@article {pmid40492738,
year = {2025},
author = {Mori, K and Hidaka, K and Tamazawa, S and Hosoyama, A and Tamaki, H and Kakegawa, T and Hanada, S},
title = {Isolation and characterization of a bacterium affiliated with the hitherto uncultured candidate phylum WOR-3 from a deep-sea hydrothermal fluid.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0018825},
doi = {10.1128/aem.00188-25},
pmid = {40492738},
issn = {1098-5336},
abstract = {UNLABELLED: A pure cultured representative, designated strain sy37, in the candidate WOR-3 lineage was obtained from a deep-sea hydrothermal fluid. This lineage was named as the candidate phylum, "Candidatus Caldipriscota," "Candidatus Hydrothermota," or "Candidatus Stahliibacteriota," based on metagenome-assembled genomes of samples from various environments. The isolated strain was a thermophilic, microaerophilic, and chemoheterotrophic rod and obtained energy through aerobic/anaerobic respiration using oxygen and elemental sulfur. The strain could not use thiosulfate, sulfate, sulfite, fumarate, nitrate, nitrite, selenate, selenite, arsenate, ferric citrate, or ferrihydrite as an electron acceptor. Genomic annotation suggested that strain sy37 possesses a novel sulfur reduction mechanism. Among members of the WOR-3 lineage, only the group containing strain sy37 possessed the oxidative phosphorylation pathway with V-type ATPase and cytochrome c oxidase and may be capable of evolving to adapt to modern oxidative environments.

IMPORTANCE: Genome analysis from various environments has revealed the overall diversity of microorganisms. However, there are many lineages for which culture representatives do not yet exist, and the characteristics and ecological significance of many of these microorganisms remain unclear: the WOR-3 lineage is one of these and has been found in various environments through the 16S rRNA gene analysis. In recent years, the metagenome-assembled genomes have been determined from the environments. In this study, we report on the successful isolation of a thermophilic microaerobic chemoorganoheterotroph, strain sy37, which is phylogenetically belonging to the WOR-3 lineage, from a deep-sea hydrothermal environment for the first time.},
}

@article {pmid40492703,
year = {2025},
author = {Alam, I and Marasco, R and Momin, AA and Aalismail, N and Laiolo, E and Martin, C and Sanz-Sáez, I and Foix, BB and Sá, EL and Kamau, A and Guzmán-Vega, FJ and Jamil, T and Acinas, SG and Gasol, JM and Gojobori, T and Agusti, S and Daffonchio, D and Arold, ST and Duarte, CM},
title = {Widespread distribution of bacteria containing PETases with a functional motif across global oceans.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf121},
pmid = {40492703},
issn = {1751-7370},
abstract = {Accumulating evidence indicates that microorganisms respond to the ubiquitous plastic pollution by evolving plastic-degrading enzymes. However, the functional diversity of these enzymes and their distribution across the ocean, including the deep sea, remain poorly understood. By integrating bioinformatics and artificial intelligence-based structure prediction, we developed a structure- and function-informed algorithm to computationally distinguish functional polyethylene terephthalate-degrading enzymes (PETases) from variants lacking PETase activity (pseudo-PETase), either due to alternative substrate specificity or pseudogene origin. Through in vitro functional screening and in vivo microcosm experiments, we verified that this algorithm identified a high-confidence, searchable sequence motif for functional PETases capable of degrading PET. Metagenomic analysis of 415 ocean samples revealed 23 PETase variants, detected in nearly 80% of the samples. These PETases mainly occur between 1000 and 2000 m deep and at the surface in regions with high plastic pollution. Metatranscriptomic analysis further identified PETase variants that were actively transcribed by marine microorganisms. In contrast to their terrestrial counterparts-where PETases are taxonomically diverse-those in marine ecosystems were predominantly encoded and transcribed by members of the Pseudomonadales order. Our study underscores the widespread distribution of PETase-containing bacteria across carbon-limited marine ecosystems, identifying and distinguishing the PETase motif that underpins the functionality of these specialised cutinases.},
}

@article {pmid40492429,
year = {2025},
author = {Meng, R and Li, J and Wang, W and Liang, D and Li, Z and Mao, C and Li, Q and Zhang, Y and Chen, H and Tang, J and Hu, P and Niu, Q and Huang, X and Shen, B and Zhang, J},
title = {Engineered Cas12j-8 is a Versatile Platform for Multiplexed Genome Modulation in Mammalian Cells.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e02593},
doi = {10.1002/advs.202502593},
pmid = {40492429},
issn = {2198-3844},
support = {2022YFC2702705//National Key Research and Development Project of China/ ; 82221005//Creative Research Groups of China/ ; 32371546//National Natural Science Foundation of China/ ; 82071434//National Natural Science Foundation of China/ ; 81971398//National Natural Science Foundation of China/ ; },
abstract = {Cas12j-8 is a compact Cas nuclease discovered from the metagenome of giant bacteriophages, consisting of only 717 amino acids and recognizing the '5-TTN-3' protospacer adjacent motif (PAM) sequence. However, its low gene editing efficiency in mammalian cells limits its application in therapeutic gene editing. To address this limitation, structure-guided mutagenesis is employed to replace key negatively charged residues with arginine, strengthening DNA binding. The resulting quintuple mutant, engineered Cas12j-8 (enCas12j-8), demonstrates robust on-target editing efficiency comparable to LbCas12a while maintaining low off-target effects. Cytosine base editors (CBEs) and adenine base editors (ABEs) are developed using enCas12j-8, achieving up to 29.54-fold C-to-T and 36.57-fold A-to-G conversion efficiency compared with the wild-type at the dominated sites, respectively. Notably, enCas12j-8 enables multiplexed editing of three genomic loci simultaneously via a single crRNA array, achieving efficiencies comparable to single-guide approaches. Additionally, enCas12j-8-ABE facilitates the disruption of splice acceptor sites, effectively inducing exon skipping in the SOD1 gene. This strategy holds potential significance for therapeutic genome modulation. These findings establish enCas12j-8 as a versatile, high-precision tool for genome engineering, combining efficient delivery, multiplexing capability, and compatibility with diverse editing modalities.},
}

