How Antibiotics May Affect the Gut-Brain Connection and Digestive Problems

The human microbiota is a collection of microorganisms that live in and on us. Over the past two decades, we have had an enormous amount of publications about gut microbiota in health and disease. Improvement in sequencing technologies coupled with bioinformatics science are making this research more feasible and cheaper. For instance, the estimated ratio of human:microbiota cells was recently revised from 10 times to 1.3 times more than human cells [1,2]. Even this 1.3 ratio (microbiota cells/human cells) is mind-blowing since these cells harbor their own genetic material. When we make a comparison between the number of genes between human and microbes in our body, over 99% of the genes in our body are microbial (numbering over 10 million). In the evolution process, we co-evolved with microbiota and they might have influenced our immune system and epigenetics [3,4,5,6,7]. Although we can modulate the expression of human genome through diet and lifestyle, human microbiome can also be directly modulated by these factors. Therefore, from a therapeutic perspective, gut microbiota can be manipulated by diet, drugs, lifestyle, etc. This opportunity gives us a new horizon for therapeutic aspect of chronic diseases. In the last decade, we had great progress in the field of molecular genetic tests and today there are evolving methods of analyzing gut microbiome [8].

Functional gastrointestinal disorders (FGID) are prevalent diseases affecting more than one third of the population [9]. Emerging evidence suggests a new definition for these disorders, involving gut-brain axis [10]. These syndromes are also pathogenetically related to disorders of gut-brain interaction [11]. Rome Criteria defines 26 distinct adult FGIDs, most well-known are irritable bowel syndrome (IBS) and functional dyspepsia (FD). The pathogenesis of these disorders is not well-defined [12] and these disorders are associated with psychiatric co-morbidities, including panic attack, anxiety disorder, depression, hypochondriac behavior and somatization [13,14,15,16,17,18]. Recent studies showed that these behavioral changes are related to disturbances in gut-brain axis, including gut microbiota [19].

The brain-gut-microbiota axis is a bidirectional system enabling gut microorganisms to communicate with the central nervous system (CNS), and the CNS with the gut [19]. The mechanisms of signal transmission are complex and not fully understood, but include neural, endocrine, immune and metabolic pathways [19]. There are many factors affecting microbiome-gut-brain-axis. These are diet, genetics, drugs, environment, exercise, cognitive behavior, stress, social interactions, and fear (Figure 1) [20,21,22,23,24,25,26,27,28].

Gut microbes are capable of producing most neurotransmitters found in the human brain. While these neurotransmitters primarily act locally in the gut, modulating the enteric nervous system, there is also undeniable evidence indicating that gut microbes can influence CNS through multiple mechanisms. The treatment with probiotic Bifidobacteria for instance, can increase the amount of tryptophan, the precursor of serotonin [29]. Some Lactobacilli species alter gamma-aminobutyric acid (GABA) metabolism and change brain GABA receptor expression and behavior [30]. Preclinical studies show that the vagus nerve is the main route for exerting the effects of gut microbiota on CNS. Lactobacillus rhamnosus has a central effect in animals and this was ameliorated by vagotomy [31]. In fact, patients with a history of vagotomy have diminished risk for certain neurological diseases [32]. Synthesis and release of neurotransmitters from bacteria have been reported: Lactobacillus and Bifidobacterium species can produce GABA; Escherichia, Bacillus and Saccharomyces spp. can produce noradrenaline; Candida, Streptococcus, Escherichia and Enterococcus spp. can produce serotonin; Bacillus can produce dopamine; Lactobacillus can produce acetylcholine [33,34,35]. Although these neurotransmitters can cross inflamed intestinal mucosal barrier, they cannot cross blood–brain-barrier (BBB) in healthy conditions. Another way of gut-brain interaction is the stimulation of hypothalamic-pituitary-adrenal (HPA) axis, which induces cortisol secretion. This system is the main stressor system in the body and it is mainly regulated by gut-HPA axis [36,37,38,39,40,41,42,43,44,45,46,47]. Psychological or physical stress can affect HPA axis and subsequently gut microbiota/barrier function (e.g., IBS) [33].

Post-infectious IBS is a prototype for gut-brain axis disorders. Water-born gastroenteritis outbreak occurred in United States and people affected from this E.coli infection later developed IBS-like symptoms including co-morbid depression, anxiety disorder [48].

There are diverse ways of communication between gut microbiota and brain such as autonomic nervous system, vagus nerve, enteric nervous system, neurotransmitters, and immune system (Figure 2).

The bi-directional communication between gut microbiota and brain ensures the maintenance of intestinal homeostasis and likely affects CNS functions in different time points of life, from early life neurodevelopment to aging and neurodegeneration [66]. Studies on the effect of antibiotics against gut microbiota-brain axis should be interpreted by considering the well-defined age-related differences in gut microbiota composition and diversity as well as its resilience and stability [69]. Moreover, the effect of antibiotics may be specific to an antibiotic group, course, and duration. Their absorption from GI tract is also critical in order to evaluate the direct effect of gut microbial perturbations without the neurologic effect of antibiotic itself [70]. For instance, metronidazole is a widely prescribed absorbable antibiotic for GI disorders, which can cross the blood–brain barrier [71]. Non-absorbable antibiotics such as vancomycin does not cross blood–brain barrier and become concentrated in the gastrointestinal tract, excluding the direct effect of antibiotics on CNS [72]. Route of antibiotic administration is also another important factor in experimental gut-brain axis studies, since oral gavage may induce stress in animals and may lead to misinterpretation of behavioral parameters [73].

