Ecological and evolutionary forces shaping microbial diversity in the human intestine

PMA1-containing extracellular vesicles of Candida albicans triggers immune responses and colitis progression

Candida albicans (C. albicans) exhibits aberrant changes in patients with colitis, and it has been reported to dominate the colonic mucosal immune response. Here, we found that PMA1 expression was significantly increased in C. albicans from patients with IBD compared to that in healthy controls. A Crispr-Cas9-based fungal strain editing system was then used to knock out PMA1 expression in C. albicans. Compared to WT-C.a, ΔPMA1-C.a could not aggravate colitis. Proteomic analysis showed that PMA1 was transported by extracellular vesicles (EVs) of C. albicans. PMA1-containing EVs aggravated colitis, modulated the migration of cDC2 from the lamina propria to mesenteric lymph nodes, and induced TH17 cell differentiation. Moreover, the adaptor protein CARD9 was critical in PMA1-containing EV-induced colitis, and CARD9-deficient DCs did not induce TH17 cell differentiation or IL-17A production. Mechanically, CARD9 combines with the glycolytic protein GAPDH (aa2-146 domain) through its CARD region. CARD9 deficiency led to decreased enzyme activity of GAPDH and decreased glycolysis of DCs. These findings indicate that PMA1 is a potential virulence factor responsible for the pathogenesis of C. albicans colitis.

Lachnospiraceae-bacterium alleviates ischemia-reperfusion injury in steatotic donor liver by inhibiting ferroptosis via the Foxo3-Alox15 signaling pathway

Ischemia-reperfusion injury (IRI) is a major obstacle in liver transplantation, especially with steatotic donor livers. Dysbiosis of the gut microbiota has been implicated in modulating IRI, and Lachnospiraceae plays a pivotal role in regulating host inflammatory and immune responses, but its specific role in liver transplantation IRI remains unclear. This study explores whether Lachnospiraceae can mitigate IRI and its underlying mechanisms. We found Lachnospiraceae-bacterium (Lachn.) abundance was significantly reduced in rats with liver cirrhosis. Lachn.-treated rats exhibited improved intestinal permeability, reduced IRI severity in both normal and steatotic donor livers, and decreased levels of neutrophil and macrophage infiltration, and inflammatory cytokines. Multi-omics analysis revealed elevated pyruvate levels in transplanted livers after Lachn. treatment, alongside reduced Alox15 and Foxo3 expression. Mechanistically, Lachn.-derived pyruvate inhibited Alox15 expression and reduced ferroptosis in normal and steatotic donor livers. Furthermore, reduced nuclear translocation of Foxo3 further suppressed Alox15 expression, alleviating IRI, especially in steatotic donor livers. Clinical samples confirmed reduced donor livers IRI in cirrhotic recipients with high Lachn. abundance after liver transplantation. In conclusion, Lachn. alleviates IRI in steatotic donor liver transplantation by inhibiting ferroptosis via the Foxo3-Alox15 axis, providing a potential therapeutic strategy to modulate gut microbiota to alleviate IRI following liver transplantation.

Multiple Sclerosis: A Story of the Interaction Between Gut Microbiome and Components of the Immune System

Multiple sclerosis (MS) is defined as an inflammatory disorder that chronically affects the central nervous system of young people mostly and is distributed globally. It is associated with degeneration and demyelination of the myelin sheath around the nerves, resulting in multiple neurological disability symptoms ranging from mild to severe cases that end with paralysis sometimes. MS is one of the rising diseases globally that is unfortunately associated with reduced quality of life and adding national economic burdens. The definite MS mechanism is not clearly defined; however, all the previous researches confirm the role of the immune system as the master contributor in the pathogenesis. Innate and adaptive immune cells are activated peripherally then attracted toward the central nervous system (CNS) due to the breakdown of the blood-brain barrier. Recently, the gut-brain axis was shown to depend on gut metabolites that are produced by different microorganisms in the colon. The difference in microbiota composition between individuals is responsible for diversity in secreted metabolites that affect immune responses locally in the gut or systemically when reach blood circulation to the brain. It may enhance or suppress immune responses in the central nervous system (CNS) (repeated short forms); consequently, it may exacerbate or ameliorate MS symptoms. Recent data showed that some metabolites can be used as adjuvant therapy in MS and other inflammatory diseases. This review sheds light on the nature of MS and the possible interaction between gut microbiota and immune system regulation through the gut-brain axis, hence contributing to MS pathogenesis.

Fire in the belly: Stress and antibiotics induce dysbiosis and inflammation in the gut of common carp

Fish are exposed to numerous stressors which negatively affect their immune response and increase infection susceptibility. The risk of bacterial infections results in the excessive and preventive use of antibiotics. Therefore, we aimed to study how antibiotic treatment and restraint stress will affect the stress response, microbiota composition, gut morphology, and inflammatory reaction in common carp. Both restraint stress and antibiotic treatment increased cortisol level. Moreover, antibiotics induced dysbiosis in fish gut, manifested by a decrease in the total abundance of bacteria, and a shift in bacteria diversity, including a reduced number of Aeromonas, Bacteroides, Barnesiellaceae, Cetobacterium and Shewanella and an increased abundance of Flavobacterium. To a lesser extent, stress modified gut microbiota, as it decreased bacteria number and slightly changed the microbiota composition by decreasing Cetobacterium abundance and increasing Vibrio abundance. Microbiota of the antibiotic-treated and stressed fish shifted from the beneficial bacterial genera - Cetobacterium and Bacteroides, to the increased presence of unfavorable bacteria such as Brevinema, Flavobacterium and Desulfovibrionaceae. Stress and antibiotic-induced changes in the gut microbiota were related to the changes in the gut morphology when the higher abundance of goblet and rodlet cells and increased secretion activity of goblet cells were observed. Moreover, up-regulation of the expression of genes encoding pro-inflammatory mediators and cytokines involved in the Th17 immune response was present in the gut of the antibiotic-treated and stressed fish. We conclude that in carp antibiotics and stress alter the abundance and composition of the microbiota and induce Th17-dependent inflammatory reaction in the gut. Moreover, our results strongly suggest the interplay of the stress axis and the brain-gut-microbiota axis.

The Role of Gut Microbiota in Modulating Brain Structure and Psychiatric Disorders: A Mendelian Randomization Study

The influence of the gut microbiome on the human brain, especially its associations with psychiatric disorders, has emerged as a focal area in contemporary neuroscience and psychiatry research. In this study, we employed a mediation Mendelian randomization approach to delve into the potential causal relationships between gut microbiota and psychiatric disorders, with a focus on the mediating role of brain structural changes. We harnessed genetic data from large - scale genome - wide association studies to analyze how 196 gut microbiota taxa affect ten psychiatric disorders via alterations in 3,143 brain structures. Our key findings revealed significant bidirectional causal relationships. In the gut microbiota - brain structure relationship, certain gut microbiota taxa, such as Bacteroides and Marvinbryantia, were associated with changes in brain activity and white matter integrity respectively. Conversely, brain structures like the right hippocampus and left superior cerebellar peduncle influenced gut microbiota composition. Regarding gut microbiota and psychiatric disorders, we identified numerous associations. For example, the genus Prevotellaceae was significantly associated with an increased risk of Autism Spectrum Disorder, while Ruminococcaceae UCG005 showed a protective effect. In Panic Disorder, Alistipes was positively associated, and for Schizophrenia, both protective (Barnesiella) and risk - associated (Phascolarctobacterium) genera were found. Moreover, through mediation analysis, we found that brain structures mediated the effects of gut microbiota on five psychiatric disorders, including bipolar disorder and anorexia nervosa. In these cases, the influence of gut microbiota on the disorders was fully transmitted through changes in brain structure. Overall, our research clarifies the role of the microbiota - gut - brain axis in mental health. It offers a new perspective on how intestinal microbes impact brain physiology and psychiatric pathology. These findings not only deepen our understanding of the biological interactions between the gut and brain but also suggest that targeted gut microbiota modifications could be novel therapeutic strategies for mental health disorders.

Evaluation of the effects of different formulations of protectants on the preservation of the microbiota in fecal microbiota transplantation

BACKGROUND

With the increasing indications for fecal microbiota transplantation for the treatment of diseases, there is a growing demand for the preparation of frozen or lyophilized fecal microbiota products that are viable and can stably colonize the recipient. The addition of protective agents plays an important role in the preparation. However, there has been no systematic evaluation of the protective agents used in fecal microbiota sample transplantation preparation for transplantation.

