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This systematic literature review and meta‐analysis provide an overview of the critical role of gut microbiota in modulating the efficacy of immunotherapy for colorectal cancer. Gut microbes influence host immune responses through multiple mechanisms including modulation of immune cell activity, metabolite action, and immune tolerance. The ability of specific gut microbes to improve the efficacy of immune checkpoint inhibitors has been linked to their ability to improve gut barrier function, modulate immune cell activity, and produce key immunomodulatory metabolites such as short‐chain fatty acids. In addition, the composition and diversity of the gut microbiota are strongly associated with the efficacy of immunotherapies, demonstrating the potential to improve therapeutic response by modifying the gut microbiota. This paper also discusses the prospect of manipulating the gut microbiota through strategies such as fecal microbial transplantation, probiotic supplementation, and dietary modifications to optimize the efficacy of immunotherapy. [ABSTRACT FROM AUTHOR]

Background: The Coronavirus disease 2019 (COVID-19) pandemic has emerged as a global health crisis, with clinical manifestations including those suggesting injury to various organs such as the ovaries, which implies that it extends beyond respiratory infections. Changes in gut microbiota may exhibit correlations with the mechanisms and stages of severity in COVID-19, as well as a link with sex hormones, embryo development, and pregnancy. Controlled ovarian stimulation (COS) is used to induce the development of multiple high-quality follicles during in vitro fertilization (IVF). Our research aimed to investigate whether patients infected with COVID-19 have altered gut microbiota compositions that would affect the outcomes of COS. Methods: Twenty-one healthy females and seventeen patients with COVID-19 were enrolled. Samples were sequenced for gut microbiota identification through 16 S rRNA V3-V4 region, including species annotation, community diversity, and community functions. Results: No significant differences were found between the groups in terms of in IVF cycle outcomes and laboratory parameters. Patients with COVID-19 and healthy women showed no significant difference in the total number of available blastocyst embryos. Furthermore, the gut microbiota alpha diversity index in the COVID-19 group were markedly reduced compared to those of healthy females. Comparing the COVID-19 group to the controls, the gut microbiota dysbiosis decreased levels of Ruminococcus, and Agathobater, and elevated levels of Achromobacter and Raistonia. Finally, we identified a series of microbial functional characteristics, including membrane transport and carbohydrate metabolism, that exhibited significant disparities between the two groups. Conclusions: Patients in the COVID-19 group exhibited significant disparities in the gut microbiota composition compared to the healthy women during COS. However, the IVF outcomes did not show any significant differences between the two groups. Collectively, our speculation suggests that SARS-COV-2 infection may alter the gut microbiota without impacting IVF outcomes. [ABSTRACT FROM AUTHOR]

Background:The gut microbiome has a significant impact on human wellness, contributing to the emergence and progression of a range of health issues including inflammatory and autoimmune conditions, metabolic disorders, cardiovascular problems, and psychiatric disorders. Notably, clinical observations have revealed that these illnesses can display differences in incidence and presentation between genders. The present study aimed to evaluate whether the composition of gut microbiota is associated with sex-specific differences and to elucidate the mechanism. Methods: 16S-rRNA-sequencing technology, hormone analysis, gut microbiota transplantation, gonadectomy, and hormone treatment were employed to investigate the correlation between the gut microbiome and sex or sex hormones. Meanwhile, genes and proteins involved bile acid signaling pathway were analyzed both in the liver and ileum tissues. Results: The composition and diversity of the microbiota from the jejunum and feces and the level of sex hormones in the serum differed between the sexes in young and middle-aged Sprague Dawley (SD) rats. However, no similar phenomenon was found in geriatric rats. Interestingly, whether in young, middle-aged, or old rats, the composition of the microbiota and bacterial diversity differed between the jejunum and feces in rats. Gut microbiota transplantation, gonadectomy, and hormone replacement also suggested that hormones, particularly testosterone (T), influenced the composition of the gut microbiota in rats. Meanwhile, the mRNA and protein level of genes involved bile acid signaling pathway (specifically SHP, FXR, CYP7A1, and ASBT) exhibited gender-specific differences, and T may play a significant role in mediating the expression of this pathway. Conclusion: Sex-specific differences in the structure of the gut microbiota are mediated by T through the bile acid signaling pathway, pointing to potential targets for disease prevention and management techniques by indicating that sex differences and T levels may alter the composition of the gut microbiota via the bile acid signaling pathway. [ABSTRACT FROM AUTHOR]

Introduction: Breastfeeding is considered the best nutrition for infants, including born preterm due to containing optimal ingredients for development and growth. Breast milk is a rich source of nutrients, it also contains diverse types of bacteria, which play a role in infant's gastrointestinal tract colonization and preserving mammary health. Composition of human milk varies depending on numerous maternal and infant factors. Aim of the study: The aim of the study was to summarize the current knowledge about the content of nutrients, bioactive factors and microbiota diversity in human milk depending on various factors. Materials and methods: The work is a review of 26 mainly English-language scientific publications from 1989-2024 posted on the PubMed platform. Results: Milk composition changes in addition to several factors. Depending on postnatal age: preterm milk has higher content of protein, fat and immunological factors and lower concentration of lactose than term milk. Depending on milk maturity: Colostrum is higher in protein but lower in lactose, fat and energy than mature milk. Human milk is also a source of viable bacteria important for developing infant's gut microbiota, but the diversity of bacterial strains in milk may vary. Depending on mode of delivery: milk of mothers after spontaneous labour contents more probiotic vaginal- and enteric-associated bacteria, while milk of mothers after C-section has more skin-associated microbiota. Depending on mother's weight: milk of overweight mothers is lower in probiotic- and higher in pathogenic bacteria. Alcohol, nicotine, and some medications also have negative impact on produced milk. Conclusions: Human milk varies from woman to woman and its composition depends on several factors. Postnatal and gestational stage, delivery mode, mother's weight and certain substances have been found to be important factors influencing the constitution of breast milk, including nutrients, microbiota and volume of milk. [ABSTRACT FROM AUTHOR]

Kimchi, a renowned and culturally significant Korean dish, has gained global recognition as a superfood due to its abundant nutritional content and positive impact on human health. The process of producing kimchi involves the fermentation of various vegetables using lactic acid bacteria (LAB). The primary genera of kimchi LAB encompass Lactobacillus, Lactococcus, Leuconostoc, Pediococcus, and Weissella. Impressively, kimchi comes in over 200 varieties with cruciferous vegetables as its main ingredients, complemented by a range of secondary ingredients that contribute to its nutritional and holistic health benefits. These secondary ingredients include salted fish, ginger, garlic, and red pepper powder. Due to its various functional properties, kimchi has attracted considerable interest. Kimchi has been extensively studied, and its recognized health benefits, including anti-oxidant, anti-tumor, anti-inflammatory, anti-microbial, anti-obesity, hepatoprotective, neuroprotection, anti-allergic, regulation of immunological responses, and many more, have been covered in many review papers. A current literature review regarding the anti-obesity properties of kimchi and kimchi LAB is currently lacking. Therefore, the present review has directed its attention towards the literature concerning the anti-obesity properties of kimchi and LAB derived from kimchi over the last five years. [ABSTRACT FROM AUTHOR]

Objective To explore the causal relationship between testosterone and endometriosis, andto identify and quantify the role of gut microbiota as a potential mediator through Mendelian randomization analysis. Methods Utilizing the summary data from the IEU GWAS database for testosterone (n=199 569) and endometriosis (8 288 cases and 68 969 controls) as the exposure and outcome variables, and the aggregated gut microbiota data from the MiBioGen Consortium (n=18 340) as the mediator, a bidirectional, two-step Mendelian randomization analysis was conducted. Causal relationships were assessed using inverse varianceweighted, MR-Egger, weighted median, weighted model, and simple modelto assess causality, while sensitivity analysis was conducted to ensure the robustness of the findings. Results Impact of testosterone on endometriosis:Inverse variance weighted estimates suggested that testosterone had negative causal effects on endometriosis (OR=0.804, 95%CI:0.670-0.964, P=0.018). Impact of endometriosis on testosterone:Reverse Mendelian randomization showed that endometriosis did not present a causal effect on testosterone (OR=0.991, 95%CI:0.958-1.026, P=0.616). The class Melainabacteria, one of the gut microbiotas, accounted for a 17.21% reduction in the risk of endometriosis associated with testosterone (mediation proportion: 17.21%, 95%CI:0.090-0.264, P=0.035). Conclusion Testosterone is one of the protective factors of endometriosis. Low testosterone levels increase the risk of endometriosis. Gut microbiota may be a mediator of the causal effect of testosterone on endometriosis. [ABSTRACT FROM AUTHOR]

