Microbiome–Gut Dissociation in the Neonate: Autism-Related Developmental Brain Disease and the Origin of the Placebo Effect

Abstract

While the importance of the intestinal microbiome has been realised for a number of years, the significance of the phrase microbiota–gut–brain axis is only just beginning to be fully appreciated. Our recent work has focused on the microbiome as if it were a single entity, modifying the expression of the genetic inheritance of the individual by the generation of interkingdom signalling molecules, semiochemicals, such as dopamine. In our view, the purpose of the microbiome is to convey information about the microbial environment of the mother so as to calibrate the immune system of the new-born, giving it the ability to distinguish harmful pathogens from the harmless antigens of pollen, for example, or to help distinguish self from non-self. In turn, this requires the partition of nutrition between the adult and its microbiome to ensure that both entities remain viable until the process of reproduction. Accordingly, the failure of a degraded microbiome to interact with the developing gut of the neonate leads to failure of this partition in the adult: to low faecal energy excretion, excessive fat storage, and concomitant problems with the immune system. Similarly, a weakened gut–brain axis distorts interoceptive input to the brain, increasing the risk of psychiatric diseases such as autism. These effects account for David Barker’s 1990 suggestion of “the fetal and infant origins of adult disease”, including schizophrenia, and David Strachan’s 1989 observation of childhood immune system diseases, such as hay fever and asthma. The industrialisation of modern life is increasing the intensity and scale of these physical and psychiatric diseases and it seems likely that subclinical heavy metal poisoning of the microbiome contributes to these problems. Finally, the recent observation of Harald Brüssow, that reported intestinal bacterial composition does not adequately reflect the patterns of disease, would be accounted for if microbial eukaryotes were the key determinant of microbiome effectiveness. In this view, the relative success of “probiotic” bacteria is due to their temporary immune system activation of the gut–brain axis, in turn suggesting a potential mechanism for the placebo effect.

1. Introduction: Non-Communicable Disease, the Microbiome, and Symbiosis

The key to understanding the puzzle of non-communicable disease lies in the findings of Denis Burkitt, who carried his surgical skills around Africa in the decades immediately following the end of the Second World War. While describing a transmissible viral disease now known as Burkitt’s lymphoma [1], he also noted the near complete absence of the non-transmissible diseases of what he described as “Modern Western Civilization” [2]. Knowing nothing of the microbiome, Burkitt settled for an environmental explanation based on the high consumption of dietary fibre in most of the peoples that he visited. Unfortunately for the full understanding of these diseases, he then assumed that the absence of disease in the Maasai (then known as the Masai) was due to them having become acclimatised to a high-cholesterol meat-based diet over many generations. Sadly, although he provided much evidence of people consuming a high-fibre diet succumbing to disease after moving to low dietary fibre environments, he did not attempt to uncover evidence of Maasai-like steppe-dwelling peoples remaining resilient to these diseases when living in such Modern Western Civilisations [2]. In addition, although he noted the, to him, inexplicable absence of non-communicable immune system diseases in his African subjects, Burkitt simply failed to mention mental health at all.

The recent emphasis placed upon the intestinal microbiota as a source of B-vitamins and the short-chain fatty acids (SCFAs), including acetate, propionate, and butyrate [3], has provided an opportunity to revisit Burkitt’s findings, including a potential explanation for immune system disease [4]. While a highly diverse bacterial microbiome has been associated with health [5], it was noted that repeated exposure to low-residue diets over several generations of mice caused the apparent disappearance of certain representatives of their normal microbiota [6]. In addition, essentially the same reduction in diversity following on from industrialisation has been noted among domesticated animals [7], who also suffer from immune system diseases similar to humans [8]. Significantly, however, the absence of specific immune-modulating bacteria in captive bred mice was shown to affect the outcome of experiments investigating aspects of amyotrophic lateral sclerosis [9], thereby posing a major question as to the relevance of disease studies using laboratory animals as a model. Not surprisingly, the potential significance of the microbiome and the microbiota–gut–brain axis for the treatment of psychological diseases has also been recognised, albeit that Ganci et al. describe the sequence as “brain–gut–microbiota”, while recognising the eventual need for a “significant paradigm shift” among practitioners in the field [10]. Importantly, however, Brüssow has recently pointed out the problems associated with the dysbiotic microbiome concept, specifically the absence of sustained scientific effort to uncover the basic “ecological and evolutionary” rationale for either the existence of the microbiome in the first place, or for the involvement of specific health-enhancing bacteria [11].

Partly in response to this dilemma, our approach has been to look at the microbiome as if it were a single entity, effectively a “black box”, in which the only measurable factors are input and output, thereby bypassing the complexity of microbe–microbe and microbe–gut interactions. A consequence of this method of analysis is that individual “good” microbes need not be specifically identified. Indeed, the observation of interkingdom signalling amines such as dopamine, serotonin, and histamine within the gut lumen [12] suggested to us that the microbiome could act as if it were an active entity, rather than just a passive supplier of nutrition [13]. Note that such agents may be defined as semiochemicals: molecules that convey information from a member of one species to a different species, often between the different “kingdoms” of life, such as bacteria to eukaryotes or vice versa. Furthermore, psychotropic effects may occur without any need for such amines to penetrate the brain if they can activate the gut wall and thereby stimulate the gut–brain axis. A combination of direct and indirect communication is likely. In this context, a new class of gut sensory epithelial cells have recently been uncovered. Called neuropod cells, they directly sense the gut contents and thereby pass information on to the brain via the vagus nerve [14]. Hormone-like substances produced by gut prokaryotes may activate the gut wall can be described as semiochemicals, prokaryote–eukaryote interkingdom signalling molecules. Serotonin, for example, can be produced both within the gut lumen itself [15] and also by the adjacent enterochromaffin cells under the influence of SCFAs [16]. This serotonin produced in the gut has positive direct gastrointestinal effects such as gastrointestinal and pancreatic secretions, or gastrointestinal motility, although it cannot cross the blood–brain barrier (BBB), as its precursor, the amino acid tryptophan (Trp), does. Tryptophan consumed in the diet can either remain in the gut or pass through the BBB, and in either case can be the precursor of serotonin and melatonin in a virtuous pathway, or be a precursor of metabolites of the kynurenine pathway, leading to neuroinflammation in a vicious cycle, which could be the origin of or contribute to various mental impairments [17]. Colonic cells of the immune system also benefit from such SCFAs [18]. Bearing in mind Burkitt’s observations, some form of immune system control must also count as an “output” of the microbiome [2].

