@article {pmid39035441,
year = {2024},
author = {Guan, Y and Zhao, S and Li, J and Zhang, W and Guo, Z and Luo, Y and Jiang, X and Li, J and Liu, J and Chen, X and Zhao, Z and Zhang, Z},
title = {Insights from metagenomics into gut microbiome associated with acute coronary syndrome therapy.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1369478},
pmid = {39035441},
issn = {1664-302X},
abstract = {Acute coronary syndrome (ACS) is a predominant cause of mortality, and the prompt and precise identification of this condition is crucial to minimize its impact. Recent research indicates that gut microbiota is associated with the onset, progression, and treatment of ACS. To investigate its role, we sequenced the gut microbiota of 38 ACS patients before and after percutaneous coronary intervention and statin therapy at three time points, examining differential species and metabolic pathways. We observed a decrease in the abundance of Parabacteroides, Escherichia, and Blautia in patients after treatment and an increase in the abundance of Gemalla, Klebsiella variicola, Klebsiella pneumoniae, and others. Two pathways related to sugar degradation were more abundant in patients before treatment, possibly correlated with disorders of sugar metabolism and risk factors, such as hyperglycemia, insulin resistance, and insufficient insulin secretion. Additionally, seven pathways related to the biosynthesis of vitamin K2 and its homolog were reduced after treatment, suggesting that ACS patients may gradually recover after therapy. The gut microbiota of patients treated with different statins exhibited notable differences after treatment. Rosuvastatin appeared to promote the growth of anti-inflammatory bacteria while reducing pro-inflammatory bacteria, whereas atorvastatin may have mixed effects on pro-inflammatory and anti-inflammatory bacteria while increasing the abundance of Bacteroides. Our research will provide valuable insights and enhance comprehension of ACS, leading to better patient diagnosis and therapy.},
}

@article {pmid39035357,
year = {2024},
author = {Qadri, H and Shah, AH and Almilaibary, A and Mir, MA},
title = {Microbiota, natural products, and human health: exploring interactions for therapeutic insights.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1371312},
pmid = {39035357},
issn = {2235-2988},
mesh = {Humans ; *Biological Products/pharmacology/metabolism ; *Gastrointestinal Microbiome/physiology ; Bacteria/metabolism/classification ; Animals ; Host Microbial Interactions ; Symbiosis ; },
abstract = {The symbiotic relationship between the human digestive system and its intricate microbiota is a captivating field of study that continues to unfold. Comprising predominantly anaerobic bacteria, this complex microbial ecosystem, teeming with trillions of organisms, plays a crucial role in various physiological processes. Beyond its primary function in breaking down indigestible dietary components, this microbial community significantly influences immune system modulation, central nervous system function, and disease prevention. Despite the strides made in microbiome research, the precise mechanisms underlying how bacterial effector functions impact mammalian and microbiome physiology remain elusive. Unlike the traditional DNA-RNA-protein paradigm, bacteria often communicate through small molecules, underscoring the imperative to identify compounds produced by human-associated bacteria. The gut microbiome emerges as a linchpin in the transformation of natural products, generating metabolites with distinct physiological functions. Unraveling these microbial transformations holds the key to understanding the pharmacological activities and metabolic mechanisms of natural products. Notably, the potential to leverage gut microorganisms for large-scale synthesis of bioactive compounds remains an underexplored frontier with promising implications. This review serves as a synthesis of current knowledge, shedding light on the dynamic interplay between natural products, bacteria, and human health. In doing so, it contributes to our evolving comprehension of microbiome dynamics, opening avenues for innovative applications in medicine and therapeutics. As we delve deeper into this intricate web of interactions, the prospect of harnessing the power of the gut microbiome for transformative medical interventions becomes increasingly tantalizing.},
}

Humans
*Biological Products/pharmacology/metabolism
*Gastrointestinal Microbiome/physiology
Bacteria/metabolism/classification
Animals
Host Microbial Interactions
Symbiosis

@article {pmid39035305,
year = {2024},
author = {Cheng, FC and Wang, LH and Lai, YJ and Chiang, CP},
title = {The utility of microbiome (microbiota) and exosomes in dentistry.},
journal = {Journal of dental sciences},
volume = {19},
number = {3},
pages = {1313-1319},
pmid = {39035305},
issn = {2213-8862},
abstract = {The concept of the oral-systemic link is important in both basic and clinical dentistry. The microbiome (microbiota) and exosomes are two prevalent issues in the modern medical researches. The common advent of oral and general microbiological investigation originated from the initial observations of oral bacteria within the dental plaque known as oral microbiome. In addition to oral diseases related to oral microbiome, the disruption of the oral and intestinal microbiome could result in the onset of systemic diseases. In the past decade, the exosomes have emerged in the field of the medical researches as they play a role in regulating the transport of intracellular vesicles. However, with the rapid advancement of exosomes researches in recent years, oral tissues (such as dental pulp stem cells and salivary gland cells) are used as the research materials to further promote the development of regenerative medicine. This article emphasized the importance of the concept of the oral-systemic link through the examples of microbiome (microbiota) and exosomes. Through the researches related to microbiome (microbiota) and exosomes, many evidences showed that as the basic dentistry developed directly from the assistance of the basic medicine, indirectly the progress of the basic dentistry turns back to promote the development of the basic medicine, indicating the importance of the concept of the oral-systemic link. The understanding of the oral-systemic link is essential for both clinicians and medical researchers, regardless of their dental backgrounds.},
}

@article {pmid39035270,
year = {2024},
author = {Dong, X and Zhao, W and Ma, S and Li, X and Li, G and Zhang, S},
title = {Oral microbial profiles of extrinsic black tooth stain in primary dentition: A literature review.},
journal = {Journal of dental sciences},
volume = {19},
number = {3},
pages = {1369-1379},
pmid = {39035270},
issn = {2213-8862},
abstract = {The extrinsic black tooth stain (EBS) is commonly found in primary dentition. Patients cannot clean the EBS; this can only be done by professional scaling and debridement. It also has a tendency to reform, which significantly compromises children's aesthetics and even affects their quality of life. However, there is no conclusive evidence on the etiology of the EBS. The associations between the EBS and related oral microbial features is one of the research hot topics. No literature review summarized these research progresses in this area. Therefore, we reviewed the literature on the microbiology of the EBS since 1931 and reported as the following 5 aspects: molecular biotechnology, morphological structure and physiochemical characteristics, microbial etiology hypothesis and core microbial characteristics. The EBS is a special dental plaque mainly composed of Gram-positive bacilli and cocci with scattered calcium deposits that acquired salivary pellicle activates. Early studies showed that the Actinomyces was the main pathogenic bacteria. With advances in biological research techniques, the 'core microbiome' was proposed. The potential pathogenic genera were Actinomyces, Prevotella nigrescens, Pseudotropinibacterium, Leptotrichia, Neisseria and Rothia. However, the pathogenic species of the above genera were still unclear. Currently, it is believed that the EBS consists of iron compounds or black substances that oral bacterial metabolism produces or that the bacterial metabolites formed after chemical reactions in the micro-ecological environment.},
}

@article {pmid39035190,
year = {2024},
author = {Kiseleva, YV and Zharikova, TS and Maslennikov, RV and Temirbekov, SM and Olsufieva, AV and Polyakova, OL and Pontes-Silva, A and Zharikov, YO},
title = {Gut Microbiota and Liver Regeneration: A Synthesis of Evidence on Structural Changes and Physiological Mechanisms.},
journal = {Journal of clinical and experimental hepatology},
volume = {14},
number = {6},
pages = {101455},
pmid = {39035190},
issn = {0973-6883},
abstract = {Liver regeneration (LR) is a unique biological process with the ability to restore up to 70% of the organ. This allows for the preservation of liver resections for various liver tumors and for living donor liver transplantation (LDLT). However, in some cases, LR is insufficient and interventions that can improve LR are urgently needed. Gut microbiota (GM) is one of the factors influencing LR, as the liver and intestine are intimately connected through the gut-liver axis. Thus, healthy GM facilitates normal LR, whereas dysbiosis leads to impaired LR due to imbalance of bile acids, inflammatory cytokines, microbial metabolites, signaling pathways, etc. Therefore, GM can be considered as a new possible therapeutic target to improve LR. In this review, we critically observe the current knowledge about the influence of gut microbiota (GM) on liver regeneration (LR) and the possibility to improve this process, which may reduce complication and mortality rates after liver surgery. Although much research has been done on this topic, more clinical trials and systemic reviews are urgently needed to move this type of intervention from the experimental phase to the clinical field.},
}

@article {pmid39034917,
year = {2024},
author = {Verhaar, BJH and Wijdeveld, M and Wortelboer, K and Rampanelli, E and Levels, JHM and Collard, D and Cammenga, M and Nageswaran, V and Haghikia, A and Landmesser, U and Li, XS and DiDonato, JA and Hazen, SL and Garrelds, IM and Danser, AHJ and van den Born, BH and Nieuwdorp, M and Muller, M},
title = {Effects of Oral Butyrate on Blood Pressure in Patients With Hypertension: A Randomized, Placebo-Controlled Trial.},
journal = {Hypertension (Dallas, Tex. : 1979)},
volume = {},
number = {},
pages = {},
doi = {10.1161/HYPERTENSIONAHA.123.22437},
pmid = {39034917},
issn = {1524-4563},
abstract = {BACKGROUND: The microbiota-derived short chain fatty acid butyrate has been shown to lower blood pressure (BP) in rodent studies. Nonetheless, the net effect of butyrate on hypertension in humans remains uncovered. In this study, for the first time, we aimed to determine the effect of oral butyrate on BP in patients with hypertension.

METHODS: We performed a double-blind randomized placebo-controlled trial including 23 patients with hypertension. Antihypertensive medication was discontinued for the duration of the study with a washout period of 4 weeks before starting the intervention. Participants received daily oral capsules containing either sodium butyrate or placebo with an equivalent dosage of sodium chloride for 4 weeks. The primary outcome was daytime 24-hour systolic BP. Differences between groups over time were assessed using linear mixed models (group-by-time interaction).

RESULTS: Study participants (59.0±3.7 years; 56.5% female) had an average baseline office systolic BP of 143.5±14.6 mm Hg and diastolic BP of 93.0±8.3 mm Hg. Daytime 24-hour systolic and diastolic BP significantly increased over the intervention period in the butyrate compared with the placebo group, with an increase of +9.63 (95% CI, 2.02-17.20) mm Hg in daytime 24-hour systolic BP and +5.08 (95% CI, 1.34-8.78) mm Hg in diastolic BP over 4 weeks. Butyrate levels significantly increased in plasma, but not in feces, upon butyrate intake, underscoring its absorption.

CONCLUSIONS: Four-week treatment with oral butyrate increased daytime systolic and diastolic BP in subjects with hypertension. Our findings implicate that butyrate does not have beneficial effects on human hypertension, which warrants caution in future butyrate intervention studies.

REGISTRATION: URL: https://clinicaltrialregister.nl/nl/trial/22936; Unique identifier: NL8924.},
}

@article {pmid39034613,
year = {2024},
author = {Krigul, KL and Feeney, RH and Wongkuna, S and Aasmets, O and Holmberg, SM and Andreson, R and Puértolas-Balint, F and Pantiukh, K and Sootak, L and Org, T and Tenson, T and Org, E and Schroeder, BO},
title = {A history of repeated antibiotic usage leads to microbiota-dependent mucus defects.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2377570},
doi = {10.1080/19490976.2024.2377570},
pmid = {39034613},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Animals ; *Anti-Bacterial Agents/pharmacology ; Mice ; *Fecal Microbiota Transplantation ; *Mucus/metabolism/microbiology ; *Bacteria/classification/genetics/drug effects/isolation & purification/metabolism ; Intestinal Mucosa/microbiology/metabolism/drug effects ; Male ; Female ; Feces/microbiology ; Adult ; Middle Aged ; Akkermansia ; Mice, Inbred C57BL ; Colon/microbiology ; Bacteroides fragilis/drug effects ; },
abstract = {Recent evidence indicates that repeated antibiotic usage lowers microbial diversity and ultimately changes the gut microbiota community. However, the physiological effects of repeated - but not recent - antibiotic usage on microbiota-mediated mucosal barrier function are largely unknown. By selecting human individuals from the deeply phenotyped Estonian Microbiome Cohort (EstMB), we here utilized human-to-mouse fecal microbiota transplantation to explore long-term impacts of repeated antibiotic use on intestinal mucus function. While a healthy mucus layer protects the intestinal epithelium against infection and inflammation, using ex vivo mucus function analyses of viable colonic tissue explants, we show that microbiota from humans with a history of repeated antibiotic use causes reduced mucus growth rate and increased mucus penetrability compared to healthy controls in the transplanted mice. Moreover, shotgun metagenomic sequencing identified a significantly altered microbiota composition in the antibiotic-shaped microbial community, with known mucus-utilizing bacteria, including Akkermansia muciniphila and Bacteroides fragilis, dominating in the gut. The altered microbiota composition was further characterized by a distinct metabolite profile, which may be caused by differential mucus degradation capacity. Consequently, our proof-of-concept study suggests that long-term antibiotic use in humans can result in an altered microbial community that has reduced capacity to maintain proper mucus function in the gut.},
}

Humans
*Gastrointestinal Microbiome/drug effects
Animals
*Anti-Bacterial Agents/pharmacology
Mice
*Fecal Microbiota Transplantation
*Mucus/metabolism/microbiology
*Bacteria/classification/genetics/drug effects/isolation & purification/metabolism
Intestinal Mucosa/microbiology/metabolism/drug effects
Male
Female
Feces/microbiology
Adult
Middle Aged
Akkermansia
Mice, Inbred C57BL
Colon/microbiology
Bacteroides fragilis/drug effects

@article {pmid39034349,
year = {2024},
author = {Zhuang, Y and Liu, S and Gao, D and Xu, Y and Jiang, W and Chen, T and Xiao, J and Wang, J and Hou, G and Li, S and Zhao, X and Huang, Y and Li, S and Zhang, S and Li, M and Wang, W and Li, S and Cao, Z},
title = {The Bifidobacterium-dominated fecal microbiome in dairy calves shapes the characteristic growth phenotype of host.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {59},
pmid = {39034349},
issn = {2055-5008},
mesh = {Animals ; *Feces/microbiology ; Cattle ; *RNA, Ribosomal, 16S/genetics ; *Bifidobacterium/genetics/growth & development ; *Gastrointestinal Microbiome ; Mice ; *Fecal Microbiota Transplantation/methods ; Phenotype ; Probiotics/administration & dosage ; Phylogeny ; DNA, Bacterial/genetics ; },
abstract = {The dominant bacteria in the hindgut of calves play an important role in their growth and health, which could even lead to lifelong consequences. However, the identification of core probiotics in the hindgut and its mechanism regulating host growth remain unclear. Here, a total of 1045 fecal samples were analyzed by 16S rRNA gene sequencing from the 408 Holstein dairy calves at the age of 0, 14, 28, 42, 56, and 70 days to characterize the dynamic changes of core taxa. Moreover, the mechanisms of nutrient metabolism of calf growth regulated by core bacteria were investigated using multi-omics analyses. Finally, fecal microbiota transplantation (FMT) in mice were conducted to illustrate the potential beneficial effects of core bacteria. Four calf enterotypes were identified and enterotypes dominated by Bifidobacterium and Oscillospiraceae_UCG-005 were representative. The frequency of enterotype conversion shifted from variable to stable. The close relationship observed between phenotype and enterotype, revealing a potential pro-growth effect of Bifidobacterium, might be implemented by promoting the use of carbohydrate, activating the synthesis of volatile fatty acids, amino acids and vitamin B6, and inhibiting methane production in the hindgut. The FMT results indicated the beneficial effect of Bifidobacterium on host growth and hindgut development. These results support the notion that the Bifidobacterium-dominated fecal microbiome would be an important driving force for promoting the host growth in the early life. Our findings provide new insights into the potential probiotic mining and application strategies to promote the growth of young animals or improve their growth retardation.},
}

Animals
*Feces/microbiology
Cattle
*RNA, Ribosomal, 16S/genetics
*Bifidobacterium/genetics/growth & development
*Gastrointestinal Microbiome
Mice
*Fecal Microbiota Transplantation/methods
Phenotype
Probiotics/administration & dosage
Phylogeny
DNA, Bacterial/genetics

@article {pmid39034003,
year = {2024},
author = {Radziemska, M and Blazejczyk, A and Gusiatin, MZ and Cydzik-Kwiatkowska, A and Majewski, G and Brtnicky, M},
title = {Compost-diatomite-based phytostabilization course under extreme environmental conditions in terms of high pollutant contents and low temperatures.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {174917},
doi = {10.1016/j.scitotenv.2024.174917},
pmid = {39034003},
issn = {1879-1026},
abstract = {The effects of changes in environmental temperatures on the immobilization or removal of cationic potentially toxic elements (PTE) in heavily polluted soils are often poorly understood, although both are widely studied in the context of phytostabilization. To address this issue, a novel compost-diatomite hybrid (CDH) amendment was developed and applied for assisted phytostabilization at two external temperature regimes. (Cd/Ni/Cu/Zn)-extremely contaminated soils (unenriched and CDH-enriched) were cultivated with perennial ryegrass and native soil microbiome under greenhouse conditions and then transferred to freeze-thaw conditions (FTC). The decrease in metal potential toxicity in soils undergoing phytostabilization following both temperature treatments was characterized by a combination of sequential extraction and atomic absorption measurements. The soil microbiome was characterized by high-throughput sequencing. In a relative comparison, the greatest decrease in the content of all different PTEs in CDH-enriched soil (compared to unenriched soil) was highest in FTC. Furthermore, under the influence of FTC, in a relative comparison between two CDH-enriched soils (exposed-, and not-exposed- to FTC) and two unenriched soils (exposed-, and not-exposed- to FTC), the content of all PTEs decreased more sharply in the CDH-enriched series than in the unenriched series. The largest redistribution into four sequentially extracted fractions in CDH-enriched soil was found for Zn. Based on the distribution pattern, Zn immobilization was greater in CDH-enriched soil in FTC. CDH increased species richness in the soil, while FTC stimulated the growth of Bacteroidia, Alphaproteobacteria, Theromomicrobia, and Gammaproteobacteria. Analysis of the functionalities of the microbiome indicated enhanced metal transportation and defense systems in samples exposed to FTC. The current research is crucial for understanding how extreme environmental conditions in the form of high contaminant levels and low temperatures affect the movement and transformation of PTEs in polluted soils during phytostabilization.},
}

@article {pmid39033820,
year = {2024},
author = {Zhang, H and Liang, S and Yin, K and Mo, Y and Li, Y and Lv, Y and Zhan, H and Zhang, Z and Shan, Z and Guo, Z and Yin, S and Yang, W},
title = {Urinary equol and equol-predicting microbial species are favorably associated with body fat measures among Chinese adults.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tjnut.2024.07.024},
pmid = {39033820},
issn = {1541-6100},
abstract = {BACKGROUND: Many studies have investigated the intake of dietary isoflavones in relation to obesity risk, while the association using objective biomarkers of isoflavones, particularly equol (a gut-derived metabolite of daidzein with greater bioavailability than other isoflavones) has been less studied. In addition, the associations between equol and gut microbiota profile at population level remain to be fully characterized.

OBJECTIVE: We aimed to identify equol-predicting microbial species and to investigate the associations of equol-predicting microbial species and urinary excretion of isoflavones including glycitein, genistein, daidzein, and equol with diverse obesity markers in free living-individuals.

METHODS: In this 1-year longitudinal study of 754 community-dwelling adults, urinary isoflavones, fecal microbiota, height, weight, and circumferences of waist and hip were measured at baseline and again after 1-year. Liver fat [indicated by controlled attenuation parameter (CAP)] and other body composition were also measured after 1-year. Linear models and linear mixed-effects models were used to analyze the associations for single measure and repeated measures, respectively.

RESULTS: Among 305 participants (median age: 50 y, IQR: 37-59 y) including 138 men and 167 women, higher urinary excretion of equol was associated with lower CAP (β = -0.013, P < 0.001) and body fat mass (β= -0.014, P = 0.046). No association was found between any other urinary isoflavones and obesity markers (all P>0.05). We identified 21 bacterial genera whose relative abundance were positively associated with urinary equol concentrations (all Pfalsediscovery rate < 0.05), and constructed an equol-predicting microbial score to reflect the overall equol-producing potential of host gut microbiota. This score was inversely associated with CAP (β = -0.040, P = 0.011).

CONCLUSIONS: High urinary equol concentrations and equol-predicting microbial species could be favorably associated with liver fat and other obesity markers.},
}

@article {pmid39033797,
year = {2024},
author = {Xia, L and Zhu, X and Wang, Y and Lu, S},
title = {The gut microbiota improves the efficacy of immune-checkpoint inhibitor immunotherapy against tumors: From association to cause and effect.},
journal = {Cancer letters},
volume = {598},
number = {},
pages = {217123},
doi = {10.1016/j.canlet.2024.217123},
pmid = {39033797},
issn = {1872-7980},
abstract = {Immune-checkpoint inhibitors (ICIs), including anti-PD-1/PD-L1 therapeutic antibodies, have markedly enhanced survival across numerous cancer types. However, the limited number of patients with durable benefits creates an urgent need to identify response biomarkers and to develop novel strategies so as to improve response. It is widely recognized that the gut microbiome is a key mediator in shaping immunity. Additionally, the gut microbiome shows significant potential in predicting the response to and enhancing the efficacy of ICI immunotherapy against cancer. Recent studies encompassing mechanistic analyses and clinical trials of microbiome-based therapy have shown a cause-and-effect relationship between the gut microbiome and the modulation of the ICI immunotherapeutic response, greatly contributing to the establishment of novel strategies that will improve response and overcome resistance to ICI treatment. In this review, we outline the current state of research advances and discuss the future directions of utilizing the gut microbiome to enhance the efficacy of ICI immunotherapy against tumors.},
}

@article {pmid39033501,
year = {2024},
author = {Kulshrestha, S and Narad, P and Singh, B and Pai, SS and Vijayaraghavan, P and Tandon, A and Gupta, P and Modi, D and Sengupta, A},
title = {Biomarker Identification for Preterm Birth Susceptibility: Vaginal Microbiome Meta-Analysis Using Systems Biology and Machine Learning Approaches.},
journal = {American journal of reproductive immunology (New York, N.Y. : 1989)},
volume = {92},
number = {1},
pages = {e13905},
doi = {10.1111/aji.13905},
pmid = {39033501},
issn = {1600-0897},
mesh = {Humans ; Female ; *Vagina/microbiology ; *Premature Birth/microbiology ; *Microbiota/genetics ; *Machine Learning ; Pregnancy ; *RNA, Ribosomal, 16S/genetics ; *Systems Biology ; Biomarkers ; Disease Susceptibility ; Infant, Newborn ; },
abstract = {PROBLEM: The vaginal microbiome has a substantial role in the occurrence of preterm birth (PTB), which contributes substantially to neonatal mortality worldwide. However, current bioinformatics approaches mostly concentrate on the taxonomic classification and functional profiling of the microbiome, limiting their abilities to elucidate the complex factors that contribute to PTB.

METHOD OF STUDY: A total of 3757 vaginal microbiome 16S rRNA samples were obtained from five publicly available datasets. The samples were divided into two categories based on pregnancy outcome: preterm birth (PTB) (N = 966) and term birth (N = 2791). Additionally, the samples were further categorized based on the participants' race and trimester. The 16S rRNA reads were subjected to taxonomic classification and functional profiling using the Parallel-META 3 software in Ubuntu environment. The obtained abundances were analyzed using an integrated systems biology and machine learning approach to determine the key microbes, pathways, and genes that contribute to PTB. The resulting features were further subjected to statistical analysis to identify the top nine features with the greatest effect sizes.

RESULTS: We identified nine significant features, namely Shuttleworthia, Megasphaera, Sneathia, proximal tubule bicarbonate reclamation pathway, systemic lupus erythematosus pathway, transcription machinery pathway, lepA gene, pepX gene, and rpoD gene. Their abundance variations were observed through the trimesters.

CONCLUSIONS: Vaginal infections caused by Shuttleworthia, Megasphaera, and Sneathia and altered small metabolite biosynthesis pathways such as lipopolysaccharide folate and retinal may increase the susceptibility to PTB. The identified organisms, genes, pathways, and their networks may be specifically targeted for the treatment of bacterial infections that increase PTB risk.},
}

Humans
Female
*Vagina/microbiology
*Premature Birth/microbiology
*Microbiota/genetics
*Machine Learning
Pregnancy
*RNA, Ribosomal, 16S/genetics
*Systems Biology
Biomarkers
Disease Susceptibility
Infant, Newborn

@article {pmid39033464,
year = {2024},
author = {Sanford, PA and Woolston, BM},
title = {Development of a Recombineering System for the Acetogen Eubacterium limosum with Cas9 Counterselection for Markerless Genome Engineering.},
journal = {ACS synthetic biology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acssynbio.4c00253},
pmid = {39033464},
issn = {2161-5063},
abstract = {Eubacterium limosum is a Clostridial acetogen that efficiently utilizes a wide range of single-carbon substrates and contributes to metabolism of health-associated compounds in the human gut microbiota. These traits have led to interest in developing it as a platform for sustainable CO2-based biofuel production to combat carbon emissions, and for exploring the importance of the microbiota in human health. However, synthetic biology and metabolic engineering in E. limosum have been hindered by the inability to rapidly make precise genomic modifications. Here, we screened a diverse library of recombinase proteins to develop a highly efficient oligonucleotide-based recombineering system based on the viral recombinase RecT. Following optimization, the system is capable of catalyzing ssDNA recombination at an efficiency of up to 2%. Addition of a Cas9 counterselection system eliminated unrecombined cells, with up to 100% of viable cells encoding the desired mutation, enabling creation of genomic point mutations in a scarless and markerless manner. We deployed this system to create a clean knockout of the extracellular polymeric substance (EPS) gene cluster, generating a strain incapable of biofilm formation. This approach is rapid and simple, not requiring laborious homology arm cloning, and can readily be retargeted to almost any genomic locus. This work overcomes a major bottleneck in E. limosum genetic engineering by enabling precise genomic modifications, and provides both a roadmap and associated recombinase plasmid library for developing similar systems in other Clostridia of interest.},
}

@article {pmid39033279,
year = {2024},
author = {Trinh, P and Teichman, S and Roberts, MC and Rabinowitz, PM and Willis, AD},
title = {A cross-sectional comparison of gut metagenomes between dairy workers and community controls.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {708},
doi = {10.1186/s12864-024-10562-1},
pmid = {39033279},
issn = {1471-2164},
support = {R35 GM133420/GM/NIGMS NIH HHS/United States ; R35 GM133420/GM/NIGMS NIH HHS/United States ; R35 GM133420/GM/NIGMS NIH HHS/United States ; T32 ES015459/ES/NIEHS NIH HHS/United States ; R21 AI168679/AI/NIAID NIH HHS/United States ; R21 AI168679/AI/NIAID NIH HHS/United States ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Cross-Sectional Studies ; *Metagenome ; Female ; Dairying ; Metagenomics/methods ; Adult ; Animals ; Middle Aged ; Bacteria/genetics/classification ; Farmers ; Male ; Drug Resistance, Bacterial/genetics ; },
abstract = {BACKGROUND: As a nexus of routine antibiotic use and zoonotic pathogen presence, the livestock farming environment is a potential hotspot for the emergence of zoonotic diseases and antibiotic resistant bacteria. Livestock can further facilitate disease transmission by serving as intermediary hosts for pathogens before a spillover event. In light of this, we aimed to characterize the microbiomes and resistomes of dairy workers, whose exposure to the livestock farming environment places them at risk for facilitating community transmission of antibiotic resistant genes and emerging zoonotic diseases.

