From Microbes to Medals: Integrative Gut Microbiome Interventions for Athletic Excellence

There is a growing interest in the potentially deleterious impact of antibiotics on gut microbiota. Patients with bone and joint infection (BJI) require prolonged treatment that may impact significantly the gut microbiota. We collected samples from patients with BJI at baseline, end of antibiotics (EOT), and 2 weeks after antibiotic withdrawal (follow-up, FU) in a multicenter prospective cohort in France. Microbiota composition was determined by shotgun metagenomic sequencing. Fecal markers of gut permeability and inflammation as well as multi-drug-resistant bacteria (MDRB) and Clostridioides difficile carriage were assessed at each time point. Sixty-two patients were enrolled: 27 native BJI, 14 osteosynthesis-related BJI, and 21 prosthetic joint infections (PJI). At EOT, there was a significant loss of alpha-diversity that recovered at FU in patients with native BJI and PJI, but not in patients with osteosynthesis-related BJI. At EOT, we observed an increase of Proteobacteria and Bacteroidetes that partially recovered at FU. The principal component analysis (PCoA) of the Bray–Curtis distance showed a significant change of the gut microbiota at the end of treatment compared to baseline that only partially recover at FU. Microbiota composition at FU does not differ significantly at the genus level when comparing patients treated for 6 weeks vs. those treated for 12 weeks. The use of fluoroquinolones was not associated with a lower Shannon index at the end of treatment; however, the PCoA of the Bray–Curtis distance showed a significant change at EOT, compared to baseline, that fully recovered at FU. Levels of fecal neopterin were negatively correlated with the Shannon index along with the follow-up (r2 = 0.17; p < 0.0001). The PCoA analysis of the Bray–Curtis distance shows that patients with an elevated plasma level of C-reactive protein (≥5 mg/L) at EOT had a distinct gut microbial composition compared to others. MDRB and C. difficile acquisition at EOT and FU represented 20% (7/35) and 37.1% (13/35) of all MDRB/C. difficile-free patients at the beginning of the study, respectively. In patients with BJI, antibiotics altered the gut microbiota diversity and composition with only partial recovery, mucosal inflammation, and permeability and acquisition of MDRB carriage. Microbiome interventions should be explored in patients with BJI to address these issues.

Diet and Microbiome-Directed Therapy 2.0 for IBD

Exploring potential therapeutic targets for myopia: Causal analysis and biological annotation with gut microbiota.

Increasing evidence suggests a correlation between intestinal microbiota and the gut-brain axis; however, the causal relationship between gut microbiota and postpartum depression (PPD) remains unclear. In this study, a two-sample Mendelian randomization (MR) design was employed to analyze the GWAS data of gut microorganisms from the Mibiogen database and PPD data from the UK biobank. Various statistical methods, including inverse variance weighted, MR-Egger, weighted median, weighted model, and MR-PRESSO, were utilized to investigate the causal relationship between gut microbiota and PPD. Additionally, sensitivity analysis was conducted to assess the robustness of the findings. Through MR analysis, it was found that phylum Actinobacteria (P=0.014, OR=0.971, 95% CI=0.948-0.994) and genus Holdemanella (P=0.023, OR=0.979, 95% CI=0.961-0.997) have protective effects on PPD, while the other two unknown genera, genus Unknown Ids 2001 (P=0.025, OR=0.972,95% CI=0.947-0.996), and genus Unknown Ids 2755 (P=0.012, OR=0.977, 95% CI=0.959-0.995) also has a protective effect on PPD. The sensitivity analysis results indicate that there is no heterogeneity or horizontal pleiotropy. This study has identified a causal association between Actinomycetota, Holdemanella, and PDD through MR analysis. These findings offer significant contributions to the development of personalized treatment approaches for PPD, encompassing interventions such as dietary modifications or microbiome interventions.