METHODS

We were used the donor bacterial flora containing 10 different formulations of protective agents were frozen, lyophilized, and stored. Plate counting, CCK8 assay, flow cytometry after LIVE/DEAD staining, and fluorescence intensity were used to assess viable bacteria in vitro. In addition, the donor bacterial flora samples containing different formulations protective agents were transplanted into antibiotic-treated SPF mice, with 3 mice in each group and a total of 5 groups. Fecal samples were collected for metagenomic sequencing to observe the colonization of the bacterial flora in the recipient mice.

RESULTS

The preliminary screening results showed that the survival rate of bacteria in the 5% trehalose (T) groups, and 5% sucrose, 5% inulin, and 1% cysteine hydrochloride (SI) groups was slightly higher than that in the other groups. SI groups tended to be more protective against anaerobes than T groups. The donor gut microbiota containing the SI groups protective agent exhibited the best colonization of the recipient mice. The protective effects of different formulations of protective agents on the colonized probiotic strains and the metabolic function of the bacterial flora in recipient mice were found to be species specific.

CONCLUSIONS

SI groups can not only better protect the activity of anaerobic bacteria in the intestine, but also effectively promote the effective colonization of donor intestinal bacteria in the recipient mice, and the effect of frozen storage method is less, and can be used at the same time as frozen and freeze-dried preparation. It can be used as a reference for the selection of protective agents in the preparation of fecal microbiota transplantation samples.

Enteropathogenic Escherichia coli induces Entamoeba histolytica superdiffusion movement on fibronectin by reducing traction forces

Amebiasis, caused by Entamoeba histolytica, is a global health concern, affecting millions and causing significant mortality, particularly in areas with poor sanitation. Although recent studies have examined E. histolytica's interaction with human intestinal microbes, the impact of bacterial presence on the parasite's motility, mechanical forces, and their potential role in altering invasiveness have not been fully elucidated. In this study, we utilized a micropillar-array system combined with live imaging to investigate the effects of enteropathogenic Escherichia coli on E. histolytica's motility characteristics, F-actin spatial localization, and traction force exerted on fibronectin-coated substrates. Our findings indicate that co-incubation with live enteropathogenic E. coli significantly enhances the motility of E. histolytica, as evidenced by superdiffusive movement-characterized by increased directionality and speed-resulting in broader dispersal and more extensive tissue/cell damage. This increased motility is accompanied by a reduction in F-actin-dependent traction forces and podosome-like structures on fibronectin-coated substrates, but with increased F-actin localization in the upper part of the cytoplasm. These findings highlight the role of physical interactions and cellular behaviors in modulating the parasite's virulence, providing new insights into the mechanistic basis of its pathogenicity.

The Role of G Protein-Coupled Receptors in the Regulation of Orthopaedic Diseases by Gut Microbiota

Exercise and diet modulate the gut microbiota, which is involved in the regulation of orthopaedic diseases and synthesises a wide range of metabolites that modulate cellular function and play an important role in bone development, remodelling and disease. G protein-coupled receptors (GPCRs), the largest family of transmembrane receptors in the human body, interact with gut microbial metabolites to regulate relevant pathological processes. This paper provides a review of different dietary and exercise effects on the pathogenic gut microbiota and their metabolites associated with GPCRs in orthopaedic diseases. RESULTS: Generally, metabolites produced by gut microbiota contribute to the maintenance of bone health by activating the corresponding GPCRs, which are involved in bone metabolism, regulation of immune response, and maintenance of gut flora homeostasis. Exercise and diet can influence gut microbiota, and an imbalance in gut microbiota homeostasis can trigger a series of adverse immune and metabolic responses by affecting GPCR function, ultimately leading to the onset and progression of various orthopaedic diseases. Understanding these relationships is crucial for elucidating the pathogenesis of orthopaedic diseases and developing personalised probiotic-based therapeutic strategies. In the future, we should further explore how to prevent and treat orthopaedic diseases through GPCR-based modulation of gut microbes and their interactions. The development of substances that precisely modulate gut microbes through different exercises and diets will provide more effective interventions to improve bone health in patients.

Beneficial effect of consuming milk containing only A2 beta-casein on gut microbiota: A single-center, randomized, double-blind, cross-over study

Cow milk contains essential nutrients, with β-casein existing in A1 and A2 forms. Studies suggest that A2 milk (containing only A2 β-casein) may offer gastrointestinal (GI) benefits compared to A1/A2 milk (containing both forms). This study investigated the effects of A2 milk consumption on the gut microbiota of South Korean cohort experiencing GI discomfort after consuming A1/A2 milk. Thirty-five participants with GI discomfort after milk consumption were included. Stool DNA was analyzed using 16S rRNA gene sequencing before and after consuming either A1/A2 or A2 milk. Beta diversity analysis using the generalized UniFrac distance method revealed a significant shift in gut microbiota composition after A2 milk consumption (p = 0.04), but no significant change after consuming A1/A2 milk. Significant differences in gut microbiota composition were found between A1/A2 and A2 milk drinkers after milk consumption (p = 0.031). Alpha diversity indices remained unchanged. Notable increases in beneficial microbes, including Bifidobacterium and Blautia, were observed after A2 milk intake. Linear discriminant analysis Effect Size (LEfSe) analysis identified significant enrichment of Actinobacteria, particularly Bifidobacterium longum and Blautia wexlerae, in the A2 group. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis highlighted enriched transport systems related to energy, peptides, sugars, and raffinose family oligosaccharides in the A2 group. Spearman correlation showed significant associations between Bifidobacterium, Blautia, and enhanced transport systems exclusively in the A2 group. Two weeks of A2 milk consumption led to significant alterations in gut microbiota, promoting beneficial microbes and related functions. A2 milk could be a suitable alternative for subjects who experience milk-intake-related GI discomfort.

Potential therapeutic strategies targeting efferocytosis for inflammation resolution and tissue repair in inflammatory bowel disease

Efferocytosis, the process by which apoptotic cells (ACs) are recognized and cleared by phagocytes, is a critical mechanism in maintaining intestinal immune homeostasis and promoting the resolution of inflammation. Inflammatory bowel disease (IBD), encompassing Crohn's disease (CD) and ulcerative colitis (UC), is characterized by chronic intestinal inflammation, wherein defective efferocytosis contributes to the accumulation of ACs, secondary necrosis, and sustained mucosal damage. This review delineates the molecular mechanisms underlying efferocytosis and systematically examines its functional roles across five key intestinal phagocytic cell types: macrophages, dendritic cells (DCs), neutrophils, intestinal epithelial cells (IECs), and Paneth cells (PCs). Particular emphasis is placed on the dysregulation of efferocytosis capacity in IBD pathogenesis and the consequences of impaired apoptotic cell clearance in both professional and non-professional phagocytes. Furthermore, we evaluate emerging therapeutic strategies designed to restore or enhance efferocytosis, including modulation of macrophage polarization, LC3-associated phagocytosis pathways, nanotechnology-enabled delivery systems, and stem cell-based interventions. A comprehensive understanding of cell-type-specific efferocytosis in the intestinal microenvironment offers promising directions for the development of targeted, inflammation-resolving therapies for IBD.

Therapeutic targeting of the host-microbiota-immune axis: implications for precision health

The human body functions as a complex ecosystem, hosting trillions of microbes that collectively form the microbiome, pivotal in immune system regulation. The host-microbe immunological axis maintains homeostasis and influences key physiological processes, including metabolism, epithelial integrity, and neural function. Recent advancements in microbiome-based therapeutics, including probiotics, prebiotics and fecal microbiota transplantation, offer promising strategies for immune modulation. Microbial therapies leveraging microbial metabolites and engineered bacterial consortia are emerging as novel therapeutic strategies. However, significant challenges remain, including individual microbiome variability, the complexity of host-microbe interactions, and the need for precise mechanistic insights. This review comprehensively examines the host microbiota immunological interactions, elucidating its mechanisms, therapeutic potential, and the future directions of microbiome-based immunomodulation in human health. It will also critically evaluate challenges, limitations, and future directions for microbiome-based precision medicine.

Evolutionary medicine and bioastronautics: an innovative approach in addressing adverse mental health effects to astronauts during long term space missions

Although evolutionary medicine has produced several novel insights for explaining prevalent health issues, it has yet to sufficiently address possible adverse mental health effects of humans during long-term space missions While evolutionary applications to medicine have increased over the past 20 years, there is scope for the integration of evolutionary applications in the new branch of space medicine called bioastronautics, which analyses the effects on human bodies when in outer space. Evolutionary principles may explain what kinds of space environments increase mental health risks to astronauts, both in the short and long term; secondly, evolutionary principles may provide a more informed understanding of the evolutionary mismatch between terrestrial and space environments in which astronauts exist. This information may assist in developing frameworks for improving mental health of astronauts and future space colonists. Consequently, this paper will focus on some of the major evolutionary mismatches currently confronting astronauts' mental health, with an aim to improve medical knowledge. It will also provide possible therapeutic countermeasures based on evolutionary principles for reducing adverse mental effects on astronauts.

