Desulfovibrio vulgaris flagellin exacerbates colorectal cancer through activating LRRC19/TRAF6/TAK1 pathway

The initiation and progression of colorectal cancer (CRC) are intimately associated with genetic, environmental and biological factors. Desulfovibrio vulgaris (DSV), a sulfate-reducing bacterium, has been found excessive growth in CRC patients, suggesting a potential role in carcinogenesis. However, the precise mechanisms underlying this association remain incompletely understood. We have found Desulfovibrio was abundant in high-fat diet-induced Apcmin/+ mice, and DSV, a member of Desulfovibrio, triggered colonocyte proliferation of germ-free mice. Furthermore, the level of DSV progressively rose from healthy individuals to CRC patients. Flagella are important accessory structures of bacteria, which can help them colonize and enhance their invasive ability. We found that D. vulgaris flagellin (DVF) drove the proliferation, migration, and invasion of CRC cells and fostered the growth of CRC xenografts. DVF enriched the epithelial-mesenchymal transition (EMT)-associated genes and characterized the facilitation of DVF on EMT. Mechanistically, DVF induced EMT through a functional transmembrane receptor called leucine-rich repeat containing 19 (LRRC19). DVF interacted with LRRC19 to modulate the ubiquitination of tumor necrosis factor receptor-associated factor (TRAF)6, rather than TRAF2. This interaction drove the ubiquitination of pivotal molecule TAK1, further enhancing its autophosphorylation and ultimately contributing to EMT. Collectively, DVF interacts with LRRC19 to activate the TRAF6/TAK1 signaling pathway, thereby promoting the EMT of CRC. These data shed new light on the role of gut microbiota in CRC and establish a potential clinical therapeutic target.

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.

Uncovering de novo polyamine biosynthesis in the gut microbiome and its alteration in inflammatory bowel disease

Polyamines are important gut microbial metabolites known to affect host physiology, yet the mechanisms behind their microbial production remain incompletely understood. In this study, we developed a stable isotope-resolved metabolomic (SIRM) approach to track polyamine biosynthesis in the gut microbiome. Viable microbial cells were extracted from fresh human and mouse feces and incubated anaerobically with [U-13C]-labeled inulin (tracer). Liquid chromatography-high resolution mass spectrometry analysis revealed distinct 13C enrichment profiles for spermidine (SPD) and putrescine (PUT), indicating that the arginine-agmatine-SPD pathway contributes to SPD biosynthesis in addition to the well-known spermidine synthase pathway (PUT aminopropylation). Species differences were observed in the 13C enrichments of polyamines and related metabolites between the human and mouse microbiome. By analyzing the fecal metabolomics and metatranscriptomic data from an inflammatory bowel disease (IBD) cohort, we found significantly higher polyamine levels in IBD patients compared to healthy controls. Further investigations using single-strain SIRM and in silico analyses identified Bacteroides spp. as key contributors to polyamine biosynthesis, harboring essential genes for this process and potentially driving the upregulation of polyamines in IBD. Taken together, this study expands our understanding of polyamine biosynthesis in the gut microbiome and will facilitate the development of precision therapies to target polyamine-associated diseases.

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.

Roseburia hominis improves host metabolism in diet-induced obesity

Next-generation live biotherapeutics are promising to aid the treatment of obesity and metabolic diseases. Here, we reported a novel anti-obesity probiotic candidate, Roseburia hominis, that was depleted in stool samples of obese subjects compared with lean controls, and its abundance was negatively correlated with body mass index and serum triglycerides. Supplementation of R. hominis prevented body weight gain and disorders of glucose and lipid metabolism, prevented fatty liver, inhibited white adipose tissue expansion and brown adipose tissue whitening in mice fed with high-fat diet, and boosted the abundance of lean-related species. The effects of R. hominis could be partially attributed to the production of nicotinamide riboside and upregulation of the Sirtuin1/mTOR signaling pathway. These results indicated that R. hominis is a promising candidate for the development of next-generation live biotherapeutics for the prevention of obesity and metabolic diseases.

Importance of intestinal microflora: Dried toad skin-radix clematidis plasma component analysis and anti-CRC core target study

The focus of this study is to explore the impact of gut microbiota in different states on the blood components of couplet medications (dried toad skin and radix clematidis) and to identify drug metabolites associated with the gut microbiota. By constructing a pseudo-sterile rat model and combining non-targeted metabolomics with plasma pharmacology, we found that the plasma metabolites of couplet medications underwent significant changes in different gut microbiome environments. The GABA and PGE1 levels in the model group and the model+TCM (traditional chinese medicine) group were both significantly lower than those in the normal+TCM group. When the gut microbiota is imbalanced, drug interventions cannot significantly increase the levels of GABA and PGE1. It further confirmed the correlation between the levels of GABA and PGE1 and the gut microbiota. Based on the results of non-targeted metabolomics, we applied network pharmacology and molecular docking to explore the core targets for colorectal cancer treatment based on gut microbiota. In the end, we identified TNF and PPARG as the two core targets. These research findings provide a possibility for clarifying the molecular mechanisms of couplet medications in the treatment of colorectal cancer. It also laid the foundation for further clarifying the molecular mechanisms of Chanling Paste in the treatment of colorectal cancer.

Gut virome: New key players in the pathogenesis of inflammatory bowel disease

Inflammatory bowel disease (IBD) is a chronic inflammatory illness of the intestine. While the mechanism underlying the pathogenesis of IBD is not fully understood, it is believed that a complex combination of host immunological response, environmental exposure, particularly the gut microbiota, and genetic susceptibility represents the major determinants. The gut virome is a group of viruses found in great frequency in the gastrointestinal tract of humans. The gut virome varies greatly among individuals and is influenced by factors including lifestyle, diet, health and disease conditions, geography, and urbanization. The majority of research has focused on the significance of gut bacteria in the progression of IBD, although viral populations represent an important component of the microbiome. We conducted this review to highlight the viral communities in the gut and their expected roles in the etiopathogenesis of IBD regarding published research to date.

Hsa_circ_0000467 promotes colorectal cancer proliferation and stem cell characteristics by activating the TCF4/Wnt/β-catenin pathway via sponging miR-520g

This study explores the role of circ_0000467 in colorectal cancer (CRC) progression and its potential as a therapeutic target. Circ_0000467 expression was analyzed using public datasets and clinical samples from 103 CRC patients. Functional assays evaluated its influence on CRC cell proliferation, migration, and stem-like properties. Molecular interactions with miR-520g and TCF4 were examined, and in vivo experiments assessed tumor growth. Circ_0000467 was significantly overexpressed in CRC and associated with poor prognosis. Its upregulation enhanced tumor growth, invasion, epithelial-mesenchymal transition, and stem-like characteristics by increasing key markers (CD44, EpCAM, SOX2, and Nanog). Mechanistically, circ_0000467 acted as a molecular sponge for miR-520g, leading to increased TCF4 expression and activation of the Wnt/β-catenin pathway. Silencing TCF4 or overexpressing miR-520g reversed these effects. Circ_0000467 promotes CRC progression by regulating the TCF4/Wnt/β-catenin pathway through miR-520g, highlighting its potential as a biomarker and therapeutic target for CRC.

Beyond Random Fecal Microbial Transplants: Next Generation Personalized Approaches to Normalize Dysbiotic Microbiota for Treating IBD

This review and commentary outline the strong rationale for normalizing the abnormal microbiota of patients with ulcerative colitis, Crohn's disease, and pouchitis and focus on strategies to improve current variable outcomes of fecal microbial transplant (FMT) in ulcerative colitis. Applying lessons from successful FMT therapy of recurrent Clostridioides difficile and insights from basic scientific understanding of host/microbial interactions provide strategies to enhance clinical outcomes in IBD. We outline promising approaches to develop novel-defined consortia of live biotherapeutic products and combination treatments to improve current results and to optimize and personalize treatment approaches in individual patients and disease subsets.

