@article {pmid39184082,
year = {2024},
author = {Larkin, AA and Brock, ML and Fagan, AJ and Moreno, AR and Gerace, SD and Lees, LE and Suarez, SA and Eloe-Fadrosh, EA and Martiny, A},
title = {Climate-driven succession in marine microbiome biodiversity and biogeochemical function.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-4682733/v1},
pmid = {39184082},
issn = {2693-5015},
abstract = {Seasonal and El Niño-Southern Oscillation (ENSO) warming result in similar ocean changes as predicted with climate change. Climate-driven environmental cycles have strong impacts on microbiome diversity, but impacts on microbiome function are poorly understood. We quantified changes in microbial genomic diversity and functioning over 11 years covering seasonal and ENSO cycles at a coastal site in the southern California Current. We observed seasonal oscillations between large genome lineages during cold, nutrient rich conditions in winter and spring versus small genome lineages, including Prochlorococcus and Pelagibacter , in summer and fall. Parallel interannual changes separated communities depending on ENSO condition. Biodiversity shifts translated into clear oscillations in microbiome functional potential. Ocean warming induced an ecosystem with less iron but more macronutrient stress genes, depressed organic carbon degradation potential and biomass, and elevated carbon-to-nutrient biomass ratios. The consistent microbial response observed across time-scales points towards large climate-driven changes in marine ecosystems and biogeochemical cycles.},
}

@article {pmid39184030,
year = {2024},
author = {Shera, S and Katzka, W and Yang, JC and Chang, C and Arias-Jayo, N and Lagishetty, V and Balioukova, A and Chen, Y and Dutson, E and Li, Z and Mayer, EA and Pisegna, JR and Sanmiguel, C and Pawar, S and Zhang, D and Leitman, M and Hernandez, L and Jacobs, JP and Dong, TS},
title = {Bariatric-induced microbiome changes alter MASLD development in association with changes in the innate immune system.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1407555},
pmid = {39184030},
issn = {1664-302X},
abstract = {INTRODUCTION: Metabolic dysfunction-associated steatotic liver disease (MASLD) affects nearly 25% of the population and is the leading cause for liver-related mortality. Bariatric surgery is a well-known treatment for MASLD and obesity. Understanding the fundamental mechanisms by which bariatric surgery can alter MASLD can lead to new avenues of therapy and research. Previous studies have identified the microbiome's role in bariatric surgery and in inflammatory immune cell populations. The host innate immune system modulates hepatic inflammation and fibrosis, and thus the progression of MASLD. The precise role of immune cell types in the pathogenesis of MASLD remains an active area of investigation. The aim of this study was to understand the interplay between microbiota composition post-bariatric surgery and the immune system in MASLD.

METHODS: Eighteen morbidly obese females undergoing sleeve gastrectomy were followed pre-and post-surgery. Stool from four patients, showing resolved MASLD post-surgery with sustained weight loss, was transplanted into antibiotic treated mice. Mice received pre-or post-surgery stool and were fed a standard or high-fat diet. Bodyweight, food intake, and physiological parameters were tracked weekly. Metabolic parameters were measured post-study termination.

RESULTS: The human study revealed that bariatric surgery led to significant weight loss (p > 0.05), decreased inflammatory markers, and improved glucose levels six months post-surgery. Patients with weight loss of 20% or more showed distinct changes in blood metabolites and gut microbiome composition, notably an increase in Bacteroides. The mouse model confirmed surgery-induced microbiome changes to be a major factor in the reduction of markers and attenuation of MASLD progression. Mice receiving post-surgery fecal transplants had significantly less weight gain and liver steatosis compared to pre-surgery recipients. There was also a significant decrease in inflammatory cytokines interferon gamma, interleukin 2, interleukin 15, and mig. This was accompanied by alterations in liver immunophenotype, including an increase in natural killer T cells and reduction of Kupfer cells in the post-surgery transplant group.

DISCUSSION: Our findings suggest surgery induced microbial changes significantly reduce inflammatory markers and fatty liver progression. The results indicate a potential causal link between the microbiome and the host immune system, possibly mediated through modulation of liver NKT and Kupffer cells.},
}

@article {pmid39184027,
year = {2024},
author = {Liu, Z and Qi, CJ and Shi, Y and Li, T and Fang, Y and Zhang, Q},
title = {Active herpesviruses are associated with intensive care unit (ICU) admission in patients pulmonary infection and alter the respiratory microbiome.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1441476},
pmid = {39184027},
issn = {1664-302X},
abstract = {BACKGROUND: The Herpesviridae family contains several human-related viruses, which are able to establish colonizing and latency in the human body, posing a significant threat to the prognosis of patients. Pulmonary infections represent one of the predominant infectious diseases globally, characterized by diverse and multifaceted clinical manifestations that have consistently attracted clinician's concern. However, the relationship of herpesviruses on the prognosis of pulmonary infections and the respiratory microbiota remains poorly understood.

METHODS: Here, we retrospectively analyzed respiratory samples from 100 patients with pulmonary infection detected by metagenomic next-generation sequencing (mNGS).

RESULTS: Employing mNGS, five herpesvirus species were detected: Human alphaherpesvirus 1 (HSV-1), Human gammaherpesvirus 4 (EBV), Human betaherpesvirus 5 (CMV), Human betaherpesvirus 7 (HHV-7), and Human betaherpesvirus 6B (HHV-6B). Regression analysis showed that the age and positivity of herpesviruses in patients were independently correlated with ICU admission rates. In addition, positivity of herpesvirus was related with increased ICU days and total hospital stay. The herpesvirus-positive group demonstrated markedly higher incidences of co-infections and fungi-positive, predominantly involving Pneumocystis jirovecii and Aspergillus fumigatus. Analysis of respiratory microbiota revealed a substantially altered community composition within the herpesvirus-positive group, and herpesviruses were significantly positively correlated with the diverse respiratory opportunistic pathogens.

CONCLUSION: Overall results substantiate that the active herpesviruses in patients with pulmonary infections were significantly associated with high ICU admission rate. Moreover, the herpesviruses promotes the dysbiosis of the respiratory microbiota and an increased proportion of co-infections. These insights could contribute to unraveling the underlying mechanisms connecting active herpesviruses to the progression of severe illnesses.},
}

@article {pmid39183982,
year = {2024},
author = {Singh, VK and Hu, XH and Singh, AK and Solanki, MK and Vijayaraghavan, P and Srivastav, R and Joshi, NK and Kumari, M and Singh, SK and Wang, Z and Kumar, A},
title = {Precision nutrition-based strategy for management of human diseases and healthy aging: current progress and challenges forward.},
journal = {Frontiers in nutrition},
volume = {11},
number = {},
pages = {1427608},
pmid = {39183982},
issn = {2296-861X},
abstract = {Currently, the treatment of various human ailments is based on different therapeutic approaches including traditional and modern medicine systems. Precision nutrition has come into existence as an emerging approach considering the diverse aspects such as age, sex, genetic and epigenetic makeup, apart from the pathophysiological conditions. The continuously and gradually evolving disciplines of genomics about nutrition have elucidated the importance of genetic variations, epigenetic information, and expression of myriads of genes in disease progression apart from the involvement in modulating therapeutic responses. Further, the investigations have presented the considerable role of gut microbiota comprising of commensal and symbionts performing innumerable activities such as release of bioactive molecules, defense against pathogenic microbes, and regulation of immunity. Noteworthy, the characteristics of the microbiome change depending on host attributes, environmental factors, and habitat, in addition to diet, and therefore can be employed as a biomarker to unravel the response to given food. The specific diet and the components thereof can be suggested for supporting the enrichment of the desired microbial community to some extent as an important part of precision nutrition to achieve not only the goal of human health but also of healthy aging.},
}

@article {pmid39183943,
year = {2024},
author = {Fitzjerrells, RL and Ollberding, NJ and Mangalam, AK},
title = {Looking at the full picture, using topic modeling to observe microbiome communities associated with disease.},
journal = {Gut microbes reports},
volume = {1},
number = {1},
pages = {1-11},
pmid = {39183943},
issn = {2993-3935},
support = {F31 DE033564/DE/NIDCR NIH HHS/United States ; I01 CX002212/CX/CSRD VA/United States ; R01 AI137075/AI/NIAID NIH HHS/United States ; T90 DE023520/DE/NIDCR NIH HHS/United States ; P30 ES005605/ES/NIEHS NIH HHS/United States ; },
abstract = {The microbiome, a complex micro-ecosystem, helps the host with various vital physiological processes. Alterations of the microbiome (dysbiosis) have been linked with several diseases, and generally, differential abundance testing between the healthy and patient groups is performed to identify important bacteria. However, providing a singular species of bacteria to an individual as treatment has not been as successful as fecal microbiota transplant therapy, where the entire microbiome of a healthy individual is transferred. These observations suggest that a combination of bacteria might be crucial for the beneficial effects. Here we provide the framework to utilize topic modeling, an unsupervised machine learning approach, to identify a community of bacteria related to health or disease. Specifically, we used our previously published gut microbiome data of patients with multiple sclerosis (MS), a neurodegenerative disease linked to a dysbiotic gut microbiome. We identified communities of bacteria associated with MS, including genera previously discovered, but also others that would have been overlooked by differential abundance testing. This method can be a useful tool for analyzing the microbiome, and it should be considered along with the commonly utilized differential abundance tests to better understand the role of the gut microbiome in health and disease.},
}

@article {pmid39183864,
year = {2024},
author = {Li, G and Shen, Q and Gao, Y and Ma, C and Song, B and Wang, C and Tang, D and He, X and Cao, Y},
title = {The microbiota continuum along the upper reproductive tract of male rat and its relation to semen parameters.},
journal = {Heliyon},
volume = {10},
number = {12},
pages = {e32556},
pmid = {39183864},
issn = {2405-8440},
abstract = {Given the physiological function and anatomical location of the reproductive tract, studying the upper reproductive tract microbiota may be essential for studying male infertility and other male diseases. This study aimed to characterize the microbiota of the upper reproductive tract male rats and investigate whether specific microbial compositions are associated with sperm parameters. 16S rRNA gene sequencing was used to characterize the microbial composition in the testis, epididymis, seminal vesicles, vas deferens and prostate tissues of the rats. The results showed significant enrichment of Methyloperoxococcus spp. in testicular tissues, Jeotgalicoccus spp. in epididymal tissues. Spearman's correlation analysis revealed that the abundance of several bacterial genera in epididymal, testicular, and seminal vesicle gland tissues correlated with several sperm activity parameters. Our findings provide detailed information on characterizing the upper reproductive tract microbiome in male rats, as well as a potentially crucial link between the reproductive system microbiota and sperm quality.},
}

@article {pmid39183848,
year = {2024},
author = {Bhuvaneshwar, K and Madhavan, S and Gusev, Y},
title = {Integrative genomic analysis of the lung tissue microenvironment in SARS-CoV-2 and NL63 patients.},
journal = {Heliyon},
volume = {10},
number = {12},
pages = {e32772},
pmid = {39183848},
issn = {2405-8440},
abstract = {The coronavirus disease 2019 (COVID-19) pandemic caused by the SARS-CoV-2 virus has affected over 700 million people, and caused over 7 million deaths throughout the world as of April 2024, and continues to affect people through seasonal waves. While over 675 million people have recovered from this disease globally, the lingering effects of the disease are still under study. Long term effects of SARS-CoV-2 infection, known as 'long COVID,' include a wide range of symptoms including fatigue, chest pain, cellular damage, along with a strong innate immune response characterized by inflammatory cytokine production. Three years after the pandemic, data about long covid studies are finally emerging. More clinical studies and clinical trials are needed to understand and determine the factors that predispose individuals to these long-term side effects. In this methodology paper, our goal was to apply data driven approaches in order to explore the multidimensional landscape of infected lung tissue microenvironment to better understand complex interactions between viral infection, immune response and the lung microbiome of patients with (a) SARS-CoV-2 virus and (b) NL63 coronavirus. The samples were analyzed with several machine learning tools allowing simultaneous detection and quantification of viral RNA amount at genome and gene level; human gene expression and fractions of major types of immune cells, as well as metagenomic analysis of bacterial and viral abundance. To contrast and compare specific viral response to SARS-COV-2, we analyzed deep sequencing data from additional cohort of patients infected with NL63 strain of corona virus. Our correlation analysis of three types of RNA-seq based measurements in patients i.e. fraction of viral RNA (at genome and gene level), Human RNA (transcripts and gene level) and bacterial RNA (metagenomic analysis), showed significant correlation between viral load as well as level of specific viral gene expression with the fractions of immune cells present in lung lavage as well as with abundance of major fractions of lung microbiome in COVID-19 patients. Our methodology-based proof-of-concept study has provided novel insights into complex regulatory signaling interactions and correlative patterns between the viral infection, inhibition of innate and adaptive immune response as well as microbiome landscape of the lung tissue. These initial findings could provide better understanding of the diverse dynamics of immune response and the side effects of the SARS-CoV-2 infection and demonstrates the possibilities of the various types of analyses that could be performed from this type of data.},
}

@article {pmid39183547,
year = {2024},
author = {Eid, M and Martínek, A and Dolina, J and Uvírová, M and Dítě, P},
title = {Gut microbio-me and pancreatic cancer.},
journal = {Klinicka onkologie : casopis Ceske a Slovenske onkologicke spolecnosti},
volume = {38},
number = {1},
pages = {20-26},
doi = {10.48095/ccko202420},
pmid = {39183547},
issn = {1802-5307},
mesh = {Humans ; *Pancreatic Neoplasms ; *Gastrointestinal Microbiome ; Carcinoma, Pancreatic Ductal ; },
abstract = {BACKGROUND: The incidence of pancreatic cancer (pancreatic ductal adenocarcinoma - PDAC) is increasing, especially in developed countries. In 2021, 496,000 new PDAC cases were dia-gnosed worldwide. In the Czech Republic, the incidence is one of the highest in the world, with 2,332 new PDAC patients dia-gnosed in 2018. Due to the absence of symptoms in the early stages, approximately 50% of patients are initially dia-gnosed with distant metastases. Mortality is slightly lower than the incidence count and, despite significant advances in cancer research, PDAC remains a fatal dia-gnosis. However, microbio-me seems to be an interesting approach, and not only in PDAC patients. Microbio-me is defined as the set of all microorganisms (microbio-ta, i.e. bacteria, fungi, viruses, archaea, and protozoa) and their genome in a certain environment. In a physiological setting, the gut microbio-me is in symbio-sis with the host organism, maintaining the balance of metabolism, mucosal immunomodulation and regulating the digestion process. When dysregulation of the number or function of intestinal microorganisms occurs, dysbio-sis is developed. It may lead to metabolic and cardiovascular diseases, nervous system disorders, induction of intestinal inflammation, or carcinogenesis. Microbio-ta can induce carcinogenesis in multiple ways, such as by activating an inflammatory response, reducing the immune system's ability to eliminate damaged cells, and deregulation of the host genome by microbial metabolites. This deregulation may lead to an activation of pro-apoptotic and pro-proliferative proteins. To date, research shows that the gut or oral microbio-me may be involved in the development of PDAC. One of the most studied bacteria is Porphyromonas gingivalis. Other bacteria, such as Fusobacteria, Enterobacter, Klebsiella, Prevotella, and Rothia, have also been shown to play a role in PDAC.

PURPOSE: The aim of this review article is to point out one of the possible mechanisms of cancerogenesis in PDAC patients and its therapeutic influence to reduce the incidence and improve the prognosis of this aggressive disease.},
}

Humans
*Pancreatic Neoplasms
*Gastrointestinal Microbiome
Carcinoma, Pancreatic Ductal

@article {pmid39183408,
year = {2024},
author = {Feng, B and Lu, J and Han, Y and Han, Y and Qiu, X and Zeng, Z},
title = {The role of short-chain fatty acids in the regulation of osteoporosis: new perspectives from gut microbiota to bone health: A review.},
journal = {Medicine},
volume = {103},
number = {34},
pages = {e39471},
pmid = {39183408},
issn = {1536-5964},
support = {2022A151511119//Guangdong Basic and Applied Basic Research Foundation/ ; JCY20220530150402004//Shenzhen Science and Technology Program/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology/drug effects ; *Fatty Acids, Volatile/metabolism ; *Osteoporosis/prevention & control ; Bone and Bones/metabolism/drug effects ; Bone Density/drug effects ; },
abstract = {Osteoporosis is a systemic skeletal disease characterized by low bone density and microarchitectural deterioration, resulting in increased fracture risk. With an aging population, osteoporosis imposes a heavy burden worldwide. Current pharmacotherapies such as bisphosphonates can reduce fracture risk but have limitations. Emerging research suggests that gut microbiota regulates bone metabolism through multiple mechanisms. Short-chain fatty acids (SCFAs) produced from microbial fermentation of dietary fiber beneficially impact bone health. Preclinical studies indicate that SCFAs such as butyrate and propionate prevent bone loss in osteoporosis models by inhibiting osteoclastogenesis and immune modulation. Early clinical data also suggest that SCFA supplementation may improve bone turnover markers in postmenopausal women. SCFAs likely act via inhibition of osteoclast differentiation, stimulation of osteoblast activity, regulation of T cells, and other pathways. However, optimal dosing, delivery methods, and long-term safety require further investigation. Modulating the gut-bone axis via supplementation, prebiotics/probiotics, diet, and lifestyle interventions represents an innovative therapeutic approach for osteoporosis. Harnessing the interplay between microbiome, metabolism, immunity, and bone may provide new directions for managing osteoporosis in the future.},
}

Humans
*Gastrointestinal Microbiome/physiology/drug effects
*Fatty Acids, Volatile/metabolism
*Osteoporosis/prevention & control
Bone and Bones/metabolism/drug effects
Bone Density/drug effects

@article {pmid39183307,
year = {2024},
author = {Beck, LC and Berrington, JE and Stewart, CJ},
title = {Impact of probiotics on gut microbiome of extremely preterm or extremely low birthweight infants.},
journal = {Pediatric research},
volume = {},
number = {},
pages = {},
pmid = {39183307},
issn = {1530-0447},
abstract = {Meta-analysis of probiotic administration to very preterm or very low birthweight (VP/VLBW) infants shows reduced risk of necrotising enterocolitis (NEC). Separately reported outcomes for extremely preterm infants (<28 weeks) or extremely low birth weight infants (<1000 g) (EP/ELBW) are lacking meaning some clinicians do not administer probiotics to EP/ELBW infants despite their high risk of NEC. We present data showing the gut microbiome is impacted in EP/ELBW infants in a similar manner to VP/VLBW infants, suggesting that risk reduction for necrotising enterocolitis that is microbiome driven will also be seen in EP/ELBW infants, making probiotic administration beneficial.},
}

@article {pmid39182818,
year = {2024},
author = {Fang, C and Liu, KD and Tian, FJ and Li, JY and Li, SJ and Zhang, RM and Sun, J and Fang, LX and Ren, H and Wang, MG and Liao, XP},
title = {Metagenomic analysis unveiled the response of microbial community and antimicrobial resistome in natural water body to duck farm sewage.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {124784},
doi = {10.1016/j.envpol.2024.124784},
pmid = {39182818},
issn = {1873-6424},
abstract = {Sewages from duck farms are often recognized as a major source of antimicrobial resistance and pathogenic bacteria discharged to natural water bodies, but few studies depicted the dynamic changes in resistome and microbial communities in the rivers under immense exposure of sewage discharge. In this study, we investigated the ecological and environmental risks of duck sewages to the rivers that geographically near to the duck farms with short-distance (< 1km) using 16S rRNA amplicon and metagenomic sequencing. The results showed that a total of 20 ARG types were identified with abundances ranged from 0.61 to 1.33 cpc. Of note, the genes modulate resistances against aminoglycoside, bacitracin and beta-lactam were the most abundant ARGs. Limnohabitans, Fluviibacter and Cyanobium were the top 3 predominant genera in the microbial community. The alpha diversity of overall microbial community decrease while the abundance of pathogen increase during the input of sewage within 200 meters. Sul1 and bacA were the dominant ARGs brought from duck farm sewage. The community variations of ARGs and microbiome were primarily driven by pH and temperature. Total phosphorus was significantly correlated to alpha diversity and top 30 ARGs subtype. Stochastic processes was the dominated microbial assembly pattern and did not be altered by sewage. We also highlighted the ecological risk caused by blaGES which possibly could be mitigated by Cyanobacteria, and the natural water body can purify partial ARGs as well as microbiome from duck farms sewage. These findings expanded our knowledge regarding the ecological risks by wastes from the livestock farm, and underscoring the necessity to monitor ARGs in farm-surrounding water bodies.},
}

@article {pmid39182764,
year = {2024},
author = {Zhao, Y and Tan, J and Fang, L and Jiang, L},
title = {Harnessing meta-omics to unveil and mitigate methane emissions in ruminants: Integrative approaches and future directions.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {175732},
doi = {10.1016/j.scitotenv.2024.175732},
pmid = {39182764},
issn = {1879-1026},
abstract = {Methane emissions from enteric fermentation present a dual challenge globally: they not only contribute significantly to atmospheric greenhouse gases but also represent a considerable energy loss for ruminant animals. Utilizing high-throughput omics technologies to analyze rumen microbiome samples (meta-omics, i.e., metagenomics, metatranscriptomics, metaproteomics, metabolomics) holds vast potential for uncovering the intricate interplay between diet, microbiota, and methane emissions in these animals. The primary obstacle is the effective integration of diverse meta-omic approaches and their broader application across different ruminant species. Genetic variability significantly impacts methane production in ruminants, suggesting that genomic selection could be a viable strategy to reduce emissions. While substantial research has been conducted on the microbiological aspects of methane production, there remains a critical need to delineate the specific genetic interactions between the host and its microbiome. Advancements in meta-omics technologies are poised to shed light on these interactions, enhancing our understanding of the genetic factors that govern methane output. This review explores the potential of meta-omics to accelerate genetic advancements that could lead to reduced methane emissions in ruminants. By employing a systems biology approach, the integration of various omics technologies allows for the identification of key genomic regions and genetic markers linked to methane production. These markers can then be leveraged in selective breeding programs to cultivate traits associated with lower emissions. Moreover, the review addresses current challenges in applying genomic selection for this purpose and discusses how omics technologies can overcome these obstacles. The systematic integration and analysis of diverse biological data provide deeper insights into the genetic underpinnings and overall biology of methane production traits in ruminants. Ultimately, this comprehensive approach not only aids in reducing the environmental impact of agriculture but also contributes to the sustainability and efficiency of livestock management.},
}

@article {pmid39182696,
year = {2024},
author = {Dabboussi, N and Debs, E and Bouji, M and Rafei, R and Fares, N},
title = {Balancing the Mind: Toward a Complete Picture of the Interplay between Gut Microbiota, Inflammation and Major Depressive Disorder.},
journal = {Brain research bulletin},
volume = {},
number = {},
pages = {111056},
doi = {10.1016/j.brainresbull.2024.111056},
pmid = {39182696},
issn = {1873-2747},
abstract = {The intricate interplay existing between gut microbiota and homeostasis extends to the realm of the brain, where emerging research underscores the significant impact of the microbiota on mood regulation and overall neurological well-being and vice-versa, with inflammation playing a pivotal role in mediating these complex interactions. This comprehensive review explores the complex interplay between inflammation, alterations in gut microbiota, and their impact on major depressive disorder (MDD). It provides a cohesive framework for the puzzle pieces of this triad, emphasizing recent advancements in understanding the gut microbiota and inflammatory states' contribution to the depressive features. Two directions of communication between the gut and the brain in depression are discussed, with inflammation serving as a potential modulator. Therapeutic implications were discussed as well, drawing insights from interventional studies on the effects of probiotics on gut bacterial composition and depressive symptoms. Ultimately, this review will attempt to provide a complete and valuable framework for future research and therapeutic interventions in MDD.},
}

@article {pmid39182606,
year = {2024},
author = {Sobhi, HF and Mercer, KE and Lan, RS and Yeruva, L and Ten Have, GAM and Deutz, NEP and Piccolo, BD and Debédat, J and Pack, LM and Adams, SH},
title = {Novel odd-chain cyclopropane fatty acids: detection in a mammalian lipidome and uptake by hepatosplanchnic tissues.},
journal = {Journal of lipid research},
volume = {},
number = {},
pages = {100632},
doi = {10.1016/j.jlr.2024.100632},
pmid = {39182606},
issn = {1539-7262},
abstract = {Microbe-produced molecules (xenometabolites) found in foods or produced by gut microbiota are increasingly implicated in microbe-microbe and microbe-host communication. Xenolipids, in particular, are a class of metabolites for which the full catalog remains to be elaborated in mammalian systems. We and others have observed that cis-3,4-methylene-heptanoylcarnitine (cis-3,4-MHC) is a lipid derivative that is one of the most abundant medium-chain acylcarnitines in human blood, hypothesized to be a product of incomplete β-oxidation of one or more "odd-chain" long-chain cyclopropane fatty acids (CpFAs). We deduced two possible candidates, cis-11,12-methylene-pentadecanoic acid (cis-11,12-MPD) and cis-13,14-methylene-heptadecanoic acid (cis-13,14 MHD). Authentic standards were synthesized: cis-11-pentadecenoic acid and cis-13-heptadecenoic acid were generated (using Jones reagent) from cis-11-pentadecene-1-ol and cis-13-heptadecene-1-ol, respectively, and these were converted to CpFAs via a reaction involving diiodomethane. Using these standards in mass spectrometry analyses, we determined presence/absence of cis-11,12-MPD and cis-13,14 MHD in archived piglet biospecimens. Both CpFAs were detected in rectal contents of sow and soy-fed piglets. Archived mass spectra were analyzed post hoc from a second, independent study that used tissue-specific catheterization to monitor net metabolite flux in growing pigs. This confirmed the presence of both CpFAs in plasma, and revealed a significant net uptake of the odd-chain CpFAs across the splanchnic tissue bed and liver. The results confirm that the novel xenolipids cis-11,12-MPD and cis-13,14 MHD can be components of the mammalian lipidome, and are viable candidate precursors of cis-3,4-MHC produced from partial β-oxidation in liver or other tissues.},
}

