Poo transplants transfer much more than bacteria

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The hodge-podge of bacteria, viruses, fungi and other bits and pieces you poo out could confer benefits to others. Exactly how, though, is largely a mystery.
Credit: Eye of Science / Getty Images

Popping faeces from one organism into the gut of another – faecal transplantation – is not a new concept. In 16th-century China, it earned the nickname “yellow soup”.

But the power of transferring gastrointestinal contents between animals to treat illness really took off in 2011 when research into faecal transplants exploded, a review published today shows.

Given a huge proportion of faeces is bacteria – some studies estimate them to constitute more than 50% of faecal matter’s dry weight – much work has concentrated on their populations.

For instance, around 95% of people suffering Clostridium difficile, a bacterium that infects the bowel causing diarrhoea, treated with faecal transplants are cured. This is because “good” bacteria populations are replenished, keeping the bad C. difficile in check.

But there’s a reason faecal transplants today transfer pretty much every component of the stool – researchers simply don’t know how much of the “other stuff” affects a patient’s outcome.

So, write Vanderbilt University’s Diana Bojanova and Seth Bordenstein in PLOS Biologywhile focus on the bacterial component does make sense in some cases, such as C. difficile treatment, it’s possible the effects of faecal transplants may be influenced by, or possibly even caused by, non-bacterial parts.

Let’s explore them.


The big one – bacteria – constitute 13% of total faecal ‘wet’ weight, or around 100 billion per gram. But are they all healthy and viable?

A 2005 study suggests not. Just half of bacteria harvested from faeces were viable; 19% were injured and a third, dead. This doesn’t mean the departed should be sieved out – their DNA or even the dead cells might have some immune functions.


These less-studied components of the gut microbiome are prevalent in your poo – up to a billion virus particles in each gram of wet faeces. They’re usually bacteriophages – viruses that infect and replicate with bacteria.

The hope is with a little fine-tuning, they may be used to target specific bacteria such as C. difficile.

Archaea and fungi

Archaea – a domain of single-celled organisms different to bacteria – and fungi are also understudied parts of poo. Methane-producing microbes constitute around 10% of faecal anaerobic organisms, although what proportion are bacterial is unknown. A 2014 study showed higher levels of gut archaea were linked to multiple sclerosis.

And let’s not forget fungi, of which there are up to a million per gram of faeces in humans. Candida albanicas, a common yeast, is usually kept in check by bacteria in a healthy gut. But if those bacteria die and C. albanicas runs rampant, it can cause inflammatory bowel disease.

Colon cells

The cells that line your colon, called colonocytes, are constantly sloughed off and excreted. You might end up with around a million colonocytes per gram of poo, but they’re constantly renewed by stem cells that reside in niches called crypts.

If colonocytes start to die in big numbers, the barrier between your microbiome and your organs also disintegrates. The good news is colonic stem cells from a healthy mouse transplanted into a mouse with colon damage integrated and replenished the blemished parts.

Stem cells haven’t yet been found in human faeces, but a transplant recipient may have much to gain if they’re able to reap their benefits too.


Here, we move away from the cells themselves and to their products – small molecules that fuel, signal, stimulate and dampen various functions. There are around 900 clusters of genes in bacteria which live in the human gut that make these small molecules.

One comes from fibre. Intestinal bacteria love it – they metabolise it to produce short-chain fatty acids that stem inflammation in the colon (from which colon cancer can develop). Fibre also makes a big dent in faecal matter weight, if an individual’s eaten loads of it.

So what does this all mean?

This is, by no means, an exhaustive list of relationships in your gut. But as research into how your resident microbial populations and their products interact with your own cells, genes and diet continues to thrive, the effects of these non-bacteria components will only become clearer.

And as for faecal transplants, Bordenstein says, “Right now [they] are used as the treatment of last resort, but their effectiveness raises an important question: when will doctors start prescribing them, or some derivative, first?”

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