Differential responses of lung and intestinal microbiota to SARS-CoV-2 infection: a comparative study of the Wuhan and Omicron strains in K18-hACE2 Tg mice

BACKGROUND

The COVID-19 pandemic, caused by SARS-CoV-2, has led to the emergence of viral variants with distinct characteristics. Understanding the differential impacts of SARS-CoV-2 variants is crucial for effective public health response and treatment development. We investigated the differential effects of the original Wuhan strain and the emergent Omicron variant of SARS-CoV-2 using a K18-hACE2 transgenic mouse model. We compared the mortality rates, viral loads, and histopathological changes in lung and tracheal tissues, as well as alterations in the lung and intestinal microbiota following infection.

RESULTS

Our findings revealed significant differences between the variants, with the Wuhan strain causing higher mortality rates, severe lung pathology, and elevated viral loads compared to the Omicron variant. Microbiome analyses uncovered novel and distinct shifts in the lung and intestinal microbiota associated with each variant, providing evidence for variant-specific microbiome alterations. These changes suggest microbiome-related mechanisms that might modulate disease severity and host responses to SARS-CoV-2 infection.

CONCLUSIONS

This study highlights critical differences between the Wuhan strain and Omicron variant in terms of mortality, lung pathology, and microbiota changes, emphasizing the role of the microbiome in influencing disease outcomes. Novel findings include the identification of variant-specific microbiota shifts, which underscore potential microbiome-related mechanisms underlying differences in disease severity. These insights pave the way for future research exploring microbiome-targeted interventions to mitigate the impacts of SARS-CoV-2 and other viral infections.

Gut microbiota and metabolome signatures in obese and normal-weight patients with colorectal tumors

Here, we aim to improve our understanding of various colorectal cancer (CRC) risk factors (obesity, unhealthy diet, and gut microbiota/metabolome alteration), analyzing 120 patients with colon polyps, divided in normal-weight (NW) or overweight/obese (OB). Dietary habits data (validated EPIC questionnaires) revealed a higher consumption of processed meat among OB vs. NW patients. Both mucosa-associated microbiota (MAM) on polyps and lumen-associated microbiota (LAM) analyses uncovered distinct bacterial signatures in the two groups. Importantly, we found an enrichment of the pathogenic species Finegoldia magna in MAM of OB patients, regardless of their polyp stage. We observed distinct mucosal-associated metabolome signatures, with OB patients showing increased pyroglutamic acid and reduced niacin levels, and performed microbiota-metabolome integrated analysis. These findings support a model where different risk factors may contribute to tumorigenesis in OB vs. NW patients, highlighting the potential impact of processed meat consumption and F. magna on CRC development among OB patients.

Coevolutionary interplay: Helminths-trained immunity and its impact on the rise of inflammatory diseases

The gut biome, a complex ecosystem of micro- and macro-organisms, plays a crucial role in human health. A disruption in this evolutive balance, particularly during early life, can lead to immune dysregulation and inflammatory disorders. 'Biome repletion' has emerged as a potential therapeutic approach, introducing live microbes or helminth-derived products to restore immune balance. While helminth therapy has shown some promise, significant challenges remain in optimizing clinical trials. Factors such as patient genetics, disease status, helminth species, and the optimal timing and dosage of their products or metabolites must be carefully considered to train the immune system effectively. We aim to discuss how helminths and their products induce trained immunity as prospective to treat inflammatory and autoimmune diseases. The molecular repertoire of helminth excretory/secretory products (ESPs), which includes proteins, peptides, lipids, and RNA-carrying extracellular vesicles (EVs), underscores their potential to modulate innate immune cells and hematopoietic stem cell precursors. Mimicking natural delivery mechanisms like synthetic exosomes could revolutionize EV-based therapies and optimizing production and delivery of ESP will be crucial for their translation into clinical applications. By deciphering and harnessing helminth-derived products' diverse modes of action, we can unleash their full therapeutic potential and pave the way for innovative treatments.

Abnormal microbiota due to prenatal antibiotic as a possible risk factor for Attention-Deficit / Hyperactivity Disorder (ADHD)

One of the major issues modern medicine faces is the increasing use of antibiotics in reaction to the increased incidence of infectious agents. The current trend of antibiotic overuse contributes to microbial dysbiosis. Recent studies have hypothesized that antibiotic exposure during pregnancy, which alters the composition of the microbiome, might increase the likelihood of attention deficit hyperactivity disorder (ADHD). In addition to the ongoing discussion about the potential links between antibiotic usage, microbiome dysbiosis, and ADHD, there is a rising interest in integrating AI and ML into healthcare practices. Diagnosis, treatment plans, and prognoses are all enhanced by these technological advancements. Remote monitors or telemedicine monitoring are among the management techniques described in this chapter for effectively managing illnesses. Also discussed are ways to halt the progression of diseases by preventative measures that use biosensor technology and dietary approaches. Personalized treatment programs, disease progression stages, and prognosis evaluations are all made possible with the use of artificial intelligence and machine learning. By using these technologies to provide individualized therapy, healthcare practitioners may get a better understanding of ADHD and perhaps improve patient outcomes.

Machine learning determines the incidence of Alzheimer's disease based on population gut microbiome profile

The human microbiome is a complex and dynamic community of microbes, thought to have symbiotic benefit to its host. Influences of the gut microbiome on brain microglia have been identified as a potential mechanism contributing to neurodegenerative diseases, such as Alzheimer's disease, motor neurone disease and Parkinson's disease (Boddy SL, Giovannelli I, Sassani M, et al. The gut microbiome: A key player in the complexity of amyotrophic lateral sclerosis (ALS). BMC Med. 2021;19(1):13). We hypothesize that population level differences in the gut microbiome will predict the incidence of Alzheimer's disease using machine learning methods. Cross-sectional analyses were performed in R, using two large, open-access microbiome datasets (n = 959 and n = 2012). Countries in these datasets were grouped based on Alzheimer's disease incidence and the gut microbiome profiles compared. In countries with a high incidence of Alzheimer's disease, there is a significantly lower diversity of the gut microbiome (P < 0.05). A permutational analysis of variance test (P < 0.05) revealed significant differences in the microbiome profile between countries with high versus low incidence of Alzheimer's disease with several contributing taxa identified: at a species level Escherichia coli, and at a genus level Haemophilus and Akkermansia were found to be reproducibly protective in both datasets. Additionally, using machine learning, we were able to predict the incidence of Alzheimer's disease within a country based on the microbiome profile (mean area under the curve 0.889 and 0.927). We conclude that differences in the microbiome can predict the varying incidence of Alzheimer's disease between countries. Our results support a key role of the gut microbiome in neurodegeneration at a population level.

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

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

Music exposure enhances resistance to Salmonella infection by promoting healthy gut microbiota

Music intervention is gaining recognition as a cost-effective therapeutic for improving human health. Despite its growing application, the mechanisms through which music exerts beneficial health effects remain largely unexplored. Here, we show that music can exert beneficial effects in mice through modulating gut microbiome composition. Adult mice were exposed to ambient noise, Mozart's Flute Quartet in D Major, K. 285, or white noise over a three-week period. Afterward, we observed treatment-specific changes in the community of gut commensal bacteria in these animals. Upon subsequent challenge with the bacterial pathogen Salmonella typhimurium, control groups exhibited significant weight loss and increased Salmonella colonization, whereas the Mozart-treated group did not. 16S ribosomal RNA gene sequencing revealed that the Mozart group showed a significant increase in Lactobacillus salivarius, a probiotic known for its antibacterial properties. Further experiments confirmed that L. salivarius mitigated Salmonella infection in mice and that L. salivarius acidified local environments in in vitro culture, thus inhibiting Salmonella growth. Additionally, mice exposed to Mozart consumed more food but showed similar body weight compared to the control groups. Behavioral assessments, including open field and object location tests, revealed that Mozart-treated mice were more active, less anxious, and exhibited enhanced spatial memory. Finally, Mozart exposure was shown to significantly boost colonization of administered L. salivarius and alter gut metabolite profiles. These findings suggest that music exposure fosters healthier gut microbiota, enhancing resistance to bacterial infections and highlighting the potential of music therapy as a novel strategy to combat drug-resistant pathogen infections.

IMPORTANCE

Music therapy is increasingly recognized as a low-cost approach to improving health, but how it works remains unclear. Our study demonstrates that music can positively influence health by altering the gut microbiome. In a mouse model, exposure to Mozart's Flute Quartet in D Major enhanced the gut microbiota, specifically increasing levels of the beneficial bacterium Lactobacillus salivarius. This probiotic protected mice from Salmonella infection by creating an acidic environment that inhibited pathogen growth. Mozart-treated mice also showed reduced anxiety, better spatial memory, and higher food intake without weight gain, suggesting the benefits of music exposure. These findings reveal a novel link between music, gut health, and disease resistance, suggesting that music therapy could be a promising strategy for enhancing gut microbiota and combating infections, including those caused by drug-resistant bacteria.