Introduction and purpose: A collection of symptoms known as cerebral palsy first manifest in early childhood and result in profound physical impairment. Cerebral palsy is thought to affect 1 in 500 live births, or roughly 17 million people worldwide. The type of cerebral palsy determines the clinical symptoms. Movement coordination disorders, epilepsy, muscle weakness, and feeding difficulties are the most common symptoms. The purpose of this article is to familiarize readers with the options for nutritional therapy for cerebral palsy patients. Material and methods The following review was based on articles from the PubMed and Google Scholar databases. Key search terms included cerebral palsy; nutrition; treatment; gut microbiota.. State of knowledge Early identification of malnutrition symptoms and appropriate interventions, such as the implantation of a percutaneous endoscopic gastrostomy tube in patients who are unable to swallow food, are the cornerstones of nutritional therapy for cerebral palsy patients. Dysphagia is a major problem in the population of patients with cerebral palsy, and multidisciplinary therapy is necessary for them. Patients' serum vitamin D levels are also influenced by their diet; 50% of those with cerebral palsy have a deficiency in this nutrient. Conclusions For people with cerebral palsy, nutrition is very important. Premature death may arise from malnutrition brought on by the disease's advancement. As a result, individuals with cerebral palsy need to receive specialized care that keeps an eye out for warning indicators and stops malnutrition from getting worse. [ABSTRACT FROM AUTHOR]

Gut microbiota dysbiosis has been implicated in rheumatoid arthritis (RA) and influences disease progression. Although molecular and culture‐independent studies revealed RA patients harbored a core microbiome and had characteristic bacterial species, the lack of cultured bacterial strains had limited investigations on their functions. This study aimed to establish an RA‐originated gut microbial biobank (RAGMB) that covers and further to correlates and validates core microbial species on clinically used and diagnostic inflammation and immune indices. We obtained 3200 bacterial isolates from fecal samples of 20 RA patients with seven improved and 11 traditional bacterial cultivation methods. These isolates were phylogenetically identified and selected for RAGMB. The RAGMB harbored 601 bacterial strains that represented 280 species (including 43 novel species) of seven bacterial phyla. The RAGMB covered 93.2% at species level of medium‐ and high‐abundant (relative abundances ≥0.2%) RA gut microbes, and included four rare species of the phylum Synergistota. The RA core gut microbiome was defined and composed of 20 bacterial species. Among these, Mediterraneibacter tenuis and Eubacterium rectale were two species that statistically and significantly correlated with clinically used diagnostic indices such as erythrocyte sedimentation rate (ESR) and IL‐10. Thus, M. tenuis and E. rectale were selected for experimental validation using DSS‐treated and not DSS‐treated mice model. Results demonstrated both M. tenuis and E. rectale exacerbated host inflammatory responses, including shortened colon length and increased spleen weight, decreased IL‐10 and increased IL‐17A levels in plasma. Overall, we established the RAGMB, defined the RA core microbiome, correlated and demonstrated core microbial species effected on host inflammatory and immune responses. This work provides diverse gut microbial resources for future studies on RA etiology and potential new targets for new biomedical practices. Highlights: An rheumatoid arthritis (RA)‐originated gut microbial biobank (RAGMB) was established, comprising 601 bacterial strains representing 280 species (including 43 novel species) across seven bacterial phyla.RAGMB covers 93.2% of medium‐ and high‐abundant RA gut microbe species from isolated samples.The RA core microbiome consists of 20 bacterial species, with Mediterraneibacter tenuis and Eubacterium rectale showing significant correlations with clinical indices such as ESR and IL‐10.RA core species Mediterraneibacter tenuis and Eubacterium rectale exacerbate inflammatory responses, including shortened colon length, enlarged spleen and altered plasma cytokine levels. [ABSTRACT FROM AUTHOR]

Abstract Background The gut-lung axis, pivotal for respiratory health, is inadequately explored in pulmonary and critical care medicine (PCCM) inpatients. Methods Examining PCCM inpatients from three medical university-affiliated hospitals, we conducted 16S ribosomal RNA sequencing on stool samples (inpatients, n = 374; healthy controls, n = 105). We conducted statistical analyses to examine the gut microbiota composition in PCCM inpatients, comparing it to that of healthy controls. Additionally, we explored the associations between gut microbiota composition and various clinical factors, including age, white blood cell count, neutrophil count, platelet count, albumin level, hemoglobin level, length of hospital stay, and medical costs. Results PCCM inpatients exhibited lower gut microbiota diversity than healthy controls. Principal Coordinates Analysis revealed marked overall microbiota structure differences. Four enterotypes, including the exclusive Enterococcaceae enterotype in inpatients, were identified. Although no distinctions were found at the phylum level, 15 bacterial families exhibited varying abundances. Specifically, the inpatient population from PCCM showed a significantly higher abundance of Enterococcaceae, Lactobacillaceae, Erysipelatoclostridiaceae, Clostridiaceae, and Tannerellaceae. Using random forest analyses, we calculated the areas under the receiver operating characteristic curves (AUCs) to be 0.75 (95% CIs 0.69–0.80) for distinguishing healthy individuals from inpatients. The four most abundant genera retained in the classifier were Blautia, Subdoligranulum, Enterococcus, and Klebsiella. Conclusions Evidence of gut microbiota dysbiosis in PCCM inpatients underscores the gut-lung axis's significance, promising further avenues in respiratory health research.

The human gut is inhabited by approximately 100 trillion of microflora, and there exists a reciprocal relationship between human health and the gut microbiota. The major reasons for the dysbiosis in the population of gut microbiota are attributed to changes in lifestyle, medication, and the intake of junk foods. In addition, the proportion of beneficial bacteria in the intestine decreases gradually with age and causes physiological disturbances, malfunctions of the immune system, and several metabolic disorders. Thus, finding safe solutions to improve the diversity of microflora is a big challenge. With an increase in health consciousness among the population, the demand for healthy and nutraceutical food products is growing gradually. Recent research has proved that consumption of probiotics promotes gut health and prevents from several metabolic and other diseases. Hence, in this present review, we will discuss the various probiotic bacteria present in ethnic foods. The importance of these probiotics in the prevention and treatment of gastrointestinal, respiratory, cancer, and metabolic disorders will be elucidated. In addition, we will highlight the importance of the development of new-generation probiotics to cater the needs of the current market. [ABSTRACT FROM AUTHOR]

Introduction: Matcha, a finely powdered form of green tea, has recently gained global popularity due to its vibrant green color, distinctive taste, and versatile applications in various food products. Despite its promising nutritional profile, matcha has not received significant attention in the academic community compared to traditional green tea. Purpose of work: The primary objective of this review is to provide a comprehensive overview of the current understanding of matcha's biological properties and its potential health benefits. Methods and materials: A review of the literature available in the PubMed database and Google Scholar, the following keywords were searched: "matcha", "catechin", "EGCG", "cognitive function", "green tea" State of knowledge: Existing studies have demonstrated that matcha exhibits anticancer properties, enhances cognitive function, improves cardio-metabolic health, and modulates the gut microbiome. Moreover, matcha is known for its anti-inflammatory and antioxidant properties. Summary: This review summarizes the latest research findings on matcha green tea and its potential health benefits. While animal studies have shown promising results, our knowledge of matcha's effects on human health remains limited. Further randomized controlled trials are necessary to fully elucidate its potential health-promoting effects. Therefore, we advocate for continued research into matcha's properties and its integration into dietary practices to promote overall health and well-being. [ABSTRACT FROM AUTHOR]

