@article {pmid39707511,
year = {2024},
author = {Ma, X and Hu, X and Liu, K and Wang, W and Jia, W and Gao, H and Lu, M and Liu, J and Chen, Y and Ma, Y and Li, Y and Nie, Y},
title = {Spatiotemporal differences induced changes in the structure and function of the gut microbiota in an endangered ungulate.},
journal = {Animal microbiome},
volume = {6},
number = {1},
pages = {74},
pmid = {39707511},
issn = {2524-4671},
support = {32225033, 32071496, 32100399//National Natural Science Foundation of China/ ; 32225033, 32071496, 32100399//National Natural Science Foundation of China/ ; 32225033, 32071496, 32100399//National Natural Science Foundation of China/ ; 32225033, 32071496, 32100399//National Natural Science Foundation of China/ ; 32225033, 32071496, 32100399//National Natural Science Foundation of China/ ; 32225033, 32071496, 32100399//National Natural Science Foundation of China/ ; 32225033, 32071496, 32100399//National Natural Science Foundation of China/ ; 32225033, 32071496, 32100399//National Natural Science Foundation of China/ ; 32225033, 32071496, 32100399//National Natural Science Foundation of China/ ; 32225033, 32071496, 32100399//National Natural Science Foundation of China/ ; 32225033, 32071496, 32100399//National Natural Science Foundation of China/ ; 32225033, 32071496, 32100399//National Natural Science Foundation of China/ ; No. 2022YFF1301500//Ministry of Science and Technology of China/ ; No. 2022YFF1301500//Ministry of Science and Technology of China/ ; No. 2022YFF1301500//Ministry of Science and Technology of China/ ; No. 2022YFF1301500//Ministry of Science and Technology of China/ ; No. 2022YFF1301500//Ministry of Science and Technology of China/ ; No. 2022YFF1301500//Ministry of Science and Technology of China/ ; No. 2022YFF1301500//Ministry of Science and Technology of China/ ; No. 2022YFF1301500//Ministry of Science and Technology of China/ ; No. 2022YFF1301500//Ministry of Science and Technology of China/ ; No. 2022YFF1301500//Ministry of Science and Technology of China/ ; No. 2022YFF1301500//Ministry of Science and Technology of China/ ; No. 2022YFF1301500//Ministry of Science and Technology of China/ ; },
abstract = {The composition and function of animal gut microbiota are shaped by various factors, among which diet is one of the major factors. Diet is affected by seasonal shifts and geographical differences, which in turn impact the host's nutritional levels. To adapt to these environmental changes, the gut microbiome often produces matching responses. Understanding the relationships among the environment, diet, host and the gut microbiome is helpful for exploring the environmental adaptation of wildlife. Here, we chose wild sika deer (Cervus nippon), which is composed natural allopatric populations, to explore how the environment shapes the gut microbiome and affects the relationship between microbiota composition and function and the mutual adaptation of the seasonal living environment to seasonal dietary changes. To this purpose we used DNA metabarcoding, 16S RNA gene amplification sequencing, metagenomic shotgun sequencing and nutritional analyses to comprehensively examine the relationships among the forage plant, nutrient status and host gut microbiome. Our analyses showed spatiotemporal differences in diet between the Tiebu and Hunchun regions, which ultimately led to varying intakes of protein, cellulose, and soluble sugar. The microbiome composition and function showed unique characteristics in each group, and significant differences were detected at the gene level for the protein absorption and metabolism pathway, the carbohydrate metabolic absorption pathway, and cellulase enzyme function, which are related to nutrition. We also found differences in the pathogenic bacteria and resistance mechanisms genes of the gut microbiota in different groups. Our results showed that the gut microbiome of allopatric populations adapts to changes in food composition and nutrition in different seasons and areas to help the host cope with spatiotemporal changes in the living environment. At the same time, varying levels of human activity can have potential health impacts on wild animals.},
}

@article {pmid39707487,
year = {2024},
author = {Xia, Y and Peng, X and Mao, J and Luo, J and Li, H and Ma, D and Yang, Z},
title = {Dietary 5-hydroxytryptophan supplementation improves growth performance and intestinal health of weaned piglets.},
journal = {Porcine health management},
volume = {10},
number = {1},
pages = {60},
pmid = {39707487},
issn = {2055-5660},
support = {No. 2023YFD1301603//National Key Research and Development Plan of China/ ; 31902167//National Natural Science Foundation of China/ ; NCTIP-XD/B02//Strategic Priority Research Program of the National Center of Technology Innovation for Pigs/ ; cx2019093//Chongqing innovation funding projects for Returned Scholars/ ; },
abstract = {This study investigated the effects of dietary 5-hydroxytryptophan (5-HTP) supplementation on growth performance, apparent total tract digestibility (ATTD), blood profile, intestinal morphology, transcriptomics, and microbial composition in weaned piglets. A total of twenty-four 28-day-old weaned piglets (Landrace × Large Yorkshire, 8.28 ± 1.09 kg) were randomly divided into 3 dietary treatments with 8 replicates. The dietary treatments include basal diet (CON), CON diet containing 250 or 500 mg/kg 5-HTP. The results revealed that supplementation with 250 mg/kg 5-HTP significantly increased (P < 0.05) the average daily gain (ADG) and resulted in a lower (P < 0.05) feed conversion ratio (FCR), while also decreased (P < 0.05) the diarrhea rate compared to the CON group. The ATTD of crude protein (CP) was lower in the 500 mg/kg group (P < 0.05) compared with the 250 mg/kg group. Furthermore, supplementation with 5-HTP led to significantly increased (P < 0.05) plasma albumin (ALB) and total protein (TP). In addition, supplementation with 5-HTP, particularly in the 250 mg/kg group, significantly increased (P < 0.05) serum serotonin (5-HT), growth hormone (GH) and insulin-like growth factor 1 (IGF-1) levels, and improved the ratio of villus height to crypt depth in the jejunum and ileum. The transcriptomic analysis revealed that the majority of differentially expressed genes (DEGs) induced by 5-HTP were related to digestion and immunity in the ileum, and 5-HTP enhanced (P < 0.05) intestinal glucose transporter 2 (GLUT2), solute carrier family 1 member 1 (SLC1A1) and solute carrier family 7 member 7 (SLC7A7) mRNA expression in weaned piglets. Furthermore, supplementation with 250 mg/kg 5-HTP increased (P < 0.05) abundance of Firmicutes, Actinobacteriota, Lachnospiracea, Ruminococcaceae and Megasphaera and decreased (P < 0.05) abundance of Spirochaetes and Treponema. Collectively, the study demonstrated that 5-HTP supplementation, particularly at 250 mg/kg, positively impacted growth performance, gut health, and microbiome composition in weaned piglets. These findings suggest the potential of using 5-HTP as a dietary supplement to enhance the health and productivity of weaned piglets.},
}

@article {pmid39707483,
year = {2024},
author = {Byrne, A and Diener, C and Brown, BP and Maust, BS and Feng, C and Alinde, BL and Gibbons, SM and Koch, M and Gray, CM and Jaspan, HB and Nyangahu, DD},
title = {Neonates exposed to HIV but uninfected exhibit an altered gut microbiota and inflammation associated with impaired breast milk antibody function.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {261},
pmid = {39707483},
issn = {2049-2618},
mesh = {Humans ; *Milk, Human/immunology ; *Gastrointestinal Microbiome ; *HIV Infections/immunology/microbiology ; Female ; Infant, Newborn ; *Inflammation ; *Immunoglobulin A/blood ; Feces/microbiology/virology ; Pregnancy ; Bacteria/classification/isolation & purification ; Adult ; Male ; Virome ; C-Reactive Protein/analysis ; },
abstract = {BACKGROUND: Infants exposed to HIV but uninfected have altered immune profiles which include heightened systemic inflammation. The mechanism(s) underlying this phenomenon is unknown. Here, we investigated differences in neonatal gut bacterial and viral microbiome and associations with inflammatory biomarkers in plasma. Further, we tested whether HIV exposure impacts antibody-microbiota binding in neonatal gut and whether antibodies in breast milk impact the growth of commensal bacteria.

RESULTS: Neonates exposed to HIV but uninfected (nHEU) exhibited altered gut bacteriome and virome compared to unexposed neonates (nHU). In addition, HIV exposure differentially impacted IgA-microbiota binding in neonates. The relative abundance of Blautia spp. in the whole stool or IgA-bound microbiota was positively associated with plasma concentrations of C-reactive protein. Finally, IgA from the breast milk of mothers living with HIV displayed a significantly lower ability to inhibit the growth of Blautia coccoides which was associated with inflammation in nHEU.

CONCLUSION: nHEU exhibits profound alterations in gut bacterial microbiota with a mild impact on the enteric DNA virome. Elevated inflammation in nHEU could be due to a lower capacity of breast milk IgA from mothers living with HIV to limit growth the of gut bacteria associated with inflammation. Video Abstract.},
}

Humans
*Milk, Human/immunology
*Gastrointestinal Microbiome
*HIV Infections/immunology/microbiology
Female
Infant, Newborn
*Inflammation
*Immunoglobulin A/blood
Feces/microbiology/virology
Pregnancy
Bacteria/classification/isolation & purification
Adult
Male
Virome
C-Reactive Protein/analysis

@article {pmid39707481,
year = {2024},
author = {Kim, MK and Lee, Y and Park, J and Lee, JY and Kang, HY and Heo, YU and Kim, DH},
title = {Short-term dynamics of fecal microbiome and antibiotic resistance in juvenile rainbow trout (Oncorhynchus mykiss) following antibiotic treatment and withdrawal.},
journal = {Animal microbiome},
volume = {6},
number = {1},
pages = {72},
pmid = {39707481},
issn = {2524-4671},
support = {RS-2024-00351648//National Research Foundation of Korea/ ; RS-2024-00351648//National Research Foundation of Korea/ ; RS-2024-00351648//National Research Foundation of Korea/ ; RS-2024-00351648//National Research Foundation of Korea/ ; RS-2024-00351648//National Research Foundation of Korea/ ; RS-2024-00351648//National Research Foundation of Korea/ ; RS-2024-00351648//National Research Foundation of Korea/ ; },
abstract = {BACKGROUND: In aquaculture, the secretions of cultured organisms contribute to the development of aquatic antibiotic resistance. However, the antibiotic-induced changes in fish feces remain poorly understood. This study aimed to assess the short-term dynamics of fecal microbiome and antibiotic resistance in juvenile rainbow trout (Oncorhynchus mykiss) upon antibiotic treatment and withdrawal period.

METHODS: Fish were orally administered diets supplemented with oxytetracycline (OTC) or sulfadiazine/trimethoprim (SDZ/TMP) for 10 consecutive days, followed by a 25-day withdrawal period. Fecal samples were collected before antibiotic treatment (day 0), and at 1, 3, 7, and 10 days post antibiotic administration (dpa), as well as 1, 3, 7, 14, and 25 days post antibiotic cessation (dpc). The fecal microbiome community was profiled using both culture-dependent and -independent methods. The relative abundance of antibiotic resistance genes (ARGs) and the class 1 integron-integrase gene (intI1) in the feces were quantified using real-time PCR.

RESULTS: Antibiotic treatment disrupted the fecal microbial communities, and this alteration persisted even after antibiotic cessation. Moreover, OTC treatment increased the relative abundance of tet genes, while sul and dfr genes increased in the SDZ/TMP-treated group. Notably, Flavobacterium, Pseudomonas, and Streptococcus exhibited a significant correlation with the abundance of ARGs, suggesting their potential role as carriers for ARGs.

CONCLUSION: This study demonstrates the antibiotic-induced changes in the fecal microbiome and the increase of ARGs in rainbow trout feces. These findings provide novel insights into the dynamics of microbiome recovery post-antibiotic cessation and suggest that fish feces provide a non-invasive approach to predict changes in the fish gut microbiome and resistome.},
}

@article {pmid39707478,
year = {2024},
author = {He, Z and Hou, Y and Li, Y and Bei, Q and Li, X and Zhu, YG and Liesack, W and Rillig, MC and Peng, J},
title = {Increased methane production associated with community shifts towards Methanocella in paddy soils with the presence of nanoplastics.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {259},
pmid = {39707478},
issn = {2049-2618},
mesh = {*Methane/metabolism ; *Soil Microbiology ; *Soil/chemistry ; *Oryza/microbiology ; Microbiota ; Polyethylene ; Soil Pollutants ; Metagenomics ; Archaea/metabolism/genetics/classification ; Carbon/metabolism ; Plastics ; },
abstract = {BACKGROUND: Planetary plastic pollution poses a major threat to ecosystems and human health in the Anthropocene, yet its impact on biogeochemical cycling remains poorly understood. Waterlogged rice paddies are globally important sources of CH4. Given the widespread use of plastic mulching in soils, it is urgent to unravel whether low-density polyethylene (LDPE) will affect the methanogenic community in flooded paddy soils. Here, we employed a combination of process measurements, short-chain and long-chain fatty acid (SCFAs and LCFAs) profiling, Fourier-transform ion cyclotron resonance mass spectrometry, quantitative PCR, metagenomics, and mRNA profiling to investigate the impact of LDPE nanoplastics (NPs) on dissolved organic carbon (DOC) and CH4 production in both black and red paddy soils under anoxic incubation over a 160-day period.

RESULTS: Despite significant differences in microbiome composition between the two soil types, both exhibited similar results to NPs exposure. NPs induced a change in DOC content and CH4 production up to 1.8-fold and 10.1-fold, respectively. The proportion of labile dissolved organic matter decreased, while its recalcitrance increased. Genes associated with the degradation of complex carbohydrates and aromatic carbon were significantly enriched. The elevated CH4 production was significantly correlated to increases in both the PCR-quantified mcrA gene copy numbers and the metagenomic methanogen-to-bacteria abundance ratio. Notably, the latter was linked to an enrichment of the hydrogenotrophic methanogenesis pathway. Among 391 metagenome-assembled genomes (MAGs), the abundance of several Syntrophomonas and Methanocella MAGs increased concomitantly, suggesting that the NPs treatments stimulated the syntrophic oxidation of fatty acids. mRNA profiling further identified Methanosarcinaceae and Methanocellaceae to be the key players in the NPs-induced CH4 production.

CONCLUSIONS: The specific enrichment of Syntrophomonas and Methanocella indicates that LDPE NPs stimulate the syntrophic oxidation of LCFAs and SCFAs, with Methanocella acting as the hydrogenotrophic methanogen partner. Our findings enhance the understanding of how LDPE NPs affect the methanogenic community in waterlogged paddy soils. Given the importance of this ecosystem, our results are crucial for elucidating the mechanisms that govern carbon fluxes, which are highly relevant to global climate change.},
}

*Methane/metabolism
*Soil Microbiology
*Soil/chemistry
*Oryza/microbiology
Microbiota
Polyethylene
Soil Pollutants
Metagenomics
Archaea/metabolism/genetics/classification
Carbon/metabolism
Plastics

@article {pmid39707461,
year = {2024},
author = {Huang, SC and Liu, KL and Chen, P and Xu, BW and Ding, WL and Yue, TJ and Lu, YN and Li, SY and Li, JK and Jian, FC},
title = {New insights into the combined effects of aflatoxin B1 and Eimeria ovinoidalis on uterine function by disrupting the gut-blood-reproductive axis in sheep.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {269},
pmid = {39707461},
issn = {2049-2618},
mesh = {Animals ; *Aflatoxin B1/toxicity ; Sheep/parasitology ; Female ; *Gastrointestinal Microbiome/drug effects ; *Eimeria ; *Uterus/drug effects/metabolism ; *Coccidiosis/veterinary ; Sheep Diseases/parasitology/chemically induced ; Reproduction/drug effects ; Animal Feed ; },
abstract = {BACKGROUND: Sheep coccidiosis is an infectious parasitic disease that primarily causes diarrhea and growth retardation in young animals, significantly hindering the development of the sheep breeding industry. Cereal grains and animal feeds are frequently contaminated with mycotoxins worldwide, with aflatoxin B1 (AFB1) being the most common form. AFB1 poses a serious threat to gastrointestinal health upon ingestion and affects the function of parenteral organs, thus endangering livestock health. However, the impact of the combined effects of coccidia and AFB1 on the reproductive system of sheep has not been reported. Therefore, this study utilized sheep as an animal model to investigate the mechanisms underlying the reproductive toxicity induced by the individual or combined effects of AFB1 and Eimeria ovinoidalis (E. ovinoidalis) on the gut-blood-reproductive axis.

RESULTS: The results showed that AFB1 and coccidia adversely affect the reproductive system defense of sheep by altering uterine histopathology and hormone levels and triggering inflammation, which is associated with changes in the gut microbiota and metabolites. Moreover, co-exposure to AFB1 and coccidia disrupted the intestinal structure of the colon, resulting in reduced crypt depth. The impaired barrier function of the colon manifests primarily through the suppression of barrier protein expression, changes in the gut microbiome composition, and disruptions in gut metabolism. Importantly, the levels of blood inflammatory factors (IL-6, IL-10, TNF-α, and LPS) increased, suggesting that exposure to AFB1 and coccidia compromises the function of uterine organs in sheep by perturbing the gut-blood-reproductive axis. Blood metabolomics analysis further revealed that the differential metabolites predominantly concentrate in the amino acid pathway, particularly N-acetyl-L-phenylalanine. This metabolite is significantly correlated with IL-6, TNF-α, LPS, ERα, and ERβ, and it influences hormone levels while inducing uterine damage through the regulation of the downstream genes PI3K, AKT, and eNOS in the relaxin signaling pathway, as demonstrated by RNA sequencing.

CONCLUSIONS: These findings reveal for the first time that the combined effects of AFB1 and E. ovinoidalis on sheep uterine function operate at the level of the gut-blood-reproductive axis. This suggests that regulating gut microbiota and its metabolites may represent a potential therapeutic strategy for addressing mycotoxins and coccidia-co-induced female reproductive toxicity.},
}

Animals
*Aflatoxin B1/toxicity
Sheep/parasitology
Female
*Gastrointestinal Microbiome/drug effects
*Eimeria
*Uterus/drug effects/metabolism
*Coccidiosis/veterinary
Sheep Diseases/parasitology/chemically induced
Reproduction/drug effects
Animal Feed

@article {pmid39707139,
year = {2024},
author = {Dantzler, MD and Miller, TA and Dougherty, MW and Quevedo, A},
title = {The Microbiome Landscape of Adenomyosis: A Systematic Review.},
journal = {Reproductive sciences (Thousand Oaks, Calif.)},
volume = {},
number = {},
pages = {},
pmid = {39707139},
issn = {1933-7205},
abstract = {Alterations in the microbiome composition have been identified in common gynecologic pathologies such as endometriosis carving a new frontier in diagnosis and treatment. We aimed to examine the existing literature on perturbations in the reproductive tract microbiome of individuals with adenomyosis informing future therapeutic targets. To examine the association between the reproductive tract microbiome composition among individuals with adenomyosis when compared to controls that can lead to new research evaluating novel mechanisms of action and treatment modalities. A systematic literature search identified studies that compared differences in microbiome composition using culture-independent microbiome analysis between individuals with adenomyosis when compared to controls. Five observational cross-sectional studies characterizing the lower and upper reproductive tract in humans were included. The diagnostic criteria of adenomyosis included surgical and imaging-based criteria. All studies used a 16S rRNA sequencing method. All individuals were recruited from either China or Thailand. An association between adenomyosis and alterations in the microbiome composition included relative deficiencies in Lactobacillus and relative enrichment of anaerobic and gram-negative bacteria when compared to control participants. Comparative studies suggest that there are significant perturbations in the microbiota composition of individuals with adenomyosis when compared with controls. Limiting conclusions include relative small sample sizes, a homogeneous population, and scant clinical phenotypic data. This systematic review identified significant alterations in the bacterial composition of adenomyosis cases that can be leveraged to design mechanistic studies and future innovative approaches to diagnose and manage this pathology. Trial registration: PROSPERO (CRD42023494563). Registered December 28, 2023.},
}

@article {pmid39706890,
year = {2024},
author = {Apte, M},
title = {PDAC: advances in tumour microenvironment, microbiome and AI.},
journal = {Nature reviews. Gastroenterology & hepatology},
volume = {},
number = {},
pages = {},
pmid = {39706890},
issn = {1759-5053},
}

@article {pmid39706502,
year = {2024},
author = {Yadav, H and Badal, VD and Masternak, MM and Leeuwenburgh, C},
title = {Editorial for the special issue on "microbiomes in extremes of aging".},
journal = {Experimental gerontology},
volume = {},
number = {},
pages = {112663},
doi = {10.1016/j.exger.2024.112663},
pmid = {39706502},
issn = {1873-6815},
abstract = {This special issue of the Journal of Experimental Gerontology explores the dynamic interplay between microbiomes and aging-related conditions. The four selected studies highlight the role of microbiota in Alzheimer's disease, cancer immunotherapy, myocardial infarction and tryptophan metabolism, providing insights into how microbiomes influence health and disease in aging. These studies underscore the potential for microbiome-targeted interventions to mitigate aging-related disorders and improve the quality of life for older adults.},
}

@article {pmid39706312,
year = {2024},
author = {Sun, L and Liu, J and Cheng, Y and Wu, Y and He, T and Zhang, Y and Bai, X and Zhou, Z and Xu, X and Yao, Y and Tan, Y and Qiu, Q and Liu, C},
title = {Metabolomics with gut microbiota analysis of podophyllotoxin-mediated cardiotoxicity in mice based on the toxicological evidence chain (TEC) concept.},
journal = {Chemico-biological interactions},
volume = {406},
number = {},
pages = {111360},
doi = {10.1016/j.cbi.2024.111360},
pmid = {39706312},
issn = {1872-7786},
abstract = {Podophyllotoxin (PPT) is a lignan isolated from the traditional Chinese medicine Dysosma Versipellis, with significant anti-tumor activity. However, its cardiotoxicity restricts its clinical application. This study aims to investigate the cardiotoxicity of PPT in mice and its underlying mechanisms based on the concept of toxicological evidence chain (TEC). In this study, alterations in body weight, behavior, and the levels of myocardial enzymes and histopathology in mice were observed. Additionally, microbiome and metabolome were integrated to identify potential microorganisms, metabolic markers and major pathways with correlation analysis. The results indicated that PPT induced pathological changes in mice, including weight loss, diarrhea, alopecia and dehydration accompanied by increased levels of serum myocardial enzymes. The results of microbiome showed that PPT altered the gut microbiota composition, changing the abundance of microbial community. The results of metabolome studies indicated total of 55 differential metabolites were involved in glycine, serine, and threonine metabolism, alanine, glutamate, and aspartate metabolism, purine, pyrimidine metabolism, and steroid hormone metabolism. Integrating the results of microbiome and metabolome, it was concluded that PPT remodeled the gut microbiota composition, which in turn modified the gut microbiota metabolism, affecting amino acid metabolisms, nucleotide metabolism, and steroid hormone metabolism in the heart, potentially leading to energy metabolism disorders, apoptosis, and oxidative stress, ultimately inducing cardiotoxicity.},
}

@article {pmid39706288,
year = {2024},
author = {In, H and Perati, SR and Usyk, M and Yang, J and Sarkar, S and Rana, B and Wang, F and Oh, A and Adams, A and Diggs, LP and Sollecito, C and Burk, RD},
title = {Oral Microbiome Signatures as Potential Biomarkers for Gastric Cancer Risk Assessment.},
journal = {Journal of gastrointestinal surgery : official journal of the Society for Surgery of the Alimentary Tract},
volume = {},
number = {},
pages = {101933},
doi = {10.1016/j.gassur.2024.101933},
pmid = {39706288},
issn = {1873-4626},
abstract = {BACKGROUND: Gastric cancer (GC) is the fifth leading cause of cancer-related death worldwide. The oral microbiota was investigated for distinguishable characteristics between GC, premalignant gastric conditions (Pre-GC), and control participants.

METHODS: Mouthwash samples from GC, Pre-GC, and control participants at a tertiary care center were prospectively collected. Following DNA extraction and sequencing, analyses of oral microbiome biodiversity and composition were performed, and receiver operating characteristic curves were created to evaluate the discriminative power of oral microbiome signatures.

RESULTS: Oral samples from 98 participants included 30 (30.6%) GC, 30 (30.6%) Pre-GC and 38 (38.8%) controls. Of these, 61 (62.2%) were female, 31 (31.6%) were Hispanic, and 18 (18.3%) were smokers. GC compared to controls demonstrated notable differences in beta diversity (Jensen-Shannon Divergence and Bray-Curtis Dissimilarity, p<0.02). 32 bacterial genera were found to be differentially abundant when comparing GC and controls, and 23 bacterial genera demonstrated differential abundance when comparing Pre-GC and controls (W-statistic >2). Minimal compositional differences between GC and Pre-GC were found, with only three differentially abundant bacterial genera (W-statistic >2). Models were constructed from the most significant bacterial signatures (W-statistic >5). These models discriminated between GC and control oral samples with an AUC of 0.880 (95% CI 0.808, 0.952) and between Pre-GC and control oral samples with an AUC of 0.943 (95% CI 0.887, 0.999).

