Effects of Antibiotics on the Intestinal Microbiome and How to Restore Internal Microbial Balance

It has been almost a hundred years since Alexander Fleming discovered penicillin. In that period, the taking of antibiotics has become a part of everyday life. Every drug has its side effect, but the side effects of antibiotics are grossly overlooked, or most times unnoticed. Antibiotics take a toll on major cells and cell components, that cause disruption in many events in their short-term and long-term dosage. Antibiotics destroy healthy needed bacteria and create an imbalance between healthy and bad bacteria. However, the normal body function and the ratio of microbes can be restored. This is done by encouraging the growth of good bacteria in the gut. The major method of this restoration is with probiotics.

Intestinal Microbiota

Intestinal Microbiota


Antibiotics are medications that are used to stop the action of bacteria, to relieve bacterial infections. They can be used for preventive or curative purposes. They work either by destroying the structure of the bacteria or disrupting their multiplication process. Every antibiotic is made with the characteristics of the target bacteria in mind. Just as bacteria can be gram-positive, gram-negative, aerobic, or anaerobic, antibiotics can be prepared specially for each group of bacteria, or broadly for a large scope of bacteria.

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Effects of antibiotics on microbes short-term

A seven-day Ph.D. research carried out in Universitat Autonoma de Barcelona (UAB) by Ms. Suchita Panda, showed the short-term effect of antibiotics in the gut microbiota. The antibiotics used for this study were fluoroquinolones and beta-lactams. These antibiotics were analyzed as the 16S rRNA was pyrosequenced with the qPCR and 454. At the end of seven days, there was a general change in the structure and population of the bacteria present. However, the first observation was a decrease in the diversity of microbiota. It was also confirmed, that irrespective of the type or dosage of antibiotics given, there is always a remarkable decrease in both Gram-positive and Gram-negative bacteria.

The decrease in microbial load as an effect of antibiotics is a very important feature that always occurs. This is important because this decrease creates space for resistant strains to populate and maintain dominance in that niche. This implies that antibiotics could be used to manipulate the local microbiome to favor resistant bacteria strains over normal bacteria in the long term.

Effects of antibiotics on microbes long-term

Over the years, scientists observed that treatment of an ailment with antibiotics for a long time produces side effects. Most of these side effects manifest as a result of over usage or abuse. The majority of these side effects are not beneficial in the long run. Singly, these side effects could lead to diabetes, immune system dysfunction, digestive problems, obesity, and much more. These side effects include:

 Destroying intestinal epithelial cells: This discovery is very new and adds to the already known effects of antibiotics. It is backed by a study done on mice, with four different antibiotics. The intestinal epithelium is made up of specialized cells that wrap the outer surface of the intestines. They compartmentalize the intestines and their bacteria, so they can do their functions. These epithelia have a velvety appearance due to tiny projections called villi. They increase the surface area for action in the intestines. This epithelium is also made up of enzymes that help in the digestion of carbohydrates, absorption of glucose, water, and essential nutrients. Immune cells also embed themselves amidst these epithelia; their function is to create a balance between the host and the bacterial colonies.

Destruction of these cells leads to the loss of all these activities. This implies defaults in immune system activity of the gut, glucose metabolism, absorption of glucose, water, and nutrients.

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Interruption of signaling between host-microbe and mitochondria: Under normal situations, there is an unending transfer of signals between the host and the gut bacteria. Note that any interruption or derailment within this communication leads to many general body problems. These problems include; digestion abnormalities, diarrhea, ulcerative colitis, less active immune function, obesity, malabsorption of food, allergies, sepsis, depression, and asthma. To add, bacteria that have developed resistance to antibiotics do that by slight changes in their mitochondria. These changes might not be major, but they affect the functioning of the cell and can lead to cell death.

Mitochondria are like powerhouses for the cell because they are the major converters of food into energy. They also participate in signaling and growth as energy is used in many forms for healthy activities. The smallest disruption in the structure or composition of the mitochondria leads to the malfunction of big events. This includes the actions of antibiotics because mitochondria are descended from bacteria, and as such, antibiotics also work on mitochondria.

Exposure to fungal infections: There are good bacteria in every human. In the process of killing harmful bacteria, good bacteria are also removed. Good bacteria protect the body from fungal infections and infections by other more virulent bacteria. Therefore, the long use of antibiotics exposes the body to these infections in the mouth, throat, gut, and vagina. In treatment scenarios, after a long-term antibiotics treatment, patients develop different ranges of infection. The symptoms of these infections could be;

    • Fever (sometimes it’ll be light and other times it’ll be intense) and chills
    • Non-stop diarrhea
    • Bloating (due to gas-forming organisms)
    • Painful ingestion and swallowing of food
    • Inactive taste buds
    • Painful intercourse
    • Burning sensation while urinating
    • Itchy and swollen vagina
    • Unusual vaginal discharge
    • A white covering in the mouth, cheeks (Thrush).
    • Cotton-like feeling in the mouth.