@article {pmid40491974,
year = {2025},
author = {Nyström-Persson, J and Bapatdhar, N and Ghosh, S},
title = {Precise and scalable metagenomic profiling with sample-tailored minimizer libraries.},
journal = {NAR genomics and bioinformatics},
volume = {7},
number = {2},
pages = {lqaf076},
pmid = {40491974},
issn = {2631-9268},
mesh = {*Metagenomics/methods ; Algorithms ; *Gene Library ; *Software ; *Metagenome ; },
abstract = {Reference-based metagenomic profiling requires large genome libraries to maximize detection and minimize false positives. However, as libraries grow, classification accuracy suffers, particularly in k-mer-based tools, as the growing overlap in genomic regions among organisms results in more high-level taxonomic assignments, blunting precision. To address this, we propose sample-tailored minimizer libraries, which improve on the minimizer-lowest common ancestor classification algorithm from the widely used Kraken 2. In this method, an initial filtering step using a large library removes non-resemblance genomes, followed by a refined classification step using a dynamically built smaller minimizer library. This 2-step classification method shows significant performance improvements compared to the state of the art. We develop a new computational tool called Slacken, a distributed and highly scalable platform based on Apache Spark, to implement the 2-step classification method, which improves speed while keeping the cost per sample comparable to Kraken 2. Specifically, in the CAMI2 'strain madness' samples, the fraction of reads classified at species level increased by 3.5×, while for in silico samples, it increased by 2.2×. The 2-step method achieves the sensitivity of large genomic libraries and the specificity of smaller ones, unlocking the true potential of large reference libraries for metagenomic read profiling.},
}

*Metagenomics/methods
Algorithms
*Gene Library
*Software
*Metagenome

@article {pmid40491912,
year = {2025},
author = {Li, Y and Ye, J and Zhang, C and Gao, W and Zhang, H and Zheng, C and Feng, Z and Song, M and Hao, J and Zuo, H and Zhao, Z and Guo, Y and Zhang, L},
title = {Case Report: Pulmonary mixed infection by Nocardia cyriacigeorgica, Stenotrophomonas maltophilia, and human cytomegalovirus in a patient with minimal change nephrotic syndrome.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1599958},
pmid = {40491912},
issn = {1664-3224},
mesh = {Humans ; Male ; *Stenotrophomonas maltophilia ; Adolescent ; *Cytomegalovirus Infections/diagnosis/drug therapy ; *Nocardia Infections/diagnosis/drug therapy ; *Nocardia ; *Cytomegalovirus ; *Gram-Negative Bacterial Infections/diagnosis/drug therapy ; *Coinfection/diagnosis/microbiology/drug therapy ; },
abstract = {To our knowledge, this is the first reported case of a pulmonary mixed infection involving Nocardia cyriacigeorgica, Stenotrophomonas maltophilia, and human cytomegalovirus (HCMV) in a patient with minimal change nephrotic syndrome (MCNS), which is of great clinical significance. We report the case of an 18-year-old male with a two-month history of MCNS who was admitted due to fever, cough, and bright red hemoptysis. Upon admission, he was treated with piperacillin/tazobactam and moxifloxacin for one week; however, the therapeutic response was suboptimal. Metagenomic Next-Generation Sequencing (mNGS) and microbiological culture of bronchoalveolar lavage fluid identified a pulmonary mixed infection involving N. cyriacigeorgica, S. maltophilia, and HCMV. Following the initiation of combination therapy with linezolid, trimethoprim-sulfamethoxazole, and ganciclovir, the patient's condition improved markedly, and he was discharged in a stable condition. One-year follow-up revealed complete recovery with no recurrence. This case highlights the critical role of incorporating advanced molecular diagnostic tools such as mNGS into clinical practice and the need to be vigilance about opportunistic infections involving multiple pathogens, especially in patients receiving immunosuppressive therapy.},
}

Humans
Male
*Stenotrophomonas maltophilia
Adolescent
*Cytomegalovirus Infections/diagnosis/drug therapy
*Nocardia Infections/diagnosis/drug therapy
*Nocardia
*Cytomegalovirus
*Gram-Negative Bacterial Infections/diagnosis/drug therapy
*Coinfection/diagnosis/microbiology/drug therapy

@article {pmid40491838,
year = {2025},
author = {Tian, C and Zhang, Z},
title = {Sociobiome signals by high income for increased mobile genetic elements in the gut microbiome of Chinese individuals.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1596101},
pmid = {40491838},
issn = {1664-302X},
abstract = {INTRODUCTION: Mobile genetic elements (MGEs) play a crucial role in the dissemination of antibiotic resistance genes (ARGs), posing significant public health concerns. Despite their importance, the impact of socioeconomic factors on MGEs within the human gut microbiome remains poorly understood.