@article {pmid39182548,
year = {2024},
author = {Xu, J and Wang, X and Xu, W and Zhang, Y and Pan, L and Gao, J},
title = {The protective effect of S-adenosylmethionine on chronic adolescent stress-induced depression-like behaviors by regulating gut microbiota.},
journal = {European journal of pharmacology},
volume = {},
number = {},
pages = {176939},
doi = {10.1016/j.ejphar.2024.176939},
pmid = {39182548},
issn = {1879-0712},
abstract = {The efficacy and tolerability of current antidepressants for adolescent depression are inadequate. S-adenosylmethionine (SAMe), known for its effectiveness and minimal side effects in adult depression, remains unstudied in adolescents. This study explored the potential of SAMe to address depression-like behaviors in juvenile rats induced by chronic unpredictable mild stress (CUMS), with a focus on gut microbiome interactions. Adolescent male Wistar rats were subjected to a 4-week CUMS regimen and received daily intraperitoneal injections of 300 mg/kg SAMe. Behavioral assessments included the sucrose preference test, elevated plus maze test, open field test, and Y-maze test. Histopathological changes of the hippocampus and colon were observed by Nissl staining and hematoxylin and eosin staining, respectively. Gut microbiome composition was analyzed using Accurate 16S absolute quantification sequencing. The results showed that SAMe significantly improved behavioral outcomes, reduced histopathological damages in hippocampal neurons and colon tissues, and modulated the gut microbiota of depressed rats. It favorably altered the ratio of Bacteroidetes to Firmicutes, decreased the absolute abundance of Deferribacteres, and adjusted levels of key microbial genera associated with depression-like behaviors. These results suggested that SAMe could effectively counter depression-like behaviors in CUMS-exposed adolescent rats by mitigating hippocampal neuronal and colon damage and modulating the gut microbiota. This supports SAMe as a viable and tolerable treatment option for adolescent depression, highlighting the importance of the gut-brain axis in therapeutic strategies.},
}

@article {pmid39182440,
year = {2024},
author = {Schettini, F and Gattazzo, F and Nucera, S and Rubio Garcia, E and López-Aladid, R and Morelli, L and Fontana, A and Vigneri, P and Casals-Pascual, C and Iebba, V and Generali, D},
title = {Navigating the complex relationship between human gut microbiota and breast cancer: Physiopathological, prognostic and therapeutic implications.},
journal = {Cancer treatment reviews},
volume = {130},
number = {},
pages = {102816},
doi = {10.1016/j.ctrv.2024.102816},
pmid = {39182440},
issn = {1532-1967},
abstract = {The human body represents the habitat of trillions of symbiotic microorganisms, collectively known as human microbiota, approximately half of which residing in the gut. The development of next-generation sequencing techniques has boosted the profiling of human microbiota in recent years. A growing body of evidence seems to support a strict relationship between the disruption of the mutualistic relationship between the microbiota and the host (i.e., dysbiosis) and the development of several diseases, including breast malignancies. Breast cancer still represents the most frequent cause of cancer-related death in women. Its complex relationship with gut microbiota is the object of a growing body of evidence. In fact, the interaction with the host immune system and a direct impact of gut microbiota on estrogen, lipid and polyphenols metabolism, seem to potentially affect breast tumor development, progression and response to treatments. In this review, in an attempt to help oncologists navigating this rapidly-evolving research field, we provide an essential overview on the taxonomy, main analytical techniques and terminology most commonly adopted. We discuss what is currently known regarding the interaction between gut microbiota and breast cancer and potential efforts to harness this complex interplay for therapeutic purposes, and revise main ongoing studies. We also briefly provide an overview on breast cancer intratumoral microbiota and its potential role beyond gut microbiota.},
}

@article {pmid39182227,
year = {2024},
author = {Chilton, PM and Ghare, SS and Charpentier, BT and Myers, SA and Rao, AV and Petrosino, JF and Hoffman, KL and Greenwell, JC and Tyagi, N and Behera, J and Wang, Y and Sloan, LJ and Zhang, J and Shields, CB and Cooper, GE and Gobejishvili, L and Whittemore, SR and McClain, CJ and Barve, SS},
title = {Age-associated temporal decline in butyrate-producing bacteria plays a key pathogenic role in the onset and progression of neuropathology and memory deficits in 3×Tg-AD mice.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2389319},
pmid = {39182227},
issn = {1949-0984},
support = {P20 GM113226/GM/NIGMS NIH HHS/United States ; R01 AG061065/AG/NIA NIH HHS/United States ; U01 AA022618/AA/NIAAA NIH HHS/United States ; P50 AA024337/AA/NIAAA NIH HHS/United States ; U01 AA026936/AA/NIAAA NIH HHS/United States ; I01 CX002219/CX/CSRD VA/United States ; },
mesh = {Animals ; *Butyrates/metabolism ; *Gastrointestinal Microbiome ; Mice ; *Alzheimer Disease/microbiology/pathology/metabolism ; *Memory Disorders/microbiology/metabolism/pathology ; *Bacteria/classification/metabolism/genetics/isolation & purification ; *Disease Models, Animal ; *Dysbiosis/microbiology ; Hippocampus/metabolism/pathology ; Mice, Transgenic ; Male ; Disease Progression ; Brain-Gut Axis/physiology ; Brain/metabolism/pathology ; },
abstract = {Alterations in the gut-microbiome-brain axis are increasingly being recognized to be involved in Alzheimer's disease (AD) pathogenesis. However, the functional consequences of enteric dysbiosis linking gut microbiota and brain pathology in AD progression remain largely undetermined. The present work investigated the causal role of age-associated temporal decline in butyrate-producing bacteria and butyrate in the etiopathogenesis of AD. Longitudinal metagenomics, neuropathological, and memory analyses were performed in the 3×Tg-AD mouse model. Metataxonomic analyses showed a significant temporal decline in the alpha diversity marked by a decrease in butyrate-producing bacterial communities and a concurrent reduction in cecal butyrate production. Inferred metagenomics analysis identified the bacterial acetyl-CoA pathway as the main butyrate synthesis pathway impacted. Concomitantly, there was an age-associated decline in the transcriptionally permissive acetylation of histone 3 at lysines 9 and 14 (H3K9/K14-Ac) in hippocampal neurons. Importantly, these microbiome-gut-brain changes preceded AD-related neuropathology, including oxidative stress, tau hyperphosphorylation, memory deficits, and neuromuscular dysfunction, which manifest by 17-18 months. Initiation of oral administration of tributyrin, a butyrate prodrug, at 6 months of age mitigated the age-related decline in butyrate-producing bacteria, protected the H3K9/K14-Ac status, and attenuated the development of neuropathological and cognitive changes associated with AD pathogenesis. These data causally implicate age-associated decline in butyrate-producing bacteria as a key pathogenic feature of the microbiome-gut-brain axis affecting the onset and progression of AD. Importantly, the regulation of butyrate-producing bacteria and consequent butyrate synthesis could be a significant therapeutic strategy in the prevention and treatment of AD.},
}

Animals
*Butyrates/metabolism
*Gastrointestinal Microbiome
Mice
*Alzheimer Disease/microbiology/pathology/metabolism
*Memory Disorders/microbiology/metabolism/pathology
*Bacteria/classification/metabolism/genetics/isolation & purification
*Disease Models, Animal
*Dysbiosis/microbiology
Hippocampus/metabolism/pathology
Mice, Transgenic
Male
Disease Progression
Brain-Gut Axis/physiology
Brain/metabolism/pathology

@article {pmid39182226,
year = {2024},
author = {Zhuang, M and Zhang, X and Cai, J},
title = {Microbiota-gut-brain axis: interplay between microbiota, barrier function and lymphatic system.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2387800},
pmid = {39182226},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Brain-Gut Axis/physiology ; Animals ; Lymphatic System/physiology/microbiology ; Brain/physiology/metabolism/microbiology ; Blood-Brain Barrier/microbiology/metabolism ; Bacteria/metabolism/genetics/classification ; Gastrointestinal Tract/microbiology/physiology ; },
abstract = {The human gastrointestinal tract, boasting the most diverse microbial community, harbors approximately 100 trillion microorganisms comprising viruses, bacteria, fungi, and archaea. The profound genetic and metabolic capabilities of the gut microbiome underlie its involvement in nearly every facet of human biology, from health maintenance and development to aging and disease. Recent recognition of microbiota - gut - brain axis, referring to the bidirectional communication network between gut microbes and their host, has led to a surge in interdisciplinary research. This review begins with an overview of the current understandings regarding the influence of gut microbes on intestinal and blood-brain barrier integrity. Subsequently, we discuss the mechanisms of the microbiota - gut - brain axis, examining the role of gut microbiota-related neural transmission, metabolites, gut hormones and immunity. We propose the concept of microbiota-mediated multi-barrier modulation in the potential treatment in gastrointestinal and neurological disorders. Furthermore, the role of lymphatic network in the development and maintenance of barrier function is discussed, providing insights into lesser-known conduits of communication between the microbial ecosystem within the gut and the brain. In the final section, we conclude by describing the ongoing frontiers in understanding of the microbiota - gut - brain axis's impact on human health and disease.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Brain-Gut Axis/physiology
Animals
Lymphatic System/physiology/microbiology
Brain/physiology/metabolism/microbiology
Blood-Brain Barrier/microbiology/metabolism
Bacteria/metabolism/genetics/classification
Gastrointestinal Tract/microbiology/physiology

@article {pmid39182153,
year = {2024},
author = {Yuan, QS and Gao, Y and Wang, L and Wang, X and Wang, L and Ran, J and Ou, X and Wang, Y and Xiao, C and Jiang, W and Guo, L and Zhou, T and Huang, L},
title = {Pathogen-driven Pseudomonas reshaped the phyllosphere microbiome in combination with Pseudostellaria heterophylla foliar disease resistance via the release of volatile organic compounds.},
journal = {Environmental microbiome},
volume = {19},
number = {1},
pages = {61},
pmid = {39182153},
issn = {2524-6372},
support = {Qian Jiao Ji (2022) 021//the Research Platform Team Project of the Education Department of Guizhou Province/ ; Qian Jiao Ji (2022) 021//the Research Platform Team Project of the Education Department of Guizhou Province/ ; Qian Jiao Ji (2022) 021//the Research Platform Team Project of the Education Department of Guizhou Province/ ; Qian Jiao Ji (2022) 021//the Research Platform Team Project of the Education Department of Guizhou Province/ ; Qian Jiao Ji (2022) 021//the Research Platform Team Project of the Education Department of Guizhou Province/ ; Qian Jiao Ji (2022) 021//the Research Platform Team Project of the Education Department of Guizhou Province/ ; Qian Jiao Ji (2022) 021//the Research Platform Team Project of the Education Department of Guizhou Province/ ; Qian Jiao Ji (2022) 021//the Research Platform Team Project of the Education Department of Guizhou Province/ ; Qian Jiao Ji (2022) 021//the Research Platform Team Project of the Education Department of Guizhou Province/ ; Qian Jiao Ji (2022) 021//the Research Platform Team Project of the Education Department of Guizhou Province/ ; Qian Jiao Ji (2022) 021//the Research Platform Team Project of the Education Department of Guizhou Province/ ; 2023YFC3503803//National key research and development program/ ; 2023YFC3503803//National key research and development program/ ; Qian Ke He Zhi Cheng (2022) Yi Ban 136//Guizhou Provincial Major Scientific and Technological Program/ ; Qian Ke He Zhi Cheng (2022) Yi Ban 136//Guizhou Provincial Major Scientific and Technological Program/ ; },
abstract = {BACKGROUND: Continuous monocropping obstacles are common in plants, especially medicinal plants, resulting in disease outbreaks and productivity reductions. Foliar disease, mainly caused by Fusarium oxysporum, results in a severe decrease in the yield of Pseudostellaria heterophylla annually. Determining an effective biomethod to alleviate this disease is urgently needed to improve its productivity and quality.

RESULTS: This study screened thirty-two keystone bacterial genera induced by pathogens in P. heterophylla rhizosphere soil under continuous monocropping conditions. Pseudomonas, Chryseobacterium, and Flavobacterium, referred to as the beneficial microbiota, were significantly attracted by pathogen infection. The P. palleroniana strain B-BH16-1 can directly inhibit the growth and spore formation of seven primary pathogens of P. heterophylla foliar disease by disrupting fusaric acid production via the emission of volatile organic compounds (VOCs). In addition, strain B-BH16-1 enhances the disease resistance of P. heterophylla by obliterating the pathogen and assembling beneficial microbiota.

CONCLUSION: Pathogen-induced Pseudomonas reshaped phyllosphere microbial communities via direct antagonism of pathogens and indirect disruption of the pathogen virulence factor biosynthesis to enhance disease suppression and improve yields. These results show that inhibiting pathogen virulence biosynthesis to reshape the plant microbial community using disease-induing probiotics will be an innovative strategy for managing plant disease, especially under continuous monoculture conditions.},
}

@article {pmid39182077,
year = {2024},
author = {Lei, S and Khan, I and Zhang, X and Chen, T and Xie, X and Zheng, X and Jianye, Z and Li, Z},
title = {Assessing oral and toothbrush microbial profiles among high-altitude individuals with and without periodontal disease: a case-control study.},
journal = {BMC oral health},
volume = {24},
number = {1},
pages = {993},
pmid = {39182077},
issn = {1472-6831},
support = {31760159//National Natural Science Foundation of China/ ; 31760159//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Altitude ; Male ; Case-Control Studies ; Female ; *Toothbrushing/instrumentation ; Adult ; *Periodontal Diseases/microbiology ; Middle Aged ; Microbiota ; Tibet ; Saliva/microbiology ; Mouth/microbiology ; },
abstract = {BACKGROUND: Periodontitis is the sixth-most common disease worldwide. The oral microbiome composition and its association with Periodontal disease (PD) have been largely explored; however, limited studies have explored the microbial profiles of both oral and toothbrushes in patients with PD. Thus, this study aimed to ascertain the oral and toothbrushes microbial composition in high-altitude populations, hypothesizing that their correlation with periodontal health would differ from those at lower altitudes, potentially indicating links between environmental factors, microbial colonization patterns, and periodontal health in distinct geographic contexts.

METHODS: In the present study, we enrolled 35 individuals including 21 healthy and 14 diagnosed with PD from the Lhasa region of Tibet, China. Saliva and toothbrush samples were collected from each participant to assess the association between toothbrush usage and oral microbiome with PD using 16 S rRNA gene-specific V3-V4 regions sequencing. To assess the oral and toothbrush microbiome composition and diversity and its possible link to PD.

RESULTS: Significantly higher Alpha diversity (Shannon index) was observed between the PD group and PD toothbrushes (p = 0.00021) and between the PD group and Healthy toothbrushes (p = 0.00041). The predominant species were Proteobacteria, Bacteroidota, Firmicutes, Actinobacteria, and Fusobacteria, with genera Pseudomonas, Veillonella, Neisseria, Acinetobacter, and Haemophilus. In addition, PICRUST2 analysis unveiled 44 significant pathways differentiating the disease and healthy groups, along with 29 pathways showing significant differences between their respective toothbrush microbial profiles. The distinct oral and toothbrush microbial composition among high-altitude populations suggests potential adaptations to the challenges of high-altitude environments.

CONCLUSION: This study emphasizes the importance of tailored dental care strategies, accounting for altitude and racial factors, to effectively manage periodontal health in these communities. Further research is warranted to investigate the specific microbial mechanisms and develop targeted interventions for optimizing oral health in populations across varying altitudes.},
}

Humans
*Altitude
Male
Case-Control Studies
Female
*Toothbrushing/instrumentation
Adult
*Periodontal Diseases/microbiology
Middle Aged
Microbiota
Tibet
Saliva/microbiology
Mouth/microbiology

@article {pmid39182075,
year = {2024},
author = {Matboli, M and Abdelbaky, I and Khaled, A and Khaled, R and Hamady, S and Farid, LM and Abouelkhair, MB and El-Attar, NE and Farag Fathallah, M and Abd El Hamid, MS and Elmakromy, GM and Ali, M},
title = {Machine learning based identification potential feature genes for prediction of drug efficacy in nonalcoholic steatohepatitis animal model.},
journal = {Lipids in health and disease},
volume = {23},
number = {1},
pages = {266},
pmid = {39182075},
issn = {1476-511X},
mesh = {Animals ; *Non-alcoholic Fatty Liver Disease/drug therapy/genetics/pathology ; *Machine Learning ; Rats ; *Disease Models, Animal ; Liver/pathology/metabolism/drug effects ; Male ; YAP-Signaling Proteins/genetics ; Biomarkers/blood ; MicroRNAs/genetics ; },
abstract = {BACKGROUND: Nonalcoholic Steatohepatitis (NASH) results from complex liver conditions involving metabolic, inflammatory, and fibrogenic processes. Despite its burden, there has been a lack of any approved food-and-drug administration therapy up till now.

PURPOSE: Utilizing machine learning (ML) algorithms, the study aims to identify reliable potential genes to accurately predict the treatment response in the NASH animal model using biochemical and molecular markers retrieved using bioinformatics techniques.

METHODS: The NASH-induced rat models were administered various microbiome-targeted therapies and herbal drugs for 12 weeks, these drugs resulted in reducing hepatic lipid accumulation, liver inflammation, and histopathological changes. The ML model was trained and tested based on the Histopathological NASH score (HPS); while (0-4) HPS considered Improved NASH and (5-8) considered non-improved, confirmed through rats' liver histopathological examination, incorporates 34 features comprising 20 molecular markers (mRNAs-microRNAs-Long non-coding-RNAs) and 14 biochemical markers that are highly enriched in NASH pathogenesis. Six different ML models were used in the proposed model for the prediction of NASH improvement, with Gradient Boosting demonstrating the highest accuracy of 98% in predicting NASH drug response.

FINDINGS: Following a gradual reduction in features, the outcomes demonstrated superior performance when employing the Random Forest classifier, yielding an accuracy of 98.4%. The principal selected molecular features included YAP1, LATS1, NF2, SRD5A3-AS1, FOXA2, TEAD2, miR-650, MMP14, ITGB1, and miR-6881-5P, while the biochemical markers comprised triglycerides (TG), ALT, ALP, total bilirubin (T. Bilirubin), alpha-fetoprotein (AFP), and low-density lipoprotein cholesterol (LDL-C).

CONCLUSION: This study introduced an ML model incorporating 16 noninvasive features, including molecular and biochemical signatures, which achieved high performance and accuracy in detecting NASH improvement. This model could potentially be used as diagnostic tools and to identify target therapies.},
}

Animals
*Non-alcoholic Fatty Liver Disease/drug therapy/genetics/pathology
*Machine Learning
Rats
*Disease Models, Animal
Liver/pathology/metabolism/drug effects
Male
YAP-Signaling Proteins/genetics
Biomarkers/blood
MicroRNAs/genetics

@article {pmid39182062,
year = {2024},
author = {Wang, L and Yi, Q and Xu, H and Liu, H and Tan, B and Deng, H and Chen, Y and Wang, R and Tang, F and Cheng, X and Zhu, J},
title = {Alterations in the gut microbiota community are associated with childhood obesity and precocious puberty.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {311},
pmid = {39182062},
issn = {1471-2180},
support = {2022064//Chengdu Medical Research Project/ ; 2022064//Chengdu Medical Research Project/ ; 22FXZD06//Scientific and technological Innovation of Maternal and Child Medicine in Sichuan Province/ ; 22FXZD06//Scientific and technological Innovation of Maternal and Child Medicine in Sichuan Province/ ; },
mesh = {Humans ; *Puberty, Precocious/microbiology ; *Gastrointestinal Microbiome ; Female ; *Pediatric Obesity/microbiology/complications ; Child ; *Bacteria/classification/genetics/isolation & purification ; *RNA, Ribosomal, 16S/genetics ; *Feces/microbiology ; Child, Preschool ; DNA, Bacterial/genetics ; },
abstract = {OBJECTIVE: To explore the distribution and differences in the intestinal microbiota in girls with obesity-related precocious puberty and the relationship between intestinal microbiota and obesity-related precocious puberty.

METHODS: 16 S rRNA gene amplicons from fecal samples from girls with precocious puberty and obesity-complicated precocious puberty and healthy children were sequenced to define microbial taxa.

RESULTS: The α- and β-diversity indices of the microbiome significantly differed among the three groups. At the phylum level, the proportions of Firmicutes, Actinobacteriota, Bacteroidota, Bacteria, Campylobacterota, and Acidobacteriota were different. At the genus level, there were differences in Bifidobacterium, Bacteroides, Anaerostipes, Fusicatenibacter, Klebsiella, Lachnospiraceae, ErysipelotrichaceaeUCG-003, Prevotella9, Ruminococcus gnavus group, and Lachnoclostridium. Additionally, Bifidobacterium, Anaerostipes, Bacteroides, Candidatus Microthrix, Eubacterium hallii group, Klebsiella, and Erysipelotrichaceae UCG-003 were identified as bacterial biomarkers by LEfSe. Furthermore, Sellimonas, Intestinibacter, Anaerostipes, Ruminococcus gnavus group, and Oscillibacter were identified as the differential biomarkers by random forest. A receiver operating characteristic (ROC) curve was used to evaluate the biomarkers with high predictive value for obesity-related precocious puberty. Spearman correlation analysis confirmed that Anaerostipes levels were negatively correlated with body weight, body mass index (BMI), bone age, luteinizing hormone, follicle-stimulating hormone, and estradiol.

CONCLUSIONS: There was a significant correlation between obesity-associated precocious puberty and gut microbiota, especially the functional characteristics of the microbiome and its interactions, which can provide a theoretical basis for the clinical intervention of obesity and precocious puberty through the microbiome.},
}

Humans
*Puberty, Precocious/microbiology
*Gastrointestinal Microbiome
Female
*Pediatric Obesity/microbiology/complications
Child
*Bacteria/classification/genetics/isolation & purification
*RNA, Ribosomal, 16S/genetics
*Feces/microbiology
Child, Preschool
DNA, Bacterial/genetics

@article {pmid39182019,
year = {2024},
author = {Dong, X and Xiong, YT and He, T and Zheng, C and Li, J and Zhuang, Y and Xu, Y and Xiu, Y and Wu, Z and Zhao, X and Xiao, X and Bai, Z and Gao, L},
title = {Protective effects of Nogo-B deficiency in NAFLD mice and its multiomics analysis of gut microbiology and metabolism.},
journal = {Genes & nutrition},
volume = {19},
number = {1},
pages = {17},
pmid = {39182019},
issn = {1555-8932},
support = {ZYYCXTD-C-202005//Innovation Team and Talents Cultivation Program of National Administration of Traditional Chinese Medicine/ ; 81721002//Foundation for lnnovative Research Groups of the National Natural ScienceFoundation of China/ ; },
abstract = {BACKGROUND: Nonalcoholic fatty liver disease (NAFLD) is a prevalent chronic liver ailment that can lead to serious conditions such as cirrhosis and hepatocellular carcinoma. Hepatic Nogo-B regulates glucose and lipid metabolism, and its inhibition has been shown to be protective against metabolic syndrome. Increasing evidence suggests that imbalances in the gut microbiota (GM) and lipid metabolism disorders are significant contributors to NAFLD progression. Nevertheless, it is not yet known whether Nogo-B can affect NAFLD by influencing the gut microbiota and metabolites. Hence, the aim of the present study was to characterize this process and explore its possible underlying mechanisms.

METHODS: A NAFLD model was constructed by administering a high-fat diet (HFD) to Nogo-B[-/-] and WT mice from the same litter, and body weight was measured weekly in each group. The glucose tolerance test (GTT) and insulin tolerance test (ITT) were performed to assess blood glucose levels. At the end of the 12-week period, samples of serum, liver, and intestinal contents were collected and used for serum biochemical marker and inflammatory factor detection; pathology evaluation; and gut microbiome and metabolomics analysis. Spearman's correlation analysis was performed to determine possible correlations between differential gut microbiota and differential serum metabolites between groups.

RESULTS: Nogo-B deficiency attenuated the effects of the HFD, including weight gain, liver weight gain, impaired glucose tolerance, hepatic steatosis, elevated serum lipid biochemicals levels, and liver function. Nogo-B deficiency suppressed M1 polarization and promoted M2 polarization, thus inhibiting inflammatory responses. Furthermore, Nogo-B[-/-]-HFD-fed mice presented increased gut microbiota richness and diversity, decreased Firmicutes/Bacteroidota (F/B) ratios, and altered serum metabolites compared with those of WT-HFD-fed mice. During analysis, several differential gut microbiota, including Lachnoclostridium, Harryflintia, Odoribacter, UCG-009, and unclassified_f_Butyricoccaceae, were screened between groups. These microbiota were found to be positively correlated with upregulated purine metabolism and bile acid metabolites in Nogo-B deficiency, while they were negatively correlated with downregulated corticosterone and tricarboxylic acid cyclic metabolites in Nogo-B deficiency.