RESULTS: Using shotgun sequencing, we investigated differences in the taxonomy, diversity and gene presence of 10 dairy farm workers and 6 community controls' gut metagenomes, contextualizing these samples with additional publicly available gut metagenomes. We found no significant differences in the prevalence of resistance genes, virulence factors, or taxonomic composition between the two groups. The lack of statistical significance may be attributed, in part, to the limited sample size of our study or the potential similarities in exposures between the dairy workers and community controls. We did, however, observe patterns warranting further investigation including greater abundance of tetracycline resistance genes and prevalence of cephamycin resistance genes as well as lower average gene diversity (even after accounting for differential sequencing depth) in dairy workers' metagenomes. We also found evidence of commensal organism association with tetracycline resistance genes in both groups (including Faecalibacterium prausnitzii, Ligilactobacillus animalis, and Simiaoa sunii).

CONCLUSIONS: This study highlights the utility of shotgun metagenomics in examining the microbiomes and resistomes of livestock workers, focusing on a cohort of dairy workers in the United States. While our study revealed no statistically significant differences between groups in taxonomy, diversity and gene presence, we observed patterns in antibiotic resistance gene abundance and prevalence that align with findings from previous studies of livestock workers in China and Europe. Our results lay the groundwork for future research involving larger cohorts of dairy and non-dairy workers to better understand the impact of occupational exposure to livestock farming on the microbiomes and resistomes of workers.},
}

Humans
*Gastrointestinal Microbiome/genetics
Cross-Sectional Studies
*Metagenome
Female
Dairying
Metagenomics/methods
Adult
Animals
Middle Aged
Bacteria/genetics/classification
Farmers
Male
Drug Resistance, Bacterial/genetics

@article {pmid39033201,
year = {2024},
author = {Fernández-Rodríguez, D and Cho, J and Chisari, E and Citardi, MJ and Parvizi, J},
title = {Nasal microbiome and the effect of nasal decolonization with a novel povidone-iodine antiseptic solution: a prospective and randomized clinical trial.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {16739},
pmid = {39033201},
issn = {2045-2322},
mesh = {Humans ; *Povidone-Iodine/pharmacology/administration & dosage ; *Anti-Infective Agents, Local/pharmacology/administration & dosage ; *Microbiota/drug effects ; Male ; Female ; Adult ; Prospective Studies ; Middle Aged ; Nose/microbiology ; Young Adult ; Bacteria/drug effects/classification/genetics ; Administration, Intranasal ; Corynebacterium/drug effects ; },
abstract = {The aim of this study was to assess the profile of nasal microbiome and evaluate the effect of a specific nasal decolonization solution on the microbiome. We conducted a randomized, placebo-controlled, and parallel-group clinical study of 50 volunteers aged 18 years and older. The subjects were randomly assigned to receive a nasal antiseptic solution, containing povidone-iodine as the main ingredient, (n = 25) or a control solution (n = 25). Nasal swabs were obtained before application (baseline) and at 3 timepoints after application (5 min, 2 h, 24 h). Nasal swabs were subjected to next generation sequencing analysis and cultured in agar plates. At baseline, there were substantial associations between anaerobic species, Corynebacterium spp., Staphylococcus spp., and Dolosigranulum spp. Then, a high bioburden reduction was observed after the application of povidone-iodine (log10 3.68 ± 0.69 at 5 min; log10 3.57 ± 0.94 at 2 h; log10 1.17 ± 1.40 at 24 h), compared to the control. The top species affected by the treatment were Cutibacterium acnes, Staphylococcus, and Corynebacterium species. None of the subjects experienced any adverse effects, nor increases in mucociliary clearance time. Antiseptic solutions applied to the anterior nares can transiently and markedly reduce the bioburden of the nose. The registration number for this clinical trial is NCT05617729.},
}

Humans
*Povidone-Iodine/pharmacology/administration & dosage
*Anti-Infective Agents, Local/pharmacology/administration & dosage
*Microbiota/drug effects
Male
Female
Adult
Prospective Studies
Middle Aged
Nose/microbiology
Young Adult
Bacteria/drug effects/classification/genetics
Administration, Intranasal
Corynebacterium/drug effects

@article {pmid39033197,
year = {2024},
author = {Visuthranukul, C and Sriswasdi, S and Tepaamorndech, S and Chamni, S and Leelahavanichkul, A and Joyjinda, Y and Aksornkitti, V and Chomtho, S},
title = {Enhancing gut microbiota and microbial function with inulin supplementation in children with obesity.},
journal = {International journal of obesity (2005)},
volume = {},
number = {},
pages = {},
pmid = {39033197},
issn = {1476-5497},
abstract = {BACKGROUND AND OBJECTIVES: Gut dysbiosis that resulted from the alteration between host-microbe interaction might worsen obesity-induced systemic inflammation. Gut microbiota manipulation by supplementation of prebiotic inulin may reverse metabolic abnormalities and improve obesity. This study aimed to determine whether inulin supplementation improved intestinal microbiota and microbial functional pathways in children with obesity.

METHODS: Children with obesity whose BMI above median + 2SDs were recruited to a randomized, double-blinded placebo-controlled study. The participants aged 7-15 years were assigned to inulin supplement extracted from Thai Jerusalem artichoke (intervention), maltodextrin (placebo), and dietary fiber advice groups. All participants received similar monthly conventional advice and follow-up for 6 months. Fecal samples were collected for gut microbiome analysis using 16S rRNA sequencing. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States was performed to infer microbial functional pathways.

RESULTS: One hundred and forty-three children with available taxonomic and functional pathway abundance profiles were evaluated. A significant increase in alpha-diversity was observed in the inulin group. Inulin supplementation substantially enhanced Bifidobacterium, Blautia, Megasphaera, and several butyrate-producing bacteria, including Agathobacter, Eubacterium coprostanoligenes, and Subdoligranulum, compared to the other groups. The inulin group showed a significant difference in functional pathways of proteasome and riboflavin metabolism. These changes correlated with clinical and metabolic outcomes exclusively in the inulin group.

CONCLUSIONS: Inulin supplementation significantly promoted gut bacterial diversity and improved gut microbiota dysbiosis in children with obesity. The modulation of functional pathways by inulin suggests its potential to establish beneficial interactions between the gut microbiota and host physiology. Inulin supplementation could be a strategic treatment to restore the balance of intestinal microbiota and regulate their functions in childhood obesity.},
}

@article {pmid39033123,
year = {2024},
author = {Mercado-Evans, V and Zulk, JJ and Hameed, ZA and Patras, KA},
title = {Gestational diabetes as a risk factor for GBS maternal rectovaginal colonization: a systematic review and meta-analysis.},
journal = {BMC pregnancy and childbirth},
volume = {24},
number = {1},
pages = {488},
pmid = {39033123},
issn = {1471-2393},
support = {AI167547//National Institute of Allergy and Infectious Diseases/ ; AI173448//National Institute of Allergy and Infectious Diseases/ ; DK136201/DK/NIDDK NIH HHS/United States ; DK128053/DK/NIDDK NIH HHS/United States ; GM136554/GM/NIGMS NIH HHS/United States ; NGP10103//Burroughs Wellcome Fund/ ; },
mesh = {Humans ; *Diabetes, Gestational/epidemiology ; Female ; Pregnancy ; Risk Factors ; *Streptococcal Infections/epidemiology ; *Streptococcus agalactiae ; *Vagina/microbiology ; *Pregnancy Complications, Infectious/epidemiology/microbiology ; *Rectum/microbiology ; },
abstract = {BACKGROUND: Maternal rectovaginal colonization by group B Streptococcus (GBS) increases the risk of perinatal GBS disease that can lead to death or long-term neurological impairment. Factors that increase the risk of rectovaginal GBS carriage are incompletely understood resulting in missed opportunities for detecting GBS in risk-based clinical approaches. There is a lacking consensus on whether gestational diabetes mellitus (GDM) is a risk factor for rectovaginal GBS. This systematic review and meta-analysis aims to address current conflicting findings and determine whether GDM should be clinically considered as a risk factor for maternal GBS colonization.

METHODS: Peer-reviewed studies that provided GDM prevalence and documented GBS vaginal and/or rectal colonization in women with and without GDM were included in this analysis. From study inception to October 30, 2023, we identified 6,275 relevant studies from EMBASE and PUBMED of which 19 were eligible for inclusion. Eligible studies were analyzed and thoroughly assessed for risk of bias with a modified Newcastle-Ottawa Scale that interrogated representativeness and comparability of cohorts, quality of reporting for GDM and GBS status, and potential bias from other metabolic diseases. Results were synthesized using STATA 18 and analyzed using random-effects meta-analyses.

RESULTS: Studies encompassed 266,706 women from 10 different countries, with study periods spanning from 1981 to 2020. Meta-analysis revealed that gestational diabetes is associated with a 16% increased risk of rectovaginal GBS carriage (OR 1.16, CI 1.07-1.26, P = 0.003). We also performed subgroup analyses to assess independent effects of pregestational vs. gestational diabetes on risk of maternal GBS carriage. Pregestational diabetes (Type 1 or Type 2 diabetes mellitus) was also associated with an increased risk of 76% (pooled OR 1.76, CI 1.27-2.45, P = 0.0008).

CONCLUSIONS: This study achieved a consensus among previously discrepant observations and demonstrated that gestational diabetes and pregestational diabetes are significant risk factors for maternal rectovaginal carriage of GBS. Recognition of GDM as a risk factor during clinical decisions about GBS screening and intrapartum antibiotic prophylaxis may decrease the global burden of GBS on maternal-perinatal health.},
}

Humans
*Diabetes, Gestational/epidemiology
Female
Pregnancy
Risk Factors
*Streptococcal Infections/epidemiology
*Streptococcus agalactiae
*Vagina/microbiology
*Pregnancy Complications, Infectious/epidemiology/microbiology
*Rectum/microbiology

@article {pmid39032735,
year = {2024},
author = {Yuan, Y and Yang, L and Wan, X and Zhao, Y and Gong, Y and Xing, W and Xue, T and Tao, J},
title = {Microplastics in heavy metal-contaminated soil drives bacterial community and metabolic changes.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {174770},
doi = {10.1016/j.scitotenv.2024.174770},
pmid = {39032735},
issn = {1879-1026},
abstract = {Microplastic (MP) and heavy metal pollution in soil are global issues. When MPs invade the soil, they combine with heavy metals and adversely affect soil organisms. Six common MPs-polyethylene, polypropylene, polystyrene, polyvinyl chloride, polyethylene terephthalate, and polytetrafluoroethylene-were selected for this study to examine the effects of various concentrations and MP types on the physicochemical properties, bacterial community, and soil metabolism of heavy metal-contaminated soil. MP enhanced predation and competition among heavy metal-contaminated soil bacteria. Heavy metal-MPs alter metabolites in lipid metabolism, other pathways, and the bacterial community. MP treatment promotes energy production and oxidative stress of soil bacteria to resist the toxicity of heavy metals and degrade MP pollution. In conclusion, MP treatment changed the metabolism of the microbiome in heavy metal-contaminated soil and increased the abundance of Proteobacteria that responded to MPs and heavy metal pollution by 11.54 % on average. This study explored bacteria for the ecological regeneration and provided ideas for MPs and heavy metal-contaminated soil remediation.},
}

@article {pmid39032655,
year = {2024},
author = {Kandel, SE and Tooker, BC and Lampe, JN},
title = {Drug metabolism of ciprofloxacin, ivacaftor, and raloxifene by Pseudomonas aeruginosa cytochrome P450 CYP107S1.},
journal = {The Journal of biological chemistry},
volume = {},
number = {},
pages = {107594},
doi = {10.1016/j.jbc.2024.107594},
pmid = {39032655},
issn = {1083-351X},
abstract = {Drug metabolism is one of the main processes governing the pharmacokinetics and toxicity of drugs via their chemical biotransformation and elimination. In humans, the liver, enriched with cytochrome P450 (CYP) enzymes, plays a major metabolic and detoxification role. The gut microbiome and its complex community of microorganisms can also contribute to some extent to drug metabolism. However, during an infection when pathogenic microorganisms invade the host, our knowledge of the impact on drug metabolism by this pathobiome remains limited. The intrinsic resistance mechanisms and rapid metabolic adaptation to new environments often allow the human bacterial pathogens to persist, despite the many antibiotic therapies available. Here, we demonstrate that a bacterial CYP enzyme, CYP107S1, from Pseudomonas aeruginosa, a predominant bacterial pathogen in cystic fibrosis (CF) patients, can metabolize multiple drugs from different classes. CYP107S1 demonstrated high substrate promiscuity and allosteric properties much like human hepatic CYP3A4. Our findings demonstrated binding and metabolism by the recombinant CYP107S1 of fluoroquinolone antibiotics (ciprofloxacin and fleroxacin), a CF transmembrane conductance regulator potentiator (ivacaftor), and a SERM antimicrobial adjuvant (raloxifene). Our in vitro metabolism data were further corroborated by molecular docking of each drug to the heme active site using a CYP107S1 homology model. Our findings raise the potential for microbial pathogens modulating drug concentrations locally at the site of infection, if not systemically, via CYP-mediated biotransformation reactions. To our knowledge, this is the first report of a CYP enzyme from a known bacterial pathogen that is capable of metabolizing clinically utilized drugs.},
}

@article {pmid39032544,
year = {2024},
author = {Ioannou, M and Borkent, J and Andreu-Sánchez, S and Wu, J and Fu, J and Sommer, IEC and Haarman, BCM},
title = {Reproducible gut microbial signatures in bipolar and schizophrenia spectrum disorders: A metagenome-wide study.},
journal = {Brain, behavior, and immunity},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.bbi.2024.07.009},
pmid = {39032544},
issn = {1090-2139},
abstract = {BACKGROUND: Numerous studies report gut microbiome variations in bipolar disorder (BD) and schizophrenia spectrum disorders (SSD) compared to healthy individuals, though, there is limited consensus on which specific bacteria are associated with these disorders.

METHODS: In this study, we performed a comprehensive metagenomic shotgun sequencing analysis in 103 Dutch patients with BD/SSD and 128 healthy controls matched for age, sex, body mass index and income, while accounting for diet quality, transit time and technical confounders. To assess the replicability of the findings, we used two validation cohorts (total n = 203), including participants from a distinct population with a different metagenomic isolation protocol.

RESULTS: The gut microbiome of the patients had a significantly different β-diversity, but not α-diversity nor neuroactive potential compared to healthy controls. Initially, twenty-six bacterial taxa were identified as differentially abundant in patients. Among these, the previously reported genera Lachnoclostridium and Eggerthella were replicated in the validation cohorts. Employing the CoDaCoRe learning algorithm, we identified two bacterial balances specific to BD/SSD, which demonstrated an area under the receiver operating characteristic curve (AUC) of 0.77 in the test dataset. These balances were replicated in the validation cohorts and showed a positive correlation with the severity of psychiatric symptoms and antipsychotic use. Last, we showed a positive association between the relative abundance of Klebsiella and Klebsiella pneumoniae with antipsychotic use and between the Anaeromassilibacillus and lithium use.

CONCLUSIONS: Our findings suggest that microbial balances could be a reproducible method for identifying BD/SSD-specific microbial signatures, with potential diagnostic and prognostic applications. Notably, Lachnoclostridium and Eggerthella emerge as frequently occurring bacteria in BD/SSD. Last, our study reaffirms the previously established link between Klebsiella and antipsychotic medication use and identifies a novel association between Anaeromassilibacillus and lithium use.},
}

@article {pmid39032424,
year = {2024},
author = {Goldstein Ascer, L and Nascimento-Silva, G and Hardoim, CCP and Custódio, MR},
title = {Effects of plasticizer Di(2-ethylhexyl) phthalate (DEHP) on the microbiome of the marine sponge Hymeniacidon heliophila.},
journal = {Aquatic toxicology (Amsterdam, Netherlands)},
volume = {273},
number = {},
pages = {107025},
doi = {10.1016/j.aquatox.2024.107025},
pmid = {39032424},
issn = {1879-1514},
abstract = {Marine pollution research in the last 15 years focused on an emerging anthropogenic contaminant: plastic debris and more specifically, microplastics. Since, not only its physical impacts on marine invertebrates were studied, but also its additives. Phthalate, a plasticizer commonly found in the ocean and known endocrine disruptor was already observed in different aquatic invertebrates, but few is known about its presence and possible effects in Porifera physiology. Our study aimed to analyze potential shifts in Hymeniacidon heliophila (Desmosponge) microbiome after exposure to Di(2-ethylhexyl) phthalate (DEHP), the most common phthalate found in the ocean, in three different doses for 4 and 24 h. Results indicate that alpha diversity had significantly changed between control and exposed organisms but not in all multicomparisons. Microbial community structure changed after exposure as well although most abundant phyla did not vary along the experiment. The core microbiome between control and each exposed organisms contained the vast majority of total ASVs and a few ASVs were exclusive to each experimental group. After DEHP exposure, microbial classes had significant changes and species with phthalate degradation enzymes were identified in a specifically dose dependent manner pointing to a possible bacterial consortium responsible for the phthalate degradation. The bacterial detoxification activity may lead to H. heliophila resistance during DEHP exposure in polluted environmental conditions.},
}

@article {pmid39032335,
year = {2024},
author = {Fan, Y and Zhou, Z and Liu, F and Qian, L and Yu, X and Huang, F and Hu, R and Su, H and Gu, H and Yan, Q and He, Z and Wang, C},
title = {The vertical partitioning between denitrification and dissimilatory nitrate reduction to ammonium of coastal mangrove sediment microbiomes.},
journal = {Water research},
volume = {262},
number = {},
pages = {122113},
doi = {10.1016/j.watres.2024.122113},
pmid = {39032335},
issn = {1879-2448},
abstract = {Mangrove aquatic ecosystems receive substantial nitrogen (N) inputs from both land and sea, playing critical roles in modulating coastal N fluxes. The microbially-mediated competition between denitrification and dissimilatory nitrate reduction to ammonium (DNRA) in mangrove sediments significantly impacts the N fate and transformation processes. Despite their recognized role in N loss or retention in surface sediments, how these two processes vary with sediment depths and their influential factors remain elusive. Here, we employed a comprehensive approach combining [15]N isotope tracer, quantitative PCR (qPCR) and metagenomics to verify the vertical dynamics of denitrification and DNRA across five 100-cm mangrove sediment cores. Our results revealed a clear vertical partitioning, with denitrification dominated in 0-30 cm sediments, while DNRA played a greater role with increasing depths. Quantification of denitrification and DNRA functional genes further explained this phenomenon. Taxonomic analysis identified Pseudomonadota as the primary denitrification group, while Planctomycetota and Pseudomonadota exhibited high proportion in DNRA group. Furthermore, genome-resolved metagenomics revealed multiple salt-tolerance strategies and aromatic compound utilization potential in denitrification assemblages. This allowed denitrification to dominate in oxygen-fluctuating and higher-salinity surface sediments. However, the elevated C/N in anaerobic deep sediments favored DNRA, tending to generate biologically available NH4[+]. Together, our results uncover the depth-related variations in the microbially-mediated competition between denitrification and DNRA, regulating N dynamics in mangrove ecosystems.},
}

@article {pmid39032183,
year = {2024},
author = {Lin, L and Huang, Y and Jia, W and Zhou, S and Gan, C and Wu, WM and Xu, M},
title = {Microbiomes on microplastics versus natural microcarriers: Stability and transformation during aquatic travel from aquaculture ponds to adjacent stream.},
journal = {Journal of hazardous materials},
volume = {477},
number = {},
pages = {135241},
doi = {10.1016/j.jhazmat.2024.135241},
pmid = {39032183},
issn = {1873-3336},
abstract = {Microplastics (MPs) with different physical-chemical properties are considered as vectors for the propagation of microbes in aquatic environments. It remains unclear how plastic types impact on the plastisphere and whether different MPs spread microbes more rapidly than natural materials in microbes across distinct water bodies as proposed previously. We used in-situ incubation to investigate the microbes attached on MPs of polyethylene (PE), polypropylene (PP), and polyvinyl chloride (PVC), versus that on two natural microcarriers (quartz sands and bamboo) during the travel from aquaculture ponds with impacted by fish farming to adjacent freshwater stream. The results showed that the microbial communities on the carriers were shaped not only by environmental conditions, which were primary determinants but also by carrier types. All the tested plastics did not carry more microbes than the natural carriers during the journey. The biofilm community composition on PVC is distinct from that on PE and PP MPs and natural carriers. The plastisphere of PE and PP kept microbial proportions as natural materials did but PVC retained less than nature materials. Bamboo carried more potential pathogens than plastic polymers and quartz. The results indicated that the communities of plastisphere is polymer-type dependent, and, compared with the natural materials, MPs did not show enhanced propagation of microbes, including pathogens, cross distinct environments.},
}

@article {pmid39031958,
year = {2024},
author = {Kwinten, KJJ and Lemain, VA and de Hullu, JA and Leenders, WPJ and Steenbeek, MP and van Altena, AM and Pijnenborg, JMA},
title = {Cervicovaginal specimen biomarkers for early detection of ovarian and endometrial cancer: A review.},
journal = {Cancer medicine},
volume = {13},
number = {14},
pages = {e70000},
pmid = {39031958},
issn = {2045-7634},
mesh = {Humans ; Female ; *Endometrial Neoplasms/diagnosis/genetics/metabolism ; *DNA Methylation ; *Early Detection of Cancer/methods ; *Ovarian Neoplasms/diagnosis/genetics ; *Biomarkers, Tumor/genetics ; Vagina/metabolism/microbiology ; Cervix Uteri/metabolism/pathology ; Proteomics/methods ; },
abstract = {BACKGROUND: In the last decade, technical innovations have resulted in the development of several minimally invasive diagnostic cancer tools. Within women at high risk of developing ovarian or endometrial cancer (EC) due to hereditary cancer syndrome, there is an urgent need for minimally invasive and patient-friendly methods to detect ovarian cancer and EC at an early stage.

MATERIALS AND METHODS: We performed a systematic search of studies using DNA methylation or mutation analysis, microbiome, or proteomics performed on cervicovaginal specimens (smear, swab, or tampon) intended to detect ovarian and EC published until January 2024.

RESULTS: Included studies (n = 36) showed high heterogeneity in terms of biomarkers used and outcomes, and only a few studies reported on the detection of biomarkers in high-risk subgroups.

