@article {pmid39692482,
year = {2024},
author = {Beattie, GA and Edlund, A and Esiobu, N and Gilbert, J and Nicolaisen, MH and Jansson, JK and Jensen, P and Keiluweit, M and Lennon, JT and Martiny, J and Minnis, VR and Newman, D and Peixoto, R and Schadt, C and van der Meer, JR},
title = {Soil microbiome interventions for carbon sequestration and climate mitigation.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0112924},
doi = {10.1128/msystems.01129-24},
pmid = {39692482},
issn = {2379-5077},
abstract = {Mitigating climate change in soil ecosystems involves complex plant and microbial processes regulating carbon pools and flows. Here, we advocate for the use of soil microbiome interventions to help increase soil carbon stocks and curb greenhouse gas emissions from managed soils. Direct interventions include the introduction of microbial strains, consortia, phage, and soil transplants, whereas indirect interventions include managing soil conditions or additives to modulate community composition or its activities. Approaches to increase soil carbon stocks using microbially catalyzed processes include increasing carbon inputs from plants, promoting soil organic matter (SOM) formation, and reducing SOM turnover and production of diverse greenhouse gases. Marginal or degraded soils may provide the greatest opportunities for enhancing global soil carbon stocks. Among the many knowledge gaps in this field, crucial gaps include the processes influencing the transformation of plant-derived soil carbon inputs into SOM and the identity of the microbes and microbial activities impacting this transformation. As a critical step forward, we encourage broadening the current widespread screening of potentially beneficial soil microorganisms to encompass functions relevant to stimulating soil carbon stocks. Moreover, in developing these interventions, we must consider the potential ecological ramifications and uncertainties, such as incurred by the widespread introduction of homogenous inoculants and consortia, and the need for site-specificity given the extreme variation among soil habitats. Incentivization and implementation at large spatial scales could effectively harness increases in soil carbon stocks, helping to mitigate the impacts of climate change.},
}

@article {pmid39692472,
year = {2024},
author = {Lawrence, GW and Garcia-Gutierrez, E and O'Mahony, AK and Walsh, CJ and O'Connor, PM and Begley, M and Guinane, CM and Cotter, PD},
title = {A gut-derived Streptococcus salivarius produces the novel nisin variant designated nisin G and inhibits Fusobacterium nucleatum in a model of the human distal colon microbiome.},
journal = {mBio},
volume = {},
number = {},
pages = {e0157324},
doi = {10.1128/mbio.01573-24},
pmid = {39692472},
issn = {2150-7511},
abstract = {Fusobacterium nucleatum is a human pathogen associated with intestinal conditions including colorectal cancer. Screening for gut-derived strains that exhibit anti-F. nucleatum activity in vitro revealed Streptococcus salivarius DPC6487 as a strain of interest. Whole-genome sequencing of S. salivarius DPC6487 identified a nisin operon with a novel structural variant designated nisin G. The structural nisin G peptide differs from the prototypical nisin A with respect to seven amino acids (Ile4Tyr, Ala15Val, Gly18Ala, Asn20His, Met21Leu, His27Asn, and His31Ile), including differences that have not previously been associated with a natural nisin variant. The nisin G gene cluster consists of nsgGEFABTCPRK with transposases encoded between the nisin G structural gene (nsgA) and nsgF, notably lacking an equivalent to the nisI immunity determinant. S. salivarius DPC6487 exhibited a narrower spectrum of activity in vitro compared to the nisin A-producing Lactococcus lactis NZ9700. Nisin G-producing S. salivarius DPC6487 demonstrated the ability to control F. nucleatum DSM15643 in an ex vivo model colonic environment while exerting minimal impact on the surrounding microbiota. The production of this bacteriocin by a gut-derived S. salivarius, its narrow-spectrum activity, and its anti-F. nucleatum activity in a model colonic environment indicates that this strain merits further attention with a view to harnessing its probiotic potential.IMPORTANCEFusobacterium nucleatum is a human pathogen associated with intestinal conditions, including colorectal cancer, making it a potentially important therapeutic target. Bacteriocin-producing probiotic bacteria demonstrate the potential to target disease-associated taxa in situ in the gut. A gut-derived strain Streptococcus salivarius DPC6487 was found to demonstrate anti-F. nucleatum activity, which was attributable to a gene encoding a novel nisin variant designated nisin G. Nisin G-producing S. salivarius DPC6487 demonstrated the ability to control an infection of F. nucleatum in a simulated model of the human distal colon while exerting minimal impact on the surrounding microbiota. Here, we describe this nisin variant produced by S. salivarius, a species that is frequently a focus for probiotic development. The production of nisin G by a gut-derived S. salivarius, its narrow-spectrum activity against F. nucleatum, and its anti-F. nucleatum activity in a model colonic environment warrants further research to determine its probiotic-related applications.},
}

@article {pmid39692258,
year = {2024},
author = {Yang, Z and Zhou, F and Zhan, D and Li, P and Pan, J},
title = {Levels of Bile Acid Metabolism Are Associated With Alterations of Gut Microbes in Hepatocellular Carcinoma.},
journal = {Molecular carcinogenesis},
volume = {},
number = {},
pages = {},
doi = {10.1002/mc.23869},
pmid = {39692258},
issn = {1098-2744},
abstract = {Hepatocellular carcinoma (HCC) is viewed as a metabolism associated disease, and bile acid metabolism is reported to occupy a significant role in the progression of HCC. However, little is known about the association between gut microbes and bile acid metabolism in HCC. Our study was designed to clarify the role of bile acid metabolism and microbiome in the progression of HCC. We investigated the relationship between bile acid metabolism and prognosis and immune cells by mining GSE14520. We studied the microbial profiles and metabolic alterations between the low bile acid group and high bile acid group using 16S rRNA sequencing and metabolomics. HCC patients in the high bile acid metabolism group showed better survival outcome compared with those in the low bile acid metabolism. Immune analysis displayed the close correlation between low bile acid metabolism and infiltration of CD4 + T cells, and the close relationship between high bile acid metabolism and infiltration of CD8 + T cells, macrophage cells in HCC. 16S rRNA sequencing results demonstrated that Blautia, Ruminococcus_gnavus_group, Erysipelotrichaceae_UCG-003 were mostly enriched in the low bile acid group. Metabolomics of the 109 fecal samples showed that the most enriched metabolites in the low total bile acid group were dihydrocytochalasin B, cucurbic acid and 27-Norcholestanehexol. Finally, KEGG enrichment analysis identified secondary bile acid biosynthesis and endocrine resistance as the most significant metabolic pathways. High bile acid metabolism was associated with more infiltration of CD8 + T cells, macrophage cells, and better prognosis in HCC. Levels of bile acid were significantly associated with altered gut microbes and metabolites in HCC. Further research related to gut microbes and bile acid metabolism may provide a novel insight into the pathogenesis and therapeutic strategy of HCC.},
}

@article {pmid39692191,
year = {2024},
author = {Zou, X and Yan, M and Wang, Y and Ni, Y and Zhao, J and Lu, B and Liu, B and Cao, B},
title = {Accurate Diagnosis of Lower Respiratory Infections Using Host Response and Respiratory Microbiome from a Single Metatranscriptome Test of Bronchoalveolar Lavage Fluid.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e2405087},
doi = {10.1002/advs.202405087},
pmid = {39692191},
issn = {2198-3844},
support = {2022YFA1304300//National Key R&D Program of China grant/ ; ZRJY2023-GG24//China-Japan Friendship Hospital elite program grant/ ; },
abstract = {Lower respiratory tract infections (LRTIs) diagnosis is challenging because noninfectious diseases mimic its clinical features. The altered host response and respiratory microbiome following LRTIs have the potential to differentiate LRTIs from noninfectious respiratory diseases (non-LRTIs). Patients suspected of having LRTIs are retrospectively enrolled and a clinical metatranscriptome test is performed on bronchoalveolar lavage fluid (BALF). Transcriptomic and metagenomic analysis profiled the host response and respiratory microbiome in patients with confirmed LRTI (n = 126) or non-LRTIs (n = 75). Patients with evidenced LRTIs exhibited enhanced pathways on chemokine and cytokine response, neutrophile recruitment and activation, along with specific gene modules linked to LRTIs status and key blood markers. Moreover, LRTIs patients exhibited reduced diversity and evenness in the lower respiratory microbiome, likely driven by an increased abundance of bacterial pathogens. Host marker genes are selected, and classifiers are developed to distinguish patients with LRTIs, non-LRTIs, and indeterminate status, achieving an area under the receiver operating characteristic curve of 0.80 to 0.86 and validated in a subsequently enrolled cohort. Incorporating respiratory microbiome features further enhanced the classifier's performance. In summary, a single metatranscriptome test of BALF proved detailed profiles of host response and respiratory microbiome, enabling accurate LRTIs diagnosis.},
}

@article {pmid39692041,
year = {2024},
author = {Yang, Z and Zhang, Z and Jiang, S and Li, A and Song, H and Zhang, J},
title = {Diet shapes and maintains the personalized native gut microbiomes in mice.},
journal = {Journal of the science of food and agriculture},
volume = {},
number = {},
pages = {},
doi = {10.1002/jsfa.14073},
pmid = {39692041},
issn = {1097-0010},
support = {//National Natural Science Foundation of China (No. 32222066 and No. 32160545)/ ; },
abstract = {BACKGROUND: The gut microbiome plays a critical role in human health and disease. Different dietary backgrounds play an important role in the uniqueness and diversity of the gut microbiota in different individuals, which promotes heterogeneity in disease phenotypes and treatment responses. Here, we explored how diet affects the composition and function of the native gut microbiome of model mice, based on the shotgun metagenomic and metabolomic, by analyzing the gut microbiome of C57B/6J mice in different dietary backgrounds.

RESULTS: The gut microbiomes of mice receiving different diets consistently exhibit distinct compositions across bacterial species, strains, fungi and phages. This implies that native microbial communities cannot 'homogenize' rapidly becaise of priority effects and unchanging diets. Notably, hotspot bacteria such as Limosilactobacillus reuteri, Parabacteroides distasonis and Akkermansia muciniphila were significantly different among the groups. These species harbor diverse adaptive mutations, reflecting genomic evolutionary diversity. The functional profiles of the gut microbiota also exhibit selective differences, involving the capacity for carbohydrate, branched-chain amino acid and fatty acid synthesis, as well as virulence factors, carbohydrate-active enzymes and antibiotic resistance. Furthermore, the differences in the gut microbiota also propagate to the host's serum, where structural and specific metabolite differences were observed. Metabolites that directly impact host health, such as d-glucosamine 6-phosphate and testolic acid, also show significant differences between the different dietary groups.

CONCLUSION: Our findings underscore the profound influence of different dietary the composition and functionality of the gut microbiome, offering valuable insights into optimizing health outcomes through personalized nutritional interventions. © 2024 Society of Chemical Industry.},
}

@article {pmid39691913,
year = {2024},
author = {Deng, K and Fan, X and Yuan, Z and Li, D},
title = {Probiotic effects on skin health: comprehensive visual analysis and perspectives.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1453755},
doi = {10.3389/fmicb.2024.1453755},
pmid = {39691913},
issn = {1664-302X},
abstract = {BACKGROUND: Bacteria play a crucial role in maintaining the health of human skin. Research has demonstrated that probiotics present notable benefits for extraintestinal organs. Despite the extensive research on the impact of probiotics on skin health, there is a notable absence of regulatory frameworks governing their external application, with no approval from the FDA for any probiotic products for external use. The aim of this study is to offer a thorough summary of the research status in the field since 2000 and project future trends.

METHOD: The Web of Science Core Collection and SCI-Expanded index were selected for an extensive search of studies concerning the role of probiotics in skin health since 2000. A total of 1,306 publications were identified. Employing a double-blind method, two subsets of literature were scrutinized and subsequently combined for analysis. Using CiteSpace, this research explored key aspects such as primary countries, institutions, authors, journals, trending topics, research frontiers, and emerging patterns in research related to application of probiotic for skin health.

RESULT: This article included 709 research papers. The number of published papers has shown a rapid increase. The United States had the highest number of research papers (128), and Canada had the highest intermediate centrality (0.23). The University of California System emerged as the most prolific institution. Huang, Chun-Ming has published the most articles, and his research is at the forefront among those prolific authors. Twelve clusters were identified, with cluster #0 skin microbiota, #3 mechanisms, and #8 antimicrobial being the most recent. As for the hot topic, "diversity," "health," "skin microbiome," "oxidative stress," "microbiota," and "antioxidants" have been at the forefront of the current field. The overall research trend has shifted from clinical trials to mechanistic exploration and from oral treatments to external applications, with the research level moving from general categories to specific strains.

CONCLUSION: This paper summarized and visualized academic achievements in the field of probiotic application for skin health using CiteSpace and VOSviewer, offering a systematic and comprehensive perspective, along with a longitudinal overview of this research field.},
}

@article {pmid39691842,
year = {2025},
author = {Paul, NJ and Sathyanarayana, HP and Kailasam, V},
title = {Microbial flora surrounding orthodontic temporary skeletal anchorage devices: A systematic review.},
journal = {Journal of oral biology and craniofacial research},
volume = {15},
number = {1},
pages = {25-32},
doi = {10.1016/j.jobcr.2024.11.005},
pmid = {39691842},
issn = {2212-4268},
abstract = {AIM: The oral cavity harbours distinct microorganisms, which create a unique microenvironment. These microorganisms might trigger inflammatory reactions in the host, potentially leading to inflammation that can question the stability of temporary skeletal anchorage devices(TSADs). This study aimed to systematically review the literature on the type of microorganisms around TSADs.

METHODS: A search of studies in six electronic databases - Cochrane Library, PubMed, OVID, Scopus, LILACS and Web of Science were performed until 30 May 2024 without any restriction in date or language of publication. The selection of articles was limited to studies evaluating the microorganisms around TSADs during orthodontic treatment. Two reviewers independently performed eligibility screening, study selection, and data extraction. The Newcastle Ottawa scale was used to assess the Risk of bias in all the included studies. Meta-analysis could not be performed because of the heterogeneity of the studies.

RESULTS: From 7020 articles, seven prospective studies were included for the qualitative analysis. Porphyromonas gingivalis and Treponema denticola were found around all TSADs used in orthodontic therapy. There was a significant difference in the type of microorganisms around successful and failed TSADs.

CONCLUSIONS: There was an overall colonization of diverse microorganisms around TSADS. Failed TSADs showed greater Porphyromonas gingivalis, Parvimonas micra and facultative anaerobic enteric commensal Enterobacter.},
}

@article {pmid39691780,
year = {2024},
author = {Ha, SM and Lee, K and Kim, GH and Hurych, J and Cinek, O and Shim, JO},
title = {Gut-microbiota-based ensemble model predicts prognosis of pediatric inflammatory bowel disease.},
journal = {iScience},
volume = {27},
number = {12},
pages = {111442},
doi = {10.1016/j.isci.2024.111442},
pmid = {39691780},
issn = {2589-0042},
abstract = {Developing microbiome-based markers for pediatric inflammatory bowel disease (PIBD) is challenging. Here, we evaluated the diagnostic and prognostic potential of the gut microbiome in PIBD through a case-control study and cross-cohort analyses. In a Korean PIBD cohort (24 patients with PIBD, 43 controls), we observed that microbial diversity and composition shifted in patients with active PIBD versus controls and recovered at remission. We employed a differential abundance meta-analysis approach to identify microbial markers consistently associated with active inflammation and remission across seven PIBD cohorts from six countries (n = 1,670) including our dataset. Finally, we trained and tested various machine learning models for their ability to predict a patient's future remission based on baseline bacterial composition. An ensemble model trained with the amplicon sequence variants effectively predicted future remission of PIBD. This research highlights the gut microbiome's potential to guide precision therapy for PIBD.},
}

@article {pmid39691697,
year = {2024},
author = {Shi, B and Chen, F and Gong, J and Khan, A and Qian, X and Xu, Z and Yang, P},
title = {Urinary microbiome profiling as a non-invasive tool for identifying biomarkers in systemic lupus erythematosus and lupus nephritis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1364333},
doi = {10.3389/fcimb.2024.1364333},
pmid = {39691697},
issn = {2235-2988},
mesh = {Humans ; *Lupus Nephritis/urine/microbiology ; *Biomarkers/urine ; *Microbiota ; *Lupus Erythematosus, Systemic/microbiology/urine ; *RNA, Ribosomal, 16S/genetics ; Female ; Adult ; Male ; Bacteria/classification/genetics/isolation & purification ; Middle Aged ; Young Adult ; ROC Curve ; DNA, Bacterial/genetics ; Dysbiosis/microbiology ; },
abstract = {INTRODUCTION: Bacteriome alterations have been implicated in the pathogenesis of systemic lupus erythematosus (SLE). However, the relationship between SLE and the urinary microbiome remains underexplored. This study aimed to characterize the urinary microbiome of SLE patients using 16S rRNA sequencing and to investigate its correlations with clinical parameters through integrative analyses.

METHODS: Urine sediment samples were collected from individuals with SLE and lupus nephritis (LN) (n = 20), SLE without LN (n = 22), and healthy controls (HCs) (n = 23). DNA was extracted and subjected to 16S rRNA sequencing to profile the urinary microbiome. Receiver operating characteristic (ROC) curve analysis was conducted to evaluate the diagnostic efficacy of urinary microbiota, while Spearman's correlation analysis was employed to identify links between specific microbial taxa and clinical parameters. Functional predictions of bacterial roles were performed using Picrust2.

RESULTS: The urinary microbiota diagnostic model exhibited excellent performance in distinguishing SLE patients from HCs. Spearman's analysis revealed significant correlations between the urinary microbiome and clinical parameters. Specifically, Sphingomonas and Lachnospiraceae genera showed positive correlations with vitamin D levels, cylinderuria, and proteinuria, while Pedobacter, Aquabacterium, Delftia, and Achromobacter displayed negative correlations with proteinuria and albumin-to-creatinine ratio (ACR). Functional predictions indicated that the urinary microbiome might influence immune regulation through modulation of signaling pathways and metabolic processes.

DISCUSSION: Our study is the first to reveal dysbiosis in the urinary microbiome of patients with SLE. Certain bacterial taxa in the urinary microbiome were identified as potential diagnostic biomarkers for SLE. Furthermore, the functional implications of these bacterial communities suggest their involvement in immune modulation, highlighting the potential for further investigation into their roles in SLE pathogenesis and diagnosis.},
}

Humans
*Lupus Nephritis/urine/microbiology
*Biomarkers/urine
*Microbiota
*Lupus Erythematosus, Systemic/microbiology/urine
*RNA, Ribosomal, 16S/genetics
Female
Adult
Male
Bacteria/classification/genetics/isolation & purification
Middle Aged
Young Adult
ROC Curve
DNA, Bacterial/genetics
Dysbiosis/microbiology

@article {pmid39691696,
year = {2024},
author = {Klvanova, E and Videnska, P and Barton, V and Bohm, J and Splichalova, P and Koksova, V and Urik, M and Lanickova, B and Prokes, R and Budinska, E and Klanova, J and Borilova Linhartova, P},
title = {Resistome in the indoor dust samples from workplaces and households: a pilot study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1484100},
doi = {10.3389/fcimb.2024.1484100},
pmid = {39691696},
issn = {2235-2988},
mesh = {*Dust/analysis ; Pilot Projects ; *Workplace ; Humans ; Air Pollution, Indoor ; Bacteria/genetics/isolation & purification/drug effects/classification ; Family Characteristics ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial/genetics ; Air Microbiology ; Metagenome ; High-Throughput Nucleotide Sequencing ; Drug Resistance, Bacterial/genetics ; Real-Time Polymerase Chain Reaction ; },
abstract = {The antibiotic resistance genes (ARGs) limit the susceptibility of bacteria to antimicrobials, representing a problem of high importance. Current research on the presence of ARGs in microorganisms focuses mainly on humans, livestock, hospitals, or wastewater. However, the spectrum of ARGs in the dust resistome in workplaces and households has gone relatively unexplored. This pilot study aimed to analyze resistome in indoor dust samples from participants' workplaces (a pediatric hospital, a maternity hospital, and a research center) and households and compare two different approaches to the ARGs analysis; high-throughput quantitative PCR (HT-qPCR) and whole metagenome shotgun sequencing (WMGS). In total, 143 ARGs were detected using HT-qPCR, with ARGs associated with the macrolides, lincosamides, and streptogramin B (MLSB) phenotype being the most abundant, followed by MDR (multi-drug resistance) genes, and genes conferring resistance to aminoglycosides. A higher overall relative quantity of ARGs was observed in indoor dust samples from workplaces than from households, with the pediatric hospital being associated with the highest relative quantity of ARGs. WMGS analysis revealed 36 ARGs, of which five were detected by both HT-qPCR and WMGS techniques. Accordingly, the efficacy of the WMGS approach to detect ARGs was lower than that of HT-qPCR. In summary, our pilot data revealed that indoor dust in buildings where people spend most of their time (workplaces, households) can be a significant source of antimicrobial-resistant microorganisms, which may potentially pose a health risk to both humans and animals.},
}

*Dust/analysis
Pilot Projects
*Workplace
Humans
Air Pollution, Indoor
Bacteria/genetics/isolation & purification/drug effects/classification
Family Characteristics
Anti-Bacterial Agents/pharmacology
Genes, Bacterial/genetics
Air Microbiology
Metagenome
High-Throughput Nucleotide Sequencing
Drug Resistance, Bacterial/genetics
Real-Time Polymerase Chain Reaction

@article {pmid39691618,
year = {2024},
author = {Hong, JS and Jeong, YD and Park, HJ and Choi, YH and Min, YJ and Kim, C and Back, SH and Kim, DW and Kim, YM and Kim, JE},
title = {Effects of Italian ryegrass with multi-enzymes supplementation on growth performance, gut microbial, and manure odor emission in finisher pig.},
journal = {Journal of animal science and technology},
volume = {66},
number = {6},
pages = {1182-1192},
pmid = {39691618},
issn = {2055-0391},
abstract = {This study investigated the effects of addition of Italian ryegrass with multi-enzyme on growth performance, fecal odor, and microbiome. The experiment had a two-factor factorial design, using three levels of Italian ryegrass (0%, 2.5%, and 5%) and two levels of multi-enzymes (no enzyme and commercially recommended level) to formulate experimental diets. In total, 60 crossbred Landrace × Yorkshire × Duroc (LYD) pigs (88.35 ± 2.57 kg) were allocated into six dietary treatments with five replicates. After four weeks, fecal samples were collected via rectal massage for microbiome and odorous compound analysis. Results showed no significant difference (p > 0.05) in growth performance, except for feed intake (p < 0.05), which was higher in enzyme-added diets. Fecal microbiome exhibited no differences (p > 0.05) between treatments, with Firmicutes and Bacteroidetes being the major phyla, similar to the general pig population. Alpha and beta diversity analyses showed no significant differences (p > 0.05). Odorous compounds displayed no significant differences (p > 0.05), except for indoles (p < 0.05) influenced by the enzyme. In conclusion, 5% Italian ryegrass with multi-enzymes can be used as an alternative feed ingredient, having no negative effects on the growth performance, microbiome, and odorous compounds of growing pigs.},
}

@article {pmid39691165,
year = {2025},
author = {Bescos, R and du Toit, L and Redondo-Rio, A and Warburton, PJ and Nicholas, TL and Kiernan, M and Burton, RA and Belfield, L and Montagut, G and Benavente, A and Vevers, W and Gabaldón, T and Brookes, Z and Casas-Agustench, P},
title = {The comparative effect of propolis and chlorhexidine mouthwash on oral nitrite-producing bacteria and blood pressure regulation.},
journal = {Journal of oral microbiology},
volume = {17},
number = {1},
pages = {2439636},
doi = {10.1080/20002297.2024.2439636},
pmid = {39691165},
issn = {2000-2297},
abstract = {BACKGROUND: Propolis mouthwash (PROP-M) has demonstrated antibacterial properties like those of chlorhexidine mouthwash (CHX-M). However, its impact on the abundance of oral nitrite-producing species (NPS) and nitrite-producing activity (NPA) remains unexplored.

METHODS: Forty-five healthy individuals were randomised into 2 groups to rinse their mouth twice a day for seven days with either CHX-M (n = 21) or PROP-M (n = 24). Metagenomic sequencing (16S rRNA) was performed on saliva samples collected before and after each treatment. Additionally, salivary biomarkers and blood pressure were measured.

RESULTS: CHX-M increased the relative abundance of NPS (p < 0.001) but significantly impaired the NPA (p < 0.001) compared to baseline and PROP-M. No significant differences in the relative abundance of NPS and NPA were observed in the PROP-M group. However, a significant increase of plasma nitrate (+7 µmol/L, p = 0.047) and a decrease in systolic BP (-2 mmHg, p = 0.022) was observed in this group compared to the baseline.