METHODS: We reanalyzed 1,382 publicly available human gut metagenomic datasets from Chinese populations, including 415 individuals from high-income eastern regions and 967 individuals from low- and middle-income western regions. MGEs were identified and categorized into functional groups, and statistical analyses were conducted to assess regional differences and correlations with economic indicators.

RESULTS: A total of 638,097 nonredundant MGEs were identified. Among these, MGEs related to integration/excision had the highest mean abundance, while those involved in stability/transfer/defense had the lowest. The abundance of MGEs was significantly higher in the eastern population compared to the western population. Moreover, MGE abundance was positively correlated with regional GDP per capita and with ARG abundance within individuals.

DISCUSSION: Our findings suggest that socioeconomic development and industrialization are associated with increased MGE abundance in the human gut microbiome, which may in turn facilitate the spread of ARGs. These results highlight a potential unintended consequence of economic advancement on public health through microbiome-mediated antibiotic resistance.},
}

@article {pmid40491516,
year = {2025},
author = {Xue, Y and Cerqueira, FM and Stevenson, HL and Williams-Bouyer, N and Fang, R},
title = {Culture-negative liver abscess identified with plasma microbial cell-free DNA sequencing: A case report.},
journal = {Infectious medicine},
volume = {4},
number = {2},
pages = {100180},
pmid = {40491516},
issn = {2772-431X},
abstract = {Pyogenic liver abscess (PLA) is a potentially life-threatening disease. Early diagnosis and appropriate treatment are crucial to ensure high-quality healthcare for patients with PLA. However, this is complicated by their non-specific clinical symptoms. In addition, the etiologic organisms responsible for PLA are frequently culture-negative, thus complicating clinical decision-making. Here, we report a case of PLA caused by Streptococcus intermedius, as identified via DNA metagenomic sequencing of plasma.},
}

@article {pmid40491436,
year = {2025},
author = {Li, D and Zhang, DY and Chen, SJ and Lv, YT and Huang, SM and Chen, C and Zeng, F and Chen, RX and Zhang, XD and Xiong, JX and Chen, FD and Jiang, YH and Chen, Z and Mo, CY and Chen, JJ and Zhu, XL and Zhang, LJ and Bai, FH},
title = {Long-term alterations in gut microbiota following mild COVID-19 recovery: bacterial and fungal community shifts.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1565887},
pmid = {40491436},
issn = {2235-2988},
mesh = {Humans ; *COVID-19/microbiology ; *Gastrointestinal Microbiome ; *Fungi/classification/genetics/isolation & purification ; Female ; *Bacteria/classification/genetics/isolation & purification ; Male ; Adult ; Middle Aged ; Feces/microbiology ; SARS-CoV-2 ; *Mycobiome ; Probiotics ; Metagenomics ; China ; },
abstract = {OBJECTIVE: COVID-19 has had a profound impact on public health globally. However, most studies have focused on patients with long COVID or those in the acute phase of infection, with limited research on the health of individuals who have recovered from mild COVID-19. This study investigates the long-term changes in bacterial and fungal communities in individuals recovering from mild COVID-19 and their clinical relevance.

METHODS: Healthy individuals from Hainan Province were enrolled before the COVID-19 outbreak, along with individuals recovering from COVID-19 at 3 months and 6 months post-recovery. Stool, blood samples, and metadata were collected. Metagenomic sequencing and Internal Transcribed Spacer (ITS) analysis characterized bacterial and fungal communities, while bacterial-fungal co-occurrence networks were constructed. A random forest model evaluated the predictive capacity of key taxa.

RESULTS: The gut microbiota of COVID-19 recoverees differed significantly from that of healthy individuals. At 3 months post-recovery, probiotics (e.g., Blautia massiliensis and Kluyveromyces spp.) were enriched, linked to improved metabolism, while at 6 months, partial recovery of probiotics (e.g., Acidaminococcus massiliensis and Asterotremella spp.) was observed alongside persistent pathogens (e.g., Streptococcus equinus and Gibberella spp.). Dynamic changes were observed, with Acidaminococcus massiliensis enriched at both baseline and 6 months but absent at 3 months. Co-occurrence network analysis revealed synergies between bacterial (Rothia spp.) and fungal (Coprinopsis spp.) taxa, suggesting their potential roles in gut restoration. The bacterial random forest model (10 taxa) outperformed the fungal model (8 taxa) in predicting recovery status (AUC = 0.99 vs. 0.80).

CONCLUSION: These findings highlight the significant long-term impacts of mild COVID-19 recovery on gut microbiota, with key taxa influencing metabolism and immune regulation, supporting microbiome-based strategies for recovery management.},
}

Humans
*COVID-19/microbiology
*Gastrointestinal Microbiome
*Fungi/classification/genetics/isolation & purification
Female
*Bacteria/classification/genetics/isolation & purification
Male
Adult
Middle Aged
Feces/microbiology
SARS-CoV-2
*Mycobiome
Probiotics
Metagenomics
China

@article {pmid40491430,
year = {2025},
author = {Chen, Z and Liu, X and Tan, L and Lyu, X and Long, Q and Wu, W and Guo, Z and Liu, Z and Li, Z and Hu, M},
title = {Comparative of metagenomic and targeted next-generation sequencing in lower respiratory tract fungal infections.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1534519},
pmid = {40491430},
issn = {2235-2988},
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Female ; Male ; Middle Aged ; Sensitivity and Specificity ; Aged ; Adult ; China ; *Fungi/genetics/isolation & purification/classification ; *Respiratory Tract Infections/microbiology/diagnosis ; Bronchoalveolar Lavage Fluid/microbiology ; *Lung Diseases, Fungal/diagnosis/microbiology ; Young Adult ; },
abstract = {OBJECTIVES: This study aims to compare the diagnostic efficiency and consistency of metagenomic next-generation sequencing (mNGS) and targeted next-generation sequencing (tNGS) in patients with lower respiratory tract fungal infections.

