Clinical Importance of Streptococcus gallolyticus infection among colorectal cancer patients: systematic review and meta-analysis

Colorectal cancer and association with anaerobic bacteraemia: A Danish nationwide population-based cohort study

OBJECTIVES

We aimed to identify specific anaerobic bacteria causing bacteraemia and a subsequent diagnosis of colorectal cancer.

METHODS

A nationwide population-based cohort study, which included all episodes of defined specific anaerobic bacteraemia from 2010 (5,534,738 inhabitants) through 2020 (5,822,763 inhabitants) and all cases of colorectal cancer diagnosed from 2010 through 2021 in Denmark. We calculated the incidence and risk of colorectal cancer after bacteraemia with specific anaerobic bacteria using Escherichia coli bacteraemia as reference.

RESULTS

Nationwide data on colorectal cancer and specific anaerobic bacteraemia (100% complete, representing 11,124 episodes). The frequencies of colorectal cancer within one year following anaerobic bacteraemia were higher for species, which almost exclusively reside in the colon, such as Phocaeicola vulgatus/dorei (5.5%), Clostridium septicum (24.2%), and Ruminococcus gnavus (4.6%) compared to 0.6% in 50,650 E. coli bacteraemia episodes. Bacteroides spp. had a subhazard ratio for colorectal cancer of 3.9 (95% confidence interval [CI], 3.0 to 5.1) and for Clostridium spp. it was 8.9 (95% CI, 6.7 to 11.8, with C. septicum 50.0 [95% CI, 36.0 to 69.5]) compared to E. coli (reference).

CONCLUSION

This nationwide study identified specific colorectal cancer-associated anaerobic bacteria, which almost exclusively reside in the colon. Bacteraemia with these bacteria could be an indicator of colorectal cancer.

Geese as reservoirs of human colon cancer-associated Streptococcus gallolyticus

Recently, an increased number of reports have described pathogens of animal origin that cause a variety of infections and a rise in their transmission to humans. Streptococcus gallolyticus, a member of the Streptococcus bovis/Streptococcus equinus complex (SBSEC), is one of these pathogens and infects a wide range of hosts from mammals to poultry and has a broad functionality ranging from pathogenicity to food fermentation. As S. gallolyticus causes complications including bacteremia, infective endocarditis, and colorectal malignancy in humans, it is important to investigate its occurrence in various hosts, including geese, to prevent potential zoonotic transmissions. This study aimed to investigate the presence of S. gallolyticus in the droppings of clinically healthy and diarrheic geese, which were raised intensively and semi-intensively, by the in vitro culture method, characterize the isolates recovered by PCR and sequence-based molecular methods and determine their antibiotic susceptibility by the disk diffusion and gradient test methods. For this purpose, 150 samples of fresh goose droppings were used. Culture positivity for S. gallolyticus was determined as 8% (12/150). PCR analysis identified 54.55% (n = 6) of the isolates as S. gallolyticus subsp. gallolyticus and 45.45% (n = 5) as S. gallolyticus subsp. pasteurianus. Following the 16S rRNA sequence and ERIC-PCR analyses, S. gallolyticus subspecies exhibited identical cluster and band profiles that could be easily distinguished from each other and were clonally identified. High rates of susceptibility to florfenicol, penicillin, rifampicin, and vancomycin were detected among the isolates, regardless of the subspecies diversity. Both subspecies showed high levels of resistance to bacitracin, clindamycin, doxycycline, tetracycline, trimethoprim-sulfamethoxazole, and erythromycin and multiple MDR profiles, indicating their potential to become superbugs. This first report from Türkiye demonstrates the occurrence of the S. gallolyticus subspecies in geese. In view of the recent increase of geese production and the consumption of goose meat in Türkiye, the occurrence of S. gallolyticus in geese should not be ignored to prevent zoonotic transmission.

The role of gut microbiota and probiotics in preventing, treating, and boosting the immune system in colorectal cancer

The gut microbiome plays a significant role in developing colorectal cancer (CRC). The gut microbiome usually acts as a protective barrier against harmful pathogens and infections in the intestine, while also regulating inflammation by affecting the human immune system. The gut microbiota and probiotics play a role not only in intestinal inflammation associated with tumor formation but also in regulating anti-cancer immune response. As a result, they associated with tumor progression and the effectiveness of anti-cancer therapies. Research indicates that gut microbiota and probiotics can be used as biomarkers to predict the impact of immunotherapy and enhance its efficacy in treating CRC by regulating it. This review examines the importance of gut microbiota and probiotics in the development and progression of CRC, as well as their synergistic impact on anti-cancer treatments.

Obesity and Inflammatory Factors in the Progression of Early-Onset Colorectal Cancer

Metabolic dysfunction associated with obesity leads to a chronic pro-inflammatory state with systemic effects, including the alteration of macrophage metabolism. Tumor-associated macrophages have been linked to the formation of cancer through the production of metabolites such as itaconate. Itaconate downregulates peroxisome proliferator-activated receptor gamma as a tumor-suppressing factor and upregulates anti-inflammatory cytokines in M2-like macrophages. Similarly, leptin and adiponectin also influence macrophage cytokine expression and contribute to the progression of colorectal cancer via changes in gene expression within the PI3K/AKT pathway. This pathway influences cell proliferation, differentiation, and tumorigenesis. This work provides a review of obesity-related hormones and inflammatory mechanisms leading to the development and progression of early-onset colorectal cancer (EOCRC). A literature search was performed using the PubMed and Cochrane databases to identify studies related to obesity and EOCRC, with keywords including 'EOCRC', 'obesity', 'obesity-related hormones', 'itaconate', 'adiponectin', 'leptin', 'M2a macrophage', and 'microbiome'. With this concept of pro-inflammatory markers contributing to EOCRC, increased use of chemo-preventative agents such as aspirin may have a protective effect. Elucidating this association between obesity-related, hormone/cytokine-driven inflammatory effects with EOCRC may help lead to new therapeutic targets in preventing and treating EOCRC.

Sciatica caused by spinal epidural abscess as the initial clinical presentation of colon cancer: a rare case report and review of literature

BACKGROUND

Colorectal cancer is one of the most frequently diagnosed forms of cancer, and it is associated with several common symptoms and signs such as rectal bleeding, altered bowel habits, abdominal pain, anemia, and unintentional weight loss. Sciatica, a debilitating condition in which the patient experiences paresthesia and pain in the dermatome of associated lumbosacral nerve roots or sciatic nerve distribution, is not considered one of these. Here we present a case of colorectal cancer manifesting symptoms of sciatica alone.

CASE PRESENTATION

A 68-year-old male presented with progressive lower back pain radiating to his left thigh and calf over L5/S1 dermatome. Sciatica was suspected and initially underwent conservative treatment with analgesics. However, the symptoms progressed and MRI revealed an epidural abscess surprisingly. Surgical debridement was performed and pus culture isolated Streptococcus gallolyticus. Based on the strong association of S. gallolyticus with colorectal cancer, the presence of this pathogen prompted further tumor evaluation, even in the absence of the typical symptoms and signs. This investigation ultimately leads to the diagnosis of sigmoid adenocarcinoma.

CONCLUSIONS

Although rare, sciatica caused by S. gallolyticus infection of the spinal epidural space may serve as the initial presentation of colorectal cancer. Physicians should be aware of the strong association between S. gallolyticus and colorectal cancer. Based on what we currently know about the condition; a thorough systematic assessment of occult neoplasia for patients with S. gallolyticus infection is recommended.

