Interplay between the human gut microbiome and host metabolism

New insights in amino sugar metabolism by the gut microbiome

Gut microorganisms inhabiting the intestinal tract play key roles in host's health and disease. A properly functioning gut microbiome requires the availability of adequate carbon, nitrogen and energy sources. One of the main sources of energy for intestinal bacteria are glycans, of which amino sugars are important components. Amino sugars are a class of carbohydrates in which one or more hydroxyl groups are substituted with amino groups. However, bacterial utilization of amino sugars and their impact on the gut microbiome and host health have not been thoroughly assessed. In this review, we summarize the latest discoveries about amino sugar metabolism by gut microbes, paying particular attention to the metabolism of N-acetyl-galactosamine (GalNAc), one of the most abundant amino sugars in the intestine, and its potential implications for microbial functionality and host health.

Exogenous prion-like proteins and their potential to trigger cognitive dysfunction

The gut is exposed to a wide range of proteins, including ingested proteins and those produced by the resident microbiota. While ingested prion-like proteins can propagate across species, their implications for disease development remain largely unknown. Here, we apply a multidisciplinary approach to examine the relationship between the biophysical properties of exogenous prion-like proteins and the phenotypic consequences of ingesting them. Through computational analysis of gut bacterial proteins, we identified an enrichment of prion-like sequences in Helicobacter pylori. Based on these findings, we rationally designed a set of synthetic prion-like sequences that form amyloid fibrils, interfere with amyloid-beta-peptide aggregation, and trigger prion propagation when introduced in the yeast Sup35 model. When C. elegans were fed bacteria expressing these prion-like proteins, they lost associative memory and exhibited increased lipid oxidation. These data suggest a link between memory impairment, the conformational state of aggregates, and oxidative stress. Overall, this work supports gut microbiota as a reservoir of exogenous prion-like sequences, especially H. pylori, and the gut as an entry point for molecules capable of triggering cognitive dysfunction.

Design of a Continuous GAA-Producing Probiotic as a Potential Mitigator of the Effects of Sleep Deprivation

Creatine is a popular athletic supplement that has also been shown to improve cognitive performance upon sleep deprivation. However, it is rapidly cleared from the gastrointestinal tract a few hours after consumption. Toward providing a persistent creatine dose, we engineered the human probiotic Escherichia coli Nissle (EcN) to produce guanidinoacetic acid (GAA), which is converted to creatine in the liver. We find GAA-producing enzymes present in the human microbiome and compare their activities to known enzymes. Three copies of arginine:glycine amidinotransferase (AGAT) from Actinokineospora terrae are expressed from the genome, and native gcvP, argR, and argA are edited or deleted to improve substrate availability without negatively impacting cell viability. A standard EcN dose (1012 cells) produces 41 ± 7 mg GAA per hour under laboratory conditions. This work demonstrates that a probiotic bacterium can be engineered to produce sustained GAA titers known to impact cognitive performance.

Zanthoxylum alkylamides improves hepatic glucose metabolism by regulating gut microbiota in STZ-induced T2DM rats

The observed beneficial impact of Zanthoxylum alkylamides (ZA) in addressing Type 2 diabetes mellitus (T2DM) suggests a potential association with short-chain fatty acids (SCFAs) and gut microbial composition. This study systematically investigated the influence of ZA on the organ index, c-peptide and lipid levels, gut microbiota composition, SCFAs production, and hepatic glucose metabolism in T2DM rats. The results indicate the success of ZA in treating T2DM rats characterized by hepatomegaly, nephromegaly, elevated blood lipids, and suppressed c-peptide levels. Following ZA intervention, the capacity of T2DM rats to produce SCFAs was not only restored but exceeded normal levels. Additionally, there was an augmentation in gut bacteria diversity, with a heightened abundance of Proteobacteria and an elevated Firmicutes/Bacteroidetes ratio. Conversely, a reduction in Actinobacteria abundance was noted. Importantly, ZA demonstrated the ability to regulate insulin activity and alleviate T2DM by activating the PI3K/Akt/mTOR signaling pathway in the liver of rats. In summary, our research reveals promising avenues for managing T2DM, encompassing diagnostic, therapeutic, monitoring, and drug discovery methodologies.

Gut microbiota-dependent increase in phenylacetic acid induces endothelial cell senescence during aging

Endothelial cell senescence is a key driver of cardiovascular aging, yet little is known about the mechanisms by which it is induced in vivo. Here we show that the gut bacterial metabolite phenylacetic acid (PAA) and its byproduct, phenylacetylglutamine (PAGln), are elevated in aged humans and mice. Metagenomic analyses reveal an age-related increase in PAA-producing microbial pathways, positively linked to the bacterium Clostridium sp. ASF356 (Clos). We demonstrate that colonization of young mice with Clos increases blood PAA levels and induces endothelial senescence and angiogenic incompetence. Mechanistically, we find that PAA triggers senescence through mitochondrial H2O2 production, exacerbating the senescence-associated secretory phenotype. By contrast, we demonstrate that fecal acetate levels are reduced with age, compromising its function as a Sirt1-dependent senomorphic, regulating proinflammatory secretion and redox homeostasis. These findings define PAA as a mediator of gut-vascular crosstalk in aging and identify sodium acetate as a potential microbiome-based senotherapy to promote healthy aging.

Synergistic role of gut-microbial L-ornithine in enhancing ustekinumab efficacy for Crohn's disease

The role of the intestinal microbiome in Crohn's disease (CD) treatment remains poorly understood. This study investigates microbe-host interactions in CD patients undergoing ustekinumab (UST) therapy. Fecal metagenome, metabolome, and host transcriptome data from 85 CD patients were analyzed using multi-omics integration and mediation analysis. Our findings reveal significant microbiome-metabolite-host interactions. Specifically, Faecalibacterium prausnitzii was linked to altered L-ornithine biosynthesis, resulting in higher L-ornithine levels in patients before UST therapy. In vivo and in vitro studies demonstrated that microbiome-derived L-ornithine enhances UST treatment sensitivity in CD by disrupting the host IL-23 receptor signaling and inhibiting Th17 cell stabilization through the IL-12RB1/TYK2/STAT3 axis. L-ornithine significantly enhances the therapeutic efficacy of UST in CD patients, as demonstrated in a prospective clinical trial. These findings suggest that targeting specific microbe-host metabolic pathways may improve the efficacy of inflammatory bowel disease (IBD) treatments.

I-SVVS: integrative stochastic variational variable selection to explore joint patterns of multi-omics microbiome data

High-dimensional multi-omics microbiome data play an important role in elucidating microbial community interactions with their hosts and environment in critical diseases and ecological changes. Although Bayesian clustering methods have recently been used for the integrated analysis of multi-omics data, no method designed to analyze multi-omics microbiome data has been proposed. In this study, we propose a novel framework called integrative stochastic variational variable selection (I-SVVS), which is an extension of stochastic variational variable selection for high-dimensional microbiome data. The I-SVVS approach addresses a specific Bayesian mixture model for each type of omics data, such as an infinite Dirichlet multinomial mixture model for microbiome data and an infinite Gaussian mixture model for metabolomic data. This approach is expected to reduce the computational time of the clustering process and improve the accuracy of the clustering results. Additionally, I-SVVS identifies a critical set of representative variables in multi-omics microbiome data. Three datasets from soybean, mice, and humans (each set integrated microbiome and metabolome) were used to demonstrate the potential of I-SVVS. The results indicate that I-SVVS achieved improved accuracy and faster computation compared to existing methods across all test datasets. It effectively identified key microbiome species and metabolites characterizing each cluster. For instance, the computational analysis of the soybean dataset, including 377 samples with 16 943 microbiome species and 265 metabolome features, was completed in 2.18 hours using I-SVVS, compared to 2.35 days with Clusternomics and 1.12 days with iClusterPlus. The software for this analysis, written in Python, is freely available at https://github.com/tungtokyo1108/I-SVVS.

Assessing the safety of microbiome perturbations

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

Regulating Intratumoral Fungi With Hydrogels: A Novel Approach to Modulating the Tumor Microbiome for Cancer Therapy

BACKGROUND

Fungi in tumors act as a double-edged sword, potentially worsening or alleviating malignancy based on the ecological balance within the tumor microenvironment (TME). Hydrogels, as innovative drug delivery systems, are poised to redefine treatment paradigms. As advanced biomaterials, they offer a versatile platform for encapsulating and releasing antifungal agents and immunomodulators, responding to the TME's unique demands.

