Role of the normal gut microbiota

Fecal microbiota transplantation modulates myeloid-derived suppressor cells and attenuates renal fibrosis in a murine model

BACKGROUND

Renal fibrosis is a hallmark of progressive chronic kidney disease (CKD), with emerging evidence linking gut microbiota dysbiosis to disease progression. Myeloid-derived suppressor cells (MDSCs) have demonstrated renoprotective effects, yet the impact of fecal microbiota transplantation (FMT) on MDSC-mediated modulation of renal fibrosis remains unclear.

METHODS

C57BL/6J mice underwent unilateral ureteral obstruction (UUO) to induce renal fibrosis, followed by FMT administration via gavage. Flow cytometry was used to quantify granulocytic (G-MDSCs) and monocytic (M-MDSCs) MDSC populations in peripheral blood, kidney, and spleen. To elucidate the role of MDSCs in FMT-mediated effects, MDSCs were depleted or adoptively transferred in vivo. Renal fibrosis severity and inflammatory cytokine expression were subsequently analyzed.

RESULTS

FMT altered MDSC distribution, increasing M-MDSC accumulation in the blood and kidney. This was associated with downregulation of proinflammatory cytokines and attenuation of renal fibrosis. Adoptive MDSC transfer similarly produced anti-inflammatory and antifibrotic effects, reinforcing their therapeutic role in FMT-mediated renal protection.

CONCLUSIONS

FMT enhances M-MDSC-mediated immunomodulation, reducing inflammation and renal fibrosis in UUO-induced CKD. These findings suggest a potential therapeutic strategy targeting the gut-kidney axis in CKD management.

Short-term antiretroviral therapy may not correct the dysregulations of plasma virome and cytokines induced by HIV-1 infection

An expansion of plasma anelloviruses and dysregulation of inflammation was associated with HIV-1 infection. However, how antiretroviral therapy (ART) affects the dynamics of plasma virome and cytokine profile remains largely unknown. To characterize the dynamics of plasma virome and cytokines in HIV-1-infected individuals before and during the first year of ART, a cohort of 26 HIV-1-infected individuals and 19 healthy controls was recruited. Blood samples were collected and subjected to metagenomic analysis and the measurement of 27 cytokines. Metagenomic analysis revealed an increased abundance and prevalence of human pegivirus type 1 (HPgV-1) and a slightly decreased diversity and abundance of anellovirus in plasma of HIV-1-infected individuals after ART. No obvious impact was observed on other plasma commensal viruses. Increased abundance and prevalence of HPgV-1 were further confirmed by RT-qPCR assay in a larger cohort of 114 HIV-1-infected individuals. Notably, most dysregulated cytokines were not fully restored by ART, with extremely abnormal levels of IL-10, GM-CSF, VEGF, and eotaxin, and a significantly increased level of plasma I-FABP. Anelloviruses showed significantly negative correlations with other commensal viruses except HPgV-1 but had positive correlations with several anti-inflammatory and Th1 cytokines. These results suggest that short-term ART may not significantly correct the virome and cytokine dysregulations induced by HIV-1 infection. The results highlight a need for further investigation into the long-term effects of ART on virome and cytokine profiles in HIV-1-infected individuals.

Fecal microbiota transplantation in allergic diseases

Microorganisms such as bacteria, fungi, viruses, parasites living in the human intestine constitute the human intestinal microbiota. Dysbiosis refers to compositional and quantitative changes that negatively affect healthy gut microbiota. In recent years, with the demonstration that many diseases are associated with dysbiosis, treatment strategies targeting the correction of dysbiosis in the treatment of these diseases have begun to be investigated. Faecal microbiota transplantation (FMT) is the process of transferring faeces from a healthy donor to another recipient in order to restore the gut microbiota and provide a therapeutic benefit. FMT studies have gained popularity after probiotic, prebiotic, symbiotic studies in the treatment of dysbiosis and related diseases. FMT has emerged as a potential new therapy in the treatment of allergic diseases as it is associated with the maintenance of intestinal microbiota and immunological balance (T helper 1/T helper 2 cells) and thus suppression of allergic responses. In this article, the definition, application, safety and use of FMT in allergic diseases will be discussed with current data.

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.

Integrative review of the gut microbiome’s role in pain management for orthopaedic conditions

The gut microbiome, a complex ecosystem of microorganisms, has a significant role in modulating pain, particularly within orthopaedic conditions. Its impact on immune and neurological functions is underscored by the gut-brain axis, which influences inflammation, pain perception, and systemic immune responses. This integrative review examines current research on how gut dysbiosis is associated with various pain pathways, notably nociceptive and neuroinflammatory mechanisms linked to central sensitization. We highlight advancements in meta-omics technologies, such as metagenomics and metaproteomics, which deepen our understanding of microbiome-host interactions and their implications in pain. Recent studies emphasize that gut-derived short-chain fatty acids and microbial metabolites play roles in modulating neuroinflammation and nociception, contributing to pain management. Probiotics, prebiotics, synbiotics, and faecal microbiome transplants are explored as potential therapeutic strategies to alleviate pain through gut microbiome modulation, offering an adjunct or alternative to opioids. However, variability in individual microbiomes poses challenges to standardizing these treatments, necessitating further rigorous clinical trials. A multidisciplinary approach combining microbiology, immunology, neurology, and orthopaedics is essential to develop innovative, personalized pain management strategies rooted in gut health, with potential to transform orthopaedic pain care.

Harnessing the human microbiome and its impact on immuno-oncology and nanotechnology for next-generation cancer therapies

The integration of microbiome research and nanotechnology represents a significant advancement in immuno-oncology, potentially improving the effectiveness of cancer immunotherapies. Recent studies highlight the influential role of the human microbiome in modulating immune responses, presenting new opportunities to enhance immune checkpoint inhibitors (ICIs) and other cancer therapies. Nanotechnology offers precise drug delivery and immune modulation capabilities, minimizing off-target effects while maximizing therapeutic outcomes. This review consolidates current knowledge on the interactions between the microbiome and the immune system, emphasizing the microbiome's impact on ICIs, and explores the incorporation of nanotechnology in cancer treatment strategies. Additionally, it provides a forward-looking perspective on the synergistic potential of microbiome modulation and nanotechnology to overcome existing challenges in immuno-oncology. This integrated approach may enhance the personalization and effectiveness of next-generation cancer treatments, paving the way for transformative patient care.

Assessment of gut microbiota in the elderly with sarcopenic obesity: a case-control study

Objectives

Sarcopenic obesity is a multifactorial disorder commonly found in elderly individuals. One contributing factor is gut microbiota dysbiosis. This study compared the abundance of certain bacteria in elderly individuals with obesity and sarcopenic obesity.

Methods

The study included 50 elderly individuals over 65 with a body mass index (BMI) of over 30 kg/m², both sexes. Participants were divided into two groups, each with 25 individuals, based on the diagnosis of sarcopenia using the EWGSOP2 criteria. Individuals with underlying diseases, those using antibiotics, and those with a history of gastrointestinal surgery were excluded. Stool samples were stored at -80 °C, and DNA was extracted using standard kits. Bacterial DNA sample quality was assessed using a Nanodrop device. Bacterial frequency was measured using qPCR. The log cfu for each bacteria was calculated and compared in both groups using an independent t-test. Spearman measured the correlation between bacterial genera and physical performance in SPSS 26.

Results

The case group had a significantly higher average age (70.96) than the control group (68.32). The average BMI was the same in both groups. The frequency of Escherichia (p-value = 0.046) and Bifidobacterium (p-value = 0.017) was significantly higher in the case group. There was no significant difference in the frequency of Lactobacillus and Akkermansia.

Conclusion

The study uncovered substantial differences in gut microbiota composition between elderly individuals experiencing sarcopenic obesity and those with obesity alone. The findings suggest that dysbiosis, characterized by an excessive presence of Bifidobacterium, Escherichia, and Akkermansia, may be associated with sarcopenic obesity.

Supplementary Information

The online version contains supplementary material available at 10.1007/s40200-025-01584-x.

Indole metabolism and its role in diabetic macrovascular and microvascular complications

Tryptophan (Trp), an essential amino acid obtained through dietary sources, plays a crucial role in various physiological processes. The metabolism of Trp branches into three principal pathways: the serotonin pathway, the kynurenine pathway, and the indole pathway. The kynurenine and serotonin pathways are host pathways while the indole pathway is solely the result of bacterial metabolism. Trp metabolites extend their influence beyond protein biosynthesis to affect a spectrum of pathophysiological mechanisms including, but not limited to, neuronal function, immune modulation, inflammatory responses, oxidative stress regulation, and maintenance of intestinal health. This review focuses on indole derivatives and their impact on vascular health. Trp-containing dipeptides are highlighted as a targeted nutraceutical approach to modulate Trp metabolism, enhance beneficial metabolite production, and mitigate risk factors for vascular diseases. The importance of optimizing Trp intake and dietary strategies to harness the benefits of Trp-derived metabolites for vascular health is underscored, bringing to light the need for further research to refine these therapeutic approaches.

