How To Recover From Antibiotics

  • 1st Revision: Tan Jit Yih

Understanding antibiotics

Antibiotics are medicines that allow humans to fight and kill pathogenic bacteria in humans.6 Considering that every surface in the world that we  come in contact with is covered with various types of microorganisms, such as bacteria and viruses, it is very important for us to have a measure of regulating and controlling those microorganisms that cause disease in humans.

Antibiotics are fairly recent medicinal compounds that allow us to either kill disease-causing (pathogenic) bacteria or restrict the efficiency with which these microorganisms multiply in the human body. These medicines are very important for us to treat bacteria-causing diseases and prevent associated deaths and complications, and it is also critical for sterilisation procedures that allow us to perform advanced surgeries safely.6

Why do we need antibiotics?

Antibiotics treat infectious diseases caused by bacteria, such as Strep throat or Urinary tract Infections (UTI).2 However, not all bacterial infections have to be treated with antibiotics since some infections tend to resolve better on their own, and use of antibiotics is often associated with unpleasant side-effects. Another important complication is related to antibiotic resistance, which is the ability of the bacteria to evolve and acquire qualities that enable it to become less sensitive to the effects of the antibiotic.1,15

If antibiotics are the best treatment option, certain rules15must be followed: 

  • Antibiotics must be taken exactly as prescribed (dosage, timing, length of the course)
  • Prescribed antibiotics must not be shared with others
  • Leftover antibiotics must be handled responsibly and medicines discarded safely
  • After finishing the course, a recovery period must follow
  • Patients must always address their uncertainties and side-effects with their doctor and pharmacist

Types of antibiotics 

There are various different forms of antibiotics.3

The differentiation is based on the range of bacteria the drug targets: broad-spectrum antibiotics target a wide range of bacteria,  while narrow-spectrum antibiotics target restricted types of bacteria.3 Broad-spectrum antimicrobials are particularly important to treat cases when disease-causing pathogenic bacteria cannot be precisely identified. While it allows the treatment of unknown infection, it often comes at the cost of having more associated adverse effects. Usually those affect gut health, associated with severe depletion of gut microbial diversity, particularly Bifidobacterium, that have protective beneficial effects. In the absence of healthy gut bacteria that resist colonisation of opportunistic pathogens, there is multiplication of opportunistic bacteria, such as Clostridium difficile, which often is a cause of antibiotic-associated diarrhoea (AAD). In juvenile patients, antibiotic use has also been linked to an increased risk of asthma and weight gain. 

Pharmacological effects of antibiotics against the microorganisms include the destruction of bacteria or diminishing the ability of bacteria to multiply within the human. Antimicrobial agents are classified based on their effect on bacteria: bactericidal and bacteriostatic antibiotics are bacteria killing and growth preventing  antibiotics respectively.3

Drug classes


  • Glycylcyclines: broad-spectrum antibiotics, derivatives of tetracyclines
  • Tetracyclines: broad-spectrum antibiotics, used against a variety of bacteria-induced acne, sexually transmitted diseases (STDs), urinary tract infections (UTIs), intestinal tract infections etc
  • Lincosamides:  wide spectrum antibiotics acting against Gram-positive bacteria
  • Macrolides: broad-spectrum of activity against a variety of Gram-positive bacteria
  • Oxazolidinones: broad-spectrum antibiotic chemotherapeutics effective against Gram-positive bacteria. Particular drugs show effectiveness against resistant species
  • Sulfonamides: broad-spectrum antimicrobials that suppress the growth of both Gram-positive and Gram-negative bacteria


  • Beta-lactams (penicillins, cephalosporins, carbapenems):  narrow-spectrum antimicrobials active against many Gram-positive, Gram-negative and anaerobic bacterial species
  • Aminoglycosides: broad-spectrum beta-lactam antibiotics that act against Gram-negative bacillary species
  • Fluoroquinolones: broad-spectrum antibiotics used widely implemented as therapy against a wide range of aerobic Gram-positive and Gram-negative bacteria
  • Glycopeptides: broad-spectrum drugs effective against Gram-positive bacteria, including several resistant strains
  • Cyclic Lipopeptides: naturally-occurring products with antibiotic properties, effective against Gram-positive bacteria
  • Nitroimidazoles: remarkably broad spectrum antibiotics with  activity against various parasites, mycobacteria, and anaerobic Gram-positive and Gram-negative bacteria

Where can we get antibiotics?

It is important to take antibiotics when it is advised to do so by a healthcare professional. Antibiotics should be only prescribed when absolutely necessary and the course of antibiotics must be completely finished. Unnecessary use of antibiotics will not only be ineffective to treating the disease, but can also cause harm by the drug's adverse effects. 

Effects of antibiotics in our body

With no doubt the use of antibiotics has dramatically changed the way that humans live now. It has been established that prevention of microbial infections by antibiotic use has contributed to a 15 year increase in average length of life. However, along with a plethora of beneficial effects, there are inevitable occurrences of unwanted side effects associated with their use.

