Tao Lin ^*

• Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States

influence human metabolic pathways, offering potential avenues for early diagnosis and targeted therapy.Therapeutic Interventions. Understanding microbiome-disease associations has led to the exploration of microbiome-based therapies. Probiotic and prebiotic interventions, as well as fecal microbiota transplantation (FMT), are being investigated for their potential to restore healthy microbiome composition and mitigate disease progression. FMT has gained traction as a treatment for recurrent Clostridioides difficile (C. difficile) infections and has been explored for its potential role in other conditions such as IBD (5). The impact of the microbiome on cancer has been one of the most intriguing areas of research. Studies suggest that the microbiota can influence cancer progression, immune response, and even the efficacy of cancer therapies. For example, research has shown that microbial species residing in the tumor microenvironment can modulate immune checkpoints and affect the response to immunotherapy. Studies have shown that certain microbial species, such as Fusobacterium nucleatum, can exacerbate colorectal cancer by promoting inflammation and genomic instability (6).Microbiome and neurological disorders. The gut-brain axis has become a focal point of research into neurodegenerative diseases. Meta-omics approaches have shown that gut dysbiosis can impact neurological health by altering microbial metabolite production, which in turn affects neuroinflammation and brain function (7). This emerging evidence suggests that gut microbiota may play a crucial role in the development of diseases such as Parkinson's and Alzheimer's, offering new opportunities for microbiome-based therapies. The microbiome profoundly impacts human susceptibility to infections and immune defense. Dysbiosis in human body such as the gut, vaginal, and skin microbiomes is associated with an increased risk of infections (8). Similarly, dysbiosis in the gut microbiome compromises immune function, leading to a greater risk of gastrointestinal infections, including C. difficile infection (9). Research also highlights the gut-lung axis, showing that gut microbial imbalances can impact respiratory infections, suggesting a systemic role of the microbiome in maintaining immune homeostasis (9). Moreover, sputum microbiota is associated with an severe and critically ill influenza patients (10), In addition, evidence indicates that the gut microbiota can alter SARS-CoV-2 virus load and COVID-19 severity (11).Microbiome and women health. The microbiome plays a critical role in women's health, particularly in the context of the vaginal and gut microbiomes. The vaginal microbiome, which is typically dominated by Lactobacillus species, is essential in maintaining a healthy environment by producing lactic acid and maintaining an acidic pH. Disruptions in this balance can result in bacterial vaginosis, yeast infections, and increased susceptibility to sexually transmitted infections (STIs) (12). In cases of bacterial vaginosis and other vaginal dysbiosis, an increase in pathogens like Gardnerella vaginalis and Prevotella has been linked to adverse reproductive outcomes, such as infertility and miscarriage (12)(13).In addition, oral microbiome changes are associated with the menstrual cycle. Different microbiome profiles were observed during the follicular phase, the early and late luteal phases. Alpha diversity and beta diversity analyses revealed distinct microbial profiles across the four menstrual phases (14). Probiotic lactobacilli were used in the treatment of vaginal infections (15). The urinary microbiota signatures are associated with different types of urinary diversion (16).Furthermore, the gut microbiome also has significant implications for hormonal regulation and immune responses, which can impact conditions like polycystic ovary syndrome (PCOS) and pregnancy outcomes. Studies have shown that alterations in the gut and vaginal microbiota are associated with insulin resistance, hormonal imbalances, and inflammation in women with PCOS, contributing to symptoms like infertility and metabolic disturbances (12) (13). The aim of this Research Topic is to offer a platform for articles that expand our understanding of host-microbiome interactions using 'meta-omics' techniques. This collection includes 5 reviews and 14 original research articles, highlighting critical associations between the microbiome and various human diseases. These contributions have made significant strides in advancing our knowledge of the complex interplay between the microbiome and disease states, including the microbiome and cancers (Lin et al. Microbial influences in cancer mechanism, prognosis, diagnosis, and therapy. A comprehensive review examines the impact of gut and intratumoral microbiota on cancer mechanisms, prognosis, diagnosis, and treatment. It delves into the systemic roles of microbiota, emphasizing their influence on the tumor microenvironment and immune responses. Additionally, the review provides an overview of recent microbiome-cancer research, summarizing key findings from the literature, highlighting past and current advancements, discussing novel techniques, identifying research gaps, and outlining future goals. It also explores the complex interactions between the microbiome and cancer, offering a detailed analysis of this rapidly evolving field (Lin, et al., 2025). Moreover, A review on respiratory tract microbiota and lung cancer investigates the bacterial communities inhabiting different regions of the respiratory system (Cheng, et al., 2024). The emerging evidence suggests that gut microbiota could play a