CONCLUSION: The results indicate that PROP-M had a smaller effect on the abundance of NPS and NPA compared to CHX-M. Additionally, PROP-M reduced blood pressure in healthy individuals, but this effect was not associated with changes in the oral microbiome.},
}

@article {pmid39690861,
year = {2025},
author = {Zheng, XQ and Wang, DB and Jiang, YR and Song, CL},
title = {Gut microbiota and microbial metabolites for osteoporosis.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2437247},
pmid = {39690861},
issn = {1949-0984},
mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; *Osteoporosis/metabolism/microbiology ; *Bone and Bones/metabolism/microbiology ; Animals ; Bacteria/metabolism/classification/genetics ; },
abstract = {Osteoporosis is an age-related bone metabolic disease. As an essential endocrine organ, the skeletal system is intricately connected with extraosseous organs. The crosstalk between bones and other organs supports this view. In recent years, the link between the gut microecology and bone metabolism has become an important research topic, both in preclinical studies and in clinical trials. Many studies have shown that skeletal changes are accompanied by changes in the composition and structure of the gut microbiota (GM). At the same time, natural or artificial interventions targeting the GM can subsequently affect bone metabolism. Moreover, microbiome-related metabolites may have important effects on bone metabolism. We aim to review the relationships among the GM, microbial metabolites, and bone metabolism and to summarize the potential mechanisms involved and the theory of the gut‒bone axis. We also describe existing bottlenecks in laboratory studies, as well as existing challenges in clinical settings, and propose possible future research directions.},
}

*Gastrointestinal Microbiome/physiology
Humans
*Osteoporosis/metabolism/microbiology
*Bone and Bones/metabolism/microbiology
Animals
Bacteria/metabolism/classification/genetics

@article {pmid39690815,
year = {2024},
author = {Jiang, H and Xu, X and Lv, L and Huang, X and Ahmed, T and Tian, Y and Hu, S and Chen, J and Li, B},
title = {Host Metabolic Alterations Mediate Phyllosphere Microbes Defense upon Xanthomonas oryzae pv oryzae Infection.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.4c09178},
pmid = {39690815},
issn = {1520-5118},
abstract = {Rice bacterial leaf blight, caused by Xanthomonas oryzae pv oryzae (Xoo), is a significant threat to global food security. Although the microbiome plays an important role in protecting plant health, how the phyllosphere microbiome is recruited and the underlying disease resistance mechanism remain unclear. This study investigates how rice phyllosphere microbiomes respond to pathogen invasion through a comprehensive multiomics approach, exploring the mechanisms of microbial defense and host resistance. We discovered that Xoo infection significantly reshapes the physicosphere microbial community. The bacterial network became more complex, with increased connectivity and interactions following infection. Metabolite profiling revealed that l-ornithine was a key compound to recruiting three keystone microbes, Brevundimonas (YB12), Pantoea (YN26), and Stenotrophomonas (YN10). These microbes reduced the disease index by up to 67.6%, and these microbes demonstrated distinct defense mechanisms. Brevundimonas directly antagonized Xoo by disrupting cell membrane structures, while Pantoea and Stenotrophomonas enhanced plant immune responses by significantly increasing salicylic acid and jasmonic acid levels and activating defense-related enzymes. Our findings provide novel insights into plant-microbe interactions, demonstrating how host metabolic changes recruit and activate beneficial phyllosphere microbes to combat pathogenic invasion. This research offers promising strategies for sustainable agricultural practices and disease management.},
}

@article {pmid39690351,
year = {2024},
author = {Ullah, H and Hassan, SHA and Yang, Q and Salama, ES and Liu, P and Li, X},
title = {Dynamic interaction of antibiotic resistance between plant microbiome and organic fertilizers: sources, dissemination, and health risks.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {1},
pages = {4},
pmid = {39690351},
issn = {1573-0972},
support = {lzujbky-2024-ey12//Fundamental Research Funds for the Central Universities/ ; },
mesh = {*Microbiota/drug effects ; *Fertilizers/analysis ; Humans ; *Anti-Bacterial Agents/pharmacology ; *Plants/microbiology ; *Soil Microbiology ; *Bacteria/drug effects/genetics/classification ; *Manure/microbiology ; Gene Transfer, Horizontal ; Agriculture/methods ; Drug Resistance, Bacterial ; Sewage/microbiology ; Drug Resistance, Microbial/genetics ; Wastewater/microbiology ; Animals ; Soil/chemistry ; },
abstract = {Antibiotic resistance is a global health problem driven by the irrational use of antibiotics in different areas (such as agriculture, animal farming, and human healthcare). Sub-lethal concentrations of antibiotic residues impose selective pressure on environmental, plant-associated, and human microbiome leading to the emergence of antibiotic-resistant bacteria (ARB). This review summarizes all sources of antibiotic resistance in agricultural soils (including manure, sewage sludge, wastewater, hospitals/pharmaceutical industry, and bioinoculants). The factors (such as the physicochemical properties of soil, root exudates, concentration of antibiotic exposure, and heavy metals) that facilitate the transmission of resistance in plant microbiomes are discussed. Potential solutions for effective measures and control of antibiotic resistance in the environment are also hypothesized. Manure exhibits the highest antibiotics load, followed by hospital and municipal WW. Chlortetracycline, tetracycline, and sulfadiazine have the highest concentrations in the manure. Antibiotic resistance from organic fertilizers is transmitted to the plant microbiome via horizontal gene transfer (HGT). Plant microbiomes serve as transmission routes of ARB and ARGS to humans. The ingestion of ARB leads to human health risks (such as ineffectiveness of medication, increased morbidity, and mortality).},
}

*Microbiota/drug effects
*Fertilizers/analysis
Humans
*Anti-Bacterial Agents/pharmacology
*Plants/microbiology
*Soil Microbiology
*Bacteria/drug effects/genetics/classification
*Manure/microbiology
Gene Transfer, Horizontal
Agriculture/methods
Drug Resistance, Bacterial
Sewage/microbiology
Drug Resistance, Microbial/genetics
Wastewater/microbiology
Animals
Soil/chemistry

@article {pmid39690257,
year = {2024},
author = {Tsuchida, S and Umemura, H and Iizuka, K and Yamamoto, H and Shimazaki, I and Shikata, E and Nakayama, T},
title = {Recent findings on metabolomics and the microbiome of oral bacteria involved in dental caries and periodontal disease.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {1},
pages = {11},
pmid = {39690257},
issn = {1573-0972},
mesh = {*Dental Caries/microbiology ; Humans ; *Microbiota ; *Mouth/microbiology ; *Metabolomics/methods ; *Periodontal Diseases/microbiology ; *Bacteria/classification/metabolism/genetics/isolation & purification ; Biofilms/growth & development ; Animals ; },
abstract = {Periodontal disease is characterized by bacterial toxins within the oral biofilm surrounding the teeth, leading to gingivitis and the gradual dissolution of the alveolar bone, which supports the teeth. Notably, symptoms in the early stages of the disease are often absent. Similarly, dental caries occurs when oral bacteria metabolize dietary sugars, producing acids that dissolve tooth enamel and dentin. These bacteria are commonly present in the oral cavity of most individuals. Metabolomics, a relatively recent addition to the "omics" research landscape, involves the comprehensive analysis of metabolites in vivo to elucidate pathological mechanisms and accelerate drug discovery. Meanwhile, the term "microbiome" refers to the collection of microorganisms within a specific environmental niche or their collective genomes. The human microbiome plays a critical role in health and disease, influencing a wide array of physiological and pathological processes. Recent advances in microbiome research have identified numerous bacteria implicated in dental caries and periodontal disease. Additionally, studies have uncovered various pathogenic factors associated with these microorganisms. This review focuses on recent findings in metabolomics and the microbiome, specifically targeting oral bacteria linked to dental caries and periodontal disease. We acknowledge the limitation of relying exclusively on the MEDLINE database via PubMed, while excluding other sources such as gray literature, conference proceedings, and clinical practice guidelines.},
}

*Dental Caries/microbiology
Humans
*Microbiota
*Mouth/microbiology
*Metabolomics/methods
*Periodontal Diseases/microbiology
*Bacteria/classification/metabolism/genetics/isolation & purification
Biofilms/growth & development
Animals

@article {pmid39690132,
year = {2024},
author = {Yang, X and Wang, X and Zhang, M and Shen, Y and Teng, Y and Li, M and Pan, H},
title = {Gut Mycobiota of Three Rhinopithecus Species Provide New Insights Into the Association Between Diet and Environment.},
journal = {Integrative zoology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1749-4877.12932},
pmid = {39690132},
issn = {1749-4877},
abstract = {Gut mycobiota are part of the gut microbiome, typically derived from the host diet and living environment. In this study, we examined the gut mycobiota of three snub-nosed monkeys: Rhinopithecus roxellana, R. bieti, and R. strykeri using next-generation amplicon sequencing targeting the fungal internal transcribed spacer. The alpha diversity indexes of gut mycobiota in R. bieti were significantly higher than R. roxellana and R. strykeri, the beta diversity indicated that R. roxellana and R. bieti had more similar feeding habits. Core mycobiota demonstrated commonalities among the three species and potentially associated with feeding habits. Mycobiota displaying significant differences exhibited the respective characteristics of the host, likely associated with the hosts' living environment. Among them, animal and plant pathogenic fungi and lichen parasites are potential threats to the survival of snub-nosed monkeys for their pathogenicity to both monkeys and their food plants. Functionally, fungal trophic modes and functional guilds revealed a strong association between gut mycobiota and host diet. We found a higher abundance and more significant correlations with lichen parasitic fungi in R. strykeri than the other two species, indicating potential threats to their foods. Accordingly, this study revealed the basic structures of gut mycobiota of three wild Rhinopithecus species and highlighted the associations between gut mycobiota and their feeding habits and living environments. Furthermore, due to the close connection between fungi and the environment, animals could ingest fungi from their diet; thus, we speculate that gut mycobiota may serve a role in environmental monitoring for wildlife.},
}

@article {pmid39690119,
year = {2024},
author = {Di Gloria, L and Baldi, S and Curini, L and Bertorello, S and Nannini, G and Cei, F and Niccolai, E and Ramazzotti, M and Amedei, A},
title = {Experimental tests challenge the evidence of a healthy human blood microbiome.},
journal = {The FEBS journal},
volume = {},
number = {},
pages = {},
doi = {10.1111/febs.17362},
pmid = {39690119},
issn = {1742-4658},
support = {//Ministry of University and Research (MUR)/ ; //FONZIE project (CUP B55F21007810001)/ ; //National Recovery and Resilience Plan (NRRP)/ ; },
abstract = {The advent of next-generation sequencing (NGS) technologies has made it possible to investigate microbial communities in various environments, including different sites within the human body. Therefore, the previously established belief of the sterile nature of several body sites, including human blood, has now been challenged. However, metagenomics investigation of areas with an anticipated low microbial biomass may be susceptible to misinterpretation. Here, we critically evaluate the results of 16S targeted amplicon sequencing performed on total DNA collected from healthy donors' blood samples while incorporating specific negative controls aimed at addressing potential bias to supplement and strengthen the research in this area. We prepared negative controls by increasing the initial DNA quantity through sequences that can be recognized and subsequently discarded. We found that only three organisms were sporadically present among the samples, and this was mostly attributable to bacteria ubiquitously present in laboratory reagents. Despite not fully confirming or denying the existence of healthy blood microbiota, our results suggest that living bacteria, or at least their residual DNA sequences, are not a common feature of human blood in healthy people. Finally, our study poses relevant questions on the design of controls in this research area that must be considered in order to avoid misinterpreted results that appear to contaminate current high-throughput research.},
}

@article {pmid39690056,
year = {2024},
author = {Gillingham, MAF and Prüter, H and Montero, BK and Kempenaers, B},
title = {The costs and benefits of a dynamic host microbiome.},
journal = {Trends in ecology & evolution},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tree.2024.11.008},
pmid = {39690056},
issn = {1872-8383},
abstract = {All species host a rich community of microbes. This microbiome is dynamic, and displays seasonal, daily, and even hourly changes, but also needs to be resilient to fulfill important roles for the host. In evolutionary ecology, the focus of microbiome dynamism has been on how it can facilitate host adaptation to novel environments. However, an hitherto largely overlooked issue is that the host needs to keep its microbiome in check, which is costly and leads to trade-offs with investing in other fitness-related traits. Investigating these trade-offs in natural vertebrate systems by collecting longitudinal data will lead to deeper insight into the evolutionary mechanisms that shape host-microbiome interactions.},
}

@article {pmid39689880,
year = {2024},
author = {Ferreira, SCM and Jarquín-Díaz, VH and Planillo, A and Ďureje, Ľ and Martincová, I and Kramer-Schadt, S and Forslund-Startceva, SK and Heitlinger, E},
title = {Eco-evolutionary dynamics of host-microbiome interactions in a natural population of closely related mouse subspecies and their hybrids.},
journal = {Proceedings. Biological sciences},
volume = {291},
number = {2037},
pages = {20241970},
pmid = {39689880},
issn = {1471-2954},
support = {//Deutsche Forschungsgemeinschaft/ ; //Bundesministerium für Bildung und Forschung/ ; },
mesh = {Animals ; Mice ; *Hybridization, Genetic ; Host Microbial Interactions ; Microbiota ; Biological Evolution ; Gastrointestinal Microbiome ; },
abstract = {Closely related host species share similar symbionts, but the effects of host genetic admixture and environmental conditions on these communities remain largely unknown. We investigated the influence of host genetic admixture and environmental factors on the intestinal prokaryotic and eukaryotic communities (fungi, parasites) of two house mouse subspecies (Mus musculus domesticus and M. m. musculus) and their hybrids in two settings: (i) wild-caught mice from the European hybrid zone and (ii) wild-derived inbred mice in a controlled laboratory environment before and during a community perturbation (infection). In wild-caught mice, environmental factors strongly predicted the overall microbiome composition. Subspecies' genetic distance significantly influenced the overall microbiome composition, and each component (bacteria, parasites and fungi). While hybridization had a weak effect, it significantly impacted fungal composition. We observed similar patterns in wild-derived mice, where genetic distances and hybridization influenced microbiome composition, with fungi being more stable to infection-induced perturbations than other microbiome components. Subspecies' genetic distance has a stronger and consistent effect across microbiome components than differences in expected heterozygosity among hybrids, suggesting that host divergence and host filtering play a key role in microbiome divergence, influenced by environmental factors. Our findings offer new insights into the eco-evolutionary processes shaping host-microbiome interactions.},
}

Animals
Mice
*Hybridization, Genetic
Host Microbial Interactions
Microbiota
Biological Evolution
Gastrointestinal Microbiome

@article {pmid39689559,
year = {2024},
author = {Zhang, W and Zong, Y and Zhang, J and Ai, J and He, H and Li, L and Peng, S and Zhou, H and Wang, D and Wang, Q},
title = {Mechanistic insights into the viral microorganism inactivation during lime stabilization for wastewater sludges.},
journal = {Journal of hazardous materials},
volume = {485},
number = {},
pages = {136884},
doi = {10.1016/j.jhazmat.2024.136884},
pmid = {39689559},
issn = {1873-3336},
abstract = {The pathogens inactivation in wastewater sludges is vitally important for safely managing solid wastes and protecting public and environmental health especially in the emergency. Reports have shown the effectiveness of lime to kill virus pathogens in sludges, but mechanism of virus inactivation and related human diseases is unclear. This study evaluated representative limes of CaO/CaO2 on actual viral microorganism inactivation by viral metagenomic sequencing technology. As results, the CaO2 treatment enhanced the sludge hydrolysis and enveloped viral pathogens suppression via EPS structure destruction by oxidative radical generations; while CaO suppressed most of none-enveloped plant related viral pathogens. Most of the viromes of plant virus including Virgaviridae and Nodaviridae were inactivated by CaO, but the human virus-Feirsviridae and plant virus-Solemoviridae were occurred after lime stabilization compared to untreated sludge, with abundances of 1 %-37 % and 21 %-32 % in CaO-treated (CaO-T) and CaO2-treated (CaO2-T) samples, respectively. In addition, metatranscriptome analysis revealed distinct gene expression patterns between the CaO-T and CaO2-T sludges, in which lipopolysaccharide biosynthesis (LPS) and aminoacyl-tRNA synthetases (ARSs) in CaO-T, the formation of ribosome in CaO2-T were crucial to RNA virus regrowth in sludge. These findings suggested neither of CaO and CaO2 could completely suppress pathogens in sludge, and the effect of representative limes of CaO and CaO2 on the viral pathogen diversity, abundance, and metabolic function of the core microbiome on virus suppression and regrowth were ignored. Therefore, combined processes were recommended to provide possible alternatives for sludge safe management in pandemic emergencies.},
}

@article {pmid39689514,
year = {2024},
author = {Thu, MS and Campbell, BJ and Hirankarn, N and Nopsopon, T and Ondee, T and Hall, SR and Jagota, A and Fothergill, JL and Pongpirul, K},
title = {Cannabis and cannabinoid-microbiome interactions in varied clinical contexts: A comprehensive systematic review.},
journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie},
volume = {182},
number = {},
pages = {117764},
doi = {10.1016/j.biopha.2024.117764},
pmid = {39689514},
issn = {1950-6007},
abstract = {With legalisation of cannabis for both medicinal and recreational use expanding to more world nations, grasping its effects on the human body is vital. The microbiome is critical to human health and disease, and accumulating data suggests that it is influenced by a variety of external variables, including marijuana/cannabis and cannabinoids. We therefore conducted a comprehensive assessment of the literature to analyse cannabis and cannabinoid effects on the human microbiota. We searched PubMed, Embase and Cochrane Library CENTRAL databases for studies involving the use of marijuana, medical cannabis, cannabinoids and cannabinoid-like lipid mediators on microbiota, across all clinical conditions. Nine studies were identified: 2 clinical trials and 7 observational studies examining cannabis and cannabinoid impact on oral, gastrointestinal, faecal and vaginal microbial abundance and diversity. Outcomes illustrated positive and negative impacts of cannabis use/cannabinoid actions on microbiota in adults with cognitive deficiency, depression, HIV infection, inflammation/pain, oral disease or obesity. Changes in alpha diversity were identified with cannabis/cannabinoid use, although this varied depending on the clinical context. A positive association exists between serum endocannabinoids and gut microbiota, via elevation in SCFAs and anti-inflammatory actions, beneficial for musculoskeletal pain relief and to counter obesity. Marijuana use in HIV patients showed protective effects by decreasing abundance of pro-inflammatory Prevotella, though excessive consumption leads to reduced microbiome richness and diversity, and increased systemic inflammation. Overall, this review underscores the need for further exploration in understanding the complex effects of cannabis, cannabinoids and cannabinoid-like mediators on composition and metabolic activity of the human microbiota.},
}

@article {pmid39689480,
year = {2024},
author = {Insawake, K and Songserm, T and Songserm, O and Plaiboon, A and Homwong, N and Adeyemi, KD and Rassmidatta, K and Ruangpanit, Y},
title = {Effects of isoquinoline alkaloids as an alternative to antibiotic on oxidative stress, inflammatory status, and cecal microbiome of broilers under high stocking density.},
journal = {Poultry science},
volume = {104},
number = {1},
pages = {104671},
doi = {10.1016/j.psj.2024.104671},
pmid = {39689480},
issn = {1525-3171},
abstract = {This study investigated the effect of isoquinoline alkaloids as an alternative to bacitracin on growth performance, oxidative stress, inflammatory status, and ceca microbiome of broilers raised under high stocking density (HSD). A total of 1,500 one-day-old male Ross 308 chicks were randomly assigned to five treatment groups, with 10 replicate pens per group and 30 birds per pen, for 37 days. The treatments included normal stocking density (NSD, 10 birds/m[2]), HSD (15 birds/m[2]), HSD with 50 ppm Bacitracin (BCT50), HSD with 80 ppm isoquinoline alkaloids (IQA80), and HSD with 100 ppm isoquinoline alkaloids (IQA100). From days 11 to 24, HSD birds had lower feed efficiency (P < 0.05) compared to those in other treatments. The heterophil-to-lymphocyte ratio and malondialdehyde levels were lower in NSD and IQA80 birds compared to HSD and BCT50 birds (P < 0.05). HSD birds had higher IL-6 and a lower villus height and villus height-to-crypt depth ratio compared to birds in other groups (P < 0.05). Serum TNF-α was lower in NSD and IQA80 birds compared to those in the HSD group. Alpha diversity was not affected by the treatments; however, beta diversity was lower in HSD birds compared to other treatments. HSD birds showed reduced microbial diversity, with a higher prevalence of Enterococcaceae and Peptostreptococcaceae. NSD enhanced the abundance of Lactobacillaceae, Clostridiaceae, and Rikenellaceae. BCT50 increased and decreased the abundance of Enterococcaceae and Rikenellaceae respectively. IQA80 and IQA100 increased the abundance of Lachnospiraceae, Leuconostocaceae, and Coriobacteriaceae. HSD altered metabolic pathways related to carbohydrate and lipid metabolism, and amino acid biosynthesis. BCT50 modulated microbial functions, particularly those related to cell wall synthesis, while isoquinoline alkaloids upregulated pathways involved in energy production, secondary metabolite biosynthesis, and antioxidant production. Both Bacitracin and isoquinoline alkaloids were effective in mitigating the negative effects of HSD on immunity, gut health and microbiota in broilers. Given the concerns about antimicrobial resistance, isoquinoline alkaloids are a potent alternative to bacitracin, with IQA80 being particularly recommended.},
}

@article {pmid39689477,
year = {2024},
author = {Li, S and Wang, K and Wang, D and Wang, H and Zhao, H and Pu, J and Wang, K and Li, C},
title = {Distribution and environmental dissemination of antibiotic resistance genes in poultry farms and surrounding ecosystems.},
journal = {Poultry science},
volume = {104},
number = {1},
pages = {104665},
doi = {10.1016/j.psj.2024.104665},
pmid = {39689477},
issn = {1525-3171},
abstract = {Antibiotic resistance poses a significant threat to human and animal health worldwide, with farms serving as crucial reservoirs of Antibiotic Resistance Genes (ARGs) and Antibiotic-resistant bacteria. However, the distribution of ARGs in poultry farms and their transmission patterns in the environment remain poorly understood. This study collected samples of aerosol microorganisms, cloacal matter, soil, and vegetables from poultry farms and surrounding environments at three different distances. We used 16S rRNA gene sequencing and HT-qPCR to analyze the characteristics of aerosol microbial communities and the abundance of ARGs. At the phylum level, Proteobacteria, Firmicutes, and Bacteroidetes were dominant in cloacal samples, aerosol samples, and vegetable samples, while Proteobacteria Actinobacteriota and Acidobacteria dominated soil. Pseudomonas was dominant in cloacal samples at the genus level, whereas Fusobacterium was prevalent in soil. The diversity and richness of bacterial communities were more similar between cloacal samples than those observed between either sample type compared with soil. Our results showed that tetracycline and aminoglycoside ARG relative abundance was high across all sample types but significantly increased within feces/air compared to soils/vegetables. Association analysis revealed five potential host genera for ARG/MGE presence among various microbiota populations studied here. Our findings confirm that farms are important sources for the environmental dissemination of pathogens and ARGs.},
}

@article {pmid39689342,
year = {2024},
author = {Chircop, O and Jaggers, C and Spiteri, M and Schembri, A and Padovese, V},
title = {DOXY do, or DOXY Don't? Syphilis and doxycycline post-exposure prophylaxis: A case report.},
journal = {International journal of STD & AIDS},
volume = {},
number = {},
pages = {9564624241308026},
doi = {10.1177/09564624241308026},
pmid = {39689342},
issn = {1758-1052},
abstract = {The resurgence of syphilis across Europe has led to a growing number of atypical cases, often characterised by varied symptoms that can delay diagnosis. We report the case of a young man who has sex with men (MSM), presenting with persistent headaches and swelling of the forehead suggestive of giant cell arteritis (GCA). Despite a recent negative syphilis test, further investigations confirmed the diagnosis of neurosyphilis. The patient had been using doxycycline post-exposure prophylaxis (DoxyPEP), which is suspected to have delayed the diagnosis by masking the typical antibody response. This case highlights concerns about DoxyPEP's impact on syphilis detection and disease progression. Further research is warranted to explore its effects on antimicrobial resistance, the human microbiome, and clinical outcomes.},
}

@article {pmid39689242,
year = {2024},
author = {Morais, VN and Moreira, LPD and Gomes, MJC and Grancieri, M and Lucio, HG and Toledo, RCL and Mishima, MDV and Costa, NMB and da Silva, BP and Stampini Duarte Martino, H},
title = {Chia Oil (Salvia hispanica L.) Improves the Intestinal Health of Wistar Rats Fed a Hypercaloric Diet.},
journal = {Journal of the American Nutrition Association},
volume = {},
number = {},
pages = {1-10},
doi = {10.1080/27697061.2024.2431271},
pmid = {39689242},
issn = {2769-707X},
abstract = {BACKGROUND: A diet rich in fat and sugar is present in society everyday life, leading to the development of metabolic changes, especially in intestinal microbiota. Chia oil is a source of alpha-linolenic acid, which has antioxidant and anti-glycemic effects. Based on this, we hypothesized that chia oil may promote intestinal health.

OBJECTIVE: The study aims to investigate the effects of chia oil on gut microbiota and intestinal health in Wistar rats fed a high-fat and high-fructose diet (HFHF).

METHODS: The animals were separated into two groups and received the following diets: standard murine diet (AIN-93M) (n = 10) and HFHF (n = 20) to induce metabolic changes (phase I) during eight weeks. After that, the AIN-93M group remained unchanged, while the HFHF group was divided into two groups: HFHF (n = 10) and HFHF with chia oil (HFHF+CO) (n = 10) for ten weeks (phase II, chia oil treatment). We analyzed immunoglobulin A (IgA) levels, cecal pH, short-chain fatty acids (SCFAs), intestinal permeability, intestinal microbiome composition, histomorphometry, and murinometric parameters.

RESULTS: Chia oil consumption increased alpha-linolenic acid intake, IgA levels, propionic acid production, cecum weight, goblet cell number, thickness and depth of intestinal crypts, and the thickness of both circular and longitudinal muscle layers of the colon, and decreased cecal pH. No change was observed in the alpha and beta diversity between the HFHF and HFHF+CO groups. The HFHF+CO diet increased the relative abundance of genera Lactobacillus sp., Faecalibacterium sp., and Erysipelatoclostridium sp., compared to the AIN-93M group. No difference was observed in the intestinal permeability among the groups.

