Get dirty, sleep, eat a diversity of real food, avoid antibiotics

The beginning of a new year is always a time for reflection and resolutions for lifestyle changes and New Year’s resolutions! I’d suggest if you want to improve your life and health, start with the very numerous, yet invisible portion of yourself – your microbiome.  The digestive system microbiome is best understood of all the human microbiomes. The importance of these invisible organisms for human health is increasingly apparent. However, scientists are still unraveling what makes up a “healthy” and “unhealthy” gut microbiome. It’s too early in the science to offer exact prescriptives, such as specific probiotics to take at certain doses or how many grams of fiber to incorporate in your diet. However, recent observational and even experimental research, points to general suggestions to improve gut microbiome health. Interestingly many of these suggestions often align with age-old healthy habits, but some may seem initially counterintuitive. 

Microbiome-friendly New Year’s Resolutions

  1. Get outside.

    Garden, hike, or otherwise go out into nature. Children growing up on farms with increased exposure to environmental microbes have been found to have fewer allergies and asthma [1]. Whether this carries over to adults has yet to be examined, though initial data from the American Gut Project suggests that adults exercising outdoors had more diverse microbiomes [2].

    Making mud pies and finding other excuses for going outside is great for you AND your microbes!
  2. Get a dog.

    Can’t get outside enough? Several studies suggest that families with dogs have less allergies and asthma [3, 4]. Individual family members also have more similar microbiomes, perhaps because the dog moves microbes between people during contact. Finally, dogs are thought to bring in soil and its associated microbes from outside into the house, which is at least another way to be exposed to environmental microbes if you are stuck in buildings most of the day.

  3. Clean less.

    Put down the bleach bottle and the vacuum. New studies in 2015 suggest that over cleaning our homes may be correlated with microbiome disruptions or increases in some illnesses. The most striking of these studies suggested that pregnant women and their 2 year old children had different microbiome communities depending on how frequently the house was vacuumed. The authors hypothesize that these microbiome differences may be due to immune system changes with increased exposure to dust mites when vacuuming more frequently [5]. Another study found households that cleaned with bleach had an increase in flu and other respiratory infections [6]. Whether this correlation is due to the air borne particulates from bleach use or disturbance of the microbiome remains to be investigated.

    Emily sharing beans with her canine best buddy.
  4. Sleep.

    In laboratory mice with a disrupted circadian rhythm and sleep cycles coupled with a high-fat and high-sugar diet had microbiomes with increases in Firmicutes and decreases in Bacteroidetes. Similar Firmicute/Bacteroidetes shifts are seen with digestive system disorders and obesity [7]. Mice fed a normal diet and disrupted sleep did not have such microbiome shifts [8].

  5. Exercise. 

    A study of rugby players showed that athletes had more diverse microbiomes than controls [9]. However, athletes also had very different diets, so these two variables could not be untangled [9]. Diet and exercise were decoupled in an experiment on lab mice. Large changes were seen in the microbiome community of laboratory mice that exercised, no matter if they were on a high fat diet or not [10]. Exercised mice also demonstrated improved memory and learning abilities and lower anxiety. Exercise did not seem to ameliorate the influence of a high fat diet [11], perhaps reinforcing the need for diet resolutions below.

  6. Eat a diet of “real”, unprocessed foods.

    Primarily fruits, vegetables, whole grains, and lean meats instead of a high fat and high sugar, processed diet. Several observational and experimental studies suggest that the gut microbiome is dramatically different between diets high in plant fiber and those high in fat [8, 11, 12]. Since your gut microbiome composition shifts rapidly with changes in diet, make this a long-term change [12, 13]. The Good Gut is an excellent book about the influence of diet on the microbiome written by two microbiome scientists.

  7. Eat a variety of fruits and vegetables.

    People eating a wider variety of plants, both fruits and vegetables, had a more diverse gut microbiome [2]. Consider this a chance to explore new areas of the produce aisle or grow your own vegetables.

  8. Eat fermented foods.

    Bonus points for you if you make them yourself. It’s surprisingly easy to conduct “controlled rotting” of food in your own kitchen. Don’t be scared, people have been doing this for centuries. Yogurt, kefir, sauerkraut, and kimchee are a great place to start, just do so in moderation. Check out Sandor Katz’s books Wild Fermentation and The Art of Fermentation for recipes and instructions.

