Paralysis and sensory loss are devastating consequences of spinal cord injury (SCI). Less obvious to the public, but not less incapacitating for the individual affected by SCI, are loss of bladder and bowel function, an increase in susceptibility to infections, depression and anxiety, fatigue, deficits in thermoregulation, and an increase in cardiovascular dysfunction and disease. All of these latter complications result from damage to the autonomic nervous system.

Within the spinal cord, autonomic function is primarily coordinated through cholinergic sympathetic preganglionic neurons (SPNs) that reside in the intermediate lateral gray matter of the thoracic and upper lumbar spinal cord. Although recent data indicate that autonomic efferents in sacral spinal cord also are sympathetic (rather than parasympathetic) [1]. When the spinal cord is injured, especially at high spinal levels, most or all brainstem circuitry that provides tonic “executive” control over SPNs is lost. Injury to these presympathetic axons “unplugs” SPNs from the brain and brainstem, eliminating feedback regulation of autonomic reflexes that are initiated below the level of injury by, for example, visceral or somatic sensory nerves that relay information into the spinal cord from the bowel, bladder, or muscle. Once activated, SPNs signal to second-order postganglionic adrenergic neurons that innervate the cardiovascular system (changing heart rate, blood pressure), other viscera (e.g., kidney, pancreas, liver, stomach, intestine, etc.), and lymphoid tissues (e.g., bone marrow, spleen). After SCI, the loss of descending control over SPNs causes autonomic reflex circuitry to become dysfunctional creating pathology including autonomic dysreflexia and SCI–immune depression syndrome [2,3,4,5,6,7]. SCI also causes an autonomic imbalance in the gastrointestinal tract, which leads to deficits in colonic motility, mucosal secretions, and vascular tone [8, 9].

The spinal cord, gut, and immune system form an interconnected triad of “super systems” that together help to maintain human health. Damage or dysfunction to any part of the triad breaks homeostasis and causes disease. After SCI, the initial break in the spinal cord–gut–immune axis occurs in the spinal cord, owing to loss of the aforementioned autonomic reflex control over the gastrointestinal tract and lymphoid tissues, including bone marrow and spleen [10, 11]. Less is known about how SCI affects the function of the immune cells that reside in gut-associated lymphoid tissues (GALT) or whether SCI-induced changes in GALT affect postinjury morbidity or mortality. A comprehensive understanding of how SCI causes cellular and molecular changes in GALT will require that we also determine how the gut microbiota are affected by SCI.

The gut microbiota are a heterogeneous community of microbes that live in the gastrointestinal tract, mostly in the large intestine. The species present and the relative abundance of these species varies throughout the length of the gastrointestinal tract (see [12,13,14] for a review of varied types and functions of gut microbiota in mammalian intestine). These microbes outnumber mammalian cells by ~10:1 and the gut microbiome (genes expressed by gut microbiota) contains ~100-fold more genes than the human genome [15, 16], although recent estimates place the ratio at ~1:1 [17]. Regardless, in mammals a vast microbial network exists that is critical for normal digestion, nutrient absorption, and the development, metabolism, and function of cells throughout the body [18,19,20]. Recent data indicate that gut microbes also regulate both normal development and disease pathogenesis in the central nervous system (CNS) [21,22,23,24].

Altering the composition of the gut microbiota creates a state of “dysbiosis” where the balance between helpful bacteria and pathogenic bacteria (“pathobionts”) is skewed, usually favoring pathobionts. Common causes of gut dysbiosis include antibiotic use, prolonged stress, and gastrointestinal dysfunction [18, 25, 26]. Autoimmune diseases (e.g., multiple sclerosis, type 1 diabetes, rheumatoid arthritis), allergy, and metabolic disorders have been linked to gut dysbiosis [27,28,29,30,31,32,33]. Similarly, dysbiosis has been implicated in the onset or progression of neurological diseases, including autism, pain, depression, anxiety, and stroke [23, 24, 34,35,36,37,38,39,40].

