Intestinal bacteria associated with irritable bowel syndrome and chronic fatigue

The etiology of irritable bowel syndrome (IBS) is unknown. Abnormal intestinal bacterial profiles and low bacterial diversity appear to play important roles in the pathophysiology of IBS. This narrative review was designed to present recent observations made relating to fecal microbiota transplantation (FMT), which implicate possible roles of 11 intestinal bacteria in the pathophysiology of IBS. The intestinal abundances of nine of these bacteria increased after FMT in patients with IBS, and these increases were inversely correlated with IBS symptoms and fatigue severity. These bacteria were Alistipes spp., Faecalibacterium prausnitzii , Eubacterium biforme , Holdemanella biformis , Prevotella spp., Bacteroides stercoris , Parabacteroides johnsonii , Bacteroides zoogleoformans , and Lactobacillus spp. The intestinal abundances of two bacteria were decreased in patients with IBS after FMT and were correlated with the severity of IBS symptoms and fatigue ( Streptococcus thermophilus and Coprobacillus cateniformis ). Ten of these bacteria are anaerobic and one ( Streptococcus thermophilus ) is facultative anaerobic. Several of these bacteria produce short-chain fatty acids, especially butyrate, which is used as an energy source by large intestine epithelial cells. Moreover, it modulates the immune response and hypersensitivity of the large intestine and decreases intestinal cell permeability and intestinal motility. These bacteria could be used as probiotics to improve these conditions. Protein-rich diets could increase the intestinal abundance of Alistipes , and plant-rich diet could increase the intestinal abundance of Prevotella spp., and consequently improve IBS and

probiotics) have been found to be relatively ineffective against IBS symptoms most probably because the beneficial bacteria needed are unknown. 13,14 Moreover, long-term intestine colonization with new bacteria through probiotic treatment is doubtful. [15][16][17] In the absence of an effective method to restore the dysbiosis, transplanting a microbiome from healthy individuals with well-functioning guts to those with IBS and dysbiosis (fecal microbiota transplantation [FMT]) is conceivable. In contrast to probiotics treatment, FMT has been found to induce long-term bacteria colonization in the intestine. 18 FMT has been applied to patients with IBS in seven randomized controlled trials (RCTs), four of which found a positive effect while the other three found no effect. 19 It is difficult to compare these RCTs due to variations in the criteria used to select the donors and patients, in the fecal transplant dose used in the FMT, the way the transplant was preserved and prepared, and the administration route. 19 Recent studies that applied FMT as a treatment for IBS have provided evidence for the involvement of several intestinal bacteria in the pathophysiology of IBS. 8,9,[20][21][22] The present narrative review was designed to reveal observations on intestinal bacteria made in studies of FMT for patients with IBS that indicate their involvement in the pathophysiology of IBS.
Using these MeSH expressions, 7861 original articles, and reviews were identified of which 35 were duplicates. Of these 7826 papers, 7560 were excluded as they were illegible to the subject of the study. The remaining 266 papers were accessed for eligibility of which 66 were included in the study and 200 were excluded because they included few patients or based on experimental animals ( Figure 1).

