GM is an association made of a huge number of bacteria (approx. 1014), and for this reason, it is considered one of the most densely-packed ecosystems we know (Gilbert et al. 2018). The composition of GM is mainly dominated by the phyla of Bacteroidetes and Firmicutes, although more than a thousand different species have been reported in human adults (Qin et al. 2010). Each individual is characterized by a specific proportion of various species and strains that constitutes her own ‘microbial fingerprint’ (Calvani et al. 2018). Despite this internal diversity, GM is quite stable in individual adults, and displays a consistent functional capacity among healthy persons, unless disturbance factors occur. Nevertheless, a significant variance has been observed among different individuals, so that configurations of GM influencing a ‘healthy state’, may be different from one subject to another (Lozupone et al. 2012; The Human Microbiome Project Consortium et al. 2012).
This section highlights the cognitive role of GM, which figures among the most striking discoveries of this decade. While interactions between the central nervous system and the gastrointestinal tract having been qualitatively recognized for many centuries, it was only in the nineteenth and early twentieth centuries that this relation was seriously assessed by physiologists and psychologists. The availability of new tools suitable to reveal the bi-directional interactions between gut physiology and nervous functions had an important role, opening new frontiers of research about the impact of GM on individual cognitive processes and behavior. Nowadays, links between the central nervous system and GM are well-known and remain one of the hottest topics of scientific research of medical interest, challenging some of the standard views in medicine and cognitive sciences (see for instance Editorial, Nature 2019, Feb; 566–7742).
Of crucial relevance for this paper, evidence suggests that the multifaceted communication between the gut and the central nervous system not only is apt to ensure the maintenance of gastrointestinal and digestive functions but also allows the gut to exert effects on emotional behavior and higher cognitive processes by means of variations in the composition and activities of GM. The relations between GM on the one hand, and emotional and cognitive functions, on the other hand, are made possible through multiple interactions, such as the existence of bi-directional neural pathways, neuroendocrine signaling, as well as the role of the immune system (Carabotti et al. 2015; Grenham et al. 2011; Mayer et al. 2014).
But how can GM exert its extra-intestinal influence? And, in this respect, how can GM be relevant for cognitive processing? The ways in which GM shapes aspects of cognitive functioning are addressed in the following subsections. We proceed by introducing basic physiological and functional evidence about the MGB axis, then we focus on its role in regulating the agent’s behavior by means of influencing emotional cognition and performance in memory tasks.
The Microbiota-Gut-Brain axis
In recent years, advancements have been made in describing the bidirectional interactions between the central nervous system, the enteric nervous system, and the gastrointestinal tract. Indeed, a number of studies have suggested a central role for GM in these interactions, leading prominent scholars to coin the notion of the Microbiota-Gut-Brain axis (Lyte and Cryan 2014). The MGB axis refers to the system of biochemical signals that takes place between the gastrointestinal tract and the nervous system and is frequently used to highlight the extra-intestinal functions of GM. As previously mentioned, it is important to recall how this axis should not be intended as a well-defined anatomical trait or structure but rather as a functional descriptor. Thus, it is not literally an ‘axis’, but rather a way to stress the presence of a great variety of modes of interactions between the gut, the brain, and microbiota.
Thus, broadly defined, the MGB axis includes the central nervous system, the neuro-immune systems, the sympathetic and parasympathetic systems, and GM. Notably, the nervous system signals to the gastrointestinal tract through a large network of neural, hormonal, and immunological routes (e.g., the sympathoadrenal axis and hypothalamic–pituitary–adrenal axis, the monoaminergic pathways). Inside the brain, signals from the gastrointestinal tract reach the hypothalamus and the amygdala which, in turn, receive inputs from a number of higher associative areas, including prefrontal cortex and cingulate cortex (Al Omran and Aziz 2014; Ongür and Price 2000).
