., 2018). Some people have even more.

Its main job is simple: it eats the fibre you can’t digest, and turns it into food for your gut lining.

Think of your gut lining as a wall, one cell thick, that separates your food from your bloodstream. That wall is doing a hard job all day, every day. And it needs fuel. Faecalibacterium makes that fuel.

What is butyrate?

Butyrate is the fuel. It’s a substance your gut bugs make when they break down fibre.

Here’s the part most people don’t know: about 70% of the energy your gut lining uses comes from butyrate (Hodgkinson et al., 2023). Not from the food on your plate. From what your bacteria make out of the fibre on your plate.

So the chain looks like this:

You eat fibre → Faecalibacterium eats the fibre → it makes butyrate → your gut lining eats the butyrate → your gut wall stays strong.

Take fibre out of that chain, and the whole thing stalls.

What does low Faecalibacterium feel like?

Honest answer: low Faecalibacterium doesn’t cause one specific symptom you can point to. Nobody can look at your symptoms and say “ah, that’s your Faecalibacterium.”

What we can say is this: low levels show up over and over in people who are struggling with their gut. It’s one of the most consistent findings in gut research (Sokol et al., 2008).

People with low levels are more likely to be dealing with:

• Bloating and a swollen, uncomfortable belly
• Gut pain and cramping
• Bowel habits that swing between too loose and too slow
• Urgency — that sudden “I need a toilet now” feeling
• Inflammation in the gut (redness, soreness and swelling inside your bowel)

It’s a bit like finding out the fire alarm in a building has been switched off. That doesn’t tell you a fire started. But it tells you an important protection isn’t working — and that’s worth fixing.

What low levels are linked to

Here’s what the research shows, and how strong that research actually is. I’ve been honest in the last column, because a lot of gut health writing isn’t.

The honest summary: low Faecalibacterium is a sign that your gut is under strain. It is not proven to be the cause of any of these conditions. And raising it is not a treatment for any of them.

If anyone tells you differently, they’ve gone further than the evidence has.

Why did my levels drop?

Most often, it comes down to one of these five things.

Look again at rows 2 and 3, because they explain why this can feel so hard to fix on your own:

Low fibre → less butyrate → your gut lining runs low on fuel → more oxygen leaks into your bowel → Faecalibacterium dies off → even less butyrate.

It’s a loop. And loops don’t break themselves. That’s not a willpower problem. That’s biology.

Can I just take it as a supplement?

No. And here’s the reason — it’s actually a fascinating one.

Faecalibacterium is what scientists call “extremely oxygen sensitive.” In plain English: it dies when it touches air. Not slowly. Straight away.

Scientists who study it have to grow it in sealed, airless containers. The lab that supplies it to researchers warns that you can’t even grow it on a normal lab dish.

So think about what that means for a capsule. A supplement gets made in a factory, packed into a pot, shipped, sat on a shelf, and opened in your kitchen. Air, air, air, air, air.

Any Faecalibacterium in that pot is long dead.

Worth knowing: scientists are working on a version that could survive as a medicine one day. It’s promising. But it’s still being tested, and it isn’t for sale (Martín et al., 2018).

The way to raise this bug is to feed it. Not to buy it.

How to raise your Faecalibacterium

Fibre. Specifically, the types of fibre this bug likes to eat. This is the only approach that’s actually been tested on real people, with real results.

Here’s what those studies found:

1. Inulin. People took 10g a day of a fibre called inulin for just over two weeks. Their Faecalibacterium went up from about 10% to 14.5% (Ramirez-Farias et al., 2009). (Inulin is in chicory root, Jerusalem artichokes, garlic, onions, leeks and asparagus.)
2. Gold kiwifruit. People with constipation took it for 4 weeks. Their levels went up from about 3.4% to 7% — they roughly doubled. 8 out of 9 people improved (Blatchford et al., 2017).
3. Resistant starch. This is starch that survives your stomach and reaches your bowel, where your bugs can eat it. You get it from potatoes, rice and pasta that have been cooked and then cooled. Also from green bananas, oats and beans.
4. Lots of different plants. Not just lots of one plant. Variety matters, because these bugs feed each other.

Foods that feed Faecalibacterium

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⚠️ Please read this before you change your diet

If you have IBS, or you bloat easily, the foods above are the exact foods most likely to set you off.

Garlic. Onions. Beans. Inulin. These are famous for causing bloating and pain in sensitive guts.

So here’s the honest warning that most articles leave out: if you go home tonight and eat a big bowl of onions, garlic and lentils, you may feel dramatically worse. And then you’ll decide fibre isn’t for you, and you’ll go right back to the safe, beige, low-fibre foods that got you here.

