Phylogenetic distribution of three pathways for propionate production within the human gut microbiota

Life-course socioeconomic position and the gut microbiome in the Hispanic Community Health Study/Study of Latinos (HCHS/SOL)

Socioeconomic position (SEP) in childhood and beyond may influence the gut microbiome, with implications for disease risk. Studies evaluating the relationship between life-course SEP and the gut microbiome are sparse, particularly among Hispanic/Latino individuals, who have a high prevalence of low SEP. We use the Hispanic Community Health Study/Study of Latinos (HCHS/SOL), a population-based cohort study conducted in four field centers in the United States (U.S.), to evaluate the association between life-course SEP and gut microbiome composition. Life-course SEP indicators included parental education (proxy of childhood SEP), current SEP (n = 2174), and childhood (n = 988) and current economic hardship (n = 994). Shotgun sequencing was performed on stool samples. Analysis of Compositions of Microbiomes was used to identify associations of life-course SEP indicators with gut microbiome species and functions. Parental education and current SEP were associated with the overall gut microbiome composition; however, parental education and current education explained more the gut microbiome variance than the current SEP. A lower parental education and current SEP were associated with a lower abundance of species from genus Bacteroides. In stratified analysis by nativity, we found similar findings mainly among foreign-born participants. Early-life SEP may have long-term effects on gut microbiome composition underscoring another biological mechanism linking early childhood factors to adult disease.

Interaction of environmental fluoride exposure and gut microbes: Potential implication in the development of fluorosis in human subjects

Fluoride exposure primarily occurs through contaminated water and leads to fluorosis, which is a global health concern. After ingestion, fluoride is absorbed via gastrointestinal tract, where it interacts with the gut microbiota. While animal studies have explored fluoride's effects on gut microbiota, no human studies have yet been conducted. Most research emphasizes metagenomic diversity, neglecting isolation and characterization of pure cultures for further applications. Additionally, the association between gut microbiota with fluorosis outcomes in fluoride-exposed populations is unexplored. This study characterizes and compares the cultivable gut microbiota in the fluoride-exposed population with (symptomatic, group II) or without (asymptomatic, group I) signs of skeletal fluorosis along with unexposed control (group III). Group I displayed higher abundance of Firmicutes (58.58 %), group II had predominance of Proteobacteria (61.25 %) while group III showed similar abundance of Proteobacteria (50.38 %) and Firmicutes (49.51 %). On analyzing short-chain fatty acid (SCFA) profiles, group I isolates produced higher isobutyric acid (1.31 ± 0.9 mM) than group II (0.71 ± 0.35 mM), while group II produced more isovaleric acid (0.8 ± 0.41 mM) than group I (0.61 ± 0.08 mM) (p < 0.05). These findings suggest that gut microbiota and SCFAs alteration may influence bone metabolism, affecting the fluorosis progression.

Structural characterization of the exopolysaccharide produced by Bacillus amyloliquefaciens JM033 and evaluation of its ability to regulate immunity and intestinal flora

The probiotic strain Bacillus amyloliquefaciens JM033 (B. amyloliquefaciens JM033), isolated from the traditional Chinese fermented food Sufu (also known as Fu-ru or fermented bean curd), is distinguished by its high production of exopolysaccharides (EPS). The EPS (BAP-1) produced by this strain was purified and its structure analyzed. BAP-1 is a novel hybrid fructan with a molecular weight of 17.6 kDa. It is composed of →6)-β-D-Fruf-(2 → and →1,6)-β-D-Fruf-(2→, which form the backbone, with a branched chain of β-D-Fruf-(2 → attached at the 1-position of residue B. In vivo studies on mice indicated that BAP-1 improves immunity in immunosuppressed mice by enhancing humoral immunity (P < 0.01), monocyte-macrophage phagocytosis (P < 0.01), and NK cell killing activity (P < 0.05). Additionally, BAP-1 was found to improve the composition of the intestinal microbiota and stimulate the production of short-chain fatty acids. Notably, BAP-1 exhibited a significant effect on the proliferation of Akkermansia. Therefore, BAP-1 shows promise as a prebiotic and may contribute to the development of new immunomodulatory agents.

Enhanced propionate and butyrate metabolism in cecal microbiota contributes to cold-stress adaptation in sheep

BACKGROUND

During cold stress, gut microbes play crucial roles in orchestrating energy metabolism to enhance environmental adaptation. In sheep, hindgut microbes ferment carbohydrates to generate short-chain fatty acids (SCFAs) as an energy source. However, the mechanisms by which hindgut microbes and their metabolites interact with the host to facilitate adaptation to cold environments remain ambiguous. Herein, we simulated a winter environment (- 20 °C) and provided a rationed diet to compare the cold adaptation mechanisms between Hulunbuir and Hu sheep.

RESULTS

Our findings show that cold exposure enhances SCFA metabolism in the sheep cecum. In Hu sheep, acetate, butyrate, and total SCFA concentrations increased, whereas in Hulunbuir sheep, propionate and butyrate concentrations increased, with a notable increase in total SCFAs. Notably, butyrate concentration was higher in Hulunbuir sheep than in Hu sheep under cold stress. Following cold exposure, the proinflammatory cytokine IL-1β levels increased in both breeds. In addition, Hu sheep showed increased IL-10, whereas Hulunbuir sheep exhibited elevated secretory IgA levels. The cecal microbiota responded differently, Hu sheep showed no notable changes in alpha and beta diversity, whereas Hulunbuir sheep exhibited considerable alterations. In Hu sheep, the abundance of fungi, specifically Blastocystis sp. subtype 4, decreased, and that of several Lachnospiraceae species (Roseburia hominis, Faecalicatena contorta, and Ruminococcus gnavus) involved in SCFA metabolism increased. Pathways related to carbohydrate metabolism, such as starch and sucrose metabolism, galactose metabolism, and pentose and glucuronate interconversions, were upregulated. In Hulunbuir sheep, the abundance of Treponema bryantii, Roseburia sp. 499, and Prevotella copri increased, with upregulation in pathways related to amino acid metabolism and energy metabolism. Cold exposure increased node connectivity within the symbiotic networks of both breeds, with increased network vulnerability in Hu sheep. Following cold exposure, the microbial community of Hulunbuir sheep showed a decrease in the influence of stochastic processes on community assembly, with a corresponding increase in the role of environmental selection. Conversely, no such shift was evident in Hu sheep. Further transcriptomic analysis revealed distinct regulatory mechanisms between breeds. In Hu sheep, protein synthesis, energy metabolism, and thermogenesis pathways were substantially upregulated. By contrast, Hulunbuir sheep showed considerable upregulation of immune pathways and energy conservation through reduced ribosome synthesis. Correlation analysis indicated that butyrate holds a central position in both networks, with Hulunbuir sheep exhibiting a more complex and tightly regulated network involving SCFAs, microbiota, microbial functions, and transcriptomes. Partial least squares path modeling revealed that cold exposure substantially altered the cecal microbiota and transcriptomes of Hulunbuir sheep, affecting SCFAs and cytokines.

CONCLUSIONS

The findings of this study suggest that under cold exposure, Hu sheep enhance acetate fermentation and rely on tissue thermogenesis for adaptation. By contrast, Hulunbuir sheep exhibit changes in microbial diversity and function, leading to increased propionate and butyrate metabolism. This may promote physiological energy conservation and innate immune defense, balancing heat loss and enhancing cold adaptation.

Multi-omics profiling of dairy cattle oxidative stress identifies hindgut-derived Phascolarctobacterium succinatutens exhibiting antioxidant activity

An imbalance between oxidative and antioxidant processes in the host can lead to excessive oxidation, a condition known as oxidative stress (OS). Although changes in the hindgut microbiota have been frequently linked to OS, the specific microbial and metabolic underpinnings of this association remain unclear. In this study, we enrolled 81 postpartum Holstein cows and stratified them into high oxidative stress (HOS, n = 9) and low oxidative stress (LOS, n = 9) groups based on the oxidative stress index (OSi). Using a multi-omics approach, we performed 16S rRNA gene sequencing to evaluate microbial diversity, conducted metagenomic analysis to identify functional bacteria, and utilized untargeted metabolomics to profile serum metabolites. Our analyses revealed elevated levels of kynurenine, formyl-5-hydroxykynurenamine, and 5-hydroxyindole-3-acetic acid in LOS dairy cows. Additionally, the LOS cows had a higher abundance of short-chain fatty acids (SCFAs)-producing bacteria, including Bacteroidetes bacterium, Paludibacter propionicigenes, and Phascolarctobacterium succinatutens (P. succinatutens), which were negatively correlated with OSi. To explore the potential role of these bacteria in mitigating OS, we administered P. succinatutens (108 cfu/day for 14 days) to C57BL/6 J mice (n = 10). Oral administration of P. succinatutens significantly increased serum total antioxidant capacity, decreased total oxidants, and reduced OSi in mice. Moreover, this treatment promoted activation of the Nrf2-Keap1 antioxidant pathway, significantly enhancing the enzymatic activities of GSH-Px and SOD, as well as the concentrations of acetate and propionate in the colon. In conclusion, our findings suggest that systemic tryptophan metabolism and disordered SCFAs production are concurrent factors influenced by hindgut microbiota and associated with OS development. Modulating the hindgut microbiota, particularly by introducing specific SCFAs-producing bacteria, could be a promising strategy for combating OS.

