Fecal detection of enterotoxigenic Bacteroides fragilis

Clinical significance of Bacteroides fragilis as a potential prognostic factor in colorectal cancer

INTRODUCTION

Bacteroides fragilis (B. fragilis) is considered to act in an anti-inflammatory manner on the intestinal tract. On the contrary, enterotoxigenic B. fragilis (ETBF), a subtype of B. fragilis, produces an enterotoxin (BFT; B. fragilis toxin), leading to asymptomatic chronic infections and colonic tumor formation. However, the impact of B. fragilis and ETBF on the clinical outcome of colorectal cancer (CRC) remains unclear. We aim to assess whether their presence affects the outcome in patients with CRC after curative resection.

METHODS

We obtained 197 pairs of matched formalin-fixed paraffin-embedded samples from cancerous and adjacent non-cancerous tissues of patients with pathological stage (pstage) II and III CRC after curative resection. The presence of B. fragilis and ETBF were estimated using real-time polymerase chain reaction, and recurrence-free survival (RFS) and overall survival (OS) of the patients were analyzed.

RESULTS

16S rRNA for B. fragilis and bft DNA were detected in 120 (60.9%) and 12 (6.1%) of the 197 patients, respectively. B. fragilis-positive patients had better RFS than B. fragilis-negative patients, although that was not statistically significant. In subgroup analysis, better outcomes on RFS were observed in the presence of B. fragilis in pstage II and left-sided CRC. The association of B. fragilis positivity on OS was accentuated in the depth of T4 subgroup. No significant differences were observed in RFS and OS between ETBF and non-toxigenic B. fragilis.

CONCLUSIONS

Our findings suggest that the presence of B. fragilis is associated with better outcomes in patients with pstage II and III CRC after curative resection.

Current advances in the anti-inflammatory effects and mechanisms of natural polysaccharides

Inflammatory bowel disease (IBD) is a chronic, multifactorial and inflammatory disease occurring in the colon tract. Bioactive polysaccharides from natural resources have attracted extensive attention due to their safety, accessibility and good bioactivities. In recent years, a variety of natural bioactive polysaccharides have been proven to possess anti-inflammatory effects on treating acute colitis. The objective of this review was to give an up-to-date review on the anti-inflammatory effects and mechanisms of natural polysaccharides on acute colitis. The anti-inflammatory effects of natural polysaccharides on acute colitis concerning clinical symptoms amelioration, colon tissue repairment, anti-oxidative stress alleviation, anti-inflammation, immune regulation, and gut microbiota modulation were comprehensively summarized. In addition, inducible murine models for assessing the anti-inflammatory effects of natural polysaccharides on acute colitis were also concluded. This review will offer the comprehensive understanding of anti-inflammatory mechanisms of natural polysaccharides in acute colitis, and render theoretical basis for the development and application of natural polysaccharides in drug and functional food.

The role of anaerobic bacteria in the development and prevention of colorectal cancer: A review study

Colorectal cancer (CRC) is the third most frequently diagnosed cancer in both males and females in the Unites States. Colonoscopy is considered a safe method for screening this disorder; however, it can be challenging for patients. As research on microbiota, especially anaerobic microbiota, has expanded substantially, new links have been determined between anaerobic bacteria and CRC progression. These associations can be useful in screening CRC in the near future. This review discusses current research investigating the presence of anaerobic bacteria, including Bacteroides fragilis, Peptostreptococcus anaerobius, Clostridium septicum, Porphyromonas gingivalis, Fusobacterium nucleatum, and Parvimonas micra in CRC and presents an overview about their mechanisms of action. We also discuss the current anaerobic probiotics used for the treatment and prevention of CRC.