Vaccarin treats lactation insufficiency through the ALKBH5-SFRP2-Wnt/β-catenin signaling pathway

ETHNOPHARMACOLOGIC SIGNIFICANCE

Vaccarin, a natural small molecule extracted from Gypsophila vaccaria (L.) Sm., is an active flavonoid glycoside.

BACKGROUND

Lactation insufficiency refers to insufficient milk secretion in women after childbirth, which affects the feeding of infants and even their development. Our preliminary experiments showed that alkylation repair homolog protein 5 (ALKBH5) was abnormally overexpressed in mammary tissue of lactation deficiency model rats, which played an important role in regulating milk secretion, but the mechanism was not clear, and no research reports were reported in this aspect.

PURPOSE

The aim of this study was to investigate whether Vaccarin (Vac) treated lactation insufficiency through the ALKBH5-SFRP2-Wnt/β-catenin signaling pathway.

METHODS

The lactation insufficiency model rats and primary cultured rat mammary epithelial cells (RMECs) were used as experimental subjects. RT-qPCR, Western blot, RNA Immunoprecipitation, immunofluorescence and related methods were used to study the mechanism of Vac treatment for lactation insufficiency.

RESULTS

Vac effectively increased the milk production, significantly improved the thickness and density of mammary ducts and follicles, and promoted the prolactin (PRL) secretion and the prolactin receptor (PRLR) expression in lactation insufficiency model rats. Vac significantly promoted the expression of FASN, CSN2, and GLUT1. ALKBH5 was upregulated in the mammary gland of model mice, promoting SFRP2 expression and inhibiting the Wnt/β-catenin signaling pathway and the expression of FASN, CSN2 and GLUT1. Furthermore, Vac inhibited the expression of SFRP2 by targeting the ALKBH5, and subsequently activated the Wnt/β-catenin signaling pathway to promote milk secretion in the lactation insufficiency model rats.

CONCLUSION

Vac promoted milk secretion and improved lactation insufficiency through the ALKBH5-SFRP2-Wnt/β-catenin signaling pathway.

Engineered Tissue Models to Decode Host-Microbiota Interactions

A mutualistic co-evolution exists between the host and its associated microbiota in the human body. Bacteria establish ecological niches in various tissues of the body, locally influencing their physiology and functions, but also contributing to the well-being of the whole organism through systemic communication with other distant niches (axis). Emerging evidence indicates that when the composition of the microbiota inhabiting the niche changes toward a pathogenic state (dysbiosis) and interactions with the host become unbalanced, diseases may present. In addition, imbalances within a single niche can cause dysbiosis in distant organs. Current research efforts are focused on elucidating the mechanisms leading to dysbiosis, with the goal of restoring tissue homeostasis. In vitro models can provide critical experimental platforms to address this need, by reproducing the niche cyto-architecture and physiology with high fidelity. This review surveys current in in vitro host-microbiota research strategies and provides a roadmap that can guide the field in further developing physiologically relevant in vitro models of ecological niches, thus enabling investigation of the role of the microbiota in human health and diseases. Lastly, given the Food and Drug Administration Modernization Act 2.0, this review highlights emerging in vitro strategies to support the development and validation of new therapies on the market.

Intestinal microbiota profiles of captive-bred cynomolgus macaques reveal influence of biogeography and age

BACKGROUND

Age-associated changes to the intestinal microbiome may be linked to inflammageing and the development of age-related chronic diseases. Cynomolgus macaques, a common animal model in biomedical research, have strong genetic physiological similarities to humans and may serve as beneficial models for the effect of age on the human microbiome. However, age-associated changes to their intestinal microbiome have previously only been investigated in faecal samples. Here, we have characterised and investigated the effects of age in the cynomolgus macaque intestinal tract in luminal samples from both the small and large intestine.

RESULTS

Whole metagenomic shotgun sequencing was used to analyse the microbial communities in intestinal content obtained from six different intestinal regions, covering the duodenum to distal colon, of 24 healthy, captive-bred cynomolgus macaques, ranging in age from 4 to 20 years. Both reference-based and assembly-based computational profiling approaches were used to analyse changes to intestinal microbiota composition and metabolic potential associated with intestinal biogeography and age. Reference-based computational profiling revealed a significant and progressive increase in both species richness and evenness along the intestinal tract. The microbial community composition also significantly differed between the small intestine, caecum, and colon. Notably, no significant changes in the taxonomic abundance of individual taxa with age were found except when sex was included as a covariate. Additionally, using an assembly-based computational profiling approach, 156 putative novel bacterial and archaeal species were identified.

CONCLUSIONS

We observed limited effects of age on the composition of the luminal microbiota in the profiled regions of the intestinal tract except when sex was included as a covariate. The enteric microbial communities of the small and the large intestine were, however, distinct, highlighting the limitations of frequently used faecal microbial profiling as a proxy for the intestinal microbiota. The identification of a number of putative novel microbial taxa contributes to knowledge of the full diversity of the cynomolgus macaque intestinal microbiome.

Therapeutic Potential and Translational Challenges for Bacterial Extracellular Vesicles in Inflammatory Bowel Disease

Despite the availability of numerous new immune-directed therapeutics, the major constituents of inflammatory bowel disease (IBD)-ulcerative colitis (UC) and Crohn's disease (CD)-continue to afflict millions worldwide, resulting in significant morbidity and long-term health risks. IBD results from a triad of immune, environmental (eg, gut microbiome), and genetic (including epigenetic) mechanisms, and therefore has been subject to a wide variety of therapeutic strategies. Among these, the administration of probiotics, particularly Gram-positive lactic acid bacteria (LAB), targeting both immune and environmental factors, has shown promising potential for efficacy in selected populations in early clinical trials. However, knowledge gaps and inconsistent efficacy currently prevent recommendations for the use of probiotics in larger IBD patient populations. The inconsistent efficacy of probiotics is likely due to variable cell viability and potency after administration, further exacerbated by IBD patient heterogeneity. Thus, an alternative to live probiotics for IBD has emerged in the form of bacterial extracellular vesicles (BEVs)-cell-secreted nanovesicles containing abundant bioactive cargo that, like live probiotics, can regulate immune and environmental factors but with fewer viability limitations and safety concerns. In this review, we summarize the work done to date establishing the potential of BEVs to provide the therapeutic benefits in IBD and discuss the hurdles BEVs must overcome to achieve clinical translation. We also consider future directions for BEV therapeutics, especially treatment potential for necrotizing enterocolitis (NEC), which shares similarities in pathophysiology with IBD.

Filamentous bacteriophage M13 induces proinflammatory responses in intestinal epithelial cells

Bacteriophages are the dominant members of the human enteric virome and can shape bacterial communities in the gut; however, our understanding of how they directly impact health and disease is limited. Previous studies have shown that specific bacteriophage populations are expanded in patients with Crohn's disease (CD) and ulcerative colitis (UC), suggesting that fluctuations in the enteric virome may contribute to intestinal inflammation. Based on these studies, we hypothesized that a high bacteriophage burden directly induces intestinal epithelial responses. We found that filamentous bacteriophages M13 and Fd induced dose-dependent IL-8 expression in the human intestinal epithelial cell line HT-29 to a greater degree than their lytic counterparts, T4 and ϕX174. We also found that M13, but not Fd, reduced bacterial internalization in HT-29 cells. This led us to investigate the mechanism underlying M13-mediated inhibition of bacterial internalization by examining the antiviral and antimicrobial responses in these cells. M13 upregulated type I and III IFN expressions and augmented short-chain fatty acid (SCFA)-mediated LL-37 expression in HT-29 cells. Taken together, our data establish that filamentous bacteriophages directly affect human intestinal epithelial cells. These results provide new insights into the complex interactions between bacteriophages and the intestinal mucosa, which may underlie disease pathogenesis.

Decreased Fecal Nicotinamide and Increased Bacterial Nicotinamidase Gene Expression in Ulcerative Colitis Patients

BACKGROUND/OBJECTIVE

Ulcerative colitis (UC) is significantly linked with gut microbiota, which is essential for maintaining gut health. Their metabolites mitigate gut inflammation and bolster barrier function. Among these metabolites, we focused on vitamin B3, which has been reported to improve the pathogenesis of UC in mice. This study aimed to compare fecal vitamin B3 and gut microbiota between non-UC and UC patients.