A Rare Case of Meningitis Caused by Streptococcus gallolyticus subsp. pasteurianus in an Immunocompetent Young Adult

Bacterial meningitis is a life-threatening condition that is mainly caused by Streptococcus pneumoniae and Neisseria meningitis. Although Streptococcus gallolyticus subsp. pasteurianus (Sgp) is also known to cause meningitis, its frequency is quite low, especially in adults. We herein report the first immunocompetent Japanese adult patient (20-year-old woman) with bacterial meningitis caused by Sgp. The patient showed dramatic improvement after antibiotic treatment. Although previous reports have described an association between Sgp infection and an immunosuppressive status, bowel and hepatobiliary diseases, or strongyloidiasis, our case did not demonstrate any of these conditions, suggesting that Sgp can cause meningitis even in young immunocompetent adults.

Streptococcus bovis infection of the central nervous system in adults: Report of 4 cases and literature review

OBJECTIVES

To describe the clinical features, history and association with intestinal disease in central nervous system (CNS) S. bovis infections.

METHODS

Four cases of S. bovis CNS infections from our institution are presented. Additionally a systematic literature review of articles published between 1975 and 2021 in PubMed/MEDLINE was conducted.

RESULTS

52 studies with 65 cases were found; five were excluded because of incomplete data. In total 64 cases were analyzed including our four cases: 55 with meningitis and 9 with intracranial focal infections. Both infections were frequently associated with underlying conditions (70.3%) such as immunosuppression (32.8%) or cancer (10.9%). In 23 cases a biotype was identified, with biotype II being the most frequent (69.6%) and S. pasteurianus the most common within this subgroup. Intestinal diseases were found in 60.9% of cases, most commonly neoplasms (41.0%) and Strongyloides infestation (30.8%). Overall mortality was 17.1%, with a higher rate in focal infection (44.4% vs 12.7%; p=0.001).

CONCLUSIONS

CNS infections due to S. bovis are infrequent and the most common clinical form is meningitis. Compared with focal infections, meningitis had a more acute course, was less associated with endocarditis and had a lower mortality. Immunosuppression and intestinal disease were frequent in both infections.

Metagenomic Analysis of Intratumoral Microbiome Linking to Response to Neoadjuvant Chemoradiotherapy in Rectal Cancer

PURPOSE

To assess taxonomic and functional characteristics of tumor-bearing microbiota and its association with response to neoadjuvant chemoradiation therapy (nCRT) in patients with locally advanced rectal cancer.

METHODS AND MATERIALS

We performed metagenomic sequencing of biopsy tumoral tissues from 73 patients with locally advanced rectal cancer before nCRT. Patients were classified into poor responders (PR) and good responders (GR) according to response to nCRT. Subsequent investigation of network alteration, key community, microbial biomarkers, and function related to nCRT responses were carried out.

RESULTS

The network-driven analysis systematically revealed 2 co-occurring bacteria modules that exhibited opposite relationship with rectal cancer radiosensitivity. In the 2 modules, prominent alteration of global graph properties and community structure was observed between networks of PR and GR group. By quantifying changes in between-group association patterns and abundances, a total of 115 discriminative biomarker species linked to nCRT response were found, and 35 microbial variables were selected to establish the optimal randomForest classifier for nCRT response prediction. It yielded an area under the curve value of 85.5% (95% CI, 73.3%-97.8%) in the training cohort and 88.4% (95% CI, 77.5%-99.4%) in the validation cohort. In a comprehensive consideration, 5 key bacteria showed high relevance with inducing resistance to nCRT, including Streptococcus equinus, Schaalia odontolytica, Clostridium hylemonae, Blautia producta, and Pseudomonas azotoformans. One key hub including several butyrate-formation bacteria involving with driving network alteration from GR to PR indicate that microbiota-derived butyrate may also be involved in reducing the antitumor effects of nCRT, especially Coprococcus. The functional analysis of metagenome linked the nitrate and sulfate-sulfur assimilation, histidine catabolic process, and resistance to cephamycin to the reduced therapeutic response. It also linked to leucine degradation, isoleucine biosynthesis, taurine, and hypotaurine metabolism to the improved response to nCRT.

CONCLUSIONS

Our data offer novel potential microbial factors and shared metagenome function linked to resistance to nCRT.

Incidence of Colorectal Cancer in Patients Diagnosed With Pyogenic Liver Abscess

Importance

Colorectal cancer (CRC) can compromise the mucosal barrier and subsequently allow a route for bacterial invasion into the portal system or systemic circulation. Despite preliminary data suggesting that patients who experienced pyogenic liver abscess (PLA) have higher CRC incidence rates, data from outside the Southeast Asian population are sparse.

Objective

To investigate whether there is an association between PLA and the subsequent incidence of diagnosed CRC using the Veterans Health Administration (VHA) cohort.

Design, Setting, and Participants

A patient-level matched retrospective cohort study was conducted at 127 VHA hospitals across the US from January 1, 2003, to December 31, 2020. Patients were followed up to 10 years from PLA diagnosis. Data analysis was performed from April 14, 2002, to October 31, 2023. All patients who were admitted to VHA hospitals with a diagnosis of PLA were included. For each patient with PLA, up to 3 controls without diagnosis of PLA, matching age, sex, and health care facility, were selected.

Exposure

Pyogenic liver abscess.

Main Outcomes and Measures

The primary outcome was CRC diagnosis during the follow-up period. A multivariable Fine-Gray subdistribution regression model with time-dependent coefficient was used to estimate the time-varying hazard ratio (HR) of CRC incidence while accounting for mortality as a competing event.

Results

A total of 8286 patients with PLA (male, 96.5%; mean [SD] age, 65.8 [11.9] years) and 23 201 patient-level matched controls (male, 96.3%; mean age, 65.3 [11.7] years) were included. A diagnosis of CRC was found in a significantly higher proportion of patients with PLA compared with controls (1.9% [159 of 8286] vs 0.8% [196 of 23 201]; P < .001). The incidence of CRC was significantly higher among patients with PLA during the first 3 years from PLA diagnosis (HR, 3.64; 95% CI, 2.70-4.91 at 0.5 years; HR, 2.51; 95% CI, 1.93-3.26 at 1 year; HR, 1.74; 95% CI, 1.33-2.28 at 2 years; and HR, 1.41; 95% CI, 1.05-1.89 at 3 years), but not significant after 3 years. This association was not observed among patients whose PLA was likely secondary to cholangitis or cholecystitis (HR, 1.78; 95% CI, 0.89-3.56 at 0.5 years).

Conclusions and Relevance

In this patient-level matched retrospective cohort study, a significantly higher incidence of CRC was observed up to 3 years from PLA diagnosis. The findings suggest that offering CRC screening for patients with cryptogenic PLA may be useful, especially patients who have not been screened according to guidelines.

Transcriptome profiling of human col\onic cells exposed to the gut pathobiont Streptococcus gallolyticus subsp. gallolyticus

Streptococcus gallolyticus sp. gallolyticus (SGG) is a gut pathobiont involved in the development of colorectal cancer (CRC). To decipher SGG contribution in tumor initiation and/or acceleration respectively, a global transcriptome was performed in human normal colonic cells (FHC) and in human tumoral colonic cells (HT29). To identify SGG-specific alterations, we chose the phylogenetically closest relative, Streptococcus gallolyticus subsp. macedonicus (SGM) as control bacterium. We show that SGM, a bacterium generally considered as safe, did not induce any transcriptional changes on the two human colonic cells. The transcriptional reprogramming induced by SGG in normal FHC and tumoral HT29 cells was significantly different, although most of the genes up- and down-regulated were associated with cancer disease. Top up-regulated genes related to cancer were: (i) IL-20, CLK1, SORBS2, ERG1, PIM1, SNORD3A for normal FHC cells and (ii) TSLP, BHLHA15, LAMP3, ZNF27B, KRT17, ATF3 for cancerous HT29 cells. The total number of altered genes were much higher in cancerous than in normal colonic cells (2,090 vs 128 genes being affected, respectively). Gene set enrichment analysis reveals that SGG-induced strong ER- (endoplasmic reticulum) stress and UPR- (unfolded protein response) activation in colonic epithelial cells. Our results suggest that SGG induces a pro-tumoral shift in human colonic cells particularly in transformed cells potentially accelerating tumor development in the colon.

