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How Do Antibiotics Affect The Microbiome

Childhood Antibiotics Affect Weight Gain

How Do Antibiotics Affect the Gut Microbiome?

Recently, a study in pre-school children found that use of macrolides in early life correlates with increased weight gain . This weight gain was also associated with microbial taxonomical changes including in the abundance of Clostridium, Akkermansia and Enterococcus. Even exposure of the fetus to antibiotics, administered to the mother during pregnancy, may result in long-term effects on growth. For instance, it was demonstrated that when pregnant women received antibiotics during the second and third trimester of pregnancy, their offspring had an 84% increased risk for childhood obesity, up to 7 years of age .

Antibiotics And The Skin Microbiome: The Damaging Effects On Your Gut Health

It is now well researched that the microbes of the skin and gut are vital to the immunologic, hormonal, and metabolic functioning of the body. With a high prevalence of antibiotic use in our society today, it is a major consideration of Naturopathic practitioners when treating a variety of conditions and being able to address the underlying cause.

What is the microbiome?

The term microbiome covers a whole range of micro-organisms, including bacteria, viruses, and fungi and the environment surrounding them. Within this array of microbes there are various groups that serve their own unique role in our overall health which include commensals, symbiotic, and pathogenic micro-organisms found in a fixed environment. The number of microbial cells in the human body alone is 10 times the number of human cells!

How do antibiotics affect the microbiome?

It is important to also note that once antibiotic treatment has stopped, the microbiota does display resilience and is capable of bouncing back to a composition similar to its original state. However, it will not be totally recovered. In fact, antibiotic-induced microbiota alterations can remain after long periods of time, spanning months and even years.

Gut-Skin Axis – how do they link?

Ive taken antibiotics – what can I do?

For further assistance and support to address your gut and skin health, book in to see one of our Melbourne Wellness Naturopaths by calling 9894 0014 or emailing .


Antibiotics Arent Effective On Viral Infections

Many of the inappropriate prescriptions of antibiotics have been targeted at viral infections. Illnesses caused by viruses cannot be treated by antibiotics. This is because viruses are structured differently than bacteria and do not replicate in the same way. So, antibiotics dont end up killing the viruses that are making you sick but just cause unnecessary harm to your microbiome.

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Effects Of Probiotic And Prebiotic Treatment On Children’s Microbiome And Overall Health

With the evident effects of antibiotics on the microbiota, it has been suggested that probiotics and prebiotics may be able to alleviate the symptoms and restore the microbial balance. Probiotics are supplements comprised of live bacteria that are considered beneficial, usually including Lactobacillus, Lactococcus or Bifidobacterium. To this end, many medical practitioners recommend probiotics following antibiotic treatment. While some studies with probiotics yielded insignificant results, other studies suggested a clear health benefit following antibiotics. Different microbial compositions were found in mice receiving probiotics after antibiotic treatment, compared with mice receiving antibiotic treatment alone . Long-term L. rhamnosus GG supplementation was found to influence the composition of the intestinal microbiota in children as well, causing an increase in the abundance of Prevotella, Lactococcus and Ruminococcus, and a decrease in Escherichia . Additionally, probiotics were suggested to alleviate some of the antibiotic-associated side effects such as diarrhea and revert the increased risk for atopic diseases following antibiotics . It has even been speculated that probiotics in combination with antibiotics may reduce antibiotic resistance, although this requires further investigation .

How To Restore Gut Flora After Antibiotics

Gut microbiome may affect some anti

If we cant avoid antibiotics, the next best thing we can do is try to restore our microbiome after them and know how to stay healthy while taking antibiotics. Diet can help ensure that your microbiome has the resources necessary to repopulate properly by providing nutrients that promote gut health and microbe diversity.

