We are not alone. Whether such statement applies to life forms beyond the planet Earth, is an area of active scientific research, but not the topic of this article. What we can say, however, is that these four words certainly hold when redirecting our attention to our inner being.
Our physical inner being, that is. As it turns out, we are accompanied by billions or perhaps even trillions of very small organisms that live inside us, for better or for worse. And it seems that our intestines are their most popular gathering place.
Who are they? Are they unique to each of us? What is their role within our intestines? And how do they manage to influence an organ that is far removed from their usual living environments?
Let’s dig up some answers.
Entire Worlds Inside Our Gut
Our body is teeming with microorganisms (also called microbiota or microbiome), including bacteria, archaea, fungi, parasites, and viruses. The largest and most diverse habitats of these tiny creatures are located within our small and large intestines and are mostly confined to the interior of the intestines (lumen) or onto the innermost layer of the gut walls (the epithelial surface).
As a matter of fact, Gail Cresci points out that the small intestines carry between 10⁴ and 10⁸ colony-forming units (CFU) per millilitre (mL) — CFU is a way in which microorganisms can be counted — while the number in the colon rises to approximately 10¹⁰–10¹² CFU/mL. In other words, the number of microbiota in our intestines oscillates between tens of thousands and several trillions. Other researchers, such as Iurii Koboziev et al. even mention estimates in the range of hundreds of trillions.
Within the human gut, most of the microorganisms appear to be bacteria. For instance, based on genetic analyses, Junjie Qin et al. find that 99.1% of the microbiota have a bacterial origin, whereas archaea (0.8%) and other microbiota (0.1%) form a relative minority. This may help explain why bacteria usually make up the main focus of research efforts.
Fig. 1. The lumen (on top) is the innermost part of the intestines where the food content passes through. The epithelium is the physical barrier generally keeping the microbiota from entering the surrounding tissue or blood vessels. (Source: Karen Madsen).
When putting the spotlight on the bacterial gut microbiota, a study conducted by Paul Eckburg et al. reveals that two strands (phyla) of bacteria, i.e., Firmicutes and Bacteroidetes, account jointly for 92.7% of the 395 observed bacterial species (phylotypes) — 301 and 65 phylotypes, respectively. In terms of the total number of species, Junjie Qin et al. establish a higher count, however: between 1000 and 1150. Similarly, Jean-Christophe Lagier et al. come up with 1,057 species (of which 65% belong to either Firmicutes or Bacteroidetes).
Still, the composition of the human gut microbiome differs markedly from person to person. As a case in point, Junjie Qin et al. suggest that every individual in their study contains a minimum of 160 different bacterial species, whereby 75 species are shared by over 50% of all individuals present and only 57 species by more than 90%. These findings imply that the greater the sample of people under consideration, the more apparent the differences between people’s gut microbiomes.
Fig. 2. Some physiological properties of the stomach, the small (the duodenum is its initial segment) and large (colon) intestines, including acidity (pH) and oxygen levels. (Source: Paper Christina Ohland and Christian Jobin).
Research furthermore highlights that the intestinal bacterial makeup can be affected by various factors, such as type of diet, infant feeding method, health status, stress levels, geography, aging process, antibiotic usage, environmental exposures, and hygienic habits. Changes in some of these (or a mixture of them) may lead to an imbalance in microbiota communities — which is referred to as dysbiosis — potentially opening the door to illness.
Although some of the microorganisms are prone to promote disease (pathogenic), the relationship of the gut microbiota with its host is overall benign (commensal) and even mutually beneficial (mutualistic). That is, in a healthy human body, the gut microbiome supports metabolic functioning (e.g. vitamin K synthesis), advances and stabilizes the immune system, properly regulates the permeability of the intestinal walls (epithelium), and protects against pathogens.
All the Way Up to the Brain
Before we explore how the gut microbiome could supposedly impact the functioning of the brain, or vice versa, let us look more closely at the entire bidirectional communication network in place that connects the intestines with the brain, the so-called gut-brain axis.
That network relies on the central nervous system, the parasympathetic and sympathetic nervous systems, and the enteric nervous system, underpinned by neuro-immuno-endocrine signalling pathways, in particular the hypothalamic-pituitary-adrenal axis.
Lots of Nerves
The enteric nervous system is the intrinsic nervous system of the gastrointestinal tract — this tract includes the mouth, the oesophagus, the stomach, the intestines, the rectum, and the anus. It is physically incorporated within the lining of this tract (more precisely, in the submucosa and muscular layers).