Background/Objectives: Metabolic dysfunction-associated steatotic liver disease (MASLD) represents a major global health challenge characterized by complex adipose–liver interactions mediated by adipokines and hepatokines. Despite rapid field evolution, a comprehensive understanding of research trends and translational advances remains fragmented. This study systematically maps the scientific landscape through bibliometric analysis, identifying emerging domains and future clinical translation directions. Methods: A comprehensive bibliometric analysis of 1002 publications from 2004 to 2025 was performed using thematic mapping, temporal trend evaluation, and network analysis. Analysis included geographical and institutional distributions, thematic cluster identification, and research paradigm evolution assessment, focusing specifically on adipokine–hepatokine signaling mechanisms and clinical implications. Results: The United States and China are at the forefront of research output, whereas European institutions significantly contribute to mechanistic discoveries. The thematic map analysis reveals the motor/basic themes residing at the heart of the field, such as insulin resistance, fatty liver, metabolic syndrome, steatosis, fetuin-A, and other related factors that drive innovation. Basic clusters include metabolic foundations (obesity, adipose tissue, FGF21) and adipokine-centered subjects (adiponectin, leptin, NASH). New themes focus on inflammation, oxidative stress, gut microbiota, lipid metabolism, and hepatic stellate cells. Niche areas show targeted fronts such as exercise therapies, pediatric/novel adipokines (chemerin, vaspin, omentin-1), and advanced molecular processes that focus on AMPK and endoplasmic-reticulum stress. Temporal analysis shows a shift from single liver studies to whole models that include the gut microbiota, mitochondrial dysfunction, and interactions between other metabolic systems. The network analysis identifies nine major clusters: cardiovascular–metabolic links, adipokine–inflammatory pathways, hepatokine control, and new therapeutic domains such as microbiome interventions and cellular stress responses. Conclusions: In summary, this study delineates current trends and emerging areas within the field and elucidates connections between mechanistic research and clinical translation to provide guidance for future research and development in this rapidly evolving area.

BackgroundMyalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is a complex disorder characterized by persistent fatigue and cognitive impairments, with emerging evidence highlighting the role of gut health in its pathophysiology. The main objective of this review was to synthesize qualitative and quantitative data from research examining the gut microbiota composition, inflammatory markers, and therapeutic outcomes of interventions targeting the microbiome in the context of ME/CFS.MethodsThe data collection involved a detailed search of peer-reviewed English literature from January 1995 to January 2025, focusing on studies related to the microbiome and ME/CFS. This comprehensive search utilized databases such as PubMed, Scopus, and Web of Science, with keywords including “ME/CFS,” “Gut-Brain Axis,” “Gut Health,” “Intestinal Dysbiosis,” “Microbiome Dysbiosis,” “Pathophysiology,” and “Therapeutic Approaches.” Where possible, insights from clinical trials and observational studies were included to enrich the findings. A narrative synthesis method was also employed to effectively organize and present these findings.ResultsThe study found notable changes in the gut microbiota diversity and composition in ME/CFS patients, contributing to systemic inflammation and worsening cognitive and physical impairments. As a result, various microbiome interventions like probiotics, prebiotics, specific diets, supplements, fecal microbiota transplantation, pharmacological interventions, improved sleep, and moderate exercise training are potential therapeutic strategies that merit further exploration.ConclusionsInterventions focusing on the gut-brain axis may help reduce neuropsychiatric symptoms in ME/CFS by utilizing the benefits of the microbiome. Therefore, identifying beneficial microbiome elements and incorporating their assessments into clinical practice can enhance patient care through personalized treatments. Due to the complexity of ME/CFS, which involves genetic, environmental, and microbial factors, a multidisciplinary approach is also necessary. Since current research lacks comprehensive insights into how gut health might aid ME/CFS treatment, standardized diagnostics and longitudinal studies could foster innovative therapies, potentially improving quality of life and symptom management for those affected.

Gut microbiota represent a potential novel target for future prediabetes and type 2 diabetes therapies. In that respect, niacin has been shown to beneficially affect the host-microbiome interaction in rodent models. We characterized more than 500 human subjects with different metabolic phenotypes regarding their niacin (nicotinic acid [NA] and nicotinamide [NAM]) status and their gut microbiome. In addition, NA and NAM delayed-release microcapsules were engineered and examined in vitro and in vivo in two human intervention studies (bioavailability study and proof-of-concept/safety study). We found a reduced α-diversity and Bacteroidetes abundance in the microbiome of obese human subjects associated with a low dietary niacin intake. We therefore developed delayed-release microcapsules targeting the ileocolonic region to deliver increasing amounts of NA and NAM to the microbiome while preventing systemic resorption to avoid negative side effects (e.g., facial flushing). In vitro studies on these delayed-release microcapsules revealed stable conditions at pH 1.4, 4.5, and 6.8, followed by release of the compounds at pH 7.4, simulating the ileocolonic region. In humans in vivo, gut-targeted delayed-release NA but not NAM produced a significant increase in the abundance of Bacteroidetes. In the absence of systemic side effects, these favorable microbiome changes induced by microencapsulated delayed-release NA were associated with an improvement of biomarkers for systemic insulin sensitivity and metabolic inflammation. Targeted microbiome intervention by delayed-release NA might represent a future therapeutic option for prediabetes and type 2 diabetes.

