Search Results (75)

Rheumatoid arthritis (RA) is a heterogeneous autoimmune disease characterized by variable clinical manifestations and a complex, often unpredictable disease trajectory, which hinders early diagnosis and personalized treatment. This review highlights recent breakthroughs in biomarker discovery, emphasizing the transformative impact of multi-omics technologies and deep profiling of the synovial microenvironment. Advances in genomics and transcriptomics have identified key genetic variants and expression signatures associated with disease susceptibility, progression, and therapeutic response. Complementary insights from proteomics and metabolomics have elucidated dynamic molecular patterns linked to inflammation and joint destruction. Concurrently, microbiome research has positioned gut microbiota as a compelling source of non-invasive biomarkers with both diagnostic and immunomodulatory relevance. The integration of these diverse data modalities through advanced bioinformatics platforms enables the construction of comprehensive biomarker panels, offering a multidimensional molecular portrait of RA. When coupled with synovial tissue profiling, these approaches facilitate the identification of spatially resolved biomarkers essential for localized disease assessment and precision therapeutics. These innovations are transforming RA care by enabling earlier detection, improved disease monitoring, and personalized treatment strategies that aim to optimize patient outcomes. Full article

Background/Objectives: Atherosclerosis is a major contributor to ischemic cardiovascular diseases (CVDs) such as myocardial infarction and stroke, which are leading causes of mortality and morbidity. The management of atherosclerosis through personalized nutrition has gained importance in recent years due to advancements in nutrigenomics, gut microbiome evaluation, and metabolomics. However, no systematic review has comprehensively evaluated the impact of personalized nutrition interventions on atherosclerotic plaque progression and clinical outcomes in humans. Methods: We adopted a systematic approach based on Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Key databases like PubMed, Cochrane, Google Scholar, and MEDLINE via EBSCOhost were searched using predefined terms related to personalized nutrition, atherosclerosis, nutrigenomics, and clinical outcomes. Results: Evidence evaluation using the framework of Boffetta et al. for cumulative evidence on the joint effects of genes and environments strongly suggested significant diet–gene interactions. Polymorphisms in the apolipoprotein A-II (APOA2) gene have been shown to influence body mass index and lipid levels. Furthermore, studies have demonstrated that omega-3 polyunsaturated fatty acids (PUFAs) can modulate microRNA expression, thereby impacting lipid metabolism. Epigenetic studies showed that dietary components can modify histone acetylation and non-coding RNA activity, which ultimately influence gene expression related to inflammation and lipid metabolism, improving clinical outcomes in atherosclerosis management. Conclusions: Integrating personalized nutrition into clinical practice promises to enhance atherosclerosis outcomes through targeted dietary interventions. Advancements in personalized nutrition offer a promising pathway toward more effective and personalized approaches to cardiovascular health. Full article

Introduction: Osteoarthritis (OA) is a chronic degenerative joint disease with limited treatment options focused primarily on symptom management. Emerging evidence suggests that dietary interventions may influence inflammation and pain through modulation of the gut microbiome and metabolome. Methods: We conducted a 4-week open-label pilot trial evaluating the effects of an anti-inflammatory dietary intervention (ITIS diet) in 20 patients with knee OA (ClinicalTrials.gov ID: NCT05559463, registered prior to enrollment; sponsor: University of California, San Diego; responsible party: Monica Guma; study start date: 1 October 2021). The following were assessed before and after the intervention: (1) clinical outcomes; (2) gut and salivary microbiomes; and (3) salivary, stool, and plasma metabolomes. Responders were defined as patients achieving ≥30% reduction in Western Ontario and McMaster Universities Arthritis Index (WOMAC) pain scores. Results: The ITIS diet was well-tolerated, with good adherence (66.2%) and a significant improvement in clinical outcomes, including reduced pain and improved overall health measured with the visual analog scale (VAS). Responders (n = 8) showed distinct gut microbiome and metabolome profiles compared to non-responders (n = 12). Notably, taxa within the Lachnospiraceae family exhibited dynamic, bidirectional shifts post-intervention: Anaerostipes and Limivivens were enriched among responders and negatively correlated with pain scores, while Oliverpabstia and Fusicatenibacter were depleted following dietary intervention. These taxa also showed strong correlations with anti-inflammatory metabolites, including hydroxydecanoic acid derivatives and pyridoxine. Furthermore, subsequent network analysis revealed more structured and selective microbiome–metabolome interactions in responders, specifically post-intervention. Conclusions: This pilot study shows that a short-term anti-inflammatory dietary intervention was associated with meaningful changes in the gut microbiome and metabolome. Members of the Lachnospiraceae family emerged as key taxa associated with pain reduction and anti-inflammatory metabolite production. Our findings suggest that specific microbial responses—rather than global diversity changes—may underlie dietary responsiveness in OA. Although exploratory and limited by sample size, our results support further investigation into personalized, microbiome-informed nutritional strategies for OA management. Full article