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Development And Maturation Of The Microbiome

As a child grows, the commensal microbiota develops in a predictable succession of species that is generalizable across human populations . The developing bacteriome, the bacterial component of the microbiome, has been profiled many times, both taxonomically and in terms of metabolic functions . These profiles have provided a view of how bacterial species are structured over time. Less is known about the gut-associated eukaryotes and viruses that develop along with the bacteriome, although they are an important part of the gut ecosystem . The disruption of the bacterial succession can be pathogenic . Critical developmental milestones for the microbiota occur, in particular, during infancy and early childhood, and both medical intervention and lack of such intervention during these periods can have lifelong consequences in the composition and function of the gut ecosystem . In this section, we discuss the instances in which antibiotics are often used during development and adulthood, the effects of antibiotics on the microbiota, and the implications of such effects for health and disease.

Fig. 1

Health consequences linked to the disruption of human-associated microbiota involving antibiotic use during development and adulthood.Red lines indicate that a single dose of antibiotics within the time period has been linked to a health consequence, whereas a dotted red line indicates that multiple doses of antibiotics within the time period are required to observe a link

Diet Impacts The Sensitivity Of Gut Microbiome To Antibiotics Study Finds

Antibiotics change the kinds of bacteria in the mouse gut as well as the bacterias metabolism but diet can exacerbate the changes, a new study showed.

PROVIDENCE, R.I. Antibiotics save countless lives each year from harmful bacterial infections but the community of beneficial bacteria that live in human intestines, known as the microbiome, frequently suffers collateral damage.

Peter Belenky, an assistant professor of molecular microbiology and immunology at Brown University, studies ways to minimize this side effect, which can lead to C. diff infections and other life-threatening imbalances in the microbiome. In a new study published on Thursday, Sept. 12, in Cell Metabolism, Belenky and his colleagues found that antibiotics change the composition and metabolism of the gut microbiome in mice, and that a mouses diet can mitigate or exacerbate these changes.

The findings are a step, Belenky said, toward helping humans to better tolerate antibiotic treatment.

Doctors now know that each antibiotic prescription has the potential to lead to some very harmful microbiome-related health outcomes, but they do not have reliable tools to protect this critical community while also treating deadly infections, Belenky said. The goal of my lab is to identify new ways to protect the microbiome, which may alleviate some of the worst antibiotic side effects.

The Department of Defense , National Science Foundation and National Institutes of Health COBREs supported the research.

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Take Probiotics And Prebiotics To Decrease The Impact Of Your Treatment

Probiotics may help the good and beneficial bacteria to grow back quicker than it would without probiotic supplements. By taking probiotic supplements, you can help to keep one strain of gut flora from taking over. Restoring gut flora after antibiotics are essential as you need a diverse gut microbiome to remain healthy. When youre taking a treatment, you can kill bad bacteriaand sometimes the good ones. You may also disturb the functions of the remaining microorganisms, and the disruption can lead to digestive symptoms. You need probiotics to help increase the population of colony-forming units in the gut. Consider it as replenishing what youre losing. Meanwhile, prebiotics can help feed the remaining microorganisms in your digestive tract. Its like helping them survive and thrive despite the treatment. There are many sources for probiotics, but the best probiotic is one that also contains fungi such as BIOHM Probiotics. Many people are not aware they have fungi in their gut too, along with viruses and bacteria.

Improving Gut Health After Antibiotics


There is increasing clinical evidence that taking probiotics during and after antibiotic use can decrease the risk of invasion by opportunistic pathogens and development of antibiotic-associated diarrhea1820. However, further research is still needed in this area and it is likely that different strains of probiotics have different levels of efficacy.

Although it is likely probiotics can protect against the invasion of opportunistic pathogens, a recent small study observed that probiotics may also inhibit the return of the native gut microbiota21. The study found it took longer for the native gut microbiota to return in individuals who consumed probiotics for 28 days following antibiotic use compared to individuals who did not take probiotics. Therefore, it appears there are both positive and negative factors to consider when deciding to take probiotics to help the gut microbiome recover from antibiotics.

A good general strategy to improve gut health is to make sure you feed your gut microbiome foods that will allow your beneficial resident microbiota to grow back. This means eating a wide variety of foods that are high in fibre and plant polyphenols such as fruits, vegetables, legumes, nuts and whole grains22.

This microbiome test is not intended to be used to diagnose or treat medical conditions. A full disclaimer is available here.


