Integrating multi-omics data to reveal the host-microbiota interactome in inflammatory bowel disease

Numerous studies have accelerated the knowledge expansion on the role of gut microbiota in inflammatory bowel disease (IBD). However, the precise mechanisms behind host-microbe cross-talk remain largely undefined, due to the complexity of the human intestinal ecosystem and multiple external factors. In this review, we introduce the interactome concept to systematically summarize how intestinal dysbiosis is involved in IBD pathogenesis in terms of microbial composition, functionality, genomic structure, transcriptional activity, and downstream proteins and metabolites. Meanwhile, this review also aims to present an updated overview of the relevant mechanisms, high-throughput multi-omics methodologies, different types of multi-omics cohort resources, and computational methods used to understand host-microbiota interactions in the context of IBD. Finally, we discuss the challenges pertaining to the integration of multi-omics data in order to reveal host-microbiota cross-talk and offer insights into relevant future research directions.

Acupuncture ameliorates inflammation by regulating gut microbiota in acute ischemic stroke

Background

Acute ischemic stroke(AIS) is a major life-threatening disease.Some studies have found that AIS may be related to gut flora and immune responses. Acupuncture is used widely in the treatment of AIS. However its relevant mechanism is unclear enough. Therefore, in this study, we wanted to confirm that acupuncture was treating AIS through gut flora and immune response.

Methods

We randomly divided 18 rats into equal three groups, including Sham, Middle Cerebral Artery Occlusion (MCAO) and Acupuncture.Rats in the Acupuncture group for a continuous period of three days after surgery. Neurological deficits were assessed using Longa's method, and detection of intestinal flora by 16s rRNA gene sequencing, determination of SCFAs by gas chromatography-mass spectrometry, detection of HDAC and inflammatory cytokines by elisa assay, detection of Th17 and Treg cells by flow cytometry and, observation of pathological and morphological changes in brain and colon tissues by HE staining.

Results

Acupuncture improved the degree of impaired neurological function in MCAO rats and regulated the type and abundance of intestinal bacteria, increased SCFAs of MCAO rats, decreased HDAC1 and HDAC2, modulated the Th17/Treg imbalance, reduced the level of inflammatory factors in the peripheral blood and altered the pathology of the intestine and brain.

Conclusion

Acupuncture repaired neurologic deficits after AIS and may be associated with an immune-inflammatory response mediated by gut microbiota.

Efficacy of melatonin for treatment and prevention of neonatal necrotizing enterocolitis: a systematic review

The purpose of this study was to systematically review the available literature evaluating the use of melatonin for preventing and treating neonatal necrotizing enterocolitis (NEC). A systematic review of studies examining the effect of melatonin on neonatal NEC was conducted. The databases of Medline, Scopus, WOS, Embase, and Cochrane Central Register of Controlled Trials were searched for relevant studies. For risk of bias and applicability, The ROB2 tool was used for randomized controlled trials, and the ROBINS-I tool was used for non-randomized controlled trials. Three studies, comprising 106 preterm neonates, were included in the review, whose mean gestational ages ranged from 31.8 to 33.53 weeks. Melatonin doses varied among the studies. A randomized, double-blind, placebo-controlled study revealed that early administration of melatonin in preterm newborns resulted in a decrease in lipid peroxidation during the initial days of life. Two studies evaluated the role of melatonin in NEC. Both reported significant clinical and laboratory improvements in the melatonin groups, including reduced abdominal distension, metabolic acidosis, thrombocytopenia, hyponatremia, and lower mortality rates compared to control groups. This systematic review suggests that melatonin may be a potential therapeutic approach for NEC in preterm infants. However, further RCTS are needed to establish its therapeutic or preventive role.

Challenges and advances in the management of inflammation in atherosclerosis

INTRODUCTION

Atherosclerosis, traditionally considered a lipid-related disease, is now understood as a chronic inflammatory condition with significant global health implications.

OBJECTIVES

This review aims to delve into the complex interactions among immune cells, cytokines, and the inflammatory cascade in atherosclerosis, shedding light on how these elements influence both the initiation and progression of the disease.

METHODS

This review draws on recent clinical research to elucidate the roles of key immune cells, macrophages, T cells, endothelial cells, and clonal hematopoiesis in atherosclerosis development. It focuses on how these cells and process contribute to disease initiation and progression, particularly through inflammation-driven processes that lead to plaque formation and stabilization. Macrophages ingest oxidized low-density lipoprotein (oxLDL), which partially converts to high-density lipoprotein (HDL) or accumulates as lipid droplets, forming foam cells crucial for plaque stability. Additionally, macrophages exhibit diverse phenotypes within plaques, with pro-inflammatory types predominating and others specializing in debris clearance at rupture sites. The involvement of CD4+ T and CD8+ T cells in these processes promotes inflammatory macrophage states, suppresses vascular smooth muscle cell proliferation, and enhances plaque instability.

RESULTS

The nuanced roles of macrophages, T cells, and the related immune cells within the atherosclerotic microenvironment are explored, revealing insights into the cellular and molecular pathways that fuel inflammation. This review also addresses recent advancements in imaging and biomarker technology that enhance our understanding of disease progression. Moreover, it points out the limitations of current treatment and highlights the potential of emerging anti-inflammatory strategies, including clinical trials for agents such as p38MAPK, tumor necrosis factor α (TNF-α), and IL-1β, their preliminary outcomes, and the promising effects of canakinumab, colchicine, and IL-6R antagonists.

CONCLUSION

This review explores cutting-edge anti-inflammatory interventions, their potential efficacy in preventing and alleviating atherosclerosis, and the role of nanotechnology in delivering drugs more effectively and safely.

Evolution of enteric viruses in the progression of colorectal cancer via the adenoma-carcinoma sequence pathway

The global incidence of colorectal cancer (CRC) is increasing. In the majority of CRC cases, colon cancer develops from alterations in the adenoma-carcinoma sequence pathway. Currently, there are few studies regarding the effects of enteric viruses on the adenoma-carcinoma sequence pathway, and subsequently, the progression and development of the CRC. Here, fecal and tissue samples from a normal control group, an adenomatous polyp group, and a colorectal adenocarcinoma group were collected to gain a deeper understanding of the variations in enteric viruses in CRC patients and to analyze their significance. With the progression of CRC from adenoma to adenocarcinoma, the number of DNA viruses in the virus-like particles (VLPs) of fecal and tissue samples gradually increased, and there were distinct differences in the composition of enteric viruses among the different groups. Multiple species correlation analysis revealed extensive interactions among viruses, bacteria, and fungi in fecal and tissue samples. Functional analysis also revealed that the functional pathways in fecal and tissue samples also underwent significant changes. In conclusion, the changes in the composition and function of enteric viruses in the progression of CRC via adenoma-carcinoma sequence pathway were analyzed in this study, and these changes hold certain importance for exploring the role of enteric viruses in the occurrence of this disease; however, their mode of action and specific mechanisms require further investigation.

Tumor-resident Malassezia can promote hepatocellular carcinoma development by downregulating bile acid synthesis and modulating tumor microenvironment

Bacterial dysbiosis coincides with the carcinogenesis in malignancies such as lung and colon cancer, and has recently been suggested to involve in the pathogenesis of hepatocellular carcinoma (HCC). However, the mycobiome has not yet been definitively linked to liver tumorigenesis. Here we showed that the microbiota composition of HCC tumors was distinct from that of the normal adjacent to tumor (NAT) on the basis of richness and beta-diversity indices. Specifically, the fungal community that infiltrated HCC tumors was markedly enriched for Malassezia spp. and genus Malassezia in tumors was substantially more abundant than that in NAT. We also discovered that the relative abundance of genus Malassezia was strongly correlated with the tumor microenvironment (TME) signatures, including stromal and immune components. In addition, tumor-resident Malassezia could inhibit bile acid synthesis by downregulating the expression level of CYP7 A1 and CYP27 A1. To improve clinical usability, we developed a set of Malassezia-related genes, called Malassezia.Sig, which could accurately predict patient survival. Collectively, our work shows that tumor-resident Malasseiza may promote HCC progression by downregulating bile acid synthesis and modulating the TME, although more studies are needed.

