Enterotoxigenic Bacteroides fragilis: a rogue among symbiotes

Interplay of m6A RNA methylation and gut microbiota in modulating gut injury

The gut microbiota undergoes continuous variations among individuals and across their lifespan, shaped by diverse factors encompassing diet, age, lifestyle choices, medication intake, and disease states. These microbial inhabitants play a pivotal role in orchestrating physiological metabolic pathways through the production of metabolites like bile acids, choline, short-chain fatty acids, and neurotransmitters, thereby establishing a dynamic "gut-organ axis" with the host. The intricate interplay between the gut microbiota and the host is indispensable for gut health, and RNA N6-methyladenosine modification, a pivotal epigenetic mark on RNA, emerges as a key player in this process. M6A modification, the most prevalent internal modification of eukaryotic RNA, has garnered significant attention in the realm of RNA epigenetics. Recent findings underscore its potential to influence gut microbiota diversity and intestinal barrier function by modulating host gene expression patterns. Conversely, the gut microbiota, through its impact on the epigenetic landscape of host cells, may indirectly regulate the recruitment and activity of RNA m6A-modifying enzymes. This review endeavors to delve into the biological functions of m6A modification and its consequences on intestinal injury and disease pathogenesis, elucidating the partial possible mechanisms by which the gut microbiota and its metabolites maintain host intestinal health and homeostasis. Furthermore, it also explores the intricate crosstalk between them in intestinal injury, offering a novel perspective that deepens our understanding of the mechanisms underlying intestinal diseases.

Gut and Intratumoral microbiota: Key to lung Cancer development and immunotherapy

Lung cancer is a common malignant tumor worldwide with high incidence and mortality rates. Previous studies have claimed that the microbial community plays an integral role in the development and progression of lung cancer. Emerging evidence reveals that gut flora plays a key role in cancer formation and evolution by participating in mechanisms such as metabolism, regulation of inflammation and immune response. Not only the gut flora, but also the presence of intratumoral microbiota may influence lung cancer progression through multiple mechanisms. These research advances suggest that intestinal flora and intratumoral microbiota may not only serve as potential biomarkers for lung cancer, but may also be targets for therapy. However, current studies on both in lung cancer are still limited. Given this, this study aimed to systematically review the latest findings on the major bacterial species of the intestinal flora and their possible protective or harmful roles in the formation, progression, and metastasis of lung cancer. In addition, we analyzed the potential mechanisms by which the intratumoral microbiota affected lung cancer and elaborated on the potential roles of the gut flora and its metabolites, as well as the intratumoral microbiota, in modulating the efficacy of immunotherapy in lung cancer.

Murine gut microbiota dysbiosis via enteric infection modulates the foreign body response to a distal biomaterial implant

The gut microbiota influences systemic immunity and the function of distal tissues, including the brain, liver, skin, lung, and muscle. However, the role of the gut microbiota in the foreign body response and fibrosis is largely unexplored. To investigate this connection, we perturbed the homeostasis of the murine gut microbiota via infection with the pathogenic bacterial species enterotoxigenic Bacteroides fragilis (ETBF) and implanted particulate material (mean particle size <600 μm) of the synthetic polymer polycaprolactone (PCL) into a distal muscle injury. ETBF infection in mice led to increased neutrophil and γδ T cell infiltration into the PCL implant site. ETBF infection alone promoted systemic inflammation, increased levels of neutrophils in lymphoid tissues, and altered skeletal muscle gene expression. At the PCL implant site, we found significant changes in the transcriptome of sorted stromal cells between infected and control mice, including differences related to ECM components such as proteoglycans and glycosaminoglycans. However, we did not observe ETBF-induced differences in fibrosis levels. These results demonstrate the ability of the gut microbiota to mediate long-distance effects such as immune and stromal responses to a distal biomaterial implant.

Intestinal dysbiosis and colorectal cancer

ABSTRACT

Colorectal cancer (CRC) is one of the leading causes of cancer-related morbidity and mortality worldwide, highlighting the urgent need for novel preventive and therapeutic strategies. Emerging research highlights the crucial role of the gut microbiota, including bacteria, fungi, viruses, and their metabolites, in the pathogenesis of CRC. Dysbiosis, characterized by an imbalance in microbial composition, contributes to tumorigenesis through immune modulation, metabolic reprogramming, and genotoxicity. Specific bacterial species, such as Fusobacterium nucleatum and enterotoxigenic Bacteroides fragilis, along with fungal agents like Candida species, have been implicated in CRC progression. Moreover, viral factors, including Epstein-Barr virus and human cytomegalovirus, are increasingly recognized for their roles in promoting inflammation and immune evasion. This review synthesizes the latest evidence on host-microbiome interactions in CRC, emphasizing microbial metabolites, such as short-chain fatty acids and bile acids, which may act as both risk factors and therapeutic agents. We further discuss the latest advances in microbiota-targeted clinical applications, including biomarker-assisted diagnosis, next-generation probiotics, and microbiome-based interventions. A deeper understanding of the role of gut microbiome in CRC pathogenesis could pave the way for diagnostic, preventive, and personalized therapeutic strategies.

Bacteroides fragilis 839 ameliorates anti-tuberculosis drugs-induced liver injury by suppressing inflammation and regulating gut microbiota in mice

Anti-tuberculosis drug-induced liver injury (ATB-DILI), caused by first-line anti-tuberculosis (anti-TB) drugs, disrupts treatment and increases the risk of drug resistance. The gut microbiota and intestinal barrier integrity play key roles in ATB-DILI susceptibility through the liver-gut axis. Probiotics, such as Bacteroides fragilis 839 (BF839), have shown therapeutic potential in modulating gut microbiota and inflammatory responses. In this study, we investigated the protective effects of BF839 on ATB-DILI in a mouse model of HRZE-induced liver injury. BF839 administration significantly alleviated HRZE-induced liver injury by reducing ALT, AST, AKP, and MDA levels, enhancing SOD and GSH levels, and improving liver histopathology. These effects were associated with restored gut microbiota diversity, enhanced intestinal barrier function, and reduced inflammatory responses. Our findings suggest that BF839 may serve as a potential preventive strategy for ATB-DILI.

Bacteroides fragilis Toxin Induces Sequential Proteolysis of E-Cadherin and Inflammatory Response in Mouse Intestinal Epithelial Cell Line

Enterotoxigenic Bacteroides fragilis (ETBF) is an intestinal bacterium that secretes the metalloprotease Bacteroides fragilis toxin (BFT), which induces E-cadherin cleavage and interleukin-8 secretion in human intestinal epithelial cell lines. ETBF-induced E-cadherin cleavage is proposed to be the underlying reason for the promotion of colitis in ETBF-infected mice. However, a BFT-responsive murine cell line has not yet been reported. In the current study, we report that the mouse colonic epithelial cell line CMT93 undergoes E-cadherin ectodomain cleavage, cell rounding, and proliferation in response to BFT treatment. The amino acid sequence of the putative cleavage site of E-cadherin is identical in both BFT-responsive (CMT93) and BFT-nonresponsive (MSIE, CT26, YAMC, and B16) cell lines, suggesting that the E-cadherin amino acid sequence is not responsible for this observation. After E-cadherin ectodomain cleavage, the membrane-bound intracellular E-cadherin domain underwent cleavage by γ-secretase and was subsequently degraded by the proteasome. Moreover, BFT induced the secretion of two chemokines (LIX and KC) and the formation of soluble TNFR1 in the CMT93 cell line. The identification of a BFT-responsive murine cell line may be used to elucidate the mechanism of ETBF pathogenesis in ETBF murine infection models.

Tryptic oncopeptide secreted from the gut bacterium Cronobacter malonaticus PO3 promotes colorectal cancer

The involvement of Cronobacter, which is frequently associated with meningitis and necrotizing enterocolitis, in human colorectal cancer remains unexplored. In this study, we isolate and characterize a novel strain of C. malonaticus designated PO3 from a fecal sample of a colon cancer patient and demonstrate its proliferative effects on colorectal cancer both in vitro and in vivo. The secretome of PO3 significantly promoted cell proliferation, as evidenced by increased cell viability, fluorescence intensity, and Ki-67 expression, without inducing cell death. Furthermore, using high-resolution mass spectrometry (HRMS), we identified a novel tryptic oncopeptide designated P506, in the PO3 secretome that promotes colorectal cancer. Synthetic P506 further stimulated human colorectal adenocarcinoma cell line HT-29 cell proliferation in a dose-dependent manner. Experiments with the BALB/c mouse model in vivo revealed that both the PO3 secretome and P506 contributed to the development of colorectal polyps and associated histological changes, including dysplasia and altered colonic architecture. These findings suggest that P506, a potent peptide from the PO3 secretome, may have oncogenic potential, promoting colorectal cancer progression.

