Image Unavailable

More than 500 species of bacteria live in an individual’s digestive tract (hereafter referred to as the gut), although most of the bacteria come from about 30 or 40 species.1 Since bacterial cells are so much smaller than our eukaryotic cells and do not require the support of our extensive connective tissue, we can house ten times as many bacterial cells in our gut (10^14) than we have human cells in the rest of our body.2 Functions of gut bacteria include digesting our food, stimulating cell growth and repressing the growth of harmful microorganisms.3 Our microbiota also have cognitive effects. It has been known for centuries than syphilitic infection (with the bacteria Treponema pallidum) can cause psychological symptoms. This “syphilitic madness” is now better characterized as causing depression, confusion, irritability, poor concentration, dementia and ultimately death without treatment.4 Another pathogenic bacteria is Toxoplasma gondii which reproduces in cats but can live and cause psychiatric effects in humans. In immunocompromised patients T. gondii infection can lead to death by brain inflammation however for most people an infection is asymptomatic. Around 10% of Americans are estimated to be infected with T. gondii,5 although the rate is higher among people with schizophrenia6 and personality disorders.7 Infection is associated with higher rates of car crashes,8 and violent suicidal behaviour.9 Negative effects (including cognitive effects) of the microbiome are not limited to pathogenic bacteria, changing the proportion of bacterial species present in healthy populations can result in intestinal disorders, metabolic disorders such as obesity and diabetes as well as psychiatric disorders such as depression and anxiety.

Human Microbiome Project

Characterizing normal microbiota is an essential first step in understanding their wide-ranging influence on human behaviour and health. To this end the Human Microbiome Project is building a microbiotic species reference database, to see how the differences in microbial affect human health. Most bacteria fall into three families, the Firmicutes, Bacteroidetes, and Actinobacteria. More than 10,000 microbial species have been found. Although these species genomes have been sequenced only 40% of these species have been studied in vitro. Most of the bacteria are anaerobic and difficult to culture. That said there is an enormous amount to learn what we do know – their genetic sequences. There are more than 360x times the number of protein-coding genes in our microbiome than in our genome.10 Together an individual’s genome and the genes of their microbiota constitute their hologenome.

Hologenome Theory

The hologenome theory originated in studies on coral reefs. The coral bleaching of the species Oculina patagonica was determined to be due to infection by the bacteria Vibrio shiloi. Bleaching was observed in a population of O. patagonica in the eastern Mediterranean from 1994 to 2002. After 2003, this coral was found to resistant to V. shiloi infection and was not becoming bleached. Since corals do not have adaptive immune systems, they should only be able to respond through natural selection. Natural selection would take longer than what was observed because the variability would have to come from natural mutations, and the colony would gain resistance more slowly than was observed because only new corals would be resistant and corals take decades to grow to the size of reefs they observed resistance in. A possible explanation for this speed of behavioural plasticity is that it was the result of a new symbiotic relationship with bacteria, which could colonize a reef faster than new corals can grow. This extended “hologenome” can change rapidly in two ways, either through the acquiring new species or by evolution of the microbiome (which would be faster since bacteria reach reproductive maturity much faster than corals).11

It was confirmed that evolution of the hologenome occurs and can drive behavioural changes in the host in 2010. Laboratory flies which were normally fed starch were switched to a diet of molasses. After two generations these flies would only mate with other molasses-fed flies. Two generations is too fast for this behavioural change to have been driven by natural selection of the host genome. When these flies were given antibiotics they began to mate indiscriminately.12 This shows that the behaviour was driven by bacterial changes although it doesn’t differentiate between bacterial evolution and colonization by new bacteria. It also suggests that changes in microbiota can drive speciation.


Since the composition of our microbiota changes as our environment changes, and these changes can have functional effects, it is important to know the changes which occur throughout typical human development. Fetuses have sterile digestive tracts, we typically acquire our microbiota from maternal vaginal and fecal flora through natural childbirth.13 Caesarean section delivery prevents exposure to maternal fecal microbes, resulting in less Bifidobacteria and more Clostridia Difficile which is associated with asthma.14 It is known that children born by C section are 20% more likely to develop asthma.15 Breastfeeding is also important for the formation of a normal microbiome, formula fed infants also had less Bifidobacteria.16 By the end of the first year of life the infant has the same density of microbiota as an adult, and the composition tends to stabilize by age four.17 Even as adults we typically still share 80% of our microbiota with our mothers.18 The most typical disturbance comes from the use of antibiotics in which it can take up to four weeks for the microbiota to stabilize. In adults the microbiota usually reverts back to its previous composition due to the presence of stable colonizers, but the effect of antibiotics can be much more severe for infants.19