CONCLUSIONS: Oral rinses of GC and Pre-GC participants exhibited distinct but similar microbiome profiles, distinguishing them from controls. This compositional difference raises the possibility of utilizing these microbial signatures to predict GC risk.},
}

@article {pmid39706191,
year = {2024},
author = {Burrows, K and Ngai, L and Chiaranunt, P and Watt, J and Popple, S and Forde, B and Denha, S and Olyntho, VM and Tai, SL and Cao, EY and Tejeda-Garibay, S and Koenig, JFE and Mayer-Barber, KD and Streutker, CJ and Hoyer, KK and Osborne, LC and Liu, J and O'Mahony, L and Mortha, A},
title = {A gut commensal protozoan determines respiratory disease outcomes by shaping pulmonary immunity.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2024.11.020},
pmid = {39706191},
issn = {1097-4172},
abstract = {The underlying mechanisms used by the intestinal microbiota to shape disease outcomes of the host are poorly understood. Here, we show that the gut commensal protozoan, Tritrichomonas musculis (T.mu), remotely shapes the lung immune landscape to facilitate perivascular shielding of the airways by eosinophils. Lung-specific eosinophilia requires a tripartite immune network between gut-derived inflammatory group 2 innate lymphoid cells and lung-resident T cells and B cells. This network exacerbates the severity of allergic airway inflammation while hindering the systemic dissemination of pulmonary Mycobacterium tuberculosis. The identification of protozoan DNA sequences in the sputum of patients with severe allergic asthma further emphasizes the relevance of commensal protozoa in human disease. Collectively, these findings demonstrate that a commensal protozoan tunes pulmonary immunity via a gut-operated lung immune network, promoting both beneficial and detrimental disease outcomes in response to environmental airway allergens and pulmonary infections.},
}

@article {pmid39706166,
year = {2024},
author = {Chandra, F and Hsiao, EY},
title = {FAAHcilitating recovery in malnourished kids.},
journal = {Cell chemical biology},
volume = {31},
number = {12},
pages = {2018-2020},
doi = {10.1016/j.chembiol.2024.11.007},
pmid = {39706166},
issn = {2451-9448},
mesh = {Humans ; *Amidohydrolases/metabolism ; *Gastrointestinal Microbiome ; Child ; Malnutrition/metabolism ; Animals ; },
abstract = {The molecular underpinnings behind the diet-microbiome-host health relationship are largely undescribed. In a recent issue of Science, Cheng et al.[1] uncovered one piece of the puzzle by describing a novel fatty acid amide hydrolase (FAAH) derived from a Faecalibacterium prausnitzii strain that correlated with improved malnutrition recovery. This emphasized the microbiome's role in supporting recovery from malnutrition.},
}

Humans
*Amidohydrolases/metabolism
*Gastrointestinal Microbiome
Child
Malnutrition/metabolism
Animals

@article {pmid39706021,
year = {2024},
author = {Dinesh, R and Sreena, CP and Sheeja, TE and Srinivasan, V and Subila, KP and Sona, C and Kumar, IPV and Anusree, M and Alagupalamuthirsolai, M and Jayarajan, K and Sajith, V},
title = {Co-resistance is the dominant mechanism of co-selection and dissemination of antibiotic resistome in nano zinc oxide polluted soil.},
journal = {Journal of hazardous materials},
volume = {485},
number = {},
pages = {136885},
doi = {10.1016/j.jhazmat.2024.136885},
pmid = {39706021},
issn = {1873-3336},
abstract = {The broader soil bacterial community responses at ecotoxicologically relevant levels of nano ZnO (nZnO) focussing on co-selection of antibiotic resistance (AR) were investigated. nZnO imposed a stronger influence than the bulk counterpart (bZnO) on antibiotic resistance genes (ARGs) with multidrug resistance (MDR) systems being predominant (63 % of total ARGs). Proliferation of biomarker ARGs especially for last resort antibiotic like vancomycin was observed and Streptomyces hosted multiple ARGs. nZnO was the major driver of the resistome with efflux systems dominating the AR mechanism. Environmental risk associated with nZnO was mediated through metal driven co-selection of ARGs and their probable transfer to eukaryotic hosts through horizontal gene transfer (HGT) via mobile genetic elements (MGEs). Novel resistance genes tetA, mdtA, int and tnpA validated in our study can be used as biomarkers for rapid detection of nZnO toxicity in soils. qRT-PCR validation of resistome in the rhizosphere soil microbiome of turmeric indicated that Zn levels decreased by 16 % compared to bulk soil with 80 % bioaccumulation in rhizomes at 1000 mg Zn kg[-1] and subsequent down regulation of ARGs. Expression of key biosynthetic genes for curcumin in turmeric rhizomes showed an increase up to 500 mg Zn kg[-1] as nZnO. Validation of co-selection phenomenon in microcosm with 10 mg kg[-1] tetracycline without added Zn indicated 20 % upregulation of Zn resistance genes (ZRGs) like czcA, yiip and zntA.},
}

@article {pmid39706018,
year = {2024},
author = {Li, S and Gao, L and Song, H and Lin, J and Zhang, S and Schmitt-Kopplin, P and Zeng, J},
title = {A comprehensive atlas of multi-tissue metabolome and microbiome shifts: Exploring obesity and insulin resistance induced by perinatal bisphenol S exposure in high-fat diet-fed offspring.},
journal = {Journal of hazardous materials},
volume = {485},
number = {},
pages = {136895},
doi = {10.1016/j.jhazmat.2024.136895},
pmid = {39706018},
issn = {1873-3336},
abstract = {Bisphenol S (BPS) is widely used as a substitute for Bisphenol A (BPA). While perinatal BPS exposure is suspected to increase susceptibility to high-caloric diet-induced adipogenesis, how BPS affects offspring remains largely unknown. This study explored effects of prenatal BPS exposure on adiposity and insulin resistance in high-fat diet (HFD)-fed C57BL/6 offspring, revealing significant changes in body weight, glucose tolerance, insulin sensitivity, and histopathology. Employing nontargeted metabolomics and 16S rRNA sequencing, we constructed a comprehensive atlas of metabolome and microbiome shifts across heart, liver, pancreas, white adipose tissue (WAT), brown adipose tissue (BAT), and feces. Male offspring showed greater metabolic and microbial disturbances. Low-dose BPS exposure (0.05 mg/kg/d) induced changes across entire atlas comparable to high-dose (5 mg/kg/d). BAT and WAT were key target tissues with the most significant metabolic disturbances. BPS disrupted fatty acid β-oxidation in WAT by reducing carnitine carriers, causing WAT fat accumulation. A resistance mechanism to BPS exposure was indicated by both mobilization of BAT compensatory thermogenesis, characterized by increased carnitines and UCP1 expression, and an increase in beneficial commensal bacteria. Their competition and imbalance contributed to obesity and insulin resistance in offspring, highlighting the potential for early interventions targeting key metabolites and microbiota.},
}

@article {pmid39705961,
year = {2024},
author = {Shi, H and Ratering, S and Schneider, B and Schnell, S},
title = {Microbiome of honey bee corbicular pollen: Factors influencing its structure and potential for studying pathogen transmission.},
journal = {The Science of the total environment},
volume = {958},
number = {},
pages = {178107},
doi = {10.1016/j.scitotenv.2024.178107},
pmid = {39705961},
issn = {1879-1026},
abstract = {Honey bees are exposed to a diverse variety of microbes in the environment. Many studies have been carried out on the microbiome of bee gut, beebread, and flower pollen. However, little is known regarding the microbiome of fresh corbicular pollen, which can directly reflect microbes acquired from the environment. Moreover, although evidences have suggested that floral resources in general can affect the bee-acquired microbes, whether specific forage plants affect the composition of these microbes is still unclear. Here, we characterized both the microbiome and plant composition of corbicular pollen in collection seasons over two years from six hives using 16S rRNA gene and ITS2 metabarcoding. The results reveal temporal changes in the microbiome and plant composition in corbicular pollen, which was influenced by environmental factors and the choice of forage plants. We identified several co-occurrences between plant and bacterial genera, indicating specific plant-microbe interactions. Many Spiroplasma species with various insect hosts, including a honey bee pathogen Spiroplasma melliferum, were shown to positively correlate with Rubus, suggesting this plant genus as an important node for microbial transmission. Overall, we demonstrated the potential of corbicular pollen for studying the transmission of microbes, especially pathogens. This framework can be applied in future research to explore the complicated pollinator-microbe-plant network in different ecosystems.},
}

@article {pmid39705829,
year = {2024},
author = {Zhu, L and Zhou, W and Wang, J and Guo, J and Zhou, C},
title = {Root exudate-mediated assemblage of rhizo-microbiome enhances Fusarium wilt suppression in chrysanthemum.},
journal = {Microbiological research},
volume = {292},
number = {},
pages = {128031},
doi = {10.1016/j.micres.2024.128031},
pmid = {39705829},
issn = {1618-0623},
abstract = {Intercropping is emerging as a sustainable strategy to manage soil-borne diseases, yet the underlying mechanisms remain largely elusive. Here, we investigated how intercropping chrysanthemum (Chrysanthemum morifolium) with ginger (Zingiber officinale) suppressed Fusarium wilt and influenced the associated rhizo-microbiome. Chrysanthemum plants in intercropping systems exhibited a marked reduction in wilt severity and greater biomass compared to those grown in monoculture. In contrast, soil sterilization intensified wilt severity and abrogated the benefits of intercropping, highlighting the critical role of soil microbiota. 16S rRNA gene amplicon analysis revealed that intercropping significantly changed the composition and structure of rhizo-bacterial communities, particularly enriching Burkholderia species, which were closely associated with plant growth and disease resistance. Further investigation demonstrated that ginger root exudates, including sinapyl alcohol and 6-gingerol, greatly promoted the proliferation and colonization of Burkholderia sp. in chrysanthemum rhizosphere, conferring the enhanced disease suppression. Metabolomic profiling revealed that ginger root exudates stimulated the release of specific metabolites by chrysanthemum roots, which promoted the growth and biofilm formation of Burkholderia sp. Our findings uncovered the mechanism by which intercropping chrysanthemum with ginger plants modulated the rhizo-microbiome and thereby resulted in the enhanced disease suppression, offering insights into optimizing plant-microbe interactions for improving crop health and productivity.},
}

@article {pmid39705298,
year = {2024},
author = {Oliveira, V and Cleary, DFR and Polónia, ARM and Huang, YM and Rocha, U and Voogd, NJ and Gomes, NCM},
title = {Unravelling a Latent Pathobiome Across Coral Reef Biotopes.},
journal = {Environmental microbiology},
volume = {26},
number = {12},
pages = {e70008},
doi = {10.1111/1462-2920.70008},
pmid = {39705298},
issn = {1462-2920},
support = {VH-NG-1248 Micro "BigData"//Helmholtz Young Investigator Grant/ ; MNPH 104403//Marine National Parks Headquarter, Taiwan/ ; MOST 105-2621-B-346-002//Ministry of Science and Technology, Taiwan/ ; DOI: 10.54499/DL57/2016/CP1482/CT0109//Foundation for Science and Technology/ ; PTDC/BIA29/MIC/6473/2014 - POCI-01-0145-FEDER-01//Foundation for Science and Technology/ ; SFRH/BPD/117563/2016//Foundation for Science and Technology/ ; UIDP/50017/2020 + UIDB/50017/2020 + LA/P/0094/2020//Foundation for Science and Technology/ ; },
mesh = {*Coral Reefs ; Animals ; *Anthozoa/microbiology ; *Bacteria/genetics/classification ; *Microbiota ; Virulence Factors/genetics ; },
abstract = {Previous studies on disease in coral reef organisms have neglected the natural distribution of potential pathogens and the genetic factors that underlie disease incidence. This study explores the intricate associations between hosts, microbial communities, putative pathogens, antibiotic resistance genes (ARGs) and virulence factors (VFs) across diverse coral reef biotopes. We observed a substantial compositional overlap of putative bacterial pathogens, VFs and ARGs across biotopes, consistent with the 'everything is everywhere, but the environment selects' hypothesis. However, flatworms and soft corals deviated from this pattern, harbouring the least diverse microbial communities and the lowest diversity of putative pathogens and ARGs. Notably, our study revealed a significant congruence between the distribution of putative pathogens, ARGs and microbial assemblages across different biotopes, suggesting an association between pathogen and ARG occurrence. This study sheds light on the existence of this latent pathobiome, the disturbance of which may contribute to disease onset in coral reef organisms.},
}

*Coral Reefs
Animals
*Anthozoa/microbiology
*Bacteria/genetics/classification
*Microbiota
Virulence Factors/genetics

@article {pmid39705185,
year = {2024},
author = {Tamkin, E and Lorenz, BP and McCarty, A and Fulte, S and Eisenmesser, E and Horswill, AR and Clark, SE},
title = {Airway Corynebacterium interfere with Streptococcus pneumoniae and Staphylococcus aureus infection and express secreted factors selectively targeting each pathogen.},
journal = {Infection and immunity},
volume = {},
number = {},
pages = {e0044524},
doi = {10.1128/iai.00445-24},
pmid = {39705185},
issn = {1098-5522},
abstract = {The composition of the respiratory track microbiome is a notable predictor of infection-related morbidities and mortalities among both adults and children. Species of Corynebacterium, which are largely present as commensals in the upper airway and other body sites, are associated with lower colonization rates of opportunistic bacterial pathogens such as Streptococcus pneumoniae and Staphylococcus aureus. In this study, Corynebacterium-mediated protective effects against S. pneumoniae and S. aureus were directly compared using in vivo and in vitro models. Pre-exposure to Corynebacterium pseudodiphtheriticum reduced the ability of S. aureus and S. pneumoniae to infect the lungs of mice, indicating a broadly protective effect. Adherence of both pathogens to human respiratory tract epithelial cells was significantly impaired following pre-exposure to C. pseudodiphtheriticum or Corynebacterium accolens, and this effect was dependent on live Corynebacterium colonizing the epithelial cells. However, Corynebacterium-secreted factors had distinct effects on each pathogen. Corynebacterium lipase activity was bactericidal against S. pneumoniae, but not S. aureus. Instead, the hemolytic activity of pore-forming toxins produced by S. aureus was directly blocked by a novel Corynebacterium-secreted factor with protease activity. Taken together, these results suggest diverse mechanisms by which Corynebacterium contribute to the protective effect of the airway microbiome against opportunistic bacterial pathogens.},
}

@article {pmid39704932,
year = {2024},
author = {Zhou, W and Zhou, Y and Zhang, S and Li, B and Li, Z and Bai, Z and Sun, D and Huangfu, C and Wang, N and Xia, T and Huang, C and Guan, L and Yang, X and Hu, Y and Zhang, P and Shen, P and Wang, R and Ni, Z and Gao, Y},
title = {Gut microbiota's role in high-altitude cognitive impairment: the therapeutic potential of Clostridium sp. supplementation.},
journal = {Science China. Life sciences},
volume = {},
number = {},
pages = {},
pmid = {39704932},
issn = {1869-1889},
abstract = {Prolonged exposure to high-altitude environments may increase the risk of cognitive decline in young migrants. Recent studies suggest that hypobaric hypoxia-induced alterations in gut microbial composition could partly contribute to this risk. However, the absence of direct evidence from cohort studies and an unclear mechanism hinder intervention development based on this hypothesis. This study recruited 109 young male migrants living in Xizang to investigate the microbial mechanisms underlying cognitive impairment associated with high-altitude migration. Multi-omic analysis revealed distinct microbiome and metabolome features in migrants with cognitive decline, notably a reduced abundance of Clostridium species and disrupted fecal absorption of L-valine. Mechanistic studies showed that hypobaric hypoxia significantly damaged the intestinal barrier, leading to lipopolysaccharide (LPS) leakage and an influx of inflammatory factors into the peripheral blood, which activated microglia and caused neuronal injury in the hippocampus of mice. Additionally, compromised L-valine absorption due to intestinal barrier damage correlated with lower hippocampal glutamate levels and neurotrophic factors. Intervention with Clostridium sp. effectively restored the intestinal barrier and enhanced L-valine absorption, which mitigated hypobaric hypoxia-induced inflammation and hippocampal neural damage in mice. In conclusion, cognitive impairment among young migrants at high altitude may be attributed to hypobaric hypoxia-induced gut microbiota disruption and subsequent intestinal barrier dysfunction. This study may provide a promising approach for preventing and treating high-altitude-associated cognitive impairment.},
}

@article {pmid39704869,
year = {2024},
author = {Bircan, H and Demircan, T and Yulek, F and Yuksel, N},
title = {PCR-based characterization of nasal and ocular surface flora and functional analysis of bacterial metabolic pathways in congenital nasolacrimal duct obstruction.},
journal = {International ophthalmology},
volume = {45},
number = {1},
pages = {17},
pmid = {39704869},
issn = {1573-2630},
mesh = {Humans ; *Lacrimal Duct Obstruction/metabolism/diagnosis/microbiology/congenital ; Female ; Male ; *Nasolacrimal Duct/microbiology/metabolism ; Child, Preschool ; Infant ; Bacteria/isolation & purification/metabolism/genetics ; Eye Infections, Bacterial/microbiology/diagnosis/metabolism ; Metabolic Networks and Pathways ; Polymerase Chain Reaction/methods ; DNA, Bacterial/analysis ; Child ; },
abstract = {PURPOSE: To evaluate the role of Streptococcus pneumoniae, Staphylococcus aureus, Haemophilus influenzae, Serratia marcescens, and Moraxella catarrhalis in the nasal and ocular surface flora, along with their metabolic activities in children with unilateral congenital nasolacrimal duct obstruction (CNLDO).

METHODS: Swabs were taken from the bilateral inferior meatus and ocular surface of 26 children with unilateral CNLDO before probing. Nasal and ocular surface swabs from non-operated eyes of children who underwent unilateral blepharoptosis or strabismus surgery formed the control group. The quantitative polymerase chain reaction (qPCR) method was used to analyze the samples.

RESULTS: The detection of Streptococcus pneumoniae in the nasal flora, Staphylococcus aureus in the ocular surface flora, and Haemophilus influenzae and Serratia marcescens in both the nasal and ocular surface flora was higher on the obstructed sides of children with CNLDO compared to the controls (p < 0.05). Obstructed sides in children with CNLDO showed a significant difference for Moraxella catarrhalis in the ocular surface and Streptococcus pneumoniae, Staphylococcus aureus, Serratia marcescens, and Moraxella catarrhalis in the nasal flora compared to the patent sides (p < 0.05). Metabolite analysis revealed that betaine, L-carnitine, L-leucine, and L-alanine were negatively regulated in the presence of these bacteria.

CONCLUSIONS: Significant changes in bacterial composition in the nasal and ocular surface flora may be a cause or a result of CNLDO. More comprehensive microbiological studies that evaluate the entire microbiome would be helpful in understanding CNLDO.},
}

Humans
*Lacrimal Duct Obstruction/metabolism/diagnosis/microbiology/congenital
Female
Male
*Nasolacrimal Duct/microbiology/metabolism
Child, Preschool
Infant
Bacteria/isolation & purification/metabolism/genetics
Eye Infections, Bacterial/microbiology/diagnosis/metabolism
Metabolic Networks and Pathways
Polymerase Chain Reaction/methods
DNA, Bacterial/analysis
Child

@article {pmid39704837,
year = {2024},
author = {Zhu, W and Wang, X and He, D and Chen, B},
title = {Causal relationships between skin microbiome and pathological scars: a bidirectional mendelian randomization study.},
journal = {Archives of dermatological research},
volume = {317},
number = {1},
pages = {139},
pmid = {39704837},
issn = {1432-069X},
support = {2022QH1103//Startup Fund for Scientific Research of Fujian Medical University/ ; 2022J011068//Natural Science Foundation of Fujian Province/ ; },
mesh = {Humans ; *Mendelian Randomization Analysis ; *Microbiota/genetics ; *Skin/microbiology/pathology ; *Polymorphism, Single Nucleotide ; *Genome-Wide Association Study ; Keloid/microbiology/genetics ; Cicatrix/microbiology/pathology ; },
abstract = {Skin bacteria infection could be a potential risk factor on wound scar formation, yet the specifics of this relationship are not fully understood. This research investigates the causal relationships between specific skin microbiome and these diseases by using bidirectional Mendelian randomization (MR). This study employed a bidirectional MR analysis using genome-wide association study (GWAS) data to analyze the associations between skin microbiome and pathological scar. Single nucleotide polymorphisms (SNPs) served as instrumental variables (IVs) in MR methods, including inverse variance weighted (IVW), and MR Egger. The IVW analysis suggested a significant relationship between specific skin microbiome and pathlogical scars. Actinomycetales_Sebaceous, Proteobacteria_Sebaceous, ASV072[Paracoccus (unc.)]_Dry, ASV008[Diaphorobacter nitroreducens]_Dry, Pseudomonadales_moist, ASV001[Propionibacterium acnes]_Moist, Moraxellaceae_moist, Flavobacteriaceae_Dry were significantly associated with keloid. Chryseobacterium_Moist, ASV016[Enhydrobacter(unc.)]_Moist, ASV021[Micrococcus(unc.)]_Moist, ASV022[Streptococcus salivarius]_Moist, Rhodobacteraceae_Dry, Staphylococcus_Moist, Micrococcaceae_Moist, ASV007[Anaerococcus(unc.)]_Dry, Betaproteobacteria_Moist and ASV001[Propionibacterium acnes]_Moist were significantly associated with hypertrophic scarring. Reverse MR analysis indicates both keloid and hypertrophic scar regulated the composition of the skin microbiome. The study revealed a possible correlation between some specific skin microbiome and pathlogical scars. Understanding these inverse relationship could help improve clinical treatment and reducing pathological scar formation.},
}

Humans
*Mendelian Randomization Analysis
*Microbiota/genetics
*Skin/microbiology/pathology
*Polymorphism, Single Nucleotide
*Genome-Wide Association Study
Keloid/microbiology/genetics
Cicatrix/microbiology/pathology

@article {pmid39704536,
year = {2024},
author = {Pulido Barriga, MF and Randolph, JWJ and Glassman, SI},
title = {Not all is lost: resilience of microbiome samples to freezer failures and long-term storage.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0060324},
doi = {10.1128/msphere.00603-24},
pmid = {39704536},
issn = {2379-5042},
abstract = {UNLABELLED: Advances in technology have facilitated extensive sample collection to explore microbiomes across diverse systems, leading to a growing reliance on ultracold freezers for storing both samples and extracted DNA. However, freezer malfunctions can jeopardize data integrity. To evaluate the impact of an unexpected -80°C freezer failure and the recoverability of thawed soil samples, we extracted DNA and compared it to long-term DNA stored at -20°C and original 16S and ITS2 sequencing data collected before the malfunction. Using Illumina MiSeq, we assessed how the freezer failure and long-term storage influenced the resilience of bacterial or fungal richness or community composition and our ability to accurately determine experimental treatment effects. Our results reveal substantial resilience in fungal richness and both bacterial and fungal beta-diversity to soil sample thawing and extended frozen DNA storage. This resilience facilitated biological inferences that closely mirrored those observed in the original study. Notably, fungi exhibited greater resilience to short-term thawing compared to bacteria, which showed sensitivity to both thawing and long-term freezing. Moreover, taxonomic composition analysis revealed the persistence of dominant microbial taxa under thawing and prolonged freezing, suggesting that dominant microbes remain viable for tracking across temporal studies. In conclusion, our study highlights that beta-diversity is more robust than alpha-diversity and fungi are more resilient to freezer failure than bacteria. Furthermore, our findings underscore the effectiveness of soil storage at -80°C compared to storage of extracted DNA at -20°C, despite potential freezer failures, as the most robust method for long-term storage in microbiome studies.

IMPORTANCE: Microbiome studies heavily rely on ultracold freezers for sample storage. Unfortunately, these freezers are prone to frequent malfunctions, resulting in the loss of invaluable samples at laboratories worldwide. Such losses can halt research progress due to potential issues with sample reliability. Our research demonstrates that not all is lost when an unforeseen freezer failure occurs. Samples can still be reliably used to assess treatment effects, which is particularly important for long-term temporal studies where samples cannot be readily obtained again.},
}

@article {pmid39704535,
year = {2024},
author = {Jones, JA and Newton, IG and Moczek, AP},
title = {Microbiome composition and turnover in the face of complex lifecycles and bottlenecks: insights through the study of dung beetles.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0127824},
doi = {10.1128/aem.01278-24},
pmid = {39704535},
issn = {1098-5336},
abstract = {UNLABELLED: Microbiome composition and function often change throughout a host's life cycle, reflecting shifts in the ecological niche of the host. The mechanisms that establish these relationships are therefore important dimensions of host ecology and evolution; yet, their nature remains poorly understood. Here, we sought to investigate the microbial communities associated with the complex life cycle of the dung beetle Onthophagus taurus and the relative contributions of host life stage, sex, and environment in determining microbiome assembly. We find that O. taurus plays host to a diverse microbiota that undergo drastic community shifts throughout host development, influenced by host life stage, environmental microbiota, and, to a lesser degree, sex. Contrary to predictions, we found that egg and pupal stages-despite the absence of a digestive tract or defined microbe-storing organs-do not constrain microbial maintenance, while host-constructed environments, such as a maternally derived fecal pellet or the pupal chamber constructed by late larvae, may still serve as complementary microbial refugia for select taxa. Lastly, we identify a small community of putative core microbiota likely to shape host development and fitness. Our results provide important insights into mechanisms employed by solitary organisms to assemble, maintain, and adjust beneficial microbiota to confront life-stage-specific needs and challenges.

IMPORTANCE: As the influence of symbionts on host ecology, evolution, and development has become more apparent so has the importance of understanding how hosts facilitate the reliable maintenance of their interactions with these symbionts. A growing body of work has thus begun to identify diverse behaviors and physiological mechanisms underpinning the selective colonization of beneficial symbionts across a range of host taxa. Yet, how organisms with complex life cycles, such as holometabolous insects, establish and maintain key symbionts remains poorly understood. This is particularly interesting considering the drastic transformations of both internal and external host morphology, and the ecological niche shifts in diet and environment, that are the hallmark of metamorphosis. This work investigates the dynamic changes of the microbiota associated with the complex life cycle and host-constructed environments of the bull-headed dung beetle, Onthophagus taurus, a useful model for understanding how organisms may maintain and modulate their microbiota across development.},
}

@article {pmid39704249,
year = {2024},
author = {Taithongchai, A and Reid, F and Agro, EF and Rosato, E and Bianchi, D and Serati, M and Da Silva, AS and Giarenis, I and Robinson, D and Abrams, P},
title = {Are We Able to Optimize Outcomes and Predict Complications in Pelvic Floor Surgery With a Better Understanding of Hormonal, Microbial and Other Factors? A Report From the ICI-RS 2024.},
journal = {Neurourology and urodynamics},
volume = {},
number = {},
pages = {},
doi = {10.1002/nau.25645},
pmid = {39704249},
issn = {1520-6777},
support = {//The authors received no specific funding for this work./ ; },
abstract = {INTRODUCTION: Pelvic organ prolapse (POP) is a common condition, affecting women worldwide and is known to have a significant impact on Health Related Quality of Life (HRQoL). Although there are various treatment options available, including pelvic floor muscle training and support pessaries, many women opt for or require surgery, with a lifetime risk of needing surgery of 12%-19%. As with any operation, this does not come without its complications and the reoperation rate following POP surgery is up to 36%. This International Consultation on Incontinence-Research Society (ICI-RS) report aims to look at the different factors which may play a role in objective and subjective outcomes following pelvic floor surgery and to summarize the evidence and uncertainties regarding prediction of POP surgical outcomes, how to optimize them and the tools available to predict them. Research question proposals to further this field have been highlighted.