METHODS

We assessed fecal metabolites and gut microbiota in 71 UC patients (UC group) and 72 non-UC patients (non-UC group) matched by sex and age in 10-year intervals. Fecal samples were collected and metabolites were analyzed using capillary electrophoresis time-of-flight mass spectrometry. Bacterial DNA was extracted for 16S rRNA gene sequencing. We analyzed fecal nicotinamide levels and gut microbiota composition, employing statistical adjustments for confounding factors.

RESULTS

We found that the UC group exhibited significantly lower fecal nicotinamide levels and α-diversity (Shannon index) compared to the non-UC group. The relative abundance of bacterial genera such as Treponema, UCG-002, and Fusicatenibacter was decreased, while Sellimonas, Fournierella, and Oscillospira were increased in the UC group. Moreover, a negative correlation was observed between Sellimonas abundance and fecal nicotinamide levels in the UC group. Additionally, the UC group showed higher expression of a bacterial gene encoding nicotinamidase compared to the non-UC group.

CONCLUSIONS

These findings suggest that gut microbiota dysbiosis contributes to reduced vitamin B3 metabolism in UC patients. The study highlights the potential of replenishing vitamin B3 metabolic pathways as a novel therapeutic approach for UC treatment.

Dendritic Poly(l-lysine)-Based Nanoparticle Loading with siDNMT1 to Alleviate Basal Cell Carcinoma Progression by Inhibiting Methylation of AXIN2

Basal cell carcinoma (BCC) is a highly invasive and metastatic non-melanoma skin tumor. Traditional treatments, such as surgery, radiation, and chemotherapy, often result in severe side effects. Recent advances in RNA interference (RNAi) have highlighted its potential in targeting cancer-causing genes. To address the complex pathology of BCC, we developed a multifunctional gene delivery system using benzylthio-modified dendritic polylysine nanoparticles loaded with siDNMT1 (siDNMT1@PDPs). This system exhibits excellent dispersibility, with over 85% of particles measuring between 50 and 80 nm, and high stability, with a zeta potential of +57.10 mV. This design enables efficient penetration into tumor cells and controlled release of siDNMT1 in the tumor microenvironment (TME), thereby improving therapeutic outcomes. Our results demonstrate that siDNMT1@PDPs significantly inhibit tumor progression and metastasis in BCC by reducing AXIN2 promoter methylation, thereby increasing AXIN2 expression. Compared to existing treatments, siDNMT1@PDPs exhibit superior biocompatibility, both in vitro and in vivo, and provide a more targeted and effective therapeutic approach. These findings suggest that siDNMT1@PDPs represent a promising advancement in RNAi-based therapies for BCC, offering potential clinical benefits over current treatment modalities.

Nutritional Deficiencies and Reduced Bone Mineralization in Ulcerative Colitis

Background: Inadequate dietary intake of vitamin D, vitamin K, and calcium, as well as sub-optimal sunlight exposure, can lead to bone loss in the general population, and more so in patients with ulcerative colitis, who are burdened by additional predisposing factors for osteoporosis, such as chronic inflammation and cortisone use. However, micronutrient deficiencies, if present, are easily corrected by nutritional intervention. While the relation between calcium and vitamin D and bone metabolism is well known, fewer data are available for vitamin K, for both healthy individuals and patients. The aim of this review is to provide an overview of recent reports focusing on nutritional deficits relevant to the development of osteoporosis/osteopenia in patients affected by ulcerative colitis. Methods: A systematic electronic search of the English literature up to January 2025 was performed using Medline and the Cochrane Library. Results: Despite being central in bone mineralization, data on dietary calcium intake in ulcerative colitis are relatively scarce, deriving mostly from mixed inflammatory bowel disease cohorts. Although lower than controls, dietary calcium intake approaches the recommended daily allowance, which establishes the necessary daily intake of nutrients. Conversely, vitamin D and vitamin K deficiencies are highly prevalent in ulcerative colitis patients. The widely shared opinion that milk and lactose-containing foods, as well as vegetables, worsen diarrhea is a prime determinant of inadequate vitamin D and vitamin K intake. Conclusions: Increased awareness of the importance of nutrition and the common occurrence of nutritional deficits represents the first step for the development of dietary intervention strategies to counteract the increased risk of osteoporosis in ulcerative colitis patients.

RNF6 Inhibits Lung Adenocarcinoma Cell Proliferation by Promoting Cyclin D2 Degradation

The E3 ubiquitin ligase RING finger protein 6 (RNF6) has been widely recognized for its role in promoting tumorigenesis in multiple cancers. However, we found that it is downregulated in lung adenocarcinoma (LUAD), and the molecular rationale for this discrepancy remains unclear. In the present study, we find that RNF6, but not its ΔRING inactive form, inhibits LUAD cell proliferation and migration and sensitizes LUAD to chemotherapy. To understand the molecular mechanism, we utilize affinity purification/tandem mass spectrometry (MS-MS) to analyze RNF6-interacting proteins and find that cyclin D2 (CCND2), a key regulator of the G1-S transition in the cell cycle. RNF6 physically binds to CCND2 and mediates its K48-linked polyubiquitination and subsequent degradation. However, ΔRING RNF6 fails to mediate CCND2 for ubiquitination and degradation. Moreover, Thr280 is critically important for CCND2 stability. When Thr280 is mutated, CCND2 becomes more stable and less ubiquitinated by RNF6. Furthermore, RNF6 arrests LUAD cell cycle at the G1 phase by inhibiting the CCND2/phospho-Rb signaling pathway, which is consistent with decreased cell proliferation. Lastly, RNF6 curtails the growth of LUAD xenografts in vivo, associated with decreased CCND2 expression. Therefore, RNF6 is a novel E3 ligase of CCND2 and suppresses LUAD cell proliferation. Implications: This study reveals a novel regulation on cell-cycle transition in LUAD and suggests the RNF6/CCND2 axis may represent an alternative therapeutic target for the treatment of LUAD.

A Consensus Statement on establishing causality, therapeutic applications and the use of preclinical models in microbiome research

The gut microbiome comprises trillions of microorganisms and profoundly influences human health by modulating metabolism, immune responses and neuronal functions. Disruption in gut microbiome composition is implicated in various inflammatory conditions, metabolic disorders and neurodegenerative diseases. However, determining the underlying mechanisms and establishing cause and effect is extremely difficult. Preclinical models offer crucial insights into the role of the gut microbiome in diseases and help identify potential therapeutic interventions. The Human Microbiome Action Consortium initiated a Delphi survey to assess the utility of preclinical models, including animal and cell-based models, in elucidating the causal role of the gut microbiome in these diseases. The Delphi survey aimed to address the complexity of selecting appropriate preclinical models to investigate disease causality and to study host-microbiome interactions effectively. We adopted a structured approach encompassing a literature review, expert workshops and the Delphi questionnaire to gather insights from a diverse range of stakeholders. Experts were requested to evaluate the strengths, limitations, and suitability of these models in addressing the causal relationship between the gut microbiome and disease pathogenesis. The resulting consensus statements and recommendations provide valuable insights for selecting preclinical models in future studies of gut microbiome-related diseases.