Advances in gut microbiota-related treatment strategies for managing colorectal cancer in humans

Colorectal cancer (CRC) is a major contributor to global cancer-related mortality with increasing incidence rates in both developed and developing regions. Therefore, CRC presents a significant challenge to global health. The development of innovative tools for enhancing early CRC screening and diagnosis, along with novel treatments and therapies for improved management, remains an urgent necessity. CRC is intricately associated with the gut microbiota, which is integral to food digestion, nutrient generation, drug metabolism, metabolite production, immune enhancement, endocrine regulation, neurogenesis modulation, and the maintenance of physiologic and psychological equilibrium. Dysbiosis or imbalances in the gut microbiome have been implicated in various disorders, including CRC. Emerging evidence highlights the critical role of the gut microbiome in CRC pathogenesis and treatment, which presents potential opportunities for early detection and diagnosis. Despite substantial advances in understanding the relationship between the gut microbiota and CRC, significant challenges persist. Gaining a deeper and more detailed understanding of the interactions between the human microbiota and cancer is essential to fully realize the potential of the microbiota in cancer management. Unlike genetic factors, the gut microbiome is subject to modification, offering a promising avenue for the development of CRC treatments and drug discovery. This review provides an overview of the interactions between the human gut microbiome and CRC, while examining prospects for precision management of CRC.

Prevalence of enterotoxigenic Bacteroides fragilis in patients with colorectal cancer: a systematic review and meta-analysis

Introduction

The gut microbiome, specifically enterotoxigenic Bacteroides fragilis (ETBF), has been reported to play a role in colorectal cancer development. We aimed to conduct a systematic review and meta-analysis of published studies to compare the prevalence of ETBF in patients with colorectal cancer and healthy controls as well as in various stages of colorectal cancer.

Methods

PubMed, EMBASE, and The Cochrane Library were systematically searched for studies published until May 2024. We utilized studies either comparing the prevalence of ETBF in patients with colorectal cancer and healthy control or examining its prevalence across different stages of colorectal cancer. The prevalence of ETBF colonization in biological samples from individuals with colorectal cancer compared to that in healthy controls or adjacent normal tissue as well as the association between the prevalence of ETBF and various stages of colorectal cancer were plotted using a random-effect or fixed-effect model.

Results

Fourteen relevant articles were identified. Meta-analyses revealed that patients with colorectal cancer had a higher likelihood of having ETBF than healthy controls (odds ratio [OR]: 2.54, 95% confidence interval [CI]: 1.63-3.98, I2 = 55%). Additionally, ETBF detection was lower in stage I/II than in stage III/IV colorectal cancer (OR: 0.61, 95% CI: 0.41-0.91, I2 = 41%).

Discussion

The prevalence of ETBF was consistently higher in the tissue and fecal samples of patients with colorectal cancer than in those of controls. A difference in ETBF prevalence between stage I/II and stage III/IV colorectal cancer was noted, but further analysis revealed that the conclusion is unreliable.

Systematic review registration

https://www.crd.york.ac.uk/prospero/, identifier CRD 42024548325.

Bacteroides fragilis Toxin Suppresses METTL3-Mediated m6A Modification in Macrophage to Promote Inflammatory Bowel Disease

BACKGROUND AND AIMS

Bacteroides fragilis toxin (BFT), produced by enterotoxigenic B. fragilis (ETBF), is crucial for ETBF-induced colitis. This study aims to investigate the impact of BFT-host interactions on N6-methyladenosine (m6A) modification of host mRNA and its underlying mechanisms.

METHODS

Single-cell sequencing was employed to identify the cell types involved in ETBF-induced colitis in inflammatory bowel disease patients and dextran sodium sulfate-induced colitis mice. An ETBF strain with the bft gene deleted (ETBF[Δbft]) was utilized to investigate the role of ETBF components. The biological functions and mechanisms of BFT-induced m6A modifications, as well as the target genes, were explored in vitro and in vivo.

RESULTS

Inflammatory macrophages are enriched in the intestinal mucosal tissue of both inflammatory bowel disease patients and mice with high levels of ETBF. Additionally, ETBF triggers the activation of inflammatory macrophages, subsequently inducing downstream inflammatory responses. Remarkably, BFT secreted by ETBF reduced METTL3 transcription by inhibiting FOXD3 expression and induced a dramatic reduction of m6A modifications in inflammatory macrophages. Moreover, BFT promotes the expression of its target ITGA5 expression by diminishing YTHDF2-dependent mRNA degradation. Targeting integrin subunit alpha 5 using Cilengitide significantly alleviated ETBF-induced colitis by decreasing the level of inflammatory factors in macrophages.

CONCLUSIONS

Our study reveals that BFT produced by ETBF leads to a reduction of m6A modifications by reducing METTL3 transcription and promotes ITGA5 expression in inflammatory macrophages. These findings provide new insights into the modulation of human m6A epitranscriptome in macrophages by gut microbiota and its significance in inflammatory bowel disease progression.

Implications of intratumoral microbiota in tumor metastasis: a special perspective of microorganisms in tumorigenesis and clinical therapeutics

Tumor metastasis is the main cause of therapeutic failure and mortality in cancer patients. The intricate metastastic process is influenced by both the intrinsic properties of tumor cells and extrinsic factors, such as microorganisms. Notably, some microbiota have been discovered to colonize tumor tissues, collectively known as intratumoral microbiota. Intratumoral microbiota can modulate tumor progression through multiple mechanisms, including regulating immune responses, inducing genomic instability and gene mutations, altering metabolic pathways, controlling epigenetic pathways, and disrupting cancer-related signaling pathways. Furthermore, intratumoral microbiota have been shown to directly impact tumor metastasis by regulating cell adhesion, stem cell plasticity and stemness, mechanical stresses and the epithelial-mesenchymal transition. Indirectly, they may affect tumor metastasis by modulating the host immune system and the tumor microenvironment. These recent findings have reshaped our understanding of the relationship between microorganims and the metastatic process. In this review, we comprehensively summarize the existing knowledge on tumor metastasis and elaborate on the properties, origins and carcinogenic mechanisms of intratumoral microbiota. Moreover, we explore the roles of intratumoral microbiota in tumor metastasis and discuss their clinical implications. Ongoing research in this field will establish a solid foundation for novel therapeutic strategies and clinical treatments for various tumors.

Tumor microbiome: roles in tumor initiation, progression, and therapy

Over the past few years, the tumor microbiome is increasingly recognized for its multifaceted involvement in cancer initiation, progression, and metastasis. With the application of 16S ribosomal ribonucleic acid (16S rRNA) sequencing, the intratumoral microbiome, also referred to as tumor-intrinsic or tumor-resident microbiome, has also been found to play a significant role in the tumor microenvironment (TME). Understanding their complex functions is critical for identifying new therapeutic avenues and improving treatment outcomes. This review first summarizes the origins and composition of these microbial communities, emphasizing their adapted diversity across a diverse range of tumor types and stages. Moreover, we outline the general mechanisms by which specific microbes induce tumor initiation, including the activation of carcinogenic pathways, deoxyribonucleic acid (DNA) damage, epigenetic modifications, and chronic inflammation. We further propose the tumor microbiome may evade immunity and promote angiogenesis to support tumor progression, while uncovering specific microbial influences on each step of the metastatic cascade, such as invasion, circulation, and seeding in secondary sites. Additionally, tumor microbiome is closely associated with drug resistance and influences therapeutic efficacy by modulating immune responses, drug metabolism, and apoptotic pathways. Furthermore, we explore innovative microbe-based therapeutic strategies, such as engineered bacteria, oncolytic virotherapy, and other modalities aimed at enhancing immunotherapeutic efficacy, paving the way for microbiome-centered cancer treatment frameworks.