CONCLUSION: Nogo-B deficiency delayed NAFLD progression, as demonstrated by reduced hepatocellular lipid accumulation, attenuated inflammation and liver injury, and ameliorated gut microbiota dysbiosis and metabolic disorders. Importantly, Odoribacter was strongly positively correlated with ALB and taurodeoxycholic acid, suggesting that it played a considerable role in the influence of Nogo-B on the progression of NAFLD, a specific feature of NAFLD in Nogo-B[-/-] mice. The regulation of bile acid metabolism by the gut microbiota may be a potential target for Nogo-B deficiency to ameliorate NAFLD.},
}

@article {pmid39181345,
year = {2024},
author = {Xu, Y and Le, J and Qin, J and Zhang, Y and Yang, J and Chen, Z and Li, C and Qian, X and Zhang, A},
title = {Decoding the microbiota metabolome in hepatobiliary and pancreatic cancers: Pathways to precision diagnostics and targeted therapeutics.},
journal = {Pharmacological research},
volume = {},
number = {},
pages = {107364},
doi = {10.1016/j.phrs.2024.107364},
pmid = {39181345},
issn = {1096-1186},
abstract = {We delve into the critical role of the gut microbiota and its metabolites in the pathogenesis and progression of hepatobiliary and pancreatic (HBP) cancers, illuminating an urgent need for breakthroughs in diagnostic and therapeutic strategies. Given the high mortality rates associated with HBP cancers, which are attributed to aggressive recurrence, metastasis, and poor responses to chemotherapy, exploring microbiome research presents a promising frontier. This research highlights how microbial metabolites, including secondary bile acids, short-chain fatty acids, and lipopolysaccharides, crucially influence cancer cell behaviors such as proliferation, apoptosis, and immune evasion, significantly contributing to the oncogenesis and progression of HBP cancers. By integrating the latest findings, we discuss the association of microbial alterations with HBP cancers, key metabolites, and their implications, and how metabolomics and microbiomics can enhance diagnostic precision. Furthermore, the paper explores strategies for targeted therapies through microbiome metabolomics, including the direct therapeutic effects of microbiome metabolites and potential synergistic effects on conventional therapies. We also recognize that the field of microbial metabolites for the diagnosis and treatment of tumors still has a lot of problems to be solved. The aim of this study is to pioneer microbial metabolite research and provide a reference for HBP cancer diagnosis, treatment, and prognosis.},
}

@article {pmid39181304,
year = {2024},
author = {Yu, Y and Ai, T and Huang, J and Jin, L and Yu, X and Zhu, X and Sun, J and Zhu, L},
title = {Metabolism of isodecyl diphenyl phosphate in rice and microbiome system: Differential metabolic pathways and underlying mechanisms.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {361},
number = {},
pages = {124803},
doi = {10.1016/j.envpol.2024.124803},
pmid = {39181304},
issn = {1873-6424},
abstract = {Isodecyl diphenyl phosphate (IDDP) is among the emerging aromatic organophosphate esters (aryl-OPEs) that pose risks to both human beings and other organisms. This study aims to investigate the translocation and biotransformation behavior of IDDP in rice and the rhizosphere microbiome through hydroponic exposure (the duration of hydroponic exposure was 10 days). The rhizosphere microbiome 9-FY was found to efficiently eliminate IDDP, thereby reducing its uptake in rice tissues and mitigating the negative impact of IDDP on rice growth. Furthermore, this study proposed the first-ever transformation pathways of IDDP, identifying hydrolysis, hydroxylation, methylation, methoxylation, carboxylation, and glucuronidation products. Notably, the methylation and glycosylation pathways were exclusively observed in rice, indicating that the transformation of IDDP in rice may be more complex than in microbiome 9-FY. Additionally, the presence of the product COOH-IDDP in rice suggested that there might be an exchange of degradation products between rice and rhizobacteria, implying their potential interaction. This finding highlights the significance of rhizobacteria's role which cannot be overlooked in the accumulation and transformation of organic pollutants in grain crops. The study revealed active members in 9-FY during IDDP degradation, and metagenomic analysis indicated that most of the active populations contained IDDP-degrading genes. Moreover, transcriptome sequencing showed that cytochrome P450, acid phosphatase, glucosyltransferase, and methyltransferases genes in rice were up-regulated, which was further confirmed by RT-qPCR. This provides insight into the intermediate products identified in rice, such as hydrolysis, hydroxylated, glycosylated, and methylated products. These results significantly contribute to our understanding of the translocation and transformation of organophosphate esters (OPEs) in plants and the rhizosphere microbiome, and reveal the fate of OPEs in rice and microbiome system to ensure the paddy yield and rice safety.},
}

@article {pmid39181210,
year = {2024},
author = {Zhang, YH and Xie, R and Dai, CS and Gao, HW and Zhou, G and Qi, TT and Wang, WY and Wang, H and Cui, YM},
title = {Thyroid hormone receptor-beta agonist HSK31679 alleviates MASLD by modulating gut microbial sphingolipids.},
journal = {Journal of hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jhep.2024.08.008},
pmid = {39181210},
issn = {1600-0641},
abstract = {BACKGROUND & AIMS: As the first approved medication for metabolic dysfunction-associated steatohepatitis (MASH), thyroid hormone receptor-beta (THR-β) agonist MGL-3196 (Resmetirom) is highly spotlighted as the liver-directed, bioactive oral drug. However, it was also identified with remarkable heterogeneity of individual clinical efficacy and its interference with gut microbiota in host hepatoenteral circulation was still undocumented.

METHODS: We compared MASH attenuation by MGL-3196 and its derivative drug HSK31679 between germ-free (GF) and specific-pathogen free (SPF) mice to evaluate the role of gut microbiota. Then cross-omics analyses of microbial metagenome, metabolome and single-cell RNA-sequencing were applied into the randomized, double-blind, placebo-controlled multiple-ascending-dose (MAD) cohort of HSK31679 treatment (n = 40), to comprehensively investigate the altered gut microbiota metabolism and circulating immune signatures.

RESULTS: HSK31679 outperformed MGL-3196 in ameliorating MASH diet-induced steatohepatitis of SPF mice but not GF mice. In the MAD cohort of HSK31679, relative abundance of B. thetaiotaomicron was significantly enriched to impair glucosylceramide synthase (GCS)-catalyzed monoglucosylation of microbial Cer(d18:1/16:0) and Cer(d18:1/24:1). In stark contrast to the non-inferiority MASH resolution between MGL-3196 and HSK31679 for GF[BTΔGCS] mice, HSK31679 manifested superior steatohepatitis alleviation than MGL-3196 for GF[BTWT] mice, due to its steric hindrance with R123 and Y401 of gut microbial GCS. For participants with high fecal GCS activity, the administration of 160 mg HSK31679 induced a shift in peripheral compartments towards an immunosuppressive niche, characterized by decreased CD8α[+] dendritic cells and MINCLE[+] macrophages.

CONCLUSIONS: This study provided novel insights into the indispensable gut microbiota for HSK31679 treatment, which revealed microbial GCS may serve as its prognostic biomarker of MASH treatment, as well as the new target for further strategies of microbiota-based MASH therapeutics.

IMPACT AND IMPLICATIONS: Remarkable heterogeneity of individual clinical efficacy of THR-β agonists and their interferences with microbiome in host hepatoenteral circulation are poorly understood. In our current germ-free mice models and randomized, double-blind multiple-dose cohort study, we identified microbial GCS as the prognostic biomarker of HSK31679 treatment, as well as the new target for further strategies of microbiota-based MASLD therapeutics.},
}

@article {pmid39181163,
year = {2024},
author = {Costabile, G and Baldassi, D and Müller, C and Groß, B and Ungaro, F and Schubert, S and Firestine, SM and Merkel, OM},
title = {Antibiotic-loaded nanoparticles for the treatment of intracellular methicillin-resistant Staphylococcus Aureus infections: In vitro and in vivo efficacy of a novel antibiotic.},
journal = {Journal of controlled release : official journal of the Controlled Release Society},
volume = {374},
number = {},
pages = {454-465},
doi = {10.1016/j.jconrel.2024.08.029},
pmid = {39181163},
issn = {1873-4995},
abstract = {Antimicrobial resistance is considered one of the biggest threats to public health worldwide. Methicillin-resistant S. aureus is the causative agent of a number of infections and lung colonization in people suffering from cystic fibrosis. Moreover, a growing body of evidence links the microbiome to the development of cancer, as well as to the success of the treatment. In this view, the development of novel antibiotics is of critical importance, and SV7, a novel antibiotic active against MRSA at low concentrations, represents a promising candidate. However, the low aqueous solubility of SV7 hampers its therapeutic translation. In this study, SV7 was encapsulated in poly(lactic-co-glycolic acid) (PLGA) nanoparticles (NPs) to improve the solubility profile, to ensure sustained release and eventually support deposition in the airways. Furthermore, PLGA NPs were formulated as dry powder to extend their shelf-life and were shown to efficiently target intracellular infections. After identifying a formulation with suitable physico-chemical characteristics, SV7-loaded NPs were investigated in vitro in terms of inhibitory activity against MRSA, and their safety profile in lung epithelial cells. Subsequently, the activity against MRSA intracellular infections was investigated in a co-culture model of MRSA and macrophages. To test the translatability of our findings, SV7-loaded NPs were tested in vivo in a Galleria mellonella infection model. In conclusion, SV7-loaded NPs showed a safe profile and efficient inhibitory activity against MRSA at low concentrations. Furthermore, their activity against intracellular infections was confirmed, and was retained in vivo, rendering them a promising candidate for treatment of MRSA lung infections.},
}

@article {pmid39180897,
year = {2024},
author = {Guo, Y and Wu, X and Wang, Y and Zeqian, Y and Cao, L and Zhu, F},
title = {Prediction of early remission after infliximab in Crohn's disease using baseline microbiome and metabolomics.},
journal = {Journal of pharmaceutical and biomedical analysis},
volume = {251},
number = {},
pages = {116424},
doi = {10.1016/j.jpba.2024.116424},
pmid = {39180897},
issn = {1873-264X},
abstract = {To characterize the microbiome and metabolic profile in Crohn's disease (CD) patients with different outcome after infliximab (IFX) treatment. The clinical data of a cohort of 35 patients with moderate-to-severe CD admitted at Jinling hospital between Oct 2022 and Dec 2023 were collected. Stool samples at baseline were collected to perform 16SrRNA and ITS2 sequencing and LC-MS untargeted metabolomics. Of these, seven discontinued IFX and underwent surgery during the induction period, and 28 received IFX at weeks 0, 2, and 6, each administered intravenously. Clinical remission was assessed based on the clinical symptoms and HBI at baseline and week 14. Baseline microbial richness and evenness was not significantly different between remission and non-remission group. The taxonomic community analysis identified decrease of Ruminococcus, Lachnoclostridium, Akkermansia in bacterial community and decrease of Asterotremella and Wallemia in fungal community in the non-remission group. LC-MS analysis showed that histamine, creatinine and L-proline significantly increased in remission group, while androsterone, berberine and episterol significantly decreased. The combined prediction model of histamine, androsterone, and episterol demonstrated a high predictive value of remission in patients after IFX treatment (AUC=0.898, p<0.001). Together, these data might facilitate a priori determination of optimal therapeutics for CD patients.},
}

@article {pmid39180778,
year = {2024},
author = {Li, W and Yang, M and Luo, Y and Liu, W and Wang, Z and Ning, Z},
title = {Effects of dietary rosemary ultrafine powder supplementation on aged hen health and productivity: a randomized controlled trial.},
journal = {Poultry science},
volume = {103},
number = {11},
pages = {104133},
doi = {10.1016/j.psj.2024.104133},
pmid = {39180778},
issn = {1525-3171},
abstract = {Recently, poultry industry has been seeking antibiotic residue-free poultry products and safe nutritious feed additives. Whether rosemary ultrafine powder (RUP) affects productive performance by regulating the intestinal microbiome of aged layers remains unclear. Here, we investigated the effects of dietary RUP supplementation on the production performance, egg quality, antioxidant capacity, intestinal microbial structure, and metabolome of aged hens. The results indicate that RUP had no significant effect on production performance but significantly enhanced Thick albumen height, Haugh unit, yolk color (P < 0.05), daily feed intake, and qualified egg rate. Serum content of non-esterified fatty acids, catalase, and glutathione peroxidase increased significantly (P < 0.05). Furthermore, the liver total protein content was significantly increased (P < 0.05). 16S rRNA sequence analysis revealed that RUP significantly impacted both α- and β-diversity of the caecum microbiota. Linear discriminant analysis of effect size and random forest identified Bacteroides, Muribaculum, Butyricimonas, Odoribacter, and Prevotella as biomarkers in groups A and B. In comparing groups A and C, Barnesiella, Turicibacter, and Acholeplasma were critical bacteria, while comparing groups A and D highlighted Barnesiella and Candidatus Saccharimonas as differential bacteria. FAPROTAX analysis of the caecum microbiota revealed that the functional genes associated with harmful substance biodegradation were significantly increased in the RUP-fed group. Based on Spearman correlation analysis, alterations in microbial genera were associated with divergent metabolites. In summary, dietary RUP can improve egg quality and antioxidant capacity and regulate the intestinal microbiome and metabolome in aged breeders. Therefore, RUP can potentially be used as a feed additive to extend breeder service life at an appropriate level of 1.0 g/kg.},
}

@article {pmid39180723,
year = {2024},
author = {Jiang, L and Hao, Y and Han, D and Dong, W and Yang, A and Sun, Z and Ge, Y and Duan, S and Zhang, X and Dai, Z},
title = {Gut microbiota dysbiosis deteriorates immunoregulatory effects of tryptophan via colonic indole and LBP/HTR2B-mediated macrophage function.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae166},
pmid = {39180723},
issn = {1751-7370},
abstract = {Tryptophan (Trp) has been shown to regulate immune function by modulating gut serotonin (5-HT) metabolism and signaling. However, the mechanisms underlying the microbial modulation of gut 5-HT signaling in gut inflammation with gut microbiota dysbiosis require further investigation. Here, we investigated the effects of Trp supplementation on the composition and metabolism of the gut microbiome and 5-HT signaling-related gut immune function using a dextran sodium sulfate (DSS)-induced colitis mouse model coupled with antibiotic exposure. The results showed that antibiotic treatment before but not during DSS treatment decreased the immunoregulatory effects of Trp and aggravated gut inflammation and body weight loss in mice. Metagenomic analysis revealed that the fecal microbiota transplantation (FMT) of Trp-enriched gut microbiota to recipient mice subject to antibiotic preexposure and DSS treatment aggravated inflammation by increasing the relative abundances of Lactobacillus and Parabacteroides and the microbial production of indole coupled with the activation of the 5-HT receptor HTR2B in the colon. Transcriptomic analysis showed that HTR2B agonist administration strengthened the beneficial effects of Trp in DSS-induced colitis mice with antibiotic exposure by reducing gut lipopolysaccharide-binding protein (LBP) production, IκB-α/nuclear factor-κB signaling, and M1 macrophage polarization. Indole treatment reduced LBP production and M1 macrophage polarization both in mice with DSS-induced colitis and in lipopolysaccharide-treated mouse macrophages; however, the HTR2B antagonist reversed the effects of indole. Our findings provide the basis for developing new dietary and therapeutic interventions to improve gut microbiota dysbiosis-associated inflammatory gut disorders and diseases.},
}

@article {pmid39180603,
year = {2024},
author = {Żak-Bochenek, A and Żebrowska-Różańska, P and Bajzert, J and Siwińska, N and Madej, JP and Kaleta-Kuratewicz, K and Bochen, P and Łaczmański, Ł and Chełmońska-Soyta, A},
title = {Comparison and characterization of the bacterial microbiota and SIgA production in different gastrointestinal segments in horses.},
journal = {Veterinary research communications},
volume = {},
number = {},
pages = {},
pmid = {39180603},
issn = {1573-7446},
abstract = {In the gastrointestinal mucosa, there is a close cooperation between secretory immunoglobulin A (SIgA) and the composition of the microbiota, which aims to maintain homeostasis as well as act as a protective barrier. The purpose of this study was to determine the composition of microbiota and SIgA production in different parts of the digestive tract (small intestine, cecum, colon and rectum) of nine healthy horses and its reflection in the feces. For this purpose, we determined: the composition of the microbiome (by next-generation Sequencing of Hypervariable Regions V3-V4 and V7-V9 of the 16 S rRNA gene analysis), the amount of SIgA in the intestinal content samples (by ELISA), as well as the number of IgA-producing cells (IgA+) in the tissue samples (by immohistochemical analysis). Significant differences were observed between the small intestine and the large colon in the composition and diversity of the microbiome, as well as the number of IgA + cells in the mucosal lamina propria and the abundance of SIgA in the intestinal lumen. The small intestine in relation to the large colon is characterised by fewer IgA + cells, more SIgA in the intestinal contents and a less diverse microbiome. However, the cecum appears to be the third separate ecosystem, with a high number of IgA + cells and a diverse microbiome. The fecal sample reflects the current state of the large colon, both in terms of the microbiome and SIgA content; however, it is not known to what extent it may be influenced by dysbiosis in other parts of the digestive tract.},
}

@article {pmid39180577,
year = {2024},
author = {Zhang, L and Jiang, Z and Hu, S and Ni, H and Zhao, Y and Tan, X and Lang, Y and Na, R and Li, Y and Du, Q and Li, QX and Dong, Y},
title = {GSK3β Substrate-competitive Inhibitors Regulate the gut Homeostasis and Barrier Function to Inhibit Neuroinflammation in Scopolamine-induced Alzheimer's Disease Model Mice.},
journal = {Inflammation},
volume = {},
number = {},
pages = {},
pmid = {39180577},
issn = {1573-2576},
support = {81973545//National Natural Science Foundation of China/ ; 81973545//National Natural Science Foundation of China/ ; 81973545//National Natural Science Foundation of China/ ; 81973545//National Natural Science Foundation of China/ ; 81973545//National Natural Science Foundation of China/ ; 81973545//National Natural Science Foundation of China/ ; 81973545//National Natural Science Foundation of China/ ; 81973545//National Natural Science Foundation of China/ ; 81973545//National Natural Science Foundation of China/ ; 81973545//National Natural Science Foundation of China/ ; 81973545//National Natural Science Foundation of China/ ; 81973545//National Natural Science Foundation of China/ ; HAW05020H//Grant USDA Hatch project/ ; HAW05020H//Grant USDA Hatch project/ ; HAW05020H//Grant USDA Hatch project/ ; HAW05020H//Grant USDA Hatch project/ ; HAW05020H//Grant USDA Hatch project/ ; HAW05020H//Grant USDA Hatch project/ ; HAW05020H//Grant USDA Hatch project/ ; HAW05020H//Grant USDA Hatch project/ ; HAW05020H//Grant USDA Hatch project/ ; HAW05020H//Grant USDA Hatch project/ ; HAW05020H//Grant USDA Hatch project/ ; HAW05020H//Grant USDA Hatch project/ ; },
abstract = {Alzheimer's disease (AD) is a neurodegenerative disease mainly characterized by cognitive impairment. Glycogen synthase kinase 3 (GSK3β) is a potential therapeutic target against AD. Isoorientin (ISO), a GSK3β substrate competitive inhibitor, plays anti-AD effects in in vitro and in vivo AD model. TFGF-18 is an ISO synthetic analog with improved potency, but its neuroprotective effect in vivo remains to be elucidated, and the underlying mechanisms of GSK3β inhibitor against AD need to be clarified. This study investigated the TFGF-18 and ISO effects on gut homeostasis and neuroinflammation in scopolamine (SCOP)-induced AD mice. And the protection on barrier function was observed in in vitro blood-brain barrier (BBB) model of mouse brain microvascular endothelial cells (bEnd.3). The results show that TFGF-18 and ISO improved cognitive function in SCOP-induced mice, and inhibited cholinergic system disorders and inflammation in the brain and intestine, decreased the level of lipopolysaccharides (LPS) in serum and intestine, protected the diversity and balance of intestinal microbiome, increased the expressions of tight junction protein (ZO-1, occludin), brain derived neurotrophic factor (BDNF) and glial cell-derived neurotrophic factor (GDNF) in the mouse brain and intestine. In addition, TFGF-18 and ISO protected against barrier damage in LPS-stimulated BBB model of bEnd.3 cells in vitro. TFGF-18 and ISO increased the ratio of p-GSK3β/GSK3β, suppressed toll-like receptors 4 (TLR-4) expression and nuclear factor kappa-B (NF-κB) activation in vivo and in vitro, and increased the expressions of β-catenin, nuclear factor erythroid 2-related factor 2 (Nrf2) and heme oxygenase-1 (HO-1) in vitro. In conclusion, The GSK3β inhibitors TFGF-18 and ISO modulate the gut homeostasis and barrier function to inhibit neuroinflammation and attenuate cognitive impairment by regulating NF-κB, β-catenin and Nrf2/HO-1 pathways.},
}

@article {pmid39180199,
year = {2024},
author = {Imataki, O and Uemura, M},
title = {Bifidobacterium Bloodstream Infection in a Lymphoma Patient Undergoing Chemotherapy: A Case Study and Implications for Probiotic Use.},
journal = {The American journal of case reports},
volume = {25},
number = {},
pages = {e944687},
doi = {10.12659/AJCR.944687},
pmid = {39180199},
issn = {1941-5923},
mesh = {Humans ; Female ; Aged ; *Probiotics/therapeutic use ; *Antineoplastic Combined Chemotherapy Protocols/therapeutic use/adverse effects ; Cyclophosphamide/therapeutic use ; Doxorubicin/therapeutic use/adverse effects ; Vincristine/therapeutic use ; Bifidobacteriales Infections/microbiology ; Rituximab/therapeutic use/adverse effects ; Prednisone/therapeutic use ; Bacteremia/drug therapy/microbiology ; Bifidobacterium breve ; Lymphoma/drug therapy ; },
abstract = {BACKGROUND Fermenting bacilli producing lactic acid, including Bifidobacterium spp., are supposed to have low pathogenicity and no virulence for humans. Probiotics consisting of those fermenting bacilli can prevent and treat symptomatic gastrointestinal conditions, such as diarrhea. We use probiotics even in cancer patients, those who are immunocompromised, because a preferable effect to the intestinal commensal microbiome has been shown in a recent report. Some case reports warn of a rare risk of bloodstream infection caused by probiotics. However, complete prohibition of probiotic use in cancer patients abandons the benefits. CASE REPORT A 75-year-old Japanese woman with malignant lymphoma was treated with immune-chemotherapy regimen consisting of rituximab plus cyclophosphamide, doxorubicin, vincristine, and prednisolone (R-CHOP). The patient had onset of febrile neutropenia during chemotherapy and had Bifidobacterium breve bloodstream infection on day 8 after the eighth R-CHOP treatment. She had usually eaten commercial yogurt every morning. This yogurt was produced from only Lactobacillus bulgaricus and Streptococcus thermophilus. It did not contain Bifidobacterium breve. The bloodstream infection in this case looked like it derived from her food; however, it was not associated with her habitual foods. The patient was treated with meropenem for 8 days and experienced complete remission of the bloodstream infection. CONCLUSIONS We speculate that fermenting bacilli can also be a source of bloodstream infection, not necessarily associated with probiotic strains, in cancer patients treated with chemotherapy. Additionally, we recommend that probiotics can alleviate alimentary tract symptoms in immunocompromised patients.},
}

Humans
Female
Aged
*Probiotics/therapeutic use
*Antineoplastic Combined Chemotherapy Protocols/therapeutic use/adverse effects
Cyclophosphamide/therapeutic use
Doxorubicin/therapeutic use/adverse effects
Vincristine/therapeutic use
Bifidobacteriales Infections/microbiology
Rituximab/therapeutic use/adverse effects
Prednisone/therapeutic use
Bacteremia/drug therapy/microbiology
Bifidobacterium breve
Lymphoma/drug therapy

@article {pmid39180136,
year = {2024},
author = {Khadem, S and Berry, D and Al-Khlifeh, E},
title = {Climate influences the gut eukaryome of wild rodents in the Great Rift Valley of Jordan.},
journal = {Parasites & vectors},
volume = {17},
number = {1},
pages = {358},
pmid = {39180136},
issn = {1756-3305},
mesh = {Animals ; Jordan/epidemiology ; Mice ; *Gastrointestinal Microbiome ; *Feces/parasitology/microbiology ; *Climate ; Eukaryota/classification/isolation & purification/genetics ; Animals, Wild/parasitology ; RNA, Ribosomal, 18S/genetics ; Rodentia/microbiology/parasitology ; Biodiversity ; Murinae/parasitology ; },
abstract = {BACKGROUND: The mammalian gut microbiome includes a community of eukaryotes with significant taxonomic and functional diversity termed the eukaryome. The molecular analysis of eukaryotic diversity in microbiomes of wild mammals is still in its early stages due to the recent emergence of interest in this field. This study aimed to fill this knowledge gap by collecting data on eukaryotic species found in the intestines of wild rodents. Because little is known about the influence of climate on the gut eukaryome, we compared the composition of the gut eukaryotes in two rodent species, Mus musculus domesticus and Acomys cahirinus, which inhabit a transect crossing a temperate and tropical zone on the Jordanian side of the Great Rift Valley (GRV).

METHODS: We used high-throughput amplicon sequencing targeting the 18S rRNA gene in fecal samples from rodents to identify eukaryotic organisms, their relative abundance, and their potential for pathogenicity.

RESULTS: Nematodes and protozoa were the most prevalent species in the eukaryome communities, whereas fungi made up 6.5% of the total. Sixty percent of the eukaryotic ASVs belonged to taxa that included known pathogens. Eighty percent of the rodents were infected with pinworms, specifically Syphacia obvelata. Eukaryotic species diversity differed significantly between bioclimatic zones (p = 0.001). Nippostrongylus brasiliensis and Aspiculuris tetraptera were found to be present exclusively in the Sudanian zone rodents. This area has not reported any cases of Trichuris infections. Yet, Capillaria infestations were unique to the Mediterranean region, while Trichuris vulpis infestations were also prevalent in the Mediterranean and Irano-Turanian regions.

CONCLUSIONS: This study highlights the importance of considering host species diversity and environmental factors when studying eukaryome composition in wild mammals. These data will be valuable as a reference to eukaryome study.},
}

Animals
Jordan/epidemiology
Mice
*Gastrointestinal Microbiome
*Feces/parasitology/microbiology
*Climate
Eukaryota/classification/isolation & purification/genetics
Animals, Wild/parasitology
RNA, Ribosomal, 18S/genetics
Rodentia/microbiology/parasitology
Biodiversity
Murinae/parasitology

@article {pmid39180084,
year = {2024},
author = {Xia, X and Wei, Q and Wu, H and Chen, X and Xiao, C and Ye, Y and Liu, C and Yu, H and Guo, Y and Sun, W and Liu, W},
title = {Bacillus species are core microbiota of resistant maize cultivars that induce host metabolic defense against corn stalk rot.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {156},
pmid = {39180084},
issn = {2049-2618},
support = {2022YFD1402000//The authors acknowledge financial support from the National Key R&D Program of China/ ; },
mesh = {*Zea mays/microbiology/metabolism ; *Plant Diseases/microbiology/immunology/prevention & control ; *Bacillus/metabolism ; *Fusarium ; *Disease Resistance ; *Microbiota ; Soil Microbiology ; Rhizosphere ; Tyrosine Decarboxylase/metabolism/genetics ; Host Microbial Interactions ; Tyramine/metabolism ; },
abstract = {BACKGROUND: Microbes colonizing each compartment of terrestrial plants are indispensable for maintaining crop health. Although corn stalk rot (CSR) is a severe disease affecting maize (Zea mays) worldwide, the mechanisms underlying host-microbe interactions across vertical compartments in maize plants, which exhibit heterogeneous CSR-resistance, remain largely uncharacterized.

