Antibiotics and Depression: Exploring the Gut Connection

21 January 2025, by SANUSq Research team
13 min reading time

Sad young woman sitting on a sofa with scattered white pills on the table in front of her

Antibiotics are among the most valuable medicines ever developed, and used well they save lives. But while they clear the bacteria behind an infection, they also disturb the trillions of helpful microbes living in your gut, and researchers are now asking what that might mean for mood. Here is what we know about antibiotics and depression, what we don't know yet, and how to look after your gut along the way.

Written by SANUSq Research Team | Medically reviewed by Dr Ajay Kumar, MD
Published: 21 January 2025 | Updated: 21 January 2025

What antibiotics do to your gut

Your digestive tract is home to a vast community of micro-organisms, known as the gut microbiota. These microbes help digest food and play a part in the normal workings of the immune system.

Antibiotics can't tell friend from foe. In targeting the bacteria causing an infection, they also knock back some of the beneficial species, temporarily shifting the balance of the whole ecosystem. This is called dysbiosis. One of the clearest changes is a drop in diversity, the number and variety of species present.

The encouraging news is that the gut is resilient. In most people, diversity returns to something close to its starting point within weeks. In others, a few species take months to come back, or don't fully return. Age, diet, the type of antibiotic and the number of courses all seem to influence how quickly things settle.

Palleja et al. (2018) followed 12 healthy young men for six months after a four-day course of three broad-spectrum antibiotics. Their gut microbiota recovered to near its original composition within about 1.5 months, but nine common species were still undetectable in most of the men after 180 days. The authors described a mild but long-lasting imprint alongside overall resilience.

The gut–brain axis: how your gut talks to your brain

Your gut and your brain are in constant two-way conversation, through nerves, hormones and the immune system. Researchers call this network the gut–brain axis. A growing body of work suggests that gut bacteria take part in that conversation, and may influence anxiety, mood and thinking.

The traffic runs both ways: stress can change the make-up of the gut microbiota, too.

In an influential review, Cryan and Dinan (2012) described accumulating evidence that the gut microbiota communicates with the central nervous system, possibly through neural, endocrine and immune pathways. Studies in germ-free animals, and in animals given probiotic bacteria or antibiotics, suggested a role for gut microbes in anxiety, mood, cognition and pain.

Much of this foundational work was done in animals, and people are far more complicated.

Foster and McVey Neufeld (2013) reviewed findings showing that gut bacteria, whether commensal, probiotic or disease-causing, can activate neural pathways and signalling systems in the central nervous system. They concluded that animal and clinical research into the microbiota–gut–brain axis may, in future, open new approaches to anxiety and depression, framing it as a direction for research rather than an established treatment.

Gut bacteria and depression: the possible pathways

Researchers have identified several routes by which the gut could, in principle, influence mood:

The vagus nerve. This long nerve runs from the brainstem to the abdomen and carries signals from the gut to the brain.
Messenger molecules. Most of the body's serotonin is made in the lining of the gut, and gut bacteria help regulate how much is produced. Gut serotonin doesn't enter the brain directly, though.
Fermentation products. When gut bacteria ferment fibre, they produce short-chain fatty acids such as butyrate, which are being studied for their effects on the gut lining, inflammation and signalling.
The immune system. A large share of the immune system sits around the gut. An imbalanced microbiota may contribute to low-grade inflammation, which has been associated with low mood.

Yano et al. (2015) showed, mainly in mice, that spore-forming bacteria from the mouse and human gut promote serotonin production by specialised cells in the colon.

Human studies are starting to fill in the picture, though they mostly show associations.

In a population study of more than 1,000 people in Belgium Valles-Colomer et al. (2019) found that butyrate-producing Faecalibacterium and Coprococcus bacteria were linked to higher quality-of-life scores, and that Coprococcus and Dialister were depleted in people with depression, even after accounting for antidepressant use. The authors emphasised the importance of confounding factors.