On the whole, it seems that the microbiome is sufficiently complex to render a purely bacterial interaction questionable and, indeed, unicellular eukaryotes have been postulated as a “missing link” between the gut and the microbiome [19]. Normally such entities have been considered to be parasites but, however, some members of the genus Blastocystis have been shown to be consistent with apparently healthy human gut microbiota [20]. Equally, the contribution of the mycobiome over the first month of life has been investigated [21]; and the involvement of archaea, bacteriophages, or other viruses in a healthy human gut has also begun to be assessed [22,23,24], although the bulk of both bioinformatic and microbiology techniques are geared towards the detection and classification of bacteria. Interestingly, we have previously suggested that the neonate immune system becomes calibrated against the microbial environment of the mother, for which we have suggested the presence of unicellular eukaryotic microbial sentinel cells [25] as a hypothetical precursor of mammalian dendritic cells [26].

Although it is not the aim of this article to discuss Margulis’ concept of the holobiont [27], Rosenburg’s extension to the hologenome [28], or their drawbacks [29], nevertheless symbiosis confers value on the combined multicellular animal and its associated microbial community. In essence, as the animal provides the stability associated with the slow changes brought about by natural selection, so the microbiome provides the speed of change associated with horizontal gene transfer and, accordingly, the combination possesses the advantages of both sides of what Woese has described as the Darwinian threshold [30]. Interestingly, it has been suggested that the genetic mechanisms to produce cell–cell signalling molecules discussed above, including dopamine, have been transferred from bacteria to animals by horizontal gene transfer [31]. In turn, this also reinforces the idea that the animal–microbial community partnership has co-evolved over time [25].

Owing to the above-mentioned flexibility of horizontal gene transfer, throughout the bulk of this article the terms microbiota (normally indicating the actual entities themselves) and microbiome (often indicating their genes) are used interchangeably in order to avoid excessive repetition. In addition, the term semiochemical is used to represent interkingdom signalling molecules produced by the microbiome, so that its output can be described as a composite immune–semiochemical system. By contrast, the normal term “hormones” is used for those messenger chemicals produced by the body to affect the behaviour of the microbiome. Interestingly, both hormones and semiochemicals may be the same molecule. Thus, for example, dopamine production may occur in the brain [32] and in the periphery [33] but, as described above, it is also produced by bacteria in the gut [12] and is therefore defined in this article as a semiochemical. Although the precise function of the dopamine synthesised in this way remains unclear, its previous description as an interkingdom signalling molecule [12] reflects the fact that bacteria and multicellular eukaryotes are exchanging information. Accordingly, dopamine would be an example of a semiochemical having functions that originally evolved within the Animalia [31], presumably as part of the development of the gut–brain axis itself [25]. After all, we must bear in mind that the brain is a very privileged organ in which glia cells, immune cells, lymphoid organs, and the microbiota that mediates numerous processes interact [34], all of these entities connected through the blood, lymphatic system, and the afferent and efferent nerves via sympathetic and parasympathetic systems.

2. Maternal Microbial Inheritance and Disease

2.1. Non-Communicable Disease

As stated above, Denis Burkitt commented on the presence of a wide variety of non-communicable diseases in what he called “Westernized Civilisations”, and their absence in the peoples he was studying in Africa [2].

Table 1. Selected Westernized non-communicable diseases noted by Burkitt [2].

Appendicitis	Coeliac Disease	Coronary Heart Disease
Deep vein thrombosis	Diabetes, type 2	Diverticular disease
Gall stones	Haemorrhoids	Hiatus hernia
Multiple sclerosis	Obesity	Pernicious anaemia
Pulmonary embolism	Rheumatoid arthritis	Thyrotoxicosis
Tumours of the bowel	Ulcerative colitis	Varicose veins

illustrates a selection of such diseases and, as we have reported before [35], it will be seen that they represent a mixture of intestinal, circulatory, and immune system conditions [2].

Although Burkitt pointed out that people could suffer from more than one of these diseases, unlike Barker he did not mention poor mental health in his analysis of non-communicable conditions. However, more recently (2014) a “p-factor” (i.e., psychopathology-factor), has been developed to acknowledge the fact that many psychiatric conditions are co-morbid with one another and, therefore, do not fit easily within the confines of the Diagnostic and Statistical Manual of Mental Disorders (DSM) [36]. This p-factor is analogous to Barker’s 1990 foetal origins hypothesis in that it recognises that such conditions seem to be inherited and start in the young [37]. Otherwise, it is entirely descriptive and does not imply any specific mechanism [36]. As explained in the following sections, the most succinct way to account for the early onset of autism and related developmental brain disease, presumably including various psychopathologies, is by the lack of communication between microbiome and gut wall in the neonate, and consequent failure of the gut–brain axis. In turn, this leads to a lack of interoceptive stimulation to the brain and subsequent distortion of its growth.