This nervous system is responsible for, among other functions, the secretion of enzymes (large biomolecules that accelerate chemical reactions), the muscular movements that facilitate the propagation of food (peristalsis), and the detection and communication of chemical and mechanical changes within the gastrointestinal system.
Fig. 3. The enteric nervous system is indicated as “intrinsic innervation” (Meissner and Auerbach plexus) in the tangential view and “intrinsic neuron” in the transverse view. (Source: Paper Manuel Jakob et al.).
Even though the enteric nervous system can perform its duties independently of any inputs from the central nervous system — which comprises the brain and the spinal cord — both these neural networks are nevertheless interconnected through the sympathetic and parasympathetic nervous systems.
The former is known as the ‘fight or flight’ mode and slows down digestive activities, because blood is reoriented towards skeletal muscles and the lungs. The sympathetic nervous system consists of nerve cells (neurons) whose cell bodies are entrenched in the middle part of the spinal cord. One of the ways the sympathetic neurons bind to the intestines is via prevertebral clusters of neuronal bodies (ganglia) and a specific kind of nerves (thoracic splanchnic nerves).
In contrast, the parasympathetic nervous system is described as the ‘rest and digest’ system which activates digestion, as less blood is now requested by the skeletal muscles and lungs. The parasympathetic cell bodies are situated in the brainstem (the brain segment that links the largest part of the brain (cerebrum) with the spinal cord) as well as in the lowest section (sacral) of the spinal cord. The neurons in the brainstem, for instance, reach the gut via the vagus nerve, which is one of the twelve cranial nerves that couple the brain to the rest of the body.
Fig. 4. A schematic overview of how the sympathetic and parasympathetic nervous systems connect to the intestines. (Source: Paper Manuel Jakob et al.).
A few words are in place about the communication between neurons. Passing along information through neurons is regulated by the difference in electric charge (membrane potential) between the inside and outside of the nerve cell. If a neuron is triggered, it releases at the nerve ending (axon terminal) certain molecules (neurotransmitters), such as acetylcholine, serotonin, and dopamine, which can either bridge a small gap (the synaptic cleft) to end up in the detectors (dendrites) of the next neuron or find their way to another type of cell.
Signals that travel from the central nervous system to the organs are called efferent signals (motor neurons), whereas afferent signals (sensory neurons) run in the opposite direction.
Throwing Hormones and Immune Cells into the Mix
The gut-brain communication hub is further reinforced by the hypothalamic-pituitary-adrenal axis. This system is activated by both stress and immune-related signalling molecules (proinflammatory cytokines).
This activation notifies — apart from the sympathetic nervous system — the hypothalamus within the limbic system of the brain (which supports, inter alia, the functions of emotions and long-term memory) to give off a certain kind of hormone (the corticotropin-releasing factor), instructing in turn the pituitary gland (which sits at the bottom of the hypothalamus) to emit another hormone (the adrenocorticotropic hormone), which eventually via the bloodstream arrives at the adrenal glands (located on top of the kidneys).
As a final result, the adrenal glands produce the steroid hormone cortisol — due to the stimulation of the sympathetic nervous system, these glands also synthesize the hormones and neurotransmitters norepinephrine and epinephrine, which impact blood flow, muscle movements (gut motility), the gastrointestinal tract’s innate immune system, and nutrient absorption.
Fig. 5. The working mechanism of the hypothalamic-pituitary-adrenal axis. (CRH: corticotropin-releasing hormone; ACTH: adrenocorticotropic hormone). (Source: Paper Angela Rodriguez et al.).
The main effect of cortisol consists of decreasing the sensitivity of fat and muscles cells to take up insulin and thereby pushing up the blood glucose (sugar) levels — insulin diverts glucose away from the bloodstream by facilitating glucose uptake into many types of cells, including tissue and fat cells. The gastrointestinal tract will counteract this cortisol-induced increasing trend by slowing down the rate of glucose absorption into the blood (through the emission of hormones, which provoke insulin secretion in the pancreas).
In addition, cortisol suppresses the immune system to free up even more glucose to extend assistance to the body’s ‘fight or flight’ mode (this biochemical state, remember, restricts digestion). To appreciate the importance of the gut in this context, it is good to realize that 70% to 80% of the body’s immune cells dwell in the gastrointestinal tract (more concretely, they are embedded in the layers just behind the epithelium — the lamina propria and the submucosa).
What is more, cortisol directly bears upon the workings of the gastrointestinal tract, for example, via mineralocorticoid receptors situated inside epithelial and neural cells within the intestines. As a result, these cells will retain more sodium and water and excrete potassium, boosting blood pressure and affecting nerve communication. Not only that, cortisol also reduces the absorption of calcium in the gastrointestinal tract which may impact gut motility and cell growth.