Association of the Streptococcus bovis/Streptococcus equinus Complex With Colorectal Neoplasia: A Systematic Review and Meta-analysis

Background

Invasive infection with Streptococcus bovis/Streptococcus equinus complex (SBSEC) bacteria is associated with underlying colorectal neoplasia. However, the link between intestinal or fecal colonization with SBSEC isolates or antibody responses to SBSEC members and colorectal cancer is not thoroughly investigated in the literature.

Methods

We searched the PubMed, EMBASE, and Web of Science databases for case-control studies as well as retrospective or prospective cohort studies reporting an association between SBSEC bacteria and colorectal neoplasia.

Results

We identified 22 studies (15 case-control and 7 cohort) that met our inclusion criteria. Among the cohort studies, patients with SBSEC bacteremia were 3.73 times more likely to have underlying colorectal cancer compared with individuals with no bacteremia (relative risk [RR], 3.73; 95% CI, 2.79-5.01), whereas the risk of underlying colorectal adenoma in patients with SBSEC bacteremia was not significantly increased (RR, 5.00; 95% CI, 0.83-30.03). In case-control studies, patients with colorectal cancer were 2.27 times more likely to have evidence of intestinal or fecal colonization with SBSEC isolates (odds ratio [OR], 2.27; 95% CI, 1.11-4.62) and immunoglobulin G (IgG) antibody responses to SBSEC antigens (OR, 2.27; 95% CI, 1.06-4.86) compared with controls. Patients with colorectal adenoma were not more likely to be colonized with SBSEC isolates compared with controls (OR, 1.12; 95% CI, 0.55-2.25).

Conclusions

Apart from the well-established association of SBSEC bacteremia and underlying colorectal cancer, intestinal or fecal colonization with SBSEC isolates and IgG antibody responses to SBSEC antigens were higher in patients with colorectal cancer compared with controls. Neither bacteremia from SBSEC isolates nor colonization with SBSEC bacteria was associated with underlying colorectal adenoma.

A new strategy for treating colorectal cancer: Regulating the influence of intestinal flora and oncolytic virus on interferon

Colorectal cancer (CRC) has the third highest incidence and the second highest mortality in the world, which seriously affects human health, while current treatments methods for CRC, including systemic therapy, preoperative radiotherapy, and surgical local excision, still have poor survival rates for patients with metastatic disease, making it critical to develop new strategies for treating CRC. In this article, we found that the gut microbiota can modulate the signaling pathways of cancer cells through direct contact with tumor cells, generate inflammatory responses and oxidative stress through interactions between the innate and adaptive immune systems, and produce diverse metabolic combinations to trigger specific immune responses and promote the initiation of systemic type I interferon (IFN-I) and anti-viral immunity. In addition, oncolytic virus-mediated immunotherapy for regulating oncolytic virus can directly lyse tumor cells, induce the immune activity of the body, interact with interferon, inhibit the anti-viral effect of IFN-I, and enhance the anti-tumor effect of IFN-II. Interferon plays an important role in the anti-tumor process. We put forward that exploring the effects of intestinal flora and oncolytic virus on interferon to treat CRC is a promising therapeutic option.

The Gum-Gut Axis: Periodontitis and the Risk of Gastrointestinal Cancers

Periodontitis has been linked to an increased risk of various chronic non-communicable diseases, including gastrointestinal cancers. Indeed, dysbiosis of the oral microbiome and immune-inflammatory pathways related to periodontitis may impact the pathophysiology of the gastrointestinal tract and its accessory organs through the so-called "gum-gut axis". In addition to the hematogenous spread of periodontal pathogens and inflammatory cytokines, recent research suggests that oral pathobionts may translocate to the gastrointestinal tract through saliva, possibly impacting neoplastic processes in the gastrointestinal, liver, and pancreatic systems. The exact mechanisms by which oral pathogens contribute to the development of digestive tract cancers are not fully understood but may involve dysbiosis of the gut microbiome, chronic inflammation, and immune modulation/evasion, mainly through the interaction with T-helper and monocytic cells. Specifically, keystone periodontal pathogens, including Porphyromonas gingivalis and Fusobacterium nucleatum, are known to interact with the molecular hallmarks of gastrointestinal cancers, inducing genomic mutations, and promote a permissive immune microenvironment by impairing anti-tumor checkpoints. The evidence gathered here suggests a possible role of periodontitis and oral dysbiosis in the carcinogenesis of the enteral tract. The "gum-gut axis" may therefore represent a promising target for the development of strategies for the prevention and treatment of gastrointestinal cancers.

Global proteomic identifies multiple cancer-related signaling pathways altered by a gut pathobiont associated with colorectal cancer

In this work, we investigated the oncogenic role of Streptococcus gallolyticus subsp. gallolyticus (SGG), a gut bacterium associated with colorectal cancer (CRC). We showed that SGG UCN34 accelerates colon tumor development in a chemically induced CRC murine model. Full proteome and phosphoproteome analysis of murine colons chronically colonized by SGG UCN34 revealed that 164 proteins and 725 phosphorylation sites were differentially regulated. Ingenuity Pathway Analysis (IPA) indicates a pro-tumoral shift specifically induced by SGG UCN34, as ~ 90% of proteins and phosphoproteins identified were associated with digestive cancer. Comprehensive analysis of the altered phosphoproteins using ROMA software revealed up-regulation of several cancer hallmark pathways such as MAPK, mTOR and integrin/ILK/actin, affecting epithelial and stromal colonic cells. Importantly, an independent analysis of protein arrays of human colon tumors colonized with SGG showed up-regulation of PI3K/Akt/mTOR and MAPK pathways, providing clinical relevance to our findings. To test SGG's capacity to induce pre-cancerous transformation of the murine colonic epithelium, we grew ex vivo organoids which revealed unusual structures with compact morphology. Taken together, our results demonstrate the oncogenic role of SGG UCN34 in a murine model of CRC associated with activation of multiple cancer-related signaling pathways.

Discovery of potent natural product higenamine derivatives as novel Anti-Fusobacterium nucleatum agents

Fusobacterium nucleatum (F. nucleatum) is closely associated with the occurrence and development of colorectal cancer (CRC). Discovery of specific antibacterial agents against F. nucleatum was urgent for the prevention and treatment of CRC. We screened a natural product library and successfully identified higenamine as an antibacterial hit against F. nucleatum. Further hit optimizations led to the discovery of new higenamine derivatives with improved anti-F. nucleatum activity. Among them, compound 7c showed potent antibacterial activity against F. nucleatum (MIC50 = 0.005 μM) with good selectivity toward intestinal bacteria and normal cells. It significantly inhibited the migration of CRC cells induced by F. nucleatum. Mechanism study revealed that compound 7c impaired the integrity of biofilm and cell wall, which represents a good starting point for the development of novel anti-F. nucleatum agents.