METHODS: A total of 115 patients with probable pulmonary infection between September 2022 and April 2023 were enrolled at the Second Xiangya Hospital, Changsha, China, of which 61 were clinically diagnosed with invasive pulmonary fungal infection (IPFI) and 54 were non-IPFI cases. All patients received bronchoalveolar lavage, with mNGS, tNGS, and cultures being conducted paralleled. Diagnostic effectiveness and consistency in detecting microorganisms were compared.

RESULTS: Both mNGS and tNGS showed high sensitivity rates of 95.08% each, with specificity of 90.74% and 85.19%, respectively. They also demonstrated positive predictive values (PPVs) of 92.1% and 87.9% and negative predictive values (NPVs) of 94.2% and 93.9%, respectively, in diagnosing IPFI. The sensitivity and NPV of mNGS and tNGS were superior to that of any individual or combined conventional microbiological tests (CMTs) (P < 0.05). The consistency of culture with mNGS and tNGS was 48.70% and 50.43%, respectively. For fungal detection, Pneumocystis jirovecii (26/61, 42.6%; and 28/61, 45.9%), Candida albicans (19/61, 31.1%; and 21/61, 34.4%), and Aspergillus fumigatus (16/61, 26.2%; and 15/61, 24.6%) are most prevalent for mNGS and tNGS in enrolled cases, and the detection rate was greatly higher than that of culture. Furthermore, mNGS and tNGS were capable of diagnosing mixed infections in 65 and 55 out of the 115 cases, whereas only nine cases of bacterial-fungal infection were detected by culture.

CONCLUSION: The diagnostic efficacy of mNGS and tNGS was comparable to that of identified IPFI. NGS-based methodologies present a promising tool for detecting IPFI, which can be a good supplement to CMT.},
}

Humans
*High-Throughput Nucleotide Sequencing/methods
*Metagenomics/methods
Female
Male
Middle Aged
Sensitivity and Specificity
Aged
Adult
China
*Fungi/genetics/isolation & purification/classification
*Respiratory Tract Infections/microbiology/diagnosis
Bronchoalveolar Lavage Fluid/microbiology
*Lung Diseases, Fungal/diagnosis/microbiology
Young Adult

@article {pmid40491146,
year = {2025},
author = {Li, YH and Zhao, YX and Liu, PL and Wang, YY and Tian, CL and Dong, YJ and Zhang, LJ and Chen, G},
title = {[Severe pneumonia, intracranial infection, and reversible splenial lesion syndrome caused by chlamydia psittacosis infection].},
journal = {Zhonghua jie he he hu xi za zhi = Zhonghua jiehe he huxi zazhi = Chinese journal of tuberculosis and respiratory diseases},
volume = {48},
number = {6},
pages = {557-559},
doi = {10.3760/cma.j.cn112147-20240809-00474},
pmid = {40491146},
issn = {1001-0939},
mesh = {Humans ; *Psittacosis/complications/drug therapy ; Male ; Chlamydophila psittaci/isolation & purification ; Minocycline/therapeutic use ; Anti-Bacterial Agents/therapeutic use ; *Pneumonia/microbiology ; Bronchoalveolar Lavage Fluid/microbiology ; },
abstract = {A patient with severe pneumonia, central nervous system infection, and reversible splenial lesion syndrome was described in this article. Metagenomic next-generation sequencing of bronchoalveolar lavage fluid and cerebrospinal fluid revealed chlamydia psittacosis. After treatment with minocycline, the patient was cured. His respiratory and neurological symptoms all disappeared.},
}

Humans
*Psittacosis/complications/drug therapy
Male
Chlamydophila psittaci/isolation & purification
Minocycline/therapeutic use
Anti-Bacterial Agents/therapeutic use
*Pneumonia/microbiology
Bronchoalveolar Lavage Fluid/microbiology

@article {pmid40490984,
year = {2025},
author = {Vargas, BO and Carazzolle, MF and Galhardo, JP and José, J and de Souza, BC and Correia, JBL and Santos, JRD and Pereira, GAG and de de Mello, FDSB},
title = {Engineering Saccharomyces Cerevisiae With Novel Functional Xylose Isomerases From Rumen Microbiota for Enhanced Biofuel Production.},
journal = {Biotechnology journal},
volume = {20},
number = {6},
pages = {e70050},
doi = {10.1002/biot.70050},
pmid = {40490984},
issn = {1860-7314},
support = {//National Agency of Petroleum, Natural Gas and Biofuels/ ; JPG: 88887.479699/2020-0//National Council for the Improvement of Higher Education/ ; JRS: 142340/2020-0//National Council for the Improvement of Higher Education/ ; BCS: 2022/05001-4//Fundação de Amparo à Pesquisa no Estado de São Paulo/ ; },
mesh = {*Saccharomyces cerevisiae/genetics/metabolism/enzymology ; Animals ; *Rumen/microbiology ; *Biofuels ; Sheep ; Xylose/metabolism ; Cattle ; Camelus/microbiology ; *Metabolic Engineering/methods ; Ethanol/metabolism ; Fermentation ; Microbiota/genetics ; Aldose-Ketose Isomerases ; },
abstract = {Xylose metabolism in Saccharomyces cerevisiae remains a significant bottleneck due to the difficulty in identifying functional and efficient xylose isomerases (XI). In the present study, publicly available metagenomic and metatranscriptomic datasets of rumen microbiota from different herbivorous mammals were used to prospect novel XIs sequences. Seven putative XIs from moose, camel, cow, and sheep were cloned into a strain modified for xylose metabolism. Out of those, five XIs demonstrated activity and efficiently converted xylose into xylulose, resulting in ethanol as the final product. A XI from camel rumen microbiota exhibited a KM of 16.25 mM, indicating high substrate affinity. The strains expressing enzymes XI11 and XI12, obtained from sheep rumen microbiota, were able to deplete 40 g/L of xylose within 72 and 96 h, achieving theoretical ethanol yields of 90% and 88%, respectively. These results are comparable to those obtained with Orpinomyces sp. ukk1 XI, a benchmark enzyme previously reported as highly efficient in S. cerevisiae. This study also provides the first report on the successful expression of XIs mined from the ruminal microbiotas of sheep and camels in S. cerevisiae, expanding the perspectives for the optimization of fermentation processes and the production of lignocellulosic biofuels from xylose.},
}