Changes of digestive and fermentation properties of Sargassum pallidum polysaccharide after ultrasonic degradation and its impacts on gut microbiota

The in vitro digestive and fermentation properties of Sargassum pallidum polysaccharide (SPP) after ultrasound degradation were investigated. The results showed that SPP and its degraded fractions were not affected by human saliva, but slightly degraded by breaking glycosidic bonds under simulated gastrointestinal digestion. The DPPH radical scavenging activity, α-glucosidase inhibitory activity, and bile acid-binding capacity of SPP and its degraded fractions were decreased after digestion, which was attributed to the reduction of molecular weights (MWs) and viscosity. Furthermore, in vitro fermentation assay indicated that SPP and its degraded fractions showed good fermentability. The predominant compositional monosaccharides including arabinose, galactose, glucose, xylose, and uronic acid were significantly decreased, and the degraded SPP fractions were more easily fermented and utilized by gut bacteria. SPP and its degraded fractions could modulate gut health by decreasing the Firmicutes/Bacteroidetes ratio and increasing the relative abundances of some beneficial genera, such as Prevotella, Dialister, Phascolarctobacterium, Ruminococcus, and Bacteroides. These findings suggested that SPP and its degraded fractions exhibited similar influence on gut microbiota community, but appropriate degraded SPP fractions were more easily fermented by gut microbiota.

To resist and persist: Important factors in the pathogenesis of Bacteroides fragilis

Bacteroides fragilis is a most frequent anaerobic pathogen isolated from human infections, particularly found in the abdominal cavity. Different factors contribute to the pathogenesis and persistence of B. fragilis at infection sites. The knowledge of the virulence factors can provide applicable information for finding alternative options for the antibiotic therapy and treatment of B. fragilis caused infections. Herein, a comprehensive review of the important B. fragilis virulence factors was prepared. In addition to B. fragilis toxin (BFT) and its potential role in the diarrhea and cancer development, some other important virulence factors and characteristics of B. fragilis are described including capsular polysaccharides, iron acquisition, resistance to antimicrobial agents, and survival during the prolonged oxidative stress, quorum sensing, and secretion systems.

Comparative Analysis of Sample Extraction and Library Construction for Shotgun Metagenomics

Human fecal specimens, serve as important materials, are widely used in the field of microbiome research, in which inconsistent results have been a pressing issue. The possible attribute factors have been proposed including the specimen status after preservation, extracted DNA quality, library preparation protocol, and sample DNA input. In this study, quality comparisons for shotgun metagenomics sequencing were performed between 2 DNA extraction methods for fresh and freeze-thaw samples, 2 library preparation protocols, and various sample inputs. The results indicate that Mag-Bind® Universal Metagenomics Kit (OM) outperformed DNeasy PowerSoil Kit (QP) with a higher DNA quantity. Controlling on library preparation protocol, OM detected on-average more genes than QP. For library construction comparison by controlling on the same DNA sample, KAPA Hyper Prep Kit (KH) outperformed the TruePrep DNA Library Prep Kit V2 (TP) with the higher number of detected genes number and Shannon index. No significant differences were found in taxonomy between 2 library preparation protocols using the fresh, freeze-thaw and mock community samples. No significant difference was observed between 250 and 50 ng DNA inputs for library preparation on both fresh and freeze-thaw samples. Through the preliminary study, a combined protocol is recommended for performing metagenomics studies, by using OM method plus KH protocol as well as suitable DNA quantity on either fresh or freeze-thaw samples. Our findings provide clues for potential variations from various DNA extraction methods, library protocols, and sample DNA inputs, which are critical for consistent and comprehensive profiling of the human gut microbiome.

Degradation of Peptide-Bound Maillard Reaction Products in Gastrointestinal Digests of Glyoxal-Glycated Casein by Human Colonic Microbiota

