If you want to know what gut health is, what causes an unhealthy gut, and how to have a healthy gut, then you want to read this article.
When we hear this word, we default to the negative connotations associated with the microscopic organisms, including illnesses and infections such as strep throat or Lyme disease.
And, it’s easy to understand why — for much of our lives bacteria have been thought of as teeny, tiny ne’er-do-wells seeking to lay waste to our immune systems and rob us of our health and vitality.
But, more and more research as of late is demonstrating that not only are all not bacteria not to be feared, they play an essential role in keeping us healthy and possible avoiding illness.
We are, of course, talking about the bacteria residing in our gut microbiome. These prokaryotic partners form a symbiotic relationship with our bodies impacts our mood, immune function, insulin sensitivity, and performance in the gym.
Ahead, we’ll dive deep into gut health — what it is, why it’s crucial, signs of poor gut health, and ways you can improve the health of your gut.
So, let’s get started!
What is Gut Health?
When we think of our gut, most of us think of our stomachs. A few of us might even think of the intestines as well.
But, the “gut” actually refers to the whole gastrointestinal (GI) tract, which includes the:
- Small Intestine
- Large Intestine
The primary function of the gut is to digest, harness, and absorb nutrients from the foods we eat and eliminate waste from the body. But, that only begins to scratch the surface of what our gut can do.
Besides nutrient acquisition, the gut also serves several other essential roles in the body, including [1,2,3,4]:
- Development of the Immune System
- Maintaining Intestinal Homeostasis (Gut Permeability)
- Energy Metabolism
- Insulin Sensitivity
- Weight Maintenance
- Neurotransmitter Synthesis
The gut also helps keep harmful substances out of the body, when it’s healthy. If it’s not in the best of shape, dysfunction follows, and illness ensues.
The gut is home to around 100 trillion micro-organisms, collectively known as the microbiome. While we typically think that only bacteria make up the microbiome, this diverse ecosystem contains viruses, fungi, and protozoa. 
Interestingly enough, your body houses roughly 40 trillion bacterial cells. Our bodies have approximately 30 trillion human cells. [6,7] This means our bodies are more bacteria than human!
And to top it off, the combined weight of the different bacteria in your body is roughly 3-5 pounds — our brains weigh, on average, three pounds! [8,9]
What Influences Gut Health?
The composition of our microbiome and the health of our gut is established from birth. The body’s first exposure to microbes comes when it crosses through the birth canal as well as when it first encounters an open environment (i.e., the hospital).
Interestingly, babies that are birthed via C-section have been found to have different gut bacteria than those that pass through the birth canal.  Some researchers have found associations between babies delivered via C-section and increased risks of disease and obesity compared to those delivered vaginally.
While the microbiome begins developing from birth, it’s always in flux throughout life. Where we live, the food we eat, supplements we use, and drugs we take to treat illnesses (antibiotics especially) all have an impact, for better or worse, on our microbiome as well as our overall health. [11,12,13] Even short courses of antibiotics (~7 days) can wipe out a significant portion of our good gut bacteria.
Other less obvious factors that can impact gut health are stress, sleep, and the amount of body fat we are carrying.
Let’s now drill a bit deeper into the ways these different factors affect the gut microbiome.
5 Factors That Affect Gut Health and the Microbiome
The foods we eat daily have a profound effect on the health and diversity of our microbiome and may account for 30 – 60% of the changes that occur in gut microbiota changes. FYI, our genes only account for 12% of gut microbiota changes, at most. 
Mostly, if we have poor, micronutrient-void diets, the good gut bacteria in our bodies have a hard time surviving. This is all the more concerning given that recent estimates suggest that less than 10% of more Westerners consume enough whole fruits and vegetables. 
This means that the vast majority of the Western population is missing out on loads of vitamins and minerals as well as fiber which serves as fodder for the gut bacteria.
Researchers have noted that temporary changes in the diet can lead to quick changes in the microbiome, but they are reversible. Long-term diet changes (e.g., going keto for years and years) could cause irreversible changes to gut microbiota. 
For example, the studies analyzing the effects of long-term consumption of a Mediterranean diet found significantly higher production of butyrate. 
Why is butyrate important?
Butyrate is a short-chain fatty acid (SCFA) produced via microbial fermentation of dietary fibers in the lower GI tract that [18,19,32]:
- Serves as a significant energy source for colon cells
- Improves insulin sensitivity
- Boosts energy expenditure by improving mitochondrial function
- Fortifies the intestinal barrier
Not having enough butyrate in the gut may lead to diarrhea, irritable bowel diseases, and possibly even colorectal cancer. [20,21,22]
This begs the question…” how do we get more butyrate?”
