Human Gut Microbiome: Function Matters

Cross-feeding-based rational design of a probiotic combination of Bacterides xylanisolvens and Clostridium butyricum therapy for metabolic diseases

The human gut microbiota has gained interest as an environmental factor that contributes to health or disease. The development of next-generation live biotherapeutic products (LBPs) is a promising strategy to modulate the gut microbiota and improve human health. In this study, we identified a novel cross-feeding interaction between Bacteroides xylanisolvens and Clostridium butyricum and developed their combination into a novel LBP for treating metabolic syndrome. Using in-silico analysis and in vitro experiments, we demonstrated that B. xylanisolvens supported the growth and butyrate production of C. butyricum by supplying folate, while C. butyricum reciprocated by providing pABA for folate biosynthesis. Animal gavage experiments showed that the two-strain combination LBP exhibited superior therapeutic efficacy against metabolic disorders in high-fat diet-induced obese (DIO) mice compared to either single-strain treatment. Further omics-based analyses revealed that the single-strain treatments exhibited distinct taxonomic preferences in modulating the gut microbiota, whereas the combination LBP achieved more balanced modulation to preserve taxonomic diversity to a greater extent, thereby enhancing the stability and resilience of the gut microbiome. Moreover, the two-strain combinations more effectively restored gut microbial functions by reducing disease-associated pathways and opportunistic pathogen abundance. This work demonstrates the development of new LBP therapy for metabolic diseases from cross-feeding microbial pairs which exerted better self-stability and robust efficacy in complex intestinal environments compared to conventional single-strain LBPs.

The gut-brain axis in early Parkinson's disease: from prodrome to prevention

Parkinson's disease is the second most common neurodegenerative disorder and fastest growing neurological condition worldwide, yet its etiology and progression remain poorly understood. This disorder is characterized pathologically by the prion-like spread of misfolded neuronal alpha-synuclein proteins in specific brain regions leading to Lewy body formation, neurodegeneration, and progressive neurological impairment. It is unclear what triggers Parkinson's and where α-synuclein protein aggregation begins, although proposed induction sites include the olfactory bulb and dorsal motor nucleus of the vagus nerve. Within the last 20 years, there has been increasing evidence that Parkinson's could be triggered by early microbiome changes and α-synuclein accumulation in the gastrointestinal system. Gut microbiota dysbiosis that alters gastrointestinal motility, permeability, and inflammation could enable prion-like spread of α-synuclein from the gut-to-brain via the enteric nervous system. Individuals with isolated rapid eye movement sleep behavior disorder have a high likelihood of developing Parkinson's and might represent a prodromal 'gut-first' subtype of the condition. The gut-first model of Parkinson's offers novel gut-based therapeutic avenues, such as anti-, pre-, and pro-biotic preparations and fecal microbiota transplants. Crucially, gut-based interventions offer an avenue to treat Parkinson's at early prodromal stages with the aim of mitigating evolution to clinically recognizable Parkinson's disease characterized by motor impairment.

Gut microbiota-derived extracellular vesicles form a distinct entity from gut microbiota

Extracellular vesicles (EVs), nanoparticles secreted by both gram-negative and gram-positive bacteria, carry various biomolecules and cross biological barriers. Gut microbiota-derived EVs are currently being investigated as a communication mechanism between the microbiota and the host. Few clinical studies, however, have investigated gut microbiota-derived EVs. Here, we show that machine learning models were able to accurately distinguish gut microbiota and respective microbiota-derived EV samples according to their taxonomic composition both within each data set (area under the curve [AUC] 0.764-1.00) and in a cross-study setting (AUC 0.701-0.997). These results show that gut microbiota-derived EVs form a distinct taxonomic entity from gut microbiota. Thus, conventional gut microbiota composition may not correctly reflect communication between the gut microbiota and the host unless microbiota-derived EVs are reported separately.IMPORTANCEGut microbiota-derived extracellular vesicles (EVs) have been suggested to be a communication mechanism between the gut microbiota and the human body. However, the data on EV secretion from the gut microbiota remain limited. To investigate and compare the composition of gut microbiota-derived EVs to gut microbiota composition, we used a machine learning approach to classify 16S rRNA gene sequencing data in seven clinical data sets incorporating both gut microbiota and gut microbiota-derived EV samples. The results of the study show that microbiota-derived EVs form a separate taxonomic entity from the gut microbiota. Gut microbiota-derived EVs should be included in clinical studies that investigate gut microbiota to gain more comprehensive insight into gut microbiota-host communication.

Temporal network analysis of gut microbiota unveils aging trajectories associated with colon cancer

The human gut microbiome's role in colorectal cancer (CRC) pathogenesis has gained increasing recognition. This study aimed to delineate the microbiome characteristics that distinguish CRC patients from healthy individuals, while also evaluating the influence of aging, through a comprehensive metagenomic approach. The study analyzed a cohort of 80 CRC patients and 80 matched healthy controls, dividing participants into a normal and a CRC group, further categorized by age into young, middle-aged, and old-aged subgroups. Extensive metagenomic sequencing of fecal samples allowed for the exploration of both the structural and functional profiles of the microbiome, with findings validated in an independent cohort to ensure robustness. Our results highlight notable differences in microbiome composition between CRC patients and healthy individuals, which exhibit age-dependent variations. Specifically, a higher prevalence of pathogenic bacteria, such as Bacteroides vulgatus, known to drive inflammation and carcinogenesis, was observed in CRC patients, alongside a reduction in beneficial microbes, including Lactobacillus. Functionally, the CRC-associated microbiome showed an increase in pathways related to DNA repair, cell cycle regulation, and metabolic activities, such as the Citrate cycle and Galactose metabolism, underscoring distinct microbial alterations in CRC patients that could influence disease onset and progression. These insights lay a foundation for future research into microbiome-based diagnostics and treatments for CRC.

IMPORTANCE

This study underscores the critical role of the gut microbiome in colorectal cancer (CRC) pathogenesis, particularly in the context of aging. By identifying age-specific microbial biomarkers and functional pathways associated with CRC, our findings provide novel insights into how microbiome composition and metabolic activities influence disease progression. These discoveries pave the way for developing personalized microbiome-based diagnostic tools and therapeutic strategies, potentially improving CRC prevention and treatment outcomes across different age groups. Understanding these microbial dynamics could also inform interventions targeting gut microbiota to mitigate CRC risk and progression.

Intestinal permeability of N-acetylcysteine is driven by gut microbiota-dependent cysteine palmitoylation

Trillions of intestinal microbiota are essential to the permeability of orally administered drugs. However, identifying microbial-drug interactions remains challenging due to the highly variable composition of intestinal flora among individuals. Using single-pass intestinal perfusion (SPIP) platform, we establish the microbiota-based permeability screening framework involving germ-free (GF) and specific-pathogen-free (SPF) rats to compare in-situ Peff-values and metabolomic profiles of 32 orally administered drugs with disputable classifications of permeability, prior to the verifications of bioorthogonal chemistry and LC-MS/MS. In contrast with SPF controls, N-Acetylcysteine (NAC) exhibits significantly increased permeability in GF rats, which is inversely related to reduced cysteine-3-ketosphinganine by Bacteroides. To further validate these microbiome features, we integrate clinical descriptors from a prospective cohort of 319 participants to optimize a 15-feature eXtreme Gradient Boosting (XGB) model, which reveal that cysteine palmitoylation by intestinal microbiota has significantly affected NAC permeability. By comparison of net reclassification improvement (NRI) index, this machine learning (ML) model of clinical prediction model encompassing intestinal microbial features outperforms other three commercial models in predicting NAC permeability. Here we have developed an intestinal microbiota-based strategy to evaluate uncharacterized NAC permeability, thus accounting for its discordant biopharmaceutics classification.

Metagenomic Comparison of Gut Microbes of Lemur catta in Captive and Semi-Free-Range Environments

In order to protect endangered species, many zoos adopt diverse rearing models to achieve optimal conservation outcomes. This study employed metagenomic approaches to assess differences in the fecal microbiome of captive and semi-free-ranging ring-tailed lemurs (Lemur catta). The results show that captivity significantly altered the microbial community structure. The inter-individual variability in the microbial community within the captive-bred (CB) group was lower than that in the semi-free-ranging (FR) group, yet these individuals harbored a higher abundance of potential pathogens (Treponema_D). In contrast, microbial genera associated with fiber degradation and short-chain fatty acid production in the FR group were significantly elevated (Faecalibacterium, Roseburia, and Megamonas) as compared to the CB group. Environmental variations between the two rearing systems led to distinct profiles in microbial functions and carbohydrate-active enzyme gene composition. Notably, the FR group of lemurs exhibited an increased abundance of enzyme genes associated with the degradation of complex polysaccharides (cellulose, hemicellulose, and pectin), suggesting that their diet, rich in natural plant fibers, enhances the capacity of their gut microbiota to extract essential energy and nutrients. Conversely, the CB group displayed a more homogeneous microbial community with a higher prevalence of potential pathogens, implying that a captive lifestyle may negatively impact gastrointestinal health. These findings offer valuable insights into the influence of rearing conditions on gut microbial ecology and its potential implications for the health management of ring-tailed lemurs.