Virulence factor discovery identifies associations between the Fic gene family and Fap2+ fusobacteria in colorectal cancer microbiomes

Fusobacterium is a bacterium associated with colorectal cancer (CRC) tumorigenesis, progression, and metastasis. Fap2 is a fusobacteria-specific outer membrane galactose-binding lectin that mediates Fusobacterium adherence to and invasion of CRC tumors. Advances in omics analyses provide an opportunity to profile and identify microbial genomic features that correlate with the cancer-associated bacterial virulence factor Fap2. Here, we analyze genomes of Fusobacterium colon tumor isolates and find that a family of post-translational modification enzymes containing Fic domains is associated with Fap2 positivity in these strains. We demonstrate that Fic family genes expand with the presence of Fap2 in the fusobacterial pangenome. Through comparative genomic analysis, we find that Fap2+ Fusobacteriota are highly enriched with Fic gene families compared to other cancer-associated and human gut microbiome bacterial taxa. Using a global data set of CRC shotgun metagenomes, we show that fusobacterial Fic and Fap2 genes frequently co-occur in the fecal microbiomes of individuals with late-stage CRC. We further characterize specific Fic gene families harbored by Fap2+ Fusobacterium animalis genomes and detect recombination events and elements of horizontal gene transfer via synteny analysis of Fic gene loci. Exposure of a F. animalis strain to a colon adenocarcinoma cell line increases gene expression of fusobacterial Fic and virulence-associated adhesins. Finally, we demonstrate that Fic proteins are synthesized by F. animalis as Fic peptides are detectable in F. animalis monoculture supernatants. Taken together, our study uncovers Fic genes as potential virulence factors in Fap2+ fusobacterial genomes.IMPORTANCEAccumulating data support that bacterial members of the intra-tumoral microbiota critically influence colorectal cancer progression. Yet, relatively little is known about non-adhesin fusobacterial virulence factors that may influence carcinogenesis. Our genomic analysis and expression assays in fusobacteria identify Fic domain-containing genes, well-studied virulence factors in pathogenic bacteria, as potential fusobacterial virulence features. The Fic family proteins that we find are encoded by fusobacteria and expressed by Fusobacterium animalis merit future investigation to assess their roles in colorectal cancer development and progression.

Alternations of the gut microbiota and the Firmicutes/Bacteroidetes ratio after biologic treatment in inflammatory bowel disease

BACKGROUND

The inflammatory bowel disease (IBD), comprising Crohn's disease (CD) and ulcerative colitis (UC) is a complex disease with multifactorial etiology. The intestinal dysbiosis have been investigated to play an important role in IBD pathogenesis and disease activity. The aim of our study was to analyze the intestinal microbiota composition in IBD across different severity levels and the impact of biologic therapy on microbiota modulation.

METHODS

In this study, 27 IBD patients were recruited, including 14 patients undergoing biologic therapy for moderate to severe disease activity and 13 controls with inactive disease. The gut microbial composition was determined by 16 S ribosomal RNA gene sequencing of stool samples.

RESULTS

Biologic therapy led to significant clinical improvement in IBD disease activity after 48 weeks. About species richness, community alpha diversity was significant lower in active CD patients and enriched gradually after biologic therapy. The beta-diversity regard to the difference of bacterial community composition showed significant difference between patients in biologic and control group. A decrease in Firmicutes and increase in Bacteroidetes abundance were observed in patients with active disease, both in CD and UC. Biologic treatment induced shifts in gut microbiota, with increased Firmicutes and decreased Bacteroidetes, as well as improved F/B ratio gradually after treatment, correlating with disease activity.

CONCLUSIONS

Our study suggested that gut microbiota differences changed after biologic therapies among IBD with different disease activity, and a rising Firmicutes/Bacteroidetes ratio could be a potential predictor for disease activity and treatment response monitoring.

Bacterial small molecule metabolites implicated in gastrointestinal cancer development

Numerous associations have been identified between cancer and the composition and function of the human microbiome. As cancer remains the second leading global cause of mortality, investigating the carcinogenic contributions of microbiome members could advance our understanding of cancer risk and support potential therapeutic interventions. Although fluctuations in bacterial species have been associated with cancer progression, studying their small molecule metabolites offers one avenue to establish support for causal relationships and the molecular mechanisms governing host-microorganism interactions. In this Review, we explore the expanding repertoire of small molecule metabolites and their mechanisms implicated in the risk of developing gastrointestinal cancers.

A review on gut microbiota and miRNA crosstalk: implications for Alzheimer's disease

Alzheimer's disease (AD) is a neurodegenerative disorder characterized by cognitive decline and progressive neuronal damage. Recent research has highlighted the significant roles of the gut microbiota and microRNAs (miRNAs) in the pathogenesis of AD. This review explores the intricate interaction between gut microbiota and miRNAs, emphasizing their combined impact on Alzheimer's progression. First, we discuss the bidirectional communication within the gut-brain axis and how gut dysbiosis contributes to neuroinflammation and neurodegeneration in AD. Changes in gut microbiota composition in Alzheimer's patients have been linked to inflammation, which exacerbates disease progression. Next, we delve into the biology of miRNAs, focusing on their roles in gene regulation, neurodevelopment, and neurodegeneration. Dysregulated miRNAs are implicated in AD pathogenesis, influencing key processes like inflammation, tau pathology, and amyloid deposition. We then examine how the gut microbiota modulates miRNA expression, particularly in the brain, potentially altering neuroinflammatory responses and synaptic plasticity. The interplay between gut microbiota and miRNAs also affects blood-brain barrier integrity, further contributing to Alzheimer's pathology. Lastly, we explore therapeutic strategies targeting this gut microbiota-miRNA axis, including probiotics, prebiotics, and dietary interventions, aiming to modulate miRNA expression and improve AD outcomes. While promising, challenges remain in fully elucidating these interactions and translating them into effective therapies. This review highlights the importance of understanding the gut microbiota-miRNA relationship in AD, offering potential pathways for novel therapeutic approaches aimed at mitigating the disease's progression.

Capilliposide A alleviates DSS-induced colitis by regulating the intestinal flora and its metabolites of origin

Ulcerative colitis is a chronic idiopathic inflammatory disease that impacts the mucous membrane of the colon. Lately, the incidence and prevalence of UC has been increasing globally. However, there are significant side effects of existing drugs for UC intervention. Accordingly, there is a pressing demand to explore novel bioactive substances for addressing UC. Natural product saponins have attracted great attention due to their obvious anti-colitis potential. Capilliposide A is a triterpenoid saponin, which is derived from Lysimachia capillipes Hemsl., exhibits good anti-inflammatory activity. Nonetheless, the impact and mechanism of CPS-A on ulcerative colitis remains obscure. This study aimed to investigate the therapeutic effects of CPS-A on the dextran sulphate sodium induced colitis mouse model and explore its mechanism. The efficacy and safety of CPS-A were evaluated in a well-established dextran sodium sulfate (DSS)-induced colitis mice model. Disease progression was monitored via clinical symptoms, histopathological examination, quantification of inflammatory cytokines, and epithelial barrier function evaluation. Plasma samples and intestinal contents were collected for non-targeted metabolomics and 16sRNA sequencing, respectively, to jointly evaluate the mechanism of action. CPS-A alleviated colitis by improving weight, Disease activity index score, histopathology, goblet cell, colon length, and expression of inflammatory factors. Moreover, CPS-A effectively preserved the integrity of the intestinal barrier by enhancing the expression of tight junction proteins and mucin in the colonic tissue of mice. Furthermore, CPS-A exerted a regulatory effect on the composition of the gut microbiota, promoting bacterial richness and diversity. It not only suppressed the abundance of detrimental bacteria while enhancing the abundance of advantageous bacteria, but also modulated the metabolites derived from the intestinal flora. Importantly, correlation analysis shows that these indicators are highly correlated. This study revealed that CPS-A exhibits a favorable therapeutic efficacy against colitis, primarily attributed to its ability to modulate the gut microbiota their associated metabolites as the key mechanisms of action.

Murine gut microbiota dysbiosis via enteric infection modulates the foreign body response to a distal biomaterial implant

The gut microbiota influences systemic immunity and the function of distal tissues, including the brain, liver, skin, lung, and muscle. However, the role of the gut microbiota in the foreign body response (FBR) and fibrosis around medical implants is largely unexplored. To investigate this connection, we perturbed the homeostasis of the murine gut microbiota via enterotoxigenic Bacteroides fragilis (ETBF) infection and implanted the synthetic polymer polycaprolactone (PCL) into a distal muscle injury. ETBF infection in mice led to increased neutrophil and γδ T cell infiltration into the PCL implant site. ETBF infection alone promoted systemic inflammation and increased levels of neutrophils in the blood, spleen, and bone marrow. At the PCL implant site, we found significant changes in the transcriptome of sorted fibroblasts but did not observe gross ETBF- induced differences in the fibrosis levels after 6 weeks. These results demonstrate the ability of the gut microbiota to mediate long-distance effects such as immune and stromal responses to a distal biomaterial implant.