Bacillus Coagulans BC99 Protects Ionizing Radiation-Induced Intestinal Injury and Modulates Gut Microbiota and Metabolites in Mice

The gastrointestinal tract is highly sensitive to ionizing radiation (IR), which causes radiation-induced intestinal injury (RIII). There are no effective drugs available for RIII in routine clinical treatment, which is a major limiting factor during the process of radiotherapy for pelvic abdominal malignancies. In this study, we aimed to elucidate the potential of probiotic Bacillus coagulans BC99 (B.coagulans BC99) in preventing RIII. C57BL/6J mice were gavage-administered with B.coagulans BC99 for 30 days and then exposed to a single dose of 12 Gy x-ray whole abdominal irradiation (WAI). B.coagulans BC99 treatment could mitigate RIII by preventing weight loss, maintaining the integrity of intestinal structure and barrier, improving inflammatory symptoms, modulating oxidative stress, and regulating the composition of gut microbiota, thereby reestablishing intestinal homeostasis. In addition, the potential radioprotective mechanism of B.coagulans BC99 was closely related to the gut microbiota-derived metabolites. This study offers a novel perspective for advancing probiotic-based treatments for RIII and enhancing strategies for the prevention of RIII.

The link between ultra-processed food consumption, fecal microbiota, and metabolomic profiles in older mediterranean adults at high cardiovascular risk

BACKGROUND

Ultra-processed food (UPF) consumption has been linked to adverse metabolic outcomes, potentially mediated by alterations in gut microbiota and metabolite production.

OBJECTIVE

This study aims to explore the cross-sectional and longitudinal associations between NOVA-classified UPF consumption, fecal microbiota, and fecal metabolome in a population of Mediterranean older adults at high cardiovascular risk.

METHODS

A total of 385 individuals, aged between 55 and 75 years, were included in the study. Dietary and lifestyle information, anthropometric measurements, and stool samples were collected at baseline and after 1-year follow-up. Fecal microbiota and metabolome were assessed using 16 S rRNA sequencing and liquid chromatography-tandem mass spectrometry, respectively.

RESULTS

At baseline, higher UPF consumption was associated with lower abundance of Ruminococcaceae incertae sedis (β = - 0.275, P = 0.047) and lower concentrations of the metabolites propionylcarnitine (β = - 0.0003, P = 0.013) and pipecolic acid (β = - 0.0003, P = 0.040) in feces. Longitudinally, increased UPF consumption was linked to reduced abundance of Parabacteroides spp. after a 1-year follow-up (β = - 0.278, P = 0.002).

CONCLUSIONS

High UPF consumption was associated with less favorable gut microbiota and metabolite profiles, suggesting a possible link to reduced short-chain fatty acid (SCFA) production, altered mitochondrial energy metabolism, and impaired amino acid metabolism. These findings support the reduction of UPF consumption and the promotion of dietary patterns rich in fiber for better gut health. Further research is needed to confirm these associations and clarify the underlying mechanisms.

TRIAL REGISTRATION

ISRCTN89898870 ( https://doi.org/10.1186/ISRCTN89898870 ).

Efficacy of a postbiotic and its components in promoting colonic transit and alleviating chronic constipation in humans and mice

This study evaluates the efficacy of the postbiotic Probio-Eco in alleviating constipation in humans and mice. A randomized, double-blind, placebo-controlled crossover trial involving 110 adults with chronic constipation (Rome IV criteria) demonstrates that a 3-week Probio-Eco intervention significantly improves constipation symptoms, stool straining, and worry scores. Gut microbiota and metabolomic analyses reveal modulations in specific gut microbiota, succinate, tryptophan derivatives, deoxycholate, propionate, butyrate, and cortisol, correlating with symptom relief. A loperamide-induced mouse model confirms that Probio-Eco and its bioactive components (succinate, 3-indoleacrylic acid, and 5-hydroxytryptophan) alleviate constipation by stimulating mucin-2 secretion, regulating intestinal transport hormones, and promoting anti-inflammatory responses. Multi-omics integration identifies key pathways, including succinate-short-chain fatty acid, tryptophan-5-hydroxytryptophan-serotonin, and tryptophan-3-indoleacrylic acid, driving intestinal homeostasis and motility. These findings highlight the comprehensive efficacy of Probio-Eco and provide robust evidence for its clinical application in constipation management. This study was registered at Chinese Clinical Trial Registry (ChiCTR2100054376).

Baseline abundance of Akkermansia muciniphila and Bacteroides acidifaciens in a healthy state predicts inflammation associated tumorigenesis in the AOM/DSS mouse model

Numerous studies demonstrate that intestinal microbiota contribute to colorectal cancer (CRC), which is often associated with dysbiosis. Most of the data were obtained from studies on CRC patients, making it challenging to determine whether alterations in microbiota are a consequence of the pathology or whether they actively drive its progression. Several studies using laboratory animals suggest that gut microbiota may be involved in both the onset and progression of CRC. In the present study we utilized the azoxymethane-dextran sulfate sodium (AOM/DSS) mouse model of CRC to investigate the contribution of healthy-state microbiota to inflammation-associated tumorigenesis. Two cohorts of C57BL/6 mice harboring different intestinal microbiota demonstrated different susceptibility to AOM/DSS treatment. Sequencing of 16S rRNA bacterial DNA from fecal samples revealed Akkermansia muciniphila and Bacteroides acidifaciens as marker features in the healthy-state microbiota (before AOM/DSS administration), which showed a strong positive correlation with tumor incidence. Moreover, the healthy-state abundance of these markers, considered beneficial bacteria, was strongly positively correlated with the sulfate-reducing bacteria Desulfovibrio fairfieldensis identified as a marker of chronic colitis-associated microbiota. Furthermore, the abundances of these marker features, associated with CRC outcome, correlated with the expression of interferon gamma and nitric oxide synthase 2 genes in colon tissue during the early stage of DSS-induced intestinal inflammation. In contrast to multiple studies demonstrating the anti-inflammatory properties of A. muciniphila and B. acidifaciens, our results point out their potential adverse effect under specific conditions of genotoxicity and inflammation in the intestine. Taken together, our findings suggest a complex, context-dependent role of commensal microbiota in inflammation-associated dysbiosis and CRC.

The current findings on the gut-liver axis and the molecular basis of NAFLD/NASH associated with gut microbiome dysbiosis