Furthermore, the vagus nerve has been shown to serve as a prominent route for the interactions between the gut and the brain (Forsythe et al. 2014; Forsythe and Kunze 2013). This stream may represent a bidirectional functional pathway, spanning from the gastrointestinal tract to the central nervous system and back to the sympathetic part of the autonomic nervous system, which is implicated in the immune regulation and homeostasis of the gut (Foster et al. 2017a, b; Perez-Burgos et al. 2014).
Recently, a great interest has been addressed toward the peculiar role of GM in regulating the gut-brain interactions (e.g., Kelly et al. 2017; Sharon et al. 2016). For example, it has been suggested that GM may modulate the synthesis of a number of neurotransmitters, including serotonin, dopamine, noradrenaline, and gamma-aminobutyric acid, which function as mediators between the activities of GM and the nervous system (e.g., Sarkar et al. 2016; Yano et al. 2015). Notably, through multiple pathways, GM may exert an extensive influence on key neurological and behavioral processes also in critical phases of early neurodevelopment and senile neurodegeneration (Dinan and Cryan 2017; Sharon et al. 2016). During early-life, GM plays a role in shaping the organization of neuronal networks influencing social and emotional domains of cognition (Kelly et al. 2017; Sharon et al. 2016). For example, animal studies have reported that antibiotic administration during the first year of life is correlated with depression and behavioral difficulties later in life (Slykerman et al. 2017). The administration of antibiotics postnatally changes the physiological status of the offspring in animal models and subsequently modulates its affective behavior. Moreover, though aging reductions in GM are usually associated with a reduction in microbial complexity, specific alterations and increased diversity in GM composition, structure, and function have been retrieved in individuals with neurodegenerative pathologies (often associated with aging) such as Alzheimer’s disease and Parkinson’s disease (e.g., Jiang et al. 2017; Scheperjans et al. 2015). Alzheimer’s disease (AD) is the most frequent cause of dementia characterized by a progressive decline in cognitive function associated with the formation of amyloid-beta plaques. A growing body of experimental and clinical data in mice and humans supports the hypothesis that so-called GM dysbiosisFootnote 5 exerts a key role in neurodegeneration and formation of amyloid-beta plaques, together with aging and other environmental factors (Kowalski and Mulak 2019).
The above-mentioned studies indicate a close connection between microbiota and behavior and suggest the presence of functional pathways through which they interact. By taking a look at this assembly of morphological and functional evidence, it is nowadays possible to appreciate the general principles regulating the extra-intestinal influence of GM. A way to address this issue is to conceive the functions exerted by microbial communities, either directly via metabolites or indirectly via the immune and endocrine systems, as providing the nervous system with information concerning the environment.
Interestingly, studies have shown how the nervous system (alone or together with the immune system) can influence microbial activities and composition. Indeed, as already mentioned, the MGB axis constitutes a bidirectional scenario. Several studies (e.g., Lyte and Cryan 2014; Zhao et al. 2018, Li et al. 2020) have highlighted the reciprocity of the MGB axis, by considering how much the brain acts on the gut, through multiple neural, hormonal, and immunological pathways.Footnote 6 First of all, the brain can affect the activities and composition of the microbiota indirectly, acting on gut motility, modulating secretions, and regulating visceral permeability. Furthermore, the brain can also act directly, through chemical-molecular signals, conveyed by certain types of cells (such as, among others, neurons), in the intestinal lumen (Rhee et al. 2009). Moreover, recent findings, due to a more profound understanding of the relations between the central nervous system (CNS) and the enteric nervous system (ENS), have revealed how the nervous system (as such) is deeply involved in shaping the gut ecosystem and thus microbial activities (Yoo and Mazmanian 2017). These aspects become particularly crucial when specific pathologies (presenting both neurological and metabolic aspects), such as obesity, are addressed since they might offer a basis for new therapeutic approaches (see Agustí et al. 2018; Niccolai et al. 2019). In addition, it has been recently reported that brain injuries can affect microbiota both in functionality and composition (Houlden et al. 2016). Furthermore, all these aspects, underlining the bidirectionality of the relationships between the microbiota and the brain, can very well serve to support the ‘holobiontic perspective’ (see "Microbiota-host relationship: beyond symbiosis and the holobiontic perspective" section).