METHODS

We have conducted and collated numerous relevant reviews and studies in recent years from three aspects: Hydrogels, intra-tumoral fungi, and tumor microbe microenvironment, in the hope of identifying the connections between hydrogels and intra-tumoral microbes.

RESULTS

This review underscores the crucial role of intra-tumoral microbes, particularly fungi, in tumorigenesis, progression, and treatment efficacy. At the same time, we concentrated on the findings of hydrogels investigations, with their remarkable adaptability to the tumor microenvironment emerge as intelligent drug delivery systems.

CONCLUSIONS

Hydrogels unique ability to precisely target and modulate the tumor microflora, including fungi, endows them with a significant edge in enhancing treatment efficacy. This innovative approach not only holds great promise for improving cancer therapy outcomes but also paves the way for developing novel strategies to control metastasis and prevent cancer recurrence.

Gut Microbiota Modulation in Osteoporosis: Probiotics, Prebiotics, and Natural Compounds

Osteoporosis is a multifactorial bone metabolic disorder characterized by the deterioration of bone mass and microarchitecture, leading to increased fragility and fracture risk. Recent advances have revealed the critical role of the gut microbiota in the pathogenesis of osteoporosis, primarily mediated by metabolite-driven and immune-mediated interactions along the gut-bone axis. Dysbiosis, or microbial imbalance, can influence bone health by modulating host metabolism, immune function, and endocrine responses. While growing evidence suggests that gut microbiota modulation holds therapeutic potential for osteoporosis, the underlying mechanisms remain poorly understood. This review examines the latest findings on the role of prebiotics, probiotics, and natural bioactive substances in modulating the gut microbiota to improve bone health. We discuss how these interventions may restore microbial balance, enhance gut barrier function, and reduce systemic inflammation, thereby influencing bone metabolism. A deeper understanding of the gut-bone axis will pave the way for more targeted, effective, and personalized therapeutic strategies for osteoporosis prevention and treatment.

Metabolic profiling of the Chinese population with extreme longevity identifies Lysophospholipid species as potential biomarkers for the human lifespan

BACKGROUND

Metabolic regulation plays a crucial role in extending the healthspan and lifespan across multiple organisms, including humans. Although numerous studies have identified the characteristics of the metabolome and potential biomarkers in long-lived populations worldwide, the metabolome landscape of Chinese centenarians remains largely unknown. This study characterised the plasma metabolic profiles of Chinese centenarians and nonagenarians and identified potential biomarkers of longevity.

METHODS

A global untargeted metabolomics approach was used to analyze plasma samples from 65 centenarians (average age 101.72 ± 1.46 years), 53 nonagenarians (average age 98.92 ± 0.27 years), 47 older individuals (average age 64.66 ± 3.31 years), and 35 middle-aged participants (average age 33.91 ± 3.53 years) recruited from the Lishui region, an area of China well known for the longevity of its population.

RESULTS

The plasma metabolic profiles of centenarians and nonagenarians differed significantly from those of the two younger populations. Specifically, 211 and 114 differentially abundant metabolites (DAMs) were identified in the centenarian and nonagenarian groups, respectively. The majority of these DAMs were glycerophosphoethanolamines, glycerophosphocholines, fatty esters, fatty alcohols, fatty acyls, and fatty acids and conjugates. For example, the circulating levels of LysoPA (20:2), LysoPA (20:3), LysoPC (16:0), LysoPC (18:2), and LysoPE (20:4) were significantly lower in centenarians than in the older and middle-aged groups. A similar pattern was also observed in the nonagenarian population. Notably, the plasma levels of five DAMs - LysoPA (20:3), LysoPC (18:2), LysoPE (20:4), PG (18:0/18:1), and PG (18:1/18:2) - were significantly and continuously reduced with the ageing process. Pearson correlation analysis revealed that the reduced abundance of LysoPA (20:3), LysoPC (18:2), LysoPE (20:4), LysoPE (24:0), PG (18:0/18:1), and PG (18:1/18:2) was significantly and negatively associated with lifespan, from middle-age to centenarian. ROC analysis indicated that LysoPA (20:3), LysoPC (18:2), LysoPE (20:4), LysoPE (24:0), PG (18:0/18:1), and PG (18:1/18:2), as well as the combination of these six DAMs (AUC = 0.9074), had high predictive power for the human longevity phenotype.

CONCLUSION

This study elucidated the plasma metabolic landscape of centenarians and nonagenarians in China and identified several potential biomarkers for predicting human lifespan. Our findings will aid in understanding the metabolic regulation of longevity and may promote the clinical practice of gerontology in the future.

Multi-omics analysis identifies Sphingomonas and specific metabolites as key biomarkers in elderly Chinese patients with coronary heart disease

Background

Abnormal component changes of gut microbiota are related to the pathogenesis and progression of coronary heart disease (CHD), and gut microbiota-derived metabolites are key factors in host-microbiome interactions. This study aimed to explore the key gut microbiota and metabolites, as well as their relationships in CHD.

Methods

Feces samples and blood samples were collected from CHD patients and healthy controls. Then, the obtained feces samples were sent for 16s rRNA gene sequencing, and the blood samples were submitted for metabolomics analysis. Finally, conjoint analysis of 16s rRNA gene sequencing and metabolomics data was performed.

Results

After sequencing, there were no significant differences in Chao 1, observed species, Simpson, Shannon, Pielou's evenness and Faith's PD between the CHD patients and controls. At phylum level, the dominant phyla were Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria. At genus level, the abundance of Sphingomonas, Prevotella, Streptococcus, Desulfovibrio, and Shigella was relatively higher in CHD patients; whereas Roseburia, Corprococcus, and Bifidobacterium was relatively lower. Randomforest analysis showed that Sphingomonas was more important for CHD. Through metabolomic analysis, a total of 155 differential metabolites were identified, and were enriched in many signaling pathways. Additionally, the AUC of the conjoint analysis (0.908) was higher than that of gut microbiota species (0.742).

Conclusion

In CHD patients, the intestinal flora was disordered, as well as Sphingomonas and the identified differential metabolites may serve as was candidate biomarkers for CHD occurrence and progression.

Critical Care Nutrition from a Metabolic Point of View: A Narrative Review

Background: Critical illness induces profound metabolic alterations, characterized by a hypermetabolic state, insulin resistance, protein catabolism, and gut barrier dysfunction, which contribute to increased morbidity and mortality. Emerging evidence highlights the role of the gut microbiome and its metabolites in modulating systemic inflammation and immune responses during critical illness. This narrative review explores the metabolic evolution of critically ill patients, the impact of gut dysbiosis on disease progression, and the potential role of nutrition in modulating metabolism and improving patient outcomes. Methods: A comprehensive literature search was conducted across PubMed and Google Scholar for articles published up to February 2025. Search terms included "critical illness", "metabolism", "gut microbiota", "nutrition", and related keywords. Articles published in English addressing metabolic alterations, microbiome changes, and nutritional strategies in critically ill patients were included. After screening for eligibility, relevant articles were synthesized to outline current knowledge and identify gaps. Results: Metabolic changes in critical illness progress through distinct phases, from catabolism-driven hypermetabolism to gradual recovery. Gut dysbiosis, characterized by a loss of microbial diversity and increased gut permeability, contributes to systemic inflammation and organ dysfunction. Nutritional strategies, including enteral nutrition, probiotics, prebiotics, and metabolomics-driven interventions, may help restore microbial balance, preserve gut barrier integrity, and modulate immune and metabolic responses. Future nutrition therapy should focus on metabolic modulation rather than solely addressing nutrient deficits. Conclusions: Advances in gut microbiome research and metabolomics offer new avenues for personalized nutrition strategies tailored to the metabolic demands of critically ill patients. Integrating these approaches may improve clinical and functional recovery while mitigating the long-term consequences of critical illness.