A Mutual Interaction Between GSTP1 and p53 Improves the Drug Resistance and Malignant Biology of Pancreatic Cancer

Glutathione S-transferase P1 (GSTP1), a classic tumor biomarker, plays a controversial role in cancer progression. However, its specific role in pancreatic cancer (PC) has rarely been investigated. In the present study, we investigated the function and relationship between GSTP1 and mutant/wild-type p53 (mtp53/wtp53) in PC in vitro and in vivo. Compared with paired adjacent normal pancreas tissue, GSTP1 was downregulated in PC tissue, which was closely correlated with lymph node metastasis, Union for International Cancer Control (UICC) stage, and a better outcome of PC patients, processes dependent on wtp53 rather than mtp53. Moreover, a mutual regulation between GSTP1 and p53 was found in wtp53 PC cells. GSTP1 overexpression inhibited cell proliferation and chemotherapy resistance in vitro via wtp53/p21 and Bax/Bcl2 signaling, which was significantly reversed by wtp53 silencing, and vice versa. Similarly, the coordination of GSTP1 and p53 regulated the invasion and migration of PC cells, which was accompanied by changes in epithelial-mesenchymal transition (EMT) signaling (E-cad, ZO-1 and MMP9). Moreover, GSTP1 overexpression inhibited tumor growth and liver metastasis in vivo, as did high wtp53 and low ki67 expression. Interestingly, GSTP1 did not coimmunoprecipitate with either mtp53 or wtp53 in vitro. However, the wtp53 protein, as a transcription factor, could bind to the GSTP1 DNA promoter to transactivate GSTP1 mRNA expression as demonstrated via a Chip assay. Additionally, GSTP1 promoted the translocation of wtp53 into the nucleus but not mtp53. These results suggest that the positive feedback regulation of GSTP1 and wtp53 plays a significant role in cell proliferation, drug resistance, cell invasion and metastasis in PC.

Food-related Quality of Life in patients with Inflammatory Bowel Disease: Translation and Validation of the German version of FR-QoL-29

The psychosocial effects of eating and drinking - summarized as food-related quality of life (FR-QoL) - are underexplored in inflammatory bowel disease (IBD). Currently, there is no German instrument to assess FR-QoL in IBD patients. This study aimed to translate the validated English FR-QoL-29 questionnaire into German and evaluate its validity and reliability.A monocentric, cross-sectional study was conducted at a tertiary referral center with IBD patients and healthy controls. Participants completed questionnaires on sociodemographics, disease history, the Malnutrition Universal Screening Tool (MUST), the German Short Health Scale (SHS), and the FR-QoL-29-German. The FR-QoL-29 was translated into German using a forward-backward method. Its reliability and validity was assessed using Pearson correlation coefficients, intraclass correlation coefficients, and Cronbach's α.N=200 IBD patients (Crohn's disease: 61.8%; women: 50.8%; remission: 56.2%) and n=10 healthy controls completed the questionnaires. Overall, 113 IBD patients repeated the questionnaires after an average of six weeks. Significant differences in FR-QoL-29-German sum scores were found between all levels of IBD disease activity, except for remission - mild disease (p = 0.423) and moderate - severe disease (p = 0.999). FR-QoL-29-German scores significantly correlated with age (p = 0.041), disease activity (p < 0.001), MUST (p = 0.015), fecal Calprotectin (p = 0.011) and SHS (p < 0.001). Overall, the FR-QoL-29-German showed excellent internal consistency (Cronbach's α = 0.965) and good test-retest reliability (ICC = 0.85 [95% CI: 0.78-0.89]).The FR-QoL-29-German is a valid and reliable tool for assessing food-related quality of life in German-speaking individuals with IBD.

Assessing the safety of microbiome perturbations

Everyday actions such as eating, tooth brushing or applying cosmetics inherently modulate our microbiome. Advances in sequencing technologies now facilitate detailed microbial profiling, driving intentional microbiome-targeted product development. Inspired by an academic-industry workshop held in January 2024, this review explores the oral, skin and gut microbiomes, focussing on the potential long-term implications of perturbations. Key challenges in microbiome safety assessment include confounding factors (ecological variability, host influences and external conditions like geography and diet) and biases from experimental measurements and bioinformatics analyses. The taxonomic composition of the microbiome has been associated with both health and disease, and perturbations like regular disruption of the dental biofilm are essential for preventing caries and inflammatory gum disease. However, further research is required to understand the potential long-term impacts of microbiome disturbances, particularly in vulnerable populations including infants. We propose that emerging technologies, such as omics technologies to characterize microbiome functions rather than taxa, leveraging artificial intelligence to interpret clinical study data and in vitro models to characterize and measure host-microbiome interaction endpoints, could all enhance the risk assessments. The workshop emphasized the importance of detailed documentation, transparency and openness in computational models to reduce uncertainties. Harmonisation of methods could help bridge regulatory gaps and streamline safety assessments but should remain flexible enough to allow innovation and technological advancements. Continued scientific collaboration and public engagement are critical for long-term microbiome monitoring, which is essential to advancing safety assessments of microbiome perturbations.

Learning a deep language model for microbiomes: The power of large scale unlabeled microbiome data

We use open source human gut microbiome data to learn a microbial "language" model by adapting techniques from Natural Language Processing (NLP). Our microbial "language" model is trained in a self-supervised fashion (i.e., without additional external labels) to capture the interactions among different microbial taxa and the common compositional patterns in microbial communities. The learned model produces contextualized taxon representations that allow a single microbial taxon to be represented differently according to the specific microbial environment in which it appears. The model further provides a sample representation by collectively interpreting different microbial taxa in the sample and their interactions as a whole. We demonstrate that, while our sample representation performs comparably to baseline models in in-domain prediction tasks such as predicting Irritable Bowel Disease (IBD) and diet patterns, it significantly outperforms them when generalizing to test data from independent studies, even in the presence of substantial distribution shifts. Through a variety of analyses, we further show that the pre-trained, context-sensitive embedding captures meaningful biological information, including taxonomic relationships, correlations with biological pathways, and relevance to IBD expression, despite the model never being explicitly exposed to such signals.

Composition of plant-based diets and the incidence and prognosis of inflammatory bowel disease: a multinational retrospective cohort study

Background

Many currently proposed diets for inflammatory bowel disease (IBD) focus on increasing plant-based foods, although a vegetarian diet can still contain products such as emulsifiers and refined grains that are believed to negatively impact IBD incidence and progression. To better inform dietary management in IBD, we investigated the association between plant-based diets and the incidence and complications of IBD.

Methods

We leveraged data from the UK Biobank (UKB, 2009-2022) including 187,888 participants free of IBD at baseline and the European Prospective Investigation into Cancer and Nutrition (EPIC, 1991-2010) cohort including 341,539 individuals free of IBD across centres among Denmark, France, Germany, Greece, Italy, the Netherlands, Sweden and UK. Healthy and unhealthy diets were characterised using plant-based diet indexes (PDIs); in individual participants, these were based on the 24-h dietary recalls for UKB and food frequency questionnaires for EPIC. The primary outcome was the incidence of IBD; secondary outcomes evaluated endpoints of disease prognosis (IBD-related surgery, diabetes, cardiovascular diease, and all-cause mortality). Cox regression was applied to estimate hazard ratios (HRs).

Findings

In the UKB (925 incident IBD, median follow-up 11.6 years, IQR 1.3 years), higher adherence to healthy PDI was associated with a lower IBD risk (HR 0.75, 95% CI 0.60-0.94), while higher alignment to an unhealthy PDI associated with an increased risk (HR 1.48, 95% CI 1.21-1.82) when comparing extreme quintiles of PDIs. Among individuals with established IBD, healthy PDI was inversely associated (HR 0.50, 95% CI 0.30-0.83) and unhealthy PDI was positively associated (HR 2.12, 95% CI 1.30-3.44) with need for IBD-related surgery. We did not observe significant associations between PDIs and risk of cardiovascular disease, diabetes mellitus or mortality. In the EPIC study (548 incident IBD, median follow-up 14.5 years, IQR 7.0 years), the HR of incident IBD for healthy PDI was 0.71 (95% CI 0.59-0.85) and for unhealthy PDI was 1.54 (95% CI 1.30-1.84).

Interpretation

We provide evidence that the composition of a plant-based diet may be an important determinant of the risk of developing IBD, and of disease course after diagnosis. Further research is needed to explore the mechanistic pathways linking plant-based diets and IBD incidence and prognosis.

Funding

National Natural Science Foundation of China, Natural Science Fund for Distinguished Young Scholars of Zhejiang Province, National Undergraduate Training Program for Innovation and Entrepreneurship, CRUK Career Development Fellowship, The "Co-PI" project, Natural Science Fund for Excellent Young Scholars of Hunan Province.