Characterization of TelE, a T7SS LXG Effector Exhibiting a Conserved C-Terminal Glycine Zipper Motif Required for Toxicity

Streptococcus gallolyticus subsp. gallolyticus (SGG) is an opportunistic bacterial pathogen strongly associated with colorectal cancer. Here, through comparative genomics analysis, we demonstrated that the genetic locus encoding the type VIIb secretion system (T7SSb) machinery is uniquely present in SGG in two different arrangements. SGG UCN34 carrying the most prevalent T7SSb genetic arrangement was chosen as the reference strain. To identify the effectors secreted by this secretion system, we inactivated the essC gene encoding the motor of this machinery. A comparison of the proteins secreted by UCN34 wild type and its isogenic ΔessC mutant revealed six T7SSb effector proteins, including the expected WXG effector EsxA and three LXG-containing proteins. In this work, we characterized an LXG-family toxin named herein TelE promoting the loss of membrane integrity. Seven homologs of TelE harboring a conserved glycine zipper motif at the C terminus were identified in different SGG isolates. Scanning mutagenesis of this motif showed that the glycine residue at position 470 was crucial for TelE membrane destabilization activity. TelE activity was antagonized by a small protein TipE belonging to the DUF5085 family. Overall, we report herein a unique SGG T7SSb effector exhibiting a toxic activity against nonimmune bacteria. IMPORTANCE In this study, 38 clinical isolates of Streptococcus gallolyticus subsp. gallolyticus (SGG) were sequenced and a genetic locus encoding the type VIIb secretion system (T7SSb) was found conserved and absent from 16 genomes of the closely related S. gallolyticus subsp. pasteurianus (SGP). The T7SSb is a bona fide pathogenicity island. Here, we report that the model organism SGG strain UCN34 secretes six T7SSb effectors. One of the six effectors named TelE displayed a strong toxicity when overexpressed in Escherichia coli. Our results indicate that TelE is probably a pore-forming toxin whose activity can be antagonized by a specific immunity protein named TipE. Overall, we report a unique toxin-immunity protein pair and our data expand the range of effectors secreted through T7SSb.

Gut Streptococcus is a microbial marker for the occurrence and liver metastasis of pancreatic cancer

Background

Gut microbiome plays an indispensable role in the occurrence and progression in various diseases. The incidence of pancreatic cancer (PC) and liver metastasis (PCLM) are high, most of them are found in advanced stage. Therefore, it is particularly necessary to search for predictive biomarkers, which are helpful for early detection and treatment, and thus improve the survival rate and quality of life of PC patients.

Methods

We retrospectively analyzed 44 pancreatic cancer patients (P group, n = 44) and 50 healthy people (N group, n = 50) from March 21, 2021 and August 2, 2022. Among all PC patients, we divided them into liver metastasis group (LM group, n = 27) and non-liver metastasis group (non-LM group, n = 17). DNA was extracted and 16S ribosomal RNA (16S rRNA) gene sequencing was performed. SPSS was used for statistical analyses and all bioinformatics analyses were based on QIIME2, p < 0.05 were considered statistically significant.

Results

The microbial richness and diversity of group P and LM were higher than that of group N and non-LM. LEfSe analysis found that Streptococcus was a significantly different microorganism, which was further identified by random forest (RF) model, and its ability to predict PC and PCLM was verified by ROC curve.

Conclusion

We demonstrated significant differences in intestinal microbiome composition between PC patients and healthy people, and found that Streptococcus is a potential biomarker for early prediction of PC and PCLM, which is critical for early diagnosis of diseases.

The interaction between liver cirrhosis, infection by Streptococcus bovis, and colon cancer

Whether cirrhotic patients with Streptococcus bovis bacteremia have an increased risk of colorectal neoplasm is uncertain. A multicentric retrospective cohort study was conducted investigating associations between S. bovis biotype and species, cirrhosis, and colorectal neoplasm. Out of 779 patients with S. bovis bacteremia, 69 (8.7%) had cirrhosis. No differences were found in the prevalence of colorectal neoplasm between cirrhotic and non-cirrhotic patients undergoing colonoscopy. Among cirrhotic patients, prevalence of colorectal neoplasms was higher in S. bovis biotype I (S. gallolyticus) bacteremia (80%) than in S. bovis biotype II (33.3%; p < 0.007). In conclusion, risk of colorectal neoplasm is high among cirrhotic patients with S. gallolyticus bacteremia.

FXR agonists for colorectal and liver cancers, as a stand-alone or in combination therapy

Farnesoid X receptor (FXR, NR1H4) is generally considered as a tumor suppressor of colorectal and liver cancers. The interaction between FXR, bile acids (BAs) and gut microbiota is closely associated with an increased risk of colorectal and liver cancers. Increasing evidence shows that FXR agonists may be potential therapeutic agents for colorectal and liver cancers. However, FXR agonists alone do not produce the desired results due to the complicated pathogenesis and single therapeutic mechanism, which suggests that effective treatments will require a multimodal approach. Based on the principle of improvingefficacy andreducingside effects, combination therapy is currently receiving considerable attention. In this review, colorectal and liver cancers are grouped together to discuss the effects of FXR agonists alone or in combination for combating the two cancers. We hope that this review will provide a theoretical basis for the clinical application of novel FXR agonists or combination with FXR agonists against colorectal and liver cancers.

Comparative Evaluation of Current Biochemical-, Sequencing-, and Proteomic-Based Identification Methods for the Streptococcus bovis Group

The Streptococcus bovis group (previously group D streptococci) consists of seven distinct species and subspecies. Definitive identification within the group is important, as certain organisms have been associated with gastrointestinal carcinoma, bacteremia, infective endocarditis, meningitis, biliary tract disease, and carcinoma, among others. Definitive identification, however, remains elusive due to limitations and inconsistencies across commonly used identification platforms in the United States. Here, we compared the performance of standard biochemical (Trek Gram-positive identification [GPID] plate, Vitek 2 GPID), sequencing (16S rDNA, sodA) databases (NCBI, RDP, CDC MicrobeNet), and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) platforms (Vitek MS, Bruker Biotyper MS) using a set of eight type strains representing all seven strains within the S. bovis group. Despite the evaluation of contemporary methods, no single platform was able to definitively identify all type strains within the S. bovis group. Vitek MS (85.7%, 7/8) provided the most accurate definitive identifications, followed by sodA sequencing (75%, 6/8). Vitek 2 and Bruker Biotyper RUO platforms performed the next best (62.5%, 5/8). All remaining platforms failed to adequately differentiate type strains within the S. bovis group (range, 0 to 37.5%). Laboratorians and clinicians should be aware of the identification limitations of routine testing algorithms and incorporate reflex testing, when appropriate, to platforms such as Vitek MS and/or sodA sequencing that are more able to definitively identify S. bovis group organisms. Further clinical evaluation was conducted using 65 clinical isolates from three geographically distinct U.S. institutions. Future improvements in identification platforms may reveal new clinical and epidemiological trends for members of the S. bovis group.

A pathogenicity locus of Streptococcus gallolyticus subspecies gallolyticus

Streptococcus gallolyticus subspecies gallolyticus (Sgg) is known to be strongly associated with colorectal cancer (CRC). Recent functional studies further demonstrated that Sgg actively stimulates CRC cell proliferation and promotes the development of colon tumors. However, the Sgg factors important for the pro-proliferative and pro-tumor activities of Sgg remain unclear. Here, we identified a chromosomal locus in Sgg strain TX20005. Deletion of this locus significantly reduced Sgg adherence to CRC cells and abrogated the ability of Sgg to stimulate CRC cell proliferation. Thus, we designate this locus as the Sgg pathogenicity-associated region (SPAR). More importantly, we found that SPAR is important for Sgg pathogenicity in vivo. In a gut colonization model, mice exposed to the SPAR deletion mutant showed significantly reduced Sgg load in the colonic tissues and fecal materials, suggesting that SPAR contributes to the colonization capacity of Sgg. In a mouse model of CRC, deletion of SPAR abolished the ability of Sgg to promote the development of colon tumors growth. Taken together, these results highlight SPAR as a critical pathogenicity determinant of Sgg.