Microbiome-metabolome dynamics associated with impaired glucose control and responses to lifestyle changes

Type 2 diabetes (T2D) is a complex disease shaped by genetic and environmental factors, including the gut microbiome. Recent research revealed pathophysiological heterogeneity and distinct subgroups in both T2D and prediabetes, prompting exploration of personalized risk factors. Using metabolomics in two Swedish cohorts (n = 1,167), we identified over 500 blood metabolites associated with impaired glucose control, with approximately one-third linked to an altered gut microbiome. Our findings identified metabolic disruptions in microbiome-metabolome dynamics as potential mediators of compromised glucose homeostasis, as illustrated by the potential interactions between Hominifimenecus microfluidus and Blautia wexlerae via hippurate. Short-term lifestyle changes, for example, diet and exercise, modulated microbiome-associated metabolites in a lifestyle-specific manner. This study suggests that the microbiome-metabolome axis is a modifiable target for T2D management, with optimal health benefits achievable through a combination of lifestyle modifications.

Gut-Microbiota-Driven Lipid Metabolism: Mechanisms and Applications in Swine Production

Background/Objectives: The gut microbiota plays a pivotal role in host physiology through metabolite production, with lipids serving as essential biomolecules for cellular structure, metabolism, and signaling. This review aims to elucidate the interactions between gut microbiota and lipid metabolism and their implications for enhancing swine production. Methods: We systematically analyzed current literature on microbial lipid metabolism, focusing on mechanistic studies on microbiota-lipid interactions, key regulatory pathways in microbial lipid metabolism, and multi-omics evidence (metagenomic/metabolomic) from swine models. Results: This review outlines the structural and functional roles of lipids in bacterial membranes and examines the influence of gut microbiota on the metabolism of key lipid classes, including cholesterol, bile acids, choline, sphingolipids, and fatty acids. Additionally, we explore the potential applications of microbial lipid metabolism in enhancing swine production performance. Conclusions: Our analysis establishes a scientific framework for microbiota-based strategies to optimize lipid metabolism. The findings highlight potential interventions to improve livestock productivity through targeted manipulation of gut microbial communities.

Regulation of microbial gene expression: the key to understanding our gut microbiome

During the past two decades, gut microbiome studies have established the significant impact of the gut microbiota and its metabolites on host health. However, the molecular mechanisms governing the production of microbial metabolites in the gut environment remain insufficiently investigated and thus are poorly understood. Here, we propose that an enhanced understanding of gut microbial gene regulation, which is responsive to dietary components and gut environmental conditions, is needed in the research field and essential for our ability to effectively promote host health and prevent diseases through interventions targeting the gut microbiome.

Supplementation With Human Foods Affects the Gut Microbiota of Wild Howler Monkeys

Wild primates face a wide range of anthropogenic influences globally that impact their health, fitness, and survival. One area of potential impact that has been particularly understudied is the supplementation of wild primate diets with human foods. Although the consumption of human foods represents a substantial dietary change for wild primates, knowledge of how it impacts their physiology and behavior is limited. Here we explore how human food supplementation impacts wild primates by comparing the gut microbiomes of free-ranging brown howler monkeys (Alouatta guariba) in periurban Brazil that do or do not have access to human foods. We found that howler monkeys consuming human foods had reduced gut microbial diversity and reduced relative abundances of fiber degrading microbial taxa, which has been associated with negative health consequences in other animals, including humans. However, the effect size of these differences was relatively small and varied over time. Additionally, the composition of the gut microbiome varied significantly across months, regardless of the access to human foods. We suggest that the biology of this howler monkey population is minimally impacted by human foods. Further empirical research will help clarify the relationship between human food supplementation and health across primate populations, facilitating conservation applications.

Gut microbiome and plasma metabolome alterations in ileostomy and after closure of ileostomy

A temporary loop ileostomy is a routine procedure for protecting the anastomosis in patients undergoing radical resection of rectal cancer. Fecal diversion by a diverting ileostomy may induce microbiota dysbiosis in the defunctioned colon; however, data on temporal and spatial microbiome and metabolome changes in these patients are sparse. Thirty patients who underwent ileostomy closure were enrolled. Fecal and plasma samples were collected successively before ileostomy closure, at the first postoperative defecation, and 1 month postoperatively. The 16S rRNA gene sequencing was used to assess changes in gut microbes, and metabolic components in the plasma were analyzed using global untargeted metabolomics. Advanced data analysis methods were used to examine the differences and correlations between flora and metabolites. The gut microbiota in the ileostomy effluent and defunctioned colon had lesser species diversity and richness, with an abundance of aerobic, gram-negative, and potentially pathogenic bacteria. After the intestinal continuity was restored with routine meal feeding, the gut microbes recovered to a standard composition within 1 month. Moreover, xanthine, traumatic acid, L-glutamine, and norepinephrine levels increased markedly in patients with ileostoma. The ileostomy closure reversed the ileostomy-associated metabolic alterations, including an increased abundance of L-leucine, creatine, and 2-ketobutyric acid. Furthermore, Agathobacter and Peptostreptococcus were most closely associated with the reconstruction of postoperative gut microbes. We described a spatiotemporal map of the intestinal microbial ecological reconstruction and metabolic recovery before and after ileostomy reversal for perioperative intervention in patients with ileostomy closure surgery.

IMPORTANCE

In this paper, the changes in the intestinal microbiome and plasma metabolome before and after temporary ileostomy were reported for the first time, and the dynamic changes in intestinal contents were described. At the same time, the key bacterial genera involved in the reestablishment of microflora after the restoration of intestinal continuity were found, and the key relationship between them and plasma metabolites was also found. More importantly, we found that patients with ileal fistula may be at risk of metabolic imbalance and that this particular metabolic state may potentially affect the course of tumor treatment. Finally, the samples in this study were obtained in their natural state and can be easily applied to the clinic to avoid unnecessary invasive examinations.

Advancing Gut Microbiome Research: The Shift from Metagenomics to Multi-Omics and Future Perspectives

The gut microbiome, a dynamic and integral component of human health, has co-evolved with its host, playing essential roles in metabolism, immunity, and disease prevention. Traditional microbiome studies, primarily focused on microbial composition, have provided limited insights into the functional and mechanistic interactions between microbiota and their host. The advent of multi-omics technologies has transformed microbiome research by integrating genomics, transcriptomics, proteomics, and metabolomics, offering a comprehensive, systems-level understanding of microbial ecology and host-microbiome interactions. These advances have propelled innovations in personalized medicine, enabling more precise diagnostics and targeted therapeutic strategies. This review highlights recent breakthroughs in microbiome research, demonstrating how these approaches have elucidated microbial functions and their implications for health and disease. Additionally, it underscores the necessity of standardizing multi-omics methodologies, conducting large-scale cohort studies, and developing novel platforms for mechanistic studies, which are critical steps toward translating microbiome research into clinical applications and advancing precision medicine.

Multi-Omics Analysis Revealed the Molecular Mechanisms Affecting Average Daily Gain in Cattle

The average daily gain (ADG) is a critical index for evaluating growth rates in cattle and is closely linked to the economic benefits of the cattle industry. Heredity is one of the factors affecting the daily gain of cattle. However, the molecular mechanisms regulating ADG remain incompletely understood. This study aimed to systematically unravel the molecular mechanisms underlying the divergence in ADG between high average daily gain (HADG) and low average daily gain (LADG) Angus cattle through integrated multi-omics analyses (microbiome, metabolome, and transcriptome), hypothesizing that the gut microbiota-host gene-metabolism axis is a key regulatory network driving ADG divergence. Thirty Angus cattle were classified according to their HADG and LADG. Fecal and serum samples were collected for 16S, fecal metabolome, and blood transcriptome analysis. The results showed that compared with the LADG group, the abundance of Firmicutes increased in the HADG group, while the abundance of Bacteroidetes and Proteobacteria decreased. Metabolomics and transcriptomic analysis revealed that KEGG pathways associated with differentially expressed genes (DEGs) and differentially abundant metabolites (DAMs) were enriched in bile acid metabolism. Spearman correlation analysis showed that Oscillospira was positively correlated with ZBTB20 and negatively correlated with RADIL. ZBTB20 was negatively correlated with dgA-11_gut_group. This study analyzed the regulatory mechanism of average daily gain of beef cattle from genetic, metabolic, and microbial levels, providing a theoretical basis for analyzing the mechanism of differential daily gain of beef cattle, and has important significance for improving the production performance of beef cattle. The multi-omics network provides biomarker foundations for machine learning-based ADG prediction models, offering potential applications in precision breeding. While these biomarkers show promise for precision breeding, their causal roles require further validation. The conclusions are derived from a single breed (Angus) and gender (castrated males). Future studies should include females and diverse breeds to assess generalizability.