Therefore, determining how GM changes with respect to environmental factors, and how this shows, in turn, an impact on the processing that underlies behavior (and vice versa), represents a fascinating challenge at the intersection between biomedical research, microbial ecology, and the cognitive sciences.
In this section, we mentioned only some preliminary physiological and functional experimental results about the MGB axis. In doing so, we paved the way for the experimental framework we use in order to defend our philosophical claim. In the next two sections, we put forward a cognitive approach to the MGB axis, focusing on some functions of GM. To this aim, we first focus on two different sets of evidence that may help to explain the role of GM in shaping specific cognitive processes. Then, we discuss a way to interpret such a role in terms of cognitive processing. This will constitute the crucial evidence at the basis of our philosophical claim.
The MGB axis and emotional processing
One of the most intriguing areas of investigation concerning the cognitive functions of the MGB axis is represented by the role of GM in shaping emotional behavior, particularly in anxiety and depression (Foster and McVey Neufeld 2013). Interestingly, it was precisely the discovery of a correlation between stress, anxiety, and the alternation of GM that alerted scholars to the possibility of bacterial involvement in psychological processes (Sarkar et al. 2018).
Before introducing the evidence suggesting the functional role of GM in the processing of emotions, it should be noted that emotions are nowadays considered as cognitive states that are essential to rational thinking and normal social behavior. Importantly, though for a long time emotions have been disregarded as mere reactions to environmental stimuli, several theoretical and empirical works have contributed to changing this paradigm, fostering the idea that processing emotional states is crucial for a plethora of cognitive activities. Emotions, indeed, determine how an individual perceives the world, organizes memories, and makes pertinent decisions (e.g., Damasio 2005; Oatley and Johnson-Laird 2014; Okon-Singer et al. 2015; Pessoa 2008; Prinz 2006; Storbeck and Clore 2007).
Over the years, most of the research on the psychological effects of GM has focused on rodents’ behavior, representing a first step toward the understanding of this phenomenon. Notably, researchers have clustered largely around negative emotional states and their behavioral manifestations. For example, emotional states related to stress and anxiety, such as fear and depression, are inferred from the time spent by the rodent to explore new and unfamiliar environments. This measure is considered a key behavioral feature of approach and orientation and is usually relevant as the agent adapts to novel situations, such as being at the center of a maze. Thus, alterations in time spent in exploration can be considered as revealing the occurrence of negative emotional states (Sarkar et al. 2018; Walf and Frye 2007).
Now, a growing body of evidence suggests an important influence of GM on emotional behavior and underlying brain mechanisms. Recent experiments revealed an anxiolytic-like behavior in germ-free rodents, compared to control rodents (Neufeld et al. 2011). Importantly, such a difference is not found in vagotimized agents, suggesting a functional role for the MGB axis in emotional processing (Bravo et al. 2011).
Interestingly, Bercik et al. (2011) have shown that transferring fecal content from an innately stress-sensitive mouse to non-anxious mice is sufficient to elicit anxiety-like reactions (i.e., reduced exploratory behavior) in the receiver animal. Correspondingly, the reverse pattern, that is, transferring portions of GM from non-anxious mice to innately anxious mice induces the latter to manifest reduced anxiety (for an analogous result, see also the more recent Chevalier et al. 2020).
For the sake of our argument, it is interesting to note that recent investigations have suggested that germ-free rodents display specific impairments in maintaining the associations involved in manifesting normal fear behavior, showing reduced reactions in response to contextual cues related to noxious stimuli (Hoban et al. 2018). Scholars found that, after training, germ-free animals displayed reduced freezing to conditioned stimuli associated with possible pain. Crucially, this evidence suggests that GM is a functional component involved in the normal development of fear-learning processes (Sarkar et al. 2018). Indeed, this altered behavioral profile can be mitigated by the successive recolonization of the rodent’s gut with a conventional GM.