Smart Bioelectronics for Real-Time Diagnosis and Therapy of Body Organ Functions

Noncommunicable diseases (NCDs) associated with cardiovascular, neurological, and gastrointestinal disorders remain a leading cause of global mortality, sounding the alarm for the urgent need for better diagnostic and therapeutic solutions. Wearable and implantable biointegrated electronics offer a groundbreaking solution, combining real-time, high-resolution monitoring with innovative treatment capabilities tailored to specific organ functions. In this comprehensive review, we focus on the diseases affecting the brain, heart, gastrointestinal organs, bladder, and adrenal gland, along with their associated physiological parameters. Additionally, we provide an overview of the characteristics of these parameters and explore the potential of bioelectronic devices for in situ sensing and therapeutic applications and highlight the recent advancements in their deployment across specific organs. Finally, we analyze the current challenges and prospects of implementing closed-loop feedback control systems in integrated sensor-therapy applications. By emphasizing organ-specific applications and advocating for closed-loop systems, this review highlights the potential of future bioelectronics to address physiological needs and serves as a guide for researchers navigating the interdisciplinary fields of diagnostics, therapeutics, and personalized medicine.

Helicobacter pylori CagA elevates FTO to induce gastric cancer progression via a "hit-and-run" paradigm

BACKGROUND

Helicobacter pylori (H. pylori) infection contributes significantly to gastric cancer (GC) progression. The intrinsic mechanisms of H. pylori-host interactions and their role in promoting GC progression need further investigation. In this study, we explored the potential role of fat mass and obesity-associated protein (FTO) in mediating Cytotoxin-associated gene A (CagA)-induced GC progression.

METHODS

The effects of H. pylori infection on N6-methyladenosine (m6A) modification were evaluated in both human samples and GC cell lines. The function of FTO in the progression of GC was elucidated through in vitro and in vivo studies. A series of techniques, including methylated RNA immunoprecipitation sequencing, RNA sequencing, RNA binding protein immunoprecipitation, and chromatin immunoprecipitation assays, were utilized to investigate the mechanism by which FTO mediates the capacity of cagA-positive H. pylori to promote GC progression. Furthermore, the therapeutic potential of the FTO inhibitor meclofenamic acid (MA) in impeding GC progression was evaluated across GC cells, animal models, and human GC organoids.

RESULTS

Infection with cagA-positive H. pylori upregulated the expression of FTO, which was essential for CagA-mediated GC metastasis and significantly associated with a poor prognosis in GC patients. Mechanistically, CagA delivered by H. pylori enhanced FTO transcription via Jun proto-oncogene. Elevated FTO induced demethylation of m6A and inhibited the degradation of heparin-binding EGF-like growth factor (HBEGF), thereby facilitating the epithelial-mesenchymal transition (EMT) process in GC cells. Interestingly, eradication of H. pylori did not fully reverse the increases in FTO and HBEGF levels induced by cagA-positive H. pylori. However, treatment with a combination of antibiotics and MA substantially inhibited cagA-positive H. pylori-induced EMT and prevented GC metastasis.

CONCLUSION

Our study revealed that FTO mediates the "hit-and-run" mechanism of CagA-induced GC progression, which suggests that the therapeutic targeting of FTO could offer a promising approach to the prevention of CagA-induced cancer progression.

Dietary Relationships between Obesity and Inflammatory Bowel Diseases: A Narrative Review of Diets Which May Promote Both Diseases

PURPOSE OF REVIEW

The pandemic of obesity preceded global spread of Inflammatory Bowel diseases by almost 2 decades. A pathogenic relationship has been described between obesity and inflammatory bowel diseases, but Crohn`s disease may be selectively impacted. The role of diet in pathogenesis has also gained significant support in the last few decades. This review explores dietary relationships to account for epidemiological observations. Quantifiable indices for diets have been described including a glycemic index, inflammatory indices and levels of food processing. Meta-analyses have been published which examine each for effects on obesity and co-morbidities as well as Crohn's disease and ulcerative colitis. This review suggests that ultra-processed foods provide the best link between obesity and Crohn's disease explaining epidemiological observations. However, the other 2 types of dietary indices likely contribute to ulcerative colitis as well as to co-morbidities related to both obesity and inflammatory bowel diseases. The term ultra-processed foods cover a large number of additives and extensive work is needed to define individual or combined harmful effects. Furthermore, the interactions among the 3 main indices need clarification in order to precisely apply therapeutic diets to both diseases (obesity and inflammatory bowel disease).

Association between sphingomyelin levels and gut microbiota abundance in Alzheimer's disease: a two-sample Mendelian randomization study

BACKGROUND

Several previous observational studies have shown that abnormal sphingomyelin metabolism may be implicated in the pathogenesis of Alzheimer's disease. To determine the causal relationship between sphingolipid abundance and gut microbiota abundance at the genetic level, we conducted a Mendelian randomization (MR) investigation.

METHODS

We first used the TwoSampleMR and MRPRESSO packages for conducting two-sample MR studies. Second, we utilized random effect inverse variance weighting (IVW) as the principal method of analysis and used MR‒Egger, the weighted median, the simple mode and the weighted mode as supplementary methods. Finally, we performed tests for heterogeneity and horizontal pleiotropy. These analyses were also conducted to evaluate the impact of individual SNPs on the outcomes of our analysis. A Bonferroni-corrected threshold of p = 2.4e-4(0.05/211) was considered significant, and p values less than 0·05 were considered to be suggestive of an association.

RESULTS

The results showed that sphingolipid levels were suggestively associated with the abundance of 6 gut microbiota taxa. Specifically, two taxa were positively correlated with sphingolipid levels, including the family Alcaligenaceae (p = 0.006, OR 95% CI = 1.109 [1.030-1.194]) and the species Ruminococcus callidus (p = 0.034, OR 95% CI = 1.217 [1.015-1.460]). In contrast, negative correlations were observed with the abundances of 4 gut microbiota taxa, including the genus Flavonifractor (p = 0.026, OR 95% CI = 0.804 [0.663-0.974]), the genus Streptococcus (p = 0.014, OR 95% CI = 0.909 [0.842-0.981]), the species Bacteroides caccae (p = 0.037, OR 95% CI = 0.870 [0.763-0.992]), and the species Haemophilus parainfluenzae (p = 0.006, beta 95% CI = -0.269 [-0.462, -0.076]). The results presented a normal distribution, with no anomalous values, heterogeneity, or horizontal pleiotropic effects detected.

CONCLUSIONS

This two-sample MR study revealed a potential causal relationship between sphingomyelin levels and gut microbiota abundance.

Gut microbiota - bidirectional modulator: role in inflammatory bowel disease and colorectal cancer

The gut microbiota is a diverse ecosystem that significantly impacts human health and disease. This article focuses on how the gut microbiota interacts with inflammatory bowel diseases and colorectal tumors, especially through immune regulation. The gut microbiota plays a role in immune system development and regulation, while the body's immune status can also affect the composition of the microbiota. These microorganisms exert pathogenic effects or correct disease states in gastrointestinal diseases through the actions of toxins and secretions, inhibition of immune responses, DNA damage, regulation of gene expression, and protein synthesis. The microbiota and its metabolites are essential in the development and progression of inflammatory bowel diseases and colorectal tumors. The complexity and bidirectionality of this connection with tumors and inflammation might render it a new therapeutic target. Hence, we explore therapeutic strategies for the gut microbiota, highlighting the potential of probiotics and fecal microbiota transplantation to restore or adjust the microbial community. Additionally, we address the challenges and future research directions in this area concerning inflammatory bowel diseases and colorectal tumors.