Short term/long term side effects

A wide spectrum of side effects from antibiotic use have been previously recorded, including:  immune-mediated response or hypersensitivity to the drug, defined as allergy; reduced metabolism and malabsorption of the medicine that leads to critically high levels of the drug in the system; impaired absorption of essential vitamins and minerals; colonisation by resistant organisms; and elevated susceptibility to secondary yeast infections. 

Short-term side effects occur immediately after administration of antibiotic drugs and often present as the occurrence of antibiotic-associated diarrhoea (AAD), electrolyte disbalance (such as, hypokalemia, hypoglycemia), drug-induced fever andmicrobiotic alterations of microbial flora of the patients (causing increased likelihood of developing subsequent diseases and symptoms).8,14 More severe complications include hepatotoxicity, myopathy andinflammation of the colon (colitis), which are more dangerous for certain patients under a higher risk of comorbidities, for instance the elderly. Adverse effects must always be anticipated prior to the beginning of antimicrobial therapy.14

A high proportion of these effects are linked to changes in microbial species colonising the host (i.e, the patient). Collectively, microbiota is formed by all microbial species, such as bacteria, fungi andviruses that colonise various parts of the human body, such as the oral and nasal cavities, the gut and urogenital tracts, skin surfaces, etc.5

Normally, microbiota has an important function in human health as it acts as a natural barrier from pathogens, contributes to certain metabolic functions, and regulates the immune system by controlling inflammatory response. Alterations of the microbiota, called dysbiosis, causes  impairment of natural individual immunity and is often associated with massive increased susceptibility to important human diseases such as inflammation-induced disorders, cardiovascular diseases and various types of cancer.

Similarly, certain severe infectious diseases require prolonged use of antibiotics, which can also result in significant alterations to the host microbiome. Recent studies have identified that long-term exposure to  antibiotic drugs can cause life-long changes in host microbiota, and predispose individuals to the emergence of cardiovascular disorders and all-cause premature death.7

The following table summarises the adverse effects of antibiotics on various organ systems.

Hematologic SystemThrombocytopenia Severe depletion of white blood cells Impaired platelet aggregation Anticoagulation (linked drug interactions)
Renal SystemInterstitial nephritis Renal failure

Dermatologic System
Skin irritations: rash, erythema multiforme, Stevens-Johnson syndrome, toxic epidermal necrolysis
Nervous SystemOtotoxicity Vestibular dysfunction Seizure Peripheral neuropathy
Cardiac System Cardiac curve changes: QT prolongation

Recovering from antibiotics after treatment

It has been established that improving gut health and re-establishing optimal gut microbiota is essential after finishing a course of antibiotics. Healthy gut microbiota is critical, since it has multiple arms of host protection against invading pathogens. Among these are production of antimicrobial compounds, outcompeting of non-beneficial pathogens for niche in the gut, maintenance of the protective mucus layer barrier that stops pathogens from invading intestinal cells and training the immune cells to produce a rapid and effective immune response to pathogens.3

Antibiotic-related depletion of resident gut microorganisms can severely affect these protective functions, thus providing an opportunity for pathogenic bacteria to colonise the gut. There is sufficient evidence from supporting clinical studies that probiotics during and after antibiotic use can significantly reduce secondary co-infection with opportunistic pathogens and associated development of antibiotic-induced diarrhoea.10

The limitations of the study include uncertainty regarding types of probiotics with highest efficacy levels. The study has identified a more rapid re-establishment of healthy-gut species and re-bounced microbiomes in individuals who have taken a combination of  probiotics with antibiotics, compared to those who took antibiotics alone. Moreover, numerous studies have highlighted that certain alterations in diet can have a dramatic impact on the human gut microbiome following a short-term macro nutrient change. 

Therefore, it appears that the introduction of certain food products is an effective measure to improve gut health and ensure re-appearance of beneficial resident microbial species after administration of antibiotics. Preferred foods include various foods rich in fibre and polyphenols such as fruits, vegetables, grains and nuts.4 Similarly, fermented food products are a great source of lactic acid bacteria  (LAB), which are highly beneficial for the maintenance of “good” bacteria and a healthy gut microbiome.11

How long does it take to recover from antibiotics?

Usually the process of recoverycan take some time as the duration of recovery is directly correlated to the length of antibiotic use. While it can take anywhere from 5 to 10 days after a short-term course, some studies have observed that in some cases the recovery can be significantly delayed (up to several months).8,12,14

Alternatively, these studies revealed that a single course of antibiotics can introduce lifelong changes in the composition of the host microbiome and lead to several complications. It is not unusual for recovery to take longer, without complete re-growth of all bacterial species even after 2-4 years following antibiotic use.12,14 Being considerate and taking important steps needed for re-establishment of the natural microbiome is highly important for overall health and prevention of various inflammatory-induced disorders.