METHODS: At ICI-RS 2024, the evidence for predicting the outcomes from POP surgery and methods to optimize outcomes were discussed and presented in this paper.

RESULTS: There are many reasons why POP surgery may fail, such as variations in lifestyle and occupation, persistent constipation, failure in the perineal body, connective tissue types or the shape of the pelvis. There may also be inherent conditions of the vagina, such as hormonal or microbial features. The literature lacks evidence about the potential use of advanced statistical modeling or supervised machine learning in the development of management plans for patients with POP. Furthermore, future research is needed to determine the role of UDS in the preoperative evaluation of POP patients.

CONCLUSIONS: High-quality powered studies are required to assess optimization for long-term outcomes of pelvic surgery and then, once these are well established, and possible interventions are elucidated, prediction modeling can have a real impact clinically.},
}

@article {pmid39703711,
year = {2024},
author = {Dias, NW and Poole, R and Soffa, DR and Brown, KJH},
title = {Dynamic principles of the microbiome and the bovine vagina: a review.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1434498},
pmid = {39703711},
issn = {1664-302X},
abstract = {The role of microbes inhabiting various body sites in supporting host physiology and health is substantial, and recent advancements in DNA sequencing technology have facilitated a more in-depth understanding of these microbial contributions. The influence of microbiota within a given organ can be broadly categorized as having two main functions: (1) promoting organ homeostasis and (2) creating conditions that inhibit the growth of pathogenic microorganisms, thereby protecting the host from diseases. In livestock production, numerous phenotypes critical to industry outcomes are affected by the microbiome, which has sparked considerable academic interest in recent years. This review aims to analyze the extensive data available on the microbiomes of humans and other mammalian species, examining microbiome ecology to elucidate principles that may assist in interpreting data on livestock microbiomes. Additionally, the review will discuss techniques available for investigating various microbiome aspects and will examine existing data on the reproductive microbiome, with a particular focus on the bovine vaginal microbiome.},
}

@article {pmid39703675,
year = {2024},
author = {Milke, F and Rodas-Gaitan, H and Meissner, G and Masson, V and Oltmanns, M and Möller, M and Wohlfahrt, Y and Kulig, B and Acedo, A and Athmann, M and Fritz, J},
title = {Enrichment of putative plant growth promoting microorganisms in biodynamic compared with organic agriculture soils.},
journal = {ISME communications},
volume = {4},
number = {1},
pages = {ycae021},
pmid = {39703675},
issn = {2730-6151},
abstract = {The potential of soils to maintain biological productivity, defined as soil health, is strongly influenced by human activity, such as agriculture. Therefore, soil management has always been a concern for sustainable agriculture and new methods that account for both soil health and crop yield must be found. Biofertilization using microbial inoculants emerges as a promising alternative to conventional interventions such as excessive mineral fertilization and herbicide use. Biodynamic preparations used as a central part of biodynamic agriculture have various effects on soil properties, such as microbial biomass and respiration. We conducted several biomarker experiments to infer the effect of biodynamic preparations on soil prokaryotic and fungal communities and compared results to organic management. Potential plant growth promoting amplicon sequence variants were quantified using a commercial database based on their taxonomic identity. We found significantly higher numbers of putative plant growth promoting amplicon sequence variants in biodynamically compared with organically treated soils. Furthermore, prokaryotic amplicon sequence variants enriched in biodynamic preparations were found in higher numbers in biodynamically treated soils, indicating successful colonization after treatment. Experiments were conducted at three locations in Germany and 21 locations in France covering different crops and soil types. Altogether, our results indicate that biodynamic preparations can act as biofertilizers that promote soil health by increasing the abundance of plant growth promoting microorganisms.},
}

@article {pmid39703608,
year = {2024},
author = {Zollner, A and Meyer, M and Jukic, A and Adolph, T and Tilg, H},
title = {The Intestine in Acute and Long COVID: Pathophysiological Insights and Key Lessons.},
journal = {The Yale journal of biology and medicine},
volume = {97},
number = {4},
pages = {447-462},
pmid = {39703608},
issn = {1551-4056},
mesh = {Humans ; *COVID-19/physiopathology/virology/immunology ; *Gastrointestinal Microbiome/physiology ; *Post-Acute COVID-19 Syndrome ; *SARS-CoV-2 ; Brain-Gut Axis/physiology ; Intestines/virology/physiopathology/microbiology ; },
abstract = {Post-Acute Sequelae of SARS-CoV-2 infection (PASC), commonly known as Long COVID, represents a significant and complex health challenge with a wide range of symptoms affecting multiple organ systems. This review examines the emerging evidence suggesting a critical role of the gut and gut-brain axis in the pathophysiology of Long COVID. It explores how changes in the gut microbiome, disruption of gut barrier integrity, and the persistence of SARS-CoV-2 antigens within the gastrointestinal tract may contribute to the prolonged and varied symptoms seen in Long COVID, including chronic inflammation and neuropsychiatric disturbances. The review also summarizes key insights gained about Long COVID, highlighting its multifactorial nature, which involves immune dysregulation, microvascular damage, and autonomic nervous system dysfunction, with the gut playing a central role in these processes. While progress has been made in understanding these mechanisms, current evidence remains inconclusive. The challenges of establishing causality, standardizing research methodologies, and addressing individual variations in the microbiome are discussed, emphasizing the need for further longitudinal studies and more comprehensive approaches to enhance our understanding of these complex interactions. This review underscores the importance of personalized approaches in developing effective diagnostic and therapeutic strategies for Long COVID, while also acknowledging the significant gaps in our current understanding. Future research should aim to further unravel the complex interplay between the gut and Long COVID, ultimately improving outcomes for those affected by this condition.},
}

Humans
*COVID-19/physiopathology/virology/immunology
*Gastrointestinal Microbiome/physiology
*Post-Acute COVID-19 Syndrome
*SARS-CoV-2
Brain-Gut Axis/physiology
Intestines/virology/physiopathology/microbiology

@article {pmid39703542,
year = {2024},
author = {Azcarate-Peril, MA},
title = {Has the two decades of research on the gut microbiome resulted in making healthier choices?.},
journal = {Gut microbiome (Cambridge, England)},
volume = {5},
number = {},
pages = {e10},
pmid = {39703542},
issn = {2632-2897},
abstract = {The gut microbiome is widely recognized for its significant contribution to maintaining human health across all life stages, from infancy to adulthood and beyond. This perspective article focuses on the impacts of well-supported microbiome research on global caesarean delivery rates, breastfeeding practices, and antimicrobial use. The article also explores the impact of dietary choices, particularly those involving ultra-processed foods, on the gut microbiota and their potential contribution to conditions like obesity, metabolic syndrome, and inflammatory diseases. This perspective aims to emphasize the need for updated guidelines and policy interventions to address the increasing global trends of caesarean deliveries, reduced breastfeeding, overuse of antibiotics, and consumption of highly processed foods to counter their adverse effects on gut health.},
}

@article {pmid39703541,
year = {2024},
author = {Shi, N and Nepal, S and Hoobler, R and Menni, C and Playdon, MC and Spakowicz, D and Wells, PM and Steves, CJ and Clinton, SK and Tabung, FK},
title = {Pro-inflammatory and hyperinsulinaemic dietary patterns are associated with specific gut microbiome profiles: a TwinsUK cohort study.},
journal = {Gut microbiome (Cambridge, England)},
volume = {5},
number = {},
pages = {e12},
pmid = {39703541},
issn = {2632-2897},
abstract = {Metabolic dietary patterns, including the Empirical Dietary Index for Hyperinsulinaemia (EDIH) and Empirical Dietary Inflammatory Pattern (EDIP), are known to impact multiple chronic diseases, but the role of the colonic microbiome in mediating such relationships is poorly understood. Among 1,610 adults with faecal 16S rRNA data in the TwinsUK cohort, we identified the microbiome profiles for EDIH and EDIP (from food frequency questionnaires) cross-sectionally using elastic net regression. We assessed the association of the dietary pattern-related microbiome profile scores with circulating biomarkers in multivariable-adjusted linear regression. In addition, we used PICRUSt2 to predict biological pathways associated with the enriched microbiome profiles, and further screened pathways for associations with the dietary scores in linear regression analyses. Microbiome profile scores developed with 32 (EDIH) and 15 (EDIP) genera were associated with higher insulin and homeostatic model assessment of insulin resistance. Six genera were associated with both dietary scores: Ruminococcaceae_UCG-008, Lachnospiraceae_UCG-008, Defluviitaleaceae_UCG-011 Anaeroplasma, inversely and Negativibacillus, Streptococcus, positively. Further, pathways in fatty acid biosynthesis, sugar acid degradation, and mevalonate metabolism were associated with insulinaemic and inflammatory diets. Dietary patterns that exert metabolic effects on insulin and inflammation may influence chronic disease risk by modulating gut microbial composition and function.},
}

@article {pmid39703540,
year = {2024},
author = {Finnegan, YE and Neill, HR and Prpa, EJ and Pot, B},
title = {"Gut" to grips with the science of the microbiome - a symposium report.},
journal = {Gut microbiome (Cambridge, England)},
volume = {5},
number = {},
pages = {e11},
pmid = {39703540},
issn = {2632-2897},
abstract = {The latest Yakult Science Study Day was held virtually on 2 November 2023. Aimed at healthcare professionals, researchers, and students, a variety of experts explored the latest gut microbiome research and what it means in practice. The morning sessions discussed the role of the microbiome in health and disease, the rapid advancements in DNA sequencing and implications for personalised nutrition, the current state of evidence on health benefits associated with fermented foods, prebiotics and probiotics and the challenges involved in interpreting research in this area. The afternoon session considered the emerging research on the microbiota-gut-brain axis in mediating effects of food on mood, the bidirectional impact of menopause on the gut microbiota, and the interplay between the gut and skin with implications for the treatment of rare and common skin disorders. The session ended with an update on the use of faecal microbiota transplant in both research and clinical practice. Undoubtedly, the gut microbiome is emerging as a key conductor of human health, both in relation to gastrointestinal and non-gastrointestinal outcomes. As research continues to elucidate mechanisms of action and confirm their effects in human trials, the gut microbiome should be a key consideration within a holistic approach to health moving forward.},
}

@article {pmid39703512,
year = {2024},
author = {Zou, J and Xu, B and Gao, H and Luo, P and Chen, T and Duan, H},
title = {Microbiome in urologic neoplasms: focusing on tumor immunity.},
journal = {Frontiers in immunology},
volume = {15},
number = {},
pages = {1507355},
pmid = {39703512},
issn = {1664-3224},
mesh = {Humans ; *Urologic Neoplasms/immunology/microbiology/therapy/etiology ; *Microbiota/immunology ; *Immunotherapy/methods ; Animals ; Gastrointestinal Microbiome/immunology ; },
abstract = {Urological tumors are an important disease affecting global human health, and their pathogenesis and treatment have been the focus of medical research. With the in - depth study of microbiomics, the role of the microbiome in urological tumors has gradually attracted attention. However, the current research on tumor - associated microorganisms mostly focuses on one type or one site, and currently, there is a lack of attention to the microbiome in the immunity and immunotherapy of urological tumors. Therefore, in this paper, we systematically review the distribution characteristics of the microbiome (including microorganisms in the gut, urine, and tumor tissues) in urologic tumors, the relationship with disease prognosis, and the potential mechanisms of microbial roles in immunotherapy. In particular, we focus on the molecular mechanisms by which the microbiome at different sites influences tumor immunity through multiple "messengers" and pathways. We aim to further deepen the understanding of microbiome mechanisms in urologic tumors, and also point out the direction for the future development of immunotherapy for urologic tumors.},
}

Humans
*Urologic Neoplasms/immunology/microbiology/therapy/etiology
*Microbiota/immunology
*Immunotherapy/methods
Animals
Gastrointestinal Microbiome/immunology

@article {pmid39703208,
year = {2024},
author = {Bamgbose, T and Quadri, A and Abdullahi, IO and Inabo, HI and Bello, M and Kori, LD and Anvikar, AR and de la Fuente, J and Piloto-Sardiñas, E and Cabezas-Cruz, A},
title = {Antiplasmodial Activity of Probiotic Limosilactobacillus fermentum YZ01 in Plasmodium berghei ANKA Infected BALB/c Mice.},
journal = {Journal of tropical medicine},
volume = {2024},
number = {},
pages = {6697859},
pmid = {39703208},
issn = {1687-9686},
abstract = {Malaria remains a significant global health challenge, with the deadliest infections caused by Plasmodium falciparum. In light of the escalating drug resistance and the limited effectiveness of available vaccines, innovative treatment approaches are urgently needed. This study explores the potential of the probiotic Limosilactobacillus fermentum YZ01, isolated from traditionally fermented kindirmo milk, to modify host responses to Plasmodium berghei ANKA infection. Twenty-five male BALB/c mice were grouped and administered various treatments, including probiotic-enriched yogurt alone or in combination with antibiotics. Parameters assessed included gut lactic acid bacteria (LAB) composition, parasitaemia progression, survival rates, and immune response dynamics over a 21-day postinfection period. The probiotic treatment significantly altered gut microbiota, evidenced by increased LAB counts and modulated immune responses, notably enhancing IgM and IL-4 production while reducing IFN-γ levels. Mice receiving prolonged probiotic treatment exhibited delayed parasitaemia onset, reduced mortality rates, and a more robust immune response compared to control groups. These outcomes suggest that probiotic intervention not only tempers the pathological effects of malaria but also enhances host resilience against infection. This study underscores the role of gut microbiota in infectious disease pathogenesis and supports probiotics as a promising adjunct therapy for malaria management.},
}

@article {pmid39605597,
year = {2024},
author = {Popowitch, EB and Tran, TH and Escapa, IF and Bhatt, E and Sozat, AK and Ahmed, N and Deming, C and Roberts, AQ and , and Segre, JA and Kong, HH and Conlan, S and Lemon, KP and Kelly, MS},
title = {Description of two novel Corynebacterium species isolated from human nasal passages and skin.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39605597},
issn = {2692-8205},
abstract = {Strains of two novel Corynebacterium species were cultured from samples of human nostrils and skin collected in the United States and Botswana. These strains demonstrated growth on Columbia Colistin-Nalidixic Acid agar with 5% sheep blood and in liquid media (brain heart infusion and tryptic soy broth) supplemented with Tween 80, a source of the fatty acid oleic acid. Cells were Gram-positive, non-spore-forming, non-motile bacilli that showed catalase but not oxidase activity. Major fatty acids in both of these species were 18:1 ω9c (oleic acid), 16:0 (palmitic acid), and 18:0 (stearic acid). Analysis of the 16S ribosomal RNA gene sequences identified these strains as belonging to the genus Corynebacterium (family Corynebacteriaceae). Whole-genome sequencing revealed that these strains formed distinct branches on a phylogenomic tree, with C. tuberculostearicum being the closest relative but with average nucleotide identities of < 95% relative to all previously described species. These results indicate that these strains represent novel species of Corynebacterium, for which we propose the names Corynebacterium hallux sp. nov., with the type strain CTNIH22[T] (=ATCC TSD-435[T]=DSM 117774[T]), and Corynebacterium nasorum sp. nov., with the type strain KPL3804[T] (=ATCC TSD-439[T]=DSM 117767[T]). We also describe the characteristics of two strains isolated from human nasal passages that are members of the recently named species Corynebacterium yonathiae.},
}

@article {pmid39703120,
year = {2024},
author = {Wu, X and Wang, L and Lu, Y and Li, MH and Liu, S and Yang, Y and Song, Y and Chen, S and Kang, J and Dong, A and Yang, YW},
title = {A Microenvironment-Responsive Graphdiyne-Iron Nanozyme Hydrogel with Antibacterial and Anti-Inflammatory Effect for Periodontitis Treatment.},
journal = {Advanced healthcare materials},
volume = {},
number = {},
pages = {e2403683},
doi = {10.1002/adhm.202403683},
pmid = {39703120},
issn = {2192-2659},
support = {22062017//National Natural Science Foundation of China/ ; 22164015//National Natural Science Foundation of China/ ; 2024ZD10//Natural Science Foundation of Inner Mongolia Autonomous Region/ ; 2019JQ03//Natural Science Foundation of Inner Mongolia Autonomous Region/ ; 2023QN02011//Natural Science Foundation of Inner Mongolia Autonomous Region/ ; 10000-22311201/035//Program of Higher-Level Talents of Inner Mongolia University/ ; NJZZ23091//Research Program of Science and Technology at Universities of Inner Mongolia Autonomous Region/ ; },
abstract = {Periodontitis is a chronic inflammatory disease caused by dental plaque, which leads to tooth loosening and shifting or even tooth loss. Current treatments, including mechanical debridement and antibiotics, often fail to eradicate recalcitrant biofilms and mitigate excessive inflammation. Moreover, these interventions can disrupt the oral microbiome, potentially compromising long-term treatment outcomes. To address these limitations, an injectable nanoenzyme hydrogel composed of a dopamine (DA)-modified hyaluronic acid (HA) scaffold and a graphdiyne-iron (GDY-Fe) complex, named GDY-Fe@HA-DA, exhibits excellent tissue adhesion, self-healing, antibacterial properties, and biocompatibility. Under near-infrared laser irradiation, GDY-Fe@HA-DA effectively eradicates a variety of pathogens, including Escherichia coli, Staphylococcus aureus, and Porphyromonas gingivalis, through a synergistic combination of chemodynamical and photothermal therapies. The hydrogel's efficacy is further validated in both bacterial-infected skin wounds and rat periodontitis models. It effectively alleviates the inflammatory environment and promotes wound healing and periodontal tissue recovery. This findings highlight the potential of GDY-Fe@HA-DA as a promising therapeutic material for periodontitis and other tissue injuries.},
}

@article {pmid39702969,
year = {2024},
author = {de Lorenzo, V},
title = {Penitentiaries: Bringing microbiological literacy to the fringes of society.},
journal = {Microbial biotechnology},
volume = {17},
number = {12},
pages = {e70052},
pmid = {39702969},
issn = {1751-7915},
support = {CEX2023-001386-S//Ministerio de Ciencia, Innovacion y Universidades/ ; Y2020/TCS- 6555//Comunidad de Madrid/ ; CL6-2021-UE 101060625//HORIZON EUROPE Framework Programme/ ; },
mesh = {Humans ; *Prisons ; Spain ; Microbiology/education ; Microbiota ; },
abstract = {This report highlights a science outreach effort for prisons launched by the Spanish National Research Council (CSIC) in collaboration with the NGO Solidarios para el Desarrollo. The Microbiology-focused part of the initiative aims at educating inmates on some basic facts, in order to raise awareness about microorganisms and their impact on daily life. The outline of the talks, inspired by the International Initiative for Microbial Literacy, aims to encourage this collective to move from passive listeners into active participants, helping them understand that Earth is a microbial planet, and that their bodies harbour vast microbiomes that affect their health and social interactions. The talks introduce Microbiology using simple metaphors and emphasize the role of beneficial microorganisms. By explaining the power of microscopes, inmates are shown the hidden microbial world that surrounds them, sparking interest and curiosity. The talks also cover microbial biotechnology, using examples such as bioplastics, anti-cavity bacteria, and skin microorganisms designed for acne prevention. Overall, this outreach initiative seeks to provide inmates with valuable scientific knowledge, fostering curiosity and critical thinking. Despite the challenges of delivering such content in a prison setting, the initiative demonstrates that even marginalized groups can benefit from microbiological literacy, helping them to both endure their terms and eventually reintegrate into society.},
}

Humans
*Prisons
Spain
Microbiology/education
Microbiota

@article {pmid39702929,
year = {2024},
author = {Hu, B and Yang, Y and Yao, J and Lin, G and He, Q and Bo, Z and Zhang, Z and Li, A and Wang, Y and Chen, G and Shan, Y},
title = {Gut Microbiota as Mediator and Moderator Between Hepatitis B Virus and Hepatocellular Carcinoma: A Prospective Study.},
journal = {Cancer medicine},
volume = {13},
number = {24},
pages = {e70454},
pmid = {39702929},
issn = {2045-7634},
support = {82072685//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Carcinoma, Hepatocellular/virology/microbiology ; *Gastrointestinal Microbiome ; *Liver Neoplasms/virology/microbiology ; Male ; Female ; Prospective Studies ; Middle Aged ; *Hepatitis B virus/isolation & purification/genetics ; Machine Learning ; Feces/microbiology/virology ; RNA, Ribosomal, 16S/genetics ; Risk Factors ; Adult ; Hepatitis B/complications/virology/microbiology ; Aged ; },
abstract = {BACKGROUND: The impact of gut microbiome on hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC) is unclear. We aimed to evaluate the potential correlation between gut microbiome and HBV-related HCC and introduced novel machine learning (ML) signatures based on gut microbe to predict the risk of HCC.

MATERIALS AND METHODS: A total of 640 patients with chronic liver diseases or HCC were prospectively recruited between 2019 and 2022. Fecal samples were collected and subjected to 16S rRNA gene sequencing. Univariate and multivariate logistic regression was applied to identify risk characteristics. Several ML methods were employed to construct gut microbe-based models and the predictive performance was evaluated.

RESULTS: A total of 571 patients were involved in the study, including 374 patients with HCC and 197 patients with chronic liver diseases. After the propensity score matching method, 147 pairs of participants were enrolled in the analysis. Bacteroidia and Bacteroidales were demonstrated to exert mediating effects between HBV and HCC, and the moderating effects varied across Bacilli, Lactobacillales, Erysipelotrichaceae, Actinomyces, and Roseburia. HBV, alpha-fetoprotein, alanine transaminase, triglyceride, and Child-Pugh were identified as independent risk factors for HCC occurrence. Seven ML-based HBV-gut microbe models were established to predict HCC, with AUCs ranging from 0.821 to 0.898 in the training set and 0.813-0.885 in the validation set. Furthermore, the merged clinical-HBV-gut microbe models exhibited a comparable performance to HBV-gut microbe models.