Remarkably, this concept has also been expanded to humans. Healthy volunteers that consumed milk containing different probiotic bacteria, which affected the equilibrium of their GM, showed altered cortical activations during the execution of an emotional faces attention task, as measured with fMRI studies (Tillisch et al. 2013). The authors administered a probiotic mixture to female participants over several weeks, and then participants viewed emotional stimuli (faces) while undergoing functional magnetic resonance imaging. As a result, with respect to controls, participants showed reduced activation in brain regions that are known to be functionally implicated in the processing of emotional information, including the insula and the somatosensory cortex. This suggests that an alteration of the MGB axis may have an impact on human emotional experience as well.
In another study, Tillisch et al. (2017) using fecal samples, magnetic resonance imaging (MRI), and an emotion induction task, assessed the relationship between GM composition in healthy women and the characteristics of brain structure and brain function as measured by affective response to emotionally related images., The authors found a correlation between the genetic profile of microbial clusters and the hippocampal activity related to the emotional experience of the subjects. This evidence suggests that the composition of the bacteria community inhabiting the agent’s gut has a functional impact on the processing of emotional stimuli in humans.
Furthermore, Bagga et al. (2018) performed a placebo-controlled randomized study aiming at investigating the effects of the administration of probiotics on emotionally driven behavior and brain activation. In this experiment, forty-five healthy participants divided into three groups (probiotic, placebo, and no intervention) were asked to perform emotional decision-making and emotional recognition memory tasks while scanned with functional MRI. Interestingly, human subjects administered with probiotics showed changes in brain activation patterns in response to emotional memory and emotional decision-making tasks.
To summarize, although most of our understanding of the emotional interaction between the microbiota and the brain has come from rodent models, in which the gut microbiota is linked to brain signaling mechanisms and affective behavioral phenotypes, there is encouraging evidence concerning the causal relationship between gut microbial community structure, brain structure and emotional processing in humans. Although this is not conclusive, the reported evidence allows us to hypothesize that GM plays a key role in the processing of emotions both in non-human and human agents, interacting closely with other brain structures involved in this function.
The MGB axis, memory, and behavioral control
Over recent years, an increasing amount of empirical research has suggested that the rate of success in executing tasks involving higher cognitive abilities may be related to the conditions of the agent’s GM (Novotný et al. 2019, Sanguinetti et al. 2019). Interestingly, studies on rodents have found significant effects of GM alteration on cognitive processes guiding behavior, such as learning and memory. For example, the experimental research has shown the effects of either gut infection or absence of GM in rodents, particularly on non-spatial memory behavior, showing that memory dysfunctions occur in infected mice exposed to acute stress, while the germ-free agents’ memory abilities are altered at baseline. Early evidence of the functional relationship between GM and higher cognitive abilities is related to the impairment of hippocampal activity and memory functions in germ-free mice as compared to normally colonized rodents (Gareau et al. 2011). Successive studies have found that exposure to antibiotics temporarily impairs learning and memory performance in mice (Wang et al. 2015).
Interestingly, further research has suggested associations between GM and cognition in human adults as well. Studies on obese individuals, for example, provide evidence of a correlation between GM composition and the agent’s performance in executing tasks involving attention and cognitive flexibility (Sarkar et al. 2018). Notably, GM influences host dietary behavior, regulating satiety, and energy intake (Fetissov 2017; Frost et al. 2014). Again, evidence of this function is illustrated by obesity, which in both mice and humans is associated with an alteration of GM composition, inducing a bacterial-dependent capacity of extracting energy from food, which in turn affect the agent’s disposition to select and ingest specific aliments (Agustí et al. 2018; Ley et al. 2006). Importantly, evidence such as this suggests that GM has a role in orienting the behavior of the agent, contributing to select specific types of interactions with the environment, like the goal of ingesting particular categories of food rather than others. In this respect, it can be said that GM performs a function similar to that of other cognitive mechanisms regulating food intake, which are classically located within the boundaries of the nervous system (e.g., the hypothalamus, see Cazettes et al. 2011). Consequently, even if the causal web of these phenomena is far from being fully understood, growing evidence allows one to consider the fruitful hypothesis according to which GM has a cognitive function in shaping the agent’s alimentary behavior.