Microbiome and fragmentation pattern of blood cell-free DNA and fecal metagenome enhance colorectal cancer micro-dysbiosis and diagnosis analysis: a proof-of-concept study

Colorectal cancer (CRC) is the third most common cancer, and it can be prevented by performing early screening. As a hallmark of cancer, the human microbiome plays important roles in the occurrence and development of CRC. Recently, the blood microbiome has been proposed as an effective diagnostic tool for various diseases, yet its performance on CRC deserves further exploration. In this study, 133 human feces and 120 blood samples are collected, including healthy individuals, adenoma patients, and CRC patients. The blood cfDNA and fecal genome are subjected to shotgun metagenome sequencing. After removing human sequences, the microbial sequences in blood are analyzed. Based on the differential microbes and functions, random forest (RF) models are constructed for adenoma and CRC diagnosis. The results show that alterations of blood microbial signatures can be captured under low coverage (even at 3×). RF diagnostic models based on blood microbial markers achieve high area under the curve (AUC) values for adenoma patients (0.8849) and CRC patients (0.9824). When the fragmentation pattern is combined with microbial and KEGG markers, higher AUC values are obtained. Furthermore, compared to the blood microbiome, the fecal microbiome shows a different community composition, whereas their changes in KEGG pathways are similar. Pathogenic bacteria Fusobacterium nucleatum (F. nucleatum) in feces increased gradually from the healthy group to the adenoma and CRC groups. Additionally, F. nucleatum in feces and blood shows a positive correlation in CRC patients. Cumulatively, the integration of blood microbiome and fragmentation pattern is promising for CRC diagnosis.IMPORTANCEThe cell-free DNA of the human microbiome can enter the blood and can be used for cancer diagnosis, whereas its diagnostic potential in colorectal cancer and association with gut microbiome has not been explored. The microbial sequences in blood account for less than 1% of the total sequences. The blood microbial composition, KEGG functions, and fragmentation pattern are different among healthy individuals, adenoma patients, and CRC patients. Machine learning models based on these differential characteristics achieve high diagnostic accuracy, especially when they are integrated with fragmentation patterns. The great difference between fecal and blood microbiomes indicates that microbial sequences in blood may originate from various organs. Therefore, this study provides new insights into the community composition and functions of the blood microbiome of CRC and proposes an effective non-invasive diagnostic tool.

Causal effect of gut microbiota on the risk of cancer and potential mediation by inflammatory proteins

BACKGROUND

While growing evidence highlights the role of gut microbiota and inflammatory proteins in cancer, with cancer-related inflammation now considered the seventh hallmark of cancer, the direct causal relationships between specific microbiota, cancer, and the potential mediating effects of inflammatory proteins have not been fully established.

METHODS

We employed Mendelian randomization (MR) to assess the causal relationships between gut microbiota, inflammatory proteins, and eighteen distinct cancers using data from extensive genome-wide association studies (GWAS). The primary statistical method utilized was inverse variance weighting (IVW). We also investigated whether inflammatory proteins could mediate the effects of gut microbiota on cancer development.

RESULTS

Our findings revealed 42 positive and 49 inverse causal impacts of gut microbiota on cancer risk (P < 0.05). Additionally, we identified 32 positive and 28 inverse causal relationships between inflammatory proteins and cancer risk. Moreover, genus Collinsella decreased the risk of lung cancer by decreasing levels of T-cell surface glycoprotein CD5 (mediating effect = 16.667%), while genus Ruminococcaceae UCG005 increased the risk of mesothelioma by increasing levels of CCL4 (mediating effect = 5.134%).

CONCLUSIONS

Our study provides evidence for a causal association between gut microbiota, inflammatory proteins, and eighteen different cancer types. Notably, the T-cell surface glycoprotein CD5 and CCL4 were identified as mediators linking the genus Collinsella with lung cancer and the genus Ruminococcaceae UCG005 with mesothelioma, respectively.

Echinacoside alleviates type 2 diabetes mellitus through inhibiting hepatic gluconeogenesis via gut bacterial-fungal trans-kingdom network reconstruction

BACKGROUND

Echinacoside (ECH), a natural phenylethanoid glycoside, has demonstrated protective effects against type 2 diabetes mellitus (T2DM). However, the mechanism underlying the low bioavailability yet advantageous anti-diabetic of ECH remains unresolved.

PURPOSE

To elucidate the mechanism of ECH against T2DM through gut microbiota-mediated host metabolism for the first time.

STUDY DESIGN AND METHODS

A T2DM mouse model was established using a high-fat diet in combination with streptozotocin injection. The therapeutic effects of ECH against T2DM were evaluated by measuring fasting blood glucose (FBG), insulin resistance, glucose intolerance, blood lipids and organ damage in mice. Fecal 16S rRNA and ITS sequencing techniques were employed to characterize the composition of gut microbiota, followed by analysis of bacterial-fungal trans-kingdom network. Metabolomics was conducted to assess the ECH-induced metabolite profile alterations. Additionally, the predicted mechanism of ECH on T2DM was investigated through measuring the hepatic gluconeogenesis markers and inflammation by western blotting, immunohistochemistry, enzymatic assays and antimicrobial mixture (ABX) experiments.

RESULTS

ECH exhibited significant protective effects against T2DM, as evidenced by reductions in FBG and fasting insulin levels, improvements in glucose and insulin tolerance, attenuations of hyperlipidemia, and alleviation of liver, kidney, and colon damage in T2DM mice. Furthermore, ECH modulated gut microbiota by decreasing the abundances of conditional pathogenic intestinal bacteria (Klebsiella and Escherichia-Shigella) and fungi (Debarymoyces), while increasing beneficial bacteria (Lactobacillus) and fungi (Wallemia and Penicillium). Moreover, ECH could restore the disrupted trans-kingdom network between gut fungi and bacteria, thereby suppressing the inflammation-mediated hepatic gluconeogenesis via downregulation of FBP1, PCK1 and G6PC expression. Correspondingly, ABX experiments indicated that once the regulatory function of gut microbiota imbalance was blocked, the anti-T2DM effects of ECH were weakened, accompanied by a failure to improve the levels of inflammation and key gluconeogenic markers in T2DM mice.

CONCLUSION

This study presents novel evidence indicating that ECH alleviates T2DM through inhibiting hepatic gluconeogenesis via gut bacterial-fungal trans-kingdom network reconstruction. These findings suggest that ECH may serve as a promising therapeutic strategy for T2DM management, providing new insights for the prevention and treatment of clinical diabetes and its complications.

Optimizing anti-PD-1/PD-L1 therapy efficacy and fecal microbiota transplantation donor selection through gut mycobiome-based enterotype

Immunotherapy has revolutionized cancer treatment, but response variability remains a challenge. The gut microbiome's role in therapeutic efficacy is well established, but the impact of the gut mycobiome is less understood. Using unsupervised clustering, we identify two gut mycobiome-based enterotypes, favorable type and unfavorable type, characterized by distinct microbial compositions linked to immunotherapy outcomes. Favorable-type enterotypes exhibit higher fungal and bacterial alpha diversity, enriched butyrate-producing bacteria, and metabolic pathways related to butyric acid and sugar/starch metabolism. External validation confirms their predictive value in assessing immunotherapy efficacy. Multi-omics analysis reveals increased CD8+ T cell infiltration in the tumor microenvironment of favorable-type patients. Fecal microbiota transplantation (FMT) from favorable-type donors enhances anti-PD-1 sensitivity, promotes CD8+ T cell infiltration, and boosts butyrate production in vivo. These findings highlight the gut mycobiome's role in immunotherapy response and support FMT from favorable-type donors as a potential strategy for improving treatment outcomes and patient stratification.

Gut microbiota plays a key role in the development of colorectal cancer

This letter addresses the recently published manuscript by Darnindro et al, which investigates the diversity and composition of colonic mucosal microbiota in Indonesian patients with and without colorectal cancer (CRC). Although the analysis revealed no statistically significant differences in alpha diversity between the CRC and non-CRC groups, the authors identified notable distinctions in the composition and diversity of colonic mucosal microbiota among patients with CRC compared to those without. At the genus level, a statistically significant difference in microbiota composition was documented between the two cohorts. Specifically, the genera Bacteroides, Campylobacter, Peptostreptococcus, and Parvimonas were found to be elevated in individuals with CRC, while Faecalibacterium, Haemophilus, and Phocaeicola were more prevalent in the non- CRC group.

Metabolomics Insights into Gut Microbiota and Functional Constipation

Background: The composition and metabolic activity of the gut microbiota play a crucial role in various health conditions, including the occurrence and development of chronic constipation. Recent metabolomic advances reveal that gut microbiota-derived metabolites-such as SCFAs, bile acids, neurotransmitters, and microbial gases-play critical roles in regulating intestinal function. Methods: We systematically analyzed the current literature on microbial metabolomics in chronic constipation. This review consolidates findings from high-throughput metabolomic techniques (GC-MS, LC-MS, NMR) comparing metabolic profiles of constipated patients with healthy individuals. It also examines diagnostic improvements and personalized treatments, including fecal microbiota transplantation and neuromodulation, guided by these metabolomic insights. Results: This review shows that reduced SCFA levels impair intestinal motility and promote inflammation. An altered bile acid metabolism-with decreased secondary bile acids like deoxycholic acid-disrupts receptor-mediated signaling, further affecting motility. Additionally, imbalances in amino acid metabolism and neurotransmitter production contribute to neuromuscular dysfunction, while variations in microbial gas production (e.g., methane vs. hydrogen) further modulate gut transit. Conclusions: Integrating metabolomics with gut microbiota research clarifies how specific microbial metabolites regulate gut function. These insights offer promising directions for precision diagnostics and targeted therapies to restore microbial balance and improve intestinal motility.