2.2. Evolution and Ecology: Maternal Microbial Inheritance

Nowadays, while there is a general recognition that Burkitt’s diseases are due to the degradation of the intestinal microbiome [4], the comments of Brüssow about the lack of evolutionary and ecological rationale for microbiome-related concepts are still applicable [11]. Accordingly, as stated above we have recently suggested a way in which the microbiome could have evolved so as to take account of the microbial environment of the parent [25]. This system seems to be optimised for the Vertebrata, so that either live birth or egg will be exposed to the intestinal microbes of the mother. Although it is perfectly possible that valuable microbes may be present in the womb prior to giving birth [38], it is reasonable to suppose that the majority will be transferred during the birth process itself, affording what we describe as a maternal microbial inheritance [25]. Unfortunately, there does not seem to be any repair mechanism in place and, accordingly, the propensity for disease is passed on from mother to child without amelioration, in turn explaining the “p-factor” described above [39].

Evidence for a much longer association between humans and their associated microbes has recently been presented. Although covering only bacteria, the authors state that their results are consistent with the transmission of microbiota out of Africa over thousands of generations [40]. Interestingly, a review of a child’s first 1000 days emphasises the “intergenerational” nature of the microbiome operating across the generations [41].

2.3. Genes versus Microbial Environment: The Trouble with Twin Studies

A perennial question in essentially all aspects of human health is the relative importance of genetic and environmental factors. Experimental design can pose problems, usually requiring enough subjects to obtain statistically significant results. In principle, monozygotic versus fraternal twins will allow a degree of control, however. Accordingly, in the 1980s an obesity study was performed in Quebec, Canada, by Claude Bouchard and his team, in which twelve pairs of monozygotic male twins were overfed by 1000 kcal per day, after an initial period to determine normal eating patterns. The interesting point is that significant differences in fat accumulation and distribution were found between twin pairs, rather than within the pairs themselves, and this result was taken as an indication of the significance of genes, i.e., that weight was primarily under genetic control [42]. Although this was an ingenious experiment, Bouchard could not have anticipated the significance of the microbiome.

The key point about twin studies is that a natural birth will give both twins, either identical or fraternal, the same maternal microbial inheritance alongside their genetic inheritance. Accordingly, the natural birth of one pair of twins may well afford a very different microbiome from another pair, dependent on the degree of degradation of the microbiome of their respective mothers. In these circumstances, it follows that deductions made about the genome of the host include its guest, the microbiome, and therefore come close to Rosenburg’s concept of the hologenome [28]. Of course, twin births carry an extra danger and are more likely to be delivered by sterile caesarean section, potentially leading to wide variation in both microbiome and health outcome, whether genetically identical or not [43].

2.4. Research Challenges Posed by Dual Genetic/Microbiome Inheritance

Gut walls represent unique intersections between the internal and external worlds and, as such, they possess an enteroendocrine system [44], including recently discovered neuropod cells [14]. While the foundations for this system were laid in the womb, the transition from dependant to independent entity is critical, and probably includes information about the microbial environment into which it is born. While everything suggests there to be a rapid, seamless association between maternal microbiome and gut wall when everything is functioning correctly, the loss of microbial diversity has introduced a disconnect into the system, leading to microbiome–gut dissociation and consequent disease. There are three sets of challenges:

• Ethical dilemmas: As Harald Brüssow reminds us [11], while it is incumbent upon scientists to design definitive experiments under controlled conditions, medicine operates under formidable ethical constraints. Nevertheless, the principles of Bouchard’s experiment [45] could be employed to design an observational study in which the health status of each of a pair of monozygotic twins was followed while noting potential microbiome-degrading factors: the degree of sterility of delivery by caesarean section, for example, or antibiotic use in mother or subject. However, as it is hard to envisage a conclusive outcome from such a study, the most likely result is for a decision on the nature of the microbiome to lie with the perceived overall balance of probability.
• Semiochemicals: Professor Nobuyuki Sudo and his team have been investigating the role of the “commensal” microbiota in the production of amine signalling molecules such as serotonin [12,15]. We have previously suggested that an ingestible sensor be developed to check the flow of such semiochemicals in response to various stimuli [45]. Although suitable for human studies, initial experiments could be carried out in animals, preferably ethically sourced from unpolluted, wild-type environments, rather than laboratory-bred.
• Sentinel cells: The most succinct way to transfer immune information between generations is by the physical transfer of potential antigens along with a method of labelling to distinguish pathogens from harmless environment components. Although no such entity has been described as yet, we have previously suggested that one may have been a eukaryotic evolutionary precursor of antigen-presenting cells [25]. Although similar cells may be present throughout unpolluted populations, they may well be absent from humans or our pets and farmed animals suffering from non-communicable diseases [39].

Although treated separately, it is possible that the immune and semiochemical systems cannot easily be separated in practice [46]. In summary: it is by observing the nature of non-communicable disease that one can discern the overall functioning of the uncompromised microbiome, although it is also in the nature of this “black box” method of investigation that the role of individual microbes cannot readily be discerned. It is important to note, however, that horizontal gene transfer implies that critical functions could be performed by a variety of different bacteria or, indeed, archaea. By contrast, in the absence of adequate information, the role of microeukaryotes remains unclear [19].