Proper joint function has a significant impact on people’s quality of life. Joints are the point of connection between two or more bones and consist of at least three elements: joint surfaces, the joint capsule, and the joint cavity. Joint diseases are a serious social problem. Risk factors for the development of these diseases include overweight and obesity, gender, and intestinal microbiome disorders. Another factor that is considered to influence joint diseases is trace elements. Under normal conditions, elements such as iron (Fe), copper (Cu), cobalt (Co), iodine (I), manganese (Mn), zinc (Zn), silver (Ag), cadmium (Cd), mercury (Hg), lead (Pb), nickel (Ni) selenium (Se), boron (B), and silicon (Si) are part of enzymes involved in reactions that determine the proper functioning of cells, regulate redox metabolism, and determine the maturation of cells that build joint components. However, when the normal concentration of the above-mentioned elements is disturbed and toxic elements are present, dangerous joint diseases can develop. In this article, we focus on the role of trace elements in joint function. We describe the molecular mechanisms that explain their interaction with chondrocytes, osteocytes, osteoblasts, osteoclasts, and synoviocytes, as well as their proliferation, apoptosis, and extracellular matrix synthesis. We also focus on the role of these trace elements in the pathogenesis of joint diseases: rheumatoid arthritis (RA), osteoarthritis (OA), psoriatic arthritis (PsA), ankylosing spondylitis (AS), and systemic lupus erythematosus (SLE). We describe the roles of increased or decreased concentrations of individual elements in the pathogenesis and development of joint diseases and their impact on inflammation and disease progression, referring to molecular mechanisms. We also discuss their potential application in the treatment of joint diseases. Full article

Osteoarthritis (OA) has traditionally been defined as a degenerative joint disease driven by mechanical wear, aging, and metabolic disturbances. However, emerging evidence suggests that joint dysbiosis, a dysregulation in the joint microbiome, may play an important role in OA pathogenesis. This review explores the mechanisms linking dysbiosis to OA. We examine the presence and origin of joint dysbiosis, also highlighting the gut–joint and oral–joint axes as potential routes for microbial translocation. However, challenges remain in distinguishing causation from correlation and addressing microbial contaminants in microbiome studies. Future research should prioritize longitudinal studies and multiomics integration to elucidate the complex interplay between microbial communities and joint health. Full article

Evidence suggests that a cross-talk between the gut microbiota and joint health exists in a paradigm known as the gut–joint axis. Recent studies have also reported the presence of microorganisms potentially involved in the pathogenesis and progression of arthritis in synovial joints, previously believed to be sterile. This systematic review describes in detail the methodologies employed to characterize the microbiota in human synovial fluid (SF). A literature search was conducted in PubMed, Embase, and Web of Science up to 5 February 2025. Nine studies aimed to characterize the SF microbiome using next-generation sequencing or polymerase chain reaction. Eight studies detected bacterial DNA in SF. However, significant heterogeneity and incomplete reporting in methodologies, including sample collection and preparation, contamination management, DNA extraction and amplification, sequencing technology, targeted 16S rRNA or ITS regions, and bioinformatics processing, limit the comparability and significance of findings. Given the potential implications for understanding arthritis mechanisms and developing targeted treatments, a standardized methodological and reporting approach in SF microbiota characterization is needed to enhance the reproducibility and the relevance of results. Full article

