What Happens to the Gut Microbiome When We Irrigate the Colon?

Written by

Emma Child

Manager, Trainer and Therapist

A fascinating human study produced a result that challenges one of the most common assumptions about bowel irrigation: after four weeks of regular transanal irrigation, microbial diversity increased rather than decreased.

One concern we hear repeatedly is: “Doesn’t washing the bowel remove all the good bacteria and damage the microbiome?”

It sounds reasonable. The colon houses an enormous microbiome—the community of microorganisms living within the gut—and irrigation introduces water and encourages evacuation. Surely that must wash the ecosystem away?

A 2022 human study suggests the relationship may be far more complex. Researchers studying transanal irrigation in people with multiple sclerosis and neurogenic bowel dysfunction did not only measure constipation, continence and bowel emptying. They also collected faecal samples and examined what happened to the gut microbiome over time.

The study: four weeks of regular bowel irrigation

Ascanelli and colleagues conducted a prospective, single-centre cohort study at the University Hospital of Ferrara in Italy. Eighty people with multiple sclerosis were screened, 37 met the study’s bowel-symptom threshold and 17 completed the diagnostic phase. Fourteen accepted transanal irrigation, two stopped near the beginning, and 12 completed the four-week treatment phase.

All 12 participants who completed irrigation were women. They used a Peristeen device to introduce 400 mL of water on alternate days. Healthcare personnel provided training, after which participants performed the treatment independently at home.

Faecal samples were collected at baseline and weekly during the four-week intervention. Samples were deliberately collected the day after an irrigation rather than immediately afterwards. Researchers used 16S rRNA gene sequencing to identify and compare groups of microorganisms present in the samples.

What is transanal irrigation?

Transanal irrigation, often shortened to TAI, introduces water through the anus using a purpose-made device to help evacuate stool from the rectum and lower colon. It may be prescribed for neurogenic bowel dysfunction—bowel problems caused by changes to the nerves controlling bowel movement, sensation and emptying.

Peristeen is not the same treatment as professional colon hydrotherapy. It is a smaller-volume system designed for trained users to operate independently or with assistance. Professional Rojas Colon Hydrotherapy uses different equipment, volumes, protocols and practitioner involvement.

There is nevertheless a relevant mechanistic similarity: both approaches introduce water rectally and encourage the evacuation of bowel contents. That makes the study informative to the wider conversation about bowel irrigation and the microbiome, while not allowing its results to be automatically transferred to Rojas Colon Hydrotherapy.

Microbial diversity increased

This was perhaps the most fascinating finding. Over four weeks of regular irrigation, two measures of alpha diversity—the number of observed operational taxonomic units and the Chao1 index—increased significantly.

Alpha diversity describes the richness and variety of microorganisms within an individual sample. Greater diversity is often associated with ecosystem resilience, but it is not a universal score of “good gut health”. A more diverse microbiome is not automatically healthier in every disease, person or context.

Even with that caution, the finding runs directly against the simple assumption that irrigation must indiscriminately strip bacteria from the colon. In these 12 participants, regular irrigation did not produce an obvious collapse in faecal microbial diversity. The measured diversity increased.

Diversity increased without major structural disruption

The researchers also measured beta diversity, which compares the overall composition of microbial communities between samples. They found no significant separation over time. At broader phylum and family levels, the microbiome’s general compositional structure was largely maintained.

That combination is interesting: the number and richness of detected groups increased, while the ecosystem did not undergo an obvious wholesale reorganisation during the short intervention.

This offers a more biologically realistic way to think about irrigation. The microbiome is not simply loose bacteria floating in stool. Microorganisms occupy different ecological niches, interact with mucus, attach to surfaces, use nutrients and metabolites, and reproduce. Removing some bowel contents is not necessarily equivalent to permanently removing the underlying microbial community.

Bowel function improved too

The study was primarily designed to assess bowel symptoms. After four weeks, all of the reported bowel-function and bowel-related quality-of-life measures improved significantly.

Faecal incontinence scores and satisfaction with bowel management also improved significantly. At a median follow-up of 28 months, 83.3% of the 12 completers were still using transanal irrigation, and the researchers reported that satisfaction remained high.

Median intestinal transit time decreased from 76.8 to 56.4 hours. However, this difference was not statistically significant, so the study did not prove that irrigation accelerated intestinal transit. Stool form and recorded diet did not change significantly during treatment.

What happened to individual microorganisms?

Before treatment, participants’ microbiomes differed from those of age- and sex-matched healthy Italian comparison samples. The researchers observed lower levels of several health-associated, short-chain-fatty-acid-producing groups and higher proportions of several taxa described as having pathogenic or pro-inflammatory potential.

During irrigation, some changes appeared potentially favourable. Prevotella decreased significantly, Enterococcus showed a downward trend, and Ruminococcus increased. The researchers also reported correlations between some health-associated taxa and better bowel-function scores.