RESULTS: Here, we investigated the microbial communities associated with CSR-resistant and CSR-susceptible maize cultivars using multi-omics analysis coupled with experimental verification. Maize cultivars resistant to CSR reshaped the microbiota and recruited Bacillus species with three phenotypes against Fusarium graminearum including niche pre-emption, potential secretion of antimicrobial compounds, and no inhibition to alleviate pathogen stress. By inducing the expression of Tyrosine decarboxylase 1 (TYDC1), encoding an enzyme that catalyzes the production of tyramine and dopamine, Bacillus isolates that do not directly suppress pathogen infection induced the synthesis of berberine, an isoquinoline alkaloid that inhibits pathogen growth. These beneficial bacteria were recruited from the rhizosphere and transferred to the stems but not grains of the CSR-resistant plants.

CONCLUSIONS: The current study offers insight into how maize plants respond to and interact with their microbiome and lays the foundation for preventing and treating soil-borne pathogens. Video Abstract.},
}

*Zea mays/microbiology/metabolism
*Plant Diseases/microbiology/immunology/prevention & control
*Bacillus/metabolism
*Fusarium
*Disease Resistance
*Microbiota
Soil Microbiology
Rhizosphere
Tyrosine Decarboxylase/metabolism/genetics
Host Microbial Interactions
Tyramine/metabolism

@article {pmid39180058,
year = {2024},
author = {Hua, X and McGoldrick, J and Nakrour, N and Staller, K and Chung, DC and Xavier, RJ and Khalili, H},
title = {Gut microbiome structure and function in asymptomatic diverticulosis.},
journal = {Genome medicine},
volume = {16},
number = {1},
pages = {105},
pmid = {39180058},
issn = {1756-994X},
support = {R01 AG068390/AG/NIA NIH HHS/United States ; DK043351//Center for the study of inflammatory bowel disease/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; Female ; Middle Aged ; Aged ; Metagenomics/methods ; Colonoscopy ; Metagenome ; Bacteria/classification/genetics ; },
abstract = {BACKGROUND: Colonic diverticulosis, the most common lesion found in routine colonoscopy, affects more than 50% of individuals aged ≥ 60 years. Emerging evidence suggest that dysbiosis of gut microbiota may play an important role in the pathophysiology of diverticular disease. However, specific changes in microbial species and metabolic functions in asymptomatic diverticulosis remain unknown.

METHODS: In a cohort of US adults undergoing screening colonoscopy, we analyzed the gut microbiota using shotgun metagenomic sequencing. Demographic factors, lifestyle, and medication use were assessed using a baseline questionnaire administered prior to colonoscopy. Taxonomic structures and metabolic pathway abundances were determined using MetaPhlAn3 and HUMAnN3. We used multivariate association with linear models to identify microbial species and metabolic pathways that were significantly different between asymptomatic diverticulosis and controls, while adjusting for confounders selected a priori including age at colonoscopy, sex, body mass index (BMI), and dietary pattern.

RESULTS: Among 684 individuals undergoing a screening colonoscopy, 284 (42%) had diverticulosis. Gut microbiome composition explained 1.9% variation in the disease status of asymptomatic diverticulosis. We observed no significant differences in the overall diversity of gut microbiome between asymptomatic diverticulosis and controls. However, microbial species Bifidobacterium pseudocatenulatum and Prevotella copri were significantly enriched in controls (q value = 0.19 and 0.14, respectively), whereas Roseburia intestinalis, Dorea sp. CAG:317, and Clostridium sp. CAG: 299 were more abundant in those with diverticulosis (q values = 0.17, 0.24, and 0.10, respectively). We observed that the relationship between BMI and diverticulosis appeared to be limited to carriers of Bifidobacterium pseudocatenulatum and Roseburia intestinalis (Pinteraction = 0.09).

CONCLUSIONS: Our study provides the first large-scale evidence supporting taxonomic and functional shifts of the gut microbiome in individuals with asymptomatic diverticulosis. The suggestive interaction between gut microbiota and BMI on prevalent diverticulosis deserves future investigations.},
}

Humans
*Gastrointestinal Microbiome
Male
Female
Middle Aged
Aged
Metagenomics/methods
Colonoscopy
Metagenome
Bacteria/classification/genetics

@article {pmid39180015,
year = {2024},
author = {Jang, JW and Capaldi, E and Smith, T and Verma, P and Varga, J and Ho, KJ},
title = {Trimethylamine N-oxide: a meta-organismal axis linking the gut and fibrosis.},
journal = {Molecular medicine (Cambridge, Mass.)},
volume = {30},
number = {1},
pages = {128},
pmid = {39180015},
issn = {1528-3658},
support = {Postdoctoral Fellowship//American Heart Association/ ; R33AR076821/AR/NIAMS NIH HHS/United States ; R01HL153306/HL/NHLBI NIH HHS/United States ; R21AG081706/AG/NIA NIH HHS/United States ; },
mesh = {*Methylamines/metabolism ; Humans ; *Gastrointestinal Microbiome ; Animals ; *Fibrosis ; Dysbiosis/metabolism ; Oxygenases/metabolism ; },
abstract = {BACKGROUND: Tissue fibrosis is a common pathway to failure in many organ systems and is the cellular and molecular driver of myriad chronic diseases that are incompletely understood and lack effective treatment. Recent studies suggest that gut microbe-dependent metabolites might be involved in the initiation and progression of fibrosis in multiple organ systems.

MAIN BODY OF THE MANUSCRIPT: In a meta-organismal pathway that begins in the gut, gut microbiota convert dietary precursors such as choline, phosphatidylcholine, and L-carnitine into trimethylamine (TMA), which is absorbed and subsequently converted to trimethylamine N-oxide (TMAO) via the host enzyme flavin-containing monooxygenase 3 (FMO3) in the liver. Chronic exposure to elevated TMAO appears to be associated with vascular injury and enhanced fibrosis propensity in diverse conditions, including chronic kidney disease, heart failure, metabolic dysfunction-associated steatotic liver disease, and systemic sclerosis.

CONCLUSION: Despite the high prevalence of fibrosis, little is known to date about the role of gut dysbiosis and of microbe-dependent metabolites in its pathogenesis. This review summarizes recent important advances in the understanding of the complex metabolism and functional role of TMAO in pathologic fibrosis and highlights unanswered questions.},
}

*Methylamines/metabolism
Humans
*Gastrointestinal Microbiome
Animals
*Fibrosis
Dysbiosis/metabolism
Oxygenases/metabolism

@article {pmid39180004,
year = {2024},
author = {Guo, X and Xu, K and Wang, Q and Han, Z and Yu, G},
title = {Assessing the impact of triiodothyronine treatment on the lung microbiome of mice with pulmonary fibrosis.},
journal = {BMC pulmonary medicine},
volume = {24},
number = {1},
pages = {405},
pmid = {39180004},
issn = {1471-2466},
support = {2019YFE0119500//State Innovation Base for Pulmonary Fibrosis (111 Project), Ministry of Science and Technology, PR China/ ; 222102310711//Henan Project of Science and Technology/ ; 21ZD002//Xinxiang Major Project/ ; },
mesh = {Animals ; Mice ; *Triiodothyronine/blood/pharmacology ; *Mice, Inbred C57BL ; *Microbiota/drug effects ; *Bleomycin ; *Disease Models, Animal ; *Lung/pathology/microbiology ; Female ; *RNA, Ribosomal, 16S/genetics ; Idiopathic Pulmonary Fibrosis/drug therapy/microbiology ; Pulmonary Fibrosis/drug therapy/microbiology ; },
abstract = {BACKGROUND: Idiopathic pulmonary fibrosis (IPF), an interstitial lung disease, is characterized by the exacerbation of progressive pulmonary fibrosis (PF). IPF primarily affects older individuals and can lead to respiratory failure. This study aimed to assess the effects of triiodothyronine (T3) treatment on the lung microbiome of mice with PF.

METHODS: Mice were perfused with bleomycin (BLM) to establish a PF model. Using a randomized design, 40 female specific pathogen-free (SPF) C57BL6/N mice were divided into four groups: saline, saline + T3, BLM, and BLM + T3. Histological morphology was assessed through Hematoxylin and Eosin staining as well as Masson's Trichrome staining. For the identification of lung bacteria, 16S rRNA gene sequencing was employed. An Enzyme-Linked Immunosorbent Assay was used to measure total T3 (TT3), free T3 (FT3, and reverse T3 (rT3) levels in the peripheral serum.

RESULTS: T3 treatment ameliorated BLM-induced lung fibrosis and structural damage. The microbiome experienced a decrease in the abundance of Proteobacteria, Bacteroides, and Actinomycetes and an increase in the abundance of Firmicutes when exposed to BLM; however, T3 treatment reversed this effect. The four groups showed no significant difference in alpha microbiome diversity (P > 0.05). Serum concentrations of TT3 and FT3 were positively correlated with microbiome abundance (P < 0.05). Administration of T3 enhanced the microbiota in PF without affecting the diversity and biological functions of the microbiome (P > 0.05).

CONCLUSION: The administration of T3 demonstrated a favorable impact on the lung microbiota of mice afflicted with PF, thereby partially substantiating the potential role of T3 as a therapeutic agent in the management of PF.},
}

Animals
Mice
*Triiodothyronine/blood/pharmacology
*Mice, Inbred C57BL
*Microbiota/drug effects
*Bleomycin
*Disease Models, Animal
*Lung/pathology/microbiology
Female
*RNA, Ribosomal, 16S/genetics
Idiopathic Pulmonary Fibrosis/drug therapy/microbiology
Pulmonary Fibrosis/drug therapy/microbiology

@article {pmid39179750,
year = {2024},
author = {Park, YS and Ahn, K and Yun, K and Jeong, J and Baek, KW and Park, DJ and Han, K and Ahn, YJ},
title = {Effect of Helicobacter pylori on sleeve gastrectomy and gastric microbiome differences in patients with obesity and diabetes.},
journal = {International journal of obesity (2005)},
volume = {},
number = {},
pages = {},
pmid = {39179750},
issn = {1476-5497},
abstract = {BACKGROUND: Obesity and diabetes mellitus (DM) have become public health concerns worldwide. Both conditions have severe consequences and are associated with significant medical costs and productivity loss. Additionally, Helicobacter pylori infection may be a risk factor for the development of these conditions. However, whether eradicating H. pylori infection directly causes weight loss or improves insulin sensitivity is unknown.

METHODS: In this study, we confirmed the effect of sleeve gastrectomy according to the state of the gastric microbiota in 40 patients with obesity, DM, and H. pylori infection. Patients with obesity were divided into four groups: non-DM without H. pylori infection (ND), non-DM with H. pylori infection (ND-HP), DM, and DM with H. pylori infection (DM-HP) using 16S V3-V4 sequencing.

RESULTS: In the DM group, ALT, hemoglobin, HbA1c, blood glucose, and HSI significantly decreased, whereas high-density lipoprotein significantly increased. However, in the H. pylori-positive group, no significant difference was observed. The diversity of gastric microbiota decreased in the order of the ND > DM > ND-HP > DM-HP groups. We also conducted a correlation analysis between the preoperative microbes and clinical data. In the ND-HP group, most of the top 20 gastric microbiota were negatively correlated with glucose metabolism. However, H. pylori infection was positively correlated with pre-insulin levels.

CONCLUSION: Therefore, these findings indicate that patients with obesity and diabetes clearly benefit from surgery, but H. pylori infection may also affect clinical improvement.},
}

@article {pmid39179632,
year = {2024},
author = {Aljohani, A and Clarke, D and Byrne, M and Fleming, G},
title = {The bacterial microbiome and resistome of house dust mites in Irish homes.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {19621},
pmid = {39179632},
issn = {2045-2322},
mesh = {Animals ; *Microbiota/genetics/drug effects ; *Dust/analysis ; *Pyroglyphidae/genetics ; Ireland ; Bacteria/genetics/drug effects/classification ; Anti-Bacterial Agents/pharmacology ; Housing ; Drug Resistance, Bacterial/genetics ; },
abstract = {Dust samples were collected from Irish homes. House Dust Mite and storage mites were separated from the dust. The microbiome and resistome of mites and originating dust were assessed using a culture-independent approach. The bacterial microbiome of mites and dust were predominantly populated by Staphylococci. There was a highly significant (P = 0.005; Spearman's rank test) correlation between the bacterial microbiome of mites and the dust. One-hundred and eighteen antimicrobial resistance genes (ARGs) were associated with mites and 176 with dust. Both contained ARGs encoding resistance for multi drug resistances, macrolide-lincosamide-streptogramin B, mobile genetic elements, Beta-lactam, Tetracycline and Aminoglycosides. By contrast, 15 ARGs were found for a laboratory-grown strain of Dermatophagoides pteronyssinus. A significant difference (P = 0.03; t test) was found in means between the resistome of mites and the household dust from which they emanated. No significant correlations (P = 0.23 and P = 0.22; Mantel test) were observed between the microbiome and resistome of mite and dust samples. There was not a significant difference (P = 0.54; t-test) between the means of ARGs for homes with and without a history of antibiotic use.},
}

Animals
*Microbiota/genetics/drug effects
*Dust/analysis
*Pyroglyphidae/genetics
Ireland
Bacteria/genetics/drug effects/classification
Anti-Bacterial Agents/pharmacology
Housing
Drug Resistance, Bacterial/genetics

@article {pmid39179487,
year = {2024},
author = {Hromić-Jahjefendić, A and Mahmutović, L and Sezer, A and Bećirević, T and Rubio-Casillas, A and Redwan, EM and Uversky, VN},
title = {The intersection of microbiome and autoimmunity in long COVID-19: Current insights and future directions.},
journal = {Cytokine & growth factor reviews},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cytogfr.2024.08.002},
pmid = {39179487},
issn = {1879-0305},
abstract = {Long COVID-19 affects a significant percentage of patients and is characterized by a wide range of symptoms, including weariness and mental fog as well as emotional symptoms like worry and sadness. COVID-19 is closely linked to the autoimmune disorders that are becoming more prevalent worldwide and are linked to immune system hyperactivation, neutrophil extracellular trap (NET) development, and molecular mimicry pathways. Long-term COVID-related autoimmune responses include a watchful immune system referring to the ability of immune system to constantly monitor the body for signs of infection, disease, or abnormal cells; altered innate and adaptive immune cells, autoantigens secreted by living or dead neutrophils, and high concentrations of autoantibodies directed against different proteins. The microbiome, which consists of billions of bacteria living in the human body, is essential for controlling immune responses and supporting overall health. The microbiome can affect the course of long COVID-associated autoimmunity, including the degree of illness, the rate of recovery, and the onset of autoimmune reactions. Although the precise role of the microbiome in long COVID autoimmunity is still being investigated, new studies indicate that probiotics, prebiotics, and dietary changes-interventions that target the microbiome-may be able to reduce autoimmune reactions and enhance long-term outcomes for COVID-19 survivors. More research is required to precisely understand how the microbiome affects COVID-19-related autoimmunity and to create tailored treatment plans.},
}

@article {pmid39179419,
year = {2024},
author = {Sierra-Garcia, IN and Ferreira, MJ and Granada, CE and Patinha, C and Cunha, Â},
title = {Rhizobacterial diversity of Portuguese olive cultivars in the Douro valley and their potential as plant growth promoters.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxae220},
pmid = {39179419},
issn = {1365-2672},
abstract = {AIMS: This study investigated the bacterial communities in the rhizosphere of two traditional Portuguese olive cultivars, Cobrançosa and Negrinha de Freixo in relation to soil properties. Additionally, we aimed to isolate and identify bacteria with potential for biocontrol and other plant growth promoting traits from these rhizosphere communities.

METHODS AND RESULTS: Bacterial communities in the olive rhizosphere were investigated using a metabarcoding approach and the soil physicochemical properties of the olive groves were also analyzed. Higher bacterial richness was associated with Negrinha de Freixo growing in soil with high organic matter content and water-holding capacity. In contrast, the soils of the Cobrançosa grove presented higher pH and electric conductivity. Negrinha de Freixo rhizosphere was enriched with ASVs (Amplicon Sequence Variants) belonging to Bacillus, Gaiella, Acidothermus, Bradyrhizobium, and uncultured Xanthobacteraceae. On the other hand, the Cobrançosa rhizosphere was characterized by higher relative abundance of Streptomyces and Sphingomonas. Bacterial isolation from the rhizosphere and screening for plant growth promoting activities were also performed. Six bacteria strains, predominantly Bacillus isolated from Negrinha de Freixo, demonstrated antagonistic activities against the olive fungal pathogen C. gloeosporoides and other plant growth promotion (PGP) traits.

CONCLUSIONS: Our findings demonstrate that the structure of rhizosphere bacterial communities associated with olive trees is shaped by both plant cultivar and soil-related factors. The higher number of bacterial species in the rhizosphere of Negrinha de Freixo was related to a higher organic matter content and a greater abundance of isolates with plant growth promotion traits, particularly Bacillus strains.},
}

@article {pmid39179206,
year = {2024},
author = {Barone Lumaga, R and Tagliamonte, S and De Rosa, T and Valentino, V and Ercolini, D and Vitaglione, P},
title = {Consumption of a sourdough-leavened croissant enriched with a blend of fibers influences fasting blood glucose in a randomized controlled trial in healthy subjects.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tjnut.2024.08.015},
pmid = {39179206},
issn = {1541-6100},
abstract = {BACKGROUND: An incorrect lifestyle, including diet, is responsible for the worldwide dramatic increase in obesity and type 2-diabetes. Increasing dietary fiber consumption may lead to health benefits and reformulation of bakery products may be a strategy to globally improve the diet.

OBJECTIVE: This study aimed to assess the impact of a two-week breakfast consumption with a sourdough-leavened croissant containing a blend of dietary fiber from 10 sources (4.8g/100g, FIBCRO), compared to a control croissant (dietary fibers 1.3g/100g, CONCRO) on daily energy intake, appetite, metabolic variables, and the gut microbiome.

METHODS: Thirty-two healthy participants were randomly allocated in two groups consuming FIBCRO or CONCRO. Participants self-recorded their diet and appetite through 7-day weighted food diaries and visual analogue scales every day over the two weeks. At baseline and after the intervention, fasting blood and urine samples, and fecal samples were collected beside blood pressure, anthropometry, and body composition. Serum glucose, lipids, C-reactive protein, and insulin according to the official methods and serum dipeptidyl peptidase-4 (DPPIV) activity by photometric method were measured. Polyphenols and urolithins in urines were analyzed by LC/MS/MS whereas gut microbiome in feces by shotgun metagenomics.

RESULTS: FIBCRO consumption improved fasting blood glucose compared to CONCRO (mean changes from baseline -2.0 mg/dL in FIBCRO vs +3.1 mg/dL in CONCRO, p=0.022), also reducing serum DPPIV activity by 1.7 IU/L (p=0.01) and increasing urinary excretion of urolithin A-sulfate by 6.9 ng/mg creatinine (p=0.04) compared to baseline. No further changes in any of monitored variables or in the gut microbiome were detected.

CONCLUSIONS: Results suggested that a two-week consumption of a sourdough croissant claimed as "source of dietary fiber" improved fasting glycemia compared to a conventional sourdough croissant in healthy subjects. The reduced serum DPPIV activity and increased bioavailability of urolithin likely contributed to determine that effect independently from gut microbiome changes.

NCT04999280 (https://clinicaltrials.gov/).},
}

@article {pmid39179176,
year = {2024},
author = {Ngo, VL and Wang, Y and Wang, Y and Shi, Z and Britton, R and Zou, J and Ramani, S and Jiang, B and Gewirtz, AT},
title = {Select gut microbiota impede rotavirus vaccine efficacy.},
journal = {Cellular and molecular gastroenterology and hepatology},
volume = {},
number = {},
pages = {101393},
doi = {10.1016/j.jcmgh.2024.101393},
pmid = {39179176},
issn = {2352-345X},
abstract = {BACKGROUND& AIMS: The protection provided by rotavirus (RV) vaccines is highly heterogeneous amongst individuals. We hypothesized that microbiota composition might influence RV vaccine efficacy.

METHODS: First, we examined the potential of segmented filamentous bacteria (SFB) colonization to influence RV vaccine efficacy in mice. Next, we probed the Influence of human microbiomes on RV vaccination via administering mice fecal microbial transplants (FMT) from children with robust or minimal RV vaccine responsiveness. Post-FMT, mice were subjected to RV vaccination followed by RV challenge.

RESULTS: SFB colonization induced a phenotype that was reminiscent of RV vaccine failure, i.e. failure to generate RV antigens and, consequently, anti-RV antibodies following RV vaccination resulting in proneness to RV challenge after SFB levels diminished. FMT from children to mice recapitulated donor vaccination phenotype. Specifically, mice receiving FMT from high-responsive vaccinees copiously shed RV antigens and robustly generated anti-RV antibodies following RV vaccination. Concomitantly, such mice were impervious to RV challenge. In contrast, mice receiving FMT from children who had not responded to RV vaccination exhibited only modest responses to RV vaccination and, concomitantly, remained prone to RV challenge. Microbiome analysis ruled out a role for SFB but suggested involvement of Clostridium perfringens. Oral administration of cultured C. perfringens to gnotobiotic mice partially recapitulated the RV vaccine non-responder phenotype. Analysis of published microbiome data found C. perfringens abundance in children modestly associated with RV vaccine failure.

CONCLUSION: Microbiota composition influences RV vaccine efficacy with C. perfringens being one, perhaps of many, potential contributing taxa.},
}

@article {pmid39179139,
year = {2024},
author = {Gao, N and Zhuang, Y and Zheng, Y and Li, Y and Wang, Y and Zhu, S and Fan, M and Tian, W and Jiang, Y and Wang, Y and Cui, M and Suo, C and Zhang, T and Jin, L and Chen, X and Xu, K},
title = {Investigating the link between gut microbiome and bone mineral density: The role of genetic factors.},
journal = {Bone},
volume = {},
number = {},
pages = {117239},
doi = {10.1016/j.bone.2024.117239},
pmid = {39179139},
issn = {1873-2763},
abstract = {Osteoporosis is a complex metabolic bone disease that severely undermines the quality of life and overall health of the elderly. While previous studies have established a close relationship between gut microbiome and host bone metabolism, the role of genetic factors has received less scrutiny. This research aims to identify potential taxa associated with various bone mineral density states, incorporating assessments of genetic factors. Fecal microbiome profiles from 605 individuals (334 females and 271 males) aged 55-65 from the Taizhou Imaging Study with osteopenia (n = 270, 170 women) or osteoporosis (n = 94, 85 women) or normal (n = 241, 79 women) were determined using shotgun metagenomic sequencing. The linear discriminant analysis was employed to identify differentially enriched taxa. Utilizing the Kyoto Encyclopedia of Genes and Genomes for annotation, functional pathway analysis was conducted to identify differentially metabolic pathways. Polygenic risk score for osteoporosis was estimated to represent genetic susceptibility to osteoporosis, followed by stratification and interaction analyses. Gut flora diversity did not show significant differences among various bone mineral groups. After multivariable adjustment, certain species, such as Clostridium leptum, Fusicatenibacter saccharivorans and Roseburia hominis, were enriched in osteoporosis patients. Statistically significant interactions between the polygenic risk score and taxa Roseburia faecis, Megasphaera elsdenii were observed (P for interaction = 0.005, 0.018, respectively). Stratified analyses revealed a significantly negative association between Roseburia faecis and bone mineral density in the low-genetic-risk group (β = -0.045, P < 0.05), while Turicimonas muris was positively associated with bone mineral density in the high-genetic-risk group (β = 4.177, P < 0.05) after multivariable adjustments. Functional predictions of the gut microbiome indicated an increase in pathways related to structural proteins in high-genetic-risk patients, while low-genetic-risk patients exhibit enrichment in enzyme-related pathways. This study emphasizes the association between gut microbes and bone mass, offering new insights into the interaction between genetic background and gut microbiome.},
}

@article {pmid39179063,
year = {2024},
author = {Li, J and Tao, W and Zhou, W and Xing, J and Luo, M and Yang, Y},
title = {The comprehensive analysis of gut microbiome and spleen transcriptome revealed the immunomodulatory mechanism of Dendrobium officinale leaf polysaccharide on immunosuppressed mice.},
journal = {International journal of biological macromolecules},
volume = {278},
number = {Pt 4},
pages = {134975},
doi = {10.1016/j.ijbiomac.2024.134975},
pmid = {39179063},
issn = {1879-0003},
abstract = {In recent years, the immunomodulatory efficacy of Dendrobium officinale leaf polysaccharide (DOLP) has attracted much attention, but its potential immunomodulatory mechanism remains unclear. Therefore, we investigated the molecular mechanism of DOLP to ameliorate cyclophosphamide-induced immunosuppressed mice based on transcriptome profiling technology. The results indicated that DOLP significantly mitigated damage to immune organs, regulated the expression levels of inflammatory factors and immunoglobulins, and restored the balance of gut microbiota. Furthermore, it modulated metabolic pathways associated with the immune system, including antigen processing and presentation, hematopoietic cell line development, and natural killer cell-mediated cytotoxicity. DOLP might promote host hematopoietic function to enhance immune cell proliferation and differentiation by up-regulating Cd19, Cr2 and Il7r but down-regulating Dntt. DOLP also up-regulated the expression of MHC-1 (Gm11127, H2-K1, H2-Q10, H2-Q6, and H2-Q7), thus promoting antigen recognition by NK cells to enhance the innate immunity and helping T cells to deliver antigen and secrete immune factors so that enhancing the adaptive immunity.},
}

@article {pmid39178987,
year = {2024},
author = {Shukla, V and Singh, S and Verma, S and Verma, S and Rizvi, AA and Abbas, M},
title = {Targeting the Microbiome to Improve Human Health with the Approach of Personalized Medicine: Latest Aspects and Current Updates.},
journal = {Clinical nutrition ESPEN},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.clnesp.2024.08.005},
pmid = {39178987},
issn = {2405-4577},
abstract = {The intricate ecosystem of microorganisms residing within and on the human body, collectively known as the microbiome, significantly influences human health. Imbalances in this microbiome, referred to as dysbiosis, have been associated with various diseases, prompting the exploration of novel therapeutic approaches. Personalized medicine, Tailors treatments to individual patient characteristics, offers a promising avenue for addressing microbiome-related health issues. This review highlights recent developments in utilizing personalized medicine to target the microbiome, aiming to enhance health outcomes. Noteworthy strategies include fecal microbiota transplantation (FMT), where healthy donor microbes are transferred to patients, showing promise in treating conditions such as recurrent Clostridium difficile infection. Additionally, probiotics, which are live microorganisms similar to beneficial gut inhabitants, and prebiotics, non-digestible compounds promoting microbial growth, are emerging as tools to restore microbiome balance. The integration of these approaches, known as synbiotics, enhances microbial colonization and therapeutic effects. Advances in metagenomics and sequencing technologies provide the means to understand individual microbiome profiles, enabling tailored interventions. This paper aims to present the latest insights in leveraging personalized medicine to address microbiome-related health concerns, envisioning a future where microbiome-based therapies reshape disease management and promote human health.},
}

@article {pmid39178919,
year = {2024},
author = {Kühn, J and Brandsch, C and Bailer, AC and Kiourtzidis, M and Hirche, F and Yu Chen, C and Markó, L and Bartolomaeus, TUP and Löber, U and Michel, S and Wensch-Dorendorf, M and Forslund-Startceva, SK and Stangl, GI},
title = {UV light exposure vs. vitamin D supplementation: a comparison of health benefits and vitamin D metabolism in a pig model.},
journal = {The Journal of nutritional biochemistry},
volume = {},
number = {},
pages = {109746},
doi = {10.1016/j.jnutbio.2024.109746},
pmid = {39178919},
issn = {1873-4847},
abstract = {There is limited data on the effect of UV light exposure versus orally ingested vitamin D3 on vitamin D metabolism and health. A 4-week study with 16 pigs (as a model for human physiology) was conducted. The pigs were either supplemented with 20 µg/d vitamin D3 or exposed to UV light for 19 min/d to standardise plasma 25-hydroxyvitamin D3 levels. Important differences were higher levels of stored vitamin D3 in skin and subcutaneous fat, higher plasma concentrations of 3-epi-25-hydroxyvitamin D3 and increases of cutaneous lumisterol3 in UV-exposed pigs compared to supplemented pigs. UV light exposure compared to vitamin D3 supplementation resulted in lower hepatic cholesterol, higher circulating plasma nitrite, a marker of the blood pressure-lowering nitric oxide, and a reduction in the release of pro- and anti-inflammatory cytokines from stimulated peripheral blood mononuclear cells. However, plasma metabolome and stool microbiome analyses did not reveal any differences between the two groups. To conclude, the current data show important health relevant differences between oral vitamin D3 supplementation and UV light exposure. The findings may also partly explain the different vitamin D effects on health parameters obtained from association and intervention studies.},
}

@article {pmid39178800,
year = {2024},
author = {Kuriki, N and Asahi, Y and Okamoto, M and Noiri, Y and Ebisu, S and Machi, H and Suzuki, M and Hayashi, M},
title = {Synergistic effects of arginine and fluoride on human dental biofilm control.},
journal = {Journal of dentistry},
volume = {149},
number = {},
pages = {105307},
doi = {10.1016/j.jdent.2024.105307},
pmid = {39178800},
issn = {1879-176X},
support = {K02 DE029531/DE/NIDCR NIH HHS/United States ; R01 DE027648/DE/NIDCR NIH HHS/United States ; },
abstract = {OBJECTIVES: The aim of this study was to quantitatively and comprehensively investigate the combined effects of arginine and fluoride on the suppression of pathogenicity using an in situ biofilm model and next-generation sequencing (NGS).