Describing a mechanism is not the same as measuring how much it matters. In people, the real weight of the gut in depression has not been established.

Antibiotics and depression: what the studies show

The most widely quoted finding comes from a large study using UK medical records.

Lurie et al. (2015) compared over 200,000 people diagnosed with depression with more than 800,000 matched controls. A single antibiotic course was associated with a higher risk of depression (around 23–25% higher for penicillins and quinolones), and the association grew with repeated courses: about 56% higher after more than five courses of penicillin. A similar pattern was seen for anxiety, but not for psychosis.

It's an interesting signal, but read it carefully.

Association is not causation. Studies like this can show that two things tend to occur together. They can't prove that one causes the other.
The infection itself may explain part of it. People who take many courses of antibiotics are, by definition, people who get ill often. Infection, inflammation and the stress of being unwell can all affect mood in their own right.
The overall evidence is limited. Most studies are observational, and they vary in quality and design.

A large Danish study of more than one million children and adolescents by Köhler-Forsberg et al. (2019) found that treated infections were associated with a higher later risk of mental disorders, with particularly high estimates for antibiotic use. The authors noted that the results cannot prove causality, and interpreted them as evidence for the involvement of infections and the immune system.

A systematic review by Pouranayatihosseinabad et al. (2023) found nine eligible studies, all observational and of relatively low quality. Together they suggested a potential association between antibiotic exposure and later depressive symptoms, but the authors concluded that methodological limits make a reliable conclusion difficult.

So the link is plausible and worth studying, but far from established.

Who might be more affected?

Not everyone starts from the same place. In the research, it is mainly repeated exposure that stands out: one justified course carries less weight than course after course, year after year.

Early life gets particular attention, because the gut microbiota is still taking shape in the first years. Your starting microbiota, diet and lifestyle also seem to shape how well your gut copes and recovers.

What about probiotics and "psychobiotics"?

The idea that gut microbes might influence mood has given rise to the term "psychobiotics": probiotics and prebiotics studied for possible effects on mood through the gut. Early results, largely from animal research and small human studies, are intriguing, but they are some way from a clinical recommendation.

A meta-analysis of 34 controlled trials by Liu et al. (2019) found that prebiotics did not differ from placebo for depression or anxiety. Probiotics showed small but significant effects on depressive symptoms, larger in clinical samples, but the authors noted that few trials involved people with diagnosed psychiatric conditions and called for more randomised trials.

Effects so far are small and strain-dependent. Probiotics are not a substitute for treatment for depression, and they should never replace antidepressants or talking therapy your doctor has recommended. If you're considering one during or after a course of antibiotics, ask your GP or pharmacist about timing and whether it suits you.

Should you worry about taking antibiotics?

The message here is not to avoid or stop antibiotics. When a doctor prescribes them, it is because you need them, and stopping early on your own can make an infection worse and encourage resistance. Take them exactly as prescribed and finish the course as directed.

The real issue is sensible use. Antibiotics should only be taken on prescription, for a bacterial infection, and never "just in case" or for a virus such as a cold or flu, against which they don't work. The best way to protect your gut is to avoid unnecessary antibiotics, not the ones you need. It also helps slow antibiotic resistance.

How to support your gut microbiota day to day

Your gut flora is resilient, and everyday habits help it recover. A few simple steps make a difference:

Varied fibre. Vegetables, pulses, fruit and wholegrains feed beneficial bacteria.
Fermented foods. Live yoghurt, kefir and unpasteurised sauerkraut provide live micro-organisms.
Less ultra-processed food and sugar, which tend to be linked with lower microbial diversity.
Sleep, movement and stress management, which also influence the gut through the gut–brain axis.
Time. Diversity rebuilds over weeks, not days, and consistency matters more than intensity.

None of this needs to be perfect. A well-fed, varied gut is a more resilient one.