The Discovery of Phages in the Substantia Nigra and Its Implication for Parkinson's Disease

Background: A century ago, a mystery between a virus and Parkinson's disease (PD) was described. Owing to the limitation of human brain biopsy and the challenge of electron microscopy in observing virions in human brain tissue, it has been difficult to study the viral etiology of PD. Recent discovery of virobiota reveals that viruses coexist with humans as symbionts. Newly developed transcriptomic sequencing and novel bioinformatic approaches for mining the encrypted virome in human transcriptome make it possible to study the relationship between symbiotic viruses and PD. Nevertheless, whether viruses exist in the human substantia nigra (SN) and whether symbiotic viruses underlie PD pathogenesis remain unknown. Methods: We collected current worldwide human SN transcriptomic datasets from the United States, the United Kingdom, the Netherlands, and Switzerland. We used bioinformatic approaches including viruSITE and the Viral-Track to identify the existence of viruses in the SN of patients. The comprehensive RNA sequencing-based virome analysis pipeline was used to characterize the virobiota in the SN. The Pearson's correlation analysis was used to examine the association between the viral RNA fragment counts (VRFCs) and PD-related human gene sequencing reads in the SN. The differentially expressed genes (DEGs) in the SN between PD patients and non-PD individuals were used to examine the molecular signatures of PD and also evaluate the impact of symbiotic viruses on the SN. Findings: We observed the existence of viruses in the human SN. A dysbiosis of virobiota was found in the SN of PD patients. A marked correlation between VRFC and PD-related human gene expression was detected in the SN of PD patients. These PD-related human genes correlated to VRFC were named as the virus-correlated PD-related genes (VPGs). We identified 3 bacteriophages (phages), including the Proteus phage VB_PmiS-Isfahan, the Escherichia phage phiX174, and the Lactobacillus phage Sha1, that might impair the gene expression of neural cells in the SN of PD patients. The Proteus phage VB_PmiS-Isfahan was a common virus in the SN of patients from the United Kingdom, the Netherlands, and Switzerland. VPGs and DEGs together highlighted that the phages might dampen dopamine biosynthesis and weaken the cGAS-STING function. Interpretation: This is the first study to discover the involvement of phages in PD pathogenesis. A lifelong low symbiotic viral load in the SN may be a contributor to PD pathogenesis. Our findings unlocked the black box between brain virobiota and PD, providing a novel insight into PD etiology from the perspective of phage-human symbiosis.

Crosstalk Between Bile Acids and Intestinal Epithelium: Multidimensional Roles of Farnesoid X Receptor and Takeda G Protein Receptor 5

Bile acids and their corresponding intestinal epithelial receptors, the farnesoid X receptor (FXR), the G protein-coupled bile acid receptor (TGR5), play crucial roles in the physiological and pathological processes of intestinal epithelial cells. These acids and receptors are involved in the regulation of intestinal absorption, signal transduction, cellular proliferation and repair, cellular senescence, energy metabolism, and the modulation of gut microbiota. A comprehensive literature search was conducted using PubMed, employing keywords such as bile acid, bile acid receptor, FXR (nr1h4), TGR5 (gpbar1), intestinal epithelial cells, proliferation, differentiation, senescence, energy metabolism, gut microbiota, inflammatory bowel disease (IBD), colorectal cancer (CRC), and irritable bowel syndrome (IBS), with a focus on publications available in English. This review examines the diverse effects of bile acid signaling and bile receptor pathways on the proliferation, differentiation, senescence, and energy metabolism of intestinal epithelial cells. Additionally, it explores the interactions between bile acids, their receptors, and the microbiota, as well as the implications of these interactions for host health, particularly in relation to prevalent intestinal diseases. Finally, the review highlights the importance of developing highly specific ligands for FXR and TGR5 receptors in the context of metabolic and intestinal disorders.

Ampullary tumors exhibit increased Fusobacterium in both the tumor surface and surrounding duodenal mucosa during carcinoma progression

Understanding the complex interplay between intestinal microbiomes and ampullary tumors is crucial for distinguishing between adenomas and carcinomas, especially when considering the role of Fusobacterium. We characterized the microbiome associated with ampullary tumors using samples collected from the tumor surface (tumor samples, TSs) and surrounding normal duodenal mucosa (normal samples, NSs) via brush rubbing. In total, samples from 17 patients, divided into an adenoma group (n = 11) and a carcinoma group (n = 6), were analyzed. The Shannon α-diversity index was significantly higher in the carcinoma group compared with the adenoma group, indicating a more diverse bacterial community in the carcinoma environment. The TSs of the carcinoma group exhibited enrichment of Fusobacterium, Leptotrichia, Methylorubrum, and Micrococcus. The relative abundance of Fusobacterium increased as the tumor progressed. The NSs of the carcinoma group showed a higher presence of Fusobacterium, Porphyromonas, Granulicatella, Rikenellaceae RC9 gut group, and Solobacterium, whereas Bergeyella was more prevalent in the adenoma group. These results suggest that ampullary carcinomas exhibit a characteristic microbiome compared to adenomas. Fusobacterium is enriched in the tumor and surrounding normal duodenal mucosa, increases in abundance as the tumor progresses, and may be associated with ampullary tumors.

Gene mutations and differentiation in laryngeal and pharyngeal squamous cell carcinoma

OBJECTIVE

To explore the characteristics of genomic variation patterns in Chinese patients with laryngeal and pharyngeal squamous cell carcinoma (SCC) and their correlation with differentiation and clinical significance.

METHODS

We analyzed genomic variations in 45 patients. Mutation patterns were evaluated using the 688 panel. We evaluated the correlation among degree of differentiation, patient prognosis, and mutation status and also analyzed 564 HNSCC samples from the UALCAN database.

RESULTS

Significant differences were observed in overall survival (OS) and progression-free survival (PFS) among patients with different degrees of differentiation. Based on the DriverML model, we found that the genes with the highest mutation rates were neurogenic locus notch homolog protein 1 (NOTCH1), tumor protein 53 (TP53), FAT atypical cadherin 1 (FAT1), and mitogen-activated protein kinase kinase kinase 4 (MAP3 K4) (over 30%). We are the first to our knowledge to propose that MAP3 K4 (33%) may be a driving gene for Chinese SCC patients. Moreover, NOTCH1 and CUB and sushi multiple domains 3 (CSMD3) were mutually exclusive (p < 0.05). CSMD3 mutations were primarily found in poorly differentiated patients (83%, 5/6). Furthermore, NOTCH1wild and MAP3 K4wild were mainly present in poorly differentiated patients (p = 0.011) as well. We also validated the differential expression of NOTCH1 and MAP3 K4 and their association (p < 0.05) with tumor differentiation using 564 HNSCC samples from the UALCAN database.

CONCLUSION

We identified a potential new driving gene, MAP3 K4, in Chinese SCC patients and confirmed that the interaction between NOTCH1-MAP3 K4 may affect the differentiation of laryngeal and pharyngeal SCC. However, further exploration and large-scale sample validation are needed.

Abundance measurements reveal the balance between lysis and lysogeny in the human gut microbiome

The human gut contains diverse communities of bacteriophage, whose interactions with the broader microbiome and potential roles in human health are only beginning to be uncovered. Here, we combine multiple types of data to quantitatively estimate gut phage population dynamics and lifestyle characteristics in human subjects. Unifying results from previous studies, we show that an average human gut contains a low ratio of phage particles to bacterial cells (∼1:100) but a much larger ratio of phage genomes to bacterial genomes (∼4:1), implying that most gut phage are effectively temperate (e.g., integrated prophage and phage-plasmids). By integrating imaging and sequencing data with a generalized model of temperate phage dynamics, we estimate that phage induction and lysis occur at a low average rate (∼0.001-0.01 per bacterium per day), imposing only a modest fitness burden on their bacterial hosts. Consistent with these estimates, we find that the phage composition of a diverse synthetic community in gnotobiotic mice can be quantitatively predicted from bacterial abundances alone while still exhibiting phage diversity comparable to native human microbiomes. These results provide a foundation for interpreting existing and future studies on links between the gut virome and human health.