Butyrate production is determined by the number of bacteria in the gut that generate butyrate as well as the pH of the stomach. Researchers have noted that Firmicutes strains of bacteria mainly produce butyrate and that more acidic (lower pH) environments are optimal.
The way to ensure your gut has the right type of bacteria and that those bacteria have the proper “raw materials” to produce butyrate is through a combination of prebiotics and probiotics.
Prebiotics are the indigestible parts of plants (fiber) that reach the colon and serve as food for the good bacteria in the gut.
Sources of fiber used by gut bacteria to produce butyrate are:
- Resistant starch — produced when certain starches are cooked and then cooled. They are also found in unripe, green bananas
- Inulin — onions, garlic, asparagus, artichokes
- Pectin — apples, carrots, oranges, and apricots
- Fructooligosaccharides (FOS) — bananas, onions, garlic, and asparagus as well as many other fruits and vegetables
- Pectin: Food sources include apples, apricots, carrots, oranges, and others
Numerous trials have found that consumption of prebiotics leads to increased growth of good gut bacteria, including Bifidobacteria and Lactobacilli in humans as well as greater butyrate production. [23,24,25]
Probiotics are live strains of bacteria that when consumed can improve and fortify gut health as well as butyrate production. [26,27] Typical strains of these “good bacteria” include Lactobacilli and Bifidobacteria. Probiotics can also help reduce levels of potentially bad, harmful bacteria. [28,29]
And, probiotics may also be useful following a course of antibiotics to help restore good bacteria wiped out by the potent medications.[ 30,31]
Not only does the food you eat have a profound impact on gut health, but so too does the amount of physical activity you get.
Research has documented that elite athletes have richer gut microbiota compared to non-athletes, including the butyrate-producing Firmicutes strain Faecalibacterium prausnitzii.
Additional research in women has noted that active women tend to have more good gut bacteria than sedentary individuals.[ 34]
And, it’s also worth noting that excessive amounts of endurance exercise have been recorded to hurt gut health. 
You want to train at a relatively high level of intensity but don’t train so long that you border on exceeding your body’s ability recovery. And, you can now add gut health to the growing list reasons (mental health, increased longevity, mood, greater focus, more muscle, etc.) of why you should be physically active.
The importance of sleep can’t be emphasized heavily enough. Poor sleep leads to feelings of low energy, difficulty concentrating, impaired recovery from exercise, and poor performance in the gym.
You can also add poorer gut health to the list of things that accompanies poor sleep hygiene.
Research has shown that sleep deprivation (even as little as two nights) negatively impacts the gut microbiome , and it also leads to increases in cortisol and decreases in testosterone as well as reduced insulin sensitivity. [36,37]
Furthermore, melatonin — the hormone the governs our circadian rhythm and sleep patterns — is produced in the gut. So not only does a bad night sleep, negatively impact your gut microbiome, it can also lead to further difficulty sleeping due to its impact on the hormones in the body that help you go to sleep. 
Many people struggle with sleep, so you’re not alone. Due to the importance sleep plays in maintaining overall health and wellbeing as well as your ability to perform at a high level, SteelFit® created Steel Dreams™ — an all-natural nighttime sleep and recovery aid that helps quiet the mind and lull the body into a state of deep relaxation promoting the optimal environment for a great night’s sleep.
When we are stressed, cortisol levels rise. Chronic elevations in stress also cause inflammation and hurt gut health.
One particularly interesting study in pregnant women observed that the babies born to mothers who were chronically stressed during pregnancy had more harmful bacteria and fewer good bacteria.  Researchers also noted that children with distorted gut bacteria were also more prone to allergic reactions and various gut disorders.
Now, it’s worth noting that not all stress is bad. Acute stressors, such as heavy back squats or high-intensity interval training, are beneficial stressors that help build muscle, and as we noted above, also improve the diversity and health of our microbiota.
Chronic stress, however, leads to prolonged elevations of cortisol, which adversely impacts health, testosterone levels, gut microbiota, recovery, mood, and performance.
Various medications have been noted to disturb the gut microbiome, with antibiotics receiving the majority of attention from researchers in the gut community due to their potential to eliminate both good and bad gut bacteria. [41,42]
The negative impact of antibiotics on good gut bacteria is usually short term; however, there is some research demonstrating that broad-spectrum usage antibiotic, such as clindamycin, can lead to disturbances in the microbiome that last over two years. Furthermore, in certain instances of prolonged antibiotic use, researchers have noted that full restoration of the gut microbiome is no longer feasible. 