Refining microbiome diversity analysis by concatenating and integrating dual 16S rRNA amplicon reads

Understanding the role of human gut microbiota in health and disease requires insights into its taxonomic composition and functional capabilities. This study evaluates whether concatenating paired-end reads enhances data output for gut microbiome analysis compared to the merging approach across various regions of the 16S rRNA gene. We assessed this approach in both mock communities and Korean cohorts with or without ulcerative colitis. Our results indicate that using the direct joining method for the V1-V3 or V6-V8 regions improves taxonomic resolution compared to merging paired-end reads (ME) in post-sequencing data. While predicting microbial function based on 16S rRNA sequencing has inherent limitations, integrating sequencing reads from both the V1-V3 and V6-V8 regions enhanced functional predictions. This was confirmed by whole metagenome sequencing (WMS) of Korean cohorts, where our approach improved taxa detection that was lost using the ME method. Thus, we propose that the integrated dual 16S rRNA sequencing technique serves as a valuable tool for microbiome research by bridging the gap between amplicon sequencing and WMS.

Intratumoral mycobiome heterogeneity influences the tumor microenvironment and immunotherapy outcomes in renal cell carcinoma

The intratumoral mycobiome plays a crucial role in the tumor microenvironment, but its impact on renal cell carcinoma (RCC) remains unclear. We collected and quantitatively profiled the intratumoral mycobiome data from 1044 patients with RCC across four international cohorts, of which 466 patients received immunotherapy. Patients were stratified into mycobiota ecology-depauperate and mycobiota ecology-flourishing (MEF) groups based on fungal abundance. The MEF group had worse prognosis, higher fungal diversity, down-regulated lipid catabolism, and exhausted CD8+ T cells. We developed the intratumoral mycobiota signature and intratumoral mycobiota-related genes expression signature, which robustly predicted prognosis and immunotherapy outcomes in RCC and other cancers. Aspergillus tanneri was identified as a potential key fungal species influencing RCC prognosis. Our findings suggest that the intratumoral mycobiome suppresses lipid catabolism and induces T cell exhaustion in RCC.

Altered microbiota of rectal mucosa in rectal cancer patients

BACKGROUND

With advances in sequencing techniques, microbiota dysbiosis and pathogenic microbes that accelerate colorectal cancer progression have been identified and widely reported. However, few studies have focused on the microbiota taxa of rectal mucus in rectal cancer (RC) patients. Here, we analyzed the composition and characteristics of the rectal mucosa microbiota of RC patients from Wenzhou city, China, and compared the results with those of healthy controls.

AIM

To explore the changes in the characteristics of the rectal mucosal flora associated with RC, and identify biomarkers of microbe taxa for RC.

METHODS

Rectal mucosa samples from a Chinese cohort of 72 recently diagnosed RC patients and 71 healthy controls were obtained. A validation cohort, which included 22 RC patients and 60 healthy controls, was also established. Changes in the rectal mucosal flora were observed by cultivation, 16S ribosomal DNA gene sequencing analysis and quantitative polymerase chain reaction analysis.

RESULTS

The 16S ribosomal DNA results demonstrated that RC patients presented increased bacterial community richness and alpha diversity as well as an altered rectal mucosal microbiota, with depletion of Proteobacteria and Thermi and enrichment of Bacteroidetes and Fusobacteria in cancerous mucosal tissues (CM) and enrichment of Firmicutes and Cyanobacteria in adjacent noncancerous mucosal tissues (AM). The culture results showed that the mean loads of Escherichia coli, Bifidobacterium, Enterococcus, and Lactobacillus were significantly reduced in RC patients. The ratios of Prevotella to Ruminococcus [areas under the receiver operating curve: 0.795 in AM vs normal control mucosa (NM), 0.77 in CM vs NM] and of Prevotella stercorea to Propionibacterium acnes (areas under the receiver operating curve: 0.808 in AM vs NM, 0.843 in CM vs NM) exhibited excellent abilities to differentiate between healthy controls and RC patients.

CONCLUSION

RC patients have an altered rectal mucosal microbiota, and the ratio of Prevotella to Ruminococcus or the ratio of Prevotella stercorea to Propionibacterium acnes may serve as a marker for RC diagnosis.

Multimodal metagenomic analysis reveals microbial InDels as superior biomarkers for pediatric Crohn's disease

BACKGROUND AND AIMS

The gut microbiome is closely associated with pediatric Crohn's disease (CD), while the multidimensional microbial signature and their capabilities for distinguishing pediatric CD are underexplored. This study aims to characterize the microbial alterations in pediatric CD and develop a robust classification model.

METHODS

A total of 1175 fecal metagenomic sequencing samples, predominantly from 3 cohorts of pediatric CD patients, were re-analyzed from raw sequencing data using uniform process pipelines to obtain multidimensional microbial alterations in pediatric CD, including taxonomic profiles, functional profiles, and multi-type genetic variants. Random forest algorithms were used to construct classification models after comparing multiple machine learning algorithms.

RESULTS

We found pediatric CD samples exhibited reduced microbial diversity and unique microbial characteristics. Pronounced abundance differences in 45 species and 1357 KEGG orthology genes. Particularly, Enterocloster bolteae emerged as a pivotal pediatric CD-associated species. Additionally, we identified a vast amount of microbial genetic variants linked to pediatric CD, including 192 structural variants, 1256 insertions/deletions (InDels), and 3567 single nucleotide variants, with a considerable portion of these variants located in non-genic regions. The InDel-based model outperformed other predictive models against multidimensional microbial signatures, achieving an area under the ROC curve (AUC) of 0.982. The robustness and disease specificity were further confirmed in an independent CD cohort (AUC = 0.996) and 5 other microbiome-associated pediatric cohorts.

CONCLUSIONS

Our study provided a comprehensive landscape of microbial alterations in pediatric CD and introduced a highly effective diagnostic model rooted in microbial InDels, which contributes to the development of noninvasive diagnostic tools and targeted therapies.

Cancer-associated fungi: An emerging powerful player in cancer immunotherapy

The role of the human microbiome in cancer has been extensively studied, focusing mainly on bacteria-host interactions and their impact on tumor development and treatment response. However, fungi, an immune-active component of the human microbiome, have received less attention regarding their roles in cancer. Recent studies have identified the widespread and specific colonization and distribution of fungi in multiple sites in patients across various cancer types. Importantly, host-fungal immune interactions significantly influence immune regulation within the tumor microenvironment. The rapid advancement of immune-checkpoint blockade (ICB)-based cancer immunotherapy creates an urgent need for effective biomarkers and synergistic therapeutic targets. Cancer-associated fungi and their associated antifungal immunity demonstrate significant potential and efficacy in enhancing cancer immunotherapy. This review summarizes and discusses the growing evidence of the functions and mechanisms of commensal and pathogenic cancer-associated fungi in cancer immunotherapy. Additionally, we emphasize the potential of fungi as predictive biomarkers and therapeutic targets in cancer immunotherapy.

Microsatellite Instability in the Tumor Microenvironment: The Role of Inflammation and the Microbiome

BACKGROUND

Microsatellite instability (MSI) is a hallmark of DNA mismatch repair (MMR) deficiency that leads to genomic instability and increased cancer risk. The tumor microenvironment (TME) significantly influences MSI-driven tumorigenesis, and emerging evidence points to a critical role of the microbiome in shaping this complex interplay.

METHODS

This review comprehensively examines the existing literature on the intricate relationship between MSI, microbiome, and cancer development, with a particular focus on the impact of microbial dysbiosis on the TME.

RESULTS

MSI-high tumors exhibited increased immune cell infiltration owing to the generation of neoantigens. However, immune evasion mechanisms such as PD-1/CTLA-4 upregulation limit the efficacy of immune checkpoint inhibitors (ICIs) in a subset of patients. Pathobionts, such as Fusobacterium nucleatum and Bacteroides fragilis, contribute to MSI through the production of genotoxins, further promoting inflammation and oxidative stress within the TME.

CONCLUSIONS

The microbiome profoundly affects MSI-driven tumorigenesis. Modulation of the gut microbiota through interventions such as fecal microbiota transplantation, probiotics, and dietary changes holds promise for improving ICI response rates. Further research into cancer pharmacomicrobiomics, investigating the interplay between microbial metabolites and anticancer therapies, is crucial for developing personalized treatment strategies.

Transmission of antimicrobial resistance genes from the environment to human gut is more pronounced in colorectal cancer patients than in healthy subjects

Antimicrobial resistance is a major global health concern. However, the source of gut resistome remains unsolved. We aimed to analyze the contribution of environmental antimicrobial resistance genes (ARGs) to colorectal cancer (CRC) patients. Here, we collected metagenomic data from 1,605 human stool samples (CRC = 748; healthy = 857) and 1,035 city-matched environmental samples, in which 110 CRC, 112 healthy, and 56 environmental samples were newly collected. Compared to healthy subjects, CRC patients had significantly higher ARG burden (p < 0.01) with increased levels of multidrug-resistant ARGs. Gut ARGs in CRC also had a closer similarity to environmental ARGs (p < 0.001). By comparing environmental and gut ARGs, 28 environmental ARGs were identified as CRC-specific ARGs, including SUL2 and MEXE, which were not identified in healthy subjects. Meanwhile, more mobile ARGs (mARGs) from the environment were observed in CRC patients compared to healthy subjects (p < 0.05). The hosts of mARGs were mainly pathogenic bacteria (e.g., Escherichia coli (E. coli) and Clostridium symbiosum (C. symbiosum)). Compared to healthy subjects, CRC patients showed elevated horizontal gene transfer efficiency from the environment to gut. Consistently, the abundance of pathobionts carrying specific mARGs (e.g., E. coli-SUL2 and C. symbiosum-SUL2) were significantly increased in CRC patients compared to healthy subjects (p < 0.05). We thus reveal a route of ARG dissemination from the environment into the gut of CRC patients.