Significance Statement

The foreign body response to implants leads to chronic inflammation and fibrosis that can be highly variable in the general patient population. Here, we demonstrate that gut dysbiosis via enteric infection promoted systemic inflammation and increased immune cell recruitment to an anatomically distant implant site. These results implicate the gut microbiota as a potential source of variability in the clinical biomaterial response and illustrate that the local tissue environment can be influenced by host factors that modulate systemic interactions.

Cell free supernatants of Bifidobacterium adolescentis and Bifidobacterium longum suppress the tumor growth in colorectal cancer organoid model

The probiotic gut microbiome and its metabolites are pivotal in regulating host metabolism, inflammation, and immunity. Host genetics, colonization at birth, the host lifestyle, and exposure to diseases and drugs determine microbial composition. Dysbiosis and disruption of homeostasis in the beneficial microbiome have been reported to be involved in the tumorigenesis and progression of colorectal cancer (CRC). However, the influence of bacteria-secreted metabolites on CRC growth is yet to be fully elucidated. In this study, we compared the microbial composition of CRC patients to healthy controls to identify distinct patterns of microbiota-derived metabolites in CRC patients. Metagenomic analysis demonstrated that beneficial bacteria strains; Blautia producta, Bifidobacterium adolescentis, and Bifidobacterium longum decreased, while Parabacteroides distasonis and Bacteroides ovatus were more prevalent in the CRC patient group. Treatment of cancer organoid lines with microbial culture supernatants from Blautia producta, Bifidobacterium adolescentis, and Bifidobacterium longum showed remarkable inhibition of cancer growth. This study demonstrates that the bacterial metabolites depleted in CRC patients may inhibit cancer growth and highlights the effects of microbiome-derived metabolites on CRC growth.

Gut microbial composition associated with risk of premature aging in women with Yin-deficiency constitution

Background

Yin-deficiency constitution (YinDC) refers to a traditional Chinese medicine concept, characterized by an imbalance state that includes an imbalance in the gut microbiota, resulting from a relative deficiency of Yin fluids within the body. In recent years, it has become apparent that the composition and structure of the gut microbiota play a significant role in the aging process. The imbalance of gut microbiota in YinDC may accelerate the aging process. However, the specific gut microbiota compositions involved in the YinDC premature aging process remain unknown.

Methods

In this study, we conducted a cohort study including 60 women with YinDC and BC to analyze their gut microbiota composition. We integrated 16S rDNA sequencing with machine learning methods to reveal the association between gut microbiota and premature aging in YinDC women.

Results

We found a significant difference in the composition of gut microbiota between the YinDC and the BC group. At the phylum level, Cyanobacteria and Synerobacteria only emerged in the YinDC group. At the genus level, Bacteroides, Bifidobacterium, Haemophilus, Alistipes, and Dialister showed higher abundance in the YinDC group. Bilophila, Eubacterium, and Aeromonas were the most significant indicators influencing the YinDC premature aging. The YinDC group had the most functional gene pathways associated with the metabolism.

Conclusion

Our study demonstrated that the gut microbiota was associated with premature aging in women with YinDC, potentially providing preliminary evidence and guidance for personalized anti-aging strategies.

Analysis of Characteristics of Bovine-Derived Non-Enterotoxigenic Bacteroides fragilis and Validation of Potential Probiotic Effects

Bacteroides fragilis is a new generation of probiotics, and its probiotic effects on humans and some animals have been verified. However, research on B. fragilis in cattle is still lacking. In this study, 24 stool samples were collected from two large-scale cattle farms in Wuzhong, Ningxia, including 12 diarrheal and 12 normal stools. A non-toxigenic Bacteroides fragilis (NTBF) was isolated and identified by 16S rRNA high-throughput sequencing and named BF-1153; genome composition and genome functional analyses were carried out to reflect the biological characteristics of the BF-1153 strain. A cluster analysis of BF-1153 was performed using Mega X to explore its genetic relationship. In addition, Cell Counting Kit-8 (CCK8) was used to determine the toxic effects of the strain on human ileocecal colorectal adenocarcinoma cell line cells (HCT-8), Madin-Darby bovine kidney cells (MDBK), and intestinal porcine epithelial cells (IPECs). The results showed that BF-1153 conformed to the biological characteristics of B. fragilis. BF-1153 had no toxic effects on HCT-8, MDBK, and IPEC. Animal experiments have shown that BF-1153 has no toxic effects on healthy SPF Kunming mice. Notably, the supernatant of BF-1153 enhanced cell activity and promoted cell growth in all three cell lines. At the same time, a cluster analysis of the isolated strains showed that the BF-1153 strain belonged to the same branch as the B. fragilis strain 23212, and B. fragilis strain 22998. The results of the animal experiments showed that BF-1153 had a certain preventive effect on diarrhea symptoms in SPF Kunming mice caused by a bovine rotavirus (BRV). In summary, the strain BF-1153 isolated in this experiment is NTBF, which has no toxic effect on MDBK, HCT-8, and IPEC, and has obvious cell growth-promoting effects, especially on MDBK. BF-1153 promotes the growth and development of SPF Kunming mice when compared with the control group. At the same time, BF-1153 alleviated the diarrhea symptoms caused by BRV in SPF Kunming mice. Therefore, BF-1153 has the potential to be a probiotic for cattle.

Harnessing Gene Editing Technology for Tumor Microenvironment Modulation: An Emerging Anticancer Strategy

Cancer is a multifaceted disease influenced by both intrinsic cellular traits and extrinsic factors, with the tumor microenvironment (TME) being crucial for cancer progression. To satisfy their high proliferation and aggressiveness, cancer cells always plunder large amounts of nutrients and release various signals to their surroundings, forming a dynamic TME with special metabolic, immune, microbial and physical characteristics. Due to the neglect of interactions between tumor cells and the TME, traditional cancer therapies often struggle with challenges such as drug resistance, low efficacy, and recurrence. Importantly, the development of gene editing technologies, particularly the CRISPR-Cas system, offers promising new strategies for cancer treatment. Combined with nanomaterial strategies, CRISPR-Cas technology exhibits precision, affordability, and user-friendliness with reduced side effects, which holds great promise for profoundly altering the TME at the genetic level, potentially leading to lasting anticancer outcomes. This review will delve into how CRISPR-Cas can be leveraged to manipulate the TME, examining its potential as a transformative anticancer therapy.

Crosstalk Between the Intratumoral Microbiota and the Tumor Microenvironment: New Frontiers in Solid Tumor Progression and Treatment

BACKGROUND

The microbiota plays a significant role in the tumor microenvironment, and its impact on tumor development and treatment outcome cannot be overlooked. Thus, it is essential to comprehend the interactions between the microbiota and the tumor microenvironment.

RECENT FINDINGS

With the advent of next-generation sequencing, microbiota research has advanced significantly in recent years. The interaction between the intratumoral microbiota and the tumor microenvironment is an emerging area of research that holds great promise for understanding and treating solid tumor progression. This crosstalk between the intratumoral microbiota and the tumor microenvironment is a complex process that involves a multitude of factors, including the immune system, cellular signaling pathways, and metabolic processes. The origin of the intratumoral microbiota differs between various solid tumor, and the quantity and diversity of intratumoral microbiota also fluctuate significantly within each solid tumor.

CONCLUSION

The aim of this review is to provide a detailed summary of the intratumoral microbiota in various types of solid tumors. This will include an analysis of their origins, differences, and how they impact the progression of solid tumors. Furthermore, we will emphasize the significant potential that the intratumoral microbiota holds for the diagnosis and treatment of solid tumors.