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Evidence From Animal Studies

Table 2 List of main studies in animals associating antibiotics exposure and obesityFull size table

Wan et al. have performed a meta-analysis of 23 observational studies including 1,253,035 children. They have reported that the administration of antibiotics only during the second trimester of pregnancy and during infancy has resulted in childhood overweight/obesity . Noteworthy, increased odds of childhood overweight/obesity were linked to the following parameters: administration of antibiotics during the first 6 months of life, repeated exposure to antibiotics for 3 courses, treatment with broad-spectrum antibiotics, and male gender .

In sharp contrast to previous studies, only two studies have reported no difference between exposure to antibiotics and childhood overweight/obesity . However, in the first study, only a single class of antibiotics was prescribed as prophylaxis therefore, the results might have been affected by the type and dosage of the administered antibiotic, while in the second study, infection per se rather than the administration of antibiotics accounted for the observed increased body weight.

What Probiotics For Antibiotic Side Effects

Typically, it will take the body time to balance the microbiome to healthy, diverse bacteria levels. In fact, research shows that it takes about 6 months to recover from the damage done by antibiotics. And even then, the body might not even be back to its pre-antibiotic state.

Saccharomyces boulardii, a probiotic yeast is particularly good at preventing and alleviating antibiotic-associated diarrhea and travellers diarrhea. Its also a friend to your gut bacteria that supports good bacteria and prevents inflammation.

Lactobacillus acidophilus, a probiotic bacterium best known for being in yoghurt is also great for your gut. Studies show that its good at treating and preventing infections, and reducing the digestive side effects of antibiotics.

Other bacteria that help recover from antibiotic use include:

  • L. casei

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Antibiotics Alter The Gut Microbiome And Host Health

Antibiotics not only act on bacteria that cause infections but also affect the resident microbiota. Although this side effect has long been appreciated, advances in sequencing technologies enabled detailed study of how antibiotics alter the gut microbiome.

Although the composition of the gut microbiota varies between individuals, the community in each individual is relatively stable over time . In 2008, Relman and colleagues studied three healthy individuals and showed that treatment with ciprofloxacin influenced the abundance of about one third of bacterial taxa in faecal samples. These changes decreased the taxonomic richness, diversity and evenness of the community. Although most bacterial groups recovered after treatment, several taxa did not and the level of reconstitution varied between the individuals. A follow-up study showed that a second course of ciprofloxacin had similar effects. There was no correlation between the magnitude of the microbiome shift in the first and second treatments within any individual each treatment was another roll of the dice.

A study looking at antibiotic perturbation of the gut microbiota and the risk of developing inflammatory bowel disease, also showed that transfer of the disturbed gut microbiota from mouse mothers to their newborn pups, promoted and accelerated the development of gut inflammation in the offspring.

Does The Gut Microbiome Ever Fully Recover From Antibiotics

Antibiotics: How They Work and Health Impact

Most gut bacteria recover quickly, but there can be long-lasting consequences from taking antibiotics.

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Q. What are the consequences of taking antibiotics on your gut microbiome? Does the gut ever fully recover?

A. Most gut bacteria recover quickly, but there can be long-lasting consequences from taking antibiotics. The changes, however, are not necessarily harmful.

The gut microbiome, the roughly 10 trillion to 100 trillion bacteria and other microorganisms that live in the digestive tract, contributes to health by synthesizing vitamins, metabolizing drugs and fighting pathogens. Anything that disrupts the balance of microorganisms, such as antibiotics, which can kill both good and bad bacteria, has the potential to cause disease.

Data from a 2016 study suggest that exposure to antibiotics in infancy can alter the gut microbiome and weaken the immune response for years to come. Other studies have linked the use of antibiotics in children to an increased lifetime risk of asthma, obesity and inflammatory bowel disease, effects thought to be mediated by the gut microbiome.

In an example of a potentially beneficial effect of altering the gut microbiome, evidence suggests that antibiotics can suppress the formation of a molecule in the gut that increases the risk for heart disease.