    Adding yogurt starter culture to our milk made some yummy yogurt!
  9. Only use antibiotics when absolutely necessary.

    Only use antibiotics to treat bacterial infections, not viruses like the common cold. Antibiotics work by targeting specific parts of bacteria, like making holes in bacterial cell membranes. Viruses have different structures that antibiotics cannot degrade, so antibiotics won’t kill viruses. However, antibiotics will destroy your body’s natural, beneficial bacteria. Removing those beneficial bacteria not only removes whatever function they provide, but also leaves an open habitat for potential pathogens to fill. Additionally, increased exposure of opportunistic pathogens to antibiotics increases the .

  10. Avoid antibiotic supplemented products.

    These include soaps, body washes, toothpaste, household cleaners, bandages, and many other common products. Look for the names of antibiotics such as triclosan and triclocarban in personal products. Firstly, antibiotic products do not clean better than regular soap and water [14]. Secondly, these products are found to disturb the native microbiome in fish [15] and may do the same in humans. The fish microbiomes do return to normal levels after an initial disturbance [15]; however, the disturbance period may allow for pathogen colonization or disruptions in the immune system. Thirdly, non-necessary exposure of opportunistic pathogenic bacteria in the environment to antibiotics increases the opportunity for antibiotic resistance to occur [16]. Finally, these antibiotics may have a role in endocrine disruption. The U.S. Environmental Protection Agency (EPA) and Food and Drug Administration (FDA) are currently reassessing regulation of triclosan. For more information on their assessments see these EPA links and FDA.

Time and time again, New Year’s resolutions are broken each year. Life gets crazy and we get out of a newly established routine or lose whatever partner/device/incentive holding us accountable. For me – thinking of New Year’s resolutions in terms of my microbial friends instead of myself just might help. After all, they are always with you and through your health – they will always hold you accountable! So for a microbially happy 2016 –  let life get a little dirty, limit your exposure to antibacterial chemicals, and feed your microbiome well!


What do you think?

Let me know in the comments section below or send an email to mostlymicrobes at gmail dot com

Will thinking about your microbiome’s health hold you more accountable?

What changes are you considering making that might be beneficial to your microbiome?

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  2. Knight R: Recent findings from the American Gut Project. In.: 5th Annual Beneficial Microbes Meeting, American Society for Microbiology; 2014.
  3. Song S, Lauber C, Costello E, Lozupone C, Humphrey G, Berg-Lyons D: Cohabiting family members share microbiota with one another and with their dogs. Elife 2013, 2:e00458.
  4. Pelucchi C, Galeone C, Bach J-F, La Vecchia C, Chatenoud L: Pet exposure and risk of atopic dermatitis at the pediatric age:meta-analysis of birth cohort studies. J Allergy Clin Immunol 2013, 132(3):616-622.e617.
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  8. Voigt RM, Forsyth CB, Green SJ, Mutlu E, Engen P, Vitaterna MH, Turek FW, Keshavarzian A: Circadian Disorganization Alters Intestinal Microbiota. PLoS ONE 2014, 9(5):e97500.
  9. Clarke SF, Murphy EF, O’Sullivan O, Lucey AJ, Humphreys M, Hogan A, Hayes P, O’Reilly M, Jeffery IB, Wood-Martin R et al: Exercise and associated dietary extremes impact on gut microbial diversity. Gut 2014, 63(12):1913-1920.
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  14. Kim SA, Moon H, Lee K, Rhee MS: Bactericidal effects of triclosan in soap both in vitro and in vivo. J Antimicrob Chemother 2015, 70(12):3345-3352.
  15. Narrowe A, Albuthi-Lantz M, Smith E, Bower K, Roane T, Vajda A, Miller C: Perturbation and restoration of the fathead minnow gut microbiome after low-level triclosan exposure. Microbiome 2015, 3(1):6.
  16. Carey DE, Mcnamara PJ: The impact of triclosan on the spread of antibiotic resistance in the environment. Frontiers in Microbiology 2015, 5.


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