Over and above the cortisol-related effects, the corticotropin-releasing factor is also produced — besides by the central nervous system — by enteric neurons and immune cells. By acting subsequently on enteric nerves, on mast cells (granulated white blood cells lodged within the intestinal barrier), and on enterocytes (the epithelial cells of the gut), this hormone is understood to have repercussions for gut motility, the permeability of the gut wall, secretion activity, the perception of pain (visceral hypersensitivity), and inflammation processes.
Fig. 6. Apart from corticotropin-releasing factor (CRF) being produced in the brain (top part: central stressors), CRF is also synthesized by enteric neurons and immune cells (lower part: peripheral stressors). (Source: Paper Nigel Bunnett).
From all the above, it becomes clear that the ensemble of neuro-immuno-endocrine communication channels of the gut-brain axis is able to influence the functioning of various intestinal cells, such as smooth muscle cells, immune cells, enteric neurons, epithelial cells, enteroendocrine cells (enterochromaffin cells) and supportive cells (e.g., interstitial cells of Cajal).
At the same time, the activities of these cells are also partially steered by the presence of the gut microbiome. Given that the gut-brain communication pathways are bidirectional, the following question automatically arises: How do gut microbiota manipulate the brain?
Microbiota Are Pulling Our Nerves
Generally, the gut microbiome assists us — as already alluded to in the above section ‘Entire Worlds Inside Our Gut’ — in a broad scope of tasks, including digesting our food, creating certain anti-inflammatory molecules, assembling short-chain fatty acids (the primary energy source for epithelial cells in the colon), and training our immune system.
What are some of the underlying mechanisms through which those activities are capable of driving, to some extent, the workings of the brain?
Bacterial Metabolites and Neuroendocrine Pathways
To start with, microbiota are able to synthesize hormones and neurotransmitters (e.g., gamma-aminobutyric acid (GABA), tryptophan, serotonin, noradrenalin, dopamine, and histamine) that act directly on neurotransmission. They reach the central nervous system either indirectly via the enteric nervous system (afferent signalling) or directly via the bloodstream as well as the vagus nerve.
Other substances (metabolites) manufactured by intestinal microorganisms also shape neuronal activities. For instance, short-chain fatty acids (e.g., butyrate, propionate, and acetate) can reportedly alter the permeability of the blood-brain barrier (which helps preserve the chemical balance within the central nervous system), while secondary bile acids trigger enteric neurons in the colon to discharge a small protein (calcitonin gene-related peptide) that controls peristalsis.
Not only can their self-made metabolites influence the body’s nervous systems, but intestinal microorganisms can also affect neural communication by mediating the release of gut hormones. That is, microbiota stimulate enteroendocrine cells to make peptides (e.g., leptin, ghrelin, gastrin, orexin, neuropeptide Y, and galanin) that are then transported to the brain via the bloodstream or, alternatively, excite enteric neurons.
Fig. 7. Schematic view of some of the pathways that connect the gut microbiota with the brain. (SCFAs: short-chain fatty acids; HPA: hypothalamic-pituitary-adrenal axis; IL: interleukins (cytokines, which are produced by immune cells); CRH: corticotropic-releasing hormone; ACTH: adrenocorticotropic hormone; CORT: cortisol). (Source: Paper Timothy Dinan and John Cryan).
Neuroimmune Routes
What is more, changes in the gut microbiome configuration itself may also impact — with the aid of the immune system — the workings of the brain.
Overall, gut microbiota play a vital role in maintaining a healthy intestinal balance (homeostasis) by working intimately with the immune system to properly regulate inflammations locally induced by some of the microorganisms so that the intestines can be protected from pathogenic infections.
Yet, an imbalance in the composition or function of the gut microbiome (dysbiosis) could possibly perturb this enteric homeostasis, paving the way for chronic intestinal inflammation, which might develop into chronic intestinal illnesses, such as Crohn’s disease and ulcerative colitis, and contribute to several brain disorders, e.g., Alzheimer’s disease, autism spectrum disorder, and schizophrenia. It is still an open question, however, whether dysbiosis is the cause or the product of chronic inflammation.
Fig. 8. The microbiota are in constant bidirectional communication with various cells in the gut wall via multiple signalling pathways, and this communication is regulated in response to perturbations of the microbiota or the brain. The brain can furthermore modulate individual intestinal cells via the hypothalamic-pituitary-adrenal axis (HPA) or the autonomous nervous system (ANS). (SMC: smooth muscle cells; ICCs: interstitional cells of Cajal; ECCs: enterochromaffin cells). (Source: Paper Robert Shulman et al.).