Differences in anti-obesity effects between raw and ripened Pu-erh tea polyphenols: impact on gut microbiota enterotypes

BACKGROUND

Pu-erh tea, a dark tea from China, is classified into raw and ripened types. Both have significant anti-obesity effects. Polyphenols are among their major bioactive components. This study aimed to explore the anti-obesity properties and mechanisms of raw (R-TP) and ripened (F-TP) Pu-erh tea polyphenols.

RESULTS

The results showed that R-TP and F-TP significantly reduced body weight, improved insulin resistance, and enhanced glucose and lipid metabolism in high-fat-diet (HFD)-induced obese mice. Mild differences were observed in their impact on fat metabolism, carbohydrate metabolism, and inflammation levels. Both R-TP and F-TP were able to restore the disrupted intestinal flora caused by HFD treatment, returning them to a composition and levels similar to those of normal mice. Interestingly, the gut microbiota of all the mice could be reclassified into three enterotypes (enterotype Type-1, Type-2, and Type-HFD). Lactobacillaceae predominated in Type-1. Lactobacillaceae, Muribaculaceae, and Lachnospiraceae were the most common in Type-2. Type-HFD was primarily composed of Atopobiaceae, Lachnospiraceae, Lactobacillaceae, Ruminococcaceae, and Erysipelotrichaceae. The small differences in the effects of R-TP and F-TP may be due to variations in enterotypes.

CONCLUSION

These findings indicate that R-TP and F-TP can alleviate obesity by regulating the enterotype of gut microbiota, suggesting that they possess the potential for application in the treatment of obesity and the development of anti-obesity agents. © 2025 Society of Chemical Industry.

Synbiotics of encapsulated Limosilactobacillus fermentum K73 promotes in vitro favorable gut microbiota shifts and enhances short-chain fatty acid production in fecal samples of children with autism spectrum disorder

Modulation of the gut microbiota has emerged as a promising approach for addressing the gastrointestinal and neurodevelopmental symptoms associated with autism spectrum disorder (ASD). Consequently, this study aimed to evaluate the impact of four formulated synbiotics comprising Limoscilactobacillus fermentum K73, high-oleic palm oil and whey, on the gut microbiota composition of Colombian children with and without ASD. These components were encapsulated through high-shear emulsification and spray drying. The four synbiotics and their individual components were subjected to in vitro digestion and fermentation using samples of Colombian children gut microbiota. Short-chain fatty acids (SCFAs), including lactic, acetic, propionic, and butyric acids, were quantified using HPLC-DAD, while serotonin was determined by an ELISA kit after in vitro fermentations. Changes in microbial structure were assessed by the sequencing of the 16S rRNA gene via next-generation sequencing (NGS). The results revealed a decrease in the abundance of genera like Bacteroides and Dorea in ASD-associated samples after the treatment with the synbiotics. Conversely, an increase in the relative abundance of probiotic-related genera, including Lactobacillus, Streptococcus, and Anaerostipes, was observed. Furthermore, the analysis of SCFAs and serotonin indicated that the synbiotic intervention resulted in an elevated butyric acid and microbial serotonin synthesis, alongside a decrease in propionic acid, which is changes considered beneficial in the context of ASD. This evidence suggests that synbiotics of L. fermentum K73 could represent a promising live biotherapeutic strategy for modulating the gut microbiota of children with ASD.

Interactions of erythromycin and an antibiotic mixture with the gut microbiome of juvenile rainbow trout

Erythromycin (ERY) is a commonly used antibiotic found in wastewater effluents and the environment globally. Due to the bioactivity by which they kill and prevent bacterial growth, ERY and other antibiotics may have significant unwanted impacts on the gut microbiome of fishes. The overall objective of this project was to assess effects on the gut microbiome in response to exposure to ERY alone or in a mixture with other common antibiotics, which was accomplished in two experiments. The objectives of experiment 1 as a pilot study were to understand uptake and depuration of ERY in juvenile rainbow trout (RBT) over a 7-d exposure to three concentrations of ERY followed by a 7-d depuration period. Furthermore, throughout the study changes in gut microbiome were assessed. In experiment 2, an identical experimental design was used to assess the effects of a mixture of antibiotics containing, in addition to ERY, 100 μg/g each of ampicillin, metronidazole, and ciprofloxacin. In that study, three matrices were analyzed, with gut collected for 16S rRNA metabarcoding, blood plasma for non-targeted metabolomics, and brain tissue for mRNA-seq analysis. ERY was relatively quickly depurated from fish and gut microbiome dysbiosis was observed at 7 d after exposure, with a slight recovery after the 7-d depuration period. A greater number of plasma metabolites was dysregulated at 14 d compared to 7 d revealing distinct temporal dynamics compared to gut microbiome dysbiosis. Furthermore, several transformation products of antibiotics and biomarker metabolites were observed in plasma due to antibiotic exposure. The transcriptome of the brain was only slightly altered due to antibiotic exposure. Results of these studies will help inform aquaculture practitioners and risk assessors when assessing the potential impacts of antibiotics present in fish feed and the environment, with implications for host health.

The conspiring role of gut microbiota as primer of autoimmune thyroid diseases: A scoping focus

The thyroid gland is the body's largest single organ specialized for endocrine hormone production, and still unraveled mechanisms regulate its interaction between the hypothalamic-pituitary-thyroid axis and composition of the gut microbiota: in particular, a disrupted integrity of the intestinal barrier, causing dysbiosis and increasing detrimental substances or reducing beneficial metabolites, such as short-chain fatty acids (SCFAs) with proinflammatory effects, may be crucial for the induction of an autoimmune thyroid disease. More specifically, Lactobacilli and Bifidobacteria have a role in this partnership through a "molecular mimicry" mechanism, as their protein sequences share structural similarity with thyroid peroxidase and thyroglobulin. Lactobacilli can also increase T helper 17 cells, modifying the number of colonic regulatory T cells, largely implicated in the maintenance of immunological tolerance at the gut barrier. Additionally, Blautia and Anaerostipes work beneficially with butyric acid, one of the SCFAs, promoting antimicrobial peptide synthesis from the intestinal cells and bolstering the innate immune system's ability to struggle against pathogens, which can also influence thyroid hormone levels by regulating iodine uptake and metabolism. This review aims to summarize the current knowledge about the contribution of gut microbiota changes in triggering immune abnormalities leading to autoimmune thyroid diseases.

Molecular characterization and virulence of fungal pathogens associated with mass mortalities in hilsa Shad (Tenualosa ilisha)

The rising incidence of invasive microbial infections and the expanding spectrum of pathogens make early and accurate identification of the causative pathogen a daunting task. Accurate diagnosis enables the identification and characterization of microbes and offers new possibilities for the control and prevention of infectious diseases. For the first time, we isolated and characterized three fungal species, viz., Mucor circinelloides, Fusarium equiseti, and F. incarnatum from hilsa (Tenualosa ilisha). The characterization was based on fungus morphology (in vitro culture and microscopy), molecular (PCR, sequencing and phylogenetic analysis) and virulence features (survival assay, histological examination). The naturally infected fish exhibited significant histomorphology alterations in the gill, liver, kidney, spleen, and muscle tissue. Furthermore, the qPCR analysis, based on Pfaffl's relative standard curve method, exhibits significant up-regulation of Heat shock protein 70 (Hsp70), inducible nitric oxide synthase (iNOS) (except spleen) and tumour necrosis factor α (TNF-α) and Chemokine receptors (CCR) (only liver) were observed during a fungal infection in liver, kidney, and spleen tissue. In contrast, nuclear factor kappa B (NF-κB) and Interferon-gamma (IFN-γ) were significantly downregulated during infection. The fungal infection strongly influences the structures of the selected bacterial population (live bacterium)/cultivable bacterial enumeration and their abundance. Naturally infected fish were found to harbor Morganella morganii, Enterobacter cloacae, Enterococcus faecalis, and Proteus penneri. In contrast, non-infected fish contained Escherichia coli, Proteus mirabilis, Enterobacter cloacae, Enterococcus lactis, and Enterococcus gallinarum. The gut bacteria from infected hilsa displayed significantly higher (P-values < 0.05) haemolysin and swimming motility activity and biofilm production compared to those from non-infected fish. Additional research is required to clarify the virulence traits of the isolated fungi, as well as the impact of one or several isolated fungal species on the host's health, to assess the mortality risks posed by these fungi. Insights gained from the first cellular and molecular characterization of Mucor circinelloides, Fusarium equiseti, and F. incarnatum have provided valuable insights into disease epidemiology in hilsa farming.