Recent research has highlighted the complex relationship between gut microbiota, metabolic pathways, and nonalcoholic fatty liver disease (NAFLD) progression. Gut dysbiosis, commonly observed in NAFLD patients, impairs intestinal permeability, leading to the translocation of bacterial products like lipopolysaccharides, short-chain fatty acids, and ethanol to the liver. These microbiome-associated mechanisms contribute to intestinal and hepatic inflammation, potentially advancing NAFLD to NASH. Dietary habits, particularly those rich in saturated fats and fructose, can modify the microbiome composition, leading to dysbiosis and fatty liver development. Metabolomic approaches have identified unique profiles in NASH patients, with specific metabolites like ethanol linked to disease progression. While bariatric surgery has shown promise in preventing NAFLD progression, the role of gut microbiome and metabolites in this improvement remains to be proven. Understanding these microbiome-related pathways may provide new diagnostic and therapeutic targets for NAFLD and NASH. A comprehensive review of current literature was conducted using multiple medical research databases, including PubMed, Scopus, Web of Science, Embase, Cochrane Library, ClinicalTrials.gov, ScienceDirect, Medline, ProQuest, and Google Scholar. The review focused on studies that examine the relationship between gut microbiota composition, metabolic pathways, and NAFLD progression. Key areas of interest included microbial dysbiosis, endotoxin production, and the influence of diet on gut microbiota. The analysis revealed that gut dysbiosis contributes to NAFLD through several mechanisms, diet significantly influences gut microbiota composition, which in turn affects liver function through the gut-liver axis. High-fat diets can lead to dysbiosis, altering microbial metabolic activities and promoting liver inflammation. Specifically, gut microbiota-mediated generation of saturated fatty acids, such as palmitic acid, can activate liver macrophages and increase TNF-α expression, contributing to NASH development. Different dietary components, including cholesterol, fiber, fat, and carbohydrates, can modulate the gut microbiome and influence NAFLD progression. This gut-liver axis plays a crucial role in maintaining immune homeostasis, with the liver responding to gut-derived bacteria by activating innate and adaptive immune responses. Microbial metabolites, such as bile acids, tryptophan catabolites, and branched-chain amino acids, regulate adipose tissue and intestinal homeostasis, contributing to NASH pathogenesis. Additionally, the microbiome of NASH patients shows an elevated capacity for alcohol production, suggesting similarities between alcoholic steatohepatitis and NASH. These findings indicate that targeting the gut microbiota may be a promising approach for NASH treatment and prevention. Recent research highlights the potential of targeting gut microbiota for managing nonalcoholic fatty liver disease (NAFLD). The gut-liver axis plays a crucial role in NAFLD pathophysiology, with dysbiosis contributing to disease progression. Various therapeutic approaches aimed at modulating gut microbiota have shown promise, including probiotics, prebiotics, synbiotics, fecal microbiota transplantation, and dietary interventions. Probiotics have demonstrated efficacy in human randomized controlled trials, while other interventions require further investigation in clinical settings. These microbiota-targeted therapies may improve NAFLD outcomes through multiple mechanisms, such as reducing inflammation and enhancing metabolic function. Although lifestyle modifications remain the primary recommendation for NAFLD management, microbiota-focused interventions offer a promising alternative for patients struggling to achieve weight loss targets.

Beyond the Gut: Unveiling Butyrate's Global Health Impact Through Gut Health and Dysbiosis-Related Conditions: A Narrative Review

Short-chain fatty acids (SCFAs), mainly produced by gut microbiota through the fermentation process of dietary fibers and proteins, are crucial to human health, with butyrate, a famous four-carbon SCFA, standing out for its inevitably regulatory impact on both gut and immune functions. Within this narrative review, the vital physiological functions of SCFAs were examined, with emphasis on butyrate's role as an energy source for colonocytes and its ability to enhance the gut barrier while exhibiting anti-inflammatory effects. Knowledge of butyrate synthesis, primarily generated by Firmicutes bacteria, can be influenced by diets with specifically high contents of resistant starches and fiber. Butyrate can inhibit histone deacetylase, modulate gene expression, influence immune functionality, and regulate tight junction integrity, supporting the idea of its role in gut barrier preservation. Butyrate possesses systemic anti-inflammatory properties, particularly, its capacity to reduce pro-inflammatory cytokines and maintain immune homeostasis, highlighting its therapeutic potential in managing dysbiosis and inflammatory diseases. Although butyrate absorption into circulation is typically minimal, its broader health implications are substantial, especially regarding obesity and type 2 diabetes through its influence on metabolic regulation and inflammation. Furthermore, this narrative review thoroughly examines butyrate's growing recognition as a modulator of neurological health via its interaction with the gut-brain axis. Additionally, butyrate's neuroprotective effects are mediated through activation of specific G-protein-coupled receptors, such as FFAR3 and GPR109a, and inhibition of histone deacetylases (HDACs). Research indicates that butyrate can alleviate neurological disorders, including Alzheimer's, Parkinson's, autism spectrum disorder, and Huntington's disease, by reducing neuroinflammation, enhancing neurotransmitter modulation, and improving histone acetylation. This focus will help unlock its full therapeutic potential for metabolic and neurological health, rather than exclusively on its well-known benefits for gut health, as these are often interconnected.

Hypercoagulable state and gut microbiota dysbiosis as predictors of poor functional outcomes in acute ischemic stroke patients

Stroke is the second leading cause of death worldwide. Acute ischemic stroke (AIS) patients often exhibit hypercoagulable state and gut microbiota dysbiosis. However, the association between coagulation abnormalities and gut microbiota dysbiosis in AIS patients and their predictive value for poor functional outcomes in AIS has not been investigated. Our study enrolled 95 AIS patients and 81 healthy controls, using 16S rRNA sequencing to analyze gut microbiota composition. Baseline fibrinogen level was found to be an independent risk factor for poor functional outcomes at 90-day follow-up (odds ratio = 2.16, 95% confidence interval: 1.02-4.59, P = 0.044). AIS patients showed significant gut microbiota dysbiosis, with significantly increased Parabacteroides and Alistipes, and decreased Prevotella and Roseburia, associated with coagulation indices. Furthermore, compared with AIS patients with normal coagulation function, those in a hypercoagulable state exhibited a significant increase in Alistipes and a decrease in Prevotella. We identified gut microbial biomarkers consisting of 15 bacteria that predicted poor functional outcome in AIS patients at 90-day follow-up. Coagulation indices improved the predictive performance of these biomarkers. In training and validation cohorts, area under the curve (AUC) values were 0.930 and 0.890 for microbial biomarkers alone, 0.691 and 0.751 for coagulation indices alone, and 0.943 and 0.944 for coagulation indices combined with gut microbial biomarkers. Our study showed that AIS patients with hypercoagulable state had gut microbiota dysbiosis, with Alistipes and Prevotella significantly associated with coagulation indices. A classification model based on coagulation indices and gut microbial biomarkers accurately predicted poor functional outcome in AIS patients at 90-day follow-up.

IMPORTANCE

Acute ischemic stroke (AIS) patients often exhibit hypercoagulable state and gut microbiota dysbiosis. However, the relationship between hypercoagulable state and gut microbiota dysbiosis in AIS patients and their predictive value for poor functional outcomes has not been fully explored. Our study of 95 AIS patients showed that baseline fibrinogen level was an independent risk factor for poor functional outcome at 90-day follow-up in AIS patients. Hypercoagulable state in AIS patients correlates with gut microbiota dysbiosis. AIS patients with hypercoagulable state had increased Alistipes abundance and decreased Prevotella abundance. A classification model based on coagulation indices and gut microbial biomarkers accurately predicted poor functional outcome in AIS patients at 90-day follow-up.

Can poly(butylene succinate) degrade in seawater?

Poly(butylene succinate) (PBSu) is a promising biodegradable polymer in natural environments. However, its biodegradability in marine environments is debatable. It is well known that the biodegradability of biodegradable polymers depends on their molecular weight. In this study, we explored the effect of the molecular weight of PBSu on its biodegradability through biochemical oxygen demand (BOD) testing in seawater. PBSu samples with different molecular weights were prepared by size-exclusion chromatography (SEC). After biodegradation testing, we extracted the residual organic matter from seawater to evaluate changes in the molecular weight by SEC, revealing that PBSu was enzymatically hydrolysed in seawater. Low-molecular-weight (LMW)-PBSu exhibited higher biodegradability in seawater while high-molecular-weight PBSu underwent hydrolysis over an extended period. Moreover, we evaluated the changes in microbial flora during biodegradation testing using amplicon sequencing of the culture media, which revealed that the microbial flora changed in response to the presence of PBSu. These findings suggest that PBSu is a potential biodegradable polymer at a sufficiently low molecular weight or when the degradation period is sufficiently long.

The role of polysaccharides in immune regulation through gut microbiota: mechanisms and implications

Polysaccharides, as complex carbohydrates, play a pivotal role in immune modulation and interactions with the gut microbiota. The diverse array of dietary polysaccharides influences gut microbial ecology, impacting immune responses, metabolism, and overall well-being. Despite their recognized benefits, there is limited understanding of the precise mechanisms by which polysaccharides modulate the immune system through the gut microbiota. A comprehensive search of Web of Science, PubMed, Google Scholar, and Embase up to May 2024 was conducted to identify relevant studies. This study employs a systematic approach to explore the interplay between polysaccharides and the gut microbiota, focusing on cytokine-mediated and short-chain fatty acid (SCFA)-mediated pathways. The findings underscore the significant role of polysaccharides in shaping the composition and function of the gut microbiota, thereby influencing immune regulation and metabolic processes. However, further research is necessary to elucidate the detailed molecular mechanisms and translate these findings into clinical applications.