Background: Both inflammatory cytokines and the gut microbiome are susceptibility factors for vascular dementia (VaD). The trends in the overall changes in the dynamics of inflammatory cytokines and in the composition of the gut microbiome are influenced by a variety of factors, making it difficult to fully explain the different effects of both on the different subtypes of VaD. Therefore, this Mendelian randomization (MR) study identified the inflammatory cytokines and gut microbiome members that influence the risk of developing VaD and their causal effects, and investigated whether inflammatory cytokines are gut microbiome mediators affecting VaD. Methods: We obtained pooled genome-wide association study (GWAS) data for 196 gut microbiota and 41 inflammatory cytokines and used GWAS data for six VaD subtypes, namely, VaD (mixed), VaD (multiple infarctions), VaD (other), VaD (subcortical), VaD (sudden onset), and VaD (undefined). We used the inverse-variance weighted (IVW) method as the primary MR analysis method. We conducted sensitivity analyses and reverse MR analyses to examine reverse causal associations, enhancing the reliability and stability of the conclusions. Finally, we used multivariable MR (MVMR) analysis to assess the direct causal effects of inflammatory cytokines and the gut microbiome on the risk of VaD, and performed mediation MR analysis to explore whether inflammatory factors were potential mediators. Results: Our two-sample MR study revealed relationships between the risk of six VaD subtypes and inflammatory cytokines and the gut microbiota: 7 inflammatory cytokines and 14 gut microbiota constituents were positively correlated with increased VaD subtype risk, while 2 inflammatory cytokines and 11 gut microbiota constituents were negatively correlated with decreased VaD subtype risk. After Bonferroni correction, interleukin-18 was correlated with an increased risk of VaD (multiple infarctions); macrophage migration inhibitory factor was correlated with an increased risk of VaD (sudden onset); interleukin-4 was correlated with a decreased risk of VaD (other); Ruminiclostridium 6 and Bacillales were positively and negatively correlated with the risk of VaD (undefined), respectively; Negativicutes and Selenomonadales were correlated with a decreased risk of VaD (mixed); and Melainabacteria was correlated with an increased risk of VaD (multiple infarctions). Sensitivity analyses revealed no multilevel effects or heterogeneity and no inverse causality between VaD and inflammatory cytokines or the gut microbiota. The MVMR results further confirmed that the causal effects of Negativicutes, Selenomonadales, and Melainabacteria on VaD remain significant. Mediation MR analysis showed that inflammatory cytokines were not potential mediators. Conclusion: This study helps us to better understand the pathological mechanisms of VaD and suggests the potential value of targeting increases or decreases in inflammatory cytokines and gut microbiome members for VaD prevention and intervention. [ABSTRACT FROM AUTHOR]

This editorial titled "Bringing Vitamin D and the Vitamin D Receptor into the Limelight" explores the growing knowledge surrounding the roles of vitamin D and the vitamin D receptor (VDR) in human health and diseases. It highlights a new clinical practice guideline recommending vitamin D supplementation for children and adolescents to prevent nutritional rickets and reduce the risk of respiratory tract infections, as well as for adults with high-risk prediabetes to lower the risk of progression to diabetes. The document also discusses the involvement of vitamin D and the VDR in innate immunity, metabolism, infection, microbiome diversity, anti-inflammatory properties, and cancer development. It includes research papers and reviews on the biological effects, molecular mechanisms, and therapeutic roles of vitamin D and the VDR, as well as their association with various health conditions such as skin health, psoriasis, atopic diseases, infant gut microbiota, colonic VDR expression, cardiological disease, and bone mineral density. The editorial concludes by emphasizing the importance of accurate supplementation schemes and dietary interventions for vitamin D. Additionally, it mentions a study that explores the association between vitamin D levels and gut microbiota composition in patients with obesity and metabolic syndrome who followed a Mediterranean diet for one year. The study suggests that both vitamin D levels and gut microbiota play a role in metabolic pathways, contributing to the understanding of the vitamin D receptor and potentially leading to further research in precision nutrition and medicine. The study was funded by various organizations, and the sponsors had no involvement in [Extracted from the article]

Introduction: Gut microbiota are associated with the health and performance of ruminant species, and they are affected by altitude, host genetics, and sex. However, there has been little research on comparing the fecal microbiota of indigenous small ruminants such as sheep and goats in Guizhou province, China. In the present study, we revealed the effect of altitude, genetics, and sex on fecal microbiota profiles and enterotypes in indigenous small ruminants of Guizhou province, China. Methods: Fecal samples were collected from Hei and Qianbei Ma goats and Weining sheep in the Chinese province of Guizhou. 16S rRNA gene sequencing targeting the V3-V4 region was performed using the Illumina MiSeq platform. Sequences were processed using QIIME2, and the qualified sequences were processed using the plugin DADA2 to generate amplicon sequence variants (ASVs). The statistical analysis was performed using R studio. Results: The fecal microbial profile was found to vary by herd (influenced by genetics/altitude) and sex. All samples were categorized into two enterotypes. The first enterotype is dominated by UCG-005, and the second enterotype is dominated by the Christensenellaceae_R-7_group, which may be highly driven by the host's genetics (breed). The predicted functional profiles of the fecal microbiota were also assigned to two clusters that corresponded exactly to the enterotypes. Cluster 1 of the functional profiling was characterized by biosynthesis pathways, and cluster 2 was characterized by energy metabolism pathways. Discussion: Our findings may provide new insights into the fecal microbial community and enterotypes in small ruminants by herds, offering clues for understanding the mechanisms by which the fecal microbiota contribute to divergent host phenotypes in indigenous small ruminants in Guizhou. [ABSTRACT FROM AUTHOR]

Recently, research has confirmed that jasmine tea may help improve the depressive symptoms that are associated with psychiatric disorders. Our team previously found that jasmine tea improved the depressive-like behavior that is induced by chronic unpredictable mild stress (CUMS) in Sprague Dawley (SD) rats. We hypothesized that the metabolic disorder component of depression may be related to the gut microbiota, which may be reflected in the metabolome in plasma. The influence of jasmine tea on gut microbiota composition and the association with depressive-related indexes were explored. Furthermore, the metabolites in plasma that are related to the gut microbiota were identified. SD rats were treated with control or CUMS and administrated jasmine tea for 8 weeks. The 16S rRNA gene amplicon sequencing was used to analyze the gut microbiota in feces samples, and untargeted metabolomics was used to analyze the metabolites in plasma. The results found that jasmine tea significantly ameliorated the depressive behavior induced by CUMS, significantly improved the neurotransmitter concentration (BDNF and 5-HT), and decreased the pro-inflammation levels (TNF-α and NF-κB). The intervention of jasmine tea also alleviated the dysbiosis caused by CUMS; increased the relative abundance of Bacteroides, Blautia, Clostridium, and Lactobacillus; and decreased Ruminococcus and Butyrivibrio in the CUMS-treated rats. Furthermore, the serum metabolites of the CUMS-treated rats were reversed after the jasmine tea intervention, i.e., 22 were up-regulated and 18 were down-regulated, which may have a close relationship with glycerophospholipid metabolism pathways, glycine serine and threonine metabolism pathways, and nicotinate and nicotinamide metabolism pathways. Finally, there were 30 genera of gut microbiota related to the depressive-related indexes, and 30 metabolites in the plasma had a strong predictive ability for depressive behavior. Potentially, our research implies that the intervention of jasmine tea can ameliorate the depression induced by CUMS via controlling the gut flora and the host's metabolism, which is an innovative approach for the prevention and management of depression. [ABSTRACT FROM AUTHOR]

Background: The gut-lung axis, pivotal for respiratory health, is inadequately explored in pulmonary and critical care medicine (PCCM) inpatients. Methods: Examining PCCM inpatients from three medical university-affiliated hospitals, we conducted 16S ribosomal RNA sequencing on stool samples (inpatients, n = 374; healthy controls, n = 105). We conducted statistical analyses to examine the gut microbiota composition in PCCM inpatients, comparing it to that of healthy controls. Additionally, we explored the associations between gut microbiota composition and various clinical factors, including age, white blood cell count, neutrophil count, platelet count, albumin level, hemoglobin level, length of hospital stay, and medical costs. Results: PCCM inpatients exhibited lower gut microbiota diversity than healthy controls. Principal Coordinates Analysis revealed marked overall microbiota structure differences. Four enterotypes, including the exclusive Enterococcaceae enterotype in inpatients, were identified. Although no distinctions were found at the phylum level, 15 bacterial families exhibited varying abundances. Specifically, the inpatient population from PCCM showed a significantly higher abundance of Enterococcaceae, Lactobacillaceae, Erysipelatoclostridiaceae, Clostridiaceae, and Tannerellaceae. Using random forest analyses, we calculated the areas under the receiver operating characteristic curves (AUCs) to be 0.75 (95% CIs 0.69–0.80) for distinguishing healthy individuals from inpatients. The four most abundant genera retained in the classifier were Blautia, Subdoligranulum, Enterococcus, and Klebsiella. Conclusions: Evidence of gut microbiota dysbiosis in PCCM inpatients underscores the gut-lung axis's significance, promising further avenues in respiratory health research. [ABSTRACT FROM AUTHOR]