Colorectal Cancer in Inflammatory Bowel Disease: A Review of the Role of Gut Microbiota and Bacterial Biofilms in Disease Pathogenesis

The risk of colorectal cancer [CRC] is increased in patients with inflammatory bowel disease [IBD], particularly in extensive ulcerative colitis [UC] and Crohn's colitis. Gut microbiota have been implicated in the pathogenesis of CRC via multiple mechanisms, including the release of reactive oxygen species and genotoxins, and induction of inflammation, as well as activation of the immune response. Gut microbiota can enhance their carcinogenic and proinflammatory properties by organising into biofilms, potentially making them more resistant to the host's immune system and to antibiotics. Colonic biofilms have the capacity to invade colonic tissue and accelerate tumorigenesis in tumour-prone models of mice. In the context of IBD, the prevalence of biofilms has been estimated to be up to 95%. Although the relationship between chronic inflammation and molecular mediators that contribute to IBD-associated CRC is well established, the role of gut microbiota and biofilms in this sequence is not fully understood. Because CRC can still arise in the absence of histological inflammation, there is a growing interest in identifying chemopreventive agents against IBD-associated CRC. Commonly used in the treatment of UC, 5-aminosalicylates have antimicrobial and anticarcinogenic properties that might have a role in the chemoprevention of CRC via the inhibition or modulation of carcinogenic gut microbiota and potentially of biofilm formation. Whether biologics and other IBD-targeted therapies can decrease the progression towards dysplasia and CRC, via mechanisms independent of inflammation, is still unknown. Further research is warranted to identify potential new microbial targets in therapy for chemoprevention of dysplasia and CRC in IBD.

Gut bacteria: an etiological agent in human pathological conditions

Through complex interactions with the host's immune and physiological systems, gut bacteria play a critical role as etiological agents in a variety of human diseases, having an impact that extends beyond their mere presence and affects the onset, progression, and severity of the disease. Gaining a comprehensive understanding of these microbial interactions is crucial to improving our understanding of disease pathogenesis and creating tailored treatment methods. Correcting microbial imbalances may open new avenues for disease prevention and treatment approaches, according to preliminary data. The gut microbiota exerts an integral part in the pathogenesis of numerous health conditions, including metabolic, neurological, renal, cardiovascular, and gastrointestinal problems as well as COVID-19, according to recent studies. The crucial significance of the microbiome in disease pathogenesis is highlighted by this role, which is comparable to that of hereditary variables. This review investigates the etiological contributions of the gut microbiome to human diseases, its interactions with the host, and the development of prospective therapeutic approaches. To fully harness the benefits of gut microbiome dynamics for improving human health, future research should address existing methodological challenges and deepen our knowledge of microbial interactions.

Development and Validation of the MAST ISOPLEX®VTEC Kit for Simultaneous Detection of Shiga Toxin/Verotoxin 1 and 2 (stx1/vt1 and stx2/vt2) with Inhibition Control (IC) in a Rapid Loop-Mediated Isothermal Amplification (LAMP) Multiplex Assay

Loop-mediated isothermal amplification (LAMP) is a cost-effective, rapid, and highly specific method of replicating nucleic acids. Adding multiple targets into a single LAMP assay to create a multiplex format is highly desirable for clinical applications but has been challenging due to a need to develop specific detection techniques and strict primer design criteria. This study describes the evaluation of a rapid triplex LAMP assay, MAST ISOPLEX®VTEC, for the simultaneous detection of Shiga toxin/verotoxin 1 and 2 (stx1/vt1 and stx2/vt2) genes in verotoxigenic Escherichia coli (E. coli) (VTEC) isolates with inhibition control (IC) synthetic DNA using a single fluorophore-oligonucleotide probe, MAST ISOPLEX®Probes, integrated into the primer set of each target. MAST ISOPLEX®Probes used in the MAST ISOPLEX®VTEC kit produce fluorescent signals as they integrate with reaction products specific to each target, allowing tracking of multiple amplifications in real time using a real-time analyzer. Initial validation on DNA extracts from fecal cultures and synthetic DNA sequences (gBlocks) showed that the MAST ISOPLEX®VTEC kit provides a method for sensitive simultaneous triplex detection in a single assay with a limit of detection (LOD) of less than 100 target copies/assay and 96% and 100% sensitivity and specificity, respectively.

Gut microbiome influences efficacy of Endostatin combined with PD-1 blockade against colorectal cancer

The combination of anti-angiogenic drugs and immune checkpoint inhibitors (ICIs) in the treatment of tumors is emerging as a way to improve ICIs-resistant tumor therapy. In addition, gut microbes (GMs) are involved in angiogenesis in the tumor microenvironment and are also associated with the antitumor function of immune checkpoint inhibitors. However, it is unclear whether gut microbes have a role in anti-tumor function in the combination of anti-angiogenic drugs and immune checkpoint inhibitors for cancer treatment. Endostatin, an angiogenesis inhibitor, has been widely used as an antiangiogenic therapy for cancer. We showed that combined therapy with an adenovirus encoding human endostatin, named Ad-E, and PD-1 blockade dramatically abrogated MC38 tumor growth. The structure of intestinal microbes in mice was changed after combination treatment. We found that the antitumor function of combination therapy was inhibited after the elimination of intestinal microbes. In mice with depleted microbiota, oral gavage of Bacteroides fragilis salvaged the antitumor effects of combination Ad-E and αPD-1 monoclonal antibody (mAb) to a certain extent. Further, Bacteroides fragilis could improve CD3+T cells, NK cells, and IFNγ+CD8+ T cells in the tumor microenvironment to inhibit tumor growth. Besides, Bacteroides fragilis might restore antitumor function by down-regulating isobutyric acid (IBA). Our results suggested that GMs may be involved in the combination of Ad-E and αPD-1 mAb for cancer treatment, which has oncological implications for tumor growth dynamics and cancer immune surveillance.

Immunomodulation aspects of gut microbiome-related interventional strategies in colorectal cancer

Colorectal cancer (CRC), the third most common cancer worldwide, develops mainly due to the accumulation of genetic and epigenetic changes over many years. Substantial evidence suggests that gut microbiota plays a significant role in the initiation, progression, and control of CRC, depending on the balance between beneficial and pathogenic microorganisms. Nonetheless, gut microbiota composition by regulating the host immune response may either promote or inhibit CRC. Thus, modification of gut microbiota potentially impacts clinical outcomes of immunotherapy. Previous studies have indicated that therapeutic strategies such as probiotics, prebiotics, and postbiotics enhance the intestinal immune system and improve the efficacy of immunotherapeutic agents, potentially serving as a complementary strategy in cancer immunotherapy. This review discusses the role of the gut microbiota in the onset and development of CRC in relation to the immune response. Additionally, we focus on the effect of strategies manipulating gut microbiome on the immune response and efficacy of immunotherapy against CRC. We demonstrate that manipulation of gut microbiome can enhance immune response and outcomes of immunotherapy through downregulating Treg cells and other immunosuppressive cells while improving the function of T cells within the tumor; however, further research, especially clinical trials, are needed to evaluate its efficacy in cancer treatment.

Targeting microbial pathogenic mechanisms as a novel therapeutic strategy in IBD

BACKGROUND

Current therapy for patients suffering from inflammatory bowel diseases (IBD) is focused on inflammatory mechanisms exclusively and not the dysbiotic microbiota, despite growing evidence implicating a role for intestinal microbes in disease.

MAIN BODY

Ongoing research into the intestinal microbiota of IBD patients, using new technologies and/or deeper application of existing ones, has identified a number of microorganisms whose properties and behaviors warrant consideration as causative factors in disease. Such studies have implicated both bacteria and fungi in the pathogenesis of disease. Some of these organisms manifest mechanisms that should be amenable to therapeutic intervention via either conventional or novel drug discovery platforms. Of particular note is a deeper characterization of microbial derived proteases and their destructive potential.

CONCLUSION

Given the steady progress on the mechanistic role of the microbiota in inflammatory diseases, it is reasonable to anticipate a future in which therapeutics targeting microbial derived pathogenic factors play an important role in improving the lives of IBD patients.

Microbiota-associated mechanisms in colorectal cancer

Colorectal cancer (CRC) is one of the most common cancers worldwide, ranking third in terms of incidence and second as a cause of cancer-related death. There is growing scientific evidence that the gut microbiota plays a key role in the initiation and development of CRC. Specific bacterial species and complex microbial communities contribute directly to CRC pathogenesis by promoting the neoplastic transformation of intestinal epithelial cells or indirectly through their interaction with the host immune system. As a result, a protumoural and immunosuppressive environment is created conducive to CRC development. On the other hand, certain bacteria in the gut microbiota contribute to protection against CRC. In this chapter, we analysed the relationship of the gut microbiota to CRC and the associations identified with specific bacteria. Microbiota plays a key role in CRC through various mechanisms, such as increased intestinal permeability, inflammation and immune system dysregulation, biofilm formation, genotoxin production, virulence factors and oxidative stress. Exploring the interaction between gut microbiota and tumourigenesis is essential for developing innovative therapeutic approaches in the fight against CRC.