Advances in in vitro cultivation techniques for comprehensive analysis of human gut microbiome

The role of gut microbiota in human health and disease is becoming increasingly recognized. Historically, the impact of human gut microbiota on health has been studied using clinical trials and animal models. However, clinical studies often struggle with controlling variables and pinpointing disease-causing factors, while animal models fall short of accurately replicating the human gut environment. Additionally, continuous sample collection for gut microbiota analysis in vivo presents significant ethical and technical challenges. To address these limitations, in vitro fermentation models have emerged as promising alternatives. These models aim to simulate the structural and functional characteristics of the human gut in a controlled setting, offering valuable insights into microbial behavior. This review highlights current knowledge and technological advances in in vitro cultivation systems for human gut microbiota, focusing on key elements such as three-dimensional scaffolds, culture media, fermentation systems, and analytical techniques. By examining these components, the review establishes a framework for improving methods to cultivate and study human gut microbiota, enhancing research methodologies for better understanding microbial interactions, behavior, and adaptation in diverse environments.

Operational Taxon-Function Framework in MetaX: Unveiling Taxonomic and Functional Associations in Metaproteomics

Metaproteomics analyzes the functional dynamics of microbial communities by identifying peptides and mapping them to the most likely proteins and taxa. One challenge in this field lies in seamlessly integrating taxonomic and functional annotations to accurately represent the contributions of individual microbial taxa to functional diversity. We introduce MetaX, a comprehensive tool for analyzing taxon-function relationships in metaproteomics by mapping peptides to their lowest common ancestors and assigning functions based on proportional thresholds, ensuring accurate peptide-level mappings. Importantly, MetaX introduces the Operational Taxon-Function (OTF), a new conceptual unit for exploring microbial roles and interactions within ecosystems. Additionally, MetaX includes extensive statistical and visualization tools, establishing it as a robust platform for metaproteomics analysis. We validated MetaX by reanalyzing ex vivo gut microbiome metaproteomic data exposed to various sweeteners, yielding more detailed results than traditional protein analysis. Furthermore, using the peptide-centric approach and OTF, we observed that Parabacteroides distasonis significantly responds to certain sweeteners, highlighting its role in modifying specific metabolic functions. With its intuitive, user-friendly interface, MetaX facilitates a detailed study of the complex interactions between microbial taxa and their functions in metaproteomics. It enhances our understanding of microbial roles in ecosystems and health.

Co-variation of Host Gene Expression and Gut Microbiome in Intestine-Specific Spp1 Conditional Knockout Mice

Osteopontin, which is a highly phosphorylated and glycosylated acidic secreted protein encoded by the secreted phosphoprotein 1 (Spp1) gene, plays a crucial role in immune regulation, inflammatory responses, and cell adhesion. However, its impact on intestinal gene expression and gut microbiota remains underexplored. In this study, we developed an Spp1 conditional knockout mouse model to investigate alterations in the intestinal transcriptome and microbiome, with particular emphasis on changes in gene expression and predicted metabolic pathways. Our findings demonstrated that Spp1 gene conditional knockout significantly modified the expression of genes involved in immune regulation and lipid metabolism. Moreover, metagenomic analysis revealed marked shifts in gut microbial diversity and predicted the metabolic pathways associated with digestion, absorption, and lipid metabolism. These results suggest that Spp1 is instrumental in maintaining gut microbial equilibrium and in regulating host lipid metabolism and immune responses. This study offers new insights into the role of Spp1 in host-microbiota interactions and the potential foundations for developing related therapeutic strategies.

Perturbed gut microbiota and serum metabolites are associated with progressive renal fibrosis

Introduction

The intricate pathogenesis of renal fibrosis necessitates identifying biomarkers at various stages to facilitate targeted therapeutic interventions, which would enhance patient survival rates and significantly improve prognosis.

Methods

We investigated the changes in gut microbiota and serum metabolites during the early, middle, and late stages of renal fibrosis in rats using 16S rDNA sequencing and UPLC-QTOF/MS-based metabolomics.

Results

We identified 5, 21, and 14 potential gut microbial markers and 19, 23, and 31 potential metabolic markers in the MOD1, MOD2, and MOD4 groups, respectively. Bifidobacterium was identified as a shared microbial marker between the MOD1 and MOD2 groups; Prevotellaceae_NK3B31_group and Bacteroides were identified as shared microbial markers between the MOD2 and MOD4 groups. The pathways of arachidonic acid metabolism and retinol metabolism were found to play a significant role in the modulation of renal fibrosis at 1, 2, and 4 weeks. Notably, the metabolic biomarkers 8,9-EET and 5(S)-HPETE within these pathways emerged as critical determinants influencing renal fibrosis.

Discussion

Our findings demonstrated that the severity of renal fibrosis is associated with dysbiosis of the gut microbiota and alterations in serum metabolites.

Mapping the global research landscape on psoriasis and the gut microbiota: visualization and bibliometric analysis

Background

Psoriasis is a common chronic inflammatory skin disease with a complex pathogenesis. Recently, the role of gut microbiota in psoriasis has attracted increasing attention. A systematic bibliometric analysis of relevant literature is necessary to understand better the current state and development trends in this field.

Materials and methods

The Web of Science Core Collection database was searched for literature indexed from 2004 to October 15, 2024. Bibliometric analysis was conducted using Bibliometrix, CiteSpace (version 6.3.R1), R 4.2.2 with the Bibliometrix package, Scimago Graphica 1.0.45, and VOSviewer (version 1.6.20.0) to visualize publication types, years, authors, countries, institutions, journal sources, references, and keywords.

Results

The development of psoriasis and gut microbiota research can be divided into two phases: slow growth (2004-2014) and rapid development (2014-2024). Lidia Rudnicka is the most active and influential author. China produced the highest number of publications, followed by the United States, which had the highest number of citations per article. The International Journal of Molecular Sciences published the most articles. In contrast, articles in the Journal of Investigative Dermatology, British Journal of Dermatology, and Journal of Allergy and Clinical Immunology were cited over 1,000 times. Keyword and co-citation analyses identified evolving research hotspots. Early studies focused on the association between gut microbiota and comorbid inflammatory diseases. Recent research has delved into specific mechanisms, such as disruption of gut barrier function, short-chain fatty acid metabolism alterations, impaired regulatory T-cell function, and excessive activation of Th17 cells. These mechanisms highlight how gut dysbiosis exacerbates psoriasis patients' systemic inflammation and skin lesions.

Conclusion

The field of psoriasis and gut microbiota research is developing rapidly despite uneven research distribution. This bibliometric evaluation assesses the current state of research and provides new perspectives for understanding the complex interactions between microbes and the host. Future efforts should strengthen international collaboration to deeply explore the mechanisms of gut microbiota's role in psoriasis, especially its potential applications in disease diagnosis and treatment.

The causal impact of gut microbiota and metabolites on myopia and pathological myopia: a mediation Mendelian randomization study

Myopia, a major cause of irreversible visual impairment globally, is projected to affect about 25% of the world's population by 2025. Myopia progresses through childhood and adolescence, necessitating frequent prescription updates. While genetic and environmental factors are well-established contributors to myopia, emerging evidence suggests a significant role of the gut microbiota (GM) in its development, mainly through metabolic interactions. This study utilized a Mendelian Randomization (MR) approach to investigate the causal relationships between GM, metabolites, and myopia and pathological myopia (PM) progression. Using genetic variants as instrumental variables, we analyzed data from extensive genome-wide association studies (GWAS) to assess the impacts of 473 GM taxa and 233 metabolites on myopia risks. Our MR analysis identified specific GM taxa and metabolites with significant causal relationship to myopia and PM. Notably, lipid metabolites were found to mediate the effects of GM on myopia, suggesting a biochemical pathway that could influence ocular development and myopia progression. We also observed significant mediation effects, indicating that specific metabolites might serve as therapeutic targets to modulate myopia progression. The findings highlight the potential of GM and metabolites as novel targets for preventing or managing myopia. This study underscores the importance of further research into the gut-metabolite-eye axis to develop targeted interventions for myopia based on modifying the GM through diet, probiotics, or other means. Future studies should aim to elucidate the specific metabolites involved and their roles in ocular health, potentially offering new avenues for treatment.

