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Antibiotics 101: What You Need To Know

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Antibiotics 101: What You Need To Know

Most people have been prescribed and taken an antibiotic at some point to treat an infection or illness. While antibiotics revolutionized medicine and the treatment of infectious disease, overuse and overprescription is becoming a global health problem. Due to the emergence of antibiotic resistance and concern for antibiotic-associated side effects, many are turning to natural medicine alternatives to support the immune system and treat bacterial infections. This article will discuss antibiotics, the potential side effects of their use, how to help the body when antibiotic therapy is indicated, and natural antibiotic agents that can be used instead of or in conjunction with prescription agents.


What Are Antibiotics?

Antibiotics are a class of medicine that fight bacterial infections in humans and animals. They work by either killing the bacteria or impairing bacterial growth and division. Antibiotics can only treat infections caused by bacterial pathogens. Common antibiotic-indicated infections include strep throat, urinary tract infections, many skin infections, ear infections, sinusitis, and bacterial pneumonia. Antibiotics are ineffective and should not be taken to treat viral, parasitic, and fungal infections. (1, 4)

There are many different types of antibiotics, which are subcategorized into classes based on their chemical structure and mechanism of action. Common antibiotic classes include penicillins, macrolides, cephalosporins, fluoroquinolones, beta-lactams, and tetracyclines.

How Do Antibiotics Work?

Antibiotics can be broadly divided into two groups based on how they treat bacterial infections. Bactericidal antibiotics directly kill bacteria, and bacteriostatic antibiotics suppress bacterial growth. (3)

There are five basic mechanisms of antibiotic action against bacteria:

Inhibition of Cell Wall Synthesis

Bacterial cells are surrounded by a cell wall made of peptidoglycans (a meshwork consisting of sugars and amino acids). Certain antibiotics, like beta-lactams, inhibit cell wall synthesis, leading to bacterial rupture and cell death. (2)

Inhibition of Protein Synthesis

Protein synthesis involves a process of DNA transcription to synthesize an RNA molecule called messenger RNA (mRNA). Then, a bacterial 70S ribosome structure synthesizes proteins from the information encoded in the mRNA in a process called translation. Antibiotics can inhibit bacterial protein synthesis by binding and inhibiting subunits of the bacterial ribosome. (2)

Alteration of Cell Membranes

Antibiotics that disrupt and alter the cellular plasma membrane cause rapid depolarization of the bacterial cell, which leads to inhibition of protein, DNA, and RNA synthesis and cell death. (2)

Inhibition of Nucleic Acid (DNA) Synthesis

Nucleic acid inhibitors work through various mechanisms to disrupt bacterial DNA synthesis and replication. For example, fluoroquinolones are a class of nucleic acid inhibitors that inhibit bacterial enzymes required for DNA replication. (2)

Antimetabolite Activity

Antimetabolites inhibit distinct steps in folic acid metabolism, ultimately disrupting bacterial DNA synthesis. (2)

How Do Antibiotics Affect the Body?

All medications have the potential to cause adverse reactions. Common side effects related to antibiotic use include (5, 6):

  • Digestive upset: nausea, vomiting, diarrhea, bloating, loss of appetite, abdominal pain, indigestion
  • Rash
  • Light sensitivity, especially when taking tetracyclines

Some antibiotic classes are associated with more unusual side effects, including (5, 6):

  • Low platelet count: cephalosporins and penicillins
  • Severe aches and pains, tendon rupture: fluoroquinolones
  • Hearing loss: macrolides and aminoglycosides
  • Kidney stones: sulfonamides

Many antibiotics are broad-spectrum, meaning they act to kill a wide variety of bacteria. These antibiotics cannot distinguish between "bad" bugs and "good" bugs, so it is common for disturbances in the healthy microbiome to occur during and after a course of antibiotic treatment. This reduction in human microbiota diversity is responsible for general digestive side effects, antibiotic-associated diarrhea, and in more severe cases, Clostridioides difficile (C. diff) infection (characterized by severe, bloody diarrhea and intestinal inflammation). (7)

Antibiotic-mediated changes to the gut microbiome lead to reduced gastric motility and negatively impacts the immune system's functioning. Reductions of beneficial bacteria and the disruption of immune function can predispose a person to develop fungal infections, commonly of the mouth, intestines, vagina, and skin. (7-9)

FAQ About Antibiotics

Below are answers to frequently asked questions about antibiotics and their use.

