Giant Bacteria Could Be Living in Your Gut, Scientists Find

Your gut microbiome is home to trillions of microbes — and some of them may not be microscopic. New research has found traces of Epulopiscium, one of the largest known types of bacteria on Earth, in human gut samples from around the world.

The finding, reported by New Scientist on Wednesday, comes from a sweeping DNA survey by microbiologist Danny Ionescu at the Technical University of Berlin, who searched more than 600,000 microbiomes for signs of the giant bacterium. The result was unexpected: thousands of human samples tested positive.

A surprise hidden in plain sight

Giant bacteria are generally defined as larger than 10 micrometres, while a typical bacterium is around 2 micrometres long. Epulopiscium dwarfs both definitions: species in the genus can reach 600 micrometres — more than half a centimetre — making them visible to the naked eye and, in cell volume, about a million times larger than a common E. coli cell.

Until now, these giants were thought to live only in niche environments: the intestines of surgeonfish, mangrove sediments and similar habitats. Ionescu first noticed Epulopiscium-related DNA sequences turning up in fish species beyond surgeonfish, and set out to find out how wide-ranging the genus really was.

How the discovery was made

Ionescu and his colleagues searched DNA sequences amplified from more than 600,000 microbiomes, mostly publicly available datasets, supplemented with samples collected by the team. The microbiomes came from a range of species across more than 80 countries.

The sweep found "tens of thousands of positives" for Epulopiscium, says Ionescu, in animals ranging from shellfish to ferrets — and, crucially, in thousands of human microbiomes. In most human samples the sequences accounted for only 1 to 2 per cent of the DNA identified, but in rare cases they reached 20 per cent.

Just how giant is giant?

Epulopiscium fishelsoni, first discovered in 1985 in the gut of surgeonfish and initially mistaken for a protist because of its size, is the second-largest known bacterium. The largest, Thiomargarita magnifica — discovered in 2022 in Guadeloupe mangroves — can reach nearly two centimetres, large enough to pick up with tweezers.

Size matters because big cells face a biological problem: how does one cell coordinate everything across such distances? Epulopiscium's answer is radical — each cell carries hundreds or even thousands of copies of its chromosomes. That polyploidy lets different parts of the cell act almost independently and tolerates mutations that would kill an ordinary bacterium.

What it could mean for your health

The most striking pattern Ionescu's team found was not just presence but abundance: the sequences were most common in the first year of life, and more likely to turn up in people with gastrointestinal conditions associated with inflammation, such as colorectal cancer and inflammatory bowel disease.

That does not mean the bacteria cause those conditions. "We think the organism is taking the opportunity of imbalance in the microbiome," Ionescu told New Scientist — in other words, an inflamed or disrupted gut may simply be a comfortable home for a giant. That opportunism could make them medically useful as an early marker of a dysregulated gut, detectable in a stool sample before symptoms appear.

The sceptics' case

Not everyone is convinced the DNA belongs to giants at all. Nicola Segata of the University of Trento called the finding "a very big surprise" and cautioned that searching for DNA sequences can pick up unrelated bacteria that happen to share similar genes but are not themselves large. "I wouldn't be surprised at all if what they are actually seeing is another, maybe unknown, bacterium," he said.

Ionescu counters that even if the genes do not belong to Epulopiscium proper, their owner is probably closely related with similar physical traits. "I would not expect it to be normal scale," he said.

What comes next: pictures or it didn't happen

The decisive test is disarmingly old-fashioned: someone has to look through a microscope and see the things. Ionescu is now running studies with fluorescent probes designed to bind to the identified sequences, which would make the bacteria glow under the microscope inside gut samples. "When we get the pictures, we'll have the proof," he said.

If the giants are confirmed, textbooks will need updating: the human gut, one of the most studied microbial habitats on the planet, would turn out to harbour organisms hundreds of times larger than microbiologists thought possible there.

FAQs

Why did DNA sequencing miss these bacteria until now?

Modern microbiome studies rarely look at cells at all: they shred DNA, sequence the fragments and try to reassemble them into genomes. That process is biased against giants. A single Epulopiscium cell carries thousands of genome copies, which confuses the assembly software, and reference databases were built mostly from bacteria that can be cultured in a lab — something Epulopiscium has never allowed. Ionescu's insight was to search the raw, unassembled sequence data directly rather than relying on assembled reference genomes.

What does "1 to 2 per cent of DNA sequences" actually mean?

When researchers sequence a microbiome sample, they count what fraction of the DNA fragments match each organism. One to two per cent is a modest but real presence — not contamination-level noise. But because one giant cell holds thousands of chromosome copies, a single cell could contribute far more DNA than its actual headcount suggests, so read percentages may overstate how many cells are present.

If they are not causing disease, why do scientists care?

Three reasons. First, a microbe that blooms during gut disruption could become an early-warning marker for conditions like inflammatory bowel disease or colorectal cancer, detectable before symptoms. Second, giant bacteria solve problems — coordinating a millimetre-scale cell, managing thousands of genomes — that push the boundaries of cell biology, with possible biotechnological uses. Third, the discovery is a reminder that even the human gut, sequenced millions of times, still holds surprises.

Have giant bacteria turned up in other unexpected places?

Yes. Beyond the shellfish and ferrets in Ionescu's survey, Volland has found Epulopiscium-related sequences in guinea pigs, and the related giant Thiomargarita magnifica was found in Caribbean mangrove sediments. The pattern is consistent: wherever researchers look carefully, giants keep appearing where the textbooks said they should not be.

How do Epulopiscium and Thiomargarita magnifica differ?

Both are giants, but they are very different organisms. Thiomargarita magnifica, the record-holder at up to two centimetres, lives in mangrove mud and stores its DNA in membrane-bound organelles called pepins. Epulopiscium, at up to 600 micrometres, is a gut symbiont that keeps its thousands of chromosome copies scattered near the cell membrane. One is a sediment dweller, the other a gut guest; both break the old rules about how big a bacterium can get.