Does Bowel Irrigation Really “Wash Away the Good Bacteria”? What a Human Microbiome Study Found

Written by

Emma Child

Manager, Trainer and Therapist

One of the most common concerns about bowel irrigation is that introducing water into the bowel will “wash away the good bacteria” and leave the gut microbiome depleted. It sounds logical—but what happens when researchers actually measure the bowel irrigation gut microbiome before and after months of regular use?

A small 2021 human study provides a fascinating early answer. Researchers followed children and adolescents with spina bifida who used transanal irrigation every second day for three months. Instead of finding a microbiome that had simply been stripped of beneficial organisms, they found changes in bacterial composition—including an increase in Roseburia, a group of bacteria associated with the production of butyrate.

The findings do not prove that all forms of bowel irrigation improve the microbiome. They also cannot be directly applied to professional colon hydrotherapy. But they do challenge the idea that water-based bowel irrigation inevitably “washes away” beneficial bacteria.

Why people worry about losing “good bacteria”

The concern is easy to understand. If water helps evacuate material from the colon, it may seem as though the bacterial community living there must be flushed away with it.

But the gut microbiome is not a loose pile of bacteria sitting in one place. Microorganisms interact with food residue, mucus, the bowel environment and one another. Stool contains bacterial DNA and provides a useful window into the gut ecosystem, but a faecal sample is not a complete census of every organism associated with the bowel.

It is also important to distinguish between bacterial quantity and bacterial composition. A study can show that the relative proportion of certain groups increased or decreased without telling us the total number of bacteria present.

That distinction is central to understanding what this study did—and did not—find.

The 2021 human microbiome study

Furuta and colleagues studied children and adolescents aged 6–17 with spina bifida, a condition that can affect the nerves responsible for bowel and bladder function.

The initial comparison included 16 participants with spina bifida and 10 healthy children of similar age and sex. Eleven of the participants with spina bifida had intractable constipation and moderate-to-severe neurogenic bowel dysfunction, and these 11 entered the three-month transanal-irrigation phase.

This was not an occasional intervention. The participants irrigated every second day for three months, making the study particularly relevant to the concern that repeated bowel irrigation might progressively remove beneficial bacteria.

What is transanal irrigation?

Transanal irrigation is a bowel-management technique in which water is introduced through the rectum using a catheter or cone system to support evacuation of retained stool. It may be used in selected people with neurogenic bowel dysfunction or difficult-to-manage constipation under appropriate clinical guidance.

Peristeen® transanal irrigation is not the same treatment as professional colon hydrotherapy. The equipment, water delivery, treatment protocols, clinical setting and intended patient population differ.

There is, however, a relevant mechanistic similarity: both involve the controlled introduction of water through the rectum, followed by evacuation of bowel contents. That makes the study useful to the broader conversation about irrigation and gut bacteria—but it does not allow its findings to be automatically transferred to Rojas Colon Hydrotherapy®.

How the researchers analysed the gut microbiome

The researchers collected faecal samples before and after the three-month intervention and used 16S rRNA gene sequencing. This technique identifies bacterial groups through characteristic genetic sequences and allows researchers to compare their relative abundance within samples.

Participants were not permitted to introduce new probiotics, prebiotics, antibiotics, dietary modifications or constipation medications during the study. This was intended to reduce some of the outside influences that can alter the gut microbiome.

The team also measured bowel function using the Bristol Stool Scale and a neurogenic bowel dysfunction score. Urine cultures were collected because urinary-tract concerns are common in people with spina bifida and neurogenic bladder.

The microbiome was already different before irrigation

Before transanal irrigation began, the children with spina bifida already showed differences in their faecal microbiota compared with the healthy control group.

At genus level, they had significantly lower relative abundance of:

• Faecalibacterium
• Blautia
• Roseburia
• Lachnospira
• Dialister

They also had a higher relative abundance of Oscillospira. At the broader phylum level, the researchers did not identify significant differences between the spina bifida and control groups.

This matters because it shows that the participants did not begin with a microbiome identical to the healthy controls. Their neurological condition, constipation, intestinal motility and other clinical factors may already have influenced the bacterial ecosystem.

What changed after three months of regular irrigation?

After three months of irrigation every second day, the microbiome had changed—but the pattern was not one of simple depletion.

Roseburia is of particular interest because members of this genus can produce butyrate, a short-chain fatty acid involved in colon-cell metabolism and the wider intestinal environment. The study also found a positive correlation between the relative abundance of Roseburia and Bristol Stool Scale scores.

These findings do not establish that irrigation directly created a “healthier microbiome.” The changes might relate to improved stool consistency, altered transit, changes in retained stool or other features of the bowel environment. What they show is that repeated irrigation was accompanied by a shift in microbial composition—not a demonstrated collapse of beneficial bacteria.

Did irrigation reduce urinary tract infections?

The proportion of participants with asymptomatic bacteriuria described by the authors as urinary tract infection decreased from 82% before irrigation to 55% afterwards.

The study also reported that faecal incontinence persisted. This reinforces why individual outcomes must be discussed carefully rather than presented as universal benefits.