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 patients and evaluates the potential connection between plant metabolites and the microbiome in the context of IBD pathophysiology.

Progress in Probiotic Science: Prospects of Functional Probiotic-Based Foods and Beverages

This comprehensive review explores the evolving role of probiotic-based foods and beverages, highlighting their potential as functional and "future foods" that could significantly enhance nutrition, health, and overall well-being. These products are gaining prominence for their benefits in gut health, immune support, and holistic wellness. However, their future success depends on addressing critical safety concerns and navigating administrative complexities. Ensuring that these products "do more good than harm" involves rigorous evaluations of probiotic strains, particularly those sourced from the human gastrointestinal tract. Lactic acid bacteria (LABs) serve as versatile and effective functional starter cultures for the development of probiotic foods and beverages. The review emphasizes the role of LABs as functional starter cultures and the development of precision probiotics in advancing these products. Establishing standardized guidelines and transparent practices is essential, requiring collaboration among regulatory bodies, industry stakeholders, and the scientific community. The review underscores the importance of innovation in developing "friendly bacteria," "super probiotics," precision fermentation, and effective safety assessments. The prospects of functional probiotic-based foods and beverages rely on refining these elements and adapting to emerging scientific advancements. Ultimately, empowering consumers with accurate information, fostering innovation, and maintaining stringent safety standards will shape the future of these products as trusted and beneficial components of a health-conscious society. Probiotic-based foods and beverages, often infused with LABs, a "friendly bacteria," are emerging as "super probiotics" and "future foods" designed to "do more good than harm" for overall health.

Uncovering the Effects of Different Formulae of Milk Powders on the Fecal Microorganisms and Metabolites of Bengal Tiger (Panthera tigris spp. tigris) Cubs

In order to optimize diets for Bengal tiger cubs and improve their health condition and survival rates, we conducted microbiota and metabolomics analyses on fecal samples from Bengal tiger cubs fed goat and dog milk replacer formulae. The results showed that there were significant differences in fecal microorganisms and metabolites between the two groups. At the phylum level, the major components of the microbial composition in the feces of cubs were Firmicutes, Actinobacteriota, Proteobacteria, Bacteroidota and Fusobacteriota. In addition, the abundance of gut microbiota varied significantly between the two groups of tiger cubs. The fecal microbiota of the tiger cubs fed dog milk replacer powder exhibited an increase in probiotic bacteria (Anaerostipes and Clostridium_scindens) (p < 0.05), and the microbial community tended to be more balanced. Metabolomics data further elucidated that feeding different milk formulae significantly affected the fecal metabolites and metabolic pathways in the Bengal tiger cubs. In the dog milk replacer powder group, 76 metabolites were up-regulated (p < 0.05), and 278 metabolites were down-regulated (p < 0.05), particularly affecting the metabolism of vitamin D3, vitamin B5, isoleucine, valine, phenylalanine and oleic acid. At the same time, 19 metabolic pathways were affected (p < 0.05), including the amino acid metabolism, lipid metabolism and nucleotide metabolism pathways. In conclusion, this study confirms that milk formula composition affects the gut microbiota and metabolism of Bengal tiger cubs. These findings may provide new insights into how different milk powder formulae and dietary strategies influence the regulation of gut microbiota and overall health in Bengal tiger cubs.

Body mass index matters: morbid obese patients have different microorganism profiles in the setting of periprosthetic hip joint infections

PURPOSE

This study investigated the relationship between BMI and microorganism profiles, with a particular focus on gut microorganisms in patients with PJI following total hip arthroplasty (THA). It also explored comorbidities, that may contribute to these variations.

METHODS

This study included all patients treated at our institution for a PJI of a THA between 1996 and 2021. Patients were categorized into four distinct BMI groups: <30; 30-34.9; 35-39.9; ≥ 40. Bivariate and logistic regression analysis were conducted, with presentation of odds ratio (OR) and 95% confidence interval (CI).

RESULTS

A total of 3645 hip PJI cases were recruited for the final analysis. Patients with a BMI ≥ 40 had approximately a ten fold higher risk for Streptococcus dysgalactiae (p < 0.001; OR = 9.92; 95% CI 3.87-25.44) and a seven fold higher risk for Proteus mirabilis (p < 0.001; OR = 7.43; 95% CI 3.13-17.67) and Klebsiella pneumoniae (p < 0.001; OR = 6.9; 95% CI 2.47-19.31). Furthermore, polymicrobial infections (p < 0.001; OR = 2.17; 95% CI 1.50-3.15) were found to be significantly more prevalent in patients with a BMI ≥ 40.

CONCLUSION

Obese patients (BMI ≥ 30) displayed a distinct microorganism profile in hip PJIs, mainly dominated by Firmicutes and Proteobacteria. Comorbidities such as diabetes, hypertension, and hyperlipidaemia may contribute to a leaky gut syndrome, increasing PJI risk caused by gut microorganisms. Optimizing comorbidities may help reduce the risk of hip PJI. Further research is needed to clarify the relationship between obesity, gut microbiome alterations and hip PJI development.

Gut microbiota diversity among humans, elephants, livestock and wild herbivores in Chitwan National Park bears implications for conservation medicine

Gut microbiome influences host health and well-being. Co-occurring hosts may exchange disease-causing bacteria belonging to these microbial communities. Therefore, monitoring gut microbiota composition in wildlife and humans is paramount to prevent zoonotic diseases, thus protecting and strengthening public health. We characterized diversity and abundance of the gut microbiome bacterial component across mahouts (captive elephant trainers and handlers), their pachyderms, livestock and wild herbivores in and around Chitwan National Park (Nepal). Firmicutes and Bacteroidota were invariably the dominant phyla. In humans, the relative abundance of Firmicutes was higher, the alpha diversity lower and beta diversity different compared to other host categories. Livestock and wild herbivores displayed similar alpha and beta diversity due to the presence of Proteobacteria, Actinobacteriota and Verrucomicrobiota. Elephants had a higher alpha diversity, and a significant beta diversity compared to other mammals. Our results suggest that taxonomic affiliation and diet niche are the main drivers of gut microbiota composition. Nevertheless, Mycobacterium and other potentially pathogenic bacteria genera were detected in elephants and livestock other than wild herbivores. These findings shed light on microbiota sharing and interlinking in each environment, thereby highlighting the importance of conservation medicine to better our understanding of health in co-occurring host species.

Effects of Different Feeding Patterns on the Gut Virome of 6-Month-Old Infants

The gut microbiome is essential for infant health, and in recent years, the impact of enteroviruses on infant health and disease has received increasing attention. The transmission of breast milk phages to the infant gastrointestinal tract contributes to the shaping of the infant gut virome, while breastfeeding regulates the colonization of the infant gut virome. In this study, we collected fecal samples from healthy infants and analyzed the distribution characteristics of infant viral communities by viral metagenomic analysis, and analyzed the differences in infant viral communities under different feeding practices. Our results indicate that the infant intestinal virome consists of phages and eukaryotic viruses. Caudovirales and Microviridae dominated the phage composition, and except for Siphoviridae, which was more predominant in the intestines of formula-fed infants, there were no significant differences in the overall abundance of other Caudovirales and Microviridae in the intestines of infants with different feeding patterns. Breastfeeding can lead to a higher diversity of infant gut viruses through vertical transmission, and a highly diverse gut virome helps maintain the maturation of the gut microbiome. This study informs the shaping of gut virome in healthy infants by breastfeeding and contributes to further research on infant gut virome characteristics and formation processes.

Advances in Fecal Microbiota Transplantation for Gut Dysbiosis-Related Diseases

This article provides an overview of the advancements in the application of fecal microbiota transplantation (FMT) in treating diseases related to intestinal dysbiosis. FMT involves the transfer of healthy donor fecal microbiota into the patient's body, aiming to restore the balance of intestinal microbiota and thereby treat a variety of intestinal diseases such as recurrent Clostridioides difficile infection (rCDI), inflammatory bowel disease (IBD), constipation, short bowel syndrome (SBS), and irritable bowel syndrome (IBS). While FMT has shown high efficacy in the treatment of rCDI, further research is needed for its application in other chronic conditions. This article elaborates on the application of FMT in intestinal diseases and the mechanisms of intestinal dysbiosis, as well as discusses key factors influencing the effectiveness of FMT, including donor selection, recipient characteristics, treatment protocols, and methods for assessing microbiota. Additionally, it emphasizes the key to successful FMT. Future research should focus on optimizing the FMT process to ensure long-term safety and explore the potential application of FMT in a broader range of medical conditions.

