Our Inner Ecosystem: Overview of the Human Gut Microbiome

This life can be a lonely one at times. But there’s good news—you’re never really alone. In fact, at any given moment, you exist in the company of 100 trillion to 1 quadrillion organisms.1 That’s more than the number of stars estimated to exist in the Milky Way Galaxy.2 Even better, many of these organisms are dedicated to protecting you from disease, supplying you with nutrients, and improving your life in a handful of other ways. We’re talking about the gut microbiota— a collection of bacteria, archaea, and eukarya that colonize the human gut and are present in your gastrointestinal (GI) tract from the moment you’re born.3 This diverse microbial ecosystem has co-evolved alongside humans for thousands of years, forming a mutually beneficial relationship that aids humans in metabolic processes, intestinal homeostasis, immune functions, and even brain function and emotional behavior.4,5 In the scientific literature, humans and their beneficial gut microbes have been referred to as a superorganism, a term coined in 1928 by myrmecologist (i.e., one who studies ants) William Morton Wheeler to describe a colony of ants, or more broadly, an association of multiple organisms of the same species working synergistically as a single unit. However, unlike ants, humans and their resident microbes are not technically a superorganism ; this is because Homo sapiens and a gut bacterium such as Lactobacillus acidophilus are not of the same species. So, while many works of scientific literature and popular media refer to the human-microbiome unit as a superorganism, some authors describe humans and their gut microbes as a holobiont, or organisms of differing species working together and responding to environmental challenges together in ways that a single organism could not.6,7

Whatever you’d like to call this unit, humans and their gut microbes are an inseparable entity with a complex composition that differs significantly from person to person. Among humans, our individual collection of microbiota differs so significantly from one another that some researchers have likened it to a fingerprint, in that the composition of our microbiome is distinct enough that we can each be identified by the genetic material present in these microbial gut organisms.8

Close study of the composition, development, and essential functions of the human gut microbiome is relatively new. The idea that human health and longevity could benefit from consuming fermented foods containing beneficial bacteria dates back to the early 1900s, but the term microbiome wasn’t coined until 2001, and the Human Microbiome Project, an initiative funded by the National Institutes of Health to characterize the human microbiome and analyze its role in health and disease, wasn’t established until 2007.9,10 Since then, advancements in the understanding of the structure and complexity of the gut microbiome has allowed scientists to further study the beneficial effects of this biological ecosystem on human health and disease.9


There are currently 1,000 different species of bacteria that have been identified as possible colonizers of the human gut. The gut microbiome of one healthy adult contains an estimated 109 species of microbes, though due to the fingerprint-like indiviuality of the gut, this number tends to vary from person to person.10 While the gut contains various types of microorganisms, bacteria is the most studied, with less research available on other microorganisms, such as fungi and archaea.11,12

Gut bacteria classification.

Bacterial species of the gut belong to a total of eight phyla, but the majority belong to three phyla: Firmicutes, Actinobacteria, and Bacteroidetes.10 More than half  of Firmicutes are members of the Clostridia (20.3%) class, which is the most abundant class, followed by Bacteroidia (18.5%), Bifidobacteriales (16.6%), Enterobacterales (14%) and Lactobacillales (14%).10 All members of the Clostridia class are members of the Clostridiales order and all of the Bacteroidia class belong to the Bacteroidales order—these two are the most abundant orders.10 There are 27 organisms which are members of Bifidobacteriaceae family, and 26 of them belong to Bifidobacterium longum, which is the most abundant species.10


Factors that have been shown to influence the specific composition
of your gut microbiome include the method by which you were born (i.e., via caesarean section [c-section] or vaginal birth), whether you were breast fed or bottle fed, where you live, what you eat, medications you take, and your stress levels.9

Development of the infant microbiota.

Exactly when bacteria first colonizes the GI tract of infants has been a point of debate over the years; initially, scientists agreed that infants receive their first dose of bacteria during the birthing process, as they exit the birth canal. Later research points to the presence of microorganisms in the placenta, amniotic fluid, and umbilical cord as evidence of earlier colonization.13–15 Because a woman’s vaginal microbiota naturally differs from her skin microbiota, the method of infant delivery will be reflected in the microbes that colonize the infant’s gut.9 Some research suggests that infants born via c-section who aren’t exposed to the vaginal microbes of their mother could suffer long- term health disadvantages, such as increased risks for asthma and obesity, but research on this isn’t definitive and other researchers have pointed
out flaws in the methodology of many studies that supports this theory.16,17 Additionally, new research has observed the differences in the gut microbiota of infants born via c-section and those born vaginally all but disappear after 6 to 9 months of life.18