Hand osteoarthritis (OA) is a prevalent and disabling condition, yet its pathogenesis remains less studied than OA in large weight-bearing joints. Emerging genetic, epigenetic, and microbiome research suggests that hand OA might be biologically distinct, involving joint-specific pathways not shared by knee or hip OA. This review integrates genome-wide association studies specific to hand OA, highlighting key molecular contributors such as inflammatory cytokines. These genetic insights, together with emerging data on epigenetic alterations and gut microbial dysbiosis, point to broader systemic and regulatory influences on hand OA onset and progression. We also assess pharmacologic interventions tested in randomized controlled trials that have attempted to target these pathways. While agents such as TNF and IL-6 inhibitors, hydroxychloroquine, and corticosteroids have shown limited success, emerging evidence supports the potential of methotrexate in synovitis-positive general hand OA, platelet-rich plasma in thumb carpometacarpal (CMC) OA, and prolotherapy in interphalangeal (IP) OA. These findings illustrate the persistent gap between mechanistic understanding and therapeutic success. Future work must prioritize multifactorial strategies for addressing pain and translational frameworks that link molecular mechanisms to treatment response. In summary, this review offers an update on hand OA and identifies key opportunities for more targeted and effective therapy. Full article

The microbiome plays a crucial role in maintaining physiological homeostasis and is intricately linked to various diseases. Traditional culture-based microbiological experiments are expensive and time-consuming. Therefore, it is essential to prioritize the development of computational methods that enable further experimental validation of disease-associated microorganisms. Existing computational methods often struggle to effectively capture nonlinear interactions and heterogeneous network structures when predicting microbiome–disease associations. To address this issue, we propose HG-LGBM, an innovative joint prediction framework that combines heterogeneous graph neural networks with a gradient boosting mechanism. We employ a hierarchical heterogeneous graph transformer (HGT) encoder, which utilizes a multi-head attention mechanism to learn higher-order node representations, while LightGBM optimizes the classification task using gradient-boosted decision trees. Evaluated through five-fold cross-validation on the HMDAD and Disbiome datasets, HG-LGBM demonstrated a state-of-the-art performance. The experimental results showed that combining heterogeneous network learning with gradient boosting strategies effectively revealed potential microbiome–disease interactions, providing a powerful tool for biomedical research and precision medicine. Finally, case studies on colorectal cancer and inflammatory bowel disease (IBD) further validated the effectiveness of HG-LGBM. Full article

Psoriatic arthritis (PsA) is a chronic inflammatory disease characterized by joint inflammation and skin lesions. Recent research has underscored the critical role of gut microbiota—comprising bacteria, fungi, viruses, and archaea—in the pathogenesis and progression of PsA. This narrative review synthesizes the latest findings on the influence of gut microbiota on PsA, focusing on mechanisms such as immune modulation, microbial dysbiosis, the gut-joint axis, and its impact on treatment. Advances in high-throughput sequencing and metagenomics have revealed distinct microbial profiles associated with PsA. Studies show that individuals with PsA have a unique gut microbiota composition, differing significantly from healthy controls. Alterations in the abundance of specific bacterial taxa, including a decrease in beneficial bacteria and an increase in potentially pathogenic microbes, contribute to systemic inflammation by affecting the intestinal barrier and promoting immune responses. This review explores the impact of various factors on gut microbiota composition, including age, hygiene, comorbidities, and medication use. Additionally, it highlights the role of diet, probiotics, and fecal microbiota transplantation as promising strategies to modulate gut microbiota and alleviate PsA symptoms. The gut-skin-joint axis concept illustrates how gut microbiota influences not only gastrointestinal health but also skin and joint inflammation. Understanding the complex interplay between gut microbiota and PsA could lead to novel, microbiome-based therapeutic approaches. These insights offer hope for improved patient outcomes through targeted manipulation of the gut microbiota, enhancing both diagnosis and treatment strategies for PsA. Full article

Diabetes mellitus (DM) is a common chronic health condition, affecting millions of people worldwide, and its incidence is projected to increase by almost 50% in the next two decades. The effects of DM on the auditory system have been reported. However, there is limited evidence on the association between DM and middle ear pathologies. This scoping review aimed to map the available evidence and identify research gaps regarding DM and middle ear pathologies in the adult population. Five electronic databases, namely Scopus, CINAHL, MEDLINE, PubMed, and Web of Science, were searched using a combination of specific key terms. This review followed the guidelines stipulated by the Joanna Briggs Institute (JBI) methodology for scoping reviews and reporting using PRISMA Extension for Scoping Reviews (PRISMA-ScR): checklist and explanation. A thematic narrative analysis was used to synthesize key findings. Of the 1809 articles, only 2 articles met the inclusion criteria. Neither of these studies focused exclusively on middle ear pathologies in DM, but they did report incidental findings related to middle ear function. Available evidence suggests that middle ear pathologies may occur in individuals with DM, with a reported prevalence ranging from 3.1% to 19.6%. Otitis media with effusion and conductive hearing loss were common middle ear pathologies identified. Additionally, recent studies have provided new evidence suggesting ossicular joint changes in individuals with DM and a causal link between DM and acute suppurative otitis media. However, age-related hearing loss (presbycusis) and sensorineural hearing loss (SNHL) were more commonly associated with DM, with studies reporting a high prevalence of SNHL in younger to middle-aged adults with diabetes. This review highlights a significant research gap in the literature, as no studies directly investigated the relationship between DM and middle ear function as a primary focus. Further research is required to investigate this potential association using methodologies explicitly designed for middle ear assessment. While some evidence suggests a possible association, the lack of age-stratified analyses, imaging data, and comprehensive diagnostic testing limits the ability to draw strong conclusions. Further research incorporating age-based analyses, radiological assessments, and microbiome studies is needed to fully understand the potential impact of DM on middle ear health. Full article