This is especially pertinent to women who have a history of antibiotic use, as research indicates that infants may have reductions in good gut bacteria as a result of the mothers’ course of antibiotics. 
To make matters worse, the disruption of good gut bacteria resulting from antibiotics use can also lead to the possibility of additional bacteria setting up home in your gut, resulting in further microbiota disturbance and illness. 
Researchers advise the use of narrow-spectrum antibiotics (antibiotics that target specific strains of bacteria) to reduce the risk of gut dysbiosis.
However, all is not doom and gloom regarding antibiotic use. They do help treat severe infections, and some research indicates they may be able to restore balance to gut bacteria by reducing the number of harmful bacteria.[ 45]
The Bottom Line on Gut Health
Gut health and the integrity of our microbiome is critical, which is why researchers continue to pour over the many ways the gut impacts our overall health and well-being. New research continues to come out about the gut furthering our understanding of this micro-organ that resides in each of us.
While we’re a long way from understanding every aspect of gut health and what is needed to create the “optimal” microbiome, we do know that forming a healthy gut is best achieved through a mixture of diet and lifestyle modifications.
- Jandhyala SM, Talukdar R, Subramanyam C, Vuyyuru H, Sasikala M, Nageshwar Reddy D. Role of the normal gut microbiota. World J Gastroenterol. 2015;21(29):8787-803.
- Soto, M., Herzog, C., Pacheco, J. A., Fujisaka, S., Bullock, K., Clish, C. B., & Kahn, C. R. (2018). Gut microbiota modulate neurobehavior through changes in brain insulin sensitivity and metabolism. Molecular Psychiatry, 2287–2301. https://doi.org/10.1038/s41380-018-0086-5
- Galland L. The gut microbiome and the brain. J Med Food. 2014;17(12):1261-72.
- Farré, N., Torres, M., Gozal, D., & Farré, R. (2018). Sleep and Circadian Alterations and the Gut Microbiome: Associations or Causality? Current Sleep Medicine Reports, 4(1), 50–57. https://doi.org/10.1007/s40675-018-0100-0
- Monda V, Villano I, Messina A, et al. Exercise Modifies the Gut Microbiota with Positive Health Effects. Oxid Med Cell Longev. 2017;2017:3831972.
- Sender R, Fuchs S, Milo R. Revised Estimates for the Number of Human and Bacteria Cells in the Body. PLoS Biol. 2016;14(8):e1002533. Published 2016 Aug 19. doi:10.1371/journal.pbio.1002533
- Qin J, Li R, Raes J, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 2010;464(7285):59-65.
- “NIH Human Microbiome Project Defines Normal Bacterial Makeup of the Body.” National Institutes of Health (NIH), 31 Aug. 2015, www.nih.gov/news-events/news-releases/nih-human-microbiome-project-defines-normal-bacterial-makeup-body.
- Hartmann, P., Ramseier, A., Gudat, F., Mihatsch, M. J., & Polasek, W. (1994). [Normal weight of the brain in adults in relation to age, sex, body height and weight]. Der Pathologe, 15(3), 165–170.
- Li H-t, Zhou YB & Liu JM (2013). The impact of cesarean section on offspring overweight and obesity: a systematic review and meta-analysis. International Journal of Obesity 37(7):893-899.
- Bäckhed F, et al. (2012). Defining a healthy human gut microbiome: current concepts, future directions, and clinical applications. Cell Host Microbe 12(5):611-622.
- Wen L, Duffy A. Factors Influencing the Gut Microbiota, Inflammation, and Type 2 Diabetes. J Nutr. 2017;147(7):1468S-1475S.