Causal relationship between gut microbiota and dental caries: a two-sample mendelian randomization study

BACKGROUND

In recent years, an increasing number of studies have revealed a close relationship between the gut microbiota and a variety of human diseases. At the same time, it has also been shown that dysregulation of the oral microbiota may lead to changes in the gut microbiota. However, it remains unclear whether the gut microbiota affects the occurrence and development of oral diseases. Therefore, the aim of this study was to explore the potential effects of gut microbiota on dental caries and to reveal possible mechanisms of the gut-oral microbiota axis.

METHODS

First, gut microbiota and dental caries data from genome-wide association studies (GWAS) were analyzed using Mendelian randomization analysis. Inverse variance weighted (IVW) was used as the main criterion (P value < 0.05). Then, MR-Egger regression, IVW regression and leave-one-out tests were used to test the reliability and stability of the mendelian randomization results. Finally, the potential mechanisms and significance of the relationship between gut microbiota and dental caries were explored.

RESULTS

The analysis showed that Eubacteriumbrachygroup [odds ratio (OR) = 1.001, 95% confidence interval (CI): 1.000-1.002, P = 0.046] and Terrisporobacter (OR = 1.002, 95% CI: 1.0001-1.0041, P = 0.035) were positively correlated with dental caries. Escherichia.Shigella (OR = 0.997, 95% CI: 0.995-0.999, P = 0.047), Oscillibacter (OR = 0.998, 95% CI: 0.997-0.999, P = 0.038), RuminococcaceaeUCG014 (OR = 0.998, 95% CI: 0.996-0.999, P = 0.044) and Oscillospira (OR = 0.997, 95% CI: 0.995-0.999, P = 0.038) were negatively correlated with dental caries.

CONCLUSION

The present study demonstrated a significant causal relationship between the gut microbiota and the development of dental caries, providing new insights into influencing the development of dental caries by affecting the composition of the gut microbiota.

Faecalibacterium prausnitzii-derived outer membrane vesicles reprogram gut microbiota metabolism to alleviate Porcine Epidemic Diarrhea Virus infection

BACKGROUND

The Porcine Epidemic Diarrhea Virus (PEDV) is one of the major challenges facing the global pig farming industry, and vaccines and treatments have proven difficult in controlling its spread. Faecalibacterium prausnitzii (F.prausnitzii), a key commensal bacterium in the gut, has been recognized as a promising candidate for next-generation probiotics due to its potential wide-ranging health benefits. A decrease in F.prausnitzii abundance has been associated with certain viral infections, suggesting its potential application in preventing intestinal viral infections. In this study, we utilized a piglet model to examine the potential role of F.prausnitzii in PEDV infections.

RESULTS

A piglet model of PEDV infection was established and supplemented with F.prausnitzii, revealing that F.prausnitzii mitigated PEDV infection. Further studies found that outer membrane vesicles (OMVs) are the main functional components of F.prausnitzii, and proteomics, untargeted metabolomics, and small RNA-seq were used to analyze the composition of OMVs. Exhaustion of the gut microbiota demonstrated that the function of Fp. OMVs relies on the presence of the gut microbiota. Additionally, metagenomic analysis indicated that Fp. OMVs altered the gut microbiota composition, enhancing the abundance of Faecalibacterium prausnitzii, Prevotellamassilia timonensis, and Limosilactobacillus reuteri. Untargeted metabolomics analysis showed that Fp. OMVs increased phosphatidylcholine (PC) levels, with PC identified as a key metabolite in alleviating PEDV infection. Single-cell sequencing revealed that PC altered the relative abundance of intestinal cells, increased the number of intestinal epithelial cells, and reduced necroptosis in target cells. PC treatment in infected IPEC-J2 and Vero cells alleviated necroptosis and reduced the activation of the RIPK1-RIPK3-MLKL signaling axis, thereby improving PEDV infection.

CONCLUSION

F.prausnitzii and its OMVs play a critical role in mitigating PEDV infections. These findings provide a promising strategy to ameliorate PEDV infection in piglets. Video Abstract.

Faecal Microbiota Transplantation Modulates Morphine Addictive-Like Behaviours Through Hippocampal Metaplasticity

The microbiota-gut-brain axis has been implicated in the pathology of substance use disorders (SUDs). In light of the brain's capability to reorganize itself in response to intrinsic and extrinsic stimuli, opioid-induced dysbiosis is likely to contribute to addictive behaviour through modulating neuroplasticity. In this study, a faecal microbiota transplantation (FMT) from a saline-donor was performed on morphine-treated rats to evaluate the effects of gut microbiota on morphine-induced metaplasticity and addictive behaviours. Male Wistar rats were treated with subcutaneous injections of 10 mg/kg morphine sulphate every 12 h for 9 days in an effort to induce dependence. The withdrawal syndrome was precipitated by injecting naloxone (1.5 mg/kg, ip) after the final dose of morphine. The tolerance was induced by repeated morphine injections over a period of 7 days (10 mg/kg, once a day, ip). FMT was applied daily through gavage of processed faeces 1 week before and during the morphine treatment. Field potential recordings (i.e., fEPSP) were carried out to assess short-term and long-term synaptic plasticity in the CA1 area of the hippocampus following Schaffer-collateral stimulation. Animals subjected to FMT exhibited significant reductions in naloxone-precipitated withdrawal syndrome (one-way ANOVA, p < 0.05). Tolerance to the analgesic effects of morphine was not affected by FMT (two-way ANOVA, p > 0.05). Following high-frequency stimulation (HFS) to induce long-term potentiation (LTP), a greater fEPSP slope was observed in morphine-treated animals (unpaired t test, p < 0.05). FMT from saline-donor rats diminished morphine-induced augmented LTP (unpaired t test, p < 0.05). These results highlighted the alleviating effects of FMT from saline-donors on morphine-induced metaplasticity and dependence potentially by modulating the dysbiosis of gut microbiota.

Metagenomic analysis characterizes stage-specific gut microbiota in Alzheimer's disease

Alzheimer's disease (AD) is a progressive neurodegenerative disorder with a decade-long preclinical pathological period that can be divided into several stages. Emerging evidence has revealed that the microbiota-gut-brain axis plays an important role in AD pathology. However, the role of gut microbiota in different AD stages has not been well characterized. In this study, we performed fecal shotgun metagenomic analysis on a Chinese cohort with 476 participants across five stages of AD pathology to characterize stage-specific alterations in gut microbiota and evaluate their diagnostic potential. We discovered extensive gut dysbiosis that is associated with neuroinflammation and neurotransmitter dysregulation, with over 10% of microbial species and gene families showing significant alterations during AD progression. Furthermore, we demonstrated that microbial gene families exhibited strong diagnostic capabilities, evidenced by an average AUC of 0.80 in cross-validation and 0.75 in independent external validation. In the optimal model, the most discriminant gene families are primarily involved in the metabolism of carbohydrates, amino acids, energy, glycan and vitamins. We found that stage-specific microbial gene families in AD pathology could be validated by an in vitro gut simulator and were associated with specific genera. We also observed that the gut microbiota could affect the progression of cognitive decline in 5xFAD mice through fecal microbiota transplantation, which could be used for early intervention of AD. Our multi-stage large cohort metagenomic analysis demonstrates that alterations in gut microbiota occur from the very early stages of AD pathology, offering important etiological and diagnostic insights.

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

PURPOSE OF REVIEW

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

RECENT FINDINGS

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

Weizmannia coagulans BC99 Improve Cognitive Impairment Induced by Chronic Sleep Deprivation via Inhibiting the Brain and Intestine's NLRP3 Inflammasome

Weizmannia coagulans BC99, a Gram-positive, spore-forming, lactic acid-producing bacterium is renowned for its resilience and health-promoting properties, W. coagulans BC99 survives harsh environments, including high temperatures and gastric acidity, enabling effective delivery to the intestines. The consequences of chronic sleep deprivation (SD) include memory deficits and gastrointestinal dysfunction. In this study, a chronic sleep deprivation cognitive impairment model was established by using a sleep deprivation instrument and W. coagulans BC99 was given by gavage for 4 weeks to explore the mechanism by which BC99 improves cognitive impairment in sleep-deprived mice. BC99 improved cognitive abnormalities in novel object recognition tests induced by chronic sleep deprivation and showed behavior related to spatial memory in the Morris water maze test. W. coagulans BC99 reduced the heart mass index of sleep-deprived mice, increased the sleep-related neurotransmitters 5-HT and DA, decreased corticosterone and norepinephrine, and increased alpha diversity and community similarity. It reduced the abundance of harmful bacteria such as Olsenella, increased the abundance of beneficial bacteria such as Lactobacillus and Bifidobacterium, and promoted the production of short-chain fatty acids (SCFAs). W. coagulans BC99 also inhibits LPS translocation and the elevation of peripheral inflammatory factors by maintaining the integrity of the intestinal barrier and inhibiting the expression of the NLRP3 signaling pathway in the jejunum, thereby inhibiting the NLRP3 inflammasome in the brain of mice and reducing inflammatory factors in the brain, providing a favorable environment for the recovery of cognitive function. The present study confirmed that W. coagulans BC99 ameliorated cognitive impairment in chronic sleep-deprived mice by improving gut microbiota, especially by promoting SCFAs production and inhibiting the NLRP3 signaling pathway in the jejunum and brain. These findings may help guide the treatment of insomnia or other sleep disorders through dietary strategies.