Background: The collection of microorganisms that colonize the human genital and urinary tract is referred to as the genitourinary microbiome. Urinary tract infections (UTIs), which predominantly affect women, are linked to alterations in the genitourinary microbiome. Cranberries (Vaccinium oxycoccos), rich in proanthocyanidins, and ascorbic acid (vitamin C), known for their urinary acidification properties, are commonly used for UTI prevention. However, their effects on the genitourinary microbiome remain inadequately characterized. This pilot study assesses the genitourinary microbiome composition in healthy women and evaluates the influence of cranberry and ascorbic acid supplementation. Methods: In a randomized, controlled, and open-label trial, 27 healthy women in their reproductive age (18–40 years) were assigned to three groups: cranberry (n = 8), ascorbic acid (n = 10), and control (n = 9). Urine samples were collected at three time points and processed for 16S rRNA gene amplicon-based microbial community composition analysis. Microbiome composition was compared within and between groups, and between study visits. Results: Sufficient microbial DNA was extracted from all midstream urine samples. The genitourinary microbiome was predominantly composed of Lactobacillus spp., as reported previously. No significant shifts in microbial composition were observed in response to cranberry or ascorbic acid supplementation, and no statistically significant differences were detected between the intervention and control groups or between study visits. Conclusion: The genitourinary microbiome of healthy women remained stable during cranberry or ascorbic acid supplementation. Further studies in patients with recurrent UTIs are needed to explore the potential impacts of these supplements on the genitourinary microbiome in disease states. Full article

Intestinal probiotics significantly regulate the growth performance of their host, with their composition being influenced by various factors. While many studies have explored how gut microbiota composition affects growth traits such as body weight and BMI, the research on probiotics influenced by host genetic factors, and their subsequent impact on host growth performance, remains limited. To address this research gap, we collected fecal and tissue samples, as well as phenotypic data, from 193 Yunong black pigs at 280 days of age. We then sequenced and genotyped all 193 subjects using the 50K SNP BeadChip, yielding a comprehensive dataset for genetic and microbiome analyses. We then employed microbiome-wide association studies (MWAS), a meta-analysis, and microbiome-wide genetic association studies (MGWASs) to examine the relationship between host genetics, gut microbiota, and growth performance. Four key microbial taxa, namely Coprococcus, Blautia, Ruminococcaceae, and RF16, were identified as being significantly associated with body weight and BMI. The MGWAS analysis revealed that both Coprococcus and Ruminococcaceae were significantly associated with host genomic variations. A total of four important single nucleotide polymorphisms (SNPs) were mapped to two chromosomal regions, corresponding to three candidate genes. Among them, the candidate genes INPP4B, SCOC, and PABPC4L were identified as being related to the abundance of key microbes. This study provides new insights into the joint contributions of host genetics and probiotics to host growth traits, offering theoretical guidance and data support for the development of efficient and targeted breeding strategies. Full article