*Saccharomyces cerevisiae/genetics/metabolism/enzymology
Animals
*Rumen/microbiology
*Biofuels
Sheep
Xylose/metabolism
Cattle
Camelus/microbiology
*Metabolic Engineering/methods
Ethanol/metabolism
Fermentation
Microbiota/genetics
Aldose-Ketose Isomerases

@article {pmid40490486,
year = {2025},
author = {Hendricks, H and Israel, S and Weitkamp, JH and Pakala, S and Rajagopala, S and Banerjee, R},
title = {Associations between antibiotic exposure intensity, intestinal microbiome perturbations, and outcomes in premature neonates with bacteremia.},
journal = {Journal of perinatology : official journal of the California Perinatal Association},
volume = {},
number = {},
pages = {},
pmid = {40490486},
issn = {1476-5543},
support = {5UL1TR002243-03//Vanderbilt Institute for Clinical and Translational Research (VICTR)/ ; },
abstract = {BACKGROUND: Neonatal microbiome dysbiosis is associated with infectious complications.

METHODS: Prospective weekly stools were collected over 1 year from hospitalized preterm infants with birthweight ≤2000 g and postnatal age (PNA) ≤2 months. Neonates with bacteremia (cases) were matched to uninfected controls. Stools were analyzed using whole metagenome sequencing. Intensity of antibiotic exposure was compared using an Antibiotic Spectrum Index (ASI).

RESULTS: We analyzed 398 stools from 40 cases and 39 controls. Cases had lower α diversity beyond 4 weeks PNA. Cases with subsequent infections after index bacteremia had persistently lower α diversity, while cases without subsequent infections demonstrated recovery of microbiome diversity. Compared to controls, cases had greater ASI at multiple timepoints, higher Enterococcus spp. and lower anaerobe abundance.

CONCLUSIONS: Compared to controls, premature neonates with bacteremia had intestinal microbiomes with lower α diversity, higher Enterococcus spp. and lower anaerobe abundance. These changes were associated with recurrent infectious complications.},
}

@article {pmid40489796,
year = {2025},
author = {Andersen, S and Kennedy, GA and Banks, M and Flanagan, BM and Henden, AS},
title = {Prebiotic fibre enteral supplementation post allogeneic transplantation; feasibility and impact on the microbiome.},
journal = {Blood advances},
volume = {},
number = {},
pages = {},
doi = {10.1182/bloodadvances.2024015703},
pmid = {40489796},
issn = {2473-9537},
abstract = {The decline in diversity of the gastrointestinal microbiome during haematopoietic stem cell transplantation (HSCT) is associated with poorer clinical outcomes. While provision of enteral nutrition (EN) is common during HSCT, provision of a prebiotic fibre containing formula has not been explored. This pilot study compared tolerance, clinical, microbiome and metabolomic outcomes between patients who received standard EN (n= 10) versus prebiotic fibre EN (n=20) post allogeneic HSCT. Stool samples were collected at baseline and at peri-engraftment and were analysed with shotgun metagenomic sequencing. Provision of prebiotic EN increased daily fibre intake post-transplant to an average 22g per day compared with 4g per day in the standard care group. High tolerance of both EN formulas was observed with only 20% (n=2) of the standard and 15% of the prebiotic group (n=3) requiring parenteral nutrition (p=1.0). There was no difference in the amount of EN provided, EN duration or clinical outcomes. Microbial diversity declined in both groups with no difference post EN provision (p=0.93), however, there was a significant difference in relative abundance of lactobacillus_C rhamnosus with an increase in the prebiotic group only (p=0.022). The relative abundance of faecalicatena gnavus increased in the standard group and declined in the prebiotic group (p=0.0027). Functional analysis of the microbial genome showed decreased expression of antibiotic resistance genes in the prebiotic group only post EN provision (p = 0.00035). A longer fibre intervention should be trialled to optimise clinical outcomes and a more diverse microbiome. The trial was registered at www.anzctr.org.au as ACTRN12621000832875.},
}