Melatonin via MTNR1B regulates METTL3 to protect ileum cell differentiation

Intestinal stem cells rapidly differentiate into various epithelial cells, playing a crucial role in maintaining intestinal homeostasis. Melatonin, a known endogenous molecule with anti-inflammatory and antioxidant properties, has its potential efficacy in ileum stem cells differentiation not fully understood to date. This study indicates that melatonin suppresses ileum inflammation and maintains normal differentiation of ileum stem cells through MTNR1B. Subsequent outcomes following treatment with MTNR1B inhibitors further substantiate these findings. Additionally, overexpression of METTL3 protein appears to be a potential instigator for promoting ileum inflammation and disruptions in cell differentiation. Treatment with the METTL3 inhibitor SAH significantly inhibits ileum inflammation and Wnt/β-catenin activity, thereby sustaining normal cellular differentiation functions. In summary, this study showed that melatonin may improve ileum inflammation and maintain cell differentiation functions by inhibiting abnormal METTL3 expression via MTNR1B.

Exploring oral microbiome in oral squamous cell carcinoma across environment-associated sample types

The relationship between the oral microbiome and oral squamous cell carcinoma (OSCC) has been extensively investigated. Nonetheless, most previous studies were single-center, resulting in the absence of systematic evaluations. To address this gap, we performed a comprehensive meta-analysis on 1,255 samples from OSCC-related 16S rRNA gene data sets, representing a diverse range of OSCC phenotypes. It is recognized that the progression of cancer is related to the alterations in the microbiome among different phenotypes. Our findings revealed distinct microbiome characteristics among different sample types, with Biopsy (Bios) and Swab samples exhibiting significant differences between phenotypes. In Bios samples, the microbiomes of the Cancer group and the normal tissue adjacent to the tumor (NAT) group display a higher similarity, while both differ from the microbiome of the Fibroepithelial polyp (FEP) group. Moreover, the identified differential genera and pathways corresponded with these observations. We developed a diagnostic model using the random forest algorithm on Swab samples, achieving an area under the receiver operating characteristic curve (AUC) of 0.918. Importantly, this model exhibited considerable effectiveness (AUC = 0.849) when applied to another sequencing platform. Taken together, our study provides a comprehensive overview of the oral microbiome during various OSCC progression stages, potentially enhancing early detection and treatment.IMPORTANCEThis study answers key questions regarding the universal microbial characteristics and comprehensive oral microbiome dynamics during oral squamous cell carcinoma (OSCC) progression. By integrating multiple data sets, we examine the following critical aspects: (1) Do different sample types harbor distinct microbial communities within the oral cavity? (2) Which sample types offer greater potential for investigating OSCC progression? (3) How are the oral microbiomes of the Cancer group, normal tissue adjacent to the tumor group, and Fibroepithelial polyp group related, and what is their potential association with OSCC development? (4) Can a diagnostic model based on microbial signatures effectively distinguish between Cancer and Health groups using Swab samples?

Metagenomic analysis characterizes stage-specific gut microbiota in Alzheimer's disease

Alzheimer's disease (AD) is a progressive neurodegenerative disorder with a decade-long preclinical pathological period that can be divided into several stages. Emerging evidence has revealed that the microbiota-gut-brain axis plays an important role in AD pathology. However, the role of gut microbiota in different AD stages has not been well characterized. In this study, we performed fecal shotgun metagenomic analysis on a Chinese cohort with 476 participants across five stages of AD pathology to characterize stage-specific alterations in gut microbiota and evaluate their diagnostic potential. We discovered extensive gut dysbiosis that is associated with neuroinflammation and neurotransmitter dysregulation, with over 10% of microbial species and gene families showing significant alterations during AD progression. Furthermore, we demonstrated that microbial gene families exhibited strong diagnostic capabilities, evidenced by an average AUC of 0.80 in cross-validation and 0.75 in independent external validation. In the optimal model, the most discriminant gene families are primarily involved in the metabolism of carbohydrates, amino acids, energy, glycan and vitamins. We found that stage-specific microbial gene families in AD pathology could be validated by an in vitro gut simulator and were associated with specific genera. We also observed that the gut microbiota could affect the progression of cognitive decline in 5xFAD mice through fecal microbiota transplantation, which could be used for early intervention of AD. Our multi-stage large cohort metagenomic analysis demonstrates that alterations in gut microbiota occur from the very early stages of AD pathology, offering important etiological and diagnostic insights.

The landscape of the microbiome at different stages of root caries

OBJECTIVE

To investigate the relationship between microorganisms and root caries, identify core species, and explore their interactions.

MATERIALS AND METHODS

Thirty patients with different levels of root caries were included. Plaques from superficial (n = 30) and deep root caries (n = 30) and sound root surfaces (n = 30) were collected. Microbial diversity and composition across different stages of root caries were analyzed using 16 S rRNA and 18 S rRNA high-throughput sequencing. Wilcoxon paired comparisons were conducted to minimize individual variations. LefSe analysis was performed to identify stage-specific microbial enrichment. In vitro biofilm models of C. albicans, S. mutans and A. viscosus were established to examine the effects of C. albicans on biofilm formation, virulence factor expression, and metabolic pathway regulation. Fungal transcriptomes were sequenced to explore how fungal species affect bacterial growth and cariogenicity.

RESULTS

No significant differences in microbial diversity or structure were observed, but relative abundances of some species differed significantly (p < 0.05). LefSe analysis showed that the genus Streptococcus, Actinomyces, Lactobacillus, and Bacillus were enriched in superficial caries, whereas Prevotella was enriched in deep lesions. C. albicans was the predominant fungal species in root plaques and positively correlated with S. mutans and Actinomyces sp. HMT448. C. albicans promoted the growth, biofilm formation, and cariogenicity of S. mutans and A. viscosus via the arginine biosynthesis pathway.

CONCLUSION

Oral microecology is stable, and species imbalance is a key factor in root caries. Cross-kingdom interactions between S. mutans, A. viscosus, and C. albicans enhance cariogenic biofilms via the arginine biosynthesis pathway, offering insights for clinical treatments of root caries.

CLINICAL RELEVANCE

Our study revealed the first landscape of the microbiome from different stages of root caries and indicated that targeting the interactions of core species may be a practical way to prevent and treat clinical root caries.

Melatonin promotes diabetic wound healing by mediating mitochondrial function in endothelial cells through the AMPK/SIRT1/HIF-1α pathway

OBJECTIVE

Diabetic wounds are open lesions that can develop on any part of the body of diabetic patients. Importantly, melatonin (Mel) exerts promotional effects on wound healing. Accordingly, this study explored the mechanism of Mel in diabetic wound healing by mediating mitochondrial function in endothelial cells.

METHODS

Human umbilical vein vascular endothelial cells (HUVECs) were exposed to high glucose (HG) to mimic a diabetic environment in vitro, followed by Mel treatment. Cell viability, invasion and angiogenic capacity were evaluated with CCK-8, Transwell, and tube formation assays, respectively. CD31 protein expression was determined with Western blot. Wound healing ability was evaluated in vitro, and the levels of adenosine triphosphate (ATP), reactive oxygen species (ROS), mitochondrial membrane potential (MMP), and apoptosis-related proteins (Bcl-2/Bax/CytC) were also detected. To verify the role of the AMPK/SIRT1/HIF-1α pathway in diabetic wound healing, HG-induced HUVECs treated with Mel were subjected to treatment with sh-HIF-1α, AMPK inhibitor (compound c), or SIRT1 inhibitor (Nicotinamide).

RESULTS

HG impaired the proliferation, invasion, angiogenesis, and wound healing ability of HUVEC, increased ROS, Bax, and CytC levels, and decreased MMP and the levels of ATP and Bcl-2. Mel facilitated viability, angiogenesis, and wound healing ability while ameliorating mitochondrial dysfunction in HG-treated HUVECs. Mel activated the AMPK/SIRT1 pathway to upregulate HIF-1α in HG-treated HUVECs. HIF-1α knockdown, CC, or Nicotinamide negated the effect of Mel on HG-treated HUVECs.

CONCLUSIONS

Mel fosters angiogenesis and represses mitochondrial dysfunction in endothelial cells by activating the AMPK/SIRT1/HIF-1α pathway, thereby promoting diabetic wound healing.

The impact of sugar-sweetened beverages consumption on constipation: evidence from NHANES

BACKGROUND

The consumption of sugar-sweetened beverages (SSBs) has increased substantially over recent decades, raising concerns about its various physiological effects on bodily function. However, the relationship between SSBs intake and constipation remains insufficiently understood.