3. The Functioning Microbiome: Microbiome–Gut Association (A Virtuous Circle)

While the word dysbiosis has been used to imply a malfunctioning microbiome, the lack of a precise meaning is unhelpful [47]. In this black box approach, however, non-communicable disease is defined as a deficiency of microbiome function and, in that sense, the nature of disease can indicate its original function. Using this principle, we have identified three basic disease types stemming from a combined immune–semiochemical system deficiency [39]. Coeliac disease, for example, includes elements of both immune system malfunction [48] and depression [49], the latter resulting from the action of an inefficient gut–brain axis on the brain [35]. Likewise, the gain of excess adiposity is, to us, not due to some lifestyle disease [50], for which the evidence is poor [51], but rather to the lack of faecal energy excretion as the microbiota fail to grow and be excreted. The key point here is that, all other lifestyle factors staying the same, the gain in weight leads to increased energy expenditure via a raised basal metabolic rate, thus directly offsetting a reduction in faecal energy loss [52].

Bearing in mind that symbiosis necessarily works across the generations, the outline of events is illustrated in Figure 1. Starting with the adult (left hand side), we envisage a partition of nutrition stimulated by the balance between bodily hormones and gut semiochemicals, influencing gut motility and peristalsis in what we have described as a virtuous circle [13]. Receiving adequate nutrition, microbiota grow and are excreted, with the faeces carrying away significant amounts of energy. We envisage that this system has evolved with the Vertebrata to respond to famine or illness, when an increase in the levels of bodily hormones will slow down peristalsis, divert extra nutrition to the body and, therefore, down-regulate microbial growth. When the emergency passes, the microbiome can revert to full growth [25]. Note that the faeces contain active intestinal cells, known to be valuable for faecal microbiota transplantation [53]. The key to health stems from the birth process (right hand side of Figure 1) as the neonate becomes contaminated with vaginal and intestinal microbes [54] in a process that we term maternal microbial inheritance. Ideally in conjunction with breast milk, these faecal microbes pass down to the gut, grow, and start to make connections with the developing gut wall. Interestingly, this process of making connections is closely analogous to the compatibility tests carried out between two items of electronic equipment prior to full communication taking place. In the electronics field this is known as handshaking and, in biology, a similar process is likely to involve epigenetic modification of the parental genes by the maternal microbiota. Active immunosuppression in infants, mediated by CD71+ erythroid cells, may also contribute to this, allowing colonisation by microbiota [55], making this handshaking easier. Unfortunately, little is known about epigenetic involvement by the microbiome [56], but it is likely that this is part of the way in which the genetic inheritance of an animal is modified by its environment [57].

As stated above, the flexibility of the microbiome is due to horizontal gene transfer which, in turn, is facilitated by bacteriophage viruses [58]. First observed by the trapping of carbon atoms in the upper layers of the sea, this situation describes an accelerated uptake of mobile genetic elements that has been called a viral shunt [59], and that has also been detected in the soil as part of biogeochemical microbial turnover [60]. Presumably, it is this same series of events within the enclosed intestinal microbiome which allows the take-up of enzymatic abilities to deal with new foods, such as those associated with seaweed digestion [61]. It is likely that this affords the rationale for increased microbial diversity to be associated with good health [5]. However, the critical point may follow when this highly diverse, fully functional microbiome is passed on from mother to neonate in the seemingly accidental process of maternal microbial inheritance. The change in microbial composition from pregnancy to early infancy has been reviewed recently, bearing in mind that modern populations are already suffering from a degree of non-communicable disease [62].

For example, an association has been found between the composition of the microbiome and the temperament of young children [63], but on the full understanding that association does not imply causality. In fact, it should be appreciated that there the complex relationships between host genetics, environmental factors—method of delivery, initial feeding (breastfeeding or formula feeding), contact with the outside world, and lifestyle from birth onwards—as well as microbial interactions may determine the risk, not conditioning, of the development of a disease [64]; and yet such factors and interactions do not seem to explain the totality of why a mental disorder does or does not develop.

4. Poor Microbial Inheritance: Microbiome–Gut Dissociation (A Vicious Circle)

While Denis Burkitt described many non-communicable conditions in the mid-20th century, albeit excluding poor mental health, by late in the same century the epidemiological studies of David Barker had identified early life as the cause of such diseases. Significantly, his 1990 paper “The fetal and infant origins of adult disease” mentioned schizophrenia in what became known as his fetal origins hypothesis [37]. Subsequent papers confirmed the validity of the epidemiology [65], and its economic relevance [66], but without elucidating any mechanism by which events in early life could give rise to the adult diseases that were becoming increasingly common. In parallel with this activity, David Strachan was pondering the cause of the rapid rise in cases of hay fever and, more worryingly, childhood asthma, writing a paper in 1989: “Hay fever, hygiene and household size” [67]. In essence, his hygiene hypothesis suggested that children were no longer being exposed to an external microbe that was calibrating our immune system, so as to tell pollen from pathogens, for example. Sadly, extensive work by Rook and his co-workers failed to find convincing evidence for these external immune modifying agents, his putative “Old Friends” [68]. By this time, food allergy [69] was joining the list of childhood-centred immune system diseases that were becoming known as the “atopic march” [70]. Equally, by the dawn of the 21st century it was no longer possible to ignore the increase in poor mental health [71], or its close association with immune system problems [72] and allergic disease [73]. Differences in maternal microbiota, drug use, or stressing conditions have been revisited to see if they might cause a type of foetal programming that results in mental health conditions in adulthood [74,75].

The situation following poor microbial inheritance is outlined in Figure 2. A failure of the microbiome to completely engage with the gut wall from birth means that the brain receives inadequate input from the gut–brain axis (indicated by the displaced arrow in Figure 2). In turn, this leads to poor brain development during its subsequent growth and, therefore, the increased chance of detectable mental illness in later childhood or as an adult. Indeed, deficiencies in the handshaking process and the gut–brain axis will change the shape of the brain as it grows into adulthood, and this may be associated with specific disease, for example, psychopathology [76] or with autism and schizophrenia [77]. While our mechanism accounts for the co-existence of developmental brain disorders with immune system disturbance, as noted above [77], it also allows for weight gain by reduction of faecal energy excretion [52]. Thus, as the compromised gut–brain axis fails to stimulate the movement of food through the gut, decreasing gut motility, so the virtuous circle of positive feedback turns into a vicious circle, reducing semiochemical output and leading to low faecal energy excretion and high weight retention [13]. Note that the whole immune–semiochemical system is affected from birth, leading to the potential for all three forms of non-communicable disease: weight gain and its consequences, e.g., type 2 diabetes, immune system problems, e.g., type 1 diabetes, and many seemingly different forms of poor mental health [39].