The MASS cohort is a study conducted in Chinese ICU settings that aims to investigate the role of the microbiome in severe pneumonia and host susceptibility. The cohort consists of 286 patients with severe pneumonia, and various biological samples are collected from them. The study highlights the need for further research to establish causality and explore the impact of environmental factors on severe pneumonia. The authors conclude that the cohort provides valuable insights into emerging pathogens, risk factors, and determinants of survival among ICU patients. [Extracted from the article]

This article discusses a recent study that examined the oral microbiome and its connection to periodontitis, a common dental condition that can have various health implications. The researchers analyzed data from multiple cohorts in different countries and continents to identify biomarkers for periodontitis. They found that certain species of bacteria and metabolic biomarkers consistently differed between healthy individuals and those with periodontitis. Machine learning models based on taxonomic profiles were able to accurately distinguish periodontitis patients from controls. The study suggests that metagenome-based diagnosis for periodontitis is possible and could lead to improved diagnostic and treatment approaches. However, further research and larger cohorts are needed to validate these findings. [Extracted from the article]

The duck gastrointestinal tract (GIT) harbors an abundance of microorganisms that play an important role in duck health and production. Here, we constructed the first relatively comprehensive duck gut microbial gene catalog (24 million genes) and 4437 metagenome‐assembled genomes using 375 GIT metagenomic samples from four different duck breeds across five intestinal segments under two distinct rearing conditions. We further characterized the intestinal region‐specific microbial taxonomy and their assigned functions, as well as the temporal development and maturation of the duck gut microbiome. Our metagenomic analysis revealed the similarity within the microbiota of the foregut and hindgut compartments, but distinctive taxonomic and functional differences between distinct intestinal segments. In addition, we found a significant shift in the microbiota composition of newly hatched ducks (3 days), followed by increased diversity and enhanced stability across growth stages (14, 42, and 70 days), indicating that the intestinal microbiota develops into a relatively mature and stable community as the host duck matures. Comparing the impact of different rearing conditions (with and without water) on duck cecal microbiota communities and functions, we found that the bacterial capacity for lipopolysaccharide biosynthesis was significantly increased in ducks that had free access to water, leading to the accumulation of pathogenic bacteria and antibiotic‐resistance genes. Taken together, our findings expand the understanding of the microbiome signatures linked to intestinal regional, temporal development, and rearing conditions in ducks, which highlight the significant impact of microbiota on poultry health and production. Highlights: A catalog of microbial genes and metagenome‐assembled genomes from the duck gut microbiome.The microbiota within different duck intestinal segments exhibits both similarities and distinctive taxonomic and functional differences.Significant shifts in microbiota composition have been observed in newly hatched ducks at 3 days of age, followed by increased diversity and enhanced stability across growth stages (14, 42, and 70 days).Ducks with free access to water have shown an increased bacterial capacity for lipopolysaccharide biosynthesis, leading to the accumulation of pathogenic bacteria and antibiotic‐resistance genes. [ABSTRACT FROM AUTHOR]

The concept of "enterotypes" in microbiome research has attracted substantial interest, particularly focusing on the abundance of Prevotella spp. in the human gut. In this study, the intricate dynamics of Prevotella spp. in the human gut microbiota was investigated, based on the metagenomic method. First, 239 fecal samples from individuals across four regions of China revealed a bimodal distribution, highlighting the abundance and variability in Prevotella spp. within the Chinese population. Second, the longitudinal cohort study included 184 fecal samples from 52 time points collected from seven individuals who demonstrated either the outbreaks or disappearances of Prevotella spp., emphasizing the transient nature of Prevotella abundance levels and suggesting shifts in Prevotella "enterotypes." Furthermore, a turnover of the dominant Prevotella spp. was observed, indicating the potential presence of diverse subtypes of Prevotella enterotype. Notably, the genomic analysis demonstrated the persistence of specific Prevotella strains within individuals over extended periods, highlighting the enduring presence of Prevotella in the human gut. In conclusion, by integrating the temporal and geographical scales in our research, we gained deeper insights into the dynamics of Prevotella, emphasizing the importance of considering the dynamics at the time and species level in gut microbiota studies and their implications on human health. [ABSTRACT FROM AUTHOR]

Background: Scavenging indigenous village chickens play a vital role in sub-Saharan Africa, sustaining the livelihood of millions of farmers. These chickens are exposed to vastly different environments and feeds compared to commercial chickens. In this study, we analysed the caecal microbiota of 243 Ethiopian village chickens living in different altitude-dependent agro-ecologies. Results: Differences in bacterial diversity were significantly correlated with differences in specific climate factors, topsoil characteristics, and supplemental diets provided by farmers. Microbiota clustered into three enterotypes, with one particularly enriched at high altitudes. We assembled 9977 taxonomically and functionally diverse metagenome-assembled genomes. The vast majority of these were not found in a dataset of previously published chicken microbes or in the Genome Taxonomy Database. Conclusions: The wide functional and taxonomic diversity of these microbes highlights their importance in the local adaptation of indigenous poultry, and the significant impacts of environmental factors on the microbiota argue for further discoveries in other agro-ecologies. EEwR8PKafK2-LVnkA2-YG- Video Abstract [ABSTRACT FROM AUTHOR]

To accurately define the role of the gut microbiota in health and disease pathogenesis, the preservation of stool sample integrity, in terms of microbial community composition and metabolic function, is critical. This presents a challenge for any studies which rely on participants self-collecting and returning stool samples as this introduces variability and uncertainty of sample storage/handling. Here, we tested the performance of three stool sample collection/preservation buffers when storing human stool samples at different temperatures (room temperature [20 °C], 4 °C and – 80 °C) for up to three days. We compared and quantified differences in 16S rRNA sequencing composition and short-chain fatty acid profiles compared against immediately snap-frozen stool. We found that the choice of preservation buffer had the largest effect on the resulting microbial community and metabolomic profiles. Collectively analysis confirmed that PSP and RNAlater buffered samples most closely recapitulated the microbial diversity profile of the original (immediately – 80 °C frozen) sample and should be prioritised for human stool microbiome studies. [ABSTRACT FROM AUTHOR]

Background: The relationship between gut microbiota and hematologic malignancies has attracted considerable attention. As research progresses, it has become increasingly clear that the composition of gut microbiota may influence the onset and progression of hematologic malignancies. However, our understanding of this association remains limited. Methods: In our study, we classified gut microbiota into five groups based on information at the phylum, class, order, family, and genus levels. Subsequently, we obtained data related to common hematologic malignancies from the IEU Open GWAS project. We then employed a bidirectional Mendelian Randomization (MR) approach to determine whether there is a causal relationship between gut microbiota and hematologic malignancies. Additionally, we conducted bidirectional MR analyses to ascertain the directionality of this causal relationship. Results: Through forward and reverse MR analyses, we found the risk of lymphoid leukemia was significantly associated with the abundance of phylum Cyanobacteria, order Methanobacteriales, class Methanobacteria, family Peptococcaceae, family Methanobacteriaceae, and genera Lachnospiraceae UCG010, Methanobrevibacter, Eubacterium brachy group, and Butyrivibrio. The risk of myeloid leukemia was significantly associated with the abundance of phylum Actinobacteria, phylum Firmicutes, order Bifidobacteriales, order Clostridiales, class Actinobacteria, class Gammaproteobacteria, class Clostridia, family Bifidobacteriaceae, and genera Fusicatenibacter, Eubacterium hallii group, Blautia, Collinsella, Ruminococcus gauvreauii group, and Bifidobacterium. The risk of Hodgkin lymphoma was significantly associated with the abundance of family Clostridiales vadinBB60 group, genus Peptococcus, and genus Ruminococcaceae UCG010. The risk of malignant plasma cell tumor was significantly associated with the abundance of genera Romboutsia and Eubacterium rectale group. The risk of diffuse large B-cell lymphoma was significantly associated with the abundance of genera Erysipelatoclostridium and Eubacterium coprostanoligenes group. The risk of mature T/NK cell lymphomas was significantly associated with the abundance of phylum Verrucomicrobia, genus Ruminococcaceae UCG013, genus Lachnoclostridium, and genus Eubacterium rectale group. Lastly, the risk of myeloproliferative neoplasms was significantly associated with the abundance of genus Coprococcus 3 and Eubacterium hallii group. Conclusion: Our study provided new evidence for the causal relationship between gut microbiota and hematologic malignancies, offering novel insights and approaches for the prevention and treatment of these tumors. [ABSTRACT FROM AUTHOR]