CONCLUSION: Chia oil consumption is an alternative for improving the intestinal health of rats fed a HFHF diet.},
}

@article {pmid39689178,
year = {2024},
author = {Li, G and Liu, T and Xie, W and Liu, Z and Li, H and Whalen, JK and Jousset, A and Wei, Z},
title = {Metabolites limiting predator growth wane with prey biodiversity.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {52},
pages = {e2410210121},
doi = {10.1073/pnas.2410210121},
pmid = {39689178},
issn = {1091-6490},
support = {32201399//MOST | National Natural Science Foundation of China (NSFC)/ ; 32171640//MOST | National Natural Science Foundation of China (NSFC)/ ; KYQN2023048//MOE | Fundamental Research Funds for the Central Universities (Fundamental Research Fund for the Central Universities)/ ; 2022YFD1500302//MOST | National Key Research and Development Program of China (NKPs)/ ; },
mesh = {Animals ; *Biodiversity ; *Nematoda/physiology ; *Food Chain ; *Predatory Behavior/physiology ; Microbiota/physiology ; Bacteria/metabolism/classification ; Soil Microbiology ; },
abstract = {Predator-prey interactions are a major driver of microbiome dynamics, but remain difficult to predict. While several prey traits potentially impact resistance to predation, their effects in a multispecies context remain unclear. Here, we leverage synthetic bacterial communities of varying complexity to identify traits driving palatability for nematodes, a main consumer of bacteria in soil. We assessed trophic interactions between four nematode species and 122 bacterial isolates, across a gradient of prey biodiversity ranging from single species to 50 species. Nematode size, a proxy for prey palatability, varied strongly with prey community composition and could be predicted by metabolic and morphological properties of the prey. However, the influence of prey traits on predators depended on biodiversity. Secondary metabolites drove palatability in monoculture, but this effect vanished under increasing prey biodiversity, where prey size became the dominant predictors of nematode size. Although idiosyncratic properties are often emphasized in the literatures, our results suggest that in biodiverse assemblages, the composition of available prey and their traits are more reliable predictors of predator-prey interactions. This study offers valuable insights into microbial ecology in the context of predator-prey interactions, as cryptic microbial responses can be guided by deductions based on generalizable biological traits.},
}

Animals
*Biodiversity
*Nematoda/physiology
*Food Chain
*Predatory Behavior/physiology
Microbiota/physiology
Bacteria/metabolism/classification
Soil Microbiology

@article {pmid39689103,
year = {2024},
author = {Milling, S and Ijaz, UZ and Venieri, D and Christidis, GE and Rattray, NJW and Gounaki, I and Andrusaite, A and Hareendran, A and Knapp, CW and Jones, AX and Photos-Jones, E},
title = {Beneficial modulation of the gut microbiome by leachates of Penicillium purpurogenum in the presence of clays: A model for the preparation and efficacy of historical Lemnian Earth.},
journal = {PloS one},
volume = {19},
number = {12},
pages = {e0313090},
pmid = {39689103},
issn = {1932-6203},
mesh = {*Penicillium/drug effects ; *Gastrointestinal Microbiome/drug effects ; Animals ; *Clay/chemistry ; Mice ; *Silicates/pharmacology ; Kaolin ; Aluminum Silicates/chemistry/pharmacology ; Coculture Techniques ; Anti-Bacterial Agents/pharmacology ; },
abstract = {The experiments presented here are based on the reconfiguration of an ancient medicine, Lemnian Earth (LE) (terra sigillata, stamped earth, sphragis), an acclaimed therapeutic clay with a 2500-year history of use. Based on our hypothesis that LE was not a natural material but an artificially modified one involving a clay-fungus interaction, we present results from experiments involving the co-culture of a common fungus, Penicillium purpurogenum (Pp), with two separate clay slurries, smectite and kaolin, which are the principal constituents of LE. Our results show: (a) the leachate of the Pp+smectite co-culture is antibacterial in vitro, inhibiting the growth of both Gram-positive and Gram-negative bacteria; (b) in vivo, supplementation of regular mouse diet with leachates of Pp+smectite increases intestinal microbial diversity; (c) Pp+kaolin does not produce similar results; (d) untargeted metabolomics and analysis of bacterial functional pathways indicates that the Pp+smectite-induced microbiome amplifies production of short-chain fatty acids (SCFAs) and amino acid biosynthesis, known to modulate intestinal and systemic inflammation. Our results suggest that the combination of increased microbial diversity and SCFA production indicates beneficial effects on the host microbiome, thus lending support to the argument that the therapeutic properties of LE may have been based on the potential for modulating the gut microbiome. Our experiments involving reconfigured LE open the door to future research into small molecule-based sources for promoting gut health.},
}

*Penicillium/drug effects
*Gastrointestinal Microbiome/drug effects
Animals
*Clay/chemistry
Mice
*Silicates/pharmacology
Kaolin
Aluminum Silicates/chemistry/pharmacology
Coculture Techniques
Anti-Bacterial Agents/pharmacology

@article {pmid39689102,
year = {2024},
author = {Cremonesi, P and Biscarini, F and Castiglioni, B and Sgoifo, CA and Compiani, R and Moroni, P},
title = {Correction: Gut microbiome modifications over time when removing in-feed antibiotics from the prophylaxis of post-weaning diarrhea in piglets.},
journal = {PloS one},
volume = {19},
number = {12},
pages = {e0316120},
doi = {10.1371/journal.pone.0316120},
pmid = {39689102},
issn = {1932-6203},
abstract = {[This corrects the article DOI: 10.1371/journal.pone.0262199.].},
}

@article {pmid39688879,
year = {2024},
author = {Mazarati, A},
title = {Gut-microbiota-brain Axis and post-traumatic epilepsy.},
journal = {Epilepsia open},
volume = {},
number = {},
pages = {},
doi = {10.1002/epi4.13113},
pmid = {39688879},
issn = {2470-9239},
abstract = {There has been growing evidence that perturbations in gut-microbiota-brain axis (GMBA) are involved in mechanisms of chronic sequelae of traumatic brain injury (TBI). This review discusses the connection between GMBA and post-traumatic epilepsy (PTE), the latter being a common outcome of TBI. The focus is on two aspects of post-TBI GMBA dysfunction that are relevant to epilepsy. First are impairments in intestinal permeability with subsequent translocation of gut bacteria into the bloodstream. Specifically, endotoxemia following TBI may have a serendipitous protective effect against PTE through lipopolysaccharide conditioning, which may be leveraged for the development of therapeutic interventions. Second are changes in microbial composition (i.e., dysbiosis). Here, the GMBA-PTE connection is explored from predictive biomarker perspective, whereby the risk of PTE can be stratified based on specific microbial profiles. Finally, microbiota transplantation is discussed both as a tool to examine the role of gut microbiota in PTE and as a prelude to novel approaches for PTE therapy and prevention.},
}

@article {pmid39688852,
year = {2024},
author = {O'Donnell, JEM and Walters, TD and Benchimol, EI},
title = {Advancements in the management of pediatric inflammatory bowel disease.},
journal = {Expert review of gastroenterology & hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1080/17474124.2024.2444555},
pmid = {39688852},
issn = {1747-4132},
abstract = {INTRODUCTION: The management of pediatric inflammatorybowel disease (PIBD) has drastically changed in the last decade. The limitedavailability of new biologics or small molecule therapies, and concerns aboutdurability in children has necessitated the development of other advances inmanagement to optimize care.

AREAS COVERED: Thisreview covers guidance for management targets andadvances in optimizing biologic therapies, newmedical therapies, adjuvant therapies, precision medicine and mental healthconcerns in PIBD. This review focused on recent advances and was not intendedas a complete overview of the investigations and management of pediatricIBD.

EXPERT OPINION: Advancements includestandardization of treatment goals via a treat-to-target strategy, optimizinganti-TNF biologics through combination therapy or proactive drug monitoring,earlier initiation of treatment for Crohn's disease, the emergence of newbiologic/advanced therapies and a growing focus on adjuvant therapies targetingthe microbiome. Future progress relies on the inclusion of children/adolescentsin clinical trials to facilitate faster regulatory approval for pediatrictherapies and the integration of precision medicine and mental health screeningto improve patient care and outcomes.},
}

@article {pmid39688845,
year = {2024},
author = {Oteo-García, G and Mutti, G and Caldon, M and Oosthuitzen, O and ManfrediniK, M and Capelli, C},
title = {Reconstructing micro-evolutionary dynamics shaping local variation in southern African populations using genomics, metagenomics and personal metadata.},
journal = {Journal of anthropological sciences = Rivista di antropologia : JASS},
volume = {102},
number = {},
pages = {},
doi = {10.4436/JASS.10204},
pmid = {39688845},
issn = {2037-0644},
abstract = {Geography is a well-known factor shaping genetic variation in human populations. However, the potential role played by cultural variables remains much understudied. This study investigates the impact of socio-cultural variables on genomic similarity and the saliva microbiome, using data from populations in Lesotho and Namibia. Geographic distance within Lesotho increases genetic differentiation, while shared clan affiliation surprisingly increases it. In Namibia, ethnicity is the predominant factor influencing genetic affinity. Saliva metagenomic data shows a negative correlation between age and alpha diversity, with notable differences in host-interacting taxa and viral load. These findings highlight the role of geography in shaping genetic affinity even at small scales and the complex influences of cultural factors. The saliva microbiome appears primarily affected by unrecorded individual behaviors rather than geographic or cultural variables. At population-level these oral microbiomes reveal insights into some dietary habits, oral health, and also the communal viral load, which appears to have greater incidence in Lesotho possibly related to the long-term effects of the HIV epidemic in the country.},
}

@article {pmid39688648,
year = {2024},
author = {Todorov, SD and Tagg, J and Algburi, A and Tiwari, SK and Popov, I and Weeks, R and Mitrokhin, OV and Kudryashov, IA and Kraskevich, DA and Chikindas, ML},
title = {The Hygienic Significance of Microbiota and Probiotics for Human Wellbeing.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {39688648},
issn = {1867-1314},
abstract = {The human body can be viewed as a combination of ecological niches inhabited by trillions of bacteria, viruses, fungi, and parasites, all united by the microbiota concept. Human health largely depends on the nature of these relationships and how they are built and maintained. However, personal hygiene practices have historically been focused on the wholesale elimination of pathogens and "hygiene-challenging microorganisms" without considering the collateral damage to beneficial and commensal species. The microbiota can vary significantly in terms of the qualitative and quantitative composition both between different people and within one person during life, and the influence of various environmental factors, including age, nutrition, bad habits, genetic factors, physical activity, medication, and hygienic practices, facilitates these changes. Disturbance of the microbiota is a predisposing factor for the development of diseases and also greatly influences the course and severity of potential complications. Therefore, studying the composition of the microbiota of the different body systems and its appropriate correction is an urgent problem in the modern world. The application of personal hygiene products or probiotics must not compromise health through disruption of the healthy microbiota. Where changes in the composition or metabolic functions of the microbiome may occur, they must be carefully evaluated to ensure that essential biological functions are unaffected. As such, the purpose of this review is to consider the microbiota of each of the "ecological niches" of the human body and highlight the importance of the microbiota in maintaining a healthy body as well as the possibility of its modulation through the use of probiotics for the prevention and treatment of certain human diseases.},
}

@article {pmid39688607,
year = {2024},
author = {Liapis, CC},
title = {["Pseudoneurotransmission" and gut microbiome - brain communication in neuropsychiatric disorders].},
journal = {Psychiatrike = Psychiatriki},
volume = {},
number = {},
pages = {},
doi = {10.22365/jpsych.2024.024},
pmid = {39688607},
issn = {1105-2333},
abstract = {The gut microbiome, which comprises symbiotic bacteria colonizing the human digestive tract, undergoes dynamic changes during the lifespan, as evidenced by the fact that the number of species and the diversity of their composition decrease significantly with age. The aim of this review is to illuminate bilateral neuroimmunological pathways that determine the role of gut microbiome dysbiosis, not only as a cause but also as a byproduct of many neurodegenerative diseases of the CNS, such as Alzheimer's disease (AD) and Parkinson's disease (PD), but also in the frame of several behavioral and psychiatric pathological conditions such as depressive and anxiety disorders, schizophrenia, and autism spectrum disorder (ASD). Dysbiosis, in particular, reveals a model of "deceptive" mimicry of host molecules that might cause abnormal folding ("misfolding") and pathological aggregation of Aβ-peptide, leading to its dispersion through the gut-brain axis, precipitating microglia cell activation. By controlling myelination at the prefrontal cortex (PFC), a crucial area for multifaceted cognitive behavior, forecasting, and decision-making, the gut/microbiome-brain axis influences mood and social behavior, since major depressive disorder is correlated to white matter disturbance in the PFC, due to disregulations in the expression of myelin-related mRNA in this area. The gut microbiome is altered in psychosis compared to healthy controls, while medication with antipsychotics may result in reduced microbial community diversity. The vagus nerve, as a key element of the parasympathetic nervous system, regulating immune responses, may "detect" gut microbiome metabolites and transfer this intestinal information to the CNS, through its afferents, as in a "pseudo-neurotransmission" process. Scientific interest towards microbiome-based therapies increases as psychobiotics (which are strains of probiotics/prebiotics with specific properties to influence the gut-brain axis) appear to be able to exercise a beneficial effect in many CNS disorders. Lifestyle modifications, such as dietary interventions via psychobiotics intake that might enhance the gut microbiome's ability to produce beneficial metabolites that exert therapeutic effects on intestinal permeability, cognitive function, and immunity, may reveal new research pathways and therapeutic directions leading to a radical change of the "epistemology paradigm" as far as prevention and treatment of major neuro-psychiatric disorders is concerned.},
}

@article {pmid39688588,
year = {2024},
author = {Jiang, H and Miao, X and Thairu, MW and Beebe, M and Grupe, DW and Davidson, RJ and Handelsman, J and Sankaran, K},
title = {Multimedia: multimodal mediation analysis of microbiome data.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0113124},
doi = {10.1128/spectrum.01131-24},
pmid = {39688588},
issn = {2165-0497},
abstract = {UNLABELLED: Mediation analysis has emerged as a versatile tool for answering mechanistic questions in microbiome research because it provides a statistical framework for attributing treatment effects to alternative causal pathways. Using a series of linked regressions, this analysis quantifies how complementary data relate to one another and respond to treatments. Despite these advances, existing software's rigid assumptions often result in users viewing mediation analysis as a black box. We designed the multimedia R package to make advanced mediation analysis techniques accessible, ensuring that statistical components are interpretable and adaptable. The package provides a uniform interface to direct and indirect effect estimation, synthetic null hypothesis testing, bootstrap confidence interval construction, and sensitivity analysis, enabling experimentation with various mediator and outcome models while maintaining a simple overall workflow. The software includes modules for regularized linear, compositional, random forest, hierarchical, and hurdle modeling, making it well-suited to microbiome data. We illustrate the package through two case studies. The first re-analyzes a study of the microbiome and metabolome of Inflammatory Bowel Disease patients, uncovering potential mechanistic interactions between the microbiome and disease-associated metabolites, not found in the original study. The second analyzes new data about the influence of mindfulness practice on the microbiome. The mediation analysis highlights shifts in taxa previously associated with depression that cannot be explained indirectly by diet or sleep behaviors alone. A gallery of examples and further documentation can be found at https://go.wisc.edu/830110.

IMPORTANCE: Microbiome studies routinely gather complementary data to capture different aspects of a microbiome's response to a change, such as the introduction of a therapeutic. Mediation analysis clarifies the extent to which responses occur sequentially via mediators, thereby supporting causal, rather than purely descriptive, interpretation. Multimedia is a modular R package with close ties to the wider microbiome software ecosystem that makes statistically rigorous, flexible mediation analysis easily accessible, setting the stage for precise and causally informed microbiome engineering.},
}

@article {pmid39688568,
year = {2024},
author = {Park, SJ and Kim, KW and Lee, EJ},
title = {Gut-brain axis and environmental factors in Parkinson's disease: bidirectional link between disease onset and progression.},
journal = {Neural regeneration research},
volume = {},
number = {},
pages = {},
doi = {10.4103/NRR.NRR-D-24-00994},
pmid = {39688568},
issn = {1673-5374},
abstract = {Parkinson's disease has long been considered a disorder that primarily affects the brain, as it is defined by the dopaminergic neurodegeneration in the substantia nigra and the brain accumulation of Lewy bodies containing alpha-synuclein protein. In recent decades, however, accumulating research has revealed that Parkinson's disease also involves the gut and uncovered an intimate and important bidirectional link between the brain and the gut, called the "gut-brain axis." Numerous clinical studies demonstrate that gut dysfunction frequently precedes motor symptoms in Parkinson's disease patients, with findings including impaired intestinal permeability, heightened inflammation, and distinct gut microbiome profiles and metabolites. Furthermore, alpha-synuclein deposition has been consistently observed in the gut of Parkinson's disease patients, suggesting a potential role in disease initiation. Importantly, individuals with vagotomy have a reduced Parkinson's disease risk. From these observations, researchers have hypothesized that alpha-synuclein accumulation may initiate in the gut and subsequently propagate to the central dopaminergic neurons through the gut-brain axis, leading to Parkinson's disease. This review comprehensively examines the gut's involvement in Parkinson's disease, focusing on the concept of a gut-origin for the disease. We also examine the interplay between altered gut-related factors and the accumulation of pathological alpha-synuclein in the gut of Parkinson's disease patients. Given the accessibility of the gut to both dietary and pharmacological interventions, targeting gut-localized alpha-synuclein represents a promising avenue for developing effective Parkinson's disease therapies.},
}

@article {pmid39688539,
year = {2024},
author = {Xiao, Q and Zhang, L and Xu, X and Dai, R and Tan, Y and Li, X and Jin, D and Fan, Y},
title = {A nitrogen-metabolism inhibitor NmrA regulates conidial production, melanin synthesis and virulence in phytopathogenic fungus Verticillium dahliae.},
journal = {Phytopathology},
volume = {},
number = {},
pages = {},
doi = {10.1094/PHYTO-07-24-0226-R},
pmid = {39688539},
issn = {0031-949X},
abstract = {NmrA homologs have been reported as conserved regulators of the nitrogen metabolite repression (NMR) in various fungi. Here, we identified a NmrA homolog in Verticillium dahliae and reported its functions in nitrogen utilization, growth and development, and pathogenesis. VdNmrA interacts with V. dahliae AreA protein and regulates the expression of a typical NCR target, the formamidase gene. VdNmrA deletion mutants exhibited significantly slower colony growth on media with Gln or Arg. Furthermore, VdNmrA deletion impaired hyphal growth, spore production, hyperosmotic stress tolerance, and melanin biosynthesis. Less ROS was produced in VdNmrA mutants, and the NADPH oxidase genes noxA and noxB showed lowered expression level compared to the wild type. VdNmrA mutants exhibited reduced virulence on cotton and Arabidopsis compared with wild type strains. Our results indicated that VdNmrA functioned as an NMR repressor and played important roles in nutrient utilization, fungal development, stress tolerance and pathogenicity in V. dahliae.},
}

@article {pmid39688441,
year = {2024},
author = {Ferreira, DO and Ferrari, M and Morais, DB and Santos, RD and Costa, MGMB and Mota, KB and Lanza, DCF},
title = {Defining a panel of principal bacteria associated with endometritis.},
journal = {JBRA assisted reproduction},
volume = {},
number = {},
pages = {},
doi = {10.5935/1518-0557.20240088},
pmid = {39688441},
issn = {1518-0557},
abstract = {The aim of this study is to present a panel that includes the main bacterial genera associated with endometritis. We conducted a search using the terms "endometritis women" OR "female endometritis" OR "pelvic inflammatory disease" AND bacteria* OR "uterine microbiome" in two databases: PubMed and Web of Science, without language or publication year restrictions. The panel is based on an analysis of 40 studies published over the past 38 years. We identified 31 bacterial genera, with the following five being the most frequently cited: Chlamydia and Ureaplasma with 11.03% each, Streptococcus and Mycoplasma with 9.56% each, and Enterococcus with 8.09%. Regarding its etiological aspects, we found that bacterial infection is the most prevalent cause of the disease, occurring because of invasive procedures such as curettage, cesarean section, or insertion of intrauterine devices (IUDs), among others. These events facilitate the entry of pathogenic microorganisms into the uterus, resulting in an inflammatory response and subsequent development of endometritis. The main techniques used to detect these pathogens were microbial culture, Polymerase Chain Reaction (PCR), and Next-Generation Sequencing, with microbial culture being the most employed, followed by PCR or a combination of both techniques. This diversity of techniques has significantly expanded our understanding of the presence and identification of microorganisms associated with the pathophysiology of endometritis. Therefore, it is understood that these findings serve as a foundation for further investigations of microorganisms related to endometritis, and such analyses will help to clarify the relationship between endometritis and the bacteria that cause it.},
}

@article {pmid39688414,
year = {2024},
author = {Yang, Y and Gao, W and Zhu, R and Tao, L and Chen, W and Zhu, X and Shen, M and Xu, T and Zhao, T and Zhang, X and Zhu, L and Jiao, N},
title = {Systematic identification of secondary bile acid production genes in global microbiome.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0081724},
doi = {10.1128/msystems.00817-24},
pmid = {39688414},
issn = {2379-5077},
abstract = {UNLABELLED: Microbial metabolism of bile acids (BAs) is crucial for maintaining homeostasis in vertebrate hosts and environments. Although certain organisms involved in bile acid metabolism have been identified, a global, comprehensive elucidation of the microbes, metabolic enzymes, and bile acid remains incomplete. To bridge this gap, we employed hidden Markov models to systematically search in a large-scale and high-quality search library comprising 28,813 RefSeq multi-kingdom microbial complete genomes, enabling us to construct a secondary bile acid production gene catalog. This catalog greatly expanded the distribution of secondary bile acid production genes across 11 phyla, encompassing bacteria, archaea, and fungi, and extended to 14 habitats spanning hosts and environmental contexts. Furthermore, we highlighted the associations between secondary bile acids (SBAs) and gastrointestinal and hepatic disorders, including inflammatory bowel disease (IBD), colorectal cancer (CRC), and nonalcoholic fatty liver disease (NAFLD), further elucidating disease-specific alterations in secondary bile acid production genes. Additionally, we proposed the pig as a particularly suitable animal model for investigating secondary bile acid production in humans, given its closely aligned secondary bile acid production gene composition. This gene catalog provides a comprehensive and reliable foundation for future studies on microbial bile acid metabolism, offering new insights into the microbial contributions to health and disease.

IMPORTANCE: Bile acid metabolism is an important function in both host and environmental microorganisms. The existing functional annotations from single source pose limitations on cross-habitat analysis. Our construction of a systematic secondary bile acid production gene catalog encompassing numerous high-quality reference sequences propelled research on bile acid metabolism in the global microbiome, holding significance for the concept of One Health. We further highlighted the potential of the microbiota-secondary bile acid axis as a target for the treatment of hepatic and intestinal diseases, as well as the varying feasibility of using animal models for studying human bile acid metabolism. This gene catalog offers a solid groundwork for investigating microbial bile acid metabolism across different compartments, including humans, animals, plants, and environments, shedding light on the contributions of microorganisms to One Health.},
}

@article {pmid39688160,
year = {2024},
author = {Gong, W and Zhou, K and Li, S and Yue, Z and Zhang, Q and Li, Y and Mi, X},
title = {Different Effects of Fixed Appliances and Clear Aligners on the Microbiome and Metabolome of Dental Plaque.},
journal = {Orthodontics & craniofacial research},
volume = {},
number = {},
pages = {},
doi = {10.1111/ocr.12883},
pmid = {39688160},
issn = {1601-6343},
support = {11402175//National Natural Science Foundation of China/ ; 202140355//Shanghai Municipal Health Commission/ ; },
abstract = {OBJECTIVE: This study aimed to uncover the microbial and metabolic changes in dental plaque during orthodontic treatments with fixed appliances (FAs) and clear aligners (CAs).

MATERIALS AND METHODS: Twenty participants were grouped by the treatment modality they received, with 10 participants each in the FA and CA groups. Supragingival plaques were collected before orthodontic treatment (T0), after 1-3 months (T1) and more than 6 months (T2) of orthodontic treatment. 16S rRNA gene sequencing and liquid chromatography-tandem mass spectrometry were employed to analyse the plaque samples.

RESULTS: No significant change was observed in the alpha and beta diversity at different time points and between the two treatment modalities. The relative abundance of genera Veillonella, Mogibacterium and unclassified_c__Actinobacteria, and species Actinomyces massiliensis, Prevotella pallens and Prevotella jejuni experienced the most significant changes. The most differential metabolites were amino acids, nucleosides and organoheterocyclic compounds. Compared to T0, downregulation of nucleotide metabolism at T1 and upregulation of amino acid metabolism at T2 were found in the FA group. Compared with the FA group, the CA group experienced metabolite enrichment in several immune pathways at T1, while linoleic acid metabolism, riboflavin metabolism and nucleotide metabolism were downregulated at T2 in the CA group. Significant correlations were identified between most differential plaque microorganisms and metabolites.

CONCLUSION: This study implied that exposure to FAs for more than 6 months resulted in the accumulation of oral disease-related bacteria in dental plaque and a metabolic shift towards a cariogenic state, whereas CAs could lead to a transient proinflammatory state.},
}

@article {pmid39688114,
year = {2024},
author = {Diao, J and Zhang, Y and Zhang, X and Jia, S and Lei, Y and Ma, B and Li, X and Zheng, S and Yuan, C},
title = {Integrated Analysis of Oral Microbiome and Metabolome in T2DM Patients With Varying Glycemic Status.},
journal = {Oral diseases},
volume = {},
number = {},
pages = {},
doi = {10.1111/odi.15220},
pmid = {39688114},
issn = {1601-0825},
support = {2022YFE0118300//National Key R&D Program of China/ ; 2022YFA1206101//National Key R&D Program of China/ ; PKUSS-2023CRF303//Peking University School and Hospital of Stomatology series of clinical research projects/ ; },
abstract = {OBJECTIVE: This study aimed to analyze the subgingival and salivary microbiome and metabolome in diabetic periodontitis patients with varying glycemic levels.

METHODS: Forty-two diabetic periodontitis patients were sampled of saliva, gingival crevicular fluid (GCF), and blood, and categorized into three groups based on systemic glycemic status. The microbiome was assessed using full-length 16S rRNA gene sequencing. Gas chromatography-mass spectrometry was performed for metabolome analysis.

RESULTS: The similarity in the structure and function of the flora in saliva and GCF was evident under good blood glucose control. Conversely, inadequate blood glucose control demonstrated a more distinct separation from saliva flora. Both salivary and GCF microorganisms exhibited greater periodontal pathogenicity, with salivary metabolites showing stronger associations with inflammation when Hemoglobin A1c (HbA1c) > 6.5%. Some periodontal pathogens, such as Veillonella atypica, showed significantly positive correlations with proinflammatory metabolites, including lactic acid and putrescine, etc. Salivary microbes demonstrated more sensitive responses than GCF to changes in blood glucose levels among type 2 diabetes mellitus (T2DM) patients.