While the flexibility of the microbiome is due to facile horizontal gene transfer of desirable attributes, such as seaweed digestion mentioned above [61], so it is likely that this process requires high microbial diversity to be successful [5]. As noted above, studies in laboratory animals indicate that the regular intake of low-residue food may eventually bring about the loss of microbial diversity [6], although it is also worth bearing in mind more recent results indicating the danger of a sole reliance upon studies involving laboratory animals [9]. Potentially, a more obvious cause of the loss of microbial diversity is the extensive use of antibiotics across the modern world, at the same time as the increase in non-communicable disease was becoming an emergency [78]. While the effect of antibiotics on the bacterial microbiome has been reviewed [79], they can also affect unicellular eukaryotes [80]. Nevertheless, the overall effect of antibiotics may be ameliorated by the presence of the appendix acting as a reservoir of valuable microbes [81]. Whilst maternal microbial inheritance proceeds via vaginal birth, delivery of the baby by caesarean section under sterile conditions will be expected to change the distribution of species within the microbiome and, indeed, this has been observed in practice [43]. Nevertheless, this change is only temporary and, after six weeks, the bacterial composition and function with the child were essentially identical regardless of the mode of delivery [82] although, by that point, any damage to the gut–brain axis may already have been done. Breast milk will contribute to the viability of the gut microbes [83], while the significance of breast milk bacteria is currently being assessed [84]. Interestingly, the vast majority of studies focussed solely on bacteria with, apart from the exception noted above, essentially no information on microeukaryotes.

The studies mentioned in the previous paragraph give no indication as to the reason for the observed drop in microbial (i.e., bacterial) diversity. Significantly, however, the first scientific investigation of non-communicable disease in people was by John Bostock early in the 19th century, who reported suffering from a mysterious summertime disease that we now know as hay fever, with all its characteristic features [85]. Intrigued, he searched across the United Kingdom and found a total of twenty-eight people, all from the rich side of society [86]. In the absence of synthetic antimicrobial agents, it seems likely that the ultimate cause of microbial, including unicellular eukaryote, depletion in Bostock’s time would be the use of toxic heavy metal salts for cosmetic purposes [87]. Although the poisonous nature of these substances was clearly understood, they would have no idea of any microbiome poisoning associated with subclinical exposure, especially as the consequences of such toxicity may only become evident as the child of a microbiome-depleted mother grew into maturity. Similar subacute poisoning would be spread around the modern world with the use of leaded petrol, starting in the 1920s and only largely discontinued by the year 2000 [88], the environmental poisoning consequences of which are still apparent today [89]. While lead contamination has decreased, other heavy metals are in extensive use [90], with some attention being paid to their toxic effects in animals at the base of the food chain [91]. Of course, such widespread contamination will have an increasing effect on animal communities, at least partly accounting for the microbe depletion experienced by domesticated animals compared to their wild equivalents, an effect that has been described as “industrialization” [7]. Proximity to human activity will doubtless be important and, accordingly, we have suggested that the 20th century disappearance of hedgehogs in the more heavily polluted parts of the United Kingdom may have been due to widespread lead pollution [25]. Furthermore, we have suggested that heavy metal pollution would be effective for the removal of microbial sentinel cells, whose specific job would be the recognition and assessment of environmental antigens in order to calibrate the immune system of the next generation [25]. It is possible that such cells simply no longer exist in populations suffering from Burkitt’s “Diseases of Modern Western Civilization” [2].

5. Temporary Stimulation of the Gut–Brain Axis: Placebo Effect and Probiotics

The concept of the placebo has had a long and distinguished history; the hope being that it could allay the symptoms of disease long enough for the underlying condition to right itself. However, the development of the double-blind, placebo controlled, randomised clinical trial let the genie firmly out of the bottle [92]. Subsequent attempts to unravel exactly why the placebo is so effective merely illustrated the difficulties posed by onion skin-like layers of bias [93]. Interestingly, of course, the gut–brain axis has evolved to transfer information faster than can be achieved by conscious thought and, as such, it can easily be confused. As an example, the well-known phenomenon of traveller’s diarrhoea is an evolved response to unknown but essentially harmless microbes [94], presumably constituting a temporary stimulation of both the immune system and the gut–brain axis, albeit with a necessarily negative effect—making you feel bad for a good reason. In a similar fashion, in certain circumstances a subconscious “placebo-like” effect can have a surprisingly negative outcome. Essentially, this nocebo effect is the antithesis of the placebo effect, and may have fatal consequences, at least in hospitalised, vulnerable populations [95]. In addition, it potentially accounts for some of the non-specific side effects of medication [96].

A potential explanation of the value of the placebo effect in the context of a malfunctioning gut–brain axis is illustrated in Figure 3. The principle here is that a strengthening of this axis from either terminus will affect the other, presumably via the intermediacy of the vagus nerve, which is also known to be involved in inflammatory disorders and a variety of psychiatric conditions [97]. Indeed, it may be that raised production of semiochemicals has subtle disease-modifying effects, for example, by increased production of dopamine in the periphery [33]. In the context of a clinical trial, it is possible that discussion with the clinician, followed by the action of taking a mock medicine, stimulates hormone levels in the brain and hence semiochemical levels in the gut. In this context, it is important to note that the placebo effect does not require the recipient to be deceived [98].