- Hospital, P. (2015). Factors influencing gastrointestinal tract and microbiota immune interaction in preterm infants, 77(6), 726–731. https://doi.org/10.1038/pr.2015.54
- Kashtanova, D. A., Popenko, A. S., Tkacheva, O. N., Tyakht, A. B., Alexeev, D. G., & Boytsov, S. A. (2016). Association between the gut microbiota and diet: Fetal life, early childhood, and further life. Nutrition (Burbank, Los Angeles County, Calif.), 32(6), 620–627. https://doi.org/10.1016/j.nut.2015.12.037
- Dreher ML. Whole Fruits and Fruit Fiber Emerging Health Effects. Nutrients. 2018;10(12):1833. Published 2018 Nov 28. doi:10.3390/nu10121833
- Gray LE, O’Hely M, Ranganathan S, Sly PD, Vuillermin P. The Maternal Diet, Gut Bacteria, and Bacterial Metabolites during Pregnancy Influence Offspring Asthma. Front Immunol. 2017;8:365. Published 2017 Mar 31. doi:10.3389/fimmu.2017.00365
- Haro, C., Montes-Borrego, M., Rangel-Zuniga, O. A., Alcala-Diaz, J. F., Gomez-Delgado, F., Perez-Martinez, P., Perez-Jimenez, F. (2016). Two Healthy Diets Modulate Gut Microbial Community Improving Insulin Sensitivity in a Human Obese Population. The Journal of Clinical Endocrinology and Metabolism, 101(1), 233–242. https://doi.org/10.1210/jc.2015-3351
- Gao Z, Yin J, Zhang J, et al. Butyrate improves insulin sensitivity and increases energy expenditure in mice. Diabetes. 2009;58(7):1509-17.
- Peng L, Li ZR, Green RS, Holzman IR, Lin J. Butyrate enhances the intestinal barrier by facilitating tight junction assembly via activation of AMP-activated protein kinase in Caco-2 cell monolayers. J Nutr. 2009;139(9):1619-25.
- Cao Y, Shen J, Ran ZH. Association between Faecalibacterium prausnitzii Reduction and Inflammatory Bowel Disease: A Meta-Analysis and Systematic Review of the Literature. Gastroenterol Res Pract. 2014;2014:872725.
- Machiels, K., Joossens, M., Sabino, J., De Preter, V., Arijs, I., Eeckhaut, V., Vermeire, S. (2014). A decrease of the butyrate-producing species Roseburia hominis and Faecalibacterium prausnitzii defines dysbiosis in patients with ulcerative colitis. Gut, 63(8), 1275–1283. https://doi.org/10.1136/gutjnl-2013-304833
- Chen W, Liu F, Ling Z, Tong X, Xiang C. Human intestinal lumen and mucosa-associated microbiota in patients with colorectal cancer. PLoS One. 2012;7(6):e39743.
- Spiller, G. A., Chernoff, M. C., Hill, R. A., Gates, J. E., Nassar, J. J., & Shipley, E. A. (1980). Effect of purified cellulose, pectin, and a low-residue diet on fecal volatile fatty acids, transit time, and fecal weight in humans. The American Journal of Clinical Nutrition, 33(4), 754–759. https://doi.org/10.1093/ajcn/33.4.754
- Ramirez-Farias, C., Slezak, K., Fuller, Z., Duncan, A., Holtrop, G., & Louis, P. (2009). Effect of inulin on the human gut microbiota: stimulation of Bifidobacterium adolescentis and Faecalibacterium prausnitzii. The British Journal of Nutrition, 101(4), 541–550. https://doi.org/10.1017/S0007114508019880
- Rivière A, Selak M, Lantin D, Leroy F, De Vuyst L. Bifidobacteria and Butyrate-Producing Colon Bacteria: Importance and Strategies for Their Stimulation in the Human Gut. Front Microbiol. 2016;7:979. Published 2016 Jun 28. doi:10.3389/fmicb.2016.00979
- Sivieri K, Morales ML, Adorno MA, Sakamoto IK, Saad SM, Rossi EA. Lactobacillus acidophilus CRL 1014 improved “gut health” in the SHIME reactor. BMC Gastroenterol. 2013;13:100. Published 2013 Jun 11. doi:10.1186/1471-230X-13-100
- Zhang, H., Sun, J., Liu, X., Hong, C., Zhu, Y., Liu, A., … Ren, F. (2013). Lactobacillus paracasei subsp. paracasei LC01 positively modulates intestinal microflora in healthy young adults. Journal of Microbiology (Seoul, Korea), 51(6), 777–782. https://doi.org/10.1007/s12275-013-3279-2
- Yamano, T., Iino, H., Takada, M., Blum, S., Rochat, F., & Fukushima, Y. (2006). Improvement of the human intestinal flora by ingestion of the probiotic strain Lactobacillus johnsonii La1. The British Journal of Nutrition, 95(2), 303–312.