What is Antibiotic Resistance?

Antibiotic resistance occurs when bacteria adapt and evolve to evade the antibiotics designed to kill them. This results in difficult-to-treat infections, leading to extended hospital stays, higher medical costs, and increased mortality. (10)

Antibiotic resistance is a threat to global health. At least 700,000 people die annually from antibiotic-resistant infections, a number anticipated to increase significantly without any action to address the problem. The increasing rates of antibiotic resistance can be attributed to antibiotic overuse and misuse, agricultural use of antibiotics, and international travel. (10, 11)

Can You Drink Alcohol While Taking Antibiotics?

It is generally recommended to avoid drinking alcohol during antibiotic therapy. Alcohol can induce blood sugar changes, dampen the immune response, and prolong recovery from illness. Alcohol and antibiotics can cause similar side effects, like stomach upset and dizziness; combining alcohol and antibiotics can increase these side effects. There are certain antibiotics where alcohol should be explicitly avoided during treatment due to the increased risk of severe side effects. These include metronidazole, tinidazole, sulfamethoxazole/trimethoprim, and linezolid. (14, 15)

How Long Does it Take for Antibiotics to Work?

Several factors can impact the length of time it takes for antibiotics to start working, including the type of infection, class of antibiotic, and overall health status of the patient. Antibiotics begin to work as soon as you start taking them, although it might take 2-3 days before you start feeling better.

Do Antibiotics Make You Tired?

Fatigue is not a common side effect of most antibiotics; however, it is possible to feel more tired when you start taking them. This fatigue may be related to being sick, an interaction with another medication, or a die-off reaction. It is recommended that you speak with your doctor if you experience fatigue that affects your ability to drive safely or prevents you from performing daily activities of living.

Functional Medicine Labs to Test for Patients Worried About Taking Antibiotics

Functional medicine labs help practitioners personalize treatment options for their patients. Additionally, labs can help confirm bacterial infection, identify the causative organism, and determine the most effective antibiotic for treatment.

Basic Health Evaluation

A basic health evaluation with a complete blood count (CBC) and comprehensive metabolic panel (CMP) can show white blood cell patterns indicative of bacterial infection and ensure the liver and kidneys are functioning optimally to prevent antibiotic-associated adverse effects. Additionally, procalcitonin is an inflammatory marker that can easily be added to this panel. Elevated procalcitonin can differentiate between bacterial and viral infections, confirming that antibiotic treatment is appropriate.

Culture & Sensitivity

The key to safely and effectively treating bacterial infections with antibiotics is identifying the presence of a bacterial pathogen and the correct antibiotic agent to use. Culture and sensitivity can be performed on a variety of bodily fluids. This test cultures and identifies the pathogenic agent and then performs susceptibility testing on it to determine antibiotic agents that will and will not be effective in treatment. The type of culture you order will depend on the patient's symptoms and the location of the infection. Common cultures include stool testing for gastrointestinal symptoms, urinalysis for urinary symptoms, throat or sputum culture for respiratory symptoms, and vaginal culture for vaginal symptoms.

Comprehensive Stool Test

A comprehensive stool analysis can be ordered as an alternative to, or in combination with, traditional stool culture for a more in-depth analysis of the gut microbiome. The benefit of a comprehensive stool test is that it screens for pathogenic infections and assesses the healthy microbiome's health and composition. Identifying imbalances in the microbiome before starting antibiotic therapy can help patients proactively initiate and dial in probiotic treatment to prevent antibiotic-induced imbalances. Comprehensive stool tests also include natural antimicrobial agents in addition to pharmaceutical antibiotics on the susceptibility portion of the test.

Yeast Culture

Because antibiotics can increase the risk for and exacerbate yeast overgrowth, identifying and treating preexisting fungal infections before and during antibiotic therapy is beneficial. Commonly ordered tests to diagnose fungal overgrowth include stool cultures and Candida antibodies.