Bearing in mind the principles behind Figure 1 and Figure 2, it is likely that the primary role of the gut microbiota lies in their initial handshaking function, while any subsequent dietary or probiotic benefits lie within the placebo concept of Figure 3. Indeed, as the damage done in early childhood is unlikely to be completely reversed, dietary and probiotic interventions must be termed amelioration rather than cure [99]. As an example of dietary action, the consumption of tea and coffee, both known for their stimulant action, have recently been associated with a reduced risk of stroke and dementia, albeit only by a prospective cohort study that cannot, in itself, determine causality [100]. Nevertheless, these beverages contain the polyphenolic compounds that seem to benefit health by stimulation of the gut microbiota [101]. Equally, it has long been known that probiotic preparations containing various bacteria can indeed influence mental health, albeit going under the term psychobiotics [102,103]. As described earlier, however, Brüssow has pointed out that the studies involving probiotic bacteria are not sufficiently detailed to be absolutely sure of the exact influence of the various bacteria of interest [11], and it remains possible that benefits accruing from semiochemical production can be expressed by different classes of bacteria among a sufficiently diverse microbiome [35]. Alongside this “horizontal gene transfer” approach to microbiome function, the possibility exists that the inadequately studied microeukaryotes carry a significant role in the fully functioning microbiome [19].

While some studies have revealed hopeful results for significant amelioration of some autistic spectrum features, those are few [104,105]. To date, several potential confounding factors have been disregarded, the most important being single- or double-blind trials to precisely assess possible placebo effects. Another problem is obtaining the cooperation of people from diverse ethnicities and nationalities, socioeconomic levels, medical histories of the mothers, etc., all well-known confusing factors for the study of mental health [106].

6. The Many Variations of Developmental Brain Disease: Do They Have the Same Underlying Cause?

While the medical model of single diagnosis and appropriate treatment remains the ideal, non-communicable disease tends to present itself as a mix of seemingly very different complaints of variable severity. This is especially so in the context of psychiatric conditions, where the Diagnostic and Statistical Manual of Mental Disorders is in its 5th Edition (DSM-5) [107], with concomitant debate about the medicalisation of society [108]. The p-factor mentioned earlier represents an attempt to account for the seeming “inheritance” of multiple varieties of poor mental health in the same individual, often starting at an early age and associated with “compromised brain integrity” [36], a concept which is entirely consistent with our own view of inappropriate brain growth following poor interoception, inefficient communication between gut and brain as outlined in Figure 2. It is reasonable to suppose that the relationship of autism spectrum disorder (ASD) with the gut microbiota, the neural, and the immune system will also apply to other non-communicable psychopathological conditions [46].

6.1. Autism Spectrum Disorder and Attention Deficit Hyperactivity Disorder

Although the division of disease into subtypes may be valuable for the precise application of therapeutic methodology, it makes the critical task of epidemiology much more difficult. Nevertheless, in a recent review Chiarotti and Venerosi have cut through all the variability to show that the incidence of ASD, one of the major forms of poor mental health, has indeed increased across all areas of the world since the establishment of the DSM-5 in 2013, at least until the date of their review in 2020 [109]. It is likely that this pattern, an overall increase in the incidence of disease combined with massive individual variation, will apply across a number of seemingly different conditions.

A recent review of the nature of ASD illustrates its pathophysiology. Characteristics include cognitive inabilities, impaired communication, and restricted social interaction, along with a wide range of co-morbidities including psychiatric illness, seizures, and gastrointestinal disorders, which are hypothesised to be due to bacterial dysbiosis [110]. While microbiome disturbances have been implicated in both ASD and attention deficit hyperactivity disorder (ADHD), a systematic literature search revealed twenty-four relevant articles, but with no consistent bacterial variation identified [111]. It is important to note, however, that once the handshaking process of Figure 1 has failed in the neonate, the exact nature of the bacterial inhabitants of the intestine may well be irrelevant to the underlying cause of the disease. Thus, as probiotics stimulate the immune system, so the gut–brain axis is temporarily strengthened, perhaps briefly lessening some of its symptoms according to the placebo effect of Figure 3.

Just as it is important to clearly define and quantify what is “normal microbiota”, it is also important to record not only brain imaging, but also the behaviour of the non-neurotypical individual beyond clinical psychiatric diagnoses that might be subjective to some degree. It is possible, for example, to parameterise the behaviour of an individual with ASD, making quantifiable what is, by definition, a spectrum [112].

6.2. Dyslexia, Anxiety, Depression, and Other Conditions

Dyslexia is often found to co-occur with ADHD, implying a similar cause and/or mechanism of action [113], and, as its precise aetiology is not understood, it has recently been suggested to be an extreme case of “specialisation in exploration” [114]. Interestingly, developmental language disorder (DLD) is presumably related to dyslexia, and striatal changes can be observed by magnetic resonance imaging (MRI) [115].

While ASD is among the most disabling of the psychiatric disorders and anorexia nervosa the most dangerous [116], the many manifestations of anxiety are the most prevalent, with a close association with depressive conditions [117]. Perhaps the most direct explanation of at least some of the various forms of anxiety is related to the phenomenon of traveller’s diarrhoea [94], in which a malfunctioning gut–brain axis falsely suggests the presence of an infection, leaving the brain uncertain as to whether to trigger the vomit reflex or not. A recent review of studies exploring the role of dietary interventions in the context of anxiety and depression has merely emphasised the complexity of the situation, emphasising the bidirectional nature of the microbiota–gut–brain axis: both being affected by, and affecting, dietary choices [118]. These complications can, perhaps, be better understood as amelioration rather than cure [99], albeit only temporarily, following the placebo concept of Figure 3.