The Gut-Brain-Microbiota Connection and Its Role in Autism Spectrum Disorders

Autism spectrum disorder (ASD) is a group of complex neurodevelopmental conditions with a heterogeneous and multifactorial etiology that is not yet fully understood. Among the various factors that may contribute to ASD development, alterations in the gut microbiota have been increasingly recognized. Microorganisms in the gastrointestinal tract play a crucial role in the gut-brain axis (GBA), affecting nervous system development and behavior. Dysbiosis, or an imbalance in the microbiota, has been linked to both behavioral and gastrointestinal (GI) symptoms in individuals with ASD. The microbiota interacts with the central nervous system through mechanisms such as the production of short-chain fatty acids (SCFAs), the regulation of neurotransmitters, and immune system modulation. Alterations in its composition, including reduced diversity or an overabundance of specific bacterial taxa, have been associated with the severity of ASD symptoms. Dietary modifications, such as gluten-free or antioxidant-rich diets, have shown potential for improving gut health and alleviating behavioral symptoms. Probiotics, with their anti-inflammatory properties, may support neural health and reduce neuroinflammation. Fecal microbiota transplantation (FMT) is being considered, particularly for individuals with persistent GI symptoms. It has shown promising outcomes in enhancing microbial diversity and mitigating GI and behavioral symptoms. However, its limitations should be considered, as discussed in this narrative review. Further research is essential to better understand the long-term effects and safety of these therapies. Emphasizing the importance of patient stratification and phenotype characterization is crucial for developing personalized treatment strategies that account for individual microbiota profiles, genetic predispositions, and coexisting conditions. This approach could lead to more effective interventions for individuals with ASD. Recent findings suggest that gut microbiota may play a key role in innovative therapeutic approaches to ASD management.

The Impact of Tetracycline on the Soil Microbiome and the Rhizosphere of Lettuce (Lactuca sativa L.)

The impact of tetracycline on the soil and rhizosphere microbiome of lettuce was analyzed. Soil was collected from an agricultural field regularly fertilized with manure, and tetracycline was added at two concentrations (5 mg/kg and 25 mg/kg). In untreated soil, dominant bacteria included Proteobacteria (43.17%), Bacteroidota (17.91%), and Firmicutes (3.06%). Tetracycline addition caused significant shifts in the microbiome composition, notably increasing Actinobacteriota (22%) and favoring Mycobacterium tuberculosis (low concentration) and Mycobacterium holsaticum (high concentration). Proteobacteria decreased by 21%, possibly indicating antibiotic resistance development. An increase in Firmicutes, particularly Bacillales, suggested a selection for resistant strains. In the lettuce rhizosphere, tetracycline-induced changes were less pronounced than in soil. Proteobacteria remained dominant, but taxa like Burkholderiales and Chitinophagales increased in response to tetracycline. The rise in chitin-degrading bacteria might result from fungal overgrowth linked to the bacteriostatic effects of tetracycline. Pathogens such as M. tuberculosis, observed in the soil, were not detected in the lettuce rhizosphere.

Perforin Generated by CD8+ T Cells Exacerbates Inflammatory Bowel Disease-Induced Depression by Promoting CXCL9 Production in Intestinal Epithelial Cells

BACKGROUND & AIMS

Approximately 25.2% of patients with inflammatory bowel disease (IBD) suffer from psychological disorders, particularly depression. Recent studies have indicated a close relationship between intestinal immunity and brain disorders.

METHODS

We performed transcriptome analysis and immunofluorescence staining of colonic samples from patients with IBD. The role of perforin generated by colonic CD8+ T cells in IBD-induced depression was investigated in dextran sulfate sodium- and CD8+ T-cell transfer-induced colitis by using Prf1-EGFP reporter and Prf1 knockout mice.

RESULTS

In this study, we revealed a significant correlation between depressive symptom severity and perforin production in CD8+ T cells in both patients with IBD and mice with colitis. Moreover, perforin deficiency in CD8+ T cells mitigated both inflammation and depressive-like behaviors in mice with colitis. Mechanistically, perforin and granzyme B were found to stimulate the expression of CXCL9 in colonic epithelial cells. CXCL9 was shown to be released into the circulation and to enter the hippocampus, where it induced endoplasmic reticulum stress in hippocampal neurons through the CXCR3-HSPA5 axis. This cascade of events subsequently was found to exacerbate depression. Neutralizing CXCL9 in vivo alleviated depression but had no effect on colitis in mice.

CONCLUSIONS

Perforin generated by colonic CD8+ T cells promotes intestinal epithelial cell CXCL9 production, which leads to neuronal endoplasmic reticulum stress in hippocampus and induces depression in IBD.

The impact of wild-boar-derived microbiota transplantation on piglet microbiota, metabolite profile, and gut proinflammatory cytokine production differs from sow-derived microbiota

Colonization of co-evolved, species-specific microbes in early life plays a crucial role in gastrointestinal development and immune function. This study hypothesized that modern pig production practices have resulted in the loss of co-evolved species and critical symbiotic host-microbe interactions. To test this, we reintroduced microbes from wild boars (WB) into conventional piglets to explore their colonization dynamics and effects on gut microbial communities, metabolite profiles, and immune responses. At postnatal day (PND) 21, 48 piglets were assigned to four treatment groups: (i) WB-derived mixed microbial community (MMC), (ii) sow-derived MMC, (iii) a combination of WB and sow MMC (Mix), or (iv) Control (PBS). Post-transplantation analyses at PND 48 revealed distinct microbial communities in WB-inoculated piglets compared with Controls, with trends toward differentiation from Sow but not Mix groups. WB-derived microbes were more successful in colonizing piglets, particularly in the Mix group, where they competed with Sow-derived microbes. WB group cecal digesta enriched with Lactobacillus helveticus, Lactobacillus mucosae, and Lactobacillus pontis. Cecal metabolite analysis showed that WB piglets were enriched in histamine, acetyl-ornithine, ornithine, citrulline, and other metabolites, with higher histamine levels linked to Lactobacillus abundance. WB piglets exhibited lower cecal IL-1β and IL-6 levels compared with Control and Sow groups, whereas the Mix group showed reduced IFN-γ, IL-2, and IL-6 compared with the Sow group. No differences in weight gain, fecal scores, or plasma cytokines were observed, indicating no adverse effects. These findings support that missing WB microbes effectively colonize domestic piglets and may positively impact metabolite production and immune responses.IMPORTANCEThis study addresses the growing concern over losing co-evolved, species-specific microbes in modern agricultural practices, particularly in pig production. The implementation of strict biosecurity measures and widespread antibiotic use in conventional farming systems may disrupt crucial host-microbe interactions that are essential for gastrointestinal development and immune function. Our research demonstrates that by reintroducing wild boar-derived microbes into domestic piglets, these microbes can successfully colonize the gut, influence microbial community composition, and alter metabolite profiles and immune responses without causing adverse effects. These findings also suggest that these native microbes can fill an intestinal niche, positively impacting immune activation. This research lays the groundwork for future strategies to enhance livestock health and performance by restoring natural microbial populations that produce immune-modulating metabolites.

Research Status and Trends of Gut Microbiota and Intestinal Diseases Based on Bibliometrics

Gut microbiota plays an important role in gut health, and its dysbiosis is closely related to the pathogenesis of various intestinal diseases. The field of gut microbiota and intestinal diseases has not yet been systematically quantified through bibliometric methods. This study conducted bibliometric analysis to delineate the evolution of research on gut microbiota and intestinal diseases. Data were sourced from the Web of Science Core Collection database from 2009 to 2023 and were scientometrically analyzed using CiteSpace. We have found that the number of annual publications has been steadily increasing and showing an upward trend. China and the Chinese Academy of Sciences are the country and institution with the most contributions, respectively. Frontiers in Microbiology and Nutrients are the journals with the most publications, while Plos One and Nature are the journals with the most citations. The field has shifted from focusing on traditional descriptive analysis of gut microbiota composition to exploring the causal relationship between gut microbiota and intestinal diseases. The research hotspots and trends mainly include the correlation between specific intestinal diseases and gut microbiota diversity, the mechanism of gut microbiota involvement in intestinal diseases, the exploration of important gut microbiota related to intestinal diseases, and the relationship between gut microbiota and human gut health. This study provides a comprehensive knowledge map of gut microbiota and intestinal diseases, highlights key research areas, and outlines potential future directions.