CONCLUSIONS: Gut microbes are important factors between HBV and HCC through its potential mediating and moderating effects, which can be used as valuable biomarkers for the pathogenesis of HBV-related HCC.},
}

Humans
*Carcinoma, Hepatocellular/virology/microbiology
*Gastrointestinal Microbiome
*Liver Neoplasms/virology/microbiology
Male
Female
Prospective Studies
Middle Aged
*Hepatitis B virus/isolation & purification/genetics
Machine Learning
Feces/microbiology/virology
RNA, Ribosomal, 16S/genetics
Risk Factors
Adult
Hepatitis B/complications/virology/microbiology
Aged

@article {pmid39702789,
year = {2024},
author = {Kaur, S and Patel, BCK and Collen, A and Malhotra, R},
title = {The microbiome and the eye: a new era in ophthalmology.},
journal = {Eye (London, England)},
volume = {},
number = {},
pages = {},
pmid = {39702789},
issn = {1476-5454},
abstract = {The human microbiome has progressively been recognised for its role in various disease processes. In ophthalmology, complex interactions between the gut and distinct ocular microbiota within each structure and microenvironment of the eye has advanced our knowledge on the multi-directional relationships of these ecosystems. Increasingly, studies have shown that modulation of the microbiome can be achieved through faecal microbiota transplantation and synbiotics producing favourable outcomes for ophthalmic diseases. As ophthalmologists, we are obliged to educate our patients on measures to cultivate a healthy gut microbiome through a range of holistic measures. Further integrative studies combining microbial metagenomics, metatranscriptomics and metabolomics are necessary to fully characterise the human microbiome and enable targeted therapeutic interventions.},
}

@article {pmid39702677,
year = {2024},
author = {Go, D and Yeon, GH and Park, SJ and Lee, Y and Koh, HG and Koo, H and Kim, KH and Jin, YS and Sung, BH and Kim, J},
title = {Integration of metabolomics and other omics: from microbes to microbiome.},
journal = {Applied microbiology and biotechnology},
volume = {108},
number = {1},
pages = {538},
pmid = {39702677},
issn = {1432-0614},
support = {RS-2024-00401586//Korea Institute of Planning and Evaluation for Technology in Food, Agriculture, Forestry and Fisheries/ ; NRF-2021M3A9I5023254//Korea Research Institute of Bioscience and Biotechnology/ ; NRF-2018M3A9H3024746//Korea Research Institute of Bioscience and Biotechnology/ ; },
mesh = {*Metabolomics/methods ; *Microbiota/physiology ; Bacteria/metabolism/genetics/classification ; Metabolic Engineering/methods ; Metabolic Networks and Pathways ; Genomics/methods ; Metabolome ; },
abstract = {Metabolomics is a cutting-edge omics technology that identifies metabolites in organisms and their environments and tracks their fluctuations. This field has been extensively utilized to elucidate previously unknown metabolic pathways and to identify the underlying causes of metabolic changes, given its direct association with phenotypic alterations. However, metabolomics inherently has limitations that can lead to false positives and false negatives. First, most metabolites function as intermediates in multiple biochemical reactions, making it challenging to pinpoint which specific reaction is responsible for the observed changes in metabolite levels. Consequently, metabolic processes that are anticipated to vary with metabolite concentrations may not exhibit significant changes, generating false positives. Second, the range of metabolites identified is contingent upon the analytical conditions employed. Until now, no analytical instrument or protocol has been developed that can capture all metabolites simultaneously. Therefore, some metabolites are changed but are not detected, generating false negatives. In this review, we offer a novel and systematic assessment of the limitations of omics technologies and propose-specific strategies to minimize false positives and false negatives through multi-omics approaches. Additionally, we provide examples of multi-omics applications in microbial metabolic engineering and host-microbiome interactions, helping other researchers gain a better understanding of these strategies. KEY POINTS: • Metabolomics identifies metabolic shifts but has inherent false positive/negatives. • Multi-omics approaches help overcome metabolomics' inherent limitations.},
}

*Metabolomics/methods
*Microbiota/physiology
Bacteria/metabolism/genetics/classification
Metabolic Engineering/methods
Metabolic Networks and Pathways
Genomics/methods
Metabolome

@article {pmid39702650,
year = {2024},
author = {Vriend, EMC and Galenkamp, H and Herrema, H and Nieuwdorp, M and van den Born, BH and Verhaar, BJH},
title = {Machine learning analysis of sex and menopausal differences in the gut microbiome in the HELIUS study.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {152},
pmid = {39702650},
issn = {2055-5008},
support = {189235//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; 09150182010020/ZONMW_/ZonMw/Netherlands ; 101141346/ERC_/European Research Council/International ; },
mesh = {*Gastrointestinal Microbiome ; Humans ; Female ; *Machine Learning ; Male ; Middle Aged ; *Menopause ; Aged ; Sex Factors ; Metagenomics/methods ; Adult ; Cohort Studies ; Bacteria/classification/genetics/isolation & purification ; Feces/microbiology ; },
abstract = {Sex differences in the gut microbiome have been examined previously, but results are inconsistent, often due to small sample sizes. We investigated sex and menopausal differences in the gut microbiome in a large multi-ethnic population cohort study, including 5166 participants. Using machine learning models, we revealed modest associations between sex and menopausal status, and gut microbiota composition (AUC 0.61-0.63). After adjustments for age, cardiovascular risk factors, and diet, a part of the associations of the highest-ranked gut microbes with sex were attenuated, but most associations remained significant. In contrast, most associations with menopausal status were driven by age and lost significance after adjustment. Using pathway analyses on metagenomic data, we identified sex differences in vitamin B6 synthesis and stachyose degradation pathways. Since some of sex differences in gut microbiome composition and function could not be explained by covariates, we recommend sex stratification in future microbiome studies.},
}

*Gastrointestinal Microbiome
Humans
Female
*Machine Learning
Male
Middle Aged
*Menopause
Aged
Sex Factors
Metagenomics/methods
Adult
Cohort Studies
Bacteria/classification/genetics/isolation & purification
Feces/microbiology

@article {pmid39702451,
year = {2024},
author = {He, W and Liang, H and Li, W and Gao, X and Hu, T and Lin, X and Wu, Z and Sun, J and Li, X and Wang, M and Hou, X and Jie, Z and Tong, X and Jin, X and Xiao, L and Zou, Y},
title = {Revealing an unprecedented diversity of episymbiotic Saccharibacteria in a high-quality genome collection.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {153},
pmid = {39702451},
issn = {2055-5008},
support = {2019B020230001//Natural Science Foundation of Guangdong Province (Guangdong Natural Science Foundation)/ ; },
mesh = {Humans ; *Genome, Bacterial ; *Microbiota ; *Symbiosis ; Phylogeny ; Mouth/microbiology ; Genetic Variation ; China ; },
abstract = {The episymbiotic Candidatus Saccharibacteria is the most studied lineage of candidate phyla radiation. Living an epiparasitic lifestyle, Saccharibacteria might be associated with human mucosal diseases by modulating the structure of the oral microbiome through interactions with host bacteria. However, the knowledge of Saccharibacterial genomic diversity and the potential underlying their adaptation to a wide range of habitats remains limited. Here, we construct a high-quality genome collection of Saccharibacteria from multiple sources, providing 2041 high-quality genomes and previously unidentified taxa. The comparative genomic analysis shows the widespread metabolic defects of Saccharibacteria. Specific metabolic modules are commonly found in Saccharibacteria of different habitats, suggesting Saccharibacteria might have undergone habitat adaptation during the transition from different environments. We additionally show that Saccharibacteria account for ~1% of the Chinese oral microbiome. A preliminary analysis of rheumatoid arthritis individuals and healthy controls implies that Saccharibacteria might be associated with human systemic disease.},
}

Humans
*Genome, Bacterial
*Microbiota
*Symbiosis
Phylogeny
Mouth/microbiology
Genetic Variation
China

@article {pmid39702426,
year = {2024},
author = {Li, J and Wu, W and Kong, X and Yang, X and Li, K and Jiang, Z and Zhang, C and Zou, J and Liang, Y},
title = {Roles of gut microbiome-associated metabolites in pulmonary fibrosis by integrated analysis.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {154},
pmid = {39702426},
issn = {2055-5008},
support = {81960019//National Natural Science Foundation of China/ ; 32372349//National Natural Science Foundation of China/ ; 2022RC3056//Science and Technology Program of Hunan Province/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; Mice ; *Pulmonary Fibrosis/metabolism/microbiology ; *Lung/microbiology/pathology/metabolism ; *Bleomycin ; *Tryptophan/metabolism ; Disease Models, Animal ; Bacteria/classification/metabolism/genetics/isolation & purification ; TOR Serine-Threonine Kinases/metabolism ; Mice, Inbred C57BL ; Male ; },
abstract = {Lung diseases often coincide with imbalances in gut microbiota, but the role of gut microbiota in pulmonary fibrosis (PF) remains unclear. This study investigates the impact of gut microbiota and their metabolites on PF. Serum and lung tissues of normal, bleomycin (BLM)- and silica-induced mice showed significant differences in gut microbiota. L-Tryptophan was upregulated within pulmonary tissue and serum metabolites both in the BLM and Silica groups. The dominant gut microbiota associated with L-tryptophan metabolism included Lachnospiraceae_NK4A136_Group, Allobaculum, Alistipes, and Candidatus_Saccharimonas. L-Tryptophan promoted BLM- and silica-induced pathological damage in PF mice. L-Tryptophan promoted TGF-β1-induced EMT and fibroblast activation in vitro via activating the mTOR/S6 pathway. In conclusion, PF mice exhibited alterations in gut microbiota and serum and lung tissue metabolites. L-Tryptophan level was associated with changes in gut microbiota, and L-tryptophan promoted PF progression in both in vivo and in vitro models, potentially through activation of the mTOR/S6 pathway.},
}

Animals
*Gastrointestinal Microbiome
Mice
*Pulmonary Fibrosis/metabolism/microbiology
*Lung/microbiology/pathology/metabolism
*Bleomycin
*Tryptophan/metabolism
Disease Models, Animal
Bacteria/classification/metabolism/genetics/isolation & purification
TOR Serine-Threonine Kinases/metabolism
Mice, Inbred C57BL
Male

@article {pmid39702405,
year = {2024},
author = {Soufi, HH and Porch, R and Korchagina, MV and Abrams, JA and Schnider, JS and Carr, BD and Williams, MA and Louca, S},
title = {Taxonomic variability and functional stability across Oregon coastal subsurface microbiomes.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {1663},
pmid = {39702405},
issn = {2399-3642},
mesh = {Oregon ; *Microbiota/genetics ; *Geologic Sediments/microbiology ; *RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification ; Phylogeny ; Metagenomics/methods ; Biodiversity ; },
abstract = {The factors shaping microbial communities in marine subsurface sediments remain poorly understood. Here, we analyzed the microbiome of subsurface sediments within a depth range of 1.6-1.9 m, at 10 locations along the Oregon coast. We used metagenomics to reconstruct the functional structure and 16S rRNA gene amplicon sequencing to estimate the taxonomic composition of microbial communities, accompanied by physicochemical measurements. Functional community structure, in terms of the proportions of various gene groups, was remarkably stable across samples, despite the latter covering a region spanning over 300 km. In contrast, taxonomic composition was highly variable, especially at the level of amplicon sequence variants (ASVs) and operational taxonomic units (OTUs). Mantel correlation tests between compositional dissimilarities and geographic distances revealed only a moderate influence of distance on composition. Regression models predicting taxonomic dissimilarities and considering up to 20 physicochemical variables as predictors, almost always failed to select a significant predictor, suggesting that variation in local conditions does not explain the high taxonomic variability. Permutation null models of community assembly revealed that taxa tend to strongly segregate, i.e., exclude each other. We conclude that biological interactions are important drivers of taxonomic variation in subsurface sediments, and that this variation can decouple from functional structure.},
}

Oregon
*Microbiota/genetics
*Geologic Sediments/microbiology
*RNA, Ribosomal, 16S/genetics
Bacteria/genetics/classification
Phylogeny
Metagenomics/methods
Biodiversity

@article {pmid39702397,
year = {2024},
author = {Shijimaya, T and Tahara, T and Yamazaki, J and Kobayashi, S and Matsumoto, Y and Nakamura, N and Takahashi, Y and Tomiyama, T and Fukui, T and Shibata, T and Naganuma, M},
title = {Distinct microbiome dysbiosis and epigenetic anomaly in esophageal adenocarcinoma and its underlying Barrett's esophagus.},
journal = {Clinical epigenetics},
volume = {16},
number = {1},
pages = {184},
pmid = {39702397},
issn = {1868-7083},
support = {22K08089//Japan Society for the Promotion of Science/ ; },
mesh = {Humans ; *Barrett Esophagus/genetics/microbiology ; *Adenocarcinoma/genetics/microbiology ; *Esophageal Neoplasms/genetics/microbiology ; *DNA Methylation/genetics ; *Dysbiosis/genetics/microbiology ; Male ; Female ; *Epigenesis, Genetic/genetics ; Middle Aged ; Aged ; RNA, Ribosomal, 16S/genetics ; Microbiota/genetics ; Adult ; },
abstract = {Interaction between host genotoxic changes and mucosa-associated microbiome (MAM) dysbiosis may have a role in various digestive cancers. We investigated MAM in Barrett's esophagus (BE) and esophageal adenocarcinoma (EAC) progression sequence and its association with host genotoxic changes. 16S rRNA gene sequencing was performed in three different groups of biopsies from nonneoplastic BE from patients without cancer (N, normal group; n = 47) and with EAC (ADJ, adjacent group; n = 27). Endoscopic biopsies were also obtained from EAC tissues (T, tumor group; n = 22). Results were correlated with TP53 mutation, telomere length and DNA methylation of candidate genes (N33, DPYS, SLC16A12, miR124A3 and miR34bc). Genome-wide DNA methylation examined by reduced representation bisulfite sequencing (RRBS) was available for 32 samples (n = 12 for N, n = 12 for ADJ and n = 22 for T groups). Lower microbial alpha diversity measures were observed in ADJ/T groups relative to N group and associated with higher mean Z score DNA methylation of candidate genes. Specific genera (n = 16) with significant change between ADJ/T groups relative to N group occurred mostly in ADJ group (13/16) and half of them (8/16) were associated with DNA methylation status. Integrated MAM and genome-wide methylation analysis demonstrated that hyper-methylated sites, associated with lower alpha diversity measures dominantly occurred within near the transcription start site, codifying genes were involved in metabolic processes. Our result shows that microbial dysbiosis in EAC mostly occurs in adjacent BE and such dysbiosis was associated with DNA methylation status, offering support for a pathogenic role of interaction between host genotoxic changes and MAM in this tumor type.},
}

Humans
*Barrett Esophagus/genetics/microbiology
*Adenocarcinoma/genetics/microbiology
*Esophageal Neoplasms/genetics/microbiology
*DNA Methylation/genetics
*Dysbiosis/genetics/microbiology
Male
Female
*Epigenesis, Genetic/genetics
Middle Aged
Aged
RNA, Ribosomal, 16S/genetics
Microbiota/genetics
Adult

@article {pmid39702387,
year = {2024},
author = {Bowser, S and Chapartegui-González, I and Torres, AG},
title = {Fecal microbiome alterations of mice following immunization with gold nanoparticle vaccines against enterohemorrhagic Escherichia coli.},
journal = {Gut pathogens},
volume = {16},
number = {1},
pages = {75},
pmid = {39702387},
issn = {1757-4749},
support = {N/A//Sealy Institute for Vaccine Sciences, University of Texas Medical Branch/ ; AI155844//National Institute of Allergy and Infectious Diseases/ ; },
abstract = {BACKGROUND: Enterohemorrhagic Escherichia coli (EHEC), a group of enteric pathogenic bacteria that is a major cause of human diarrheal disease, must interact with the diverse intestinal microbiome during colonization and subsequently overcome the environmental challenges to survive and cause disease. While this relationship, and how the microbiome modulates infection of EHEC, has been studied, it is less understood how the microbiome is impacted during treatment for an EHEC infection. One area that is notably lacking in knowledge is how vaccination can impact the intestinal microbiome composition, and therefore, influence vaccine efficacy. We previously developed vaccine formulations consisting of gold nanoparticles (AuNPs) conjugated to various EHEC antigens and tested them in mice models using both EHEC and its murine counterpart Citrobacter rodentium. The goal of this study was to evaluate the relationship between these EHEC vaccines and their effects on the gut microbiome.

RESULTS: We found that immunization with the vaccines or adjuvant-only control did not lead to major alterations in the composition of the fecal microbiome; however, there were measurable variations in individual mice within the same vaccine group housed in separate cages. Also, immunization with one vaccine (AuNP-EscC) prevented both a decrease in the diversity of the fecal microbiome and an increase in detectable C. rodentium following infection compared to control animals.

CONCLUSIONS: Overall, our small study argues in favor of evaluating the intestinal microbiome during vaccine development not just for EHEC, but for other enteric pathogens.},
}

@article {pmid39702294,
year = {2024},
author = {Gui, WY and Yin, JG and Liao, JC and Luo, HZ and You, Q and Gong, JH and Xiang, J and Zou, JD and Li, CY},
title = {Integrated analysis of metabolome, lipidome, and gut microbiome reveals the immunomodulation of Astragali radix in healthy human subjects.},
journal = {Chinese medicine},
volume = {19},
number = {1},
pages = {174},
pmid = {39702294},
issn = {1749-8546},
support = {No. BK20201502//Natural Science Foundation of Jiangsu Province/ ; },
abstract = {BACKGROUND: As a typical medicinal food homology species, Chinese herbal medicine Astragali radix (AR) has been widely used to regulate the human immune system worldwide. However, the human immunomodulation of AR and its corresponding mechanisms remain unclear.

METHODS: First, following a fortnight successive AR administration, the changes in immune cytokines and immune cells from 20 healthy human subjects were used as immune indicators to characterize the immunomodulatory effects of AR. Subsequently, ultra-high-performance liquid chromatography coupled with quadrupole-time-of-flight mass spectrometry (UHPLC-Q-TOF/MS) based lipidomics and metabolomics analysis was performed on human serum, urine, and feces samples to investigate the changes in metabolic profiles. Then, 16S rRNA gene sequencing of feces samples was adopted for the changes of human gut microbiota. Finally, correlation analysis was conducted on the gut microbiome, metabolome/lipidome data, and immune indicators.

RESULTS: AR displayed good safety in clinical use and posed a minor impact on gut microbiota major genera, global metabolic profiles, and immune cells. Meanwhile, AR could significantly up-regulate anti-inflammatory cytokines, down-regulate serum creatinine and pro-inflammatory cytokines, promote the anabolism of arginine, glycerolipid, sphingolipid, and purine, and the catabolism of phenylalanine and glycerophospholipid. Moreover, these AR-induced changes were closely correlated with significantly decreased Granulicatella, slightly higher Bifidobacterium, Ruminococcus, and Subdoligranulum, and slightly lower Blautia.

CONCLUSION: The study clearly demonstrated that AR could modulate the human immune, by modifying the metabolism of amino acids, lipids, and purines in a microbiota-related way. Trial registration ChiCTR, ChiCTR2100054765. Registered 26 December 2021-Prospectively registered, https://www.chictr.org.cn/historyversionpub.html?regno=ChiCTR2100054765.},
}

@article {pmid39702006,
year = {2024},
author = {Demirkan, A and van Dongen, J and Finnicum, CT and Westra, HJ and Jankipersadsing, S and Willemsen, G and Ijzerman, RG and Boomsma, DI and Ehli, EA and Bonder, MJ and Fu, J and Franke, L and Wijmenga, C and de Geus, EJC and Kurilshikov, A and Zhernakova, A},
title = {Linking the gut microbiome to host DNA methylation by a discovery and replication epigenome-wide association study.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {1224},
pmid = {39702006},
issn = {1471-2164},
mesh = {*DNA Methylation ; *Gastrointestinal Microbiome/genetics ; Humans ; *Epigenome ; *Genome-Wide Association Study ; Male ; Female ; RNA, Ribosomal, 16S/genetics ; CpG Islands/genetics ; Middle Aged ; Adult ; Netherlands ; },
abstract = {Microbiome influences multiple human systems, but its effects on gene methylation is unknown. We investigated the relations between gene methylation in blood and the abundance of common gut bacteria profiled by 16s rRNA gene sequencing in two population-based Dutch cohorts: LifeLines-Deep (LLD, n = 616, discovery) and the Netherlands Twin Register (NTR, n = 296, replication). In LLD, we also explored microbial pathways using data generated by shotgun metagenomic sequencing (n = 683). Methylation in both cohorts was profiled in blood samples using the Illumina 450K array. Discovery and replication analysis identified two independent CpGs associated with the genus Eggerthella: cg16586104 (Pmeta-analysis = 3.21 × 10[-11]) and cg12234533 (Pmeta-analysis = 4.29 × 10[-10]). We also show that microbiome can mediate the effect of environmental factors on host gene methylation. In this first association study linking epigenome to microbiome, we found and replicated the associations of two CpGs to the abundance of genus Eggerthella and identified microbiome as a mediator of the exposome. These associations are observational and suggest further investigation in larger and longitudinal set-ups.},
}

*DNA Methylation
*Gastrointestinal Microbiome/genetics
Humans
*Epigenome
*Genome-Wide Association Study
Male
Female
RNA, Ribosomal, 16S/genetics
CpG Islands/genetics
Middle Aged
Adult
Netherlands

@article {pmid39701930,
year = {2024},
author = {Wen, J and Wang, S and Sun, K and Wang, H and Yuan, Z and Deng, W},
title = {Chang-Wei-Qing Combined with PD-1 Inhibitor Alleviates Colitis-Associated Colorectal Tumorigenesis by Modulating the Gut Microbiota and Restoring Intestinal Barrier.},
journal = {Biological procedures online},
volume = {26},
number = {1},
pages = {32},
pmid = {39701930},
issn = {1480-9222},
support = {ptkwws202002//Shanghai Putuo District Health and Health System Science and Technology Innovation Project/ ; 2021tszk01//Shanghai Putuo District Health and Health System Clinical Specialty Construction Project/ ; ZY[2021-2023]-0302//Shanghai Municipal Health Commission's Shanghai Further Accelerating Traditional Chinese Medicine Development Three-Year Action Plan Project/ ; },
abstract = {Chang-Wei-Qing (CWQ) is a widely recognized Traditional Chinese Medicine (TCM) formulation composed of Astragalus, Codonopsis, Atractylodes, Poria, Coix seed, Akebia trifoliata Koidz, Sargentodoxa cuneata, and Vitis quinquangularis Rehd. This formulation has garnered significant interest for its positive effects in mitigating colorectal cancer, and when combined with PD-1, it affects some gut microbiota associated with tumor infiltrating lymphocytes cells. However, the biological rationale underlying the suppression of colitis-associated colorectal cancer (CAC) in AOM/DSS-treated mice by CWQ combined with PD-1 inhibitor remains to be explored. Our aim is to explore the chemopreventive effect of CWQ combined with PD-1 inhibitor on CAC, with a focus on modulating the gut microbiota. A mouse model of CAC was established using azoxymethane (AOM) and dextran sulfate sodium (DSS) treatment. Pathological evaluation of tissue samples included immunohistochemistry and hematoxylin and eosin staining. Intestinal barrier function was assessed by transmission electron microscopy. Fecal microbiota and metabolites were analyzed through 16 S rRNA gene sequencing and liquid chromatography-mass spectrometry, respectively. Mice treated with antibiotics served as models for fecal microbiota transplantation. CWQ combined with PD-1 inhibitor suppressed CAC in AOM/DSS-treated mice. This combined therapy effectively alleviated gut dysbiosis in the CAC model by increasing microbial diversity, enriching probiotic populations such as Limosilactobacillus and Bifidobacterium, and reducing pathogenic bacteria like Desulfovibrio. Additionally, CWQ combined with PD-1 inhibitor downregulated metabolites associated with the NF-kappa B signaling pathway. The combined treatment also significantly improved intestinal barrier function in CAC mice. Transmission electron microscopy of the CWQ combined with PD-1 inhibitor group showed enhanced cellular integrity, a relatively normal mitochondrial structure with intact membranes, and a more abundant, unexpanded endoplasmic reticulum, underscoring the protective effects of this combination on intestinal barrier integrity. Transcriptomic analysis further demonstrated that the combined therapy upregulated genes involved in tight and adherens junctions, while downregulating genes linked to innate immune responses. CWQ combined with PD-1 inhibitor can ameliorate dysbiosis in the AOM/DSS mouse model, with the metabolites of the gut microbiome potentially possessing anti-inflammatory activity. Moreover, CWQ combined with PD-1 inhibitor improves intestinal barrier function, thereby effectively inhibiting the occurrence and development of CAC.},
}

@article {pmid39701859,
year = {2024},
author = {Barnes, CJ and Bahram, M and Nicolaisen, M and Gilbert, MTP and Vestergård, M},
title = {Microbiome selection and evolution within wild and domesticated plants.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2024.11.011},
pmid = {39701859},
issn = {1878-4380},
abstract = {Microbes are ubiquitously found across plant surfaces and even within their cells, forming the plant microbiome. Many of these microbes contribute to the functioning of the host and consequently affect its fitness. Therefore, in many contexts, including microbiome effects enables a better understanding of the phenotype of the plant rather than considering the genome alone. Changes in the microbiome composition are also associated with changes in the functioning of the host, and there has been considerable focus on how environmental variables regulate plant microbiomes. More recently, studies suggest that the host genome also preconditions the microbiome to the environment of the plant, and the microbiome is therefore subject to evolutionary forces. Here, we outline how plant microbiomes are governed by both environmental variables and evolutionary processes and how they can regulate plant health together.},
}

@article {pmid39701829,
year = {2024},
author = {McAlister, JS and Blum, MJ and Bromberg, Y and Fefferman, NH and He, Q and Lofgren, E and Miller, DL and Schreiner, C and Candan, KS and Szabo-Rogers, H and Reed, JM},
title = {An interdisciplinary perspective of the built-environment microbiome.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiae166},
pmid = {39701829},
issn = {1574-6941},
abstract = {The built environment provides an excellent setting for interdisciplinary research on the dynamics of microbial communities. The system is simplified compared to many natural settings, and to some extent the entire environment can be manipulated, from architectural design to materials use, air flow, human traffic, and capacity to disrupt microbial communities through cleaning. Here we provide an overview of the ecology of the microbiome in the built environment. We address niche space and refugia, population and community (metagenomic) dynamics, spatial ecology within a building, including the major microbial transmission mechanisms, as well as evolution. We also address landscape ecology, connecting microbiomes between physically separated buildings. At each stage we pay particular attention to the actual and potential interface between disciplines, such as ecology, epidemiology, materials science, and human social behavior. We end by identifying some opportunities for future interdisciplinary research on the microbiome of the built environment.},
}

@article {pmid39701818,
year = {2024},
author = {Evans, SE and Valentine, ME and Gallimore, F and Meka, Y and Koehler, SI and Yu, HD and Valentovic, MA and Long, TE},
title = {Perturbations in the Gut Microbiome of C57BL/6J Mice by the Sobriety Aid Antabuse® (Disulfiram).},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxae305},
pmid = {39701818},
issn = {1365-2672},
abstract = {AIMS: Disulfiram (Antabuse®) is an oral alcohol sobriety medication that exhibits antimicrobial activity against Gram-positive facultative anaerobes. The aims of this study were to measure the antimicrobial activity against anaerobic bacteria of the gut human microbiome and establish the extent that disulfiram alters the microbial composition of the ileum, cecum, and feces using C57BL/6 mice.

METHODS AND RESULTS: Antimicrobial susceptibility testing by the microdilution method revealed that disulfiram inhibits the in vitro growth of gut anaerobic species of Bacteroides, Clostridium, Peptostreptococcus, and Porphyromonas. Differential sequencing of 16S rRNA isolated from the ileum, cecum, and feces contents of treated vs. untreated mice showed disulfiram enriches the Gram-negative enteric population. In female mice, the enrichment was greatest in the ileum whereas the feces composition in male mice was the most heavily altered.

CONCLUSIONS: Daily administration of oral disulfiram depletes the enteric Gram-positive anaerobe population as predicted by the MIC data for isolates from the human gut microbiota.},
}

@article {pmid39701663,
year = {2024},
author = {Golshany, H and Helmy, SA and Morsy, NFS and Kamal, A and Yu, Q and Fan, L},
title = {The gut microbiome across the lifespan: how diet modulates our microbial ecosystem from infancy to the elderly.},
journal = {International journal of food sciences and nutrition},
volume = {},
number = {},
pages = {1-27},
doi = {10.1080/09637486.2024.2437472},
pmid = {39701663},
issn = {1465-3478},
abstract = {This comprehensive review examines the impact of dietary patterns on gut microbiome composition and diversity from infancy to old age, linking these changes to age-related health outcomes. It investigates how the gut microbiome develops and changes across life stages, focusing on the influence of dietary factors. The review explores how early-life feeding practices, including breastfeeding and formula feeding, shape the infant gut microbiota and have lasting effects. In elderly individuals, alterations in the gut microbiome are associated with increased susceptibility to infections, chronic inflammation, metabolic disorders and cognitive decline. The critical role of diet in modulating the gut microbiome throughout life is emphasised, particularly the potential benefits of probiotics and fortified foods in promoting healthy ageing. By elucidating the mechanisms connecting food systems to gut health, this review provides insights into interventions that could enhance gut microbiome resilience and improve health outcomes across the lifespan.},
}

@article {pmid39701568,
year = {2025},
author = {Deflorin, N and Ehlert, U and Amiel Castro, RT},
title = {Associations of Maternal Salivary Cortisol and Psychological Symptoms With Human Milk's Microbiome Composition.},
journal = {Psychosomatic medicine},
volume = {87},
number = {1},
pages = {33-45},
doi = {10.1097/PSY.0000000000001351},
pmid = {39701568},
issn = {1534-7796},
mesh = {Humans ; Female ; *Milk, Human/chemistry/microbiology ; *Saliva/chemistry/microbiology ; *Hydrocortisone/analysis/metabolism ; Adult ; Pregnancy ; *Microbiota/physiology ; *Anxiety/metabolism ; *Stress, Psychological/metabolism ; *Depression/microbiology ; Postpartum Period ; },
abstract = {OBJECTIVE: Human milk (HM) is considered the best source of infant nutrition with many benefits for the infant. However, pregnancy changes can lead to increased stress in some women, which might affect HM composition. Although studies have demonstrated a link between maternal psychopathology and child development, it remains unclear how maternal psychobiological changes can be intergenerationally transmitted. We aimed to investigate the associations of maternal stress, depressive symptoms, and anxiety symptoms with the HM microbiome; to analyze these parameters in relation to HM glucocorticoid concentrations; and to explore the influence of HM glucocorticoids on HM bacterial composition.