The breakdown of semiochemical and/or neural connection between gut and brain following microbiome–gut dissociation may have consequences for many other conditions. Although the details remain to be discovered, the microbiome is somehow connected to the Parkinson’s disease-related loss of dopamine in the substantia nigra, for example [119]. Interestingly, dopamine also has a role in dynamic emotion perception [120], which may be related to the observation of alexithymia, the neurodevelopmental disorder-related difficulty of classifying one’s own emotions [121]. Probably involving a similar mechanism, people suffering from depressive states have difficulty making the fast, intuitive decisions that are associated with the phrase “gut feeling” [122]. One significant finding is that the disturbance of the skin microbiota has a depressive effect operating through the gut: an example of a gut–brain–skin axis but, seemingly, with the gut microbiota themselves exerting the major emotional influence on the brain [123].

6.3. Unexpected Strengths and the Problems of Definition in Psychology

Following an initial failure of the handshaking process in the neonate, the asymmetric development of the brain, clearly revealed by structural magnetic resonance imaging [124] and convolutional neural networks [125], probably contributes to a number of developmental issues that may actually be associated with unexpected strengths. One is the above-mentioned “specialisation in exploration” hypothesised to accompany developmental dyslexia [114], but possibly the most extreme example of disability combined with exceptional skills is that of savant syndrome [126]. It has even been suggested that ASD may be a variation of “normality” [127], and that individuals with ASD only need certain specific integration requirements to be functional in society [128]. Equally, leaving aside the question of the precise definitions of the terms used, the question has been asked as to whether “genius” is related to “madness”, or whether it can also be expressed by “normal” people; it seems that the answer is not clear-cut [129]. A further study along similar lines has discussed creativity in the context of psychopathology, calling for better definitions and for more methodological rigour [130], in a similar fashion to Brüssow’s call for greater clarity in the field of probiotic bacteria.

7. Microbiome Measurement: Semiochemicals and Sentinel Cells

Although the human neonatal gut microbiome has been well studied by now, the overall message is that the microbiota transferred by maternal microbial inheritance must be fully functional both in the neonate [131] and throughout childhood if the worse consequences of adult disease are to be avoided [35,39]. As the enclosed intestinal microbiome would have evolved with the vertebrates [25], so animal studies should be helpful. Equally, it should be possible to obtain information from people living in unpolluted places not suffering from non-communicable disease. In principle, such peoples should still have properly functioning semiochemical messenger systems and also, probably, eukaryote microbial sentinel cells capable of passing environmental antigen information onwards from mother to child [13]. Peoples such as the African Hadza have been cooperating with medical teams for a number of years, and their microbiomes have been assessed, in terms of the bacteria, at least [132]. Nevertheless, it is feasible that their microbiota has already been degraded, bearing in mind that any medical consequences may not show up until subsequent generations. Essentially, the same comments apply to the South American Tsimane, except that, to our knowledge, their microbiota have not yet been investigated [133]. Any information gained from them should be compensated for, perhaps in a similar way as for cancer medicines, for example [134].

7.1. Semiochemical Measurement: An Ingestible Sensor

Although function is important, it seems that the exact species-level bacterial composition of the maternal microbiome may be irrelevant as a measure of its value to the neonate. In addition to in vitro studies, one option would be to detect potential semiochemicals [12] in animal faeces under different conditions, such as fed, fasting, or pregnant, bearing in mind previous experience suggesting that laboratory-raised animals may not have the full complement of necessary microbes [9]. Although the presence of candidate messaging compounds in faeces would provide a suggestion of their activity, significantly more information would be gained after the development of an ingestible sensor, a pill-like device equipped with a detector calibrated for molecules such as dopamine, and a transmitter allowing the readout of real-time information on their ebb and flow under different conditions [45]. Such studies could also be performed in humans as ingestible sensors are currently considered to be minimally invasive [135]. Nevertheless, essentially the same strictures apply to humans as to laboratory-raised animals: that even apparently healthy individuals can only be considered to have an intact microbiome if the whole population is free from non-communicable disease [39].

7.2. Microeukaryotes and Microbial Sentinel Cells

Given the apparent complexity of microbiome function, alongside Brüssow’s observation of the “problems of … gut microbiota dysbiosis” [11] it would be surprising if unicellular eukaryotes were not critical to the functioning of the microbiome, as has been suggested already [19]. Granted a co-evolutionary relationship between microbiome and vertebrate animals [25], and the importance of immune system disease [35], the possibility of microbial sentinel cells as precursors of the dendritic cells that link the innate and adaptive aspects of our immune system [26] must be taken into consideration. Eukaryotes such as the Blastocystis genus have been mentioned [20], but it is possible that such entities can no longer be found in heavily polluted communities suffering from extensive levels of non-communicable disease [39]. Interestingly, human coprolites have been studied for evidence of now-extinct microbiomes but, as usual, the focus remains on bacteria [136]. It is important to note, however, that pre-modern communities could still have high levels of pollution due to complex trading societies spreading the results of mining activities [137]. Although such societies could stretch back into the Stone Age, certainly the Egyptians and Romans used lead extensively and have been confirmed as suffering from non-communicable disease, for example, atherosclerosis [138] and coeliac disease [139], respectively. Although it may prove difficult to find examples of immune system-related microeukaryotes associated with undegraded human microbiota, the fact that domesticated animals suffer from immune system diseases implies that wild animal populations could be used as a proxy for human microbial biology [8].