Deconstruct the link between gut microbiota and neurological diseases: application of Mendelian randomization analysis

Background

Recent research on the gut-brain axis has deepened our understanding of the correlation between gut bacteria and the neurological system. The inflammatory response triggered by gut microbiota may be associated with neurodegenerative diseases. Additionally, the impact of gut microbiota on emotional state, known as the "Gut-mood" relationship, could play a role in depression and anxiety disorders.

Results

This review summarizes recent data on the role of gut-brain axis in the pathophysiology of neuropsychiatric and neurological disorders including epilepsy, schizophrenia, Alzheimer's disease, brain cancer, Parkinson's disease, bipolar disorder and stroke. Also, we conducted a Mendelian randomization study on seven neurological disorders (Epilepsy, schizophrenia, Alzheimer's disease, brain cancer, Parkinson's disease, bipolar disorder and stroke). MR-Egger and MR-PRESSO tests confirmed the robustness of analysis against horizontal pleiotropy.

Conclusions

By comparing the protective and risk factors for neurological disorders found in our research and other researches, we can furtherly determine valuable indicators for disease evolution tracking and potential treatment targets. Future research should explore extensive microbiome genome-wide association study datasets using metagenomics sequencing techniques to deepen our understanding of connections and causality between neurological disorders.

Akkermansia muciniphila: promises and pitfallsfor next-generation beneficial microorganisms

Akkermansia muciniphila, a microorganism ubiquitously colonizing the mucosal layer of the human gut, has garnered significant scientific interest as a promising candidate for probiotic therapeutics. Its persistent identification in both laboratory and living organism studies underscores its potential physiological benefits, positioning it as a bacterium of paramount importance in promoting host health. This review examines the diversity and abundance of gut microbiota members, emphasizing the identification of microbial species engaged in cross-feeding networks with A. muciniphila. Insightful exploration into the mechanisms of cross-feeding, including mucin-derived nutrient exchange and metabolite production, unveils the intricate dynamics shaping microbial community stability. Such interactions contribute not only to the availability of essential nutrients within the gut environment but also to the production of metabolites influencing microbial community dynamics and host health. In conclusion, the cumulative evidence from in vitro and in vivo perspectives substantiates the notion that A. muciniphila holds tremendous promise as a next-generation probiotic. By leveraging its unique physiological benefits, particularly in mucosal health and metabolic regulation, A. muciniphila stands poised to revolutionize the landscape of probiotic interventions for enhanced host well-being.

Advancements in the investigation of gut microbiota-based strategies for stroke prevention and treatment

Stroke represents a predominant cause of mortality and disability on a global scale, impacting millions annually and exerting a considerable strain on healthcare systems. The incidence of stroke exhibits regional variability, with ischemic stroke accounting for the majority of occurrences. Post-stroke complications, such as cognitive impairment, motor dysfunction, and recurrent stroke, profoundly affect patients' quality of life. Recent advancements have elucidated the microbiota-gut-brain axis (MGBA), underscoring the complex interplay between gut health and brain function. Dysbiosis, characterized by an imbalance in gut microbiota, is significantly linked to an elevated risk of stroke and unfavorable outcomes. The MGBA plays a crucial role in modulating immune function, neurotransmitter levels, and metabolic byproducts, which may intensify neuroinflammation and impair cerebral health. This review elucidates the role of MGBA in stroke pathophysiology and explores potential gut-targeted therapeutic strategies to reduce stroke risk and promote recovery, including probiotics, prebiotics, pharmacological interventions, and dietary modifications. However, the current prevention and treatment strategies based on intestinal flora still face many problems, such as the large difference of individual intestinal flora, the stability of efficacy, and the long-term safety need to be considered. Further research needs to be strengthened to promote its better application in clinical practice.

Pathogenic bacterial taxa constitute a substantial portion of fecal microbiota in common migratory bats and birds in Europe

Identifying the wildlife reservoirs of bacterial pathogens, spatially and temporally, is important for assessing the threats to human and the rest of the biosphere. Our objective was to study Europe-wide characteristics of the fecal microbiota of four highly mobile migratory vertebrates, that is, one bat (Pipistrellus nathusii) and three bird species (Turdus merula, Anas platyrhynchos, Columba palumbus). The 351 sample PacBio data set of almost the entire 16S rRNA gene with 438,997 amplicon sequence variants (ASVs) assigned 3,277 bacterial species. A significant proportion of the ASVs were assigned to bacterial genera having species pathogenic to human or animals. These pathogen ASVs accounted for 45% of all the ASVs and statistically were more frequent at higher latitudes and in younger age groups. In 36 samples, more than >90% of all the PacBio reads were assigned to these pathogenic genera. We designate to individuals of these samples a new term, that is, a pathogen bloomer. The pathogen bloomers, which did not display apparent macroscopic disease symptoms, were detected in Nathusius bat (n = 8; Finland and Latvia), blackbird (n = 6; Finland, Latvia and Denmark), and wood pigeon (n = 22; Finland and France), but not in mallard. Key species-level taxonomic assignments in the pathogen bloomers were the two well-known enteropathogens (Campylobacter jejuni or Escherichia coli) and one emerging enteropathogen (Escherichia marmotae). Our data imply that the studied common migratory vertebrates may contribute to the transmission of bacterial pathogens across the European continent.

IMPORTANCE

The understanding of gut microbiota composition and dynamics in wild vertebrate populations, especially in highly mobile vertebrates, birds and bats, remains limited. Our study sheds light on the critical knowledge gap in how common pathogenic bacterial taxa of fecal microbiota are in migratory bats and birds in Europe. We found out that bacterial genera having species pathogenic to human or animals constituted a substantial portion of the fecal microbiota in all the studied host taxa. Most importantly, we identified asymptomatic individuals that were dysbiotic with bacterial pathogen overgrowth. These previously unknown pathogen bloomers appear as potent Europe-wide transmitters of bacterial pathogens, which cause, for example, diarrhea and bacteremia in human. Our findings may contribute to better understanding of seasonal disease hotspots and pathogen spillover risks related to migratory vertebrates.

Microbial signatures and therapeutic strategies in neurodegenerative diseases

Neurodegenerative diseases (NDs), including Alzheimer's disease (AD), Parkinson's disease (PD), amyotrophic lateral sclerosis (ALS), and multiple sclerosis (MS), arise from complex interactions between genetic factors, environmental exposures, and aging. Additionally, gut dysbiosis has been linked to systemic inflammation and neurodegeneration. Advances in microbiome and metabolome profiling techniques have provided deeper insights into how alterations in gut microbiota and dietary patterns affect metabolic pathways and contribute to the progression of NDs. This review explores the profiles of gut microbiome and metabolome derived biomarkers and their roles in NDs. Across phyla, families, and genera, we identified 55 microbial alterations in PD, 24 in AD, 4 in ALS, and 17 in MS. Some notable results include an increase in Akkermansia in PD, AD, and MS and a decrease in short-chain fatty acids (SCFAs) in PD and AD. We examined the effects of probiotics, prebiotics, fecal microbiota transplants (FMT), sleep, exercise, and diet on the microbiota, all of which contributed to delayed onset and alleviation of symptoms. Further, artificial intelligence (AI) and machine learning (ML) algorithms applied to omics data have been crucial in identifying novel therapeutic targets, diagnosing and predicting prognosis, and enabling personalized medicine using microbiota-modulating therapies in NDs patients.