| Alistipes spp.
The Alistipes genus was first described in 2003 23 and belongs to the Rikenellaceae family within the Bacteroidales order of the Bacteroidetes phylum. 23,24 The Alistipes genus comprises 13 species 24 that are mostly localized in the gastrointestinal tracts of humans. 25 Alistipes spp. are gram-negative, rod-shaped, anaerobic, nonspore-forming, and bile-resistant bacteria. 23,26,27 This bileresistant genus is expected to be more abundant in the terminal ileum. 28 Tryptophan is a precursor for serotonin and Alistipes hydrolyse tryptophan to produce indole, and so an increased Alistipes level would decrease serotonin availability. 24 Alistipes also expresses F I G U R E 1 Transparent Reporting of Systematic Reviews and Meta-Analysis (PRISMA) flow diagram. http://www.prism a-state ment.org/ | 3 of 10 EL-SALHY glutamate decarboxylase, an enzyme that metabolizes glutamate into γ-aminobutyric acid. 24 In addition, Alistipes also produces SCFAs with anti-inflammatory effects, such as acetic, succinic, and propionic acids. 24,29 Propionic acid exerts neurobiological effects in rats. 30 Moreover, Alistipes expresses methylmalonyl-CoA epimerase, the gene for which is located on an operon of the acetyl-CoA carboxylase gene. 24 The relative abundance of Alistipes spp. appears to play a role in gut transit times and relative abundance of Alistipes spp. has been found to be higher in healthy subjects with longer gut transit times. 31 The abundance of Alistipes spp. is associated with aging and several gastrointestinal diseases such as inflammatory bowel disease and lever cirrhosis and nongastrointestinal diseases such as chronic fatigue syndrome, depression, anxiety, and autism. 24,[32][33][34] Several immuno-inflammatory and metabolic mechanisms have been proposed for their role in human health and association with diseases. 24,32,33 Interestingly, subjects with asymptomatic colonization with Clostridioides difficile and patients with COVID-19 infection have lower abundance of Alistipes spp. than healthy subjects. 35,36 The fecal levels of Alistipes spp. have been reported to be lower in IBS patients than healthy subjects. 37 The fecal levels of Alistipes spp.
increased significantly in patients who received FMT after 1 month and remained high at 1, 2, and 3 years after FMT ( Figure 2). These levels were inversely correlated with total scores on the IBS Symptom Severity Scale (IBS-SSS) and Fatigue Assessment Scale (FAS) at 1 month, 1 year, 2 years and 3 years after FMT ( Figure 3). 8,9,20,21 Among the bacteria levels that changed after FMT and were correlated with IBS-SSS and FAS scores (Table 1) Patients with IBS who did not respond to FMT had lower Alistipes spp. levels at the baseline compared with those who responded to FMT. 22 Furthermore, patients with IBS who initially responded to FMT after 3 months and relapsed after 1 year had lower Alistipes levels at the baseline than those did who maintained a response at 1 year after FMT ( Figure 4). 21 These findings suggest that Alistipes spp. levels are important for initial responses to FMT and for maintaining that response.
It has been reported that female patients with IBS respond to FMT better than do male patients with IBS. 26 A sex difference has been reported in the gastrointestinal microbiota of healthy subjects, with Alistipes spp. being more abundant in females than in males. 38 Analysis of our previous data also indicated that the Alistipes spp. levels were higher in female than in male patients with IBS ( Figure 5). 20 It is reasonable to assume that like nonresponders to FMT, low Alistipes spp. levels could underlie the lesser response to FMT in males.
In summary, the observations presented above suggest that Alistipes spp. are involved in the pathophysiology of IBS and the coexisting fatigue in patients with IBS ( Figure 6).

| Faecalibacterium prausnitzii
Faecalibacterium prausnitzii is a gram-negative, anaerobic, nonsporeforming, and rod-shaped bacterium. 39 It is the most abundant bacterium in the healthy adults and amounts to over 5% of the intestinal bacteria. 40,41 Faecalibacterium prausnitzii is the primary butyrate producer in the large intestines of humans. 40,[42][43][44][45] Butyric acid levels were found to be inversely correlated with IBS-SSS and FAS total scores at 1 years after FMT ( Figure 7). Moreover, Faecalibacterium prausnitzii produces an anti-inflammatory single 15 kDa protein, which blocks the NF-κB pathway pathways. 46 Faecalibacterium prausnitzii has also been reported to increase the serotonin level through its impact on the expression of major genes involved in the serotonin system. 47 Changes in the abundance of Faecalibacterium prausnitzii are associated with several diseases such as metabolic syndrome and diabetes. 23,41 A decreased abundance of Faecalibacterium prausnitzii has been reported in inflammatory bowel disease, chronic fatigue and Clostridioides difficile, and COVID-19 infections. 35,36,46,48,49 The abundance of Faecalibacterium prausnitzii has been found to be negatively correlates to the activity of inflammatory bowel disease, fatigue severity, and colorectal cancer as well as to correlate with cognitive scores and decreases in the Alzheimer's-type dementia. 42,49,50 The fecal levels of Faecalibacterium in IBS patients have been shown to be lower than those of healthy subjects. 37,51 The level of Faecalibacterium prausnitzii in the feces increased significantly in patients with IBS after FMT and was inversely correlated with both IBS symptoms and fatigue ( Figure 7 and Table 1). 8,37 Furthermore, decreased relative abundance of Faecalibacterium prausnitzii has been reported in patients with IBS and chronic fatigue, and it is associated with worse fatigue scores and worse pain scores. 52 F I G U R E 2 Fluorescence signals of Alistipes spp. in patients who received 30 and 60 g of donor feces at the baseline and at 1 month, 1 year, 2 years, and 3 years after fecal microbiota transplantation (FMT). The figure is based on previous data. 22-24 *, p < 0.05; ***, p < 0.001, ****, p < 0.0001 compared with baseline values.