When to talk to someone

If your mood stays low for more than a couple of weeks after a course of antibiotics, or at any other time, you don't have to deal with it alone. Speak to your GP, who can look at the whole picture and talk you through the options.

If you are on antidepressants, don't stop or change them without talking to your doctor, and let your prescriber know about any other medicines or supplements you take.

If you ever feel unable to keep yourself safe, or are having thoughts of suicide, call your local emergency number or a crisis line straight away. In the UK and Ireland, Samaritans are available day and night on 116 123.

The bottom line

Large observational studies link repeated antibiotic use with a higher risk of depression, but association isn't proof, infections may explain part of the link, and gut–mood research in humans is early. Take antibiotics when they're prescribed and as directed, look after your gut with fibre, fermented foods and good daily habits, and talk to your GP if your mood is low.

Frequently asked questions

Can antibiotics cause depression?

No study has shown that they do. Large observational studies have found an association between repeated antibiotic courses and a higher risk of depression or anxiety, but the underlying infections and other factors may explain some or all of that link. It is a lead worth investigating, not proof.

Should I stop my antibiotics if I feel low?

No. Never stop antibiotics on your own: an unfinished course can make an infection worse and encourage resistance. Tell your doctor or pharmacist how you're feeling. In a crisis, call your local emergency number or Samaritans on 116 123 (UK and Ireland).

How can I help my gut recover after antibiotics?

Eat varied fibre, include fermented foods, cut back on ultra-processed foods and look after your sleep. In most people the gut flora recovers by itself over time.

Do probiotics help during a course of antibiotics?

The evidence is mixed and depends on the strain. It's worth discussing with your GP or pharmacist, including when to take a probiotic relative to your antibiotic doses.

How long does gut bacteria take to recover after antibiotics?

In many healthy adults, the gut microbiota returns close to its original state within about six weeks after a short course, although a few species can take longer or not fully return. After repeated or prolonged courses, recovery may be slower and less complete.

References

Lurie I, Yang YX, Haynes K, Mamtani R, Boursi B. Antibiotic exposure and the risk for depression, anxiety, or psychosis: a nested case-control study. Journal of Clinical Psychiatry. 2015;76(11):1522–1528. PMID 26580313
Cryan JF, Dinan TG. Mind-altering microorganisms: the impact of the gut microbiota on brain and behaviour. Nature Reviews Neuroscience. 2012;13(10):701–712. PMID 22968153
Foster JA, McVey Neufeld KA. Gut-brain axis: how the microbiome influences anxiety and depression. Trends in Neurosciences. 2013;36(5):305–312. PMID 23384445
Palleja A, Mikkelsen KH, Forslund SK, et al. Recovery of gut microbiota of healthy adults following antibiotic exposure. Nature Microbiology. 2018;3(11):1255–1265. PMID 30349083
Yano JM, Yu K, Donaldson GP, et al. Indigenous bacteria from the gut microbiota regulate host serotonin biosynthesis. Cell. 2015;161(2):264–276. PMID 25860609
Valles-Colomer M, Falony G, Darzi Y, et al. The neuroactive potential of the human gut microbiota in quality of life and depression. Nature Microbiology. 2019;4(4):623–632. PMID 30718848
Köhler-Forsberg O, Petersen L, Gasse C, et al. A nationwide study in Denmark of the association between treated infections and the subsequent risk of treated mental disorders in children and adolescents. JAMA Psychiatry. 2019;76(3):271–279. PMID 30516814
Pouranayatihosseinabad M, Bezabih Y, Hawrelak J, et al. Antibiotic use and the development of depression: a systematic review. Journal of Psychosomatic Research. 2023;164:111113. PMID 36502554
Liu RT, Walsh RFL, Sheehan AE. Prebiotics and probiotics for depression and anxiety: a systematic review and meta-analysis of controlled clinical trials. Neuroscience and Biobehavioral Reviews. 2019;102:13–23. PMID 31004628

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