Roselle Extract Ameliorates Abnormal Glucolipid Metabolism and Gut Microbiota in Obese Mice Fed With High-Fat Diet

Roselle extract (RE) is rich in anthocyanins and chlorogenic acids. This study investigated the health-promoting effects of RE on lipid metabolism, oxidative stress, glycometabolism, and gut microbiota in obese mice fed a high-fat diet (HFD). The obesity model was induced by feeding mice a HFD, with RE supplementation added to their drinking water at concentrations of 2 and 4 mg/mL for 12 weeks. RE significantly reduced body weight gain and fat accumulation compared to the control group, alleviated hepatic steatosis, and improved insulin sensitivity. Additionally, RE restored antioxidative enzyme activities such as SOD and GSH-PX while reducing MDA levels. Transcriptomic analysis of the liver was performed to evaluate gene expression related to lipid metabolism, particularly in the PPAR signaling pathway. Gut microbiota analysis showed that RE increased beneficial bacteria and reduced the Firmicutes-to-Bacteroidetes ratio, suggesting an improvement in gut dysbiosis caused by the HFD. RE enhanced lipid metabolism, reduced oxidative stress, and improved insulin sensitivity in obese mice, potentially through modulation of the PPAR signaling pathway and gut microbiota, suggesting its potential as a therapeutic candidate for obesity-related metabolic disorders.

Innovative Therapeutic Strategies for Asthma: The Role of Gut Microbiome in Airway Immunity

There is a growing acknowledgment of the gut microbiome's impact on widespread immune responses, which holds considerable importance for comprehending and addressing asthma. Recent research has clarified the complex interactions between gut microbiota and airway immune systems, demonstrating that microbial diversity and composition can affect both the initiation and advancement of asthma. Gut microbial species and metabolites primarily short-chain fatty acids (SCFAs) may either worsen or reduce airway inflammation by regulating the balance of helper T cell 1 (Th1) / helper T cell 2 (Th2) and other immune mediators. This interaction presents innovative therapeutic possibilities, including modulation of gut microbiome during early life through breastfeeding and control of antibiotic use, particularly with prebiotics, which could selectively stimulate the growth of beneficial bacteria, promote immune maturation, reducing susceptibility to asthma and allergic airway inflammation. Besides, investigating the gut-lung axis reveals new opportunities for personalized medicine in asthma treatment, emphasizing the necessity for integrated strategies that take individual microbiome profiles into account. This paper examines the latest developments in comprehending the mechanisms by which gut microbiota affect airway inflammation and hypersensitivity, especially focusing on treatment strategies.

Dual graph-embedded fusion network for predicting potential microbe-disease associations with sequence learning

Recent studies indicate that microorganisms are crucial for maintaining human health. Dysbiosis, or an imbalance in these microbial communities, is strongly linked to a variety of human diseases. Therefore, understanding the impact of microbes on disease is essential. The DuGEL model leverages the strengths of graph convolutional neural network (GCN) and graph attention network (GAT), ensuring that both local and global relationships within the microbe-disease association network are captured. The integration of the Long Short-Term Memory Network (LSTM) further enhances the model's ability to understand sequential dependencies in the feature representations. This comprehensive approach allows DuGEL to achieve a high level of accuracy in predicting potential microbe-disease associations, making it a valuable tool for biomedical research and the discovery of new therapeutic targets. By combining advanced graph-based and sequence-based learning techniques, DuGEL addresses the limitations of existing methods and provides a robust framework for the prediction of microbe-disease associations. To evaluate the performance of DuGEL, we conducted comprehensive comparative experiments and case studies based on two databases, HMDAD, and Disbiome to demonstrate that DuGEL can effectively predict potential microbe-disease associations.

The forgotten link: how the oral microbiome shapes childhood growth and development

Childhood stunting, defined as impaired linear growth and development, remains a significant global health challenge with long-term consequences on cognitive and physical well-being. Emerging evidence highlights the pivotal role of the oral microbiome-a dynamic microbial ecosystem-in influencing nutritional status, immune response, and overall systemic health. This review explores the intricate interplay between the oral microbiome and stunting, emphasizing mechanisms such as microbial dysbiosis, its impact on nutrient absorption, and immune modulation. Disruptions in the oral microbiome can lead to nutrient malabsorption and systemic inflammation, further exacerbating growth impairments in children. Furthermore, the potential for microbiome-targeted diagnostics and interventions, including probiotics and prebiotics, offers novel strategies to address stunting. A deeper understanding of these interactions may inform innovative diagnostic tools and therapeutic interventions aimed at mitigating stunting through oral microbiome modulation. Integrating oral microbiome research into stunting prevention efforts could provide valuable insights for public health strategies to improve child growth and development, particularly in resource-limited settings. Future research should focus on elucidating the molecular pathways linking the oral microbiome to stunting and developing personalized interventions that optimize microbiome health in early life.

CRAmed: a conditional randomization test for high-dimensional mediation analysis in sparse microbiome data

MOTIVATION

Numerous microbiome studies have revealed significant associations between the microbiome and human health and disease. These findings have motivated researchers to explore the causal role of the microbiome in human complex traits and diseases. However, the complexities of microbiome data pose challenges for statistical analysis and interpretation of causal effects.

RESULTS

We introduced a novel statistical framework, CRAmed, for inferring the mediating role of the microbiome between treatment and outcome. CRAmed improved the interpretability of the mediation analysis by decomposing the natural indirect effect into two parts, corresponding to the presence-absence and abundance of a microbe, respectively. Comprehensive simulations demonstrated the superior performance of CRAmed in Recall, precision, and F1 score, with a notable level of robustness, compared to existing mediation analysis methods. Furthermore, two real data applications illustrated the effectiveness and interpretability of CRAmed. Our research revealed that CRAmed holds promise for uncovering the mediating role of the microbiome and understanding of the factors influencing host health.

AVAILABILITY AND IMPLEMENTATION

The R package CRAmed implementing the proposed methods is available online at https://github.com/liudoubletian/CRAmed.

Time-restricted feeding mediated modulation of microbiota leads to changes in muscle physiology in Drosophila obesity models

Recent research has highlighted the essential role of the microbiome in maintaining skeletal muscle physiology. The microbiota influences muscle health by regulating lipid metabolism, protein synthesis, and insulin sensitivity. However, metabolic disturbances such as obesity can lead to dysbiosis, impairing muscle function. Time-restricted feeding (TRF) has been shown to mitigate obesity-related muscle dysfunction, but its effects on restoring healthy microbiomes remain poorly understood. This study utilizes 16S microbiome analysis and bacterial supplementation to investigate the bacterial communities influenced by TRF that may benefit skeletal muscle physiology. In wild-type and obese Drosophila models (axenic models devoid of natural microbial communities), the absence of microbiota influence muscle performance and metabolism differently. Specifically, axenic wild-type Drosophila exhibited reduced muscle performance, higher glucose levels, insulin resistance, ectopic lipid accumulation, and decreased ATP levels. Interestingly, in obese Drosophila (induced by a high-fat diet or predisposed obesity mutant Sk2), the absence of microbiota improved muscle performance, lowered glucose levels, reduced insulin resistance, and increased ATP levels. TRF was found to modulate microbiota composition, notably increasing Acetobacter pasteurianus (AP) and decreasing Staphylococcus aureus (SA) in both obesity models. Supplementation with AP improved muscle performance and reduced glucose and insulin resistance, while SA supplementation had the opposite effect. This study provides novel insights into the complex interactions between TRF, microbiota, and skeletal muscle physiology in different Drosophila models.

Bacterial Nanovesicles as Interkingdom Signaling Moieties Mediating Pain Hypersensitivity

Gut dysbiosis contributes to multiple pathologies, yet the mechanisms of the gut microbiota-mediated influence on systemic and distant responses remain largely elusive. This study aimed to identify the role of nanosized bacterial extracellular vesicles (bEVs) in mediating allodynia, i.e., pain hypersensitivity, in a diet-induced obesity (DIO) gut dysbiosis model. bEVs were enriched from the feces of lean (bEVLean) and DIO (bEVDIO) mice by an approach combining ultracentrifugation and immunoprecipitation and then extensively analyzed for purity and bacterial characteristics. Next, bEVs were injected, either intraplantarly or intravenously, in mice to assess pain sensitivity. Fluorescence-labeled bEVs were injected in mice by enema to assess biodistribution. The effect of bEV on immune cells and inflammation was analyzed by array, immunophenotyping, microscopy, NF-κB activation, and cellular uptake assays. Results showed that bEVDIO administration in wild-type mice replicated the allodynia phenotype observed in DIO mice for both mechanical and thermal stimuli. Importantly, this effect was compromised in TRPA1/TRPV1 double-knockout mice. Biodistribution analyses showed bEV entry into systemic circulation with subsequent localization at distant sites. Multiple analyses revealed that bEVDIO exposure incited systemic inflammation, primarily through modulating the innate immune system. This inflammatory mechanism involved LPS on the bEV surface, activating TLR2- and TLR4-related pathways, as confirmed using TLR2 and TLR4 inhibitors and shaving bEV surface proteins. Interestingly, the enhanced cellular uptake of bEVDIO was contingent on interactions involving LPS and proteins on bEVs and TLR2/TLR4 on monocytes. These findings illuminate the hitherto unexplored role of bEV as pivotal mediators of allodynia and inflammation linked to gut dysbiosis.