New approaches in childhood IgE-mediated food allergy treatment

PURPOSE OF REVIEW

This review aims to provide an overview of the current and future treatment options for children with food allergies (FAs), highlighting the latest research findings and the potential impact of these new approaches on improving patients' and caregivers' quality of life.

RECENT FINDINGS

In the last decade, many promising approaches have emerged as an alternative to the standard avoidance of the culprit food with the risk of severe accidental reactions. Desensitization through oral immunotherapy has been introduced in clinical settings as a therapeutic approach, and more recently also omalizumab. In addition, alternative routes of administration for immunotherapy, other biologics, small molecules, probiotics or prebiotics, microbiota transplantation therapy, IGNX001, and PVX108 are being investigated.

SUMMARY

The portfolio of available treatment options for food allergies is increasing but several relevant unmet needs remain. This review aims to provide a brief overview of the existing and future treatment options for IgE-mediated food allergies.

The Gut Microbiome and Joint Microbiome Show Alterations in Patients With Knee Osteoarthritis Versus Controls: A Systematic Review

PURPOSE

To assess the current scientific literature on the microbiome's relation with knee osteoarthritis (OA), with specific focuses on the gut microbiome-joint axis and joint microbiome-joint axis.

METHODS

A systematic review was conducted following the Preferred Reporting Items for Systematic Reviews and Meta-analyses guidelines; the PubMed, Embase, and Cochrane databases were searched for relevant English-language clinical studies on the gut and/or joint microbiomes' association with knee OA in humans. Bias was evaluated using the Methodological Index for Non-randomized Studies score.

RESULTS

Thirty-five thousand bacterial species comprise the gut microbiome; approximately 90% are members of the phyla Bacteroides and Firmicutes. Symbiosis between the gut microbiome and host under normal physiological conditions positively affects host growth, development, immunity, and longevity. Gut microbiome imbalance can negatively influence various physiological processes, including immune response, inflammation, metabolism, and joint health including the development of knee OA. In addition, next-generation gene sequencing suggests the presence of microorganisms in the synovial fluid of OA knees, and distinct microbiome profiles detected are presumed to play a role in the development of OA. Regarding the gut microbiome, consistent alterations in microbial composition between OA patients and controls are noted, in addition to several associations between certain gut bacteria and OA-related knee pain, patient-reported outcome measure performance, imaging findings, and changes in metabolic and inflammatory pathways. Regarding the joint microbiome, studies have revealed that increased levels of lipopolysaccharide and lipopolysaccharide-binding protein in synovial fluid are associated with activated macrophages-and are correlated with worsened osteophyte severity, joint space narrowing, and pain scores in knee OA patients. In addition, studies have shown various microbial composition differences in OA patients compared with controls, with certain joint microbes directly associated with OA pathogenesis, inflammation, and metabolic dysregulation.

CONCLUSIONS

The gut microbiome-joint axis and joint microbiome show alterations in microbial composition between patients with OA and controls. These alterations are associated with perturbations of metabolic and inflammatory pathways, imaging findings, OA-related pain, and patient-reported outcome measure performance.

LEVEL OF EVIDENCE

Level III, systematic review of Level II and III studies.

Rare taxa in the core microbiome

Rare taxa are an important constituent of the microbiome and play a crucial role in maintaining biodiversity and ecosystem dynamics. However, little is known about rare taxa within the core microbiome (i.e., core rare taxa), nor do we understand the factors that drive their distribution and occupancy in ecosystems. In this opinion article, we define and explore the role of core rare taxa and the ecological and genetic drivers of their persistence. We also discuss 'innate' and 'adaptive' resilience in relation to core rare taxa and their drivers. Finally, we emphasize the need to develop appropriate metrics to quantify core rare taxa and their functions, as this can have significant implications for biodiversity conservation and microbiome engineering in the long run.

Comparative analysis of the fecal microbiota in Père David's deer and five other captive deer species

Introduction

Gut microbes are essential for host nutrition, immunity, and development. Various factors influence the composition and function of the gut microbial community. However, there is limited knowledge regarding the comparison of gut microbiota across different deer species, particularly those in the World Deer Park of Baotou (Inner Mongolia, China).

Methods

This study utilized 16S rRNA gene amplicon sequencing to analyze the fecal microbiota and potential microbial function in Père David's Deer (Elaphurus davidianus), Sika deer (Cervus nippon), American Wapiti (Cervus canadensis), Red Deer (Cervuselaphus), Fallow Deer (Dama dama), and Reindeer (Rangifer tarandus).

Results and discussion

The findings indicated no significant differences in alpha diversity, yet there was a noteworthy distinction in beta diversity among the six deer groups. At the phylum level, the predominant bacteria in the deer populations were Firmicutes, Bacteroidetes, and Proteobacteria. At the genus level, 54 core bacterial microbiota were identified. The top four genera in AW, FD, PD, and SD were Ruminococcaceae UCG-005, Rikenellaceae RC9 gut group, RuminococcaceaeUCG-010 and Christensenellaceae R-7 group. The results of the neutral model revealed that neutral processes predominantly governed the gut microbiota community assembly in different deer species, particularly in Père David's deer. PICRUSt2 predictions showed significant enrichment of fecal bacterial functions related to fatty acid, lipid, metabolic regulator, and amino acid biosynthesis. This comparative analysis sheds light on the microbial community structure, community assembly, and potential functions, offering improved insights into the management and conservation of deer species, especially Père David's deer. Future research might focus on exploring metagenomic functions and dynamics in wild settings or across different seasons using metagenomics or metatranscriptomics.

Heterologous Expression of a Cryptic BGC from Bilophila sp. Provides Access to a Novel Family of Antibacterial Thiazoles

Human health is greatly influenced by the gut microbiota and microbiota imbalance can lead to the development of diseases. It is widely acknowledged that the interaction of bacteria within competitive ecosystems is influenced by their specialized metabolites, which act, e.g., as antibacterials or siderophores. However, our understanding of the occurrence and impact of such natural products in the human gut microbiome remains very limited. As arylthiazole siderophores are an emerging family of growth-promoting molecules in pathogenic bacteria, we analyzed a metagenomic data set from the human microbiome and thereby identified the bil-BGC, which originates from an uncultured Bilophila strain. Through gene synthesis and BGC assembly, heterologous expression and mutasynthetic experiments, we discovered the arylthiazole natural products bilothiazoles A-F. While established activities of related molecules indicate their involvement in metal-binding and -uptake, which could promote the growth of pathogenic strains, we also found antibiotic activity for some bilothiazoles. This is supported by biosensor-experiments, where bilothiazoles C and E show PrecA-suppressing activity, while bilothiazole F induces PblaZ, a biosensor characteristic for β-lactam antibiotics. These findings serve as a starting point for investigating the role of bilothiazoles in the pathogenicity of Bilophila species in the gut.

Role of gut microbiota in thalassemia: a review of therapeutic prospects

In recent years, the study of gut microbiota has gradually become a research hotspot in the field of medicine, as gut microbiota dysbiosis is closely related to various diseases. Thalassemia, as a hereditary hemoglobinopathy, has a complex pathophysiological mechanism, and traditional treatment methods show limited efficacy. With a deeper understanding of the gut microbiome, researchers have begun to focus on its role in the pathogenesis of thalassemia and its therapeutic effects. This article aims to review the role of gut microbiota in thalassemia and its potential therapeutic prospects, analyze the latest research findings, and explore the impact and mechanisms of gut microbiota on patients with thalassemia, with the goal of providing new ideas and directions for future research and clinical treatment of thalassemia.

Effect of Probiotics on Improving Intestinal Mucosal Permeability and Inflammation after Surgery

Background/Aims

We explored the mechanisms underlying the improvement of postoperative ileus (POI) following probiotic pretreatment. We assessed intestinal permeability, inflammation, tight junction (TJ) protein expression in the gut epithelium, and plasma interleukin (IL)-17 levels in a guinea pig model of POI.

Methods

Guinea pigs were divided into control, POI, and probiotic groups. The POI and probiotic groups underwent surgery, but the probiotic group received probiotics before the procedure. The ileum and proximal colon were harvested. Intestinal permeability was measured via horseradish peroxidase permeability. Inflammation was evaluated via leukocyte count in the intestinal wall muscle layer, and calprotectin expression in each intestinal wall layer was analyzed immunohistochemically. TJ proteins were analyzed using immunohistochemical staining, and plasma IL-17 levels were measured using an enzyme-linked immunosorbent assay.