METHODS

Data from 7,979 participants sourced from the National Health and Nutrition Examination Survey (NHANES) were analyzed in this study. Dietary intake of SSBs was assessed using two 24-hour dietary recall interviews, and constipation was defined according to the Bristol Stool Form Scale (BSFS) Cards. We employed weighted logistic regression analysis to examine the relationship between SSBs consumption (quantified in grams and kilocalories) and the risk of constipation, while stratified and restricted cubic spline (RCS) analyses explored population variability.

RESULTS

After adjusting for all relevant variables, SSBs quantified in grams (SSBs-grams) (ORQ3 vs. Q1 = 1.419, 95% CI: 1.064-1.893, p = 0.019; p for trend = 0.02) and SSBs quantified in kilocalories (SSBs-kcal) (ORQ4 vs. Q1 = 1.567, 95% CI: 1.100-2.234, p = 0.015; p for trend = 0.016) showed a significant positive association with constipation. Furthermore, the weighted RCS and stratified analyses indicated that the association varied among subgroups, with a non-linear relationship between SSBs-kcal and constipation (SSBs-grams: p non-linear = 0.100, SSBs-kcal: p non-linear = 0.026).

CONCLUSIONS

Our findings indicated that increased SSBs consumption is associated with a higher risk of constipation. The results underscore the need for public health interventions aimed at reducing the intake of SSBs and promoting healthier alternatives.

The Microbiome and Metabolic Dysfunction-Associated Steatotic Liver Disease

Metabolic dysfunction-associated steatotic liver disease (MASLD) is a condition wherein excessive fat accumulates in the liver, leading to inflammation and potential liver damage. In this narrative review, we evaluate the tissue microbiota, how they arise and their constituent microbes, and the role of the intestinal and hepatic microbiota in MASLD. The history of bacteriophages (phages) and their occurrence in the microbiota, their part in the potential causation of MASLD, and conversely, "phage therapy" for antibiotic resistance, obesity, and MASLD, are all described. The microbiota metabolism of bile acids and dietary tryptophan and histidine is defined, together with the impacts of their individual metabolites on MASLD pathogenesis. Both periodontitis and intestinal microbiota dysbiosis may cause MASLD, and how individual microorganisms and their metabolites are involved in these processes is discussed. Novel treatment opportunities for MASLD involving the microbiota exist and include fecal microbiota transplantation, probiotics, prebiotics, synbiotics, tryptophan dietary supplements, intermittent fasting, and phages or their holins and endolysins. Although FDA is yet to approve phage therapy in clinical use, there are multiple FDA-approved clinical trials, and this may represent a new horizon for the future treatment of MASLD.

Fecal bacterial biomarkers and blood biochemical indicators as potential key factors in the development of colorectal cancer

The incidence of colorectal cancer (CRC) has been increasing in recent decades. Current methods for CRC screening have their own drawbacks, thus there is an urgent need to identify the key microbes that drive the development of CRC for wider application in the early detection and prevention of CRC. To address this issue, we performed fecal microbiome analysis by high-throughput sequencing of 16S rRNA gene combined with blood biochemical indicators in patients with CRC stages I, II, III, and IV, healthy people, and patients with polyps. Fecal microbiota of patients with CRC was disturbed, as evidenced by significantly reduced α-diversity in patients with CRC stage IV and markedly different β-diversity. The random forest model identified the top 25 genera from 174 training data, resulting in a diagnostic accuracy of 87.95%. Further, by combining with differential genera analysis, we screened out 11 biomarkers that significantly changed in different groups. Peptostreptococcus, Parvimonas, Shewanella, Oscillibacter, Eggerthella, and Gemella associated with the development of CRC were significantly enriched, while Fenollaria, Staphylococcus, Ezakiella, Finegoldia, and Neisseria associated with the remission of CRC were significantly suppressed in patients with CRC. Importantly, carcinoembryonic antigen (CEA) was significantly correlated with these 11 microbial biomarkers, and carbohydrate antigen 19-9 (CA 19-9) was markedly correlated with Oscillibacter. Notably, co-occurrence network analysis at the genus level exhibited that the microbial co-occurrence network of CRC IV was the most complex and stable. These results suggested that CEA, CA 19-9 and 11 microbial biomarkers may be co-biomarkers for the disease occurrence and development, and non-invasive diagnosis of CRC.

IMPORTANCE

Identifying the key microbes that drive the development of colorectal cancer (CRC) has been important in this field. We delved into the research on the association between CRC and fecal microbiota in this study, providing a detailed analysis of the characteristics of fecal microbiota during the transition from normal intestine to polyps to cancer. Fecal bacterial biomarkers and blood biochemical indicators may be co-biomarkers in the development of CRC.

Mycobiome: an underexplored kingdom in cancer

SUMMARYThe human microbiome, including bacteria, fungi, archaea, and viruses, is intimately linked to both health and disease. The relationship between bacteria and disease has received much attention and intensive investigation, while that of the fungal microbiome, also known as mycobiome, has lagged far behind bacteria. There is growing evidence showing mycobiome dysbiosis in cancer patients, and certain cancer-specific fungi may contribute to cancer progression by interacting with both host and bacteria. It was also demonstrated that the role of fungi-derived products in cancer should also not be underestimated. Therefore, investigating how fungal pathogenesis contributes to the onset and spread of cancer would yield crucial information for cancer diagnosis, prevention, and anti-cancer therapy.

Analysis of expression characteristics of ferroptosis-related lncRNAs in gastrointestinal cancer patients in Asia

BACKGROUND

Asian cancer patients have become the highest morbidity and mortality group, and gastrointestinal tumors account for the majority of them, so it is urgent to find effective targets. Therefore, ferroptosis-related lncRNAs models were established to predict the prognosis and clinical immune characteristics of GI cancer.

METHODS

RNA sequencing and clinical data were collected from the TCGA database (LIHC, STAD, ESCA, PAAD, COAD, CHOL, and READ) of patients with gastrointestinal cancer in Asia. Download ferrodroptosis genes from FerrDb. Through R language, differential genes were identified, prognostic related LncRNAs were screened, and risk scores were obtained by risk formula to build models. Survival analysis, risk heat map, COX regression and ROC were used to evaluate the risk model. Establish Nomogram and clinically relevant heat maps. GSEA software was used to analyze gene enrichment and immune-related characteristics in high and low risk groups. LncRNA expression was validated through paired sample differential analysis and qRT-PCR, and the drug sensitivity of genes was also analyzed.

RESULTS

The transcriptome data of 297 cases and clinical data of 322 cases were downloaded from TCGA, and the intersection of ferroptosis-related genes were obtaine. Cox analysis revealed 48 ferroptosis-related LncRNAs associated with prognosis. Through survival analysis, risk heatmap, COX regression and ROC, it was found that the risk model was highly accurate and efficient in predicting prognosis. KEGG-related GSEA enrichment analysis showed that 12 related pathways were significantly expressed in the low-risk group. Four immune-related functions were significantly higher in the high-risk group than in the low-risk group, and the expression of all immune checkpoints were significantly higher in the high-risk group than in the low-risk group. The three LncRNAs in the model exhibited varying expression levels across different tumors and obtained drug sensitivity data.

CONCLUSIONS

Our results reveal innovative and strong evidence that ferroptosis-related lncRNAs can be used as biomarkers for the treatment and prognosis of Asian GI cancer.

Intervention and research progress of gut microbiota-immune-nervous system in autism spectrum disorders among students

Autism Spectrum Disorder (ASD) is a neurodevelopmental disorder characterized by difficulties in social interaction and communication, repetitive and stereotyped behaviors, restricted interests, and sensory abnormalities. Its etiology is influenced by both genetic and environmental factors, with no definitive cause identified and no specific pharmacological treatments available, posing a significant burden on patients' families and society. In recent years, research has discovered that gut microbiota dysbiosis plays a crucial role in the pathogenesis of ASD. The gut microbiota can influence brain function and behavior through the gut-brain axis via the nervous system, immune system, and metabolic pathways. On the one hand, specific gut microbes such as Clostridium and Prevotella species are found to be abnormal in ASD patients, and their metabolic products, like short-chain fatty acids, serotonin, and GABA, are also involved in the pathological process of ASD. On the other hand, ASD patients exhibit immune system dysfunction, with gut immune cells and related cytokines affecting neural activities in the brain. Currently, intervention methods targeting the gut microbiota, such as probiotics, prebiotics, and fecal microbiota transplantation, have shown some potential in improving ASD symptoms. However, more studies are needed to explore their long-term effects and optimal treatment protocols. This paper reviews the mechanisms and interrelationships among gut microbiota, immune system, and nervous system in ASD and discusses the challenges and future directions of existing research, aiming to provide new insights for the prevention and treatment of ASD.