Recent data from our laboratory show that traumatic SCI also causes gut dysbiosis and that dysbiosis impairs functional recovery and exacerbates intraspinal inflammation and lesion pathology (Fig. 1) [41]. Specifically, mice (C57BL/6, females) received mid-thoracic SCIs using a clinically relevant model of controlled contusion injury. At baseline and at different times postinjury, fecal samples were collected and 16s rRNA sequencing was used to quantify time-dependent changes in gut microbiota. The 16S rRNA gene contains hypervariable regions (V1–9) that, when sequenced, provide specific identification of bacterial communities. Data analyses revealed that Bacteroidales and Clostridiales, the 2 major bacterial orders in the gut [42, 43], were inversely regulated by SCI—by 3 weeks postinjury, Bacteroidales (phylum Bacteroidetes) decreased ~30%, whereas Clostridiales (phylum Firmicutes) increased ~250% relative to preinjury values. Significant changes in these major bacterial taxa were accompanied by lesser but consistent changes in minor taxa, including Anaeroplasmatales, Turicibacterales, and Lactobacillales. These changes in gut bacteria populations persisted, and in some cases increased by 4 weeks postinjury. Given that the bacterial orders Bacteroidales and Clostridiales together constitute >80% of all species residing in the gut, significant and lasting changes in their relative population densities after SCI will likely influence numerous physiological processes, both within and outside the gastrointestinal tract. Indeed, although gut microbiota live in the gastrointestinal tract, these bacteria likely affect spinal cord structure and function by various modes of communication. For example, the constant dialogue that occurs between gut microbiota and GALT immune cells produces cytokines and other metabolites that circulate and affect CNS function [44]. After SCI, we found that gut dysbiosis is associated with marked changes in the relative proportion of immune cells found in mesenteric lymph nodes and Peyer’s patches. An increase in the synthesis of inflammatory and immunoregulatory cytokines also occurred in GALT in parallel with changes in immune cell populations [41]. Gut microbes also produce neuroactive metabolites (short-chain fatty acids, choline) and neurotransmitters (γ-aminobutyric acid, serotonin, dopamine, acetylcholine), which can affect CNS function by activating vagal afferent nerve fibers in the intestines [19, 22, 34, 45, 46].

Fig. 1
figure 1

Spinal cord injury (SCI) disrupts brain and brainstem control over the sympathetic preganglionic neurons (SPNs) that are located in the thoracic spinal cord. This break in executive control over SPNs breaks homeostasis and control over postganglionic neurons (e.g., projecting from celiac ganglia) that innervate the gastrointestinal (GI) tract. Loss of coordinated neural control over the GI tract will impair motility, mucous secretion, immune surveillance, and epithelial barrier permeability in the small and large intestines. Together, these changes in the GI tract can cause bacterial translocation and gut dysbiosis (a). After SCI, probiotic treatment may normalize the gut microbiota leading to improvements in gut barrier integrity (b)

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Gut microbes may also exit the gastrointestinal tract and colonize other tissues. Indeed, in our mouse model of SCI, we found evidence of increased intestinal barrier permeability with bacterial translocation to mesenteric lymph nodes, liver, spleen, kidney, and blood [41]. Chronic systemic immune suppression, intestinal obstruction, and impaired intestinal motility—all complications of SCI—can independently cause bacterial translocation [47]. When this occurs, gut microbes or microbial components (e.g., endotoxin, peptidoglycan) can directly activate immune receptors (e.g., Toll-like receptors) on glia, neurons, hematopoietic stem/precursor cells, and mature immune cells [48, 49]. These are important considerations given that gut dysbiosis also develops in people after a SCI [50].

In a small cohort of SCI and able-bodied human subjects (30 SCI patients vs 10 age-matched able-bodied controls), gut microbe population dynamics were evaluated from fecal samples using 16s rRNA sequencing. All individuals had sustained a SCI at least 12 months prior to sample collection. Data from this study showed that butyrate-producing bacteria, such as Roseburia and Pseudobutyrivibrio, decreased in individuals with SCI [50]. Although the mechanisms responsible for the onset or maintenance of gut dysbiosis were not evaluated in this clinical cohort, it is logical to assume that dysbiosis develops secondary to the loss of autonomic control over the gastrointestinal tract. Repeat or sustained antibiotic use and psychological stress, which are common after SCI, can also exacerbate the effects of dysautonomia on the gut microbiome. This creates a feed-forward system; SCI-induced dysautonomia causes dysbiosis and impairs immune function, which, in turn, increases susceptibility to infections [2, 3, 6, 51,52,53,54,55]. High rates of infection in SCI populations increase the need for repeat dosing with antibiotics [56,57,58]. Precisely how repeat antibiotic use affects people with a SCI has not been studied, but antibiotics can disrupt bacterial gene and protein expression in the gut [59] and the composition of the gut microbiota can be changed for months or years after taking a single prescription of antibiotics [60, 61]. Thus, the conditions are ripe in both SCI animals and people for prolonged gut dysbiosis, which could adversely affect organ systems throughout the body.

Gut Dysbiosis as a Therapeutic Target After SCI

Restoring effective dialogue between the spinal cord, gut, and immune system would undoubtedly improve recovery and/or quality of life for individuals living with SCI. However, repair of the injured spinal cord is a formidable therapeutic target. Both the gut and immune system are more tractable targets and since each is affected by changes in the gut microbiota, efforts to modify postinjury gut dysbiosis could have therapeutic value. In this context, oral probiotics must be considered for use in human SCI.