Results

The POI group exhibited increased intestinal permeability and inflammation, whereas probiotic pretreatment reduced the extent of these POI-induced changes. Probiotics restored the expression of TJ proteins occludin and zonula occludens-1 in the proximal colon, which were increased in the POI group. Calprotectin expression significantly increased in the muscle layer of the POI group and was downregulated in the probiotic group; however, no distinct differences were observed between the mucosal and submucosal layers. Plasma IL-17 levels did not significantly differ among the groups.

Conclusions

Probiotic pretreatment may relieve POI by reducing intestinal permeability and inflammation and TJ protein expression in the gut epithelium. These findings suggest a potential therapeutic approach for POI management.

Poncirus trifoliata Extract and Its Active Coumarins Alleviate Dexamethasone-Induced Skeletal Muscle Atrophy by Regulating Protein Synthesis, Mitochondrial Biogenesis, and Gut Microbiota

Sarcopenia, an age-related decline in skeletal muscle mass and function, contributes to frailty and increased morbidity in the elderly. This necessitates the development of effective interventions to combat muscle atrophy. This study investigated the therapeutic potential of Poncirus trifoliata ethanol extract (PT) and its coumarin derivatives against dexamethasone (DEX)-induced muscle atrophy. We employed in vitro and in vivo models of DEX-induced muscle atrophy. C2C12 myotubes were used for mechanistic studies. C57BL/6J mice received DEX injections and oral PT supplementation (50 mg/kg/day) to evaluate effects on muscle mass, function, gene expression, and gut microbiota composition. In vitro, PT enhanced protein synthesis, mitochondrial biogenesis, and myogenic differentiation in DEX-exposed myotubes, with auraptene, ponciol, and triphasiol identified as key bioactive coumarins. In vivo, PT significantly attenuated DEX-induced muscle atrophy, increasing tibialis anterior muscle mass by 36% (p < 0.01), grip strength by 31% (p < 0.001), and maximal running speed by 18% (p < 0.05). Mechanistically, PT upregulated genes associated with muscle function and mitochondrial health. Furthermore, PT modulated gut microbiota composition, notably increasing Phocaeicola vulgatus abundance 2.2-fold, which correlated with improved muscle performance (R = 0.58, p < 0.01). These findings suggest that PT and its coumarin derivatives, particularly auraptene, ponciol, and triphasiol, hold promise as therapeutic agents for combating muscle atrophy. The observed benefits may be mediated through enhanced protein synthesis, improved mitochondrial function, and modulation of the gut-muscle axis.

Traumatic Brain Injury and Gut Microbiome: The Role of the Gut-Brain Axis in Neurodegenerative Processes

PURPOSE OF REVIEW

A deeper understanding of the communication network between the gut microbiome and the central nervous system, termed the gut-brain axis (GBA), has revealed new potential targets for intervention to prevent the development of neurodegenerative disease associated with tramatic brain injury (TBI). This review aims to comprehensively examine the role of GBA post-traumatic brain injury (TBI).

RECENT FINDINGS

The GBA functions through neural, metabolic, immune, and endocrine systems, creating bidirectional signaling pathways that modulate brain and gastrointestinal (GI) tract physiology. TBI perturbs these signaling pathways, producing pathophysiological feedback loops in the GBA leading to dysbiosis (i.e., a perturbed gut microbiome, impaired brain-blood barrier, impaired intestinal epithelial barrier (i.e., "leaky gut"), and a maladaptive, systemic inflammatory response. Damage to the CNS associated with TBI leads to GI dysmotility, which promotes small intestinal bacterial overgrowth (SIBO). SIBO has been associated with the early stages of neurodegenerative conditions such as Parkinson's and Alzheimer's disease. Many of the bacteria associated with this overgrowth promote inflammation and, in rodent models, have been shown to compromise the structural integrity of the intestinal mucosal barrier, causing malabsorption of essential nutrients and further exacerbating dysbiosis. TBI-induced pathophysiology is strongly associated with an increased risk of neurodegenerative diseases, including Parkinson's and Alzheimer's diseases, which represents a significant public health burden and challenge for patients and their families. A healthy gut microbiome has been shown to promote improved recovery from TBI and prevent the development of neurodegenerative disease, as well as other chronic complications. The role of the gut microbiome in brain health post-TBI demonstrates the potential for microbiome-targeted interventions to mitigate TBI-associated comorbidities. Promising new evidence on prebiotics, probiotics, diet, and fecal microbiota transplantation may lead to new therapeutic options for improving the quality of life for patients with TBI. Still, many of these preliminary findings must be explored further in clinical settings. This review covers the current understanding of the GBA in the setting of TBI and how the gut microbiome may provide a novel therapeutic target for treatment in this patient population.

Gut microbiota as a new target for anticancer therapy: from mechanism to means of regulation

In order to decipher the relationship between gut microbiota imbalance and cancer, this paper reviewed the role of intestinal microbiota in anticancer therapy and related mechanisms, discussed the current research status of gut microbiota as a biomarker of cancer, and finally summarized the reasonable means of regulating gut microbiota to assist cancer therapy. Overall, our study reveals that the gut microbiota can serve as a potential target for improving cancer management.

Research progress on the kidney-gut-brain axis in brain dysfunction in maintenance hemodialysis patients

Maintenance hemodialysis (MHD) has become the primary renal replacement therapy for patients with end-stage renal disease. The kidney-gut-brain axis represents a communication network connecting the kidney, intestine and brain. In MHD patients, factors such as uremic toxins, hemodynamic changes, vascular damage, inflammation, oxidative stress, and intestinal dysbiosis in MHD patients refers to a range of clinical syndromes, including brain injury, and is manifested by conditions such as white matter disease, brain atrophy, cerebrovascular disease, cognitive impairment, depression, anxiety, and other behavioral or consciousness abnormalities. Numerous studies have demonstrated the prevalence of these brain disorders in MHD patients. Understanding the mechanisms of brain disorders in MHD patients, particularly through the lens of kidney-gut-brain axis dysfunction, offers valuable insights for future research and the development of targeted therapies. This article reviews the brain dysfunction associated with MHD, the impact of the kidney-brain axis, intestinal barrier damage, gut microbiota dysbiosis caused by MHD, and the role of the gut-brain axis in brain dysfunction.

The Effects of Sika Deer Antler Peptides on 3T3-L1 Preadipocytes and C57BL/6 Mice via Activating AMPK Signaling and Gut Microbiota

(1) Background: To explore the anti-obesity effects and mechanisms of sika deer velvet antler peptides (sVAP) on 3T3-L1 preadipocytes and in high-fat diet (HFD)-induced obese mice. (2) Methods: sVAP fractions of different molecular weights were obtained via enzymatic hydrolysis and ultrafiltration. Their anti-lipid effects on 3T3-L1 cells were assessed with Oil Red O staining. The optimal fraction was tested in HFD-induced obese C57BL/6 mice to explore anti-obesity mechanisms. Peptide purification used LC-MS/MS, followed by sequence analysis and molecular docking for activity prediction. (3) Results: The peptide with the best anti-obesity activity was identified as sVAP-3K (≤3 kDa). sVAP-3K reduced lipid content and proliferation in 3T3-L1 cells, improved lipid profiles and ameliorated adipocyte degeneration in HFD mice, promoted the growth of beneficial gut microbiota, and maintained lipid metabolism. Additionally, sVAP-3K activated the AMP-activated protein kinase (AMPK) signaling pathway, regulating adipogenic transcription factors. sVAP-3K exhibited ten major components (peak area ≥ 1.03 × 108), with four of the most active components being newly discovered natural oligopeptides: RVDPVNFKL (m/z 363.21371), GGEFTPVLQ (m/z 474.24643), VDPENFRL (m/z 495.25735), and VDPVNFK (m/z 818.44043). (4) Conclusion: This study identifies four novel oligopeptides in sVAP-3K as key components for anti-obesity effects, offering new evidence for developing natural weight-loss drugs from sika deer velvet.