Gut microbiota in diabetic-linked polycystic ovarian syndrome: Mechanisms and therapeutic insights

Polycystic ovarian syndrome (PCOS) is a complex multisystem disorder prevalent among women of reproductive age, commonly marked by insulin resistance, hyperinsulinemia, and metabolic disruptions such as hypertension and dyslipidemia, which elevate risks of cardiovascular disease and hepatic steatosis. Recent advances underscore the gut microbiome's critical role in modulating insulin resistance and metabolic homeostasis in PCOS. This review highlights novel insights into gut dysbiosis-driven inflammation, gut-brain hormonal signaling, and immune modulation as underlying mechanisms connecting PCOS with metabolic dysfunction and diabetes. We comprehensively analyzed studies up to September 2024 on gut microbiota, diabetes, PCOS, and metformin, exploring emerging perspectives on the microbiome's therapeutic potential in managing PCOS. Metformin's dual role in insulin sensitivity improvement and gut microbiome modulation is emphasized, including its indirect effects on weight management. This review also identifies gaps in current research, urging a shift toward precision therapies targeting microbiome-related pathways in PCOS. Further exploration of the gut-brain axis, pathogen-associated molecular patterns, and the need for controlled clinical trials are discussed to enhance therapeutic approaches.

The Role of Short-Chain Fatty Acids in Metabolic Dysfunction-Associated Steatotic Liver Disease and Other Metabolic Diseases

With its increasing prevalence, metabolic dysfunction-associated steatotic liver disease (MASLD) has emerged as a major global public health concern over the past few decades. Growing evidence has proposed the microbiota-derived metabolites short-chain fatty acids (SCFAs) as a potential factor in the pathophysiology of MASLD and related metabolic conditions, such as obesity and type 2 diabetes mellitus (T2DM). By influencing key pathways involved in energy homeostasis, insulin sensitivity, and inflammation, SCFAs play an important role in gut microbiota composition, intestinal barrier function, immune modulation, and direct metabolic signaling. Furthermore, recent animal and human studies on therapeutic strategies targeting SCFAs demonstrate their potential for treating these metabolic disorders.

The hypoglycemic effect of mulberry (Morus atropurpurea) fruit lacking fructose and glucose by regulation of the gut microbiota

Mulberries are known to be rich in hypoglycemic active substances such as anthocyanins and dietary fiber, which primarily aid in regulating gut microbiota. However, their high sugar content, such as fructose, hinders their application in hypoglycemic functional foods. This research utilized microbial fermentation technology to remove the fructose and glucose in mulberries (FM), subsequently evaluating their hypoglycemic properties and balancing gut microbiota. Results indicated that administering varying doses of FM to type 2 diabetic mice for five weeks notably decreased blood sugar and insulin levels, improved dyslipidemia and insulin resistance, enhanced antioxidant capacity, repaired organ damage, and regulated hypoglycemic activity by influencing mRNA expression of key signaling factors in the PI3K/Akt and AMPK pathways. Analysis of the intestinal microbiota composition revealed that FM can modulate specific bacterial populations, increasing beneficial bacteria like Lactobacillus, Bifidobacterium and Akkermansia while inhibiting harmful bacteria like Escherichia-Shigella and Helicobacter. This restoration of the intestinal microecological balance helped regulate host sugar metabolism homeostasis and affect the secretion of short chain fatty acid (SCFA) synthase in the gut microbiota to increase the production of SCFAs. These findings offer significant support for the potential use of FM in the treatment of diabetes.

Remodeling of Gut Microbiome of Pakistani Expats in China After Ramadan Fasting

Time-restricted intermittent fasting (TRIF) has gained popularity as an intervention for addressing overweight, obesity, and metabolic syndrome. It may influence the composition of the gut microbiome, potentially affecting various microbiome-mediated functions in humans. However, limited studies have been conducted involving TRIF and microbiome on developing and underdeveloped populations. Here, we investigated the impact of TRIF/Ramadan fasting (16:8) on the changes of gut microbiome and functional profiling of microbial communities during and after the month of Ramadan in Pakistani Expats living in China. We observed substantial change in alpha diversity during TRIF; the changes in gut microbial structure by the end of TRIF were higher vis-a-vis in the beginning. Significant differences were observed among individuals; several bacteria (Clostridium perfringens, Coprococcus comes, and Lactococcus lactis, among others) were changed significantly (p < 0.05). Additionally, amino acid, carbohydrate, and energy metabolism; glycan biosynthesis; and metabolism of cofactors and vitamins were significantly affected by TRIF. Pyridoxamine, glutamate, citrulline, arachidonic acid, and short-chain fatty acids showed substantial differences at different time points based on the predicted metabolic pathways. The preliminary results from this study demonstrate significant potential for elucidating the mechanisms underlying gut microbiome stability and enhancing the effectiveness of microbiome-tailored interventions among the Pakistani populace to ameliorate metabolic disorders.

Cecal microbial composition and serum concentration of short-chain fatty acids in laying hens fed different fiber sources

The intestinal microbiota is widely recognized as an integral factor in host health, metabolism, and immunity. In this study, the impact of dietary fiber sources on the intestinal microbiota and the production of short-chain fatty acids (SCFAs) was evaluated in Lohmann White laying hens. The hens were divided into four treatment groups: a control diet without fiber, a diet with wheat bran (mixed fibers), a diet with insoluble fiber (cellulose), and a diet with soluble fiber (pectin), with six replicates of four hens each. Cecal content from 24 hens was analyzed using 16 S rRNA sequencing, while SCFA concentrations were measured in blood serum. Alpha diversity analysis revealed significant variations in microbial richness and diversity among treatments, with higher species richness observed in hens fed wheat bran and cellulose, as indicated by Shannon indices. Principal Coordinates Analysis (PCoA) showed significant differences in microbial composition between the control group and the fiber-supplemented groups. The predominant phyla were Bacteroidetes, Campilobacterota, Firmicutes, and Spirochaetota, with a notable increase in Bacteroidetes in fiber-supplemented groups. Regarding SCFAs, fiber inclusion increased acetic and propionic acid concentrations compared to the control group. Diets with mixed fibers (wheat bran) resulted in the highest acetic acid levels, while propionic acid was most abundant in hens fed soluble fiber (pectin). These findings demonstrate that dietary fiber inclusion to laying hens enhances microbial diversity, stimulates SCFA production, and contributes to host metabolism and health.

The role of kratom (Mitragyna speciosa Korth.) extract in medical foods for obese patients: Effects on gut microbiota in a colon model

Kratom (Mitragyna speciosa Korth.), rich in mitragynine and polyphenols, suppresses and affects the metabolism of macronutrients, making it a functional ingredient in medical food for obese patients. This research focuses on the formulation of a kratom-supplemented medical food (MKT) and its effects on the gut microbiota of obese patients using in vitro fecal fermentation, as well as the production of their metabolites in a simulated human colon system. The 16S rRNA gene sequencing and studies on α- and β-diversity revealed favorable outcomes for MKT, demonstrating the promotion of beneficial bacteria and the suppression of pathogens in obese patients. However, the commercial medical food (MC) resulted in the production of more short-chain fatty acids. In conclusion, the developed kratom-supplemented formula shows potential for use in the diets of obese patients. However, further investigation through animal and human trials is needed to confirm its safety and effectiveness.

Metabolic network reconstruction as a resource for analyzing Salmonella Typhimurium SL1344 growth in the mouse intestine

Nontyphoidal Salmonella strains (NTS) are among the most common foodborne enteropathogens and constitute a major cause of global morbidity and mortality, imposing a substantial burden on global health. The increasing antibiotic resistance of NTS bacteria has attracted a lot of research on understanding their modus operandi during infection. Growth in the gut lumen is a critical phase of the NTS infection. This might offer opportunities for intervention. However, the metabolic richness of the gut lumen environment and the inherent complexity and robustness of the metabolism of NTS bacteria call for modeling approaches to guide research efforts. In this study, we reconstructed a thermodynamically constrained and context-specific genome-scale metabolic model (GEM) for S. Typhimurium SL1344, a model strain well-studied in infection research. We combined sequence annotation, optimization methods and in vitro and in vivo experimental data. We used GEM to explore the nutritional requirements, the growth limiting metabolic genes, and the metabolic pathway usage of NTS bacteria in a rich environment simulating the murine gut. This work provides insight and hypotheses on the biochemical capabilities and requirements of SL1344 beyond the knowledge acquired through conventional sequence annotation and can inform future research aimed at better understanding NTS metabolism and identifying potential targets for infection prevention.