CONCLUSION: Under active blood glucose control, it indicates lower periodontal pathogenicity and inflammatory correlation in the oral microecology of T2DM patients. Saliva appears to offer superior diagnostic and monitoring value compared to GCF in the context of systemic disease surveillance.},
}

@article {pmid39687970,
year = {2024},
author = {Schifano, N and Capogrosso, P and Baldini, S and Villano, A and Antonini, G and Deho', F},
title = {The role of the urinary microbiome on male benign prostatic hyperplasia (BPH) and its management using probiotic supplementation: a narrative review.},
journal = {European review for medical and pharmacological sciences},
volume = {28},
number = {23},
pages = {4671-4679},
doi = {10.26355/eurrev_202412_36978},
pmid = {39687970},
issn = {2284-0729},
mesh = {Humans ; Male ; *Prostatic Hyperplasia/therapy/microbiology ; *Probiotics/administration & dosage/therapeutic use ; Microbiota ; Lower Urinary Tract Symptoms/therapy/microbiology ; Gastrointestinal Microbiome ; Dietary Supplements ; },
abstract = {Benign prostatic hyperplasia (BPH) is highly prevalent and associated with a significant impact on individuals' well-being. Initial management involves various medications, but their benefits can be limited by side effects, particularly concerning young people. In this context, novel and better-tolerated therapeutic strategies have been proposed, thus including the modulation of the gut microbiome through probiotic ingestion. We aimed to examine the available evidence linking the urinary microbiome to lower urinary tract symptoms (LUTS) and to evaluate the possible usefulness of probiotic supplementation as a novel treatment option for LUTS/BPH. A narrative review design was preferred to fulfill our purpose. The search strategy included a range of terms, e.g., "microbiome," "microbiota," "urobiome," AND/OR "probiotics" AND "benign prostatic hyperplasia," "benign prostatic enlargement," "lower urinary tract symptoms." A range of studies aimed to investigate the possible impact of urinary microbiome on BPH. Gut and/or urinary dysbiosis can alter the gut permeability and initiate/maintain inflammatory and oxidative processes in the prostate, which may contribute to the cell-hyper-proliferation leading to BPH. The modulation of the urinary and/or gut microbiome through probiotic supplementation seems to provide levels of clinical effectiveness in the management of BPH. Although different probiotics have been tested, a combination of B. Longum and F. Psychaerophilum seems to be particularly promising due to their capability of modulating both the inflammatory pathway and the intestinal barrier permeability. Gut and/or urinary microbiome dysbiosis is most likely contributing to the BPH pathogenesis. Even though only scarce evidence on the potential usefulness of probiotic supplementation in the management of BPH is currently available, the available studies seem to provide encouraging results. Further prospective trials are warranted in order to confirm these findings and to clarify which probiotic strains are more suitable for supplementation in this setting.},
}

Humans
Male
*Prostatic Hyperplasia/therapy/microbiology
*Probiotics/administration & dosage/therapeutic use
Microbiota
Lower Urinary Tract Symptoms/therapy/microbiology
Gastrointestinal Microbiome
Dietary Supplements

@article {pmid39687876,
year = {2024},
author = {Tarantino, G and Cataldi, M and Citro, V},
title = {Could chronic opioid use be an additional risk of hepatic damage in patients with previous liver diseases, and what is the role of microbiome?.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1319897},
doi = {10.3389/fmicb.2024.1319897},
pmid = {39687876},
issn = {1664-302X},
abstract = {Among illicit drugs, addiction from opioids and synthetic opioids is soaring in an unparalleled manner with its unacceptable amount of deaths. Apart from these extreme consequences, the liver toxicity is another important aspect that should be highlighted. Accordingly, the chronic use of these substances, of which fentanyl is the most frequently consumed, represents an additional risk of liver damage in patients with underlying chronic liver disease. These observations are drawn from various preclinical and clinical studies present in literature. Several downstream molecular events have been proposed, but recent pieces of research strengthen the hypothesis that dysbiosis of the gut microbiota is a solid mechanism inducing and worsening liver damage by both alcohol and illicit drugs. In this scenario, the gut flora modification ascribed to non-alcoholic fatty liver disease performs an additive role. Interestingly enough, HBV and HCV infections impact gut-liver axis. In the end, the authors tried to solicit the attention of operators on this major healthcare problem.},
}

@article {pmid39687871,
year = {2024},
author = {Peng, C and Ghanbari, M and May, A and Abeel, T},
title = {Effects of antibiotic growth promoter and its natural alternative on poultry cecum ecosystem: an integrated analysis of gut microbiota and host expression.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1492270},
doi = {10.3389/fmicb.2024.1492270},
pmid = {39687871},
issn = {1664-302X},
abstract = {BACKGROUND: In-feed antibiotic growth promoters (AGPs) have been a cornerstone in the livestock industry due to their role in enhancing growth and feed efficiency. However, concerns over antibiotic resistance have driven a shift away from AGPs toward natural alternatives. Despite the widespread use, the exact mechanisms of AGPs and alternatives are not fully understood. This necessitates holistic studies that investigate microbiota dynamics, host responses, and the interactions between these elements in the context of AGPs and alternative feed additives.

METHODS: In this study, we conducted a multifaceted investigation of how Bacitracin, a common AGP, and a natural alternative impact both cecum microbiota and host expression in chickens. In addition to univariate and static differential abundance and expression analyses, we employed multivariate and time-course analyses to study this problem. To reveal host-microbe interactions, we assessed their overall correspondence and identified treatment-specific pairs of species and host expressed genes that showed significant correlations over time.

RESULTS: Our analysis revealed that factors such as developmental age substantially impacted the cecum ecosystem more than feed additives. While feed additives significantly altered microbial compositions in the later stages, they did not significantly affect overall host gene expression. The differential expression indicated that with AGP administration, host transmembrane transporters and metallopeptidase activities were upregulated around day 21. Together with the modulated kininogen binding and phenylpyruvate tautomerase activity over time, this likely contributes to the growth-promoting effects of AGPs. The difference in responses between AGP and PFA supplementation suggests that these additives operate through distinct mechanisms.

CONCLUSION: We investigated the impact of a common AGP and its natural alternative on poultry cecum ecosystem through an integrated analysis of both the microbiota and host responses. We found that AGP appears to enhance host nutrient utilization and modulate immune responses. The insights we gained are critical for identifying and developing effective AGP alternatives to advance sustainable livestock farming practices.},
}

@article {pmid39687868,
year = {2024},
author = {Frazier, AN and Beck, MR and Waldrip, H and Koziel, JA},
title = {Connecting the ruminant microbiome to climate change: insights from current ecological and evolutionary concepts.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1503315},
doi = {10.3389/fmicb.2024.1503315},
pmid = {39687868},
issn = {1664-302X},
abstract = {Ruminant livestock provide meat, milk, wool, and other products required for human subsistence. Within the digestive tract of ruminant animals, the rumen houses a complex and diverse microbial ecosystem. These microbes generate many of the nutrients that are needed by the host animal for maintenance and production. However, enteric methane (CH4) is also produced during the final stage of anaerobic digestion. Growing public concern for global climate change has driven the agriculture sector to enhance its investigation into CH4 mitigation. Many CH4 mitigation methods have been explored, with varying outcomes. With the advent of new sequencing technologies, the host-microbe interactions that mediate fermentation processes have been examined to enhance ruminant enteric CH4 mitigation strategies. In this review, we describe current knowledge of the factors driving ruminant microbial assembly, how this relates to functionality, and how CH4 mitigation approaches influence ecological and evolutionary gradients. Through the current literature, we elucidated that many ecological and evolutionary properties are working in tandem in the assembly of ruminant microbes and in the functionality of these microbes in methanogenesis. Additionally, we provide a conceptual framework for future research wherein ecological and evolutionary dynamics account for CH4 mitigation in ruminant microbial composition. Thus, preparation of future research should incorporate this framework to address the roles ecology and evolution have in anthropogenic climate change.},
}

@article {pmid39687852,
year = {2024},
author = {Marcato, F and Schokker, D and Kar, SK and Bossers, A and Harders, F and Rebel, JMJ and Jansen, CA and van der Valk, E and Kruijt, L and Te Beest, DE and de Jong, IC},
title = {Effects of breed and early feeding on intestinal microbiota, inflammation markers, and behavior of broiler chickens.},
journal = {Frontiers in veterinary science},
volume = {11},
number = {},
pages = {1492274},
doi = {10.3389/fvets.2024.1492274},
pmid = {39687852},
issn = {2297-1769},
abstract = {Recently, the Netherlands has shifted toward more welfare-friendly broiler production systems using slower-growing broiler breeds. Early post-hatch feeding (EF) is a dietary strategy that is currently used in commercial broiler production to modulate the gut microbiota and improve performance and welfare. However, there is a knowledge gap in how both breed and EF and their interplay affect gut microbiota composition and diversity, inflammatory status, and broiler behavior. Therefore, the aim of this study was to investigate the effects of breed (fast vs. slower-growing), EF, and their interaction on jejunum microbiota, inflammation, and behavior of broiler chickens. The study included a total of 416 Ross 308 and 416 Hubbard JA757 day-old male broiler chickens, observed until they were 37 days and 51 days old, respectively. Within each breed, one-half of the chickens received EF and the other half did not. A total of two chickens per pen were euthanized at two time points, that is, target body weight (BW) of 200 g and 2.5 kg, and jejunum samples were collected. The jejunum content samples (N = 96) were analyzed for their microbiota, whereas the jejunum tissue (N = 96) was used for the detection of mRNA levels of cytokines (IL-17, IL-22, and IFNγ). Two behavioral tests were performed to assess fear responses: (1) a novel environment test at a target BW of 200 g and (2) a tonic immobility test at a target BW of 2.5 kg. Breed affected the microbiota at a target BW of 2.5 kg (p = 0.04). A breed × EF interaction (p = 0.02) was present for IFNγ at a target BW of 200 g. During the novel environment test, Ross 308 chickens exhibited a shorter latency to vocalize and a higher number of vocalizations compared to Hubbard JA757 chickens (p < 0.05). Early-fed broiler chickens vocalized less compared to not early-fed chickens (Δ = -27.8 on average; p < 0.01). During the tonic immobility test, Hubbard JA757 chickens exhibited a shorter latency to stand compared to Ross 308 chickens. In conclusion, using a slower-growing breed has beneficial effects on gut microbiota and fear responses of broilers, especially at slaughter age, whereas EF seems to have an impact only at an early stage of the life of broilers.},
}

@article {pmid39687766,
year = {2024},
author = {Fleischer, R and Velling, M and Peters, W and Peterka, T and Franke, F and Vymyslická, PJ and Rehbein, S and Heurich, M and Sommer, S},
title = {Invasive Fascioloides magna infections impact gut microbiota in a definitive host in Europe.},
journal = {International journal for parasitology. Parasites and wildlife},
volume = {25},
number = {},
pages = {101024},
doi = {10.1016/j.ijppaw.2024.101024},
pmid = {39687766},
issn = {2213-2244},
abstract = {Invasive parasites that expand their natural range can be a threat to wildlife biodiversity and may pose a health risk to non-adapted, naive host species. The invasive giant liver fluke, Fascioloides magna, native to North America, has extended its range in Europe and uses mainly red deer (Cervus elaphus) as definitive hosts. The penetration of the intestinal barrier by the young flukes to reach the liver via the abdominal cavity as well as the release of fluke metabolism products and excreta with the bile and/or changes in the microbial community of the biliary system may enable the translocation of intestinal bacteria across the intestinal barrier and, in turn, could be associated with inflammation and changes in the intestinal bacterial community. The gut commensal community plays a key role in host nutrition and interacts with cells of the immune system to maintain host health. For this study, the gut bacterial community of red deer infected with F. magna and of non-infected red deer from one of the largest forest ecosystems in Central Europe, located on the border between the Czech Republic and Germany, was investigated. The individual fluke burden was associated with changes in the gut microbial composition of the gut of infected individuals, whereas the diversity and composition of the gut bacteria were only slightly different between fluke-infected and uninfected deer. Several bacterial taxa at the genus level were unique to individuals carrying either one or many liver flukes. Our results suggest that the microbiota of red deer is stable to perturbation by low numbers of F. magna. However, a larger parasite burden may cause changes in the gut microbial composition in definitive hosts implying that non-invasive fecal microbiome assessments could serve as indicator for wildlife health monitoring.},
}

@article {pmid39687638,
year = {2024},
author = {Wen, NN and Sun, LW and Geng, Q and Zheng, GH},
title = {Gut microbiota changes associated with frailty in older adults: A systematic review of observational studies.},
journal = {World journal of clinical cases},
volume = {12},
number = {35},
pages = {6815-6825},
pmid = {39687638},
issn = {2307-8960},
abstract = {BACKGROUND: Frailty is a complex aging-related syndrome characterized by a cumulative loss of physiological reserve and increased vulnerability to adverse clinical outcomes, including falls, disability, incapacity and death. While an increasing number of studies suggest that the gut microbiota may play a key role in the pathophysiology of frailty, direct evaluation of the association between gut microbiome alterations and frailty in older adults remains limited.

AIM: To gain insight into gut dysbiosis in frail older adults.

METHODS: Seven electronic databases (China National Knowledge Infrastructure, VIP, SinoMed, Wanfang, PubMed, Web of Science and EMBASE) were searched for articles published before October 31, 2023 to identify observational studies that compared the microbiomes of older adults with and without frailty. The diversity and composition of the gut microbiota were the main outcomes used to analyze the associations of changes in the gut microbiota with frailty in older adults. The quality of the included studies was assessed via the Newcastle-Ottawa Scale and the Agency for Healthcare Research and Quality.

RESULTS: Eleven observational studies with 912 older adults were included in this review. Consistent results revealed a significant difference in the gut microbiota composition between frail and non-frail older adults, with a significant decrease in α diversity and a significant increase in β diversity in frail older adults. The pooled results revealed that at the phylum level, four microbiota (Actinobacteria, Proteobacteria, Verrucomicrobia and Synergistetes) were significantly enriched, and two microbiota (Firmicutes and Fusobacteria) were significantly depleted in frail older adults. At the family level, the results consistently revealed that the abundances of 6 families, most of which belong to the Actinobacteria or Proteobacteria phylum, were greater in frail than in non-frail older adults. At the genus or species level, consistent results from more than two studies revealed that the abundances of the genera Prevotella, Faecalibacterium, and Roseburia were significantly lower in frail older adults; individual studies revealed that the abundances of some genera or species (e.g., Megamonas, Blautia, and Megasphaera) were significantly lower, whereas those of other genera or species (e.g., Bifidobacterium, Oscillospira, Ruminococcus and Pyramidobacter) were significantly greater in frail older adults.

CONCLUSION: This systematic review suggests that changes in the gut microbiota are associated with frailty in older adults, which is commonly reflected by a reduction in beneficial species and an increase in pathogenic species. However, further studies are needed to confirm these findings.},
}

@article {pmid39687478,
year = {2024},
author = {Falconer, JL and Rajani, R and Androshchuk, V and Yogarajah, A and Greenbury, RA and Ismail, A and Oh, N and Nibali, L and D'Agostino, EM and Sousa, V},
title = {Exploring links between oral health and infective endocarditis.},
journal = {Frontiers in oral health},
volume = {5},
number = {},
pages = {1426903},
doi = {10.3389/froh.2024.1426903},
pmid = {39687478},
issn = {2673-4842},
abstract = {Infective endocarditis (IE) is a bacterial infection of the heart's inner lining. A low incidence rate combined with a high mortality rate mean that IE can be difficult to treat effectively. There is currently substantial evidence supporting a link between oral health and IE with the oral microbiome impacting various aspects of IE, including pathogenesis, diagnosis, treatment, and mortality rates. The oral microbiome is highly diverse and plays a crucial role in maintaining oral health by providing protective functions. However, when dysbiosis occurs, conditions such as periodontal or peri-implant disease can arise, offering a pathway for bacteraemia to develop. The role of the oral microbiome as a coloniser, facilitator and driver of IE remains to be uncovered by next-generation sequencing techniques. Understanding the dysbiosis and ecology of the oral microbiome of IE patients will allow improvements into the diagnosis, treatment, and prognosis of the disease. Furthermore, an increased awareness amongst those at high-risk of developing IE may encourage improved oral hygiene methods and lower incidence rates. This narrative review examines current findings on the relationship between oral health and IE. It draws from key studies on both topics, with manuscripts selected for their pertinence to the subject. It highlights the link between the oral microbiome and IE by exploring diagnostic techniques and treatments for IE caused by oral commensals.},
}

@article {pmid39687430,
year = {2024},
author = {Alemu, BK and Wang, CC and Li, L and Zhu, Z and Li, Q and Wang, Y},
title = {Effect of preconception antibiotics exposure on female reproductive health and pregnancy outcomes: a systematic review and meta-analysis.},
journal = {EClinicalMedicine},
volume = {78},
number = {},
pages = {102935},
doi = {10.1016/j.eclinm.2024.102935},
pmid = {39687430},
issn = {2589-5370},
abstract = {BACKGROUND: The preconception period is a window of opportunity to influence maternal and pregnancy outcomes. Inappropriate use of antibiotics results in gut dysbiosis and may affect host reproductive health through multiple dimensions. Animal studies demonstrate that antibiotic treatment profoundly affects ovarian functions and the estrous cycle, and it has a direct implication for infertility. Infertility was defined as the inability to conceive after 12 months of unprotected intercourse. However, whether antibiotic exposure in the preconception period influences female fertility, miscarriage, and congenital malformation remains obscure and controversial.

METHODS: A systematic review and meta-analysis until April 20, 2024, was conducted by searching PubMed, Web of Science, Scopus, and Science Direct without restrictions to designs and language. The risk of bias was assessed by two independent reviewers using the Newcastle Ottawa Scale (NOS) and the Risk of Bias 2 (RoB-2) tools. The report followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Relative risks (RR), odds ratios (OR), and fecundability ratios (FR) with a 95% confidence interval (CI) were effect size measures determined with a random effect model. Heterogeneity across included studies was assessed using I [2] , T2, and H[2]. The review protocol is registered in PROSPERO, CRD42024515680.

FINDINGS: Fifteen studies with a total of 1,206,583 participants were included. Preconception exposure to macrolides reduced the FR by 35% (FR: 0.65, 95% CI: 0.48, 0.88, P < 0.001). Sulfonamide users were also at 2.35 times (OR:2.35, 95% CI: 1.86, 2.97; P < 0.001) more risk of developing infertility. Using beta-lactams other than penicillin G reduced the odds of infertility by 64% (OR: 0.36, 95% CI: 0.26,0.50; P < 0.001). The possibility of infertility among quinolone users was 13% lower (OR: 0.87, 95% CI: 0.77, 0.99; P = 0.03) than non-users. Preconception antibiotics exposure increased the risk of spontaneous miscarriage by 34% (RR: 1.34, 95% CI: 1.16, 1.53; P < 0.001). Moreover, trimethoprim intake also increased the odds of congenital malformations by 85% (OR:1.85, 95% CI: 1.54, 2.23; P < 0.001).

INTERPRETATION: Preconception antibiotics exposure in females increases the risk of infertility, miscarriage, and congenital anomalies. Macrolides, sulfonamides, and trimethoprim increase the risk of infertility, spontaneous miscarriage, and congenital malformation while beta-lactams and quinolones reduce the risk. Clinicians, pregnancy planners, and health care policymakers should be warranted for pregnancy needs and success. Further clinical and mechanistic studies are required to illustrate their specific functions and cause effects.

FUNDING: Funded by Leading Discipline Development Fund (No. 403947), The Second Affiliated Hospital of Shaanxi University of Traditional Chinese Medicine; and The Hong Kong Obstetrical and Gynaecological Trust Fund.},
}

@article {pmid39687379,
year = {2024},
author = {Lee, D and Oliveira, FCC and Conant, RT and Kim, M},
title = {Microbial community assembly across agricultural soil mineral mesocosms revealed by 16S rRNA gene amplicon sequencing data.},
journal = {Data in brief},
volume = {57},
number = {},
pages = {111125},
doi = {10.1016/j.dib.2024.111125},
pmid = {39687379},
issn = {2352-3409},
abstract = {Increasing atmospheric carbon dioxide (CO2) concentrations are impacting the global climate, resulting in significant interest in soil carbon sequestration as a mitigation strategy. While recognized that mineral-associated organic matter (MAOM) in soils is mainly formed through microbial activity, our understanding of microbial-derived MAOM formation processes remains limited due to the complexity of the soil environment. To gain insights into this issue, we incubated fresh soil samples for 45 days with one of three mineral additions: Sand, Kaolinite+Sand, or Illite+Sand. 16S rRNA V3/V4 gene amplicon sequencing was then conducted on samples using an Illumina NextSeq 2000 flow cell. The reads were analyzed and taxonomically assigned with QIIME2 v2023.5.1 and SILVA 138. The dataset has been made publicly available through NCBI GenBank under BioProject ID PRJNA1124235. This dataset is important and useful as it provides valuable insights into the interactions between soil minerals and microbial communities, which can inform strategies for enhancing soil carbon sequestration and mitigating climate change. Moreover, it serves as a crucial reference for future studies, offering a foundational understanding of microbial dynamics in soil systems and guiding further research in microbial ecology and carbon cycling.},
}

@article {pmid39687297,
year = {2024},
author = {Zhang, C and Sui, C and Ma, X and Ma, C and Sun, X and Zhai, C and Cao, P and Zhang, Y and Cheng, J and Li, T and Sai, J},
title = {Therapeutic potential of Xihuang Pill in colorectal cancer: Metabolomic and microbiome-driven approaches.},
journal = {Frontiers in pharmacology},
volume = {15},
number = {},
pages = {1402448},
doi = {10.3389/fphar.2024.1402448},
pmid = {39687297},
issn = {1663-9812},
abstract = {INTRODUCTION: The Xihuang Pill (XHP), a venerated traditional Chinese medicine, has demonstrated significant anti-cancer capabilities. Despite its proven efficacy, the scarcity of comprehensive pharmacological studies limits the widespread application of XHP. This research endeavor seeks to demystify the therapeutic underpinnings of XHP, particularly in the realm of colorectal cancer (CRC) therapy.

METHODS: In this study, mice harboring CT26 tumors were divided into four groups, each administered with either XHP monotherapy, 5-fluorouracil (5-FU), or a combination of both. The tumor growth trajectory was closely monitored to evaluate the effectiveness of these anti-neoplastic interventions. Advanced techniques, including 16S-rDNA gene sequencing and ultra-high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS), were harnessed to scrutinize the gut microbiota and serum metabolite profiles. Immunohistochemical assays were employed to gauge the expression levels of CD4, CD8, and Foxp3, thereby providing insights into the dynamics of tumor-infiltrating lymphocytes within the tumor microenvironment.

RESULTS: Our findings indicate that XHP effectively suppresses the initiation and progression of colorectal tumors. The combinatorial therapy of XHP with 5-FU exhibited an enhanced inhibitory effect on tumor growth. Metabolic profiling revealed that XHP induced notable metabolic shifts, particularly impacting pathways such as steroid hormone synthesis, arachidonic acid metabolism, purine biosynthesis, and renin secretion. Notably, 17α-ethinyl estradiol and α-ergocryptine were identified as serum metabolites with the most substantial increase following XHP administration. Analysis of the gut microbiome suggested that XHP promoted the expansion of specific bacterial taxa, including Lachnospiraceae_NK4A136_group, Clostridiales, Desulfovibrionaceae, and Anaerotignum_sp., while suppressing the proliferation of others such as Ligilactobacilus, Lactobacillus_taiwanensis, and Candidatus_saccharimonas. Immunohistochemical staining indicated an upregulation of CD4 and CD8 post-XHP treatment.

CONCLUSION: This study delineates a potential mechanism by which XHP inhibits CRC tumorigenesis through modulating the gut microbiota, serum metabolites, and reshaping the tumor immune microenvironment in a murine CRC model. These findings contribute to a more profound understanding and potentially broaden the clinical utility of XHP in oncology.},
}

@article {pmid39687136,
year = {2024},
author = {Jørgensen, AB and Almer, L and Samaniego Castruita, JA and Pedersen, MS and Kirkby, NS and Jensen, EA and Alfaro-Núñez, A and Friis-Hansen, L and Brandstrup, B},
title = {The baseline fecal microbiome differs in patients with and without anastomotic leakage after colorectal cancer surgery.},
journal = {Heliyon},
volume = {10},
number = {23},
pages = {e40616},
doi = {10.1016/j.heliyon.2024.e40616},
pmid = {39687136},
issn = {2405-8440},
abstract = {BACKGROUND: Anastomotic leakage (AL) is a severe complication of colorectal surgery. The risk of AL is affected by both surgery and patient factors. Gut microbiomes can be generated from the residual material from the fecal immunochemical test (FIT). We, therefore, examined if AL after colorectal cancer surgery could be associated with specific baseline microbiomes in the FIT screening sampling tubes collected weeks before surgery.

METHODS: Samples from patients participating in the Danish colorectal cancer screening program were biobanked from 2016 to 2018, and samples from patients who had surgery for screening-detected cancer were included. They were matched with patients without AL in a 1:2 ratio based on age, sex, location of anastomosis (colonic/rectal), ASA classification, and smoking habits. Bacterial DNA was extracted from the sampling tubes, and the fecal microbiomes were analyzed with targeted 16S ribosomal RNA third-generation sequencing.

RESULTS: 18 patients who developed AL after surgery were matched with 36 without AL. The alpha diversity was lower in the AL group (p = 0.035), and the AL group separated from the Controls in the PCoA plot (p < 0.001). This was due to the patients undergoing rectal resections, with significant differences in alpha- and beta diversity (p = 0.025 and p = 0.002, respectively). The prevalence of bacteria with the potential to produce collagenase was higher in patients who developed AL (odds ratio 1.29 (95% CI 1.28-1.30), p < 0.001).

CONCLUSIONS: We found differences in the baseline microbiome profile associated with subsequent development of AL after surgery for screening-detected rectal cancer.},
}

@article {pmid39687078,
year = {2024},
author = {Liu, C and Zhou, S and Li, Y and Yin, X and Li, P},
title = {Metabolomic disorders caused by an imbalance in the gut microbiota are associated with central precocious puberty.},
journal = {Frontiers in endocrinology},
volume = {15},
number = {},
pages = {1481364},
doi = {10.3389/fendo.2024.1481364},
pmid = {39687078},
issn = {1664-2392},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Puberty, Precocious/microbiology/metabolism ; Female ; Child ; Male ; *Metabolomics ; Feces/microbiology ; Dysbiosis/microbiology ; Case-Control Studies ; Metabolome ; Child, Preschool ; },
abstract = {BACKGROUND: Central precocious puberty (CPP) is characterized by the premature activation of the hypothalamic-pituitary-gonadal axis, resulting in early onset of sexual development. The incidence of CPP has been rising in recent years, with approximately 90% of cases lacking a clearly identifiable etiology. While an association between precocious puberty and gut microbiota has been observed, the precise causal pathways and underlying mechanisms remain poorly understood. The study aims to investigate the potential mechanisms through which gut microbiota imbalances may contribute to CPP.

METHODS: In this study, clinical information and fecal samples were collected from 50 CPP patients and 50 healthy control subjects. The fecal samples were analyzed by 16S rDNA sequencing and UPLC-MS/MS metabolic analysis. Spearman correlation analysis was used to identify the relationships between gut microbiota and metabolites.

RESULTS: The gut microbiota composition in CPP patients was significantly different from that in healthy controls, characterized by an increased abundance of Faecalibacterium and a decreased abundance of Anaerotruncus. Additionally, significant differences were observed in metabolite composition between the CPP and control groups. A total of 51 differentially expressed metabolites were identified, with 32 showing significant upregulation and 19 showing significant downregulation in the CPP group. Furthermore, Spearman correlation analysis indicated that gut microbiota dysbiosis may contribute to altered metabolic patterns in CPP, given its involvement in the regulation of several metabolic pathways, including phenylalanine and tyrosine biosynthesis and metabolism, the citrate cycle (TCA cycle), glyoxylate and dicarboxylate metabolism, and tryptophan metabolism.