  Additionally, breastfeeding has been shown to be vital to the development of the infant microbiome; human breastmilk can contain over 700 possible species of beneficial bacteria, and during breastfeeding, this bacteria further colonize the newborn’s gut. Another important component of breastmilk is human milk oligosaccharides, a special type of sugar found exclusively in breast milk that acts as a prebiotic to feed those beneficial microbes; so far, researchers have identified over 100 different types of oligosaccharides that can be present in human breast milk.19 In the same way that each human’s gut microbiome is unique to the individual, the composition of bacteria and oligosaccharides in each mother’s breast milk will be unique and correspond to the needs of her baby.20

A child’s microbiome fully matures at around three years of age, and at this time, resembles a fully-grown adult’s gut microbiome. Save for external disruptions, such as drastic diet changes and antibiotic use, this will remain stable until natural changes related to old age begin to occur.9


Short-chain fatty acids (SCFAs).

As researchers continue to explore how the gut microbiome benefits the human that it inhabits, the importance of these mysterious critters becomes increasingly more apparent. One well-studied process that has been shown to be beneficial to humans is the production of short-chain fatty acids by their gut microbes. Because we humans lack the enzymes to digest most dietary fibers, our bodies have outsourced this job to our gut microbiome, resulting in a number of benefits.21 SCFAs are the main byproduct of the fermentation of partially digestible and nondigestible polysaccharides (i.e., fiber) by the microbes in our large intestine.21,22 Fermentable fibers include pectin, beta-glucans, guar gum, inulin, oligofructose, and resistant starches.23 Acetate, propionate, and butyrate are the most abundant SCFAs produced by our gut microbes. Research in the past few decades suggests SCFAs can prevent colon cancer and bowel disorders,24 as well as increase insulin sensitivity and prevent metabolic syndrome—a condition that increases the risk of heart disease, Type 2 diabetes, and stroke.21 A diagnosis of metabolic syndrome is based on the presence of at least three of the following five symptoms: high blood pressure, high fasting glucose, abdominal obesity, high blood triglycerides (i.e., dyslipidemia), and low high-density lipoprotein (HDL) cholesterol.25

Immune regulation.

In addition to the vital production of SCFAs, our gut microbes are thought to play a crucial role in the regulation of our immune system. SCFAs also play an important role in gut-associated immunity by decreasing inflammation and promoting the generation of immune cells, such  as T cells. In studies using germ-free mice, or mice that have been raised in an isolated environment so as to never develop a microbiome, researchers have observed abnormal and impaired immune function, including the absence or underdevelopment of lymph nodes both throughout the body and specifically in lymphoid tissues associated with the gut.26 DISRUPTION OF THE HEALTHY GUT MICROBIOTA

At any stage of life, various external factors can lead to changes in the gut microbiota; research suggests that this disruption of microbial homeostasis in the gut, also referred to as dysbiosis, can contribute to a host of health conditions, including obesity and Type 2 diabetes.26 Earlier, we touched on the factors that influence the development of the infant microbiome, including delivery and feeding method, and how this development might affect the health of an infant in his or her adult life. In addition to infant development, antibiotic use and diet throughout a person’s lifetime can lead to unfavorable changes in the gut microbiome.


Broad-spectrum antibiotics, such as clindamycin, are a less-than-elegant approach to treating bacterial infections, as these antibiotics don’t discriminate between killing the bacteria causing the infection and the diverse beneficial bacteria in the gut. This disruption of the normal balance of bacteria in the gut has been shown to lead to persistent problems later on, including inflammatory bowel disease, diabetes, and obesity.26 While antibiotics have saved millions of lives, and no health professional or medical researcher would argue for the eradication of their use, further understanding of the effects and their long-term consequences of antibiotic use on the human microbiome can help healthcare professionals and patients take preventative steps when antibiotic use is necessary. Currently
used methods cited in the literature include the use of commercial probiotic supplements containing Lactobacillus and Bifidobacterium species and prebiotic supplements, as well as increased intake of fermented vegetables (e.g., kimchi, sauerkraut) and fermented dairy products (e.g., kefir, yogurt).27 Possible future methods that have been proposed include developing narrow-spectrum antibiotics that target a single pathogen; advanced, pharmaceutical-grade probiotics tailored to the specific needs of each patient’s microbial composition; and banking pretreatmed fecal specimens of patients taking antibiotics for posttreatment transplantation.28


Diet is believed to be even more influential than antibiotics when it comes to the composition of an individual’s gut microbiota. Available research on
the effects that diet can have on the gut microbiome suggests that minimally processed, high-fiber, lower-fat diets promote the healthiest gut microbiome compared to other diets.29 In addition, prebiotic foods containing fermentable fiber are thought to be essential for the gut to produce SCFAs. For a list of prebiotic foods that you can eat to support the health of your gut, check out PAGE XX.

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