METHODS: One hundred women completed psychological questionnaires (e.g., EPDS, STAI, GAS) at 34-36 weeks' gestation and in the early postpartum period and provided saliva at 34-36 and 38 weeks' gestation. HM samples were collected in the early postpartum. Microbiota were analyzed using 16S rRNA amplicon sequencing.

RESULTS: Birth anxiety was negatively correlated with Alphaproteobacteria (τ = -0.20, FDR = 0.01), whereas in the postpartum period, anxiety symptoms were negatively correlated with different taxa. The sum of postpartum-related symptoms was linked to lower Propionibacteriales. Salivary cortisol AUCg at 34-36 weeks was negatively correlated with Stenotrophomonas (τ = -0.24, FDR = 0.05), whereas HM cortisol was positively correlated with Streptococcus mitis (τ = 0.26, FDR = 0.03) and Gemella haemolysans (τ = 0.24, FDR = 0.02). No associations emerged between psychobiological parameters and HM glucocorticoids.

CONCLUSIONS: Higher perinatal psychological symptoms and prenatal salivary cortisol AUCg were associated with lower relative abundances of different bacteria, whereas higher HM cortisol was linked to higher Gemella and Streptococcus. These findings suggest a negative association between high maternal psychobiological symptoms and relative abundances of the milk microbiota.},
}

Humans
Female
*Milk, Human/chemistry/microbiology
*Saliva/chemistry/microbiology
*Hydrocortisone/analysis/metabolism
Adult
Pregnancy
*Microbiota/physiology
*Anxiety/metabolism
*Stress, Psychological/metabolism
*Depression/microbiology
Postpartum Period

@article {pmid39701529,
year = {2024},
author = {Firkins, JL and Henderson, EL and Duan, H and Pope, PB},
title = {International Symposium on Ruminant Physiology: Current perspective on rumen microbial ecology to improve fiber digestibility.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2024-25863},
pmid = {39701529},
issn = {1525-3198},
abstract = {Although cellulose has received the most attention, further research is needed for a complete comprehension of other fiber components in forage and nonforage fiber sources corresponding with the array of enzymes needed for depolymerization and resulting fermentation of sugars. The carbohydrate-active enzymes (CAZymes) have been described in detail herein, although new information will no doubt accumulate in the future. Known CAZymes are attributed to taxa that are easily detected via 16S rRNA gene profiling techniques, but such approaches have limitations. We describe how closely related species or strains expand into different niches depending on diet and the dynamic availability of remaining fibrous substrates. Moreover, expression of CAZymes and other enzymes such as in fermentation pathways can shift among strains and even within strains over time of incubation. We describe unique fibrolytic components of bacteria, protozoa, and fungi while emphasizing the development of consortia that efficiently increase neutral detergent fiber degradability (NDFD). For example, more powerful genome-centric functional omics approaches combined with expanded bioinformatics and network analyses are needed to expand our current understanding of ruminal function and the bottlenecks that lead to among-study variation in NDFD. Specific examples highlighted include our lack of fundamental understanding why starch limits NDFD, whereas moderate inclusion of rumen-degraded protein, certain supplemental fatty acids (especially palmitic), and supplemental sugars sometimes stimulates NDFD. Current and future research must uncover deeper complexity in the rumen microbiome through a combination of approaches described herein to be followed by validation using novel cultivation studies and, ultimately, NDFD measured in vivo for integration with ruminant productivity traits.},
}

@article {pmid39701424,
year = {2024},
author = {Hong, SW and Page, R and Truman, P},
title = {Smoking, coffee intake, and Parkinson's disease: Potential protective mechanisms and components.},
journal = {Neurotoxicology},
volume = {106},
number = {},
pages = {48-63},
doi = {10.1016/j.neuro.2024.12.003},
pmid = {39701424},
issn = {1872-9711},
abstract = {Parkinson's disease (PD) is a common progressive neurodegenerative disease characterized by the loss of dopaminergic neurons in the substantia nigra pars compacta (SNpc). Environmental and lifestyle factors, such as smoking and coffee drinking, have been associated with a decreased risk for PD. However, the biological mechanisms underlying protective effects on PD are still not fully understood. It has been suggested that non-nicotine components in cigarette smoke and non-caffeine components in coffee may contribute to this protective effect. The aim of this review was to explore candidate molecules and mechanisms behind the effects of smoking and coffee drinking on PD by integrating findings from previous studies. By cross-referencing an index of tobacco constituents and a list of coffee constituents with existing literature on natural compounds and their structural analogs that show inhibitory activities against monoamine oxidase B, catechol O-methyltransferase, and α-synuclein fibrillation, we have identified tobacco and coffee components that inhibit these targets. Furthermore, tobacco and coffee components potentially play roles in suppressing neuroinflammation, activating the Nrf2 pathway as natural activators, and altering the gut microbiome. This review suggests that the phenolic compounds from tobacco and coffee investigated may contribute to the low incidence of PD in smokers and coffee drinkers, showing moderate to strong potential as therapeutic interventions. The current review suggests that multifunctional molecules found in coffee and cigarette smoke may have potential neuroprotective effects, but none of the data indicates that multifunctionality is required for these effects. This review will deepen our understanding of how smoking and coffee drinking are linked to a reduced risk of PD and will also be important in elucidating the mechanisms underlying the protective effects of smoking and coffee drinking on PD.},
}

@article {pmid39701375,
year = {2024},
author = {Corbett, GA and Corcoran, S and Feehily, C and Soldati, B and Rafferty, A and MacIntyre, DM and Cotter, PD and McAuliffe, FM},
title = {Preterm-birth-prevention with Lactobacillus Crispatus oral probiotics: Protocol for a double blinded randomised placebo-controlled trial (the PrePOP study).},
journal = {Contemporary clinical trials},
volume = {},
number = {},
pages = {107776},
doi = {10.1016/j.cct.2024.107776},
pmid = {39701375},
issn = {1559-2030},
abstract = {INTRODUCTION: Effective spontaneous preterm birth (sPTB) prevention is an urgent unmet clinical need. Vaginal depletion of Lactobacillus crispatus is linked to sPTB. This trial will investigate impact of an oral Lactobacillus spp. probiotic product containing an L. crispatus strain with other Lactobacilli spp., on the maternal vaginal and gut microbiome in pregnancies high-risk for sPTB.

METHODS: A double-blind, placebo-controlled, randomised trial will be performed at the National Maternity Hospital Dublin, Ireland. Inclusion criteria are women with history of sPTB or mid-trimester loss, cervical surgery (cone biopsy or two previous large-loop-excision-of-transformation-zone) or uterine anomaly. The intervention is oral supplementation for twelve weeks with probiotic or identical placebo. The probiotic will contains: ◦ 4 billion CFU Lactobacillus crispatus Lbv 88(2x10[9]CFU/Capsule) ◦ 4 billion CFU Lactobacillus rhamnosus Lbv 96(2x10[9]CFU/Capsule) ◦ 0.8 billion CFU Lactobacillus jensenii Lbv 116(0.4x10[9]CFU/Capsule) ◦ 1.2 billion CFU Lactobacillus gasseri Lbv 150(0.6x10[9]CFU/Capsule) Investigators and participants will be blinded to assignment.

RESULTS: The primary outcome is detectable L. crispatus in the vaginal microbiome after twelve weeks of treatment, measured using high-throughput DNA sequencing. A total of 126 women are required to detect a 25 % increase in detectable L. crispatus. Secondary outcomes include impact of intervention on the gut microbiome and metabolome, rate of sPTB and mid-trimester loss, neonatal outcomes and maternal morbidity.

CONCLUSIONS: This randomised trial will investigate ability of an oral probiotic containing L. crispatus to increase its abundance in the vaginal microbiome, both directly by horizontal transfer and indirectly via microbiome and metabolome of the gut.},
}

@article {pmid39701354,
year = {2024},
author = {Liu, J and Zhou, M and Zhou, L and Dang, R and Xiao, L and Tan, Y and Li, M and Yu, J and Zhang, P and Hernández, M and Lichtfouse, E},
title = {Methane production related to microbiota in dairy cattle feces.},
journal = {Environmental research},
volume = {},
number = {},
pages = {120642},
doi = {10.1016/j.envres.2024.120642},
pmid = {39701354},
issn = {1096-0953},
abstract = {Methane (CH4) emission from livestock feces, led by ruminants, shows a profound impact on global warming. Despite this, we have almost no information on the syntrophy of the intact microbiome metabolisms, from carbohydrates to the one-carbon units, covering multiple stages of ruminant development. In this study, syntrophic effects of polysaccharide degradation and acetate-producing bacteria, and methanogenic archaea were revealed through metagenome-assembled genomes from water saturated dairy cattle feces. Although CH4 is thought to be produced by archaea, more edges, nodes, and balanced interaction types revealed by network analysis provided a closed bacteria-archaea network. The CH4 production potential and pathways were further evaluated through dynamic, thermodynamic and [13]C stable isotope analysis. The powerful CH4 production potential benefited from the metabolic flux: classical polysaccharides, soluble sugar (glucose, galactose, lactose), acetate, and CH4 produced via typical acetoclastic methanogenesis. In comparison, a cooperative model dominated by hydrogenotrophic methanogenic archaea presented a weak ability to generate CH4. Our findings comprehensively link carbon and CH4 metabolism paradigm to specific microbial lineages which are shaped related to developmental stages of the dairy cattle, directing influencing global warming from livestock and waste treatment.},
}

@article {pmid39701328,
year = {2024},
author = {Zhou, X and Ganz, AB and Rayner, A and Cheng, TY and Oba, H and Rolnik, B and Lancaster, S and Lu, X and Li, Y and Johnson, JS and Hoyd, R and Spakowicz, DJ and Slavich, GM and Snyder, MP},
title = {Dynamic human gut microbiome and immune shifts during an immersive psychosocial intervention program.},
journal = {Brain, behavior, and immunity},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.bbi.2024.12.027},
pmid = {39701328},
issn = {1090-2139},
abstract = {BACKGROUND: Although depression is a leading cause of disability worldwide, the pathophysiological mechanisms underlying this disorder-particularly those involving the gut microbiome-are poorly understood.

METHOD: To investigate, we conducted a community-based observational study to explore complex associations between changes in the gut microbiome, cytokine levels, and depression symptoms in 52 participants (Mage = 49.56, SD = 13.31) receiving an immersive psychosocial intervention. A total of 142 multi-omics samples were collected from participants before, during, and three months after the nine-day inquiry-based stress reduction program.

RESULTS: Results revealed that depression was associated with both an increased presence of putatively pathogenic bacteria and reduced microbial beta-diversity. Following the intervention, we observed reductions in neuroinflammatory cytokines and improvements in several mental health indicators. Interestingly, participants with a Prevotella-dominant microbiome showed milder symptoms when depressed, along with a more resilient microbiome and more favorable inflammatory cytokine profile, including reduced levels of CXCL-1.

CONCLUSIONS: These findings reveal a potentially protective link between the Prevotella-dominant microbiome and depression, as evidenced by a reduced pro-inflammatory environment and fewer depressive symptoms. These insights, coupled with observed improvements in neuroinflammatory markers and mental health from the intervention, may highlight potential avenues for microbiome-targeted therapies for managing depression.},
}

@article {pmid39701092,
year = {2024},
author = {Lee, HI and Jang, BS and Chang, JH and Kim, E and Lee, TH and Park, JH and Chie, EK},
title = {Relationships between the Microbiome and Response to Neoadjuvant Chemoradiotherapy in Locally Advanced Rectal Cancer.},
journal = {Cancer research and treatment},
volume = {},
number = {},
pages = {},
doi = {10.4143/crt.2024.521},
pmid = {39701092},
issn = {2005-9256},
abstract = {PURPOSE: This study aimed to investigate the dynamic changes in the microbiome of patients with locally advanced rectal cancer (LARC) undergoing neoadjuvant chemoradiotherapy (nCRT), focusing on the relationship between the microbiome and response to nCRT.

MATERIALS AND METHODS: We conducted a longitudinal study involving 103 samples from 26 patients with LARC. Samples were collected from both the tumor and normal rectal tissues before and after nCRT. Diversity, taxonomic, and network analyses were performed to compare the microbiome profiles across different tissue types, pre- and post-nCRT time-points, and nCRT responses.

RESULTS: Between the tumor and normal tissue samples, no differences in microbial diversity and composition were observed. However, when pre- and post-nCRT samples were compared, there was a significant decrease in diversity, along with notable changes in composition. Non-responders exhibited more extensive changes in their microbiome composition during nCRT, characterized by an increase in pathogenic microbes. Meanwhile, responders had relatively stable microbiome communities with more enriched butyrate-producing bacteria. Network analysis revealed distinct patterns of microbial interactions between responders and non-responders, where butyrate-producing bacteria formed strong networks in responders, while opportunistic pathogens formed strong networks in non-responders. A Bayesian network model for predicting the nCRT response was established, with butyrate-producing bacteria playing a major predictive role.

CONCLUSION: Our study demonstrated a significant association between the microbiome and nCRT response in LARC patients, leading to the development of a microbiome-based response prediction model. These findings suggest potential applications of microbiome signatures for predicting and optimizing nCRT treatment in LARC patients.},
}

@article {pmid39701054,
year = {2024},
author = {Hongler, K and Lounici, A and Maurer, E and Lanz, U and Szathmari, O and Reuter, Y and Nussbaum, S and Steinborn, I and Haedrich, A and Mölling, MA and Wein, U and Bocek, I and Hersberger, L and Brühl, AB and Lang, UE and Liwinski, T},
title = {KETO-MOOD: Ketogenic Diet for Microbiome Optimization and Overcoming Depression: A Protocol for a Randomized Controlled Trial.},
journal = {Neuroimmunomodulation},
volume = {},
number = {},
pages = {1-23},
doi = {10.1159/000542979},
pmid = {39701054},
issn = {1423-0216},
abstract = {Major Depressive Disorder (MDD) significantly impacts millions worldwide, with limited success in achieving remission for many patients, leading to high disease burden and increased suicide risk. Psychotherapy and antidepressants, although effective, do not provide relief for all, prompting the search for alternative treatments. Ketogenic diets have demonstrated positive effects on brain health. Our study aims to investigate the efficacy of the ketogenic diet in alleviating MDD symptoms, filling a critical gap in psychiatric treatment options and offering a novel dietary approach with potential to mitigate disease burden and enhance mental well-being. This phase randomized controlled trial will evaluate the efficacy of a ten-week program of dietitian counseling and ketogenic meal provision versus an intervention with similar dietetic contact promoting a healthy, insulin-lowering, non-ketogenic diet. The primary outcome is the change in the Patient Health Questionnaire nine-item depression score. Secondary outcomes include cognitive and affective mindfulness, self-efficacy, sleep, cognitive function, work and social adjustment, and various immunological, metabolic, and microbiome markers at weeks 6 and 10. This study addresses a critical gap in depression treatment by exploring the ketogenic diet's potential as a novel intervention. Given the global impact of depression and limitations of current therapies, this research is valuable for its potential neuroprotective and metabolic benefits. It aims to advance psychiatric treatment strategies by clarifying the diet's effects on depression and its underlying mechanisms.},
}

@article {pmid39700995,
year = {2024},
author = {Xu, X and Hao, Y and Cai, Z and Cao, Y and Jia, W and Zhao, J and White, JC and Ma, C},
title = {Nanoscale‑boron nitride positively alters rhizosphere microbial communities and subsequent cucumber (Cucumis sativa) growth: A metagenomic analysis.},
journal = {The Science of the total environment},
volume = {958},
number = {},
pages = {178115},
doi = {10.1016/j.scitotenv.2024.178115},
pmid = {39700995},
issn = {1879-1026},
abstract = {Boron (B) deficiency affects over 132 crop species globally, making effective B supplement crucial for enhancing agricultural yield and health. This study explores an innovative application of nanoscale boron nitride (nano-BN) as a sustainable solution for addressing B deficiency in crops. Cucumber seedlings were treated with different contents of nano-BN under greenhouse conditions and both B and N ionic treatments were set as comparisons. Results show that soil application of 10 mg/kg nano-BN achieved a remarkable 15.8 % increase in fresh weight compared to the control. Notably, nano-BN exhibited superior efficiency in providing essential micronutrients without inducing toxicity as compared to traditional ionic B sources. Phytohormone correlation analysis reveals that nano-BN application significantly enhances levels of indole-3-acetic acid (IAA) and cytokinins while reducing abscisic acid (ABA), fostering optimal plant growth conditions. Furthermore, increases in dissolved organic matter (DOM) and dissolved organic carbon (DOC) levels in the rhizosphere improve nutrient availability and promote beneficial microbial activity in the soil as affected by nano-BN. Metagenomics techniques were used to investigate the impact of nano-BN on soil carbon and nitrogen cycling, alongside its effects on the soil microbiome. The upregulation of genes associated with fermentation pathways as affected by nano-BN suggests the enhanced carbon cycling. Additionally, nano-BN upregulated a number of functional genes involved in nitrogen-based processes, leading to a significant increase in microorganisms harboring nitrogen-fixing genes, including Phenylobacterium, Novosphingobium, and Reyranella. Overall, these findings provide valuable insight into the application of nano-BN in agriculture to sustainably increase crop productivity and enhance the efficiency of carbon and nitrogen cycling.},
}

@article {pmid39700931,
year = {2024},
author = {Wang, L and Tian, Y and Sun, J and Li, Y and Yang, Z},
title = {The efficacy of bioretention systems amended with iron-modified biochar for the source-separated and component-specific treatment of rainwater runoff: A microbiome perspective.},
journal = {Journal of environmental management},
volume = {373},
number = {},
pages = {123728},
doi = {10.1016/j.jenvman.2024.123728},
pmid = {39700931},
issn = {1095-8630},
abstract = {Bioretention systems offer advantages in controlling non-point source pollution from runoff rainwater. However, the systems frequently encounter challenges, including insufficient stability of nitrogen and phosphorus removal. Limited research has been performed on bioretention systems which integrate actual data from non-point source pollution cases for the quantitative and qualitative refinement of initial and non-initial rainwater. Moreover, the potential linkages between amended media and microbial communities in bioretention systems with the addition of novel functional filler have not been explored. In this study, a system for treating both initial and non-initial rainwater was established through measurements including iron-modified biochar (FeBC) packing and the optimization of the layer structures. In system treating initial rainwater, the systems loaded with FeBC maintained stable NH4[+]-N and NO3[-]-N removal rates of over 95% and 80%, respectively under 12 rainfall simulation events. After a 10-day antecedent drying duration (ADD), the removal rates for NH4[+]-N and PO4[3-]-P remained above 78% and 85%. In systems designed to process non-initial rainwater, increasing the height of the transition layer effectively enhanced the NH4[+]-N removal stability. Meanwhile, increasing the height of the drainage layer could promote PO4[3-]-P removal rates to over 75%. The addition of FeBC facilitated the growth of certain denitrifiers improved overall NO3[-]-N removal during successive rainfall events. The microbial communities may adapt to variations in the external environment by enhancing the synthesis of ribosome and the metabolism of pyrimidine and purine, further improving the stability of NH4[+]-N removal. This study provides a theoretical basis for the precise enhancement of nitrogen and phosphorus removal and the design of bioretention systems for differentiated treatment of rainwater, guiding their design and applications in different regions.},
}

@article {pmid39700897,
year = {2024},
author = {Pirola, CJ and Salatino, A and Fernández Gianotti, T and Castaño, GO and Garaycoechea, M and Sookoian, S},
title = {Corrigendum to "Cross talk between the liver microbiome and epigenome in patients with metabolic dysfunction-associated steatotic liver disease".},
journal = {EBioMedicine},
volume = {111},
number = {},
pages = {105525},
doi = {10.1016/j.ebiom.2024.105525},
pmid = {39700897},
issn = {2352-3964},
}

@article {pmid39700680,
year = {2024},
author = {Wang, Z and Zhang, L and Liu, X and Xu, L},
title = {The role of reproductive tract microbiota in gynecological health and diseases.},
journal = {Journal of reproductive immunology},
volume = {167},
number = {},
pages = {104418},
doi = {10.1016/j.jri.2024.104418},
pmid = {39700680},
issn = {1872-7603},
abstract = {The reproductive tract, as a lumen connected to the outside world, its microbial community is influenced by various factors. The changes in its microbiome are closely related to women's health. The destruction of the micro ecological environment will lead to various infections, such as Bacterial vaginosis, sexually transmitted infections, adverse pregnancy outcomes, infertility and tumors. In recent years, with the continuous development and progress of molecular biology, research on reproductive tract microbiota has become a clinical hotspot. The reproductive tract microbiota is closely related to the occurrence and development of female reproductive tract diseases such as vaginitis, pelvic inflammation, PCOS, cervical lesions, and malignant tumors. This article reviews the research on the relationship between vaginal microbiota and female reproductive tract diseases, in order to provide theoretical basis for the prevention and treatment of female reproductive tract diseases.},
}

@article {pmid39699589,
year = {2024},
author = {Fredriksen, S and Neila-Ibáñez, C and Hennig-Pauka, I and Guan, X and Dunkelberger, J and de Oliveira, IF and Ferrando, ML and Correa-Fiz, F and Aragon, V and Boekhorst, J and van Baarlen, P and Wells, JM},
title = {Streptococcus suis infection on European farms is associated with an altered tonsil microbiome and resistome.},
journal = {Microbial genomics},
volume = {10},
number = {12},
pages = {},
pmid = {39699589},
issn = {2057-5858},
mesh = {Animals ; Swine ; *Streptococcus suis/genetics ; *Streptococcal Infections/microbiology/veterinary ; *Swine Diseases/microbiology ; *Microbiota ; *Farms ; *Palatine Tonsil/microbiology ; Case-Control Studies ; Europe ; Cross-Sectional Studies ; Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Streptococcus suis is a Gram-positive opportunistic pathogen causing systemic disease in piglets around weaning age. The factors predisposing to disease are not known. We hypothesized that the tonsillar microbiota might influence disease risk via colonization resistance and/or co-infections. We conducted a cross-sectional case-control study within outbreak farms complemented by selective longitudinal sampling and comparison with control farms without disease occurrence. We found a small but significant difference in tonsil microbiota composition between case and control piglets (n=45+45). Variants of putative commensal taxa, including Rothia nasimurium, were reduced in abundance in case piglets compared to asymptomatic controls. Case piglets had higher relative abundances of Fusobacterium gastrosuis, Bacteroides heparinolyticus and uncultured Prevotella and Alloprevotella species. Piglets developing disease post-weaning had reduced alpha diversity pre-weaning. Despite case-control pairs receiving equal antimicrobial treatment, case piglets had a higher abundance of antimicrobial resistance genes conferring resistance to antimicrobial classes used to treat S. suis. This might be an adaption of disease-associated strains to frequent antimicrobial treatment.},
}

Animals
Swine
*Streptococcus suis/genetics
*Streptococcal Infections/microbiology/veterinary
*Swine Diseases/microbiology
*Microbiota
*Farms
*Palatine Tonsil/microbiology
Case-Control Studies
Europe
Cross-Sectional Studies
Drug Resistance, Bacterial/genetics
Anti-Bacterial Agents/pharmacology

@article {pmid39699254,
year = {2024},
author = {Weaver, D and Gago, S and Bassetti, M and Giacobbe, DR and Prattes, J and Hoenigl, M and Reizine, F and Guegan, H and Gangneux, J-P and Bromley, MJ and Bowyer, P},
title = {Mycobiome analyses of critically ill COVID-19 patients.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0411023},
doi = {10.1128/spectrum.04110-23},
pmid = {39699254},
issn = {2165-0497},
abstract = {Coronavirus disease 2019 (COVID-19)-associated pulmonary aspergillosis (CAPA) is a life-threatening complication in patients with severe COVID-19. Previously, acute respiratory distress syndrome in patients with COVID-19 has been associated with lung fungal dysbiosis, evidenced by reduced microbial diversity and Candida colonization. Increased fungal burden in the lungs of critically ill COVID-19 patients is linked to prolonged mechanical ventilation and increased mortality. However, specific mycobiome signatures associated with severe COVID-19 in the context of survival and antifungal drug prophylaxis have not yet been determined, and such knowledge could have an important impact on treatment. To understand the composition of the respiratory mycobiome in critically ill COVID-19 patients with and without CAPA and the impact of antifungal use in patient outcome, we performed a multinational study of 39 COVID-19 patients in intensive care units (ICUs). Respiratory mycobiome was profiled using internal transcribed spacer 1 sequencing, and Aspergillus fumigatus burden was further validated using quantitative PCR. Fungal communities were investigated using alpha diversity, beta diversity, taxa predominance, and taxa abundances. Respiratory mycobiomes of COVID-19 patients were dominated by Candida and Aspergillus. There was no significant association with corticosteroid use or CAPA diagnosis and respiratory fungal communities. Increased A. fumigatus burden was associated with mortality and, the use of azoles at ICU admission was linked with an absence of A. fumigatus. Our findings suggest that mold-active antifungal treatment at ICU admission may be linked with reduced A. fumigatus-associated mortality in severe COVID-19. However, further studies are warranted on this topic.IMPORTANCEInvasive fungal infections are a serious complication affecting up to a third of patients with severe COVID-19. Nevertheless, our understanding of the fungal communities in the lungs during critically ill COVID-19 remains limited. Evidence suggests a higher fungal burden is associated with prolonged ventilation and higher mortality, although the particular organisms responsible for this link are unclear. Antifungal prophylaxis may be beneficial for reducing the burden of fungal co-infections in COVID-19 intensive care. However, the composition of the fungal microbiome in severe COVID-19 in relation to prophylactic antifungals, as well as how this is associated with survival outcomes, is yet to be studied. Our study provides insights into the lung fungal microbiome in severe COVID-19 and has found antifungal treatment to be associated with lower Aspergillus fumigatus burden and that higher levels of this pathogen are associated with mortality. Therefore, our study suggests mold-active antifungal prophylaxis may be beneficial in severe COVID-19.},
}

@article {pmid39699251,
year = {2024},
author = {Mottawea, W and Yousuf, B and Sultan, S and Ahmed, T and Yeo, J and Hüttmann, N and Li, Y and Bouhlel, NE and Hassan, H and Zhang, X and Minic, Z and Hammami, R},
title = {Multi-level analysis of gut microbiome extracellular vesicles-host interaction reveals a connection to gut-brain axis signaling.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0136824},
doi = {10.1128/spectrum.01368-24},
pmid = {39699251},
issn = {2165-0497},
abstract = {UNLABELLED: Microbiota-released extracellular vesicles (MEVs) have emerged as a key player in intercellular signaling. However, their involvement in the gut-brain axis has been poorly investigated. We hypothesize that MEVs cross host cellular barriers and deliver their cargoes of bioactive compounds to the brain. In this study, we aimed to investigate the cargo capacity of MEVs for bioactive metabolites and their interactions with the host cellular barriers. First, we conducted a multi-omics profiling of MEVs' contents from ex vivo and stool samples. Metabolomics analysis identified various neuro-related compounds encapsulated within MEVs, such as arachidonyl-dopamine, gabapentin, glutamate, and N-acylethanolamines. Metaproteomics unveiled an enrichment of enzymes involved in neuronal metabolism, primarily in the glutamine/glutamate/gamma-aminobutyric acid (GABA) pathway. These neuro-related proteins and metabolites were correlated with Bacteroides spp. We isolated 18 Bacteroides strains and assessed their GABA production capacity in extracellular vesicles (EVs) and culture supernatant. A GABA-producing Bacteroides finegoldii, released EVs with a high GABA content (4 µM) compared to Phocaeicola massiliensis. Upon testing the capacity of MEVs to cross host barriers, MEVs exhibited a dose-dependent paracellular transport and were endocytosed by Caco-2 and hCMEC/D3 cells. Exposure of Caco-2 cells to MEVs did not alter expression of genes related to intestinal barrier integrity, while affected immune pathways and cell apoptosis process as revealed by RNA-seq analyses. In vivo, MEVs biodistributed across mice organs, including the brain, liver, stomach, and spleen. Our results highlight the ability of MEVs to cross the intestinal and blood-brain barriers to deliver their cargoes to distant organs, with potential implication for the gut-brain axis.