When short-chain fatty acids meet type 2 diabetes mellitus: Revealing mechanisms, envisioning therapies

Evidence is accumulating that short-chain fatty acids (SCFAs) produced by the gut microbiota play pivotal roles in host metabolism. They contribute to the metabolic regulation and energy homeostasis of the host not only by preserving intestinal health and serving as energy substrates but also by entering the systemic circulation as signaling molecules, affecting the gut-brain axis and neuroendocrine-immune network. This review critically summarizes the current knowledge regarding the effects of SCFAs in the fine-tuning of the pathogenesis of type 2 diabetes mellitus (T2DM) and insulin resistance, with an emphasis on the complex relationships among diet, microbiota-derived metabolites, T2DM inflammation, glucose metabolism, and the underlying mechanisms involved. We hold an optimistic view that elucidating how diet can influence gut bacterial composition and activity, SCFA production, and metabolic functions in the host will advance our understanding of the mutual interactions of the intestinal microbiota with other metabolically active organs, and may pave the way for harnessing these pathways to develop novel personalized therapeutics for glucometabolic disorders.

Association between plasma short-chain fatty acids and inflammation in human immunodeficiency virus-associated neurocognitive disorder: a pilot study

BACKGROUND AND AIMS

Short-chain fatty acids (SCFAs), key metabolites produced by gut microbiota, have neuroprotective effects in neurodegenerative diseases by modulating immune responses. However, their role in human immunodeficiency virus (HIV)-associated neurocognitive disorder (HAND) remains largely unexplored.

METHODS

We recruited HAND patients, HIV Control, and healthy controls (HC). Plasma SCFAs and SCFA-producing gut microbiota were quantified via gas chromatography-mass spectrometry and fecal metagenomic analysis. Inflammatory cytokine levels were measured using liquid chromatography. Receiver operating characteristic (ROC) curves were generated to evaluate the predictive accuracy of SCFAs for HAND.

RESULTS

Plasma SCFAs were significantly reduced in HAND patients, correlating with a decrease in SCFA-producing gut bacteria, such as Prevotella and its related species. Reduced SCFAs were positively correlated with pro-inflammatory cytokines and cognitive impairment, while being negatively correlated with anti-inflammatory cytokines. ROC curve analysis demonstrated that several SCFAs exhibited strong predictive accuracy for HAND status.

CONCLUSIONS

SCFAs may influence cognitive function by modulating inflammatory responses, and identifies plasma SCFAs as potential biomarkers and therapeutic targets for HAND. Further investigation is needed to delineate the mechanisms that SCFAs influence HAND pathology.

Gut microbiome alterations precede graft rejection in kidney transplantation patients

Kidney transplantation (KT) is the best treatment for end-stage kidney disease, with graft survival critically affected by the recipient's immune response. The role of the gut microbiome in modulating this immune response remains underexplored. Our study investigates how microbiome alterations might associate with allograft rejection by analyzing the gut microbiome using 16S rRNA gene amplicon sequencing of a multicenter prospective study involving 562 samples from 245 individuals of which 217 received KT. Overall, gut microbiome composition showed gradual recovery post-KT, mirroring CKD-to-health transition as indicated by an increase of Shannon diversity. Prior to graft rejection, we observed a decrease in microbial diversity and SCFA-producing taxa. Functional analysis highlighted a decreased potential for SCFA production in patients preceding the rejection event, validated by quantitative PCR for the production potential of propionate and butyrate. Post-rejection analysis revealed normalization of these microbiome features. Comparison to published microbiome signatures from CKD patients demonstrated a partial overlap of the microbiome alterations preceding graft rejection with the alterations typically found in CKD. Our findings suggest that alterations in gut microbiome composition and function may precede and influence KT rejection, suggesting potential implications as biomarkers or for early therapeutic microbiome-targeting interventions.

Metabolic outcomes of Cordyceps fungus and Goji plant polysaccharides during in vitro human fecal fermentation

This study was to assess the digestion and colonic fermentation of two bioactive polysaccharides, EPS-LM and LBPS, and the subsequent influences on human gut microbiota through simulated gastrointestinal systems. EPS-LM, an exopolysaccharide isolated from mycelial culture of a medicinal fungus Cordyceps sinensis Cs-HK1, was characterized as a heteropolysaccharide consisting of Man(108):Gal(52.7):Glc(29.2) (molar ratio) with an average molecular weight (MW) 5.513 × 106. LBPS was isolated from a well-known medicinal plant (Lycium barbarum L.) which was also characterized as a heteropolysaccharide (1.236 × 105 MW). Both polysaccharides were highly resistant to saliva, gastric and small-intestine digestion with negligible MW reduction and release of reducing sugars but were quickly degraded to lower MW during in vitro human fecal fermentation. They were consumed as a carbon source by the gut bacteria to produce short-chain fatty acids (SCFAs). In comparison, the carbohydrate content of EPS-LM was more completely consumed than LBPS and there were also notable differences in consumption of specific monosaccharides and production of specific SCFAs, propionic and butyric acid, and relative abundance of gut bacterial populations between EPS-LM and LBPS group. The results suggest that metabolic outcomes and modulating effects of EPS-LM and LBPS on the gut microbiota are highly dependent on their molecular composition.

Treatment of Acute Ulcerative Colitis with Zinc Hyaluronate in Mice

Ulcerative colitis (UC) is a type of inflammatory bowel disease arising from numerous factors, while UC patients face insufficient treatment options and a high incidence of adverse reactions to the current therapies. As a functional food additive, hyaluronic acid plays a certain role in intestinal repair. In this study, we constructed a mouse model of dextran sulfate sodium (DSS)-induced UC to examine the effects and underlying mechanisms of action of zinc hyaluronate (ZnHA) on the pathogenesis of UC. ZnHA effectively alleviated key clinical UC symptoms, such as weight loss, loose stools, and bloody stools. Mechanistically, ZnHA attenuated the expression of inflammatory factors, such as tumor necrosis factor-α, interleukin (IL)-6, and myeloperoxidase while upregulating the expression of IL-10. Furthermore, through intestinal flora and short-chain fatty acid analyses, ZnHA was found to promote propionic acid production by enriching beneficial bacteria. ZnHA simultaneously enhanced the expression of tight junction proteins, specifically ZO-1 and occludin, thereby restoring intestinal barrier function. Overall, our findings elucidate the therapeutic potential of ZnHA in treating acute UC by inhibiting intestinal inflammation and regulating flora, while also providing further theoretical support for development of hyaluronic acid to treat this disease.

Exploring the microbiota-gut-brain axis: impact on brain structure and function

The microbiota-gut-brain axis (MGBA) plays a significant role in the maintenance of brain structure and function. The MGBA serves as a conduit between the CNS and the ENS, facilitating communication between the emotional and cognitive centers of the brain via diverse pathways. In the initial stages of this review, we will examine the way how MGBA affects neurogenesis, neuronal dendritic morphology, axonal myelination, microglia structure, brain blood barrier (BBB) structure and permeability, and synaptic structure. Furthermore, we will review the potential mechanistic pathways of neuroplasticity through MGBA influence. The short-chain fatty acids (SCFAs) play a pivotal role in the MGBA, where they can modify the BBB. We will therefore discuss how SCFAs can influence microglia, neuronal, and astrocyte function, as well as their role in brain disorders such as Alzheimer's disease (AD), and Parkinson's disease (PD). Subsequently, we will examine the technical strategies employed to study MGBA interactions, including using germ-free (GF) animals, probiotics, fecal microbiota transplantation (FMT), and antibiotics-induced dysbiosis. Finally, we will examine how particular bacterial strains can affect brain structure and function. By gaining a deeper understanding of the MGBA, it may be possible to facilitate research into microbial-based pharmacological interventions and therapeutic strategies for neurological diseases.

Reducing methane emissions by developing low-fumarate high-ethanol eco-friendly rice

Methane in rice paddies is mainly produced by methanogenic communities feeding on carbon from root exudates and debris. However, the dominant root secretion governing methane emissions is not yet identified after decades of studies, even though secreted carbohydrates and organic acids have been shown to contribute to methane emissions. In this study, we discovered that fumarate and ethanol are two major rice-orchestrated secretions and play a key role in regulating methane emissions. Fumarate released in the rhizosphere is metabolized by microorganisms, supporting the growth of methanogenic archaea that produce methane as an end carbon product, while ethanol mitigates methane emissions through inhibition of methanogenic activity and growth as well as reducing fumarate synthesis in the rice root. Furthermore, we elucidated the route of fumarate metabolism in the anoxic rhizospheric zone. We found that fumarate in the rice root is produced from acetate via propionate and succinate, and when released into soil directly is oxidized to propionate before conversion via acetate into methane as the end product. The knowledge on fumarate and ethanol metabolism in rice was then used for hybrid breeding of new rice varieties with the property of low methane emission. Cultivation of these novel rice lines or employing our findings for rice cultivation managements showed up to 70% reductions in methane production from seven paddy field sites during 3 years of cultivation trials. Taken together, these findings offer great possibilities for effective mitigation of the global climatic impact of rice cultivation.