Human Milk Oligosaccharides Modulating Inflammation in Infants, Adults, and Older Individuals-From Concepts to Applications

The increasing global prevalence of inflammatory diseases, such as ulcerative colitis and irritable bowel syndrome, represents a challenging task for healthcare systems. Several approaches to disease management target the intestinal microbiome, which plays a key role in health and disease. One promising approach is modulating the microbiome using human milk oligosaccharides (HMOs). Originating from human milk, HMOs are indigestible carbohydrates that act in a host-optimized prebiotic fashion by providing an energy source for health-promoting intestinal bacteria and exhibiting systemic effects. Commercial products supporting infant health and development have been the primary fields of HMO application. Advancements in the large-scale production of HMOs through bioengineering and precision fermentation have led to evaluation of their potential for managing inflammatory diseases. Several in vitro studies and observations on model systems have been clinically validated in infants, resulting in a large body of evidence supporting the safety and efficacy of HMOs in inflammatory disorders. Although novel approaches seek to explore interventions in adults, the primary goal for the future is to provide cost-efficient, safe, and reliable healthcare compounds across all age groups.

Comparison of phage and plasmid populations in the gut microbiota between Parkinson's disease patients and controls

The aging population worldwide is on the rise, leading to a higher number of Parkinson's disease (PD) cases each year. PD is presently the second most prevalent neurodegenerative disease, affecting an estimated 7-10 million individuals globally. This research aimed to identify mobile genetic elements in human fecal samples using a shotgun metagenomics approach. We identified over 44,000 plasmid contigs and compared plasmid populations between PD patients (n = 68) and controls (n = 68). Significant associations emerged between groups (control vs PD) based on plasmid alpha and beta diversity. Moreover, the gene populations present on plasmids displayed marked differences in alpha and beta diversity between PD patients and controls. We identified a considerable number of phage contigs that were differentially abundant in the two groups. We also developed a predictive machine learning model based on phage abundance data, achieving a mean Area Under the Curve (AUC) of 0.74 with a standard deviation of 0.105 and a mean F1 score of 0.68 with a standard deviation of 0.14 across cross-validation folds, indicating moderate discriminatory power. Additionally, when tested on external data, the model yielded an AUC of 0.74 and an F1 score of 0.8, further demonstrating the predictive potential of phage populations in Parkinson's disease. Further, we improved the continuity and identification of the protein coding regions of the phage contigs by implementing alternative genetic codes.

Faecal microbiota transplantation in Crohn's disease: an Australian randomised placebo-controlled trial protocol

INTRODUCTION

The enteric microbiota drives inflammation in Crohn's disease. Yet, there are no placebo controlled trials evaluating the efficacy and safety of faecal microbiota transplantation (FMT) in inducing and maintaining remission in patients with active Crohn's disease. The Microbial Restoration (MIRO) study aims to establish this evidence.

METHODS AND ANALYSIS

At two specialist inflammatory bowel disease centres, 120 enrolled patients will have a 3-week period of diet optimisation (removal of ultra-processed foods) together with a 7-day course of antibiotics (to facilitate subsequent FMT engraftment). Patients will then be stratified to upper gut (for disease proximal to the splenic flexure) or lower gut (distal to the splenic flexure) disease. Patients will then be randomised in a 2:1 ratio to receive anaerobically prepared stool or placebo for 8 weeks either by gastroscopy, or colonoscopy and enemas. Clinical response at 8 weeks (Crohn's Disease Activity Index (CDAI) reduction ≥100 points or to <150 points) is the primary outcome measure. Non-responders to placebo and partial responders to FMT (CDAI decrease <100 but >70) receive FMT for weeks 8-16.Patients achieving clinical response from FMT after 8 or 16 weeks will be randomised in a 1:1 ratio to either a 44-week maintenance phase of FMT or placebo. Patients will receive FMT from one donor throughout the study.The MIRO study will establish whether FMT is an effective and safe therapy to induce and maintain remission in patients with active Crohn's disease.

ETHICS AND DISSEMINATION

Ethical approval has been received by the St Vincent's Hospital Melbourne Human Research Ethics Committee (HREC-A 084/21). The results will be disseminated in peer-reviewed journals and presented at international conferences.

TRIAL REGISTRATION NUMBER

ClinicalTrials.gov: NCT04970446; Registered on 20 July 2021.

A systematic review on the role of gut microbiome in inflammatory bowel disease: Spotlight on virome and plant metabolites

Inflammatory bowel diseases (IBD), including ulcerative colitis and Crohn's disease, arise from various factors such as dietary, genetic, immunological, and microbiological influences. The gut microbiota plays a crucial role in the development and treatment of IBD, though the exact mechanisms remain uncertain. Current research has yet to definitively establish the beneficial effects of the microbiome on IBD. Bacteria and viruses (both prokaryotic and eukaryotic) are key components of the microbiome uniquely related to IBD. Numerous studies suggest that dysbiosis of the microbiota, including bacteria, viruses, and bacteriophages, contributes to IBD pathogenesis. Conversely, some research indicates that bacteria and bacteriophages may positively impact IBD outcomes. Additionally, plant metabolites play a crucial role in alleviating IBD due to their anti-inflammatory and microbiome-modulating properties. This systematic review discusses the role of the microbiome in IBD pathogenesis and evaluates the potential connection between plant metabolites and the microbiome in the context of IBD pathophysiology.

UBTF facilitates acute myeloid leukemia development and immune escape via PD-L1 regulation

UBTF has been implicated in the development of multiple cancers, yet its specific biological function in acute myeloid leukemia (AML) remains unclear. This study utilized expression profiles and clinical data from The Cancer Genome Atlas (TCGA) and Therapeutically Applicable Research to Generate Effective Treatments (TARGET) databases, with UBTF expression data obtained from the GEPIA database. Analysis via the R software package CIBERSORT explored immune cell infiltration levels under different UBTF expression levels. LASSO Cox analysis with optimized penalty parameters identified genes associated with survival outcomes, leading to the construction of a prognostic risk model using multivariate Cox regression analysis. Prognostic significance was evaluated and validated through Kaplan-Meier survival analysis and receiver operating characteristic curve analysis. Experimental validation using stable AML cell lines with UBTF overexpression or knockdown, transcriptome sequencing, and a CD8+ T cell killing assay were performed. Ultimately, in vivo experimental validation was conducted. Results revealed that UBTF is overexpressed in AML compared to normal tissues and correlates with poor clinical prognosis. UBTF overexpression is associated with increased expression of PD-L1 (CD274) and immune cell infiltration, suggesting its role in promoting AML progression via PD-L1 (CD274)-mediated immune evasion. These findings highlight UBTF as a potential prognostic biomarker and a novel therapeutic target for tumor immunotherapy in AML.

Deciphering Gut Microbiome in Colorectal Cancer via Robust Learning Methods

BACKGROUND

Colorectal cancer (CRC) is one of the most prevalent cancers worldwide and is closely linked to the gut microbiota. Identifying reproducible and generalizable microbial signatures holds significant potential for enhancing early detection and advancing treatment for this deadly disease.

METHODS

This study integrated various publicly available case-control datasets to identify microbial signatures for CRC. Alpha and beta diversity metrics were evaluated to characterize differences in gut microbial richness, evenness, and overall composition between CRC patients and healthy controls. Differential abundance analysis was conducted using ANCOM-BC and LEfSe to pinpoint individual taxa that were enriched or depleted in CRC patients. Additionally, sccomp, a Bayesian machine learning method from single-cell analysis, was adapted to provide a more robust validation of compositional differences in individual microbial markers.

RESULTS

Gut microbial richness is significantly higher in CRC patients, and overall microbiome composition differs significantly between CRC patients and healthy controls. Several taxa, such as Fusobacterium and Peptostreptococcus, are enriched in CRC patients, while others, including Anaerostipes, are depleted. The microbial signatures identified from the integrated data are reproducible and generalizable, with many aligning with findings from previous studies. Furthermore, the use of sccomp enhanced the precision of individual microbial marker identification.

CONCLUSIONS

Biologically, the microbial signatures identified from the integrated data improve our understanding of the gut microbiota's role in CRC pathogenesis and may contribute to the development of translational targets and microbiota-based therapies. Methodologically, this study demonstrates the effectiveness of adapting robust techniques from single-cell research to improve the precision of microbial marker discovery.