Moreover, there is evidence that greater diversity in GM (composition and population interactions) is related to variation in the microstructures of brain areas, including those functionally connected to learning and memory tasks (Fernandez-Real et al. 2015). Studies in infants found that a greater GM diversity impacts exploratory and communicative behaviors and cognitive performances (Carlson et al. 2018). Interestingly, results suggest that higher levels of diversity are not always correlated with cognitive improvements, but also with lower performances. Nonetheless, findings of this sort highlight the function of the MGB axis in human cognition, stimulating new research on the regulating role of GM (see Sanguinetti et al. 2019).
Importantly, also several indirect results point toward the cognitive role of GM. For example, patients suffering from Irritable Bowel Syndrome (IBS), i.e. a functional gastrointestinal disorder associated with an altered GM (and possibly alterations of the MGB axis), display an increased recognition memory concerning words with a negative emotional connotation in contrast to either healthy controls or patients with different gastrointestinal diseases (Gareau 2014; Ringel and Maharshak 2013). Related to this effect, Gibbs-Gallagher et al. (2001) have shown that patients with IBS have difficulties in recalling words and phrases concerning gastrointestinal symptoms, while they do not show the same difficulty in recalling phrases and words associated with respiratory symptoms. Evidence such as this supports the hypothesis that IBS impacts on the agent’s cognitive functions subserving attention and behavioral responses.
Furthermore, an important role in this research area is played by the correlations between cognitive pathologies, the composition, and the activity of the agent’s GM. In a recent review published in Science, Sherwin et al. (2019) have collected evidence suggesting an important role of the microbiota in disorders of social behavior in both non-humans and humans. For example, the authors have reported that the analysis of the fecal microbiota of children with autism spectrum disorder (ASD), which involves an impairment of normal social behavior, shows a strong alteration in the composition of GM, with peculiar losses in key bacterial taxa along with the presence of harmful strains, frequently associated with gastrointestinal pathologies (Finegold, 2011; Góra et al. 2018; Son et al. 2015). Though such evidence needs further discussion and confirmation, it nevertheless suggests the hypothesis according to which GM has a functional role in regulating the cognitive activity involved in high-level processes such as those underlying social behavior.
Before concluding this section, if the reader were not convinced about the deep impact of GM on cognitive functions, it is noteworthy that variation in GM composition has been associated also with the manifestation of mental disorders consisting of highly distorted contact with reality. More precisely, several common classes of antibiotics used for the treatment of various infections, whose lethal effect on GM is known, have been recognized also to induce non-permanent psychosis in certain patients. Among the most common antibiotics known to have psychotic inducing effects are, for example, penicillin, quinolones, macrolides, and anti-tuberculosis agents (Cummings et al. 1986; Kass and Shandera 2010; McCue and Zandt 1991). Symptoms develop within the first days of treatment and include visual and auditory hallucinations, loss of orientation, space and time delusions, and agitation. For the sake of the present argument, it is interesting to note that antibiotic-induced changes in GM also induce changes in brain chemistry and behavior. Bercik and Collins (2014) have shown that an intraperitoneal administration of antibiotics failed to show an impact on the behavior of rodents, while the oral administration of the same antibiotic mixture has relevant behavioral consequences. The authors interpreted this finding to mean that the altered GM profile was responsible for the changes in behavior by means of effects on the hippocampus and the amygdala mediated by the MGB axis.