The Gut Microbiome, Microsatellite Status and the Response to Immunotherapy in Colorectal Cancer

There is increasing evidence in a range of cancer types that the microbiome plays a direct role in modulating the anti-cancer immune response both at the gut level and systemically. Differences in the gut microbiota have been shown to correlate with differences in immunotherapy responses in a range of non-gastrointestinal tract cancers. DNA mismatch repair-deficient (dMMR) colorectal cancer (CRC) is radically different to DNA mismatch repair-proficient (pMMR) CRC in clinical phenotype and in its very good responses to immunotherapy. While this has usually been thought to be due to the high mutational burden in dMMR CRC, the gut microbiome is radically different in dMMR and pMMR CRC in terms of both composition and diversity. It is probable that differences in the gut microbiota contribute to the varied responses to immunotherapy in dMMR versus pMMR CRC. Targeting the microbiome offers a way to boost the response and increase the selection of patients who might benefit from this therapy. This paper reviews the available literature on the role of the microbiome in the response to immunotherapy in dMMR and pMMR CRC, explores the potential causal relationship and discusses future directions for study in this exciting and rapidly changing field.

Microbial Metabolite Dysbiosis and Colorectal Cancer

The global burden of colorectal cancer (CRC) is expected to continuously increase. Through research performed in the past decades, the effects of various environmental factors on CRC development have been well identified. Diet, the gut microbiota and their metabolites are key environmental factors that profoundly affect CRC development. Major microbial metabolites with a relevance for CRC prevention and pathogenesis include dietary fiber-derived short-chain fatty acids, bile acid derivatives, indole metabolites, polyamines, trimethylamine-N-oxide, formate, and hydrogen sulfide. These metabolites regulate various cell types in the intestine, leading to an altered intestinal barrier, immunity, chronic inflammation, and tumorigenesis. The physical, chemical, and metabolic properties of these metabolites along with their distinct functions to trigger host receptors appear to largely determine their effects in regulating CRC development. In this review, we will discuss the current advances in our understanding of the major CRC-regulating microbial metabolites, focusing on their production and interactive effects on immune responses and tumorigenesis in the colon.

Prolonged Streptococcus gallolyticus subsp. pasteurianus gut colonization in healthcare workers and potential transmission role in neonatal sepsis

BACKGROUND

Streptococcus gallolyticus subsp. pasteurianus (SGSP) is a commensal in the intestinal tract and a potential pathogen of neonatal sepsis. During an 11-month period, four consecutive cases of SGSP sepsis were identified in one postnatal care unit (unit A) without evidence of vertical transmission. Therefore, we initiated this study to investigate the reservoir and mode of transmission of SGSP.

METHOD

We performed cultures of stool samples from healthcare workers in unit A and unit B (another unit without SGSP sepsis). If SGSP was positive in feces, we performed isolate pulsotyping and genotyping by using pulsed-field gel electrophoresis (PFGE) and analyzing random amplified polymorphic DNA (RAPD) patterns, respectively.

RESULTS

Five staff members in unit A showed positivity for SGSP. All samples from unit B were negative. We identified two major pulsogroups (groups C and D) by PFGE. In group D, the strains isolated from 3 consecutive sepsis patients (P1, P2 and P3) were closely related and clustered together as those from 2 staff members (C1/C2, C6). One staff (staff 4) had a direct contact history with patient (P1) confirmed to have the same clone. The last isolate of the patient in our study (P4) belonged to a distinct clone.

CONCLUSION

We found prolonged gut colonization of SGSP in healthcare workers and its epidemiological relatedness to neonatal sepsis. Fecal-oral or contact transmission is a possible route of SGSP infection. Fecal shedding among staff may be associated with neonatal sepsis in healthcare facilities.

Gut Microbiota in Colorectal Cancer: Biological Role and Therapeutic Opportunities

Colorectal cancer (CRC) is the second-leading cause of cancer-related deaths worldwide. While CRC is thought to be an interplay between genetic and environmental factors, several lines of evidence suggest the involvement of gut microbiota in promoting inflammation and tumor progression. Gut microbiota refer to the ~40 trillion microorganisms that inhabit the human gut. Advances in next-generation sequencing technologies and metagenomics have provided new insights into the gut microbial ecology and have helped in linking gut microbiota to CRC. Many studies carried out in humans and animal models have emphasized the role of certain gut bacteria, such as Fusobacterium nucleatum, enterotoxigenic Bacteroides fragilis, and colibactin-producing Escherichia coli, in the onset and progression of CRC. Metagenomic studies have opened up new avenues for the application of gut microbiota in the diagnosis, prevention, and treatment of CRC. This review article summarizes the role of gut microbiota in CRC development and its use as a biomarker to predict the disease and its potential therapeutic applications.

Oral Microbiota as Novel Biomarkers for Colorectal Cancer Screening

Alterations of the gut microbiome in cases of colorectal cancer (CRC) hint at the involvement of host-microbe interactions in the onset and progression of CRC and also, possibly, provide novel ways to detect and prevent CRC early. The aim of the present study was to evaluate whether the oral and fecal microbiomes of an individual can be suitable for CRC screening. Oral and fecal samples (n = 80) were gathered in Taleghani hospital, affiliated with Shahid Beheshti University of Medical Sciences, Tehran-Iran, from CRC stage 0 and I patients and healthy controls (HCs), who were screened for the first time. Microbial metagenomics assays were performed for studying microbiota profiles in all oral and fecal samples gathered. An abundance of top bacterial genera from both types of specimens (fecal and saliva samples) revealed a distinction between CRC patients and HCs. In saliva samples, the α diversity index was different between the microbiome of HCs and CRC patients, while β diversity showed a densely clustered microbiome in the HCs but a more dispersed pattern in CRC cases. The α and β diversity of fecal microbiota between HCs and CRC patients showed no statistically significant differences. Bifidobacterium was identified as a potential bacterial biomarker in CRC saliva samples, while Fusobacterium, Dialister, Catonella, Tennerella, Eubacterium-brachy-group, and Fretibacterium were ideal to distinguish HCs from CRC patients. One of the reasons for the heterogeneity of CRC may be the gastrointestinal (GI) tract microbiota, which can also cause systematic resistance to CRC. Moreover, an evaluation of saliva microbiota might offer a suitable screening test for the early detection of this malignancy, providing more accurate results than its fecal counterpart.

Carcinogenic microbiota and its role in colorectal cancer development

Colorectal cancer (CRC) is one of the most common malignancies worldwide. The main risk factors for CRC are family history of colon or rectal cancer, familial polyposis syndrome or hereditary nonpolyposis, and chronic inflammatory bowel diseases (ulcerative colitis and Crohn's disease). Recent studies show that the gastrointestinal microbiota play a significant role in colorectal carcinogenesis. In this review we present the microorganisms, whose influence on the development of CRC has been proven: Bacteroides fragilis, Clostridioides and Clostridium spp., Enterococcus faecalis, Escherichia coli, Fusobacterium nucleatum, Helicobacter pylori, Peptostreptococcus anaerobius, Streptococcus bovis group, and sulfate-reducing bacteria. Moreover, the carcinogenic mechanisms of action mediated by the above bacteria are laid out.

Use of Bacteriocins and Bacteriocinogenic Beneficial Organisms in Food Products: Benefits, Challenges, Concerns

This review’s objective was to critically revisit various research approaches for studies on the application of beneficial organisms and bacteriocins as effective biopreservatives in the food industry. There are a substantial number of research papers reporting newly isolated bacterial strains from fermented food products and their application as potential probiotics, including partial characterization of bacteriocins produced by these microorganisms. Most of these studies follow scientific community-accepted standard procedures and propose various applications of the studied strains and bacteriocins as potential biopreservatives for the food industry. A few investigations go somewhat further, performing model studies, exploring the application of expressed bacteriocins in a designed food product, or trying to evaluate the effectiveness of the studied potential probiotics and bacteriocins against foodborne pathogens. Some authors propose applications of bacteriocin producers as starter cultures and are exploring in situ bacteriocin production to aid in the effective control of foodborne pathogens. However, few studies have evaluated the possible adverse effects of bacteriocins, such as toxicity. This comes from well-documented reports on bacteriocins being mostly non-immunogenic and having low cytotoxicity because most of these proteinaceous molecules are small peptides. However, some studies have reported on bacteriocins with noticeable cytotoxicity, which may become even more pronounced in genetically engineered or modified bacteriocins. Moreover, their cytotoxicity can be very specific and is dependent on the concentration of the bacteriocin and the nature of the targeted cell. This will be discussed in detail in the present review.

