Do Antibiotics Cause Constipation?

Do Antibiotics Cause Constipation

Research has clearly established that antibiotics can cause significant shifts in the composition of the gut microbiome that are similar to those observed in constipation-dominant irritable bowel syndrome (IBS-C). The question as to whether antibiotics cause constipation is further supported by evidence from both cohort and case-control studies, demonstrating that antibiotic treatment is associated with an increased risk of IBS (without specifying the subtype).

The 3 Types Of Constipation

Let’s dive into this question in more detail, starting by differentiating the types of constipation.      

Functional constipation is typically categorised into:

1. Normal transit constipation.

2. Slow transit constipation.

3. Defecatory or rectal evacuation disorders.

Until recently, constipation was studied in terms of gut function, for example, transit time (or how quickly food travels through the digestive system). However, more recent research has been investigating, and revealing, that imbalances in the gut microbiome can be detected in constipated patients compared with healthy controls.

A Common Cause Of Constipation: Dysynergia

Dysynergia is a rectal evacuation disorder – so an example of the third type of constipation from above. 

This type of constipation is caused by pelvic floor dyssynergia (which is a disturbance in muscular coordination, resulting in uncoordinated movements) as well as reduced intra-abdominal pressure (the act of bearing down), rectal sensory perception, and rectal contraction.

This all demonstrates that this type of constipation is not related to the gut microbiome and, therefore, will not be caused or successfully treated by antibiotics. 

Research has theorised this is a behavioural issue – perhaps learned during potty training. However, consider our societal relationship with pooing. I know many people who don’t feel comfortable going for a poo in public toilets, at work, or at friends houses. When we resist the urge to poo, we are conditioning ourselves to not poo, meaning we may develop a rectal sensory perception issue!

I have spoken previously about how I feel this contributed to my constipation and the health issues that came with it. After an extremely embarrassing experience when I was five years old at school, I refused to go for a poo at school. This naturally would lead to issues around constipation. With chronic constipation may come issues with the microbiome and liver also.

The Majority Of Constipation Types Are Associated With The Gut Microbiome

In contrast, normal transit constipation and slow transit constipation are associated with the gut microbiome. 

Let’s look at the evidence here. 

The Gut Microbiome in Constipation

To help answer the question of whether antibiotics can cause constipation, let’s look at what the evidence says about the microbiome and constipation. Here are some common themes and highlights:  

  • One study that compared healthy volunteers with patients diagnosed with constipation found that, compared with healthy subjects, patients with constipation had a lower level of Actinobacteria, including Bifidobacteria. (source)
  • In another study, the researchers found that those with constipation had reduced levels of Bifidobacterium, Lactobacillus, Bacteroides, and Clostridium species and an increased level of Enterobacteriaceae, such as Escherichia coli, as well as Staphylococcus aureus and fungi. (source)
  • In another study, patients with functional constipation had significantly lower levels of Bacteroidetes, in particular Prevotella, and an increased level of several species of Firmicutes, including Lactobacillus. Although Bifidobacteria species were not reduced. (source)
  • Finally, another study found that patients with constipation had significantly lower levels of Bifidobacterium and Bacteroides (source).

“These studies suggest that compared with healthy subjects, IBS-C patients have a lower level of Actinobacteria, including Bifidobacteria, in their fecal samples” (source)

So, it seems that the research is a little inconsistent, and the verdict is that currently, no consensus exists. But it is clear there is a trend to low levels of certain bacteria such as bifidobacteria. 

Gut Microbiome Metabolites And Constipation

Before we move on to how antibiotics might shape the microbiome, it is important to acknowledge that it’s not just about the amount of bacteria present but what they are doing. So, let’s look at some research that has looked into this in the context of constipation.

GLP-1 & Constipation:

Short-chain fatty acids, secondary bile acids, and the metabolite indole, produced by certain bacteria in the gut, including Clostridium, Bacteroides, and Ruminococcus, stimulate a specific type of cell found on the gut wall, called intestinal L-cells, to secrete GLP-1. 

GLP-1 reduces post-meal motility in the upper gut and decreased colonic transit time. One study found decreased levels of GLP-1 in patients with constipation. The authors of the study suggested that decreased levels of GLP-1 may reduce its prokinetic effects in the large intestine, resulting in constipation.

Serotonin & Constipation:

Secondary bile acids and short-chain fatty acids also promote serotonin synthesis from specialised cells called enterochromaffin cells. You’re likely familiar with serotonin – it’s an important neurotransmitter known for influencing mood. But among its other functions, it also regulates gut motility. Serotonin levels were found to be increased in those with diarrhoea-predominant IBS and reduced in those with constipation dominant IBS.

Do Antibiotics Cause Constipation? The Effects Of Antibiotics On The Microbiome

So, we know that constipation can be caused by changes to the gut microbiome. Now, let’s look at how antibiotics contribute to changes in the gut microbiome, namely through reduced diversity, composition changes, and reduced metabolic function.