A large portion of Maillard reaction products (MRPs) cannot be absorbed in the upper gut and therefore may be further decomposed and utilized by colonic microbiota (CM). This work reported the stability of UV-absorbent MRPs, fluorescent MRPs and peptide-bound N(ε)-(carboxymethyl)-lysine (CML) in high molecular weight (HMW, >10 kDa), medium molecular weight (MMW, 1-10 kDa), and low molecular weight (LMW, <1 kDa) gastrointestinal digests of glyoxal-glycated casein in the presence of CM. Fluorescent MRPs showed high stability, whereas UV-absorbent MRPs may be partially decomposed. A higher depletion rate of CML was found in the LMW fraction (38.7%) than in the MMW (21.7%) and HMW (9.6%) fractions. The 16S rRNA sequencing results revealed both beneficial and detrimental changes in CM composition induced by the glycated fractions. Generation of short-chain and branched-chain fatty acids in fermentation solutions with glycated fractions was significantly suppressed compared with that in fermentation solution with unglycated digests. This work revealed the possible interplay between peptide-bound MRPs and CM.

Inhibition of enterohemorrhagic Escherichia coli O157:H7 infection in a gnotobiotic mouse model with pre-colonization by Bacteroides strains

Enterohemorrhagic Escherichia coli (EHEC) O157:H7 has been known to cause outbreaks of hemorrhagic colitis and hemolytic uremic syndrome. We previously demonstrated that intestinal flora contribute to the prevention of EHEC infection in a mouse model. However, it has not yet been determined whether Bacteroides, a predominant genus in the human intestine, contributes to the prevention of EHEC infection. The aim of the present study was to investigate the effect of Bacteroides fragilis (B. fragilis) and Bacteroides vulgatus (B. vulgatus) on EHEC O157:H7 infection in vivo using gnotobiotic mice. These strains were inoculated into germ-free mice to create a gnotobiotic mouse model. EHEC was inoculated into the mice, which were then monitored for 7 days for any change in symptoms. The mice that had been pre-colonized with the Bacteroides strains did not develop lethal EHEC infection, although several inflammatory symptoms were observed in the B. vulgatus pre-colonized group. However, no inflammatory symptoms were identified in the B. fragilis pre-colonized group. Moreover, B. fragilis exerted an inhibitory effect on enterocyte-like cell apoptosis. B. fragilis protected HT29 cells from apoptosis caused by Shiga toxin. In conclusion, the findings of the present study demonstrated that colonization by Bacteroides strains can inhibit EHEC infection.

Gastrointestinal Pathobionts in Pediatric Crohn's Disease Patients

Crohn's disease (CD) is an inflammatory disease of the gastrointestinal tract, with a rising incidence worldwide, particularly in children. CD is thought to arise due to an immune response to environmental factors. The role of bacteria in CD has recently been highlighted, and here, we examine the prevalence of two bacterial species, enterotoxigenic Bacteroides fragilis (ETBF) and Fusobacterium nucleatum, implicated in gastrointestinal pathologies, in a pediatric CD cohort. Stool samples from 30 children with treatment-naïve CD and 30 age- and sex-matched controls were collected, and DNA was extracted. Quantitative PCR was used to determine the levels of ETBF and F. nucleatum in stool samples. Bacterial positivity and relative abundance were assessed between cases and controls and in relation to disease severity. No associations were found between colonization with ETBF and CD, or between colonization with either ETBF or F. nucleatum and disease severity or presence of C. concisus. However, a strong association was observed between positivity for F. nucleatum in the stool samples and the occurrence of CD in patients (25/30) as compared to controls (8/30) (P=0.003). F. nucleatum is more prevalent in the stool samples of pediatric CD patients, compared to healthy controls, and may have potential use as a biomarker of pediatric CD.

The gut microbiome and colorectal cancer: a review of bacterial pathogenesis

Colorectal cancer (CRC) is the third most common newly diagnosed cancer in both men and women in the Unites States. Colonoscopy has become increasingly popular in CRC screening and represents the gold standard for detecting and removing pre-cancerous lesions. Although colonoscopy is considered a relatively safe procedure, it is invasive and bowel preparation can be challenging for patients. As interest in the gut microbiome has expanded, there have been new links established between bacteria and the development of CRC. These developing associations could prove to be a useful adjunct to colonoscopy for CRC screening in the future. This review examines current research evaluating multiple proposed pathogenic microorganisms including sulfidogenic bacteria such as Bilophila wadsworthia, as well as Streptococcus bovis, Helicobacter pylori, Bacteroides fragilis, and Clostridium septicum. This discussion primarily focuses on bacterial pathogenesis, evidence of association with CRC, and the proposed mechanisms of carcinogenesis.