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.

Deciphering the coordinated roles of the host genome, duodenal mucosal genes, and microbiota in regulating complex traits in chickens

BACKGROUND

The complex interactions between host genetics and the gut microbiome are well documented. However, the specific impacts of gene expression patterns and microbial composition on each other remain to be further explored.

RESULTS

Here, we investigated this complex interplay in a sizable population of 705 hens, employing integrative analyses to examine the relationships among the host genome, mucosal gene expression, and gut microbiota. Specific microbial taxa, such as the cecal family Christensenellaceae, which showed a heritability of 0.365, were strongly correlated with host genomic variants. We proposed a novel concept of regulatability ( r b 2 ), which was derived from h2, to quantify the cumulative effects of gene expression on the given phenotypes. The duodenal mucosal transcriptome emerged as a potent influencer of duodenal microbial taxa, with much higher r b 2 values (0.17 ± 0.01, mean ± SE) than h2 values (0.02 ± 0.00). A comparative analysis of chickens and humans revealed similar average microbiability values of genes (0.18 vs. 0.20) and significant differences in average r b 2 values of microbes (0.17 vs. 0.04). Besides, cis ( h cis 2 ) and trans heritability ( h trans 2 ) were estimated to assess the effects of genetic variations inside and outside the cis window of the gene on its expression. Higher h trans 2 values than h cis 2 values and a greater prevalence of trans-regulated genes than cis-regulated genes underscored the significant role of loci outside the cis window in shaping gene expression levels. Furthermore, our exploration of the regulatory effects of duodenal mucosal genes and the microbiota on 18 complex traits enhanced our understanding of the regulatory mechanisms, in which the CHST14 gene and its regulatory relationships with Lactobacillus salivarius jointly facilitated the deposition of abdominal fat by modulating the concentration of bile salt hydrolase, and further triglycerides, total cholesterol, and free fatty acids absorption and metabolism.

CONCLUSIONS

Our findings highlighted a novel concept of r b 2 to quantify the phenotypic variance attributed to gene expression and emphasize the superior role of intestinal mucosal gene expressions over host genomic variations in elucidating host‒microbe interactions for complex traits. This understanding could assist in devising strategies to modulate host-microbe interactions, ultimately improving economic traits in chickens.

Structural characteristics of a heteropolysaccharide from Ganoderma lucidum and its protective effect against Alzheimer's disease via modulating the microbiota-gut-metabolomics

Ganoderma lucidum is a traditional Chinese medicine used to treat Alzheimer's disease (AD), whose main active ingredient is polysaccharides. A heteropolysaccharide named GLPZ-1 was isolated from Ganoderma lucidum. GLPZ-1 (6.608 kDa) predominantly consisted of Glc and minor Gal. The results of GC-MS and NMR analyses indicated that the backbone of GLPZ-1 was mainly composed of 1,4-α-D-Glcp, 1,4,6-α-Glcp and a minor amount of 1,3,4-β-D-Glcp, which was substituted with complex side chains at C-6 of 1,4,6-α-D-Glcp and at C-3 of 1,3,4-β-D-Glcp. GLPZ-1 demonstrated a protective effect on AD rats by improving behavioral abnormalities, alleviating pathological damage and ameliorating levels of IL-6, IL-1β, TNF-α and Th17, which were associated with GLPZ-1 modulating the microbiota-gut-metabolomics of AD rats. GLPZ-1 regulated the gut microbiota in AD rats by increasing the abundance of Bacteroides, unclassified_Lachnospiraceae, Lactobacillus, Pediococcus, Oscillibacter, Lachnoclostridium and Bifidobacterium, while simultaneously reducing the abundance of Pseudomonas and Desulfovibrio. GLPZ-1 could regulate fecal metabolites in AD rats tending towards the normal levels. These regulated fecal metabolites belonged to fatty acid metabolism, cholesterol and bile acid metabolism, neurotransmitters and aromatic amino acid metabolism. These findings provide a preliminary research basis for the exploitation of GLPZ-1 as an effective drug to prevent and delay AD.

Targeted gut microbiome therapy: Applications and prospects of probiotics, fecal microbiota transplantation and natural products in the management of type 2 diabetes

Type 2 diabetes mellitus (T2DM) is considered as one of the most pressing public health challenges worldwide. Studies have shown significant differences in the gut microbiota between healthy individuals and T2DM patients, suggesting that gut microorganisms may play a key role in the onset and progression of T2DM. This review systematically summarizes the relationship between gut microbiota and T2DM, and explores the mechanisms through which gut microorganisms may alleviate T2DM. Additionally, it evaluates the potential of probiotics, fecal microbiota transplantation (FMT)/virome transplantation (FVT), and natural products in modulating gut microbiota to treat T2DM. Although existing studies have suggested that these interventions may delay or even halt the progression of T2DM, most research remained limited to animal models and observational clinical studies, with a lack of high-quality clinical data. This has led to an imbalance between theoretical research and clinical application. Although some studies have explored the regulatory role of the gut virome on the gut microbiota, research in this area remains in its early stages. Based on these current studies, future research should be focused on large-scale, long-term clinical studies and further investigation on the potential role of the gut virome in T2DM. In conclusion, this review aims to summarize the current evidence and explore the applications of gut microbiota in T2DM treatment, as well as providing recommendations for further investigation in this field.

Exploring the Utility of the Gut Microbiome as a Longitudinal Health Monitoring Tool in Sanctuary Chimpanzees (Pan troglodytes)

The primary goal of captive primate management is to ensure optimal health and welfare of the animals in our care. Given that the gut microbiome interacts closely with host metabolism, immunity, and even cognition, it represents a potentially powerful tool for identifying subtle changes in health status across a range of body systems simultaneously. However, thus far, it has not been widely tested or implemented as a monitoring tool. In this study, we used longitudinal microbiome sampling of newly arrived chimpanzees at Chimp Haven to explore the feasibility of using the gut microbiome as a health and welfare biomarker in a sanctuary environment. We also tested the hypothesis that a transition to a new living environment, and integration into new social groupings, would result in temporal changes in chimpanzee gut microbiome composition. The collection of longitudinal microbiome data at Chimp Haven was feasible, and it revealed temporal shifts that were unique to each individual and, in some cases, correlated to other known impacts on health and behavior. We found limited evidence for microbial change over time after arrival at Chimp Haven that was consistent across individuals. In contrast, social group and enclosure, and to a lesser extent, age and sex, were associated with differences in gut microbiome composition. Microbiome composition was also associated with overall health status categories. However, many of the effects we detected were most apparent when using longitudinal data, as opposed to single time point samples. Additionally, we found important effects of technical factors, specifically outdoor temperature and time to collection, on our data. Overall, we demonstrate that the gut microbiome has the potential to be effectively deployed as a tool for health and environmental monitoring in a population of sanctuary chimpanzees, but the design must be carefully considered. We encourage other institutions to apply these approaches and integrate health and physiology data to build on the utility of gut microbiome analysis for ensuring the welfare of captive primates in a range of contexts.

A critical review of microbiome-derived metabolic functions and translational research in liver diseases

Significant changes in gut microbial composition are associated with chronic liver disease. Using preclinical models, it has been demonstrated that ethanol/alcohol-induced liver disease is transmissible through fecal microbiota transplantation (FMT). So, the survival rate of people with severe alcoholic hepatitis got better, which suggests that changes in the makeup and function of gut microbiota play a role in metabolic liver disease. The leaky intestinal barrier plays a major role in influencing metabolic-related liver disease development through the gut microbiota. As a result, viable bacteria and microbial products can be transported to the liver, causing inflammation, contributing to hepatocyte death, and causing the fibrotic response. As metabolic-related liver disease starts and gets worse, gut dysbiosis is linked to changes in the immune system, the bile acid composition, and the metabolic function of the microbiota in the gut. Metabolic-related liver disease, as well as its self-perpetuation, will be demonstrated using data from preclinical and human studies. Further, we summarize how untargeted treatment approaches affect the gut microbiota in metabolic-related liver disease, including dietary changes, probiotics, antibiotics, and FMT. It discusses how targeted therapies can improve liver disease in various areas. These approaches may improve metabolic-related liver disease treatment options.