Research progress on the correlation between intestinal flora and colorectal cancer

Colorectal cancer (CRC) is one of the most common gastrointestinal malignancies in the world. With the rapid pace of life and changes in diet structure, the incidence and mortality of CRC increase year by year posing a serious threat to human health. As the most complex and largest microecosystem in the human body, intestinal microecology is closely related to CRC. It is an important factor that affects and participates in the occurrence and development of CRC. Advances in next-generation sequencing technology and metagenomics have provided new insights into the ecology of gut microbes. It also helps to link intestinal flora with CRC, and the relationship between intestinal flora and CRC can be continuously understood from different levels. This paper summarizes the relationship between intestinal flora and CRC and its potential role in the diagnosis of CRC providing evidence for early screening and treatment of CRC.

Characteristics of gut microbiota and its correlation with hs-CRP and somatic symptoms in first-episode treatment-naive major depressive disorder

OBJECTIVE

Most patients with major depressive disorder (MDD) have somatic symptoms, but little studies pay attention in the microbial-inflammatory mechanisms of these somatic symptoms. Our study aimed to investigate alterations in gut microbiota and its correlation with inflammatory marker levels and somatic symptoms in first-episode treatment-naive MDD.

METHODS

Subjects contained 160 MDD patients and 101 healthy controls (HCs). MDD patients were divided into MDD with somatic symptoms group (MDDS) and MDD without somatic symptoms group (MDDN) based on Somatic Self-rating Scale (SSS). 16S ribosomal RNA sequencing were performed to analyze the composition of the fecal microbiota. The inflammatory factors were measured using enzyme linked immunosorbent assay (ELISA). Correlation among the altered gut microbiota, inflammatory factor and severity of clinical symptoms were analysized.

RESULTS

Relative to HCs, MDD patients had higher levels of high-sensitivity C-reactive protein (hs-CRP) as well as disordered α-diversity and β-diversity of gut microbiota. Linear discriminant effect size (LEfSe) analysis showed that MDD patients had higher proportions of Bifidobacterium, Blautia, Haemophilus and lower proportions of Bacteroides, Faecalibacterium, Roseburia, Dialister, Sutterella, Parabacteroides, Bordetella, and Phascolarctobacterium from the genus aspect. Furthermore, correlation analysis showed Bacteroides and Roseburia had negative correlations with the hs-CRP, HAMD-24, the total and factor scores of SSS in all participants. Further, compared with MDDN, the Pielous evenness was higher in MDDS. Random Forest (RF) analysis showed 20 most important genera discriminating MDD-S and MDDN, HCs. The ROC analysis showed that the AUC was 0.90 and 0.81 combining these genera respectively.

CONCLUSION

Our study manifested MDD patients showed disordered gut microbiota and elevated hs-CRP levels, and altered gut microbiota was closely associated with hs-CRP, depressive symptoms, and somatic symptoms.

Natural products can be potential inhibitors of metalloproteinase II from Bacteroides fragilis to intervene colorectal cancer

Bacteroides fragilis, a gram negative and obligate anaerobe bacterium, is a member of normal gut microbiota and facilitates many essential roles being performed in human body in normal circumstances specifically in Gastrointestinal or GI tract. Sometimes, due to genetics, epigenetics, and environmental factors, Bacteroides fragilis and their protein(s) start interacting with intestinal epithelium thus damaging the lining leading to colorectal cancers (CRC). To identify these protein(s), we incorporated a novel subtractive proteomics approach in the study. Metalloproteinase II (MPII), a Bacteroides fragilis toxin (bft), was investigated for its virulence and unique pathways to demonstrate its specificity and uniqueness in pathogenicity followed by molecular docking against a set of small drug-like natural molecules to discover potential inhibitors against the toxin. All these identified inhibitor-like molecules were analyzed for their ADMET calculations and detailed physiochemical properties to predict their druggability, GI absorption, blood brain barrier and skin permeation, and others. Resultantly, a total of ten compounds with the least binding energies were obtained and were subjected to protein-compound interaction analysis. Interaction analysis revealed the most common ligand-interacting residues in MPII are His 345, Glu 346, His 339, Gly 310, Tyr 341, Pro 340, Asp 187, Phe 309, Lys 307, Ile 185, Thr 308, and Pro 184. Therefore, top three compounds complexed with MPII having best binding energies were selected in order to analyze their trajectories. RMSD, RMSF, Rg and MMPBSA analysis revealed that all compounds showed good binding and keeping the complex stable and compact throughout the simulation time in addition to all properties and qualities of being a potential inhibitor against MPII.

Pathogenic Bacteroides fragilis strains can emerge from gut-resident commensals

Bacteroides fragilis is a prominent member of the human gut microbiota, playing crucial roles in maintaining gut homeostasis and host health. Although it primarily functions as a beneficial commensal, B. fragilis can become pathogenic. To determine the genetic basis of its duality, we conducted a comparative genomic analysis of 813 B. fragilis strains, representing both commensal and pathogenic origins. Our findings reveal that pathogenic strains emerge across diverse phylogenetic lineages, due in part to rapid gene exchange and the adaptability of the accessory genome. We identified 16 phylogenetic groups, differentiated by genes associated with capsule composition, interspecies competition, and host interactions. A microbial genome-wide association study identified 44 genes linked to extra-intestinal survival and pathogenicity. These findings reveal how genomic diversity within commensal species can lead to the emergence of pathogenic traits, broadening our understanding of microbial evolution in the gut.

Post-stroke cognitive impairment: exploring molecular mechanisms and omics biomarkers for early identification and intervention

Post-stroke cognitive impairment (PSCI) is a major stroke consequence that has a severe impact on patients' quality of life and survival rate. For this reason, it is especially crucial to identify and intervene early in high-risk groups during the acute phase of stroke. Currently, there are no reliable and efficient techniques for the early diagnosis, appropriate evaluation, or prognostication of PSCI. Instead, plenty of biomarkers in stroke patients have progressively been linked to cognitive impairment in recent years. High-throughput omics techniques that generate large amounts of data and process it to a high quality have been used to screen and identify biomarkers of PSCI in order to investigate the molecular mechanisms of the disease. These techniques include metabolomics, which explores dynamic changes in the organism, gut microbiomics, which studies host-microbe interactions, genomics, which elucidates deeper disease mechanisms, transcriptomics and proteomics, which describe gene expression and regulation. We looked through electronic databases like PubMed, the Cochrane Library, Embase, Web of Science, and common databases for each omics to find biomarkers that might be connected to the pathophysiology of PSCI. As all, we found 34 studies: 14 in the field of metabolomics, 5 in the field of gut microbiomics, 5 in the field of genomics, 4 in the field of transcriptomics, and 7 in the field of proteomics. We discovered that neuroinflammation, oxidative stress, and atherosclerosis may be the primary causes of PSCI development, and that metabolomics may play a role in the molecular mechanisms of PSCI. In this study, we summarized the existing issues across omics technologies and discuss the latest discoveries of PSCI biomarkers in the context of omics, with the goal of investigating the molecular causes of post-stroke cognitive impairment. We also discuss the potential therapeutic utility of omics platforms for PSCI mechanisms, diagnosis, and intervention in order to promote the area's advancement towards precision PSCI treatment.

The role of the microscopic world: Exploring the role and potential of intratumoral microbiota in cancer immunotherapy

Microorganisms, including bacteria, viruses, and fungi, coexist in the human body, forming a symbiotic microbiota that plays a vital role in human health and disease. Intratumoral microbial components have been discovered in various tumor tissues and are closely linked to the occurrence, progression, and treatment results of cancer. The intratumoral microbiota can enhance antitumor immunity through mechanisms such as activating the stimulator of interferon genes signaling pathway, stimulating T and NK cells, promoting the formation of TLS, and facilitating antigen presentation. Conversely, the intratumoral microbiota might suppress antitumor immune responses by increasing reactive oxygen species levels, creating an anti-inflammatory environment, inducing T cell inactivation, and enhancing immune suppression, thereby promoting cancer progression. The impact of intratumoral microbiota on antitumor immunity varies based on microbial composition, interactions with cancer cells, and the cancer's current state. A deep understanding of the complex interactions between intratumoral microbiota and antitumor immunity holds the potential to bring new therapeutic strategies and targets to cancer immunotherapy.