The gut microbiota during tamoxifen therapy in patients with breast cancer

Tamoxifen is essential in treating estrogen receptor-positive (ER+) breast cancer, primarily through its active metabolite, endoxifen. Emerging research suggests potential interactions between tamoxifen and gut microbiota. This study investigates the effects of tamoxifen on gut microbiota composition in postmenopausal ER+ and human epidermal growth factor receptor 2 negative (HER2-) breast cancer patients and explores correlations between gut microbiota and endoxifen plasma levels. This prospective observational study included postmenopausal ER+/HER2- breast cancer patients. Fecal and blood samples were collected before and during 6-12 weeks of tamoxifen therapy. Gut microbiota composition was analyzed using 16S rRNA amplicon sequencing of the hypervariable V4 gene region, and plasma endoxifen levels were measured using liquid chromatography-mass spectrometry. Changes in microbial diversity and composition were assessed, with correlations to endoxifen levels. A total of 62 patients were included. Tamoxifen significantly increased microbial richness (p = 0.019), although overall community structure remained consistent between pre- and during-treatment samples. Notable changes were observed in specific microbial taxa, with significant increases in genera such as Blautia (padjusted = 0.003) and Streptococcus (padjusted = 0.010), and decreases in Prevotella_9 (padjusted = 0.006). No significant correlations between gut microbiota and endoxifen levels were identified after multiple comparisons. Tamoxifen therapy increases gut microbial diversity in postmenopausal ER+/HER2- breast cancer patients, though overall microbial community structure remains stable. The absence of significant correlations with endoxifen levels suggests that while tamoxifen affects the gut microbiota, its role in endoxifen metabolism requires further study. More comprehensive research is needed to understand the relationship between tamoxifen, gut microbiota, and therapeutic outcomes.

Tryptophan and Its Metabolite Serotonin Impact Metabolic and Mental Disorders via the Brain-Gut-Microbiome Axis: A Focus on Sex Differences

The crisis of metabolic and mental disorders continues to escalate worldwide. A growing body of research highlights the influence of tryptophan and its metabolites, such as serotonin, beyond their traditional roles in neural signaling. Serotonin acts as a key neurotransmitter within the brain-gut-microbiome axis, a critical bidirectional communication network affecting both metabolism and behavior. Emerging evidence suggests that the gut microbiome regulates brain function and behavior, particularly through microbial influences on tryptophan metabolism and the serotonergic system, both of which are essential for normal functioning. Additionally, sex differences exist in multiple aspects of serotonin-mediated modulation within the brain-gut-microbiome axis, affecting feeding and affective behaviors. This review summarizes the current knowledge from human and animal studies on the influence of tryptophan and its metabolite serotonin on metabolic and behavioral regulation involving the brain and gut microbiome, with a focus on sex differences and the role of sex hormones. We speculate that gut-derived tryptophan and serotonin play essential roles in the pathophysiology that modifies neural circuits, potentially contributing to eating and affective disorders. We propose the gut microbiome as an appealing therapeutic target for metabolic and affective disorders, emphasizing the importance of understanding sex differences in metabolic and behavioral regulation influenced by the brain-gut-microbiome axis. The therapeutic targeting of the gut microbiota and its metabolites may offer a viable strategy for treating serotonin-related disorders, such as eating and affective disorders, with potential differences in treatment efficacy between men and women. This review would promote research on sex differences in metabolic and behavioral regulation impacted by the brain-gut-microbiome axis.

Amelioration of metabolic syndrome in high-fat diet-fed mice by total sesquiterpene lactones of chicory via modulation of intestinal flora and bile acid excretion

Chicory (Cichorium intybus L.) is a commonly used vegetable in Europe and is also regarded as a plant for both medicinal and edible uses in China. Chicory exhibits a substantial abundance of sesquiterpene lactone compounds within its composition. The prevalence of metabolic syndrome (MetS) is increasing and has become a global public health issue threatening the well-being of the general population. Recent studies have identified plant secondary metabolites as potential substances for treating MetS. Sesquiterpene lactones, a type of secondary metabolite with diverse biological activities, have been reported to exhibit anti-inflammatory effects, reduce lipid accumulation, and normalize blood glucose levels. However, the therapeutic effects of chicory sesquiterpene lactones on MetS remain to be explored, and little is known about sesquiterpene lactones' effects on intestinal flora and bile acids (BAs). Therefore, the effects of total sesquiterpene lactones (TSLs) from chicory on metabolic disorders, intestinal flora, and BAs were investigated in this study. In this study, C57BL/6J mice were fed a high-fat diet (HFD) for 8 weeks, followed by administration of TSLs, total chicory extract (TCE), and pioglitazone (Pio) for another 8 weeks. TSL, TCE, and Pio interventions reduced body weight gain, hepatic lipid accumulation, and lipogenesis in HFD-fed mice and attenuated plasma biochemical parameters. Among them, TSLs exhibited more significant effects, prompting further analysis of their impact on intestinal flora and bile acid metabolism. TSL intervention influenced the composition and structure of intestinal flora and BAs. TSL intervention impacted the composition and structure of the intestinal flora, characterized by a decrease in the abundances of Allobaculum, unidentified_Coriobacteriaceae, and Odoribacter, while the abundances of Prevotella, unidentified_Erysipelotrichaceae and Akkermansia were increased. Additionally, the levels of BAs TCDCA, GDCA, UDCA, 12-ketoLCA, 7-ketoLCA, and 6,7-diketoLCA were reduced. The research results indicated that TSLs from chicory may serve as potential agents for regulating metabolic abnormalities associated with MetS, as their effects can influence intestinal flora and BAs. The conclusions of this study are expected to open new research trajectories in the field of food science and nutrition, providing a solid scientific basis and innovative intervention approaches for the development of strategies targeting MetS prevention and management.

Deciphering the tripartite interaction of urbanized environment, gut microbiome and cardio-metabolic disease

The world is experiencing a sudden surge in urban population, especially in developing Asian and African countries. Consequently, the global burden of cardio-metabolic disease (CMD) is also rising owing to gut microbiome dysbiosis due to urbanization factors such as mode of birth, breastfeeding, diet, environmental pollutants, and soil exposure. Dysbiotic gut microbiome indicated by altered Firmicutes to Bacteroides ratio and loss of beneficial short-chain fatty acids-producing bacteria such as Prevotella, and Ruminococcus may disrupt host-intestinal homeostasis by altering host immune response, gut barrier integrity, and microbial metabolism through altered T-regulatory cells/T-helper cells balance, activation of pattern recognition receptors and toll-like receptors, decreased mucus production, elevated level of trimethylamine-oxide and primary bile acids. This leads to a pro-inflammatory gut characterized by increased pro-inflammatory cytokines such as tumour necrosis factor-α, interleukin-2, Interferon-ϒ and elevated levels of metabolites or metabolic endotoxemia due to leaky gut formation. These pathophysiological characteristics are associated with an increased risk of cardio-metabolic disease. This review aims to comprehensively elucidate the effect of urbanization on gut microbiome-driven cardio-metabolic disease. Additionally, it discusses targeting the gut microbiome and its associated pathways via strategies such as diet and lifestyle modulation, probiotics, prebiotics intake, etc., for the prevention and treatment of disease which can potentially be integrated into clinical and professional healthcare settings.

Gut-brain axis and neuroplasticity in health and disease: a systematic review

The gut microbiota emerged as a potential modulator of brain connectivity in health and disease. This systematic review details current evidence on the gut-brain axis and its influence on brain connectivity. The initial set of studies included 532 papers, updated to January 2024. Studies were selected based on employed techniques. We excluded reviews, studies without connectivity focus, studies on non-human subjects. Forty-nine papers were selected. Employed techniques in healthy subjects included 15 functional magnetic resonance imaging studies (fMRI), 5 diffusion tensor imaging, (DTI) 1 electroencephalography (EEG), 6 structural magnetic resonance imaging, 2 magnetoencephalography, 1 spectroscopy, 2 arterial spin labeling (ASL); in patients 17 fMRI, 6 DTI, 2 EEG, 9 structural MRI, 1 transcranial magnetic stimulation, 1 spectroscopy, 2 R2*MRI. In healthy subjects, the gut microbiota was associated with connectivity of areas implied in cognition, memory, attention and emotions. Among the tested areas, amygdala and temporal cortex showed functional and structural differences based on bacteria abundance, as well as frontal and somatosensory cortices, especially in patients with inflammatory bowel syndrome. Several studies confirmed the connection between microbiota and brain functions in healthy subjects and patients affected by gastrointestinal to renal and psychiatric diseases.