| Eubacterium biforme
Eubacterium biforme is a gram-positive, anaerobic, nonspore forming, and rod-shaped bacterium, 53 and it produces large amounts of butyric acid. 44,54,55 Decreased abundance of Eubacterium biforme has been reported in patients with Parkinson's disease. 55 The changes in fecal levels of Eubacterium biforme and the correlations to IBS and fatigue following FMT are presented in Table 1. 21

| Holdemanella biformis
The fecal levels of Holdemanella biformis increased in patients with IBS following FMT and were inversely correlated with both IBS symptoms and fatigue. 8 Holdemanella biformis is a coccus-shaped, anaerobic bacterium 56,57 that produces the long-chain fatty acid 3-hydroxyoctadecaenoic acid, which has an anti-inflammatory effect in colitis and protects against intestinal tumor growth. 56,57

| Prevotella spp.
Prevotella is a genus of gram-negative, anaerobic, rod-shaped common commensal bacteria comprising 50 species. 58 The abundance of Prevotella is higher in non-westerners who consume plant-rich diets. 59,60 Prevotella spp. can improve glucose metabolism and is abundant in inflammatory conditions, such as inflammatory bowel disease, rheumatoid arthritis, and periodontitis. 61 The role of Prevotella spp. in inflammation and whether the increase in their abundance is the cause of or is secondary to the inflammation remain to be determined. 61 On the contrary, in subjects with either asymptomatic colonization with Clostridioides difficile (CD) or suffering from CDI infection have lower abundance of Prevotella spp. 35 The fecal levels of Prevotella spp. have been reported to be lower in IBS patients than those of healthy subjects. 37 The abundance of fecal Prevotella spp. increased significantly in patients with IBS after FMT (Table 1). 21,62,63

| Bacteroides stercoris
Bacteroides stercoris is a gram-negative, anaerobic, nonsporeforming, rod-shaped, and bile-resistant bacteria. 64 It ferments carbohydrates via the production of a pool of volatile fatty acids that are reabsorbed through the large intestine and utilized by the host as an energy source. 64 The abundance of Bacteroides stercoris has been found to be inversely correlated with disease activity in ulcerative colitis. 34 The abundance of Bacteroides stercoris in patients with IBS after FMT is summarized in Table 1

| Parabacteroides johnsonii
Parabacteroides is a relatively new genus with distinctive features shared among other intestinal commensal bacteria, and comprises 15 species. 65 Parabacteroides johnsonii is a gram-negative, anaerobic, nonspore-forming, and rod-shaped bacterium. [65][66][67] The fecal levels of Parabacteroides have been reported to be lower in IBS patients than those of healthy subjects. 37 The levels of Parabacteroides johnsonii increase in patients with IBS after FMT and are inversely correlated with both the IBS symptoms and fatigue (Table 1). 9,21

| 7 of 10
EL-SALHY thermophilus is low in patients with colorectal cancer and it secretes β-galactosidase, which inhibits tumor genesis. 74 It also has antiinflammatory effects via NF-κB pathway activation. 73,75 However, bacteremia was reported in a regular consumer of probiotics including Streptococcus thermophilus. 76 The fecal levels of Streptococcus have been found to be higher in IBS patients than those of healthy subjects. 37 The fecal levels of Streptococcus thermophilus changed significantly in patients with IBS after FMT (Table 1). 8