Objective: Bladder cancer(BCa) was a disease that seriously affects patients' quality of life and prognosis. To address this issue, many researches suggested that the gut microbiota modulated tumor response to treatment; however, this had not been well-characterized in bladder cancer. In this study, our objective was to determine whether the diversity and composition of the gut microbiota or the density of specific bacterial genera influence the prognosis of patients with bladder cancer. Methods: We collected fecal samples from a total of 50 bladder cancer patients and 22 matched non-cancer individuals for 16S rDNA sequencing to investigate the distribution of Parabacteroides in these two groups. Further we conducted follow-up with cancer patients to access the impact of different genera of microorganisms on patients survival. We conducted a Fecal Microbiota Transplantation (FMT) and mono-colonization experiment with Parabacteroides distasonis to explore its potential enhancement of the efficacy of anti-PD-1 immunotherapy in MB49 tumor-bearing mice. Immunohistochemistry, transcriptomics and molecular experiment analyses were employed to uncover the underlying mechanisms. Results: The 16S rDNA showed that abundance of the genus Parabacteroides was elevated in the non-cancer control group compared to bladder cancer group. The results of tumor growth curves showed that a combination therapy of P. distasonis and ICIs treatment significantly delayed tumor growth and increased the intratumoral densities of both CD4+T and CD8+T cells. The results of transcriptome analysis demonstrated that the pathways associated with antitumoral immune response were remarkably upregulated in the P. distasonis gavage group. Conclusion: P. distasonis delivery combined with α-PD-1 mAb could be a new strategy to enhance the effect of anti-PD-1 immunotherapy. This effect might be achieved by activating immune and antitumor related pathways. [ABSTRACT FROM AUTHOR]

Objective: Enterotypes (ETs) are the clustering of gut microbial community structures, which could serve as indicators of growth performance and carcass traits. However, ETs have been sparsely investigated in waterfowl. The objective of this study was to identify the ileal ETs and explore the correlation of the ETs with growth performance and carcass traits in Muscovy ducks. Methods: A total of 200 Muscovy ducks were randomly selected from a population of 5,000 ducks at 70-day old, weighed and slaughtered. The growth performance and carcass traits, including body weight, dressed weight and evidenced weight, dressed percentage, percentage of apparent yield, breast muscle weight, leg muscle weight, percentage of leg muscle and percentage of breast muscle, were determined. The contents of ileum were collected for the isolation of DNA and 16S rRNA gene sequencing. The ETs were identified based on the 16S rRNA gene sequencing data and the correlation of the ETs with growth performance and carcass traits was performed by Spearman correlation analysis. Results: Three ETs (ET1, ET2, and ET3) were observed in the ileal microbiota of Muscovy ducks with significant differences in number of features and α-diversity among these ETs (p<0.05). Streptococcus, Candida Arthritis, and Bacteroidetes were the presentative genus in ET1 to ET3, respectively. Correlation analysis revealed that Lactococcus and Bradyrhizobium were significantly correlated with percentage of eviscerated yield and leg muscle weight (p<0.05) while ETs were found to have a close association with percentage of eviscerated yield, leg muscle weight, and percentage of leg muscle in Muscovy ducks. However, the growth performance of ducks with different ETs did not show significant difference (p>0.05). Lactococcus were found to be significantly correlated with leg muscle weight, dressed weight, and percentage of eviscerated yield. Conclusion: Our findings revealed a substantial variation in carcass traits associated with ETs in Muscovy ducks. It is implied that ETs might have the potential to serve as a valuable biomarker for assessing duck carcass traits. It would provide novel insights into the interaction of gut microbiota with growth performance and carcass traits of ducks. [ABSTRACT FROM AUTHOR]

Gut microbes is a crucial factor in the pathogenesis of type 1 diabetes (T1D). However, it is still unclear which gut microbiota are the key factors affecting T1D and their influence on the development and progression of the disease. To fill these knowledge gaps, we constructed a model to find biomarker from gut microbiota in patients with T1D. We first identified microbial markers using Linear discriminant analysis Effect Size (LEfSe) and random forest (RF) methods. Furthermore, by constructing co-occurrence networks for gut microbes in T1D, we aimed to reveal all gut microbial interactions as well as major beneficial and pathogenic bacteria in healthy populations and type 1 diabetic patients. Finally, PICRUST2 was used to predict Kyoto Encyclopedia of Genes and Genomes (KEGG) functional pathways and KO gene levels of microbial markers to investigate the biological role. Our study revealed that 21 identified microbial genera are important biomarker for T1D. Their AUC values are 0.962 and 0.745 on discovery set and validation set. Functional analysis showed that 10 microbial genera were significantly positively associated with D-arginine and D-ornithine metabolism, spliceosome in transcription, steroid hormone biosynthesis and glycosaminoglycan degradation. These genera were significantly negatively correlated with steroid biosynthesis, cyanoamino acid metabolism and drug metabolism. The other 11 genera displayed an inverse correlation. In summary, our research identified a comprehensive set of T1D gut biomarkers with universal applicability and have revealed the biological consequences of alterations in gut microbiota and their interplay. These findings offer significant prospects for individualized management and treatment of T1D. [ABSTRACT FROM AUTHOR]

Background: Previous research has hinted at a crucial link between gut microbiota and arterial embolism and thrombosis, yet the causal relationship remains enigmatic. To gain a deeper understanding, we aimed to comprehensively explore the causal relationship and elucidate the impact of the gut microbiota on the risk through a two-sample Mendelian randomization (MR) study. Methods: Genetic instrumental variables for gut microbiota were identified from a genome-wide association study (GWAS) of 18,340 participants. Summary statistics for IBS were drawn from a GWAS including 1,076 cases and 381,997 controls. We used the inverse-variance weighted (IVW) method as the primary analysis. To test the robustness of our results, we further performed the weighted median method, MR-Egger regression, and MR pleiotropy residual sum and outlier test. Results: We identified three bacterial traits that were associated with the risk of arterial embolism and thrombosis: odds ratio (OR): 1.58, 95% confidence interval (CI): 1.08-2.31, p = 0.017 for genus Catenibacterium; OR: 0.64, 95% CI: 0.42-0.96, p = 0.031 for genus Dialister; and OR: 2.08, 95% CI: 1.25-3.47, p = 0.005 for genus Odoribacter. The results of sensitivity analyses for these bacterial traits were consistent (P<0.05). Conclusion: Our systematic analyses provided evidence to support a potential causal relationship between several gut microbiota taxa and the risk of arterial embolism and thrombosis. More studies are required to show how the gut microbiota affects the development of arterial embolism and thrombosis. [ABSTRACT FROM AUTHOR]

ABSTRACTXanthohumol (XN), a polyphenol found in the hop plant (Humulus lupulus), has antioxidant, anti-inflammatory, prebiotic, and anti-hyperlipidemic activity. Preclinical evidence suggests the gut microbiome is essential in mediating these bioactivities; however, relatively little is known about XN’s impact on human gut microbiota in vivo. We conducted a randomized, triple-blinded, placebo-controlled clinical trial (ClinicalTrials.gov NCT03735420) to determine safety and tolerability of XN in healthy adults. Thirty healthy participants were randomized to 24 mg/day XN or placebo for 8 weeks. As secondary outcomes, quantification of bacterial metabolites and 16S rRNA gene sequencing were utilized to explore the relationships between XN supplementation, gut microbiota, and biomarkers of gut health. Although XN did not significantly change gut microbiota composition, it did re-shape individual taxa in an enterotype-dependent manner. High levels of inter-individual variation in metabolic profiles and bioavailability of XN metabolites were observed. Moreover, reductions in microbiota-derived bile acid metabolism were observed, which were specific to Prevotella and Ruminococcus enterotypes. These results suggest interactions between XN and gut microbiota in healthy adults are highly inter-individualized and potentially indicate that XN elicits effects on gut health in an enterotype-dependent manner.