Mechanisms of Bacteroides fragilis resistance to metronidazole

Metronidazole-resistant Bacteroides fragilis (B. fragilis) have been reported worldwide. Several mechanisms contribute to B. fragilis resistance to metronidazole. In some cases, the mechanisms of metronidazole resistance are unknown. Understanding the mechanisms of resistance is important for therapy, the design of new alternative drugs, and control of resistant strains. In this study, a comprehensive review of the B. fragilis resistance mechanisms to metronidazole was prepared. The rate of metronidazole-resistant B. fragilis has been reported as ranging from 0.5% to 7.8% in many surveys. According to CLSI, isolates with MICs ≥32 μg/mL are considered to be metronidazole-resistant. In the majority of cases, metronidazole resistance in B. fragilis is coupled with the existence of nim genes. Metronidazole resistance could be induced in nim-negative strains by exposure to sub-MIC levels of metronidazole. There are multi-drug efflux pumps in B. fragilis which can pump out a variety of substrates such as metronidazole. The recA overexpression and deficiency of feoAB are other reported metronidazole resistance mechanisms in this bacterium.

Simulated Digestion and Fermentation in Vitro by Human Gut Microbiota of Polysaccharides from Bee Collected Pollen of Chinese Wolfberry

Digestion and fermentation in vitro of polysaccharides from bee collected pollen of Chinese wolfberry (WBPPS) were investigated in the present study. It was found that WBPPS mainly consisted of mannose, ribose, rhamnose, galacturonic acid, glucose, galactose, xylose, and arabinose in a molar ratio of 0.38:0.09:0.17:0.64:0.22:0.67:0.08:1.03, respectively. WBPPS was not affected by human saliva. The fraction A (molecular weight 1340 kDa) of WBPPS was not broken down in simulated gastric and small intestinal juices, while the small fraction B (molecular weight 523 kDa) of WBPPS was degraded. Moreover, fermentation in vitro revealed that WBPPS could significantly enhance the production of short-chain fatty acids and modulate gut microbiota composition via increasing the relative abundances of genera Prevotella, Dialister, Megamonas, Faecalibacterium, and Alloprevotella and decreasing the numbers of genera Bacteroides, Clostridium XlVa, Parabacteroides, Escherichia/Shigella, Phascolarctobacterium, Parasutterella, Clostridium sensu stricto, and Fusobacterium.

Colonization with enterotoxigenic Bacteroides fragilis is associated with early-stage colorectal neoplasia

BACKGROUND

Enterotoxigenic Bacteroides fragilis (ETBF) is a toxin-producing bacteria thought to possibly promote colorectal carcinogenesis by modulating the mucosal immune response and inducing epithelial cell changes. Here, we aim to examine the association of colonic mucosal colonization with ETBF and the presence of a range of lesions on the colonic neoplastic spectrum.

METHODS

Mucosal tissue from up to four different colonic sites was obtained from a consecutive series of 150 patients referred for colonoscopy. The presence and relative abundance of the B. fragilis toxin gene (bft) in each tissue sample was determined using quantitative PCR, and associations with clinicopathological characteristics were analysed.

FINDINGS

We found a high concordance of ETBF between different colonic sites (86%). Univariate analysis showed statistically significant associations between ETBF positivity and the presence of low-grade dysplasia (LGD), tubular adenomas (TA), and serrated polyps (P-values of 0.007, 0.027, and 0.007, respectively). A higher relative abundance of ETBF was significantly associated with LGD and TA (P-values of < 0.0001 and 0.025, respectively). Increased ETBF positivity and abundance was also associated with left-sided biopsies, compared to those from the right side of the colon.