CONCLUSION: Based on the findings in this review, DNA methylation techniques seem to be the most promising for detecting ovarian and EC at early stages in the general population. Future validation of cervicovaginal DNA methylation techniques is needed to determine whether this technique might be beneficial in hereditary high-risk subgroups.},
}

Humans
Female
*Endometrial Neoplasms/diagnosis/genetics/metabolism
*DNA Methylation
*Early Detection of Cancer/methods
*Ovarian Neoplasms/diagnosis/genetics
*Biomarkers, Tumor/genetics
Vagina/metabolism/microbiology
Cervix Uteri/metabolism/pathology
Proteomics/methods

@article {pmid39031813,
year = {2024},
author = {de Celis, M and Fernández-Alonso, MJ and Belda, I and García, C and Ochoa-Hueso, R and Palomino, J and Singh, BK and Yin, Y and Wang, JT and Abdala-Roberts, L and Alfaro, FD and Angulo-Pérez, D and Arthikala, MK and Corwin, J and Gui-Lan, D and Hernandez-Lopez, A and Nanjareddy, K and Pasari, B and Quijano-Medina, T and Rivera, DS and Shaaf, S and Trivedi, P and Yang, Q and Zaady, E and Zhu, YG and Delgado-Baquerizo, M and Milla, R and García-Palacios, P},
title = {The abundant fraction of soil microbiomes regulates the rhizosphere function in crop wild progenitors.},
journal = {Ecology letters},
volume = {27},
number = {6},
pages = {e14462},
doi = {10.1111/ele.14462},
pmid = {39031813},
issn = {1461-0248},
support = {//Ministerio de Universidades/ ; PID2021-122296NB-100//Ministerio de Ciencia e Innovación/ ; PID2020-113021RA-I00//Ministerio de Ciencia e Innovación/ ; //Fundación BBVA/ ; },
mesh = {*Rhizosphere ; *Soil Microbiology ; *Microbiota ; *Crops, Agricultural/microbiology ; Soil/chemistry ; Fungi/physiology ; Animals ; Bacteria/classification/isolation & purification ; Invertebrates/microbiology/physiology ; },
abstract = {The rhizosphere influence on the soil microbiome and function of crop wild progenitors (CWPs) remains virtually unknown, despite its relevance to develop microbiome-oriented tools in sustainable agriculture. Here, we quantified the rhizosphere influence-a comparison between rhizosphere and bulk soil samples-on bacterial, fungal, protists and invertebrate communities and on soil multifunctionality across nine CWPs at their sites of origin. Overall, rhizosphere influence was higher for abundant taxa across the four microbial groups and had a positive influence on rhizosphere soil organic C and nutrient contents compared to bulk soils. The rhizosphere influence on abundant soil microbiomes was more important for soil multifunctionality than rare taxa and environmental conditions. Our results are a starting point towards the use of CWPs for rhizosphere engineering in modern crops.},
}

*Rhizosphere
*Soil Microbiology
*Microbiota
*Crops, Agricultural/microbiology
Soil/chemistry
Fungi/physiology
Animals
Bacteria/classification/isolation & purification
Invertebrates/microbiology/physiology

@article {pmid39031531,
year = {2024},
author = {Lee, SY and Roh, E and Kim, SG and Kong, HG},
title = {Competition for nutrient niches within the apple blossom microbiota antagonizes the initiation of fire blight infection.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.19971},
pmid = {39031531},
issn = {1469-8137},
support = {//National Academy of Agricultural Sciences/ ; //Cooperative Research Program for Agriculture Science and Technology Development, Rural Development Administration, Republic of Korea/ ; },
abstract = {Changes in the plant microbiota composition are intimately associated with the health of the plant, but factors controlling the microbial community in flowers are poorly understood. In this study, we used apple flowers and fire blight as a model system to investigate the effects of floral microbiota and microbial competition on disease development and suppression. To compare changes in microbial flora with the RNA expression patterns of plants, the flower samples were collected in three different flowering stages (Bud, Popcorn, and Full-bloom). Using advanced sequencing technology, we analyzed the data and conducted both in vitro and in vivo experiments to validate our findings. Our results show that the Erwinia amylovora use arabinogalactan, which is secreted on the flowers, for early colonization of apple flowers. Pantoea agglomerans was more competitive for arabinogalactan than E. amylovora. Additionally, P. agglomerans suppressed the expression of virulence factors of E. amylovora by using arabinose, which is a major component of arabinogalactan, which induces virulence gene expression. The present data provide new insights into developing control strategies for diverse plant diseases, including fire blight, by highlighting the importance of nutrients in disease development or suppression.},
}

@article {pmid39031274,
year = {2024},
author = {Chong, AC and Navarro-Triviño, FJ and Su, M and Park, CO},
title = {Fungal Head and Neck Dermatitis: Current Understanding and Management.},
journal = {Clinical reviews in allergy & immunology},
volume = {},
number = {},
pages = {},
pmid = {39031274},
issn = {1559-0267},
abstract = {Head and neck dermatitis (HND) is a form of atopic dermatitis (AD) that affects the seborrheic areas of the body and causes greater quality of life detriments than other types of AD. HND can be challenging to treat since first-line topical therapies may be ineffective or intolerable for long-term use on areas affected by HND while dupilumab may cause dupilumab-associated HND (DAHND). Current evidence implicates fungi, particularly Malassezia spp., in the pathogenesis of HND. Penetration of fungal antigens through the defective AD skin barrier activates the innate and adaptive immune systems to cause cutaneous inflammation via the T helper (Th)17 and/or Th2 axes. Malassezia sensitization may distinguish HND from other forms of AD. Multiple double-blind, placebo-controlled trials have shown antifungals to benefit HND, yet the persistence of symptom relief with sustained use remains unclear. Oral antifungals appear more effective than topical antifungals but may be harmful with long-term use. DAHND may also be fungal-mediated given improvement with antifungals and evidence of an overactive immune response against Malassezia in these patients. Janus kinase inhibitors are effective for HND, including DAHND, but may cause significant side effects when administered systemically. OX40/OX40L inhibitors and tralokinumab may be promising options for HND on the horizon. Demographic and environmental factors influence the host mycobiome and should be considered in future precision-medicine approaches as microbiome composition and diversity are linked to severity of HND.},
}

@article {pmid39030978,
year = {2024},
author = {Dong, Y and Dong, J and Xiao, H and Li, Y and Wang, B and Zhang, S and Cui, M},
title = {A gut microbial metabolite cocktail fights against obesity through modulating the gut microbiota and hepatic leptin signaling.},
journal = {Journal of the science of food and agriculture},
volume = {},
number = {},
pages = {},
doi = {10.1002/jsfa.13758},
pmid = {39030978},
issn = {1097-0010},
abstract = {BACKGROUND: Excessive body weight and obesity elevate the risk of chronic non-communicable diseases. The judicious application of the gut microbiome, encompassing both microorganisms and their derived compounds, holds considerable promise in the treatment of obesity.

RESULTS: In this study, we showed that a cocktail of gut microbiota-derived metabolites, comprising indole 3-propionic acid (IPA), sodium butyrate (SB) and valeric acid (VA), alleviated various symptoms of obesity in both male and female mice subjected to a high-fat diet (HFD). The 16S ribosomal RNA (rRNA) sequencing revealed that administering the cocktail via oral gavage retained the gut microbiota composition in obese mice. Fecal microbiota transplantation using cocktail-treated mice as donors mitigated the obesity phenotype of HFD-fed mice. Transcriptomic sequencing analysis showed that the cocktail preserved the gene expression profile of hepatic tissues in obese mice, especially up-regulated the expression level of leptin receptor. Gene delivery via in vivo fluid dynamics further validated that the anti-obesity efficacy of the cocktail was dependent on leptin signaling at least partly. The cocktail also inhibited the expression of appetite stimulators in hypothalamus. Together, the metabolite cocktail combated adiposity by retaining the gut microbiota configuration and activating the hepatic leptin signaling pathway.

CONCLUSIONS: Our findings provide a sophisticated regulatory network between the gut microbiome and host, and highlight a cocktail of gut microbiota-derived metabolites, including IPA, SB, and VA, might be a prospective intervention for anti-obesity in a preclinical setting. © 2024 Society of Chemical Industry.},
}

@article {pmid39030898,
year = {2024},
author = {Stevens, C and Norris, S and Arbeeva, L and Carter, S and Enomoto, M and Nelson, AE and Lascelles, BDX},
title = {Gut microbiome and osteoarthritis: insights from the naturally occurring canine model of OA.},
journal = {Arthritis & rheumatology (Hoboken, N.J.)},
volume = {},
number = {},
pages = {},
doi = {10.1002/art.42956},
pmid = {39030898},
issn = {2326-5205},
abstract = {OBJECTIVES: The purpose was to enhance the current knowledge of the relationship between the gut microbiome and osteoarthritis (OA) and associated pain using pet dogs as a clinically relevant translational model.

METHODS: Fecal samples were collected from 93 owned pet dogs. Dogs were designated either clinically healthy or OA-pain using validated methods. Metagenomic profiling was performed through shotgun sequencing using the Illumina Novaseq platform. MetaPhlAn2 and HUMAnN2 were used to evaluate bacterial taxonomic and pathway relative abundance. Comparisons between healthy and OA-pain groups were performed individually for each taxa using non-parametric tests following Benjamini and Hochberg adjustment for multiple comparisons. Permutation analysis of variance was performed using Bray-Curtis distance matrices. All downstream analyses were completed in R.

RESULTS: No significant differences between healthy and OA-pain dogs were observed for alpha and beta-diversity. We found 13 taxa with nominally significant (p<0.05) associations with OA case status, but none of the associations remained significant after adjustment for multiple comparisons. No differences in alpha, beta diversities or Firmicutes/Bacteroidetes ratio (FBR) were found regarding pain severity, mobility/ activity level, age, or body composition score.

CONCLUSIONS: Similar to recent studies in humans, the present study did not demonstrate a significant difference in the fecal microbial communities between dogs with OA pain and healthy control dogs. Future research in this naturally occurring model should expand on these data and relate the gut microbiome to gut permeability and circulating pro- and anti-inflammatory molecules to better understand the influence of the gut microbiome on OA and OA-pain.},
}

@article {pmid39030691,
year = {2024},
author = {Gan, D and Lin, Z and Zeng, L and Deng, H and Walsh, TR and Zhou, S and Yang, QE},
title = {Housefly gut microbiomes as a reservoir and facilitator for the spread of antibiotic resistance.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae128},
pmid = {39030691},
issn = {1751-7370},
abstract = {Arthropods, such as houseflies, play a significant role on the dissemination of antimicrobial resistance (AMR); however, their impact has often been overlooked in comparison to other AMR vectors. Understanding the contribution of arthropods to the spread of AMR is critical for implementing robust policies to mitigate the spread of AMR across "One Health" sectors. Herein, we investigated the in-situ transfer of a gfp-labelled AMR plasmid (IncA/C carrying a mcr-8 gene, pA/C_MCR-8) in the gut microbiota of housefly (Musca domestica) by applying single-cell sorting, 16S rRNA gene amplicon sequencing, and whole genome sequencing. Our findings demonstrate that the pA/C_MCR-8 positive E. coli donor strain is capable of colonizing the gut microbiome of houseflies and persists in the housefly intestine for five days, however, no transfer was detectable above the detection threshold of 10-5 per cell. The conjugative plasmid, pA/C_MCR-8 demonstrated a high transfer frequency ranging from 4.1 × 10-3 to 5.0 × 10-3 per cell in vitro, and exhibited transfer across various bacterial phyla, primarily encompassing Pseudomonadota and Bacillota. Phylogenic analysis has revealed that Providencia stuartii, a human opportunistic pathogen, was a notable recipient of pA/C_MCR-8. The conjugation assays further revealed that newly formed P. stuartii transconjugants readily transfer pA/C_MCR-8 to other clinically relevant pathogens (e.g. Klebsiella pneumoniae). Our findings indicate the potential transfer of AMR plasmids from houseflies to human opportunistic pathogens and further advocates the adoption of a One Health approach in developing infection control policies that address AMR across clinical settings.},
}

@article {pmid39030654,
year = {2024},
author = {Drake, MJ and Daniel, SG and Baker, LD and Indugu, N and Bittinger, K and Dickens, C and Zackular, JP and Pitta, D and Redding, LE},
title = {Effects of dietary zinc on the gut microbiome and resistome of the gestating cow and neonatal calf.},
journal = {Animal microbiome},
volume = {6},
number = {1},
pages = {39},
pmid = {39030654},
issn = {2524-4671},
support = {R35GM138369//National Institutes of General Medical Sciences, National Institutes of Health/ ; 5K23AI163351/NH/NIH HHS/United States ; },
abstract = {Zinc is an essential trace element required in the diet of all species. While the effects of zinc have been studied in growing calves, little is known about the effect of zinc on the microbiota of the gestating cow or her neonatal calf. Understanding factors that shape the gut health of neonatal animals and evaluating the effect of dietary supplements in adult gestating animals is important in promoting animal health and informing feeding practices. The aims of this study were to determine the effect of dietary zinc on the microbiota and resistome of the gestating cow and calf. Gestating cows received standard (40 ppm) or high (205 ppm) dietary zinc levels from dry off to calving. Fecal samples were collected from cows upon enrollment and at calving and from neonatal calves. Fecal samples underwent 16S rRNA sequencing and a subset also underwent shotgun metagenomic sequencing. The effect of zinc supplementation on the diversity and composition of the cow and calf microbiome and resistome was assessed. Alpha and beta diversity and composition of the microbiota were significantly altered over time but not by treatment in the cows, with alpha diversity decreasing and 14 genera found at significantly higher relative abundances at calving compared to enrollment. Levels of 27 antimicrobial resistance genes significantly increased over time. Only a small number of taxa were differentially expressed at calving in treatment and control groups, including Faecalibacterium, Bacteroides, Turicibacter, and Bifidobacterium pseudolongum. No effect of the dam's treatment group was observed on the diversity or composition of the neonatal calf microbiota. The calf resistome, which was relatively rich and diverse compared to the cow, was also unaffected by the dam's treatment group. The impact of high levels of dietary zinc thus appeared to be minimal, with no observed changes in alpha or beta diversity, and few changes in the relative abundance of a small number of taxa and antimicrobial resistance genes.},
}

@article {pmid39030648,
year = {2024},
author = {Moretti, LG and Crusciol, CAC and Leite, MFA and Momesso, L and Bossolani, JW and Costa, OYA and Hungria, M and Kuramae, EE},
title = {Diverse bacterial consortia: key drivers of rhizosoil fertility modulating microbiome functions, plant physiology, nutrition, and soybean grain yield.},
journal = {Environmental microbiome},
volume = {19},
number = {1},
pages = {50},
pmid = {39030648},
issn = {2524-6372},
support = {2016/23699-8; 2018/14892-4//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 151120/2020-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; },
abstract = {Soybean cultivation in tropical regions relies on symbioses with nitrogen-fixing Bradyrhizobium and plant growth-promoting bacteria (PGPBs), reducing environmental impacts of N fertilizers and pesticides. We evaluate the effects of soybean inoculation with different bacterial consortia combined with PGPBs or microbial secondary metabolites (MSMs) on rhizosoil chemistry, plant physiology, plant nutrition, grain yield, and rhizosphere microbial functions under field conditions over three growing seasons with four treatments: standard inoculation of Bradyrhizobium japonicum and Bradyrhizobium diazoefficiens consortium (SI); SI plus foliar spraying with Bacillus subtilis (SI + Bs); SI plus foliar spraying with Azospirillum brasilense (SI + Az); and SI plus seed application of MSMs enriched in lipo-chitooligosaccharides extracted from B. diazoefficiens and Rhizobium tropici (SI + MSM). Rhizosphere microbial composition, diversity, and function was assessed by metagenomics. The relationships between rhizosoil chemistry, plant nutrition, grain yield, and the abundance of microbial taxa and functions were determined by generalized joint attribute modeling. The bacterial consortia had the most significant impact on rhizosphere soil fertility, which in turn affected the bacterial community, plant physiology, nutrient availability, and production. Cluster analysis identified microbial groups and functions correlated with shifts in rhizosoil chemistry and plant nutrition. Bacterial consortia positively modulated specific genera and functional pathways involved in biosynthesis of plant secondary metabolites, amino acids, lipopolysaccharides, photosynthesis, bacterial secretion systems, and sulfur metabolism. The effects of the bacterial consortia on the soybean holobiont, particularly the rhizomicrobiome and rhizosoil fertility, highlight the importance of selecting appropriate consortia for desired outcomes. These findings have implications for microbial-based agricultural practices that enhance crop productivity, quality, and sustainability.},
}

@article {pmid39030619,
year = {2024},
author = {Wu, Z and Xiao, C and Wang, J and Zhou, M and You, F and Li, X},
title = {17β-estradiol in colorectal cancer: friend or foe?.},
journal = {Cell communication and signaling : CCS},
volume = {22},
number = {1},
pages = {367},
pmid = {39030619},
issn = {1478-811X},
support = {82205072//National Natural Science Foundation of China/ ; 2023NSFSC1830//Natural Science Foundation project of Sichuan Science and Technology Department/ ; 2023NSFSC1830//Natural Science Foundation project of Sichuan Science and Technology Department/ ; },
mesh = {Humans ; *Colorectal Neoplasms/metabolism/pathology/genetics ; *Estradiol/metabolism ; Animals ; Estrogen Receptor beta/metabolism/genetics ; Tumor Microenvironment ; Signal Transduction ; },
abstract = {Colorectal cancer (CRC) is a common gastrointestinal malignancy with higher incidence and mortality rates in men compared to women, potentially due to the effects of estrogen signaling. There is substantial evidence supporting the significant role of 17β-Estradiol (E2) in reducing CRC risk in females, although this perspective remains debated. E2 has been demonstrated to inhibit CRC cell proliferation and migration at the cellular level by enhancing DNA mismatch repair, modulating key gene expression, triggering cell cycle arrest, and reducing activity of migration factors. Furthermore, E2 contributes to promote a tumor microenvironment unfavorable for CRC growth by stimulating ERβ expression, reducing inflammatory responses, reversing immunosuppression, and altering the gut microbiome composition. Conversely, under conditions of high oxidative stress, hypoxia, and nutritional deficiencies, E2 may facilitate CRC development through GPER-mediated non-genomic signaling. E2's influence on CRC involves the genomic and non-genomic signals mediated by ERβ and GPER, respectively, leading to its dual roles in anticancer activity and carcinogenesis. This review aims to summarize the potential mechanisms by which E2 directly or indirectly impacts CRC development, providing insights into the phenomenon of sexual dimorphism in CRC and suggesting potential strategies for prevention and treatment.},
}

Humans
*Colorectal Neoplasms/metabolism/pathology/genetics
*Estradiol/metabolism
Animals
Estrogen Receptor beta/metabolism/genetics
Tumor Microenvironment
Signal Transduction

@article {pmid39030599,
year = {2024},
author = {Xu, SY and Feng, XR and Zhao, W and Bi, YL and Diao, QY and Tu, Y},
title = {Rumen and hindgut microbiome regulate average daily gain of preweaning Holstein heifer calves in different ways.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {131},
pmid = {39030599},
issn = {2049-2618},
mesh = {Animals ; Cattle ; *Rumen/microbiology/metabolism ; *Gastrointestinal Microbiome ; *Weaning ; Bacteria/classification/isolation & purification/metabolism/genetics ; Female ; Fermentation ; Metagenomics/methods ; Metabolomics ; Fatty Acids, Volatile/metabolism/analysis ; Weight Gain ; Butyrates/metabolism ; },
abstract = {BACKGROUND: The average daily gain (ADG) of preweaning calves significantly influences their adult productivity and reproductive performance. Gastrointestinal microbes are known to exert an impact on host phenotypes, including ADG. The aim of this study was to investigate the mechanisms by which gastrointestinal microbiome regulate ADG in preweaning calves and to further validate them by isolating ADG-associated rumen microbes in vitro.

RESULTS: Sixteen Holstein heifer calves were selected from a cohort with 106 calves and divided into higher ADG (HADG; n = 8) and lower ADG (LADG; n = 8) groups. On the day of weaning, samples of rumen contents, hindgut contents, and plasma were collected for rumen metagenomics, rumen metabolomics, hindgut metagenomics, hindgut metabolomics, and plasma metabolomics analyses. Subsequently, rumen contents of preweaning Holstein heifer calves from the same dairy farm were collected to isolate ADG-associated rumen microbes. The results showed that the rumen microbes, including Pyramidobacter sp. C12-8, Pyramidobacter sp. CG50-2, Pyramidobacter porci, unclassified_g_Pyramidobacter, Pyramidobacter piscolens, and Acidaminococcus fermentans, were enriched in the rumen of HADG calves (LDA > 2, P < 0.05). Enrichment of these microbes in HADG calves' rumen promoted carbohydrate degradation and volatile fatty acid production, increasing proportion of butyrate in the rumen and ultimately contributing to higher preweaning ADG in calves (P < 0.05). The presence of active carbohydrate degradation in the rumen was further suggested by the negative correlation of the rumen microbes P. piscolens, P. sp. C12-8 and unclassified_g_Pyramidobacter with the rumen metabolites D-fructose (R <  - 0.50, P < 0.05). Widespread positive correlations were observed between rumen microbes (such as P. piscolens, P. porci, and A. fermentans) and beneficial plasma metabolites (such as 1-pyrroline-5-carboxylic acid and 4-fluoro-L-phenylalanine), which were subsequently positively associated with the growth rate of HADG calves (R > 0.50, P < 0.05). We succeeded in isolating a strain of A. fermentans from the rumen contents of preweaning calves and named it Acidaminococcus fermentans P41. The in vitro cultivation revealed its capability to produce butyrate. In vitro fermentation experiments demonstrated that the addition of A. fermentans P41 significantly increased the proportion of butyrate in the rumen fluid (P < 0.05). These results further validated our findings. The relative abundance of Bifidobacterium pseudolongum in the hindgut of HADG calves was negatively correlated with hindgut 4-hydroxyglucobrassicin levels, which were positively correlated with plasma 4-hydroxyglucobrassicin levels, and plasma 4-hydroxyglucobrassicin levels were positively correlated with ADG (P < 0.05).

CONCLUSIONS: This study's findings unveil that rumen and hindgut microbes play distinctive roles in regulating the preweaning ADG of Holstein heifer calves. Additionally, the successful isolation of A. fermentans P41 not only validated our findings but also provided a valuable strain resource for modulating rumen microbes in preweaning calves. Video Abstract.},
}

Animals
Cattle
*Rumen/microbiology/metabolism
*Gastrointestinal Microbiome
*Weaning
Bacteria/classification/isolation & purification/metabolism/genetics
Female
Fermentation
Metagenomics/methods
Metabolomics
Fatty Acids, Volatile/metabolism/analysis
Weight Gain
Butyrates/metabolism

@article {pmid39030597,
year = {2024},
author = {Eraqi, WA and El-Sabbagh, WA and Aziz, RK and Elshahed, MS and Youssef, NH and Elkenawy, NM},
title = {Gastroprotective and microbiome-modulating effects of ubiquinol in rats with radiation-induced enteropathy.},
journal = {Animal microbiome},
volume = {6},
number = {1},
pages = {40},
pmid = {39030597},
issn = {2524-4671},
abstract = {Radiation enteritis is a frequently encountered issue for patients receiving radiotherapy and has a significant impact on cancer patients' quality of life. The gut microbiota plays a pivotal role in intestinal function, yet the impact of irradiation on gut microorganisms is not fully understood. This study explores the gastroprotective effect and gut microbiome-modulating potential of ubiquinol (Ubq), the reduced form of the powerful antioxidant CoQ-10. For this purpose, male albino rats were randomly assigned to four groups: Control, IRR (acute 7 Gy γ-radiation), Ubq_Post (Ubq for 7 days post-irradiation), and Ubq_Pre/Post (Ubq for 7 days pre and 7 days post-irradiation). The fecal microbiomes of all groups were profiled by 16S rRNA amplicon sequencing followed by bioinformatics and statistical analysis. Histopathological examination of intestinal tissue indicated severe damage in the irradiated group, which was mitigated by ubiquinol with enhanced regeneration, goblet cells, and intestinal alkaline phosphatase expression. Compared to the irradiated group, the Ubq-treated groups had a significant recovery of intestinal interleukin-1β, caspase-3, nitric oxide metabolites, and thio-barbituric reactive substances to near-healthy levels. Ubq_Pre/Post group displayed elevated peroxisome proliferator-activated receptor (PPAR-γ) level, suggesting heightened benefits. Serum insulin reduction in irradiated rats improved post-Ubq treatment, with a possible anti-inflammatory effect on the pancreatic tissue. Fecal microbiota profiling revealed a dysbiosis state with a reduction of bacterial diversity post-irradiation, which was re-modulated in the Ubq treated groups to profiles that are indistinguishable from the control group. These findings underscore Ubq's gastroprotective effects against radiation-induced enteritis and its potential in restoring the gut microbiota's diversity and balance.},
}

@article {pmid39030586,
year = {2024},
author = {Liu, J and Spencer, N and Utter, DR and Grossman, AS and Lei, L and Dos Santos, NC and Shi, W and Baker, JL and Hasturk, H and He, X and Bor, B},
title = {Persistent enrichment of multidrug-resistant Klebsiella in oral and nasal communities during long-term starvation.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {132},
pmid = {39030586},
issn = {2049-2618},
support = {T90 fellowship/DE/NIDCR NIH HHS/United States ; 1R01DE023810/DE/NIDCR NIH HHS/United States ; 1K99DE027719/DE/NIDCR NIH HHS/United States ; },
mesh = {Humans ; *Drug Resistance, Multiple, Bacterial/genetics ; *Klebsiella/genetics/isolation & purification/drug effects ; *Mouth/microbiology ; *Microbiota/drug effects/genetics ; Klebsiella Infections/microbiology ; Anti-Bacterial Agents/pharmacology ; Klebsiella pneumoniae/genetics/isolation & purification/drug effects ; Starvation ; Nasal Cavity/microbiology ; Nose/microbiology ; },
abstract = {BACKGROUND: The human oral and nasal cavities can act as reservoirs for opportunistic pathogens capable of causing acute infection. These microbes asymptomatically colonize the human oral and nasal cavities which facilitates transmission within human populations via the environment, and they routinely possess clinically significant antibiotic resistance genes. Among these opportunistic pathogens, the Klebsiella genus stands out as a notable example, with its members frequently linked to nosocomial infections and multidrug resistance. As with many colonizing opportunistic pathogens, the essential transmission factors influencing the spread of Klebsiella species among both healthy and diseased individuals remain unclear.

RESULTS: Here, we explored a possible explanation by investigating the ability of oral and nasal Klebsiella species to outcompete their native microbial community members under in vitro starvation conditions, which could be analogous to external hospital environments or the microenvironment of mechanical ventilators. When K. pneumoniae and K. aerogenes were present within a healthy human oral or nasal sample, the bacterial community composition shifted dramatically under starvation conditions and typically became enriched in Klebsiella species. Furthermore, introducing K. pneumoniae exogenously into a native microbial community lacking K. pneumoniae, even at low inoculum, led to repeated enrichment under starvation. Precise monitoring of K. pneumoniae within these communities undergoing starvation indicated rapid initial growth and prolonged viability compared to other members of the microbiome. K. pneumoniae strains isolated from healthy individuals' oral and nasal cavities also exhibited resistance to multiple classes of antibiotics and were genetically similar to clinical and gut isolates. In addition, we found that in the absence of Klebsiella species, other understudied opportunistic pathogens, such as Peptostreptococcus, increased in relative abundance under starvation conditions.

