Top 3 Ways to Restore the Microbiome after Antibiotics

By Qiara Probiotics  15 November 2024 

The widespread use of antibiotics is proving to have major impacts on our microbiome and overall health. While antibiotics can be lifesaving, the ‘’blanket use’’ commonly seen in mainstream medicine is contributing to the worldwide epidemic of antibiotic resistance.

Previously, it was believed to be simply a matter of ‘re-seeding’ the gut with probiotics after a course of antibiotics to rectify any disruption that may have been caused. However, it is now known from clinical research, this is not necessarily the case.

So, what are the top 3 ways Health Professionals can help restore the microbiome and support our patients/clients after antibiotic use?

1. DIET & LIFESTYLE

The very foundation of maintaining health and wellness and promoting a robust microbiome long term is a healthy diet and lifestyle which encompasses the following:

  • Pre and probiotics (from food and supplemental sources, more on this below)
  • Plant food DIVERSITY – research shows 30-40 different types of plant foods per week is an ideal benchmark
  • Polyphenols - the colourful chemicals naturally occurring in plant foods (the blues, purples and blacks begin the highest concentration). Polyphenols contribute to a healthy microbiome by suppressing the growth of pathobionts and encouraging the growth of probiotics
  • Consuming organic, local, home grown produce (when possible) and minimising highly processed food and drink
  • Reducing environmental toxins, including EMFs and radiation exposure
  • Addressing stress with holistic lifestyle practices
  • Ensuring quality sleep

When educating your patients/clients on this topic, empowerment comes with increasing awareness of the microbiome – individuals will make healthier choices if they understand every time they eat, they have an opportunity to nourish their good gut bugs or alternatively feed their bad bugs.

2. PREBIOTICS

Of our food intake, dietary prebiotics have the most influence on the gut microbiome. The beneficial bacteria (also known as probiotics) which make up our gut microbiome reside mostly in our large bowel and it’s these bacteria that metabolise the prebiotics as they pass through. This process results in the production of crucial beneficial bio-actives, also referred to as ‘metabolites’ or more recently ‘post-biotics’. Bio-actives are varied substances and include such things as vitamins and neurotransmitters.

To understand how important prebiotics are, consider human milk. As a human’s first food source, it is weighted more than being considered solely as a ‘fuel’ source. Human breastmilk and its make-up could easily be considered as personalised medicine.


Fig. 1 Schematic summary of the beneficial roles human milk oligosaccharides (HMOs) play in the digestive tract of breast fed infants

Prebiotic HMOs (human milk oligosaccharides) are the third highest component of breastmilk having many biological roles in the foundation stages of an infant’s developing microbiome (fig 1);

  • Feeding specific bifidobacteria (the dominant bacteria in a healthy infant microbiome)
  • Acting as decoys to pathogens (protecting against ‘first exposures’ which is a critical in modulating the developing immune system and learning appropriate responses)
  • Producing post-biotics which contribute to healthy development of the epithelial and mucosal barrier
  • Modulating the immune response and reducing inflammation Including food based or supplemental prebiotics is central to restoring the microbiome after antibiotics – particularly in the longer term and for ongoing maintenance.

3. PROBIOTICS

Probiotics are the best proven clinical tool we have for protecting and restoring the microbiome acutely during and after antibiotics. However, not all probiotics are created equal!

Historically, probiotics were formulated from the ‘more is better’ construct i.e: include many strains and consequently the benefits will be wide and of greater significance.

However, as we learn more and more about probiotics, the science clearly shows this concept is simply not true.

Instead, probiotics need to be considered as ‘gardeners’ who tend to the environment. With their transient beneficial effects they create favourable conditions for the indigenous flora to re-establish itself.

Additionally, recent clinical findings present the importance of understanding the mechanisms of action of specific strains and how this translates to clinical results and health outcomes.

It’s safe to consider ‘most’ probiotics are generally beneficial, but with more thorough research we can also consider specific strains are superior, having multiple mechanisms of action. Moreover, these ‘superior strains’ display their mechanism of action across multiple body sites and encompass ‘rare’ mechanisms (fig 2).


Fig. 2 Possible distribution of mechanisms among probiotics. Some mechanisms might be widespread among commonly studied probiotic genera; others might be frequently observed among most stralns of problotlc species; others may be rare and present in only a few strains of a given species. Evidence is accumulating on a cross-section of probiotic strains that suggest some generalisations can be made beyond strain-specific effects. Abbreviation: SCFA, short-chain fatty acid.

Breastmilk (BM) strains are somewhat of the ‘new kids on the block’ when it comes to supplemental probiotics and are proving to be standouts in this space.

It has been shown that BM strains are selected from other body sites to compile the ‘foundation strains’ for colonising an infant’s microbiome (along with the HMO’s) during this critical early developmental stage. With this in mind, we can make sense of BM probiotics being ’big players’ amongst the array of probiotics available and their potential is being clearly demonstrated in clinical research over the last decade.

Limosilactobacillus fermentum CECT5716 (formerly Lactobacillus fermentum CECT5716) is a thoroughly researched BM strain which offers multiple mechanisms of action, including the particularly unique ‘maternal transfer’ (which translocates to mammary tissue and breast milk when taken orally). L. fermentum CECT5716 helps to relieve symptoms and reduce the occurrence of mild mastitis, as well as being the strain the can be used for numerous applications, across all life stages (6).

Mechanisms of Action L. fermentum CECT5716 is a highly effective and researched probiotic strain (6).

  • Maintains and supports healthy pregnancy and maternal health
  • Helps to relieve symptoms and reduce the occurrence of mild mastitis. Use at the first signs of mild mastitis [1][2]
  • Helps restore good gut flora during and after antibiotic use, important for C-section or GBS positive mums and their babies[3]
  • Improves healthy digestive system function,
  • Maintains and supports gastrointestinal system health
  • Helps increase the growth of good bacteria
  • Maintains and supports immune system health
  • Maintains and supports healthy gastrointestinal immune function
  • Helps to stimulate a healthy immune system response

Understanding the more recent clinical insights into how probiotics work in the body - using single strain, small doses with multiple mechanisms of actions (along with diet, lifestyle & prebiotics) has become best practice when using probiotics as part of your treatment plan to restore the microbiome after antibiotics. Additionally, by using probiotics and prebiotics concurrently, the adverse effects or the collateral damage of antibiotics therapy can be minimised.

For a thorough understanding into the microbiome and probiotics across the life stages including during pregnancy and breastfeeding, join the Qiara Stockist and Health Professional Portal for free accredited (CPE/CPD) eduction modules.

L. fermentum CECT5716 is commercially available in the evidence-based Qiara Probiotics range.


Qiara is a family of breastmilk isolated probiotics for pregnancy, breastfeeding, infant, kid and adult. Supporting lifelong gut health with our awarded brand, most highly rated “Vitamin and Supplement” for Mum at @TellmebabyAU 2020 and 2021. Evidence-based for 7 health outcomes including : reducing mild mastitis, restore gut flora after antibiotic recovery, restoring good bacteria after csection, supporting immunity, improve good bacteria growth and supporting gastrointestinal health. Read over 2000 brand reviews and probiotic insights @Qiaraprobiotics : Buy online www.qiara.com.au