METHODS: Using the in situ model, dental biofilms were formed and the viable bacterial counts and arginine activity in the arginine- and fluoride-containing dentifrice and control groups were measured. We also compared their effects on the bacterial microbiota and predictive functional factors in the control, arginine (arg), and arginine + fluoride (argF) groups using NGS analysis.

RESULTS: Compared to the control treatment, the use of 8 % arginine and 1450 ppm fluoride toothpaste resulted in significantly high oral NH4[+] concentrations without affecting the number of viable bacteria (P < 0.05). NGS analysis revealed that the oral microbiota of the control, arg, and argF groups were significantly different. Heat map analysis of the predicted functional factors revealed that the arg group had different properties from the other groups and activated specific substrate metabolic pathways; contrastingly, argF treatment inhibited the activity of these pathways and prevented an increase in the abundance of bacterial genera that utilize substrates such as sucrose, suggesting the synergistic effect of arginine and fluoride.

CONCLUSIONS: This study indicates that the combination of arginine and fluoride has a synergistic effect on the bacterial microbiota and pathogenicity of dental biofilms compared with arginine alone.

CLINICAL SIGNIFICANCE: Our findings suggest that the combination of arginine and fluoride could be used as an effective prebiotic and may inhibit the growth of bacteria associated with dental diseases.},
}

@article {pmid39178663,
year = {2024},
author = {Indriani, S and Srisakultiew, N and Benjakul, S and Boonchuen, P and Petsong, K and Pongsetkul, J},
title = {The impact of hot-air oven drying combined with Bacillus subtilis KC3 inoculation on quality characteristics and microbial profiles of salted shrimp paste.},
journal = {International journal of food microbiology},
volume = {425},
number = {},
pages = {110867},
doi = {10.1016/j.ijfoodmicro.2024.110867},
pmid = {39178663},
issn = {1879-3460},
abstract = {This study used hot-air oven drying with Bacillus subtilis KC3 inoculation to improve shrimp paste production. The fermentation rate, quality characteristics, as well as microbial profiles, were compared to those produced using sun-drying with/without inoculation. B. subtilis inoculation increased the degree of hydrolysis of shrimp paste (22.3-32.1 %) during fermentation, compared to those without inoculation (12.7-25.4 %), regardless of different drying methods (p < 0.05). The result corresponded to the faster development of shrimp paste characteristics, particularly color and browning intensity of inoculated samples when fermented for the same duration. More abundant halophilic, proteolytic, and lipolytic bacteria (p < 0.05) were also obtained in inoculated samples, confirming accelerated fermentation. Interestingly, there was no difference in proximate composition, pH, and aw among samples (p > 0.05), which were still in the range regulated by the product's standard. However, the protein and lipid degradation products such as nitrogen contents, 5'-nucleotides, free fatty acids or TBARS values, varied among samples, potentially influencing the release of desirable flavor precursors to a certain extent. The inoculation increased microbial richness and evenness/uniformity, according to next-generation sequencing analysis on microbiota profiles. Pearson's correlation also revealed that these microbiota profiles were correlated with several desirable quality characteristics to varying degrees. Thus, combining the inoculation with B. subtilis KC3 can enhance shrimp paste fermentation and quality when produced using an alternative hot-air oven while maintaining quality characteristics. The findings suggested the possibility of achieving a more efficient and consistent production process for shrimp paste.},
}

@article {pmid39178596,
year = {2024},
author = {Oh, S and Byeon, H and Wijaya, J},
title = {Machine learning surveillance of foodborne infectious diseases using wastewater microbiome, crowdsourced, and environmental data.},
journal = {Water research},
volume = {265},
number = {},
pages = {122282},
doi = {10.1016/j.watres.2024.122282},
pmid = {39178596},
issn = {1879-2448},
abstract = {Clostridium perfringens (CP) is a common cause of foodborne infection, leading to significant human health risks and a high economic burden. Thus, effective CP disease surveillance is essential for preventive and therapeutic interventions; however, conventional practices often entail complex, resource-intensive, and costly procedures. This study introduced a data-driven machine learning (ML) modeling framework for CP-related disease surveillance. It leveraged an integrated dataset of municipal wastewater microbiome (e.g., CP abundance), crowdsourced (CP-related web search keywords), and environmental data. Various optimization strategies, including data integration, data normalization, model selection, and hyperparameter tuning, were implemented to improve the ML modeling performance, leading to enhanced predictions of CP cases over time. Explainable artificial intelligence methods identified CP abundance as the most reliable predictor of CP disease cases. Multi-omics subsequently revealed the presence of CP and its genotypes/toxinotypes in wastewater, validating the utility of microbiome-data-enabled ML surveillance for foodborne diseases. This ML-based framework thus exhibits significant potential for complementing and reinforcing existing disease surveillance systems.},
}

@article {pmid39178591,
year = {2024},
author = {Gao, FZ and Hu, LX and Liu, YS and Qiao, LK and Chen, ZY and Su, JQ and He, LY and Bai, H and Zhu, YG and Ying, GG},
title = {Unveiling the overlooked small-sized microbiome in river ecosystems.},
journal = {Water research},
volume = {265},
number = {},
pages = {122302},
doi = {10.1016/j.watres.2024.122302},
pmid = {39178591},
issn = {1879-2448},
abstract = {Enriching microorganisms using a 0.22-μm pore size is a general pretreatment procedure in river microbiome research. However, it remains unclear the extent to which this method loses microbiome information. Here, we conducted a comparative metagenomics-based study on microbiomes with sizes over 0.22 μm (large-sized) and between 0.22 μm and 0.1 μm (small-sized) in a subtropical river. Although the absolute concentration of small-sized microbiome was about two orders of magnitude lower than that of large-sized microbiome, sequencing only large-sized microbiome resulted in a significant loss of microbiome diversity. Specifically, the microbial community was different between two sizes, and 347 genera were only detected in small-sized microbiome. Small-sized microbiome had much more diverse viral community than large-sized fraction. The viruses had abundant ecological functions and were hosted by 825 species of 169 families, including pathogen-related families. Small-sized microbiome had distinct antimicrobial resistance risks from large-sized microbiome, showing an enrichment of eight antibiotic resistance gene (ARG) types as well as the detection of 140 unique ARG subtypes and five enriched risk rank I ARGs. Draft genomes of five major resistant pathogens having diverse ecological and pollutant-degrading functions were only assembled in small-sized microbiome. These findings provide novel insights into river ecosystems, and highlight the overlooked small-sized microbiome in the environment.},
}

@article {pmid39178327,
year = {2024},
author = {Xia, P and Li, R and Chen, M and Zeng, F and Zhou, W and Hou, T},
title = {Proanthocyanidins and β-Glucan Synergistically Regulate Intestinal Inflammation in Dextran Sulfate Sodium-Induced Colitis Mice.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.4c03544},
pmid = {39178327},
issn = {1520-5118},
abstract = {Proanthocyanidins (PA) have been proven to have an anti-inflammation effect in multiple models by regulating oxidative stress. β-glucan (BG) could alleviate colitis from the perspectives of intestinal permeability and gut microbiota. In the present study, the synergistic anti-inflammatory function of PA and BG was explored from multiple aspects including immune response, intestinal barrier, gut microbiota, and differential metabolites. The results showed that the supplementation of PA and BG improved the colitis symptoms including atrophy of the colon, body weight loss, and organ index increase. Additionally, inflammatory cytokine levels and oxidative stress status were significantly regulated with the intake of PA and BG. Moreover, PA and BG intervention improved intestinal permeability and promoted the expression of barrier proteins. The microbiome and metabolic profile of cecal contents showed that PA and BG supplementation increased the abundance of anti-inflammatory bacteria and decreased the abundance of pro-inflammatory bacteria. Furthermore, some beneficial metabolites involved in amino acid metabolism, carbohydrate metabolism, and biosynthesis of other secondary metabolite pathways were increased. Overall, these findings have demonstrated the regulation of the inflammatory response and remodel of metabolite profiles by PA and BG complexes, indicating that it may serve as a new strategy for inflammatory bowel disease treatment in the future.},
}

@article {pmid39178312,
year = {2024},
author = {Glaser-Schmitt, A and Lemoine, M and Kaltenpoth, M and Parsch, J},
title = {Pervasive tissue-, genetic background-, and allele-specific gene expression effects in Drosophila melanogaster.},
journal = {PLoS genetics},
volume = {20},
number = {8},
pages = {e1011257},
doi = {10.1371/journal.pgen.1011257},
pmid = {39178312},
issn = {1553-7404},
abstract = {The pervasiveness of gene expression variation and its contribution to phenotypic variation and evolution is well known. This gene expression variation is context dependent, with differences in regulatory architecture often associated with intrinsic and environmental factors, and is modulated by regulatory elements that can act in cis (linked) or in trans (unlinked) relative to the genes they affect. So far, little is known about how this genetic variation affects the evolution of regulatory architecture among closely related tissues during population divergence. To address this question, we analyzed gene expression in the midgut, hindgut, and Malpighian tubule as well as microbiome composition in the two gut tissues in four Drosophila melanogaster strains and their F1 hybrids from two divergent populations: one from the derived, European range and one from the ancestral, African range. In both the transcriptome and microbiome data, we detected extensive tissue- and genetic background-specific effects, including effects of genetic background on overall tissue specificity. Tissue-specific effects were typically stronger than genetic background-specific effects, although the two gut tissues were not more similar to each other than to the Malpighian tubules. An examination of allele specific expression revealed that, while both cis and trans effects were more tissue-specific in genes expressed differentially between populations than genes with conserved expression, trans effects were more tissue-specific than cis effects. Despite there being highly variable regulatory architecture, this observation was robust across tissues and genetic backgrounds, suggesting that the expression of trans variation can be spatially fine-tuned as well as or better than cis variation during population divergence and yielding new insights into cis and trans regulatory evolution.},
}

@article {pmid39178258,
year = {2024},
author = {Zhang, Y and Zhou, C and Tian, B and Xu, J and Wang, X and Dai, H and Wang, H and Xu, F and Wang, C},
title = {3D printed spiral tube-like cellulose scaffold for oral delivery of probiotics.},
journal = {Science advances},
volume = {10},
number = {34},
pages = {eadp3654},
pmid = {39178258},
issn = {2375-2548},
mesh = {*Probiotics/administration & dosage ; *Cellulose/chemistry ; *Printing, Three-Dimensional ; Administration, Oral ; *Gastrointestinal Microbiome ; Animals ; Mice ; Humans ; Tissue Scaffolds/chemistry ; },
abstract = {Introducing specific strains of probiotics into the gut microbiome is a promising way to modulate the intestinal microbiome to treat various health conditions clinically. However, oral probiotics typically have a temporary or limited impact on the gut microbiome and overall health benefits. Here, we reported a 3D printed cellulose-derived spiral tube-like scaffold that enabled high efficacy of the oral delivery of probiotics. Benefiting from the unique surface pattern, this system can effectively extend the retention time of loaded probiotics in the gut without invading nearby tissues, provide a favorable environment for the survival and long-term colonization of loaded probiotics, and influence the intestinal ecosystem as a dietary fiber after degradation. We demonstrate Roseburia intestinalis-loaded scaffold exerts noticeable impacts on the regulation of the gut microbiome to treat various gut-related diseases, including obesity and inflammatory bowel disease; thus, we provide a universal platform for oral delivery of probiotics.},
}

*Probiotics/administration & dosage
*Cellulose/chemistry
*Printing, Three-Dimensional
Administration, Oral
*Gastrointestinal Microbiome
Animals
Mice
Humans
Tissue Scaffolds/chemistry

@article {pmid39178199,
year = {2024},
author = {Munley, JA and Kelly, LS and Park, G and Pons, EE and Kannan, KB and Bible, LE and Efron, PA and Nagpal, R and Mohr, AM},
title = {Postinjury Pneumonia Induces a Unique Blood Microbiome Signature.},
journal = {Shock (Augusta, Ga.)},
volume = {},
number = {},
pages = {},
doi = {10.1097/SHK.0000000000002428},
pmid = {39178199},
issn = {1540-0514},
abstract = {BACKGROUND: Previous preclinical studies have demonstrated a pathobiome after traumatic injury; however, the impact of post-injury sepsis on gut epithelial permeability and bacterial translocation remains unknown. We hypothesized that polytrauma with post-injury pneumonia would result in impaired gut permeability leading to specific blood microbiome arrays.

METHODS: Male and proestrus female Sprague-Dawley rats were subjected to either polytrauma (PT), PT plus 2-hours daily chronic restraint stress (PT/CS), PT with postinjury day 1 inoculation with pseudomonas pneumonia (PT + PNA), PT/CS + PNA, or naive controls. Whole blood microbiome was measured serially using high-throughput 16S rRNA sequencing and QIIME2 bioinformatics analyses. Microbial diversity was assessed using Chao1/Shannon indices and principle coordinate analysis. Intestinal permeability was evaluated by plasma occludin and lipopolysaccharide-binding protein (LBP) assays.

RESULTS: PT/CS + PNA had increased intestinal permeability compared to uninfected counterparts (PT/CS) with significantly elevated occludin (p < 0.01). Bacteria was not detected in the blood of naïve controls, PT or PT/CS, but was present in both PT + PNA and PT/CS + PNA on days two and seven. The PT/CS + PNA blood biome showed dominance of Streptococcus compared to PT + PNA at day two (p < 0.05). Females PT/CS + PNA had a significant abundance of Staphylococcus at day two and Streptococcus at day seven in the blood biome compared to male counterparts (p < 0.05).

CONCLUSIONS: Multicompartmental trauma with post-injury pneumonia results in increased intestinal permeability and bacteremia with a unique blood biome, with sexual dimorphisms evident in the blood biome composition. These findings suggest that post-injury sepsis has clinical significance and could influence outcomes after severe trauma and critical illness.},
}

@article {pmid39177281,
year = {2024},
author = {Sun, Y and Zhao, H and Chang, M and Yue, T and Yuan, Y and Shi, Y},
title = {Prophylactic effects of Tibetan goat kefir on depression-like behaviors in chronic unpredictable stress model through the gut-brain axis.},
journal = {Journal of the science of food and agriculture},
volume = {},
number = {},
pages = {},
doi = {10.1002/jsfa.13825},
pmid = {39177281},
issn = {1097-0010},
support = {//The Key R&D projects of Ningxia Autonomous Region/ ; //The 13th five-year Plan Key R&D projects/ ; //The National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Depression is a common psychological disorder, and traditional therapeutic drugs often result in side effects such as emesis, dry mouth, headache, dysentery and constipation. Probiotics and goat milk have garnered widespread attention for their ability to modulate immune function and regulate the endocrine system, and for their anti-inflammatory effects. In this work, the effects of Tibetan goat kefir on the behavior, immune status, neuroendocrine response and gut microbiological composition of chronic unpredictable mild stress (CUMS) mouse models were evaluated.

RESULTS: The results indicated that Tibetan kefir goat milk significantly alleviated behavioral despair in mice. Furthermore, the results demonstrated that Tibetan kefir goat milk mitigated the inflammatory response in the mice and moderated the hyperactivity of the hypothalamic-pituitary-adrenal axis and the expression of brain-derived neurotrophic factor. Meanwhile, chronic stress-induced gut microbial abnormalities were restored. In addition, the correlation between gut microbiota and nervous system was evaluated.

CONCLUSION: These results explained the potential mechanism of Tibetan kefir in the antidepressant effect on the CUMS model and enriched diets for depressed patients. © 2024 Society of Chemical Industry.},
}

@article {pmid39176279,
year = {2024},
author = {Alzate Zuluaga, MY and Fattorini, R and Cesco, S and Pii, Y},
title = {Plant-microbe interactions in the rhizosphere for smarter and more sustainable crop fertilization: the case of PGPR-based biofertilizers.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1440978},
pmid = {39176279},
issn = {1664-302X},
abstract = {Biofertilizers based on plant growth promoting rhizobacteria (PGPR) are nowadays gaining increasingly attention as a modern tool for a more sustainable agriculture due to their ability in ameliorating root nutrient acquisition. For many years, most research was focused on the screening and characterization of PGPR functioning as nitrogen (N) or phosphorus (P) biofertilizers. However, with the increasing demand for food using far fewer chemical inputs, new investigations have been carried out to explore the potential use of such bacteria also as potassium (K), sulfur (S), zinc (Zn), or iron (Fe) biofertilizers. In this review, we update the use of PGPR as biofertilizers for a smarter and more sustainable crop production and deliberate the prospects of using microbiome engineering-based methods as potential tools to shed new light on the improvement of plant mineral nutrition. The current era of omics revolution has enabled the design of synthetic microbial communities (named SynComs), which are emerging as a promising tool that can allow the formulation of biofertilizers based on PGPR strains displaying multifarious and synergistic traits, thus leading to an increasingly efficient root acquisition of more than a single essential nutrient at the same time. Additionally, host-mediated microbiome engineering (HMME) leverages advanced omics techniques to reintroduce alleles coding for beneficial compounds, reinforcing positive plant-microbiome interactions and creating plants capable of producing their own biofertilizers. We also discusses the current use of PGPR-based biofertilizers and point out possible avenues of research for the future development of more efficient biofertilizers for a smarter and more precise crop fertilization. Furthermore, concerns have been raised about the effectiveness of PGPR-based biofertilizers in real field conditions, as their success in controlled experiments often contrasts with inconsistent field results. This discrepancy highlights the need for standardized protocols to ensure consistent application and reliable outcomes.},
}

@article {pmid39176109,
year = {2024},
author = {Shi, H and She, Y and Mao, W and Xiang, Y and Xu, L and Yin, S and Zhao, Q},
title = {16S rRNA Sequencing Reveals Alterations of Gut Bacteria in Hirschsprung-Associated Enterocolitis.},
journal = {Global medical genetics},
volume = {11},
number = {4},
pages = {263-269},
pmid = {39176109},
issn = {2699-9404},
abstract = {Hirschsprung-associated enterocolitis (HAEC) stands as most common and serious complication of Hirschsprung's disease. Variations in the microbiota composition may account for the differences observed between HAEC and healthy individuals, offering crucial insights into the disease's pathogenesis. Here, we performed a study to changes in the gut microbiome using 16sRNA amplicon sequencing in a cohort of HAEC patients (n = 16) and healthy controls (n = 14). Our result revealed a significant disparity in beta diversity between the two groups. Following correction for false discovery rate, a rank-sum test at the genus level indicated a notable decrease in the relative abundance of Bifidobacterium , Lactobacillus , and Veillonella , whereas the Enterococcus genus exhibited a substantial increase in HAEC, a finding further supported by additional linear discriminant analysis effect size analysis. Functional analysis showed that putative transport and catabolism, digestive system, and metabolism of cofactors and vitamins were proved to be some abundant KOs (Kyoto Encyclopedia of Genes and Genomes [KEGG] orthologs) in healthy group, whereas infectious disease, membrane transport, and carbohydrate metabolism were the three KOs with the higher abundance in the HAEC group. Our data increased our insight into the HAEC, which may shed further light on HAEC pathogenesis. Our study firstly demonstrated the difference between fecal microbiota of HAEC patients and healthy individuals, which made a step forward in the understanding of the pathophysiology of HAEC.},
}

@article {pmid39176096,
year = {2024},
author = {Einenkel, R and Ehrhardt, J and Zygmunt, M and Muzzio, DO},
title = {Less is more! Low amount of Fusobacterium nucleatum supports macrophage-mediated trophoblast functions in vitro.},
journal = {Frontiers in immunology},
volume = {15},
number = {},
pages = {1447190},
pmid = {39176096},
issn = {1664-3224},
mesh = {Humans ; *Trophoblasts/immunology/microbiology/metabolism ; *Fusobacterium nucleatum/immunology/physiology ; *Macrophages/immunology/microbiology/metabolism ; Female ; Pregnancy ; Cytokines/metabolism ; THP-1 Cells ; NF-kappa B/metabolism ; Fusobacterium Infections/immunology/microbiology ; Vascular Endothelial Growth Factor A/metabolism ; },
abstract = {F. nucleatum, involved in carcinogenesis of colon carcinomas, has been described as part of the commensal flora of the female upper reproductive tract. Although its contribution to destructive inflammatory processes is well described, its role as commensal uterine bacteria has not been thoroughly investigated. Since carcinogenesis shares similar mechanisms with early pregnancy development (including proliferation, invasion, blood supply and the induction of tolerance), these mechanisms induced by F. nucleatum could play a role in early pregnancy. Additionally, implantation and placentation require a well-balanced immune activation, which might be suitably managed by the presence of a limited amount of bacteria or bacterial residues. We assessed the effect of inactivated F. nucleatum on macrophage-trophoblast interactions. Monocytic cells (THP-1) were polarized into M1, M2a or M2c macrophages by IFN-γ, IL-4 or TGF-β, respectively, and subsequently treated with inactivated fusobacteria (bacteria:macrophage ratio of 0.1 and 1). Direct effects on macrophages were assessed by viability assay, flow cytometry (antigen presentation molecules and cytokines), qPCR (cytokine expression), in-cell Western (HIF and P-NF-κB) and ELISA (VEGF secretion). The function of first trimester extravillous trophoblast cells (HTR-8/SVneo) in response to macrophage-conditioned medium was microscopically assessed by migration (scratch assay), invasion (sprouting assay) and tube formation. Underlying molecular changes were investigated by ELISA (VEGF secretion) and qPCR (matrix-degrading factors and regulators). Inflammation-primed macrophages (M1) as well as high bacterial amounts increased pro-inflammatory NF-κB expression and inflammatory responses. Subsequently, trophoblast functions were impaired. In contrast, low bacterial stimulation caused an increased HIF activation and subsequent VEGF-A secretion in M2c macrophages. Accordingly, there was an increase of trophoblast tube formation. Our results suggest that a low-mass endometrial/decidual microbiome can be tolerated and while it supports implantation and further pregnancy processes.},
}

Humans
*Trophoblasts/immunology/microbiology/metabolism
*Fusobacterium nucleatum/immunology/physiology
*Macrophages/immunology/microbiology/metabolism
Female
Pregnancy
Cytokines/metabolism
THP-1 Cells
NF-kappa B/metabolism
Fusobacterium Infections/immunology/microbiology
Vascular Endothelial Growth Factor A/metabolism

@article {pmid39176086,
year = {2024},
author = {Wu, M and Huang, H and Tang, Y and Ren, X and Jiang, X and Tian, M and Li, W},
title = {Unveiling the multifaceted realm of human papillomavirus: a comprehensive exploration of biology, interactions, and advances in cancer management.},
journal = {Frontiers in immunology},
volume = {15},
number = {},
pages = {1430544},
pmid = {39176086},
issn = {1664-3224},
mesh = {Humans ; *Papillomavirus Infections/therapy/virology/immunology ; *Neoplasms/therapy/immunology/etiology/virology ; *Papillomaviridae/physiology/immunology ; Coinfection ; Host-Pathogen Interactions/immunology ; Papillomavirus Vaccines/immunology/therapeutic use ; Animals ; Human Papillomavirus Viruses ; },
abstract = {Human Papillomavirus (HPV), an extensive family of DNA viruses, manifests as a persistent global health challenge. Persistent HPV infection is now firmly established as a significant aetiological factor for a spectrum of malignancies. In this review, we examine the latest insights into HPV biology and its intricate relationship with the host. We delve into the complex dynamics of co-infections involving HPV alongside other viruses, such as HIV, EBV, and HSV, as well as the burgeoning role of the microbiome in cancer development. We also explore recent advancements in understanding the specific contributions of HPV in the development of various cancers, encompassing cancers of the anogenital region, head and neck, as well as breast, lung, and prostate. Moreover, we focus on the current preventive strategies, including vaccination and screening methods, and therapeutic interventions that range from traditional approaches like surgery and chemotherapy to emerging modalities such as targeted therapies and immunotherapies. Additionally, we provide a forward-looking view on the future directions of HPV research, highlighting potential areas of exploration to further our understanding and management of HPV and its associated cancers. Collectively, this review is positioned to deepen readers' understanding of HPV biology and its complex interplay with cancer biology. It presents innovative strategies for the prevention, management, and therapeutic intervention of HPV-associated malignancies.},
}