Probiotics influence mucosal homeostasis by regulating intestinal microbe population dynamics, stabilizing gut epithelial barrier function, and by modulating local (GALT) and systemic immune responses [62, 63]. In patients with SCI, probiotics have been used to treat urinary tract infections and gastrointestinal distress [64, 65]. Whether probiotics can confer neuroprotection or ameliorate a range of comorbidities and neurological complications caused by a traumatic SCI has not been tested. Recently, using a mouse model of SCI, we showed that sustained postinjury delivery of VSL#3, a medical-grade probiotic, improved immune function and promoted recovery of locomotor function [41].

VSL#3 is a commercial probiotic formula comprised of 8 distinct lactic acid bacteria, primarily Lactobacillus and Bifidobacterium. These and other probiotic bacteria exert diverse effects throughout the body. In addition to their immunomodulatory effects, Lactobacillus and Bifidobacterium produce neuroactive metabolites (butyrate and other short-chain fatty acids) and neurotransmitters (serotonin, dopamine, γ-aminobutyric acid) [26, 46, 66]. These neurometabolites, produced locally in the gut, can spill over into the circulation where they can influence systemic inflammation and immune function [19, 66, 67]. These metabolites also can bypass the blood–brain barrier to affect CNS structure and function including mood, appetite, sleep, memory and learning, temperature regulation, and social behaviors [19, 66, 67]. Data from our laboratory show that SCI mice fed VSL#3 daily for 5 weeks show improvements in spontaneous locomotor recovery with reduced neuropathology [41]. Importantly, in the mesenteric lymph nodes of VSL#3-treated mice, CD4+CD25+FoxP3+ regulatory T cells (Tregs) increased significantly. Tregs, a population of T lymphocytes that express the transcription factor FoxP3, play a crucial role in immune homeostasis; Tregs actively suppress potentially damaging self-reactive (autoreactive) T cells [68]. Loss of Treg function is implicated in the onset or progression of multiple sclerosis, rheumatoid arthritis, graft versus host disease, and irritable bowel disease. Probiotics, especially those containing Lactobacillus and Bifidobacterium, significantly boost Treg activity in vivo and can ameliorate disease in multiple sclerosis models [69, 70].

Because gut microbes exert profound biological effects throughout the body, the translocation of bacteria and the development of gut dysbiosis after SCI could contribute to the various comorbidities typically attributed to paralysis or the psychological stress associated with adapting to life after SCI. Indeed, in able-bodied individuals gut dysbiosis has been linked to major depressive disorders and gastrointestinal and metabolic diseases (e.g., obesity, diabetes, Crohn’s disease, irritable bowel syndrome, etc.) (Fig. 2) [34, 46, 62, 71]. Dysbiosis and “leaky gut” also have been implicated in the onset and progression of chronic fatigue syndrome. Chronic fatigue syndrome is a multisystem disease characterized by persistent fatigue, postexertion malaise, cognitive impairment, mood changes, and gastrointestinal disturbances. Despite persistent fatigue, people with chronic fatigue syndrome often report difficulty sleeping. Many of these same symptoms also plague people with SCI [72,73,74]. In fact, fatigue affects most SCI individuals [75]. Fatigue in people with SCI is an amalgam of changes in physiological and behavioral factors including innate neuromuscular ability, motivation, resilience, and depressive-like mood swings, and is influenced by one’s overall sense of quality of life [76, 77]. As such, measures of fatigue are closely linked to social and mental health after SCI [75].

Fig. 2
figure 2

Gut dysbiosis is a disease-modifying comorbidity that likely causes or exacerbates many other comorbidities associated with spinal cord injury (SCI). Gut microbiota can directly influence immune function, neurocognitive function, and mood, metabolism, and energy/fatigue. Each of these can, in turn, influence the gut microbiota. Thus, gut dysbiosis creates a feed-forward cycle that can contribute to lasting pathophysiology, which will impair function and quality of life after SCI

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SCI also enhances the risk or frequency of developing heart disease or metabolic disorders, including obesity, diabetes, and liver dysfunction [78,79,80,81,82,83,84,85]. The development of these diverse multisystem pathologies is often attributed to inactivity in people with SCI; however, changes in muscle mass and adiposity take time to develop and the onset of insulin resistance and hyperinsulinemia are not immediate consequences of SCI [86]. Similarly, cardiovascular disease and/or the consequences of chronic low-grade systemic inflammation do not manifest soon after SCI. The postinjury onset of gut dysbiosis could contribute to or cause cardiometabolic disease. After SCI in mice, the relative abundance of Bacteroidetes (order Bacteroidales) decreases as a function of time postinjury with a corresponding time-dependent increase in Firmicutes (order Clostridiales) [41]. These are the 2 major bacterial phyla that comprise both mouse and human microbiota [42, 43]. A reciprocal change in the Bacteroidetes-to-Firmicutes ratio also occurs in obese humans and rodents [87]. Gut microbiota are now believed to represent novel genetic determinants that, together with changes in diet and lifestyle, contribute to the pathophysiology of obesity [32, 88,89,90]. Precisely how obesity dysbiosis causes or exacerbates adiposity is not known; however, a high Firmicutes-to-Bacteroidetes ratio was found to increase energy harvest from the diet. Indeed, an obese microbiota is more efficient than nonobese microbiota at metabolizing and absorbing dietary substrates from food [87, 91, 92].