Effects of Monascus pilosus SWM 008-Fermented Red Mold Rice and Its Functional Components on Gut Microbiota and Metabolic Health in Rats

Red mold rice, fermented by Monascus spp., has been reported to modulate gut microbiota composition and improve metabolic health. Previous studies indicate that red mold rice can reduce cholesterol, inhibit hepatic lipid accumulation, and enhance bile acid excretion, while also altering gut microbiota under high-fat dietary conditions. However, it remains unclear whether these effects are directly due to Monascus-derived products modulating gut microbiota or are a consequence of improved metabolic health conditions, which indirectly influence gut microbiota. This study aimed to evaluate the effects of Monascus pilosus SWM 008 fermented red mold rice and its components-monascin, monascinol, ankaflavin, and polysaccharides-on gut microbiota and metabolic health in rats fed a normal diet. Over eight weeks, physiological, biochemical, and gut microbiota parameters were assessed. Results showed no significant changes in body weight or liver/kidney function, confirming safety. Gut microbiota analysis revealed that red mold rice, monascin, monascinol, and polysaccharides significantly altered gut microbiota composition by increasing the relative abundance of beneficial bacteria, such as Akkermansia muciniphila, Ligilactobacillus murinus, and Duncaniella dubosii. Functional predictions indicated enhanced vitamin K2 biosynthesis, nucleotide metabolism, and other metabolic pathways linked to improved gut health. In conclusion, Monascus pilosus SWM 008 fermented red mold rice demonstrated safety and beneficial effects, suggesting its potential as a functional food to maintain gut microbiota balance under normal dietary conditions.

Reproduction in yellow drum (Nibea albiflora): insights from endocrine regulation and intestinal microbiota changes during reproductive season

The yellow drum (Nibea albiflora), a pivotal species within the Sciaenidae family, is economically important in the mariculture along the coastal regions of China. A comprehensive understanding gonadal maturation and spawning processes is crucial for seed production in the artificial propagation of yellow drum. This study investigates serum hormonal fluctuations, gonadal histological features, sex hormone receptor gene expression, and intestinal microbiota composition in both male and female yellow drum during the reproductive season. Twenty individuals were sampled from reproductive stages IV, V, and VI, respectively. During the spawning season, no significant differences were observed in the levels of PROG, E2, and 11-KT across different stages, in both males and females, with no significant sex-based differences. Subsequent analysis indicated a significant upregulation of fshr, lhcgr, and esr expression in the ovary during spawning stages. In contrast, within the testis, the expression levels of fshr, ar, and esr remained relatively constant across different stages, whereas lhcgr expression was markedly higher during the spawning stages compared with prespawning and post-spawning stages. Analysis of intestinal microbiota revealed a predominance of Bacteroidota, Firmicutes, and Proteobacteria, with no significant sex differences. At the class level, the abundances of Alphaproteobacteria, Gammaproteobacteria, and Bacilli exhibited significant fluctuations during the spawning and post-spawning stages in both sexes. At the genus level, g_Muribaculaceae and g_Bacteroides were abundant during spawning stages in both sexes. A Mantel test showed significant positive correlations between PROG levels and the abundances of g_Bacteroides in males. In females, PROG levels were positively correlated with the abundance of g_Prevotella. These findings enhance our understanding of the interplay between reproductive biology and the biological functions of intestinal microbiota in yellow drum broodstock during the reproductive season, thereby laying a foundation for the development of artificial propagation technology in this species.

Gut Microbiome, Diet and Depression: Literature Review of Microbiological, Nutritional and Neuroscientific Aspects

PURPOSE OF REVIEW

This review explores the intricate relationships among the gut microbiota, dietary patterns, and mental health, focusing specifically on depression. It synthesizes insights from microbiological, nutritional, and neuroscientific perspectives to understand how the gut-brain axis influences mood and cognitive function.

RECENT FINDINGS

Recent studies underscore the central role of gut microbiota in modulating neurological and psychological health via the gut-brain axis. Key findings highlight the importance of dietary components, including probiotics, prebiotics, and psychobiotics, in restoring microbial balance and enhancing mood regulation. Different dietary patterns exhibit a profound impact on gut microbiota composition, suggesting their potential as complementary strategies for mental health support. Furthermore, mechanisms like tryptophan metabolism, the HPA axis, and microbial metabolites such as SCFAs are implicated in linking diet and microbiota to depression. Clinical trials show promising effects of probiotics in alleviating depressive symptoms. This review illuminates the potential of diet-based interventions targeting the gut microbiota to mitigate depression and improve mental health. While the interplay between microbial diversity, diet, and brain function offers promising therapeutic avenues, further clinical research is needed to validate these findings and establish robust, individualized treatment strategies.

Early-life gut mycobiome core species modulate metabolic health in mice

The gut microbiome causally contributes to obesity; however, the role of fungi remains understudied. We previously identified three core species of the infant gut mycobiome (Rhodotorula mucilaginosa, Malassezia restricta and Candida albicans) that correlated with body mass index, however their causal contributions to obesity development are unknown. Here we show the effects of early-life colonization by these fungal species on metabolic health in gnotobiotic mice fed standard (SD) or high-fat-high-sucrose (HFHS) diets. Each species resulted in bacterial microbiome compositional and functional differences. R. mucilaginosa and M. restricta increased adiposity in mice fed SD, while only R. mucilaginosa exacerbated metabolic disease. In contrast, C. albicans resulted in leanness and resistance to diet-induced obesity. Intestinal nutrient transporter expression was unaffected by the presence of fungi in jejunal enteroids, yet the immune landscape in white adipose tissue was distinctly impacted by each fungal species, suggesting that these phenotypes may be a result of fungal immune regulation. This work revealed that three common fungal colonizers have distinct causal influences on obesity and metabolic inflammation and justifies the consideration of fungi in microbiome research on host metabolism.

The Future of Microbiome Therapeutics

The human microbiome exerts profound influence over various biological processes within the body. Unlike many host determinants, it represents a readily accessible target for manipulation to promote health benefits. However, existing commercial microbiome-directed products often exhibit low efficacy. Advancements in technology are paving the way for the development of novel microbiome therapeutics, across a wide range of indications. In this narrative review, we provide an overview of state-of-the-art technologies in late-stage development, examining their advantages and limitations. By covering a spectrum, from fecal-derived products to live biotherapeutics, phage therapy, and synthetic biology, we illuminate the path toward the future of microbiome therapeutics.

The microbiome and the eye: a new era in ophthalmology

The human microbiome has progressively been recognised for its role in various disease processes. In ophthalmology, complex interactions between the gut and distinct ocular microbiota within each structure and microenvironment of the eye has advanced our knowledge on the multi-directional relationships of these ecosystems. Increasingly, studies have shown that modulation of the microbiome can be achieved through faecal microbiota transplantation and synbiotics producing favourable outcomes for ophthalmic diseases. As ophthalmologists, we are obliged to educate our patients on measures to cultivate a healthy gut microbiome through a range of holistic measures. Further integrative studies combining microbial metagenomics, metatranscriptomics and metabolomics are necessary to fully characterise the human microbiome and enable targeted therapeutic interventions.

Serum metabolomics and 16S rRNA amplicon sequencing reveal the role of puerarin in alleviating bone loss aggravated by antidiabetic agent pioglitazone in type 2 diabetic mice

ETHNOPHARMACOLOGICAL RELEVANCE

Pioglitazone (PIO) was an anti type 2 diabetes (T2D) agent but caused bone loss and bone marrow fat accumulation. Puerarin (PUE) was a natural component of herbal medicine extracted from Pueraria lobata (Willd.) Ohwi and reduced glycemia and improved bone mass as a supplementary drug. A combination of PIO and PUE might be good for maintaining bone mass and blood glucose.

AIM OF THE STUDY

We aimed to elucidate the potential correlation and underlying mechanisms of dietary supplement PUE in reducing side effects caused by PIO.

MATERIALS AND METHODS

In vitro, alkaline phosphatase (ALP) staining, alizarin S (ARS) staining and qRT-PCR were performed to detect the osteogenesis activity in MC3T3-E1 cells. In vivo, we established the T2D model by treating C57BL6/J mice with high-fat diets and streptozotocin (STZ). Micro-CT, hematoxylin and eosin (H&E) staining and tartrate-resistant acid phosphatase (TRAcP) staining were performed to observe the difference in skeletal phenotype. Serum metabolomics and 16S rRNA amplicon sequencing were applied to analyze the potential effect of the combination of PIO and PUE.