CONCLUSIONS: Our findings establish an environmental and microbiome community circumstance that allows for the enrichment of Klebsiella species and other opportunistic pathogens. Klebsiella's enrichment may hinge on its ability to quickly outgrow other members of the microbiome. The ability to outcompete other commensal bacteria and to persist under harsh environmental conditions could be an important factor that contributes to enhanced transmission in both commensal and pathogenic contexts. Video Abstract.},
}

Humans
*Drug Resistance, Multiple, Bacterial/genetics
*Klebsiella/genetics/isolation & purification/drug effects
*Mouth/microbiology
*Microbiota/drug effects/genetics
Klebsiella Infections/microbiology
Anti-Bacterial Agents/pharmacology
Klebsiella pneumoniae/genetics/isolation & purification/drug effects
Starvation
Nasal Cavity/microbiology
Nose/microbiology

@article {pmid39030525,
year = {2024},
author = {Lu, L and Li, F and Gao, Y and Kang, S and Li, J and Guo, J},
title = {Microbiome in radiotherapy: an emerging approach to enhance treatment efficacy and reduce tissue injury.},
journal = {Molecular medicine (Cambridge, Mass.)},
volume = {30},
number = {1},
pages = {105},
pmid = {39030525},
issn = {1528-3658},
support = {31920210037//Fundamental Research Funds for Central Universities of the Central South University/ ; No. xbmuyjrc202217//Northwest Minzu University/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/radiation effects ; *Neoplasms/radiotherapy/microbiology/immunology/therapy ; *Probiotics/therapeutic use ; *Radiotherapy/adverse effects/methods ; Animals ; Microbiota/radiation effects ; Radiation Injuries/microbiology/therapy/etiology ; Treatment Outcome ; },
abstract = {Radiotherapy is a widely used cancer treatment that utilizes powerful radiation to destroy cancer cells and shrink tumors. While radiation can be beneficial, it can also harm the healthy tissues surrounding the tumor. Recent research indicates that the microbiota, the collection of microorganisms in our body, may play a role in influencing the effectiveness and side effects of radiation therapy. Studies have shown that specific species of bacteria living in the stomach can influence the immune system's response to radiation, potentially increasing the effectiveness of treatment. Additionally, the microbiota may contribute to adverse effects like radiation-induced diarrhea. A potential strategy to enhance radiotherapy outcomes and capitalize on the microbiome involves using probiotics. Probiotics are living microorganisms that offer health benefits when consumed in sufficient quantities. Several studies have indicated that probiotics have the potential to alter the composition of the gut microbiota, resulting in an enhanced immune response to radiation therapy and consequently improving the efficacy of the treatment. It is important to note that radiation can disrupt the natural balance of gut bacteria, resulting in increased intestinal permeability and inflammatory conditions. These disruptions can lead to adverse effects such as diarrhea and damage to the intestinal lining. The emerging field of radiotherapy microbiome research offers a promising avenue for optimizing cancer treatment outcomes. This paper aims to provide an overview of the human microbiome and its role in augmenting radiation effectiveness while minimizing damage.},
}

Humans
*Gastrointestinal Microbiome/radiation effects
*Neoplasms/radiotherapy/microbiology/immunology/therapy
*Probiotics/therapeutic use
*Radiotherapy/adverse effects/methods
Animals
Microbiota/radiation effects
Radiation Injuries/microbiology/therapy/etiology
Treatment Outcome

@article {pmid39030520,
year = {2024},
author = {Joo, M and Nam, S},
title = {Adolescent gut microbiome imbalance and its association with immune response in inflammatory bowel diseases and obesity.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {268},
pmid = {39030520},
issn = {1471-2180},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Adolescent ; *RNA, Ribosomal, 16S/genetics ; *Obesity/microbiology/immunology ; Female ; Male ; *Bacteria/classification/genetics/isolation & purification ; *Phylogeny ; Inflammatory Bowel Diseases/microbiology/immunology ; Crohn Disease/microbiology/immunology ; Colitis, Ulcerative/microbiology/immunology ; Dysbiosis/microbiology ; Prevotella/genetics/classification/isolation & purification ; Faecalibacterium prausnitzii/genetics ; Feces/microbiology ; },
abstract = {BACKGROUND: Recently, there has been an increase in the number of studies focusing on the association between the gut microbiome and obesity or inflammatory diseases, especially in adults. However, there is a lack of studies investigating the association between gut microbiome and gastrointestinal (GI) diseases in adolescents.

METHOD: We obtained 16S rRNA-seq datasets for gut microbiome analysis from 202 adolescents, comprising ulcerative colitis (UC), Crohn's disease (CD), obesity (Ob), and healthy controls (HC). We utilized Quantitative Insights Into Microbial Ecology (QIIME) and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) to acquire Operational Taxonomic Units (OTUs). Subsequently, we analyzed Kyoto Encyclopedia of Genes and Genomes (KEGG) Orthology (KO) terms and pathway enrichment for the identified OTUs.

RESULTS: In this study, we investigated the difference between the gut microbiomes in adolescents with GI diseases and those in healthy adolescents using 202 samples of 16S rRNA sequencing data. The distribution of the six main gut microbiota (i.e., unclassified Dorea, unclassified Lachnospiraceae, unclassified Ruminococcus, Faecalibacterium prausnitzii, Prevotella copri, unclassified Sutterella) was different based on the status of obesity and inflammatory diseases. Dysbiosis was observed within Lachnospiraceae in adolescents with inflammatory diseases (i.e., UC and CD), and in adolescents with obesity within Prevotella and Sutterella. More specifically, our results showed that the relative abundance of Faecalibacterium prausnitzii and unclassified Lachnospiraceae was more than 10% and 8% higher, respectively, in the UC group compared to the CD, Ob, and HC groups. Additionally, the Ob group had over 20% and over 3% higher levels of Prevotella copri and unclassified Sutterella, respectively, compared to the UC, CD, and HC groups. Also, inspecting associations between the six specific microbiota and KO terms, we found that the six microbiota -relating KO terms were associated with NOD-like receptor signaling. These six taxa differences may affect the immune system and inflammatory response by affecting NOD-like receptor signaling in the host during critical adolescence.

CONCLUSION: In this study, we discovered that dysbiosis of the microbial community had varying degrees of influence on the inflammatory and immune response pathways in adolescents with inflammatory diseases and obesity.},
}

Humans
*Gastrointestinal Microbiome/genetics
Adolescent
*RNA, Ribosomal, 16S/genetics
*Obesity/microbiology/immunology
Female
Male
*Bacteria/classification/genetics/isolation & purification
*Phylogeny
Inflammatory Bowel Diseases/microbiology/immunology
Crohn Disease/microbiology/immunology
Colitis, Ulcerative/microbiology/immunology
Dysbiosis/microbiology
Prevotella/genetics/classification/isolation & purification
Faecalibacterium prausnitzii/genetics
Feces/microbiology

@article {pmid39030484,
year = {2024},
author = {Siegieda, D and Panek, J and Frąc, M},
title = {Ecological processes of bacterial microbiome assembly in healthy and dysbiotic strawberry farms.},
journal = {BMC plant biology},
volume = {24},
number = {1},
pages = {692},
pmid = {39030484},
issn = {1471-2229},
support = {BIOSTRATEG3/344433/16/NCBR/2018//Narodowe Centrum Badań i Rozwoju/ ; },
mesh = {*Fragaria/microbiology ; *Microbiota ; *Soil Microbiology ; *Rhizosphere ; *Bacteria/classification/genetics ; Plant Roots/microbiology ; Plant Shoots/microbiology ; Farms ; },
abstract = {The bacterial microbiome plays crucial role in plants' resistance to diseases, nutrient uptake and productivity. We examined the microbiome characteristics of healthy and unhealthy strawberry farms, focusing on soil (bulk soil, rhizosphere soil) and plant (roots and shoots). The relative abundance of most abundant taxa were correlated with the chemical soil properties and shoot niche revealed the least amount of significant correlations between the two. While alpha and beta diversities did not show differences between health groups, we identified a number of core taxa (16-59) and marker bacterial taxa for each healthy (Unclassified Tepidisphaerales, Ohtaekwangia, Hydrocarboniphaga) and dysbiotic (Udaeobacter, Solibacter, Unclassified Chitinophagales, Unclassified Nitrosomonadaceae, Nitrospira, Nocardioides, Tardiphaga, Skermanella, Pseudomonas, Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Curtobacterium) niche. We also revealed selective pressure of strawberry rhizosphere soil and roots plants in unhealthy plantations increased stochastic ecological processes of bacterial microbiome assembly in shoots. Our findings contribute to understanding sustainable agriculture and plant-microbiome interactions.},
}

*Fragaria/microbiology
*Microbiota
*Soil Microbiology
*Rhizosphere
*Bacteria/classification/genetics
Plant Roots/microbiology
Plant Shoots/microbiology
Farms

@article {pmid39030411,
year = {2024},
author = {Yang, Q and Yang, B and Yang, B and Zhang, W and Tang, X and Sun, H and Zhang, Y and Li, J and Ling, J and Dong, J},
title = {Alleviating Coral Thermal Stress via Inoculation with Quorum Quenching Bacteria.},
journal = {Marine biotechnology (New York, N.Y.)},
volume = {},
number = {},
pages = {},
pmid = {39030411},
issn = {1436-2236},
support = {2021YFC3100500//National Key Research and Development Program of China/ ; 2022YFC3102003//National Key Research and Development Program of China/ ; 2022YFC3102004//National Key Research and Development Program of China/ ; 42106197//National Natural Science Foundation of China/ ; 42276160//National Natural Science Foundation of China/ ; 422QN440//Hainan Provincial Natural Science Foundation of China, China/ ; ISEE2021ZD03//Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences/ ; ISEE2021ZD03//Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences/ ; 2021B1212050023//Science and Technology Planning Project of Guangdong Province, China/ ; },
abstract = {In the background of global warming, coral bleaching induced by elevated seawater temperature is the primary cause of coral reef degradation. Coral microbiome engineering using the beneficial microorganisms for corals (BMCs) has become a hot spot in the field of coral reef conservation and restoration. Investigating the potential of alleviating thermal stress by quorum quenching (QQ) bacteria may provide more tools for coral microbial engineering remediation. In this study, QQ bacteria strain Pseudoalteromonas piscicida SCSIO 43740 was screened among 75 coral-derived bacterial strains, and its quorum sensing inhibitor (QSI) compound was isolated and identified as 2,4-di-tert-butylphenol (2,4-DTBP). Then, the thermal stress alleviating potential of QQ bacteria on coral Pocillopora damicornis was tested by a 30-day controlled experiment with three different treatments: control group (Con: 29 °C), high temperature group (HT: 31 °C), and the group of high temperature with QQ bacteria inoculation (HTQQ: 31 °C + QQ bacteria). The results showed that QQ bacteria SCSIO 43740 inoculation can significantly mitigate the loss of symbiotic algae and impairment of photosynthesis efficiency of coral P. damicornis under thermal stress. Significant difference in superoxide dismutase (SOD) and catalase (CAT) enzyme activities between HT and HTQQ was not observed. In addition, QQ bacteria inoculation suppressed the coral microbial community beta-dispersion and improved the stability of microbial co-occurrence network under thermal stress. It was suggested that QQ bacteria inoculation can alleviate coral thermal stress via reshaping microbial interaction and maintain community stability of coral microbiome. This study provided new evidence for the probiotic function of QQ bacteria in corals, which shedding light on the development of new microbiological tools for coral reef conservation.},
}

@article {pmid39030408,
year = {2024},
author = {Gilbert, JA and Hartmann, EM},
title = {The indoors microbiome and human health.},
journal = {Nature reviews. Microbiology},
volume = {},
number = {},
pages = {},
pmid = {39030408},
issn = {1740-1534},
abstract = {Indoor environments serve as habitat for humans and are replete with various reservoirs and niches for microorganisms. Microorganisms enter indoor spaces with their human and non-human hosts, as well as via exchange with outdoor sources, such as ventilation and plumbing. Once inside, many microorganisms do not survive, especially on dry, barren surfaces. Even reduced, this microbial biomass has critical implications for the health of human occupants. As urbanization escalates, exploring the intersection of the indoor environment with the human microbiome and health is increasingly vital. The indoor microbiome, a complex ecosystem of microorganisms influenced by human activities and environmental factors, plays a pivotal role in modulating infectious diseases and fostering healthy immune development. Recent advancements in microbiome research shed light on this unique ecological system, highlighting the need for innovative approaches in creating health-promoting living spaces. In this Review, we explore the microbial ecology of built environments - places where humans spend most of their lives - and its implications for immune, endocrine and neurological health. We further propose strategies to harness the indoor microbiome for better health outcomes.},
}

@article {pmid39030381,
year = {2024},
author = {Noruzpour, A and Gholam-Mostafaei, FS and Looha, MA and Dabiri, H and Ahmadipour, S and Rouhani, P and Ciacci, C and Rostami-Nejad, M},
title = {Assessment of salivary microbiota profile as a potential diagnostic tool for pediatric celiac disease.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {16712},
pmid = {39030381},
issn = {2045-2322},
mesh = {Humans ; *Celiac Disease/microbiology/diagnosis ; *Saliva/microbiology ; Child ; Female ; Male ; Cross-Sectional Studies ; *Microbiota ; *RNA, Ribosomal, 16S/genetics ; Diet, Gluten-Free ; Adolescent ; Child, Preschool ; Dysbiosis/microbiology/diagnosis ; Case-Control Studies ; Bacteria/genetics/classification/isolation & purification ; },
abstract = {The association between oral dysbiosis and celiac disease (CD) remains poorly understood, as does the impact of CD-associated dysbiosis on disease development or exacerbation. This study aims to investigate alterations in salivary microbial composition among children with CD. In this cross-sectional study, saliva samples from 12 children with active CD (A-CD group), 14 children with CD on a gluten-free diet (GFD), and 10 healthy control (HC) children were analyzed using DNA sequencing targeting the 16S ribosomal RNA. Both patients in A-CD and GFD groups showed a significant increase (p = 0.0001) in the Bacteroidetes phylum, while the Actinobacteria phylum showed a significant decrease (p = 0.0001). Notably, the Rothia genus and R.aeria also demonstrated a significant decrease (p = 0.0001) within the both CD groups as compare to HC. Additionally, the control group displayed a significant increase (p = 0.006) in R.mucilaginosa species compared to both CD patient groups. Distinct bacterial strains were abundant in the saliva of patients with active CD, indicating a unique composition of the salivary microbiome in individuals with CD. These findings suggest that our approach to assessing salivary microbiota changes may contribute to developing noninvasive methods for diagnosing and treating CD.},
}

Humans
*Celiac Disease/microbiology/diagnosis
*Saliva/microbiology
Child
Female
Male
Cross-Sectional Studies
*Microbiota
*RNA, Ribosomal, 16S/genetics
Diet, Gluten-Free
Adolescent
Child, Preschool
Dysbiosis/microbiology/diagnosis
Case-Control Studies
Bacteria/genetics/classification/isolation & purification

@article {pmid39030253,
year = {2024},
author = {Moadi, L and Turjeman, S and Asulin, N and Koren, O},
title = {The effect of testosterone on the gut microbiome in mice.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {880},
pmid = {39030253},
issn = {2399-3642},
support = {101001355//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; ERC-2020-COG No. 101001355//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; },
mesh = {Animals ; *Testosterone/metabolism/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Female ; Male ; Mice ; *Feces/microbiology ; Mice, Inbred C57BL ; Bacteria/metabolism/drug effects ; },
abstract = {The role of hormones in gut-brain crosstalk is largely elusive, but recent research supports specific changes in hormone levels correlated with the gut microbiota. An interesting but unstudied area in microbial endocrinology is the interplay between the microbiota and sex hormones. The aim of this study is to investigate the effect of testosterone and sex on the mouse gut microbiome. We use in vitro experiments to test direct effects of testosterone on bacteria in fecal samples collected from male and female mice pre- and post-puberty. Sex-specific microbial and metabolic differences surrounding puberty are also examined in vivo. We then explore effects of testosterone supplementation in vivo, characterizing microbiota and metabolomes of male and female mice. We detect sex-specific differences in microbiota and associated metabolites of mice post-puberty, but in vitro experiments reveal that testosterone only affects microbiota of fecal samples collected before puberty. Testosterone supplementation in vivo affects gut microbiota and metabolomes in both male and female mice. Taking our results from in vitro and in vivo experiments, we conclude that the shift in the microbiome after puberty is at least partially caused by the higher levels of sex hormones, mainly testosterone, in the host.},
}

Animals
*Testosterone/metabolism/pharmacology
*Gastrointestinal Microbiome/drug effects
Female
Male
Mice
*Feces/microbiology
Mice, Inbred C57BL
Bacteria/metabolism/drug effects

@article {pmid39029911,
year = {2024},
author = {Tyagi, S and Katara, P},
title = {Metatranscriptomics: A Tool for Clinical Metagenomics.},
journal = {Omics : a journal of integrative biology},
volume = {},
number = {},
pages = {},
doi = {10.1089/omi.2024.0130},
pmid = {39029911},
issn = {1557-8100},
abstract = {In the field of bioinformatics, amplicon sequencing of 16S rRNA genes has long been used to investigate community membership and taxonomic abundance in microbiome studies. As we can observe, shotgun metagenomics has become the dominant method in this field. This is largely owing to advancements in sequencing technology, which now allow for random sequencing of the entire genetic content of a microbiome. Furthermore, this method allows profiling both genes and the microbiome's membership. Although these methods have provided extensive insights into various microbiomes, they solely assess the existence of organisms or genes, without determining their active role within the microbiome. Microbiome scholarship now includes metatranscriptomics to decipher how a community of microorganisms responds to changing environmental conditions over a period of time. Metagenomic studies identify the microbes that make up a community but metatranscriptomics explores the diversity of active genes within that community, understanding their expression profile and observing how these genes respond to changes in environmental conditions. This expert review article offers a critical examination of the computational metatranscriptomics tools for studying the transcriptomes of microbial communities. First, we unpack the reasons behind the need for community transcriptomics. Second, we explore the prospects and challenges of metatranscriptomic workflows, starting with isolation and sequencing of the RNA community, then moving on to bioinformatics approaches for quantifying RNA features, and statistical techniques for detecting differential expression in a community. Finally, we discuss strengths and shortcomings in relation to other microbiome analysis approaches, pipelines, use cases and limitations, and contextualize metatranscriptomics as a tool for clinical metagenomics.},
}

@article {pmid39029779,
year = {2024},
author = {Shatunova, S and Aktar, R and Peiris, M and Lee, JYP and Vetter, I and Starobova, H},
title = {The Role of the Gut Microbiome in Neuroinflammation and Chemotherapy-Induced Peripheral Neuropathy.},
journal = {European journal of pharmacology},
volume = {},
number = {},
pages = {176818},
doi = {10.1016/j.ejphar.2024.176818},
pmid = {39029779},
issn = {1879-0712},
abstract = {Chemotherapy-induced peripheral neuropathy (CIPN) is one of the most debilitating adverse effects caused by chemotherapy drugs such as paclitaxel, oxaliplatin and vincristine. It is untreatable and often leads to the discontinuation of cancer therapy and a decrease in the quality of life of cancer patients. It is well-established that neuroinflammation and the activation of immune and glial cells are among the major drivers of CIPN. However, these processes are still poorly understood, and while many chemotherapy drugs alone can drive the activation of these cells and consequent neuroinflammation, it remains elusive to what extent the gut microbiome influences these processes. In this review, we focus on the peripheral mechanisms driving CIPN, and we address the bidirectional pathways by which the gut microbiome communicates with the immune and nervous systems. Additionally, we critically evaluate literature addressing how chemotherapy-induced dysbiosis and the consequent imbalance in bacterial products may contribute to the activation of immune and glial cells, both of which drive neuroinflammation and possibly CIPN development, and how we could use this knowledge for the development of effective treatment strategies.},
}

@article {pmid39029767,
year = {2024},
author = {Lanfranchi, A and Desmond-Le Quéméner, E and Magdalena, JA and Cavinato, C and Trably, E},
title = {Conversion of wine lees and waste activated sludge into caproate and heptanoate: Thermodynamic and microbiological insights.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {131126},
doi = {10.1016/j.biortech.2024.131126},
pmid = {39029767},
issn = {1873-2976},
abstract = {In this study, wine lees and waste activated sludge (WAS) were co-fermented for the first time in a 4:1 ratio (COD basis) at 20, 40, 70 and 100 gCOD/L, in batch at 37 °C and pH 7.0. The substrates were successfully converted to caproate (C6) and heptanoate (C7) with a high selectivity (40.2 % at 40 gCOD/L). The rapidly-growing chain-elongating microbiome was enriched inClostridiaceaeandOscillospiraceae, representing together 3.4-8.8 % of the community. Substrate concentrations higher than 40 gCOD/L negatively affected C6 and C7 selectivities and yields, probably due to microbial inhibition by high ethanol concentrations (15.82-22.93 g/L). At 70 and 100 gCOD/L, chain elongation shifted from ethanol-based to lactate-based, with a microbiome enriched in the lactic acid bacteriaRoseburia intestinalis(27.3 %) andEnterococcus hirae(13.8 %). The partial pressure of H2(pH2) was identified by thermodynamic analysis as a fundamental parameter for controlling ethanol oxidation and improving C6 and C7 selectivities.},
}

@article {pmid39029595,
year = {2024},
author = {Hermanson, JB and Tolba, SA and Chrisler, EA and Leone, VA},
title = {Gut Microbes, Diet, and Genetics as Drivers of Metabolic Liver Disease: A Narrative Review Outlining Implications for Precision Medicine.},
journal = {The Journal of nutritional biochemistry},
volume = {},
number = {},
pages = {109704},
doi = {10.1016/j.jnutbio.2024.109704},
pmid = {39029595},
issn = {1873-4847},
abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD) is rapidly increasing in prevalence, impacting over a third of the global population. The advanced form of MASLD, Metabolic dysfunction-associated steatohepatitis (MASH), is on track to become the number one indication for liver transplant. FDA-approved pharmacological agents are limited for MASH, despite over 400 ongoing clinical trials, with only a single drug (resmetirom) currently on the market. This is likely due to the heterogeneous nature of disease pathophysiology, which involves interactions between highly individualized genetic and environmental factors. To apply precision medicine approaches that overcome interpersonal variability, in-depth insights into interactions between genetics, nutrition, and the gut microbiome are needed, given that each have emerged as dynamic contributors to MASLD and MASH pathogenesis. Here, we discuss the associations and molecular underpinnings of several of these factors individually and outline their interactions in the context of both patient-based studies and preclinical animal model systems. Finally, we highlight gaps in knowledge that will require further investigation to aid in successfully implementing precision medicine to prevent and alleviate MASLD and MASH.},
}

@article {pmid39029396,
year = {2024},
author = {Fan, X and Kong, L and Wang, J and Tan, Y and Xu, X and Li, M and Zhu, L},
title = {Surface-programmed microbiome assembly in phycosphere to microplastics contamination.},
journal = {Water research},
volume = {262},
number = {},
pages = {122064},
doi = {10.1016/j.watres.2024.122064},
pmid = {39029396},
issn = {1879-2448},
abstract = {Recalcitrance in microplastics accounts for ubiquitous white pollution. Of special interest are the capabilities of microorganisms to accelerate their degradation sustainably. Compared to the well-studied pure cultures in degrading natural polymers, the algal-bacterial symbiotic system is considered as a promising candidate for microplastics removal, cascading bottom-up impacts on ecosystem-scale processes. This study selected and enriched the algae-associated microbial communities hosted by the indigenous isolation Desmodesmus sp. in wastewater treatment plants with micro-polyvinyl chloride, polyethylene terephthalate, polyethylene, and polystyrene contamination. Results elaborated that multiple settled and specific affiliates were recruited by the uniform algae protagonist from the biosphere under manifold microplastic stress. Alteration of distinct chemical functionalities and deformation of polymers provide direct evidence of degradation in phycosphere under illumination. Microplastic-induced phycosphere-derived DOM created spatial gradients of aromatic protein, fulvic and humic acid-like and tryptophan components to expanded niche-width. Surface thermodynamic analysis was conducted to simulate the reciprocal and reversible interaction on algal-bacterial and phycosphere-microplastic interface, revealing the enhancement of transition to stable and irreversible aggregation for functional microbiota colonization and microplastics capture. Furthermore, pangenomic analysis disclosed the genes related to the chemotaxis and the proposed microplastics biodegradation pathway in enriched algal-bacterial microbiome, orchestrating the evidence for common synthetic polymer particles and ultimately to confirm the effectiveness and potential. The present study emphasizes the necessity for future endeavors aimed at fully leveraging the potential of algal-bacterial mutualistic systems within sustainable bioremediation strategies targeting the eradication of microplastic waste.},
}

@article {pmid39029191,
year = {2024},
author = {Wang, N and Zhang, R and Wang, Y and Zhang, L and Sun, A and Zhang, Z and Shi, X},
title = {Accumulation and growth toxicity mechanisms of fluxapyroxad revealed by physiological, hepatopancreas transcriptome, and gut microbiome analysis in Pacific white shrimp (Litopenaeus vannamei).},
journal = {Journal of hazardous materials},
volume = {476},
number = {},
pages = {135206},
doi = {10.1016/j.jhazmat.2024.135206},
pmid = {39029191},
issn = {1873-3336},
abstract = {Fluxapyroxad (FX), a typical succinate dehydrogenase inhibitor fungicide, is causing increased global concerns due to its fungicide effects. However, the accumulation and grow toxicity of FX to Litopenaeus vannamei (L. vannamei) is poorly understand. Therefore, the accumulation pattern of FX in L. vannamei was investigated for the first time in environmental concentrations. FX accumulated rapidly in shrimp muscle. Meanwhile, growth inhibition was observed and the mechanism derived by primarily accelerated glycolipid metabolism and reduced glycolipid content. Moreover, exposure to environmental concentrations of FX induced significant growth inhibition and oxidative stress and inhibited oxidative phosphorylation and TCA cycle in L. vannamei. The endocytosis signaling pathway genes were activated, thereby driving growth toxicity. Oxidative phosphorylation and cytosolic gene expression were further rescued in elimination experiments, demonstrating the mechanism of growth toxicity by FX exposure. The results revealed that FX persistently altered the gut microbiome of L. vannamei using gut microbiome sequencing, particularly with increased Garcinia Purple Pseudoalteromonas luteoviolacea for organic pollutant degradation. This study provided new insights into the potential toxicity of FX to marine organisms, emphasizing the need for further investigation and potential regulatory considerations.},
}