Natural Antibiotics & Their Comparison to Pharmaceutical Antibiotics

Great natural antibiotic alternatives exist for those wishing to avoid pharmaceutical antibiotic therapy. The antimicrobial activity of plants depends on their antibacterial constituents, including phenols, polyphenols, terpenoids, essential oils, alkaloids, lectins, and polypeptides. Because plant metabolites can induce bacterial death by affecting the human's cellular and immune processes, as well as acting to disrupt multiple bacterial sites, bacteria are less likely to develop resistance to herbal products. (12)

Many herbs have been found to have just as or more effective antibacterial properties than their pharmaceutical counterparts. For example, a 2014 study found that herbal formulas containing Pau D'Arco, thyme, mugwort, yarrow, sage, oregano, and berberine (among others) were just as effective as the antibiotic rifaximin for treating patients with small intestinal overgrowth (SIBO).

Some plant constituents with the most potent antimicrobial potential include berberine, piperine, eugenol, tannins, allicin, berberine, and thymol.

Studies also show that using herbal extracts in combination with prescription antibiotics creates a synergistic antimicrobial effect, making therapy more effective and preventing antibiotic resistance. (13)

Additionally, herbs, unlike prescription antibiotics, have the benefit of being broadly antimicrobial and possess antibacterial, antiviral, antifungal, and antiparasitic properties (13). Natural supplements, including caprylic acid, oregano oil, garlic, and berberine, can therefore be utilized to treat bacterial infections and prevent antibiotic-associated fungal overgrowth.



Antibiotics are medicinal agents that treat bacterial infections. They are often, but not always, indicated in treating bacterial illness. With antibiotic resistance on the rise and the growing concern about antibiotic side effects, seeking natural antibiotic therapy is of growing interest. If you are sick, talk to a functional medicine doctor about whether antibiotic treatment is needed. Functional medicine testing can help with medical decision-making to initiate correct and effective therapies. A holistic and preventive approach can also provide adjunctive, individualized support to address common antibiotic-induced microbiome disruptions and fungal infections.

The information provided is not intended to be a substitute for professional medical advice. Always consult with your doctor or other qualified healthcare provider before taking any dietary supplement or making any changes to your diet or exercise routine.
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Lab Tests in This Article

1. National Library of Medicine. Antibiotics. MedlinePlus.

2. Kapoor, G., Saigal, S., & Elongavan, A. (2017). Action and resistance mechanisms of antibiotics: A guide for clinicians. Journal of Anaesthesiology Clinical Pharmacology, 33(3), 300.

3. Bernatová, S., Samek, O., Pilát, Z., et al. (2013). Following the Mechanisms of Bacteriostatic versus Bactericidal Action Using Raman Spectroscopy. Molecules, 18(11), 13188–13199.

4. Antibiotic Use Questions and Answers. (2021, October 6). Centers for Disease Control and Prevention.

5. Calhoun, C., Wermuth, H.R., & Hall, G.A. (2023). Antibiotics. StatPearls Publishing.

6. Felman, A. (2023, January 3). What to know about antibiotics.

7. Patangia, D., Ryan, C., Dempsey, E.M., et al. (2022). Impact of antibiotics on the human microbiome and consequences for host health. MicrobiologyOpen, 11(1).

8. University of Birmingham. (2022, May 13). Antibiotics can lead to fungal infection because of disruption to the gut's immune system. ScienceDaily.

9. Huizen, J. (2021, December 17). What are the side effects of antibiotics?

10. Cloyd, J. (2023, April 5). Treatment of Antibiotic Resistance Through Functional Medicine. Rupa Health.

11. WHO. (2019, April 29). New report calls for urgent action to avert antimicrobial resistance crisis. World Health Organization.

12. Pancu, D.F., Scurtu, A., Macasoi, I., et al. (2021). Antibiotics: Conventional Therapy and Natural Compounds with Antibacterial Activity—A Pharmaco-Toxicological Screening. Antibiotics, 10(4), 401.

13. Khameneh, B., Iranshahy, M., Soheili, V., et al. (2019). Review on plant antimicrobials: a mechanistic viewpoint. Antimicrobial Resistance and Infection Control, 8(1).

14. Antibiotics and alcohol. (2022, March 19). Mayo Clinic.

15. Freeland, M. N. (2022, January 26). Alcohol and Antibiotics: Is Mixing Them Really That Dangerous? GoodRx.

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