Gut microbiota in multiple sclerosis and animal models

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

Perspective: Multiomics and Artificial Intelligence for Personalized Nutritional Management of Diabetes in Patients Undergoing Peritoneal Dialysis

Managing diabetes in patients on peritoneal dialysis (PD) is challenging due to the combined effects of dietary glucose, glucose from dialysate, and other medical complications. Advances in technology that enable continuous biological data collection are transforming traditional management approaches. This review explores how multiomics technologies and artificial intelligence (AI) are enhancing glucose management in this patient population. Continuous glucose monitoring (CGM) offers significant advantages over traditional markers, such as hemoglobin A1c (HbA1c). Unlike HbA1c, which reflects an mean glucose level, CGM provides real-time, dynamic glucose data that allow clinicians to make timely adjustments, leading to better glycemic control and outcomes. Multiomics approaches are valuable for understanding genetic factors that influence susceptibility to diabetic complications, particularly those related to advanced glycation end products (AGEs). Identifying genetic polymorphisms that modify a patient's response to AGEs allows for personalized treatments, potentially reducing the severity of diabetes-related pathologies. Metabolomic analyses of PD effluent are also promising, as they help identify early biomarkers of metabolic dysregulation. Early detection can lead to timely interventions and more tailored treatment strategies, improving long-term patient care. AI integration is revolutionizing diabetes management for PD patients by processing vast datasets from CGM, genetic, metabolic, and microbiome profiles. AI can identify patterns and predict outcomes that may be difficult for humans to detect, enabling highly personalized recommendations for diet, medication, and dialysis management. Furthermore, AI can assist clinicians by automating data interpretation, improving treatment plans, and enhancing patient education. Despite the promise of these technologies, there are limitations. CGM, multiomics, and AI require significant investment in infrastructure, training, and validation studies. Additionally, integrating these approaches into clinical practice presents logistical and financial challenges. Nevertheless, personalized, data-driven strategies offer great potential for improving outcomes in diabetes management for PD patients.

The Gut Microbiota Characterization of a World-Class Mountain Trail Runner During a Complete Competition Season: A Case Report

In the present case study, the gut microbiota (GM) profile of a male elite mountain runner (34 years, 171 cm, 59 kg, VO2max = 92 mL/min/kg) was analyzed over a 5-month competitive period (6 samples). Gut microbiota diversity increased throughout the season, where higher levels coincided with peak performance, and shorter and longer races (42 km versus 172 km) produced different phenotypic GM changes. Shorter races promoted elevation of protective bacteria related to positive benefits (higher production of short-chain fatty acids, lactate resynthesis, and mucin degraders). By contrast, longer races promoted an elevation of opportunistic pathogenic bacteria while reducing protective commensal bacteria. The present findings indicate that a higher resilience of the GM after competitions may support rapid recovery from maximal exercise. Gut microbiota analyses before and after competition could represent a rapid indicator for the (patho) physiological impact of exercise and provide information on gut health and the recovery time needed.

Alteration of Immune Function and Gut Microbiome Composition in Carassius auratus Challenged With Rahnella aquatilis

Rahnella aquatilis as an emerging pathogen can cause bacterial enteritis in cyprinid fish such as crucian carp Carassius auratus. Currently, the characterisation of immune function and gut microbiome composition in C. auratus orally challenged by R. aquatilis were yet unknown. In this study, we therefore investigated the changes of histopathology, white blood cells (i.e., LEU, NEU and LYM), serum biochemical indicators (e.g., CRE, CK and CHO) and digestive enzyme activity (e.g., LYS, AST, ALT, GSH-Px and AKP), as well as complements and immune-related genes (e.g., C3, F2, LysC, TLR3, MyD88, TGF-β, TNF-α and IL-15) that were significantly altered after the oral administration of R. aquatilis KCL-5. Moreover, the gut microbiome composition and diversity were analysed by using 16S rRNA gene high-throughput sequencing analysis. The correlation analysis showed that the high abundance of phylum Proteobacteria, Actinobacteria, Firmicutes and Fusobacteria was related to the pathogenesis of enteritis caused by oral infection. KEGG enrichment analysis indicated that fatty acid, carbon and pyruvate metabolism were significantly increased pathways (p < 0.05). To our best knowledge, this is a rare report of physicochemical properties and gut microbiome in C. auratus by R. aquatilis infection, which will provide a scientific reference for the clinical diagnosis and prevention of bacterial enteritis in cyprinid fish.

Akkermansia muciniphila: biology, microbial ecology, host interactions and therapeutic potential

Akkermansia muciniphila is a gut bacterium that colonizes the gut mucosa, has a role in maintaining gut health and shows promise for potential therapeutic applications. The discovery of A. muciniphila as an important member of our gut microbiome, occupying an extraordinary niche in the human gut, has led to new hypotheses on gut health, beneficial microorganisms and host-microbiota interactions. This microorganism has established a unique position in human microbiome research, similar to its role in the gut ecosystem. Its unique traits in using mucin sugars and mechanisms of action that can modify host health have made A. muciniphila a subject of enormous attention from multiple research fields. A. muciniphila is becoming a model organism studied for its ability to modulate human health and gut microbiome structure, leading to commercial products, a genetic model and possible probiotic formulations. This Review provides an overview of A. muciniphila and Akkermansia genus phylogeny, ecophysiology and diversity. Furthermore, the Review discusses perspectives on ecology, strategies for harnessing beneficial effects of A. muciniphila for human mucosal metabolic and gut health, and its potential as a biomarker for diagnostics and prognostics.

Comparison of Negative Pressure Wound Therapy Systems and Conventional Non-Pressure Dressings on Surgical Site Infection Rate After Stoma Reversal: Systematic Review and Meta-Analysis of Randomized Controlled Trials

Background/Objectives: Surgical Site Infections (SSIs) rank among the most common complications following stoma takedown and lead to increased morbidity, increased Length of Hospital Stay (LOS), and higher healthcare costs. Negative Pressure Wound Therapy (NPWT) systems have emerged as a promising option for optimizing wound management and minimizing SSI rates. This systematic review and meta-analysis compares postoperative outcomes of NPWT and conventional Non-Pressure Dressings following stoma reversal. Methods: A search of the literature published up to 1 September 2024 was conducted across MEDLINE/PubMed, and the Cochrane Central Register of Controlled Trials (CENTRAL), and Scopus, as well as ClinicalTrials.gov. Only Randomized Controlled Trials (RCTs) were included. The primary outcome was SSI rate, while secondary outcomes included time to complete wound healing, LOS, and patient-reported wound cosmesis. Quality assessment was performed using the Cochrane Risk of Bias 2 (RoB 2) tool. The results were synthesized using means and Standard Deviations for continuous variables, counts and percentages for categorical variables, and presented as Odds Ratios (OR) or Mean Differences (MD) with 95% Confidence Intervals, using random or fixed effects models based on heterogeneity (I2). Results: Six RCTs, including 328 patients, were ultimately eligible for inclusion. No significant difference was revealed in SSI rates between the NPWT and conventional dressing groups (OR = 0.95; 95% CI: 0.27-3.29; p = 0.94; I2 = 38%). Time to complete wound healing was significantly lower in the NPWT group compared to conventional dressings (MD = -3.78 days; 95% CI: -6.29 to -1.27; p = 0.003). Two studies reported a lower rate of wound healing complications other than SSIs in the NPWT group (OR = 0.22; 95% CI: 0.05-1.09; p = 0.06). No substantial differences were observed in terms of LOS (MD = -0.02 days; 95% CI: -1.22 to 1.17; p = 0.97) and patient-reported wound cosmesis (SMD = 0.31; 95% CI: -0.49 to 1.11; p = 0.44). The review's limitations include potential risk of bias, variability in study designs, and heterogeneity between studies. Conclusions: NPWT contributes to improved wound management through reducing wound healing time compared to Non-Pressure Dressings after stoma reversal, although it does not appear to substantially impact SSI rates, LOS, or patient-assessed wound cosmesis. Further large-scale, multicenter RCTs are necessary to validate these results and identify patient populations most likely to benefit from NPWT application.

Changes of potential shorty-chain fatty acids producing bacteria in the gut of patients with spinal cord injury: a systematic review and meta-analysis

Gut bacteria that potential produce short-chain fatty acids (SCFAs) influences the recovery of motor function in the host in patients with spinal cord injury (SCI). We aimed to conduct a review and meta-analysis of the literature on gut microbiota in SCI patients. Following the Preferred Reporting Project for Systematic Review and Meta-Analysis (PRISMA), we searched Embase, PubMed, Cochrane Library, Web of Science (WOS) and ClinicalTrials.gov. The search period was from inception to March 31, 2024. We reported standardized mean differences (d) with 95% confidence intervals (CI) and used funnel plots and Egger tests to assess publication bias. The subacute of SCI data set revealed the microflora changes in the subacute phase, and meta-analysis summarized the changes in the chronic phase. Eleven studies (720 participants) were included, 2 phyla, 1 order, and 14 genus meta-analyses performed. No substantial heterogeneity was observed, and significant publication bias was not found among the studies included. In the subacute phase of spinal cord injury, the relative abundance of Bacteroidetes, Clostridiales, Faecalbacterium, Ruminococcus, Coprococcus, Lachnospira, Dorea, Prevotella, Roseburia, Atopobium, Bifidobacterium, Bacteroides, and Blautia increased. Firmicutes and Lactobacillus decreased. In the chronic phase, Firmicutes decreased in the SCI group. Bifidobacterium, Bacteroides, Blautia, and Eubacterium were found to have a higher average proportion of abundance in patients with SCI compared to non-SCI persons, and Clostridiales, Ruminococcus, Faecalbacterium, Coprococcus, and Lachnospira showed a lower relative abundance in SCI. The genus of potential SCFAs-producing bacteria is lower in the chronic phase of spinal cord injury than in the subacute phase, and gut dysbiosis is present in both the subacute and chronic phases.