Humans
*Papillomavirus Infections/therapy/virology/immunology
*Neoplasms/therapy/immunology/etiology/virology
*Papillomaviridae/physiology/immunology
Coinfection
Host-Pathogen Interactions/immunology
Papillomavirus Vaccines/immunology/therapeutic use
Animals
Human Papillomavirus Viruses

@article {pmid39176025,
year = {2024},
author = {Gérard, P and Li, CG and Bhuyan, DJ},
title = {Editorial: Fruits, vegetables, and biotics for a healthy gut microbiome.},
journal = {Frontiers in nutrition},
volume = {11},
number = {},
pages = {1468453},
pmid = {39176025},
issn = {2296-861X},
}

@article {pmid39175996,
year = {2024},
author = {Zanella, R and de Camargo, J and Scariot, CA and Marques, MG},
title = {The microbiome effect on the female reproductive performance.},
journal = {Animal reproduction},
volume = {21},
number = {3},
pages = {e20240063},
pmid = {39175996},
issn = {1984-3143},
abstract = {The female reproductive function is coordinated by the endocrine system driven by the hypothalamic-pituitary-gonadal (HPG) axis. While not directly part of the female reproductive system, the gut microbiome plays a crucial role in overall health, including reproductive health. The gut microbiome communicates bidirectionally with the brain via the gut-brain axis, influencing stress levels, mood, and hormonal balance, which can impact reproductive health and fertility. In addition to that, the vaginal and uterine microbiome are directly involved with the reproductive success of farm animals, including female fertility and offspring development. In this paper, we summarize some of the effects of bacterial contamination in the female reproductive tract and their association with reproductive performance in farm animals.},
}

@article {pmid39175767,
year = {2024},
author = {Ribeiro, FM and Petriz, B and Anderson, M and Assis, V and Dos Santos, TR and Correa, H and Cavichiolli de Oliveira, N and Passos, L and Fonseca, A and Brito, LA and Silva, O and Castro, A and Franco, OL},
title = {Discontinuation of HIIT restores diabesity while retraining increases gut microbiota diversity.},
journal = {iScience},
volume = {27},
number = {8},
pages = {110365},
pmid = {39175767},
issn = {2589-0042},
abstract = {Investigations involving high-intensity interval training (HIIT) have proven to be efficient in controlling diabesity. This study aimed to assess the impact of discontinuing HIIT and retraining within the context of diabesity. 75 C57BL6 mice went through 5 stages: baseline, induction of diabesity with Western diet, training, detraining, and retraining (6 weeks each period). Detraining led to elevated adiposity, exacerbated metabolic parameters and intestinal health, and altered gut microbiota composition. Retraining restored blood glucose regulation and enhanced intestinal health yet did not induce fat reduction. While both training and retraining exerted an effect on the composition of the gut microbiota, the impact of diet demonstrates a more substantial potency compared to that of exercise concerning intestinal health and microbiome. These findings may contribute to a broader understanding of diabesity management and introduce perspectives for the use of specific physical training to enhance patient outcomes and intestine health.},
}

@article {pmid39175739,
year = {2024},
author = {Ke, X and Wei, Q and Sun, L and Yang, H},
title = {Liver microbiome: an intrahepatic resident playing a role in liver diseases.},
journal = {Hepatobiliary surgery and nutrition},
volume = {13},
number = {4},
pages = {686-689},
pmid = {39175739},
issn = {2304-3881},
}

@article {pmid39175566,
year = {2024},
author = {Shi, Y and Li, X and Zhang, J},
title = {Systematic review on the role of the gut microbiota in tumors and their treatment.},
journal = {Frontiers in endocrinology},
volume = {15},
number = {},
pages = {1355387},
pmid = {39175566},
issn = {1664-2392},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Neoplasms/microbiology/therapy ; *Tumor Microenvironment ; Animals ; },
abstract = {Tumors present a formidable health risk with limited curability and high mortality; existing treatments face challenges in addressing the unique tumor microenvironment (hypoxia, low pH, and high permeability), necessitating the development of new therapeutic approaches. Under certain circumstances, certain bacteria, especially anaerobes or parthenogenetic anaerobes, accumulate and proliferate in the tumor environment. This phenomenon activates a series of responses in the body that ultimately produce anti-tumor effects. These bacteria can target and colonize the tumor microenvironment, promoting responses aimed at targeting and fighting tumor cells. Understanding and exploiting such interactions holds promise for innovative therapeutic strategies, potentially augmenting existing treatments and contributing to the development of more effective and targeted approaches to fighting tumors. This paper reviews the tumor-promoting mechanisms and anti-tumor effects of the digestive tract microbiome and describes bacterial therapeutic strategies for tumors, including natural and engineered anti-tumor strategies.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Neoplasms/microbiology/therapy
*Tumor Microenvironment
Animals

@article {pmid39175504,
year = {2024},
author = {Coretti, L and Buommino, E and Lembo, F},
title = {The aryl hydrocarbon receptor pathway: a linking bridge between the gut microbiome and neurodegenerative diseases.},
journal = {Frontiers in cellular neuroscience},
volume = {18},
number = {},
pages = {1433747},
pmid = {39175504},
issn = {1662-5102},
abstract = {The Aryl hydrocarbon receptor (AHR) is a cytosolic receptor and ligand-activated transcription factor widely expressed across various cell types in the body. Its signaling is vital for host responses at barrier sites, regulating epithelial renewal, barrier integrity, and the activities of several types of immune cells. This makes AHR essential for various cellular responses during aging, especially those governing inflammation and immunity. In this review, we provided an overview of the mechanisms by which the AHR mediates inflammatory response at gut and brain level through signals from intestinal microbes. The age-related reduction of gut microbiota functions is perceived as a trigger of aberrant immune responses linking gut and brain inflammation to neurodegeneration. Thus, we explored gut microbiome impact on the nature and availability of AHR ligands and outcomes for several signaling pathways involved in neurodegenerative diseases and age-associated decline of brain functions, with an insight on Parkinson's and Alzheimer's diseases, the most common neurodegenerative diseases in the elderly. Specifically, we focused on microbial tryptophan catabolism responsible for the production of several AHR ligands. Perspectives for the development of microbiota-based interventions targeting AHR activity are presented for a healthy aging.},
}

@article {pmid39175265,
year = {2024},
author = {Pereira, TJ and De Santiago, A and Bik, HM},
title = {Soil properties predict below-ground community structure, but not nematode microbiome patterns in semi-arid habitats.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e17501},
doi = {10.1111/mec.17501},
pmid = {39175265},
issn = {1365-294X},
support = {//Center for Conservation Biology at the University of California, Riverside and The Shipley-Skinner Reserve - Riverside County Endowment/ ; },
abstract = {Microbial and microeukaryotic communities are extremely abundant and diverse in soil habitats where they play critical roles in ecosystem functioning and services that are essential to soil health. Soil biodiversity is influenced by above-ground (vegetation) and below-ground factors (soil properties), which together create habitat-specific conditions. However, the compound effects of vegetation and soil properties on soil communities are less studied or often focused on one component of the soil biota. Here, we integrate metabarcoding (16S and 18S rRNA genes) and nematode morphology to assess the effects of habitat and soil properties shaping microbial and microeukaryotic communities as well as nematode-associated microbiomes. We show that both vegetation and soil properties (soil bulk density) were major factors structuring microbial and microeukaryotic communities in semi-arid soil habitats. Despite having lower nutrients and lower pH, denser soils displayed significantly higher alpha diversity than less dense soils across datasets. Nematode-associated microbiomes have lower microbial diversity, strongly differ from soil microbes and are more likely to respond to microscale variations among samples than to vegetation or soil bulk density. Consequently, different nematode lineages and trophic groups are likely to display similar associated microbiomes when sharing the same microhabitat. Different microbiome taxa were enriched within specific nematode lineages (e.g. Mycobacterium, Candidatus Cardinium) highlighting potentially new species-specific associations that may confer benefits to their soil nematode hosts. Our findings highlight the importance of exploring above- and below-ground effects to assess community structure in terrestrial habitats, and how fine-scale analyses are critical for understanding patterns of host-associated microbiomes.},
}

@article {pmid39175183,
year = {2024},
author = {Castro, AM and Sabater, C and Navarro, S and Rodriguez, S and Molinos, C and Jiménez, S and Claver, A and Espin, B and Domínguez, G and Coronel, C and Toyos, P and Gutiérrez-Díaz, I and Sariego, L and Fernández, P and Perez, D and Margolles, A and Díaz, JJ and Delgado, S},
title = {The intestinal microbiome of infants with cow's milk-induced FPIES is enriched in taxa and genes of enterobacteria.},
journal = {Journal of pediatric gastroenterology and nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1002/jpn3.12356},
pmid = {39175183},
issn = {1536-4801},
abstract = {OBJECTIVES: Food protein-induced enterocolitis syndrome (FPIES) is a severe type of non-IgE (immunoglobulin E)-mediated (NIM) food allergy, with cow's milk (CM) being the most common offending food. The relationship between the gut microbiota and its metabolites with the inflammatory process in infants with CM FPIES is unknown, although evidence suggests a microbial dysbiosis in NIM patients. This study was performed to contribute to the knowledge of the interaction between the gut microbiota and its derived metabolites with the local immune system in feces of infants with CM FPIES at diagnosis.

METHODS: Twelve infants with CM FPIES and a matched healthy control group were recruited and the gut microbiota was investigated by 16S amplicon and shotgun sequencing. Fatty acids (FAs) were measured by gas chromatography, while immune factors were determined by enzyme-linked immunosorbent assay and Luminex technology.

RESULTS: A specific pattern of microbiota in the gut of CM FPIES patients was found, characterized by a high abundance of enterobacteria. Also, an intense excretion of FAs in the feces of these infants was observed. Furthermore, correlations were found between fecal bifidobacteria and immune factors.

CONCLUSION: These fecal determinations may be useful to gain insight into the pathophysiology of this syndrome and should be taken in consideration for future studies of FPIES patients.},
}

@article {pmid39175157,
year = {2024},
author = {Hu, JC and Sethi, S},
title = {New methods to detect bacterial or viral infections in patients with chronic obstructive pulmonary disease.},
journal = {Expert review of respiratory medicine},
volume = {},
number = {},
pages = {},
doi = {10.1080/17476348.2024.2396413},
pmid = {39175157},
issn = {1747-6356},
abstract = {INTRODUCTION: Patients with chronic obstructive pulmonary disease (COPD) are frequently colonized and infected by respiratory pathogens. Identifying these infectious etiologies is critical for understanding the microbial dynamics of COPD and for the appropriate use of antimicrobials during exacerbations.

AREAS COVERED: Traditional methods, such as bacterial and viral cultures, have been standard in diagnosing respiratory infections. However, these methods have significant limitations, including lack of sensitivity and prolonged turnaround time. Modern molecular approaches offer rapid, sensitive, and specific detection, though they also come with their own challenges. This review explores and evaluates the clinical utility of the latest advancements in detecting bacterial and viral respiratory infections in COPD, encompassing molecular techniques, biomarkers, and emerging technologies.

EXPERT OPINION: In the evolving landscape of COPD management, integrating molecular diagnostics and emerging technologies holds great promise. The enhanced sensitivity of molecular techniques has significantly advanced our understanding of the role of microbes in COPD. However, many of these technologies have primarily been developed for pneumonia diagnosis or research applications, and their clinical utility in managing COPD requires further evaluation.},
}

@article {pmid39175147,
year = {2024},
author = {Hong, BY and Chhaya, A and Robles, A and Cervantes, JL and Tiwari, S},
title = {EXPRESS: The role of Fusobacterium nucleatum in the pathogenesis of colon cancer.},
journal = {Journal of investigative medicine : the official publication of the American Federation for Clinical Research},
volume = {},
number = {},
pages = {10815589241277829},
doi = {10.1177/10815589241277829},
pmid = {39175147},
issn = {1708-8267},
abstract = {Previously, many studies have reported changes in the gut microbiota of patients with colorectal cancer (CRC). While CRC is a well-described disease, the relationship between its development and features of the intestinal microbiome are still becoming understood. Evidence linking Fusobacterium nucleatum enrichment in colorectal tumor tissue has prompted the elucidation of various molecular mechanisms and tumor-promoting attributes. In this review we highlight various aspects of our understanding of the relationship between the development of CRC and the alteration of intestinal microbiome, focusing specifically on the role of F. nucleatum. As the amount of F. nucleatum DNA in CRC tissue is associated with shorter survival, it may potentially serve as a prognostic biomarker, and most importantly may open the door for a role in CRC treatment.},
}

@article {pmid39175056,
year = {2024},
author = {Sbardellati, DL and Vannette, RL},
title = {Targeted viromes and total metagenomes capture distinct components of bee gut phage communities.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {155},
pmid = {39175056},
issn = {2049-2618},
support = {2023-67011-40501//U.S. Department of Agriculture/ ; 1929516//National Science Foundation/ ; },
mesh = {Bees/virology/microbiology ; Animals ; *Bacteriophages/genetics/isolation & purification/classification ; *Virome ; *Metagenome ; Gastrointestinal Microbiome/genetics ; Metagenomics/methods ; Gastrointestinal Tract/microbiology/virology ; },
abstract = {BACKGROUND: Despite being among the most abundant biological entities on earth, bacteriophage (phage) remain an understudied component of host-associated systems. One limitation to studying host-associated phage is the lack of consensus on methods for sampling phage communities. Here, we compare paired total metagenomes and viral size fraction metagenomes (viromes) as methods for investigating the dsDNA viral communities associated with the GI tract of two bee species: the European honey bee Apis mellifera and the eastern bumble bee Bombus impatiens.

RESULTS: We find that viromes successfully enriched for phage, thereby increasing phage recovery, but only in honey bees. In contrast, for bumble bees, total metagenomes recovered greater phage diversity. Across both bee species, viromes better sampled low occupancy phage, while total metagenomes were biased towards sampling temperate phage. Additionally, many of the phage captured by total metagenomes were absent altogether from viromes. Comparing between bees, we show that phage communities in commercially reared bumble bees are significantly reduced in diversity compared to honey bees, likely reflecting differences in bacterial titer and diversity. In a broader context, these results highlight the complementary nature of total metagenomes and targeted viromes, especially when applied to host-associated environments.

CONCLUSIONS: Overall, we suggest that studies interested in assessing total communities of host-associated phage should consider using both approaches. However, given the constraints of virome sampling, total metagenomes may serve to sample phage communities with the understanding that they will preferentially sample dominant and temperate phage. Video Abstract.},
}

Bees/virology/microbiology
Animals
*Bacteriophages/genetics/isolation & purification/classification
*Virome
*Metagenome
Gastrointestinal Microbiome/genetics
Metagenomics/methods
Gastrointestinal Tract/microbiology/virology

@article {pmid39175946,
year = {2020},
author = {Louime, CJ and Vazquez-Sanchez, F and Derilus, D and Godoy-Vitorino, F},
title = {Divergent Microbiota Dynamics along the Coastal Marine Ecosystem of Puerto Rico.},
journal = {Microbiology research},
volume = {11},
number = {2},
pages = {45-55},
pmid = {39175946},
issn = {2036-7473},
support = {P20 GM103475/GM/NIGMS NIH HHS/United States ; },
abstract = {Understanding the different factors shaping the spatial and temporal distribution of marine microorganisms is fundamental in predicting their responses to future environmental disturbances. There has been, however, little effort to characterize the microbial diversity including the microbiome dynamics among regions in the Caribbean Sea. Toward this end, this study was designed to gain some critical insights into microbial diversity within the coastal marine ecosystem off the coast of Puerto Rico. Using Illumina MiSeq, the V4 region of the 16S rRNA gene was sequenced with the goal of characterizing the microbial diversity representative of different coastal sites around the island of Puerto Rico. This study provided valuable insights in terms of the local bacterial taxonomic abundance, α and β diversity, and the environmental factors shaping microbial community composition and structure. The most dominant phyla across all 11 sampling sites were the Proteobacteria, Bacteroidetes, and Planctomycetes, while the least dominant taxonomic groups were the NKB19, Tenericutes, OP3, Lentisphaerae, and SAR406. The geographical area (Caribbean and Atlantic seas) and salinity gradients were the main drivers shaping the marine microbial community around the island. Despite stable physical and chemical features of the different sites, a highly dynamic microbiome was observed. This highlights Caribbean waters as one of the richest marine sources for a microbial biodiversity hotspot. The data presented here provide a basis for further temporal evaluations aiming at deciphering microbial taxonomic diversity around the island, while determining how microbes adapt to changes in the climate.},
}

@article {pmid39174963,
year = {2024},
author = {Liu, Y and Qiao, F and Wang, Z and Meng, G and Gu, Y and Wu, H and Liu, D and Niu, K},
title = {Analysis of the microbial community diversity in various regions of the healthy oral cavity.},
journal = {BMC oral health},
volume = {24},
number = {1},
pages = {978},
pmid = {39174963},
issn = {1472-6831},
support = {ZC20132//Science and Technology Project of Tianjin Municipal Health Commission/ ; ZC0178//Science and Technology Project of Tianjin Municipal Health Commission/ ; ZC20134//Science and Technology Project of Tianjin Municipal Health Commission/ ; 82071079//National Natural Science Foundation of China/ ; 81302422//National Natural Science Foundation of China/ ; TJSJMYXYC -D2-025//Jinmen Medical Talents Project of Tianjin Municipal People`s Government/ ; 11ZCGYSY05700//Key Technologies R&D Program of Tianjin/ ; },
mesh = {Humans ; *Mouth Mucosa/microbiology ; *Microbiota ; *Mouth/microbiology ; Adult ; Male ; *In Situ Hybridization, Fluorescence ; Female ; RNA, Ribosomal, 16S/analysis ; DNA, Bacterial/analysis ; Young Adult ; Bacteria/classification/isolation & purification ; Specimen Handling/methods ; Molar/microbiology ; Porphyromonas gingivalis/isolation & purification ; Feasibility Studies ; },
abstract = {BACKGROUND: Microbiomics offers new methods for conducting epidemiological surveys of oral microbiota in large populations. Compared to curette sampling, swab sampling is more convenient and less technically sensitive, making it more suitable for such surveys. To verify the feasibility of using swabs for buccal mucosa sampling in large-scale studies, we collected samples from the buccal mucosa and tooth surfaces of healthy individuals using both swabs and curettes. Microbiomics was employed to analyze and compare microbial abundance and diversity between these two methods.

METHODS: Four sites were assessed: the buccal mucosa on both sides and the buccal surfaces of the left and right mandibular first molars. Two sampling methods, swab and curette, were used to collect bacterial communities from healthy individuals. Specifically, buccal mucosa samples (n = 10) and tooth surface samples (n = 20) were analyzed using 16 S rDNA gene sequencing. Bacterial signals were detected through fluorescence in situ hybridization (FISH), targeting the bacterial 16 S rDNA gene. Metastats analysis and Wilcoxon test were used.

RESULTS: A total of 383 OTUs were detected in the 30 samples, which belonged to 1 kingdom (bacteria), 11 phyla, 23 classes, 40 orders, 75 families, 143 genus, and 312 species. Among them, 223 OTUs were found on both the buccal mucosa and tooth surfaces. The statistics suggest that although there were no significant differences in colony composition, there were differences in the abundance and distribution of colonies on the dental and buccal mucosal surfaces. When detecting oral disease-causing pathogens such as Enterococcus faecalis and Porphyromonas gingivalis, the efficiency of detection is higher when using curette sampling. Compared to right tooth sampling with a curette, the swab sampling group had higher levels of Firmicutes, while Fusobacteria and Bacteroidetes were more prevalent in the curette tissues.

CONCLUSIONS: In oral health individuals, there is no difference in the bacterial composition of the oral buccal mucosa and the dental surface, differing only in abundance. Thus, the buccal mucosa can act as a substitute for the teeth in epidemiological investigations exploring the bacterial composition of the oral cavity.},
}

Humans
*Mouth Mucosa/microbiology
*Microbiota
*Mouth/microbiology
Adult
Male
*In Situ Hybridization, Fluorescence
Female
RNA, Ribosomal, 16S/analysis
DNA, Bacterial/analysis
Young Adult
Bacteria/classification/isolation & purification
Specimen Handling/methods
Molar/microbiology
Porphyromonas gingivalis/isolation & purification
Feasibility Studies

@article {pmid39174936,
year = {2024},
author = {Farrugia, A and Williams, N and Khan, S and P Arasaradnam, R},
title = {Bile acid diarrhoea and metabolic changes after cholecystectomy: a prospective case-control study.},
journal = {BMC gastroenterology},
volume = {24},
number = {1},
pages = {282},
pmid = {39174936},
issn = {1471-230X},
mesh = {Humans ; Case-Control Studies ; *Diarrhea/etiology/metabolism ; Prospective Studies ; *Bile Acids and Salts/blood/metabolism ; Female ; Male ; Middle Aged ; *Fibroblast Growth Factors/blood/metabolism ; *PPAR alpha/metabolism ; Adult ; Triglycerides/blood ; Cholecystectomy/adverse effects ; Gallbladder/metabolism/surgery ; Postoperative Complications/etiology ; Enterohepatic Circulation ; Aged ; Cholestenones/blood ; },
abstract = {INTRODUCTION: Bile acid diarrhoea (BAD) can occur due to disruption to the enterohepatic circulation such as following cholecystectomy. However, the mechanism behind this is as yet unknown. The aim of this study was to determine the rate of post-cholecystectomy diarrhoea and to assess whether FGF19 within the gallbladder was associated with the development of BAD.

METHODS: This was a prospective case-control study in which patients were assessed pre- and post- cholecystectomy (study group) and compared with patients also having laparoscopic surgery but not cholecystectomy (control group). Their bowel habits and a GIQLI questionnaire was performed to compare the pre- and post-operative condition of the two groups. Gallbladder tissue sample was tested for FGF19 and PPARα in the study group patients. A subset had serum lipid levels, FGF19 and C4 measurements.