Friend or Foe: Exploring the Relationship between the Gut Microbiota and the Pathogenesis and Treatment of Digestive Cancers

Digestive cancers are among the leading causes of cancer death in the world. However, the mechanisms of cancer development and progression are not fully understood. Accumulating evidence in recent years pointing to the bidirectional interactions between gut dysbiosis and the development of a specific type of gastrointestinal cancer is shedding light on the importance of this "unseen organ"-the microbiota. This review focuses on the local role of the gut microbiota imbalance in different digestive tract organs and annexes related to the carcinogenic mechanisms. Microbiota modulation, either by probiotic administration or by dietary changes, plays an important role in the future therapies of various digestive cancers.

Dissecting Gut-Microbial Community Interactions using a Gut Microbiome-on-a-Chip

While the human gut microbiota has a significant impact on gut health and disease, understanding of the roles of gut microbes, interactions, and collective impact of gut microbes on various aspects of human gut health is limited by the lack of suitable in vitro model system that can accurately replicate gut-like environment and enable the close visualization on causal and mechanistic relationships between microbial constitutents and the gut. , In this study, we present a scalable Gut Microbiome-on-a-Chip (GMoC) with great imaging capability and scalability, providing a physiologically relevant dynamic gut-microbes interfaces. This chip features a reproducible 3D stratified gut epithelium derived from Caco-2 cells (µGut), mimicking key intestinal architecture, functions, and cellular complexity, providing a physiolocially relevant gut environment for microbes residing in the gut. Incorporating tumorigenic bacteria, enterotoxigenic Bacteroides fragilis (ETBF), into the GMoC enable the observation of pathogenic behaviors of ETBF, leading to µGut disruption and pro-tumorigenic signaling activations. Pre-treating the µGut with a beneficial gut microbe Lactobacillus spp., effectively prevent ETBF-mediated gut pathogenesis, preserving the healthy state of the µGut through competition-mediated colonization resistance. The GMoC holds potential as a valuable tool for exploring unknown roles of gut microbes in microbe-induced pathogenesis and microbe-based therapeutic development.

Unveiling intratumoral microbiota: An emerging force for colorectal cancer diagnosis and therapy

Microbes, including bacteria, viruses, fungi, and other eukaryotic organisms, are commonly present in multiple organs of the human body and contribute significantly to both physiological and pathological processes. Nowadays, the development of sequencing technology has revealed the presence and composition of the intratumoral microbiota, which includes Fusobacterium, Bifidobacteria, and Bacteroides, and has shed light on the significant involvement in the progression of colorectal cancer (CRC). Here, we summarized the current understanding of the intratumoral microbiota in CRC and outline the potential translational and clinical applications in the diagnosis, prevention, and treatment of CRC. We focused on reviewing the development of microbial therapies targeting the intratumoral microbiota to improve the efficacy and safety of chemotherapy and immunotherapy for CRC and to identify biomarkers for the diagnosis and prognosis of CRC. Finally, we emphasized the obstacles and potential solutions to translating the knowledge of the intratumoral microbiota into clinical practice.

Overview of Bacterial Protein Toxins from Pathogenic Bacteria: Mode of Action and Insights into Evolution

Bacterial protein toxins are secreted by certain bacteria and are responsible for mild to severe diseases in humans and animals. They are among the most potent molecules known, which are active at very low concentrations. Bacterial protein toxins exhibit a wide diversity based on size, structure, and mode of action. Upon recognition of a cell surface receptor (protein, glycoprotein, and glycolipid), they are active either at the cell surface (signal transduction, membrane damage by pore formation, or hydrolysis of membrane compound(s)) or intracellularly. Various bacterial protein toxins have the ability to enter cells, most often using an endocytosis mechanism, and to deliver the effector domain into the cytosol, where it interacts with an intracellular target(s). According to the nature of the intracellular target(s) and type of modification, various cellular effects are induced (cell death, homeostasis modification, cytoskeleton alteration, blockade of exocytosis, etc.). The various modes of action of bacterial protein toxins are illustrated with representative examples. Insights in toxin evolution are discussed.

The microbial landscape of colorectal cancer

Colorectal cancer (CRC) is a substantial source of global morbidity and mortality in dire need of improved prevention and treatment strategies. As our understanding of CRC grows, it is becoming increasingly evident that the gut microbiota, consisting of trillions of microorganisms in direct interface with the colon, plays a substantial role in CRC development and progression. Understanding the roles that individual microorganisms and complex microbial communities play in CRC pathogenesis, along with their attendant mechanisms, will help yield novel preventive and therapeutic interventions for CRC. In this Review, we discuss recent evidence concerning global perturbations of the gut microbiota in CRC, associations of specific microorganisms with CRC, the underlying mechanisms by which microorganisms potentially drive CRC development and the roles of complex microbial communities in CRC pathogenesis. While our understanding of the relationship between the microbiota and CRC has improved in recent years, our findings highlight substantial gaps in current research that need to be filled before this knowledge can be used to the benefit of patients.

The microbiota and renal cell carcinoma

Renal cell carcinoma (RCC) accounts for about 2% of cancer diagnoses and deaths worldwide. Recent studies emphasized the critical involvement of microbial populations in RCC from oncogenesis, tumor growth, and response to anticancer therapy. Microorganisms have been shown to be involved in various renal physiological and pathological processes by influencing the immune system function, metabolism of the host and pharmaceutical reactions. These findings have extended our understanding and provided more possibilities for the diagnostic or therapeutic development of microbiota, which could function as screening, prognostic, and predictive biomarkers, or be manipulated to prevent RCC progression, boost anticancer drug efficacy and lessen the side effects of therapy. This review aims to present an overview of the roles of microbiota in RCC, including pertinent mechanisms in microbiota-related carcinogenesis, the potential use of the microbiota as RCC biomarkers, and the possibility of modifying the microbiota for RCC prevention or treatment. According to these scientific findings, the clinical translation of microbiota is expected to improve the diagnosis and treatment of RCC.

Multi-omics analysis revealed the regulation mode of intratumor microorganisms and microbial signatures in gastrointestinal cancer

OBJECTIVE

Gastrointestinal cancer is one of the most common malignant tumors in the world, and its incidence rate is always high. In recent years, research has shown that microorganisms may play a broad role in the diagnosis, pathogenesis, and treatment of cancer.

METHODS

In this study, samples were first classified according to the microbial expression data of Gastrointestinal cancer, followed by functional enrichment and Immunoassay. In order to better understand the role of intratumor microorganisms in the prognosis, we screened gene signatures and constructed risk model through univariate cox and lasso regression and multivariable cox, then screened microbial signatures using zero-inflated model regression model and constructed risk index (RI), and finally predicted the immunotherapeutic effect of the risk model.

RESULTS

The results indicate that the composition of tumor microorganisms in the C3 subtype is closely related to tumor angiogenesis, and there is a significant difference in the proportion of innate and acquired immune cells between the C2 and C1 subtypes, as well as differences in the physiological functions of immune cells. There are significant differences in the expression of microbial signatures between high and low risk subtypes, with 9 microbial signatures upregulated in high risk subtypes and 15 microbial signatures upregulated in low risk subtypes. These microbial signatures were significantly correlated with the prognosis of patients. The results of immunotherapy indicate that immunotherapy for high-risk subtypes is more effective.

CONCLUSION

Overall, we analyze from the perspective of microorganisms within tumors, pointing out new directions for the diagnosis and treatment of cancer.