Low molecular weight galactomannan alleviates diarrhea induced by senna leaf in mice via intestinal barrier improvement and gut microbiota modulation

Low molecular weight galactomannan (LMGM), a soluble dietary fibre derived from guar gum, is recognized for its prebiotic functions, including promoting the growth of beneficial intestinal bacteria and the production of short-chain fatty acids, but the mechanism of alleviating diarrhea is not fully understood. This study established an acute diarrhea mouse model using senna leaf decoction and evaluated the therapeutic effects of LMGM by monitoring diarrhea scores, loose stool prevalence, intestinal tissue pathology and gene expression, and gut microbiota composition and metabolisms. The results indicated that LMGM significantly reduced diarrhea scores and loose stool prevalence within two hours post-treatment. Hematoxylin and eosin staining and quantitative real-time polymerase chain reaction analysis revealed that LMGM improved intestinal epithelial structure and up-regulated the expression of zonula occludens 1, occludin, mucin 2, aquaporin 3, and aquaporin 4 in ileum, jejunum, and colon tissues. Moreover, LMGM increased the abundance of beneficial bacteria such as Lactobacillaceae and Lachnospiraceae, and decreased Prevotellaceae in the cecum. Furthermore, LMGM promoted short-chain fatty acid production and reduced ammonia nitrogen and skatole concentrations in the intestinal content. The study suggests that LMGM could serve as a functional prebiotic for diarrhea alleviation, potentially by enhancing the intestinal barrier, modulating water transportation, and regulating the microbiota composition.

Integrated Metabolomics and Proteomics Analysis of the Myocardium in a Mouse Model of Acute Viral Myocarditis

BACKGROUND

Acute viral myocarditis (AVMC) is a common inflammatory disease affecting the myocardium and is often accompanied by severe metabolic disturbances. The molecular mechanisms underlying this disease are complex and not yet fully understood.

METHODS AND RESULTS

Coxsackievirus B3 (CVB3)-induced AVMC mouse models were established. By integrating ultra-high-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS)-based metabolomics and data-independent acquisition (DIA)-based proteomics, we aimed to investigate the global influence of CVB3 infection on the myocardial metabolome and proteome in mice. Based on the criterion of OPLS-DA VIP > 1.0 and p value < 0.05, a total of 149 differential metabolites (DMs) were identified, including 64 upregulated and 85 downregulated metabolites. Bioinformatics analysis revealed that these DMs were mostly enriched in Global and overview maps (Metabolic pathways), Energy metabolism (Sulfur metabolism and Nitrogen metabolism), Amino acid metabolism (Taurine and hypotaurine metabolism, Lysine degradation, and Arginine and proline metabolism), and Carbohydrate metabolism (Propanoate metabolism). Differential analysis also identified 1385 differential proteins (DPs) between the two groups (|Fold Change| >1.5 and p value < 0.05), including 1092 upregulated and 293 downregulated proteins. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of DPs indicated that metabolism-related pathways were significant components of the AVMC process. Next, we mined many DPs engaged in the above metabolic pathways through an integrated analysis of KEGG pathway-based metabolomics and proteomics data.

CONCLUSIONS

Our integrated metabolomics and proteomics analysis revealed characteristic alterations in metabolites and proteins in the myocardium of AVMC, as well as the associations between them. This not only extends the existing understanding of the molecular basis of the pathogenesis and progression of AVMC but also suggests new directions for its treatment.

The gut microbiota in thrombosis

The gut microbiota has emerged as an environmental risk factor that affects thrombotic phenotypes in several cardiovascular diseases. Evidence includes the identification of marker species by sequencing studies of the gut microbiomes of patients with thrombotic disease, the influence of antithrombotic therapies on gut microbial diversity, and preclinical studies in mouse models of thrombosis that have demonstrated the functional effects of the gut microbiota on vascular inflammatory phenotypes and thrombus formation. In addition to impaired gut barrier function promoting low-grade inflammation, gut microbiota-derived metabolites have been shown to act on vascular cell types and promote thrombus formation. Therefore, these meta-organismal pathways that link the metabolic capacities of gut microorganisms with host immune functions have emerged as potential diagnostic markers and novel drug targets. In this Review, we discuss the link between the gut microbiota, its metabolites and thromboembolic diseases.

Precision Dietary Intervention: Gut Microbiome and Meta-metabolome as Functional Readouts

Gut microbiome, the group of commensals residing within the intestinal tract, is closely associated with dietary patterns by interacting with food components. The gut microbiome is modifiable by the diet, and in turn, it utilizes the undigested food components as substrates and generates a group of small molecule-metabolites that addressed as "meta-metabolome" in this review. Profiling and mapping of meta-metabolome could yield insightful information at higher resolution and serve as functional readouts for precision nutrition and formation of personalized dietary strategies. For assessing the meta-metabolome, sample preparation is important, and it should aim for retrieval of gut microbial metabolites as intact as possible. The meta-metabolome can be investigated via untargeted and targeted meta-metabolomics with analytical platforms such as nuclear magnetic resonance spectroscopy and mass spectrometry. Employing flux analysis with meta-metabolomics using available database could further elucidate metabolic pathways that lead to biomarker discovery. In conclusion, integration of gut microbiome and meta-metabolomics is a promising supplementary approach to tailor precision dietary intervention. In this review, relationships among diet, gut microbiome, and meta-metabolome are elucidated, with an emphasis on recent advances in alternative analysis techniques proposed for nutritional research. We hope that this review will provide information for establishing pipelines complementary to traditional approaches for achieving precision dietary intervention.

Short-Chain Fatty Acids: Promising Therapeutic Targets for Respiratory Syncytial Virus Infection

The intestinal microbiota is a complex community of organisms present in the human gastrointestinal tract, some of which can produce short-chain fatty acids (SCFAs) through the fermentation of dietary fiber. SCFAs play a major role in mediating the intestinal microbiota's regulation of host immunity and intestinal homeostasis. Respiratory syncytial virus (RSV) can cause an imbalance between anti-inflammatory and proinflammatory responses in the host. In addition, changes in SCFA levels and the structure of the intestinal microbiota have been observed after RSV infection. Therefore, there may be a link between SCFAs and RSV infection, and SCFAs are expected to be therapeutic targets for RSV infection.

Functional regulation of cytotoxic T cells by gut microbial metabolites

Metabolites from gut microbes have a wide range of functions within the host body. One important function of these metabolites is to either positively or negatively control CD8+ cytotoxic T lymphocytes (CTLs), which can kill cancer and virus-infected cells. In healthy conditions, gut microbes produce a mixture of metabolites that promote CTL activity but also suppress excessive inflammatory responses. However, gut microbial dysbiosis occurs in patients with cancer, and this leads to changes in the production of gut microbial metabolites that can suppress CTL activity, promote inflammatory responses, and/or aid cancer growth. Decreased levels of CTL-promoting metabolites such as short-chain fatty acids, indole metabolites and polyamines but increased levels of CTL-suppressing metabolites, such as certain bile acids along with oncogenic metabolites, have been observed in patients with cancer. This review summarizes the altered production of major microbial metabolites in patients with cancer and discusses the impact of these changes on anti-cancer CTL responses.