Human papillomavirus, vaginal microbiota and metagenomics: the interplay between development and progression of cervical cancer

Persistent infection with oncogenic human papillomavirus (HPV) types, such as HPV 16 or 18, is a major factor in cervical cancer development. However, only a small percentage of infected women develop cancer, indicating that other factors are involved. Emerging evidence links vaginal microbiota with HPV persistence and cancer progression. Alterations in microbial composition, function, and metabolic pathways may contribute to this process. Despite the potential of metagenomics to explore these interactions, studies on the vaginal microbiota's role in cervical cancer are limited. This review systematically examines the relationship between cervical microbiota, HPV, and cervical cancer by analyzing studies from PubMed, EBSCO, and Scopus. We highlight how microbial diversity influences HPV persistence and cancer progression, noting that healthy women typically have lower microbiota diversity and higher Lactobacillus abundance compared to HPV-infected women, who exhibit increased Gardenella, Prevotella, Sneathia, Megasphaera, Streptococcus, and Fusobacterium spp., associated with dysbiosis. We discuss how microbial diversity is associated with HPV persistence and cancer progression, noting that studies suggest healthy women typically have lower microbiota diversity and higher Lactobacillus abundance, while HPV-infected women exhibit increased Gardnerella, Prevotella, Sneathia, Megasphaera, Streptococcus, and Fusobacterium spp., indicative of dysbiosis. Potential markers such as Gardnerella and Prevotella have been identified as potential microbiome biomarkers associated with HPV infection and cervical cancer progression. The review also discusses microbiome-related gene expression changes in cervical cancer patients. However, further research is needed to validate these findings and explore additional microbiome alterations in cancer progression.

Cross-Sectional Comparative Analysis of Gut Microbiota in Spanish Adolescents with Mediterranean and Western Diets

Dietary patterns, such as the Mediterranean diet (MD) and the Western diet (WD), influence gut microbiota composition and functionality, which play important roles in energy metabolism and nutrient absorption.

OBJECTIVES

A descriptive cross-sectional study was designed to evaluate the gut microbiota of 19 Spanish adolescents and to investigate the association of MD and ultra-processed food (UPF) intake with microbial diversity and community structure.

METHODS

Functional diversity of gut microbiota was evaluated using Biolog EcoPlates, taxonomic composition was assessed with 16S rRNA sequencing via MinION, and phenotypic responses to antibiotics were analyzed using the cenoantibiogram technique under aerobic and anaerobic conditions.

RESULTS

Adolescents with higher adherence to the MD exhibited greater functional diversity, as per the Shannon-Weaver index. In addition, this group showed higher abundance of bacterial genera previously described as beneficial, such as Paraclostridium, Anaerobutyricum, Romboutsia, and Butyricicoccus. In contrast, adolescents reporting greater UPF intakes had a microbiota composition similar to those with low adherence to the MD, characterized by decreased abundance of beneficial genera. Regarding antibiotic resistance, significant differences were only observed under anaerobic conditions, with individuals with low adherence to the MD showing more sensitivity for most antibiotics tested.

CONCLUSIONS

These results suggest that the MD promotes a healthier and more balanced gut environment, potentially improving metabolic functions in adolescents. Despite the lack of differences in α-diversity, comparisons of microbial community structure between adolescents following the MD and those with high UPF (characteristic of the WD) showed clear differences in terms of β-diversity. These findings suggest that dietary patterns influence the composition of the gut microbiota in a more complex manner, beyond just taxonomic richness. The outcomes of this exploratory study highlight opportunities for future research to deepen understanding of the long-term health implications of these dietary patterns, as well as the mechanisms regulating the composition, functionality, and phenotypic responses to antibiotics of gut microbial communities.

Metagenome-guided culturomics for the targeted enrichment of gut microbes

The gut microbiome significantly impacts human health, yet cultivation challenges hinder its exploration. Here, we combine deep whole-metagenome sequencing with culturomics to selectively enrich for taxa and functional capabilities of interest. Using a modified commercial base medium, 50 growth modifications were evaluated, spanning antibiotics, physico-chemical conditions, and bioactive compounds. Whole-metagenome sequencing identified medium additives, like caffeine, that enhance taxa often associated with healthier subjects (e.g., Lachnospiraceae, Oscillospiraceae, Ruminococcaceae). We also explore the impact of modifications on the composition of cultured communities and establish a link between medium preference and microbial phylogeny. Leveraging these insights, we demonstrate that combinations of media modifications can further enhance the targeted enrichment of taxa and metabolic functions, such as Collinsella aerofaciens, or strains harboring biochemical pathways involved in dopamine metabolism. This streamlined, scalable approach unlocks the potential for selective enrichment, advancing microbiome research by understanding the impact of different cultivation parameters on gut microbes.

Effect of folpet on hypoglycaemia, intestinal microbiota, and drug resistance genes in mice

BACKGROUND

Folpet is a nonspecific sulfonamide fungicide widely used to protect crops from mildew. However, the in vivo effects of folpet on glucose metabolism homeostasis, gut microbiota, and abundance of drug resistance genes remain unknown. The purpose of this study was to assess the effects of the pesticide, folpet, on glucose metabolism homeostasis, and folpet-induced changes in the intestinal microbiota and resistance genes in mice.

METHODS

Mice were orally administered folpet at 0, 1, 10, and 100 mg/kg body weight/day for 5 weeks. Blood sugar levels in mice were measured after 5 weeks of folpet administration. Metagenomic sequencing and drug resistance gene analyses were performed to explore changes in the abundance of gut microbiota members and drug resistance genes in mice after folpet administration. Correlation analysis was performed using metabolomics to explore the relationship between intestinal microbiota, drug resistance genes, and glucose metabolism.

RESULTS

Mice in the folpet group had significantly lower blood glucose levels than those in the control group. The abundance of Atopobium, Libanicoccus, Collinsella, and Parabacteroides in the intestinal microbiota of folpet-treated mice was significantly higher than that in the control group. However, the abundance of Mailhella, Bilophila, Roseburia, and Bacteroides were reduced in folpet-treated mice. Compared with the control group, the abundance of APH6-Ic and AAC6-Ie-APH2-Ia resistance genes in mice treated with folpet significantly increased. The abundance of tetQ, ermE, and BahA resistance genes was significantly reduced after folpet treatment.

CONCLUSIONS

Folpet is associated with changes in the abundance of gut microbiota in mice and may also affect the abundance of drug-resistance genes and the regulation of blood glucose levels.

Gut-Heart Axis: Microbiome Involvement in Restrictive Cardiomyopathies

An intriguing aspect of restrictive cardiomyopathies (RCM) is the microbiome role in the natural history of the disease. These cardiomyopathies are often difficult to diagnose and so result in significant morbidity and mortality. The human microbiome, composed of billions of microorganisms, influences various physiological and pathological processes, including cardiovascular health. Studies have shown that gut dysbiosis, an imbalance in the composition of intestinal bacteria, can contribute to systemic inflammation, a key factor in many cardiovascular conditions. An increase in gut permeability, frequently caused by dysbiosis, allows bacterial endotoxins to enter the bloodstream, activating inflammatory pathways that exacerbate cardiac dysfunction. Recent reports highlight the potential role of microbiome in amyloidogenesis, as certain bacteria produce proteins that accelerate the formation of amyloid fibrils. Concurrently, advancements in amyloidosis treatments have sparked renewed hopes, marking a promising era for managing these kinds of diseases. These findings suggest that the gut-heart axis may be a potential factor in the development and progression of cardiovascular disease like RCM, opening new paths for therapeutic intervention. The aim of this review is to provide a detailed overview of the gut-heart axis, focusing on RCM.

Covariation Between Microbiome Composition and Host Transcriptome in the Gut of Wild Drosophila melanogaster: A Re-Analysis

Gut microbiota are fundamental for healthy animal function, but the evidence that host function can be predicted from microbiota taxonomy remains equivocal, and natural populations remain understudied compared to laboratory animals. Paired analyses of covariation in microbiota and host parameters are powerful approaches to characterise host-microbiome relationships mechanistically, especially in wild populations of animals that are also lab models, enabling insight into the ecological basis of host function at molecular and cellular levels. The fruitfly Drosophila melanogaster is a preeminent model organism, amenable to field investigation by 'omic analyses. Previous work in wild male D. melanogaster guts analysed paired measurements of (A) bacterial diversity and abundance, measured by 16S amplicon sequencing; and (B) the host gut transcriptome, but no signature of covariation was detected. Here, we re-analyse those data comprehensively. We find orthogonal axes of microbial genera, which correspond to differential expression of host genes. The differentially expressed gene sets were enriched in functions including protein translation, mitochondrial respiration, immunity and reproduction. Each gene set had a distinct functional signature, suggesting that wild flies exhibit a range of distinct axes of functional variation, which correspond to orthogonal axes of microbiome variation. These findings lay a foundation to better connect ecology and functional genetics of a leading host-microbiome model.