Assessing the gut microbiota composition in older adults: connections to physical activity and healthy ageing

The composition and functionality of the gut microbiota (GM) changes throughout the life course. As we move into older age, it starts to shift towards a less healthy one, which may lead to an imbalance in the GM community. Strategies that can reverse age-related dysbiosis are an important part of healthy aging. Little is known about the GM composition of older adults with different physical activity (PA) levels and whether it might contribute to healthy ageing. The aim of this study was to compare the GM composition of older adults with different PA levels and assess if it is associated with healthy ageing. 101 participants aged between 65-85 years undertook anthropometric measures, a 6-min walking test, wore an accelerometer for 7 days and provided a faecal sample. Faecal GM composition was analysed using 16S rRNA sequencing. We found that those who fulfilled the WHO/UK PA recommendations had higher relative abundance of several health-related bacteria such as Lactobacillus, F. prausnitzii and Roseburia intestinalis and lower abundance of disease-associated bacteria such as D.piger or Enterobacterales when compared to those who did not reach PA recommendations. These findings suggest that PA might improve the GM composition and has the potential to, at least partially, revert age-associated dysbiosis and promote healthy ageing.

Gut dysbiosis as a driver of neuroinflammation in attention-deficit/hyperactivity disorder: A review of current evidence

There is mounting evidence for the involvement of the immune system, neuroinflammation and disturbed gut microbiota, or dysbiosis, in attention-deficit/hyperactivity disorder (ADHD). Gut dysbiosis is strongly implicated in many physical, autoimmune, neurological, and neuropsychiatric conditions, however knowledge of its particular pathogenic role in ADHD is sparse. As such, this narrative review examines and synthesizes the available evidence related to inflammation, dysbiosis, and neural processes in ADHD. Minimal differences in microbiota diversity measures between cases and controls were found, however many relative abundance differences were observed at all classification levels (phylum to strain). Compositional differences of taxa important to key gut-brain axis pathways, in particular Bacteroides species and Faecalibacterium, may contribute to inflammation, brain functioning differences, and symptoms, in ADHD. We have identified one possible model of ADHD etiopathogenesis involving systemic inflammation, an impaired blood-brain barrier, and neural disturbances as downstream consequences of gut dysbiosis. Nevertheless, studies conducted to date have varied degrees of methodological rigour and involve diverse participant characteristics and analytical techniques, highlighting a need for additional research.

The microbiome: what a neurologist needs to know

The gastrointestinal tract is inhabited by trillions of micro-organisms that form the gut microbiome, which serves various functions that can influence neurological pathways. It can release metabolites that could affect the nervous system. The bidirectional communication between the intestine and the central nervous system is known as the gut-brain axis. This communication can be impacted by the microbiota in various direct and indirect ways. There has been a suggested connection between the microbiome and many neurological disorders, including epilepsy, Alzheimer's disease, Parkinson's disease and multiple sclerosis. This has been explored in human and animal studies. While no microbial biomarkers have been identified yet, alterations in several taxa have been suggested to be associated with disease states. The potential of the microbiome to modulate neurological function has sparked multiple clinical trials using gut-altering treatments, some with positive preliminary results.

Gut bacterial and fungal communities of François' langur (Trachypithecus francoisi) changed coordinate to different seasons

Introduction

François' langur (Trachypithecus francoisi), an endangered primate endemic to limestone forests in Vietnam and China, relies on gut microbiota to maintain gastrointestinal stability and adapt to dietary shifts. While gut microbial communities are dynamic and sensitive to seasonal and resource variations, their specific responses in François' langurs remain poorly characterized. This study investigates seasonal variations in the composition and diversity of gut bacterial and fungal communities in this species to enhance understanding of its ecological adaptations.

Methods

Fresh fecal samples from 22 François' langurs in Mayanghe National Nature Reserve, China, were collected across four seasons. Bacterial and fungal communities were analyzed using high-throughput sequencing to assess taxonomic composition and α-diversity. Statistical comparisons were conducted to evaluate seasonal differences at phylum and genus levels.

Results

Significant seasonal shifts occurred in both bacterial and fungal communities. Bacterial α-diversity peaked in warmer seasons, whereas fungal diversity was higher in colder months. At the genus level, Akkermansia (1.3% relative abundance in summer), a mucin-degrading bacterium linked to gut health, dominated warmer seasons. In contrast, the fungal genus Cercophora, associated with plant biomass degradation, was enriched during colder seasons. Seasonal factors strongly influenced microbial structure, with distinct community assemblages observed across all seasons.

Discussion

The inverse diversity patterns of bacterial and fungal communities suggest complementary roles in nutrient extraction under seasonal dietary constraints. Akkermansia's summer prevalence may reflect enhanced mucin utilization during fruit-rich periods, while Cercophora's cold-season dominance likely aids cellulose breakdown in leaf-heavy diets. These dynamics highlight the microbiota's role in optimizing energy harvest from seasonally variable diets. By elucidating microbial seasonal plasticity, this study provides critical insights for developing conservation strategies tailored to the nutritional ecology of François' langurs.

Ensemble learning based on matrix completion improves microbe-disease association prediction

Microbes have a profound impact on human health. Identifying disease-associated microbes would provide helpful guidance for drug development and disease treatment. Through an enormous experimental effort, limited disease-associated microbes have been determined. Accurate computational approaches are needed to predict potential microbe-disease associations for biomedical screening. In this study, we present an ensemble learning framework entitled SABMDA to improve microbe-disease association inference. We first integrate multi-source of information from both microbes and diseases, and develop two matrix completion algorithms to predict microbe-disease associations successively. Ablation tests show combining the two matrix completion algorithms can receive better prediction performance. Moreover, comprehensive experiments, including cross-validations and independent test, demonstrate that SABMDA outperforms seven recent baseline methods significantly. Finally, we apply SABMDA to three diseases to predict their associated microbes, and results show SABMDA's remarkable prediction ability in real situations.

Metabolic pathways associated with Firmicutes prevalence in the gut of multiple livestock animals and humans

Dynamic interspecific interactions and environmental factors deeply impact the composition of microbiotic communities in the gut. These factors intertwined with the host's genetic background and social habits cooperate synergistically as a hidden force modulating the host's physiological and health determinants, with certain bacterial species being maintained from generation to generation. Firmicutes, one of the dominant bacterial phyla present across vertebrate classes, exhibits a wide range of functional capabilities and colonization strategies. While ecological scenarios involving microbial specialization and metabolic functions have been hypothesized, the specific mechanisms that sustain the persistence of its microbial taxa in a high diversity of hosts remain elusive. This study fills this gap by investigating the Firmicutes metabolic mechanisms contributing to their prevalence and heritability in the host gut on metagenomes-assembled bacterial genomes collected from 351 vertebrate samples, covering 18 food-producing animals and humans, specific breeds and closely-related species. We observed that taxa belonging to Acetivibrionaceae, Clostridiaceae, Lachnospiraceae, Ruminococcaceae, and the not well understood CAG-74 family were evolutionarily shared across all hosts. These prevalent taxa exhibit metabolic pathways significantly correlated with extra-host survival mechanisms, cell adhesion, colonization and host transmission, highlighted by sporulation, glycan biosynthesis, bile acid metabolism, and short-chain fatty acid encoded genes. Our findings provide a deeper understanding of the ecological foundations governing distinct transmission modes, effective colonization establishment, and maintenance of Firmicutes, offering new perspectives on both well-known and poorly characterized species.

Interactions of the maternal microbiome with diet, stress, and infection influence fetal development

Humans and other animals contain multitudes of microorganisms including bacteria, fungi, and viruses, which make up a diverse microbiome. Across body sites including skin, gastrointestinal tract, and oral cavity there are distinct microbial niches that are made up of trillions of microorganisms that have co-evolved to inhabit and interact with the host. The microbiome also interacts with the changing environment. This tripartite interaction between the host, microbiome, and environment suggests microbial communities play a key role in the biological processes of the host, such as development and behaviors. Over the past two decades, emerging research continues to reveal how host and microbe interactions impact nervous system signaling and behaviors, and influence neurodevelopmental, neurological, and neurodegenerative disorders. In this review, we will describe the unique features of the maternal microbiome that exist during the perinatal period and discuss evidence for the function of the maternal microbiome in offspring development. Finally, we will discuss how the maternal environment interacts with the microbiome and nervous system development and then postulate how the maternal microbiome can modify early offspring development to have lasting influence on brain health.