Crohn's Disease and Ulcerative Colitis Share 2 Molecular Subtypes With Different Mechanisms and Drug Responses

BACKGROUND AND AIMS

Several therapies have been approved to treat Crohn's disease (CD) and ulcerative colitis (UC), indicating that both diseases may share the same molecular subtypes. The aim of this study is to identify shared patient subtypes with common molecular drivers of disease.

METHODS

Five public datasets with 406 CD and 421 UC samples were integrated to identify molecular subtypes. Then, the patient labels from 6 independent datasets and 8 treatment datasets were predicted for validating subtypes and identifying the relationship with response status of corticosteroids, infliximab, vedolizumab, and ustekinumab.

RESULTS

Two molecular subtypes were identified from the training datasets, in which CD and UC patients were relatively evenly represented in each subtype. We found 6 S1-specific gene modules related to innate/adaptive immune responses and tissue remodeling and 9 S1-specific cell types (cycling T cells, Tregs, CD8+ lamina propria, follicular B cells, cycling B cells, plasma cells, inflammatory monocytes, inflammatory fibroblasts, and postcapillary venules). Subtype S2 was associated with 3 modules related to metabolism functions and 4 cell types (immature enterocytes, transit amplifying cells, immature goblet cells, and WNT5B+ cells). The subtypes can be replicated in 6 independent datasets based on a 20-gene classifier. Furthermore, response rates to 4 treatments in subtype S2 were significantly higher than those in subtype S1.

CONCLUSIONS

This study discovered and validated a robust transcriptome-based molecular classification shared by CD and UC and built a 20-gene classifier. Because 2 subtypes have different molecular mechanisms and drug response, our classification may aid interpretation of heterogeneous molecular and clinical information in inflammatory bowel disease patients.

Feature selection with vector-symbolic architectures: a case study on microbial profiles of shotgun metagenomic samples of colorectal cancer

The continuously decreasing cost of next-generation sequencing has recently led to a significant increase in the number of microbiome-related studies, providing invaluable information for understanding host-microbiome interactions and their relation to diseases. A common approach in metagenomics consists of determining the composition of samples in terms of the amount and types of microbial species that populate them, with the goal of identifying microbes whose profiles are able to differentiate samples under different conditions with advanced feature selection techniques. Here, we propose a novel backward variable selection method based on the hyperdimensional computing (HDC) paradigm, which takes inspiration from how the human brain works in the classification of concepts by encoding features into vectors in a high-dimensional space. We validated our method on public metagenomic samples collected from patients affected by colorectal cancer in a case/control scenario, by performing a comparative analysis with other state-of-the-art feature selection methods, obtaining promising results.

AUTHOR SUMMARY

Characterizing the microbial composition of metagenomic samples is crucial for identifying potential biomarkers that can distinguish between healthy and diseased states. However, the high dimensionality and complexity of metagenomic data present significant challenges in the context of accurately selecting features. Our backward variable selection method, based on the HDC paradigm, offers a promising approach to overcoming these challenges. By effectively reducing the feature space while preserving essential information, this method enhances the ability to detect critical microbial signatures associated with diseases like colorectal cancer, leading to more precise diagnostic tools.

Is the oral pathogen, Porphyromona gingivalis, associated to colorectal cancer?: a systematic review

BACKGROUND

The association between the oral pathogen Porphyromonas gingivalis (PG) and the gut microbiota in colorectal cancer (CRC) patients has been explored with inconsistent results. This study aims to systematically assess this potential association.

MATERIALS AND METHODS

A systematic review was conducted across three databases (Pubmed, Embase and Web of Science) from inception up to January 2023 and updated until November 2024. Inclusion criteria were observational studies examining PG in the microbiota of adults with CRC compared to healthy controls. Exclusion criteria were studies without control group of healthy individuals, other designs or without full-text access. Two reviewers independently selected and extracted data following a pre-registered protocol. Disagreements were resolved by consensus or with a third reviewer. Risk of bias (RoB) was assessed using the Newcastle-Ottawa Scale (NOS). Results were summarized with a flow diagram, tables, and narrative descriptions. Meta-analysis was not feasible, so Fisher's method for combining p-values and the sign test were used as alternative integration methods.

RESULTS

Finally, 18 studies, with 23 analysis units were included, providing a total sample of 4,373 participants (48.0% cases and 52.0%controls), 38.2% men and 61.8% women, with a similar distribution among cases and controls. The mean (SD) age of cases was 63.3 (4.382) years old and 57.0 (7.753) years for controls. Most of the studies analyzed the presence of PG in feces (70.0%) collected before colonoscopy (55.0%) and were classified with good quality (70.0%) in the RoB assessment. Results suggested an effect (Fisher's test, p = .000006) with some evidence towards a positive association of PG in CRC patients compared to healthy controls (Sign test, p = .039).

CONCLUSIONS

Results of the systematic review suggest that PG is associated with the microbiota of CRC patients. Lack of information to calculate the effect size prevented the performance of a meta-analysis. Future research should aim for standardized protocols and statistical approaches.

FUNDING

No funding was received for this work.

SYSTEMATIC REVIEW REGISTRATION

The research protocol was registered with the International Prospective Register of Systematic Reviews (PROSPERO) on 2023 (registration number: CRD42023399382).

Global trends and regime state shifts of lacustrine aquatic vegetation

Aquatic vegetation (AV) is vital for maintaining the health of lake ecosystems, with submerged aquatic vegetation (SAV) and floating/emergent aquatic vegetation (FEAV) representing clear and shaded states, respectively. However, global SAV and FEAV dynamics are poorly understood due to data scarcity. To address this gap, we developed an innovative AV mapping algorithm and workflow using satellite imagery (1.4 million Landsat images) from 1989 to 2021 and created a global database of AV across 5,587 shallow lakes. Our findings suggest that AV covers 108,186 km2 on average globally, accounting for 28.9% (FEAV, 15.8%; SAV, 13.1%) of the total lake area. Over two decades, we observed a notable transition: SAV decreased by 30.4%, while FEAV increased by 15.6%, leading to a substantial net loss of AV. This global trend indicates a shift from clear to shaded conditions, increasingly progressing toward turbid states dominated by phytoplankton. We found that human-induced eutrophication was the primary driver of change until the early 2010s, after which global warming and rising lake temperatures became the dominant drivers. These trends serve as a warning sign of deteriorating lake health worldwide. With future climate warming and intensified eutrophication, these ongoing trends pose a significant risk of disrupting lake ecosystems.

Prediction of colorectal cancer based on taxonomic levels of microorganisms and discovery of taxonomic biomarkers using the Grouping-Scoring-Modeling (G-S-M) approach

Colorectal cancer (CRC) is one of the most prevalent forms of cancer globally. The human gut microbiome plays an important role in the development of CRC and serves as a biomarker for early detection and treatment. This research effort focuses on the identification of potential taxonomic biomarkers of CRC using a grouping-based feature selection method. Additionally, this study investigates the effect of incorporating biological domain knowledge into the feature selection process while identifying CRC-associated microorganisms. Conventional feature selection techniques often fail to leverage existing biological knowledge during metagenomic data analysis. To address this gap, we propose taxonomy-based Grouping Scoring Modeling (G-S-M) method that integrates biological domain knowledge into feature grouping and selection. In this study, using metagenomic data related to CRC, classification is performed at three taxonomic levels (genus, family and order). The MetaPhlAn tool is employed to determine the relative abundance values of species in each sample. Comparative performance analyses involve six feature selection methods and four classification algorithms. When experimented on two CRC associated metagenomics datasets, the highest performance metric, yielding an AUC of 0.90, is observed at the genus taxonomic level. At this level, 7 out of top 10 groups (Parvimonas, Peptostreptococcus, Fusobacterium, Gemella, Streptococcus, Porphyromonas and Solobacterium) were commonly identified for both datasets. Moreover, the identified microorganisms at genus, family, and order levels are thoroughly discussed via refering to CRC-related metagenomic literature. This study not only contributes to our understanding of CRC development, but also highlights the applicability of taxonomy-based G-S-M method in tackling various diseases.

Ex Vivo Analysis of the Effect of Endoscopic Premedications on the Microbiota Profile in Gastric Juice

Background and Aim

Dimethicone (GAS), lidocaine (XYL), and protease (PRO) are commonly used as premedications during esophagogastroduodenoscopy (EGD). However, the effects of these drugs on the gastric microbiota remain unexplored. Therefore, we aimed to investigate the effects of these premedications on gastric juice collected from patients undergoing EGD.

Methods

Gastric juice was endoscopically aspirated from six patients and divided into six aliquots for in vitro analysis. The samples were mixed with premedications in corresponding treatment sets: GAS, XYL, PRO, MIX (a mixture of GAS, XYL, and PRO), and control (CTL1 and 2; no medication treatment). After extraction of microbial DNA from the treated samples, the 16S rRNA amplicon sequence was analyzed to determine the microbiota profile in terms of (1) the amount of genomic DNA (gDNA), (2) α-diversity indices, Shannon index, number of observed operational taxonomic units (OTUs), and Chao1 index, (3) weighted and unweighted UniFrac distances, and (4) the relative abundance of phyla and genera.