Recently, an increasing number of scholars have started to investigate how microbiota can improve drug discovery for psychiatric and behavioral disorders, launching the idea that in the future the term ‘psychobiome’ could represent a solid area of scientific inquiry and not just a fancy speculative term (Pennisi 2020). For instance, some researchers (Valles-Colomer et al. 2019) have shown that the number of bacteria belonging to genera Coprococcus and Dialister, was diminished in patients with depression. Moreover, they also confirmed a positive correlation between quality of life and the capacity of some bacterial strains “to synthesize a breakdown product of the neurotransmitter dopamine, called 3,4-dihydroxyphenylacetic acid. The results are some of the strongest yet to show that a person’s microbiota can influence their mental health” (Editorial, Nature 2019, Feb; 566–7742). Other groups revealed that diverse bacterial strains can modulate, produce, and consume neurotransmitter inhibitors, such as GABA (Strandwitz et al. 2019). In addition to that, another venue of studies has started to accumulate evidence supporting the view that microbiota can be implicated in the evolution of social behavior in complex social eukaryotes (including humans) and in the functional development of the structures allowing it (Sherwin et al. 2019).
As already mentioned, one crucial issue of many studies concerning the impact of microbiota on cognitive functions depends on the fact that most of them show interesting correlations but a mechanistic understanding is yet to come. Therefore, before going on with our proposal, it is necessary to spend some words on the causal aspects concerning this area of scientific investigation.
On causality
A fil rouge of this work is the notion that the microbiota, being a crucial component of a network of symbiotic relationships, is at the center of causal connections that, first, involve different populations of microorganisms and, second, the other component, the ‘host’. This has prompted much host-microbiota research to postulate the presence of a causal dependence for a variety of phenomena, in both physiology and behavior, concerning the human being. According to recent work (Lynch et al. 2019), many studies that support a causal role of the microbiota in phenomena concerning the physiology of the host organism seem not to respect crucial epistemic conditions for ‘causality’. This possibility could, at first glance, constitute an objection to the thesis presented here. However, we believe this is not the case. Although we do not have space here to go into the details of the general debate about causality, to clarify our line of thought, we believe that some points need to be addressed.
First of all, given the systemic nature of the object of our analysis (the microbiota-host relationship), we believe that the accounts of causality examined in the criticism (e.g. interventionist causal framework) may not be the most suitable for the situation. In particular, as recently argued (Lean 2019; Klassen 2019), microbiota, in its ecological dimension, can have a causal influence on higher, systemic properties. The recent attempts to influence, and experimentally intervene on microbiota according to new manipulation criteria derived from disciplines other than molecular sciences, such as ecology (Boem et al. 2020), also go in this direction. Moreover, the adoption of the so-called ‘holobiontic perspective’ (see on this "Microbiota-host relationship: beyond symbiosis and the holobiontic perspective" section), makes this possibility even more established and concrete.
Secondly, from the point of view of cognitive sciences, there is currently no single causal account shared by the scientific community, but rather a plethora of hypotheses on causality that compete on empirical ground. For our purposes, in relation to cognitive sciences literature, it is evident that the microbiota can be seen as a ‘difference maker’, concerning the determination of some crucial cognitive functions, even if the mechanistic description of these interactions is still partially incomplete.
Finally, our argument, in fact, explores a theoretical possibility: if the empirical evidence examined is to be considered solid, then there are good reasons to argue that the activity of the microbiota constitutes a legitimate extension of cognitive functions.
In what follows, we offer an innovative account of extended cognition, according to which it can be seen as being realized outside the brain, but still inside the body. This is what we call the ‘Internally Extended Cognition Thesis’. We believe that not only our thesis but also our approach for defending it is innovative, as the argument we offer is supported by recent empirical findings in the life sciences and biomedicine, which suggest that the gut microbiota’s activity might have a functional role in regulating our cognitive processes and behaviors.
Our opinion is that these sets of evidence would be better framed in light of the so-called holobiontic-perspective. According to this view, what we call biological individuals are not autonomous entities with clear boundaries, but should rather be seen as networks of multiple species interactions (see "Microbiota-host relationship: beyond symbiosis and the holobiontic perspective" section). Consequently, we argue that gut microbiota could be seen as a component of our organism (Bordenstein and Theis 2015). On this basis, we claim that gut microbiota can be plausibly seen as a functional part of our cognitive system. However, if that is the case, this requires us to extend cognition out of the agent’s skull, though still restricting it within other internal parts of the organismic agent: its own gut.