So, does bowel irrigation wash away good bacteria?

This study did not find evidence of a microbiome simply stripped of beneficial bacteria after three months of regular transanal irrigation. Instead, it found compositional changes, including an increase in the butyrate-associated genus Roseburia.

However, the strongest scientifically accurate answer is:

The study challenges the “wash away all the good bacteria” assumption, but it does not prove that bowel irrigation has no effect on total bacterial load or that every microbiome change is beneficial.

The researchers measured the relative abundance of bacterial groups in faecal samples. They did not measure the absolute number of bacteria before and after irrigation, directly sample mucosa-associated communities, assess microbial function in detail or measure short-chain fatty acids such as butyrate.

In other words, this was a study of how the visible bacterial pattern changed—not a complete audit of every bacterium or microbial function in the colon.

Important limitations of the study

This research is valuable because it examined humans over three months, but it remains an early, exploratory study. Its key limitations include:

• Very small treatment group: only 11 participants received transanal irrigation.
• Highly specific population: all participants were children or adolescents with spina bifida and neurogenic bowel dysfunction.
• No untreated treatment-phase control: the study did not randomise participants to irrigation versus no irrigation for the three-month period.
• No direct comparison with colon hydrotherapy: Peristeen® transanal irrigation and professional Rojas Colon Hydrotherapy® are different interventions.
• Relative rather than absolute measurement: 16S sequencing described bacterial composition but did not quantify the total bacterial population.
• No metabolite analysis: the researchers did not measure short-chain fatty acids or directly demonstrate changes in microbial activity.
• Funding disclosure: Coloplast Japan, the manufacturer associated with the irrigation system, supported the cost of microbiome sequencing. The paper states that the company had no influence on study design, analysis or interpretation.

These limitations do not make the study meaningless. They define the boundaries of what can responsibly be concluded.

What this research means for colon hydrotherapy

It would be inaccurate to say that this study proves Rojas Colon Hydrotherapy® improves the gut microbiome. It did not test the Rojas Technique, professional colon hydrotherapy or a general wellness population.

What it contributes is a human observation that challenges an overly simple narrative: regular water-based bowel irrigation did not merely correspond with the disappearance of “good bacteria.” The microbial community changed, and at least one bacterial genus commonly discussed in relation to butyrate production increased.

For clinicians and health professionals, the study supports a more precise question than “does irrigation remove bacteria?” Future research should ask which organisms change, whether absolute bacterial load changes, how quickly the microbiome responds, what functions are affected, whether changes persist and how results differ between irrigation techniques and patient populations.

You can explore the broader evidence in our article, What a New Scientific Review Says About Colon Hydrotherapy, or read What Is Colon Hydrotherapy? A Complete Beginner’s Guide.

The bottom line

The claim that bowel irrigation inevitably “washes away the good bacteria” is not supported by this human study. After three months of transanal irrigation every second day, the researchers observed a changed microbiome rather than a simply depleted one. Roseburia and Bacteroides increased, while measured bowel-function outcomes improved.

That is encouraging and scientifically interesting—but it is not the final answer. The study was small, involved a specialised paediatric population and examined a different intervention from colon hydrotherapy. Larger, independent studies measuring bacterial quantity, composition, metabolites and longer-term outcomes are still needed.

The most responsible conclusion is neither fear nor overstatement. It is that the relationship between bowel irrigation and the gut microbiome appears more complex—and potentially more adaptive—than the phrase “washing away good bacteria” suggests.

Frequently asked questions

Does bowel irrigation remove gut bacteria?

Bacteria are present in evacuated bowel contents, but this study did not show that regular transanal irrigation simply depleted the gut microbiome. It found changes in relative bacterial composition, including increases in Roseburia and Bacteroides. It did not measure the total number of bacteria.

Did good bacteria increase after transanal irrigation?

The relative abundance of Roseburia, a genus associated with butyrate production, increased significantly after three months. Calling any bacterial group universally “good” can be an oversimplification because microbial effects depend on species, function, abundance and the wider gut environment.

Is transanal irrigation the same as colon hydrotherapy?

No. They both involve water introduced through the rectum, but the devices, protocols, water delivery, treatment settings and intended uses differ. Results from transanal irrigation cannot automatically be applied to Rojas Colon Hydrotherapy®.

Does this study prove colon hydrotherapy improves the microbiome?

No. The study examined Peristeen® transanal irrigation in 11 children with spina bifida and neurogenic bowel dysfunction. It did not study colon hydrotherapy, adults seeking general wellness support or the Rojas Technique.

Was the study independent?

The research was conducted by an academic clinical team. Coloplast Japan supported the cost of the 16S rRNA microbiome sequencing. The authors reported that the company had no influence on study design, data analysis or interpretation.

Reference

1. Furuta A, Suzuki Y, Takahashi R, et al. Effects of Transanal Irrigation on Gut Microbiota in Pediatric Patients with Spina Bifida. Journal of Clinical Medicine. 2021;10(2):224. doi:10.3390/jcm10020224.