IMPORTANCE: Microbiota-released extracellular vesicles (MEVs) have emerged as a key player in intercellular signaling. In this study, a multi-level analysis revealed presence of a diverse array of biologically active molecules encapsulated within MEVs, including neuroactive metabolites, such as arachidonyl-dopamine, gabapentin, glutamate, and N-acylethanolamines, and gamma-aminobutyric acid (GABA). Metaproteomics also unveiled an enrichment of neural-related proteins, mainly the glutamine/glutamate/GABA pathway. MEVs were able to cross epithelial and blood-brain barriers in vitro. RNA-seq analyses showed that MEVs stimulate several immune pathways while suppressing cell apoptosis process. Furthermore, MEVs were able to traverse the intestinal barriers and reach distal organs, including the brain, thereby potentially influencing brain functionality and contributing to mental and behavior.},
}

@article {pmid39699199,
year = {2024},
author = {Almeida-Santos, AC and Duarte, B and Tedim, AP and Teixeira, MJ and Prata, JC and Azevedo, RMS and Novais, C and Peixe, L and Freitas, AR},
title = {The healthy human gut can take it all: vancomycin-variable, linezolid-resistant strains and specific bacteriocin-species interplay in Enterococcus spp.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0169924},
doi = {10.1128/aem.01699-24},
pmid = {39699199},
issn = {1098-5336},
abstract = {Enterococcus spp. are opportunistic human pathogens colonizing the human gut and a significant reservoir for the continuous adaptation of hospital clones. However, studies on the features of enterococci species co-colonizing healthy individuals are scarce. We investigated the prevalence, antibiotic resistance, and bacteriocin profiles of Enterococcus species in fecal samples from healthy adults in Portugal using culture-based methods, WGS, and bacteriocin inhibition assays. Results were compared with data from a 2001 study in the same region. Enterococcus spp. (n = 315; 24% MDR) were recovered from all volunteers. Enterococcus lactis was the prevalent species (75%), followed by Enterococcus faecalis (65%) and Enterococcus faecium (47%). E. lactis prevalence increased 2.5-fold since 2001. Linezolid resistance genes (optrA/poxtA) were detected in E. faecium and Enterococcus thailandicus isolates, while a vancomycin-variable E. faecium was also identified. Virulence and plasmid profiles were diverse across species, with evidence of exchange of virulence markers and plasmid replicons between E. faecium and E. lactis. Bacteriocin gene repertoires were extensive and species-specific. Higher numbers of bacteriocin genes were associated with stronger inhibition profiles, and 25% of E. faecium and E. lactis isolates were capable of inhibiting relevant VRE clones. This study unveils the co-occurrence and ecological dynamics of Enterococcus species in the healthy human gut, reinforcing its role as a reservoir for key antibiotic resistance genes and potentially pathogenic strains. The shift toward E. lactis prevalence and the detection of linezolid resistance genes in healthy individuals underscore the need for ongoing surveillance of the gut microbiome to guide public health strategies and antibiotic stewardship efforts.IMPORTANCEThis study highlights the role of Enterococcus species in the healthy human gut, revealing important insights into their prevalence and antibiotic resistance. It emphasizes that the human gut serves as a significant reservoir for antibiotic-resistant strains and shows a notable increase and prevalence of Enterococcus lactis, which has been underappreciated due to identification challenges. The research also underscores the bacteriocins' role in microbial competition, where commensal strains inhibit clinical VRE, potentially aiding the restoration of the gut microbiota, after antibiotic treatment. The findings accentuate the need for ongoing surveillance to track changes in gut bacteria, especially with the emergence of resistance genes to last resort antibiotics. Such monitoring is crucial for shaping public health strategies and managing the growing threat of antibiotic-resistant infections. Profiling bacteriocins at the species and strain level can identify ecological adaptation factors and inform strategies to target high-risk clones.},
}

@article {pmid39699194,
year = {2024},
author = {Nerva, L and Gambino, G and Moffa, L and Spada, A and Falginella, L and De Luca, E and Zambon, Y and Chitarra, W},
title = {Conjoined partners: efficacy and side effects of grafting and dsRNA application on the microbial endophyte population of grapevine plants inoculated with two esca-related fungal pathogens.},
journal = {Journal of experimental botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/jxb/erae461},
pmid = {39699194},
issn = {1460-2431},
support = {CN00000022//Agritech National Research Center/ ; //European Union/ ; },
abstract = {Grafting has been exploited since 7000 BC to enhance productivity, disease resistance, and adaptability of cultivated plants to stressful conditions especially in woody crops such as grapevine (Vitis spp.). In contrast, the application of sequence specific double-stranded RNAs (dsRNAs) to control fungal pathogens and insect pests has only been recently developed. The possibility of combining these approaches to enhance plant resilience, reducing reliance on pesticides, offers new perspectives for a more sustainable agriculture. In this study, we assessed the potential of utilizing dsRNAs to enhance resilience against esca-related wood fungal pathogens in grapevine, considering various rootstock-scion combinations. The results showed that the scion genotype modulates the ability of the rootstock to cope with the inoculated wood fungal pathogens, mainly by altering the efficacy of producing stilbene compounds. Additionally, we found that dsRNAs reduced the growth of two inoculated esca-related fungal pathogens but they did not completely stop their colonization. Furthermore, wood microbiome data showed that the scion genotype (always belonging to Vitis vinifera species) was also able to influence the rootstock-associated microbiota, with a major effect on the fungal community. Lastly, adverse effects on non-target microorganisms are reported, raising questions on the environmental fate of dsRNAs and how dsRNAs can directly or indirectly affect plant-associated microbial communities.},
}

@article {pmid39699190,
year = {2024},
author = {Prattico, C and Gonzalez, E and Dridi, L and Jazestani, S and Low, KE and Abbott, DW and Maurice, CF and Castagner, B},
title = {Identification of novel fructo-oligosaccharide bacterial consumers by pulse metatranscriptomics in a human stool sample.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0066824},
doi = {10.1128/msphere.00668-24},
pmid = {39699190},
issn = {2379-5042},
abstract = {UNLABELLED: Dietary fibers influence the composition of the human gut microbiota and directly contribute to its downstream effects on host health. As more research supports the use of glycans as prebiotics for therapeutic applications, the need to identify the gut bacteria that metabolize glycans of interest increases. Fructo-oligosaccharide (FOS) is a common diet-derived glycan that is fermented by the gut microbiota and has been used as a prebiotic. Despite being well studied, we do not yet have a complete picture of all FOS-consuming gut bacterial taxa. To identify new bacterial consumers, we used a short exposure of microbial communities in a stool sample to FOS or galactomannan as the sole carbon source to induce glycan metabolism genes. We then performed metatranscriptomics, paired with whole metagenomic sequencing, and 16S amplicon sequencing. The short incubation was sufficient to cause induction of genes involved in carbohydrate metabolism, like carbohydrate-active enzymes (CAZymes), including glycoside hydrolase family 32 genes, which hydrolyze fructan polysaccharides like FOS and inulin. Interestingly, FOS metabolism transcripts were notably overexpressed in Blautia species not previously reported to be fructan consumers. We therefore validated the ability of different Blautia species to ferment fructans by monitoring their growth and fermentation in defined media. This pulse metatranscriptomics approach is a useful method to find novel consumers of prebiotics and increase our understanding of prebiotic metabolism by CAZymes in the gut microbiota.

IMPORTANCE: Complex carbohydrates are key contributors to the composition of the human gut microbiota and play an essential role in the microbiota's effects on host health. Understanding which bacteria consume complex carbohydrates, or glycans, provides a mechanistic link between dietary prebiotics and their beneficial health effects, an essential step for their therapeutic application. Here, we used a pulse metatranscriptomics pipeline to identify bacterial consumers based on glycan metabolism induction in a human stool sample. We identified novel consumers of fructo-oligosaccharide among Blautia species, expanding our understanding of this well-known glycan. Our approach can be applied to identify consumers of understudied glycans and expand our prebiotic repertoire. It can also be used to study prebiotic glycans directly in stool samples in distinct patient populations to help delineate the prebiotic mechanism.},
}

@article {pmid39699186,
year = {2024},
author = {Lei, Y and Li, M and Zhang, H and Deng, Y and Dong, X and Chen, P and Li, Y and Zhang, S and Li, C and Wang, S and Tao, R},
title = {Comparative analysis of the human microbiome from four different regions of China and machine learning-based geographical inference.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0067224},
doi = {10.1128/msphere.00672-24},
pmid = {39699186},
issn = {2379-5042},
abstract = {The human microbiome, the community of microorganisms that reside on and inside the human body, is critically important for health and disease. However, it is influenced by various factors and may vary among individuals residing in distinct geographic regions. In this study, 220 samples, consisting of sterile swabs from palmar skin and oral and nasal cavities were collected from Chinese Han individuals living in Shanghai, Chifeng, Kunming, and Urumqi, representing the geographic regions of east, northeast, southwest, and northwest China. The full-length 16S rRNA gene of the microbiota in each sample was sequenced using the PacBio single-molecule real-time sequencing platform, followed by clustering the sequences into operational taxonomic units (OTUs). The analysis revealed significant differences in microbial communities among the four regions. Cutibacterium was the most abundant bacterium in palmar samples from Shanghai and Kunming, Psychrobacter in Chifeng samples, and Psychrobacillus in Urumqi samples. Additionally, Streptococcus and Staphylococcus were the dominant bacteria in the oral and nasal cavities. Individuals from the four regions could be distinguished and predicted based on a model constructed using the random forest algorithm, with the predictive effect of palmar microbiota being better than that of oral and nasal cavities. The prediction accuracy using hypervariable regions (V3-V4 and V4-V5) was comparable with that of using the entire 16S rRNA. Overall, our study highlights the distinctiveness of the human microbiome in individuals living in these four regions. Furthermore, the microbiome can serve as a biomarker for geographic origin inference, which has immense application value in forensic science.IMPORTANCEMicrobial communities in human hosts play a significant role in health and disease, varying in species, quantity, and composition due to factors such as gender, ethnicity, health status, lifestyle, and living environment. The characteristics of microbial composition at various body sites of individuals from different regions remain largely unexplored. This study utilized single-molecule real-time sequencing technology to detect the entire 16S rRNA gene of bacteria residing in the palmar skin, oral, and nasal cavities of Han individuals from four regions in China. The composition and structure of the bacteria at these three body sites were well characterized and found to differ regionally. The results elucidate the differences in bacterial communities colonizing these body sites across different regions and reveal the influence of geographical factors on human bacteria. These findings not only contribute to a deeper understanding of the diversity and geographical distribution of human bacteria but also enrich the microbiome data of the Asian population for further studies.},
}

@article {pmid39699131,
year = {2024},
author = {Romano, J and Hoyer, N and Krumbeck, JA and Goodnight, A and Brandão, J and Sadar, MJ},
title = {ORAL MICROBIOME OF BENNETT'S (NOTAMACROPUS RUFOGRISEUS) AND YELLOW-FOOTED (PETROGALE XANTHOPUS) ROCK WALLABIES AND THE IMPACT OF INTRAORAL DISEASE.},
journal = {Journal of zoo and wildlife medicine : official publication of the American Association of Zoo Veterinarians},
volume = {55},
number = {4},
pages = {849-857},
doi = {10.1638/2023-0028},
pmid = {39699131},
issn = {1042-7260},
mesh = {Animals ; *Macropodidae/microbiology ; *Microbiota ; *Mouth/microbiology ; Mouth Diseases/veterinary/microbiology ; Bacteria/isolation & purification/classification ; Female ; Male ; },
abstract = {Intraoral disease, including macropod progressive periodontal disease, is one of the leading causes of morbidity and mortality for wallabies under human care. Clinical signs associated with intraoral disease vary, and diagnostic findings can be difficult to interpret without intraoral radiographs or advanced imaging; therefore, this disease process can be challenging to detect in its early stages. Previous studies have investigated the effects of intraoral disease on the normal oral microbiome of various domestic species. Results from these studies demonstrate specific changes to the oral microbiome that have the potential to be used as an early indicator of intraoral disease. The purpose of this study was to evaluate the oral microbiome of 12 Bennett's wallabies (Notamacropus rufogriseus) and 3 yellow-footed rock wallabies (Petrogale xanthopus), using next-generation sequencing, to determine if intraoral disease influences the oral microbiome, as demonstrated in other species. The study identified a total of 295 bacterial species and 388 fungal species from the oral cavity of 15 wallabies. Although not statistically significant, the results of the study suggest an increase in the number of anaerobic bacterial species in sites of disease, including Actinomyces bowdenii, a species from the family Propionibacteriaceae, Peptostreptococcus canis, Fretibacterium sp., and Synergistes jonesii. It also revealed a decrease in microbial diversity in animals with active intraoral disease compared with animals without active disease, as well as at the site of disease compared with the control site. Results from this study support the findings of similar studies assessing the oral microbiome of macropods. Additional studies are warranted to better understand the normal oral microbiome of Bennett's and yellow-footed rock wallabies and the dynamic changes in the microbiome that occur in animals with intraoral disease.},
}

Animals
*Macropodidae/microbiology
*Microbiota
*Mouth/microbiology
Mouth Diseases/veterinary/microbiology
Bacteria/isolation & purification/classification
Female
Male

@article {pmid39698753,
year = {2024},
author = {Stothart, MR and Lavergne, S and McCaw, L and Singh, H and de Vega, W and Amato, K and Poissant, J and Boonstra, R},
title = {Population Dynamics and the Microbiome in a Wild Boreal Mammal: The Snowshoe Hare Cycle and Impacts of Diet, Season and Predation Risk.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e17629},
doi = {10.1111/mec.17629},
pmid = {39698753},
issn = {1365-294X},
support = {//Polar Knowledge Canada/ ; //Natural Sciences and Engineering Research Council of Canada/ ; },
abstract = {The North American boreal forest is a massive ecosystem, and its keystone herbivore is the snowshoe hare (Lepus americanus). Hares are exposed to considerable environmental extremes in diet and weather, food availability, and predation risk. Gut microbiomes have been suggested to facilitate adaptive animal responses to environmental change, but severe environmental challenges to homeostasis can also disrupt host-microbiome relationships. To better understand gut microbiome contributions to animal acclimation, we studied the faecal bacterial microbiome of wild hares across two types of extreme environmental change that are integral to their natural history: (1) seasonal transitions between summer and winter, and (2) changes over the ~10 year 'boom-bust' population cycles that are characterised by shifting food resource availability and predation pressure. When compared to summer, hares in winter had lower bacterial richness and were depleted in 20 families (including Oxalobacteraceae and Christensenellaceae) but enriched for Ruminococcaceae (a family which contains plant fibre degrading bacteria) alongside nine other bacterial groups. Marked bacterial microbiome differences also occurred across phases of the population cycle. Bacterial microbiomes were lower in richness and compositionally distinct in the peak compared to the increase or decline phases of the population cycle. Direct measures of host physiology and diet quality (faecal fibre contents) most strongly supported food resource availability as a mechanism underlying phase-based differences in bacterial communities, but faecal fibre contents could not fully account for bacterial microbiome variation across phases.},
}

@article {pmid39698548,
year = {2024},
author = {Pitell, S and Spencer-Williams, I and Huffman, D and Moncure, P and Millstone, J and Stout, J and Gilbertson, L and Haig, SJ},
title = {Not the Silver Bullet: Uncovering the Unexpected Limited Impacts of Silver-Containing Showerheads on the Drinking Water Microbiome.},
journal = {ACS ES&T water},
volume = {4},
number = {12},
pages = {5364-5376},
pmid = {39698548},
issn = {2690-0637},
abstract = {The incidence of waterborne disease outbreaks in the United States attributed to drinking water-associated pathogens that can cause infections in the immunocompromised DWPIs (e.g., Legionella pneumophila, nontuberculous mycobacteria (NTM), and Pseudomonas aeruginosa, among others) appears to be increasing. An emerging technology adopted to reduce DWPIs are point-of-use devices, such as showerheads that contain silver, a known antimicrobial material. In this study, we evaluate the effect of silver-containing showerheads on DWPI density and the broader microbiome in shower water under real-use conditions in a full-scale shower system, considering three different silver-modified showerhead designs: (i) silver mesh within the showerhead, (ii) silver-coated copper mesh in the head and hose, and (iii) silver-embedded polymer composite compared to conventional plastic and metal showerheads. We found no significant difference in targeted DWPI transcriptional activity in collected water across silver and nonsilver shower head designs. Yet, the presence of silver and how it was incorporated in the showerhead influenced the metal concentrations, microbial rare taxa, and microbiome functionality. Microbial dynamics were also influenced by the showerhead age (i.e., time after installation). The results of this study provide valuable information for consumers and building managers to consider when choosing a showerhead meant to reduce microorganisms in shower water.},
}

@article {pmid39698531,
year = {2024},
author = {Christou, D and Stevanovic, K and Evers, S and Weide, M and Zuberbier, T},
title = {Evaluating the Impact of Laundry Detergents on the Skin Microbiome of Atopic Dermatitis Patients-A Clinical Study.},
journal = {Health science reports},
volume = {7},
number = {12},
pages = {e70261},
pmid = {39698531},
issn = {2398-8835},
abstract = {BACKGROUND AND AIMS: Remnants of laundry detergent ingredients are suspected to be in constant contact with the skin. Allergy sufferers need assurance that the chemicals in everyday products do not cause such disruption. The purpose of this study was to evaluate the effects and tolerability of common laundry detergents on the skin microbiome in individuals with atopic dermatitis.

METHODS: Two laundry detergents for sensitive skin were tested on subjects with atopic dermatitis by having to wear detergent-washed socks for 7 days. The bacterial population from volunteers' skin swabs was determined and bacterial viability and biodiversity was evaluated before and after wearing the detergent-washed socks. The tolerability and effect on atopic dermatitis was also evaluated.

RESULTS: The results showed that the tested laundry detergents did not have a negative effect on bacterial viability or biodiversity on the skin after being exposed to the detergent-washed socks for a week. The laundry detergents were rated as very good on the tolerability scale and no worsening of skin itch was reported with the use of either detergent.

CONCLUSION: The results of the study showed that both laundry detergents are skin and allergy friendly and do not alter the skin microbiome.},
}

@article {pmid39698218,
year = {2024},
author = {Ibeanu, GC and Rowaiye, AB and Okoli, JC and Eze, DU},
title = {Microbiome Differences in Colorectal Cancer Patients and Healthy Individuals: Implications for Vaccine Antigen Discovery.},
journal = {ImmunoTargets and therapy},
volume = {13},
number = {},
pages = {749-774},
pmid = {39698218},
issn = {2253-1556},
abstract = {BACKGROUND: Colorectal cancer (CRC) is the third most prevalent cancer worldwide, with numerous risk factors contributing to its development. Recent research has illuminated the significant role of the gut microbiota in CRC pathogenesis, identifying various microbial antigens as potential targets for vaccine development.

AIM: This review aimed at exploring the potential sources of microbial antigens that could be harnessed to create effective CRC vaccines and understand the role of microbiome-CRC interactions in carcinogenesis.

METHODS: A comprehensive search of original research and review articles on the pathological links between key microbial candidates, particularly those more prevalent in CRC tissues, was conducted. This involved extensive use of the PubMed and Medline databases, as well as the Google Scholar search engine, utilizing pertinent keywords. A total of one hundred and forty-three relevant articles in English, mostly published between 2018 and 2024, were selected.

RESULTS: Numerous microbes, particularly bacteria and viruses, are significantly overrepresented in CRC tissues and have been shown to promote tumorigenesis by inducing inflammation and modulating the immune system. This makes them promising candidates for antigens in the development of CRC vaccines.

CONCLUSION: The selection of microbial antigens focuses on their capacity to trigger a strong immune response and their link to tumor presence and progression. Identifying and validating these antigens through preclinical testing is essential in developing a CRC vaccine.},
}

@article {pmid39698189,
year = {2024},
author = {Nazir, A and Hussain, FHN and Raza, A},
title = {Advancing microbiota therapeutics: the role of synthetic biology in engineering microbial communities for precision medicine.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {12},
number = {},
pages = {1511149},
pmid = {39698189},
issn = {2296-4185},
abstract = {Over recent years, studies on microbiota research and synthetic biology have explored novel approaches microbial manipulation for therapeutic purposes. However, fragmented information is available on this aspect with key insights scattered across various disciplines such as molecular biology, genetics, bioengineering, and medicine. This review aims to the transformative potential of synthetic biology in advancing microbiome research and therapies, with significant implications for healthcare, agriculture, and environmental sustainability. By merging computer science, engineering, and biology, synthetic biology allows for precise design and modification of biological systems via cutting edge technologies like CRISPR/Cas9 gene editing, metabolic engineering, and synthetic oligonucleotide synthesis, thus paving the way for targeted treatments such as personalized probiotics and engineered microorganisms. The review will also highlight the vital role of gut microbiota in disorders caused by its dysbiosis and suggesting microbiota-based therapies and innovations such as biosensors for real-time gut health monitoring, non-invasive diagnostic tools, and automated bio foundries for better outcomes. Moreover, challenges including genetic stability, environmental safety, and robust regulatory frameworks will be discussed to understand the importance of ongoing research to ensure safe and effective microbiome interventions.},
}

@article {pmid39697933,
year = {2024},
author = {More, K and Hanumantharaju, A and Amrit, A and Nimbalkar, SM and Patole, S},
title = {Use of Probiotics for Preventing Necrotizing Enterocolitis in Preterm Infants: A Survey of Current Practices Among Indian Neonatologists.},
journal = {Cureus},
volume = {16},
number = {11},
pages = {e73923},
pmid = {39697933},
issn = {2168-8184},
abstract = {OBJECTIVE: Probiotics are known to reduce the risk of necrotizing enterocolitis (NEC≥ Stage II) significantly, as well as all-cause mortality, late-onset sepsis (LOS), and feeding intolerance in preterm infants. Probiotics have been reported to have comparable benefits in high- and low-middle-income countries (LMICs). We aimed to assess the current practices of neonatologists in India for using probiotics in preterm infants.

MATERIAL AND METHODS: A questionnaire created using Survey Monkey's web-based tool was sent to neonatologists in India. Survey forms automatically converted responses into Excel files (Microsoft® Corp., Redmond, WA). Data were analyzed using SPSS (IBM Corp., Armonk, NY).

RESULTS: A total of 615 responses were received from various neonatal intensive care units (NICUs) in India (Level I: 43 (7%), II: 124 (20.8%), III: 448 (72.8%)). Around 431 (70%) of the units had either National Neonatology Forum (NNF) accreditation or IAP fellowships or were affiliated with private or government medical colleges. The remaining 184 (30%) were in private setups. Routine probiotic supplementation (RPS) was provided in 241 (39.1%) of the responding units; 179 (48%) quoted inadequate evidence as the reason for not providing RPS, 125 (33.43%) quoted difficulty in sourcing safe and effective products, whereas others were concerned about adverse effects. Most centers provided RPS for preterm infants <32 weeks and 1500 g at birth. The clinical practice was influenced by the judgment of the attending clinician. Significant variation was noticed in the protocol for RPS.