Crosstalk between gut microbiotas and fatty acid metabolism in colorectal cancer

Colorectal cancer (CRC) is the third most common malignancy globally and the second leading cause of cancer-related mortality. Its development is a multifactorial and multistage process influenced by a dynamic interplay between gut microbiota, environmental factors, and fatty acid metabolism. Dysbiosis of intestinal microbiota and abnormalities in microbiota-associated metabolites have been implicated in colorectal carcinogenesis, highlighting the pivotal role of microbial and metabolic interactions. Fatty acid metabolism serves as a critical nexus linking dietary patterns with gut microbial activity, significantly impacting intestinal health. In CRC patients, reduced levels of short-chain fatty acids (SCFAs) and SCFA-producing bacteria have been consistently observed. Supplementation with SCFA-producing probiotics has demonstrated tumor-suppressive effects, while therapeutic strategies aimed at modulating SCFA levels have shown potential in enhancing the efficacy of radiation therapy and immunotherapy in both preclinical and clinical settings. This review explores the intricate relationship between gut microbiota, fatty acid metabolism, and CRC, offering insights into the underlying mechanisms and their potential translational applications. Understanding this interplay could pave the way for novel diagnostic, therapeutic, and preventive strategies in the management of CRC.

Intestinal Microbiota Dysbiosis Role and Bacterial Translocation as a Factor for Septic Risk

The human immune system is closely linked to microbiota such as a complex symbiotic relationship during the coevolution of vertebrates and microorganisms. The transfer of microorganisms from the mother's microbiota to the newborn begins before birth during gestation and is considered the initial phase of the intestinal microbiota (IM). The gut is an important site where microorganisms can establish colonies. The IM contains polymicrobial communities, which show complex interactions with diet and host immunity. The tendency towards dysbiosis of the intestinal microbiota is influenced by local but also extra-intestinal factors such as inflammatory processes, infections, or a septic state that can aggravate it. Pathogens could trigger an immune response, such as proinflammatory responses. In addition, changes in the host immune system also influence the intestinal community and structure with additional translocation of pathogenic and non-pathogenic bacteria. Finally, local intestinal inflammation has been found to be an important factor in the growth of pathogenic microorganisms, particularly in its role in sepsis. The aim of this article is to be able to detect the current knowledge of the mechanisms that can lead to dysbiosis of the intestinal microbiota and that can cause bacterial translocation with a risk of infection or septic state and vice versa.

Exploring the role of oral bacteria in oral cancer: a narrative review

A growing body of research indicates that a wide range of cancer types may correlate with human microbiome components. On the other hand, little is known about the potential contribution of the oral microbiota to oral cancer. However, some oral microbiome components can stimulate different tumorigenic processes associated with the development of cancer. In this line, two prevalent oral infections, Porphyromonas gingivalis, and Fusobacterium nucleatum can increase tumor growth. The microbiome can impact the course of the illness through direct interactions with the human body and major modifications to the toxicity and responsiveness to different kinds of cancer therapy. Recent research has demonstrated a relationship between specific phylogenetic groupings and the results of immunotherapy treatment for particular tumor types. Conversely, there has been a recent upsurge in interest in the possibility of using microbes to treat cancer. At the moment, some species, such as Salmonella typhimurium and Clostridium spp., are being explored as possible cancer treatment vectors. Thus, understanding these microbial interactions highlights the importance of maintaining a healthy oral microbiome in preventing oral cancers. From this perspective, this review will discuss the role of the microbiome on oral cancers and their possible application in oral cancer treatment/improvement.

Impact of a 7-day short peptide diet on gut microbiota and metabolomics in septic mice

Objective

Our study aim is to explore the mechanisms of short peptide passages on intestinal dysfunction in septic mice utilizing a metabolomics approach, which provides a new scientific basis for the clinical study of sepsis.

Methods

Mices were allocated at random into four groups: control (Con), cecal ligation and puncture followed by one, three or 7 day short-peptide-based enteral nutrition group (CLP + SPEN1), (CLP + SPEN3), and (CLP + SPEN7) groups. A liquid chromatography-mass spectrometry-based metabolomics method was used to analyze changes in serum metabolites in septic mice.

Results

Short peptides showed effectiveness in reducing symptoms, mucosal inflammation, and intestinal function damage scores in septic mice. The 16sRNA analysis showcased significant variances in the distribution of bacterial communities between the CLP + SPEN1, CLP + SPEN3, and CLP + SPEN7 groups. At the phylum level, statistically significant variances in the relative abundance of Proteobacteria, Firmicutes, and Bacteroidetes were recognized. The metabolomics analysis results showed significant separation of metabolites between the CLP + SPEN1 and CLP + SPEN3 groups, as well as significant differences in metabolite profiles between the CLP + SPEN3 and CLP + SPEN7 groups. Utilizing a differential Venn diagram, four metabolites were commonly different; 10-heptadecanoic and dodecanoic acids had statistical significance. The abundance of both dodecanoic and lactic acid bacteria was negatively associated at the genus level.

Conclusion

Short peptides were found to promote the growth of beneficial bacteria, Lactobacillus and uncultured_bacterium_f_Muribaculaceae, while reducing intestinal metabolites such as Dodecanoic acid and 10-Heptadecenoic acid. Moreover the Lactobacillus may play a significant therapeutic role in the treatment of sepsis. However, due to the limited number of experimental samples, the exact mechanism of action of short peptides awaits further confirmation.

Gut Dysbiosis Exacerbates Intestinal Absorption of Cadmium and Arsenic from Cocontaminated Rice in Mice Due to Impaired Intestinal Barrier Functions

Globally, humans face gut microbiota dysbiosis; however, its impact on the bioavailability of cadmium (Cd) and arsenic (As) from rice consumption─a major source of human exposure to these metals─remains unclear. In this study, we compared Cd and As accumulation in the liver and kidneys of mice with disrupted gut microbiota (administered cefoperazone sodium), restored microbiota (administered probiotics and prebiotics following antibiotic exposure), and normal microbiota, all after consuming cocontaminated rice. Compared to normal mice, microbiota-disrupted mice exhibited 30.9-119% and 30.0-100% (p < 0.05) higher Cd and As levels in tissues after a 3 week exposure period. The increased Cd and As bioavailability was not due to changes in the duodenal expression of Cd-related transporters or As speciation biotransformation in the intestine. Instead, it was primarily attributed to a damaged mucus layer and depleted tight junctions associated with gut dysbiosis, which increased intestinal permeability. These mechanisms were confirmed by observing 34.3-74.3% and 25.0-75.0% (p < 0.05) lower Cd and As levels in the tissues of microbiota-restored mice with rebuilt intestinal barrier functions. This study enhances our understanding of the increased risk of dietary metal(loid) exposure in individuals with gut microbiota dysbiosis due to impaired intestinal barrier functions.

Advances in gut microbiota functions in inflammatory bowel disease: Dysbiosis, management, cytotoxicity assessment, and therapeutic perspectives

Inflammatory bowel disease (IBD), including Crohn's disease and ulcerative colitis, have become increasingly prevalent across all human generations. Despite advances in diagnosis, effective long-term therapeutic options remain limited, with many patients experiencing recurrent symptoms after treatment. The multifactorial origins of ulcerative colitis are widely recognized, but the intestinal microbiome, particularly bacteria from the Desulfovibrionaceae family, is thought to play a central role in the pathogenesis of the disease. These bacteria contribute significantly to gut microbial functions, yet their cytotoxic and viability characteristics under disease conditions remain poorly understood. Our review provides insights on recent advancements in methodologies for assessing the cytotoxicity and viability of anaerobic intestinal bacteria, with a specific focus on their relevance to gut health and disease. We introduce overview from current literature on modern techniques including flow cytometry, high-throughput screening, and molecular-based assays, highlighting their applications in understanding the role of Desulfovibrionaceae and other gut microbes in IBD pathogenesis. By bridging methodological advancements with functional implications, this review aims to enhance our understanding of gut microbiota-host interactions, which are crucial for maintaining health and preventing disease through immune modulation, where microbiota help regulate immune responses and prevent excessive inflammation; nutrient metabolism, including the breakdown of dietary fibers into short-chain fatty acids that support gut health; and colonization resistance, where beneficial microbes outcompete harmful pathogens to maintain microbial balance.