RESULTS: Gallbladder PPAR α was found to have a significant correlation with stool consistency, with the lower the PPARα concentration the higher the Bristol stool chart number (i.e. looser stool). There were no significant correlation when assessing the effect of gallbladder FGF19 concentration on bowel habit, stool consistency, lipid levels, BMI or smoking. The study group showed a significant increase in triglycerides post-operatively, however there were no changes in cholesterol, HDL and LDL levels. Correlation of the increased triglyceride levels with stool consistency and frequency showed no significant results DISCUSSION AND CONCLUSION: We did not find any direct evidence that FGF19 levels within the gallbladder impact the development of post-cholecystectomy diarrhoea. There was however a significant increase in triglycerides postoperatively. There was also no correlation of bowel habits with PPARα suggesting the observed rise is independent of this pathway. Further work is required particularly relating to the gut microbiome to further investigate this condition.},
}

Humans
Case-Control Studies
*Diarrhea/etiology/metabolism
Prospective Studies
*Bile Acids and Salts/blood/metabolism
Female
Male
Middle Aged
*Fibroblast Growth Factors/blood/metabolism
*PPAR alpha/metabolism
Adult
Triglycerides/blood
Cholecystectomy/adverse effects
Gallbladder/metabolism/surgery
Postoperative Complications/etiology
Enterohepatic Circulation
Aged
Cholestenones/blood

@article {pmid39174732,
year = {2024},
author = {Jo, A and Kim, KS and Won, J and Shin, H and Kim, S and Kim, B and Kim, DJ and Cho, JY and Kim, HJ},
title = {Nasal symbiont Staphylococcus epidermidis restricts influenza A virus replication via the creation of a polyamine-deficient cellular environment.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {1031},
pmid = {39174732},
issn = {2399-3642},
mesh = {*Staphylococcus epidermidis/physiology/metabolism ; *Virus Replication ; Humans ; *Polyamines/metabolism ; *Influenza A virus/physiology ; *Nasal Mucosa/microbiology/virology/metabolism ; *Symbiosis ; Influenza, Human/virology/metabolism ; },
abstract = {Studies on the immune-regulatory roles played by the commensal microbes residing in the nasal mucosa consider the contribution of antiviral immune responses. Here, we sought to identify the nasal microbiome, Staphylococcus epidermidis-regulated antiviral immune responses and the alteration of polyamine metabolites in nasal epithelium. We found that polyamines were required for the life cycle of influenza A virus (IAV) and depletion of polyamines disturbed IAV replication in normal human nasal epithelial (NHNE) cells. Inoculation of S. epidermidis also suppressed IAV infection and the concentration of polyamines including putrescine, spermidine, and spermine was completely attenuated in S. epidermidis-inoculated NHNE cells. S. epidermidis activated the enzyme involved in the production of ornithine from arginine and downregulated the activity of the enzyme involved in the production of putrescine from ornithine in nasal epithelium. S. epidermidis also induced the activation of enzymes that promote the extracellular export of spermine and spermidine in NHNE cells. Our findings demonstrate that S. epidermidis is shown to be able of creating an intracellular environment lacking polyamines in the nasal epithelium and promote the balance of cellular polyamines in favor of the host to restrict influenza virus replication.},
}

*Staphylococcus epidermidis/physiology/metabolism
*Virus Replication
Humans
*Polyamines/metabolism
*Influenza A virus/physiology
*Nasal Mucosa/microbiology/virology/metabolism
*Symbiosis
Influenza, Human/virology/metabolism

@article {pmid39174731,
year = {2024},
author = {Koc, F and Magner, C and Murphy, K and Kelleher, ST and Tan, MH and O'Toole, M and Jenkins, D and Boyle, J and Lavelle, M and Maguire, N and Ross, PR and Stanton, C and McMahon, CJ},
title = {Gut Microbiome in Children with Congenital Heart Disease After Cardiopulmonary Bypass Surgery (GuMiBear Study).},
journal = {Pediatric cardiology},
volume = {},
number = {},
pages = {},
pmid = {39174731},
issn = {1432-1971},
support = {12/RC/2273_P2/SFI_/Science Foundation Ireland/Ireland ; 12/RC/2273_P2/SFI_/Science Foundation Ireland/Ireland ; 12/RC/2273_P2/SFI_/Science Foundation Ireland/Ireland ; 12/RC/2273_P2/SFI_/Science Foundation Ireland/Ireland ; 12/RC/2273_P2/SFI_/Science Foundation Ireland/Ireland ; 12/RC/2273_P2/SFI_/Science Foundation Ireland/Ireland ; 12/RC/2273_P2/SFI_/Science Foundation Ireland/Ireland ; 12/RC/2273_P2/SFI_/Science Foundation Ireland/Ireland ; 12/RC/2273_P2/SFI_/Science Foundation Ireland/Ireland ; 12/RC/2273_P2/SFI_/Science Foundation Ireland/Ireland ; 12/RC/2273_P2/SFI_/Science Foundation Ireland/Ireland ; 12/RC/2273_P2/SFI_/Science Foundation Ireland/Ireland ; },
abstract = {The gut microbiome of infants with congenital heart disease (CHD) undergoing cardiopulmonary bypass surgery (CPB) is at risk of profound alteration. The aim of this study was to examine the gut microbiome pre- and post-bypass surgery to explore potential implications of altered gut biodiversity. A prospective cohort study involving infants with CHD who underwent CPB was performed. Faecal samples were collected from infants alongside the collection of demographic and clinical data in order to examine gut microbiome changes before and after surgery. 16S rRNA sequencing analysis was performed on DNA isolated from stool samples to determine changes in gut microbiome composition. Thirty-three patients were recruited, with samples from thirteen of these available for final analysis. Compared with healthy, matched controls, at a genus level, pre-operative samples for infants with CHD demonstrated a higher relative abundance of Escherichia-Shigella (31% vs 2-6%) and a lower relative abundance of Bifidobacterium (13% vs 40-60%). In post-operative samples, the relative abundance of Escherichia-Shigella (35%), Enterococcus (11%), Akkermansia (6%), and Staphylococcus (5%) were higher than pre-op samples. One infant developed post-operative necrotising-enterocolitis (NEC). They displayed a marked abundance of the Enterococcus (93%) genus pre-operatively. This study demonstrates that infants with CHD have an altered gut microbiome when compared with healthy controls and there might be a possible link between an abundance of virulent species and NEC.},
}

@article {pmid39174555,
year = {2024},
author = {Shijimaya, T and Tahara, T and Yamazaki, J and Kobayashi, S and Matsumoto, Y and Nakamura, N and Takahashi, Y and Tomiyama, T and Fukui, T and Shibata, T and Naganuma, M},
title = {Microbiome of esophageal endoscopic wash samples is associated with resident flora in the esophagus and incidence of cancer.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {19525},
pmid = {39174555},
issn = {2045-2322},
support = {22K08089//Japan Society for the Promotion of Science London/ ; },
mesh = {Humans ; *Esophageal Neoplasms/microbiology ; Male ; Female ; Middle Aged ; Aged ; Incidence ; *RNA, Ribosomal, 16S/genetics ; *Esophagus/microbiology/pathology ; Microbiota ; Bacteria/isolation & purification/classification/genetics ; Esophageal Mucosa/microbiology/pathology ; Biopsy ; },
abstract = {Change in mucosal microbiome is associated with various types of cancer in digestive tract. We hypothesized that microbial communities in the esophageal endoscopic wash fluids reflects resident flora in esophageal mucosa that is associated with esophageal carcinoma (EC) risk and/or directly correlates microbiome derived from EC tumor tissue. Studying microbial communities in esophageal endoscopic wash samples would be therefore useful to predict the incidence or risk of EC. We examined microbial communities of the endoscopic wash samples from 45 primary EC and 20 respective non-EC controls using 16S rRNA V3-V4 amplicon sequencing. The result was also compared with microbial communities in matched endoscopic biopsies from EC and non-cancerous esophageal mucosa. Compared with non-EC controls, 6 discriminative bacterial genera were detected in EC patients. Among them, relative abundance ratio of Prevotella and Shuttlewarthia, as well as decrease of genus Prevotella presented good prognostic performance to discriminate EC from controls (area under curve, 0.86, 0.82, respectively). Multivariate analysis showed occurrence of EC was an independent factor associated with decrease of this bacteria. Abundance of genus Prevotella in the esophageal endoscopic wash samples was significantly correlated with the abundance of this bacteria in the matched endoscopic biopsies from non-cancerous esophageal mucosa but not in the EC tissues. Our findings suggest that microbiome composition in the esophageal endoscopic wash samples reflects resident flora in the esophagus and significantly correlates with the incidence of EC.},
}

Humans
*Esophageal Neoplasms/microbiology
Male
Female
Middle Aged
Aged
Incidence
*RNA, Ribosomal, 16S/genetics
*Esophagus/microbiology/pathology
Microbiota
Bacteria/isolation & purification/classification/genetics
Esophageal Mucosa/microbiology/pathology
Biopsy

@article {pmid39174449,
year = {2024},
author = {Presley, CJ and Grogan, M and Compston, A and Hock, K and Knauss, B and Redder, E and Arrato, NA and Lo, SB and Janse, S and Benedict, J and Hoyd, R and Williams, N and Hayes, S and Wells-Di Gregorio, S and Gill, TM and Allore, H and Focht, B and Quist, M and Carbone, DP and Spakowicz, D and Paskett, ED and Andersen, BL},
title = {Resiliency among older adults receiving lung cancer treatment (ROAR-LCT): A novel supportive care intervention for older adults with advanced lung cancer.},
journal = {Journal of geriatric oncology},
volume = {},
number = {},
pages = {101844},
doi = {10.1016/j.jgo.2024.101844},
pmid = {39174449},
issn = {1879-4076},
abstract = {INTRODUCTION: Novel supportive care interventions designed for an aging population with lung cancer are urgently needed. We aimed to determine the feasibility of a novel supportive care physical therapy (PT) plus progressive muscle relaxation (PMR) intervention delivered to older adults with advanced lung cancer in the United States (US).

MATERIALS AND METHODS: This clinical trial, Resiliency Among Older Adults Receiving Lung Cancer Treatment (ROAR-LCT: NCT04229381), recruited adults aged ≥60 years with unresectable stage III/IV non-small cell (NSCLC) or small cell lung cancer (SCLC) receiving cancer treatment at The James Thoracic Oncology Center (planned enrollment, N = 20). There were no exclusion criteria pertaining to performance status, laboratory values, prior cancer diagnoses, comorbidities, or brain metastases. Participants were evaluated by PT and psychology and given an exercise pedaler, resistance bands, a relaxation voice recording, and instructions at study initiation. Participants were evaluated in-person by PTs and psychologists at the start and end of the 12-session intervention, with the intervening sessions conducted via virtual health. Participants completed self-reported measures of functional status, symptoms, and mood longitudinally with the following instruments: EQ-5D-5L, Patient Health Questionnaire-9, and General Anxiety Disorder-7. PT assessments included the Short Physical Performance Battery (SPPB) and the two-minute walk test. Feasibility was defined as at least 60% of participants completing at least 70% of all intervention sessions. Optional gut microbiome samples and activity monitoring data (ActiGraph®) were also collected.

RESULTS: The ROAR-LCT study concluded after consenting 22 patients. Among the 22 consented, 18 (81.8%) started the intervention; 11 participants (61.1%) completed at least 70% of all study sessions. All participants with SCLC completed the intervention. Reasons for withdrawal included progression of disease or hospitalization. The majority (88.9%) of patients who started were able to complete at least one virtual health session. Participants' functional status, SPPB, depression, and anxiety scores were stable from pre- to post-intervention. Participants who withdrew had worse baseline scores across domains. Seven microbiome and six ActiGraph® samples were collected.

DISCUSSION: This is one of the first PT + PMR supportive care interventions using virtual health among older adults with advanced lung cancer to achieve feasibility in the US.},
}

@article {pmid39173973,
year = {2024},
author = {Oliver, A and Alkan, Z and Stephensen, CB and Newman, JW and Kable, ME and Lemay, DG},
title = {Diet, microbiome, and inflammation predictors of fecal and plasma short-chain fatty acids in humans.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tjnut.2024.08.012},
pmid = {39173973},
issn = {1541-6100},
abstract = {BACKGROUND: Gut microbes produce short-chain fatty acids (SCFAs) which are associated with broad health benefits. However, it is not fully known how diet and/or the gut microbiome could be modulated to improve SCFA production.

OBJECTIVE: To identify dietary, inflammatory, and/or microbiome predictors of SCFAs in a cohort of healthy adults.

METHODS: SCFAs were measured in fecal and plasma samples from 359 healthy adults in the USDA Nutritional Phenotyping Study. Habitual and recent diet was assessed using a Food Frequency Questionnaire and ASA24 dietary recalls. Markers of systemic and gut inflammation were measured in fecal and plasma samples. The gut microbiome was assessed using shotgun metagenomics. Using statistics and machine learning, we determined how the abundance and composition of SCFAs varied with measures of diet, inflammation, and the gut microbiome.

RESULTS: We show that fecal pH may be a good proxy for fecal SCFA abundance. A higher Healthy Eating Index for habitual diet was associated with a compositional increase in fecal butyrate, relative to acetate and propionate. SCFAs were associated with markers of subclinical GI inflammation. Fecal SCFA abundance was inversely related to plasma lipopolysaccharide binding protein. When we analyzed hierarchically organized diet and microbiome data with taxonomy-aware algorithms, we observed that diet and microbiome features were far more predictive of fecal SCFA abundances compared to plasma SCFA abundances. The top diet and microbiome predictors of fecal butyrate included potatoes and the thiamine biosynthesis pathway, respectively.

CONCLUSION: These results suggest that resistant starch in the form of potatoes and microbially produced thiamine provide a substrate and essential cofactor, respectively, for butyrate synthesis. Thiamine may be a rate-limiting nutrient for butyrate production in adults. Overall, these findings illustrate the complex biology underpinning SCFA production in the gut. This trial was registered on clinicaltrials.gov as NCT02367287.},
}

@article {pmid39173907,
year = {2024},
author = {Kotowska, M and Kołodziej, M and Szajewska, H and Łukasik, J},
title = {The impact of probiotics on core autism symptoms - a systematic review and meta-analysis of randomized clinical trials.},
journal = {Clinical nutrition ESPEN},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.clnesp.2024.08.010},
pmid = {39173907},
issn = {2405-4577},
abstract = {BACKGROUND & AIMS: Studies have shown evidence of gut dysbiosis in individuals with autism spectrum disorder (ASD). Various microbiome-modifying treatments, including probiotics, have been proposed. This review systematically assessed the evidence on the effects of probiotics on core autism symptoms in children with ASD.

METHODS: We performed a comprehensive literature search in Medline, Embase, CENTRAL, PsycInfo, and clinical trial registries, up to March 2023, and updated on January 10, 2024. Randomized controlled trials (RCTs) of parallel-group and cross-over designs were eligible. The population included individuals below 20 years of age diagnosed with ASD. Trials evaluating the effects of probiotics (any strain or dose) compared to placebo, no treatment, or another intervention were included. The outcomes of interest included the core autism symptoms: deficits in social skills, communication skills, and restricted, repetitive behaviors. No language restrictions were applied. Studies were excluded if an additional active compound was administered. The risk of bias was assessed using the Revised Cochrane Risk of Bias tool (RoB 2). This review was registered in PROSPERO (CRD42023393000).

RESULTS: In total, 12 RCTs assessing 630 participants were included. A borderline significant beneficial effect of probiotics on core ASD symptoms was found (8 RCTs, mean difference -0.21; 95% CI -0.39 to -0.03). Subgroup analysis according to study type showed a significant positive effect in parallel group trials (6 RCTs, mean difference -0.26; 95% CI -0.48 to -0.05). The pooled effect estimates for the other outcomes didn't reveal significant differences between the groups. Importantly, the risk of bias was high in nine studies.

CONCLUSIONS: Available data do not provide high-quality evidence supporting the use of probiotics for ASD symptoms in children.},
}

@article {pmid39173885,
year = {2024},
author = {MacGibeny, MA and Adjei, S and Pyle, H and Bunick, CG and Ghannoum, M and Grada, A and Harris-Tryon, T and Tyring, SK and Kong, HH},
title = {Alterations in the Skin Microbiome in Dermatologic Diseases and with External Exposures: CME Part 2.},
journal = {Journal of the American Academy of Dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaad.2024.07.1499},
pmid = {39173885},
issn = {1097-6787},
abstract = {In Part I of our CME we reviewed the skin microbiome in healthy individuals. Part II reviews the evolving understanding of alterations in the skin microbiome in specific human diseases. We also discuss how the skin microbiome can change with environmental exposures and medications such as antibiotics as well as ongoing research on microbiome-based interventions.},
}

@article {pmid39173756,
year = {2024},
author = {Liu, J and Zhang, Z and Zhong, S and Zhang, X and Yang, J and Zhou, Q and Wang, D and Chang, X and Wang, H},
title = {Fecal microbiome transplantation alleviates manganese-induced neurotoxicity by altering the composition and function of the gut microbiota via the cGAS-STING/NLRP3 pathway.},
journal = {The Science of the total environment},
volume = {951},
number = {},
pages = {175681},
doi = {10.1016/j.scitotenv.2024.175681},
pmid = {39173756},
issn = {1879-1026},
abstract = {Manganese (Mn) is an environmental pollutant, and overexposure can cause neurodegenerative disorders similar to Alzheimer's disease and Parkinson's disease that are characterized by β-amyloid (Aβ) overexpression, Tau hyperphosphorylation and neuroinflammation. However, the mechanisms of Mn neurotoxicity are not clearly defined. In our study, a knockout mouse model of Mn exposure combined with gut flora-induced neurotoxicity was constructed to investigate the effect of gut flora on Mn neurotoxicity. The results showed that the levels of Tau, p-Tau and Aβ in the hippocampus of C57BL/6 mice were greater than those in the hippocampus of control mice after 5 weeks of continuous exposure to manganese chloride (Mn content of 200 mg/L). Transplanted normal and healthy fecal microbiota from mice significantly downregulated Tau, p-Tau and Aβ expression and ameliorated brain pathology. Moreover, Mn exposure activated the cGAS-STING pathway and altered the cecal microbiota profile, characterized by an increase in Clostridiales, Pseudoflavonifractor, Ligilactobacillus and Desulfovibrio, and a decrease in Anaerotruncus, Eubacterium_ruminantium_group, Fusimonas and Firmicutes, While fecal microbiome transplantation (FMT) treatment inhibited this pathway and restored the microbiota profile. FMT alleviated Mn exposure-induced neurotoxicity by inhibiting activation of the NLRP3 inflammasome triggered by overactivation of the cGAS-STING pathway. Deletion of the cGAS and STING genes and FMT altered the gut microbiota composition and its predictive function. Phenotypic prediction revealed that FMT markedly decreased the abundances of anaerobic and stress-tolerant bacteria and significantly increased the abundances of facultative anaerobic bacteria and biofilm-forming bacteria after blocking the cGAS-STING pathway compared to the Mn-exposed group. FMT from normal and healthy mice ameliorated the neurotoxicity of Mn exposure, possibly through alterations in the composition and function of the microbiome associated with the cGAS-STING/NLRP3 pathway. This study provides a prospective direction for future research on the mechanism of Mn neurotoxicity.},
}

@article {pmid39173719,
year = {2024},
author = {Conroy, ER and Peterson, R and Phipatanakul, W and Sheehan, WJ},
title = {Increasing Awareness Regarding the Relationship between Environmental Exposures and Allergic Disease.},
journal = {The Journal of allergy and clinical immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaci.2024.08.008},
pmid = {39173719},
issn = {1097-6825},
abstract = {This review highlights studies from the past 3 years that add to the understanding of the impact of environmental exposures on allergic disease. These include aeroallergens, air quality, prenatal or early life exposures, and occupational exposures. Recent studies focused on the relationship between the environment, the microbiome, and allergic disease as well as new therapeutic options are also reviewed. Lastly, there has been significant recent research that improves our knowledge of the link between health disparities and environmental exposures. These scientific advances have resulted in a better understanding that sets the foundation for current and future research dedicated to improving health outcomes by modifying environmental exposures.},
}

@article {pmid39173527,
year = {2024},
author = {Conley, TE and Slater, R and Moss, S and Bulmer, DC and Negro, JR and Ijaz, UZ and Pritchard, DM and Parkes, M and Probert, C},
title = {Microbiome-driven IBS metabotypes influence response to the low FODMAP diet: insights from the faecal volatome.},
journal = {EBioMedicine},
volume = {107},
number = {},
pages = {105282},
doi = {10.1016/j.ebiom.2024.105282},
pmid = {39173527},
issn = {2352-3964},
abstract = {BACKGROUND: Irritable bowel syndrome (IBS) is a common and debilitating disorder manifesting with abdominal pain and bowel dysfunction. A mainstay of treatment is dietary modification, including restriction of FODMAPs (fermentable oligosaccharides, disaccharides, monosaccharides and polyols). A greater response to a low FODMAP diet has been reported in those with a distinct IBS microbiome termed IBS-P. We investigated whether this is linked to specific changes in the metabolome in IBS-P.

METHODS: Solid phase microextraction gas chromatography-mass spectrometry was used to examine the faecal headspace of 56 IBS cases (each paired with a non-IBS household control) at baseline, and after four-weeks of a low FODMAP diet (39 pairs). 50% cases had the IBS-P microbial subtype, while the others had a microbiome that more resembled healthy controls (termed IBS-H). Clinical response to restriction of FODMAPs was measured with the IBS-symptom severity scale, from which a pain sub score was calculated.

FINDINGS: Two distinct metabotypes were identified and mapped onto the microbial subtypes. IBS-P was characterised by a fermentative metabolic profile rich in short chain fatty acids (SCFAs). After FODMAP restriction significant reductions in SCFAs were observed in IBS-P. SCFA levels did not change significantly in the IBS-H group. The magnitude of pain and overall symptom improvement were significantly greater in IBS-P compared to IBS-H (p = 0.016 and p = 0.026, respectively). Using just five metabolites, a biomarker model could predict microbial subtype with accuracy (AUROC 0.797, sensitivity 78.6% (95% CI: 0.78-0.94), specificity 71.4% (95% CI: 0.55-0.88).

INTERPRETATION: A metabotype high in SCFAs can be manipulated by restricting fermentable carbohydrate, and is associated with an enhanced clinical response to this dietary restriction. This implies that SCFAs harbour pro-nociceptive potential when produced in a specific IBS niche. By ascertaining metabotype, microbial subtype can be predicted with accuracy. This could allow targeted FODMAP restriction in those seemingly primed to respond best.

FUNDING: This research was co-funded by Addenbrooke's Charitable Trust, Cambridge University Hospitals and the Wellcome Sanger Institute, and supported by the NIHR Cambridge Biomedical Research Centre (BRC-1215-20014).},
}

@article {pmid39173404,
year = {2024},
author = {Zhang, Q and Song, J and Wu, H and Wang, L and Zhuo, G and Li, H and He, S and Pan, Y and Liu, G},
title = {Intratumoral microbiota associates with systemic immune inflammation state in nasopharyngeal carcinoma.},
journal = {International immunopharmacology},
volume = {141},
number = {},
pages = {112984},
doi = {10.1016/j.intimp.2024.112984},
pmid = {39173404},
issn = {1878-1705},
abstract = {BACKGROUND: The nasopharynx serves as a crucial niche for the microbiome of the upper respiratory tract. However, the association between the intratumoral microbiota and host systemic inflammation and immune status in nasopharyngeal carcinoma (NPC) remain uncertain.

METHODS: We performed 5R 16S rDNA sequencing on NPC tissue samples, followed by diversity analysis, LEfSe differential analysis, and KEGG functional prediction. The analyses were based on indices such as AISI, SIRI, PAR, PLR, and NAR. Correlation analyses between microbes and these indices were performed to identify microbes associated with inflammation and immune status. Additionally, regression analysis based on tumor TNM stage was performed to identify key microbes linked to tumor progression. The head and neck squamous cell carcinoma (HNSC) transcriptome and the paired HNSC microbiome data from TCGA were utilized to validate the analyses.

RESULTS: The Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes were the most enriched phyla in NPC tissues. Microbes within these phyla demonstrated high sensitivity to changes in host systemic inflammation and immune status. Proteobacteria and Firmicutes showed significant differences between inflammation groups. Actinobacteria varied specifically with platelet-related inflammatory indices, and Bacteroidetes genera exhibited significant differences between NAR groups. Corynebacterium and Brevundimonas significantly impacted the T stage of tumors, with a high load of Corynebacterium within tumors associated with a better prognosis CONCLUSION: Our analysis indicates that Proteobacteria play a crucial role in the inflammatory state of NPC, while Bacteroidetes are more sensitive to the tumor immune status.},
}

@article {pmid39173370,
year = {2024},
author = {Oh, S and Nguyen, AH and Kim, JS and Chung, SY and Maeng, SK and Jung, YH and Cho, K},
title = {A microbiome-biochar composite synergistically eliminates the environmental risks of antibiotic mixtures and their toxic byproducts.},
journal = {Journal of hazardous materials},
volume = {478},
number = {},
pages = {135474},
doi = {10.1016/j.jhazmat.2024.135474},
pmid = {39173370},
issn = {1873-3336},
abstract = {This study developed a continuous reactor system employing a hybrid hydrogel composite synthesized using a complex sludge microbiome and an adsorbent (HSA). This HSA-based system effectively eliminated the environmental risks associated with a mixture of the antibiotics ciprofloxacin and sulfamethoxazole, which exhibited higher toxicity in combination than individually at environmentally relevant levels. Analytical chemistry experiments revealed the in-situ generation of various byproducts (BPs) within the bioreactor system, with two of these BPs recording toxicity levels that surpassed those of their parent compound. The HSA approach successfully prevented the functional microbiome from being washed out of the reactor, while HSA efficiently removed antibiotic residues in their original and BP forms through synergistic adsorptive and biotransformation mechanisms, ultimately reducing the overall ecotoxicity. The use of HSA thus demonstrates promise not only as a mean to reduce the threat posed by toxic antibiotic residues to aquatic ecosystems but also as a practical solution to operational challenges, such as biomass loss/washout, that are frequently encountered in various environmental bioprocesses.},
}

@article {pmid39173279,
year = {2024},
author = {Du, L and Chen, J and Yan, J and Xie, H and Wang, L and Wang, R and Han, X and Wang, Y},
title = {Lingguizhugan decoction ameliorates cognitive impairment in AD-like mice by influencing the microbiome-gut-brain axis mediated by SCFAs.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {133},
number = {},
pages = {155942},
doi = {10.1016/j.phymed.2024.155942},
pmid = {39173279},
issn = {1618-095X},
abstract = {BACKGROUND: Lingguizhugan (LGZG) decoction, an ancient Chinese herbal remedy originating from the Eastern Han Dynasty, consists of Poria cocos, Cinnamomi ramulus, Atractylodes macrocephala, and Glycyrrhiza, as described in the Golden Chamber Synopsis. It has a history spanning over 1600 years, in which it has been primarily used for the treatment of inflammation, injuries, and fluid retention; however, the potential of LGZG decoction to ameliorate Alzheimer's disease (AD) progression by modulating the gut-brain axis through attenuation of gut microbiota and their metabolites remains unknown.

PURPOSE: To examine the in vivo anti-AD effects and mechanism of LGZG decoction in alleviating AD cognitive impairment.

STUDY DESIGN: Two-part experiments in vivo were designed, one for behavior tests, intestinal and brain histopathology, intestinal microbiome and quantitative determination, and another one for metabolite supplementation study.

METHODS: AlCl3/D-gal was used to establish an AD-like mouse model. Behavioral tests, such as the Morris water maze test, were used to assess the effect of LGZG decoction on cognitive dysfunction. The concentration of proinflammatory mediators was measured by ELISA. The protein content was detected by western blot analysis and immunohistochemistry. The content of short-chain fatty acids was measured by LC-MS/MS. Evaluation of 16S rRNA gene sequencing for species and strain-level gut microbiome analysis was performed.

RESULTS: LGZG decoction mitigated cognitive impairment in an AD-like mouse model, and decreased the deposition of amyloid-β and the production of proinflammatory cytokines in the brain. LGZG decoction remodeled the intestinal microecology, enhanced the integrity of the intestinal and brain tissue barriers, and modulated Aβ transportation through gut microbiota metabolite SCFAs. The neuroprotective effect of SCFAs on the AD-like model mice may be manifested through the inhibition of pP38 of the MAPK signaling pathway.