CONCLUSION: Findings of the survey suggest that approximately 39% of the participating neonatologists in India currently offer RPS for preterm infants. A significant variation exists in the selection of probiotic strains, products, dose, and duration of supplementation. Despite limitations, our findings are useful in guiding clinical practice and further research to optimize the safety and efficacy of RPS for preterm infants.},
}

@article {pmid39697649,
year = {2024},
author = {Aluthge, N and Adams, S and Davila, CA and Gocchi Carrasco, NR and Chiou, KS and Abadie, R and Bennett, SJ and Dombrowski, K and Major, AM and Valentín-Acevedo, A and West, JT and Wood, C and Fernando, SC},
title = {Gut microbiota profiling in injection drug users with and without HIV-1 infection in Puerto Rico.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1470037},
pmid = {39697649},
issn = {1664-302X},
abstract = {INTRODUCTION: The full extent of interactions between human immunodeficiency virus (HIV) infection, injection drug use, and the human microbiome is unclear. In this study, we examined the microbiomes of HIV-positive and HIV-negative individuals, both drug-injecting and non-injecting, to identify bacterial community changes in response to HIV and drug use. We utilized a well-established cohort of people who inject drugs in Puerto Rico, a region with historically high levels of injection drug use and an HIV incidence rate disproportionately associated with drug use.

METHODS: Using amplicon-based 16S rDNA sequencing, we identified amplicon sequence variants (ASVs) that demonstrated significant variations in the composition of microbial communities based on HIV status and drug use.

RESULTS AND DISCUSSION: Our findings indicate that the HIV-positive group exhibited a higher abundance of ASVs belonging to the genera Prevotella, Alloprevotella, Sutterella, Megasphaera, Fusobacterium, and Mitsuokella. However, Bifidobacteria and Lactobacillus ASVs were more abundant in injectors than in non-injectors. We examined the effect of drug use on the gut microbiome in both HIV-infected and non-infected patients, and found that multiple drug use significantly affected the microbial community composition. Analysis of differential of bacterial taxa revealed an enrichment of Bifidobacterium spp., Faecalibacterium spp., and Lactobacillus spp. in the multiple drug-injecting group. However, in the non-injecting group, Parabacteroides spp., Prevotella spp., Paraprevotella spp., Sutterella spp., and Lachnoclostridium spp. The presence of multiple drug-injecting groups was observed to be more prevalent. Our findings provide detailed insight into ASV-level changes in the microbiome in response to HIV and drug use, suggesting that the effect of HIV status and drug injection may have different effects on microbiome composition and in modulating gut bacterial populations.},
}

@article {pmid39697547,
year = {2024},
author = {Khan, I and Gouxin, H and Khan, S and Ali, A},
title = {Editorial: The roles of pathogens in gut-related diseases and the strategies for inhibiting their growth.},
journal = {Frontiers in pharmacology},
volume = {15},
number = {},
pages = {1513694},
pmid = {39697547},
issn = {1663-9812},
}

@article {pmid39696724,
year = {2024},
author = {Cruciata, I and Scirè Calabrisotto, L and Carpani, G and Poppa, L and Modica, A and Pace, A and Catania, V and Quatrini, P},
title = {1,2-DCA biodegradation potential of an aquifer assessed in situ and in aerobic and anaerobic microcosms.},
journal = {Environmental microbiome},
volume = {19},
number = {1},
pages = {106},
pmid = {39696724},
issn = {2524-6372},
support = {PJ_GEST_DOTT_ENI_D15//Eni Corporate University (ENI-ECU) S.p.A./ ; National Recovery and Resilience Plan - NRRP, Mission 4, Component 2, Investment 1.3 - D.D. 1243 2/8/2022, PE0000005//European Union Next-Generation EU (RETURN Extended Partnership)/ ; IR0000005//European Commission-NextGenerationEUProject "Strengthening the MIRRI Italian Research Infrastructure for Sustainable Bioscience and Bioeconomy"/ ; },
abstract = {BACKGROUND: 1,2-dichloroethane (1,2-DCA) biodegradation can occur through aerobic or anaerobic pathways that can be exploited in bioremediation strategies. Bioremediation interventions are site specific and generally based on anaerobic pathways, nevertheless expanding knowledge on proper conditions favoring the biodegradation and especially on 1,2-DCA degrading microorganisms is crucial. In this work the intrinsic biodegradation potential of an aquifer impacted by Chlorinated Aliphatic Hydrocarbons (mainly 1,2-DCA) was evaluated by characterizing the aquifer microbiome across space and time and by setting up biostimulation treatments in microcosms under different aerobic and anaerobic conditions, in parallel.

RESULTS: The microbial profiling of the aquifer revealed noticeable alpha and beta diversity across the sampling sites within the aquifer and strong fluctuations over time. Surprisingly both the anaerobic and aerobic biostimulation treatments led to the successful removal of 1,2-DCA in microcosms, the enrichment of known 1,2-DCA degraders and the detection of reductive or hydrolytic dehalogenases. Ancylobacter and Starkeya were enriched in aerobic microcosms. Desulfovibrio and Desulfuromonas, known as perchloroethylene degraders, were enriched in anaerobic microcosms, suggesting they could be yet unknown 1,2-DCA respirers.

CONCLUSIONS: Our results demonstrate the occurrence of both aerobic and anaerobic bioremediation potential in the aquifer despite its negative redox potential. Due to the feasibility of direct oxidation with oxygen insufflation, we propose that an enhanced bioremediation strategy based on direct oxidation of 1,2-DCA could be applied to the contaminated aquifer as an ecofriendly, efficient and cost-effective approach as an alternative to anaerobic biodegradation.},
}

@article {pmid39697987,
year = {2023},
author = {Kelwick, RJR and Webb, AJ and Freemont, PS},
title = {Opportunities for engineering outer membrane vesicles using synthetic biology approaches.},
journal = {Extracellular vesicles and circulating nucleic acids},
volume = {4},
number = {2},
pages = {255-261},
pmid = {39697987},
issn = {2767-6641},
abstract = {Gram-negative bacteria naturally shed lipid vesicles, which contain complex molecular cargoes, from their outer membrane. These outer membrane vesicles (OMVs) have important biological functions relating to microbial stress responses, microbiome regulation, and host-pathogen interactions. OMVs are also attractive vehicles for delivering drugs, vaccines, and other therapeutic agents because of their ability to interact with host cells and their natural immunogenic properties. OMVs are also set to have a positive impact on other biotechnological and medical applications including diagnostics, bioremediation, and metabolic engineering. We envision that the field of synthetic biology offers a compelling opportunity to further expand and accelerate the foundational research and downstream applications of OMVs in a range of applications including the provision of OMV-based healthcare technologies. In our opinion, we discuss how current and potential future synergies between OMV research and synthetic biology approaches might help to further accelerate OMV research and real-world applications for the benefit of animal and human health.},
}

@article {pmid39696657,
year = {2024},
author = {Armstrong, C and Ganasamurthy, S and Wigley, K and Mercier, C and Wakelin, S},
title = {The microorganisms and metabolome of Pinus radiata Pollen.},
journal = {Environmental microbiome},
volume = {19},
number = {1},
pages = {103},
pmid = {39696657},
issn = {2524-6372},
support = {C04 × 2002//Ministry of Business, Innovation and Employment/ ; },
abstract = {BACKGROUND: Pollen is a crucial source of nutrients and energy for pollinators. It also provides a unique habitat and resource for microbiota. Previous research on the microbiome of pollen has largely focused on angiosperm systems, with limited research into coniferous gymnosperms. This study characterises the pollen microbiome and metabolome associated with one of the world's most widely grown tree species, Pinus radiata. Trees were sampled from locations across Canterbury, New Zealand. Repeated collections were undertaken in 2020 and 2021.

RESULTS: Metabolomic analysis revealed the main compounds present on P. radiata pollen to be amino acids (principally proline), and carbohydrates (fructose, glucose, and sucrose). Although phenolic compounds such as ρ-coumaric acid and catechin, and terpenoids such as dehydroabietic acid, were present at low concentrations, their strong bioactive natures mean they may be important in ecological filtering of microbiome communities on pollen. The P. radiata pollen microbiome was richer in fungal taxa compared with bacteria, which differs from many angiosperm species. Geographic range and annual variation were evaluated as drivers of microbiome assembly. Neither sampling location (geographic range) nor annual variation significantly influenced the fungal community which exhibited remarkable conservation across samples. However, some bacterial taxa exhibited sensitivity to geographic distances and yearly variations, suggesting a secondary role of these factors for some taxa. A core microbiome was identified in P. radiata pollen, characterized by a consistent presence of specific fungal and bacterial taxa across samples. While the dominant phyla, Proteobacteria and Ascomycota, align with findings from other pollen microbiome studies, unique core members were unidentified at genus level.

CONCLUSION: This tree species-specific microbiome assembly emphasizes the crucial role of the host plant in shaping the pollen microbiome. These findings contribute to a deeper understanding of pollen microbiomes in gymnosperms, shedding light on the need to look further at their ecological and functional roles.},
}

@article {pmid39696594,
year = {2024},
author = {Shi, P and Martino, C and Han, R and Janssen, S and Buck, G and Serrano, M and Owzar, K and Knight, R and Shenhav, L and Zhang, AR},
title = {TEMPTED: time-informed dimensionality reduction for longitudinal microbiome studies.},
journal = {Genome biology},
volume = {25},
number = {1},
pages = {317},
pmid = {39696594},
issn = {1474-760X},
support = {DP2AI185753//Division of Intramural Research, National Institute of Allergy and Infectious Diseases/ ; R01HD092415//National Institute of Child Health and Human Development/ ; DP1AT010885/AT/NCCIH NIH HHS/United States ; 75D301-22-C-14717/CC/CDC HHS/United States ; Distinguished Investigator Award//Emerald Foundation/ ; R01CA241728//Division of Cancer Prevention, National Cancer Institute/ ; U24CA248454//Center for Strategic Scientific Initiatives, National Cancer Institute/ ; R01HL169347//NHLBI Division of Intramural Research/ ; R01HL168940//NHLBI Division of Intramural Research/ ; CAREER-2203741//Division of Mathematical Sciences/ ; },
mesh = {Humans ; *Microbiota ; Longitudinal Studies ; Female ; Vagina/microbiology ; Algorithms ; },
abstract = {Longitudinal studies are crucial for understanding complex microbiome dynamics and their link to health. We introduce TEMPoral TEnsor Decomposition (TEMPTED), a time-informed dimensionality reduction method for high-dimensional longitudinal data that treats time as a continuous variable, effectively characterizing temporal information and handling varying temporal sampling. TEMPTED captures key microbial dynamics, facilitates beta-diversity analysis, and enhances reproducibility by transferring learned representations to new data. In simulations, it achieves 90% accuracy in phenotype classification, significantly outperforming existing methods. In real data, TEMPTED identifies vaginal microbial markers linked to term and preterm births, demonstrating robust performance across datasets and sequencing platforms.},
}

Humans
*Microbiota
Longitudinal Studies
Female
Vagina/microbiology
Algorithms

@article {pmid39696556,
year = {2024},
author = {Amano, Y and Sachdeva, R and Gittins, D and Anantharaman, K and Lei, S and Valentin-Alvarado, LE and Diamond, S and Beppu, H and Iwatsuki, T and Mochizuki, A and Miyakawa, K and Ishii, E and Murakami, H and Jaffe, AL and Castelle, C and Lavy, A and Suzuki, Y and Banfield, JF},
title = {Diverse microbiome functions, limited temporal variation and substantial genomic conservation within sedimentary and granite rock deep underground research laboratories.},
journal = {Environmental microbiome},
volume = {19},
number = {1},
pages = {105},
pmid = {39696556},
issn = {2524-6372},
support = {JPJ007597//The Ministry of Economy, Trade and Industry of Japan/ ; 19K05342//the Japan Society for the Promotion of Science/ ; OCE2049478//National Science Foundation/ ; DE-AC02-05CH11231//the Watershed Function Scientific Focus Area funded by the U.S. Department of Energy/ ; 2230766//NSF "Four Networks for Geologic Hydrogen Storage"/ ; },
abstract = {BACKGROUND: Underground research laboratories (URLs) provide a window on the deep biosphere and enable investigation of potential microbial impacts on nuclear waste, CO2 and H2 stored in the subsurface. We carried out the first multi-year study of groundwater microbiomes sampled from defined intervals between 140 and 400 m below the surface of the Horonobe and Mizunami URLs, Japan.

RESULTS: We reconstructed draft genomes for > 90% of all organisms detected over a four year period. The Horonobe and Mizunami microbiomes are dissimilar, likely because the Mizunami URL is hosted in granitic rock and the Horonobe URL in sedimentary rock. Despite this, hydrogen metabolism, rubisco-based CO2 fixation, reduction of nitrogen compounds and sulfate reduction are well represented functions in microbiomes from both URLs, although methane metabolism is more prevalent at the organic- and CO2-rich Horonobe URL. High fluid flow zones and proximity to subsurface tunnels select for candidate phyla radiation bacteria in the Mizunami URL. We detected near-identical genotypes for approximately one third of all genomically defined organisms at multiple depths within the Horonobe URL. This cannot be explained by inactivity, as in situ growth was detected for some bacteria, albeit at slow rates. Given the current low hydraulic conductivity and groundwater compositional heterogeneity, ongoing inter-site strain dispersal seems unlikely. Alternatively, the Horonobe URL microbiome homogeneity may be explained by higher groundwater mobility during the last glacial period. Genotypically-defined species closely related to those detected in the URLs were identified in three other subsurface environments in the USA. Thus, dispersal rates between widely separated underground sites may be fast enough relative to mutation rates to have precluded substantial divergence in species composition. Species overlaps between subsurface locations on different continents constrain expectations regarding the scale of global subsurface biodiversity.

CONCLUSIONS: Our analyses reveal microbiome stability in the sedimentary rocks and surprising microbial community compositional and genotypic overlap over sites separated by hundreds of meters of rock, potentially explained by dispersal via slow groundwater flow or during a prior hydrological regime. Overall, microbiome and geochemical stability over the study period has important implications for underground storage applications.},
}

@article {pmid39696486,
year = {2024},
author = {Shi, M and Li, Z and Hu, S and Zhang, P and Meng, S and Huang, L and Miao, Z and Zhang, J},
title = {Microbiome-proteome analysis of gastrointestinal microbiota and longissimus thoracis muscle proteins in cattle with high and low grades of marbling.},
journal = {BMC veterinary research},
volume = {20},
number = {1},
pages = {563},
pmid = {39696486},
issn = {1746-6148},
support = {2202036A//The Core Technology Research Projects in Luoyang City/ ; 232102110079, 232102111055, 222102110021, 202102110241//The Provincial Key Technology Research and Development Program of Henan/ ; 23B230003//The Key Scientific Research Projects of Colleges and Universities in Henan Province/ ; 22IRTSTHN026//Innovative Research Team (in Science and Technology) at the University of Henan Province/ ; },
mesh = {Animals ; Cattle ; *Gastrointestinal Microbiome ; *Proteome ; *Muscle Proteins/metabolism ; *Muscle, Skeletal/metabolism ; *Fatty Acids, Volatile/metabolism/analysis ; *Rumen/microbiology/metabolism ; Meat/analysis/microbiology ; Cecum/microbiology ; },
abstract = {Marbling is a key indicator of the meat quality of ruminants. Gastrointestinal microbiota may regulate the formation of marbling by influencing the nutritional metabolism of animals. This study analyzed the composition and functional differences of microbiota in the rumen and cecum, the differences in volatile fatty acids (VFAs) content in the longissimus thoracis muscle, and the differences in protein abundance in the longissimus thoracis muscle of ruminants with different marbling grades through microbiome-proteome analysis. The results showed that the diversity of gastrointestinal microbiota in high-marbling ruminants was significantly higher than that in low-marbling ruminants. The relative abundance of Firmicutes and Akkermansia in the gastrointestinal of high-marbling ruminants was higher than that in low-marbling ruminants, while the relative abundance of Bacteroidetes and Prevotella was lower. In addition, PICRUST2 functional prediction results of the microbiota revealed that the gastrointestinal microbiota of high-marbling ruminants was mainly involved in the biosynthesis pathways of fat and lipids. The metabolomics results showed that the content of VFAs (acetic acid, propionic acid, butyric acid, isovaleric acid, valeric acid, and hexanoic acid) in the rumen of high-marbling ruminants was significantly higher than that in low-marbling ruminants. The proteome analysis results indicated that the differential proteins in the longissimus thoracis muscle of high-marbling ruminants were mainly involved in lipid transport and metabolism compared to low-marbling ruminants. In summary, the differences in the composition and function of the gastrointestinal microbiota led to higher levels of VFAs in the gastrointestinal tract of high-marbling ruminants, which provides the basis for lipid/fat synthesis. The proteome results of the longissimus thoracis muscle support the view that high-marbling ruminants have richer lipid transport and metabolic functions in their muscle.},
}

Animals
Cattle
*Gastrointestinal Microbiome
*Proteome
*Muscle Proteins/metabolism
*Muscle, Skeletal/metabolism
*Fatty Acids, Volatile/metabolism/analysis
*Rumen/microbiology/metabolism
Meat/analysis/microbiology
Cecum/microbiology

@article {pmid39696340,
year = {2024},
author = {Gan, M and Liu, N and Li, W and Chen, M and Bai, Z and Liu, D and Liu, S},
title = {Metabolic targeting of regulatory T cells in oral squamous cell carcinoma: new horizons in immunotherapy.},
journal = {Molecular cancer},
volume = {23},
number = {1},
pages = {273},
pmid = {39696340},
issn = {1476-4598},
mesh = {Humans ; *T-Lymphocytes, Regulatory/immunology/metabolism ; *Mouth Neoplasms/immunology/therapy/metabolism/pathology ; *Immunotherapy/methods ; *Tumor Microenvironment/immunology ; Carcinoma, Squamous Cell/immunology/therapy/metabolism/pathology ; Animals ; Signal Transduction ; Metabolic Networks and Pathways ; },
abstract = {Oral squamous cell carcinoma (OSCC) is a prevalent oral malignancy, which poses significant health risks with a high mortality rate. Regulatory T cells (Tregs), characterized by their immunosuppressive capabilities, are intricately linked to OSCC progression and patient outcomes. The metabolic reprogramming of Tregs within the OSCC tumor microenvironment (TME) underpins their function, with key pathways such as the tryptophan-kynurenine-aryl hydrocarbon receptor, PI3K-Akt-mTOR and nucleotide metabolism significantly contributing to their suppressive activities. Targeting these metabolic pathways offers a novel therapeutic approach to reduce Treg-mediated immunosuppression and enhance anti-tumor responses. This review explores the metabolic dependencies and pathways that sustain Treg function in OSCC, highlighting key metabolic adaptations such as glycolysis, fatty acid oxidation, amino acid metabolism and PI3K-Akt-mTOR signaling pathway that enable Tregs to thrive in the challenging conditions of the TME. Additionally, the review discusses the influence of the oral microbiome on Treg metabolism and evaluates potential therapeutic strategies targeting these metabolic pathways. Despite the promising potential of these interventions, challenges such as selectivity, toxicity, tumor heterogeneity, and resistance mechanisms remain. The review concludes with perspectives on personalized medicine and integrative approaches, emphasizing the need for continued research to translate these findings into effective clinical applications for OSCC treatment.},
}

Humans
*T-Lymphocytes, Regulatory/immunology/metabolism
*Mouth Neoplasms/immunology/therapy/metabolism/pathology
*Immunotherapy/methods
*Tumor Microenvironment/immunology
Carcinoma, Squamous Cell/immunology/therapy/metabolism/pathology
Animals
Signal Transduction
Metabolic Networks and Pathways

@article {pmid39696220,
year = {2024},
author = {Mavrides, DE and Liapi, M and Ierodiakonou, D and Pipis, C and Malas, S and Gentekaki, E and Tsaousis, AD},
title = {The cow GUTBIOME CY study: investigating the composition of the cattle gut microbiome in health and infectious disease transmission in cyprus.},
journal = {BMC veterinary research},
volume = {20},
number = {1},
pages = {566},
pmid = {39696220},
issn = {1746-6148},
support = {AIRCOMM//University of Nicosia/ ; AIRCOMM//University of Nicosia/ ; 1HEALTH-GUTBIOME//University of Nicosia/ ; H4DC//Interreg-2-seas/ ; },
mesh = {Animals ; Cattle ; Cyprus ; *Gastrointestinal Microbiome ; Feces/microbiology ; Cattle Diseases/microbiology/transmission/epidemiology ; Animal Husbandry/methods ; Female ; Milk/microbiology/chemistry ; Dairying ; },
abstract = {BACKGROUND: Recent evidence suggests that the lower gut microbiome of ruminants presents roles in their health and environment, including the development of the mucosal immune system, milk production efficiency and quality and subsequent methane emissions. However, there are proportionately fewer studies on this complex microbial community in cattle and region-focus studies are non- existent.

METHODS: Herein, we present the research protocol of the GUTBIOME CY project pertaining to determine the composition of the lower gut microbiome in dairy cows situated in 37 farms across five districts of the island of Cyprus. Detailed questionnaires on animal husbandry and farming practices will be gathered from each farm. Faecal, milk (individual and bulk) and water samples will also be collected from cows and their offspring. Samples will be analysed using a combination of molecular biology and bioinformatics pipelines to define microbiome profiles and antimicrobial resistance (AMR). Information collected from the questionnaires will be used to test for associations between animal husbandry or farming practices and microbiome components and AMR.

DISCUSSION: Collected samples will establish the first dairy cattle biobank in the country for contributing substantially towards scientific advancements in microbiome research and providing insights to all stakeholders, tailored to the unique agricultural context of Cyprus.},
}

Animals
Cattle
Cyprus
*Gastrointestinal Microbiome
Feces/microbiology
Cattle Diseases/microbiology/transmission/epidemiology
Animal Husbandry/methods
Female
Milk/microbiology/chemistry
Dairying

@article {pmid39696186,
year = {2024},
author = {Salenius, K and Väljä, N and Thusberg, S and Iris, F and Ladd-Acosta, C and Roos, C and Nykter, M and Fasano, A and Autio, R and Lin, J and , },
title = {Exploring autism spectrum disorder and co-occurring trait associations to elucidate multivariate genetic mechanisms and insights.},
journal = {BMC psychiatry},
volume = {24},
number = {1},
pages = {934},
pmid = {39696186},
issn = {1471-244X},
support = {825033//Horizon 2020 Framework Programme/ ; 825033//Horizon 2020 Framework Programme/ ; 825033//Horizon 2020 Framework Programme/ ; 825033//Horizon 2020 Framework Programme/ ; 825033//Horizon 2020 Framework Programme/ ; 825033//Horizon 2020 Framework Programme/ ; 825033//Horizon 2020 Framework Programme/ ; 825033//Horizon 2020 Framework Programme/ ; 825033//Horizon 2020 Framework Programme/ ; 825033//Horizon 2020 Framework Programme/ ; 825033//Horizon 2020 Framework Programme/ ; },
mesh = {Humans ; *Autism Spectrum Disorder/genetics ; *Genome-Wide Association Study ; *Mendelian Randomization Analysis ; Genetic Predisposition to Disease/genetics ; Polymorphism, Single Nucleotide/genetics ; Quantitative Trait Loci/genetics ; Comorbidity ; Attention Deficit Disorder with Hyperactivity/genetics ; },
abstract = {BACKGROUND: Autism spectrum disorder (ASD) is a partially heritable neurodevelopmental trait, and people with ASD may also have other co-occurring trait such as ADHD, anxiety disorders, depression, mental health issues, learning difficulty, physical health traits and communication challenges. The concomitant development of ASD and other neurological traits is assumed to result from a complex interplay between genetics and the environment. However, only a limited number of studies have performed multivariate genome-wide association studies (GWAS) for ASD.

METHODS: We conducted to-date the largest multivariate GWAS on ASD and 8 ASD co-occurring traits (ADHD, ADHD childhood, anxiety stress (ASDR), bipolar (BIP), disruptive behaviour (DBD), educational attainment (EA), major depression, and schizophrenia (SCZ)) using summary statistics from leading studies. Multivariate associations and central traits were further identified. Subsequently, colocalization and Mendelian randomization (MR) analysis were performed on the associations identified with the central traits containing ASD. To further validate our findings, pathway and quantified trait loci (QTL) resources as well as independent datasets consisting of 112 (45 probands) whole genome sequence data from the GEMMA project were utilized.

RESULTS: Multivariate GWAS resulted in 637 significant associations (p < 5e-8), among which 322 are reported for the first time for any trait. 37 SNPs were identified to contain ASD and one or more traits in their central trait set, including variants mapped to known SFARI ASD genes MAPT, CADPS and NEGR1 as well as novel ASD genes KANSL1, NSF and NTM, associated with immune response, synaptic transmission, and neurite growth respectively. Mendelian randomization analyses found that genetic liability for ADHD childhood, ASRD and DBT has causal effects on the risk of ASD while genetic liability for ASD has causal effects on the risk of ADHD, ADHD childhood, BIP, WA, MDD and SCZ. Frequency differences of SNPs found in NTM and CADPS genes, respectively associated with neurite growth and neural/endocrine calcium regulation, were found between GEMMA ASD probands and controls. Pathway, QTL and cell type enrichment implicated microbiome, enteric inflammation, and central nervous system enrichments.