@article {pmid39029147,
year = {2024},
author = {Taveira, I and Castro, RO and Cypriano, J and Santos, HF and Abreu, F and de Araújo, FV},
title = {Retrieving the real microbial diversity in aquatic plastisphere.},
journal = {Marine pollution bulletin},
volume = {206},
number = {},
pages = {116719},
doi = {10.1016/j.marpolbul.2024.116719},
pmid = {39029147},
issn = {1879-3363},
abstract = {Disposed plastics in oceans provide a substrate to which microbes can adhere and structure the biofilm, namely the plastisphere. In this study, we showed that the mesoplastic density-based separation, routinely used in quantification assays, is detrimental to studying the microbiome diversity and ecology as it underestimates the real microbial diversity within these samples. Based on SEM and microbiome observations, we propose that chemically fixing samples before density separation preserves cellular diversity (2.32-fold change) and richness (1.12-fold change) that would be naturally lost due to the current methodology. OTUs assigned to Gram-negative bacterial species are the most negatively affected by omitting fixation and polymer composition was not decisive in shifting microbiome composition. Considering our findings, the formaldehyde-fixation step should be incorporated into the current methodology described in most studies as this is crucial to promote a deeper understanding of the microbial community in this ecosystem and biofilm-adhered scattering through aquatic ecosystems.},
}

@article {pmid39029010,
year = {2024},
author = {Kim, B and Song, A and Son, A and Shin, Y},
title = {Gut microbiota and epigenetic choreography: Implications for human health: A review.},
journal = {Medicine},
volume = {103},
number = {29},
pages = {e39051},
doi = {10.1097/MD.0000000000039051},
pmid = {39029010},
issn = {1536-5964},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Epigenesis, Genetic ; DNA Methylation ; Obesity/microbiology/genetics ; Inflammatory Bowel Diseases/microbiology/genetics ; },
abstract = {The interwoven relationship between gut microbiota and the epigenetic landscape constitutes a pivotal axis in understanding human health and disease. Governed by a myriad of dietary, genetic, and environmental influences, the gut microbiota orchestrates a sophisticated metabolic interplay, shaping nutrient utilization, immune responses, and defenses against pathogens. Recent strides in genomics and metabolomics have shed light on the intricate connections between these microbial influencers and the host's physiological dynamics, presenting a dynamic panorama across diverse disease spectra. DNA methylation and histone modifications, as key players in epigenetics, intricately align with the dynamic orchestration of the gut microbiota. This seamless collaboration, notably evident in conditions like inflammatory bowel disease and obesity, has captured the attention of researchers, prompting an exploration of its nuanced choreography. Nevertheless, challenges abound. Analyzing data is intricate due to the multifaceted nature of the gut microbiota and the limitations of current analytical methods. This underscores the need for a multidisciplinary approach, where diverse disciplines converge to pave innovative research pathways. The integration of insights from microbiome and epigenome studies assumes paramount importance in unraveling the complexities of this intricate partnership. Deciphering the synchronized interactions within this collaboration offers a deeper understanding of these delicate interplays, potentially heralding revolutionary strides in treatment modalities and strategies for enhancing public health.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Epigenesis, Genetic
DNA Methylation
Obesity/microbiology/genetics
Inflammatory Bowel Diseases/microbiology/genetics

@article {pmid39028631,
year = {2024},
author = {Ottinger, MA and Mani, S and Krüger, S and Coverdale, B and Willows-Munro, S and Combrink, L},
title = {Microbiomes in Birds: A Review of Links to Health and Reproduction.},
journal = {Reproduction & fertility},
volume = {},
number = {},
pages = {},
doi = {10.1530/RAF-23-0076},
pmid = {39028631},
issn = {2633-8386},
abstract = {Microbiomes have emerged as a key component essential for maintaining the health of an organism. Additionally, the roles of microbiomes are multifaceted, some unique to specific body areas and organs while others, particularly the gut microbiome, having broader effects on the entire organism. Comparative literature is emerging that compares microbiomes across mammals and birds. Domestic poultry have been the most extensively studied relative to their role in production agriculture. These data have provided a great deal of information about the effects of diet and nutritional requirements relative to the gut microbiome, productivity, and resilience to diseases. Conversely, limited such research has been conducted on wild birds, despite them inhabiting a broad array of ecological niches and environments, providing a rich diversity in their adaptations to different habitats. Migratory birds and raptors are of particular interest. Migratory birds encounter a range of ecosystems and provide a link between allopatric populations. Raptors occupy high positions in the food chain, with potential exposure to biomagnification of environmental contaminants and pathogens. This review overviews our current understanding of the structure and function of avian microbiomes as related to avian health and reproduction in domestic and wild birds, highlighting knowledge gaps in need of further investigation for more effective conservation of rapidly declining avian populations.},
}

@article {pmid39028556,
year = {2024},
author = {Tian, Y and Cheng, J and Yang, Y and Wang, H and Fu, Y and Li, X and Wang, W and Ma, S and Xu, X and Lu, F and Feng, P and Han, S and Chen, H and Hou, H and Hu, Q and Wu, C},
title = {A 90-day subchronic exposure to heated tobacco product aerosol caused differences in intestinal inflammation and microbiome dysregulation in rats.},
journal = {Nicotine & tobacco research : official journal of the Society for Research on Nicotine and Tobacco},
volume = {},
number = {},
pages = {},
doi = {10.1093/ntr/ntae179},
pmid = {39028556},
issn = {1469-994X},
abstract = {INTRODUCTION: Smoking is one of the most important predisposing factors of intestinal inflammatory diseases. Heated tobacco product (HTP) is a novel tobacco category that is claimed to deliver reduced chemicals to human those reported in combustible cigarette smoke (CS). However, the effect of HTP on intestine is still unknown.

METHODS: In the framework of Organization for Economic Co-operation and Development guidelines 413 guidelines, Sprague-Dawley rats were exposed to HTP aerosol and CS for 13 weeks. The atmosphere was characterized and oxidative stress and inflammation of intestine were investigated after exposure. Furthermore, the faeces we performed with 16S sequencing and metabolomics analysis.

RESULTS: HTP aerosol and CS led to obvious intestinal damage evidenced by increased intestinal pro-inflammatory cytokines and oxidative stress in male and female rats After HTP and CS exposure, the abundance that obviously changed were Lactobacillus and Turiciacter in male rats and Lactobacillus and Prevotella in female rats. HTP mainly induced the metabolism of amino acids and fatty acyls such as short-chain fatty acids and tryptophan, while CS involved into the main metabolism of bile acids, especially indole and derivatives. Although different metabolic pathways in the gut mediated by HTP and CS, both to inflammation and oxidative stress were ultimately induced.

CONCLUSIONS: HTP aerosol and CS induced intestinal damage mediated by different gut microbiota and metabolites, while both lead to inflammation and oxidative stress.

IMPLICATIONS: The concentration of various harmful components in heated tobacco product aerosol is reported lower than that of traditional cigarette smoke, however, its health risk impact on consumers remains to be studied. Our research findings indicate that heated tobacco product and cigarette smoke inhalation induced intestinal damage through different metabolic pathways mediated by gut microbiome, indicating the health risk of heated tobacco product in intestine.},
}

@article {pmid39028343,
year = {2024},
author = {Hao, Y and Hao, Z and Zeng, X and Lin, Y},
title = {Gut microbiota and metabolites of cirrhotic portal hypertension: a novel target on the therapeutic regulation.},
journal = {Journal of gastroenterology},
volume = {},
number = {},
pages = {},
pmid = {39028343},
issn = {1435-5922},
support = {PWZxq2022-06//the Key Disciplines Group Construction Project of Shanghai Pudong New Area Health Commission/ ; 82270636//the National Natural Science Foundation of China/ ; 82070616//the National Natural Science Foundation of China/ ; PWYgf2021-02//Medical Discipline Construction Project of Pudong Health Committee of Shanghai/ ; PW2022D08//the Joint Tackling Project of Pudong Health Committee of Shanghai/ ; 2019lhrcjh//the Pilot Talent Plan of Shanghai East Hospital/ ; },
abstract = {BACKGROUND: The regulatory role of gut microbiota and gut-derived metabolites through the gut-liver axis in the development of cirrhotic portal hypertension (PH) has received increasing attention.

METHODS: The review summarized a series of investigations on effects of metabolites derived from microbiota and medicines targeting microbiome including rifaximin, VSL#3, statins, propranolol, FXR agonists as well as drugs derived from bile acids (BAs) on PH progression.

RESULTS: Patients with PH exhibit alterations in gut microbial richness and differential overall microbiota community, and several results clearly displayed the correlation of PH with enrichment of Veillonella dispar or depletion of Clostridiales, Peptostreptococcaceae, Alistipes putredinis, Roseburia faecis and Clostridium cluster IV. The gut-derived metabolites including hydrogen sulfide, tryptophan metabolites, butyric acid, secondary BAs and phenylacetic acid (PAA) participate in a range of pathophysiology process of PH through modulating intrahepatic vascular resistance and portal blood flow associated with the formation and progression of PH. Established and emerging drugs targeting on bacterial translocation and intestinal eubiosis are gradually identified as potential strategies for treatments of liver cirrhosis and PH by modulating intestinal inflammation, splanchnic arterial vasodilation and endothelial dysfunction.

CONCLUSIONS: Future explorations should further characterize the alteration of the fecal microbiome and metabolite profiles in PH and elucidate the regulatory mechanism of the intestinal microbiome, gut-derived metabolites and gut microbiota targeted pharmaceutical treatments involved in PH.},
}

@article {pmid39028257,
year = {2024},
author = {Brosse, A and Coullon, H and Janoir, C and Péchiné, S},
title = {The state of play of rodent models for the study of Clostridioides difficile infection.},
journal = {Journal of medical microbiology},
volume = {73},
number = {7},
pages = {},
doi = {10.1099/jmm.0.001857},
pmid = {39028257},
issn = {1473-5644},
mesh = {Animals ; *Clostridium Infections/microbiology ; *Disease Models, Animal ; *Clostridioides difficile/pathogenicity ; Mice ; Cricetinae ; Humans ; Rodentia/microbiology ; Germ-Free Life ; },
abstract = {Clostridioides difficile is the most common cause of nosocomial antibiotic-associated diarrhoea and is responsible for a spectrum of diseases characterized by high levels of recurrence and morbidity. In some cases, complications can lead to death. Currently, several types of animal models have been developed to study various aspects of C. difficile infection (CDI), such as colonization, virulence, transmission and recurrence. These models have also been used to test the role of environmental conditions, such as diet, age and microbiome that modulate infection outcome, and to evaluate several therapeutic strategies. Different rodent models have been used successfully, such as the hamster model and the gnotobiotic and conventional mouse models. These models can be applied to study either the initial CDI infectious process or recurrences. The applications of existing rodent models and their advantages and disadvantages are discussed here.},
}

Animals
*Clostridium Infections/microbiology
*Disease Models, Animal
*Clostridioides difficile/pathogenicity
Mice
Cricetinae
Humans
Rodentia/microbiology
Germ-Free Life

@article {pmid39028195,
year = {2024},
author = {Li, Y and Xu, T and Tu, Y and Li, T and Wei, Y and Zhou, Y},
title = {An aldolase-dependent phloroglucinol degradation pathway in Collinsella sp. zg1085.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0104724},
doi = {10.1128/aem.01047-24},
pmid = {39028195},
issn = {1098-5336},
abstract = {Phloroglucinol (1,3,5-trihydroxybenzene) is a key intermediate in the degradation of polyphenols such as flavonoids and hydrolysable tannins and can be used by certain bacteria as a carbon and energy source for growth. The identification of enzymes that participate in the fermentation of phloroglucinol to acetate and butyrate in Clostridia was recently reported. In this study, we present the discovery and characterization of a novel metabolic pathway for phloroglucinol degradation in the bacterium Collinsella sp. zg1085, from marmot respiratory tract. In both the Clostridial and Collinsella pathways, phloroglucinol is first reduced to dihydrophoroglucinol by the NADPH-dependent phloroglucinol reductase (PGR), followed by ring opening to form (S)-3-hydroxy-5-oxohexanoate by a Mn[2+]-dependent dihydrophloroglucinol cyclohydrolase (DPGC). In the Collinsella pathway, (S)-3-hydroxy-5-oxohexanoate is then cleaved to form malonate semialdehyde and acetone by a newly identified aldolase (HOHA). Finally, a NADP[+]-dependent malonate-semialdehyde dehydrogenase converts malonate semialdehyde to CO2 and acetyl-CoA, an intermediate in carbon and energy metabolism. Recombinant expression of the Collinsella PGR, DPGC, and HOHA in E. coli enabled the conversion of phloroglucinol into acetone, providing support for the proposed pathway. Experiments with Olsenella profusa, another bacterium containing the gene cluster of interest, show that the PGR, DPGC, HOHA, and MSDH are induced by phloroglucinol. Our findings add to the variety of metabolic pathways for the degradation of phloroglucinol, a widely distributed phenolic compound, in the anaerobic microbiome.IMPORTANCEPhloroglucinol is an important intermediate in the bacterial degradation of polyphenols, a highly abundant class of plant natural products. Recent research has identified key enzymes of the phloroglucinol degradation pathway in butyrate-producing anaerobic bacteria, which involves cleavage of a linear triketide intermediate by a beta ketoacid cleavage enzyme, requiring acetyl-CoA as a co-substrate. This paper reports a variant of the pathway in the lactic acid bacterium Collinsella sp. zg1085, which involves cleavage of the triketide intermediate by a homolog of deoxyribose-5-phosphate aldolase, highlighting the variety of mechanisms for phloroglucinol degradation by different anaerobic bacterial taxa.},
}

@article {pmid39028146,
year = {2024},
author = {Ding, L and Wang, Y and Jiang, Z and Tang, X and Mao, B and Zhao, J and Chen, W and Zhang, Q and Cui, S},
title = {Effects of Lactiplantibacillus plantarum CCFM1214 and Ligilactobacillus salivarius CCFM1215 on halitosis: a double-blind, randomized controlled trial.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d4fo02280g},
pmid = {39028146},
issn = {2042-650X},
abstract = {The purpose of this study was to evaluate the effects of known probiotic species Lactiplantibacillus plantarum CCFM1214 and Ligilactobacillus salivarius CCFM1215 on halitosis, the oral status, and the oral microbiome. In a double-blind, randomized controlled trial that lasted for five weeks, 43 participants were divided into an oral probiotics group and a control group and given probiotics or control powder for the first four weeks, with the fifth week being the discontinuation period. 33 participants (probiotics group = 21, control group = 12) completed the entire experiment in the end. Oral samples were taken as part of oral health examinations during the baseline period (day 0) and four weeks after (day 28). The nucleotide sequence of the V3-V4 region of 16S rRNA was determined to examine the impact of intervention and time on the oral microbiome. The effects of L. plantarum CCFM1214 and L. salivarius CCFM1215 on the number of Fusobacterium nucleatum in gingival crevicular fluid (GCF) samples of participants were detected by quantitative PCR. After the intervention, L. plantarum CCFM1214 and L. salivarius CCFM1215 significantly reduced the levels of volatile sulfur compounds (VSCs) and the quantity of F. nucleatum in GCF samples, where the average DNA copy number per ng (log) of F. nucleatum decreased from 7.12 ± 0.04 to 6.01 ± 0.09. The β diversity of the probiotics group, on the whole, tended to be more concentrated and stable after the intervention. In addition, after probiotic intervention, the abundance of Lactobacillus and Bifidobacterium increased, while the abundance of Fusobacterium, Acinetobacter, Porphyromonas, and Aggregatibacter decreased significantly. In general, L. plantarum CCFM1214 and L. salivarius CCFM1215 can alleviate halitosis and considerably lower the value of VSCs and improve the oral microbiota in participants with halitosis.},
}

@article {pmid39027867,
year = {2024},
author = {Upadhyay, K and Nigam, N and Gupta, S and Tripathi, SK and Jain, A and Puri, B},
title = {Current and future therapeutic approaches of CFTR and airway dysbiosis in an era of personalized medicine.},
journal = {Journal of family medicine and primary care},
volume = {13},
number = {6},
pages = {2200-2208},
pmid = {39027867},
issn = {2249-4863},
abstract = {Cystic fibrosis (CF) is a life-threatening genetic disorder caused by mutations in the CFTR gene. This leads to a defective protein that impairs chloride transport, resulting in thick mucus buildup and chronic inflammation in the airways. The review discusses current and future therapeutic approaches for CFTR dysfunction and airway dysbiosis in the era of personalized medicine. Personalized medicine has revolutionized CF treatment with the advent of CFTR modulator therapies that target specific genetic mutations. These therapies have significantly improved patient outcomes, slowing disease progression, and enhancing quality of life. It also highlights the growing recognition of the airway microbiome's role in CF pathogenesis and discusses strategies to modulate the microbiome to further improve patient outcomes. This review discusses various therapeutic approaches for cystic fibrosis (CFTR) mutations, including adenovirus gene treatments, nonviral vectors, CRISPR/cas9 methods, RNA replacement, antisense-oligonucleotide-mediated DNA-based therapies, and cell-based therapies. It also introduces airway dysbiosis with CF and how microbes influence the lungs. The review highlights the importance of understanding the cellular and molecular causes of CF and the development of personalized medicine to improve quality of life and health outcomes.},
}

@article {pmid39027755,
year = {2024},
author = {Pereira, MP and Jones, S and Costin, JM},
title = {Association of Polycystic Ovarian Syndrome (PCOS) With Vaginal Microbiome Dysbiosis: A Scoping Review.},
journal = {Cureus},
volume = {16},
number = {6},
pages = {e62611},
pmid = {39027755},
issn = {2168-8184},
abstract = {The aim of this scoping review was to explore the potential relationship between vaginal microbiome dysbiosis and polycystic ovarian syndrome (PCOS). Four databases were utilized to identify primary literature based on a pre-determined exclusion and inclusion criteria. The electronic databases searched include MEDLINE, Embase, Cochrane Register of Controlled Trials (CENTRAL), Cumulative Index to Nursing and Allied Health Literature (CINAHL), and Web of Science. After an initial double-blind screening and removal of duplicates, 81 articles remained. Articles were included based on preselected inclusion and exclusion criteria, type of study, and date of publishing. Specifically, primary literature that focused on subjects that were diagnosed with PCOS and that discussed PCOS in relation to the vaginal microbiome was included. Literature reviews, studies with animal subjects, and studies that did not discuss PCOS and the vaginal microbiome were excluded. Current data from the five articles included in this review suggests that there is a relationship between PCOS and vaginal microbiome dysbiosis. Specifically, dysbiosis of the vaginal flora may be due to vaginal pH alterations secondary to decreased vaginal Lactobacillus species and elevated pathogenic species including Streptococcus, Actinomyces, Prevotella, Gardnerella, and Mycoplasma species. The manifestation of this vaginal microbiome dysbiosis is often bacterial and fungal vaginitis. Therefore, more studies are needed to explore the possibility of treating PCOS with probiotics designed to reestablish a healthy Lactobacillus-dominant vaginal microbiome. In addition, further studies on the microbial composition of the vaginal microbiota in PCOS patients could identify microbial biomarkers for diagnosing PCOS.},
}

@article {pmid39027559,
year = {2024},
author = {Gobert, AP and Finley, J and Asim, M and Barry, DP and Allaman, MM and Hawkins, CV and Williams, KJ and Delagado, AG and Mirmira, RG and Zhao, S and Piazuelo, MB and Washington, MK and Coburn, LA and Wilson, KT},
title = {Analysis of the effect of hypusination in myeloid cells on colitis and colitis-associated cancer.},
journal = {Heliyon},
volume = {10},
number = {13},
pages = {e33838},
pmid = {39027559},
issn = {2405-8440},
support = {P01 CA028842/CA/NCI NIH HHS/United States ; R01 DK128200/DK/NIDDK NIH HHS/United States ; I01 CX002473/CX/CSRD VA/United States ; P30 DK058404/DK/NIDDK NIH HHS/United States ; P01 CA116087/CA/NCI NIH HHS/United States ; I01 CX002171/CX/CSRD VA/United States ; },
abstract = {Hypusine is an amino acid synthesized by the enzyme deoxyhypusine synthase (DHPS). It is critical for the activity of eukaryotic translation initiation factor 5A (EIF5A). We reported that hypusination i) in macrophages supports the innate response towards pathogenic bacteria and ii) in epithelial cells maintains intestinal homeostasis. Herein, we investigated the effect of myeloid hypusination on the outcome of colitis and colitis-associated cancer. We found that patients with Crohn's disease exhibit increased levels of DHPS and EIF5A[Hyp] in cells infiltrating the colon lamina propria. However, the specific deletion of Dhps in myeloid cells had no impact on clinical, histological, or inflammatory parameters in mice treated with dextran sulfate sodium (DSS). Further, tumorigenesis and level of dysplasia were not affected by myeloid deletion of Dhps in the azoxymethane-DSS model. The composition of the fecal and the mucosa-associated microbiome was similar in animals lacking or not DHPS in myeloid cells. Thus, hypusination in myeloid cells does not regulate colitis associated with epithelial injury and colitis-associated cancer. Enhancement of the DHPS/hypusine pathway in patients with inflammatory bowel disease could have therapeutic impact through epithelial effects, but modulation of hypusination in myeloid cells will be unlikely to affect the disease.},
}

@article {pmid39027446,
year = {2024},
author = {Khaledi, M and Sameni, F and Gholipour, A and Shahrjerdi, S and Golmohammadi, R and Gouvarchin Ghaleh, HE and Poureslamfar, B and Hemmati, J and Mobarezpour, N and Milasi, YE and Rad, F and Mehboodi, M and Owlia, P},
title = {Potential role of gut microbiota in major depressive disorder: A review.},
journal = {Heliyon},
volume = {10},
number = {12},
pages = {e33157},
pmid = {39027446},
issn = {2405-8440},
abstract = {Interactions between the gut microbiota and host immunity are sophisticated, dynamic, and host-dependent. Scientists have recently conducted research showing that disturbances in the gut bacterial community can lead to a decrease in some metabolites and, consequently, to behaviors such as depression. Exposure to stressors dropped the relative abundance of bacteria in the genus Bacteroides while soaring the relative abundance of bacteria in the genus Clostridium, Coprococcus, Dialister, and Oscillibacter, which were also reduced in people with depression. Microbiota and innate immunity are in a bilateral relationship. The gut microbiota has been shown to induce the synthesis of antimicrobial proteins such as catalysidins, type C lectins, and defensins. Probiotic bacteria can modulate depressive behavior through GABA signaling. The gut microbiome produces essential metabolites such as neurotransmitters, tryptophan metabolites, and short-chain fatty acids (SCFAs) that can act on the CNS. In the case of dysbiosis, due to mucin changes, the ratio of intestinal-derived molecules may change and contribute to depression. Psychotropics, including Bifidobacterium longum NCC3001, Clostridium butyricum CBM588, and Lactobacillus acidophilus, have mental health benefits, and can have a positive effect on the host-brain relationship, and have antidepressant effects. This article reviews current studies on the association between gut microbiota dysbiosis and depression. Comprehensively, these findings could potentially lead to novel approaches to improving depressive symptoms via gut microbiota alterations, including probiotics, prebiotics, and fecal microbiota transplantation.},
}

@article {pmid39027370,
year = {2024},
author = {Yuan, X and Yang, X and Xu, Z and Li, J and Sun, C and Chen, R and Wei, H and Chen, L and Du, H and Li, G and Yang, Y and Chen, X and Cui, L and Fu, J and Wu, J and Chen, Z and Fang, X and Su, Z and Zhang, M and Wu, J and Chen, X and Zhou, J and Luo, Y and Zhang, L and Wang, R and Luo, F},
title = {The profile of blood microbiome in new-onset type 1 diabetes children.},
journal = {iScience},
volume = {27},
number = {7},
pages = {110252},
pmid = {39027370},
issn = {2589-0042},
abstract = {Blood microbiome signatures in patients with type 1 diabetes (T1D) remain unclear. We profile blood microbiome using 16S rRNA gene sequencing in 77 controls and 64 children with new-onset T1D, and compared it with the gut and oral microbiomes. The blood microbiome of patients with T1D is characterized by increased diversity and perturbed microbial features, with a significant increase in potentially pathogenic bacteria compared with controls. Thirty-six representative genera of blood microbiome were identified by random forest analysis, providing strong discriminatory power for T1D with an AUC of 0.82. PICRUSt analysis suggested that bacteria capable of inducing inflammation were more likely to enter the bloodstream in T1D. The overlap of the gut and oral microbiome with the blood microbiome implied potential translocation of bacteria from the gut and oral cavity to the bloodstream. Our study raised the necessity of further mechanistic investigations into the roles of blood microbiome in T1D.},
}

@article {pmid39027140,
year = {2024},
author = {Mendes-Frias, A and Moreira, M and Vieira, MC and Gaifem, J and Costa, P and Lopes, L and Silvestre, R},
title = {Akkermansia muciniphila and Parabacteroides distasonis as prognostic markers for relapse in ulcerative colitis patients.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1367998},
pmid = {39027140},
issn = {2235-2988},
mesh = {Humans ; *Colitis, Ulcerative/microbiology ; Female ; Male ; Adult ; *Recurrence ; Prognosis ; *Gastrointestinal Microbiome ; *Akkermansia ; Middle Aged ; *Bacteroidetes/isolation & purification ; *Feces/microbiology ; Biomarkers/blood ; Verrucomicrobia/isolation & purification ; Young Adult ; Aged ; },
abstract = {INTRODUCTION: Ulcerative colitis is an inflammatory disorder characterized by chronic inflammation in the gastrointestinal tract, mainly in the colon and rectum. Although the precise etiology of ulcerative colitis remains unclear, recent research has underscored the significant role of the microbiome in its development and progression.