Results

The total amount of extracted gDNA did not significantly differ between the six groups. The α-diversity indices did not significantly differ between treatment groups. Although GAS, PRO, and MIX differed significantly from the technical replicates in the weighted UniFrac distance (p = 0.03 all), no significant difference was observed in the unweighted UniFrac distance. However, significant differences were observed in the relative abundance of several bacterial microbiota at the phylum and genus levels.

Conclusions

Premedications affect the microbiota profile of specific phylum- and genus-level bacterial groups. Trial Registration: University Hospital Medical Information Network Clinical Trials Registry: UMIN-CTR 000040192 and UMIN-CTR 000051289.

Gut microbiota in multiple sclerosis and animal models

Multiple sclerosis (MS) is a chronic central nervous system (CNS) neurodegenerative and neuroinflammatory disease marked by a host immune reaction that targets and destroys the neuronal myelin sheath. MS and correlating animal disease models show comorbidities, including intestinal barrier disruption and alterations of the commensal microbiome. It is accepted that diet plays a crucial role in shaping the microbiota composition and overall gastrointestinal (GI) tract health, suggesting an interplay between nutrition and neuroinflammation via the gut-brain axis. Unfortunately, poor host health and diet lead to microbiota modifications that could lead to significant responses in the host, including inflammation and neurobehavioral changes. Beneficial microbial metabolites are essential for host homeostasis and inflammation control. This review will highlight the importance of the gut microbiota in the context of host inflammatory responses in MS and MS animal models. Additionally, microbial community restoration and how it affects MS and GI barrier integrity will be discussed.

Composition, Influencing Factors, and Effects on Host Nutrient Metabolism of Fungi in Gastrointestinal Tract of Monogastric Animals

Intestinal fungi, collectively referred to as mycobiota, constitute a small (0.01-2%) but crucial component of the overall intestinal microbiota. While fungi are far less abundant than bacteria in the gut, the volume of an average fungal cell is roughly 100-fold greater than that of an average bacterial cell. They play a vital role in nutrient metabolism and maintaining intestinal health. The composition and spatial organization of mycobiota vary across different animal species and are influenced by a multitude of factors, including age, diet, and the host's physiological state. At present, quantitative research on the composition of mycobiota in monogastric animals remains scarce, and investigations into the mechanisms underlying their metabolic functions are also relatively restricted. This review delves into the distribution characteristics of mycobiota, including Candida albicans, Saccharomyces cerevisiae, Kazachstania slooffiae, in monogastric animals, the factors influencing their composition, and the consequent impacts on host metabolism and health. The objective is to offer insights for a deeper understanding of the nutritional significance of intestinal fungi in monogastric animals and to explore the mechanisms by which they affect host health in relation to inflammatory bowel disease (IBD), diarrhea, and obesity. Through a systematic evaluation of their functional contributions, this review shifts our perception of intestinal fungi from overlooked commensals to key components in gut ecosystem dynamics, emphasizing their potential in personalized metabolic control regulation and the enhancement of disease prevention and treatment strategies.

After Surgically Induced Remission, Ileal and Colonic Mucosa-Associated Microbiota Predicts Crohn's Disease Recurrence

BACKGROUND & AIMS

Investigating the tissue-associated microbiota after surgically induced remission may help to understand the mechanisms initiating intestinal inflammation in Crohn's disease.

METHODS

Patients with Crohn's disease undergoing ileocolic resection were prospectively recruited in 6 academic centers. Biopsy samples from the neoterminal ileum, colon, and rectosigmoid were obtained from colonoscopies performed after surgery. Microbial DNA was extracted for 16S rRNA gene sequencing. Microbial diversity and taxonomic differential relative abundance were analyzed. A random forest model was applied to analyze the performance of clinical and microbial features to predict recurrence. A Rutgeerts score ≥i2 was deemed as endoscopic recurrence.

RESULTS

A total of 349 postoperative colonoscopies and 944 biopsy samples from 262 patients with Crohn's disease were analyzed. Ileal inflammation accounted for most of the explained variance of the ileal and colonic mucosa-associated microbiota. Samples obtained from 97 patients who were in surgically induced remission at first postoperative colonoscopy who went on to develop endoscopic recurrence at second colonoscopy showed lower diversity and microbial deviations when compared with patients who remained in endoscopic remission. Depletion of genus Anaerostipes and increase of several genera from class Gammaproteobacteria at the 3 biopsy sites increase the risk of further recurrence. Gut microbiome was able to predict future recurrence better than clinical features.

CONCLUSIONS

Ileal and colonic mucosa-associated microbiome deviations precede development of new-onset ileal inflammation after surgically induced remission and show good predictive performance for future recurrence. These findings suggest that targeted microbial modulation is a plausible modality to prevent postoperative Crohn's disease recurrence.

A meta-analysis of the efficacy and safety of immunomodulators in the treatment of severe COVID-19

ObjectiveTo evaluate the efficacy and adverse events of immunomodulators in the treatment of severe coronavirus disease 2019 (COVID-19).MethodsA literature search for the meta-analysis was performed using PubMed, The Cochrane Library, Embase, Wanfang Data, CNKI, and Web of Science to identify randomized controlled trials assessing the outcomes of patients treated with corticosteroids alone and/or interleukin-6 receptor antagonists for COVID-19. The risk of bias was assessed using the Cochrane method. The protocol was registered with PROSPERO (registry number: CRD42022356904).ResultsCompared with patients receiving standard of care, patients treated with corticosteroids alone had an increased risk of 14-day in-hospital death, whereas those treated with interleukin-6 receptor antagonists alone or in combination with corticosteroids had a lower risk of 14-day in-hospital death. Corticosteroid therapy alone was associated with increased risk of several adverse events, including intensive care unit admission and non-invasive ventilation, whereas interleukin-6 receptor antagonists alone or in combination with corticosteroids were not linked to adverse effects.ConclusionsThe findings supported the safety and efficacy of interleukin-6 receptor antagonists, either alone or together with corticosteroids, in patients with severe COVID-19; evidence supporting the efficacy and safety of corticosteroids monotherapy is lacking.

The Impacts of Seasonal Factors on Psoriasis

Psoriasis is a chronic inflammatory skin condition driven by immune system dysfunction, genetic predisposition and environmental factors. Patients with psoriasis experience a well-known clinical phenomenon of 'winter severity and summer relief', in which seasonal environmental factors play critical roles in the onset and progression of psoriasis. These factors include temperature, humidity, infection, light exposure and psychological stress. Seasonal changes in temperature and humidity can compromise skin barrier function and exacerbate inflammatory responses, thereby worsening psoriasis symptoms. Notably, during the winter, decreased light exposure leads to reduced vitamin D (VD) levels, reaching their lowest levels from late winter to early spring. This decline in VD levels is associated with increased disease activity, greater disease severity and more frequent flare-ups in patients with psoriasis. During the winter, influenza and Streptococcus pneumoniae infections are more prevalent, which can further exacerbate psoriasis symptoms. Moreover, the environmental conditions in winter can trigger or intensify feelings of depression, which may adversely affect psoriasis through the brain-skin axis. In this comprehensive review, we thoroughly examined the influence of seasonal environmental factors on the incidence, recurrence and severity of psoriasis. By clarifying these complex relationships, we aimed to support the future development of more personalised and effective treatment and management strategies for patients with psoriasis.

Multi-Cohort Analysis Reveals Altered Archaea in Colorectal Cancer Fecal Samples Across Populations

BACKGROUND & AIMS

Archaea are important components of the host microbiome, but their roles in colorectal cancer (CRC) remain largely unclear. We aimed to elucidate the contribution of gut archaea to CRC across multiple populations.

METHODS

This study incorporated fecal metagenomic data from 10 independent cohorts across 7 countries and an additional in-house cohort, totaling 2101 metagenomes (748 CRC, 471 adenoma, and 882 healthy controls [HCs]). Taxonomic profiling was performed using Kraken2 against the Genome Taxonomy Database. Alterations of archaeal communities and their interactions with bacteria, as well as methanogenic functions were analyzed. A Random Forest model was used to identify multicohort diagnostic microbial biomarkers in CRC.

RESULTS

The overall archaeal alpha diversity shifted from HCs, patients with adenoma, to patients with CRC with the Methanobacteriota phylum enriched while the order Methanomassiliicoccales depleted. At the species level, Methanobrevibacter_A smithii and Methanobrevibacter_A sp002496065 were enriched, whereas 8 species, including Methanosphaera stadtmanae and Methanomassiliicoccus_A intestinalis, were depleted in patients with CRC across multiple cohorts. Among them, M stadtmanae, Methanobrevibacter_A sp900314695, and Methanocorpusculum sp001940805 exhibited a progressive decrease in the HC-adenoma-CRC sequence. CRC-depleted methanogenic archaea exhibited enhanced co-occurring interactions with butyrate-producing bacteria. Consistently, methanogenesis-related genes and pathways were enriched in patients with CRC. A model incorporating archaeal and bacterial biomarkers outperformed single-kingdom models in discriminating patients with CRC from healthy individuals with the area under the curve ranging from 0.744 to 0.931 in leave-one-cohort-out analysis.