When to seek medical attention

It is normal and anticipated to experience some unwanted adverse effects, often right after the administration of the antibiotics; however, if a patient experiences a critical onset of any side-effects/ allergies related to antibiotics use, it is very important to seek immediate professional help.

Critical emergencies are most commonly recorded among children that arrive in emergency departments with severe antibiotic-induced reactions.  

Common signs are highly versatile and vary from mild to critically severe.

Some symptoms can include:

  • Skin rash
  • Nausea
  • Acute episodes of loose watery bowel movements
  • Secondary yeast infections


In conclusion, antibiotics are life-saving therapeutics that can be applied when other traditional and topical treatments are failing. Not all bacterial infections must be treated with antibiotics, because of drug-related side effects and a phenomenon known as antibiotic resistance. Prescription of these drugs should never be pressured and benefits of the antimicrobial therapy should outweigh the risks. It is often the case that optimal treatment is non-antibiotic over-the-counter medication. 

However, in certain cases, use of antibiotics is essential and can reverse an otherwise lethal disease. After the fully finished course of antibiotic therapy, the immediate recovery steps must be taken. As numerous side-effects relate to dysbalance of normal microbiome, re-establishment of beneficial bacterial gut species is highly important to prevent serious complications and associated co-infections.


  1. Adedeji WA. The treasure is called antibiotics [Internet]. Annals of Ibadan postgraduate medicine. Association of Resident Doctors (ARD), University College Hospital, Ibadan; 2016 [cited 2022Oct14]. Available from:
  2. Antibiotic use questions and answers [Internet]. Centers for Disease Control and Prevention. Centers for Disease Control and Prevention; 2021 [cited 2022Oct14]. Available from:
  3. Calhoun C, Wermuth HR, Hall GA. Antibiotics - statpearls - NCBI bookshelf [Internet]. Antibiotics. [cited 2022Oct14]. Available from: 
  4. David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE, Wolfe BE, et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature. 2013;505(7484):559–63.
  5. Dethlefsen L, Huse S, Sogin ML, Relman DA. The pervasive effects of an antibiotic on the human gut microbiota, as revealed by Deep 16S rrna sequencing. PLoS Biology. 2008;6(11).
  6. GALLAGHER JASONC. Antibiotics simplified. SUDBURY: JONES & BARTLETT LEARNING; 2022.
  7. Heianza Y, Ma W, Li X, Cao Y, Chan AT, Rimm EB, et al. Duration and life-stage of antibiotic use and risks of all-cause and cause-specific mortality. Circulation Research. 2020;126(3):364–73.
  8. Jakobsson HE, Jernberg C, Andersson AF, Sjölund-Karlsson M, Jansson JK, Engstrand L. Short-term antibiotic treatment has differing long-term impacts on the human throat and Gut Microbiome. PLoS ONE. 2010;5(3).
  9. Jernberg C, Löfmark S, Edlund C, Jansson JK. Long-term ecological impacts of antibiotic administration on the human intestinal microbiota. The ISME Journal. 2007;1(1):56–66.
  10. Johnston BC, Ma SSY, Goldenberg JZ, Thorlund K, Vandvik PO, Loeb M, et al. Probiotics for the prevention of clostridium difficile–associated diarrhea. Annals of Internal Medicine. 2012;157(12):878.  
  11. GMFH Editing Team GMFH Editing Team. Lactic acid bacteria in fermented foods can be transferred to the human gut [Internet]. Gut Microbiota for Health. 2020 [cited 2022Oct14]. Available from: 
  12. Lofmark S, Jernberg C, Jansson JK, Edlund C. Clindamycin-induced enrichment and long-term persistence of resistant bacteroides spp. and resistance genes. Journal of Antimicrobial Chemotherapy. 2006;58(6):1160–7.
  13. Mary Ann E. Zagaria PD. Antibiotic therapy: Adverse effects and dosing considerations [Internet]. U.S. Pharmacist – The Leading Journal in Pharmacy. 2013 [cited 2022Oct14]. Available from:
  14. Meropol SB, Chan KA, Chen Z, Finkelstein JA, Hennessy S, Lautenbach E, et al. Adverse events associated with prolonged antibiotic use. Pharmacoepidemiology and Drug Safety. 2008;17(5):523–32.
  15. Using medication: Using antibiotics correctly - NCBI bookshelf [Internet]. [cited 2022Oct14]. Available from: 
This content is purely informational and isn’t medical guidance. It shouldn’t replace professional medical counsel. Always consult your physician regarding treatment risks and benefits. See our editorial standards for more details.

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Nafisa Djumaeva

Bachelor's degree, Applied Medical Science, UCL

Biomedical scientist with professional experience in health communications. Experienced in medical writing and account management, I am a believer that translation of most recent research and HCP/patient education drives improved quality of medical care.

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