CONCLUSIONS: Our study, combining multivariate GWAS with systematic decomposition, identified novel genetic associations related to ASD and ASD co-occurring driver traits. Statistical tests were applied to discern evidence for shared and interpretable liability between ASD and co-occurring traits. These findings expand upon the current understanding of the complex genetics regulating ASD and reveal insights of neuronal brain disruptions potentially driving development and manifestation.},
}

Humans
*Autism Spectrum Disorder/genetics
*Genome-Wide Association Study
*Mendelian Randomization Analysis
Genetic Predisposition to Disease/genetics
Polymorphism, Single Nucleotide/genetics
Quantitative Trait Loci/genetics
Comorbidity
Attention Deficit Disorder with Hyperactivity/genetics

@article {pmid39695983,
year = {2024},
author = {Su, L and Guo, J and Shi, W and Tong, W and Li, X and Yang, B and Xiang, Z and Qin, C},
title = {Metagenomic analysis reveals the community composition of the microbiome in different segments of the digestive tract in donkeys and cows: implications for microbiome research.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {530},
pmid = {39695983},
issn = {1471-2180},
support = {2021YFF0702900//National Key Research and Development Program of China/ ; 2023-PT180-01//Non-profit Central Research Institute Fund of Chinese Academy of Medical Sciences/ ; 2021-I2M-1-039, 2021-I2M-1-034//CAMS initiative for Innovative Medicine of China/ ; },
mesh = {Animals ; *Equidae/microbiology ; Cattle/microbiology ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; *Feces/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Gastrointestinal Tract/microbiology ; Sequence Analysis, DNA/methods ; Metagenome ; Bacteroidetes/genetics/isolation & purification/classification ; },
abstract = {INTRODUCTION: The intestinal microbiota plays a crucial role in health and disease. This study aimed to assess the composition and functional diversity of the intestinal microbiota in donkeys and cows by examining samples collected from different segments of the digestive tract using two distinct techniques: direct swab sampling and faecal sampling.

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

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

Animals
*Equidae/microbiology
Cattle/microbiology
*Metagenomics/methods
*Gastrointestinal Microbiome/genetics
*Feces/microbiology
*Bacteria/classification/genetics/isolation & purification
*Gastrointestinal Tract/microbiology
Sequence Analysis, DNA/methods
Metagenome
Bacteroidetes/genetics/isolation & purification/classification

@article {pmid39695939,
year = {2024},
author = {Li, P and Zhang, H and Gao, X and Chen, L and Chen, H and Yuan, S and Chen, W and Dai, M},
title = {Difference in fecal and oral microbiota between pancreatic cancer and benign/low-grade malignant tumor patients.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {527},
pmid = {39695939},
issn = {1471-2180},
support = {2021-I2M-1-002//Chinese Academy of Medical Sciences Innovation Fund for Medical Sciences/ ; 82073238//the project of National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Pancreatic Neoplasms/microbiology/diagnosis ; *Feces/microbiology ; Male ; Female ; Middle Aged ; Aged ; *RNA, Ribosomal, 16S/genetics ; *Mouth/microbiology ; Bacteria/classification/isolation & purification/genetics ; Gastrointestinal Microbiome/genetics ; Adult ; Microbiota/genetics ; },
abstract = {BACKGROUND: Significant gaps exist in understanding the gastrointestinal microbiota in patients with pancreatic cancer (PCA) versus benign or low-grade malignant pancreatic tumors (NPCA). This study aimed to analyze these microbiota characteristics and explore their potential use in distinguishing malignant pancreatic lesions.

METHODS: Between September 2020 and May 2024, fecal and oral samples were collected from 121 patients undergoing surgical resection or diagnostic biopsy of pancreatic lesions, including 75 patients with PCA and 46 patients with NPCA, and 16s rRNA sequencing was performed. Random forest models based using fecal and oral microbiota data were developed to diagnose PCA and NPCA, with performance assessed using the leave-one-out cross validation method.

RESULTS: The Shannon index and PCoA analysis revealed significant differences in oral microbiota composition between PCA and NPCA (p < 0.001 and p = 0.001, respectively). Fecal microbiome richness differed significantly (p = 0.02), though composition similarity was noted (p = 0.238). LEfSe identified 16 and 23 genera with significant differences in fecal and oral microbiomes, respectively. Random forest classifiers based on fecal and oral microbiota achieved areas under the curves (AUCs) of 89.4% and 96.3%, respectively, for distinguishing PCA and NPCA. In the mucinous tumor cohort, oral and fecal microbiome classifiers outperformed CA19-9, yielding AUCs of 83.0% and 85.2%, respectively.

CONCLUSION: Fecal and oral microbiota compositions were significantly different between PCA and NPCA patients. Random forest classifiers utilizing fecal and oral microbiota data effectively distinguish between benign or low-grade malignant and malignant pancreatic lesions.},
}

Humans
*Pancreatic Neoplasms/microbiology/diagnosis
*Feces/microbiology
Male
Female
Middle Aged
Aged
*RNA, Ribosomal, 16S/genetics
*Mouth/microbiology
Bacteria/classification/isolation & purification/genetics
Gastrointestinal Microbiome/genetics
Adult
Microbiota/genetics

@article {pmid39695885,
year = {2024},
author = {Galic, I and Bez, C and Bertani, I and Venturi, V and Stankovic, N},
title = {Herbicide-treated soil as a reservoir of beneficial bacteria: microbiome analysis and PGP bioinoculants in maize.},
journal = {Environmental microbiome},
volume = {19},
number = {1},
pages = {107},
pmid = {39695885},
issn = {2524-6372},
support = {451-03-47/2023-01/ 200042//Ministarstvo Prosvete, Nauke i Tehnološkog Razvoja/ ; 451-03-47/2023-01/ 200042//Ministarstvo Prosvete, Nauke i Tehnološkog Razvoja/ ; Research and Training Grant 1818//FEMS/ ; },
abstract = {BACKGROUND: Herbicides are integral to agricultural weed management but can adversely affect non-target organisms, soil health, and microbiome. We investigated the effects of herbicides on the total soil bacterial community composition using 16S rRNA gene amplicon community profiling. Further, we aimed to identify herbicide-tolerant bacteria with plant growth-promoting (PGP) capabilities as a mitigative strategy for these negative effects, thereby promoting sustainable agricultural practices.

RESULTS: A bacterial community analysis explored the effects of long-term S-metolachlor application on soil bacterial diversity, revealing that the herbicide's impact on microbial communities is less significant than the effects of temporal factors (summer vs. winter) or agricultural practices (continuous maize cultivation vs. maize-winter wheat rotation). Although S-metolachlor did not markedly alter the overall bacteriome structure in our environmental context, the application of enrichment techniques enabled the selection of genera such as Pseudomonas, Serratia, and Brucella, which were rare in metagenome analysis of soil samples. Strain isolation revealed a rich source of herbicide-tolerant PGP bacteria within the culturable microbiome fraction, termed the high herbicide concentration tolerant (HHCT) bacterial culture collection. Within the HHCT collection, we isolated 120 strains that demonstrated significant in vitro PGP and biocontrol potential, and soil quality improvement abilities. The most promising HHCT isolates were combined into three consortia, each exhibiting a comprehensive range of plant-beneficial traits. We evaluated the efficacy and persistence of these multi-strain consortia during 4-week in pot experiments on maize using both agronomic parameters and 16S rRNA gene community analysis assessing early-stage plant development, root colonization, and rhizosphere persistence. Notably, 7 out of 10 inoculated consortia partners successfully established themselves and persisted in the maize root microbiome without significantly altering host root biodiversity. Our results further evidenced that all three consortia positively impacted both seed germination and early-stage plant development, increasing shoot biomass by up to 47%.

CONCLUSIONS: Herbicide-treated soil bacterial community analysis revealed that integrative agricultural practices can suppress the effects of continuous S-metolachlor application on soil microbial diversity and stabilize microbiome fluctuations. The HHCT bacterial collection holds promise as a source of beneficial bacteria that promote plant fitness while maintaining herbicide tolerance.},
}

@article {pmid39695869,
year = {2024},
author = {Rodriguez, J and Cordaillat-Simmons, M and Badalato, N and Berger, B and Breton, H and de Lahondès, R and Deschasaux-Tanguy, M and Desvignes, C and D'Humières, C and Kampshoff, S and Lavelle, A and Metwaly, A and Quijada, NM and Seegers, JFML and Udocor, A and Zwart, H and , and Maguin, E and Doré, J and Druart, C},
title = {Microbiome testing in Europe: navigating analytical, ethical and regulatory challenges.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {258},
pmid = {39695869},
issn = {2049-2618},
mesh = {Humans ; Europe ; *Feces/microbiology ; Microbiota ; Reproducibility of Results ; },
abstract = {BACKGROUND: In recent years, human microbiome research has flourished and has drawn attention from both healthcare professionals and general consumers as the human microbiome is now recognized as having a significant influence on human health. This has led to the emergence of companies offering microbiome testing services. Some of these services are sold directly to the consumer via companies' websites or via medical laboratory websites.

METHODOLOGY: In order to provide an overview of the consumer experience proposed by these microbiome testing services, one single faecal sample was sent to six different companies (five based in Europe and one based in the USA). Two out of the six testing kits were commercialized by medical laboratories, but without any requirement for a medical prescription. The analyses and reports received were discussed with a panel of experts (21 experts from 8 countries) during an online workshop.

RESULTS: This workshop led to the identification of several limitations and challenges related to these kits, including over-promising messages from the companies, a lack of transparency in the methodology used for the analysis and a lack of reliability of the results. The experts considered the interpretations and recommendations provided in the different reports to be premature due to the lack of robust scientific evidence and the analyses associated with the reports to be of limited clinical utility. The experts also discussed the grey areas surrounding the regulatory status of these test kits, including their positioning in the European market. The experts recommended a distinction between regulatory requirements based on the intended use or purpose of the kit: on the one hand, test kits developed to satisfy consumer curiosity, with a clear mention of this objective, and no mention of any disease or risk of disease, and on the other hand, in vitro diagnostic (IVD) CE-marked test kits, which could go deeper into the analysis and interpretation of samples, as such a report would be intended for trained healthcare professionals.

CONCLUSIONS: Recommendations or actions, specific to the context of use of microbiome testing kits, are listed to improve the quality and the robustness of these test kits to meet expectations of end users (consumers, patients and healthcare professionals). The need for standardization, robust scientific evidence, qualification of microbiome-based biomarkers and a clear regulatory status in Europe are the main issues that will require attention in the near future to align laboratory development with societal needs and thus foster translation into daily health practice.},
}

Humans
Europe
*Feces/microbiology
Microbiota
Reproducibility of Results

@article {pmid39695840,
year = {2024},
author = {Gomathinayagam, S and Kanagalingam, S and Chandrasekaran, S and Krishnan, T and Kodiveri Muthukaliannan, G},
title = {Millennial-scale microbiome analysis reveals ancient antimicrobial resistance conserved despite modern selection pressures.},
journal = {Environmental microbiome},
volume = {19},
number = {1},
pages = {110},
pmid = {39695840},
issn = {2524-6372},
support = {AMR/Fellowship/20/2022-ECD-lI//Indian Council of Medical Research/ ; },
abstract = {BACKGROUND: Antimicrobial resistance presents a formidable challenge, yet its existence predates the introduction of antibiotics. Our study delves into the presence of antimicrobial resistance genes (ARGs) in ancient permafrost microbiomes, comparing them with contemporary soil and pristine environments. Majority of the samples are from regions around Beringia, encompassing parts of Russia and Alaska, with only one sample originating from the Tien Shan Mountain range in Kyrgyzstan.

RESULTS: From over 2.3 tera basepairs of raw metagenomic data, retrieved from samples ranging in age from approximately 7,000 years to 1.1 million years, we assembled about 1.3 billion metagenomic contigs and explored the prevalence of ARGs within them. Our findings reveal a diverse array of ARGs in ancient microbiomes, akin to contemporary counterparts. On average, we identified 2 ARGs per rRNA gene in ancient samples. Actinomycetota, Bacillota, and several thermophiles were prominent carriers of ARGs in Chukochi and Kamchatkan samples. Conversely, ancient permafrost from the Tien Shan Mountain range exhibited no Thermophiles or Actinomycetota carrying ARGs. Both ancient and contemporary microbiomes showcased numerous divergent ARGs, majority of which have identity between 40 and 60% to genes in antibiotic resistance gene databases. To study the selection pressure on ARGs, we performed dN/dS analysis specifically on antibiotic inactivation-type ARGs, which exhibited purifying selection compared to contemporary genes.

CONCLUSION: Antibiotic resistance has existed throughout microbial evolution and will likely persist, as microbes have the capacity to develop and retain resistance genes through evolutionary processes. The classes of antimicrobial resistance genes profiled and the function of antibiotic-inactivating enzymes from ancient permafrost microbiomes do not seem to be very different from the genes found in the antibiotic era. Additionally, we retrieved 359 putative complete viruses from ancient microbiomes and none of them harboured any ARGs.},
}

@article {pmid39695422,
year = {2024},
author = {Czapar, AE and Paul, S and Zulaika, G and Otieno, F and Agingu, W and Chaudhary, A and Bhaumik, R and van Eijk, AM and Green, SJ and Nyothach, E and Phillips-Howard, PA and Mehta, SD},
title = {Water source, latrine type, and rainfall are associated with detection of non-optimal and enteric bacteria in the vaginal microbiome: a prospective observational cohort study nested within a cluster randomized controlled trial.},
journal = {BMC infectious diseases},
volume = {24},
number = {1},
pages = {1419},
pmid = {39695422},
issn = {1471-2334},
support = {R01HD093780/NH/NIH HHS/United States ; R01HD093780/NH/NIH HHS/United States ; R01HD093780/NH/NIH HHS/United States ; R01HD093780/NH/NIH HHS/United States ; R01HD093780/NH/NIH HHS/United States ; R01HD093780/NH/NIH HHS/United States ; R01HD093780/NH/NIH HHS/United States ; R01HD093780/NH/NIH HHS/United States ; MR/N006046/1/MRC_/Medical Research Council/United Kingdom ; MR/N006046/1/MRC_/Medical Research Council/United Kingdom ; MR/N006046/1/MRC_/Medical Research Council/United Kingdom ; MR/N006046/1/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Humans ; Female ; *Vagina/microbiology ; Prospective Studies ; *Toilet Facilities ; Adolescent ; *Microbiota ; *Vaginosis, Bacterial/microbiology ; *Rain ; RNA, Ribosomal, 16S/genetics ; Sanitation ; Hygiene ; Enterobacteriaceae/isolation & purification/classification/genetics ; Young Adult ; Bacteria/classification/isolation & purification/genetics ; },
abstract = {BACKGROUND: Less than one-third of sub-Saharan Africans have access to improved water sources. In US, Indian, and African studies, Bacterial vaginosis (BV) is increased among women with poor water, sanitation, and hygiene (WASH). We examined water source, sanitation (latrine type), and rainfall in relation to the vaginal microbiome (VMB).

METHODS: In a cluster randomized controlled trial of menstrual cups and cash transfer, we measured the impact of cups on VMB via 16S rRNA gene amplicon sequencing in a subset of 436 adolescent girls. We analyzed how self-reported water source and latrine type at home related to VMB over 18-months, examining community state type I (CST-I, L. crispatus dominant) vs. other CST; alpha diversity; targeted taxa (coliform and other water-related pathogens); and non-targeted taxa via machine learning approaches. Mixed effects multivariable longitudinal models were adjusted for intervention arm, age, socioeconomic status, sexual activity, and cluster-level school WASH and rainfall (in millimeters).

RESULTS: Adjusting for all covariates in all models: (1) the odds of CST-I were increased among participants with piped water (vs. pond), and decreased with traditional pit latrine vs. flush toilet. (2) Alpha diversity varied by water source and latrine type without consistent trends. (3) Coliform bacteria relative abundance (RA) was higher among participants with traditional pit or ventilated improved pit latrines vs. flush toilet, and higher among participants relying on stream vs. pond water. Streptococcus agalactiae RA was higher among participants with non-flush toilets, while Bacteroides fragilis RA was lower with non-flush toilets. (4) Key taxa from non-targeted analyses associated with water source and latrine type included typical vaginal bacteria, opportunistic pathogens, and urinary tract pathobionts. (6) Increased rainfall was associated with decreased odds of CST-I.

TRIAL REGISTRATION: ClinicalTrials.gov NCT03051789, February 14, 2017.},
}

Humans
Female
*Vagina/microbiology
Prospective Studies
*Toilet Facilities
Adolescent
*Microbiota
*Vaginosis, Bacterial/microbiology
*Rain
RNA, Ribosomal, 16S/genetics
Sanitation
Hygiene
Enterobacteriaceae/isolation & purification/classification/genetics
Young Adult
Bacteria/classification/isolation & purification/genetics

@article {pmid39695352,
year = {2025},
author = {Moore, M and Whittington, HD and Knickmeyer, R and Azcarate-Peril, MA and Bruno-Bárcena, JM},
title = {Non-stochastic reassembly of a metabolically cohesive gut consortium shaped by N-acetyl-lactosamine-enriched fibers.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2440120},
pmid = {39695352},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; Infant ; *Bacteria/metabolism/classification/isolation & purification/genetics ; Feces/microbiology ; Lactose/metabolism ; Dietary Fiber/metabolism ; Oligosaccharides/metabolism ; Amino Sugars ; },
abstract = {Diet is one of the main factors shaping the human microbiome, yet our understanding of how specific dietary components influence microbial consortia assembly and subsequent stability in response to press disturbances - such as increasing resource availability (feeding rate) - is still incomplete. This study explores the reproducible re-assembly, metabolic interplay, and compositional stability within microbial consortia derived from pooled stool samples of three healthy infants. Using a single-step packed-bed reactor (PBR) system, we assessed the reassembly and metabolic output of consortia exposed to lactose, glucose, galacto-oligosaccharides (GOS), and humanized GOS (hGOS). Our findings reveal that complex carbohydrates, especially those containing low inclusion (~1.25 gL[-1]) components present in human milk, such as N-acetyl-lactosamine (LacNAc), promote taxonomic, and metabolic stability under varying feeding rates, as shown by diversity metrics and network analysis. Targeted metabolomics highlighted distinct metabolic responses to different carbohydrates: GOS was linked to increased lactate, lactose to propionate, sucrose to butyrate, and CO2, and the introduction of bile salts with GOS or hGOS resulted in butyrate reduction and increased hydrogen production. This study validates the use of single-step PBRs for reliably studying microbial consortium stability and functionality in response to nutritional press disturbances, offering insights into the dietary modulation of microbial consortia and their ecological dynamics.},
}

Humans
*Gastrointestinal Microbiome
Infant
*Bacteria/metabolism/classification/isolation & purification/genetics
Feces/microbiology
Lactose/metabolism
Dietary Fiber/metabolism
Oligosaccharides/metabolism
Amino Sugars

@article {pmid39695297,
year = {2024},
author = {Conteville, LC and Silva, JVD and Andrade, BGN and Coutinho, LL and Palhares, JCP and Regitano, LCA},
title = {Recovery of metagenome-assembled genomes from the rumen and fecal microbiomes of Bos indicus beef cattle.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {1385},
pmid = {39695297},
issn = {2052-4463},
mesh = {Animals ; Cattle/microbiology ; *Feces/microbiology ; *Metagenome ; *Rumen/microbiology ; *Phylogeny ; Gastrointestinal Microbiome ; Brazil ; Male ; Archaea/genetics/classification ; Bacteria/genetics/classification ; Microbiota ; },
abstract = {Nelore is a Bos indicus beef breed that is well-adapted to tropical environments and constitutes most of the world's largest commercial cattle herd: the Brazilian bovine herd. Despite its significance, microbial genome recovery from ruminant microbiomes has largely excluded representatives from Brazilian Nelore cattle. To address this gap, this study presents a comprehensive dataset of microbial genomes recovered from the rumen and feces of 52 Brazilian Nelore bulls. A total of 1,526 non-redundant metagenome-assembled genomes (MAGs) were recovered from their gastrointestinal tract, with 497 ruminal and 486 fecal classified as high-quality. Phylogenetic analysis revealed that the bacterial MAGs fall into 12 phyla, with Firmicutes and Bacteroidota being the most predominant, while all archaeal MAGs belong to the genus Methanobrevibacter. The exploration of these microbial genomes will provide valuable insights into the metabolic potential and functional roles of individual microorganisms within host-microbiome interactions, contributing to a better understanding of the microbiome's roles in bovine performance.},
}

Animals
Cattle/microbiology
*Feces/microbiology
*Metagenome
*Rumen/microbiology
*Phylogeny
Gastrointestinal Microbiome
Brazil
Male
Archaea/genetics/classification
Bacteria/genetics/classification
Microbiota

@article {pmid39695280,
year = {2024},
author = {Sinclair, DA},
title = {A bile acid could explain how calorie restriction slows ageing.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {39695280},
issn = {1476-4687},
}

@article {pmid39695182,
year = {2024},
author = {Bell, CJ and Sena, JA and Fajardo, DA and Lavelle, EM and Costa, MA and Herman, B and Davin, LB and Lewis, NG and Berry, AM},
title = {A root nodule microbiome sequencing data set from red alder (Alnus rubra Bong.).},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {1343},
pmid = {39695182},
issn = {2052-4463},
support = {1547842//National Science Foundation (NSF)/ ; 1547842//National Science Foundation (NSF)/ ; 1547842//National Science Foundation (NSF)/ ; 1547842//National Science Foundation (NSF)/ ; 1547842//National Science Foundation (NSF)/ ; 1547842//National Science Foundation (NSF)/ ; 1547842//National Science Foundation (NSF)/ ; 1547842//National Science Foundation (NSF)/ ; },
mesh = {*Microbiota ; *Root Nodules, Plant/microbiology ; *Alnus/microbiology ; *High-Throughput Nucleotide Sequencing ; *Symbiosis ; Frankia/genetics ; },
abstract = {There have been frequent reports of more than one strain of the nitrogen-fixing symbiont, Frankia, in the same root nodule of plants in the genus Alnus, but quantitative assessments of their relative contributions have not been made to date. Neither has the diversity of other microbes, having potential functional roles in symbiosis, been systematically evaluated. Alnus rubra root nodule microbiota were studied using Illumina short read sequencing and kmer-based read classification. Single end 76 bp sequencing was done to a median depth of 96 million reads per sample. Reads were assigned to taxa using KrakenUniq, with taxon abundances being estimated using its companion program Bracken. This was the first high resolution study of Alnus root nodules using next generation sequencing (NGS), quantifying multiple Cluster 1 A Frankia strains in single nodules, and in some cases, a Cluster 4 strain. Root nodules were found to contain diverse bacteria, including several genera containing species known to have growth-promoting effects. Evidence was found for partitioning of some bacterial strains in older versus younger lobes.},
}

*Microbiota
*Root Nodules, Plant/microbiology
*Alnus/microbiology
*High-Throughput Nucleotide Sequencing
*Symbiosis
Frankia/genetics

@article {pmid39695168,
year = {2024},
author = {Park, SG and Kim, JW and Song, JH and Kwon, SH and Oh, SH and Piao, X and Wang, Z and Ryu, JH and Kim, N and Kim, OS and Koh, JT},
title = {The microbial metabolite imidazole propionate dysregulates bone homeostasis by inhibiting AMP-activated protein kinase (AMPK) signaling.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {1644},
pmid = {39695168},
issn = {2399-3642},
support = {2019R1A5A2027521//National Research Foundation of Korea (NRF)/ ; NRF-2020R1I1A1A01061824//National Research Foundation of Korea (NRF)/ ; NRF-2021R1C1C2009626//National Research Foundation of Korea (NRF)/ ; },
mesh = {Animals ; *Imidazoles/pharmacology ; Mice ; *AMP-Activated Protein Kinases/metabolism ; *Homeostasis/drug effects ; *Osteoblasts/drug effects/metabolism ; *Signal Transduction/drug effects ; *Cell Differentiation/drug effects ; *Osteogenesis/drug effects ; Mesenchymal Stem Cells/metabolism/drug effects ; Mice, Inbred C57BL ; Bone and Bones/metabolism/drug effects ; Male ; Osteoclasts/drug effects/metabolism ; Adipocytes/metabolism/drug effects ; },
abstract = {Microbial metabolites provide numerous benefits to the human body but can also contribute to diseases such as obesity, diabetes, cancer, and bone disorders. However, the role of imidazole propionate (ImP), a histidine-derived metabolite produced by the intestinal microbiome, in bone metabolism and the development of osteoporosis is still poorly understood. In this study, we investigated the role of ImP and its underlying mechanisms in regulating bone homeostasis. When ImP was administered to 8-week-old mice for 4 weeks, bone loss was observed, along with a decrease in alkaline phosphatase-positive osteoblast cells. Additionally, bone marrow stromal cells (BMSCs) isolated from ImP-treated mice exhibited reduced osteogenic potential. In BMSCs from control mice, ImP treatment inhibited BMP2-induced osteoblast differentiation while promoting adipocyte differentiation. However, ImP had no effect on RANKL-induced osteoclast differentiation or activity in bone marrow macrophages. Mechanistically, ImP treatment increased p38γ phosphorylation and decreased AMPK (T172) phosphorylation in BMSCs. Suppression of p38γ expression using si-p38γ reversed the inhibitory effects of ImP on osteoblast differentiation, with a concurrent increase in AMPK (T172) phosphorylation. Conversely, ImP stimulated adipocyte differentiation by decreasing AMPK (T172) phosphorylation. Treatment with the AMPK agonist metformin significantly reversed the inhibitory effects of ImP on osteoblast differentiation and the promotion of adipocyte differentiation, along with enhanced AMPK (T172) phosphorylation. These findings suggest that the microbial metabolite ImP may disrupt bone homeostasis by stimulating p38γ phosphorylation and inhibiting the AMPK pathway, presenting a potential therapeutic target for managing metabolic bone diseases.},
}

Animals
*Imidazoles/pharmacology
Mice
*AMP-Activated Protein Kinases/metabolism
*Homeostasis/drug effects
*Osteoblasts/drug effects/metabolism
*Signal Transduction/drug effects
*Cell Differentiation/drug effects
*Osteogenesis/drug effects
Mesenchymal Stem Cells/metabolism/drug effects
Mice, Inbred C57BL
Bone and Bones/metabolism/drug effects
Male
Osteoclasts/drug effects/metabolism
Adipocytes/metabolism/drug effects