| Coprobacillus cateniformis
Coprobacillus cateniformis is a gram-positive, nonsporulating, anaerobic, and rod-shaped bacterium, which has been described recently. 77 The abundance of Coprobacillus cateniformis increases with biological age and it has been reported to cause bacteremia in an immunesuppressed patient. 78 The fecal levels of Coprobacillus cateniformis decreased significantly in patients with IBS after FMT and were positively correlated with both IBS symptoms and fatigue. 8

| CON CLUS ION
It is not clear yet whether bacterial dysbiosis or difference in abundance of certain bacteria in IBS patients is a factor involved in the pathophysiology of IBS. 79 A large proportion of IBS patient do not exhibit dysbiosis and reanalyzing the data from our previous studies showed that 58% out of 165 IBS patients and 33% out of 186 IBS patients had dysbiosis. [8][9][10] However, other studies showed that over 70% of IBS patients had dysbiosis. 6,11,12 Following the application of an effective FMT protocol for IBS treatment, Barbara and Ianiro furthered their vision that FMT may lead to identifying the bacteria that are beneficial for IBS, and reconstructed them in the laboratory. 20,80 The present review presented 11 intestinal bacteria that were associated with IBS symptoms and fatigue severity. All of the bacteria that seem to be associated with IBS and fatigue are anaerobic, with the exception of Streptococcus salivarius 81 subsp. thermophilus, which is a facultative anaerobic bacterium. Freezing the fecal samples of patients with IBS directly and keeping them frozen until the analysis was performed without ambient air exposure may explain why changes could be detected in these bacteria in FMT studies that directly froze the feces of the patients. 8,9,20,21,82 In other FMT studies the fecal samples of IBS patients exposed to ambient air, which may reduce the abundance of important commensal bacteria up to 12-folds reduction. 82 It is too early to draw any definite conclusions about their roles in the pathophysiology of IBS and fatigue, and so these bacteria require further investigations.
Chronic fatigue occurred in up to 96% of patients with IBS, raising the question of whether these conditions have the same underlying mechanisms. 5,83 The intestinal bacteria described above that were correlated with IBS symptom severity were also correlated with fatigue severity. This observation is consistent with the suggestion that these two conditions having common mechanisms. 5 Several of these bacteria produce short-chain fatty acids (SCFAs), especially butyrate. The butyrate levels in patients with IBS increased after FMT and were correlated with both IBS symptoms and fatigue ( Figure 6). 84 Butyrate provides large intestine epithelial cells with energy, modulates the immune response and hypersensitivity of the large intestine, and decreases intestinal cell permeability and intestinal motility. 19 Butyrate also has protective properties against colorectal cancer and inflammatory bowel diseases. 40,[42][43][44][45] Assuming that future studies confirm the roles of these bacteria in the pathophysiology of IBS and its coexisting fatigue, these species could be used as probiotics to improve these conditions. Some of these bacteria such as Lactobacillus spp. and Streptococcus salivarius subsp. thermophilus are actually already used as probiotics. 85,86 However, the observations made in this review that Streptococcus salivarius subsp. thermophilus worsen both IBS symptoms and fatigue in patients with IBS should be considered when recommending probiotics containing them.
Consuming a diet based on animal proteins for 5 days can rapidly increase Alistipes spp. levels. 87

AUTH O R CO NTR I B UTI O N S
Magdy El-Salhy: Collected and reviewed the data and wrote the manuscript.

FU N D I N G I N FO R M ATI O N
This work was supported by Helse Fonna (grant no. 40415) and Helse Vest (grant no. F-12854-D10484).

CO N FLI C T O F I NTE R E S T S TATE M E NT
The author has nothing to disclose.

DATA AVA I L A B I L I T Y S TAT E M E N T
The data that support the findings of this study are available from the corresponding author upon reasonable request.