RESULTS

We showed that the PUE could increase ALP activity and mineralization nodes of MC3T3-E1 with PIO. PIO could aggravate bone loss but PUE alleviated the effect caused by PIO in T2D mice. PUE promoted alpha-linolenic acid metabolism and glycerophospholipid metabolism, and affected the alpha diversity of the gut microbiome by regulating the genera of Alloprevotella, Fusobacterium, Rodentibacter, etc. Correlation analysis indicated that sphingosine-1-phosphate, nonadecylic acid, and margaric acid were associated with the effect of PUE.

CONCLUSIONS

Taken together, we demonstrated that PIO combined with PUE was able to lower blood sugar levels without causing bone loss. The effect of PUE mainly correlated with the genua of Alloprevotella, Fusobacterium, Rodentibacter, and Alistipes. Also, alpha-linolenic acid metabolism and glycerophospholipid metabolism were major targets of PUE.

Predicting metabolite response to dietary intervention using deep learning

Due to highly personalized biological and lifestyle characteristics, different individuals may have different metabolite responses to specific foods and nutrients. In particular, the gut microbiota, a collection of trillions of microorganisms living in the gastrointestinal tract, is highly personalized and plays a key role in the metabolite responses to foods and nutrients. Accurately predicting metabolite responses to dietary interventions based on individuals' gut microbial compositions holds great promise for precision nutrition. Existing prediction methods are typically limited to traditional machine learning models. Deep learning methods dedicated to such tasks are still lacking. Here we develop a method McMLP (Metabolite response predictor using coupled Multilayer Perceptrons) to fill in this gap. We provide clear evidence that McMLP outperforms existing methods on both synthetic data generated by the microbial consumer-resource model and real data obtained from six dietary intervention studies. Furthermore, we perform sensitivity analysis of McMLP to infer the tripartite food-microbe-metabolite interactions, which are then validated using the ground-truth (or literature evidence) for synthetic (or real) data, respectively. The presented tool has the potential to inform the design of microbiota-based personalized dietary strategies to achieve precision nutrition.

A Small-Molecule Inhibitor of Gut Bacterial Urease Protects the Host from Liver Injury

Hyperammonemia is characterized by the accumulation of ammonia within the bloodstream upon liver injury. Left untreated, hyperammonemia contributes to conditions such as hepatic encephalopathy that have high rates of patient morbidity and mortality. Previous studies have identified gut bacterial urease, an enzyme that converts urea into ammonia, as a major contributor to systemic ammonia levels. Here, we demonstrate use of benurestat, a clinical candidate used against ureolytic organisms in encrusted uropathy, to inhibit urease activity in gut bacteria. Benurestat inhibits ammonia production by urease-encoding gut bacteria and is effective against individual microbes and complex gut microbiota. When administered to conventional mice with liver injury induced by thioacetamide exposure, benurestat reduced gut and serum ammonia levels and rescued 100% of mice from lethal acute liver injury. Overall, this study provides an important proof-of-concept for modulating host ammonia levels and microbiota-driven risks for hyperammonemia with gut microbiota-targeted small-molecule inhibitors.

16S rRNA and metabolomics reveal the key microbes and key metabolites that regulate diarrhea in Holstein male calves

Introduction

Diarrhea is a prevalent disease among calves, which significantly hinders their growth and development, thereby impacting farm productivity and revenue. This study aimed to investigate the impact of diarrhea on calf growth.

Methods

Holstein male calves with similar birth weight (39.5 ± 4.2 kg) were included in this study, and key parameters such as fecal score, diarrhea incidence, and growth performance from birth to weaning were measured. Rectal fecal samples from both diarrheic (n = 24) and healthy calves (n = 24) aged 1-4 weeks were analyzed using 16S rRNA gene sequencing and untargeted metabolomics.

Results

Our findings indicated a high prevalence of diarrhea among calves between 1-4 weeks of age on pasture, which led to a marked decrease in growth performance, including average daily gain. At the genus level, the relative abundance of GCA-900066575 in one-week-old diarrheic calves was significantly higher; Escherichia-Shigella and Pseudoflavonifractor were more abundant in two-week-old calves; while Tyzzerella and Lachnospiraceae_UCG-004 increased significantly in four-week-old calves, and correlated negatively with average daily gain, suggesting that these bacteria may promote the occurrence of diarrhea. Correlation analysis revealed that fecal metabolites such as arachidonic acid, cis-vaccenic acid, oleic acid, choline, creatinine, and others were significantly negatively correlated with calf growth performance and were significantly increased in diarrheic calves. WGNCA identified that dark magenta module metabolites were significantly associated with diarrhea traits from 1-4 weeks. Thirteen metabolites, including glycerophospholipids (such as 1-stearoyl-2-hydroxy-sn-glycero-3-phosphoethanolamine), fatty acids (such as dodecanoic acid), and arachidonic acid, were positively correlated with GCA-900066575, Escherichia-shigella, Tyzzerella, and Clostridium_butyricum, but negatively correlated with UBA1819, Lachnoclostridium_sp_YL32, and Clostridium_scindens.

Discussion

Therefore, GCA-900066575, Escherichia-shigella, Lachnospiraceae_UCG-004, and Tyzzerella are likely key bacterial genera causing diarrhea in calves, while arachidonic acid, glycerol phospholipids, and fatty acids are critical metabolites associated with this condition. These alterations in the fecal microbiota and metabolite composition were found to be the principal contributors to growth retardation in diarrheic calves.

The mycobiome in human cancer: analytical challenges, molecular mechanisms, and therapeutic implications

The polymorphic microbiome is considered a new hallmark of cancer. Advances in High-Throughput Sequencing have fostered rapid developments in microbiome research. The interaction between cancer cells, immune cells, and microbiota is defined as the immuno-oncology microbiome (IOM) axis. Fungal microbes (the mycobiome), although representing only ∼ 0.1-1% of the microbiome, are a critical immunologically active component of the tumor microbiome. Accumulating evidence suggests a possible involvement of commensal and pathogenic fungi in cancer initiation, progression, and treatment responsiveness. The tumor-associated mycobiome mainly consists of the gut mycobiome, the oral mycobiome, and the intratumoral mycobiome. However, the role of fungi in cancer remains poorly understood, and the diversity and complexity of analytical methods make it challenging to access this field. This review aims to elucidate the causal and complicit roles of mycobiome in cancer development and progression while highlighting the issues that need to be addressed in executing such research. We systematically summarize the advantages and limitations of current fungal detection and analysis methods. We enumerate and integrate these recent findings into our current understanding of the tumor mycobiome, accompanied by the prospect of novel and exhilarating clinical implications.

Understanding Patterns of the Gut Microbiome May Contribute to the Early Detection and Prevention of Type 2 Diabetes Mellitus: A Systematic Review

The rising burden of type 2 diabetes mellitus (T2DM) is a growing global public health problem, particularly prominent in developing countries. The early detection of T2DM and prediabetes is vital for reversing the outcome of disease, allowing early intervention. In the past decade, various microbiome-metabolome studies have attempted to address the question of whether there are any common microbial patterns that indicate either prediabetic or diabetic gut microbial signatures. Because current studies have a high methodological heterogeneity and risk of bias, we have selected studies that adhered to similar design and methodology. We performed a systematic review to assess if there were any common changes in microbiome belonging to diabetic, prediabetic and healthy individuals. The cross-sectional studies presented here collectively covered a population of 65,754 people, with 1800 in the 2TD group, 2770 in the prediabetic group and 61,184 in the control group. The overall microbial diversity scores were lower in the T2D and prediabetes cohorts in 86% of the analyzed studies. Re-programming of the microbiome is potentially one of the safest and long-lasting ways to eliminate diabetes in its early stages. The differences in the abundance of certain microbial species could serve as an early warning for a dysbiotic gut environment and could be easily modified before the onset of disease by changes in lifestyle, taking probiotics, introducing diet modifications or stimulating the vagal nerve. This review shows how metagenomic studies have and will continue to identify novel therapeutic targets (probiotics, prebiotics or targets for elimination from flora). This work clearly shows that gut microbiome intervention studies, if performed according to standard operating protocols using a predefined analytic framework (e.g., STORMS), could be combined with other similar studies, allowing broader conclusions from collating all global cohort studies efforts and eliminating the effect-size statistical insufficiency of a single study.