@article {pmid40489603,
year = {2025},
author = {Cao, J and He, Q and Zhang, M and Zhou, R and Feng, C},
title = {Characteristics and Clinical Significance of Gut Microbiota in Patients with Invasive Pulmonary Aspergillosis.},
journal = {Polish journal of microbiology},
volume = {},
number = {},
pages = {},
doi = {10.33073/pjm-2025-011},
pmid = {40489603},
issn = {2544-4646},
abstract = {Gut microbiota acts on the lungs through the gut-lung axis and play an important role in lung diseases. However, there are no reports on the gut microbiota characteristics in patients with invasive pulmonary aspergillosis (IPA). We aimed to analyze changes in gut microbiota in IPA patients, correlate these changes with clinical indicators and disease prognosis, and explore the application value of these characteristic changes in diagnosing IPA. The objective was to provide a theoretical basis for preventing and treating individual immunity. We conducted metagenomic next-generation sequencing of fecal samples from 43 patients with IPA and 31 healthy controls to analyze changes in the gut microbiota of these patients. We also built a random forest model for diagnosing IPA based on the gut microbiota. Compared to healthy controls, IPA patients showed a decrease in gut microbiota diversity and metabolic levels. Changes in the microbiota were characterized by a significant reduction in anti-inflammatory species that produce short-chain fatty acids, such as Faecalibacterium, Blautia, Roseburia, Phocaeicola, and Bacteroides. In contrast, opportunistic pathogens, such as Enterococcus, Corynebacterium, Escherichia, Staphylococcus, Haemophilus, and Finegoldia, were significantly enriched. The classification model based on Clostridium fessum, Blautia wexlerae, Streptococcus pseudopneumoniae, Corynebacterium striatum, and Faecalibacterium prausnitzii showed high value in distinguishing patients with IPA from healthy controls. Patients with IPA exhibit gut microbiota imbalance. The gut microbiota can serve as a biomarker that helps in diagnosing IPA. Our findings support the potential use of gut microbiota as a target for IPA prevention and treatment.},
}

@article {pmid40489326,
year = {2025},
author = {Sun, Y and Guo, K and Tang, J and Zhao, J and Zhang, X and Yan, Y and Yuan, L and Zhang, Y and Qiu, C and Luo, J and Zhang, W and Fang, H and Chen, J},
title = {Changes of respiratory microbiota associated with prognosis in pulmonary infection patients with invasive mechanical ventilation-supported respiratory failure.},
journal = {Annals of medicine},
volume = {57},
number = {1},
pages = {2514093},
doi = {10.1080/07853890.2025.2514093},
pmid = {40489326},
issn = {1365-2060},
mesh = {Humans ; Male ; Female ; Retrospective Studies ; *Respiration, Artificial/methods/adverse effects ; Prognosis ; *Respiratory Insufficiency/therapy/microbiology/mortality ; Middle Aged ; Aged ; *Microbiota/genetics ; Intensive Care Units/statistics & numerical data ; High-Throughput Nucleotide Sequencing ; *Respiratory Tract Infections/microbiology/mortality ; Anti-Bacterial Agents/therapeutic use ; Risk Factors ; },
abstract = {BACKGROUND: Respiratory failure (RF) is an important cause of intensive care unit (ICU) admission and mortality due to respiratory diseases. This study aimed to evaluate the clinical performance of metagenomic next-generation sequencing (mNGS) testing in pathogen diagnosis, medication guidance and to explore dynamic changes in the respiratory microbiota associated with prognosis.

METHODS: This multicenter retrospective study enrolled ICU patients from five hospitals who underwent invasive mechanical ventilation (IMV) and had pathogenic microorganisms identified by both mNGS and conventional microbiological tests (CMT) from December 2021 to April 2024. Patients were classified into two groups based on discharge outcomes: survivors (n=122) and non-survivors (n=35).

RESULTS: Compared with the survivors, non-survivors had a significantly higher proportion of smokers, dyspnea, type I RF, blood urea nitrogen, and C-reactive protein (p < 0.05). All the above indicators were identified as independent risk factors for mortality, except for type I RF. mNGS showed a better performance for pathogen identification than CMT in both groups, and nearly 60% showed consistent results between the two methods. Among survivors, antibiotic adjustment was mainly based on mNGS results (35.25%), whereas non-survivors more frequently received adjustments based on mNGS and CMT results (34.29%). The richness and abundance of lung microorganisms in the non-survivors were significantly lower than those in the survivors (p < 0.05).

CONCLUSIONS: mNGS is a promising method for identifying pathogens in pulmonary infections in IMV-supported RF patients and for exploring changes in lung microbial composition to provide a reference for patient prognosis.},
}

Humans
Male
Female
Retrospective Studies
*Respiration, Artificial/methods/adverse effects
Prognosis
*Respiratory Insufficiency/therapy/microbiology/mortality
Middle Aged
Aged
*Microbiota/genetics
Intensive Care Units/statistics & numerical data
High-Throughput Nucleotide Sequencing
*Respiratory Tract Infections/microbiology/mortality
Anti-Bacterial Agents/therapeutic use
Risk Factors