key role in mediating oncogenesis through various mechanisms, potentially opening new avenues for therapeutic interventions (Li, et al. 2023). In addition, new Colorectal cancer (CRC)-associated species, such as Porphyromonas endodontalis, Ruminococcus torques, and Odoribacter splanchnicus. Additionally, certain stage-specific bacterial taxa were identified, which may aid in diagnosing colorectal polyps (BP) and the four distinct CRC stages (Cai et al., 2023). Furthermore, specific bacterial species and metabolic pathways may influence the occurrence of a series of immune-related adverse events (irAEs) in gastric, esophageal, and colon cancers. Notably, Ruminococcus callidus and Bacteroides xylanisolvens were enriched in patients without severe irAEs. Several microbial metabolic pathways, including citrulline and arginine biosynthesis, were associated with irAE development (Zhang et al., 2023). The authors reviewed innovative microbial single cell sequencing techniques, highlighting their broad applications in addressing critical questions regarding microbiome composition and spatial heterogeneity. These advancements offer deeper insights into the functional roles and interactions of individual microbial cells within complex communities (Madhu, etal., 2023). The microbiota-gut-brain axis plays a pivotal role in regulating neuroprotective functions in the host. Patients with Parkinson's disease (PD) often exhibit gut microbiota dysbiosis (Jia, et al., 2023). Moreover, he gut microbiome and its associated metabolic pathways appear to play a significant role in the long-term development of depression (Li et al., 2023). In addition, the identification of bacterial classes like Negativicutes and Selenomonadales provides a new direction for therapeutic strategies to manage sleep disorders via microbiota modulation (Wang, et al., 2024). In another study, ten gut microbiome (GM) taxa were found to have causal associations with insomnia (Li et al. 2023). Oral microbiome changes associated with the menstrual cycle. During the follicular phase, the relative abundance of the Streptococcus genus was significantly higher compared to the early and late luteal phases, while the Prevotella 7 and Prevotella 6 genera exhibited significantly lower abundance during the follicular phase than in the luteal phases. Alpha diversity was notably lower in the follicular phase, and beta diversity analyses revealed distinct microbial profiles across the four menstrual phases (Yamazaki et al., 2023).Use of probiotic lactobacilli in the treatment of vaginal infections. Probiotic Lactobacilli play a crucial role in maintaining the balance of the vaginal microenvironment. A review explores their therapeutic potential in treating female vaginal infections. Probiotic lactobacilli contribute to restoring and preserving vaginal health by competing with pathogenic bacteria, enhancing the local immune response, and producing antimicrobial substances (Liu, et al., 2023).The urinary microbiota signatures and urinary diversion. The urinary microbiota signatures associated with different types of urinary diversion was studied. Urinary microbial landscapes of radical cystectomy and urinary diversion (UD) patients were analyzed (Liu, et al., 2024). Sputum microbiota characteristics and severe and critically ill influenza patients. Bacteroidetes showed significant depletion in the critically ill cohort. The sputum microbiomes in the severe influenza group were marked by an overrepresentation of Neisseria, Porphyromonas, Actinobacillus, Alloprevotella, Nanosynbacter lyticus TM7x, and Clostridia UCG-014. Notably, Alloprevotella exhibited an inverse correlation with influenza cycle threshold (Ct) values. Additionally, C-reactive protein (CRP) levels demonstrated a positive correlation with the presence of Haemophilus and Porphyromonas (Gu, et al., 2023). The gut microbiome and Clostridioides difficile infection. Distinct microbiome patterns were identified among healthy individuals, colonized patients, those with Clostridioides difficile infection (CDI), recurrent Clostridioides difficile infection (R-CDI), and patients with non-Clostridioides difficile infection (NOCDI) diarrhea. Potential microbiome biomarkers were discovered that may be valuable in distinguishing true CDI infections from other conditions, improving diagnostic accuracy and guiding treatment strategies (Vázquez-Cuesta, et al., 2023).Gut microbiota in children with split-dose bowel preparations. In pediatric patients undergoing split-dose PEG bowel preparation and colonoscopy, gut microbiota showed significant alterations at the genus, species, and functional pathway levels. However, no significant changes were observed at the phylum level (Zou, et al., 2023). Correlations between specific oral and gut fungal species with clinical parameters were identified from patients with Metabolic Dysfunction-Associated Fatty Liver Disease (MAFLD) patients (Niu, et al., 2023). One study reveals significant differences in microbial profiles between cholesterol and pigment gallstone patients (Zhang et al., 2024). A combination of NaClO and H₂O₂ has shown potential as a more effective disinfectant, particularly against fungal pathogens, offering an alternative solution for more efficient microbial control (Li et al., 2022). In conclusion, the integration of meta-omics techniques has revolutionized our ability to explore the microbiome's contributions to human diseases, providing a more detailed understanding of microbial functions and their impact on human health and diseases. As these techniques continue to evolve, they hold immense promise for identifying novel diagnostic biomarkers and therapeutic targets across a wide range of diseases.