Personalized nutrition studies of human gut microbiome-polyphenol interactions utilizing continuous multistaged in vitro fermentation models-a narrative review

The gut microbiota, a complex community of microorganisms primarily inhabiting the human large intestine, plays a crucial role in human health. Gut dysbiosis, characterized by an imbalance in gut bacterial populations, has been increasingly recognized as a significant factor in the pathogenesis of metabolic diseases such as type 2 diabetes, inflammatory bowel disease, and colorectal cancer. Polyphenols are critical modulators of gut microbial composition and metabolism. However, the extent of polyphenol-induced modulation of the gut microbiome remains largely unexplored. In vitro models offer a convenient and ethical alternative to in vivo studies for investigating nutrient-gut microbiome interactions, facilitating easy sampling and controlled experimental conditions. Among these, continuous multistaged in vitro fermentation models, which simulate different sections of the human gastrointestinal tract (e.g., proximal colon, transverse colon, and distal colon), provide a more accurate representation of the human gut environment compared to single-batch fermentation. Various configurations of these multistaged models have been developed and widely employed in studies examining the effects of polyphenols on the gut microbiome. This review aims to summarize the different configurations of multistaged in vitro fermentation models and recent advancements in their development, highlight key aspects of experimental design, outline commonly used analytical workflows with complementary analyses, and review the restorative effects of polyphenol interventions on dysregulated gut microbiota.

Gut Microbiota Alterations in Patients With Kawasaki Disease

The intestinal microbiota influences many host biological processes, including metabolism, intestinal barrier functions, and immune responses in the gut and distant organs. Alterations in its composition have been associated with the development of inflammatory disorders and cardiovascular diseases, including Kawasaki disease (KD). KD is an acute pediatric vasculitis of unknown etiology and the leading cause of acquired heart disease in children in the United States. The presence of gastrointestinal symptoms in the acute phase of KD has been associated with an increased risk of treatment resistance and the development of coronary artery aneurysms. Studies report alterations in fecal bacterial communities of patients with KD, characterized by the blooming of pathogenic bacteria and decreased relative abundance of short-chain fatty acid-producing bacteria. However, causality and functionality cannot be established from these observational patient cohorts of KD. This highlights the need for more advanced and rigorous studies to establish causality and functionality in both experimental models of KD vasculitis and patient cohorts. Here, we review the evidence linking an altered gut microbiota composition to the development of KD, assess the potential mechanisms involved in this process, and discuss the potential therapeutic value of these observations.

A guide to germ-free and gnotobiotic mouse technology to study health and disease

The intestinal microbiota has major influence on human physiology and modulates health and disease. Complex host-microbe interactions regulate various homeostatic processes, including metabolism and immune function, while disturbances in microbiota composition (dysbiosis) are associated with a plethora of human diseases and are believed to modulate disease initiation, progression and therapy response. The vast complexity of the human microbiota and its metabolic output represents a great challenge in unraveling the molecular basis of host-microbe interactions in specific physiological contexts. To increase our understanding of these interactions, functional microbiota research using animal models in a reductionistic setting are essential. In the dynamic landscape of gut microbiota research, the use of germ-free and gnotobiotic mouse technology, in which causal disease-driving mechanisms can be dissected, represents a pivotal investigative tool for functional microbiota research in health and disease, in which causal disease-driving mechanisms can be dissected. A better understanding of the health-modulating functions of the microbiota opens perspectives for improved therapies in many diseases. In this review, we discuss practical considerations for the design and execution of germ-free and gnotobiotic experiments, including considerations around germ-free rederivation and housing conditions, route and timing of microbial administration, and dosing protocols. This comprehensive overview aims to provide researchers with valuable insights for improved experimental design in the field of functional microbiota research.

Microbiome analysis of gut microbiota in patients with colorectal polyps and healthy individuals

Colorectal polyps serve as the primary precursors for colorectal cancer. A close relationship has been observed between colorectal polyps and gut microbiota. However, the composition and role of the microbiome associated with tubular adenoma are not well understood. In this study, we prospectively evaluated alterations in gut microbiota among patients with colorectal polyps. A total of 60 subjects were enrolled in this study, including 30 patients with colorectal polyps (CP group) and 30 healthy controls (control group). The 16S rRNA sequencing was employed to characterize the gut microbiome in fecal samples. The results revealed that the beta diversity of the gut microbiota in the CP group significantly differs from that of the control group (p = 0.001). At the phylum level, the relative abundance of Bacteroides, Fusobacteria, and Proteobacteria was higher in the CP group compared to the control group (p < 0.05), whereas the relative abundance of Actinobacteria was higher in the control group in comparison to the CP group (p < 0.05). At the genus level, the abundance of Bacteroides increased in the CP group (p < 0.05), while Bifidobacterium declined in the CP group (p < 0.05). At the species level, the abundance of Clostridium perfringens, unidentified_Bacteroides, unidentified_Dorea, Escherichia coli, Clostridium ramosum, and Ruminococcus gnavus was higher (p < 0.05), whereas the abundance of Bifidobacterium adolescentis, unclassified_Bifidobacterium, Bifidobacterium longum, Faecalibacterium prausnitzii, and unidentified_Bifidobacterium is lower in CP group compared to the control group (p < 0.05). There was a structural imbalance in the composition of intestinal colonization flora for CP patients, characterized by a decrease in beneficial bacteria and an increase in harmful bacteria. Escherichia, Shigella, and Bacteroides may serve as promising biomarkers for early detection of colorectal polyps.

Malted Barley as a Potential Feed Supplementation for the Reduction of Enteric Methane Emissions, Rumen Digestibility, and Microbiome Community Changes in Laboratory Conditions

Three sets of in vitro rumen fermentation experiments were conducted to determine the effects of diets that included malted barley (MB) and basal diets (grain- and forage-based) on the in vitro gas production, greenhouse gas (GHG) emissions, rumen fermentation profiles, and microbiome changes in the rumen when supplemented with feedlot or dairy rations. The first experiment (Exp. 1) was conducted to evaluate the effects of various levels of MB (0% [referred to as a control], 10%, 20%, and 30%, as-fed basis) supplemented with a grain-based diet in a feedlot ration (2.5 g/bottle) after 48 h ruminal incubation on the in vitro gas production, GHG emissions, and rumen fermentation rate. The second two sets of in vitro experiments (Exp. 2a, b) were conducted to determine (1) the effects of linear dose levels of malted barley (MB; 0%, 10%, 20%, 30%, and 40% as-fed) with two different basal diets (grain-based and forage-based) and (2) the effects of different sources of MB (control, Korean, Canadian, and the USA; 30% MB, as-fed) in a dairy ration after 24 h incubation on in vitro gas production, rumen fermentation profiles, GHG emissions (methane [CH4] and nitrous oxide [N2O]), in vitro dry matter disappearance rate (IVDMD), and microbiome changes. Commercially available α-amylase (0.2 g/100 mL) was used as a sub-control in Exp. 2a. Using gas chromatography, all gases were collected using an ANKOM Gas Production system and analyzed for CH4 and N2O. In Exp. 1, total gas production, cumulative gas, and GHG productions (CH4, N2O) linearly decreased (p ≤ 0.05) with increasing MB supplementation. In Exp. 2a, cumulative in vitro gas, total gas production, and rumen fermentation profiles (e.g., total VFA, acetate, butyrate, iso-butyrate, valerate, and iso-valerate) linearly decreased (p < 0.05-0.01) with increasing MB supplementation, with diet-treatment interactions (p < 0.001). In addition, CH4 and N2O production (mL/g DM) linearly and quadratically decreased (p < 0.01) with increasing MB supplementation across the diets. However, IVDMD linearly and/or quadratically increased (p < 0.01) with increasing MB, with diet-treatment interactions (p < 0.001). The average populations of Bacteroidetes, Proteobacteria, and Spirochaetes were significantly decreased (p < 0.01-0.001) for MB treatment groups compared to the control group. Therefore, it may be possible to suppress methane production directly and indirectly by adding MB and α-amylase by modifying ruminal fermentation profiles.

Microbiome metabolic capacity is buffered against phylotype losses by functional redundancy

Many animals contain a species-rich and diverse gut microbiota that likely contributes to several host-supportive services that include diet processing and nutrient provisioning. Loss of microbiome taxa and their associated metabolic functions as result of perturbations may result in loss of microbiome-level services and reduction of metabolic capacity. If metabolic functions are shared by multiple taxa (i.e., functional redundancy), including deeply divergent lineages, then the impact of taxon/function losses may be dampened. We examined to what degree alterations in phylotype diversity impact microbiome-level metabolic capacity. Feeding two nutritionally imbalanced diets to omnivorous Periplaneta americana over 8 weeks reduced the diversity of their phylotype-rich gut microbiomes by ~25% based on 16S rRNA gene amplicon sequencing, yet PICRUSt2-inferred metabolic pathway richness was largely unaffected due to their being polyphyletic. We concluded that the nonlinearity between taxon and metabolic functional losses is due to microbiome members sharing many well-characterized metabolic functions, with lineages remaining after perturbation potentially being capable of preventing microbiome "service outages" due to functional redundancy.