Heart failure (HF) is a global health challenge characterized by the heart’s inability to satisfy metabolic demands, driven by renin-angiotensin-aldosterone system (RAAS) overactivation, neurohormonal imbalance, and emerging mechanisms like the gut-heart axis and mitochondrial dysfunction. Affecting over 6 million adults in the US alone, HF incurs a 5-year mortality rate of 50% and escalating costs projected to double by 2030. This review examines HF’s molecular paradigms, integrating established pathways with advances in omics, stem cell therapy, genetic modification, and personalized medicine. RAAS blockade remains central, yet its efficacy is limited in HF with preserved ejection fraction (HFpEF). Stem cell therapies (mesenchymal and induced pluripotent stem cells) show regenerative potential but face poor retention (10% survival at 30 days). CRISPR/Cas9 offers precision, though off-target effects persist. The gut microbiome, via trimethylamine N-oxide, exacerbates inflammation, while omics technologies promise biomarkers for tailored treatments. Challenges include translating these innovations into practice, particularly for HFpEF. Future directions involve novel HFpEF therapies, enhanced stem cell delivery, precise genetic tools, and microbiome interventions, supported by artificial intelligence. By 2030, these advances could shift HF management toward regeneration, contingent on overcoming translational barriers through global collaboration.

Managing the gut microbiome with a personalized approach can significantly improve surgical outcomes, leading to reduced risk of infections, improved immune function, faster recovery and healing, and decreased risk of postoperative complications. This review explores microbiome-based interventions, such as probiotics, prebiotics, synbiotics, and fecal microbiota transplantation, and their roles in perioperative, preoperative, and postoperative care. Electronic databases, such as PubMed, ScienceDirect, and Google Scholar, were searched using topic-related keywords and MeSH terms. The literature search was limited to English-language peer-reviewed articles within the last 10 years, but the majority of the literature was from the last five years. Microbiome interventions have been associated with reduced postoperative complications and enhanced recovery times. The study found that changing the gut microbiome in specific ways, like using probiotics and synbiotics before and after surgery, can lead to better surgical results. For example, these treatments can lower the risk of infection at the surgery site by 40%-80% compared to standard care, help patients recover their bowel function one to two days faster, and reduce hospital stays by up to 30%. They also decrease levels of important inflammation markers like IL-6 and CRP. Using probiotics and synbiotics before surgery and continuing them for two weeks can lower infection rates and enhance recovery while managing inflammation. The beneficial effects of probiotics, prebiotics, and synbiotics support their use as effective strategies in perioperative care. However, people react differently to probiotics, prebiotics, and synbiotics because of factors like genetics, age, hormonal differences between sexes, and variations in gut microbiota based on race. Future research should focus on developing personalized microbiome-based interventions and establishing standardized protocols tailored to individual patient characteristics to enhance their effectiveness.

Background Recent explorations into the gut microbiome of humans and animals reveal implications in chronic physical and mental health disorders. Relatively little is known regarding the relationship of gut microbiome and depression. In the current review, we reviewed existing scientific data related to the gut microbiome and healthy patients versus patients with depression. Additionally, scientific literature containing the utility of microbiome interventions to improve depression symptoms was reviewed. Methods A PubMed and Clinical Key literature search combined the key terms ‘gut,’ ‘microbiome,’ ‘bacteria,’ and ‘depression’ to identify studies investigating these relationships. Results 76 relevant articles were identified. Human and animal studies reviewed examined marked alterations in the dominant bacterial phyla in the gut of individuals with depression, the connection between leaky gut and neuroinflammation in depression, brain regulatory centers impacted by changes in the gut microbiome, and the benefits of the addition of a probiotic/prebiotic for gut and mental health. Conclusions The current review confirmed the suspected direct communication between the gut microbiome, brain functioning, and depression. Additionally, studies suggest antibiotics disrupt the gut microbiome. There are important implications for psychiatrists in providing opportunities for intervention and enhancement of current treatments for individuals with depression.

