Microbiome – How trillions of microorganisms work to keep you healthy
What is the microbiome?
We have trillions of bacteria living in our bodies. Different groups of bacteria live in different parts of the body (skin, mouth, nose, reproductive system, digestive tract), with the vast majority in the gut. They all work to keep us healthy.
Most of our bacteria are helpful to us and are sometimes called “good bacteria” or our “microbiome”.
The word microbiome comes from the Greek micro – meaning small, and bios – meaning life. The term describes the microorganisms, like bacteria, viruses and fungi, that live on and in a person’s body and all around us.1
Each individual has a their own microbiome, much like a fingerprint.
Many factors such as diet, environment, having pets and our overall health affect our microbiome.
Our microbiome is priceless to us
Bacteria have always lived on and in our bodies and are necessary for good health.1
Bacteria in our gut help us digest our food, train our immune system, and even help our brain develop.
The good bacteria take up space and crowd out disease-causing harmful bacteria.
The good bacteria contain far more genes than our human genome and produce important components for our body such as vitamin K (blood health) and serotonin (nerve health).1
Although we don’t understand exactly how, it seems that changes to our microbiome could result in diseases such as asthma, inflammatory bowel disease and Parkinson’s Disease.1
Our bodies contain more bacterial than human cells and genes
Eat a balanced diet rich in fibre, whole grains, fruits and vegetables.2,3 These provide a food source for the good bacteria in your gut. Dietary fibre is sometimes referred to as a form of “prebiotic” as it assists in the growth of these good bacteria.
Fermented (probiotic) foods such as cultured milk products (certain yogurts), miso, kimchi and sauerkraut contain beneficial live bacteria that can sometimes have a helpful effect on the microbiome.4,5
Exercise is thought to have a helpful effect on the microbiome; however, one study found that high intensity endurance training might be harmful to the microbiome.7
Wash your hands often with plain soap (no need for antibacterial soap) which protects you against illness and from getting harmful bacteria into your body. It’s especially important to wash your hands after you have been to the washroom, before you eat, when you’ve been in public spaces and after coughing or sneezing.
Stay up to date with immunizations and immunize your children to avoid the need for antibiotics.
Take antibiotics when you understand you have a bacterial infection that requires antibiotics. Antibiotics do not work against viruses.
Antibiotics are designed to kill the bacteria causing an infection, but they also kill many of the good bacteria. Antibiotics cause the most damage to the microbiome compared to any other factor.1 When your microbiome is affected by antibiotics, it takes time for the good bacteria to grow back, and repeated antibiotic exposure permanently harms your microbiome.10
Sometimes when a lot of good bacteria are killed, potentially harmful bacteria can grow and cause infection, such as bad diarrhea from a bacterium called Clostridioides difficile (C. diff.).11
Some sources suggest that an animal-based diet (which is composed of red meats, eggs and cheeses, and processed foods such as white sugar and flour) can weaken the microbiome when compared to a plant-based diet, which is rich in grains, legumes, fruits and vegetables.2
The current evidence about probiotics
Probiotics are supplements that contain live bacteria that have a potential health benefit.
Current research does not show that probiotic supplements available on the market have an impact on restoring the bacterial diversity of the gut microbiome following antibiotic treatment.12 In contrast, some research suggests that probiotics can even direct the microbiome towards less diversity if taken after the microbiome was harmed by antibiotics.13 The best way to restore the microbiome after taking antibiotics is improved diet, exercise, and exposure to microbes (through pets, nature, etc.).
Some studies show that specific types of bacteria can help certain diseases. As with any supplement, you should talk to your healthcare provider if you have questions, especially for young children, older adults, and people with weakened immune systems.
Research related to manipulating or altering the gut microbiome to prevent or treat disease is ongoing and in the future may involve clinically administered pre/probiotics that are specific to the underlying imbalance.14
Prebiotics are substances that feed the good bacteria in the gut. Fibres from whole grain, fruits and vegetables are excellent prebiotics. However, there are no scientific studies demonstrating a defined benefit for prebiotics yet.
Commercially sold probiotics are not regulated by Health Canada, so are not as rigourously tested as medicines. Therefore, their quality cannot be guaranteed and the health effects have not been studied for many of them.