CONCLUSIONS: The study revealed the gut microbial and metabolite characteristics of CPP patients by integrating microbiome and metabolomics analyses. Moreover, several key metabolic pathways involved in the onset and progression of CPP were identified, which were regulated by gut microbiota. These findings broaden the current understanding of the complex interactions between gut microbial metabolites and CPP, and provide new insights into the pathogenesis and clinical management of CPP.},
}

Humans
*Gastrointestinal Microbiome
*Puberty, Precocious/microbiology/metabolism
Female
Child
Male
*Metabolomics
Feces/microbiology
Dysbiosis/microbiology
Case-Control Studies
Metabolome
Child, Preschool

@article {pmid39686807,
year = {2024},
author = {Ghosh, U and Tal-Gan, Y},
title = {Designing Highly Potent Side-Chain Lactam-Bridged Cyclic Competence-Stimulating Peptide-Based Quorum-Sensing Modulators in Streptococcus oligofermentans.},
journal = {ACS infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsinfecdis.4c00773},
pmid = {39686807},
issn = {2373-8227},
abstract = {Streptococcus oligofermentans, a Gram-positive bacterium found in the oral microbiome, shows promise as an oral probiotic for preventing dental caries. It exhibits a reverse correlation with Streptococcus mutans, a key caries-causing pathogen, likely due to its production of hydrogen peroxide, a process mediated by quorum sensing (QS). In this work, we set out to develop novel lactam-based cyclic analogues of the competence stimulating peptide (CSP) signal utilized by S. oligofermentans for QS activation. To this end, we first conducted a ring position scan, where we determined the best positions within the CSP sequence to use for macrolactamization. We then conducted systematic ring size and bridge position scans to fine-tune the cyclic peptide conformation and identified a cyclic analogue, CSP-cyc(K2E2), with enhanced biological activity, 7-fold more active than the native CSP signal. This analogue also exhibited improved stability toward enzymatic degradation, demonstrating this analogue's potential utility as a chemical probe to study interspecies interactions between oral microbes and as a potential therapeutic agent. Overall, our lead cyclic analogue could be applied to augment the biotherapeutic potential of S. oligofermentans against S. mutans infections.},
}

@article {pmid39685893,
year = {2024},
author = {España-Pamplona, P and Bernés-Martínez, L and Andrés-Castelló, C and Bolás-Colveé, B and Adobes-Martín, M and Garcovich, D},
title = {Changes in the Oral Microbiota with the Use of Aligners vs. Braces: A Systematic Review.},
journal = {Journal of clinical medicine},
volume = {13},
number = {23},
pages = {},
pmid = {39685893},
issn = {2077-0383},
abstract = {Background: Orthodontic treatments have evolved significantly, with clear aligners becoming increasingly popular due to their aesthetic appeal and ease of use. This study systematically reviewed the impact of clear aligners in the changes in the oral microbiota compared to traditional fixed appliances. Methods: Following PRISMA guidelines, a systematic review was conducted using two databases such as Scopus, Web of Science, and the PubMed search engine. The studies included were those published between 2010 and 2023, involving adults over 18 years using clear aligners and fixed appliances. The data on oral microbiota changes were extracted and analyzed. Results: The review included eight studies, highlighting the differences in microbial changes associated with clear aligners versus fixed appliances. Clear aligners were associated with fewer detrimental changes in the oral microbiota, potentially due to their removable nature allowing for better hygiene. Fixed appliances showed a tendency to harbor more pathogenic bacteria, which is likely due to their difficulty to clean. Conclusions: Clear aligners may offer a better alternative to fixed appliances in terms of maintaining a healthier oral microbiota. Their design and ease of hygiene contribute to less accumulation of pathogenic bacteria, showing a more positive impact on maintaining a balanced oral microbiota when compared to fixed appliances.},
}

@article {pmid39685594,
year = {2024},
author = {Stabile, G and Doria, A and Bruno, M and D'Indinosante, M and Gallotta, V and Fanfani, F and Scambia, G and Restaino, S and Vizzielli, G and Carlucci, S and Nappi, L},
title = {The Role of the Endometrial Microbiota in Endometrial Cancer: A Systematic Review of the Literature.},
journal = {Journal of clinical medicine},
volume = {13},
number = {23},
pages = {},
pmid = {39685594},
issn = {2077-0383},
abstract = {Background: Endometrial cancer is currently the sixth most frequent cancer in women, and scientific research is focusing on the search for particular features of the endometrium that may explain a further predisposition to the onset of endometrial cancer, aimed at improving knowledge of the pathogenetic factors of this disease. The aim of our review is to analyze in detail the results of the literature on the endometrial microbiota in patients with endometrial cancer and to investigate its role. Methods: We performed our research on the Pubmed, Web of Science, and Scopus databases. We searched up to December 2023 and considered manuscripts published from 2000. Only articles in English were included in the search. We excluded studies in which the endometrial microbiota were collected through the vagina or cervical canal. Results: We included in our review a total of five manuscripts at the end of the screening process, and the total number of patients involved was 190. Four studies considered only post-menopausal patients, while one study considered both pre- and post-menopausal patients. In all studies, the microbiota analysis was derived from a post-hysterectomy biopsy. From our review, it emerged that Bacteroidetes, Actinobacteria, Firmicutes, and Proteobacteria are the most represented bacteria in patients with endometrial cancer. These are both Gram-positive and Gram-negative, but predominantly anaerobic bacteria. Conclusions: The reduced microbial diversity and the presence of specific bacteria is often associated with endometrial cancer. Further work on larger population samples, and on healthy women and those affected by endometrial carcinoma, is needed to understand how the endometrial microbiota changes and influences the development of the tumor and whether intervening in the changes in the microbiota will have a therapeutic impact on endometrial carcinoma.},
}

@article {pmid39685282,
year = {2024},
author = {Gerengi, H and Kaya, E and Solomon, MM and Snape, M and Koerdt, A},
title = {Advances in the Mitigation of Microbiologically Influenced Concrete Corrosion: A Snapshot.},
journal = {Materials (Basel, Switzerland)},
volume = {17},
number = {23},
pages = {},
pmid = {39685282},
issn = {1996-1944},
support = {CA20130//European Cooperation in Science and Technology/ ; },
abstract = {Concrete, a versatile construction material, faces pervasive deterioration due to microbiologically influenced corrosion (MIC) in various applications, including sewer systems, marine engineering, and buildings. MIC is initiated by microbial activities such as involving sulfate-reducing bacteria (SRB), sulfur-oxidizing bacteria (SOB), etc., producing corrosive substances like sulfuric acid. This process significantly impacts structures, causing economic losses and environmental concerns. Despite over a century of research, MIC remains a debated issue, lacking standardized assessment methods. Microorganisms contribute to concrete degradation through physical and chemical means. In the oil and gas industry, SRB and SOB activities may adversely affect concrete in offshore platforms. MIC challenges also arise in cooling water systems and civil infrastructures, impacting concrete surfaces. Sewer systems experience biogenic corrosion, primarily driven by SRB activities, leading to concrete deterioration. Mitigation traditionally involves the use of biocides and surface coatings, but their long-term effectiveness and environmental impact are questionable. Nowadays, it is important to design more eco-friendly mitigation products. The microbial-influenced carbonate precipitation is one of the green techniques and involves incorporating beneficial bacteria with antibacterial activity into cementitious materials to prevent the growth and the formation of a community that contains species that are pathogenic or may be responsible for MIC. These innovative strategies present promising avenues for addressing MIC challenges and preserving the integrity of concrete structures. This review provides a snapshot of the MIC in various areas and mitigation measures, excluding underlying mechanisms and broader influencing factors.},
}

@article {pmid39684937,
year = {2024},
author = {Balla, B and Illés, A and Tobiás, B and Pikó, H and Beke, A and Sipos, M and Lakatos, P and Kósa, JP},
title = {The Role of the Vaginal and Endometrial Microbiomes in Infertility and Their Impact on Pregnancy Outcomes in Light of Recent Literature.},
journal = {International journal of molecular sciences},
volume = {25},
number = {23},
pages = {},
pmid = {39684937},
issn = {1422-0067},
support = {2020-4.1.1.-TKP2020-MOLORKIV//Hungarian Ministry of Innovation and Technology/ ; },
mesh = {Humans ; Female ; *Vagina/microbiology ; Pregnancy ; *Microbiota ; *Endometrium/microbiology/metabolism ; *Pregnancy Outcome ; Dysbiosis/microbiology ; Infertility, Female/microbiology ; Infertility/microbiology ; },
abstract = {The Human Microbiome Project (HMP), initiated in 2007, aimed to gather comprehensive knowledge to create a genetic and metabolic map of human-associated microorganisms and their contribution to physiological states and predisposition to certain diseases. Research has revealed that the human microbiome is highly diverse and exhibits significant interpersonal variability; consequently, its exact impact on health remains unclear. With the development of next-generation sequencing (NGS) technologies, the broad spectrum of microbial communities has been better characterized. The lower female genital tract, particularly the vagina, is colonized by various bacterial species, with Lactobacillus spp. predominating. The upper female genital tract, especially the uterus, was long considered sterile. However, recent studies have identified a distinct endometrial microbiome. A Lactobacillus-dominated microbiome of the female genital tract is associated with favorable reproductive outcomes, including higher success rates in natural conception and assisted reproductive technologies (ART). Conversely, microbial imbalances, or dysbiosis, marked by reduced Lactobacilli as well as an increased diversity and abundance of pathogenic species (e.g., Gardnerella vaginalis or Prevotella spp.), are linked to infertility, implantation failure, and pregnancy complications such as miscarriage and preterm birth. Dysbiosis can impair the vaginal or endometrial mucosal barrier and also trigger pro-inflammatory responses, disrupting essential reproductive processes like implantation. Despite growing evidence supporting the associations between the microbiome of the female genital tract and certain gynecological and obstetric conditions, clear microbial biomarkers have yet to be identified, and there is no consensus on the precise composition of a normal or healthy microbiome. The lack of standardized protocols and biomarkers limits the routine use of microbiome screening tests. Therefore, larger patient cohorts are needed to facilitate comparative studies and improve our understanding of the physiological microbiome profiles of the uterus and vagina, as well as how dysbiosis may influence clinical outcomes. Further research is required to refine diagnostic tools and develop personalized therapeutic strategies to improve fertility and pregnancy outcomes.},
}

Humans
Female
*Vagina/microbiology
Pregnancy
*Microbiota
*Endometrium/microbiology/metabolism
*Pregnancy Outcome
Dysbiosis/microbiology
Infertility, Female/microbiology
Infertility/microbiology

@article {pmid39684918,
year = {2024},
author = {Li, C and Chen, S and Wang, Y and Su, Q},
title = {Microbiome-Based Therapeutics for Insomnia.},
journal = {International journal of molecular sciences},
volume = {25},
number = {23},
pages = {},
pmid = {39684918},
issn = {1422-0067},
mesh = {Humans ; *Sleep Initiation and Maintenance Disorders/therapy/microbiology ; *Gastrointestinal Microbiome ; *Fecal Microbiota Transplantation/methods ; *Probiotics/therapeutic use ; *Prebiotics/administration & dosage ; Animals ; Synbiotics ; },
abstract = {Insomnia poses considerable risks to both physical and mental health, leading to cognitive impairment, weakened immune function, metabolic dysfunction, cardiovascular issues, and reduced quality of life. Given the significant global increase in insomnia and the growing scientific evidence connecting gut microbiota to this disorder, targeting gut microbiota as an intervention for insomnia has gained popularity. In this review, we summarize current microbiome-based therapeutics for insomnia, including dietary modifications; probiotic, prebiotic, postbiotic, and synbiotic interventions; and fecal microbiota transplantation. Moreover, we assess the capabilities and weaknesses of these technologies to offer valuable insights for future studies.},
}

Humans
*Sleep Initiation and Maintenance Disorders/therapy/microbiology
*Gastrointestinal Microbiome
*Fecal Microbiota Transplantation/methods
*Probiotics/therapeutic use
*Prebiotics/administration & dosage
Animals
Synbiotics

@article {pmid39684900,
year = {2024},
author = {Vo, DK and Trinh, KTL},
title = {Emerging Biomarkers in Metabolomics: Advancements in Precision Health and Disease Diagnosis.},
journal = {International journal of molecular sciences},
volume = {25},
number = {23},
pages = {},
pmid = {39684900},
issn = {1422-0067},
mesh = {Humans ; *Metabolomics/methods ; *Precision Medicine/methods ; *Biomarkers/metabolism ; Neoplasms/metabolism/diagnosis ; Cardiovascular Diseases/metabolism/diagnosis ; Neurodegenerative Diseases/metabolism/diagnosis ; Metabolome ; Gastrointestinal Microbiome ; },
abstract = {Metabolomics has come to the fore as an efficient tool in the search for biomarkers that are critical for precision health approaches and improved diagnostics. This review will outline recent advances in biomarker discovery based on metabolomics, focusing on metabolomics biomarkers reported in cancer, neurodegenerative disorders, cardiovascular diseases, and metabolic health. In cancer, metabolomics provides evidence for unique oncometabolites that are important for early disease detection and monitoring of treatment responses. Metabolite profiling for conditions such as neurodegenerative and mental health disorders can offer early diagnosis and mechanisms into the disease especially in Alzheimer's and Parkinson's diseases. In addition to these, lipid biomarkers and other metabolites relating to cardiovascular and metabolic disorders are promising for patient stratification and personalized treatment. The gut microbiome and environmental exposure also feature among the influential factors in biomarker discovery because they sculpt individual metabolic profiles, impacting overall health. Further, we discuss technological advances in metabolomics, current clinical applications, and the challenges faced by metabolomics biomarker validation toward precision medicine. Finally, this review discusses future opportunities regarding the integration of metabolomics into routine healthcare to enable preventive and personalized approaches.},
}

Humans
*Metabolomics/methods
*Precision Medicine/methods
*Biomarkers/metabolism
Neoplasms/metabolism/diagnosis
Cardiovascular Diseases/metabolism/diagnosis
Neurodegenerative Diseases/metabolism/diagnosis
Metabolome
Gastrointestinal Microbiome

@article {pmid39684893,
year = {2024},
author = {Parkar, N and Young, W and Olson, T and Hurst, C and Janssen, P and Spencer, NJ and McNabb, WC and Dalziel, JE},
title = {Peripherally Restricted Activation of Opioid Receptors Influences Anxiety-Related Behaviour and Alters Brain Gene Expression in a Sex-Specific Manner.},
journal = {International journal of molecular sciences},
volume = {25},
number = {23},
pages = {},
pmid = {39684893},
issn = {1422-0067},
support = {C10X1706//Ministry of Business, Innovation and Employment/ ; },
mesh = {Animals ; Male ; Female ; *Anxiety/metabolism ; Rats ; *Loperamide/pharmacology ; *Brain/metabolism/drug effects ; *Rats, Sprague-Dawley ; *Receptors, Opioid/metabolism/genetics ; Behavior, Animal/drug effects ; Gastrointestinal Microbiome/drug effects ; Hippocampus/metabolism/drug effects ; Enteric Nervous System/metabolism ; Gene Expression Regulation/drug effects ; Sex Factors ; Sex Characteristics ; },
abstract = {Although effects of stress-induced anxiety on the gastrointestinal tract and enteric nervous system (ENS) are well studied, how ENS dysfunction impacts behaviour is not well understood. We investigated whether ENS modulation alters anxiety-related behaviour in rats. We used loperamide, a potent μ-opioid receptor agonist that does not cross the blood-brain barrier, to manipulate ENS function and assess changes in behaviour, gut and brain gene expression, and microbiota profile. Sprague Dawley (male/female) rats were acutely dosed with loperamide (subcutaneous) or control solution, and their behavioural phenotype was examined using open field and elevated plus maze tests. Gene expression in the proximal colon, prefrontal cortex, hippocampus, and amygdala was assessed by RNA-seq and caecal microbiota composition determined by shotgun metagenome sequencing. In female rats, loperamide treatment decreased distance moved and frequency of supported rearing, indicating decreased exploratory behaviour and increased anxiety, which was associated with altered hippocampal gene expression. Loperamide altered proximal colon gene expression and microbiome composition in both male and female rats. Our results demonstrate the importance of the ENS for communication between gut and brain for normo-anxious states in female rats and implicate corticotropin-releasing hormone and gamma-aminobutyric acid gene signalling pathways in the hippocampus. This study also sheds light on sexually dimorphic communication between the gut and the brain. Microbiome and colonic gene expression changes likely reflect localised effects of loperamide related to gut dysmotility. These results suggest possible ENS pharmacological targets to alter gut to brain signalling for modulating mood.},
}

Animals
Male
Female
*Anxiety/metabolism
Rats
*Loperamide/pharmacology
*Brain/metabolism/drug effects
*Rats, Sprague-Dawley
*Receptors, Opioid/metabolism/genetics
Behavior, Animal/drug effects
Gastrointestinal Microbiome/drug effects
Hippocampus/metabolism/drug effects
Enteric Nervous System/metabolism
Gene Expression Regulation/drug effects
Sex Factors
Sex Characteristics

@article {pmid39684874,
year = {2024},
author = {Galappaththi, SPL and Smith, KR and Alsatari, ES and Hunter, R and Dyess, DL and Turbat-Herrera, EA and Dasgupta, S},
title = {The Genomic and Biologic Landscapes of Breast Cancer and Racial Differences.},
journal = {International journal of molecular sciences},
volume = {25},
number = {23},
pages = {},
pmid = {39684874},
issn = {1422-0067},
support = {1R21MD019400-01/MD/NIMHD NIH HHS/United States ; },
mesh = {Humans ; *Breast Neoplasms/genetics/pathology/epidemiology ; Female ; *Genomics/methods ; Dysbiosis ; Racial Groups/genetics ; },
abstract = {Breast cancer is a significant health challenge worldwide and is the most frequently diagnosed cancer among women globally. This review provides a comprehensive overview of breast cancer biology, genomics, and microbial dysbiosis, focusing on its various subtypes and racial differences. Breast cancer is primarily classified into carcinomas and sarcomas, with carcinomas constituting most cases. Epidemiology and breast cancer risk factors are important for public health intervention. Staging and grading, based on the TNM and Nottingham grading systems, respectively, are crucial to determining the clinical outcome and treatment decisions. Histopathological subtypes include in situ and invasive carcinomas, such as invasive ductal carcinoma (IDC) and invasive lobular carcinoma (ILC). The review explores molecular subtypes, including Luminal A, Luminal B, Basal-like (Triple Negative), and HER2-enriched, and delves into breast cancer's histological and molecular progression patterns. Recent research findings related to nuclear and mitochondrial genetic alterations, epigenetic reprogramming, and the role of microbiome dysbiosis in breast cancer and racial differences are also reported. The review also provides an update on breast cancer's current diagnostics and treatment modalities.},
}

Humans
*Breast Neoplasms/genetics/pathology/epidemiology
Female
*Genomics/methods
Dysbiosis
Racial Groups/genetics

@article {pmid39684853,
year = {2024},
author = {Tynior, W and Kłósek, M and Salatino, S and Cuber, P and Hudy, D and Nałęcz, D and Chan, YT and Gustave, C and Strzelczyk, JK},
title = {Metagenomic Analysis of the Buccal Microbiome by Nanopore Sequencing Reveals Structural Differences in the Microbiome of a Patient with Molar Incisor Hypomineralization (MIH) Compared to a Healthy Child-Case Study.},
journal = {International journal of molecular sciences},
volume = {25},
number = {23},
pages = {},
pmid = {39684853},
issn = {1422-0067},
support = {PCN-1-111/N/2/O//Medical University of Silesia/ ; },
mesh = {Humans ; *Microbiota/genetics ; *Metagenomics/methods ; *Nanopore Sequencing/methods ; *Dental Enamel Hypoplasia/microbiology/genetics ; Child ; Mouth Mucosa/microbiology/pathology ; Male ; Female ; Bacteria/genetics/classification/isolation & purification ; Case-Control Studies ; Metagenome ; Incisor/microbiology ; Molar Hypomineralization ; },
abstract = {Molar incisor hypomineralization (MIH) is a qualitative developmental defect that affects the enamel tissue of permanent molars and can also occur in permanent incisors. Enamel affected by MIH has reduced hardness, increased porosity, and a higher organic content than unaffected enamel. These characteristics predispose the enamel to accumulation of bacteria and a higher prevalence of caries lesions. Through a groundbreaking metagenomic analysis of the buccal mucosal sample from a patient with MIH, we explored the intricacies of its microbiome compared to a healthy control using state-of-the-art nanopore long-read sequencing. Out of the 210 bacterial taxa identified in the MIH microbiome, we found Streptococcus and Haemophilus to be the most abundant genera. The bacteria with the highest read counts in the patient with MIH included Streptococcus mitis, Haemophilus parainfluenzae, Streptococcus pneumoniae, Rothia dentocariosa, and Gemella haemolysans. Our results revealed a striking contrast between healthy and MIH affected children, with a higher dominance and number of pathogenic species (S. pneumoniae, H. influenzae, and N. meningitidis) and reduced diversity in the MIH-affected patient. This distinct microbial profile not only sheds light on MIH-affected patients, but paves the way for future research, inspiring deeper understanding and larger scale studies.},
}

Humans
*Microbiota/genetics
*Metagenomics/methods
*Nanopore Sequencing/methods
*Dental Enamel Hypoplasia/microbiology/genetics
Child
Mouth Mucosa/microbiology/pathology
Male
Female
Bacteria/genetics/classification/isolation & purification
Case-Control Studies
Metagenome
Incisor/microbiology
Molar Hypomineralization

@article {pmid39684832,
year = {2024},
author = {Wu, K and Kwon, SH and Zhou, X and Fuller, C and Wang, X and Vadgama, J and Wu, Y},
title = {Overcoming Challenges in Small-Molecule Drug Bioavailability: A Review of Key Factors and Approaches.},
journal = {International journal of molecular sciences},
volume = {25},
number = {23},
pages = {},
pmid = {39684832},
issn = {1422-0067},
support = {U54MD007598//NIH-NIMHD/ ; U54CA14393//NIH/NCI1/ ; BC043180//Department-of-Defense Breast Cancer Research Program grant/ ; UL1TR000124//NIH/NCATS CTSI/ ; G0812D05//Accelerating Excellence in Translational Science Pilot Grants/ ; G003PP07//ACS DCRIDG/ ; SC1CA200517//NIH/NCI/ ; GM135050-05//9 SC1/ ; },
mesh = {*Biological Availability ; Humans ; Drug Delivery Systems/methods ; Animals ; Drug Design ; Pharmaceutical Preparations/metabolism/chemistry ; Artificial Intelligence ; Small Molecule Libraries/pharmacokinetics/chemistry/pharmacology ; Nanotechnology/methods ; },
abstract = {The bioavailability of small-molecule drugs remains a critical challenge in pharmaceutical development, significantly impacting therapeutic efficacy and commercial viability. This review synthesizes recent advances in understanding and overcoming bioavailability limitations, focusing on key physicochemical and biological factors influencing drug absorption and distribution. We examine cutting-edge strategies for enhancing bioavailability, including innovative formulation approaches, rational structural modifications, and the application of artificial intelligence in drug design. The integration of nanotechnology, 3D printing, and stimuli-responsive delivery systems are highlighted as promising avenues for improving drug delivery. We discuss the importance of a holistic, multidisciplinary approach to bioavailability optimization, emphasizing early-stage consideration of ADME properties and the need for patient-centric design. This review also explores emerging technologies such as CRISPR-Cas9-mediated personalization and microbiome modulation for tailored bioavailability enhancement. Finally, we outline future research directions, including advanced predictive modeling, overcoming biological barriers, and addressing the challenges of emerging therapeutic modalities. By elucidating the complex interplay of factors affecting bioavailability, this review aims to guide future efforts in developing more effective and accessible small-molecule therapeutics.},
}

*Biological Availability
Humans
Drug Delivery Systems/methods
Animals
Drug Design
Pharmaceutical Preparations/metabolism/chemistry
Artificial Intelligence
Small Molecule Libraries/pharmacokinetics/chemistry/pharmacology
Nanotechnology/methods

@article {pmid39684802,
year = {2024},
author = {Ma, Y and Roeder, T},
title = {Macrostomum lignano Complements the Portfolio of Simple Animal Models Used for Marine Toxicological Studies.},
journal = {International journal of molecular sciences},
volume = {25},
number = {23},
pages = {},
pmid = {39684802},
issn = {1422-0067},
support = {JC2023043//Nantong Jiangsu Scientific Research Project/ ; BK20240948//Natural Science Foundation of Jiangsu Province/ ; 24KJD430010//Natural Science Research of Jiangsu Higher Education Institutions/ ; },
mesh = {Animals ; *Aquatic Organisms/drug effects ; Ecosystem ; Models, Animal ; *Water Pollutants, Chemical/toxicity ; },
abstract = {Macrostomum lignano is gaining increasing recognition as a model organism for toxicological studies in marine ecosystems and expands the range of simple animal models currently used. Water pollution caused by human activities not only endangers environmental integrity but also affects human health, underlining the need to monitor water pollution effectively. This review describes the distinctive characteristics of M. lignano, including its rapid reproductive cycle, increased sensitivity to environmental variability, and remarkable regenerative abilities. Over the last thirty years, M. lignano has been used in various research areas, particularly molecular biology and toxicology. This endeavor has benefited from significant advances in genome and transcriptome technologies. Recent investigations have revealed its sensitivity to various pollutants and highlighted its potential for assessing toxicological effects at the physiological and molecular levels. Furthermore, the ecological versatility and stable microbiome of M. lignano make it an exemplary model for research into pollutant interactions in marine ecosystems. Despite challenges associated with its complex genomic architecture, ongoing genomic efforts are promising to significantly enhance its utility in toxicological research. This review underscores the pivotal role of M. lignano in advancing environmental health studies and outlines future research directions to maximize its potential as a model organism.},
}

Animals
*Aquatic Organisms/drug effects
Ecosystem
Models, Animal
*Water Pollutants, Chemical/toxicity