Gut microbiota in pathophysiology, diagnosis, and therapeutics of inflammatory bowel disease

Inflammatory bowel disease (IBD) is a multifactorial disease, which is thought to be an interplay between genetic, environment, microbiota, and immune-mediated factors. Dysbiosis in the gut microbial composition, caused by antibiotics and diet, is closely related to the initiation and progression of IBD. Differences in gut microbiota composition between IBD patients and healthy individuals have been found, with reduced biodiversity of commensal microbes and colonization of opportunistic microbes in IBD patients. Gut microbiota can, therefore, potentially be used for diagnosing and prognosticating IBD, and predicting its treatment response. Currently, there are no curative therapies for IBD. Microbiota-based interventions, including probiotics, prebiotics, synbiotics, and fecal microbiota transplantation, have been recognized as promising therapeutic strategies. Clinical studies and studies done in animal models have provided sufficient evidence that microbiota-based interventions may improve inflammation, the remission rate, and microscopic aspects of IBD. Further studies are required to better understand the mechanisms of action of such interventions. This will help in enhancing their effectiveness and developing personalized therapies. The present review summarizes the relationship between gut microbiota and IBD immunopathogenesis. It also discusses the use of gut microbiota as a noninvasive biomarker and potential therapeutic option.

Microbial Biomarkers in Liquid Biopsy for Cancer: An Overview and Future Directions

In recent years, the relationship between microbes and tumors has led to a new wave of scholarly pursuits. Due to the growing awareness of the importance of microbiota, including those within tumors, for cancer onset, progression, metastasis, and treatment, researchers have come to understand that microbiota and the tumor microenvironment together form a dynamic and complex ecosystem. Liquid biopsy technology, a non-invasive and easily repeatable method for sample collection, combined with emerging multi-omics techniques, allows for a more comprehensive and in-depth exploration of microbial signals and characteristics in bodily fluids. Microbial biomarkers hold immense potential in the early diagnosis, treatment stratification, and prognosis prediction of cancer. In this review, we describe the significant potential of microbial biomarkers in liquid biopsy for clinical applications in cancer, including early diagnosis, predicting treatment responses, and prognosis. Moreover, we discuss current limitations and potential solutions related to microbial biomarkers. This review aims to provide an overview and future directions of microbial biomarkers in liquid biopsy for cancer clinical practice.

Antibody response to enterotoxigenic Bacteroides fragilis of Filipino colorectal cancer patients

Background

Several species of the gut microbiota have been implicated in colorectal cancer (CRC) development. The anaerobic bacterium enterotoxigenic Bacteroides fragilis (ETBF), has been identified to produce fragilysin, a toxin known to cleave E-cadherin, thereby leading to carcinogenesis.

Objective

To determine the antibody response of CRC patients against ETBF to ascertain whether significant difference exists or whether antibody response is related to tumor grade and tumor stage.

Methods

Informed consent was obtained from histologically confirmed CRC casesand their age- and sex-matched clinically healthy controls. Plasma samples from the participants were subjected to in-house enzyme-linked immunosorbent assay (ELISA) to determine their antibody levels.

Results

Using ETBF total protein as coating antigen, 38/39 (97%) CRC cases and 36/39 (92%) controls showed anti-ETBF IgG above cut-off, while all (100%) CRC cases and 36/39 (92%) controls had anti-ETBF IgA levels above cut-off. With culture broth as coating antigen, all (100%) CRC cases and 37/39 (95%) controls had anti-ETBF IgG levels above cut-off. For anti-ETBF IgA, all (100%) cases and controls had levels above cut-off. Statistical analysis reveals no significant difference (P > 0.05) on the number of CRC cases and controls with IgG and IgA antibody levels above cut-off value. Also, there's no significant difference (P > 0.05) in the mean anti-ETBF antibody levels of cases who were at different tumor grade (well differentiated and moderately and poorly differentiated) and tumor stage (early and advanced).

Conclusions

These results suggest that Filipino CRC cases and their clinically healthy matched controls exhibit antibody responses against ETBF.

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.

Using 16S rDNA and metagenomic sequencing technology to analyze the fecal microbiome of children with avoidant/restrictive food intake disorder

To investigate the gut microbiota distribution and its functions in children with avoidant/restrictive food intake disorder (ARFID). A total of 135 children were enrolled in the study, including 102 children with ARFID and 33 healthy children. Fecal samples were analyzed to explore differences in gut microbiota composition and diversity and functional differences between the ARFID and healthy control (HC) groups via 16S rDNA and metagenomic sequencing. The gut microbiota composition and diversity in children with ARFID were different from those in heathy children, but there is no difference in the composition and diversity of gut microbiota between children at the age of 3-6 and 7-12 with ARFID. At the phylum level, the most abundant microbes in the two groups identified by 16S rDNA and metagenomic sequencing were the same. At the genus level, the abundance of Bacteroides was higher in the ARFID group (P > 0.05); however, different from the result of 16SrDNA sequencing, metagenomic sequencing showed that the abundance of Bacteroides in the ARFID group was significantly higher than that in the HC group (P = 0.041). At the species level, Escherichia coli, Streptococcus thermophilus and Lachnospira eligens were the most abundant taxa in the ARFID group, and Prevotella copri, Bifidobacterium pseudocatenulatum, and Ruminococcus gnavus were the top three microbial taxa in the HC group; there were no statistically significant differences between the abundance of these microbial taxa in the two groups. LefSe analysis indicated a greater abundance of the order Enterobacterales and its corresponding family Enterobacteriaceae, the family Bacteroidaceae and corresponding genus Bacteroides, the species Bacteroides vulgatus in ARFID group, while the abundance of the phylum Actinobacteriota and its corresponding class Actinobacteria , the order Bifidobacteriales and corresponding family Bifidobacteriaceae, the genus Bifidobacterium were enriched in the HC group. There were no statistically significant differences in the Chao1, Shannon and Simpson indices between the Y1 and Y2 groups (P = 0.1, P = 0.06, P = 0.06). At the phylum level, Bacillota, Bacteroidota, Proteobacteria and Actinobacteriota were the most abundant taxa in both groups, but there were no statistically significant differences among the abundance of these bacteria (P = 0.958, P = 0.456, P = 0.473, P = 0.065). At the genus level, Faecalibacterium was more abundant in the Y2 group than in the Y1 group, and the difference was statistically significant (P = 0.037). The KEGG annotation results showed no significant difference in gut microbiota function between children with ARFID and healthy children; however, GT26 was significantly enriched in children with ARFID based on the CAZy database. The most abundant antibiotic resistance genes in the ARFID group were the vanT, tetQ, adeF, ermF genes, and the abundance of macrolide resistance genes in the ARFID group was significantly higher than that in the HC group (P = 0.041). Compared with healthy children, children with ARFID have a different distribution of the gut microbiota and functional genes. This indicates that the gut microbiome might play an important role in the pathogenesis of ARFID.Clinical trial registration: ChiCTR2300074759.

Genomic analyses of Bacteroides fragilis: subdivisions I and II represent distinct species

Introduction. Bacteroides fragilis is a Gram-negative anaerobe that is a member of the human gastrointestinal microbiota and is frequently found as an extra-intestinal opportunistic pathogen. B. fragilis comprises two distinct groups - divisions I and II - characterized by the presence/absence of genes [cepA and ccrA (cfiA), respectively] that confer resistance to β-lactam antibiotics by either serine or metallo-β-lactamase production. No large-scale analyses of publicly available B. fragilis sequence data have been undertaken, and the resistome of the species remains poorly defined.Hypothesis/Gap Statement. Reclassification of divisions I and II B. fragilis as two distinct species has been proposed but additional evidence is required.Aims. To investigate the genomic diversity of GenBank B. fragilis genomes and establish the prevalence of division I and II strains among publicly available B. fragilis genomes, and to generate further evidence to demonstrate that B. fragilis division I and II strains represent distinct genomospecies.Methodology. High-quality (n=377) genomes listed as B. fragilis in GenBank were included in pangenome and functional analyses. Genome data were also subject to resistome profiling using The Comprehensive Antibiotic Resistance Database.Results. Average nucleotide identity and phylogenetic analyses showed B. fragilis divisions I and II represent distinct species: B. fragilis sensu stricto (n=275 genomes) and B. fragilis A (n=102 genomes; Genome Taxonomy Database designation), respectively. Exploration of the pangenome of B. fragilis sensu stricto and B. fragilis A revealed separation of the two species at the core and accessory gene levels.Conclusion. The findings indicate that B. fragilis A, previously referred to as division II B. fragilis, is an individual species and distinct from B. fragilis sensu stricto. The B. fragilis pangenome analysis supported previous genomic, phylogenetic and resistome screening analyses collectively reinforcing that divisions I and II are two separate species. In addition, it was confirmed that differences in the accessory genes of B. fragilis divisions I and II are primarily associated with carbohydrate metabolism and suggest that differences other than antimicrobial resistance could also be used to distinguish between these two species.