- Satomi K, et al. (1999). Effects of Culture-Powder Microflora of Propionibacterium of Normal freudenreichii ET-3 on Fecal Microflora of Normal Adults, Central Research Institute, Meiji Milk Products Co., 1-21-3 Sakae-cho, Higashimurayama, Tokyo 189-8530, Japan
- Wang, T., Hu, X., Liang, S., Li, W., Wu, X., Wang, L., & Jin, F. (2015). Lactobacillus fermentum NS9 restores the antibiotic induced physiological and psychological abnormalities in rats. Beneficial Microbes, 6(5), 707–717. https://doi.org/10.3920/BM2014.0177
- Rodgers B, Kirley K, Mounsey A. PURLs: prescribing an antibiotic? Pair it with probiotics. J Fam Pract. 2013;62(3):148-50.
- den Besten G, van Eunen K, Groen AK, Venema K, Reijngoud DJ, Bakker BM. The role of short-chain fatty acids in the interplay between diet, gut microbiota, and host energy metabolism. J Lipid Res. 2013;54(9):2325-40.
- Clarke, S. F., Murphy, E. F., O’Sullivan, O., Lucey, A. J., Humphreys, M., Hogan, A., Cotter, P. D. (2014). Exercise and associated dietary extremes impact on gut microbial diversity. Gut, 63(12), 1913–1920. https://doi.org/10.1136/gutjnl-2013-306541
- Bressa C, Bailén-Andrino M, Pérez-Santiago J, et al. Differences in gut microbiota profile between women with active lifestyle and sedentary women. PLoS One. 2017;12(2):e0171352. Published 2017 Feb 10. doi:10.1371/journal.pone.0171352
- Benedict C, Vogel H, Jonas W, et al. Gut microbiota and glucometabolic alterations in response to recurrent partial sleep deprivation in normal-weight young individuals. Mol Metab. 2016;5(12):1175-1186. Published 2016 Oct 24. doi:10.1016/j.molmet.2016.10.003
- Donga, E., van Dijk, M., van Dijk, J. G., Biermasz, N. R., Lammers, G.-J., van Kralingen, K. W., … Romijn, J. A. (2010). A single night of partial sleep deprivation induces insulin resistance in multiple metabolic pathways in healthy subjects. The Journal of Clinical Endocrinology and Metabolism, 95(6), 2963–2968. https://doi.org/10.1210/jc.2009-2430
- Leproult R, Van Cauter E. Effect of 1 week of sleep restriction on testosterone levels in young healthy men. JAMA. 2011;305(21):2173-4.
- Chen CQ, Fichna J, Bashashati M, Li YY, Storr M. Distribution, function and physiological role of melatonin in the lower gut. World J Gastroenterol. 2011;17(34):3888-98.
- Fakhoury M, Negrulj R, Mooranian A, Al-Salami H. Inflammatory bowel disease: clinical aspects and treatments. J Inflamm Res. 2014;7:113-20. Published 2014 Jun 23. doi:10.2147/JIR.S65979
- Zijlmans, M. A. C., Korpela, K., Riksen-Walraven, J. M., de Vos, W. M., & de Weerth, C. (2015). Maternal prenatal stress is associated with the infant intestinal microbiota. Psychoneuroendocrinology, 53, 233–245. https://doi.org/10.1016/j.psyneuen.2015.01.006
- Kim D, Zeng MY, Núñez G. The interplay between host immune cells and gut microbiota in chronic inflammatory diseases. Exp Mol Med. 2017;49(5):e339. Published 2017 May 26. doi:10.1038/emm.2017.24
- Thursby E, Juge N. Introduction to the human gut microbiota. Biochem J. 2017;474(11):1823-1836. Published 2017 May 16. doi:10.1042/BCJ20160510
- Jernberg, C., Lofmark, S., Edlund, C., & Jansson, J. K. (2007). Long-term ecological impacts of antibiotic administration on the human intestinal microbiota. The ISME Journal, 1(1), 56–66. https://doi.org/10.1038/ismej.2007.3
- Fallani, M., Young, D., Scott, J., Norin, E., Amarri, S., Adam, R., Dore, J. (2010). Intestinal microbiota of 6-week-old infants across Europe: geographic influence beyond delivery mode, breast-feeding, and antibiotics. Journal of Pediatric Gastroenterology and Nutrition, 51(1), 77–84. https://doi.org/10.1097/MPG.0b013e3181d1b11e
- Sharara, A. I., Aoun, E., Abdul-Baki, H., Mounzer, R., Sidani, S., & Elhajj, I. (2006). A randomized double-blind placebo-controlled trial of rifaximin in patients with abdominal bloating and flatulence. The American Journal of Gastroenterology, 101(2), 326–333. https://doi.org/10.1111/j.1572-0241.2006.00458.x