Relative to other tumors in smokers, KRAS-mutant lung adenocarcinomas (LUADs) display dismal prognosis warranting the need for early management of this disease. Limiting these advances is our gap in knowledge of events that drive KRAS-mutant LUAD oncogenesis. Host defense systems, such as those elicited by the gut microbiome, were recently shown to influence tumors external to the gastrointestinal tract (e.g. melanomas), thus highlighting the microbiome as an orchestrator of oncogenesis. Yet, gut microbiome changes in early stages of KRAS-mutant LUAD development are not known. We recently reported that mice with knockout of G-protein coupled receptor 5A (Gprc5a-/-), in contrast to wild type (WT) littermates, develop LUADs which are accelerated following exposure to tobacco carcinogen (nicotine-specific nitrosamine ketone/NNK). LUADs in the tobacco exposed Gprc5a-/- mouse model exhibit high somatic mutation burdens, driver Kras variants and other co-occurring drivers, features constituting a “perfect storm” for LUAD pathogenesis in smokers. Using this human-relevant model, we performed 16S-Seq of fecal samples collected prior to and at several time points post-NNK exposure during LUAD development. We found significant, some progressive, microbial changes during the pathogenesis of LUAD, including abolishment of phylum Verrucomicrobia, progressive increase in tumor-promoting genera Odoribacter spp., gradual decrease in Akkermansia spp., which was previously shown to be associated with response to PD-1 blockade, as well as reduced abundance of Ruminococcus which was previously reported to be suppressed during colon carcinogenesis. Additionally, and prior to tumor onset, lungs and immune cells of these Gprc5a-/- mice exhibited markedly elevated expression of lipocalin 2 (LCN2), an antimicrobial protein released from host cells during microbiome imbalance and inflammation. We further found that Gprc5a-/- mice with knockout of Lcn2 exhibited increased tumors compared to similarly exposed Gprc5a-/- with intact Lcn2. These effects were accompanied by widespread changes in the gut microbiome including increased abundance of tumor-promoting Alistipes spp. and, conversely, reduced abundance of Lactobacillus spp. Our data show that host defense mediated by LCN2 counteracts Kras-mutant LUAD development by restricting gut microbiome imbalance (i.e., maintaining gut microbiome homeostasis and diversity), suggesting a protective role during Kras-mutant LUAD development. Our overall findings inform on novel pathways implicating antimicrobial host defense mechanisms in the development of smoking-associated Kras-mutant LUAD. Efforts are underway to discern specific microbiome profiles that are likely causally related to smoking-associated Kras-mutant LUAD development as well as to develop and test preclinical microbiome intervention strategies for this malignancy. Citation Format: Warapen Treekitkarnmongkol, Casey Finnicum, Ansam Sinjab, Maya Hassane, Christel Davis, Gareth E. Davies, Kristi L. Hoffman, Junya Fujimoto, Florencia McAllister, Boris Sepesi, Tina Cascone, Robert R. Jenq, Joseph Petrosino, Erik Ehli, Seyed J. Moghaddam, Humam Kadara. Evolution of the gut microbiome during the pathogenesis of smoking-associated Kras-mutant lung cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3349.

This review explores the transformative potential of gut microbiota modulation in sports medicine, where the convergence of advanced technology, rigorous training, and injury management aims to mitigate sports-related injuries. Athletes in high-intensity sports demand exceptional physical prowess, adhering to grueling training regimens for peak fitness levels. However, the pursuit of athletic excellence often leads to exhaustive physical stress and sport-specific injuries. Personalized sports medicine has emerged as an adaptive discipline, utilizing diverse technologies and methods to deliver customized medical care and enhance performance. The gut microbiota, a complex microbial community in the gastrointestinal system, significantly influences energy production, digestion, and immune defense. Similar to personalized sports medicine, the gut microbiota of every individual is unique, shaped by genetics, diet, lifestyle, and environment. Recent research underscores the profound impact of gut microbiota on athletic performance, recovery, and overall health. This review consolidates current knowledge regarding gut microbiota modulation in sports medicine, revealing its potential to revolutionize athlete care and performance enhancement. The uniqueness of our review lies in considering the interplay between gut health and personalized sports medicine, a relatively unexplored area. The study highlights the prospect of tailoring nutritional and training regimens based on the unique gut microbiota profile of every individual, marking a new era in sports medicine. Addressing a significant literature gap, this review emphasizes the importance of gut microbiota modulation in personalized sports medicine—a paradigm shift poised to enhance athletic performance, expedite recovery, and reduce injury risk.