CONCLUSIONS

This multicohort analysis uncovered significant alterations in gut archaea and their interactions with bacteria in healthy individuals, patients with adenoma, and patients with CRC. Archaeal biomarkers, combined with bacterial features, have potential as noninvasive diagnostic biomarkers for CRC.

From silent partners to potential therapeutic targets: macrophages in colorectal cancer

Cancer cells grow and survive in the tumor microenvironment, which is a complicated process. As a key part of how colorectal cancer (CRC) progresses, tumor-associated macrophages (TAMs) exhibit a double role. Through angiogenesis, this TAM can promote the growth of cancers. Although being able to modify and adjust immune cells is a great advantage, these cells can also exhibit anti-cancer properties including direct killing of cancer cells, presenting antigens, and aiding T cell-mediated responses. The delicate regulatory mechanisms between the immune system and tumors are composed of a complex network of pathways regulated by several factors including hypoxia, metabolic reprogramming, cytokine/chemokine signaling, and cell interactions. Decoding and figuring out these complex systems become significant in building targeted treatment programs. Targeting TAMs in CRC involves disrupting chemokine signaling or adhesion molecules, reprogramming them to an anti-tumor phenotype using TLR agonists, CD40 agonists, or metabolic modulation, and selectively removing TAM subsets that promote tumor growth. Multi-drug resistance, the absence of an accurate biomarker, and drug non-specificity are also major problems. Combining macrophage-targeted therapies with chemotherapy and immunotherapy may revolutionize treatment. Macrophage studies will advance with new technology and multi-omics methodologies to help us understand CRC and build specific and efficient treatments.

Droplet microfluidics: unveiling the hidden complexity of the human microbiome

The human body harbors diverse microbial communities essential for maintaining health and influencing disease processes. Droplet microfluidics, a precise and high-throughput platform for manipulating microscale droplets, has become vital in advancing microbiome research. This review introduces the foundational principles of droplet microfluidics, its operational capabilities, and wide-ranging applications. We emphasize its role in enhancing single-cell sequencing technologies, particularly genome and RNA sequencing, transforming our understanding of microbial diversity, gene expression, and community dynamics. We explore its critical function in isolating and cultivating traditionally unculturable microbes and investigating microbial activity and interactions, facilitating deeper insight into community behavior and metabolic functions. Lastly, we highlight its broader applications in microbial analysis and its potential to revolutionize human health research by driving innovations in diagnostics, therapeutic development, and personalized medicine. This review provides a comprehensive overview of droplet microfluidics' impact on microbiome research, underscoring its potential to transform our understanding of microbial dynamics and their relevance to health and disease.

Melatonin Exerts Positive Effects on Sepsis Through Various Beneficial Mechanisms

In recent years, our understanding of sepsis has greatly advanced. However, due to the complex pathological and physiological mechanisms of sepsis, the mechanisms of sepsis are currently not fully elucidated, and it is difficult to translate the research results into specific sepsis treatment methods. Melatonin possesses broad anti-inflammatory, antioxidant, and immune-regulatory properties, making it a promising therapeutic agent for sepsis. In recent years, further research has deepened our understanding of the potential mechanisms and application prospects of melatonin in sepsis. The mechanisms underlying the protective effects of melatonin in sepsis are multifaceted. In this review, based on a substantial body of clinical trials and animal research findings, we first highlighted the significance of melatonin as an important biomarker for disease progression and prognosis in sepsis. We also described the extensive regulatory mechanisms of melatonin in sepsis-induced organ damage. In addition to its broad anti-inflammatory, and anti-oxidant effects, melatonin exerts positive effects by regulating metabolic disorders, hemodynamics, cell autophagy, cellular ion channels, endothelial cell permeability, ferroptosis and other complex pathological mechanisms. Furthermore, as a safe exogenous supplement with low toxicity, melatonin demonstrates positive synergistic effects with other anti-sepsis agents. In the face of the urgent medical challenge of transforming the increasing knowledge of sepsis molecular mechanisms into therapeutic interventions to improve patient prognosis, melatonin seems to be a promising option.

Examining the relationship between secondhand smoke and non-malignant digestive system diseases: Mendelian randomization evidence

INTRODUCTION

Secondhand smoke (SHS) may exacerbate the global disease burden, particularly in workplace settings. Observational studies have implicated SHS as a risk factor for various non-malignant digestive system diseases (NMDSD), yet establishing a causal relationship remains challenging. Therefore, we conducted a Mendelian randomization (MR) study to explore whether workplace exposure to SHS is associated with NMDSD.

METHODS

This study utilized a secondary dataset analysis based on Genome-Wide association study (GWAS) summary data. Genetic variants associated with exposure to SHS in the workplace were used as instrumental variables. Genome-wide association study (GWAS) summary data for SHS were obtained from the UK Biobank. GWAS summary data for NMDSD were sourced from the FinnGen study, the International Inflammatory Bowel Disease Genetics Consortium (IIBDGC), and a large-scale study conducted in Japan. We employed inverse variance-weighted (IVW), MR-Egger, and weighted median methods for MR analysis. Additionally, sensitivity analyses were conducted to ensure the robustness of our findings.

RESULTS

According to the IVW model, SHS in the workplace was positively associated with ulcerative colitis (UC) (OR=2.03; 95% CI: 1.03-4.05; p=0.04). There was no evidence of horizontal pleiotropy biasing causality (p>0.05), and leave-one-out analysis confirmed the stability and robustness of this association.

CONCLUSIONS

Our study identifies an association between regular exposure to SHS in the workplace and an increased risk of ulcerative colitis. However, the potential influence of active smoking or exposure to SHS from other sources cannot be excluded. Further research is needed to confirm these findings.

Preferential apical infection of Caco-2 intestinal cell monolayers by SARS-CoV-2 is associated with damage to cellular barrier integrity: Implications for the pathophysiology of COVID-19

SARS-CoV-2 can infect different organs, including the intestine. In an in vitro model of Caco-2 intestinal cell line, we previously found that SARS-CoV-2 modulates the ACE2 receptor expression and affects the expression of molecules involved in intercellular junctions. To further explore the possibility that the intestinal epithelium can serve as an alternative infection route for SARS-CoV-2, we used a model of polarized monolayers of Caco-2 cells (or co-cultures of two intestinal cell lines: Caco-2 and HT29) grown on the polycarbonate membrane of Transwell inserts, inoculated with the virus either in the upper or lower chamber of culture to determine the tropism of the virus for the apical or basolateral pole of these cells. In both polarized Caco-2 cell monolayers and co-culture Caco-2/HT29 cell monolayer, apical SARS-CoV-2 inoculation was found to be much more effective in establishing infection than basolateral inoculation. In addition, apical SARS-CoV-2 infection triggers monolayer degeneration, as shown by histological examination, measurement of trans-epithelial electrical resistance, and cell adhesion molecule expression. During apical infection, the infectious viruses reach the lower chamber, suggesting either a transcytosis mechanism from the apical side to the basolateral side of cells, a paracellular trafficking of the virus after damage to intercellular junctions in the epithelial barrier, or both. Taken together, these data indicate a preferential tropism of SARS-CoV-2 for the apical pole of the human intestinal tract and suggest that infection via the intestinal lumen leads to a systemic infection.

Intestinal microbiota as biomarkers for different colorectal lesions based on colorectal cancer screening participants in community

Introduction

The dysregulation of intestinal microbiota has been implicated in the pathogenesis of colorectal cancer (CRC). However, the utilization of intestinal microbiota for identify the lesions in different procedures in CRC screening populations remains limited.

Methods

A total of 529 high-risk individuals who underwent CRC screening were included, comprising 13 advanced adenomas (Aade), 5 CRC, 59 non-advanced adenomas (Nade), 129 colon polyps (Pol), 99 cases of colorectal inflammatory disease (Inf), and 224 normal controls (Nor). 16S rRNA gene sequencing was used to profile the intestinal microbiota communities. The Gut Microbiota Health Index (GMHI) and average variation degree (AVD) were employed to assess the health status of the different groups.

Results

Our findings revealed that the Nor group exhibited significantly higher GMHIs and the lowest AVD compared to the four Lesion groups. The model incorporating 13 bacterial genera demonstrated optimal efficacy in distinguishing CRC and Aade from Nor, with an area under the curve (AUC) of 0.81 and a 95% confidence interval (CI) of 0.72 to 0.89. Specifically, the 55 bacterial genera combination model exhibited superior performance in differentiating CRC from Nor (AUC 0.98; 95% CI, 0.96-1), the 25 bacterial genera combination showed superior performance in distinguishing Aade from Nor (AUC 0.95). Additionally, the 27 bacterial genera combination demonstrated superior efficacy in differentiating Nade from Nor (AUC 0.82). The 13 bacterial genera combination exhibited optimal performance in distinguishing Inf from Nor (AUC 0.71).

Discussion

Our study has identified specific microbial biomarkers that can differentiate between colorectal lesions and healthy individuals. The intestinal microbiota markers identified may serve as valuable tools in community-based CRC screening programs.

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.