Characterization of the phyllosphere virome of fresh vegetables and potential transfer to the human gut

Fresh vegetables harbor diverse microorganisms on leaf surfaces, yet their viral communities remain unexplored. We investigate the diversity and ecology of phyllosphere viromes of six leafy green vegetables using virus-like particle (VLP) enrichment and shotgun metagenome sequencing. On average, 9.2 × 107 viruses are present per gram of leaf tissue. The majority (93.1 ± 6.2%) of these viruses are taxonomically unclassified. Virome compositions are distinct among vegetable types and exhibit temporal variations. Virulent phages with replication-enhancing auxiliary metabolic genes (AMGs) are more dominant than temperate phages with host fitness-benefiting AMGs. Analysis of 1498 human fecal VLP metagenomes reveals that approximately 10% of vegetable viruses are present in the human gut virome, including viruses commonly observed in multiple studies. These gut-associated vegetable viruses are enriched with short-term vegetable intake, and depleted in individuals with metabolic and immunologic disorders. Overall, this study elucidates the ecological contribution of the fresh vegetable virome to human gut virome diversity.

Food-Based Interventions as Therapy for Inflammatory Bowel Disease: Important Steps in Diet Trial Design and Reporting of Outcomes

Diet therapy for inflammatory bowel disease (IBD) is an international research priority but guidance for IBD-specific diet trial design is lacking. This review critically evaluates key elements of prospective IBD food-based intervention trials and identifies gaps. Electronic databases were searched for interventional IBD diet studies. Prospective primary studies/trials were included if used food-based dietary strategies. Forty studies/trials evaluating 29 food-based strategies as therapy for IBD were identified. Considerable heterogeneity in diets, trial design, and methodology exists. Thirty-one trials (78%) intended the diet to modulate inflammation but 14/31 (46%) did not have a primary endpoint measuring an objective change in inflammatory activity and 20/31 (65%) controlled for medication stability prior to application of diet at baseline. Higher-quality IBD diet trials used symptom-based assessment tools coupled with an objective evaluation of inflammatory activity. Dietary advice trials are the most common. One-third of trials developed and administered diet education without a dietitian. Evaluation and reporting on adherence to diet therapy occurred in <60% of trials. Failure to include or report on key elements of trial design reduced the interpretability and validity of the results. This is a considerable limitation to advancing scientific knowledge in this area. Diet therapy trials should adhere to similar rigorous quality standards used to develop other IBD therapies. Therefore, a set of practical recommendations was generated to provide the authors' perspective to help inform the future design of high-quality IBD diet trials.

Baseline abundance of Akkermansia muciniphila and Bacteroides acidifaciens in a healthy state predicts inflammation associated tumorigenesis in the AOM/DSS mouse model

Numerous studies demonstrate that intestinal microbiota contribute to colorectal cancer (CRC), which is often associated with dysbiosis. Most of the data were obtained from studies on CRC patients, making it challenging to determine whether alterations in microbiota are a consequence of the pathology or whether they actively drive its progression. Several studies using laboratory animals suggest that gut microbiota may be involved in both the onset and progression of CRC. In the present study we utilized the azoxymethane-dextran sulfate sodium (AOM/DSS) mouse model of CRC to investigate the contribution of healthy-state microbiota to inflammation-associated tumorigenesis. Two cohorts of C57BL/6 mice harboring different intestinal microbiota demonstrated different susceptibility to AOM/DSS treatment. Sequencing of 16S rRNA bacterial DNA from fecal samples revealed Akkermansia muciniphila and Bacteroides acidifaciens as marker features in the healthy-state microbiota (before AOM/DSS administration), which showed a strong positive correlation with tumor incidence. Moreover, the healthy-state abundance of these markers, considered beneficial bacteria, was strongly positively correlated with the sulfate-reducing bacteria Desulfovibrio fairfieldensis identified as a marker of chronic colitis-associated microbiota. Furthermore, the abundances of these marker features, associated with CRC outcome, correlated with the expression of interferon gamma and nitric oxide synthase 2 genes in colon tissue during the early stage of DSS-induced intestinal inflammation. In contrast to multiple studies demonstrating the anti-inflammatory properties of A. muciniphila and B. acidifaciens, our results point out their potential adverse effect under specific conditions of genotoxicity and inflammation in the intestine. Taken together, our findings suggest a complex, context-dependent role of commensal microbiota in inflammation-associated dysbiosis and CRC.

Prebiotics empower probiotics with gastrointestinal stress resistance for colon-targeted release to synergistically alleviate colitis

Oral administration of probiotics holds promise for alleviating ulcerative colitis (UC), yet their efficacy is inevitably compromised by the hostile gastrointestinal (GI) environment. Here, we devised a strategy by coating β-glucan (GN) prebiotic onto the surface of Lactobacillus plantarum (Lp) probiotic at the single-cell level (Lp@CGN) based on bioorthogonal chemistry in a layer-by-layer manner. This achieved to form a firm, dense, and multifunctional GN-based "armor" with advances of superior protective properties, colon-targeted degradation, and prebiotic benefits. Under the protection of the prebiotic-based "armor", Lp@CGN exhibited a notable 276-fold increase in the survival rate compared to naïve Lp after exposure to whole GI conditions. Upon reaching the colon, the "armor" was metabolized into short-chain fatty acids (SCFAs) by gut microbiota, facilitating the timely release of Lp within colon, thereby achieving a synergistic treatment effect due to sustained SCFAs generation and Lp liberation. As a result, oral administration of Lp@CGN efficiently realized the alleviation of UC in both preventative and therapeutic models through restoring intestinal mucosal barriers, positively regulating inflammatory cytokines, renovating the dysbiosis of gut microbiota, and promoting SCFAs production. In sum, our strategy marks the reconstruction of probiotics with chemical tools, offering useful insights into powering probiotics for disease treatment.

Multi-cohort analysis reveals colorectal cancer tumor location-associated fecal microbiota and their clinical impact

Microbial alterations in different tumor locations of colorectal cancer (CRC) remain unclear. Here, 1,375 fecal metagenomes from six in-house and published datasets were analyzed, including 128 right-sided CRC (rCRC), 168 left-sided CRC (lCRC), 250 rectal cancer (RC), and 829 controls. Firmicutes progressively increase from rCRC, lCRC, to RC, in contrast to the gradual decrease of Bacteroidetes. Tumor location-associated fecal microbes are identified, including Veillonella parvula for rCRC, Streptococcus angionosus for lCRC, and Peptostreptococcus anaerobius for RC, while Fusobacterium nucleatum is enriched in all tumor locations. Tumor location-associated bacteria correlate with patient survival. Clinically, we establish a microbial biomarker panel for each tumor location that accurately diagnoses rCRC (area under the receiver operating characteristic curve [AUC] = 91.59%), lCRC (AUC = 91.69%), or RC (AUC = 90.53%) from controls. Tumor location-specific biomarkers also have higher diagnostic accuracy (AUC = 91.38%) than location-non-specific biomarkers (AUC = 82.92%). Overall, we characterize fecal microbes associated with different CRC tumor locations, highlighting that tumor location should be considered in non-invasive diagnosis.

Association of Fusobacterium nucleatum with colorectal cancer molecular subtypes and its outcome: a systematic review

Colorectal cancer (CRC) represents a relevant public health problem, with high incidence and mortality in Western countries. CRC can occur as sporadic (65%-75%), common familial (25%), or as a consequence of an inherited predisposition (up to 10%). While unravelling its genetic basis has been a long trip leading to relevant clinical implementation over more than 30 years, other contributing factors remain to be clarified. Among these, micro-organisms have emerged as critical players in the development and progression of the disease, as well as for CRC treatment response. Fusobacterium nucleatum (Fn) has been associated with CRC development in both pre-clinical models and clinical settings. Fusobacteria are core members of the human oral microbiome, while being less prevalent in the healthy gut, prompting questions about their localization in CRC and its precursor lesions. This review aims to critically discuss the evidence connecting Fn with CRC pathogenesis, its molecular subtypes and clinical outcomes.