@article {pmid40489211,
year = {2025},
author = {Gautam, P and Yadav, R and Vishwakarma, RK and Shekhar, S and Pathak, A and Singh, C},
title = {An Integrative Analysis of Metagenomic and Metabolomic Profiling Reveals Gut Microbiome Dysbiosis and Metabolic Alterations in ALS: Potential Biomarkers and Therapeutic Insights.},
journal = {ACS chemical neuroscience},
volume = {},
number = {},
pages = {},
doi = {10.1021/acschemneuro.5c00254},
pmid = {40489211},
issn = {1948-7193},
abstract = {ALS is a severe neurodegenerative disorder characterized by motor neuron degeneration, gut dysbiosis, immune dysregulation, and metabolic disturbances. In this study, shotgun metagenomics and [1]H nuclear magnetic resonance (NMR)-based metabolomics were employed to investigate the altered gut microbiome and metabolite profiles in individuals with ALS, household controls (HCs), and nonhousehold controls (NHCs). The principal component analysis (PCA) explained 33% of the variance, and the partial least-squares discriminant analysis (PLS-DA) model demonstrate R[2] and Q[2] values of 0.97 and 0.84, respectively, indicating an adequate model fit. The relative bacterial abundance was 99.34% in the ALS group and 98.94% in the HC group. Among the ten identified genera, Bifidobacterium, Lactobacillus, and Enterococcus were more prevalent in ALS individuals, while Lactiplantibacillus and Klebsiella were more abundant in the HC group. We identified 70 metabolites, including short-chain fatty acids (SCFAs), branched-chain amino acids (BCAAs), carbohydrates, and aromatic compounds, using NMR. Orthogonal partial least-squares discriminant analysis (O-PLS-DA) explained 15.8% of the variance, with a clear separation between the ALS and HC groups. Univariate receiver operating characteristic (ROC) analysis identified three fecal metabolites with AUC values above 0.70, including butyrate (0.798), propionate (0.727), and citrate (0.719). These metabolites may serve as potential biomarkers for ALS. The statistical model for metabolic pathway analysis revealed interconnected pathways, highlighting the complexity of metabolic dysregulation, as well as potential microbial and metabolic biomarkers in ALS. These results highlight the role of gut microbiome alterations in ALS and suggest potential avenues for therapeutic intervention.},
}

@article {pmid40488951,
year = {2025},
author = {Liu, Y and Huang, G and Wei, F and Hu, Y},
title = {Non-negligible role of gut morphology in shaping mammalian gut microbiomes.},
journal = {Science China. Life sciences},
volume = {},
number = {},
pages = {},
pmid = {40488951},
issn = {1869-1889},
abstract = {Because of the overemphasis on the roles of diet and phylogeny in shaping the gut microbiome, the gut morphology is seldom independently considered and even often ignored. To address this research gap, we investigated a large-scale dataset of mammalian gut microbiomes, comprising 16S ribosomal RNA and metagenomic sequencing data from 292 species spanning 20 orders. We dissected the effects of various factors on the gut microbiome across four distinct gut morphology categories (foregut/hindgut/simple, foregut/hindgut, functional ruminant/ruminant-like, and colon fermenter/cecum fermenter) and uncovered the synergistic effect between phylogeny and gut morphology. Moreover, we identified the significant role of gut morphology in the gut microbiomes of hosts occupying specific niches, as well as those within the same taxonomic order but with different gut morphologies. We also identified three enterotype indices-Fusobacterium, UCG-005, and Prevotella-which could predict the three gut morphology types of mammals: simple, foregut, and hindgut. These findings enhance our understanding of mammalian gut microbial assembly and provide novel insights into host-microbe coevolution.},
}

@article {pmid40488937,
year = {2025},
author = {Paul, C and Roy, T and Roy, M and Rajeev, AC and Pan, A and Maitra, M and Das, N},
title = {Genome wide analysis of Priestia aryabhattai_OP, an endobacterium, modulating growth, development and biochemical compositions of sporophores in edible oyster mushroom Pleurotus ostreatus (MTCC 1802).},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {6},
pages = {194},
pmid = {40488937},
issn = {1573-0972},
support = {G.O. No. 52-Edn (B)/5B-15/2017//by Higher Education Department, Govt. of West Bengal, India as fellowship/ ; BT/INF/22/SP41296/2020//Department of Biotechnology (DBT), Govt. of India as DBT Builder Grant/ ; },
mesh = {*Pleurotus/growth & development/metabolism ; *Genome, Bacterial ; Phylogeny ; Laccase/metabolism/biosynthesis ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; Siderophores/metabolism ; Whole Genome Sequencing ; Fruiting Bodies, Fungal/growth & development ; },
abstract = {The increasing global interest in the consuming and producing of edible oyster mushrooms (Pleurotus spp.) is driven by their well-documented nutritional and health benefits. The metagenomic analysis of fruiting body revealed a distinct microbial composition in P. ostreatus, predominantly comprising Pseudomonodota (~ 82%) and Bacillota (~ 10%). An endobacterium Priestia aryabhattai_OP, associated with internal tissue of P. ostreatus (MTCC 1802), was isolated and characterized through biochemical and microscopic analyses as well as 16 S rRNA and whole genome sequencing. Co-cultivation of P. ostreatus with this bacterium significantly enhanced the in vitro production of laccase, a key growth-promoting enzyme. Additionally, the endobacterium improved the biological efficiency (BE) of the mushroom, enriched its nutraceutical profile, and facilitated the biosynthesis of beneficial compounds, including IAA, siderophores, and antimicrobials like lassopeptides, phosphonates, non-ribosomal iron-binding siderophores (NI- siderophore), carotenoids, paeninodins, synechobactins, and surfactins. The present findings offer novel insights into microbe-microbe interactions and their pivotal roles in fungal biology, with significant implications for sustainable mushroom production as well as nutrient enrichment and biotechnological advancements.},
}

*Pleurotus/growth & development/metabolism
*Genome, Bacterial
Phylogeny
Laccase/metabolism/biosynthesis
RNA, Ribosomal, 16S/genetics
Metagenomics
Siderophores/metabolism
Whole Genome Sequencing
Fruiting Bodies, Fungal/growth & development