Go slowly. Add small amounts. Add one new food at a time. Give your gut a week to adjust before you add more.

And if you’ve already tried adding fibre and it made things worse — that doesn’t mean you failed. It usually means the order or the pace was wrong, or something else needs sorting out first. That’s a good moment to get help rather than to give up.

How is Faecalibacterium tested?

With a stool test. You send off a sample, and a lab reads the DNA in it to work out which bugs are living in your gut and roughly how many of each.

There are two main types:

• 16S sequencing — cheaper. It can tell you that you have Faecalibacterium, but it usually can’t tell you exactly which type.
• Shotgun sequencing — more expensive. It can tell you the exact type.

What counts as a normal level?

About 5 out of every 100 bacteria in your stool. Healthy people range from roughly 5% to 15% (Martín et al., 2018). In people with gut disease, it often drops to somewhere between 1% and 6%.

Two things to keep in mind before you panic at a “low” flag:

• Every lab uses slightly different ranges. So compare your result to your own lab’s normal range, not to a number you read online.
• One test is one snapshot. Your gut bugs shift with what you ate that week. A single low result is a reason to look into things — not a diagnosis.

When you should see a doctor

Some symptoms need a GP, not a gut test. Please book an appointment if you have any of these:

• Blood in your poo
• Losing weight without trying to
• A change in your bowel habits that’s lasted more than 3 weeks
• Symptoms that wake you up at night
• A family history of bowel cancer
• You’ve been told you’re low in iron

These need proper medical checks. A microbiome test cannot rule out a serious problem, and it should never be used instead of seeing a doctor.

The bottom line

You are not imagining it, and you are not being dramatic. Living with an unpredictable gut is exhausting, and it costs you things other people never have to think about — meals out, holidays, work days, confidence.

Faecalibacterium is one small piece of that picture. It’s a real, well-studied bug with a real job: turning your fibre into fuel for your gut wall. Low levels are a genuine clue that your gut is under strain.

But it’s a clue, not an answer. And it can’t be fixed with a capsule — only with food, time, and usually a bit of help working out where to start.

That’s a slower story than a supplement label promises. It’s also the true one.

Frequently asked questions

Is Faecalibacterium good or bad? Good. It’s one of the most helpful bugs in your gut. It makes butyrate, which feeds your gut lining, and it helps calm swelling. It’s low levels that are linked to problems — not high ones (Sokol et al., 2008).

What does Faecalibacterium do? It eats the fibre your body can’t digest and turns it into butyrate. Butyrate is the fuel your gut lining runs on — about 70% of its energy comes from it (Hodgkinson et al., 2023).

What is a normal Faecalibacterium level? Around 5 out of every 100 bacteria in a healthy adult’s stool sample. Healthy ranges run from about 5% to 15% (Martín et al., 2018). Every lab is a bit different, so check your own lab’s range.

Can I take Faecalibacterium as a probiotic? No. This bug dies as soon as it touches air, so it can’t survive in a normal supplement capsule (DSMZ, strain DSM 17677). Scientists are working on a version that might survive one day, but it isn’t for sale yet.

What foods increase Faecalibacterium? Chicory root, Jerusalem artichoke, garlic, onions, leeks and asparagus (these contain inulin). Also cooked-and-cooled potatoes and rice, green bananas, oats and beans (resistant starch), and apples, pears and carrots (pectin). One study found 10g of inulin a day raised levels from 10% to 14.5% in just over two weeks (Ramirez-Farias et al., 2009). Add them slowly if you bloat easily.

Why are my levels low? The most common reasons are: recent antibiotics, not eating enough fibre, swelling in your gut, long-term stress, and smoking.

How long does it take to raise my levels? Studies have seen levels go up in as little as 2 to 4 weeks with the right fibre (Ramirez-Farias et al., 2009; Blatchford et al., 2017). But feeling better usually takes longer than the numbers take to move, and it depends on sticking with it.

Does low Faecalibacterium cause bloating? Not exactly. Low levels are often found in people with bloating and gut pain, but we can’t say low levels are the cause. It’s a sign your gut is under strain, and it’s worth acting on — but it’s not the whole answer.

How is it tested? With a stool test. A lab reads the DNA in your sample to see which bugs are there and how many. One test is a snapshot, so it’s best read alongside your symptoms and history.

Is Faecalibacterium prausnitzii the same thing? Nearly. Faecalibacterium prausnitzii is the best-known type within the Faecalibacterium family. In 2022, scientists renamed the most-studied strain to Faecalibacterium duncaniae (Sakamoto et al., 2022). So you may see two different names for the same bug — both older and newer research are talking about the same thing.