@article {pmid39684788,
year = {2024},
author = {Moreno, RJ and Ashwood, P},
title = {An Update on Microbial Interventions in Autism Spectrum Disorder with Gastrointestinal Symptoms.},
journal = {International journal of molecular sciences},
volume = {25},
number = {23},
pages = {},
pmid = {39684788},
issn = {1422-0067},
support = {HD090214/HD/NICHD NIH HHS/United States ; },
mesh = {Humans ; *Autism Spectrum Disorder/therapy/microbiology ; *Gastrointestinal Microbiome ; *Probiotics/therapeutic use ; *Fecal Microbiota Transplantation/methods ; *Dysbiosis/therapy/microbiology ; *Prebiotics ; Gastrointestinal Diseases/therapy/microbiology ; Anti-Bacterial Agents/therapeutic use ; Animals ; },
abstract = {In the United States, autism spectrum disorder (ASD) affects 1 in 33 children and is characterized by atypical social interactions, communication difficulties, and intense, restricted interests. Microbial dysbiosis in the gastrointestinal (GI) tract is frequently observed in individuals with ASD, potentially contributing to behavioral manifestations and correlating with worsening severity. Moreover, dysbiosis may contribute to the increased prevalence of GI comorbidities in the ASD population and exacerbate immune dysregulation, further worsening dysbiosis. Over the past 25 years, research on the impact of microbial manipulation on ASD outcomes has gained substantial interest. Various approaches to microbial manipulation have been preclinically and clinically tested, including antibiotic treatment, dietary modifications, prebiotics, probiotics, and fecal microbiota transplantation. Each method has shown varying degrees of success in reducing the severity of ASD behaviors and/or GI symptoms and varying long-term efficacy. In this review, we discuss these microbiome manipulation methods and their outcomes. We also discuss potential microbiome manipulation early in life, as this is a critical period for neurodevelopment.},
}

Humans
*Autism Spectrum Disorder/therapy/microbiology
*Gastrointestinal Microbiome
*Probiotics/therapeutic use
*Fecal Microbiota Transplantation/methods
*Dysbiosis/therapy/microbiology
*Prebiotics
Gastrointestinal Diseases/therapy/microbiology
Anti-Bacterial Agents/therapeutic use
Animals

@article {pmid39684563,
year = {2024},
author = {Gomes, SF and Valois, A and Estevinho, MM and Santiago, M and Magro, F},
title = {Association of Gut Microbiome and Dipeptidyl Peptidase 4 in Immune-Mediated Inflammatory Bowel Disease: A Rapid Literature Review.},
journal = {International journal of molecular sciences},
volume = {25},
number = {23},
pages = {},
pmid = {39684563},
issn = {1422-0067},
support = {GEDII Innovate 2023 Fellowship//Portuguese Study Group of Inflammatory Bowel Disease (GEDII)/ ; UI/BD/150826/2021//Portuguese Foundation for Science and Technology (FCT)/ ; },
mesh = {*Gastrointestinal Microbiome ; Humans ; *Inflammatory Bowel Diseases/microbiology/immunology ; *Dipeptidyl Peptidase 4/metabolism ; Animals ; Dysbiosis/microbiology/immunology ; },
abstract = {Immune-mediated inflammatory diseases (IMIDs) are characterized by dysregulated immune responses and chronic tissue inflammation. In the setting of inflammatory bowel disease (IBD), dipeptidyl peptidase 4 (DPP4) and gut microorganisms have been proved to interplay, potentially influenced by dietary factors. This rapid review aimed to study the DPP4-gut microbiome link in IBD. A search across five databases and two gray literature sources identified seven relevant studies reporting data on DPP4 and gut microbiome in patients with IBD-related IMIDs or in vitro or in vivo models: one cross-sectional, one in vitro, and five in vivo studies. The findings revealed a significant impact of DPP4 and its substrates, i.e., glucagon-like peptide-1/2 (GLP-1/2), on the composition of gut microbiome and on the development of dysbiosis. Increased DPP4 activity is associated with decreased GLP-1/2; increased pathogenic bacterial phyla such as Actinobacteria, Bacteroidetes, Deferribacteres, Firmicutes, Fusobacteriota, Proteobacteria, and Verrucomicrobia; and decreased alpha diversity of beneficial gut microbes, including Clostridiaceae, Lachnospiraceae, and Ruminococcaceae families and short-chain fatty acid-producing bacteria like Odoribacter and Butryvibrio spp., with exacerbation of intestinal inflammation. This overview revealed that understanding the DPP4-gut microbiome association is critical for the development of DPP4-targeted therapeutic strategies to guarantee gut microbiome balance and modulation of immune response in IBD.},
}

*Gastrointestinal Microbiome
Humans
*Inflammatory Bowel Diseases/microbiology/immunology
*Dipeptidyl Peptidase 4/metabolism
Animals
Dysbiosis/microbiology/immunology

@article {pmid39684532,
year = {2024},
author = {Ma, H and Zhang, H and Zheng, C and Liu, Z and Wang, J and Tian, P and Wu, Z and Zhang, H},
title = {Synthetic Microbial Community Isolated from Intercropping System Enhances P Uptake in Rice.},
journal = {International journal of molecular sciences},
volume = {25},
number = {23},
pages = {},
pmid = {39684532},
issn = {1422-0067},
support = {32101398, 32301449//National Natural Science Foundation of China/ ; 20240303024NC//Jilin Science and Technology Development Plan Project/ ; },
mesh = {*Oryza/microbiology/growth & development/metabolism ; *Phosphorus/metabolism ; *Rhizosphere ; *Microbiota ; *Plant Roots/microbiology/metabolism/growth & development ; *Soil Microbiology ; Biomass ; Bacteria/metabolism/genetics/classification/growth & development ; Glycine max/microbiology/metabolism/growth & development ; },
abstract = {Changes in root traits and rhizosphere microbiome are important ways to optimize plant phosphorus (P) efficiency and promote multifunctionality in intercropping. However, whether and how synthetic microbial communities isolated from polyculture systems can facilitate plant growth and P uptake are still largely unknown. A field experiment was first carried out to assess the rice yield and P uptake in the rice/soybean intercropping systems, and a synthetic microbial community (SynCom) isolated from intercropped rice was then constructed to elucidate the potential mechanisms of growth-promoting effects on rice growth and P uptake in a series of pot experiments. Our results showed that the yield and P uptake of intercropped rice were lower than those of rice grown in monoculture. However, bacterial networks in the rice rhizosphere were more stable in polyculture, exhibiting more hub nodes and greater modularity compared to the rice monoculture. A bacterial synthetic community (SynCom) composed of four bacterial strains (Variovorax paradoxus, Novosphingobium subterraneum, Hydrogenophaga pseudoflava, Acidovorax sp.) significantly enhanced the biomass and P uptake of potted rice plants. These growth-promoting effects are underpinned by multiple pathways, including the direct activation of soil available P, increased root surface area and root tip number, reduced root diameter, and promotion of root-to-shoot P translocation through up-regulation of Pi transporter genes (OsPht1;1, OsPht1;2, OsPht1;4, OsPht1;6). This study highlights the potential of harnessing synthetic microbial communities to enhance nutrient acquisition and improve crop production.},
}

*Oryza/microbiology/growth & development/metabolism
*Phosphorus/metabolism
*Rhizosphere
*Microbiota
*Plant Roots/microbiology/metabolism/growth & development
*Soil Microbiology
Biomass
Bacteria/metabolism/genetics/classification/growth & development
Glycine max/microbiology/metabolism/growth & development

@article {pmid39684528,
year = {2024},
author = {Pei, XM and Zhou, LX and Tsang, MW and Tai, WC and Wong, SC},
title = {The Oral Microbial Ecosystem in Age-Related Xerostomia: A Critical Review.},
journal = {International journal of molecular sciences},
volume = {25},
number = {23},
pages = {},
pmid = {39684528},
issn = {1422-0067},
support = {N-ZJNN//External donation funding/ ; },
mesh = {Humans ; *Xerostomia/microbiology/etiology ; *Mouth/microbiology ; *Microbiota ; *Dysbiosis/microbiology ; Aged ; Oral Health ; Aging ; Quality of Life ; },
abstract = {Xerostomia is a widespread condition among the elderly, impacting as many as 50% of individuals within this demographic. This review aims to analyze the association between age-related xerostomia and the oral microbial ecosystem. Xerostomia not only induces discomfort but also heightens the susceptibility to oral diseases, including dental caries and infections. The oral microbial ecosystem, characterized by a dynamic equilibrium of microorganisms, is integral to the maintenance of oral health. Dysbiosis, defined as a microbial imbalance, can further aggravate oral health complications in those suffering from xerostomia. This review investigates the composition, diversity, and functionality of the oral microbiota in elderly individuals experiencing xerostomia, emphasizing the mechanisms underlying dysbiosis and its ramifications for both oral and systemic health. A comprehensive understanding of these interactions is vital for the formulation of effective management and prevention strategies aimed at enhancing the quality of life for older adults.},
}

Humans
*Xerostomia/microbiology/etiology
*Mouth/microbiology
*Microbiota
*Dysbiosis/microbiology
Aged
Oral Health
Aging
Quality of Life

@article {pmid39684393,
year = {2024},
author = {Majumdar, R and Kandel, SL and Strausbaugh, CA and Singh, A and Pokhrel, S and Bill, M},
title = {Root Microbiome and Metabolome Traits Associated with Improved Post-Harvest Root Storage for Sugar Beet Breeding Lines Under Southern Idaho Conditions.},
journal = {International journal of molecular sciences},
volume = {25},
number = {23},
pages = {},
pmid = {39684393},
issn = {1422-0067},
mesh = {*Beta vulgaris/microbiology/metabolism ; *Plant Roots/microbiology/metabolism ; *Metabolome ; *Microbiota ; Disease Resistance/genetics ; RNA, Ribosomal, 16S/genetics ; Plant Breeding/methods ; Bacteria/metabolism/genetics/classification ; Plant Diseases/microbiology/genetics ; },
abstract = {Post-harvest storage loss in sugar beets due to root rot and respiration can cause >20% sugar loss. Breeding strategies focused on factors contributing to improved post-harvest storage quality are of great importance to prevent losses. Using 16S rRNA and ITS sequencing and sugar beet mutational breeding lines with high disease resistance (R), along with a susceptible (S) commercial cultivar, the role of root microbiome and metabolome in storage performance was investigated. The R lines in general showed higher abundances of bacterial phyla, Patescibacteria at the M time point, and Cyanobacteria and Desulfobacterota at the L time point. Amongst fungal phyla, Basidiomycota (including Athelia) and Ascomycota were predominant in diseased samples. Linear discriminant analysis Effect Size (LEfSe) identified bacterial taxa such as Micrococcales, Micrococcaceae, Bacilli, Glutamicibacter, Nesterenkonia, and Paenarthrobacter as putative biomarkers associated with resistance in the R lines. Further functional enrichment analysis showed a higher abundance of bacteria, such as those related to the super pathway of pyrimidine deoxyribonucleoside degradation, L-tryptophan biosynthesis at M and L, and fungi, such as those associated with the biosynthesis of L-iditol 2-dehydrogenase at L in the R lines. Metabolome analysis of the roots revealed higher enrichment of pathways associated with arginine, proline, alanine, aspartate, and glutamate metabolism at M, in addition to beta-alanine and butanoate metabolism at L in the R lines. Correlation analysis between the microbiome and metabolites indicated that the root's biochemical composition, such as the presence of nitrogen-containing secondary metabolites, may regulate relative abundances of key microbial candidates contributing to better post-harvest storage.},
}

*Beta vulgaris/microbiology/metabolism
*Plant Roots/microbiology/metabolism
*Metabolome
*Microbiota
Disease Resistance/genetics
RNA, Ribosomal, 16S/genetics
Plant Breeding/methods
Bacteria/metabolism/genetics/classification
Plant Diseases/microbiology/genetics

@article {pmid39684390,
year = {2024},
author = {Burge, KY and Zhong, H and Wilson, AP and Chaaban, H},
title = {Network-Based Bioinformatics Highlights Broad Importance of Human Milk Hyaluronan.},
journal = {International journal of molecular sciences},
volume = {25},
number = {23},
pages = {},
pmid = {39684390},
issn = {1422-0067},
support = {R01HD109784/GF/NIH HHS/United States ; 5P20GM134973/GF/NIH HHS/United States ; },
mesh = {Animals ; Humans ; *Hyaluronic Acid/metabolism/pharmacology ; Mice ; *Milk, Human/chemistry/metabolism ; *Computational Biology/methods ; Enterocolitis, Necrotizing/metabolism/prevention & control ; Ileum/metabolism/drug effects ; Animals, Newborn ; Female ; Transcriptome ; Gene Regulatory Networks/drug effects ; },
abstract = {Human milk (HM) is rich in bioactive factors promoting postnatal small intestinal development and maturation of the microbiome. HM is also protective against necrotizing enterocolitis (NEC), a devastating inflammatory condition predominantly affecting preterm infants. The HM glycosaminoglycan, hyaluronan (HA), is present at high levels in colostrum and early milk. Our group has demonstrated that HA with a molecular weight of 35 kDa (HA35) promotes maturation of the murine neonatal intestine and protects against two distinct models of NEC. However, the molecular mechanisms underpinning HA35-induced changes in the developing ileum are unclear. CD-1 mouse pups were treated with HA35 or vehicle control daily, from P7 to P14, and we used network and functional analyses of bulk RNA-seq ileal transcriptomes to further characterize molecular mechanisms through which HA35 likely influences intestinal maturation. HA35-treated pups separated well by principal component analysis, and cell deconvolution revealed increases in stromal, Paneth, and mature enterocyte and progenitor cells in HA35-treated pups. Gene set enrichment and pathway analyses demonstrated upregulation in key processes related to antioxidant and growth pathways, such as nuclear factor erythroid 2-related factor-mediated oxidative stress response, hypoxia inducible factor-1 alpha, mechanistic target of rapamycin, and downregulation of apoptotic signaling. Collectively, pro-growth and differentiation signals induced by HA35 may present novel mechanisms by which this HM bioactive factor may protect against NEC.},
}

Animals
Humans
*Hyaluronic Acid/metabolism/pharmacology
Mice
*Milk, Human/chemistry/metabolism
*Computational Biology/methods
Enterocolitis, Necrotizing/metabolism/prevention & control
Ileum/metabolism/drug effects
Animals, Newborn
Female
Transcriptome
Gene Regulatory Networks/drug effects

@article {pmid39684324,
year = {2024},
author = {Toader, C and Tataru, CP and Munteanu, O and Serban, M and Covache-Busuioc, RA and Ciurea, AV and Enyedi, M},
title = {Decoding Neurodegeneration: A Review of Molecular Mechanisms and Therapeutic Advances in Alzheimer's, Parkinson's, and ALS.},
journal = {International journal of molecular sciences},
volume = {25},
number = {23},
pages = {},
pmid = {39684324},
issn = {1422-0067},
mesh = {Humans ; *Alzheimer Disease/therapy/metabolism/genetics ; *Parkinson Disease/therapy/genetics/metabolism ; *Amyotrophic Lateral Sclerosis/therapy/genetics/metabolism ; Animals ; Neurodegenerative Diseases/therapy/metabolism/genetics ; Drug Delivery Systems ; Gene Editing ; },
abstract = {Neurodegenerative diseases, such as Alzheimer's, Parkinson's, ALS, and Huntington's, remain formidable challenges in medicine, with their relentless progression and limited therapeutic options. These diseases arise from a web of molecular disturbances-misfolded proteins, chronic neuroinflammation, mitochondrial dysfunction, and genetic mutations-that slowly dismantle neuronal integrity. Yet, recent scientific breakthroughs are opening new paths to intervene in these once-intractable conditions. This review synthesizes the latest insights into the underlying molecular dynamics of neurodegeneration, revealing how intertwined pathways drive the course of these diseases. With an eye on the most promising advances, we explore innovative therapies emerging from cutting-edge research: nanotechnology-based drug delivery systems capable of navigating the blood-brain barrier, gene-editing tools like CRISPR designed to correct harmful genetic variants, and stem cell strategies that not only replace lost neurons but foster neuroprotective environments. Pharmacogenomics is reshaping treatment personalization, enabling tailored therapies that align with individual genetic profiles, while molecular diagnostics and biomarkers are ushering in an era of early, precise disease detection. Furthermore, novel perspectives on the gut-brain axis are sparking interest as mounting evidence suggests that microbiome modulation may play a role in reducing neuroinflammatory responses linked to neurodegenerative progression. Taken together, these advances signal a shift toward a comprehensive, personalized approach that could transform neurodegenerative care. By integrating molecular insights and innovative therapeutic techniques, this review offers a forward-looking perspective on a future where treatments aim not just to manage symptoms but to fundamentally alter disease progression, presenting renewed hope for improved patient outcomes.},
}

Humans
*Alzheimer Disease/therapy/metabolism/genetics
*Parkinson Disease/therapy/genetics/metabolism
*Amyotrophic Lateral Sclerosis/therapy/genetics/metabolism
Animals
Neurodegenerative Diseases/therapy/metabolism/genetics
Drug Delivery Systems
Gene Editing

@article {pmid39684314,
year = {2024},
author = {Domingo-Bretón, R and Moroni, F and Toxqui-Rodríguez, S and Belenguer, Á and Piazzon, MC and Pérez-Sánchez, J and Naya-Català, F},
title = {Moving Beyond Oxford Nanopore Standard Procedures: New Insights from Water and Multiple Fish Microbiomes.},
journal = {International journal of molecular sciences},
volume = {25},
number = {23},
pages = {},
pmid = {39684314},
issn = {1422-0067},
support = {871108//Horizon H2020/ ; PRTR-C17.I1//Ministerio de Ciencia e Innovación/ ; THINKINAZUL/2021/024//Generalitat Valenciana/ ; },
mesh = {Animals ; *Microbiota/genetics ; *Fishes/microbiology ; Nanopores ; Feces/microbiology ; Water Microbiology ; DNA Barcoding, Taxonomic/methods ; High-Throughput Nucleotide Sequencing/methods ; },
abstract = {Oxford Nanopore Technology (ONT) allows for the rapid profiling of aquaculture microbiomes. However, not all the experimental and downstream methodological possibilities have been benchmarked. Here, we aimed to offer novel insights into the use of different library preparation methods (standard-RAP and native barcoding-LIG), primers (V3-V4, V1-V3, and V1-V9), and basecalling models (fast-FAST, high-HAC, and super-accuracy-SUP) implemented in ONT to elucidate the microbiota associated with the aquatic environment and farmed fish, including faeces, skin, and intestinal mucus. Microbial DNA from water and faeces samples could be amplified regardless of the library-primer strategy, but only with LIG and V1-V3/V1-V9 primers in the case of skin and intestine mucus. Low taxonomic assignment levels were favoured by the use of full-length V1-V9 primers, though in silico hybridisation revealed a lower number of potential matching sequences in the SILVA database, especially evident with the increase in Actinobacteriota in real datasets. SUP execution allowed for a higher median Phred quality (24) than FAST (11) and HAC (17), but its execution time (6-8 h) was higher in comparison to the other models (0.6-7 h). Altogether, we optimised the use of ONT for water- and fish-related microbial analyses, validating, for the first time, the use of the LIG strategy. We consider that LIG-V1-V9-HAC is the optimal time/cost-effective option to amplify the microbial DNA from environmental samples. However, the use of V1-V3 could help to maximise the dataset microbiome diversity, representing an alternative when long amplicon sequences become compromised by microbial DNA quality and/or high host DNA loads interfere with the PCR amplification/sequencing procedures, especially in the case of gut mucus.},
}

Animals
*Microbiota/genetics
*Fishes/microbiology
Nanopores
Feces/microbiology
Water Microbiology
DNA Barcoding, Taxonomic/methods
High-Throughput Nucleotide Sequencing/methods

@article {pmid39684312,
year = {2024},
author = {Bellver, J and Gonzalez-Monfort, M and González, S and Toson, B and Labarta, E and Castillón, G and Mariani, G and Vidal, C and Giles, J and Cruz, F and Ballesteros, A and Ferrando, M and García-Velasco, JA and Valbuena, D and Vilella, F and Parras-Molto, M and Tercero-Atencia, E and Simon, C and Moreno, I},
title = {An Analysis of the Digestive and Reproductive Tract Microbiota in Infertile Women with Obesity.},
journal = {International journal of molecular sciences},
volume = {25},
number = {23},
pages = {},
pmid = {39684312},
issn = {1422-0067},
support = {GRISOLIAP/2021/176//Generalitat Valenciana/ ; INVEST/2022/478//Generalitat Valenciana/ ; PI21/00528//Instituto de Salud Carlos III/ ; GA101080219//European Union/ ; RTI2018-094946-B-I00//Agencia Estatal de Investigación/ ; PI21/00235//Instituto de Salud Carlos III/ ; },
mesh = {Humans ; Female ; *Obesity/microbiology/complications ; *Infertility, Female/microbiology ; Adult ; *RNA, Ribosomal, 16S/genetics ; Gastrointestinal Microbiome/genetics ; Vagina/microbiology ; Microbiota ; Endometrium/microbiology ; Prospective Studies ; Saliva/microbiology ; Feces/microbiology ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {Previous studies have linked the microbiome of distinct body habitats to obesity and infertility; however, the often-divergent results observed have left the role of the so-called "second genome" in obese infertile patients incompletely explored. Here, we present a prospective observational multicenter study of oral, gut, endometrial, and vaginal microbiota of infertile patients classified according to BMI. Patients collected saliva/fecal samples, while vaginal/endometrial fluid samples were collected in the clinic. Total bacterial DNA was extracted, and microbiota profiles were analyzed by 16S rRNA gene sequencing. Our results showed no differences in the Bacteroidetes/Firmicutes ratio (proposed obesity hallmark) in the gut microbiota between patients with obesity and normal weight; however, a tendency for higher levels of genera such as Escherichia-Shigella in normal-weight patients was observed; in comparison, patients with obesity possessed increased numbers of Parasutterella and Roseburia. In the reproductive tract, vaginal samples possessed a similar microbiota to endometrial fluid, both largely colonised by Lactobacillus, Gardnerella, and Streptococcus, supporting the hypothesis that uterine colonisation proceeds from vaginal bacteria ascension. Additionally, higher prevalence of a Streptococcus-dominated (>50%) endometrial microbiota was observed among patients with obesity. This first description of the human digestive and reproductive tract microbiota in infertile women with obesity may explain their poor reproductive outcomes.},
}

Humans
Female
*Obesity/microbiology/complications
*Infertility, Female/microbiology
Adult
*RNA, Ribosomal, 16S/genetics
Gastrointestinal Microbiome/genetics
Vagina/microbiology
Microbiota
Endometrium/microbiology
Prospective Studies
Saliva/microbiology
Feces/microbiology
Bacteria/classification/genetics/isolation & purification

@article {pmid39687223,
year = {2023},
author = {Sahni, S and Schott, EM and Carroll, D and Soto-Giron, MJ and Corbett, S and Toledo, GV and Kiel, DP},
title = {Randomized clinical trial to test the safety and tolerability of SBD111, an optimized synbiotic medical food combination designed for the dietary management of the metabolic processes underlying osteopenia and osteoporosis.},
journal = {Journal of microbiology & experimentation},
volume = {11},
number = {1},
pages = {1-11},
pmid = {39687223},
issn = {2373-437X},
abstract = {To determine the effect of a twice daily administration of SBD111 on safety and tolerability in healthy adults in a randomized, placebo-controlled trial over 28-days. Participants were randomized to either SBD111 (n=15) or placebo (n=17). The outcomes were the number, frequency, and severity of Gastrointestinal (GI) symptoms and the number and severity of adverse events (AEs) over 28-days. Stool samples were collected and analyzed at baseline, after 28- and 56-days. Groups were compared (P< 0.05) using an intention-to-treat approach. The two groups were similar at baseline. After 28-days, the presence of GI symptoms tended to be higher with SBD111 use vs placebo (P=0.08) but the total number, frequency/severity of GI symptoms did not significantly differ. The number of AEs possibly related to the study were higher with SBD111 use vs placebo (P=0.05), there were no significant differences in the mean number/severity of AEs. The majority of reported AEs were mild, some were moderate, but none were severe. There were no significant differences in alpha diversity indices between the two groups at baseline or follow-up. SBD111 strains were identified in stool, enriched metabolic pathways for menaquinone (vitamin K2) production at 28-days, and were not detected at 56-days. The relatively low frequency and mild severity of GI symptoms and AEs suggests that SBD111 at the level tested is safe for human consumption.},
}

@article {pmid39684246,
year = {2024},
author = {Domínguez-Pino, M and Mellado, S and Cuesta, CM and Grillo-Risco, R and García-García, F and Pascual, M},
title = {Metagenomics Reveals Sex-Based Differences in Murine Fecal Microbiota Profiles Induced by Chronic Alcohol Consumption.},
journal = {International journal of molecular sciences},
volume = {25},
number = {23},
pages = {},
pmid = {39684246},
issn = {1422-0067},
support = {2023-I024//the Spanish Ministry of Health-PNSD/ ; CIAICO/2021/203//GVA/ ; RD21/0009/0005//the Primary Addiction Care Research Network/ ; pro-ject IMPaCT-Data, exp. IMP/00019//FGG and RGR were supported by and partially funded by the Institute of Health Carlos III/ ; PID2023-146865OB-I00 and PID2021-124430OA-I00//MCIN/AEI/10.13039/501100011033/ FEDER/ ; },
mesh = {Animals ; Female ; Male ; *Feces/microbiology ; Mice ; *Gastrointestinal Microbiome/drug effects ; *Toll-Like Receptor 4/genetics/metabolism ; *Metagenomics/methods ; *Mice, Knockout ; *RNA, Ribosomal, 16S/genetics ; *Ethanol/adverse effects ; Alcohol Drinking/adverse effects ; Mice, Inbred C57BL ; Sex Factors ; Dysbiosis/microbiology/chemically induced ; Sex Characteristics ; },
abstract = {Chronic ethanol exposure induces an inflammatory response within the intestinal tract, compromising mucosal and epithelial integrity and leading to dysbiosis of the gut microbiome. However, the specific roles of the gut microbiota in mediating ethanol-induced effects, as well as their interactions with the immune system, remain poorly characterized. This study aimed to evaluate sex-based differences in fecal microbiota profiles induced by chronic alcohol consumption and to assess whether TLR4 is involved in these effects. We analyzed the 16S rRNA gene sequencing of fecal samples from male and female wild-type (WT) and TLR4-knockout (TLR4-KO) mice with and without chronic ethanol exposure over a three-month period. Our findings provide evidence, for the first time, that male mice are more susceptible to the effects of ethanol on the fecal microbiota, since ethanol exposure induced greater alterations in the Gram-negative and -positive bacteria with immunogenic capacity in the WT male mice than in the female mice. We also demonstrate that the absence of immune receptor TLR4 leads to different microbiota in both sexes, showing anti-inflammatory and protective properties for intestinal barrier function and resulting in a phenotype more resistant to ethanol's effects. These findings may open new avenues for understanding the relationship between gut microbiota profiles and inflammation in the digestive system induced by chronic alcohol consumption.},
}