METHODS: The aim of this study was to establish a relationship between the levels of specific gut bacterial species and disease relapse in ulcerative colitis. For this study, we recruited 105 ulcerative colitis patients in remission and collected clinical data, blood, and stool samples. Akkermansia muciniphila and Parabacteroides distasonis levels were quantified in the stool samples of ulcerative colitis patients. Binary logistic regression was applied to collected data to predict disease remission.

RESULTS: The median time in remission in this cohort was four years. A predictive model incorporating demographic information, clinical data, and the levels of Akkermansia muciniphila and Parabacteroides distasonis was developed to understand remission patterns.

DISCUSSION: Our findings revealed a negative correlation between the levels of these two microorganisms and the duration of remission. These findings highlight the importance of the gut microbiota in ulcerative colitis for disease prognosis and for personalized treatments based on microbiome interventions.},
}

Humans
*Colitis, Ulcerative/microbiology
Female
Male
Adult
*Recurrence
Prognosis
*Gastrointestinal Microbiome
*Akkermansia
Middle Aged
*Bacteroidetes/isolation & purification
*Feces/microbiology
Biomarkers/blood
Verrucomicrobia/isolation & purification
Young Adult
Aged

@article {pmid39027134,
year = {2024},
author = {Rizo, J and Encarnación-Guevara, S},
title = {Bacterial protein acetylation: mechanisms, functions, and methods for study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1408947},
pmid = {39027134},
issn = {2235-2988},
mesh = {Acetylation ; *Bacterial Proteins/metabolism/genetics ; *Protein Processing, Post-Translational ; *Bacteria/metabolism/genetics ; Lysine/metabolism ; Lysine Acetyltransferases/metabolism/genetics ; Acetyl Coenzyme A/metabolism ; },
abstract = {Lysine acetylation is an evolutionarily conserved protein modification that changes protein functions and plays an essential role in many cellular processes, such as central metabolism, transcriptional regulation, chemotaxis, and pathogen virulence. It can alter DNA binding, enzymatic activity, protein-protein interactions, protein stability, or protein localization. In prokaryotes, lysine acetylation occurs non-enzymatically and by the action of lysine acetyltransferases (KAT). In enzymatic acetylation, KAT transfers the acetyl group from acetyl-CoA (AcCoA) to the lysine side chain. In contrast, acetyl phosphate (AcP) is the acetyl donor of chemical acetylation. Regardless of the acetylation type, the removal of acetyl groups from acetyl lysines occurs only enzymatically by lysine deacetylases (KDAC). KATs are grouped into three main superfamilies based on their catalytic domain sequences and biochemical characteristics of catalysis. Specifically, members of the GNAT are found in eukaryotes and prokaryotes and have a core structural domain architecture. These enzymes can acetylate small molecules, metabolites, peptides, and proteins. This review presents current knowledge of acetylation mechanisms and functional implications in bacterial metabolism, pathogenicity, stress response, translation, and the emerging topic of protein acetylation in the gut microbiome. Additionally, the methods used to elucidate the biological significance of acetylation in bacteria, such as relative quantification and stoichiometry quantification, and the genetic code expansion tool (CGE), are reviewed.},
}

Acetylation
*Bacterial Proteins/metabolism/genetics
*Protein Processing, Post-Translational
*Bacteria/metabolism/genetics
Lysine/metabolism
Lysine Acetyltransferases/metabolism/genetics
Acetyl Coenzyme A/metabolism

@article {pmid39027091,
year = {2024},
author = {Li, J and Li, J and Liu, Y and Zeng, J and Liu, Y and Wu, Y},
title = {Large-scale bidirectional Mendelian randomization study identifies new gut microbiome significantly associated with immune thrombocytopenic purpura.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1423951},
pmid = {39027091},
issn = {1664-302X},
abstract = {INTRODUCTION: A variety of studies have shown a link between the gut microbiota and autoimmune diseases, but the causal relationship with Henoch-Schönlein purpura (HSP) and immune thrombocytopenic purpura (ITP) is unknown.

METHODS: This study investigated the bidirectional causality between gut microbiota and HSP and ITP using Mendelian randomization (MR). Large-scale genetic data of gut microbiota at phylum to species level from the MiBioGen consortium and the Dutch Microbiome Project were utilized. Genome-wide association studies (GWAS) summary statistics for HSP and ITP came from FinnGen R10. Various MR methods were applied to infer causal relationships, including inverse variance weighted (IVW), maximum likelihood (ML), cML-MA, MR-Egger, weighted median, weighted model, and MR-PRESSO. Multiple sensitivity analyses and Bonferroni correction were conducted to enhance robustness and reliability.

RESULTS: Based on the IVW estimates, 23 bacterial taxa were identified to have suggestive associations with HSP and ITP. Remarkably, after Bonferroni correction, family Alcaligenaceae (OR = 2.86, 95% CI = 1.52-5.37; IVW, p = 1.10 × 10[-3], ML, p = 1.40 × 10[-3]) was significantly associated with ITP as a risk factor, while family Bacteroidales S24 7group (OR = 0.46, 95% CI = 0.29-0.74; IVW, p = 1.40 × 10[-3]) was significantly associated with ITP as a protective factor. No significant associations between HSP and ITP and gut microbiota were found in reverse analyses.

CONCLUSION: Our study provides evidence of causal effects of gut microbiota on HSP and ITP, highlighting the importance of further research to clarify the underlying mechanisms and develop targeted therapeutic interventions for these autoimmune diseases.},
}

@article {pmid39027090,
year = {2024},
author = {Vasileva, S and Yap, CX and Whitehouse, AJO and Gratten, J and Eyles, D},
title = {Absence of association between maternal adverse events and long-term gut microbiome outcomes in the Australian autism biobank.},
journal = {Brain, behavior, & immunity - health},
volume = {39},
number = {},
pages = {100814},
pmid = {39027090},
issn = {2666-3546},
abstract = {INTRODUCTION: Maternal immune activation (MIA) and prenatal maternal stress (MatS) are well-studied risk factors for psychiatric conditions such as autism and schizophrenia. Animal studies have proposed the gut microbiome as a mechanism underlying this association and have found that risk factor-related gut microbiome alterations persist in the adult offspring. In this cross-sectional study, we assessed whether maternal immune activation and prenatal maternal stress were associated with long-term gut microbiome alterations in children using shotgun metagenomics.

METHODS: This cross-sectional study included children diagnosed with autism (N = 92), siblings without a diagnosis (N = 42), and unrelated children (N = 40) without a diagnosis who were recruited into the Australian Autism Biobank and provided a faecal sample. MIA exposure was inferred from self-reported data and included asthma/allergies, complications during pregnancy triggering an immune response, auto-immune conditions, and acute inflammation. Maternal stress included any of up to 9 stressful life events during pregnancy, such as divorce, job loss, and money problems. Data were analysed for a total of 174 children, of whom 63 (36%) were born to mothers with MIA and 84 (48%) were born to mothers who experienced maternal stress during pregnancy (where 33 [19%] experienced both). Gut microbiome data was assessed using shotgun metagenomic sequencing of the children's faecal samples.

RESULTS: In our cohort, MIA, but not MatS, was associated with ASD. Variance component analysis revealed no associations between any of the gut microbiome datasets and neither MIA nor MatS. After adjusting for age, sex, diet and autism diagnosis, there was no significant difference between groups for bacterial richness, α-diversity or β-diversity. We found no significant differences in species abundance in the main analyses. However, when stratifying the cohort by age, we found that Faecalibacterium prausnitzii E was significantly decreased in MIA children aged 11-17.

DISCUSSION: Consistent with previous findings, we found that children who were born to mothers with MIA were more likely to be diagnosed with autism. Unlike within animal studies, we found negligible microbiome differences associated with MIA and maternal stress. Given the current interest in the microbiome-gut-brain axis, researchers should exercise caution in translating microbiome findings from animal models to human contexts and the clinical setting.},
}

@article {pmid39026939,
year = {2024},
author = {Du, X and Cui, X and Fan, R and Pan, J and Cui, X},
title = {Characteristics of gut microbiome in patients with pediatric solid tumor.},
journal = {Frontiers in pediatrics},
volume = {12},
number = {},
pages = {1388673},
pmid = {39026939},
issn = {2296-2360},
abstract = {BACKGROUND: Pediatric solid tumors are a common malignant disease in children, and more and more studies have proved that there is an inseparable relationship between adult tumors and intestinal microbiome, but the changes in the intestinal microbiota of pediatric solid tumor (PST) patients have been scarcely examined. This study aims to examine the differences in the intestinal microbiota features between patients diagnosed with PST and healthy controls (HCs).

METHODS: To elucidate the unique characteristics of the gut microbiota in pediatric patients with solid tumors, we recruited 23 PST patients and 20 HCs. A total of 43 stool samples were gathered, and then 16S rRNA sequencing was performed.

RESULTS: We noticed a noticeable pattern of elevated diversity in the gut microbiota within the PST groups. The differences in microbial communities among two groups were remarkable, regarding the analysis at the class level, the abundance of Bacilli was markedly increased in PST patients compared to HCs (P < 0.05), regarding the analysis at the genus level, The presence of Enterococcus was significantly higher in PST cases compared to HCs (P < 0.01), while Lachnospiraceae unclassified, Lachnospira, Haemophilus and Colidextribacter in PST cases, the abundance was significantly reduced. (P < 0.05), 6 genera, including Bacilli, Lactobacillales, Enterococcaceae and Morganella, showed a significant enrichment compared to healthy controls, while 10 genera, including Bilophila, Colidextribacter, Pasteurellales, Haemophilus, Lachnospiraceae unclassified, Lachnospira and Fusobacteriales, were significant reduction in the PST groups.

CONCLUSION: Our research conducted the characterization analysis of the gut microbiota in PST patients for the first time. More importantly, there are some notable differences in the gut microbiota between PST patients and healthy controls, which we believe is an interesting finding.},
}

@article {pmid39026867,
year = {2024},
author = {Rudzite, M and O'Toole, GA},
title = {An energy coupling factor transporter of Streptococcus sanguinis impacts antibiotic susceptibility as well as metal and membrane homeostasis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.07.12.603315},
pmid = {39026867},
issn = {2692-8205},
abstract = {UNLABELLED: Streptococcus sanguinis is a prevalent member of human microbiome capable of acting as a causative agent of oral and respiratory infections. S. sanguinis competitive success within the infection niche is dependent on acquisition of metal ions and vitamins. Among the systems that bacteria use for micronutrient uptake is the energy coupling factor (ECF) transporter system EcfAAT. Here we describe physiological changes arising from EcfAAT transporter disruption. We found that EcfAAT contributes to S. sanguinis antibiotic sensitivity as well as metal and membrane homeostasis. Specifically, our work found that disruption of EcfAAT results in increased polymyxin susceptibility. We performed assessment of cell-associated metal content and found depletion of iron, magnesium, and manganese. Furthermore, membrane composition analysis revealed significant enrichment in unsaturated fatty acid species resulting in increased membrane fluidity. Our results demonstrate how disruption of a single EcfAAT transporter can have broad consequences on bacterial cell homeostasis. ECF transporters are of interest within the context of infection biology in bacterial species other than streptococci, hence work described here will further the understanding of how micronutrient uptake systems contribute to bacterial pathogenesis.

IMPORTANCE: Proficiency in micronutrient uptake is key for pathogen success in bacteria-bacteria and bacteria-host interactions within the infection context. Micronutrient uptake mechanisms are of interest in furthering the understanding of bacterial physiology within infection niche and as targets for design of antimicrobials. Here we describe how a deletion of a nutrient uptake transporter in S. sanguinis alters bacterial sensitivity to antibiotics. We also show that a defect in this candidate nutrient uptake system has consequences on the intracellular metal content, and also results in changes in membrane fatty acid composition and fluidity. This study demonstrates how disruption of a single nutrient uptake system disrupts bacterial physiology resulting in increased antibiotic sensitivity.},
}

@article {pmid39026780,
year = {2024},
author = {Bashor, L and Rawlinson, JE and Kozakiewicz, CP and Behzadi, E and Miller, C and Kim, J and Conry, M and Nehring, M and Carver, S and Abdo, Z and VandeWoude, S},
title = {Impacts of Antiretroviral Therapy on the Oral Microbiome and Periodontal Health of Feline Immunodeficiency Virus Positive Cats.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.07.10.602918},
pmid = {39026780},
issn = {2692-8205},
abstract = {UNLABELLED: Feline immunodeficiency virus (FIV) is the domestic cat analogue of HIV infection in humans. Both viruses induce oral disease in untreated individuals, with clinical signs that include gingivitis and periodontal lesions. Oral disease manifestations in HIV patients are abated by highly effective combination antiretroviral therapy (cART), though certain oral manifestations persist despite therapy. Microorganisms associated with oral cavity opportunistic infections in patients with HIV cause similar pathologies in cats. To further develop this model, we evaluated characteristics of feline oral health and oral microbiome during experimental FIV infection over an 8-month period following cART. Using 16S metagenomics sequencing, we evaluated gingival bacterial communities at four timepoints in uninfected and FIV-infected cats treated with cART or placebo. Comprehensive oral examinations were also conducted by a veterinary dental specialist over the experimental period. Gingival inflammation was higher in FIV-infected cats treated with placebo compared to cART-treated cats and controls at study endpoint. Oral microbiome alpha diversity increased in all groups, while beta diversity differed among treatment groups, documenting a significant effect of cART therapy on microbiome community composition. This finding has not previously been reported and indicates cART ameliorates immunodeficiency virus-associated oral disease via preservation of oral mucosal microbiota. Further, this study illustrates the value of the FIV animal model for investigations of mechanistic associations and therapeutic interventions for HIV oral manifestations.

IMPORTANCE: Feline Immunodeficiency Virus (FIV) is the viral analogue to HIV in humans, and both infections are associated with oral disease. Our study explored how antiretroviral treatment affects the oral health and microbiome of domestic cats infected with FIV. Cats treated with antiretroviral therapy had less gum inflammation and a different community of oral bacteria compared to untreated FIV-positive cats. This suggests that antiretroviral therapy not only helps in controlling FIV infection but also benefits feline oral health. These findings advance our understanding of antiretroviral treatment for lentiviral-associated oral disease and highlight FIV as a valuable experimental model for the similar condition in humans.},
}

@article {pmid39026688,
year = {2024},
author = {Agnew, A and Humm, E and Zhou, K and Gunsalus, RP and Zhou, ZH},
title = {Reconstruction and identification of the native PLP synthase complex from Methanosarcina acetivorans lysate.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.07.09.602819},
pmid = {39026688},
issn = {2692-8205},
abstract = {Many protein-protein interactions behave differently in biochemically purified forms as compared to their in vivo states. As such, determining native protein structures may elucidate structural states previously unknown for even well-characterized proteins. Here we apply the bottom-up structural proteomics method, cryoID , toward a model methanogenic archaeon. While they are keystone organisms in the global carbon cycle and active members of the human microbiome, there is a general lack of characterization of methanogen enzyme structure and function. Through the cryoID approach, we successfully reconstructed and identified the native Methanosarcina acetivorans pyridoxal 5'-phosphate (PLP) synthase (PdxS) complex directly from cryogenic electron microscopy (cryoEM) images of fractionated cellular lysate. We found that the native PdxS complex exists as a homo-dodecamer of PdxS subunits, and the previously proposed supracomplex containing both the synthase (PdxS) and glutaminase (PdxT) was not observed in cellular lysate. Our structure shows that the native PdxS monomer fashions a single 8α/8β TIM-barrel domain, surrounded by seven additional helices to mediate solvent and interface contacts. A density is present at the active site in the cryoEM map and is interpreted as ribose 5-phosphate. In addition to being the first reconstruction of the PdxS enzyme from a heterogeneous cellular sample, our results reveal a departure from previously published archaeal PdxS crystal structures, lacking the 37 amino acid insertion present in these prior cases. This study demonstrates the potential of applying the cryoID workflow to capture native structural states at atomic resolution for archaeal systems, for which traditional biochemical sample preparation is nontrivial.},
}

@article {pmid39026515,
year = {2024},
author = {Raboso, B and Pou, C and Abril, R and Erro, M and Sánchez, C and Manzano, C and Zamarrón, E and Suarez-Cuartin, G and González, J},
title = {Bronchiectasis.},
journal = {Open respiratory archives},
volume = {6},
number = {3},
pages = {100339},
pmid = {39026515},
issn = {2659-6636},
abstract = {Non-cystic fibrosis bronchiectasis, a condition that remains relatively underrecognized, has garnered increasing research focus in recent years. This scientific interest has catalyzed advancements in diagnostic methodologies, enabling comprehensive clinical and molecular profiling. Such progress facilitates the development of personalized treatment strategies, marking a significant step toward precision medicine for these patients. Bronchiectasis poses significant diagnostic challenges in both clinical settings and research studies. While computed tomography (CT) remains the gold standard for diagnosis, novel alternatives are emerging. These include artificial intelligence-powered algorithms, ultra-low dose chest CT, and magnetic resonance imaging (MRI) techniques, all of which are becoming recognized as feasible diagnostic tools. The precision medicine paradigm calls for refined characterization of bronchiectasis patients by analyzing their inflammatory and molecular profiles. Research into the underlying mechanisms of inflammation and the evaluation of biomarkers such as neutrophil elastase, mucins, and antimicrobial peptides have led to the identification of distinct patient endotypes. These endotypes present variable clinical outcomes, necessitating tailored therapeutic interventions. Among these, eosinophilic bronchiectasis is notable for its prevalence and specific prognostic factors, calling for careful consideration of treatable traits. A deeper understanding of the microbiome's influence on the pathogenesis and progression of bronchiectasis has inspired a holistic approach, which considers the multibiome as an interconnected microbial network rather than treating pathogens as solitary entities. Interactome analysis therefore becomes a vital tool for pinpointing alterations during both stable phases and exacerbations. This array of innovative approaches has revolutionized the personalization of treatments, incorporating therapies such as inhaled mannitol or ARINA-1, brensocatib for anti-inflammatory purposes, and inhaled corticosteroids specifically for patients with eosinophilic bronchiectasis.},
}

@article {pmid39026297,
year = {2024},
author = {Mabaso, NG and Ngobese, B and Ganesan, H and van der Westhuizen, D and Hassan, WM and Abbai, NS},
title = {The vaginal microbiome of South African pregnant women living with human immunodeficiency virus (HIV) with and without Chlamydia trachomatis infection.},
journal = {BMC women's health},
volume = {24},
number = {1},
pages = {410},
pmid = {39026297},
issn = {1472-6874},
support = {132729//National Research Foundation/ ; productivity funding//University of KwaZulu-Natal/ ; },
mesh = {Humans ; Female ; South Africa/epidemiology ; *Vagina/microbiology ; Adult ; Pregnancy ; *Chlamydia Infections/epidemiology/microbiology ; Cross-Sectional Studies ; *HIV Infections/microbiology/complications ; *Chlamydia trachomatis/isolation & purification ; *Microbiota ; Pregnancy Complications, Infectious/microbiology/epidemiology ; Young Adult ; Gardnerella ; Lactobacillus/isolation & purification ; },
abstract = {BACKGROUND: Chlamydia genital infections continue to be a serious health concern globally. Previous studies have reported that Chlamydia trachomatis infection alters the vaginal microbiota of infected women. This study investigated differences in the vaginal microbiome of South African pregnant women living with HIV with and without C. trachomatis infection.

METHODS: This was a cross-sectional study among 385 pregnant women, recruited from the King Edward VIII Hospital in Durban, South Africa. C. trachomatis was detected using the Applied Biosystems™ TaqMan[®] Assays. A total of 40 samples, 20 C. trachomatis positive and 20 C. trachomatis negative, were selected for sequencing. The sequencing of the vaginal microbiome was performed using the PacBio platform. Statistical analysis was performed on IBM SPSS version 26.

RESULTS: The prevalence of C. trachomatis infection was 12.2% (47/385). The genus Gardnerella (32.14% vs. 24.02%) and species in the genus Gardnerella (31.97% vs. 24.03%) were more abundant in the C. trachomatis-infected group compared to the uninfected group. Lactobacillus iners were also more abundant in the C. trachomatis-infected women (28.30%) compared to the uninfected women. However, these observed patterns did not reach statistical significance. Discriminant analysis showed that the class Alpha-Proteobacteria; order Bacillales; family Enterococcaceae; the genera Enhydrobacter, Enterococcus, and Parabacteroides; Enterococcus spp.; and Pseudomonas stutzeri significantly contributed to a model separating C. trachomatis-infected women from the uninfected group (p < 0.05).

CONCLUSION: The organisms and taxa that significantly contributed to separating the vaginal microbiota of C. trachomatis-infected women from the uninfected women in this study cohort have not been previously observed in association with C. trachomatis infection or the vaginal microbiota. Future studies in larger cohorts that will investigate the role of these microorganisms in C. trachomatis infection and the vaginal microbiota are required.},
}

Humans
Female
South Africa/epidemiology
*Vagina/microbiology
Adult
Pregnancy
*Chlamydia Infections/epidemiology/microbiology
Cross-Sectional Studies
*HIV Infections/microbiology/complications
*Chlamydia trachomatis/isolation & purification
*Microbiota
Pregnancy Complications, Infectious/microbiology/epidemiology
Young Adult
Gardnerella
Lactobacillus/isolation & purification

@article {pmid39026296,
year = {2024},
author = {Abdelfadil, MR and Patz, S and Kolb, S and Ruppel, S},
title = {Unveiling the influence of salinity on bacterial microbiome assembly of halophytes and crops.},
journal = {Environmental microbiome},
volume = {19},
number = {1},
pages = {49},
pmid = {39026296},
issn = {2524-6372},
abstract = {BACKGROUND: Climate change and anthropogenic activities intensify salinity stress impacting significantly on plant productivity and biodiversity in agroecosystems. There are naturally salt-tolerant plants (halophytes) that can grow and withstand such harsh conditions. Halophytes have evolved along with their associated microbiota to adapt to hypersaline environments. Identifying shared microbial taxa between halophyte species has rarely been investigated. We performed a comprehensive meta-analysis using the published bacterial 16S rRNA gene sequence datasets to untangle the rhizosphere microbiota structure of two halophyte groups and non-halophytes. We aimed for the identification of marker taxa of plants being adapted to a high salinity using three independent approaches.

RESULTS: Fifteen studies met the selection criteria for downstream analysis, consisting of 40 plants representing diverse halophyte and non-halophyte species. Microbiome structural analysis revealed distinct compositions for halophytes that face high salt concentrations in their rhizosphere compared to halophytes grown at low salt concentrations or from non-halophytes. For halophytes grown at high salt concentrations, we discovered three bacterial genera that were independently detected through the analysis of the core microbiome, key hub taxa by network analysis and random forest analysis. These genera were Thalassospira, Erythrobacter, and Marinobacter.

CONCLUSIONS: Our meta-analysis revealed that salinity level is a critical factor in affecting the rhizosphere microbiome assembly of plants. Detecting marker taxa across high-halophytes may help to select Bacteria that might improve the salt tolerance of non-halophytic plants.},
}

@article {pmid39026261,
year = {2024},
author = {Lee, M and Kaul, A and Ward, JM and Zhu, Q and Richards, M and Wang, Z and González, A and Parks, CG and Beane Freeman, LE and Umbach, DM and Motsinger-Reif, AA and Knight, R and London, SJ},
title = {House dust metagenome and pulmonary function in a US farming population.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {129},
pmid = {39026261},
issn = {2049-2618},
support = {Z01-ES049030 and Z01-ES102385//National Institutes of Health, the National Institute of Environmental Health Sciences/ ; Z01-ES049030 and Z01-ES102385//National Institutes of Health, the National Institute of Environmental Health Sciences/ ; Z01-ES049030 and Z01-ES102385//National Institutes of Health, the National Institute of Environmental Health Sciences/ ; Z01-CP010119B/CA/NCI NIH HHS/United States ; },
mesh = {*Dust/analysis ; Humans ; *Metagenome ; Female ; Male ; United States ; *Microbiota/genetics ; Middle Aged ; Lung/microbiology ; Adult ; Bacteria/classification/genetics/isolation & purification ; Forced Expiratory Volume ; Agriculture ; Respiratory Function Tests ; Vital Capacity ; Metagenomics/methods ; },
abstract = {BACKGROUND: Chronic exposure to microorganisms inside homes can impact respiratory health. Few studies have used advanced sequencing methods to examine adult respiratory outcomes, especially continuous measures. We aimed to identify metagenomic profiles in house dust related to the quantitative traits of pulmonary function and airway inflammation in adults. Microbial communities, 1264 species (389 genera), in vacuumed bedroom dust from 779 homes in a US cohort were characterized by whole metagenome shotgun sequencing. We examined two overall microbial diversity measures: richness (the number of individual microbial species) and Shannon index (reflecting both richness and relative abundance). To identify specific differentially abundant genera, we applied the Lasso estimator with high-dimensional inference methods, a novel framework for analyzing microbiome data in relation to continuous traits after accounting for all taxa examined together.

RESULTS: Pulmonary function measures (forced expiratory volume in one second (FEV1), forced vital capacity (FVC), and FEV1/FVC ratio) were not associated with overall dust microbial diversity. However, many individual microbial genera were differentially abundant (p-value < 0.05 controlling for all other microbial taxa examined) in relation to FEV1, FVC, or FEV1/FVC. Similarly, fractional exhaled nitric oxide (FeNO), a marker of airway inflammation, was unrelated to overall microbial diversity but associated with differential abundance for many individual genera. Several genera, including Limosilactobacillus, were associated with a pulmonary function measure and FeNO, while others, including Moraxella to FEV1/FVC and Stenotrophomonas to FeNO, were associated with a single trait.