Performance improvements and increased ruminal microbial interactions in Angus heifers via supplementation with native rumen bacteria during high-grain challenge

Feedlot cattle may be subjected to digestive disorders, including ruminal acidosis, due to high concentration of grain in their diet. Therefore, novel feeding strategies are required to maximize animal performance and mitigate economic losses in the operation. This study employed a two-period crossover design to assess the effect of direct ruminal administration of native rumen microorganisms (NRM) inoculation on cattle that underwent a high-grain challenge. The NRM inoculation consisted of six microorganisms (1.70 M CFU /day/animal) isolated from the rumen of healthy feedlot cattle: Succinivibrio dextrinosolvens ASCUSBF53, Prevotella albensis ASCUSBF41, Chordicoccus furentiruminis ASCUSBF65, Bacteroides xylanisolvens ASCUSBF52, Clostridium beijerinckii ASCUSBF26, and Syntrophococcus sp. ASCUSBF60. The trial consisted of 16 Angus heifers receiving NRM (n = 8) or a CON (CON = Carrier Buffer; n = 8) inoculation daily for 14-days as pre-challenge while on a high-grain diet and continued daily for a 21-day treatment period. The combined 35 days of microbial supplementation resulted in an improved average daily gain (ADG) of 29% (P = 0.037) and a tendency toward a 19% decrease in the feed efficiency metric, gain to feed ratio (G: F) (P = 0.055). Additionally, administration of NRM to animals on a high-grain diet, improved ruminal microbiome stability (P < 0.001), potentially encouraging the conversion of rumen lactate to propionate over time via the succinate pathway and alleviating metabolic stress.

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.

ISCAZIM: Integrated statistical correlation analysis for zero-inflated microbiome data

Microbiome-metabolome association analysis is critical to reveal the key pairs of gut microbiota and metabolites for discovery of the microbial biomarkers in chronic diseases. However, the characteristics of microbiome data, such as zero inflation, over dispersion, may impair the confidence of association analysis between microbiome and metabolome data. The objectives of this study are to evaluate the strengths and weaknesses of existing statistical methods and to develop a computational framework tailored to the unique characteristics of microbiome data. We designed a computational framework called Integrated Statistical Correlation Analysis for Zero-Inflated Microbiome data (ISCAZIM) that takes account of complicated microbiome data characteristics, including zero inflation rates (ZIRs), dispersion and correlation patterns. ISCAZIM first benchmarked prevalent statistical correlation methods, Pearson, Spearman, zero inflated negative binomial (ZINB) model, mutual information and Maximal Information Coefficient. ISCAZIM then classifies the correlation pattern to linear or non-linear and applies the correlation method according to the ZIRs status. Applying to multiple real-world microbiome-metabolomics data, ISCAZIM is overall more accurate than using a single method with more truly significant association pairs included. Therefore, ISCAZIM will significantly facilitate the association analysis using zero-inflated microbiome data for multi-omics integration.

Tungsten is utilized for lactate consumption and SCFA production by a dominant human gut microbe Eubacterium limosum

Eubacterium limosum is a dominant member of the human gut microbiome and produces short-chain fatty acids (SCFAs). These promote immune system function and inhibit inflammation, making this microbe important for human health. Lactate is a primary source of gut SCFAs but its utilization by E. limosum has not been explored. We show that E. limosum growing on lactate takes up added tungstate rather than molybdate and produces the SCFAs acetate and butyrate, but not propionate. The genes encoding an electron bifurcating, tungsten-containing oxidoreductase (WOR1) and a tungsten-containing formate dehydrogenase (FDH), along with an electron bifurcating lactate dehydrogenase (LCT), lactate permease, and enzymes of the propanediol pathway, are all up-regulated on lactate compared to growth on glucose. Lactate metabolism is controlled by a GntR-family repressor (LctR) and two global regulators, Rex and CcpA, where Rex in part controls W storage and tungstopyranopterin (Tuco) biosynthesis. Tuco-dependent riboswitches, along with CcpA, also control two iron transporters, consistent with the increased iron demand for many iron-containing enzymes, including WOR1 and FDH, involved in SCFA production. From intracellular aldehyde concentrations and the substrate specificity of WOR1, we propose that WOR1 is involved in detoxifying acetaldehyde produced during lactate degradation. Lactate to SCFA conversion by E. limosum is clearly highly tungstocentric and tungsten might be an overlooked micronutrient in the human microbiome and in overall human health.

Oral administration of Bifidobacterium longum and Bifidobacterium infantis ameliorates cefcapene pivoxil-induced attenuation of anti-programmed cell death protein-1 antibody action in mice

Gut bacteria play pivotal roles in the antitumor effects of immune checkpoint inhibitors (ICIs). However, antimicrobial therapy, often necessary for infections in cancer patients, can reduce the efficacy of ICIs. The potential of probiotics to restore ICI efficacy remains uncertain. This study evaluated the effects of Bifidobacterium longum and Bifidobacterium infantis (BLBI) in a CT-26 subcutaneous tumor mouse model treated with anti-programmed cell death protein 1 antibody (αPD-1) and cefcapene pivoxil (CFPN-PI). BALB/c mice received daily oral gavage of CFPN-PI for 5 days before tumor inoculation, followed by weekly αPD-1 administration and tumor growth monitoring. BLBI was administered via ad libitum feeding, mixed in powdered feed. Gut microbiota composition and fecal short-chain fatty acid concentrations were assessed, along with gene expression and immune cell populations in the tumor microenvironment, using quantitative RT-PCR and flow cytometry, respectively. CFPN-PI alone increased tumor growth and attenuated the antitumor effect of αPD-1. In contrast, BLBI inhibited CFPN-PI-induced tumor growth and improved the efficacy of αPD-1. Probiotic treatment increased the stool propionic acid concentration and the number of tumor-infiltrating conventional type 1 dendritic cells. Relative decreases in Bacteroides and Lachnospiraceae _NK4A136_group species and relative increases in Muribaculaceae and Unclassified_f_Oscillospiraceae species correlated with an improved αPD-1 response. These results suggest that probiotic administration may be a new therapeutic strategy to rescue the attenuated efficacy of ICIs in patients with cancer who require antimicrobial therapy.

Early subclinical stages of the inflammatory bowel diseases: insights from human and animal studies

The inflammatory bowel diseases (IBD) occur in genetically susceptible individuals that mount inappropriate immune responses to their microbiota leading to chronic intestinal inflammation. The natural history of IBD progression begins with early subclinical stages of disease that occur before clinical diagnosis. Improved understanding of those early subclinical stages could lead to new or improved strategies for IBD diagnosis, prognostication, or prevention. Here, we review our current understanding of the early subclinical stages of IBD in humans including studies from first-degree relatives of patients with IBD and members of the general population who go on to develop IBD. We also discuss representative mouse models of IBD that can be used to investigate disease dynamics and host-microbiota relationships during these early stages. In particular, we underscore how mouse models of IBD that develop disease later in life with variable penetrance may present valuable opportunities to discern early subclinical mechanisms of disease before histological inflammation and other severe symptoms become apparent.

Microbial Metabolites-induced Epigenetic Modifications for Inhibition of Colorectal Cancer: Current Status and Future Perspectives

Globally, one of the most prevalent cancers is colorectal cancer (CRC). Chemotherapy and surgery are two common conventional CRC therapies that are frequently ineffective and have serious adverse effects. Thus, there is a need for complementary and different therapeutic approaches. The use of microbial metabolites to trigger epigenetic alterations as a way of preventing CRC is one newly emerging field of inquiry. Small chemicals called microbial metabolites, which are made by microbes and capable of altering host cell behaviour, are created. Recent research has demonstrated that these metabolites can lead to epigenetic modifications such as histone modifications, DNA methylation, and non-coding RNA regulation, which can control gene expression and affect cellular behaviour. This review highlights the current knowledge on the epigenetic modification for cancer treatment, immunomodulatory and anti-carcinogenic attributes of microbial metabolites, gut epigenetic targeting system, and the role of dietary fibre and gut microbiota in cancer treatment. It also focuses on short-chain fatty acids, especially butyrates (which are generated by microbes), and their cancer treatment perspective, challenges, and limitations, as well as state-of-the-art research on microbial metabolites-induced epigenetic changes for CRC inhibition. In conclusion, the present work highlights the potential of microbial metabolites-induced epigenetic modifications as a novel therapeutic strategy for CRC suppression and guides future research directions in this dynamic field.

Intratumoral Fusobacterium nucleatum in Pancreatic Cancer: Current and Future Perspectives

The intratumoral microbiome plays a significant role in many cancers, such as lung, pancreatic, and colorectal cancer. Pancreatic cancer (PC) is one of the most lethal malignancies and is often diagnosed at advanced stages. Fusobacterium nucleatum (Fn), an anaerobic Gram-negative bacterium primarily residing in the oral cavity, has garnered significant attention for its emerging role in several extra-oral human diseases and, lately, in pancreatic cancer progression and prognosis. It is now recognized as oncobacterium. Fn engages in pancreatic tumorigenesis and metastasis through multifaceted mechanisms, including immune response modulation, virulence factors, control of cell proliferation, intestinal metabolite interactions, DNA damage, and epithelial-mesenchymal transition. Additionally, compelling research suggests that Fn may exert detrimental effects on cancer treatment outcomes. This paper extends the perspective to pancreatic cancer associated with Fn. The central focus is to unravel the oncogenomic changes driven by Fn in colonization, initiation, and promotion of pancreatic cancer development. The presence of Fusobacterium species can be considered a prognostic marker of PC, and it is also correlated to chemoresistance. Furthermore, this review underscores the clinical research significance of Fn as a potential tumor biomarker and therapeutic target, offering a novel outlook on its applicability in cancer detection and prognostic assessment. It is thought that given the role of Fn in tumor formation and metastasis processes via its FadA, FapA, Fap2, and RadD, new therapies for tumor treatment targeting Fn will be developed.