ABSTRACTUlcerative colitis (UC) is a chronic inflammatory intestinal disease affecting the colon and rectum, with its pathogenesis attributed to genetic background, environmental factors, and gut microbes. This study aimed to investigate the role of enterotypes in UC by conducting a hierarchical analysis, determining differential bacteria using machine learning, and performing Species Co-occurrence Network (SCN) analysis. Fecal bacterial data were collected from UC patients, and a 16S rRNA metagenomic analysis was performed using the QIIME2 bioinformatics pipeline. Enterotype clustering was conducted at the family level, and deep neural network (DNN) classification models were trained for UC and healthy controls (HC) in each enterotype. Results from eleven 16S rRNA gut microbiome datasets revealed three enterotypes: Bacteroidaceae (ET-B), Lachnospiraceae (ET-L), and Clostridiaceae (ET-C). Ruminococcus (R. gnavus) abundance was significantly higher in UC subjects with ET-B and ET-C than in those with ET-L. R. gnavus also showed a positive correlation with Clostridia in UC SCN for ET-B and ET-C subjects, with a higher correlation in ET-C subjects. Conversely, Odoribacter (O.) splanchnicus and Bacteroides (B.) uniformis exhibited a positive correlation with tryptophan metabolism and AMP-activated protein kinase (AMPK) signaling pathways, while R. gnavus showed a negative correlation. In vitro co-culture experiments with Clostridium (C.) difficile demonstrated that fecal microbiota from ET-B subjects had a higher abundance of C. difficile than ET-L subjects. In conclusion, the ET-B enterotype predisposes individuals to UC, with R. gnavus as a potential risk factor and O. splanchnicus and B. uniformis as protective bacteria, and those with UC may have ultimately become ET-C.

Background: Population stratification based on interindividual variability in gut microbiota composition has revealed the existence of several ecotypes named enterotypes in humans and various animal species. Enterotypes are often associated with environmental factors including diet, but knowledge of the role of host genetics remains scarce. Moreover, enterotypes harbor functionalities likely associated with varying abilities and susceptibilities of their host. Previously, we showed that under controlled conditions, 60-day-old pig populations consistently split into two enterotypes with either Prevotella and Mitsuokella (PM enterotype) or Ruminococcus and Treponema (RT enterotype) as keystone taxa. Here, our aim was to rely on pig as a model to study the influence of host genetics to assemble enterotypes, and to provide clues on enterotype functional differences and their links with growth traits. Results: We established two pig lines contrasted for abundances of the genera pairs specifying each enterotype at 60 days of age and assessed them for fecal microbiota composition and growth throughout three consecutive generations. Response to selection across three generations revealed, per line, an increase in the prevalence of the selected enterotype and in the average relative abundances of directly and indirectly selected bacterial genera. The PM enterotype was found less diverse than the RT enterotype but more efficient for piglet growth during the post-weaning period. Shotgun metagenomics revealed differentially abundant bacterial species between the two enterotypes. By using the KEGG Orthology database, we show that functions related to starch degradation and polysaccharide metabolism are enriched in the PM enterotype, whereas functions related to general nucleoside transport and peptide/nickel transport are enriched in the RT enterotype. Our results also suggest that the PM and RT enterotypes might differ in the metabolism of valine, leucin, and isoleucine, favoring their biosynthesis and degradation, respectively. Conclusion: We experimentally demonstrated that enterotypes are functional ecosystems that can be selected as a whole by exerting pressure on the host genetics. We also highlight that holobionts should be considered as units of selection in breeding programs. These results pave the way for a holistic use of host genetics, microbiota diversity, and enterotype functionalities to understand holobiont shaping and adaptation. 4B2VhAArUR-Phf8Fa7EFRX Video Abstract [ABSTRACT FROM AUTHOR]

Background: Previous studies have highlighted a robust correlation between gut microbiota/immune cells and ischemic stroke (IS). However, the precise nature of their causal relationship remains uncertain. To address this gap, our study aims to meticulously investigate the causal association between gut microbiota/immune cells and the likelihood of developing IS, employing a two-sample Mendelian randomization (MR) analysis. Methods: Our comprehensive analysis utilized summary statistics from genome-wide association studies (GWAS) on gut microbiota, immune cells, and IS. The primary MR method employed was the inverse variance-weighted (IVW) approach. To address potential pleiotropy and identify outlier genetic variants, we incorporated the Mendelian randomization pleiotropy residual sum and outlier (MR-PRESSO) technique, along with MR-Egger regression. Heterogeneity was assessed using Cochran’s Q-test. Additionally, leave-one-out analysis was conducted to pinpoint any individual genetic variant influencing the observed causal associations. Finally, a reverse MR analysis was performed to explore the potential of reverse causation. Results: Our investigation revealed four gut microbial taxa and 16 immune cells with a significant causal relationship with IS (p < 0.05). Notably, two bacterial features and five immunophenotypes were strongly associated with a lower IS risk: genus.Barnesiella.id.944 (OR: 0.907, 95% CI: 0.836–0.983, p = 0.018), genus.LachnospiraceaeNK4A136group.id.11319 (OR: 0.918, 95% CI: 0.853–0.983, p = 0.988), Activated & resting Treg % CD4++ (OR: 0.977, 95% CI: 0.956–0.998, p = 0.028). Additionally, significant associations between IS risk and two bacterial features along with eleven immunophenotypes were observed: genus.Paraprevotella.id.962 (OR: 1.106, 95% CI: 1.043–1.172, p < 0.001), genus.Streptococcus.id.1853 (OR: 1.119, 95% CI: 1.034–1.210, p = 0.005), CD127 on granulocyte (OR: 1.039, 95% CI: 1.009–1.070, p = 0.011). Our analyses did not reveal heterogeneity based on the Cochrane’s Q-test (p > 0.05) nor indicate instances of horizontal pleiotropy according to MR-Egger and MR-PRESSO analyses (p > 0.05). Furthermore, the robustness of our MR results was confirmed through leave-one-out analysis. Conclusion: Our study provides further evidence supporting the potential association between gut microbiota and immune cells in relation to IS, shedding light on the underlying mechanisms that may contribute to this condition. These findings lay a solid foundation for future investigations into targeted prevention strategies. [ABSTRACT FROM AUTHOR]

Much research has been conducted to describe the factors that determine the fecal microbiome, with diet and host phylogeny as the main drivers. The influence of diet has been described at different levels. Firstly, there are major differences in the microbiomes of herbivorous and carnivorous species and secondly the morphology of the digestive system also determines the composition and diversity of the microbiota. In this study, we aim to describe the influence of the three factors - diet, digestive system and host - on the microbiota in order to develop a model that is able to characterize host-specific metadata from an unknown fecal sample. We therefore analyzed the 16s rRNA from 525 fecal samples of 14 zoo-housed species belonging to different phylogenetic groups including herbivores, carnivores and omnivores. We found significant differences in the bacterial taxa correlated with these groups. While herbivores show positive correlations with a large number of bacterial taxa, we found fewer taxa correlating with carnivores or omnivores. We also detected considerable differences in the microbiota of the ruminant, hindgut fermenting and simple digestive system. Based on these results, we developed a logistic ensemble model, that predicts the diet and based on these findings either the herbivorous digestive system or the carnivorous host-family from a given fecal microbiota composition. This model is able to effectively discriminate herbivores, omnivores and carnivores. It also excels at predicting the herbivore-specific digestive system with 98% accuracy, further reinforcing the strong link between microbiota and digestive system morphology. Carnivorous host-family identification achieves an overall accuracy of 79%, although this performance varies between families. We provide this trained model as a tool to enable users to generate host-specific information from their microbiome data. In future research, tools such as the one presented here could lead to a combined approach of microbiome and host-specific analyses which would be a great advantage in non-invasive wildlife monitoring. [ABSTRACT FROM AUTHOR]