Influence of gut flora on diabetes management after kidney transplantation

Post-transplant diabetes mellitus (PTDM) is a common complication following renal transplantation, and its incidence has been gradually increasing in recent years, posing a significant public health challenge. Managing PTDM is complex, as studies suggest that it involves changes in the microbial flora across multiple organs. Recent research highlights the critical role of gut flora metabolism in the development of diabetes among post-renal transplant patients. This paper reviews the alterations in gut flora observed in PTDM patients and explores how gut flora influences PTDM. These findings may offer new perspectives on targeting gut flora metabolites for the prevention and treatment of PTDM.

Exploring the Prebiotic Potential of Fermented Astragalus Polysaccharides on Gut Microbiota Regulation In Vitro

Astragalus polysaccharides (APS) are known for their prebiotic properties, and fermentation by probiotics is a promising strategy to enhance the prebiotic activity of polysaccharides. In this study, Lactobacillus rhamnosus was used to ferment APS, and response surface methodology was applied to optimize the fermentation parameters. The optimal conditions were determined as follows: 10.28% APS addition, 5.83% inoculum, 35.6 h of fermentation time, and a temperature of 34.6 °C. Additionally, the effects of Fermented Astragalus polysaccharides (FAPS) on human gut microbiota were investigated through in vitro anaerobic incubation. Fecal samples were obtained from 6 healthy volunteers, which were then individually incubated with FAPS. Results demonstrated that FAPS significantly regulated microbial composition and diversity, increasing the abundance of beneficial gut bacteria such as Lactobacillus, E. faecalis, and Brautobacterium, while inhibiting harmful species such as Shigella, Romboutsia, and Clostridium_sensu_stricto_1. Furthermore, FAPS enhanced the production of short-chain fatty acids (SCFAs), which are increasingly recognized to play a role in intestinal homeostasis. These findings suggested that FAPS offers several advantages in terms of increasing beneficial metabolites and regulating gut microbial composition. This study provides valuable insights for expanding the use of plant-derived polysaccharides in the food industry and for developing functional dietary supplements.

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.

DeepPhylo: Phylogeny-Aware Microbial Embeddings Enhanced Predictive Accuracy in Human Microbiome Data Analysis

Microbial data analysis poses significant challenges due to its high dimensionality, sparsity, and compositionality. Recent advances have shown that integrating abundance and phylogenetic information is an effective strategy for uncovering robust patterns and enhancing the predictive performance in microbiome studies. However, existing methods primarily focus on the hierarchical structure of phylogenetic trees, overlooking the evolutionary distances embedded within them. This study introduces DeepPhylo, a novel method that employs phylogeny-aware amplicon embeddings to effectively integrate abundance and phylogenetic information. DeepPhylo improves both the unsupervised discriminatory power and supervised predictive accuracy of microbiome data analysis. Compared to the existing methods, DeepPhylo demonstrates superiority in informing biologically relevant insights across five real-world microbiome use cases, including clustering of skin microbiomes, prediction of host chronological age and gender, diagnosis of inflammatory bowel disease (IBD) across 15 studies, and multilabel disease classification.

The gut microbiome and the brain

PURPOSE OF REVIEW

The importance of the gut microbiome for human health and well-being is generally accepted, and elucidating the signaling pathways between the gut microbiome and the host offers novel mechanistic insight into the (patho)physiology and multifaceted aspects of healthy aging and human brain functions.

RECENT FINDINGS

The gut microbiome is tightly linked with the nervous system, and gut microbiota are increasingly emerging as important regulators of emotional and cognitive performance. They send and receive signals for the bidirectional communication between gut and brain via immunological, neuroanatomical, and humoral pathways. The composition of the gut microbiota and the spectrum of metabolites and neurotransmitters that they release changes with increasing age, nutrition, hypoxia, and other pathological conditions. Changes in gut microbiota (dysbiosis) are associated with critical illnesses such as cancer, cardiovascular, and chronic kidney disease but also neurological, mental, and pain disorders, as well as chemotherapies and antibiotics affecting brain development and function.

SUMMARY

Dysbiosis and a concomitant imbalance of mediators are increasingly emerging both as causes and consequences of diseases affecting the brain. Understanding the microbiota's role in the pathogenesis of these disorders will have major clinical implications and offer new opportunities for therapeutic interventions.

Exploring the relationship between gut microbiota and breast diseases using Mendelian randomization analysis

Background

Growing evidence suggests a relationship between gut microbiota composition and breast diseases, although the precise nature of this association remains uncertain. To investigate the causal relationship between gut microbiota and breast diseases, we utilized two-way Mendelian randomization (MR) analysis.

Methods

Four common diseases were included as outcomes: breast cancer, breast cysts, inflammatory disorders of the breast, and infections of the breast associated with childbirth, along with their subtypes. Genetic data on gut microbiota were extracted from genome-wide association studies (GWAS). The primary approach used to investigate the association between these genetic factors and gut microbiota was the inverse-variance-weighted (IVW) method with random-effects types. Sensitivity analyses, such as Cochran's Q test, the MR-Egger intercept test, and leave-one-out analysis, were conducted to ensure the stability and reliability of the MR findings.

Results

We discovered plausible causal links between 20 microbial categories and the breast diseases, with a significance level of p < 0.05. Notably, Family.Rikenellaceae (p: 0.0013) maintained a significant inverse relationship with overall breast cancer (BC), after the Bonferroni correction. In the reverse MR analysis, interactions were observed between Genus.Adlercreutzia and estrogen receptor-positive cancer. In addition, Genus.Sellimonas, Family.Rikenellaceae, and Genus.Paraprevotella were associated with ER+ and overall breast cancer, whereas Genus.Dorea was linked to both estrogen receptor-negative and overall breast cancer. Family.Prevotellaceae was the only category correlated with inflammatory breast disorders. Moreover, Genus Eubacteriumruminantiumgroup, Genus.Lactococcus, and Family.Alcaligenaceae were associated with breast cysts, while Genus.Anaerofilum, Genus.Butyricimonas, Order.Coriobacteriales, Order.Pasteurellales, and Order.Verrucomicrobiales showed significant associations with infections of the breast associated with childbirth. No evidence of heterogeneity or horizontal pleiotropy was found.

Conclusion

Our Mendelian randomization analysis confirmed a causal relationship between gut microbiota and breast diseases. Early stool tests may be a viable method for screening diseases to identify people at higher risk of breast diseases.

SPARTA: Interpretable functional classification of microbiomes and detection of hidden cumulative effects

The composition of the gut microbiota is a known factor in various diseases and has proven to be a strong basis for automatic classification of disease state. A need for a better understanding of microbiota data on the functional scale has since been voiced, as it would enhance these approaches' biological interpretability. In this paper, we have developed a computational pipeline for integrating the functional annotation of the gut microbiota into an automatic classification process and facilitating downstream interpretation of its results. The process takes as input taxonomic composition data, which can be built from 16S or whole genome sequencing, and links each component to its functional annotations through interrogation of the UniProt database. A functional profile of the gut microbiota is built from this basis. Both profiles, microbial and functional, are used to train Random Forest classifiers to discern unhealthy from control samples. SPARTA ensures full reproducibility and exploration of inherent variability by extending state-of-the-art methods in three dimensions: increased number of trained random forests, selection of important variables with an iterative process, repetition of full selection process from different seeds. This process shows that the translation of the microbiota into functional profiles gives non-significantly different performances when compared to microbial profiles on 5 of 6 datasets. This approach's main contribution however stems from its interpretability rather than its performance: through repetition, it also outputs a robust subset of discriminant variables. These selections were shown to be more consistent than those obtained by a state-of-the-art method, and their contents were validated through a manual bibliographic research. The interconnections between selected taxa and functional annotations were also analyzed and revealed that important annotations emerge from the cumulated influence of non-selected taxa.