CONCLUSION

Our results showing association of ETBF positivity and increased abundance with early-stage carcinogenic lesions underlines its importance in the development of colorectal cancer, and we suggest that detection of ETBF may be a potential marker of early colorectal carcinogenesis.

Comparison of standard, quantitative and digital PCR in the detection of enterotoxigenic Bacteroides fragilis

Gut colonization with enterotoxigenic Bacteroides fragilis (ETBF) appears to be associated with the development of colorectal cancer. However, differences in carriage rates are seen with various testing methods and sampling sites. We compared standard PCR, SYBR green and TaqMan quantitative PCR (qPCR) and digital PCR (dPCR) in detecting the B. fragilis toxin (bft) gene from cultured ETBF, and from matched luminal and faecal stool samples from 19 colorectal cancer patients. Bland-Altman analysis found that all three quantitative methods performed comparably in detecting bft from purified bacterial DNA, with the same limits of detection (<1 copy/μl). However, SYBR qPCR under-performed compared to TaqMan qPCR and dPCR in detecting bft in clinical stool samples; 13/38 samples were reported positive by SYBR, compared to 35 and 36 samples by TaqMan and dPCR, respectively. TaqMan qPCR and dPCR gave bft copy numbers that were 48-fold and 75-fold higher for the same samples than SYBR qPCR, respectively (p < 0.001). For samples that were bft-positive in both fecal and luminal stools, there was no difference in relative abundance between the sites, by any method tested. From our findings, we recommend the use of TaqMan qPCR as the preferred method to detect ETBF from clinical stool samples.

Screening for enterotoxigenic Bacteroides fragilis in stool samples

Bacteroides fragilis is a commensal bacterium found in the gut of most humans, however enterotoxigenic B. fragilis strains (ETBF) have been associated with diarrhoea and colorectal cancer (CRC). The purpose of this study was to establish a method of screening for the Bacteroides fragilis toxin (bft) gene in stool samples, as a means of determining if carriage of ETBF is detected more often in CRC patients than in age-matched healthy controls. Stool samples from 71 patients recently diagnosed with CRC, and 71 age-matched controls, were screened by standard and quantitative PCR using primers specific for the detection of the bft gene. Bacterial template DNA from stool samples was prepared by two methods: a sweep, where all colonies growing on Bacteroides Bile Esculin agar following stool culture for 48 h at 37 °C in an anaerobic environment were swept into sterile water and heat treated; and a direct DNA extraction from each stool sample. The bft gene was detected more frequently from DNA isolated from bacterial sweeps than from matched direct DNA extractions. qPCR was found to be more sensitive than standard PCR in detecting bft. The cumulative total of positive qPCR assays from both sample types revealed that 19 of the CRC patients had evidence of the toxin gene in their stool sample (27%), compared to seven of the age-matched controls (10%). This difference was significant (P = 0.016). Overall, ETBF carriage was detected more often in CRC patient stool samples compared to controls, but disparate findings from the different DNA preparations and testing methods suggests that poor sensitivity may limit molecular detection of ETBF in stool samples.

Isolation, Detection, and Characterization of Enterotoxigenic Bacteroides fragilis in Clinical Samples

Bacteroides fragilis is an extensively studied anaerobic bacterium comprising the normal flora of the human gut. B. fragilis is known to be one of the most commonly isolated species from clinical samples and has been shown to cause a wide range of pathologies in humans [1, 2]. As an opportunistic pathogen B. fragilis can cause abscess formation and bacteremia [2]. Additionally in its enterotoxigenic form, B. fragilis is a known cause of diarrheal illness, is associated with inflammatory bowel disease, and has been recently characterized in patients with colon cancer [3 - 5]. As research in the field of the gut microbiome continues to expand at an ever increasing rate due to advances in the availability of next generation sequencing and analysis tools it is important to outline various molecular methods that can be employed in quickly detecting and isolating relevant strains of B. fragilis. This review outlines methods that are routinely employed in the isolation and detection of B. fragilis, with an emphasis on characterizing enterotoxigenic B. fragilis (ETBF) strains.