First, it’s important to acknowledge the inconsistency in the results of various studies. This can be attributed to substantial variety in participant characteristics (age, ethnicity, diet, etc.) as well as study methodology. Also, there is variety within antibiotics, such as their class, pharmacokinetics (absorption and excretion), range of action, and dose used. These have all been shown in the research to influence the response of the gut microbiome to the antibiotic taken.

Microbiome Diversity & Changed Composition

Antibiotic use is associated with reduced microbiome diversity – thought to be one of the most important elements of a healthy gut. Research has shown that the administration of a combination of antibiotics (meropenem, gentamicin, and vancomycin) resulted in an increase in the prevalence of Enterobacteriaceae and other pathobionts and a decrease in Bifidobacterium and butyrate-producing species. (source) These have been discussed throughout this blog as being detected low in patients with constipation! There is plenty of additional evidence that demonstrates how bifidobacteria are highly susceptible to most antibiotics (source)

While the gut microbiome was mostly restored after 1.5 months of the antibiotic treatment, several common species of bacteria remained undetectable after 180 days!! (source)

Finally, in a recent systematic review, the authors of the paper took data from 129 studies on the effect of antibiotics on the composition of the gut microbiome. They concluded that the majority of antibiotics increase the abundance of Enterobacteriaceae, mainly Citrobacter spp., Enterobacter spp., and Klebsiella spp. 

These bacteria contain molecules that directly enhance the inflammatory response of the host.

Reduced Metabolic Function of The Microbiome After Antibiotics

We mentioned earlier that certain bacteria produce metabolites such as serotonin that can be helpful in maintaining regular bowel movements. Well, research has found that some antibiotics can deplete the gut of some of these key bacteria (source). This then negatively affects gut motility and may result in constipation. 

Considerations To Improve Constipation

In most randomised controlled and parallel-group trials, probiotics, prebiotics, synbiotics, antibiotics, and FMT therapy for chronic constipation were effective with few side effects.

Prebiotics: Lactulose

Research has demonstrated that lactulose, an indigestible carbohydrate, is as effective as the laxative polyethylene glycol in improving constipation. The researchers in one study also examined poo samples of patients taking lactulose and detected a significant increase in the level of Bifidobacteria. As mentioned, these are the bacteria often found to be low in those with constipation. (source)

Does lactulose sound familiar? That might be because it can be in the solution you drink before completing a SIBO breath test!

Prebiotics: PHGG

In one study (there are others), participants who had been diagnosed with constipation took a four-week course of PHGG. It was found to improve colon transit time, especially in those with slow transit. As a result, it improved many of the participants’ symptoms, including frequency of bowel movements (source).


“single-strain probiotic studies seem to have more effect on defecation frequency, stool consistency, and constipation-related symptoms, compared to multistrain probiotic studies.” (source)

With this in mind, let’s look at the two most evidenced strains.

B. lactis HN019 has evidence behind it for constipation. It has various ways it may help, including via the exclusion of potential pathogens. Furthermore, B. lactis HN019 has also been shown to reduce intestinal transit time and increased bowel movement frequency in functional constipation. It is thought to do this via two mechanisms: (1) modulating the gut–brain–microbiome axis via serotonin and (2) through the production of short-chain fatty acids derived from the fermentation of dietary fiber. 

B. lactis HN019™ is thus a probiotic that can contribute to relieving gut dysmotility related disorde (source)

In another study looking at L. casei Shirota, the researchers found that, in constipated patients, the probiotic significantly improved defecation frequency (from 4.81 to 7.81 times per week), stool consistency, and constipation-related symptoms. (source)


Synbiotics are a mixture of probiotics and prebiotics. In one study, the researchers administered either the synbiotic or maltodextrin as a placebo for 8 weeks. The researchers demonstrated that patients receiving the synbiotic had a significant improvement in defecation frequency and also in stool consistency. Not surprisingly, colonic transit time significantly reduced in the synbiotic group – transit time influences stool consistency and also microbiome composition and diversity. (source)

Fecal Microbiota Transplants

Leaving the least accessible to last!

Research has demonstrated that fecal microbiota transplants may be helpful in improving constipation also. In one study, on 4 patients with chronic constipation, immediate improvements in symptoms were experienced. This included improvements in abdominal pain, early satiety, and nausea, as well as a significant improvement in defecation frequency to once or twice daily. (source)

In another case report of a patient with treatment-resistant constipation, it was demonstrated that fecal microbiota transplant effectively induced defecation 2–3 days after the transplant, with a defecation frequency of once or twice daily. (source)


So it seems we don’t have direct evidence if antibiotics cause constipation, but I know through 15 years of working in a clinic and seeing countless reports online that, yes, it happens. I have done my best to demonstrate some of the links that we are aware of – both changes to the composition of the microbiome but also to the metabolic function of the microbiome (i.e., what the bacteria are producing or not producing). I hope it’s helped!


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