Gut microbiota and skin pathologies: Mechanism of the gut-skin axis in atopic dermatitis and psoriasis

Atopic dermatitis (AD) and psoriasis are chronic skin diseases with a global impact, posing significant challenges to public health systems and severely affecting patients' quality of life. This review delves into the key role of the gut microbiota in these diseases, emphasizing the importance of the gut-skin axis in inflammatory mediators and immune regulation and revealing a complex bidirectional communication system. We comprehensively assessed the pathogenesis, clinical manifestations, and treatment strategies for AD and psoriasis, with a particular focus on how the gut microbiota and their metabolites influence disease progression via the gut-skin axis. In addition, personalized treatment plans based on individual patient microbiome characteristics have been proposed, offering new perspectives for future treatment approaches. We call for enhanced interdisciplinary cooperation to further explore the interactions between gut microbiota and skin diseases and to assess the potential of drugs and natural products in modulating the gut-skin axis, aiming to advance the treatment of skin diseases.

Gut microbiota of children with autism spectrum disorder and healthy siblings: A comparative study

Autism spectrum disorder (ASD) is a neurodevelopmental abnormality that impairs social communication. The human gut microbiome (GM) influences a variety of local processes, including dysbiosis and the defense against pathogenic microorganisms. The aim of the present study was to categorize and identify molecular biomarkers for ASD. In the present study, metagenomics whole genome shotgun sequencing was used to identify the gut microbiota in autistic individuals. Fecal samples from four children with ASD and four healthy control siblings, aged 3-10 years old, were examined using bioinformatics analysis. A total of 673,091 genes were cataloged, encompassing 25 phyla and 2 kingdoms based on the taxonomy analysis. The results revealed 257 families, 34 classes, 84 orders, and 1,314 genera among 4,339 species. The top 10 most abundant genes and corresponding functional genes for each group were determined after the abundance profile was screened. The results showed that children with ASD had a higher abundance of certain gut microbiomes than their normal siblings and vice versa. The phyla Firmicutes and Proteobacteria were the most abundant in ASD. The Thermoanaerobacteria class was also restricted to younger healthy individuals. Moreover, the Lactobacillaceae family was more abundant in children with ASD. Additionally, it was discovered that children with ASD had a higher abundance of the Bacteroides genus and a lower abundance of the Bifidobacterium and Prevotella genera. In conclusion, there were more pathogenic genera and species and higher levels of biomass, diversity and richness in the GM of children with ASD.

The Novel Insight of Gut Microbiota from Mouse Model to Clinical Patients and the Role of NF-κB Pathway in Polycystic Ovary Syndrome

Polycystic Ovary Syndrome (PCOS) is a metabolic disorder characterized by hyperandrogenism and related symptoms in women of reproductive age. Emerging evidence suggests that chronic low-grade inflammation plays a significant role in the development of PCOS. The gut microbiota, a complex bacterial ecosystem, has been extensively studied for various diseases, including PCOS, while the underlying mechanisms are not fully understood. This review comprehensively summarizes the changes in gut microbiota and metabolites observed in PCOS and their potential association with the condition. Additionally, we discuss the role of abnormal nuclear factor κB signaling in the pathogenesis of PCOS. These findings offer valuable insights into the mechanisms of PCOS and may pave the way for the development of control and therapeutic strategies for this condition in clinical practice. By bridging the gap between mouse models and clinical patients, this review contributes to a better understanding of the interplay between gut microbiota and inflammation in PCOS, thus paving new ways for future investigations and interventions.

Gut Microbiota and Liver Regeneration: A Synthesis of Evidence on Structural Changes and Physiological Mechanisms

Liver regeneration (LR) is a unique biological process with the ability to restore up to 70% of the organ. This allows for the preservation of liver resections for various liver tumors and for living donor liver transplantation (LDLT). However, in some cases, LR is insufficient and interventions that can improve LR are urgently needed. Gut microbiota (GM) is one of the factors influencing LR, as the liver and intestine are intimately connected through the gut-liver axis. Thus, healthy GM facilitates normal LR, whereas dysbiosis leads to impaired LR due to imbalance of bile acids, inflammatory cytokines, microbial metabolites, signaling pathways, etc. Therefore, GM can be considered as a new possible therapeutic target to improve LR. In this review, we critically observe the current knowledge about the influence of gut microbiota (GM) on liver regeneration (LR) and the possibility to improve this process, which may reduce complication and mortality rates after liver surgery. Although much research has been done on this topic, more clinical trials and systemic reviews are urgently needed to move this type of intervention from the experimental phase to the clinical field.

Long-chain polyunsaturated fatty acids influence colorectal cancer progression via the interactions between the intestinal microflora and the macrophages

The metabolism of long-chain polyunsaturated fatty acids (LCPUFAs) is closely associated with the risk and progression of colorectal cancer (CRC). This paper aims to investigate the role of LCPUFA in the crosstalk between intestinal microflora and macrophages, as well as the effects of these three parties on the progression of CRC. The metabolism and function of LCPUFA play important roles in regulating the composition of the human gut microflora and participating in the regulation of inflammation, ultimately affecting macrophage function and polarization, which is crucial in the tumor microenvironment. The effects of LCPUFA on cellular interactions between the two species can ultimately influence the progression of CRC. In this review, we explore the molecular mechanisms and clinical applications of LCPUFA in the interactions between intestinal microflora and intestinal macrophages, as well as its significance for CRC progression. Furthermore, we reveal the role of LCPUFA in the construction of the CRC microenvironment and explore the key nodes of the interactions between intestinal flora and intestinal macrophages in the environment. It provides potential targets for the metabolic diagnosis and treatment of CRC.

Stage dependent microbial dynamics in hepatocellular carcinoma and adjacent normal liver tissues

The interactive pathway of the gut-liver axis underscores the significance of microbiome modulation in the pathogenesis and progression of various liver diseases, including hepatocellular carcinoma (HCC). This study aims to investigate the disparities in the composition and functionality of the hepatic microbiota between tumor tissues and adjacent normal liver tissues, and their implications in the etiology of HCC. We conducted a comparative analysis of the hepatic microbiome between adjacent normal liver tissues and tumor tissues from HCC patients. Samples were categorized according to the modified Union for International Cancer Control (mUICC) staging system into Non-tumor, mUICC stage I, mUICC stage II, and mUICC stage III groups. Microbial richness and community composition were analyzed, and phylogenetic profiles were examined to identify significantly altered microbial taxa among the groups. Predicted metabolic pathways were analyzed using PICRUSt2. Our analysis did not reveal significant differences in microbial richness and community composition with the development of HCC. However, phylogenetic profiling identified significantly altered microbial taxa among the groups. Sphingobium, known for degrading polychlorinated biphenyls (PCBs), exhibited a significantly negative correlation with clinical indices in HCC patients. Conversely, Sphingomonas, a gut bacterium associated with various liver diseases, showed a positive correlation. Predicted metabolic pathways suggested a correlation between atrazine degradation and valine, leucine, and isoleucine biosynthesis with mUICC stage and tumor size. Our results underscore the critical link between hepatic microbial composition and function and the HCC tumor stage, suggesting a potentially pivotal role in the development of HCC. These findings highlight the importance of targeting the hepatic microbiome for therapeutic strategies in HCC.

Genetic evidence of bidirectional mendelian randomization study on the causality between gut microbiome and respiratory diseases contributes to gut-lung axis

Observational studies and clinical trials have suggested the relationship between the gut microbiome and respiratory diseases, but the causality between them remains unclear. Firstly, we selected eight respiratory diseases Genome-wide association study (GWAS) datasets mainly from the FinnGen collaboration as outcomes. The exposure was based on GWAS statistics about the gut microbiome, sourced from the MiBioGen consortium, including gut microbial taxa. The causal link between the gut microbiome and respiratory illnesses was then estimated using a Two-sample Mendelian randomization (MR) analysis, including the inverse-variance weighted (IVW), weighted median, MR-Egger, simple mode, and weighted mode. To ensure reliability, F-statistics and sensitivity tests were conducted. Furthermore, we performed a reverse MR analysis of the pre-Mendelian positive findings to possible reverse causality. For the 196 gut microbe taxa, the IVW analysis suggested 88 potential associations with eight clinically prevalent respiratory diseases. Among them, 30 causal associations were found in more than one MR method. Multiple statistical corrections have confirmed three causal associations: genus Holdemanella was a risk factor for chronic obstructive pulmonary disease (COPD) (P = 1.3 × 10-4, OR = 1.18), family FamilyXIII was a protective factor for COPD (P = 1.3 × 10-3, OR = 0.75), and genus Oxalobacter was a risk factor for asthma (P = 2.1 × 10-4, OR = 1.09). Our MR analysis results indicate that there would be a causal relationship between the gut microbiome and respiratory diseases, contributing to the gut-lung axis. This finding offers new insights into the gut microbiome's roles in respiratory diseases' clinical prevention, pathogenesis, and improvement of clinical symptoms. Further randomized controlled trials are necessary to clarify the protective effect of probiotics and fecal microbial transplantation on respiratory health.