Relevance of [18F]FDG-PET/CT in the detection of colon pathology, in patients studied by bacteriemia or infectious endocarditis caused by enteropathogenic microorganisms

PURPOSE

Association between S. gallolyticus infective endocarditis (IE) and malignant lesions of the gastrointestinal tract is well described. We hypothesize that other enteropathogenic microorganisms, such as S. viridans and E. faecalis are also related with colorectal pathology. Our aim is to determine the frequency of focal colorectal FDG deposits, suggestive of tumoral lesions and their correlation with colorectal pathology, in patients with infection caused by different commensal microorganisms of the gastrointestinal tract.

METHODS

We retrospectively examined 61 patients diagnosed with bacteremia (BSI) and IE (possible or definite) according to Duke's criteria, caused by enteropathogenic microorganisms, who underwent a full-body [¹⁸F]FDG-PET/CT in our institution. We looked for colorrectal FDG deposits and morphological lesions. All IE patients underwent a complete colonoscopy and the histological results were classified into four groups: malignant lesion, premalignant lesion, benign lesion and no lesion. We evaluated the correlation between the findings of the [¹⁸F]FDG-PET/CT with the histopathological diagnosis and the involved microorganism.

RESULTS

PET/CT detected 20 colorectal FDG deposits (32.79%-OR: 47.28), 2 within bacteriemic patients (16.7%) confirmed as malignant and premalignant lesions and 18 in IE group (36.6%), 17 of them corresponding to colorrectal pathology: 11 malignant, 5 premalignant and 1 benign lesions. In the IE subgroup, the colonoscopy detected colorectal lesions in 51.02% of the patients: 11malignant, 8premalignant and 6benign. We found a higher incidence of colorectal FDG deposits in Streptococcus spp. subgroup. Regarding the anatomopathological colonic findings there was a predominance of patients affected by S. viridans, followed by E. faecalis and S. gallolyticus.

CONCLUSION

Patients studied by PET/CT for systemic infection, especially IE, caused by S. viridans or E. faecalis, in addition to S. gallolyticus, show a greater probability of presenting incidental colorectal FDG deposits, mostly corresponding to malignant or pre-malignant lesions. Therefore, it is necessary to carry out an exhaustive search of possible colorectal foci in these exams.

Modulation of the extracellular matrix by Streptococcus gallolyticus subsp. gallolyticus and importance in cell proliferation

Streptococcus gallolyticus subspecies gallolyticus (Sgg) has a strong clinical association with colorectal cancer (CRC) and actively promotes the development of colon tumors. Previous work showed that this organism stimulates CRC cells proliferation and tumor growth. However, the molecular mechanisms underlying these activities are not well understood. Here, we found that Sgg upregulates the expression of several type of collagens in HT29 and HCT116 cells, with type VI collagen (ColVI) being the highest upregulated type. Knockdown of ColVI abolished the ability of Sgg to induce cell proliferation and reduced the adherence of Sgg to CRC cells. The extracellular matrix (ECM) is an important regulator of cell proliferation. Therefore, we further examined the role of decellularized matrix (dc-matrix), which is free of live bacteria or cells, in Sgg-induced cell proliferation. Dc-matrix prepared from Sgg-treated cells showed a significantly higher pro-proliferative activity than that from untreated cells or cells treated with control bacteria. On the other hand, dc-matrix from Sgg-treated ColVI knockdown cells showed no difference in the capacity to support cell proliferation compared to that from untreated ColVI knockdown cells, suggesting that the ECM by itself is a mediator of Sgg-induced cell proliferation. Furthermore, Sgg treatment of CRC cells but not ColVI knockdown CRC cells resulted in significantly larger tumors in vivo, suggesting that ColVI is important for Sgg to promote tumor growth in vivo. These results highlight a dynamic bidirectional interplay between Sgg and the ECM, where Sgg upregulates collagen expression. The Sgg-modified ECM in turn affects the ability of Sgg to adhere to host cells and more importantly, acts as a mediator for Sgg-induced CRC cell proliferation. Taken together, our results reveal a novel mechanism in which Sgg stimulates CRC proliferation through modulation of the ECM.

Bacteraemia and Associated Complications on Imaging as a Clue to Colorectal Malignancy

Streptococcus gallolyticus (SG) – among other bacterial infections – is associated with colorectal malignancy and adenoma. It is reported that patients with SG bacteraemia have a concomitant colorectal tumour in 25–80% of cases. We present a case of a patient with complications of this septicaemia associated with a rectal adenocarcinoma, as an example of this important radiological and clinical correlation.

Teaching Point: Always screen for primary colorectal malignancy in a patient with malignancy-associated bacterial infection.

Correlation between Olive Oil Intake and Gut Microbiota in Colorectal Cancer Prevention

Extra virgin olive oil (EVOO) is a mainstay of the Mediterranean diet with its excellent balance of fats and antioxidant bioactive compounds. Both the phenolic and lipid fractions of EVOO contain a variety of antioxidant and anticancer substances which might protect from the development of colorectal cancer (CRC). The function of the intestinal microbiome is essential for the integrity of the intestinal epithelium, being protective against pathogens and maintaining immunity. Indeed, dysbiosis of the microbiota alters the physiological functions of the organ, leading to the onset of different diseases including CRC. It is known that some factors, including diet, could deeply influence and modulate the colon microenvironment. Although coming from animal models, there is increasing evidence that a diet rich in EVOO is linked to a significant reduction in the diversity of gut microbiome (GM), causing a switch from predominant bacteria to a more protective group of bacteria. The potential beneficial effect of the EVOO compounds in the carcinogenesis of CRC is only partially known and further trials are needed in order to clarify this issue. With this narrative review, we aim at discussing the available evidence on the effect of olive oil consumption on GM in the prevention of CRC.

Streptococcus gallolyticus subspecies pasteurianus bacteremia accompanied by acute pancreatitis

INTRODUCTION

While Streptococcus gallolyticus subsp. gallolyticus has a well-known association with colorectal cancer, an epidemiological association between S. gallolyticus subsp. pasteurianus (SGSP) and hepatobiliary diseases has been suggested. Here we described a case of gallstone pancreatitis and SGSP bacteremia in which species-identification by Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight Mass Spectrometry (MALDI-TOF MS) helped to diagnose the biliary etiology.

CASE REPORT

A 61-year-old Japanese man without history of alcohol consumption was hospitalized for acute pancreatitis. His past medical history included endoscopically treated familial adenomatous polyposis. A blood culture grew gram-positive cocci, identified to be SGSP by MALDI-TOF MS. A contrast-enhanced computed tomography scan showed pancreatic enlargement and increased fatty tissue concentration around the perirenal and pararenal space. He was diagnosed with acute pancreatitis and subsequently recovered after appropriate antimicrobial therapy and supportive care. Subsequent magnetic resonance cholangiopancreatography showed gallstones in the gallbladder neck, suggesting the cause of the acute pancreatitis. Seven months after admission, cholecystectomy was performed for cholelithiasis.

CONCLUSION

This case highlights that the identification of subspecies enabled by MALDI-TOF MS supports the diagnosis of the underlying etiology from the microbiological point of view.