Initial colonization of the gut begins in early life and mainly shaped by gestational age [74], mode of delivery (vaginal birth vs. Caesarean section) [75], method of feeding (breastfeeding vs. formula feeding) [76], and antibiotic exposure [77]. The early postnatal period is critical for microbial community and immune cell development. During this critical window, morphological and functional development in CNS also takes place, which is likely to be directly or indirectly influenced by gut microbiota [78,79]. A growing body of evidence from both epidemiological [80,81,82] and experimental studies [71,83,84] indicates that the gut microbiota has a crucial role in modulating brain function and behavior via gut-brain axis.

The majority of the studies providing evidence for the role of the gut microbiota in neurodevelopment come from germ-free animal experiments including altered hippocampal neurogenesis and decreased expression of brain-derived neurotrophic factors in germ-free mice [66,85,86]. Unlike germ-free conditions, antibiotics can selectively deplete microbial populations which is advantageous to design flexible experimental models and to determine targeted approaches for specific bacterial taxa [73]. Disruptive effect of antibiotic use especially in early life has known to cause long lasting consequences on microbial community and immunity, which may lead to increased predisposition and susceptibility to further disease progression such as IBD [77,87]. Majority of the studies using broad spectrum antibiotic cocktails showed comparable results with those observed in germ-free mice involving impaired social behaviors, neurogenesis and cognitive function together with the perturbations in gut microbiota [88,89].

In addition to evidence from experimental studies, a recent longitudinal population-based study reported that early-life antibiotic exposure is associated with an increased risk for psychiatric disorders [81]. Another recent clinical study also showed an altered auditory processing and recognition memory responses in infants who received intravenous antibiotics after delivery, supporting the importance of microbiota-gut-brain axis in humans during early life [80]. As a neurodevelopmental condition, autism spectrum disorder has also been linked to gut microbiota-brain axis dysfunction [90]. According to a recent meta-analysis, prenatal antibiotic exposure significantly increased the ASD risk in children. Interestingly, non-absorbable antibiotic vancomycin treatment, which mainly target Gram positive bacteria such as Clostridium spp., resulted in improved eye contact behavior and less constipation in autistic children [82].

Although not specifically focused in this review, neurodegenerative disorders such as Alzheimer’s disease (AD) are another consequence of gut microbiota-brain axis impairment. Minter et al. [78] reported that broad-spectrum postnatal antibiotic use reduced the amyloid plaque deposition in aged APPSWE/PS1ΔE9 transgenic mice suggesting that selective, targeted microbiome-based treatments can be used in early stage AD. A possible potential mechanism might be blooming in Lachnospiraceae family, one of the main butyrate-producers of the gut microbiota, after antibiotic treatment [91]. The increased butyrate production may induce T-reg differentiation, which has beneficial effect in AD pathogenesis by modulating microglial response amyloid-β deposition [92].

In addition to early life being of critical importance in terms of disruptive antibiotic effect on gut microbiota, antibiotic studies on adult animals also showed impaired behavior and brain function [71,83,93,94,95] and neurodegenerative disorders [96] both in prolonged and short courses, supporting the crucial role of gut microbiota-brain axis during lifespan. Some of the studies showed that these disruptive effects can be rescued by probiotic administrations [89,97].

Experimental reports summarizing the effect of antibiotics by considering the type of antibiotic, duration, route and age of exposure on gut-brain axis are depicted in Table 1. These experimental studies can be evaluated by considering broad-spectrum antibiotic cocktail strategies, which can broadly target gut microbiota including anaerobic bacteria causing germ-free like conditions [73], and targeted therapies using specific antibiotic groups such as Vancomycin. Both approaches lead to brain and behavioral impairments suggesting the role of disruption in both structure and function of the microbiota together, rather than a specific taxonomic group. A study by Erny et al. [98] also highlights the importance of gut microbial metabolites in microglia maturation and function. They showed that gut microbiota depletion by antibiotics resulted in defective microglia, which can be restored by microbiota-derived metabolites such as SCFA. Accordingly, antibiotic-driven disruption in gut microbiota may cause perturbation in functional gut microbiota, leading to alterations in microbial metabolites such as SCFA, as possible regulators of CNS inflammation [99].

While majority of the experimental studies in Table 1 highlight the complex role of gut microbiota in brain function both in early-life and adult age, the study by Minter et al. suggested a potential protective role of postnatal antibiotics in further AD progression, which provides a mechanism for Aβ deposition as a consequence of gut microbiota driven neuroinflammation [78].

Gut microbiota plays a vital role in the pathogenesis of functional gastrointestinal disorder. Gut microbiota and brain interactions are important factors for prevention and therapy. Further clinical studies are required for understanding the true effect of gut microbiota on disease progression in humans. While antibiotics are essential treatment strategies in most conditions, the long-lasting effects on host microbiome and immune functions, especially during early life should be interpreted with caution. We need prospective randomized trials for the therapeutic potential of gut microbiota modulation in functional gastrointestinal disorders.