Special groups
Infants
Infants start to develop their gut microbiome in the womb, during birth when they pass through the birth canal and through skin-to-skin exposure with their caregivers. Breastmilk/human milk also plays a key role in developing an infants’ microbiome.15
In the first few months of life a healthy microbiome is very important in helping to develop a healthy immune system.
Disruptions to the gut bacteria at this age can have impacts on immune system development and leave children susceptible to allergic diseases (such as asthma) later in childhood.16,17
Healthcare providers are careful about using antibiotics for infants because their developing microbiome is especially susceptible to disruption.
Feeding with breastmilk/human milk throughout infancy helps to establish and protect the microbiome, even when antibiotics may be needed.18
Older Adults
As we age, the number of different microorganisms in our microbiome decreases.19
This means the microbiome is less able to keep bad bacteria from spreading and can lead to a higher risk of some infections, such as C. difficile infection.
An ageing microbiome also recovers slower from the effects of antibiotics
It is important to only take antibiotics when they are prescribed to you by a health care provider. This protects your microbiome and minimizes interactions with other medications.
Gilbert JA, Blaser MJ, Caporaso JG, Jansson JK, Lynch S V., Knight R. Current understanding of the human microbiome. Nat Med. 2018;24(4):392-400. doi:10.1038/nm.4517
David LA, Maurice CF, Carmody RN, et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature. 2014;505(7484):559-563. doi:10.1038/nature12820
Wu GD, Chen J, Hoffmann C, et al. Linking Long-Term Dietary Patternswith Gut Microbial Enterotypes. Science (80- ). 2011;334(October):105-109. doi:10.1126/science.1208344.
Taylor BC, Lejzerowicz F, Poirel M, et al. Consumption of Fermented Foods Is Associated with Systematic Differences in the Gut Microbiome and Metabolome. mSystems. 2020;5(2). doi:10.1128/msystems.00901-19
Leeuwendaal NK, Stanton C, O’toole PW, Beresford TP. Fermented Foods, Health and the Gut Microbiome. Nutrients. 2022;14(7):1-26. doi:10.3390/nu14071527
Ortiz-Alvarez L, Xu H, Martinez-Tellez B. Influence of Exercise on the Human Gut Microbiota of Healthy Adults: A Systematic Review. Clin Transl Gastroenterol. 2020;11(2):e00126. doi:10.14309/ctg.0000000000000126
Bonomini-Gnutzmann R, Plaza-Díaz J, Jorquera-Aguilera C, Rodríguez-Rodríguez A, Rodríguez-Rodríguez F. Effect of Intensity and Duration of Exercise on Gut Microbiota in Humans: A Systematic Review. Int J Environ Res Public Health. 2022;19(15). doi:10.3390/ijerph19159518
Maillard JY, Pascoe M. Disinfectants and antiseptics: mechanisms of action and resistance. Nat Rev Microbiol. 2024;22(1):4-17. doi:10.1038/s41579-023-00958-3
Yang QE, Ma X, Li M, et al. Evolution of triclosan resistance modulates bacterial permissiveness to multidrug resistance plasmids and phages. Nat Commun. 2024;15(1). doi:10.1038/s41467-024-48006-9
Modi SR, Collins JJ, Relman DA. Antibiotics and the gut microbiota. J Clin Invest. 2014;124(10):4212-4218. doi:10.1172/JCI72333
Brown KA, Khanafer N, Daneman N, Fisman DN. Meta-analysis of antibiotics and the risk of community-associated Clostridium difficile infection. Antimicrob Agents Chemother. 2013;57(5):2326-2332. doi:10.1128/AAC.02176-12
Éliás AJ, Barna V, Patoni C, et al. Probiotic supplementation during antibiotic treatment is unjustified in maintaining the gut microbiome diversity: a systematic review and meta-analysis. BMC Med. 2023;21(1):1-18. doi:10.1186/s12916-023-02961-0
Suez J, Zmora N, Zilberman-Schapira G, et al. Post-Antibiotic Gut Mucosal Microbiome Reconstitution Is Impaired by Probiotics and Improved by Autologous FMT. Cell. 2018;174(6):1406-1423.e16. doi:10.1016/j.cell.2018.08.047
Cunningham M, Azcarate-Peril MA, Barnard A, et al. Shaping the Future of Probiotics and Prebiotics. Trends Microbiol. 2021;29(8):667-685. doi:10.1016/j.tim.2021.01.003
Fehr K, Moossavi S, Sbihi H, et al. Breastmilk Feeding Practices Are Associated with the Co-Occurrence of Bacteria in Mothers’ Milk and the Infant Gut: the CHILD Cohort Study. Cell Host Microbe. 2020;28(2):285-297.e4. doi:10.1016/j.chom.2020.06.009