For these reasons, some specialists strongly advise against the long-term usage of antibiotics for the treatment of infections unless it is necessary. Instead, it is most beneficial if the population, condition, and action of healthy bacteria are improved to resolve these infections. This would lead to healthy competition and healthy results.

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How to restore your body microbiome after long-term antibiotics usage

After the use of antibiotics, the only way to restore the body condition and get rid of the side effects is to restore the healthy bacteria and rebuild the destroyed microbiome. The aim of restoring these healthy bacteria is to bring back the balance of good and bad bacteria in the gut. This healthy bacteria helps prevent inflammatory bowel sickness (IBS) and inflammatory bowel disease (IBD). If this is not done the side effects can become very intense, leading to other serious complications in the gut and body as a whole. These methods are a wide range of recommendations and can be taken by anyone. However, patients with IBD should contact their physician before taking them, as they are very sensitive to food. These methods are:

  • Include fermented foods in your diet: Foods that are fermented contain healthy bacteria that are partially broken down. A clear example is the bacteria in yogurt. This bacteria is not fully broken down,  but it helps to give yogurt its texture and sloppy flavor by fermenting lactose (the sugar in milk). When taken in, the bacteria can replace the loss of its kind, and continue the function. There are many fermented foods including; cheese, kefir, cider, kimchi, miso, kombucha, temper, etc.
  • Eat fibers that help to grow healthy bacteria: Various food sources are fibrous and also support the growth and regeneration of healthy bacteria. These include; nuts, beans, leeks, asparagus, garlic, bananas, pears, watermelons, onion, whole grains, flaxseed, raspberries, Jerusalem artichokes, etc.
  • Directly take high-quality probiotics: This depends on your exact need for probiotics at the moment. If you take in random probiotics from a random brand you have done no research on, you can do more harm than good. Make sure to buy living bacteria. The best advice on this quest is to target probiotics containing Lactobacilli and Bifidobacteria. For intense diarrhea, look for Saccharomyces boulardii.
  • Decrease your level of sugar intake: Taking artificially manufactured foods and high sugar, can decrease and kill good bacteria. If there is already IBD, high sugar can lead to intense inflammation which would increase the symptoms of IBD. If the body is in its recovery state from antibiotics, there is no effective absorption of glucose and a high intake of sugar increases the effect of this issue.
  • Managing stress: from various studies, psychological stressors cause an imbalance between good and bad bacteria. However, when good bacteria like Lactobacillus and Bifidobacteria are given to people under chronic stress, there is an obvious improvement from anxiety symptoms and other fatigue symptoms. During the recovery from a recent treatment with antibiotics, reduce stress and stay away from stress triggers for better gut health.
  • Ensure your liver is healthy: The liver has many functions including removing bacteria destroyed by antibiotics. This function is very necessary as new healthy bacteria will not grow successfully in the presence of dead old bacteria.  To support this function, green leaves, cardoons, artichokes, carrots, avocados, beets are advisable. Supplements like milk thistle also help in supporting this function. It can be taken as a pill or as a tea.
  • Eat small portions of food: The gut is not as effective in this state, meaning that it cannot carry out cumbersome activities. Therefore, do not overload your system with too much food, to prevent more complications while in this state.
  • Increase your daily water intake: Water plays an essential role in diluting food. This makes the digestion process in this body state, easier. During recovery, a person is expected to take at least 8 servings of water per day.

Read Also: IBS: How to Treat the Diarrhea, Bloating, Flatulence and Abdominal Pain


Probiotics are living bacteria in the body. They are mostly found in the gut. They help in solving many ailments in the body including, diarrhea, inflammatory bowel disease, high cholesterol, infection, high blood pressure, and many others. They also help in food digestion, immunity of the gut snd production of vitamins. Some foods contain probiotics like yogurt, cheese, etc. these foods should be taken in according to body conditions. Examples of probiotics are; Lactobacillus (found in fermented foods), Bifidobacteria (found in dairy products), Saccharomyces Boulardii (it is a yeast, and helps in digestive problems)

Probiotics and bloating

Excessive production of gas and bloating is majorly due to flatulence. There are many other causes of gas:

  • Maturity of bad bacteria in the gut.
  • An unbalanced diet like carbonated drinks, spicy foods, fatty foods, beans, cold or hot drinks, foods containing mannitol, sorbitol or maltitol, etc.
  • Malfunction in food digestion and slow digestion.
  • A wrong eating pattern like talking while eating, using a straw, eating very fast, smoking, chewing gum, deep sighing, overeating, etc.
  • Stress and anxiety.
  • Hormonal imbalances.
  • Weakness in muscles of the gut that aid digestion.
  • Inflammatory bowel disease.
  • Small intestine bacterial overgrowth.
  • Inflammatory bowel sickness.
  • Other digestive disorders.