When immune cells in the gut are activated, they expel cell signalling peptides (cytokines) and neurotransmitters that can adjust neuronal activities in the brain.
Cytokines find their way to the central nervous system either directly (via carrier-mediated transport through the blood-brain barrier) or indirectly (via the activation of secondary messengers, including nitric oxide). When the blood-brain barrier is compromised, both immune cells and cytokines are able to enter the brain directly. Additionally, local sites of cytokine production can trigger the nerve endings of enteric neurons or fire signals via the vagus nerve to the cerebral neurons.
Once introduced into the central nervous system, cytokines can spur local immune cells (microglia) to produce even more cytokines. If such inflammatory responses become chronic (neuroinflammation), the presence of cytokines in the brain may lead to neuron death which has been associated with the development of neurodegenerative diseases.
Interconnected Communication
It is good to recall at this point — as elaborated upon in the above subsection ‘Throwing Hormones and Immune Cells into the Mix’ — that proinflammatory cytokines in the brain can switch on the hypothalamic-pituitary-adrenal axis, enhancing blood glucose levels and potentially further destabilizing the intestinal health balance.
In this context, Aitak Farzi et al. remind us of the interconnectedness of all the communication channels between the intestines and the brain. More specifically, they argue that “the communication between the gut microbiota and the [hypothalamic-pituitary-adrenal] axis is closely interrelated with other systems, such as the immune system, the intestinal barrier and blood-brain barrier, microbial metabolites, and gut hormones, as well as the sensory and autonomic nervous systems.”
Fig. 9. An example of interconnected gut-brain pathways in the case of autism spectrum disorder. (SCFA: short-chain fatty acid; 5’-HT: 5-hydroxytryptamine or better known as the neurotransmitter serotonin; GI: gastrointestinal; IL: interleukin (a type of cytokines); LPS: lipopolysaccharides; HPA: hypothalamic-pituitary-adrenal axis). (Source: Paper Maria Vittoria Ristori et al.).
The microbiota-gut-brain interdependence is furthermore elucidated by research studies with mice that do not possess a gut microbiome: These experiments report considerable dynamical and structural changes in the brain relative to regular mice (e.g., memory dysfunction and a different composition of neurotransmitters). They equally demonstrate that the gut microbiome is of paramount importance to the enteric nervous system and to sensory-motor functions (e.g., delayed gastric emptying).
Moreover, these physiological alterations purportedly account for “the differences in stress reactivity, anxiety-related, depressive-like, and social behaviors as well as cognition observed in germ-free animals”, according to Christine Fülling et al.
Under the Lens
In view of the sheer number of microbiota operative in the gut, it might be insightful to direct our focus onto just one bacterial species, i.e., the bacterium Bacteroides fragilis (B. fragilis) belonging to the B. fragilis group within the phylum Bacteroidetes.
B. fragilis is an anaerobic (it survives in areas with little oxygen present) and rod-shaped bacterium that resides in the large intestine. Of all the species within the B. fragilis group, B. fragilis is the most prevalent (62%) one in the colon. Usually, it is harmless to its host and supports the human body by contributing to the digestion of carbohydrates, sustaining the immune system, and assisting in vitamin synthesis, among other biochemical functions.
Fig. 10. The species B. fragilis belongs to the family Bacteroidaceae (green dots). The more we move towards the end of the large intestine, the larger the number of bacteria, the lower the oxygen levels, the less acidic the gut content, and the fewer the number of simple nutrients. Also, the lumen (the inner part of the intestines) has a lower oxygen level relative to the more outward layers. (Source: Paper Fátima Pereira and David Berry).
Nonetheless, if it enters the bloodstream or surrounding tissue — for instance, after intra-abdominal surgery — it can turn into an opportunistic pathogen and cause infection. As a case in point, this bacterium has been identified as a pathogen in brain abscesses, meningitis (an inflammation of the protective cover around the brain and spinal cord), and peritonitis (an inflammation of the membrane that envelops all the internal organs of the abdomen).
What is more, Walter Lukiw provides evidence that, given its ability to engineer proinflammatory neurotoxins, B. fragilis has an important role to play in inflammatory neurodegeneration in the brain, which, for example, typifies Alzheimer’s disease, especially when the integrity of the gastrointestinal and the blood-brain barriers deteriorates with aging and disease.
These observations reflect the alleged prominence of B. fragilis within the gut-brain axis. Several studies based on mouse models affirm such apparent significance by, conversely, investigating its therapeutic potential — its curative effect seems most notably pronounced when the bacterium produces the molecule polysaccharide A.