Animals
Female
Male
*Feces/microbiology
Mice
*Gastrointestinal Microbiome/drug effects
*Toll-Like Receptor 4/genetics/metabolism
*Metagenomics/methods
*Mice, Knockout
*RNA, Ribosomal, 16S/genetics
*Ethanol/adverse effects
Alcohol Drinking/adverse effects
Mice, Inbred C57BL
Sex Factors
Dysbiosis/microbiology/chemically induced
Sex Characteristics

@article {pmid39684223,
year = {2024},
author = {Jaworska, K and Kopacz, W and Koper, M and Ufnal, M},
title = {Microbiome-Derived Trimethylamine N-Oxide (TMAO) as a Multifaceted Biomarker in Cardiovascular Disease: Challenges and Opportunities.},
journal = {International journal of molecular sciences},
volume = {25},
number = {23},
pages = {},
pmid = {39684223},
issn = {1422-0067},
support = {UMO-2020/37/B/NZ5/00366//National Science Centre, Poland/ ; },
mesh = {*Methylamines/metabolism/blood ; Humans ; *Biomarkers/blood ; *Cardiovascular Diseases/metabolism/diagnosis ; Prognosis ; Microbiota ; Gastrointestinal Microbiome ; Animals ; },
abstract = {Biomarkers play a crucial role in various stages of disease management, including screening, diagnosis, prediction, prognosis, treatment, and safety monitoring. Although they are powerful tools in disease diagnosis, management, and drug development, identifying and validating reliable biomarkers remains a significant challenge. Among potential microbiome-derived biomarkers, trimethylamine N-oxide (TMAO) has gained notable attention for its link to atherosclerosis and cardiovascular risk. However, despite the growing body of research on TMAO, its practical application in clinical settings for disease management and patient outcome enhancement is still not a reality. This paper presents recent data on the utility of TMAO as a cardiovascular biomarker, categorized by its various roles: diagnostic, prognostic, susceptibility/risk, monitoring, pharmacodynamic/response, predictive, and safety. It also briefly discusses research on TMAO's potential role in cardiovascular disease development. While TMAO shows promise, particularly in prognostic applications, its reliability as a biomarker has been inconsistent across studies. These variances may result from several confounding factors that affect TMAO plasma levels, including diet, kidney function, and demographic variables. The review aims to elucidate the specific contexts in which TMAO can be valuable, potentially leading to more personalized and effective management of cardiovascular disease.},
}

*Methylamines/metabolism/blood
Humans
*Biomarkers/blood
*Cardiovascular Diseases/metabolism/diagnosis
Prognosis
Microbiota
Gastrointestinal Microbiome
Animals

@article {pmid39684211,
year = {2024},
author = {Zhao, Z and Zhang, X and Zhao, F and Luo, T},
title = {Microbiome-Metabolomics Analysis Insight into the Effects of Starvation and Refeeding on Intestinal Integrity in the Juvenile Largemouth Bass (Micropterus salmoides).},
journal = {International journal of molecular sciences},
volume = {25},
number = {23},
pages = {},
pmid = {39684211},
issn = {1422-0067},
mesh = {Animals ; *Bass/metabolism/microbiology ; *Gastrointestinal Microbiome ; *Starvation/metabolism ; Metabolomics/methods ; Metabolome ; Intestines/microbiology/pathology ; Oxidative Stress ; },
abstract = {The effects of starvation and refeeding on the gut condition of juvenile largemouth bass (Micropterus salmoides) remain unclear. Therefore, our research aimed to explore these effects. Amylase and lipase activities were remarkably decreased in the starvation (ST) group, yet prominently increased in the refeeding (RE) group (p < 0.05). In addition to the malondialdehyde (MDA) level, catalase (CAT) and superoxide dismutase (SOD) activities were significantly upregulated in the ST group (p < 0.05) in marked contrast to those in the controls; however, the RE group showed no substantial variations in CAT and SOD activities or the MDA level (p > 0.05). During starvation, the expression of Nrf2-Keap1 pathway-associated genes was significantly upregulated (p < 0.05). The comparative levels of TNF-α, IL-1β, and IL-15 were highly increased, with the levels of TGF-β1 and IL-10 apparently downregulated in the ST group; in contrast, these levels were restored to their original values in the RE group (p < 0.05). In contrast to the controls, the ST group showed significantly lower height and width of the villi, muscle thickness, and crypt depth and a higher goblet cell number; however, these values were recovered to some extent in the RE group (p < 0.05). The dominant bacterial phyla in the intestines of both groups were Proteobacteria, Firmicutes, Bacteroidetes, Acidobacteria, and Actinobacteria, with marked inter-group differences in the genera Serratia and Lactobacillus. Metabolomics analysis showed that amino acid metabolism is disrupted during starvation and is restored after refeeding. In summary, this study expands our comprehension of the interaction between oxidative stress and antioxidant defenses among juvenile largemouth bass subjected to starvation and refeeding.},
}

Animals
*Bass/metabolism/microbiology
*Gastrointestinal Microbiome
*Starvation/metabolism
Metabolomics/methods
Metabolome
Intestines/microbiology/pathology
Oxidative Stress

@article {pmid39683623,
year = {2024},
author = {Vaduva, CC and Petrescu, AM and Dira, LM and Ruican, D and Pana, RC},
title = {Probiotics in the Prophylaxis of Premature Rupture of Membranes and Cervical Incompetence.},
journal = {Nutrients},
volume = {16},
number = {23},
pages = {},
pmid = {39683623},
issn = {2072-6643},
mesh = {Humans ; *Probiotics/therapeutic use/administration & dosage ; *Fetal Membranes, Premature Rupture/prevention & control ; Female ; Pregnancy ; *Vagina/microbiology ; *Premature Birth/prevention & control ; *Uterine Cervical Incompetence ; Microbiota ; Lactobacillus ; Vaginosis, Bacterial/prevention & control/microbiology ; },
abstract = {UNLABELLED: Premature rupture of membranes (PROM) and cervical incompetence (CI) are major contributors to preterm birth, a leading cause of neonatal morbidity and mortality.

BACKGROUND/OBJECTIVES: Disorders of the vaginal microbiota, such as bacterial vaginosis, have been associated with an increased risk of PROM, CI, and subsequent preterm birth. Probiotics, particularly Lactobacillus strains, have been proposed as a preventive strategy to restore and maintain a healthy vaginal microbiome. This review aims to summarize the latest evidence on the role of probiotics in the prevention of PROM and CI.

METHODS: A comprehensive review was conducted to evaluate the effectiveness of probiotic interventions in the prevention of PROM and CI, yielding 1809 records from 2005 to 2024. Seven relevant studies were selected by searching medical databases and focusing on studies that investigated the restoration of healthy vaginal flora, the reduction of pathogenic bacteria colonization, and the modulation of immune responses by probiotics.

RESULTS: The studies analyzed suggest that probiotics may help restore healthy vaginal flora, reduce pathogenic bacterial colonization, and modulate immune responses, thereby reducing the risk of membrane rupture and cervical insufficiency. Evidence from randomized controlled trials and observational studies shows that the use of probiotics is associated with a lower incidence of PROM and preterm birth, especially in high-risk groups.

CONCLUSIONS: Probiotics emerge as a potential non-invasive and cost-effective strategy to improve pregnancy outcomes in women at risk of preterm birth due to PROM. According to our research, probiotic prophylaxis of cervical insufficiency has not yet been sufficiently investigated. Despite the promising findings, further research is needed to determine standardized probiotic formulations, optimal timing, and routes of administration. Personalized probiotic therapies may represent the future of preterm birth prevention as they offer targeted interventions based on individual microbiome composition.},
}

Humans
*Probiotics/therapeutic use/administration & dosage
*Fetal Membranes, Premature Rupture/prevention & control
Female
Pregnancy
*Vagina/microbiology
*Premature Birth/prevention & control
*Uterine Cervical Incompetence
Microbiota
Lactobacillus
Vaginosis, Bacterial/prevention & control/microbiology

@article {pmid39683613,
year = {2024},
author = {Prapa, I and Yanni, AE and Kompoura, V and Mitropoulou, G and Panas, P and Kostomitsopoulos, N and Kourkoutas, Y},
title = {Functional Modulation of Gut Microbiota and Blood Parameters in Diabetic Rats Following Dietary Intervention with Free or Immobilized Pediococcus acidilactici SK Cells on Pistachio Nuts.},
journal = {Nutrients},
volume = {16},
number = {23},
pages = {},
pmid = {39683613},
issn = {2072-6643},
support = {Operational Pro-gramme "Human Resources Development, Education and Lifelong Learning 2014-2020" in the context of the project "Strengthening Human Resources Research Potential via Doctorate Re-search - 2nd Cycle" (MIS 5000432)//Greece and the European Union (European Social Fund- ESF)/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; Male ; *Pistacia ; *Rats, Wistar ; *Pediococcus acidilactici ; *Diabetes Mellitus, Experimental/microbiology/blood/diet therapy/therapy ; *Probiotics/pharmacology/administration & dosage ; Rats ; *Nuts ; *Feces/microbiology ; },
abstract = {BACKGROUND/OBJECTIVES: The gut microbiota is linked to the pathogenesis of type 1 diabetes mellitus (T1DM), while supplementation with probiotics may result in positive alterations in the composition of the gut microbiome. This research aimed to map the changes in the gut microbiome and blood markers of streptozotocin-induced diabetic rats after a dietary intervention with free or immobilized cells of the presumptive probiotic Pediococcus acidilactici SK on pistachio nuts.

METHODS: Twenty-four male Wistar rats were studied and divided into four groups (healthy or diabetic) which received the free or the immobilized P. acidilactici SK cells on pistachio nuts for 4 weeks. Blood, fecal, and intestinal tissue samples were examined.

RESULTS: The diabetic rats exhibited an elevated concentration of HDL-c, while the inflammatory IL-1β levels were significantly lower in the diabetic animals that received the immobilized cells compared to the group that received the free cells. The dietary intervention with immobilized cells led to decreased counts of fecal staphylococci and enterococci in the diabetic animals, while the diet with both free and immobilized P. acidilactici SK cells rendered levels of these populations in normal values in the feces and intestinal tissue of the diabetic animals. Noticeably, the Lactobacillus and Bifidobacterium genera were elevated after the supplementation with immobilized P. acidilactici SK cells on pistachio nuts.

CONCLUSIONS: Dietary supplementation with P. acidilactici SK cells (in free or in immobilized form) beneficially affected the gut microbiota/microbiome of streptozotocin-induced diabetic rats, leading to the alleviation of dysbiosis and inflammation and control over their lipid levels.},
}

Animals
*Gastrointestinal Microbiome
Male
*Pistacia
*Rats, Wistar
*Pediococcus acidilactici
*Diabetes Mellitus, Experimental/microbiology/blood/diet therapy/therapy
*Probiotics/pharmacology/administration & dosage
Rats
*Nuts
*Feces/microbiology

@article {pmid39683612,
year = {2024},
author = {Turbić, A and Vandenput, L and Gandham, A and Lorentzon, M},
title = {Effects of Synbiotic Supplementation on Bone and Metabolic Health in Caucasian Postmenopausal Women: Rationale and Design of the OsteoPreP Trial.},
journal = {Nutrients},
volume = {16},
number = {23},
pages = {},
pmid = {39683612},
issn = {2072-6643},
support = {904165//Australian Catholic University/ ; },
mesh = {Humans ; Female ; *Synbiotics/administration & dosage ; *Postmenopause ; Double-Blind Method ; *Bone Density/drug effects ; *Gastrointestinal Microbiome ; *Dietary Supplements ; Middle Aged ; White People ; Osteoporosis, Postmenopausal/prevention & control ; Aged ; Absorptiometry, Photon ; Bone and Bones/metabolism ; Blood Glucose/metabolism ; White ; },
abstract = {BACKGROUND/OBJECTIVES: Correction of decreased diversity of the gut microbiome, which is characteristic of menopause, by supplementation with a synbiotic may attenuate or prevent dysbiosis processes and preserve bone mass. We describe the rationale and design of the OsteoPreP trial aimed at evaluating the effects of 12 months of supplementation with a synbiotic on bone and metabolic health in postmenopausal Caucasian women.

METHODS: This is a randomized, double-blinded, placebo-controlled trial among 160 Caucasian, postmenopausal women with no current diagnosis of osteoporosis or supplementation with pro- or prebiotics, and no medical treatment affecting bone turnover. Dual-energy X-ray absorptiometry scans will be conducted at screening to confirm absence of osteoporosis. The primary outcome is the relative change (%) in total bone mineral density of the distal tibia at 12 months post-treatment between the active and placebo groups, as determined via high-resolution peripheral quantitative computed tomography. Secondary outcomes are the effects on immune system modulation and cognition, gut microbiota composition, and musculoskeletal and metabolic functions, with particular emphasis on blood glucose regulation.

CONCLUSIONS: The trial will inform on the efficacy and safety of a synbiotic containing both aerobic and anerobic bacterial strains and a prebiotic fiber on reduction in bone loss and on indices of blood glucose regulation. This trial may pave the way for an exciting field of translational research and be the underpinnings of the prevention strategy of osteoporosis and the management of metabolic dysfunction in postmenopausal women. The trial is registered with clinicaltrials.gov (NCT05348694).},
}

Humans
Female
*Synbiotics/administration & dosage
*Postmenopause
Double-Blind Method
*Bone Density/drug effects
*Gastrointestinal Microbiome
*Dietary Supplements
Middle Aged
White People
Osteoporosis, Postmenopausal/prevention & control
Aged
Absorptiometry, Photon
Bone and Bones/metabolism
Blood Glucose/metabolism
White

@article {pmid39683595,
year = {2024},
author = {Deleu, S and Becherucci, G and Godny, L and Mentella, MC and Petito, V and Scaldaferri, F},
title = {The Key Nutrients in the Mediterranean Diet and Their Effects in Inflammatory Bowel Disease: A Narrative Review.},
journal = {Nutrients},
volume = {16},
number = {23},
pages = {},
pmid = {39683595},
issn = {2072-6643},
support = {NA//European Crohn's and Colitis Organisation/ ; },
mesh = {Animals ; Humans ; *Diet, Mediterranean ; Fruit ; *Gastrointestinal Microbiome ; *Inflammatory Bowel Diseases/diet therapy/microbiology ; Nutrients/administration & dosage ; },
abstract = {The gut microbiome, a collection of gut microorganisms, is crucial in the development and progression of inflammatory bowel diseases (IBD). Therefore, diet and dietary interventions are promising strategies to shape the gut microbiota for IBD management. Of all the diets studied in the IBD field, the Mediterranean diet has the least restrictive nature, promoting long-term adherence. The Mediterranean diet is rich in plants, with a high daily intake of fruits and vegetables (high in fiber, antioxidants, and vitamins), olive oil, whole grains, legumes, and nuts. It includes the moderate consumption of animal products such as oily fish (rich in mono- and polyunsaturated fatty acids), dairy products, and poultry, with a limited intake of red meat and processed foods. This diet is associated with a decreased risk of chronic diseases, including IBD. However, the mechanisms of specific nutrients behind these effects in the Mediterranean diet remain under investigation. Therefore, in this review, we aim to provide an overview of the nutrients that are abundant in the Mediterranean diet and their effects on IBD, with a main focus on preclinical evidence. While several nutrients like fructo-oligosaccharide, chitosan, plant-derived protein, polyphenols, omega-3 polyunsaturated fatty acids, and resveratrol have shown potential beneficial effects in preclinical models, clinical evidence is often limited. However, understanding the complex interactions between specific nutrients and IBD is essential to developing a tailored, multidisciplinary, and personalized approach for disease management; therefore, further research is required.},
}

Animals
Humans
*Diet, Mediterranean
Fruit
*Gastrointestinal Microbiome
*Inflammatory Bowel Diseases/diet therapy/microbiology
Nutrients/administration & dosage

@article {pmid39683552,
year = {2024},
author = {Bender, M and Santos, JM and Dufour, JM and Deshmukh, H and Trasti, S and Elmassry, MM and Shen, CL},
title = {Peanut Shell Extract Improves Markers of Glucose Homeostasis in Diabetic Mice by Modulating Gut Dysbiosis and Suppressing Inflammatory Immune Response.},
journal = {Nutrients},
volume = {16},
number = {23},
pages = {},
pmid = {39683552},
issn = {2072-6643},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Arachis ; *Mice, Inbred C57BL ; *Dysbiosis ; *Homeostasis/drug effects ; Mice ; *Plant Extracts/pharmacology ; Male ; Liver/metabolism/drug effects ; Blood Glucose/metabolism/drug effects ; Immunity, Innate/drug effects ; Diabetes Mellitus, Type 2 ; Inflammation ; Diabetes Mellitus, Experimental ; Biomarkers/blood ; Dietary Supplements ; },
abstract = {BACKGROUND/OBJECTIVE: There is strong evidence that the tripartite interaction between glucose homeostasis, gut microbiota, and the host immune system plays a critical role in the pathophysiology of type 2 diabetes mellitus (T2DM). We reported previously that peanut shell extract (PSE) improves mitochondrial function in db/db mice by suppressing oxidative stress and inflammation in the liver, brain, and white adipose tissue. This study evaluated the impacts of PSE supplementation on glucose homeostasis, liver histology, intestinal microbiome composition, and the innate immune response in diabetic mice.

METHODS: Fourteen db/db mice were randomly assigned to a diabetic group (DM, AIN-93G diet) and a PSE group (1% wt/wt PSE in the AIN-93G diet) for 5 weeks. Six C57BL/6J mice received the AIN-93G diet for 5 weeks (control group). Parameters of glucose homeostasis included serum insulin, HOMA-IR, HOMA-B, and the analysis of pancreatic tissues for insulin and glucagon. We assessed the innate immune response in the colon and liver using a microarray. Gut microbiome composition of cecal contents was analyzed using 16S rRNA gene amplicon sequencing.

RESULTS: PSE supplementation improved glucose homeostasis (decreased serum insulin concentration, HOMA-IR, and HOMA-B) and reduced hepatic lipidosis in diabetic mice. PSE supplementation reversed DM-induced shifts in the relative abundance of amplicon sequence variants of Enterorhabdus, Staphylococcus, Anaerotruncus, and Akkermansia. Relative to the DM mice, the PSE group had suppressed gene expression levels of Cd8α, Csf2, and Irf23 and increased expression levels of Tyk2, Myd88, and Gusb in the liver.

CONCLUSIONS: This study demonstrates that PSE supplementation improves T2DM-associated disorders of diabetic mice, in part due to the suppression of innate immune inflammation.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Arachis
*Mice, Inbred C57BL
*Dysbiosis
*Homeostasis/drug effects
Mice
*Plant Extracts/pharmacology
Male
Liver/metabolism/drug effects
Blood Glucose/metabolism/drug effects
Immunity, Innate/drug effects
Diabetes Mellitus, Type 2
Inflammation
Diabetes Mellitus, Experimental
Biomarkers/blood
Dietary Supplements

@article {pmid39683451,
year = {2024},
author = {Protasiewicz-Timofticiuc, DC and Bădescu, D and Moța, M and Ștefan, AG and Mitrea, A and Clenciu, D and Efrem, IC and Roșu, MM and Vladu, BE and Gheonea, TC and Moța, E and Vladu, IM},
title = {Back to Roots: Dysbiosis, Obesity, Metabolic Syndrome, Type 2 Diabetes Mellitus, and Obstructive Sleep Apnea-Is There an Objective Connection? A Narrative Review.},
journal = {Nutrients},
volume = {16},
number = {23},
pages = {},
pmid = {39683451},
issn = {2072-6643},
mesh = {Humans ; *Dysbiosis ; *Gastrointestinal Microbiome/physiology ; *Metabolic Syndrome/etiology ; *Sleep Apnea, Obstructive ; *Diabetes Mellitus, Type 2/microbiology ; *Obesity ; *Circadian Rhythm/physiology ; Sleep/physiology ; },
abstract = {In recent decades, it has become clear that the gut is more than just a digestive organ; it also functions as an immune organ with regulatory capabilities and acts as a "second brain" that influences brain function due to the presence and regulatory roles of the gut microbiota (GM). The GM is a crucial component of its host and significantly impacts human health. Dysbiosis, or microbial imbalance, has been closely linked to various diseases, including gastrointestinal, neurological, psychiatric, and metabolic disorders. The aim of this narrative review is to highlight the roles of the GM in maintaining metabolic health. Sleep is a vital biological necessity, with living organisms having evolved an internal sleep-wake rhythm that aligns with a roughly 24 h light/dark cycle, and this is known as the circadian rhythm. This cycle is essential for tissue repair, restoration, and overall optimal body functioning. Sleep irregularities have become more prevalent in modern society, with fast-paced lifestyles often disrupting normal sleep patterns. Urban living factors, such as fast food consumption, shift work, exposure to artificial light and nighttime noise, medications, and social activities, can adversely affect circadian rhythms, with dysbiosis being one of the many factors incriminated in the etiology of sleep disorders.},
}

Humans
*Dysbiosis
*Gastrointestinal Microbiome/physiology
*Metabolic Syndrome/etiology
*Sleep Apnea, Obstructive
*Diabetes Mellitus, Type 2/microbiology
*Obesity
*Circadian Rhythm/physiology
Sleep/physiology

@article {pmid39683427,
year = {2024},
author = {Pokushalov, E and Ponomarenko, A and Shrainer, E and Kudlay, D and Miller, R},
title = {Biomarker-Guided Dietary Supplementation: A Narrative Review of Precision in Personalized Nutrition.},
journal = {Nutrients},
volume = {16},
number = {23},
pages = {},
pmid = {39683427},
issn = {2072-6643},
mesh = {Humans ; *Dietary Supplements ; *Precision Medicine/methods ; *Biomarkers/blood ; Nutritional Status ; Artificial Intelligence ; Metabolomics/methods ; },
abstract = {Background: Dietary supplements (DS) are widely used to address nutritional deficiencies and promote health, yet their indiscriminate use often leads to reduced efficacy, adverse effects, and safety concerns. Biomarker-driven approaches have emerged as a promising strategy to optimize DS prescriptions, ensuring precision and reducing risks associated with generic recommendations. Methods: This narrative review synthesizes findings from key studies on biomarker-guided dietary supplementation and the integration of artificial intelligence (AI) in biomarker analysis. Key biomarker categories-genomic, proteomic, metabolomic, lipidomic, microbiome, and immunological-were reviewed, alongside AI applications for interpreting these biomarkers and tailoring supplement prescriptions. Results: Biomarkers enable the identification of deficiencies, metabolic imbalances, and disease predispositions, supporting targeted and safe DS use. For example, genomic markers like MTHFR polymorphisms inform folate supplementation needs, while metabolomic markers such as glucose and insulin levels guide interventions in metabolic disorders. AI-driven tools streamline biomarker interpretation, optimize supplement selection, and enhance therapeutic outcomes by accounting for complex biomarker interactions and individual needs. Limitations: Despite these advancements, AI tools face significant challenges, including reliance on incomplete training datasets and a limited number of clinically validated algorithms. Additionally, most current research focuses on clinical populations, limiting generalizability to healthier populations. Long-term studies remain scarce, raising questions about the sustained efficacy and safety of biomarker-guided supplementation. Regulatory ambiguity further complicates the classification of supplements, especially when combinations exhibit pharmaceutical-like effects. Conclusions: Biomarker-guided DS prescription, augmented by AI, represents a cornerstone of personalized nutrition. While offering significant potential for precision and efficacy, advancing these strategies requires addressing challenges such as incomplete AI data, regulatory uncertainties, and the lack of long-term studies. By overcoming these obstacles, clinicians can better meet individual health needs, prevent diseases, and integrate precision nutrition into routine care.},
}

Humans
*Dietary Supplements
*Precision Medicine/methods
*Biomarkers/blood
Nutritional Status
Artificial Intelligence
Metabolomics/methods

@article {pmid39683390,
year = {2024},
author = {Patloka, O and Komprda, T and Franke, G},
title = {Review of the Relationships Between Human Gut Microbiome, Diet, and Obesity.},
journal = {Nutrients},
volume = {16},
number = {23},
pages = {},
pmid = {39683390},
issn = {2072-6643},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Obesity/microbiology ; *Dietary Fiber/administration & dosage ; *Diet ; Fatty Acids, Volatile/metabolism ; Bile Acids and Salts/metabolism ; Diet, High-Fat/adverse effects ; },
abstract = {Obesity is a complex disease that increases the risk of other pathologies. Its prevention and long-term weight loss maintenance are problematic. Gut microbiome is considered a potential obesity modulator. The objective of the present study was to summarize recent findings regarding the relationships between obesity, gut microbiota, and diet (vegetable/animal proteins, high-fat diets, restriction of carbohydrates), with an emphasis on dietary fiber and resistant starch. The composition of the human gut microbiome and the methods of its quantification are described. Products of the gut microbiome metabolism, such as short-chain fatty acids and secondary bile acids, and their effects on the gut microbiota, intestinal barrier function and immune homeostasis are discussed in the context of obesity. The importance of dietary fiber and resistant starch is emphasized as far as effects of the host diet on the composition and function of the gut microbiome are concerned. The complex relationships between human gut microbiome and obesity are finally summarized.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Obesity/microbiology
*Dietary Fiber/administration & dosage
*Diet
Fatty Acids, Volatile/metabolism
Bile Acids and Salts/metabolism
Diet, High-Fat/adverse effects

@article {pmid39683382,
year = {2024},
author = {Abulughod, N and Valakas, S and El-Assaad, F},
title = {Dietary and Nutritional Interventions for the Management of Endometriosis.},
journal = {Nutrients},
volume = {16},
number = {23},
pages = {},
pmid = {39683382},
issn = {2072-6643},
mesh = {Humans ; *Endometriosis/diet therapy/therapy ; Female ; Diet ; Estrogens ; Quality of Life ; Inflammation/diet therapy ; Pelvic Pain/therapy/diet therapy/etiology ; Nutrition Therapy/methods ; Nutritional Status ; },
abstract = {Endometriosis is a chronic, complex, systemic inflammatory condition that impacts approximately 190 million girls and women worldwide, significantly impacting their quality of life. The effective management of endometriosis requires a multi-disciplinary and holistic approach, one that includes surgical and medical management, such as a laparoscopy and a chronic medical management plan, as well as dietary, nutritional, and lifestyle adjunct interventions, such as pelvic pain physiotherapy and acupuncture. There is growing evidence to support the role of dietary and nutritional interventions in the adjunct management of endometriosis-related pain and gastrointestinal symptoms. However, the implementation of these interventions is often not regulated, as patients with endometriosis often adopt self-management strategies. Diet and nutrition can modulate key players integral to the pathophysiology of endometriosis, such as, but not limited to, inflammation, estrogen, and the microbiome. However, it is unclear as to whether diet plays a role in the prevention or the onset of endometriosis. In this review, we discuss three key players in the pathogenesis of endometriosis-inflammation, estrogen, and the microbiome-and we summarize how diet and nutrition can influence their mechanisms, and consequently, the progression and manifestation of endometriosis. There is a major need for evidence-based, non-invasive adjunct management of this debilitating disease, and diet and nutritional interventions may be suitable.},
}