But the organism-level story was not uniformly positive. Peptostreptococcaceae, which the authors noted may have pro-inflammatory characteristics, increased. Methanobrevibacter, previously reported as enriched in multiple sclerosis, also increased. Other genera moved in different directions, while Faecalibacterium and Veillonella initially decreased and then returned to their baseline proportions.

Could changing bowel emptying change the microbial environment?

This study cannot tell us exactly why diversity increased. One plausible hypothesis is that regular emptying changed the physical and chemical environment of the colon—such as stool retention, available nutrients, fermentation conditions and microbial competition—allowing a different range of organisms to be detected.

That is a biological interpretation, not a proven mechanism. Faecal sequencing shows which microbial groups were detected and their relative proportions; it does not directly measure the full mucosal microbiome, microbial function, metabolite production or inflammation inside the bowel.

The findings invite a more useful research question. Rather than asking only, “What bacteria might irrigation remove?”, we can also ask, “How does changing stool retention and the colonic environment affect the microbial ecosystem that remains and regrows?”

What this study does—and does not—show

What it supports

• Regular transanal irrigation did not reduce measured faecal microbial diversity in this small group.
• Alpha diversity increased significantly over the four-week intervention.
• The microbiome’s broad community structure remained comparatively stable.
• Multiple measures of bowel dysfunction and bowel-related quality of life improved alongside the microbial changes.

What it cannot establish

• It cannot prove that irrigation caused every microbiome change because there was no randomised or untreated comparison group.
• It cannot establish that increased diversity was clinically beneficial or improved multiple sclerosis.
• It cannot determine whether the findings apply to people without multiple sclerosis or neurogenic bowel dysfunction.
• It cannot be treated as a direct trial of professional colon hydrotherapy or the Rojas method.
• It cannot establish long-term microbiome effects from only four weeks of microbial sampling.

Important limitations for medical professionals

The intervention analysis included only 12 participants, all women, at one Italian centre. Attrition was substantial between screening and treatment completion, creating a risk of selection bias. Participants acted as their own pre–post comparison, with no concurrent untreated control group.

The microbiome was assessed through 16S rRNA sequencing of faecal samples. This is useful for taxonomic profiling but cannot provide the functional detail of shotgun metagenomics, metabolomics or direct mucosal sampling. The comparison samples from healthy people and people with multiple sclerosis without significant bowel symptoms came from previous datasets rather than a newly recruited parallel control group.

Diet diaries did not identify significant dietary change, reducing—but not eliminating—diet as an explanation. Medication, disease characteristics, home treatment performance, ordinary week-to-week microbiome variability and increased clinical attention may also have influenced the results.

The authors declared no financial support or conflicts of interest. They acknowledged Coloplast Italy for a substantive contribution involving use of the Peristeen device.

Two participants stopped treatment

One participant with a history of diverticulosis developed diverticulitis and discontinued irrigation. Another with endometriosis stopped because of non-specific abdominal pain, which continued after stopping and was later associated with adhesions. The authors considered these events relevant to patient selection rather than evidence of a general procedural safety problem.

However, such events reinforce why bowel irrigation should not be treated as universally suitable. Proper screening, contraindication checks, training and clinical oversight matter.

What does this mean for colon hydrotherapy?

The study offers human evidence against the simplistic claim that introducing water into the bowel inevitably “washes away all the good bacteria”. That outcome was not observed after alternate-day transanal irrigation in this small cohort.

It does not provide direct evidence about Rojas Colon Hydrotherapy because the treatment and population were different. Still, it demonstrates why assumptions about irrigation and microbial depletion should be tested rather than repeated as settled fact.

It also complements a separate human study in children with spina bifida, where three months of transanal irrigation was associated with compositional microbiome changes rather than simple depletion. Together, these small studies justify better research into bowel irrigation, microbial ecology and clinically meaningful outcomes.

For the broader evidence base, visit our colon hydrotherapy scientific review.

The bottom line

After four weeks of regular transanal irrigation, 12 women with multiple sclerosis and neurogenic bowel dysfunction showed increased faecal microbial diversity, no major shift in overall community structure and significant improvements across several bowel-symptom and quality-of-life measures.

That does not prove irrigation creates a healthier microbiome, and it cannot be generalised directly to professional colon hydrotherapy. But it does challenge the assumption that bowel irrigation simply strips the colon of its microbial ecosystem.

The more accurate conclusion is both more cautious and more interesting: changing how the bowel empties may change the microbial environment in ways we are only beginning to understand.

Frequently asked questions

Reference

Ascanelli S, Bombardini C, Chimisso L, et al. Trans-anal irrigation in patients with multiple sclerosis: Efficacy in treating disease-related bowel dysfunctions and impact on the gut microbiota: A monocentric prospective study. Multiple Sclerosis Journal—Experimental, Translational and Clinical. 2022;8(3). doi:10.1177/20552173221109771.