CONCLUSIONS: Using state-of-the-art metagenomic sequencing, we identified specific microorganisms in indoor dust related to pulmonary function and airway inflammation. Some were previously associated with respiratory conditions; others were novel, suggesting specific environmental microbial components contribute to various respiratory outcomes. The methods used are applicable to studying microbiome in relation to other continuous outcomes. Video Abstract.},
}

*Dust/analysis
Humans
*Metagenome
Female
Male
United States
*Microbiota/genetics
Middle Aged
Lung/microbiology
Adult
Bacteria/classification/genetics/isolation & purification
Forced Expiratory Volume
Agriculture
Respiratory Function Tests
Vital Capacity
Metagenomics/methods

@article {pmid39026121,
year = {2024},
author = {Couture, G and Cheang, SE and Suarez, C and Chen, Y and Bacalzo, NP and Jiang, J and Weng, CC and Stacy, A and Castillo, JJ and Delannoy-Bruno, O and Webber, DM and Barratt, MJ and Gordon, JI and Mills, DA and German, JB and Fukagawa, NK and Lebrilla, CB},
title = {A multi-glycomic platform for the analysis of food carbohydrates.},
journal = {Nature protocols},
volume = {},
number = {},
pages = {},
pmid = {39026121},
issn = {1750-2799},
support = {R01 DK124193/DK/NIDDK NIH HHS/United States ; },
abstract = {Carbohydrates comprise the largest fraction of most diets and exert a profound impact on health. Components such as simple sugars and starch supply energy, while indigestible components, deemed dietary fiber, reach the colon to provide food for the tens of trillions of microbes that make up the gut microbiota. The interactions between dietary carbohydrates, our gastrointestinal tracts, the gut microbiome and host health are dictated by their structures. However, current methods for analysis of food glycans lack the sensitivity, specificity and throughput needed to quantify and elucidate these myriad structures. This protocol describes a multi-glycomic approach to food carbohydrate analysis in which the analyte might be any food item or biological material such as fecal and cecal samples. The carbohydrates are extracted by ethanol precipitation, and the resulting samples are subjected to rapid-throughput liquid chromatography (LC)-tandem mass spectrometry (LC-MS/MS) methods. Quantitative analyses of monosaccharides, glycosidic linkages, polysaccharides and alcohol-soluble carbohydrates are performed in 96-well plates at the milligram scale to reduce the biomass of sample required and enhance throughput. Detailed stepwise processes for sample preparation, LC-MS/MS and data analysis are provided. We illustrate the application of the protocol to a diverse set of foods as well as different apple cultivars and various fermented foods. Furthermore, we show the utility of these methods in elucidating glycan-microbe interactions in germ-free and colonized mice. These methods provide a framework for elucidating relationships between dietary fiber, the gut microbiome and human physiology. These structures will further guide nutritional and clinical feeding studies that enhance our understanding of the role of diet in nutrition and health.},
}

@article {pmid39026037,
year = {2024},
author = {Migaud, ME and Ziegler, M and Baur, JA},
title = {Regulation of and challenges in targeting NAD[+] metabolism.},
journal = {Nature reviews. Molecular cell biology},
volume = {},
number = {},
pages = {},
pmid = {39026037},
issn = {1471-0080},
abstract = {Nicotinamide adenine dinucleotide, in its oxidized (NAD[+]) and reduced (NADH) forms, is a reduction-oxidation (redox) co-factor and substrate for signalling enzymes that have essential roles in metabolism. The recognition that NAD[+] levels fall in response to stress and can be readily replenished through supplementation has fostered great interest in the potential benefits of increasing or restoring NAD[+] levels in humans to prevent or delay diseases and degenerative processes. However, much about the biology of NAD[+] and related molecules remains poorly understood. In this Review, we discuss the current knowledge of NAD[+] metabolism, including limitations of, assumptions about and unappreciated factors that might influence the success or contribute to risks of NAD[+] supplementation. We highlight several ongoing controversies in the field, and discuss the role of the microbiome in modulating the availability of NAD[+] precursors such as nicotinamide riboside (NR) and nicotinamide mononucleotide (NMN), the presence of multiple cellular compartments that have distinct pools of NAD[+] and NADH, and non-canonical NAD[+] and NADH degradation pathways. We conclude that a substantial investment in understanding the fundamental biology of NAD[+], its detection and its metabolites in specific cells and cellular compartments is needed to support current translational efforts to safely boost NAD[+] levels in humans.},
}

@article {pmid39026025,
year = {2024},
author = {Perry, RW and Mullish, BH and Alexander, JL and Shah, R and Danckert, NP and Blanco, JM and Roberts, L and Liu, Z and Chrysostomou, D and Radhakrishnan, ST and Balarajah, S and Barry, R and Hicks, LC and Williams, HRT and Marchesi, JR},
title = {3D printed rectal swabs for assessing the gut microbiome, metabolome and inflammation.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {16613},
pmid = {39026025},
issn = {2045-2322},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Feces/microbiology ; *Metabolome ; *Inflammatory Bowel Diseases/microbiology/metabolism ; *Printing, Three-Dimensional ; *RNA, Ribosomal, 16S/genetics ; Male ; Female ; Adult ; Rectum/microbiology/metabolism ; Leukocyte L1 Antigen Complex/metabolism/analysis ; Inflammation/microbiology/metabolism ; Middle Aged ; Specimen Handling/methods ; },
abstract = {Investigating the gut microbiome and metabolome frequently requires faecal samples, which can be difficult to obtain. Previous studies have shown that rectal swabs are comparable to faecal samples for analysing gut microbiota composition and key metabolites. In this study, 3D printed rectal swabs were compared with conventional flocked swabs and faecal samples, due to the potential advantages 3D printing as a technique offers for swab production and development. 16S rRNA gene sequencing, qPCR and metabolite profiling (using [1]H-NMR spectroscopy) were performed on swab and faecal samples from healthy participants. Faecal calprotectin and total protein analysis were performed on samples from inflammatory bowel disease (IBD) patients. There were no significant differences between both swab types and faecal samples when assessing key measures of alpha and beta diversity, and differences in the abundance of major phyla. There was a strong correlation between both swab types and faecal samples for all combined metabolites detected by NMR. In IBD patients, there was no significant difference in faecal calprotectin and total protein levels between both swab types and faecal samples. These data lead us to conclude that 3D printed swabs are equivalent to flocked swabs for the analysis of the gut microbiome, metabolome and inflammation.},
}

Humans
*Gastrointestinal Microbiome
*Feces/microbiology
*Metabolome
*Inflammatory Bowel Diseases/microbiology/metabolism
*Printing, Three-Dimensional
*RNA, Ribosomal, 16S/genetics
Male
Female
Adult
Rectum/microbiology/metabolism
Leukocyte L1 Antigen Complex/metabolism/analysis
Inflammation/microbiology/metabolism
Middle Aged
Specimen Handling/methods

@article {pmid39025794,
year = {2024},
author = {Overbeek, MF and Rutters, F and Nieuwdorp, M and Davids, M and van Valkengoed, I and Galenkamp, H and van den Born, BJ and Beulens, JWJ and Muilwijk, M},
title = {Plasma sphingolipids mediate the association between gut microbiome composition and type 2 diabetes risk in the HELIUS cohort: a case-cohort study.},
journal = {BMJ open diabetes research & care},
volume = {12},
number = {4},
pages = {},
pmid = {39025794},
issn = {2052-4897},
mesh = {Humans ; *Diabetes Mellitus, Type 2/microbiology/blood/epidemiology ; *Sphingolipids/blood ; *Gastrointestinal Microbiome ; Middle Aged ; Male ; Female ; Adult ; Aged ; Case-Control Studies ; Cohort Studies ; Young Adult ; Adolescent ; Risk Factors ; Follow-Up Studies ; Biomarkers/blood/analysis ; RNA, Ribosomal, 16S/analysis ; Prognosis ; },
abstract = {INTRODUCTION: The association between the gut microbiome and incident type 2 diabetes (T2D) is potentially partly mediated through sphingolipids, however these possible mediating mechanisms have not been investigated. We examined whether sphingolipids mediate the association between gut microbiome and T2D, using data from the Healthy Life in an Urban Setting study.

RESEARCH DESIGN AND METHODS: Participants were of Dutch or South-Asian Surinamese ethnicity, aged 18-70 years, and without T2D at baseline. A case-cohort design (subcohort n=176, cases incident T2D n=36) was used. The exposure was measured by 16S rRNA sequencing (gut microbiome) and mediator by targeted metabolomics (sphingolipids). Dimensionality reduction was achieved by principle component analysis and Shannon diversity. Cox regression and procrustes analyses were used to assess the association between gut microbiome and T2D and sphingolipids and T2D, and between gut microbiome and sphingolipids, respectively. Mediation was tested familywise using mediation analysis with permutation testing and Bonferroni correction.

RESULTS: Our study confirmed associations between gut microbiome and T2D and sphingolipids and T2D. Additionally, we showed that the gut microbiome was associated with sphingolipids. The association between gut microbiome and T2D was partly mediated by a sphingolipid principal component, which represents a dominance of ceramide species over more complex sphingolipids (HR 1.17; 95% CI 1.08 to 1.28; proportional explained 48%), and by Shannon diversity (HR 0.97; 95% CI 0.95 to 0.99; proportional explained 24.8%).

CONCLUSIONS: These data suggest that sphingolipids mediate the association between microbiome and T2D risk. Future research is needed to confirm observed findings and elucidate causality on a molecular level.},
}

Humans
*Diabetes Mellitus, Type 2/microbiology/blood/epidemiology
*Sphingolipids/blood
*Gastrointestinal Microbiome
Middle Aged
Male
Female
Adult
Aged
Case-Control Studies
Cohort Studies
Young Adult
Adolescent
Risk Factors
Follow-Up Studies
Biomarkers/blood/analysis
RNA, Ribosomal, 16S/analysis
Prognosis

@article {pmid39025292,
year = {2024},
author = {Guo, X and Zhao, W and Yin, D and Mei, Z and Wang, F and Tiedje, J and Ling, S and Hu, S and Xu, T},
title = {Aspirin altered antibiotic resistance genes response to sulfonamide in the gut microbiome of zebrafish.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {359},
number = {},
pages = {124566},
doi = {10.1016/j.envpol.2024.124566},
pmid = {39025292},
issn = {1873-6424},
abstract = {Pharmaceuticals are widespread in aquatic environments and might contribute to the prevalence of antibiotic resistance. However, the co-effect of antibiotics and non-antibiotic pharmaceuticals on the gut microbiome of fish is poorly understood. In this study, we characterized the variation of the zebrafish gut microbiome and resistome after exposure to sulfamethoxazole (SMX) and aspirin under different treatments. SMX contributed to the significant increase in the antibiotic resistance genes (ARGs) richness and abundance with 46 unique ARGs and five mobile genetic elements (MGEs) detected. Combined exposure to SMX and aspirin enriched total ARGs abundance and rearranged microbiota under short-term exposure. Exposure time was more responsible for resistome and the gut microbiome than exposure concentrations. Perturbation of the gut microbiome contributed to the functional variation related to RNA processing and modification, cell motility, signal transduction mechanisms, and defense mechanisms. A strong significant positive correlation (R = 0.8955, p < 0.001) was observed between total ARGs and MGEs regardless of different treatments revealing the key role of MGEs in ARGs transmission. Network analysis indicated most of the potential ARGs host bacteria belonged to Proteobacteria. Our study suggested that co-occurrence of non-antibiotics and antibiotics could accelerate the spread of ARGs in gut microbial communities and MGEs played a key role.},
}

@article {pmid39025154,
year = {2024},
author = {Keshri, J and Mankazana, BBJ and Kachieng'a, L and Momba, MNB},
title = {Indigenous metal-tolerant mine water bacterial populations under varying metal stresses.},
journal = {The Science of the total environment},
volume = {948},
number = {},
pages = {174830},
doi = {10.1016/j.scitotenv.2024.174830},
pmid = {39025154},
issn = {1879-1026},
abstract = {The present study investigated the indigenous metal-tolerant bacterial populations in the mine-water microbiome. Our intention was to assess the effects of the metal concentrations in mine water on the bacterial community of mine waters. The bacterial communities in Vanadium and Gold mine-water samples were exposed to different heavy-metal Arsenic, Cadmium, Chromium, Nickel, Mercury and Vanadium at two different concentrations (5 and 25 mM). The 16S rRNA amplicon from mine waters were sequenced using the Illumina's NGS MiSeq platform. Data analysis revealed a high diversity in the bacterial populations associated with the different heavy metals at different concentrations. The taxonomic profiles obtained after the exposure were different in different salts, but mostly dominated by Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria and Firmicutes at variable relative abundance. Principal Component Analysis (PCoA) predicts the clear community shift after exposure with heavy metals salts and emergence of tolerant community depending upon the specific community present in the original mine water.},
}

@article {pmid39025064,
year = {2024},
author = {Mbatchou, J and McPeek, MS},
title = {JASPER: Fast, powerful, multitrait association testing in structured samples gives insight on pleiotropy in gene expression.},
journal = {American journal of human genetics},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajhg.2024.06.010},
pmid = {39025064},
issn = {1537-6605},
abstract = {Joint association analysis of multiple traits with multiple genetic variants can provide insight into genetic architecture and pleiotropy, improve trait prediction, and increase power for detecting association. Furthermore, some traits are naturally high-dimensional, e.g., images, networks, or longitudinally measured traits. Assessing significance for multitrait genetic association can be challenging, especially when the sample has population sub-structure and/or related individuals. Failure to adequately adjust for sample structure can lead to power loss and inflated type 1 error, and commonly used methods for assessing significance can work poorly with a large number of traits or be computationally slow. We developed JASPER, a fast, powerful, robust method for assessing significance of multitrait association with a set of genetic variants, in samples that have population sub-structure, admixture, and/or relatedness. In simulations, JASPER has higher power, better type 1 error control, and faster computation than existing methods, with the power and speed advantage of JASPER increasing with the number of traits. JASPER is potentially applicable to a wide range of association testing applications, including for multiple disease traits, expression traits, image-derived traits, and microbiome abundances. It allows for covariates, ascertainment, and rare variants and is robust to phenotype model misspecification. We apply JASPER to analyze gene expression in the Framingham Heart Study, where, compared to alternative approaches, JASPER finds more significant associations, including several that indicate pleiotropic effects, most of which replicate previous results, while others have not previously been reported. Our results demonstrate the promise of JASPER for powerful multitrait analysis in structured samples.},
}

@article {pmid39024951,
year = {2024},
author = {Li, L and Xiao, S and Dai, X and Tang, Z and Wang, Y and Ali, M and Ataya, FS and Sahar, I and Iqbal, M and Wu, Y and Li, K},
title = {Multi-omics analysis and the remedial effects of Swertiamarin on hepatic injuries caused by CCl4.},
journal = {Ecotoxicology and environmental safety},
volume = {282},
number = {},
pages = {116734},
doi = {10.1016/j.ecoenv.2024.116734},
pmid = {39024951},
issn = {1090-2414},
abstract = {Hepatic diseases pose a significant threat to community health, impacting the quality of life and longevity of millions worldwide. Despite revolutionary advancements in treatment, liver diseases remain a pressing issue, necessitating the development of more effective therapeutic approaches. Here, we conducted a comprehensive multi-omics analysis to investigate the underlying mechanism of Swertiamarin in alleviating hepatic injuries induced by CCl4 in mice. We divided 100 Kunming mice into five groups: RC (control), RM (CCl4), RD (15 mg/Kg Swertiamarin), RZ (30 mg/Kg Swertiamarin), and RG (60 mg/Kg Swertiamarin). Animals in groups RD, RZ, and RG received daily Swertiamarin via gavage, while those in groups RM, RD, RZ, and RG were treated with CCl4 solution intraperitoneally every four days, nine times in total. Our findings revealed that mice in the RM group exhibited slightly lower average weights compared to other groups, along with significantly higher liver weight (p<0.0001) and liver index (p<0.0001). Pathological analysis indicated liver damage characterized by cell degeneration, inflammatory cell infiltration, and hepatic fibrosis in the CCl4-induced group. In contrast, Swertiamarin supplementation mitigated these effects, reducing denatured cells, inflammatory cells, and collagenous fibers in the liver. Serum analysis showed elevated levels of TNF-α (p<0.001), IL-6 (p<0.05), ALT (p<0.001), AST (p<0.0001), MDA (p<0.001), and Hyp (p<0.001) in CCl4-induced animals, along with lower levels of T-AOC (p<0.001), GSH-px (p<0.0001), SOD (p<0.001), and CAT (p<0.01). Microbiome analysis revealed significant differences among groups, with pathogenic taxa such as Arthrinium and Aureobasidium, and probiotic Saccharomyces showing notable variations. Metabolomics analysis identified numerous differentially abundant metabolites, with Swertiamarin-treated animals exhibiting distinct profiles. Our findings highlight the potential of Swertiamarin ameliorating CCl4-induced liver toxicity through modulation of antioxidant capacity, inflammatory response, gut microbiota, and metabolites. These insights may inform the development of novel therapies for liver injury.},
}

@article {pmid39024947,
year = {2024},
author = {Wueppenhorst, K and Alkassab, AT and Beims, H and Ernst, U and Friedrich, E and Illies, I and Janke, M and Kirchner, WH and Seidel, K and Steinert, M and Yurkov, A and Erler, S and Odemer, R},
title = {Honey bee colonies can buffer short-term stressor effects of pollen restriction and fungicide exposure on colony development and the microbiome.},
journal = {Ecotoxicology and environmental safety},
volume = {282},
number = {},
pages = {116723},
doi = {10.1016/j.ecoenv.2024.116723},
pmid = {39024947},
issn = {1090-2414},
abstract = {Honey bees (Apis mellifera) have to withstand various environmental stressors alone or in combination in agriculture settings. Plant protection products are applied to achieve high crop yield, but residues of their active substances are frequently detected in bee matrices and could affect honey bee colonies. In addition, intensified agriculture could lead to resource limitation for honey bees. This study aimed to compare the response of full-sized and nucleus colonies to the combined stressors of fungicide exposure and resource limitation. A large-scale field study was conducted simultaneously at five different locations across Germany, starting in spring 2022 and continuing through spring 2023. The fungicide formulation Pictor® Active (active ingredients boscalid and pyraclostrobin) was applied according to label instructions at the maximum recommended rate on oil seed rape crops. Resource limitation was ensured by pollen restriction using a pollen trap and stressor responses were evaluated by assessing colony development, brood development, and core gut microbiome alterations. Furthermore, effects on the plant nectar microbiome were assessed since nectar inhabiting yeast are beneficial for pollination. We showed, that honey bee colonies were able to compensate for the combined stressor effects within six weeks. Nucleus colonies exposed to the combined stressors showed a short-term response with a less favorable brood to bee ratio and reduced colony development in May. No further impacts were observed in either the nucleus colonies or the full-sized colonies from July until the following spring. In addition, no fungicide-dependent differences were found in core gut and nectar microbiomes, and these differences were not distinguishable from local or environmental effects. Therefore, the provision of sufficient resources is important to increase the resilience of honey bees to a combination of stressors.},
}

@article {pmid39024858,
year = {2024},
author = {Janse van Rensburg, H and Stengele, K and Schlaeppi, K},
title = {Understanding plant responsiveness to microbiome feedbacks.},
journal = {Current opinion in plant biology},
volume = {81},
number = {},
pages = {102603},
doi = {10.1016/j.pbi.2024.102603},
pmid = {39024858},
issn = {1879-0356},
abstract = {Plant microbiome interactions are bidirectional with processes leading to microbiome assembly and processes leading to effects on plants, so called microbiome feedbacks. With belowground focus we systematically decomposed both of these directions into plant and (root and rhizosphere) microbiome components to identify methodological challenges and research priorities. We found that the bidirectionality of plant microbiome interactions presents a challenge for genetic studies. Establishing causality is particularly difficult when a plant mutant has both, an altered phenotype and an altered microbiome. Is the mutation directly affecting the microbiome (e.g., through root exudates), which then causes an altered phenotype of the plant and/or is the altered microbiome the consequence of the mutation altering the plant's phenotype (e.g., root architecture)? Here, we put forward that feedback experiments allow to separate cause and effect and furthermore, they are useful for investigating plant interactions with complex microbiomes in natural soils. They especially allow to investigate the plant genetic basis how plants respond to soil microbiomes and we stress that such microbiome feedbacks are understudied compared to the mechanisms contributing to microbiome assembly. Thinking towards application, this may allow to develop crops with both abilities to assemble a beneficial microbiome and to actively exploit its feedbacks.},
}

@article {pmid39024793,
year = {2024},
author = {Jiang, Y and Jian, T and Song, H and Zhang, G and Ling, J},
title = {Amelioration of hyperuricemia by cordycepin and Cordyceps militaris aqueous extract in mice via modulating gut microbiota and restoring metabolic profile.},
journal = {Journal of pharmaceutical and biomedical analysis},
volume = {249},
number = {},
pages = {116368},
doi = {10.1016/j.jpba.2024.116368},
pmid = {39024793},
issn = {1873-264X},
abstract = {In this study, we first screened and evaluated the inhibitory effects of seven medicinal fungi on diseases such as hyperuricemia (HUA). Then, using metabolomics and gut microbiome methods, the focus was on analyzing and evaluating the effects of the aqueous extract of Cordyceps. militaris (CME) and cordycepin on potassium oxyzinate induced HUA mice. It was found that CME exhibits good uric acid lowering activity in both in vivo and in vitro experiments. It can relieve hyperuricemia by inhibiting xanthine oxidase enzyme activity, reducing the production of xanthine precursors, and inhibiting insulin resistance. The uric acid-lowering efficacy of cordycepin in vivo is comparable to that of CME. The species abundance of Oscillibacter, Alistipes, Prevotellaaceae_NK3B31, Lachnospiraceae_NK4A136 were decreased after treatment with CME and cordycepin. The metabolomics analysis of cecal contents and fecal samples elucidated the mechanism of intervention of CME on hyperuricemia from different perspectives. This suggests that we should consider carefully when selecting samples. This current research provides the scientific foundation for the medicinal research of C. militaris and the maintenance of human health.},
}

@article {pmid39024753,
year = {2024},
author = {Park, EJ and Kim, JY and Jaiswal, V and Park, HS and Ki, DB and Lee, YS and Lee, HJ},
title = {High-molecular-weight Fucoidan exerts an immune-enhancing effect in RAW 264.7 cells and cyclophosphamide-induced immunosuppression rat by altering the gut microbiome.},
journal = {International immunopharmacology},
volume = {139},
number = {},
pages = {112677},
doi = {10.1016/j.intimp.2024.112677},
pmid = {39024753},
issn = {1878-1705},
abstract = {High-molecular-weight fucoidan (Fucoidan P), sourced from Undaria pinnatifida exhibits several health benefits, including immunomodulation. However, the mechanisms underlying the immune-enhancing effects of Fucoidan P remain unclear. Here, we investigated the immune-enhancing effects and the potential mechanisms of Fucoidan P using RAW 264.7 macrophages and cyclophosphamide (CP)-induced immunosuppression rat model. In macrophages, Fucoidan P showed dose-dependent stimulation by increasing cell proliferation, nitric oxide production, and gene expression of inducible nitric oxide synthase, cyclooxygenase-2, and proinflammatory cytokines. These effects are mediated through the activation of the nuclear factor-kappa B (NF-κB) signaling pathway. Moreover, orally administered Fucoidan P was evaluated in immunosuppressed rats treated with CP. Fucoidan P administration increased hematological values and natural killer cell activity, and positively affected nitrite and prostaglandin E2 levels. The Fucoidan P treatment groups exhibited improved serum cytokine levels as well as splenic and intestinal cytokine mRNA expression compared to the model group. Fucoidan P also mitigated splenic damage and increased the phosphorylation of NF-κB and NF-κB inhibitor alpha (IκBα). Furthermore, Fucoidan P treatment altered the gut microbiota composition, enhancing the alpha diversity, evenness, and abundance of Bacteroidetes, which are associated with immune function. Taken together, our findings suggest that Fucoidan P exerts beneficial effects on immune function by activating NF-κB and modulating gut microbiota. These findings suggested its potential as a therapeutic agent for immune enhancement.},
}

@article {pmid39024554,
year = {2024},
author = {Lacunza, E and Fink, V and Salas, ME and Gun, AM and Basiletti, JA and Picconi, MA and Golubicki, M and Robbio, J and Kujaruk, M and Iseas, S and Williams, SL and Figueroa, M and Coso, O and Cahn, P and Ramos, JC and Abba, MC},
title = {Transcriptome and microbiome-immune changes across preinvasive and invasive anal cancer lesions.},
journal = {JCI insight},
volume = {},
number = {},
pages = {},
doi = {10.1172/jci.insight.180907},
pmid = {39024554},
issn = {2379-3708},
abstract = {Anal squamous cell carcinoma (ASCC) is a rare gastrointestinal malignancy linked to high-risk Human papillomavirus (HPV) infection, which develops from precursor lesions like Low-Grade Squamous Intraepithelial Lesions (LGSIL) and High-Grade Squamous Intraepithelial Lesions (HGSIL). ASCC incidence varies across populations, posing increased risk for People Living with HIV (PLWH). Our investigation focused on transcriptomic and metatranscriptomic changes from Squamous Intraepithelial Lesions (SILs) to ASCC. Metatranscriptomic analysis highlighted specific bacterial species (e.g., Fusobacterium nucleatum, Bacteroides fragilis) more prevalent in ASCC than precancerous lesions. These species correlated with gene encoding enzymes (Acca, glyQ, eno, pgk, por) and oncoproteins (FadA, dnaK), presenting potential diagnostic or treatment markers. Unsupervised transcriptome analysis identified distinct sample clusters reflecting histological diagnosis, immune infiltrate, HIV/HPV status, and pathway activities, recapitulating anal cancer progression's natural history. Our study unveiled molecular mechanisms in anal cancer progression, aiding in stratifying HGSIL cases based on low- or high-risk progression to malignancy.},
}