Interaction between microbiota and immunity and its implication in colorectal cancer

Colorectal cancer (CRC) is one of the leading causes of cancer-related death in the world. Besides genetic causes, colonic inflammation is one of the major risk factors for CRC development, which is synergistically regulated by multiple components, including innate and adaptive immune cells, cytokine signaling, and microbiota. The complex interaction between CRC and the gut microbiome has emerged as an important area of current CRC research. Metagenomic profiling has identified a number of prominent CRC-associated bacteria that are enriched in CRC patients, linking the microbiota composition to colitis and cancer development. Some microbiota species have been reported to promote colitis and CRC development in preclinical models, while a few others are identified as immune modulators to induce potent protective immunity against colitis and CRC. Mechanistically, microbiota regulates the activation of different immune cell populations, inflammation, and CRC via crosstalk between innate and adaptive immune signaling pathways, including nuclear factor kappa B (NF-κB), type I interferon, and inflammasome. In this review, we provide an overview of the potential interactions between gut microbiota and host immunity and how their crosstalk could synergistically regulate inflammation and CRC, thus highlighting the potential roles and mechanisms of gut microbiota in the development of microbiota-based therapies to prevent or alleviate colitis and CRC.

Colon Tumors in Enterotoxigenic Bacteroides fragilis (ETBF)-Colonized Mice Do Not Display a Unique Mutational Signature but Instead Possess Host-Dependent Alterations in the APC Gene

Enterotoxigenic Bacteroides fragilis (ETBF) is consistently found at higher frequency in individuals with sporadic and hereditary colorectal cancer (CRC) and induces tumorigenesis in several mouse models of CRC. However, whether specific mutations induced by ETBF lead to colon tumor formation has not been investigated. To determine if ETBF-induced mutations impact the Apc gene, and other tumor suppressors or proto-oncogenes, we performed whole-exome sequencing and whole-genome sequencing on tumors isolated after ETBF and sham colonization of Apcmin/+ and Apcmin/+Msh2fl/flVC mice, as well as whole-genome sequencing of organoids cocultured with ETBF. Our results indicate that ETBF-induced tumor formation results from loss of heterozygosity (LOH) of Apc, unless the mismatch repair system is disrupted, in which case, tumor formation results from new acquisition of protein-truncating mutations in Apc. In contrast to polyketide synthase-positive Escherichia coli (pks+ E. coli), ETBF does not produce a unique mutational signature; instead, ETBF-induced tumors arise from errors in DNA mismatch repair and homologous recombination DNA damage repair, established pathways of tumor formation in the colon, and the same genetic mechanism accounting for sham tumors in these mouse models. Our analysis informs how this procarcinogenic bacterium may promote tumor formation in individuals with inherited predispositions to CRC, such as Lynch syndrome or familial adenomatous polyposis (FAP). IMPORTANCE Many studies have shown that microbiome composition in both the mucosa and the stool differs in individuals with sporadic and hereditary colorectal cancer (CRC). Both human and mouse models have established a strong association between particular microbes and colon tumor induction. However, the genetic mechanisms underlying putative microbe-induced colon tumor formation are not well established. In this paper, we applied whole-exome sequencing and whole-genome sequencing to investigate the impact of ETBF-induced genetic changes on tumor formation. Additionally, we performed whole-genome sequencing of human colon organoids exposed to ETBF to validate the mutational patterns seen in our mouse models and begin to understand their relevance in human colon epithelial cells. The results of this study highlight the importance of ETBF colonization in the development of sporadic CRC and in individuals with hereditary tumor conditions, such as Lynch syndrome and familial adenomatous polyposis (FAP).

Bacterial driver-passenger model in biofilms: a new mechanism in the development of colorectal cancer

Colorectal cancer (CRC) is a heterogeneous disease of the intestinal epithelium and ranks the third largest diagnosed malignancy in the world. Many studies have shown that the high risk of CRC is believed to be related to the formation of biofilms. To prove causation, it will be significant to decipher which specific bacteria in biofilms initiate and maintain CRC and fully describe their underlying mechanisms. Here we introduce a bacterial driver-passenger model. This model added a novel and compelling angle to the role of microorganisms, putting more emphasis on the transformation of bacterial composition in biofilms which play different roles in the development of CRC. In this model, bacterial drivers can initiate the formation of CRC through genotoxicity, while bacterial passengers maintain the CRC process through metabolites. On the basis of these pathogens, we further turned our attention to strategies that can inhibit and eradicate these pathogenic biofilms, with the aim of finding new ways to hinder colorectal carcinogenesis.

Human disease prediction from microbiome data by multiple feature fusion and deep learning

Human disease prediction from microbiome data has broad implications in metagenomics. It is rare for the existing methods to consider abundance profiles from both known and unknown microbial organisms, or capture the taxonomic relationships among microbial taxa, leading to significant information loss. On the other hand, deep learning has shown unprecedented advantages in classification tasks for its feature-learning ability. However, it encounters the opposite situation in metagenome-based disease prediction since high-dimensional low-sample-size metagenomic datasets can lead to severe overfitting; and black-box model fails in providing biological explanations. To circumvent the related problems, we developed MetaDR, a comprehensive machine learning-based framework that integrates various information and deep learning to predict human diseases. Experimental results indicate that MetaDR achieves competitive prediction performance with a reduction in running time, and effectively discovers the informative features with biological insights.

Colorectal microbiota after removal of colorectal cancer

The colonic microbiome has been implicated in the pathogenesis of colorectal cancer (CRC) and intestinal microbiome alterations are not confined to the tumour. Since data on whether the microbiome normalises or remains altered after resection of CRC are conflicting, we studied the colonic microbiota of patients after resection of CRC. We profiled the microbiota using 16S rRNA gene amplicon sequencing in colonic biopsies from patients after resection of CRC (n = 63) in comparison with controls (n = 52), subjects with newly diagnosed CRC (n = 93) and polyps (i = 28). The colonic microbiota after surgical resection remained significantly different from that of controls in 65% of patients. Genus-level profiling and beta-diversity confirmed two distinct groups of patients after resection of CRC: one with an abnormal microbiota similar to that of patients with newly diagnosed CRC and another similar to non-CRC controls. Consumption levels of several dietary ingredients and cardiovascular drugs co-varied with differences in microbiota composition suggesting lifestyle factors may modulate differential microbiome trajectories after surgical resection. This study supports investigation of the colonic microbiota as a marker of risk for development of CRC.

Malignancy and Endocarditis: Divulging Into the Intertwined Association

Cancer is an immunosuppressive disorder with characteristic features of unchecked cell growth, invasion, and sometimes thromboembolism leading to multiple systemic sequelae, including infective endocarditis. This article has compiled some of the crucial mechanisms by which infective endocarditis occurs in cancer patients, its risk factors, and the existing treatment interventions. It has focused on the necessity of being aware that these multiple pathogeneses are involved in the development of infective endocarditis (IE) in cancer patients, which would help delineate the risk factors associated with the condition and help physicians screen better for specific red flags. Identifying these risk factors and patient-oriented therapy, targeting the necessary elements such as causative organism, patient immune status, type of cancer, choosing evidence-based treatment modalities, and to improve the outcome of the disease in an already exasperating condition called cancer.

Bacteremia with Anaerobic Bacteria and Association with Colorectal Cancer: A Population-based Cohort Study

BACKGROUND

There is a well-described association between bacteremia with bovis group streptococci or Clostridium septicum and an increased risk of a colorectal cancer (CRC) diagnosis. We wanted to investigate the possible existence of a similar association between CRC and bacteremia with other bacteria belonging to the gut microbiota.