IMPORTANCE

Diet can affect gut microbiome taxonomic composition and diversity, but its impacts on community-level functional capabilities are less clear. Host health and fitness are increasingly being linked to microbiome composition and further modeling of the relationship between microbiome taxonomic and metabolic functional capability is needed to inform these linkages. Invertebrate animal models like the omnivorous American cockroach are ideal for this inquiry because they are amenable to various diets and provide high replicates per treatment at low costs and thus enabling rigorous statistical analyses and hypothesis testing. Microbiome taxonomic composition is diet-labile and diversity was reduced after feeding on unbalanced diets (i.e., post-treatment), but the predicted functional capacities of the post-treatment microbiomes were less affected likely due to the resilience of several abundant taxa surviving the perturbation as well as many metabolic functions being shared by several taxa. These results suggest that both taxonomic and functional profiles should be considered when attempting to infer how perturbations are altering gut microbiome services and possible host outcomes.

Effect of fecal microbiota transplantation on ulcerative colitis model in rats: The gut-brain axis

Study objectives

The impact of fecal microbiota transplantation (FMT) on the TLR4/MYD88/NF-kB signaling pathway in the colon in the ulcerative colitis model, as well as the incidence of anxiety behaviors caused by the colitis model was investigated.

Methods

Twenthy four ats were induced with ulcerative colitis using a 4 % acetic acid solution administered intrarectally and were subsequently treated with prednisolone and FMT. The study examined several indicators, such as TLR4, MYD88, and NF-κB mRNA expression, along with oxidative stress factors. Additionally, it examined the relationship between anxiety-related behaviors and colitis and assessed the pro-inflammatory cytokines in the hippocampus.

Results

FMT led to lower disease score index and improved colon tissue pathology findings. This was associated with reduced mRNA expression of TLR4, MYD88, and NF-κB, as well as lower levels of TOS, and higher levels of TAC, GSH, and GSSG in colon tissues. FMT was found to reduce anxiety in both the open field and elevated plus maze tests. Additionally, levels of IL-6 and TNF-a were decreased in the hippocampus.

Conclusions

FMT suppressed acetic acid-induced colitis by inhibiting the TLR4/MYD88/NF-kB signaling pathway. FMT reduced anxiety in open field and plus maze tests, and resulted in decreased levels of IL-6 and TNF-a in the hippocampus.

Dynamic Impacts of Stock Enhancement on Kaluga Sturgeon (Huso dauricus): Novel Conservation Strategy Insights from the Gut Microbe Composition and Gene Expression Mode

The sturgeon population has experienced strict threats due to inordinate human activities in the last decade and has been classified into the Red List of Threatened Species in recent years. Stock enhancement is one effective practice for the conservation of wild sturgeons. However, the survival conditions for sturgeon were not satisfactory after they were directly restocked into their natural habitat. Huso dauricus is an important protected sturgeon species, and finding an appropriate conservation strategy for the wild population is urgent. To clarify the dynamic adaptability of Huso dauricus to its wild environment, 1000 individuals were released into a natural river. On the 0th, 7th, 14th, and 30th days, five recaptured individuals were used to evaluate the dynamic trends in biochemical biomarkers, intestinal histomorphology, gut microbe taxon composition, and transcription profile over 30 days of stock enhancement. Our results indicated that Huso dauricus individuals still had a physiological stress status on the seventh day and then gradually adapted to the wild habitat 14 days after reintroduction based on the serum cortisol level. Meanwhile, the feeding habitat, organ function indicators, and growth performance showed similar dynamic changes within 30 days. Interestingly, their gut bacterial diversity and taxon structure also fluctuated over the 30 days after restocking, and they were accompanied by dynamic changes in intestinal pathological injury and tight junction protein expression in this period. The transcriptome analysis revealed the dynamic adaptability of Huso dauricus to wild habitats associated with the expression modes of genes related to the FoxO family, immune system, cytochrome family, and ATP metabolism. Taken together, the findings of the present research demonstrated that artificial reintroduction had dynamic impacts on the health condition of Huso dauricus and that 14 days of wilderness training might be essential for sturgeon restocking practices. Our study revealed the adaption mechanism of Huso dauricus at the molecular level during the restocking period and shed light on the theoretical guidelines for wild sturgeon conservation.

Health-Improving Effects of Polyphenols on the Human Intestinal Microbiota: A Review

Dietary polyphenols are garnering attention in the scientific community due to their potential health-beneficial properties and preventative effects against chronic diseases, viz. cardiovascular diseases, diabetes, obesity, and neurodegenerative diseases. Polyphenols are antioxidants that change microbial composition by suppressing pathogenic bacteria and stimulating beneficial bacteria. The interaction of polyphenols with dietary fibers affects their bioaccessibility in the upper and lower parts of the digestive tract. Dietary fibers, polyphenols, their conjugates, and their metabolites modulate microbiome population and diversity. Consuming polyphenol-rich dietary fibers such as pomegranate, cranberry, berries, and tea improves gut health. A complex relationship exists between polyphenol-rich diets and gut microbiota for functioning in human health. In this review, we provide an overview of the interactions of dietary polyphenols, fibers, and gut microbiota, improving the understanding of the functional properties of dietary polyphenols.

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.

The Gut Microbiota-Related Antihyperglycemic Effect of Metformin

It is critical to sustain the diversity of the microbiota to maintain host homeostasis and health. Growing evidence indicates that changes in gut microbial biodiversity may be associated with the development of several pathologies, including type 2 diabetes mellitus (T2DM). Metformin is still the first-line drug for treatment of T2DM unless there are contra-indications. The drug primarily inhibits hepatic gluconeogenesis and increases the sensitivity of target cells (hepatocytes, adipocytes and myocytes) to insulin; however, increasing evidence suggests that it may also influence the gut. As T2DM patients exhibit gut dysbiosis, the intestinal microbiome has gained interest as a key target for metabolic diseases. Interestingly, changes in the gut microbiome were also observed in T2DM patients treated with metformin compared to those who were not. Therefore, the aim of this review is to present the current state of knowledge regarding the association of the gut microbiome with the antihyperglycemic effect of metformin. Numerous studies indicate that the reduction in glucose concentration observed in T2DM patients treated with metformin is due in part to changes in the biodiversity of the gut microbiota. These changes contribute to improved intestinal barrier integrity, increased production of short-chain fatty acids (SCFAs), regulation of bile acid metabolism, and enhanced glucose absorption. Therefore, in addition to the well-recognized reduction of gluconeogenesis, metformin also appears to exert its glucose-lowering effect by influencing gut microbiome biodiversity. However, we are only beginning to understand how metformin acts on specific microorganisms in the intestine, and further research is needed to understand its role in regulating glucose metabolism, including the impact of this remarkable drug on specific microorganisms in the gut.

Deterministic succession patterns in the rumen and fecal microbiome associate with host metabolic shifts in peripartum dairy cattle

BACKGROUND

Metabolic disorders in peripartum ruminants affect health and productivity, with gut microbiota playing a key role in host metabolism. Therefore, our study aimed to characterize the gut microbiota of peripartum dairy cows to better understand the relationship between metabolic phenotypes and the rumen and fecal microbiomes during the peripartum period.

RESULTS

In a longitudinal study of 91 peripartum cows, we analyzed rumen and fecal microbiomes via 16S rRNA and metagenomic sequencing across six time points. By using enterotype classification, ecological model, and random forest analysis, we identified distinct deterministic succession patterns in the rumen and fecal microbiomes (rumen: rapid transition-transition-stable; hindgut: stable-transition-stable). Key microbes, such as Succiniclasticum and Bifidobacterium, were found to drive microbial succession by balancing stochastic and deterministic processes. Notably, we observed that changes in gut microbiota succession patterns significantly influenced metabolic phenotypes (e.g., serum non-esterified fatty acid, glucose, and insulin levels). Mediation analysis suggested that specific gut microbes (e.g., Prevotella sp900315525 in the rumen and Alistipes sp015059845 in the hindgut) and metabolic pathways (e.g., glucose-related pathway) were associated with host metabolic phenotypes.

CONCLUSIONS

Overall, utilizing a large gut microbiome dataset and enterotype- and ecological model-based microbiome analyses, we comprehensively elucidated the succession and assembly of the gut microbiota in peripartum dairy cows. We further confirmed that changes in gut microbiota succession patterns were significantly related to the metabolic phenotypes of peripartum dairy cows. These findings provide valuable insights for developing health management strategies for peripartum ruminants.