8. Microbiome Degradation and the Development of Society: Where Are We Now?

While birds are renowned for lining their nests with attractive shiny objects, only mankind has the ability to delve deeply for those metal ores that are the basis of high-status objects with a similar function. Coloured metal salts provide extra distinguishing features for the ruling class and, while it seems reasonable to assume that overt toxicity due to excessive application of cosmetics would eventually be recognised and avoided, our interpretation of Bostock’s observations [86] suggests that covert toxicity via damage to the microbiome may have been common in the richer elements of society [35]. Although it might be thought that the lifestyle of the early hunter–gatherer peoples would guarantee a slim and healthy physique, nevertheless we have these so-called Venus figurines: representations of seemingly obese female statuettes sculpted around Europe in the Palaeolithic, earlier than 23,000 years ago. While the original reasons for these figurines naturally remain obscure [140], a representation of the actual daughters of real families of a priestly and/or kingly class must remain a possibility.

Although toxic cosmetics remained in use throughout the European medieval period, the extent of the ruling class gradually increased in subsequent centuries as European countries became richer. It was in the early 19th century that Bostock noted his hay fever [85] and, while great works of art, science, and engineering increased, so too did eccentricity, leaving open the question of the relationship between genius and madness [129]. In time, however, mere eccentricity turned into a slew of previously unknown psychiatric conditions. Based in Vienna, the capital of the rich Austro-Hungarian Empire in the late 19th century, Sigmund Freud found himself faced with people suffering from mysterious psychosomatic phenomena and, having no physical data to measure, he began the process of developing psychoanalysis [141].

Without focusing on this new phenomenon of poor mental health, an interesting 2012 review charts the change in the nature of disease over the two hundred years following 1812, albeit from the point of view of the doctor–patient relationship. Nevertheless, the slow but steady change in the nature of disease is noticeable: from infectious to non-communicable, including the rise in atherosclerotic heart disease, cancer, and other immune system diseases, and also obesity [142]. Interestingly, there has recently been a recognition that body temperature of United States service personnel has dropped from the previously accepted standard of 37 °C to 36.6 °C since the middle of the 19th century [143] and, presumably, since the beginning of their obesity crisis. We have assigned this steady temperature reduction as being due to the phenomenon of energy compensation as the movement of the heavier body produces a response mimicking greater levels of voluntary exercise [52].

During the 20th century, medical knowledge rose alongside the intergenerational increase in non-communicable disease, so much so that Denis Burkitt was surprised to find that a large part of his hard-earned medical skills were simply not applicable to people living traditional lives in many parts of the African continent [2]. Of course, the latter half of the last century was notable for the almost unrestrained spread of industrial pollution. Plastics range from the visible to the microscopic, with as-yet-unknown health risks [144]. Heavy metals, by contrast, are clearly toxic, both to multicellular creatures [145] and to their microbiota, albeit that only the bacteria are normally considered [146]. It is feasible that the addition of lead to petrol is an important factor in the spread of subclinical lead poisoning from the richer elements of society to the many [88], probably also affecting our domesticated animals [8]. It would be interesting to see if the increase in non-communicable disease in different parts of the world followed one generation after the import of significant numbers of cars using leaded petrol.

The current situation is that nothing seems to stop the spread of obesity [147], while its co-existence with problems of the immune system [69] and poor mental health [71] receives little recognition. While some obesity studies assign little weight to the microbiome [148], others focus only on bacteria [149], though not without criticism [150]. Although the existence of the microbiota–gut–brain axis has been connected with obesity [151], it is not known how. Sadly, the obvious failure to understand the causes of these diseases, especially obesity and autism, has led to a broader antiscience movement, whose complaints are not easily answered [152]. New ideas are badly needed.

9. Conclusions and Recommendations

It would seem that, following the late 20th century insights of David Barker and his “fetal and infant origins of adult health”, the potential for non-communicable disease in the adult arises after the “handshaking” interaction between the maternal microbiota and the developing gut of the neonate starts to go wrong in the infant. While such failure gives rise to the potential for psychiatric disease and for excessive adiposity from later childhood onwards, it is possible that the early immune system disorders noted by David Strachan arise via a different mechanism: the loss of the to date hypothetical microbial sentinel cells potentially related to dendritic cells. Whatever the exact reason for such non-infectious, non-communicable diseases, it would seem that the output of the microbiome is a combined immune–semiochemical system operating through the gut–brain axis. In this way, “placebo” stimulation of the brain can, by temporarily strengthening this axis, stimulate the gut and, therefore, the peripheral immune system. On this theory, stimulation of the gut by so-called prebiotics may alert the brain, while activation of the immune system by probiotics containing harmless live bacteria may have the same “psychobiotic” effect. In both cases, the customer will feel a little better, at least for a while. In addition to effects on the brain, however, stimulation of the immune–semiochemical system may have measurable physical effects in the rest of the body. This non-specific effect of probiotic bacteria echoes Brüssow’s observation of the lack of any compelling evidence for causal relationships between specific bacteria and specified diseases.

Following the logic of maternal microbial inheritance, we make three main recommendations:

• Search in faecal samples of wild animal populations, preferably primates, looking specifically for any microbial or semiochemical changes in late-stage pregnancy or, indeed, when giving birth. The aim is to detect those microbes, including eukaryotes, which are being transferred to the neonate. Bearing in mind any cultural sensitivities, the same could be asked of humans, comparing populations with and without evidence of non-communicable disease.
• Commence a research programme to discover key semiochemicals in the gut lumen, and their effect on receptors both within and outside the gut wall. In principle, an ingestible sensor could be developed as an aid to research, tracking the rise and fall of these semiochemicals under different circumstances.
• Once key microbes are detected, they would be added to the head of a new-born baby in order to re-introduce functionalities that have been lost through industrialisation.