Contaminations are challenging for monocultures, as they impact the culture conditions and thus influence the growth of the target organism and the overall biomass composition. In phycology, axenic cultures comprising a single living species are commonly strived for both basic research and industrial applications, because contaminants reduce significance for analytic purposes and interfere with the safety and quality of commercial products. We aimed to establish axenic cultures of Limnospira fusiformis, known as the food additive “Spirulina”. Axenicity is strived because it ensures that pathogens or harmful microorganisms are absent and that the harvested biomass is consistent in terms of quality and composition. For the axenic treatment, we applied sterile filtration, ultrasonication, pH treatment, repeated centrifugation, and administration of antibiotics. For testing axenicity, we considered the most common verification method plate tests with Lysogeny Broth (LB) medium, which indicated axenicity after treatments were performed. In addition, we included plate tests with Reasoner’s 2A (R2A) agar and modified Zarrouk+ medium, the latter comparable to the biochemical properties of L. fusiformis’ cultivation medium. In contrast to LB plates, the other media, particularly Zarrouk+, indicated bacterial contamination. We conclude that LB-agar plates are inappropriate for contamination screening of extremophiles. Contamination was also verified by cultivation-independent methods like flow cytometry and 16S rRNA genome amplicon sequencing. We detected taxa of the phyla Proteobacteria, Bacteriodota, Firmicutes and to a lesser extent Verrucomicrobiota. Contaminants are robust taxa, as they survived aggressive treatments. Sequencing data suggest that some of them are promising candidates for in-depth studies to commercially exploit them. Full article

Background/Objectives: The integration of microbiome and metabolome data could unveil profound insights into biological processes. However, widely used multi-omic data analyses often employ a stepwise mining approach, failing to harness the full potential of multi-omic datasets and leading to reduced detection accuracy. Synergistic analysis incorporating microbiome/metabolome data are essential for deeper understanding. Method: This study introduces a Coupled Matrix and Tensor Factorization (CMTF) framework for the joint analysis of microbiome and metabolome data, overcoming these limitations. Two CMTF frameworks were developed to factorize microbial taxa, functional pathways, and metabolites into latent factors, facilitating dimension reduction and biomarker identification. Validation was conducted using three diverse microbiome/metabolome datasets, including built environments and human gut samples from inflammatory bowel disease (IBD) and COVID-19 studies. Results: Our results revealed biologically meaningful biomarkers, such as Bacteroides vulgatus and acylcarnitines associated with IBD and pyroglutamic acid and p-cresol associated with COVID-19 outcomes, which provide new avenues for research. The CMTF framework consistently outperformed traditional methods in both dimension reduction and biomarker detection, offering a robust tool for uncovering biologically relevant insights. Conclusions: Despite its stringent data requirements, including the reliance on stratified microbial-based pathway abundances and taxa-level contributions, this approach provides a significant step forward in multi-omics integration and analysis, with potential applications across biomedical, environmental, and agricultural research. Full article

Introduction: Osteoarthritis (OA) is the most prevalent form of arthritis and affects over 528 million people worldwide. Degenerative joint disease involves cartilage degradation, subchondral bone remodeling, and synovial inflammation, leading to chronic pain, stiffness, and impaired joint function. Initially regarded as a “wear and tear” condition associated with aging and mechanical stress, OA is now recognized as a multifaceted disease influenced by systemic factors such as metabolic syndrome, obesity, and chronic low-grade inflammation. Recent studies have focused on the gut-joint axis to investigate how the gut microbiome modulates inflammation and pain in OA. Materials and Methods: A systematic review was conducted following the PRISMA guidelines and was registered with PROSPERO (CRD42024556265). This review included studies involving adults with symptomatic OA and analyzed the relationship between the gut microbiome and OA-related pain. Randomized and non-randomized clinical trials, case reports, editorials, and pilot studies were excluded. Searches were performed in PubMed, Cochrane Library, and Web of Science without publication date restrictions, and filtered for “observational studies”. The study selection and data extraction were performed by two independent researchers, and the risk of bias was assessed using appropriate tools. Results: Five observational studies were included in the systematic review, and three were included in the meta-analysis. Two studies reported an association between different tryptophan metabolites and pain levels in patients with OA. Two other studies demonstrated a correlation between lipopolysaccharide levels and pain in OA. A fifth study confirmed the relationship between Streptococcus relative abundance of Streptococcus spp. and knee pain. These results were not supported by a meta-analysis, which found no significant association between the presence of pain in OA and the presence of bacilli of the genus Streptococcus or plasma markers of the tryptophan pathway. Conclusions: Current evidence indicates a potential link between gut microbiome dysbiosis and OA-related pain. However, methodological limitations preclude definitive conclusions. Further research using advanced techniques and larger cohorts is needed to validate and extend these findings and elucidate the underlying mechanisms. Targeted manipulation of the gut microbiome may be a valuable strategy for pain management in OA patients. Full article