Each of these multiorgan “failures” develop over time and each can be linked to preceding changes in gastrointestinal dysfunction, dysbiosis, and leaky gut. Individuals with SCI also suffer from dysfunctional immune responses that exacerbate the above conditions and impair host defense, rendering individuals with SCI more susceptible to infection [2, 54, 93]. Since gut dysbiosis will affect nutrient absorption, mental health, whole-body metabolism, and systemic immune function, oral probiotics could be a “magic bullet” therapy that would simultaneously benefit various neurological and behavioral manifestations of SCI.

Future Directions and Challenges

The continuing analyses of genomic and metagenomic changes in gut microbiota will allow scientists to map the dynamic patterns of dysbiosis caused by SCI. Data from these analyses can then be used to estimate how the biological functions attributed to specific gut microbiota (e.g., metabolism of amino acids by Lactobacilli) are affected by SCI and whether these and other changes can predict the probability or severity of various SCI comorbidities including infection, anemia, obesity/metabolic syndrome, and, perhaps, secondary neurological deterioration or improvement. To date, this type of analysis in preclinical studies has been limited to fecal samples obtained from a single mouse strain affected by a moderate level of mid-thoracic SCI [41]. A similarly narrow scope of genomic analysis has been completed in fecal samples obtained from human subjects with SCI human [50].

One might predict that the magnitude of gut dysbiosis after SCI will vary as a function of injury level, injury severity, and time postinjury in both males and females after SCI. Indeed, the gut microbiota affect serotonin synthesis, metabolism, and neurotransmission in a sex-specific manner [45, 46, 94]. Also, the magnitude of innervation to the intestine by the sympathetic nervous system will vary as a function of injury severity and the spinal level affected by injury. Comparative studies of dysbiosis should also incorporate an analysis of the much less accessible small intestine microbiota [95]. The small intestine contains fewer microbiota than the large intestine, but most (~90%) energy absorption from the diet occurs in the small intestine [95, 96]. Future studies should determine whether SCI-induced changes in intestinal microbiota contribute to the high incidence of metabolic disease and increased adiposity that develop in individuals with SCI [80,81,82,83,84,85, 97,98,99]. The clinical value of considering changes in the microbiota after SCI seems obvious given that changes in the relative abundance of discrete gut microbiota (e.g., Bacteroidetes:Firmicutes) can contribute to the pathophysiology of obesity [32, 87,88,89,90,91,92]. These and other changes in the population dynamics of gut microbes represent “druggable” targets and can be manipulated in future studies using custom diets, personalized nutraceuticals (e.g., pre- or probiotics), or possibly by altering the composition of bacteriophages in the intestine that feed on pathobionts (“phage therapy”) [100, 101].

To understand how SCI-induced changes in gut microbial communities affect human physiology and pathophysiology, comparative preclinical studies are essential. In humans, it is exceedingly difficult to control the many variables that influence gut microbiota, including diet, environment, and genetics. These variables are easy to control in mice. Because mice and humans have the same core bacteria in their intestines [43, 102], mice have proven to be a productive and tractable model system for dissecting host–microbiota functional relationships. In a large multicenter study, 184 fecal samples were collected from several strains of mice housed in various laboratories around the world. A comparison of the microbiota (bacterial species) and microbiome (genes expressed by these bacteria) in these mouse samples with a human gut gene catalog revealed that the mouse and human gut microbiomes encode proteins that control nearly identical biological functions including nutrient harvest and metabolism [102]. Thus, there is remarkable conservation of function between mouse and human microbiota, making it reasonable to predict that the functional implications of large shifts in gut bacterial communities in rodent SCI models are relevant to human SCI. Still, species-specific variables do exist that can critically impact microbiota studies, many of which are driven by dietary differences between rodents and humans [103, 104]. Accordingly, researchers must remain vigilant about these (and other) differences as they design and interpret data regarding the microbiota. By doing so, the “hype” that often surrounds new microbiota research findings can be placed into context to appropriately manage the scientific and public expectations of these new data [105].