MicrobiomeNet: exploring microbial associations and metabolic profiles for mechanistic insights

The growing volumes of microbiome studies over the past decade have revealed a wide repertoire of microbial associations under diverse conditions. Microbes produce small molecules to interact with each other as well as to modulate their environments. Their metabolic profiles hold the key to understanding these association patterns for translational applications. Based on this concept, we developed MicrobiomeNet, a comprehensive database that integrates microbial associations with their metabolic profiles for mechanistic insights. It currently contains a total of ∼5.8 million known microbial associations, coupled with >12 400 genome-scale metabolic models (GEMs) covering ∼6000 microbial species. Users can intuitively explore microbial associations and compare their corresponding metabolic profiles. Our case studies show that MicrobiomeNet can provide mechanistic insights that are consistent with the literature. MicrobiomeNet is freely available at https://www.microbiomenet.com/.

Dietary inclusion of high-amylose cornstarch increased Lactobacillus and Terrisporobacter and decreased Streptococcus in the cecal digesta of weanling pigs

The study investigated the effect of dietary inclusion of high-amylose cornstarch (HA-starch) on cecal microbiota composition and volatile fatty acid (VFA) concentrations in weanling pigs fed high levels of cold-pressed canola-cake (CPCC). Weaned pigs (240 mixed sex; 7.1 ± 1.2 kg) were housed in 40 pens (6 pigs/pen) and fed a common commercial diet for 7 d, followed by the experimental diets for 28-d, which contained either 0% or 40% CPCC with either 0% or 40% HA-starch. At the end of the study, one pig from each pen (n = 8) was selected and euthanized to collect cecal digesta for microbial and VFA composition analyses. The HA-starch increased (P < 0.001) acetate, propionate, and butyrate concentrations, thereby increasing total VFA concentration (P < 0.001). There was a tendency for cecal butyrate and total VFA concentrations to decrease when pigs were fed the 40% CPCC diet without HA-starch but increase when fed the 40% CPCC diet containing 40% HA-starch (CPCC × HA-starch effect; P = 0.09), indicating HA-starch can increase cecal butyrate and total VFA concentrations in pigs fed a diet with high-CPCC level. The proportions of Lactobacillus and Terrisporobacter were high, whereas low proportions of Streptococcus genus were observed in the cecal microbiota of pigs fed diets containing 40% HA-starch. Also, pathways consistent with carbohydrate digestion, absorption, and phosphate metabolism were enriched in pigs when the diet included 40% HA-starch. In summary, incorporating high amounts of HA-starch in a weanling pig diet containing high levels of CPCC may benefit intestinal health and digestive performance by enhancing the abundance of probiotic commensal bacteria, contributing to increased enzymatic activity and carbohydrate metabolism.

Metagenomic Insights into Pigeon Gut Microbiota Characteristics and Antibiotic-Resistant Genes

BACKGROUND

Antibiotics were extensively used in the pigeon breeding industry previously to promote growth and prevent disease, leading to the spread of antibiotic-resistant genes (ARGs) in gut microbes, which has become a major public health concern.

METHODS

A metagenomic analysis was performed to investigate the gut microbial communities and ARGs in young and older pigeons in Nanjing, Jiangsu Province, China.

RESULTS

There were obviously distinct gut microbiota and functional compositions between young and older pigeons. Both Pseudomonadota and Uroviricota were dominant in young and older pigeons. Although sharing 24 gut microbiota phyla between young and older pigeons, Bacillota and Pseudomonadota were the dominant microbial phyla in them, respectively. Besides the shared metabolic pathways and biosynthesis of secondary metabolites, biosynthesis of amino acids was the most abundant Kyoto Encyclopedia of Genes and Genomes (KEGG) function in young pigeons, while microbial metabolism in diverse environments was abundant in older pigeons. A total of 142 ARGs conferring multidrug resistance, tetracycline, and aminoglycoside resistance were identified; the most abundant gene in young pigeons was tetracycline-tetW, while in older pigeons, it was multidrug-acrB.

CONCLUSIONS

Our findings revealed significant differences in the gut microbial communities and ARGs between young and older pigeons. This study enhances our understanding of pigeon gut microbiota and antibiotic resistomes, contributing to knowledge-based sustainable pigeon meat production.

Research Progress in the Relationship between Intestinal Flora and Diabetes Mellitus

Diabetes mellitus is a common chronic metabolic disease characterized by a high incidence and disability rate. Intestinal flora refers to the microbial community that lives in the intestines and plays a crucial role in maintaining intestinal health and the human immune system. In recent years, an increasing body of research has revealed a close relationship between intestinal flora and diabetes. The pathophysiological mechanisms between them have also been constantly uncovered, and the regulation of intestinal flora has shown promising efficacy in the adjuvant treatment of diabetes. This study mainly summarized the characteristics and mechanisms of intestinal flora in patients with diabetes in recent years, as well as the methods of regulating intestinal flora to prevent and treat diabetes, and prospected the future research direction. This will offer a theoretical basis for the clinical adjuvant treatment of diabetes with intestinal flora and the development of new drugs.

Microbial Dynamics in COVID-19: Unraveling the Impact of Human Microbiome on Disease Susceptibility and Therapeutic Strategies

This review explores the bidirectional relationship between the human microbiome and SARS-CoV-2 infection, elucidating its implications for COVID-19 susceptibility, severity, and therapeutic strategies. Metagenomic analyses reveal notable alterations in microbiome composition associated with SARS-CoV-2 infection, impacting disease severity and clinical outcomes. Dysbiosis within the respiratory, gastrointestinal, oral, and skin microbiomes exacerbates COVID-19 pathology through immune dysregulation and inflammatory pathways. Understanding these microbial shifts is pivotal for devising targeted therapeutic interventions. Notably, co-infection of oral pathogens with SARS-CoV-2 worsens lung pathology, while gut microbiome dysbiosis influences viral susceptibility and severity. Potential therapeutic approaches targeting the microbiome include probiotics, antimicrobial agents, and immunomodulatory strategies. This review underscores the importance of elucidating host-microbiota interactions to advance precision medicine and public health initiatives in combating COVID-19 and other infectious diseases.

Exploring the Adaptation Process of Huso dauricus to High Temperatures Based on Changes in Intestinal Microbiota

Global warming has led to rising water temperatures, posing a significant threat to fish survival. Understanding the mechanisms by which fish respond to and adapt to temperature variations is thus of considerable importance. This study employed high-throughput 16S rRNA gene sequencing and bioinformatics to investigate changes in the intestinal microbiota of the kaluga sturgeon (Huso dauricus) under four temperature conditions (19 °C, 25 °C, 28 °C, and 31 °C) and its relationship with adaptation to high-temperature stress. The results indicated that temperature variations caused significant changes in the intestinal microbiota. Over time, differences in the microbiota structure became more pronounced under different temperature conditions, and within-group variability gradually decreased. At higher temperatures, the relative abundance of Sphingomonas significantly decreased, while that of Clostridium sensu stricto 1, Cetobacterium, and Plesiomonas exhibited a significant increase in relative abundance. Upon the cessation of rapid mortality under various high-temperature conditions, the intestinal microbiota structure and composition became highly similar, with Clostridium sensu stricto 1 dominating both in terms of composition and relative abundance, suggesting a central role in adaptation to high-temperature stress. This study preliminarily confirms that the high-temperature adaptability of Huso dauricus is closely related to the structure and composition of its intestinal microbiota, with bacteria such as Clostridium sensu stricto 1 playing an important role. These findings provide new scientific insights into enhancing fish adaptability to high-temperature stress.

Bifidobacterium animalis Probio-M8 improves sarcopenia physical performance by mitigating creatine restrictions imposed by microbial metabolites

Sarcopenia is a major health challenge due to an aging population. Probiotics may improve muscle function through gut-muscle axis, but their efficacy and mechanisms in treating sarcopenia remain unclear. This study investigated the impact of Bifidobacterium animalis subsp. lactis Probio-M8 (Probio-M8) on old mice and sarcopenia patients. We analyzed 43 subjects, including gut microbiome, fecal metabolome, and serum metabolome, using a multi-omics approach to assess whether Probio-M8 can improve sarcopenia by modulating gut microbial metabolites. Probio-M8 significantly improved muscle function in aged mice and enhanced physical performance in sarcopenia patients. It reduced pathogenic gut species and increased beneficial metabolites such as indole-3-lactic acid, acetoacetic acid, and creatine. Mediating effect analyses revealed that Probio-M8 effectively reduced n-dodecanoyl-L-homoserine lactone level in gut concurrent with increased creatine circulation, to significantly enhance host physical properties. These findings provide new insights into probiotics as a potential treatment for sarcopenia by modulating gut microbiota metabolism.