Donald K, Finlay BB. Early-life interactions between the microbiota and immune system: impact on immune system development and atopic disease. Nat Rev Immunol. 2023;23(11):735-748. doi:10.1038/s41577-023-00874-w
Patrick DM, Sbihi H, Dai DLY, et al. Decreasing antibiotic use, the gut microbiota, and asthma incidence in children: evidence from population-based and prospective cohort studies. Lancet Respir Med. 2020;8(11):1094-1105. doi:10.1016/S2213-2600(20)30052-7
Dai DLY, Petersen C, Hoskinson C, et al. Breastfeeding enrichment of B. longum subsp. infantis mitigates the effect of antibiotics on the microbiota and childhood asthma risk. Med. 2023;4(2):92-112.e5. doi:10.1016/j.medj.2022.12.002
Bosco N, Noti M. The aging gut microbiome and its impact on host immunity. Genes Immun. 2021;22(5-6):289-303. doi:10.1038/s41435-021-00126-8
Antibiotic Resistance, Overuse and Misuse in Adults Over 65
Misinformation about antibiotics leads to overuse, misuse and resistance
Antibiotics are the most common treatment for bacterial infections. They don’t work for viral infections like colds, flu or COVID-19. Antibiotic resistant bacteria develop if you take antibiotics when you don’t need them. When these bacteria spread, it undermines modern medicine.
Why should adults over 65 be concerned about antibiotic resistance?
If you are over 65 years of age you are more likely to have an infection. You may have a weakened immune system or live in a care home in close contact with others who may be ill.
As well, you may visit health care settings like hospitals more often. Infections can spread easily in these settings. Antibiotics may also interact with other medications you are already taking.
What you can do to prevent antibiotic resistance
If you are being prescribed antibiotics, ask your health-care provider about the best option for you.
If prescribed antibiotics, discuss with your health-care provider side effects and interactions with other medications.
Always follow your health-care provider’s directions on how to take antibiotics.
Reduce the spread of infections to help yourself and others.
Reducing and preventing the spread of infections in the first place decreases the need for antibiotics, and will help us all to stay healthier.
Wash your hands often with plain soap and water.
Clean common surfaces with regular cleaner and water – you don’t need antibacterial cleaners for most home cleaning.
Store, handle and prepare food safely.
Sneeze into a sleeve or tissue to avoid spreading germs
Stay active and develop healthy habits to keep your immune system strong.
Download and display this poster in your practice.
Penicillin Allergy – Things You Need to Know
What is penicillin?
Penicillin is one of the first antibiotics discovered, and has been used for nearly 80 years to treat common bacterial infections such as bronchitis and laryngitis. It is inexpensive and can treat skin, ear, sinus and upper respiratory tract infections.
Penicillin is one of the safer antibiotics
Compared to other antibiotics, penicillin can be more effective and less likely to result in antibiotic-resistant bacteria. It also has a lower risk of causing C. difficile infection, a severe and hard to treat diarrhea.
Do you have a penicillin allergy?
You may have had a reaction when taking penicillin in the past in the form of hives, itchiness, rashes or swelling. These are common side effects and do not necessarily indicate an allergy. Fewer than 5 in 10,000 people have a true penicillin allergy.
In fact, 80 per cent of adverse effects related to penicillin disappear over time. This means that you may be able to take penicillin safely again the next time you need it, even if you have had reactions to the antibiotic in the past.
Should you take penicillin?
Always share any past penicillin reactions with your health-care provider. They will let you know if you should try penicillin again or use another antibiotic. While your health-care provider may avoid prescribing you penicillin, they may also determine that it is safe to try again.
This is important as the alternatives to penicillin are often stronger antibiotics which may have a higher risk of side effects and should be saved for times when they are truly needed. If these alternative antibiotics are used too much, bacteria may develop resistance to these drugs, and they may not work in future.