@article {pmid39024520,
year = {2024},
author = {de Castilhos, J and Tillmanns, K and Blessing, J and Laraño, A and Borisov, V and Stein-Thoeringer, CK},
title = {Microbiome and pancreatic cancer: time to think about chemotherapy.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2374596},
pmid = {39024520},
issn = {1949-0984},
mesh = {Humans ; *Pancreatic Neoplasms/drug therapy/microbiology ; *Gastrointestinal Microbiome/drug effects ; *Carcinoma, Pancreatic Ductal/drug therapy/microbiology ; *Tumor Microenvironment/drug effects ; *Antineoplastic Agents/therapeutic use ; Animals ; Bacteria/metabolism/drug effects/genetics/classification ; Precision Medicine ; Drug Resistance, Neoplasm ; },
abstract = {Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive cancer characterized by late diagnosis, rapid progression, and a high mortality rate. Its complex biology, characterized by a dense, stromal tumor environment with an immunosuppressive milieu, contributes to resistance against standard treatments like chemotherapy and radiation. This comprehensive review explores the dynamic role of the microbiome in modulating chemotherapy efficacy and outcomes in PDAC. It delves into the microbiome's impact on drug metabolism and resistance, and the interaction between microbial elements, drugs, and human biology. We also highlight the significance of specific bacterial species and microbial enzymes in influencing drug action and the immune response in the tumor microenvironment. Cutting-edge methodologies, including artificial intelligence, low-biomass microbiome analysis and patient-derived organoid models, are discussed, offering insights into the nuanced interactions between microbes and cancer cells. The potential of microbiome-based interventions as adjuncts to conventional PDAC treatments are discussed, paving the way for personalized therapy approaches. This review synthesizes recent research to provide an in-depth understanding of how the microbiome affects chemotherapy efficacy. It focuses on elucidating key mechanisms and identifying existing knowledge gaps. Addressing these gaps is crucial for enhancing personalized medicine and refining cancer treatment strategies, ultimately improving patient outcomes.},
}

Humans
*Pancreatic Neoplasms/drug therapy/microbiology
*Gastrointestinal Microbiome/drug effects
*Carcinoma, Pancreatic Ductal/drug therapy/microbiology
*Tumor Microenvironment/drug effects
*Antineoplastic Agents/therapeutic use
Animals
Bacteria/metabolism/drug effects/genetics/classification
Precision Medicine
Drug Resistance, Neoplasm

@article {pmid39024464,
year = {2024},
author = {Hernández-Melgar, AG and Guerrero, A and Moreno-Ulloa, A},
title = {Chronic Exposure to Petroleum-Derived Hydrocarbons Alters Human Skin Microbiome and Metabolome Profiles: A Pilot Study.},
journal = {Journal of proteome research},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jproteome.4c00256},
pmid = {39024464},
issn = {1535-3907},
abstract = {Petroleum-derived substances, like industrial oils and grease, are ubiquitous in our daily lives. Comprised of petroleum hydrocarbons (PH), these substances can come into contact with our skin, potentially causing molecular disruptions and contributing to the development of chronic disease. In this pilot study, we employed mass spectrometry-based untargeted metabolomics and 16S rRNA gene sequencing analyses to explore these effects. Superficial skin samples were collected from subjects with and without chronic dermal exposure to PH at two anatomical sites: the fingers (referred to as the hand) and arms (serving as an intersubject variability control). Exposed hands exhibited higher bacterial diversity (Shannon and Simpson indices) and an enrichment of oil-degrading bacteria (ODB), including Dietzia, Paracoccus, and Kocuria. Functional prediction suggested enriched pathways associated with PH degradation in exposed hands vs non-exposed hands, while no differences were observed when comparing the arms. Furthermore, carboxylic acids, glycerophospholipids, organooxygen compounds, phenol ethers, among others, were found to be more abundant in exposed hands. We observed positive correlations among multiple ODB and xenobiotics, suggesting a chemical remodeling of the skin favorable for ODB thriving. Overall, our study offers insights into the complex dysregulation of bacterial communities and the chemical milieu induced by chronic dermal exposure to PH.},
}

@article {pmid39024451,
year = {2024},
author = {Wilde, J and Slack, E and Foster, KR},
title = {Host control of the microbiome: Mechanisms, evolution, and disease.},
journal = {Science (New York, N.Y.)},
volume = {385},
number = {6706},
pages = {eadi3338},
doi = {10.1126/science.adi3338},
pmid = {39024451},
issn = {1095-9203},
mesh = {Animals ; Humans ; *Biological Evolution ; Homeostasis ; *Host Microbial Interactions/genetics ; *Microbiota/genetics ; *Selection, Genetic ; *Symbiosis ; },
abstract = {Many species, including humans, host communities of symbiotic microbes. There is a vast literature on the ways these microbiomes affect hosts, but here we argue for an increased focus on how hosts affect their microbiomes. Hosts exert control over their symbionts through diverse mechanisms, including immunity, barrier function, physiological homeostasis, and transit. These mechanisms enable hosts to shape the ecology and evolution of microbiomes and generate natural selection for microbial traits that benefit the host. Our microbiomes result from a perpetual tension between host control and symbiont evolution, and we can leverage the host's evolved abilities to regulate the microbiota to prevent and treat disease. The study of host control will be central to our ability to both understand and manipulate microbiotas for better health.},
}

Animals
Humans
*Biological Evolution
Homeostasis
*Host Microbial Interactions/genetics
*Microbiota/genetics
*Selection, Genetic
*Symbiosis

@article {pmid39024228,
year = {2024},
author = {Ravelo, AD and Ferm, P and Guo, Y and Omontese, BO and Morley, PS and Chen, C and Noyes, NR and Caixeta, LS},
title = {Using a multi-omics approach to explore potential associations with rumen content and serum of cows with different milk production levels based on genomic predicted transmitting ability for milk and phenotypic milk production.},
journal = {PloS one},
volume = {19},
number = {7},
pages = {e0305674},
pmid = {39024228},
issn = {1932-6203},
mesh = {Animals ; Cattle ; *Rumen/microbiology/metabolism ; Female ; *Milk/metabolism/microbiology ; *Lactation ; Phenotype ; Metabolome ; Microbiota ; Genomics/methods ; Metagenome ; Metabolomics/methods ; Multiomics ; },
abstract = {This study aims to compare rumen microbiome and metabolites between second lactation dairy cows in the 75th percentile (n = 12; 57.2 ± 5.08 kg/d) of production according to genomic predicted transmitting ability for milk (GPTAM) and their counterparts in the 25th percentile (n = 12; 47.2 ± 8.61 kg/d). It was hypothesized that the metagenome and metabolome would differ between production levels. Cows were matched by days in milk (DIM), sire, occurrence of disease, and days open in previous lactation. For an additional comparison, the cows were also divided by phenotype into high (n = 6; 61.3 ± 2.8 kg/d), medium (n = 10; 55 ± 1.2 kg/d), and low (n = 8; 41.9 ± 5.6 kg/d) based on their milk production. Samples were collected 65 ± 14 DIM. Rumen content was collected using an oro-gastric tube and serum samples were collected from the coccygeal vessels. High-resolution liquid chromatography-mass spectrometry (LC-MS) was used for rumen and serum metabolite profiling. Shotgun metagenomics was used for rumen microbiome profiling. Microbiome sample richness and diversity were used to determine alpha and Bray-Curtis dissimilarity index was used to estimate beta diversity. Differences in metabolites were determined using t-tests or ANOVA. Pearson correlations were used to consider associations between serum metabolites and milk production. There was no evidence of a difference in rumen metabolites or microbial communities by GPTAM or phenotype. Cows in the phenotypic low group had greater serum acetate to propionate ratio and acetate proportion compared to the cows in the phenotypic medium group. Likewise, serum propionate proportion was greater in the medium compared to the low phenotypic group. Serum acetate, butyrate, and propionate concentrations had a weak positive correlation with milk production. When investigating associations between rumen environment and milk production, future studies must consider the impact of the ruminal epithelium absorption and post-absorption processes in relation to milk production.},
}

Animals
Cattle
*Rumen/microbiology/metabolism
Female
*Milk/metabolism/microbiology
*Lactation
Phenotype
Metabolome
Microbiota
Genomics/methods
Metagenome
Metabolomics/methods
Multiomics

@article {pmid39023942,
year = {2024},
author = {Yirmiya, K and Turjeman, S and Shtossel, O and Zagoory-Sharon, O and Moadi, L and Rubin, E and Sharon, E and Louzoun, Y and Koren, O and Feldman, R},
title = {Microbiome signature of posttraumatic stress disorder and resilience in youth.},
journal = {Psychological trauma : theory, research, practice and policy},
volume = {},
number = {},
pages = {},
doi = {10.1037/tra0001727},
pmid = {39023942},
issn = {1942-969X},
support = {//Bezos Family Foundation/ ; //theHarris Corporation/ ; //European Research Council (ERC)/ ; //Azrieli Foundation/ ; },
abstract = {OBJECTIVE: Identifying biomarkers that can distinguish trauma-exposed youth at risk for developing posttraumatic pathology from resilient individuals is essential for targeted interventions. As trauma can alter the microbiome with lasting effects on the host, our longitudinal, multimeasure, cross-species study aimed to identify the microbial signature of posttraumatic stress disorder (PTSD).

METHOD: We followed children exposed to war-related trauma and matched controls from early childhood (Mage = 2.76 years, N = 232) to adolescence (Mage = 16.13 years, N = 84), repeatedly assessing posttraumatic symptomatology and maternal caregiving. In late adolescence, we collected fecal samples from mothers and youth and assessed microbiome composition, diversity, and mother-child microbial synchrony. We then transplanted adolescents' fecal samples into germ-free mice to determine if behavioral changes are observed.

RESULTS: Youth with PTSD exhibited a distinct gut microbiome profile and lower diversity compared to resilient individuals, and microbiome diversity mediated the continuity of posttraumatic symptomatology throughout development. Low microbiome diversity correlated with more posttraumatic symptoms in early childhood, more emotional and behavioral problems in adolescence, and poor maternal caregiving. Youth with PTSD demonstrated less mother-child microbial synchrony, suggesting that low microbial concordance between mother and child may indicate susceptibility to posttraumatic illness. Germ-free mice transplanted with microbiomes from individuals with PTSD displayed increased anxious behavior.

CONCLUSIONS: Our findings provide evidence that the trauma-associated microbiome profile is at least partially responsible for the anxiety component of the PTSD phenotype and highlight microbial underpinnings of resilience. Further, our results suggest that the microbiome may serve as additional biological memory of early life stress and underscore the potential for microbiome-related diagnosis and treatment following trauma. (PsycInfo Database Record (c) 2024 APA, all rights reserved).},
}

@article {pmid39023417,
year = {2024},
author = {Tian, K and Jing, D and Lan, J and Lv, M and Wang, T},
title = {Commensal microbiome and gastrointestinal mucosal immunity: Harmony and conflict with our closest neighbor.},
journal = {Immunity, inflammation and disease},
volume = {12},
number = {7},
pages = {e1316},
pmid = {39023417},
issn = {2050-4527},
support = {82072648//National Natural Science Foundation of China/ ; 81772542//National Natural Science Foundation of China/ ; BK20211508//Natural Science Foundation of Jiangsu Province/ ; 021414380500//Fundamental Research Funds for the Central Universities/ ; JQX21009//Nanjing Medical Science and Technique Development Foundation/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Immunity, Mucosal/immunology ; *Intestinal Mucosa/immunology/microbiology ; Animals ; Symbiosis/immunology ; Homeostasis/immunology ; },
abstract = {BACKGROUND: The gastrointestinal tract contains a wide range of microorganisms that have evolved alongside the immune system of the host. The intestinal mucosa maintains balance within the intestines by utilizing the mucosal immune system, which is controlled by the complex gut mucosal immune network.

OBJECTIVE: This review aims to comprehensively introduce current knowledge of the gut mucosal immune system, focusing on its interaction with commensal bacteria.

RESULTS: The gut mucosal immune network includes gut-associated lymphoid tissue, mucosal immune cells, cytokines, and chemokines. The connection between microbiota and the immune system occurs through the engagement of bacterial components with pattern recognition receptors found in the intestinal epithelium and antigen-presenting cells. This interaction leads to the activation of both innate and adaptive immune responses. The interaction between the microbial community and the host is vital for maintaining the balance and health of the host's mucosal system.

CONCLUSION: The gut mucosal immune network maintains a delicate equilibrium between active immunity, which defends against infections and damaging non-self antigens, and immunological tolerance, which allows for the presence of commensal microbiota and dietary antigens. This balance is crucial for the maintenance of intestinal health and homeostasis. Disturbance of gut homeostasis leads to enduring or severe gastrointestinal ailments, such as colorectal cancer and inflammatory bowel disease. Utilizing these factors can aid in the development of cutting-edge mucosal vaccines that have the ability to elicit strong protective immune responses at the primary sites of pathogen invasion.},
}

Humans
*Gastrointestinal Microbiome/immunology
*Immunity, Mucosal/immunology
*Intestinal Mucosa/immunology/microbiology
Animals
Symbiosis/immunology
Homeostasis/immunology

@article {pmid39023219,
year = {2024},
author = {López-Beltrán, A and Botelho, J and Iranzo, J},
title = {Dynamics of CRISPR-mediated virus-host interactions in the human gut microbiome.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae134},
pmid = {39023219},
issn = {1751-7370},
abstract = {Arms races between mobile genetic elements and prokaryotic hosts are major drivers of ecological and evolutionary change in microbial communities. Prokaryotic defense systems such as CRISPR-Cas have the potential to regulate microbiome composition by modifying the interactions among bacteria, plasmids, and phages. Here, we used longitudinal metagenomic data from 130 healthy and diseased individuals to study how the interplay of genetic parasites and CRISPR-Cas immunity reflects on the dynamics and composition of the human gut microbiome. Based on the coordinated study of 80 000 CRISPR-Cas loci and their targets, we show that CRISPR-Cas immunity effectively modulates bacteriophage abundances in the gut. Acquisition of CRISPR-Cas immunity typically leads to a decrease in the abundance of lytic phages but does not necessarily cause their complete disappearance. Much smaller effects are observed for lysogenic phages and plasmids. Conversely, phage-CRISPR interactions shape bacterial microdiversity by producing weak selective sweeps that benefit immune host lineages. We also show that distal (and chronologically older) regions of CRISPR arrays are enriched in spacers that are potentially functional and target crass-like phages and local prophages. This suggests that exposure to reactivated prophages and other endemic viruses is a major selective pressure in the gut microbiome that drives the maintenance of long-lasting immune memory.},
}

@article {pmid39023197,
year = {2024},
author = {Brasino, DSK and Speese, SD and Schilling, K and Schutt, CE and Barton, MC},
title = {A Linkable, Polycarbonate Gut Microbiome-Distal Tumor Chip Platform for Interrogating Cancer Promoting Mechanisms.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e2309220},
doi = {10.1002/advs.202309220},
pmid = {39023197},
issn = {2198-3844},
support = {//Cancer Early Detection Advanced Research Center at Oregon Health & Science University's Knight Cancer Institute and the Collins Medical Trust in Portland, Oregon/ ; //National Institute of General Medical Sciences (NIGMS)/ ; R35GM151057/NH/NIH HHS/United States ; //Collins Medical Trust/ ; Exploratory6781119//Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health and Science University/ ; Full6950120//Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health and Science University/ ; Full 2021-1391//Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health and Science University/ ; Full 2023-1773//Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health and Science University/ ; },
abstract = {Gut microbiome composition is tied to diseases ranging from arthritis to cancer to depression. However, mechanisms of action are poorly understood, limiting development of relevant therapeutics. Organ-on-chip platforms, which model minimal functional units of tissues and can tightly control communication between them, are ideal platforms to study these relationships. Many gut microbiome models are published to date but devices are typically fabricated using oxygen permeable polydimethylsiloxane, requiring interventions to support anaerobic bacteria. To address this challenge, a platform is developed where the chips are fabricated entirely from gas-impermeable polycarbonate without tapes or gaskets. These chips replicate polarized villus-like structures of the native tissue. Further, they enable co-cultures of commensal anaerobic bacteria Blautia coccoides on the surface of gut epithelia for two days within a standard incubator. Another complication of commonly used materials in organ-on-chip devices is high ad-/absorption, limiting applications in high-resolution microscopy and biomolecule interaction studies. For future communication studies between gut microbiota and distal tumors, an additional polycarbonate chip design is developed to support hydrogel-embedded tissue culture. These chips enable high-resolution microscopy with all relevant processing done on-chip. Designed for facile linking, this platform will make a variety of mechanistic studies possible.},
}

@article {pmid39023095,
year = {2024},
author = {Zhang, P and Ma, S and Guo, R and Li, L and Guo, X and Chang, D and Li, S and Zhang, H and Fu, C and Yang, L and Zhang, Y and Jiang, J and Wang, T and Wang, J and Shi, H},
title = {Metagenomic analysis of the gut virome in patients with irritable bowel syndrome.},
journal = {Journal of medical virology},
volume = {96},
number = {7},
pages = {e29802},
doi = {10.1002/jmv.29802},
pmid = {39023095},
issn = {1096-9071},
mesh = {Humans ; *Irritable Bowel Syndrome/virology/microbiology ; *Virome ; *Gastrointestinal Microbiome/genetics ; *Metagenomics ; *Feces/virology/microbiology ; Viruses/classification/genetics/isolation & purification ; Adult ; Male ; Female ; Middle Aged ; Bacteria/classification/genetics/isolation & purification ; Metagenome ; },
abstract = {Irritable bowel syndrome (IBS), a chronic functional gastrointestinal disorder, is recognized for its association with alterations in the gut microbiome and metabolome. This study delves into the largely unexplored domain of the gut virome in IBS patients. We conducted a comprehensive analysis of the fecal metagenomic data set from 277 IBS patients and 84 healthy controls to characterize the gut viral community. Our findings revealed a distinct gut virome in IBS patients compared to healthy individuals, marked by significant variances in between-sample diversity and altered abundances of 127 viral operational taxonomic units (vOTUs). Specifically, 111 vOTUs, predominantly belonging to crAss-like, Siphoviridae, Myoviridae, and Quimbyviridae families, were more abundant in IBS patients, whereas the healthy control group exhibited enrichment of 16 vOTUs from multiple families. We also investigated the interplay between the gut virome and bacteriome, identifying a correlation between IBS-enriched bacteria like Klebsiella pneumoniae, Fusobacterium varium, and Ruminococcus gnavus, and the IBS-associated vOTUs. Furthermore, we assessed the potential of gut viral signatures in predicting IBS, achieving a notable area under the receiver operator characteristic curve (AUC) of 0.834. These findings highlight significant shifts in the viral diversity, taxonomic distribution, and functional composition of the gut virome in IBS patients, suggesting the potential role of the gut virome in IBS pathogenesis and opening new avenues for diagnostic and therapeutic strategies targeting the gut virome in IBS management.},
}

Humans
*Irritable Bowel Syndrome/virology/microbiology
*Virome
*Gastrointestinal Microbiome/genetics
*Metagenomics
*Feces/virology/microbiology
Viruses/classification/genetics/isolation & purification
Adult
Male
Female
Middle Aged
Bacteria/classification/genetics/isolation & purification
Metagenome

@article {pmid39022685,
year = {2024},
author = {Khosrojerdi, M and Azad, FJ and Yadegari, Y and Ahanchian, H and Azimian, A},
title = {The role of microRNAs in atopic dermatitis.},
journal = {Non-coding RNA research},
volume = {9},
number = {4},
pages = {1033-1039},
pmid = {39022685},
issn = {2468-0540},
abstract = {Atopic dermatitis (AD), known as eczema, is a chronic inflammatory skin condition affecting millions worldwide. This abstract provides an overview of the clinical features and underlying pathogenesis of AD, highlighting the role of specific microRNAs (miRNAs) in its development and progression. AD presents with distinct clinical manifestations that evolve with age, starting in infancy with dry, itchy skin and red patches, which can lead to sleep disturbances. In childhood, the rash spreads to flexural areas, resulting in lichenification. In adulthood, lesions may localize to specific areas, including the hands and eyelids. Pruritus (itchiness) is a hallmark symptom, often leading to excoriations and increased vulnerability to skin infections. The pathogenesis of AD is multifaceted, involving genetic, immunological, and environmental factors. Skin barrier dysfunction, immune dysregulation, genetic predisposition, microbiome alterations, and environmental triggers contribute to its development. Recent research has uncovered the role of miRNAs, such as miR-10a-5p, miR-29b, miR-124, miR-143, miR-146a-5p, miR-151a, miR-155, and miR-223, in AD pathogenesis. These microRNAs play crucial roles in regulating various aspects of immune responses, keratinocyte dynamics, and inflammation. MicroRNA-10a-5p orchestrates keratinocyte proliferation and differentiation, while miR-29b regulates keratinocyte apoptosis and barrier integrity. MicroRNA-124 exhibits anti-inflammatory effects by targeting the NF-κB signaling pathway. MicroRNANA-143 counters allergic inflammation by modulating IL-13 signaling. MicroRNA-146a-5p regulates immune responses and correlates with IgE levels in AD. MicroRNA-151a shows diagnostic potential and modulates IL-12 receptor β2. MicroRNA-155 plays a central role in immune responses and Th17 cell differentiation, offering diagnostic and therapeutic potential. MicroRNA-223 is linked to prenatal smoke exposure and immune modulation in AD. Understanding these microRNAs' intricate roles in AD pathogenesis promises more effective treatments, personalized approaches, and enhanced diagnostic tools. Further research into these molecular orchestrators may transform the landscape of AD management, improving the quality of life for affected individuals.},
}

@article {pmid39022135,
year = {2020},
author = {Jiang, J and Warren, CM and Browning, RL and Ciaccio, CE and Gupta, RS},
title = {Food allergy epidemiology and racial and/or ethnic differences.},
journal = {Journal of food allergy},
volume = {2},
number = {1},
pages = {11-16},
pmid = {39022135},
issn = {2689-0275},
abstract = {In recent decades, immunoglobulin E (IgE) mediated food allergy has become a growing public health concern. Converging evidence from cross-sectional prevalence studies, health care utilization records, and cohort studies indicate that food allergies are increasingly prevalent and often severe. Although IgE-mediated food allergy has long been considered a predominantly pediatric concern, analysis of recent self-reported data suggests that food allergies may be more prevalent among adult populations than previously acknowledged, with many reported cases of adult-onset allergies as well as persistent childhood-onset allergies. Results of studies also suggest that food allergy-related health care utilization is increasing as more individuals seek emergency treatment for food-induced anaphylaxis. Analysis of epidemiologic data also indicates that the burden of food allergies is unequally distributed. Published prevalence rates are highest in Western countries, e.g., the United States, United Kingdom, and Australia. Within these countries, there also is heterogeneity across racial and/or ethnic groups, with non-White and second-generation immigrant populations disproportionately affected. Importantly, such observations can shed light on the etiology of food allergy and inform improved clinical management, treatment, and prevention efforts. For example, there is a growing consensus that earlier introduction of allergenic foods, e.g., peanut, promotes oral tolerance and can dramatically reduce food allergy risk. In addition, much attention has been paid to the potentially deleterious effects of cutaneous allergen exposure, e.g., through eczematous skin, which can skew the immune response away from tolerance and toward allergic sensitization, thereby increasing food allergy risk. Furthermore, there is a growing appreciation for the potential protective effects of diverse microbial exposures, given mounting evidence for the immunomodulatory effects of the human microbiome. Also, when considering the geographic variability in the prevalence of certain food and environmental allergies as well as their structural similarities at the molecular level, it is believed that co-sensitization between food and environmental allergens may be a key driver of rising food allergy prevalence.},
}

@article {pmid39022133,
year = {2020},
author = {Leonard, SA},
title = {Food allergy prevention, including early food introduction.},
journal = {Journal of food allergy},
volume = {2},
number = {1},
pages = {69-74},
pmid = {39022133},
issn = {2689-0275},
abstract = {As the prevalence of immunoglobulin E (IgE)-mediated food allergy continues to increase without an imminent cure, prevention has become an urgent need. A breakthrough study that shows that early consumption of peanut can prevent the development of peanut allergy has led for a push in early interventions. Theories associated with the increasing prevalence of food allergy lend themselves to areas of potential intervention, e.g., age at time of food introduction, infant feeding practices, microbiome influences, diet composition, vitamin D deficiency, and increasing rates of eczema. This review focused on the available data from studies that investigated early interventions to decrease the risk of food allergy.},
}

@article {pmid39021924,
year = {2024},
author = {Xu, D and Ren, L and Zhang, W and Wu, S and Yu, M and He, X and Wei, Z},
title = {Therapeutic effects and mechanisms of fecal microbiota transplantation on EAE partly through HPA axis-mediated neuroendocrine regulation.},
journal = {Heliyon},
volume = {10},
number = {12},
pages = {e33214},
pmid = {39021924},
issn = {2405-8440},
abstract = {BACKGROUND: The pathogenesis of multiple sclerosis (MS) may be closely related to immune regulation and inflammatory cytokines induced by specific flora. Repairing the intestinal flora may alter the immune response in MS patients, thus opening up novel approaches for the treatment of MS.

OBJECTIVE: We aimed to test the therapeutic effect of fecal microbiota transplantation (FMT) on experimental autoimmune encephalomyelitis (EAE) and the characteristics of intestinal microbiota composition changes, explore the potential mechanisms of FMT treatment.

METHODS: EAE animals were treated with FMT, with the therapeutic effects were evaluated by observing neurological scores and measuring serum levels of cortisol, IL-17, and TLR-2. Fecal microbiome 16S rRNA sequencing was used to profile changes in microbiota composition, and adrenalectomy pretreatment was used to test whether FMT effects were dependent on HPA axis function.

RESULTS: FMT improved neurological function and reduced serum IL-17 to levels that were close to the control group. FMT reestablished intestinal homeostasis by altering the structure of the intestinal flora, increasing the abundance of beneficial flora, and regulating intestinal metabolites. We found that the therapeutic effects of FMT depended partly on the efferent function of the HPA axis; surgical disruption of the HPA axis altered the abundance and diversity of the intestinal flora.

CONCLUSION: FMT showed a neuroprotective effect on EAE by increasing the abundance of the beneficial flora, rebuilding intestinal homeostasis, reducing IL-17 and cortisol serum levels, and promoting serum TLR-2; the therapeutic effect of FMT on EAE is partly dependent on the HPA axis.},
}