Mucin-driven ecological interactions in an in vitro synthetic community of human gut microbes

Specific human gut microbes inhabit the outer mucus layer of the gastrointestinal tract. Certain residents of this niche can degrade the large and complex mucin glycoproteins that constitute this layer and utilise the degradation products for their metabolism. In turn, this microbial mucin degradation drives specific microbiological ecological interactions in the human gut mucus layer. However, the exact nature of these interactions remains unknown. In this study, we designed and studied an in vitro mucin-degrading synthetic community that included mucin O-glycan degraders and cross-feeding microorganisms by monitoring community composition and dynamics through a combination of 16S rRNA gene amplicon sequencing and qPCR, mucin glycan degradation with PGC-LC-MS/MS, production of mucin-degrading enzymes and other proteins through metaproteomics, and metabolite production with HPLC. We demonstrated that specialist and generalist mucin O-glycan degraders stably co-exist and found evidence for cross-feeding relationships. Cross-feeding on the products of mucin degradation by other gut microbes resulted in butyrate production, hydrogenotrophic acetogenesis, sulfate reduction and methanogenesis. Metaproteomics analysis revealed that mucin glycan degraders Akkermansia muciniphila, Bacteroides spp. and Ruminococcus torques together contributed 92% of the total mucin O-glycan degrading enzyme pool of this community. Furthermore, comparative proteomics showed that in response to cultivation in a community compared to monoculture, mucin glycan degraders increased carbohydrate-active enzymes whereas we also found indications for niche differentiation. These results confirm the complexity of mucin-driven microbiological ecological interactions and the intricate role of carbohydrate-active enzymes in the human gut mucus layer.

Fructo-oligosaccharides promote butyrate production over citrus pectin during in vitro fermentation by colonic inoculum from pig

OBJECTIVES

Fructo-oligosaccharide (FOS) and citrus pectin (CP) are soluble fibers with different chemical composition. However, their fermentation pattern in the large intestine remains unclear.

METHODS

An in vitro batch fermentation using colonic digesta from pigs as inoculum was employed to investigate the fermentation dynamics of FOS and CP. The monosaccharides and SCFAs contents were assayed by high-performance liquid chromatography and gas chromatography, respectively. And the microbiota community was assessed by 16S rRNA gene high-throughput sequencing.

RESULTS

Both FOS and CP were degraded after 6 h; FOS to a negligible level. The FOS group showed higher abundances of butyrate-producing bacteria such as Eubacterium rectale, Roseburia faecis and Coprococcus comes and butyrate compared to CP. CP stimulated the growth of pectinolytic microbes Lachnospira pectinoschiza, succinate-producing bacteria Succinivibrio dextrinosolvens, succinate-utilizing bacteria Phascolarctobacterium succinatutens and the production of acetate and propionate compared to FOS. Moreover, the relative abundances of key enzymes (e.g. butyrate kinase) involved in butyrate formation via the butyrate kinase route were upregulated in the FOS group, and the key enzymes (e.g. acetyl-CoA synthetase) associated with propionate production through the succinate pathway were upregulated in the CP group.

CONCLUSIONS

FOS was preferable for fermentation by butyrate-producing bacteria to yield a higher level of butyrate via the butyrate kinase pathway, while CP enhanced the cross-feeding of succinate-producing and succinate-utilizing bacteria to form propionate through the succinate pathway. These findings deepen our understanding of the fermentation characteristics of the soluble fibers, and also provide guidelines for fiber choice in precisely modulating the microbial composition and metabolism in large intestine.

Gut-Brain Axis a Key Player to Control Gut Dysbiosis in Neurological Diseases

Parkinson's disease is a chronic neuropathy characterised by the formation of Lewy bodies (misfolded alpha-synuclein) in dopaminergic neurons of the substantia nigra and other parts of the brain. Dopaminergic neurons play a vital role in generating both motor and non-motor symptoms. Finding therapeutic targets for Parkinson's disease (PD) is hindered due to an incomplete understanding of the disease's pathophysiology. Existing evidence suggests that the gut microbiota participates in the pathogenesis of PD via immunological, neuroendocrine, and direct neural mechanisms. Gut microbial dysbiosis triggers the loss of dopaminergic neurons via mitochondrial dysfunction. Gut dysbiosis triggers bacterial overgrowth in the small intestine, which increases the permeability barrier and induces systemic inflammation. It results in excessive stimulation of the innate immune system. In addition to that, activation of enteric neurons and enteric glial cells initiates the aggregation of alpha-synuclein. This alpha-synucleinopathy thus affects all levels of the brain-gut axis, including the central, autonomic, and enteric nervous systems. Though the neurobiological signaling cascade between the gut microbiome and the central nervous system is poorly understood, gut microbial metabolites may serve as a promising therapeutic strategy for PD. This article summarises all the known possible ways of bidirectional signal communication, i.e., the "gut-brain axis," where microbes from the middle gut interact with the brain and vice versa, and highlights a unique way to treat neurodegenerative diseases by maintaining homeostasis. The tenth cranial nerve (vagus nerve) plays a significant part in this signal communication. However, the leading regulatory factor for this axis is a diet that helps with microbial colonisation and brain function. Short-chain fatty acids (SCFAs), derived from microbially fermented dietary fibres, link host nutrition to maintain intestinal homeostasis. In addition to that, probiotics modulate cognitive function and the metabolic and behavioural conditions of the body. As technology advances, new techniques will emerge to study the tie-up between gut microbes and neuronal diseases.

Inside the microbial black box: a redox-centric framework for deciphering microbial metabolism

Microbial metabolism influences the global climate and human health and is governed by the balance between NADH and NAD+ through redox reactions. Historically, oxidative (i.e., catabolism) and reductive (i.e., fermentation) pathways have been studied in isolation, obscuring the complete metabolic picture. However, new omics technologies and biotechnological tools now allow an integrated system-level understanding of the drivers of microbial metabolism through observation and manipulation of redox reactions. Here we present perspectives on the importance of viewing microbial metabolism as the dynamic interplay between oxidative and reductive processes and apply this framework to diverse microbial systems. Additionally, we highlight novel biotechnologies to monitor and manipulate microbial redox status to control metabolism in unprecedented ways. This redox-focused systems biology framework enables a more mechanistic understanding of microbial metabolism.

Hypoglycemic effects of a new heteropolysaccharide from common bean (Phaseolus vulgaris L.) seeds in type 2 diabetes mellitus mice via modulating gut microbiota

Type 2 diabetes poses significant health issues worldwide; however, relatively few effective treatment strategies are currently available. This research seeks to explore the potential hypoglycemic impact of compounds derived from common bean (Phaseolus vulgaris L.) by structurally characterizing a new type of heteropolysaccharide (CIE2-F) and evaluating its hypoglycemic effects in a murine model. CIE2-F primarily comprises 10 monosaccharides, Mw: 9.25 × 105 Da. The polysaccharide exhibited significant anti-obesity effects, alleviated pathological liver damage, and reduced hyperglycemia. In addition, the polysaccharide mitigated insulin resistance and regulated dyslipidemia by increasing serum HDL-C and reducing LDL-C, total cholesterol, and triglycerides in diabetic mice. Furthermore, 16S rRNA sequencing revealed that CIE2-F enriched beneficial gut microbiota, including Akkermansia and Verrucomicrobia, while decreasing pathogenic bacteria.

Recent advances on the impact of protumorigenic dietary‐derived bacterial metabolites on the intestinal stem cell

The links between diet, microbiome, immunity, and colorectal cancer are well established. The metabolite output of the microbiome, which has a large influence over host health and disease, is related to the composition of the diet. These metabolites subsequently impact on immune and intestinal epithelial either directly or indirectly via production of secondary metabolites. Here we summarize the latest findings and briefly discuss their potential for managing disease risk.