Penicillin allergy and what you can do
Before asking to be prescribed a different antibiotic, talk to your health-care provider. They will be able to evaluate your allergy or refer you to an allergist.
Did you know that half of all penicillin allergies go away within 5 years? Learn more about why penicillin may still be the right choice even if you have been told you have an allergy.
Patient and provider information on antibiotic allergies.
Using Antibacterial Products at Home
Using antibacterial products in your home washes away the good bacteria
Millions of good bacteria live on our bodies to protect against infections caused by bad bacteria. Good bacteria also keep harmful bacteria from multiplying. Antibacterial cleaners, makeup and body products wash away the good and the bad. Antibacterial use makes bacteria more resistant to antibiotics.
Using antibacterial products in your home impacts hospital disinfectants
Researchers have found little difference between using plain soap or antibacterial soap in a home or community setting and there is no added benefit of using antimicrobial soap in preventing infections. Similarly, antibacterial ingredients added to makeup, hygiene products, and surfaces of children’s toys have no added benefit to protect against the common cold or the flu. Moreover, some antimicrobial chemicals (such as Triclosan) are harmful to plants and animals when the chemicals are washed down the drain. Triclosan also kills good bacteria and can cause antibiotic resistance over time.
What household products may be labelled as antibacterial, antimicrobial or antiseptic?
Soaps and cleaners
Disinfectant wipes
Window cleaners
Cleaning cloths
Toothpastes
Mouthwashes
Facial cleaners
Makeup and makeup brushes
Pillowcases
Garbage bags and plastic wrap
Child and baby products
What are alternatives to antibacterial products?
Plain soap or detergent and water (any temperature) are the only tools you need to get things clean. Most households don’t need antibacterial cleaning products.
There’s little difference between plain soap versus antibacterial soap when you’re at home. Antibacterial ingredients don’t protect you better from cold or flu. Handwashing with plain soap is extremely effective at reducing the spread of germs.
The David Suzuki Foundation have provided alternative non-toxic disinfecting solutions for at-home use.
Antibiotics for Cold, Flu and COVID-19
Antibiotics for cold, flu and COVID-19 do not work
Antibiotics treat bacterial infections. Colds, COVID-19 and the flu are viral infections, so antibiotics won’t help. Using antibiotics when you have these illnesses can lead to the development of antibiotic resistant bacteria.
There are a few ways to help prevent colds, flu and COVID-19
The best way to recover from a cold or flu is to drink plenty of fluids, get rest, and give your body time to do its job.
Do I have COVID-19?
If you experience any of these symptoms, stay home and contact your healthcare provider. You may just have a cold or the flu but stay home to keep others safe. Here is a link to the BC COVID-19 Self-assessment Tool.
Symptoms of COVID-19 include new or worsening:
Fever or chills
Cough
Loss of sense of smell or taste
Difficulty breathing
Sore throat
Loss of appetite
Runny nose
Sneezing
Extreme fatigue or tiredness
Headache
Body aches
Nausea or vomiting
Diarrhea
COVID-19 symptoms can range from mild to severe. Sometimes people with COVID-19 have mild illness, but their symptoms may suddenly worsen in a few days.
Go to an urgent care clinic or emergency department if you:
Antibiotics don’t help most respiratory infections, and they can even be harmful. See ways you can help treat symptoms from colds and flu without unnecessary antibiotics.
Poster with the six steps for proper hand washing.
Antibiotics and Dental Care – Things You Need to Know
You don’t always need antibiotics at the dentist
Antibiotics are appropriate for some dental procedures. They are used to prevent or fight infections, but many toothaches and oral infections do not need antibiotics. Discuss options with your dentist. Always tell your dentist about any medical conditions or health changes.
What are antibiotics for dental care?
Antibiotics are medicines for treating bacterial infections. They play a vital part in modern medicine and dentistry.
When taken incorrectly or overused, bacteria can develop resistance to antibiotics. This means antibiotics may not work the next time you need them. When antibiotics for serious bacterial infections stop working, lives are lost.
Antibiotics and Dental Care – How Can I Help?
Maintaining a healthy dental routine helps prevent oral infections that require antibiotics. Eat well, brush, floss and visit your dentist regularly. These are all important steps in preventing dental disease.
Did you know that half of all penicillin allergies go away within 5 years? Learn more about why penicillin may still be the right choice even if you have been told you have an allergy.