Advancing therapeutic strategies for graft-versus-host disease by targeting gut microbiome dynamics in allogeneic hematopoietic stem cell transplantation: current evidence and future directions

Hematopoietic stem cell transplantation (HSCT) is a highly effective therapy for malignant blood illnesses that pose a high risk, as well as diseases that are at risk due to other variables, such as genetics. However, the prevalence of graft-versus-host disease (GVHD) has impeded its widespread use. Ensuring the stability of microbial varieties and associated metabolites is crucial for supporting metabolic processes, preventing pathogen intrusion, and modulating the immune system. Consequently, it significantly affects the overall well-being and susceptibility of the host to disease. Patients undergoing allogeneic hematopoietic stem cell transplantation (allo-HSCT) may experience a disruption in the balance between the immune system and gut bacteria when treated with medicines and foreign cells. This can lead to secondary intestinal inflammation and GVHD. Thus, GM is both a reliable indicator of post-transplant mortality and a means of enhancing GVHD prevention and treatment after allo-HSCT. This can be achieved through various strategies, including nutritional support, probiotics, selective use of antibiotics, and fecal microbiota transplantation (FMT) to target gut microbes. This review examines research advancements and the practical use of intestinal bacteria in GVHD following allo-HSCT. These findings may offer novel insights into the prevention and treatment of GVHD after allo-HSCT.

Unveiling gut microbiota's role: Bidirectional regulation of drug transport for improved safety

Drug safety is a paramount concern in the field of drug development, with researchers increasingly focusing on the bidirectional regulation of gut microbiota in this context. The gut microbiota plays a crucial role in maintaining drug safety. It can influence drug transport processes in the body through various mechanisms, thereby modulating their efficacy and toxicity. The main mechanisms include: (1) The gut microbiota directly interacts with drugs, altering their chemical structure to reduce toxicity and enhance efficacy, thereby impacting drug transport mechanisms, drugs can also change the structure and abundance of gut bacteria; (2) bidirectional regulation of intestinal barrier permeability by gut microbiota, promoting the absorption of nontoxic drugs and inhibiting the absorption of toxic components; (3) bidirectional regulation of the expression and activity of transport proteins by gut microbiota, selectively promoting the absorption of effective components or inhibiting the absorption of toxic components. This bidirectional regulatory role enables the gut microbiota to play a key role in maintaining drug balance in the body and reducing adverse reactions. Understanding these regulatory mechanisms sheds light on novel approaches to minimize toxic side effects, enhance drug efficacy, and ultimately improve drug safety. This review systematically examines the bidirectional regulation of gut microbiota in drug transportation from the aforementioned aspects, emphasizing their significance in ensuring drug safety. Furthermore, it offers a prospective outlook from the standpoint of enhancing therapeutic efficacy and reducing drug toxicity, underscoring the importance of further exploration in this research domain. It aims to provide more effective strategies for drug development and treatment.

Gut microbiome-gut brain axis-depression: interconnection

OBJECTIVES

The relationship between the gut microbiome and mental health, particularly depression, has gained significant attention. This review explores the connection between microbial metabolites, dysbiosis, and depression. The gut microbiome, comprising diverse microorganisms, maintains physiological balance and influences health through the gut-brain axis, a communication pathway between the gut and the central nervous system.

METHODS

Dysbiosis, an imbalance in the gut microbiome, disrupts this axis and worsens depressive symptoms. Factors like diet, antibiotics, and lifestyle can cause this imbalance, leading to changes in microbial composition, metabolism, and immune responses. This imbalance can induce inflammation, disrupt neurotransmitter regulation, and affect hormonal and epigenetic processes, all linked to depression.

RESULTS

Microbial metabolites, such as short-chain fatty acids and neurotransmitters, are key to gut-brain communication, influencing immune regulation and mood. The altered production of these metabolites is associated with depression. While progress has been made in understanding the gut-brain axis, more research is needed to clarify causative relationships and develop new treatments. The emerging field of psychobiotics and microbiome-targeted therapies shows promise for innovative depression treatments by harnessing the gut microbiome's potential.

CONCLUSIONS

Epigenetic mechanisms, including DNA methylation and histone modifications, are crucial in how the gut microbiota impacts mental health. Understanding these mechanisms offers new prospects for preventing and treating depression through the gut-brain axis.

Investigation of Intestinal Microbes of Five Zokor Species Based on 16S rRNA Sequences

Zokor is a group of subterranean rodents that are adapted to underground life and feed on plant roots. Here, we investigated the intestinal microbes of five zokor species (Eospalax cansus, Eospalax rothschildi, Eospalax smithi, Myospalax aspalax, and Myospalax psilurus) using 16S amplicon technology combined with bioinformatics. Microbial composition analysis showed similar intestinal microbes but different proportions among five zokor species, and their dominant bacteria corresponded to those of herbivores. To visualize the relationships among samples, PCoA and PERMANOVA tests showed that the intestinal microbes of zokors are largely clustered by host species, but less so by genetics and geographical location. To find microbes that differ among species, LefSe analysis identified Lactobacillus, Muribaculaceae, Lachnospiraceae_NK4A136_group, unclassified_f_Christensenellaceae, and Desulfovibrio as biomarkers for E. cansus, E. rothschildi, E. smithi, M. aspalax, and M. psilurus, respectively. PICRUSt metagenome predictions revealed enriched microbial genes for carbohydrate and amino acid metabolism in E. cansus and E. smithi, and for cofactor and vitamin metabolism as well as glycan biosynthesis and metabolism in E. rothschildi, M. aspalax, and M. psilurus. Our results demonstrated differences in the microbial composition and functions among five zokor species, potentially related to host genetics, and host ecology including dietary habits and habitat environment. These works would provide new insight into understanding how subterranean zokors adapt to their habitats by regulating intestinal microbes.

Gut Dysbiosis and Adult Atopic Dermatitis: A Systematic Review

Background/Objectives: Research on the relationship between gut microbiota (GM) and atopic dermatitis (AD) has seen a growing interest in recent years. The aim of this systematic review was to determine whether differences exist between the GM of adults with AD and that of healthy adults (gut dysbiosis). Methods: We conducted a systematic review based on the PRISMA guidelines (Preferred Reporting Items for Systematic Reviews and Meta-Analyses). The search was performed using PubMed, EMBASE, and Web of Science. Observational and interventional studies were analyzed. Results: Although the studies showed heterogeneous results, some distinguishing characteristics were found in the intestinal microbial composition of adults with dermatitis. Even though no significant differences in diversity were found between healthy and affected adults, certain microorganisms, such as Bacteroidales, Enterobacteriaceae, and Clostridium (perfringens), were more characteristic of the fecal microbiota in adults with AD. Healthy individuals exhibited lower abundances of aerobic bacteria and higher abundances of short-chain fatty acid-producing species and polyamines. Clinical trials showed that the consumption of probiotics (Bifidobacterium and/or Lactobacillus), fecal microbiota transplants, and balneotherapy modified the fecal microbiota composition of participants and were associated with significant improvements in disease management. Conclusions: In anticipation of forthcoming clinical trials, it is essential to conduct meta-analyses that comprehensively evaluate the effectiveness and safety of interventions designed to modify intestinal flora in the context of AD. Preliminary evidence suggests that certain interventions may enhance adult AD management.

Metagenomic analysis reveals the community composition of the microbiome in different segments of the digestive tract in donkeys and cows: implications for microbiome research

INTRODUCTION

The intestinal microbiota plays a crucial role in health and disease. This study aimed to assess the composition and functional diversity of the intestinal microbiota in donkeys and cows by examining samples collected from different segments of the digestive tract using two distinct techniques: direct swab sampling and faecal sampling.

RESULTS

In this study, we investigated and compared the effects of multiple factors on the composition and function of the intestinal microbial community. Approximately 300 GB of metagenomic sequencing data from 91 samples obtained from various segments of the digestive tract were used, including swabs and faecal samples from monogastric animals (donkeys) and polygastric animals (cows). We assembled 4,004,115 contigs for cows and 2,938,653 contigs for donkeys, with a total of 9,060,744 genes. Our analysis revealed that, compared with faecal samples, swab samples presented a greater abundance of Bacteroidetes, whereas faecal samples presented a greater abundance of Firmicutes. Additionally, we observed significant variations in microbial composition among different digestive tract segments in both animals. Our study identified key bacterial species and pathways via different methods and provided evidence that multiple factors can influence the microbial composition. These findings provide new insights for the accurate characterization of the composition and function of the gut microbiota in microbiome research.

CONCLUSIONS

The results obtained by both sampling methods in the present study revealed that the composition and function of the intestinal microbiota in donkeys and cows exhibit species-specific and region-specific differences. These findings highlight the importance of using standardized sampling protocols to ensure accurate and consistent characterization of the intestinal microbiota in various animal species. The implications and underlying mechanisms of these associations provide multiple perspectives for future microbiome research.