Humans
*Endometriosis/diet therapy/therapy
Female
Diet
Estrogens
Quality of Life
Inflammation/diet therapy
Pelvic Pain/therapy/diet therapy/etiology
Nutrition Therapy/methods
Nutritional Status

@article {pmid39683174,
year = {2024},
author = {Pishchik, VN and Chizhevskaya, EP and Chebotar, VK and Mirskaya, GV and Khomyakov, YV and Vertebny, VE and Kononchuk, PY and Kudryavtcev, DV and Bortsova, OA and Lapenko, NG and Tikhonovich, IA},
title = {PGPB Isolated from Drought-Tolerant Plants Help Wheat Plants to Overcome Osmotic Stress.},
journal = {Plants (Basel, Switzerland)},
volume = {13},
number = {23},
pages = {},
pmid = {39683174},
issn = {2223-7747},
support = {No 23-66-10013//Russian Science Foundation/ ; },
abstract = {The aim of this research was to study the effect of plant-growth-promoting bacteria (PGPB) isolated from the drought-tolerant plants camel thorn (Alhagi pseudoalhagi (M.Bieb.) Fisch) and white pigweed (Chenopodium album L.) on wheat (Triticum aestivum L.) plants cv. Lenigradskaya 6, growing under hydroponic conditions and osmotic stress (generated by 12% polyethylene glycol-6000 (PEG)). Based on the assumption that plants create a unique microbiome that helps them overcome various stresses, we hypothesized that bacteria isolated from drought-tolerant plants may assist cultivated wheat plants in coping with drought stress. PGPB were isolated from seeds and leaves of plants and identified as Bacillus spp. (strains Cap 07D, Cap 09D, and App 11D); Paenibacillus sp. (Cap 286); and Arthrobacter sp. (Cap 03D). All bacteria produced different phytohormones such as indole acetic acid (IAA), abscisic acid (ABA), and gibberellic acid (GAS3) and were capable of stimulating wheat growth under normal and osmotic stress conditions. All PGPB reduced the malondialdehyde (MDA) content, increased the total chlorophyll content by increasing chlorophyll a, and modulated wheat hormone homeostasis and CAT and POX activities under osmotic conditions. Selected strains can be promising candidates for the mitigating of the drought stress of wheat plants.},
}

@article {pmid39683103,
year = {2024},
author = {Jeong, DH and Yun, YB and Son, HJ and Um, Y and Song, JH and Kim, J},
title = {Correlation Analysis of Soil Microbial Communities and Physicochemical Properties with Growth Characteristics of Sageretia thea Across Different Habitats.},
journal = {Plants (Basel, Switzerland)},
volume = {13},
number = {23},
pages = {},
pmid = {39683103},
issn = {2223-7747},
support = {FP0802-2023-01-2023//National Institute of Forest Science/ ; },
abstract = {This study aimed to investigate the growth characteristics of Sageretia thea and analyze the correlations between soil physicochemical properties and microbial communities in its native habitats. Soil physicochemical properties were characterized by organic matter (0.37-36.43%), available phosphate (57.96-315.90 mg/kg), potassium (0.11-1.17 cmol[+]kg[-1]), calcium (1.23-25.97 cmol[+]kg[-1]), magnesium (0.43-15.01 cmol[+]kg[-1]), sodium (0.04-6.16 cmol[+]kg[-1]), and pH (4.68-7.05), indicating slightly acidic to neutral conditions. S. thea exhibited variable growth characteristics across habitats; leaf length and width were largest in Jangnam-ri and Hacka-ri, respectively, whereas Docheong-ri promoted higher fruit growth. The soil microbial community composition was dominated by Proteobacteria, Actinobacteria, and Acidobacteria at the phylum level (76.09%) and by Alphaproteobacteria, Actinobacteria_c, and Vicinamibacter_c at the class level (40%). Soil physicochemical properties were significantly correlated with Actinobacteria, Acidobacteria, and Chloroflexi at the phylum level, and all microbial groups except Spartobacteria at the class level. Furthermore, growth characteristics were significantly correlated with all microbial communities except Acidobacteria and Firmicutes at the phylum level, and Acidobacteria, Thermoleophilia, and Rubrobacteria at the class level. These findings provide a foundation for developing efficient cultivation techniques for S. thea based on its soil microbiome and habitat conditions.},
}

@article {pmid39683003,
year = {2024},
author = {Zhang, R and Liu, S and Liu, T and Chang, R and Liu, G and Li, M and Mao, J},
title = {The Microbial Diversity and Flavor Metabolism Regulation of Xiangzao During Different Natural Fermentation Time Periods.},
journal = {Foods (Basel, Switzerland)},
volume = {13},
number = {23},
pages = {},
pmid = {39683003},
issn = {2304-8158},
support = {2022YFD2101204//the National Key R&D Program of the 14th Five-Year Plan/ ; 22138004//the National Natural Science Foundation of China/ ; 2022B43001, 2023B43001//Shaoxing Science and Technology Plan Project/ ; JUSRP202401019//the Fundamental Research Funds for the Central Universities/ ; },
abstract = {Xiangzao brine is a special flavored food produced by the natural fermentation of Huangjiu lees. To clarify fermentation time on its quality, this study integrated flavoromics analysis, macro-genomics, and polypeptide omics to analyze the volatile flavor components, microbial species, and flavor peptide distributions of four groups of samples (XZ-1Y, XZ-2Y, XZ-3Y, and XZ-4Y) fermented for 1-4 years. The results showed that the samples fermented for 1 year had the highest contents of umami amino acids and umami peptides, and the samples fermented for 4 years had the highest contents of organic acids and fruity components. In addition, 42 volatile flavor components and 532 peptides were identified, including 393 umami taste peptides and only 37 bitter taste peptides. Correlation analysis showed that ethyl lactate and furfural were positively correlated with the abundance of Nocardioides and Stenotrophomonas, respectively. The abundance of Pseudomonas was positively correlated with four previously unreported umami peptides (FATPR, RELER, FNLERP, and RSSFLGQ) screened by molecular docking. This study provides a reference for the flavor metabolism regulation of Xiangzao brine.},
}

@article {pmid39682952,
year = {2024},
author = {Ma, H and Mueed, A and Ma, Y and Ibrahim, M and Su, L and Wang, Q},
title = {Fecal Microbiota Transplantation Activity of Floccularia luteovirens Polysaccharides and Their Protective Effect on Cyclophosphamide-Induced Immunosuppression and Intestinal Injury in Mice.},
journal = {Foods (Basel, Switzerland)},
volume = {13},
number = {23},
pages = {},
pmid = {39682952},
issn = {2304-8158},
support = {2021YFD1600401//National Key Research and Development Program of China/ ; },
abstract = {Floccularia luteovirens polysaccharides (FLP1s) have potential biological activities. Our previous study showed that FLP1s positively regulated gut immunity and microbiota. However, it is still unclear whether FLP1s mediate gut microbiota in immunosuppressed mice. This research aims to explore the relationship between FLP1-mediated gut microbes and intestinal immunity in immunosuppressed mice through fecal microbiota transplantation (FMT). The results demonstrated that FLP1s exhibited prebiotic and anti-immunosuppressive effects on CTX-induced immunosuppressed mice. FFLP1 treatment (microbiota transplantation from the fecal sample) remarkably elevated the production of sIgA and secretion of the anti-inflammatory cytokines IL-4, TNF-α, and IFN-γ in the intestine of CTX-treated mice, inducing activation of the MAPK pathway. Moreover, FFLP1s mitigated oxidative stress by activating the Nrf2/Keap1 signaling pathway and strengthened the intestinal barrier function by upregulating the expression level of tight junction proteins (occludin, claudin-1, MUC-2, and ZO-1). Furthermore, FFPL1s restored gut dysbiosis in CTX-treated immunosuppressed mice by increasing the abundance of Alloprevotella, Lachnospiraceae, and Bacteroides. They also modified the composition of fecal metabolites, leading to enhanced regulation of lipolysis in adipocytes, the cGMP-PKG pathway, the Rap1 signaling pathway, and ovarian steroidogenesis, as indicated by KEGG pathway analysis. These findings indicate that FLP1s could modulate the response of the intestinal immune system through regulation of the gut microbiota, thus promoting immune activation in CTX-treated immunosuppressed mice. FLP1s can serve as a natural protective agent against CTX-induced immune injury.},
}

@article {pmid39682785,
year = {2024},
author = {Anumudu, CK and Miri, T and Onyeaka, H},
title = {Multifunctional Applications of Lactic Acid Bacteria: Enhancing Safety, Quality, and Nutritional Value in Foods and Fermented Beverages.},
journal = {Foods (Basel, Switzerland)},
volume = {13},
number = {23},
pages = {},
pmid = {39682785},
issn = {2304-8158},
abstract = {Lactic Acid Bacteria (LAB) have garnered significant attention in the food and beverage industry for their significant roles in enhancing safety, quality, and nutritional value. As starter cultures, probiotics, and bacteriocin producers, LAB contributes to the production of high-quality foods and beverages that meet the growing consumer demand for minimally processed functional and health-promoting food products. Industrial food processing, especially in the fresh produce and beverage sector, is shifting to the use of more natural bioproducts in food production, prioritizing not only preservation but also the enhancement of functional characteristics in the final product. Starter cultures, essential to this approach, are carefully selected for their robust adaptation to the food environment. These cultures, often combined with probiotics, contribute beyond their basic fermentation roles by improving the safety, nutritional value, and health-promoting properties of foods. Thus, their selection is critical in preserving the integrity, quality, and nutrition of foods, especially in fresh produce and fruits and vegetable beverages, which have a dynamic microbiome. In addition to reducing the risk of foodborne illnesses and spoilage through the metabolites, including bacteriocins they produce, the use of LAB in these products can contribute essential amino acids, lactic acids, and other bioproducts that directly impact food quality. As a result, LAB can significantly alter the organoleptic and nutritional quality of foods while extending their shelf life. This review is aimed at highlighting the diverse applications of LAB in enhancing safety, quality, and nutritional value across a range of food products and fermented beverages, with a specific focus on essential metabolites in fruit and vegetable beverages and their critical contributions as starter cultures, probiotics, and bacteriocin producers.},
}

@article {pmid39682776,
year = {2024},
author = {Kim, S and Rahim, MA and Tajdozian, H and Barman, I and Park, HA and Yoon, Y and Jo, S and Lee, S and Shuvo, MSH and Bae, SH and Lee, H and Ju, S and Park, CE and Kim, HK and Han, JH and Kim, JW and Yoon, SG and Kim, JH and Choi, YG and Lee, S and Seo, H and Song, HY},
title = {Clinical Potential of Novel Microbial Therapeutic LP51 Based on Xerosis-Microbiome Index.},
journal = {Cells},
volume = {13},
number = {23},
pages = {},
pmid = {39682776},
issn = {2073-4409},
support = {RS-2023-00219563//National Research Foundation of Korea/ ; P248400003//Korea Institute for Advancement of Technology/ ; },
mesh = {Humans ; Female ; *Microbiota/drug effects ; Double-Blind Method ; Adult ; Skin/microbiology/pathology ; Middle Aged ; },
abstract = {Xerosis, characterized by dry, rough skin, causes discomfort and aesthetic concerns, necessitating effective treatment. Traditional treatments often show limited efficacy, prompting the need for innovative therapies. This study highlights the efficacy of microbiome therapeutic LP51, derived from a healthy vaginal microbiome, in improving xerosis. A double-blind clinical trial involving 43 subjects with dry inner arm skin compared the effects of a 2.9% LP51 extract formulation to a placebo over 4 weeks. The LP51 group exhibited a significant increase in stratum corneum hydration (10.0 A.U.) compared to the placebo group (4.8 A.U.) and a 21.4% decrease in transepidermal water loss (TEWL), whereas the placebo group showed no significant change. LP51 also demonstrated benefits in enhancing skin hydration, improving the skin barrier, and exhibited anti-atopic, anti-inflammatory, and antioxidant properties. Safety was confirmed through in vitro cytotoxicity tests. These effects are attributed to the microbiome-safe component in LP51 and its role in improving xerosis, reflected by an increase in the xerosis-microbiome index, defined by the Firmicutes/Actinobacteria ratio. These findings position microbiome therapeutic LP51 as a promising novel treatment for xerosis.},
}

Humans
Female
*Microbiota/drug effects
Double-Blind Method
Adult
Skin/microbiology/pathology
Middle Aged

@article {pmid39682754,
year = {2024},
author = {Robles, V and Balaguer, F and Maicas, M and Martínez-Vázquez, JM and Martorell, P and Tortajada, M and Ramón, D and Valcarce, DG},
title = {The Effect of the Combination of Two Postbiotics on Anxiety-like Behavior in Animal Models.},
journal = {Cells},
volume = {13},
number = {23},
pages = {},
pmid = {39682754},
issn = {2073-4409},
mesh = {Animals ; *Anxiety/therapy ; *Zebrafish ; *Caenorhabditis elegans/drug effects ; *Behavior, Animal/drug effects ; Disease Models, Animal ; Lacticaseibacillus rhamnosus ; Probiotics/pharmacology/therapeutic use ; Bifidobacterium longum ; Dietary Supplements ; },
abstract = {With increasing evidence showing the connections between the microbiome, neurophysiology, and behavior, our research endeavors to investigate whether the consumption of a combination of two postbiotics with antioxidant effects can affect behavior regulation in model species. Here, we worked with a combination (1:1 ratio) of heat-treated Bifidobacterium longum subsp. longum ES1 (CECT7347) and Lacticaseibacillus rhamnosus BPL15 (CECT8361) as a dietary supplement. To examine the potential benefit of using this formulation to alleviate anxiety-like behavior, we employed two model species, Caenorhabditis elegans and adult Danio rerio. In C. elegans, the postbiotic supplementation reduced the anxiety-related behavior analyzed by means of the octanol avoidance test. In zebrafish, the novel tank test indicated a different swimming pattern 2 and 4 months after the animals were fed with the postbiotic combination. While fish did not exhibit any variance in their locomotion parameters such as pace and speed, they showed a statistically significant preference to spend more time in the upper zone of the water tank, a behavior that is correlated with a lower anxiety-like behavior in these species. Our aim with this study is to present evidence that can be used to develop whole-cell postbiotic-based novel and innovative dietary supplements for anxiety-related conditions.},
}

Animals
*Anxiety/therapy
*Zebrafish
*Caenorhabditis elegans/drug effects
*Behavior, Animal/drug effects
Disease Models, Animal
Lacticaseibacillus rhamnosus
Probiotics/pharmacology/therapeutic use
Bifidobacterium longum
Dietary Supplements

@article {pmid39682751,
year = {2024},
author = {Seo, H and Kim, S and Beck, S and Song, HY},
title = {Perspectives on Microbiome Therapeutics in Infectious Diseases: A Comprehensive Approach Beyond Immunology and Microbiology.},
journal = {Cells},
volume = {13},
number = {23},
pages = {},
pmid = {39682751},
issn = {2073-4409},
support = {RS-2023-00219563//Ministry of Science and ICT/ ; P248400003//Korea Institute for Advancement of Technology/ ; Soonchunhyang University Research Fund//Soonchunhyang University Research Fund/ ; },
mesh = {Humans ; *Microbiota/immunology ; *Probiotics/therapeutic use ; *COVID-19/immunology/virology/therapy ; Communicable Diseases/microbiology/therapy/immunology ; SARS-CoV-2/immunology ; },
abstract = {Although global life expectancy has increased over the past 20 years due to advancements in managing infectious diseases, one-fifth of people still die from infections. In response to this ongoing threat, significant efforts are underway to develop vaccines and antimicrobial agents. However, pathogens evolve resistance mechanisms, complicating their control. The COVID-19 pandemic has underscored the limitations of focusing solely on the pathogen-killing strategies of immunology and microbiology to address complex, multisystemic infectious diseases. This highlights the urgent need for practical advancements, such as microbiome therapeutics, that address these limitations while complementing traditional approaches. Our review emphasizes key outcomes in the field, including evidence of probiotics reducing disease severity and insights into host-microbiome crosstalk that have informed novel therapeutic strategies. These findings underscore the potential of microbiome-based interventions to promote physiological function alongside existing strategies aimed at enhancing host immune responses and pathogen destruction. This narrative review explores microbiome therapeutics as next-generation treatments for infectious diseases, focusing on the application of probiotics and their role in host-microbiome interactions. While offering a novel perspective grounded in a cooperative defense system, this review also addresses the practical challenges and limitations in translating these advancements into clinical settings.},
}

Humans
*Microbiota/immunology
*Probiotics/therapeutic use
*COVID-19/immunology/virology/therapy
Communicable Diseases/microbiology/therapy/immunology
SARS-CoV-2/immunology

@article {pmid39682735,
year = {2024},
author = {Hemmati, MA and Monemi, M and Asli, S and Mohammadi, S and Foroozanmehr, B and Haghmorad, D and Oksenych, V and Eslami, M},
title = {Using New Technologies to Analyze Gut Microbiota and Predict Cancer Risk.},
journal = {Cells},
volume = {13},
number = {23},
pages = {},
pmid = {39682735},
issn = {2073-4409},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Neoplasms/microbiology ; Machine Learning ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; },
abstract = {The gut microbiota significantly impacts human health, influencing metabolism, immunological responses, and disease prevention. Dysbiosis, or microbial imbalance, is linked to various diseases, including cancer. It is crucial to preserve a healthy microbiome since pathogenic bacteria, such as Escherichia coli and Fusobacterium nucleatum, can cause inflammation and cancer. These pathways can lead to the formation of tumors. Recent advancements in high-throughput sequencing, metagenomics, and machine learning have revolutionized our understanding of the role of gut microbiota in cancer risk prediction. Early detection is made easier by machine learning algorithms that improve the categorization of cancer kinds based on microbiological data. Additionally, the investigation of the microbiome has been transformed by next-generation sequencing (NGS), which has made it possible to fully profile both cultivable and non-cultivable bacteria and to understand their roles in connection with cancer. Among the uses of NGS are the detection of microbial fingerprints connected to treatment results and the investigation of metabolic pathways implicated in the development of cancer. The combination of NGS with machine learning opens up new possibilities for creating customized medicine by enabling the development of diagnostic tools and treatments that are specific to each patient's microbiome profile, even in the face of obstacles like data complexity. Multi-omics studies reveal microbial interactions, biomarkers for cancer detection, and gut microbiota's impact on cancer progression, underscoring the need for further research on microbiome-based cancer prevention and therapy.},
}

Humans
*Gastrointestinal Microbiome
*Neoplasms/microbiology
Machine Learning
High-Throughput Nucleotide Sequencing/methods
Metagenomics/methods

@article {pmid39682542,
year = {2024},
author = {Morales, C and Ballestero, L and Del Río, P and Barbero-Herranz, R and Olavarrieta, L and Gómez-Artíguez, L and Galeano, J and Avendaño-Ortiz, J and Basterra, J and Del Campo, R},
title = {Should the Faecal Microbiota Composition Be Determined to Certify a Faecal Donor?.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {14},
number = {23},
pages = {},
pmid = {39682542},
issn = {2075-4418},
support = {XX//Mikrobiomik/ ; },
abstract = {BACKGROUND/OBJECTIVES: Faecal microbiota transplantation (FMT) is considered a safe and effective therapy for recurrent Clostridioides difficile infection. It is the only current clinical indication for this technique, although numerous clinical research studies and trials propose its potential usefulness for treating other pathologies. Donor selection is a very rigorous process, based on a personal lifestyle interview and the absence of known pathogens in faeces and serum, leading to only a few volunteers finally achieving the corresponding certification. However, despite the high amount of data generated from the ongoing research studies relating microbiota and health, there is not yet a consensus defining what is a "healthy" microbiota. To date, knowledge of the composition of the microbiota is not a requirement to be a faecal donor. The aim of this work was to evaluate whether the analysis of the composition of the microbiota by massive sequencing of 16S rDNA could be useful in the selection of the faecal donors.

METHODS: Samples from 10 certified donors from Mikrobiomik Healthcare Company were collected and sequenced using 16S rDNA in a MiSeq (Illumina) platform. Alpha (Chao1 and Shannon indices) and beta diversity (Bray-Curtis) were performed using the bioinformatic web server Microbiome Analyst. The differences in microbial composition at the genera and phyla levels among the donors were evaluated.

RESULTS: The microbial diversity metric by alpha diversity indexes showed that most donors exhibited a similar microbial diversity and richness, whereas beta diversity by 16S rDNA sequencing revealed significant inter-donor differences, with a more stable microbial composition over time in some donors. The phyla Bacillota and Bacteroidota were predominant in all donors, while the density of other phyla, such as Actinomycota and Pseudomonota, varied among individuals. Each donor exhibited a characteristic genera distribution pattern; however, it was possible to define a microbiome core consisting of the genera Agathobacter, Eubacterium, Bacteroides, Clostridia UCG-014 and Akkermansia. Conclusions: The results suggest that donor certification does not need to rely exclusively on their microbiota composition, as it is unique to each donor. While one donor showed greater microbial diversity and richness, clear criteria for microbial normality and health have yet to be established. Therefore, donor certification should focus more on clinical and lifestyle aspects.},
}

@article {pmid39682493,
year = {2024},
author = {Jia, M and Lei, J and Dong, Y and Guo, Y and Zhang, B},
title = {The Interactive Effects of Nutrient Density and Breed on Growth Performance and Gut Microbiota in Broilers.},
journal = {Animals : an open access journal from MDPI},
volume = {14},
number = {23},
pages = {},
pmid = {39682493},
issn = {2076-2615},
support = {2022YFE0111100//National Key R&D Program of China/ ; CARS-41-G11//China Agriculture Research System/ ; 2115 Talent Development Program//China Agricultural University/ ; },
abstract = {This study investigated whether variations in growth response to low nutrient density across breeds are linked to microbiota regulation. Arbor Acres (AA) and Beijing-You (BY) were fed high- (HN) and low-nutrient (LN) diets from day (d) 0 to d42. Body weight, feed intake, and intestinal measurements were recorded, and microbiota from the ileum and cecum were analyzed on d7, d21, and d42. Results showed that AA broilers had greater growth performance with a lower feed conversion ratio (FCR) and greater average daily gain (ADG) than BY chickens. The LN diet negatively affected AA broiler growth due to impaired intestinal development, while BY chickens compensated by increasing feed intake. Microbiota composition was primarily affected by breed than by nutrient density, with AA broilers having more beneficial bacteria and BY chickens having more short-chain fatty acid (SCFA)-producing bacteria. The LN diets reduced anti-inflammatory bacteria such as Shuttleworthia and Eisenbergiella in the cecum on d7. By d21, LN diets decreased Lactobacillus and increased proinflammatory Marvinbryantia, potentially impairing growth. However, LN diets enriched SCFA-producing bacteria like Ruminococcaceae_UCG.013, Eisenbergiella, and Tyzzerella in BY chickens and Faecalitalea in AA broilers by d21, which may benefit gut health. By d42, LN diets reduced genera linked to intestinal permeability and fat deposition, including Ruminococcus_torques_group, Romboutsia, Erysipelatoclostridium, and Oscillibacter. Additionally, LN diets enriched Christensenellaceae_R-7_group in AA broilers, associated with intestinal barrier integrity, and increased anti-inflammatory bacteria Alistipes and Barnesiella in AA broilers and BY chickens, respectively, by d42. Overall, AA broilers were more susceptible to reduced nutrient density due to impaired intestinal development, while BY chickens adapted better by increasing feed intake. The microbiota responses to low nutrient density varied over time, potentially negatively affecting gut health in the early stage and growth in the middle stage but possibly improving lipid deposition and gut health in the middle and late stages.},
}

@article {pmid39682463,
year = {2024},
author = {Yan, S and Zhang, Y and Huang, J and Liu, Y and Li, S},
title = {Comparative Study of Gut Microbiome in Urban and Rural Eurasian Tree Sparrows.},
journal = {Animals : an open access journal from MDPI},
volume = {14},
number = {23},
pages = {},
pmid = {39682463},
issn = {2076-2615},
support = {32170481//National Natural Sciences Foundation of China/ ; },
abstract = {Gut microbiota play a significant role in various physiological functions, including digestion, nutritional metabolism, and host immune function. The composition of these gut microbes is largely influenced by habitats. This study examines the gut microbiota of the Eurasian tree sparrow (Passer montanus) inhabiting rural and urban environments to understand the effects of habitat variation on microbial composition. We captured 36 rural and 29 urban adult tree sparrows and observed minor differences in body mass but substantial differences in foraging microhabitats between the two groups. Fecal samples from adult males with similar body mass were selected for a gut microbiome analysis to mitigate potential confounding effects, resulting in 20 successfully sequenced samples. The analysis disclosed disparities in gut microbiota diversity and composition between rural and urban sparrows. The urban group demonstrated slightly higher alpha diversity and distinct dominant phyla and genera compared to the rural group. Additionally, differences in the relative abundance of potentially pathogenic bacteria were observed between the groups. Several potentially pathogenic bacteria (e.g., TM7, Staphylococcus, Helicobacter, and Shigella) were more abundant in the urban group, suggesting that tree sparrows may act as transmission vectors and develop stronger immune systems. This could potentially facilitate pathogen dissemination while also contributing to the natural cycling of nutrients and maintaining ecosystem health in urban environments. The beta diversity analysis confirmed structural differences in microbial communities, implicating habitat variation as a contributing factor. Furthermore, the LEfSe analysis emphasized significant differences in gut bacteria abundance (across two phyla, three classes, six orders, seven families, and eight genera) between urban and rural sparrows, with predicted functional differences in metabolic pathways. Notably, lipid metabolism was enriched in urban sparrows, indicating enhanced lipid synthesis and metabolism in urban habitats. In conclusion, this study underscores the profound influence of habitat on the gut microbiota composition and functional potential in tree sparrows. Our findings highlight that urbanization alters the gut microbes and, consequently, the physiological functions of bird species.},
}