Can I have too much Faecalibacterium? There’s no known condition caused by having too much of it. The concern in research is always about having too little.

My test says my levels are low. Should I worry? It’s worth acting on, not worrying about. Low levels are common and usually reflect things you can change — like fibre, recent antibiotics, or gut inflammation. Read it alongside your symptoms and the rest of your results. And if you have blood in your poo or you’re losing weight without trying, see your GP first.

References

1. Sokol H, Pigneur B, Watterlot L, Lakhdari O, Bermúdez-Humarán LG, Gratadoux JJ, Blugeon S, Bridonneau C, Furet JP, Corthier G, Grangette C, Vasquez N, Pochart P, Trugnan G, Thomas G, Blottière HM, Doré J, Marteau P, Seksik P, Langella P. Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients. Proceedings of the National Academy of Sciences (PNAS). 2008;105(43):16731–16736. doi:10.1073/pnas.0804812105. https://pubmed.ncbi.nlm.nih.gov/18936492/
2. Sokol H, Seksik P, Furet JP, Firmesse O, Nion-Larmurier I, Beaugerie L, Cosnes J, Corthier G, Marteau P, Doré J. Low counts of Faecalibacterium prausnitzii in colitis microbiota. Inflammatory Bowel Diseases. 2009;15(8):1183–1189. doi:10.1002/ibd.20903. https://pubmed.ncbi.nlm.nih.gov/19235886/
3. Ramirez-Farias C, Slezak K, Fuller Z, Duncan A, Holtrop G, Louis P. Effect of inulin on the human gut microbiota: stimulation of Bifidobacterium adolescentis and Faecalibacterium prausnitzii. British Journal of Nutrition. 2009;101(4):541–550. doi:10.1017/S0007114508019880. https://pubmed.ncbi.nlm.nih.gov/18590586/
4. Blatchford P, Stoklosinski H, Eady S, Wallace A, Butts C, Gearry R, Gibson G, Ansell J. Consumption of kiwifruit capsules increases Faecalibacterium prausnitzii abundance in functionally constipated individuals: a randomised controlled human trial. Journal of Nutritional Science. 2017;6:e52. doi:10.1017/jns.2017.52. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5672330/
5. Sakamoto M, Sakurai N, Tanno H, Iino T, Ohkuma M, Endo A. Genome-based, phenotypic and chemotaxonomic classification of Faecalibacterium strains: proposal of three novel species Faecalibacterium duncaniae sp. nov., Faecalibacterium hattorii sp. nov. and Faecalibacterium gallinarum sp. nov. International Journal of Systematic and Evolutionary Microbiology. 2022;72(4):005379. doi:10.1099/ijsem.0.005379. https://pubmed.ncbi.nlm.nih.gov/35438610/
6. Martín R, Miquel S, Benevides L, Bridonneau C, Robert V, Hudault S, Chain F, Berteau O, Azevedo V, Chatel JM, Sokol H, Bermúdez-Humarán LG, Thomas M, Langella P. Functional characterization of novel Faecalibacterium prausnitzii strains isolated from healthy volunteers: a step forward in the use of F. prausnitzii as a next-generation probiotic (and related review: “Searching for the bacterial effector: the example of the multi-skilled commensal bacterium Faecalibacterium prausnitzii”). Frontiers in Microbiology. 2017–2018;8:1226 / 9:346. doi:10.3389/fmicb.2018.00346. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5845625/
7. Hodgkinson K, El Abbar F, Dobranowski P, Manoogian J, Butcher J, Figeys D, Mack D, Stintzi A. Butyrate’s role in human health and the current progress towards its clinical application to treat gastrointestinal disease. Clinical Nutrition. 2023;42(2):61–75. doi:10.1016/j.clnu.2022.10.024. https://pubmed.ncbi.nlm.nih.gov/36502573/
8. Leibniz Institute DSMZ (German Collection of Microorganisms and Cell Cultures). Faecalibacterium duncaniae (formerly Faecalibacterium prausnitzii), strain DSM 17677 — “This strain is extremely sensitive towards oxygen.” DSMZ Culture Collection catalogue. https://www.dsmz.de/collection/catalogue/details/culture/DSM-17677

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Medical disclaimer

This article is for information only. It is not medical advice, and it is not meant to diagnose or treat any condition. Gut microbiome tests are not a way to diagnose disease. If you have ongoing gut symptoms — and especially if you have blood in your poo, are losing weight without trying, or your bowel habits have changed for more than three weeks — please speak to your GP.