Simple Summary: In recent years, research has shown that animals' gut microbiota can regulate various physiological functions such as nutrition, metabolism, and immunity, and play an indispensable role in maintaining host gut health. At present, there are few reports on the establishment of rabbits' gut microbiota and its relationship with the host. To clarify the colonization of rabbits' gut microbiota, the changes in species during development, and the relationship between gut microbiota and rabbits' growth and development, this study determined the 16s rRNA of gut microbiota in rabbits of different age groups and preliminarily explored the changes in the types of gut microbiota during the colonization process. Six amplicon sequence variants (ASVs) that significantly affect body weight were obtained. The research results provide a firm theoretical basis for maintaining gut health and constructing new methods for rabbit breeding. This study used feces from 0-day-old (36 rabbits), 10-day-old (119 rabbits), and 60-day-old (119 rabbits) offspring rabbits and their corresponding female rabbits (36 rabbits) as experimental materials. Using 16s rRNA sequencing, the study analyzed the types and changes of gut microbiota in rabbits at different growth and development stages, as well as the correlation between gut microbiota composition and the weight of 60-day-old rabbits. All experimental rabbits were placed in the same rabbit shed. Juvenile rabbits were fed solid feed at 18 days of age and weaned at 35 days of age. In addition to identifying the dominant bacterial phyla of gut microbiota in rabbits at different age stages, it was found that the abundance of Clostridium tertium and Clostridium paraputrificum in all suckling rabbits (10-day-old) was significantly higher than that in rabbits fed with whole feed (60-day-old) (p < 0.05), while the abundance of Gram-negative bacterium cTPY13 was significantly lower (p < 0.05). In addition, Fast Expected Maximum Microbial Source Tracing (FEAST) analysis showed that the contribution of female rabbits' gut microbiota to the colonization of offspring rabbits' gut microbiota was significantly higher than that of unrelated rabbits' gut microbiota (p < 0.05). The contribution of female rabbits' gut microbiota to the colonization of gut microbiota in 0-day-old rabbits was significantly higher than that to the colonization of gut microbiota in the 10- and 60-day-old rabbits (p < 0.05). Finally, the correlation between gut microbiota composition and body weight of 60-day-old rabbits was analyzed based on a mixed linear model, and six ASVs significantly affecting body weight were screened. The above results provide important theoretical and practical guidance for maintaining gut health, improving growth and development performance, and feeding formulation in rabbits. [ABSTRACT FROM AUTHOR]

Inflammatory Bowel Disease (IBD) is a complex health problem that affects millions of individuals worldwide. It consists of two main types, Ulcerative Colitis (UC) and Crohn's Disease (CD), which have distinct characteristics and symptoms. Both UC and CD can lead to intestinal fibrosis, a condition characterized by excessive tissue scarring. Current therapies for IBD aim to induce remission, improve quality of life, and prevent complications, but there is still a need for more effective treatments. Recent research has also highlighted the role of the gut microbiota in IBD and the potential for targeting it to modulate inflammation and fibrosis. Overall, understanding the molecular mechanisms underlying IBD is crucial for developing targeted therapies and improving long-term outcomes for patients. [Extracted from the article]

Background: Postmenopausal osteoporosis is a prevalent disease that affects the bone health of middle-aged and elderly women. The link between gut microbiota and bone health, known as the gut-bone axis, has garnered widespread attention. Methods: We employed a two-sample Mendelian randomization approach to assess the associations between gut microbiota with osteoclasts and postmenopausal osteoporosis, respectively. Single nucleotide polymorphisms associated with the composition of gut microbiota were used as instrumental variables. By analyzing large-scale multi-ethnic GWAS data from the international MiBioGen consortium, and combining data from the eQTLGen consortium and the GEFOS consortium, we identified microbiota related to osteoclasts and postmenopausal osteoporosis. Key genes were further identified through MAGMA analysis, and validation was performed using single-cell data GSE147287. Results: The outcomes of this study have uncovered significant associations within the gut microbiome community, particularly with the Burkholderiales order, which correlates with both an increase in osteoclasts and a reduced risk of postmenopausal osteoporosis. with an odds ratio (OR) of 0.400, and a P-value of 0.011. Further analysis using single-cell data allowed us to identify two key genes, FMNL2 and SRBD1, that are closely linked to both osteoclasts and osteoporosis. Conclusion: This study utilizing Mendelian randomization and single-cell data analysis, provides new evidence of a causal relationship between gut microbiota and osteoclasts, as well as postmenopausal osteoporosis. It was discovered that the specific microbial group, the Burkholderiales order, significantly impacts both osteoporosis and osteoclasts. Additionally, key genes FMNL2 and SRBD1 were identified, offering new therapeutic strategies for the treatment of postmenopausal osteoporosis. [ABSTRACT FROM AUTHOR]

Cholesterol-dependent cytolysins (CDCs) comprise a large family of pore-forming toxins produced by Gram-positive bacteria, which are used to attack eukaryotic cells. Here, we functionally characterize a family of 2-component CDC-like (CDCL) toxins produced by the Gram-negative Bacteroidota that form pores by a mechanism only described for the mammalian complement membrane attack complex (MAC). We further show that the Bacteroides CDCLs are not eukaryotic cell toxins like the CDCs, but instead bind to and are proteolytically activated on the surface of closely related species, resulting in pore formation and cell death. The CDCL-producing Bacteroides is protected from the effects of its own CDCL by the presence of a surface lipoprotein that blocks CDCL pore formation. These studies suggest a prevalent mode of bacterial antagonism by a family of two-component CDCLs that function like mammalian MAC and that are wide-spread in the gut microbiota of diverse human populations. Pathogenic bacteria produce cholesterol-dependent cytolysins to form pores in eukaryotic membranes. Here, the authors show that human gut bacteria use a related family of pore-forming toxins for intra- and interspecies antagonism. [ABSTRACT FROM AUTHOR]

The gut microbiota plays a crucial role in host physiology and the disruption of host-microbiota relationships caused by environmental stressors can impact host growth and survival. In this study, we used Daphnia galeata as a model organism to investigate the interactive effects of fish kairomones on the life-history traits and gut microbiota alterations of D. galeata, as well as the relationship between life-history traits and gut microbiota composition. The presence of fish kairomones enhanced fecundity, decreased growth, and altered gut microbiota, with significant changes in alpha diversity but not in beta diversity in the genotype KB5 of D. galeata. Statistical analysis revealed that the relative abundance of the Pseudomonadaceae family significantly increased upon exposure to fish kairomone, while the relative abundance of the Comamonadaceae family significantly decreased. The decreased growth in genotype KB5 may be associated with a significant increase in Pseudomonas, a member of the family Pseudomonadaceae, which is generally deficient in essential fatty acids, potentially negatively impacting growth. Meanwhile, it is speculated that the significant decrease in Limnohabitans belonging to the Comamonadaceae family is associated with the reduction of body size and increased fecundity of KB5 when exposed to fish kairomones. Furthermore, the genus Candidatus Protochlamydia was observed only under the fi sh kairomones-treated condition. These data suggest that variations in host life-history traits related to reproduction and growth are potentially associated with the relative abundance or presence of these microbial genera. Our research findings provide valuable insights into understanding the impact of biotic stress on the interaction between hosts and microbiota. [ABSTRACT FROM AUTHOR]

This article explores the potential use of pathobiome strains as live biotherapeutic products for human health. It emphasizes the importance of evaluating these strains at a detailed level, considering factors such as functional genes, ecological niche, and drug interactions. The article acknowledges the role of the gut microbiota in human health and discusses the potential benefits and risks of using pathobiome strains. It also addresses the challenges in developing these products, particularly in terms of safety, efficacy, and quality management. The authors propose further research into gene functions, ecological influences, and the pathogenicity of specific strains, and suggest expanding the applications of live biotherapeutics beyond gastrointestinal diseases. They discuss various development methods, such as large-scale screening and gene editing technology, and highlight the need for further investigation in this field. [Extracted from the article]

This article explores the role of Akkermansia muciniphila, a type of gut bacteria, in preventing Listeria monocytogenes infection in mice. The study found that mice treated with A. muciniphila had reduced bacterial loads and improved intestinal barrier function compared to control mice. A. muciniphila was also found to increase levels of linoleic acid in the intestines, which strengthened the epithelial barrier and protected against L. monocytogenes infection. These findings suggest that A. muciniphila or linoleic acid-based strategies could be potential approaches for preventing listeriosis. [Extracted from the article]

The microbial ecology of the human gut is made up of many different species of beneficial microorganisms, mostly bacteria. The integrity of the gut and general health are crucially dependent on these beneficial bacterial species. A variety of microbial communities reside in the human gut in symbiotic interactions, the majority of which are advantageous. According to reports, aberrant bacterial species colonization causes gut dysbiosis and serves as a catalyst for a number of human diseases. Understanding the diverse microbial species that live in the human gut and how they are related to human health and a number of disorders has been the subject of extensive research. Less research has been done on the postbiotics, such as chemistry and biochemistry, and their connections to human health. Postbiotics are defined as non-viable microbial cells, metabolic metabolites, and their microbial by-products released after lysis. Understanding the postbiotic landscape is essential to determining its source and method of synthesis, whether natural or artificial. Therefore, it is crucial to profile the ecology of the gut's microbes as well as the habitat since these factors have an impact on the postbiotic metabolites that are created. In order to relate human health and disease based on postbiotic rather than microbial species, it will be more important to address specific metabolites. The present study stresses the importance of gut microbial ecology in human physiology and health. Postbiotics profiles may be helpful in gaining access to gut ecology, and these molecular markers may act as early diagnostic tools for a variety of disorders. The most recent studies show that postbiotics increase immunological function, allergic reactions, neurological diseases, acute and chronic diarrhoea, and immune function. In the future, effort can be made to develop a quantitative-effect relationship evaluation method that is more rational, scientific, and better to give stronger support for the healthy and long-term development of postbiotic preparations. [ABSTRACT FROM AUTHOR]