Do you have a health question?Ask Well

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What Can Restore Gut Flora After Taking An Antibiotic

The best way to restore gut flora after an antibiotic is to establish healthy eating habits even before the start of taking medicine. A well-balanced diet can help the body recover from disruption to the microbiome whether it’s caused by an antibiotic or an infection and help relieve digestive side effects.

Another approach to consider, in addition to eating healthy, is making sure your diet includes prebiotics.

“Prebiotics create a favorable environment for probiotics to live and grow in,” Dr. Gurram explains. “Many people are using prebiotics and probiotics together to create a favorable and sustainable environment for gut flora to live and thrive before, during or after antibiotic use.”

Good sources of prebiotics include:

  • Fruits and vegetables
  • Grains and legumes
  • Fermented products like yogurt, kefir and sauerkraut

Avoiding Antibiotics In Foods

Taking antibiotics is not the only way we are exposed to them, antibiotics and antibiotic resistant bacteria can also enter into our system through foods. Many animals are fed antibiotics to promote growth and by consuming meat products from these animals we may be putting are self at larger risk of antibiotic resistance.

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How Do Antibiotics Affect The Long

In a 2019 study published out of New Zealand, 474 mothers were enrolled with infants categorized into the first antibiotic exposure, whether at

  • 0-6 months,
  • 6-12 months,
  • 12-24 months, or no antibiotic use.

At 11 years old, these grown children completed a variety of neurocognitive assessments administered by a psychologist, and reports by both parents and the child.

Of the 72% that participated, it was determined that there was an increased risk of problems associated with:

  • impulsivity, and
  • metacognition following early exposure to antibiotics.

A similar study from the University of Auckland in 2017 demonstrated more behavioural difficulties and symptoms of depression at three-and-a-half years following early antibiotic exposure.

The Harmful Effects Of Antibiotics On The Human Microbiome

How Antibiotics Affect Gut Bacteria?

How many articles about the importance of the microbiome and the relationship between microbiome health and chronic, devastating diseases need to come out in order for the cognitive dissonance around antibiotic safety to stop?

People assume that all antibiotics are safe drugs, that they damage bacteria but leave people and animals unharmed. People assume that bacteria are bad, that they are harmful and make us sick, and that human life is improved when they are killed. Many also assume that all antibiotics are created equally and that the more powerful an antibiotic, the better. Most people assume that there are no long-term consequences from taking antibiotics.

There is ample evidence that these assumptions are false, and that a microbiome that is disturbed by antibiotics makes people more anxious, intolerant of pain, and sick with a variety of diseases.

A disrupted microbiome has been connected with development of Parkinsons Disease , as shown in Gut microbiota are related to Parkinsons Disease and clinical phenotype, published in the journal Movement Disorder. It was found that patients with PD had less Prevotellaceae than those in the control group, and that, The relative abundance of Enterobacteriaceae was positively associated with the severity of postural instability and gait difficulty. It is also pointed out in the study that the reason for examining the relationship between PD and the gut microbiome is that:


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Alterations Of The Gut Microbiome By Antibiotics

Antibiotics, as lifesaving medicines for over a century, have been in the front line for combating infections, preventing various medical conditions, and promoting animal growth . However, they present certain disadvantages including antimicrobial resistance and adverse drug events . As gut microbiota is characterized by multiple shifts from the endometrial period till the end of life, antibiotics are suggested to represent one of the most pivotal factors for these alterations stimulating or promoting various diseases.

Since 1940, it has been known that antimicrobials may affect the intestinal microbiota. In 1950, terramycin proved to alter the gut microbiota in patients submitted to bowel surgery . Dysbiosis is closely related to the use of medication, being characterized by the flourishing of the pathobionts, i.e., resident microbes with pathogenic potential the loss of -diversity, i.e., the mean species diversity in the intestinal tract the recruitment of inflammatory cells the leaky gut syndrome and the impaired protection against pathogens . Figure 2 depicts the main mechanisms interconnecting gut dysbiosis triggered by environmental exposures such as diet and antibiotics and obesity.

Fig. 2

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