METHODS

A population based cohort study in a population about 2 million people including 45,774 bacteremia episodes and 231,387 blood culture negative cases was performed in the Region of Southern Denmark and Region Zealand (Denmark) from 2007-2016. Episodes of bacteremia were combined with the Danish central register for CRC. We performed Cox's regression analysis with hazard ratios (HRs) and 95% confidence intervals (CIs).

RESULTS

The study results confirmed previous findings of an increased risk of a CRC diagnosis after bacteremia with the bovis group streptococci (risk within a year: 4.3%; HR [95% CI]: 8.46 [3.51-20.4]) or C. septicum (20.8%; 76.2 [42.0-138]). Furthermore, Bacteroides ovatus (6.7%; 20.3 [5.04-81.8]), Bacteroides uniformis (5.4%; 16.2 [4.02-65.7]), Clostridium tertium (3.6 %; 13.9 [1.96-99.4]), Fusobacterium spp. (excluding F. necrophorum) (3.0 %; 8.51 [2.73-26.5]), and Gram-positive anaerobic cocci (3.6 %; 10.9 [4.50-26.3]) were also associated with an increased risk of a CRC diagnosis compared to patients with negative blood cultures (0.4%).

CONCLUSIONS

Bacteremia with several specific gut microbiota anaerobic bacteria is associated with a high risk of a diagnosis of CRC, indicating the need for colorectal workup in such cases. Importantly, this strategy also holds the possible additional benefit of detecting adenomas or other premalignant conditions, which were not included in the present study.

Consistent Alterations of Human Fecal Microbes After Transplantation into Germ-free Mice

Fecal microbiota transplantation (FMT) of human fecal samples into germ-free (GF) mice is useful for establishing causal relationships between the gut microbiota and human phenotypes. However, due to the intrinsic differences between human and mouse intestines and the different diets of the two organisms, it may not be possible to replicate human phenotypes in mice through FMT; similarly, treatments that are effective in mouse models may not be effective in humans. In this study, we aimed to identify human gut microbes that undergo significant and consistent changes (i.e., in relative abundances) after transplantation into GF mice in multiple experimental settings. We collected 16S rDNA-seq data from four published studies and analyzed the gut microbiota profiles from 1713 human-mouse pairs. Strikingly, on average, we found that only 47% of the human gut microbes could be re-established in mice at the species level, among which more than 1/3 underwent significant changes (referred to as "variable taxa"). Most of the human gut microbes that underwent significant changes were consistent across multiple human-mouse pairs and experimental settings. Consequently, about 1/3 of human samples changed their enterotypes, i.e., significant changes in their leading species after FMT. Mice fed with a controlled diet showed a lower enterotype change rate (23.5%) than those fed with a noncontrolled diet (49.0%), suggesting a possible solution for rescue. Most of the variable taxa have been reported to be implicated in human diseases, with some recognized as the causative species. Our results highlight the challenges of using a mouse model to replicate human gut microbiota-associated phenotypes, provide useful information for researchers using mice in gut microbiota studies, and call for additional validations after FMT. An online database named FMT-DB is publicly available at http://fmt2mice.humangut.info/#/.

Infective Endocarditis: New Challenges in a Classic Disease

Infective endocarditis is a relatively rare, but deadly infection, with an overall mortality of around 20% in most series. Clinical manifestations have evolved in response to significant epidemiological shifts in industrialized nations, with a move toward a nosocomial or health-care-related pattern, in older patients, with more episodes associated with prostheses and/or intravascular electronic devices and a predominance of staphylococcal and enterococcal etiology.Diagnosis is often challenging and is based on the conjunction of clinical, microbiological, and imaging information, with notable progress in recent years in the accuracy of echocardiographic data, coupled with the recent emergence of other useful imaging techniques such as cardiac computed tomography (CT) and nuclear medicine tools, particularly ¹⁸F-fluorodeoxyglucose positron emission/CT.The choice of an appropriate treatment for each specific case is complex, both in terms of the selection of the appropriate agent and doses and durations of therapy as well as the possibility of using combined bactericidal antibiotic regimens in the initial phase and finalizing treatment at home in patients with good evolution with outpatient oral or parenteral antimicrobial therapies programs. A relevant proportion of patients will also require valve surgery during the active phase of treatment, the timing of which is extremely difficult to define. For all the above, the management of infective endocarditis requires a close collaboration of multidisciplinary endocarditis teams.

Profiling the Bladder Microbiota in Patients With Bladder Cancer

Evidence suggests that microbiota may contribute to the pathogenesis of several diseases, including cancer. In the case of bladder cancer, preliminary studies have found alterations in the urinary microbiota of patients with urothelial carcinoma compared with healthy individuals. Conversely, the urinary microbiota differ between men and women, and it has been hypothesized that these differences are associated with the lower incidence of bladder cancers in women. The objective of this study was to characterize the bladder microbiota in paired samples of tumor and non-tumor mucosa of patients with malignant bladder neoplasia using next-generation sequencing. In addition, we aimed to study potential differences in microbial composition in tumor samples according to clinical and pathological variables, and to determine possible microbial profiles. We found significant differences in microbial richness at the genus level, with a higher richness observed in the non-tumor compared with the tumor mucosa. It was also shown that Actinobacteria were significantly more enriched in the non-tumor compared with the tumor mucosa (P = 0.014). In the multivariate analysis, we found significant differences in microbial composition according to tumor grade (P = 0.03 and 0.04 at the phylum and genus levels, respectively). Moreover, we detected a higher microbial richness in non-tumor vs. tumor tissues which agrees with the global assumption that microbial richness is an indicator of health. The greater abundance of members of the Actinobacteria phylum in the non-neoplastic bladder mucosa samples supports the hypothesis that a higher abundance of Actinomycetes is associated with a lower rate of bladder cancer in women and suggests a protective role for these microbiota. We detected a microbial profile that was enriched for Enterococcus in low-grade tumors. Finally, we identified the presence of two clusters in the microbial composition of the tumor mucosa samples, significantly enriched for the genera Barnesiella, Parabacteroides, Prevotella, Alistipes, and Lachnospiracea_incertae_sedis (Cluster 1), or Staphylococcus (Cluster 2). Further longitudinal studies are needed to assess the role of the bladder microbiota in carcinogenesis.

Bacteriophages and their potential for treatment of gastrointestinal diseases

Although bacteriophages have been overshadowed as therapeutic agents by antibiotics for decades, the emergence of multidrug-resistant bacteria and a better understanding of the role of the gut microbiota in human health and disease have brought them back into focus. In this Perspective, we briefly introduce basic phage biology and summarize recent discoveries about phages in relation to their role in the gut microbiota and gastrointestinal diseases, such as inflammatory bowel disease and chronic liver disease. In addition, we review preclinical studies and clinical trials of phage therapy for enteric disease and explore current challenges and potential future directions.

Distribution, Diversity and Roles of CRISPR-Cas Systems in Human and Animal Pathogenic Streptococci

Streptococci form a wide group of bacteria and are involved in both human and animal pathologies. Among pathogenic isolates, differences have been highlighted especially concerning their adaptation and virulence profiles. CRISPR-Cas systems have been identified in bacteria and many streptococci harbor one or more systems, particularly subtypes I-C, II-A, and III-A. Since the demonstration that CRISPR-Cas act as an adaptive immune system in Streptococcus thermophilus, a lactic bacteria, the diversity and role of CRISPR-Cas were extended to many germs and functions were enlarged. Among those, the genome editing tool based on the properties of Cas endonucleases is used worldwide, and the recent attribution of the Nobel Prize illustrates the importance of this tool in the scientific world. Another application is CRISPR loci analysis, which allows to easily characterize isolates in order to understand the interactions of bacteria with their environment and visualize species evolution. In this review, we focused on the distribution, diversity and roles of CRISPR-Cas systems in the main pathogenic streptococci.