Ulcerative colitis is an inflammatory disorder characterized by chronic inflammation in the gastrointestinal tract, mainly in the colon and rectum. Although the precise etiology of ulcerative colitis remains unclear, recent research has underscored the significant role of the microbiome in its development and progression. The aim of this study was to establish a relationship between the levels of specific gut bacterial species and disease relapse in ulcerative colitis. For this study, we recruited 105 ulcerative colitis patients in remission and collected clinical data, blood, and stool samples. Akkermansia muciniphila and Parabacteroides distasonis levels were quantified in the stool samples of ulcerative colitis patients. Binary logistic regression was applied to collected data to predict disease remission. The median time in remission in this cohort was four years. A predictive model incorporating demographic information, clinical data, and the levels of Akkermansia muciniphila and Parabacteroides distasonis was developed to understand remission patterns. Our findings revealed a negative correlation between the levels of these two microorganisms and the duration of remission. These findings highlight the importance of the gut microbiota in ulcerative colitis for disease prognosis and for personalized treatments based on microbiome interventions.

Hepatocellular carcinoma (HCC) is a leading cause of cancer mortality, and pathogenic gut bacteria contribute to its pathogenesis. This review explains how gut microbiota dysbiosis drives hepatocarcinogenesis through inflammation, metabolic dysregulation, and immune modulation. Pathogens like Fusobacterium nucleatum, Helicobacter pylori, Clostridium spp., Enterococcus faecalis, and Escherichia coli disrupt intestinal barrier integrity, alter bile acid metabolism, and induce DNA damage. These interactions activate oncogenic pathways and suppress apoptosis, thereby creating a tumor-permissive environment. Risk factors, including viral hepatitis, non-alcoholic fatty liver disease, alcohol consumption, and dietary imbalances, combined with microbial dysbiosis to increase HCC risk. Genetic susceptibility affects host-microbe interactions, with polymorphisms in TLR4, ATM, and PNPLA3 worsening inflammation and metabolic dysfunction. Early detection through ultrasound surveillance, biomarkers, and microbiome interventions is key to improving patient outcomes. Clinical trials investigating H. pylori eradication, F. nucleatum detection, and E. faecalis-mediated inflammation have demonstrated the translational potential of microbiota modulation. Molecular docking analyses revealed pathogen-host receptor interactions (E. coli-TLR4 and H. pylori-PD-L1) that drive immune evasion and barrier disruption. These insights support integrated approaches that combine genetic screening, microbiome profiling, and precision therapies. This review establishes the gut-liver axis as a therapeutic target, calling for efforts to understand host-microbe dynamics and advance cancer therapies.

Inflammatory bowel diseases (IBDs), including Crohn’s disease (CD) and ulcerative colitis (UC), are chronic immune-mediated disorders characterized by mucosal injury, cycles of inflammation and repair, and tissue damage. Persistent inflammation accelerates epithelial turnover, generates oxidative and replication stress, and remodels the stromal niche, contributing to the risk of colorectal cancer (CRC). Systematic dysplasia surveillance remains essential. Cellular senescence has emerged as a unifying mechanism linking inflammation, impaired epithelial repair, fibrosis, and neoplasia. In UC, p16/p21 upregulation, telomere erosion, and loss of lamin B1 accumulate and adopt a senescence-associated secretory phenotype (SASP) that perpetuates barrier dysfunction. In CD, senescence within stem and stromal compartments limits regeneration, promotes pro-fibrotic remodeling, and sustains cycles of injury and repair via chronic SASP signaling. IBD prevalence continues to rise from environmental factors, dietary changes, antibiotic exposures, and gut microbiota alterations. Pathogenesis integrates genetic factors (e.g., NOD2, IL23R, HLA, and ATG16L1 mutations), environmental modifiers, dysbiosis characterized by loss of short-chain fatty-acid-producing Gram-positive bacteria and expansion of Proteobacteria, and a dysregulated immune system. Therapeutic strategies have shifted toward targeted biologics and small molecules to promote mucosal healing. In this review, we recapitulate the mechanistic axes of inflammation, oxidative stress, and senescence in IBD and then critically evaluate emerging targeted therapies. Topics include anti-TNFα, integrin blockade, IL-12/23 and IL-23 inhibition, JAK inhibitors, S1P receptor modulators, microRNA modulation, senomorphics, mesenchymal cell therapy, and microbiome interventions. We endorse biomarker-guided therapy and propose future directions to break the SASP-driven inflammatory loop and mitigate long-term carcinogenic risk.