CONCLUSION: Our results suggest that LGZG decoction reshapes the gut microbiota. SCFAs derived from the gut microbiota ameliorate the cognitive decline induced by AlCl3/D-gal through the gut-brain axis and reduce brain Aβ aggregation. We propose LGZG decoction as a potential therapeutic option for AD.},
}

@article {pmid39173234,
year = {2024},
author = {Jia, P and Liang, JL and Lu, JL and Zhong, SJ and Xiong, T and Feng, SW and Wang, Y and Wu, ZH and Yi, XZ and Gao, SM and Zheng, J and Wen, P and Li, F and Li, Y and Liao, B and Shu, WS and Li, JT},
title = {Soil keystone viruses are regulators of ecosystem multifunctionality.},
journal = {Environment international},
volume = {191},
number = {},
pages = {108964},
doi = {10.1016/j.envint.2024.108964},
pmid = {39173234},
issn = {1873-6750},
abstract = {Ecosystem multifunctionality reflects the capacity of ecosystems to simultaneously maintain multiple functions which are essential bases for human sustainable development. Whereas viruses are a major component of the soil microbiome that drive ecosystem functions across biomes, the relationships between soil viral diversity and ecosystem multifunctionality remain under-studied. To address this critical knowledge gap, we employed a combination of amplicon and metagenomic sequencing to assess prokaryotic, fungal and viral diversity, and to link viruses to putative hosts. We described the features of viruses and their potential hosts in 154 soil samples from 29 farmlands and 25 forests distributed across China. Although 4,460 and 5,207 viral populations (vOTUs) were found in the farmlands and forests respectively, the diversity of specific vOTUs rather than overall soil viral diversity was positively correlated with ecosystem multifunctionality in both ecosystem types. Furthermore, the diversity of these keystone vOTUs, despite being 10-100 times lower than prokaryotic or fungal diversity, was a better predictor of ecosystem multifunctionality and more strongly associated with the relative abundances of prokaryotic genes related to soil nutrient cycling. Gemmatimonadota and Actinobacteria dominated the host community of soil keystone viruses in the farmlands and forests respectively, but were either absent or showed a significantly lower relative abundance in that of soil non-keystone viruses. These findings provide novel insights into the regulators of ecosystem multifunctionality and have important implications for the management of ecosystem functioning.},
}

@article {pmid39173215,
year = {2024},
author = {Wickramasuriya, SS and Park, I and Lee, Y and Richer, LM and Przybyszewski, C and Gay, CG and van Oosterwijk, JG and Lillehoj, HS},
title = {Effect of orally administered B. subtilis-cNK-2 on growth performance, immunity, gut health, and gut microbiome in chickens infected with Eimeria acervulina and its potential as an alternative to antibiotics.},
journal = {Poultry science},
volume = {103},
number = {11},
pages = {104156},
doi = {10.1016/j.psj.2024.104156},
pmid = {39173215},
issn = {1525-3171},
abstract = {This study investigated the best oral delivery strategy (gavage or feed) for the B. subtilis expressing the chicken anti-microbial peptide cNK-2 (B. subtilis-cNK-2) in comparison to monensin, in chickens challenged with Eimeria acervulina (E. acervulina). A total of 120 broiler chickens were randomly allocated into 5 treatment groups in a completely randomized design: 1) uninfected chickens fed with basal diet (NC), 2) E. acervulina-infected chickens fed a basal diet (PC), 3) E. acervulina-infected chickens fed a basal diet supplemented with 90 mg monensin/kg feed (MO), 4) E. acervulina-infected chickens fed a basal diet and orally gavaged with B. subtilis-cNK-2 at 1 × 10[10] cfu/d (CNK-O), and 5) E. acervulina-infected chickens fed a basal diet mixed with B. subtilis-cNK-2 at 1 × 10[10] cfu/kg feed (CNK-F). The challenge consisted of 5,000 sporulated E. acervulina oocysts through oral gavage on d 15. Body weights were measured on d 7, 14, 21, and 23. Duodenal tissue and digesta samples were collected at 6 d postinfection (dpi) to assess the gut integrity, oxidative stress, mucosal immunity, and the gut microbiome. Fecal samples were collected from 6 to 8 dpi to enumerate the oocyst shedding. Chickens in the CNK-O group showed improved (P < 0.05) growth performance, gut integrity, and mucosal immunity compared to PC, comparable to chickens in the MO group. Chickens in the MO, CNK-F, and CNK-O treatment groups all showed lower (P < 0.05) oocyst shedding compared to PC chickens. Moreover, distinct cytokine profile, oxidative stress measures, tight junction proteins, and shifts in the gut microbiome with associated functional changes were observed in all challenge groups. In conclusion, we showed that the oral administration of B. subtilis-cNK-2 improved growth performance, enhanced local protective immunity, and reduced fecal oocyst shedding in broiler chickens infected with E. acervulina, demonstrating potential use of B. subtilis-cNK-2 as an alternative to antibiotics to protect chickens against coccidiosis.},
}

@article {pmid39173024,
year = {2024},
author = {Sato, Y and Shioya, H and Uda, Y and Asano, H and Nagao, Y and Kuno, H and Yoshizawa, F},
title = {Effects of two types of Coccomyxa sp. KJ on in vitro ruminal fermentation, methane production, and the rumen microbiota.},
journal = {PloS one},
volume = {19},
number = {8},
pages = {e0308646},
pmid = {39173024},
issn = {1932-6203},
mesh = {Animals ; *Rumen/microbiology/metabolism ; *Methane/metabolism/biosynthesis ; *Fermentation ; Gastrointestinal Microbiome/drug effects ; Chlorophyta/metabolism ; Microbiota/drug effects ; Digestion ; Nitrogen/metabolism ; Cattle ; Silage ; },
abstract = {Coccomyxa sp. KJ is a unicellular green microalga that accumulates abundant lipids when cultured under nitrogen-deficient conditions (KJ1) and high nitrogen levels when cultured under nitrogen-sufficient conditions (KJ2). Considering the different characteristics between KJ1 and KJ2, they are expected to have different effects on rumen fermentation. This study aimed to determine the effects of KJ1 and KJ2 on in vitro ruminal fermentation, digestibility, CH4 production, and the ruminal microbiome as corn silage substrate condition. Five treatments were evaluated: substrate only (CON) and CON + 0.5% dry matter (DM) KJ1 (KJ1_L), 1.0% DM KJ1 (KJ1_H), 0.5% DM KJ2 (KJ2_L), and 1.0% DM KJ2 (KJ2_H). DM degradability-adjusted CH4 production was inhibited by 48.4 and 40.8% in KJ2_L and KJ2_H, respectively, compared with CON. The proportion of propionate was higher in the KJ1 treatments than the CON treatment and showed further increases in the KJ2 treatments. The abundances of Megasphaera, Succiniclasticum, Selenomonas, and Ruminobacter, which are related to propionate production, were higher in KJ2_H than in CON. The results suggested that the rumen microbiome was modified by the addition of 0.5-1.0% DM KJ1 and KJ2, resulting in increased propionate and reduced CH4 production. In particular, the KJ2 treatments inhibited ruminal CH4 production more than the KJ1 treatments. These findings provide important information for inhibiting ruminal CH4 emissions, which is essential for increasing animal productivity and sustaining livestock production under future population growth.},
}

Animals
*Rumen/microbiology/metabolism
*Methane/metabolism/biosynthesis
*Fermentation
Gastrointestinal Microbiome/drug effects
Chlorophyta/metabolism
Microbiota/drug effects
Digestion
Nitrogen/metabolism
Cattle
Silage

@article {pmid39172990,
year = {2024},
author = {Wang, KA and Singh, J and Albin, JS and Pentelute, BL and Nolan, EM},
title = {Class IIb Microcin MccM Interferes with Oxidative Phosphorylation in Escherichia coli.},
journal = {ACS chemical biology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acschembio.4c00226},
pmid = {39172990},
issn = {1554-8937},
abstract = {Dysbiosis of the human gut microbiota is linked to numerous diseases. Understanding the molecular mechanisms by which microbes interact and compete with one another is required for developing successful strategies to modulate the microbiome. The natural product Microcin M (MccM) consists of a 77-residue bioactive peptide conjugated to a siderophore and is a class II microcin involved in microbial competition with an enigmatic mode-of-action. In this work, we investigated the basis for MccM activity and leveraged bioinformatics to expand the known chemical diversity of class II microcins. We applied automated fast-flow solid phase peptide synthesis coupled with chemoenzymatic chemistry to acquire MccM and demonstrated that its activity was bacteriostatic. We then used our synthetic molecule to ascertain that catecholate siderophore transporters in Escherichia coli K-12 are necessary for MccM import. Once inside the cell, we found that MccM treatment decreased the levels of intracellular ATP and interfered with gene expression. These effects were ameliorated in genetic mutants lacking ATP synthase or in conditions that support substrate-level phosphorylation. Further, we showed that MccM elevated the levels of reactive oxygen species within the target cell. We propose that MccM effects its bacteriostatic activity by decreasing the total energy level of the cell through inhibition of oxidative phosphorylation. Lastly, using genome mining, we bioinformatically identified 171 novel putative class II microcins. Our investigation sheds light on the natural processes involved in microbial competition and provides inspiration, in the form of new molecules, for future therapeutic endeavors.},
}

@article {pmid39172818,
year = {2024},
author = {Frazier, AN and Belk, AD and Beck, MR and Koziel, JA},
title = {Impact of methane mitigation strategies on the native ruminant microbiome: A protocol for a systematic review and meta-analysis.},
journal = {PloS one},
volume = {19},
number = {8},
pages = {e0308914},
pmid = {39172818},
issn = {1932-6203},
mesh = {*Methane/metabolism ; *Ruminants/microbiology ; Animals ; *Microbiota ; *Systematic Reviews as Topic ; *RNA, Ribosomal, 16S/genetics ; *Meta-Analysis as Topic ; },
abstract = {Recently, research has investigated the role of the ruminant native microbiome, and the role microbes play in methane (CH4) production and mitigation. However, the variation across microbiome studies makes implementing impactful strategies difficult. The first objective of this study is to identify, summarize, compile, and discuss the current literature on CH4 mitigation strategies and how they interact with the native ruminant microbiome. The second objective is to perform a meta-analysis on the identified16S rRNA sequencing data. A literature search using Web of Science, Scopus, AGRIS, and Google Scholar will be implemented. Eligible criteria will be defined using PICO (population, intervention, comparator, and outcomes) elements. Two independent reviewers will be utilized for both the literature search and data compilation. Risk of bias will be assessed using the Cochrane Risk Bias 2.0 tool. Publicly available 16S rRNA amplicon gene sequencing data will be downloaded from NCBI Sequence Read Archive, European Nucleotide Archive or similar database using appropriate extraction methods. Data processing will be performed using QIIME2 following a standardized protocol. Meta-analyses will be performed on both alpha and beta diversity as well as taxonomic analyses. Alpha diversity metrics will be tested using a Kruskal-Wallis test with a Benjamini-Hochberg multiple testing correction. Beta diversity will be statistically tested using PERMANOVA testing with multiple test corrections. Hedge's g standardized mean difference statistic will be used to calculate fixed and random effects model estimates using a 95% confidence interval. Heterogeneity between studies will be assessed using the I2 statistic. Potential publication bias will be further assessed using Begg's correlation test and Egger's regression test. The GRADE approach will be used to assess the certainty of evidence. The following protocol will be used to guide future research and meta-analyses for investigating CH4 mitigation strategies and ruminant microbial ecology. The future work could be used to enhance livestock management techniques for GHG control. This protocol is registered in Open Science Framework (https://osf.io/vt56c) and available in the Systematic Reviews for Animals and Food (https://www.syreaf.org/contact).},
}

*Methane/metabolism
*Ruminants/microbiology
Animals
*Microbiota
*Systematic Reviews as Topic
*RNA, Ribosomal, 16S/genetics
*Meta-Analysis as Topic

@article {pmid39172632,
year = {2024},
author = {Blount, KF and Papazyan, R and Ferdyan, N and Srinivasan, K and Gonzalez, C and Shannon, WD and Fuchs, BC},
title = {Microbiome and Metabolome Restoration After Administration of Fecal Microbiota, Live-jslm (REBYOTA®) for Preventing Recurrent Clostridioides difficile Infection.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiae418},
pmid = {39172632},
issn = {1537-6613},
abstract = {BACKGROUND: Microbiota-based treatments are effective in preventing recurrent Clostridioides difficile infection (rCDI). Fecal microbiota, live-jslm (REBYOTA®; RBL, previously RBX2660) was shown to prevent rCDI in a phase 3, randomized, double-blinded placebo controlled clinical trial (PUNCH™ CD3).

METHODS: Stool samples from participants in PUNCH™ CD3 who received a single blinded dose of rectally administered RBL or placebo were sequenced to determine microbial community composition and calculate the Microbiome Health Index for post-antibiotic dysbiosis (MHI-A). The composition of bile acids (BAs) in the same samples was quantified by liquid chromatography mass spectrometry. Relationships between BA composition and microbiota community structure and correlations with treatment outcomes were assessed.

RESULTS: Before administration, Gammaproteobacteria and Bacilli dominated the microbiota community and primary BAs were more prevalent than secondary BAs. Clinical success after administration correlated with shifts to predominantly Bacteroidia and Clostridia, a significant increase in MHI-A, and a shift from primary to secondary BAs. Several microbiota and BA changes were more extensive in RBL-treated responders compared to placebo-treated responders, and microbiota changes correlated with BA changes.

CONCLUSIONS: Clinical response and RBL administration were associated with significant restoration of microbiota and BA composition.

CLINICAL TRIALS REGISTRATION: NCT03244644.},
}

@article {pmid39172626,
year = {2024},
author = {Li, M and Xue, Y and Lu, H and Bai, J and Cui, L and Ning, Y and Yuan, Q and Jia, X and Wang, S},
title = {Relationship between infant gastrointestinal microorganisms and maternal microbiome within 6 months of delivery.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0360823},
doi = {10.1128/spectrum.03608-23},
pmid = {39172626},
issn = {2165-0497},
abstract = {To investigate the association between the microbiota in mothers and gut microbiota in infants from 0 to 6 months, the microbiotas in infant feces, maternal feces, and breast milk were determined by 16S rRNA gene sequencing. The contribution of each maternal microbiome to the infant was assessed using fast expectation-maximization for microbial source tracking calculations. The levels of short-chain fatty acids (SCFAs) and secretory immunoglobulin A (sIgA) in the feces of infants were also determined using gas chromatography and IDK-sIgA ELISA to gain a more comprehensive understanding of the infant gut microbiome. The results of this study showed that in addition to Firmicutes (E1) and Bifidobacterium (E2), the dominant microorganisms of the intestinal microbiota of infants aged 0-6 months include Proteobacteria, which is different from previous findings. Acetic acid, the most abundant SCFA in the infant gut, was positively correlated with Megasphaera (P < 0.01), whereas sIgA was positively correlated with Bacteroides (P < 0.05) and negatively correlated with Klebsiella and Clostridium_XVIII (P < 0.05). The maternal gut microbiota contributed more to the infant gut microbiota (43.58% ± 11.13%) than the breast milk microbiota, and significant differences were observed in the contribution of the maternal microbiota to the infant gut microbiota based on the delivery mode and feeding practices. In summary, we emphasize the key role of maternal gut health in the establishment and succession of infant gut microbiota.IMPORTANCEThis study aims to delineate the microbial connections between mothers and infants, leveraging the fast expectation-maximization for microbial source tracking methodology to quantify the contribution of maternal microbiota to the constitution of the infant's gut microbiome. Concurrently, it examines the correlations between the infant gut microbiota and two distinctive biomolecules, namely short-chain fatty acids (SCFAs) and secretory immunoglobulin A (sIgA). The findings indicate that the maternal gut microbiota exerts a greater influence on the infant's gut microbial composition than does the microbiota present in breast milk. Infants born via vaginal delivery and receiving mixed feeding display gut microbiota profiles more similar to their mothers'. Notably, the SCFA acetate displays positive associations with beneficial bacteria and inverse relationships with potentially harmful ones within the infant's gut. Meanwhile, sIgA positively correlates with Bacteroides species and negatively with potentially pathogenic bacteria. By delving into the transmission dynamics of maternal-infant microbiota, exploring the impacts of metabolic byproducts within the infant's gut, and scrutinizing how contextual factors such as birthing method and feeding practices affect the correlation between maternal and infant microbiota, this research endeavors to establish practical strategies for optimizing early-life gut health management in infants. Such insights promise to inform targeted interventions that foster healthier microbial development during the critical first 6 months of life.},
}

@article {pmid39172545,
year = {2024},
author = {Chen, G and Jiang, J and Sun, Y},
title = {RNAVirHost: a machine learning-based method for predicting hosts of RNA viruses through viral genomes.},
journal = {GigaScience},
volume = {13},
number = {},
pages = {},
pmid = {39172545},
issn = {2047-217X},
support = {//Research Grants Council, University Grants Committee/ ; },
mesh = {*Machine Learning ; *Genome, Viral ; *RNA Viruses/genetics/classification ; High-Throughput Nucleotide Sequencing/methods ; Computational Biology/methods ; Software ; },
abstract = {BACKGROUND: The high-throughput sequencing technologies have revolutionized the identification of novel RNA viruses. Given that viruses are infectious agents, identifying hosts of these new viruses carries significant implications for public health and provides valuable insights into the dynamics of the microbiome. However, determining the hosts of these newly discovered viruses is not always straightforward, especially in the case of viruses detected in environmental samples. Even for host-associated samples, it is not always correct to assign the sample origin as the host of the identified viruses. The process of assigning hosts to RNA viruses remains challenging due to their high mutation rates and vast diversity.

RESULTS: In this study, we introduce RNAVirHost, a machine learning-based tool that predicts the hosts of RNA viruses solely based on viral genomes. RNAVirHost is a hierarchical classification framework that predicts hosts at different taxonomic levels. We demonstrate the superior accuracy of RNAVirHost in predicting hosts of RNA viruses through comprehensive comparisons with various state-of-the-art techniques. When applying to viruses from novel genera, RNAVirHost achieved the highest accuracy of 84.3%, outperforming the alignment-based strategy by 12.1%.

CONCLUSIONS: The application of machine learning models has proven beneficial in predicting hosts of RNA viruses. By integrating genomic traits and sequence homologies, RNAVirHost provides a cost-effective and efficient strategy for host prediction. We believe that RNAVirHost can greatly assist in RNA virus analyses and contribute to pandemic surveillance.},
}

*Machine Learning
*Genome, Viral
*RNA Viruses/genetics/classification
High-Throughput Nucleotide Sequencing/methods
Computational Biology/methods
Software

@article {pmid39172513,
year = {2024},
author = {Łaniewski, P and Joe, TR and Jimenez, NR and Eddie, TL and Bordeaux, SJ and Quiroz, V and Peace, DJ and Cui, H and Roe, DJ and Caporaso, JG and Lee, NR and Herbst-Kralovetz, MM},
title = {Viewing Native American Cervical Cancer Disparities through the Lens of the Vaginal Microbiome: A Pilot Study.},
journal = {Cancer prevention research (Philadelphia, Pa.)},
volume = {},
number = {},
pages = {},
doi = {10.1158/1940-6207.CAPR-24-0286},
pmid = {39172513},
issn = {1940-6215},
abstract = {Vaginal dysbiosis is implicated in persistent HPV infection and cervical cancer. Yet, there is a paucity of data on the vaginal microbiome in Native American communities. Here, we aimed to elucidate the relationships between microbiome, HPV, sociodemographic and behavioral risk factors to better understand an increased cervical cancer risk in Native American women. In this pilot study, we recruited 31 participants (16 Native American, 15 non-Native women) in Northern Arizona and examined vaginal microbiota composition, HPV status, and immune mediators. We also assessed individuals' sociodemographic information, and physical, mental, sexual, and reproductive health. Overall, microbiota profiles were dominated by common Lactobacillus species (associated with vaginal health) or a mixture of bacterial vaginosis-associated bacteria. Only 44% of Native women exhibited Lactobacillus dominance, compared to 58% of non-Native women. Women with vaginal dysbiosis also had elevated vaginal pH and were more frequently infected with high-risk HPV. Furthermore, we observed associations of multiple people in a household, lower level of education, and high parity with vaginal dysbiosis and abundance of specific bacterial species. Finally, women with dysbiotic microbiota presented with elevated vaginal levels of proinflammatory cytokines. Altogether, these findings indicate an interplay between HPV, vaginal microbiota, and host defense, which may play a role in the cervical cancer disparity among Native American women. Future longitudinal studies are needed to determine the mechanistic role of vaginal microbiota in HPV persistence in the context of social determinants of health toward the long-term goal of reducing health disparities between non-Hispanic White and Native American populations.},
}

@article {pmid39172274,
year = {2024},
author = {Skičková, Š and Kratou, M and Svobodová, K and Maitre, A and Abuin-Denis, L and Wu-Chuang, A and Obregón, D and Said, MB and Majláthová, V and Krejčí, A and Cabezas-Cruz, A},
title = {Functional redundancy and niche specialization in honeybee and Varroa microbiomes.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
pmid = {39172274},
issn = {1618-1905},
abstract = {The honeybee (Apis mellifera) is a key pollinator critical to global agriculture, facing threats from various stressors, including the ectoparasitic Varroa mite (Varroa destructor). Previous studies have identified shared bacteria between Varroa mites and honeybees, yet it remains unclear if these bacteria assemble similarly in both species. This study builds on existing knowledge by investigating co-occurrence patterns in the microbiomes of both Varroa mites and honeybees, shedding light on potential interactions. Leveraging 16S rRNA datasets, we conducted co-occurrence network analyses, explored Core Association Networks (CAN) and assess network robustness. Comparative network analyses revealed structural differences between honeybee and mite microbiomes, along with shared core features and microbial motifs. The mite network exhibited lower robustness, suggesting less resistance to taxa extension compared to honeybees. Furthermore, analyses of predicted functional profiling and taxa contribution revealed that common central pathways in the metabolic networks have different taxa contributing to Varroa mites and honeybee microbiomes. The results show that while both microbial systems exhibit functional redundancy, in which different taxa contribute to the functional stability and resilience of the ecosystem, there is evidence for niche specialization resulting in unique contributions to specific pathways in each part of this host-parasite system. The specificity of taxa contribution to key pathways offers targeted approaches to Varroa microbiome management and preserving honeybee microbiome. Our findings provide valuable insights into microbial interactions, aiding farmers and beekeepers in maintaining healthy and resilient bee colonies amid increasing Varroa mite infestations.},
}

@article {pmid39171904,
year = {2024},
author = {Rao, G and Song, W-L and Yan, S-Z and Chen, S-L},
title = {Unraveling the distribution pattern and driving forces of soil microorganisms under geographic barriers.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0135924},
doi = {10.1128/aem.01359-24},
pmid = {39171904},
issn = {1098-5336},
abstract = {The Altai Mountains (ALE) and the Greater Khingan Mountains (GKM) in northern China are forest regions dominated by coniferous trees. These geographically isolated regions provide an ideal setting for studying microbial biogeographic patterns. In this study, we employed high-throughput techniques to obtain DNA sequences of soil myxomycetes, bacteria, and fungi and explored the mechanisms underlying the assembly of both local and cross-regional microbial communities in relation to environmental factors. Our investigation revealed that the environmental heterogeneity in ALE and GKM significantly affected the succession and assembly of soil bacterial communities at cross-regional scales. Specifically, the optimal environmental factors affecting bacterial Bray-Curtis similarity were elevation and temperature seasonality. The spatial factors and climate change impact on bacterial communities under the geographical barriers surpassed that of local soil microenvironments. The assembly pattern of bacterial communities transitions from local drift to cross-regional heterogeneous selection. Environmental factors had a relatively weak influence on myxomycetes and fungi. Both soil myxomycetes and fungi faced considerable dispersal limitation at local and cross-regional scales, ultimately leading to weak geographical distribution patterns.IMPORTANCEThe impact of environmental selection and dispersal on the soil microbial spatial distribution is a key concern in microbial biogeography, particularly in large-scale geographical patterns. However, our current understanding remains limited. Our study found that soil bacteria displayed a distinct cross-regional geographical distribution pattern, primarily influenced by environmental selection. Conversely, the cross-regional geographical distribution patterns of soil myxomycetes and fungi were relatively weak. Their composition exhibited a weak association with the environment at local and cross-regional scales, with assembly primarily driven by dispersal limitation.},
}

@article {pmid39171766,
year = {2024},
author = {Ingram, K and Ngalame Eko, E and Nunziato, J and Ahrens, M and Howell, B},
title = {Impact of obesity on the perinatal vaginal environment and bacterial microbiome: effects on birth outcomes.},
journal = {Journal of medical microbiology},
volume = {73},
number = {8},
pages = {},
doi = {10.1099/jmm.0.001874},
pmid = {39171766},
issn = {1473-5644},
mesh = {Humans ; Female ; *Vagina/microbiology ; Pregnancy ; *Obesity/microbiology ; Adult ; *Microbiota ; *Pregnancy Outcome ; Hydrogen-Ion Concentration ; Dysbiosis/microbiology ; Pregnancy Complications/microbiology ; Estrogens/blood/metabolism ; Bacteria/classification/isolation & purification/genetics ; Glycogen/metabolism/analysis ; Young Adult ; Lactobacillus/isolation & purification ; Premature Birth ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Introduction. Lactobacillus species predominate the human vagina and are associated with positive vaginal health, including an acidic pH (<4.5). The prevalence of vaginal Lactobacilli increases with increased oestrogen due to increased glycogen production within the vagina. Lactobacilli produce lactic acid, thereby lowering vaginal pH, preventing growth of other bacteria, and lowering microbial diversity. Lower placental oestrogen levels in obese pregnant women could dampen the mechanism to initiate this process, which may be associated with vaginal dysbiosis and unfavourable pregnancy outcomes.Hypothesis. We hypothesize that oestrogen and glycogen levels will be lower, vaginal pH will be higher, and vaginal microbiome diversity will be greater during pregnancy in obese and overweight women compared to healthy weight women.Aim. Pregnancy complications (e.g. preterm birth) are more common in overweight and obese women. If vaginal dysbiosis plays a role, and quantifiable predictors of this increased risk can be determined, these measures could be used to prospectively identify women at risk for pregnancy complications early in pregnancy.Methodology. Vaginal samples were collected at 10-14, 18-24, 26-30, and 34-37 weeks gestation and at delivery from 67 pregnant participants (23 healthy weight, 22 overweight, 22 obese). A blood sample to quantify serum oestrogen was collected at 10-14 weeks. Vaginal samples were collected to test vaginal pH using pH paper, glycogen abundance using fluorometry, and the vaginal microbiome using 16S rRNA amplicon sequencing.Results. Vaginal pH was higher in obese participants compared to healthy weight participants (P=<0.001). Vaginal glycogen levels increased over time in obese participants (P=0.033). The vaginal bacterial alpha diversity was higher in obese participants compared to healthy weight participants (P=0.033). The relative abundances of Peptoniphilus and Anaerococcus were increased in overweight and obese participants, as well as in complicated pregnancies, at 10-14 weeks gestation.Conclusion. The relative abundance of specific vaginal bacteria, like Peptoniphilus and Anaerococcus, in early pregnancy could predict pregnancy outcomes. Our goal is to use the information gathered in this pilot study to further determine the feasibility of assessing the vaginal environment during pregnancy to identify women at risk for negative pregnancy and birth outcomes in the context of a larger study.},
}

Humans
Female
*Vagina/microbiology
Pregnancy
*Obesity/microbiology
Adult
*Microbiota
*Pregnancy Outcome
Hydrogen-Ion Concentration
Dysbiosis/microbiology
Pregnancy Complications/microbiology
Estrogens/blood/metabolism
Bacteria/classification/isolation & purification/genetics
Glycogen/metabolism/analysis
Young Adult
Lactobacillus/isolation & purification
Premature Birth
RNA, Ribosomal, 16S/genetics