Simple Summary: Simple Summary: The production of eggs is a crucial aspect of the chicken industry. Recent research has indicated that the gut microbiota undergoes dynamic changes and plays a significant role in egg production. However, the relationship between the gut microbiota and host gene expression remains unclear. To investigate this, we collected samples from the intestine (i.e., duodenum, jejunum, and ileum) and its microbiota at different stages of egg-laying (i.e., pre-, peak-, and late-laying) in chickens. Our findings showed that intestinal flora underwent significant changes during different laying periods that included changed genes (i.e., APOA1, APOB, TST, CCDC93, and TMEM175) involved in several transport processes, response to DNA damage, and development of intestinal structure. Additionally, our analysis suggested that specific intestinal microbes were significantly correlated with host gene expression, which indicated an interaction between the gut microbiota and the chicken host. Eggs are a vital dietary component for humans, and it is beneficial to increase egg production to support poultry farming. Initially, the egg production rate rises rapidly with young hens until it reaches its peak, and then it declines gradually. By extending the duration of peak egg production, the hens' performance can be enhanced significantly. Previous studies found dynamic changes in gut microbiota during egg-laying, and several species of microbiota isolated from the chicken gut improved egg-laying performance. However, the interaction between microbes and host gene expression is still unclear. This study provides a more comprehensive understanding of chicken egg-laying by examining dynamic alterations in the microbiota of the entire intestinal tract (i.e., duodenum, jejunum, and ileum) and gene expression. The microbial community in the intestine underwent significant changes during different egg-laying periods (i.e., pre-, peak-, and late-laying periods). Metagenomic functional analysis showed that the relative abundance of biosynthesis of amino acids, secondary metabolites, and cofactors decreased significantly in the duodenum, jejunum, and ileum of aging hens. The relative levels of aldosterone, GnRH, insulin, growth hormone, and other hormone-related pathways increased dramatically in the intestinal microbiota during egg-laying, but only in the microbiota located in the duodenum and ileum. Transcriptome analysis suggested that genes associated with various transport processes were upregulated consistently in the small intestine during egg-laying; genes involved in the development of intestinal structure were down-regulated; and genes involved in response to DNA damage and stress were consistent with changes in laying rate. The abundance of Lactobacillus was related to the expression of ANGPTRL1, ANGPTRL2, ANGPT1L, and NOXO1 in the duodenum; Muricomes was correlated significantly with NFKBIZ, LYG2, and IRG1L expression in the jejunum; and Campylobacter was correlated positively with the expression of KMT2A and USF3 in the ileum. These results indicated that the intestinal microbiota and host gene expression may influence egg production jointly. [ABSTRACT FROM AUTHOR]

Intestinal epithelium renewal strictly depends on fine regulation between cell proliferation, differentiation, and apoptosis. While murine intestinal microbiota has been shown to modify some epithelial cell kinetics parameters, less is known about the role of the human intestinal microbiota. Here, we investigated the rate of intestinal cell proliferation in C3H/HeN germ-free mice associated with human flora (HFA, n = 8), and in germ-free (n = 15) and holoxenic mice (n = 16). One hour before sacrifice, all mice were intraperitoneally inoculated with 5-bromodeoxyuridine (BrdU), and the number of BrdU-positive cells/total cells (labelling index, LI), both in the jejunum and the colon, was evaluated by immunohistochemistry. Samples were also observed by scanning electron microscopy (SEM). Moreover, the microbiota composition in the large bowel of the HFA mice was compared to that of of human donor's fecal sample. No differences in LI were found in the small bowels of the HFA, holoxenic, and germ-free mice. Conversely, the LI in the large bowel of the HFA mice was significantly higher than that in the germ-free and holoxenic counterparts (p = 0.017 and p = 0.048, respectively). In the holoxenic and HFA mice, the SEM analysis disclosed different types of bacteria in close contact with the intestinal epithelium. Finally, the colonic microbiota composition of the HFA mice widely overlapped with that of the human donor in terms of dominant populations, although Bifidobacteria and Lactobacilli disappeared. Despite the small sample size analyzed in this study, these preliminary findings suggest that human intestinal microbiota may promote a high proliferation rate of colonic mucosa. In light of the well-known role of uncontrolled proliferation in colorectal carcinogenesis, these results may deserve further investigation in a larger population study. [ABSTRACT FROM AUTHOR]

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Different modifications of the standard bread recipe have been proposed to improve its nutritional and health benefits. Here, we utilized the in vitro Human Gut Simulator (HGS) to assess the fermentation of one such artisan bread by human gut microbiota. Dried and milled bread, composed of almond flour, psyllium husks, and flax seeds as its three main ingredients, was first subjected to an in vitro protocol designed to mimic human oro-gastro-intestinal digestion. The bread digest was then supplied to complex human gut microbial communities, replacing the typical Western diet-based medium (WM) of the GHS system. Switching the medium from WM to bread digest resulted in statistically significant alterations in the community structure, encoded functions, produced short-chain fatty acids, and available antioxidants. The abundances of dietary fiber degraders Enterocloster, Mitsuokella, and Prevotella increased; levels of Gemmiger, Faecalibacterium, and Blautia decreased. These community alterations resembled the previously revealed differences in the distal gut microbiota of healthy human subjects consuming typical Mediterranean vs. Western-pattern diets. Therefore, the consumption of bread high in dietary fiber and unsaturated fatty acids might recapitulate the beneficial effects of the Mediterranean diet on the gut microbiota. [ABSTRACT FROM AUTHOR]

Background: Multiple studies have suggested a possible connection between the gut microbiota and the development of lymphoma, though the exact nature of this relationship remains unclear. This study aimed to explore whether a causal association exists between gut microbiota and lymphoma. Methods: A bidirectional two-sample Mendelian randomization (MR) approach was conducted to investigate potential causal effects between gut microbiota and various lymphoma subtypes. The primary method employed for MR analysis was inverse variance weighted (IVW), supplemented by additional methods including MR-Egger, weighted median, and weighted mode approaches. The Cochrane Q test, MR-PRESSO global test and MR-Egger intercept test were performed to assess pleiotropy and heterogeneity. Furthermore, a reverse MR analysis was performed to explore potential reverse causal effect. Results: The primary MR analysis identified 36 causal relationships between genetic liabilities in gut microbiota and different lymphoma subtypes. Neither the MR-PRESSO test nor the MR-Egger regression detected any pleiotropy, and Cochran's Q test indicated no significant heterogeneity. Conclusions: Our MR analysis revealed substantial causal associations between gut microbiota and lymphoma, offering new insights into lymphoma prevention and management microbiota. [ABSTRACT FROM AUTHOR]

Background: The application of reduced metagenomic sequencing approaches holds promise as a middle ground between targeted amplicon sequencing and whole metagenome sequencing approaches but has not been widely adopted as a technique. A major barrier to adoption is the lack of read simulation software built to handle characteristic features of these novel approaches. Reduced metagenomic sequencing (RMS) produces unique patterns of fragmentation per genome that are sensitive to restriction enzyme choice, and the non-uniform size selection of these fragments may introduce novel challenges to taxonomic assignment as well as relative abundance estimates. Results: Through the development and application of simulation software, readsynth, we compare simulated metagenomic sequencing libraries with existing RMS data to assess the influence of multiple library preparation and sequencing steps on downstream analytical results. Based on read depth per position, readsynth achieved 0.79 Pearson's correlation and 0.94 Spearman's correlation to these benchmarks. Application of a novel estimation approach, fixed length taxonomic ratios, improved quantification accuracy of simulated human gut microbial communities when compared to estimates of mean or median coverage. Conclusions: We investigate the possible strengths and weaknesses of applying the RMS technique to profiling microbial communities via simulations with readsynth. The choice of restriction enzymes and size selection steps in library prep are non-trivial decisions that bias downstream profiling and quantification. The simulations investigated in this study illustrate the possible limits of preparing metagenomic libraries with a reduced representation sequencing approach, but also allow for the development of strategies for producing and handling the sequence data produced by this promising application. [ABSTRACT FROM AUTHOR]