Metabolic Conditions

To model type 1 diabetes we have a genetically engineered mouse model called NODs (non-obese diabetics). Over 80 per cent NOD mice develop diabetes in germ-free environments, however when they are given probiotics mimicking normal human microbiota, only 34 per cent of the mice developed diabetes.20 In humans we find it is the proportions of normal bacteria which are implicated in metabolic conditions. People with Type 1 diabetes have microbiomes with less Firmicutes and more Bacteroidetes.21 In contrast obese populations have more Firmicutes bacteria and less Bacteroidetes.22 In addition obese populations have reduced microbial diversity.23 The authors of this study suggest the following analogy with ecological models. The western high-fat sugar rich diet is not like a rainforest which is adapted to a high energy flux and have high biodiversity, but like an unnatural fertilizer runoff in which a few species outcompete all the others resulting in an initial algal bloom and then a hypoxic dead zone. Germ free mice do not become obese when fed a high-fat, sugar-rich diet.24 However when microbes from obese mice were transplanted into the germ free mice, they became obese.25 Germ free mice which did not receive a microbial transplant but had a genetic knock out for fasting-induced adipose factor (Fiaf) – an enzyme involved in fatty acid oxidation show the same pattern of weight gain suggesting that the microbes are causing weight gain by inhibiting this enzyme.26

Chronic, low doses of antibiotics cause mice to gain 15% more body fat. This is consistent with the weight gain found in farm animals who are put on similar antibiotic regiments.27 Early exposure to antibiotics also causes weight gain in humans.28

Support for the microbial theory of obesity comes from the effectiveness of human fecal transplants in reducing metabolic symptoms, such as weight and insulin sensitivity.29 It is not suprising that fecal transplantation has been successful in treating symptoms of a metabolic disorders such as obesity and diabetes. It is also a successful therapy for sufferers of Irritiable Bowel Syndrome30 which is co-morbid with psychiatric illness in 50–90% of cases.31 The tight link between gut bacteria and higher cognition may surprising but there is a growing body of literature which supports it. For example fecal transplantation can also improve symptoms in Multiple Scherlosis,32 Chronic Fatigue Syndrome33 and Parkinson’s.34 It is known that Parkinson’s progresses from the vagus nerve to cerebral cortex. Parkinson’s patients also have damage to their enteric nervous system, which connects the gut to the brain via the vagus nerve. Considering that fecal transplantation reduces symptoms, it is thought that a microbial breach of the intestine may be the ultimate source of Parkinson’s disease.35


Microbes are also implicated in depression. The pathogenic bacteria Borrelia burgdorferii causes Lyme disease which causes depression in up to 2/3 of all cases.36 Non-pathogenic bacteria are also implicated in depression in which bacterial populations are suppressed. One model of depression is periodic separation of infant mice from their mothers. These mice show reductions in Lactobacillus and Bifidobacterium species, functional gut abnormalities, increased corticosterone (stress hormone) levels, weight loss, and causes them to not swim as much in a forced swim test as control mice indicating behavioural despair. Treating the mice with Lactobacillus lowered corticosterone levels and gut abnormalities.37 Another experiment has replicated the effect that germ free mice have an exaggerated stress response and also found reduced expression of brain-derived neurotrophic factor in the cortex and hippocampus.38 Another experiment showed that treating the maternally separated mice with a probiotic culture of Bifodobacterium infantis minimizes weight loss, causes mice to swim longer and causes an increase in the amount of the secotonin precursor tryptophan produced.39 Increasing serotonin levels through selective serotonin reuptake inhibitors is the primary treatment of depression in humans. Human patients with depression are less able to properly digest fructose,40 which is also associated with a reduction in tryptophan production.41 Eliminating fructose from their diet improved their depression.42


Gut microbes are also implicated in anxiety disorders. In humans anxiety disorders are common in patients with disturbed gut flora.43 The bacteria Campylobacter jejuni has been shown to cause anxious behaviour in mice.44 Germ free mice show less anxious behaviour and also less NR2B mRNA expression selectively in the central amygdala which might be responsible for the anxiolytic behaviour since NR2B antagonists have an anxiolytic effect on behaviour.45 The behavioural change might also be caused by increased brain derived neurotrophic factor (BDNF) mRNA expression possibly inducing plasticity in the dentate granular layer of the hippocampus.46 BDNF and the hippocampus are implicated in memory. It is fitting that gut bacterial diversity has been shown to improve both working and reference memory as well as reducing anxiety-like behaviour.47


Autistic populations have a unique microbiome consisting of more clostridial species.48 Half of all autistic children with gastrointestinal dysfunction were found to have the bacteria Sutterella which was completely absent in non-autistic children with gastrointestinal dysfunction.49 There is evidence that for some children with late-onset autism antibiotics can allievate symptoms temporarily.50

Mechanism of action

Although we are starting to uncover links between different microbiotic profiles and functional cognitive effects, the mechanism by which these effects are mediated is not yet understood. Some microbial organisms can produce neurochemicals such as serotonin, melatonin, gamma-aminobutyric acid (GABA) catecholamines, histamine and acetylcholine51 as well as nitric oxide, hydrogen sulfide and carbon monoxide.52 Enterochromafin cells, which are interspersed among epithelial cells throughout the intestines, can secrete serotonin - which is a signaling molecule for both neurons and many gut bacteria - on both sides of the intestinal epithelium. This makes it uniquely suited to be a signal transducer between the microbiome and the nervous system.53

Add a New Comment
Unless otherwise stated, the content of this page is licensed under Creative Commons Attribution-ShareAlike 3.0 License