The gut bacteria control a large percentage of food digestion. This means that if the cause of bloating is digestion malfunction or in a case where the cause is unknown, there is a probability of imbalance of microbes. The major corrective action should be to bring balance between the microbes of the gut. Over years of practice, it has become common knowledge that taking a high-quality multispecies, multistrain yet targeted probiotic can help promote digestion. For this reason, there are specific beneficial bacteria produced for the singular purpose of bloating. These bacteria aid restoration of digestive functions, reduce gas production, reduce flatulence which will reduce its cohorts. The reason why probiotic strains cure bloating or flatulence has not been scientifically proven, but scientists are very sure that probiotics healthily get rid of bloating and induce microbial balance in the gut. The probiotics that specifically attack bloating are Lactobacillus acidophilus and Bifidobacterium lactis.

Read Also: Study Shows That Probiotics Can Evolve Making Them Highly Unpredictable

Antibiotics and bloating

In most cases, antibiotics are a strong cause of bloating. This is because it leads to an imbalance in microbes by destroying good bacteria. This means an improper digestion process which can lead to various digestive complications including flatulence.

However, there is an antibiotic that aids in reducing bloating. The antibiotic is called Rifaximin. It has made itself a name in the treatment of travelers’ diarrhea that is majorly caused by Escherichia coli. Rifaximin is a broad-spectrum antibiotic with a commendable safety profile. Its safety profile is because it is not easily absorbed. It reduces bloating and gas production, by reducing the amount of hydrogen gas produced by the large intestine. 500mg of Rifaximin daily, for two weeks, resolved all symptoms of bloating, flatulence, and other digestive disorders. This is a direct approach. Rifaximin can be used for chronic digestive complications like irritable bowel syndrom (IBS) because it is non-absorbable, and it is no side effects.


Prebiotics are non-digestible fibers found in food, that encourage the growth and multiplication of probiotics. Prebiotics are degraded to small chain fatty acids by good bacteria in the gut and transported to where needed. By helping probiotics, they improve gut activities and enhance the immune system of the gut. There are many that lay a claim on the name, but for a food to be considered a prebiotic, there are certain criteria that have to be naturally present. These criteria include;

  • The food must not be affected by the acidic pH of the stomach. This means food must not be basic by nature.
  • The food must be resistant to the effects of the gastrointestinal tract enzymes.
  • There should be a low or totally no absorption of the food into the gastrointestinal tract.
  • The microbes of the gut must be able to degrade and ferment this food.
  • The activity or growth of intestinal bacteria can be stimulated by this food. This is very necessary to improve the individual’s health.

In meeting these criteria, there are four types of prebiotics namely;

  • Fructans.: are prebiotics that can stimulate lactic acid bacteria. However, they also stimulate other groups of bacteria.
  • Galactic-oligosaccharides: These prebiotics majorly stimulate Bifidobacteria and Lactobacilli. They also stimulate EnterobacteriaBacteroidetes, and Firmicutes to a very minor level.
  • Starch and glucose-derived polysaccharides: The specific starch that serves as a prebiotic is Resistant Starch. This starch is resistant to the upper part of the gut. It is considered a prebiotic because it produces a high level of butyrate in the gut.
  • Non-carbohydrate prebiotics: a good example of non-carbohydrate prebiotics is cocoa-derived flavanols. According to a study, flavanols stimulate lactic acid bacteria
  • Other oligosaccharides

Read Also: Stevia-Based Sweeteners May Disturb the Balance of the Intestinal Microbiome


Although antibiotics are arguably the best discovery ever in pharmaceutical sciences, they are neither a cure-all nor a magic bullet. During infections, it may be best to seek probiotics to increase the balance of good bacteria over bad bacteria. If the need arises to take antibiotics for a long or short period, do so with extreme caution. After taking antibiotics, proper care of the gut with probiotics and prebiotics should not be neglected. Gut health holds extreme importance as the majority of food nutrients are absorbed and digested through this route. This means that proper care for the gut should be an essential activity for every individual.


Rifaximin: MedlinePlus Drug Information



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