For one, June Round et al. find that B. fragilis safeguards the mice from experimental colitis (a chronic inflammatory disease of the colon and the rectum). Next, Lloyd Kasper et al. report that it protects the animals from neuroinflammation (more accurately, from experimental autoimmune encephalomyelitis) in the case of multiple sclerosis (a chronic disease of the central nervous system).
Fig. 11. The bacterium Bacteriodes fragilis (left, boxed) spotted just above the epithelium of an intestinal mouse cell. Right: a reconstruction of the bacterium. (Source: ScienceNews).
A third illustration is the research conducted by Sophia Hsien et al., demonstrating that this bacterium can ameliorate gastrointestinal and behavioural symptoms (e.g., increased gut permeability and anxiety) related to autism spectrum disorder (a neurodevelopmental illness).
Against the backdrop of neurodegenerative diseases, such research studies are instrumental to better comprehend the behaviour of microbiota more generally.
Parkinson’s Disease
Let us consider an example with regard to the hypothesized relationship between gut immune responses and the incidence of a brain disorder: Scientists suggest that chronic proinflammatory immune activity in the intestines plays a part in the development of Parkinson’s disease.
In the context of this disease, the brain is lacking in dopamine due to the degeneration and death of dopaminergic neurons — these neurons are the main sites of production of the neurotransmitter dopamine in the central nervous system — resulting in both motor symptoms (e.g., loss of normal muscle functioning, slowness of movement, tremor, speech deficits, gait impairment, and rigidity) and non-motor symptoms (e.g., constipation, anxiety, depression, and lesser sensitivity to odours).
Reserving a role for gut microbiota, Madelyn Houser and Malú Tansey propose a model that describes the course of neuro-immunological events leading up to the observed symptoms of Parkinson’s disease.
In a first step, a toxic substance or an infection in the intestines elicits a proinflammatory immune reaction. If this defensive response is sustained over a longer period of time, it might in a next phase contribute to dysbiosis and heightened permeability of the gut walls. A weakened intestinal epithelium then encourages leakage of bacterial metabolites and inflammatory mediators (e.g., cytokines and prostaglandins) from the gut, cultivating a more systemic immune response throughout the body and thereby possibly debilitating the blood-brain barrier.
Meanwhile, a positive feedback loop ensues: proinflammatory activities boost the levels of alpha-synuclein in the gut as well as the brain — alpha-synuclein is a protein particularly present in large numbers at nerve endings — which, in turn, instigates immune cells to continue to engage in proinflammatory activities.
Not only can systemic inflammation upgrade the expression of alpha-synuclein in the brain, but the protein itself can also make its way to the brain via a hampered blood-brain barrier. What is more, alpha-synuclein is able to travel directly from the gut to the central nervous system via the vagus nerve. All these routes enable an aggregation of alpha-synuclein within the brain where they incite the cerebral immune cells (microglia).
In the final stage of the model, these enduring proinflammatory responses in the brain (neuroinflammation) — accompanied by a subsequent degeneration of neurons — start in a specific region in the brainstem (the dorsal motor nucleus of the vagus nerve) to eventually spread out to other brain regions, including the site where dopaminergic neurons amass (in the substantia nigra of the midbrain). Their degeneration and death cause the symptoms typical of Parkinson’s disease.
Fig. 12. In a susceptible individual, inflammatory triggers (1) initiate immune responses in the gut that deleteriously impact the microbiota, increase intestinal permeability, and induce increased expression and aggregation of αSYN (2). Synucleinopathy may be transmitted from the gut to the brain via the vagus nerve (3b), and chronic intestinal inflammation and permeability promote systemic inflammation, which, among other things, can increase blood-brain barrier permeability (3a). Intestinal inflammation, systemic inflammation, and synuclein pathology in the brain all promote neuroinflammation (4) which drives the neurodegeneration that characterizes PD (5). (Source: Paper Madelyn Houser and Malú Tansey).
One Step at a Time
For years, we have been living with our body and introducing every day food and liquids into our gastrointestinal tract, yet at the same time there is still so much going on inside us about which we are clueless, especially when it comes to the role of our smallest inhabitants — the microbiota.
That is why research exploring the significance of the gut microbiome within the gut-brain axis is so fascinating. Moreover, such academic investigations become highly pertinent and needed if we consider the interlinkages that some of these microorganisms appear to manifest between neurodegenerative diseases and gastrointestinal ailments.
Even though most of these experimental studies are currently still based on animal models, they nevertheless signal a promising potential in general for the treatment of human-related brain disorders and intestinal maladies.
After all, that first step on the moon had surely not been possible without the innumerable preceding steps of scientific progress along the way.
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