Beetroot juice intake positively influenced gut microbiota and inflammation but failed to improve functional outcomes in adults with long COVID: A pilot randomized controlled trial

BACKGROUND & AIMS

Long-term effects of coronavirus disease 2019 (long COVID) develop in a substantial number of people following an acute COVID-19 episode. Red beetroot juice may have positive effects on multiple pathways involved in long COVID. The aim of this pilot study was to explore the impact of beetroot juice supplementation on physical function, gut microbiota, and systemic inflammation in adults with long COVID.

METHODS

A single-center, double-blind, placebo-controlled randomized trial was conducted to test the effects of 14 days of beetroot juice supplementation, rich in nitrates and betalains, on functional and biological outcomes in adults aged between 20 and 60 years with long COVID. Participants were randomized 1:1 to receive either daily oral supplementation with 200 mL beetroot juice (∼600 mg nitrate) or placebo (∼60 mg nitrate) for 14 days. The primary endpoint was the change from baseline to day 14 in a fatigue resistance test. Secondary outcomes included the distance walked on the 6-min walk test, handgrip strength, and flow-mediated dilation. Secondary endpoints also included changes from baseline in circulating inflammatory mediators and metagenomic and fecal water metabolomic profiles. Partial least squares discriminant analysis (PLS-DA) models were built to evaluate the differences in biological variables associated with the interventions.

RESULTS

Thirty-one participants were randomized in the study. Twenty-five of them (median (interquartile range) age 40 (10), 14 [56 %] women), received either beetroot juice (15) or placebo (10) and completed the study. At 14 days, fatigue resistance significantly improved from baseline (mean difference [standard error]: +21.8 [3.7] s; p < 0.001) with no significant differences between intervention groups. A significant increase from baseline in the distance walked on the 6-min walk test was observed (mean difference [standard error]: +30.0 [9.4] m; p = 0.03), which was not different between groups. Flow-mediated dilation did not differ between participants who received beetroot juice and those on placebo. PLS-DA models allowed correct classification of participants with 92.2 ± 4.4 % accuracy. Those who ingested red beetroot juice had a greater abundance of bacteria with well-known beneficial effects, including Akkermansia, Oscillospira, Prevotella, Roseburia, Ruminococcaceae, and Turicibacter, compared with placebo. Participants allocated to beetroot juice supplementation were also characterized by significantly higher levels of fecal nicotinate, trimethylamine, and markers of beetroot juice intake (e.g., 5,6-dihydroxyindole). Finally, higher levels of interferon gamma and macrophage inflammatory protein-1β were found in participants who consumed beetroot juice.

CONCLUSION

Beetroot juice supplementation for two weeks did not to induce significant improvements in functional outcomes in adults with long COVID compared with placebo. Beneficial effects were observed in both gut microbiota composition (i.e., increase in probiotic species) and inflammatory mediators.

TRIAL REGISTRATION

Trial was registered under ClinicalTrials.gov. Identifier no. NCT06535165.

Microbial functional pathways based on metatranscriptomic profiling enable effective saliva-based health assessments for precision wellness

It is increasingly recognized that an important step towards improving overall health is to accurately measure biomarkers of health from the molecular activities prevalent in the oral cavity. We present a general methodology for computationally quantifying the activity of microbial functional pathways using metatranscriptomic data. We describe their implementation as a collection of eight oral pathway scores using a large salivary sample dataset (n = 9350), and we evaluate score associations with oropharyngeal disease phenotypes within an unseen independent cohort (n = 14,129). Through this validation, we show that the relevant oral pathway scores are significantly worse in individuals with periodontal disease, acid reflux, and nicotine addiction, compared with controls. Given these associations, we make the case to use these oral pathway scores to provide molecular health insights from simple, non-invasive saliva samples, and as molecular endpoints for actionable interventions to address the associated conditions.

Characterizing the role of the microbiota-gut-brain axis in cerebral small vessel disease: An integrative multi‑omics study

BACKGROUND

Prior efforts have revealed changes in gut microbiome, circulating metabolome, and multimodal neuroimaging features in cerebral small vessel disease (CSVD). However, there is a paucity of research integrating the multi-omic information to characterize the role of the microbiota-gut-brain axis in CSVD.

METHODS

We collected gut microbiome, fecal and blood metabolome, multimodal magnetic resonance imaging data from 37 CSVD patients with white matter hyperintensities and 46 healthy controls. Between-group comparison was performed to identify the differential gut microbial taxa, followed by performance of multi-stage microbiome-metabolome-neuroimaging-neuropsychology correlation analyses in CSVD patients.

RESULTS

Our data showed both depleted and enriched gut microbes in CSVD patients. Among the differential microbes, Haemophilus and Akkermansia were associated with a range of metabolites enriched for Aminoacyl-tRNA biosynthesis pathway. Furthermore, the affected metabolites were associated with neuroimaging measures involving gray matter morphology, spontaneous intrinsic brain activity, white matter integrity, and global structural network topology, which were in turn related to cognition and emotion in CSVD patients.

CONCLUSION

Our findings provide an integrative framework to understand the pathophysiological mechanisms underlying the interplay between gut microbiota dysbiosis and CSVD, highlighting the potential of targeting the microbiota-gut-brain axis as a therapeutic strategy in CSVD patients.

A new target for treating intervertebral disk degeneration: gut microbes

Intervertebral disk degeneration (IDD) is a common clinical spinal disease and one of the main causes of low back pain (LBP). Generally speaking, IDD is considered a natural degenerative process with age. However, with the deepening of research, people have discovered that IDD is not only related to age, but also has many factors that can induce and accelerate its progression. In addition, the pathogenesis of IDD remains unclear, resulting in limited traditional treatment methods that cannot effectively prevent and treat IDD. Conservative treatment may lead to patients' dependence on drugs, and the pain relief effect is not obvious. Similarly, surgical treatment is highly invasive, with a longer recovery time and a higher recurrence rate. With the deepening of exploration, people have discovered that intestinal microorganisms are an important symbiotic microbial community in the human body and are closely related to the occurrence and development of various diseases. Changes in intestinal microorganisms and their metabolites may affect the body's inflammatory response, immune regulation, and metabolic processes, thereby affecting the health of the intervertebral disk. In this context, the gut microbiota has received considerable attention as a potential target for delaying or treating IDD. This article first introduces the impact of gut microbes on common distal organs, and then focuses on three potential mechanisms by which gut microbes and their metabolites influence IDD. Finally, we also summarized the methods of delaying or treating IDD by interfering with intestinal microorganisms and their metabolites. Further understanding of the potential mechanisms between intestinal microorganisms and IDD will help to formulate reasonable IDD treatment strategies to achieve ideal therapeutic effects.

NMFGOT: a multi-view learning framework for the microbiome and metabolome integrative analysis with optimal transport plan

The rapid development of high-throughput sequencing techniques provides an unprecedented opportunity to generate biological insights into microbiome-related diseases. However, the relationships among microbes, metabolites and human microenvironment are extremely complex, making data analysis challenging. Here, we present NMFGOT, which is a versatile toolkit for the integrative analysis of microbiome and metabolome data from the same samples. NMFGOT is an unsupervised learning framework based on nonnegative matrix factorization with graph regularized optimal transport, where it utilizes the optimal transport plan to measure the probability distance between microbiome samples, which better dealt with the nonlinear high-order interactions among microbial taxa and metabolites. Moreover, it also includes a spatial regularization term to preserve the spatial consistency of samples in the embedding space across different data modalities. We implemented NMFGOT in several multi-omics microbiome datasets from multiple cohorts. The experimental results showed that NMFGOT consistently performed well compared with several recently published multi-omics integrating methods. Moreover, NMFGOT also facilitates downstream biological analysis, including pathway enrichment analysis and disease-specific metabolite-microbe association analysis. Using NMFGOT, we identified the significantly and stable metabolite-microbe associations in GC and ESRD diseases, which improves our understanding for the mechanisms of human complex diseases.