@article {pmid40488750,
year = {2025},
author = {Jin, L and Huaijie, J and Shuaiyang, Z and Qiaoyun, R and Qingli, N and Jifei, Y and Obaid, MK and Guiquan, G and Guangyuan, L and Hong, Y},
title = {Microbial Pathogen Community in Ornithodoros lahorensis (Acari: Argasidae) in China.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {39},
number = {11},
pages = {e70694},
doi = {10.1096/fj.202500105R},
pmid = {40488750},
issn = {1530-6860},
support = {2021YFD1800101//MOST | National Key Research and Development Program of China (NKPs)/ ; },
mesh = {Animals ; *Ornithodoros/virology/microbiology ; China ; Phylogeny ; Genome, Viral ; *RNA Viruses/genetics ; },
abstract = {The prevalence of tick-borne bacterial and viral diseases, which pose a serious threat to human and livestock health, is increasing worldwide. At present, only a limited number of tick-borne pathogens have been reported, and no analysis of the microbial pathogen community in ticks has been carried out. We sequenced the viral metagenome of Ornithodoros lahorensis species of ticks from the Chinese mainland and identified 390 RNA viruses with unique microbial compositions. A total of 992 assembled viral transcriptomes revealed the breadth and diversity of the genome structure of tick-borne viruses, reflecting the importance of ticks as RNA viral pools. We analyzed the phylogeny of different virus families to investigate virus evolution and found that the most diverse tick-associated viruses belonged to the family Siphoviridae, which diverged earlier in evolutionary time than other arboviruses. There were only a few tick-specific viruses, whereas the number of vertebrate-infecting viruses in ticks was greater. We hope that our virus sequencing dataset will facilitate future important research on viruses carried by ticks that can infect vertebrates.},
}

Animals
*Ornithodoros/virology/microbiology
China
Phylogeny
Genome, Viral
*RNA Viruses/genetics

@article {pmid40488653,
year = {2025},
author = {Shajahan, RM and M, A and A, FT and Sreekumaran, S and Lakshmanan, D and Jaiswal, M and K, RE},
title = {Targeted Antimicrobial Resistance Gene Screening from Metagenomic DNA of Raw Milk Samples Identifies the Presence of Multiple Genes Including the mcr9.},
journal = {Foodborne pathogens and disease},
volume = {},
number = {},
pages = {},
doi = {10.1089/fpd.2024.0187},
pmid = {40488653},
issn = {1556-7125},
abstract = {The current study has investigated the prevalence of antimicrobial resistance (AMR) genes in cow and goat raw milk samples. The misuse of antibiotics in the livestock sector has already been reported to be a major factor contributing to AMR risk. For the study, milk samples were collected from five different farms, and metagenomic DNA was extracted. Then, PCR amplification was carried out using primers specific to 15 different AMR genes. From the results obtained, the prevalence of β-lactam resistance genes, particularly blaTEM (24%), along with other genes like blaZ (12%) and blaSHV (8%), were observed in addition to the transmissible mcr9 gene (12%) conferring resistance to colistin. These findings underscore the urgent need for monitoring AMR genes and regulating antibiotic use in dairy farming to safeguard public health, as it poses a potential risk with the consumption of unpasteurized milk.},
}

@article {pmid40488505,
year = {2025},
author = {Hoque, MN and Rana, ML and Gilman, MAA and Pramanik, PK and Islam, MS and Punom, SA and Hassan, J and Islam, T and Ramasamy, S and Schreinemachers, P and Oliva, R and Rahman, MT},
title = {Mapping of urban garden soil microbiomes in Bangladesh.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0037525},
doi = {10.1128/mra.00375-25},
pmid = {40488505},
issn = {2576-098X},
abstract = {Shotgun metagenomics revealed distinct microbiome profiles in the garden soils of Dhaka and Gazipur district, Bangladesh, with Bacillus spp. demonstrating ecological dominance (>53% relative abundance) and location-specific distribution patterns. These findings highlight Bacillus species as prevalent microbes in urban garden soils.},
}

@article {pmid40488500,
year = {2025},
author = {Berríos-Farías, V and Guajardo-Leiva, S and Gallardo-Cerda, J and Galbán-Malagón, C and Ballesteros, G and Egas, C and Molina-Montenegro, M and Castro-Nallar, E},
title = {Rhizosphere and soil metagenomes and metagenome-assembled genomes from the Byers Peninsula, Livingston Island (62°S), Antarctica.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0017125},
doi = {10.1128/mra.00171-25},
pmid = {40488500},
issn = {2576-098X},
abstract = {Rhizosphere microbes establish functional interactions with their hosts, impacting plant fitness. To further understand plant effects on microbial composition and functional diversity, we present 52 metagenomes and 1,484 metagenome-assembled genomes (MAGs) from soil and the rhizosphere of Colobanthus quitensis and Deschampsia antarctica.},
}

@article {pmid40488474,
year = {2025},
author = {Li, P and Chen, Y and Cao, X and Wang, Z and Sai, L and Wang, L},
title = {Diagnosis of invasive pulmonary aspergillosis using metagenomic next-generation sequencing and conventional microbial tests post-COVID-19 pandemic.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0012125},
doi = {10.1128/spectrum.00121-25},
pmid = {40488474},
issn = {2165-0497},
abstract = {UNLABELLED: Early recognition and timely diagnosis are crucial for improving the clinical outcome of invasive pulmonary aspergillosis (IPA) patients. Metagenomic next-generation sequencing (mNGS) shows immense advantages in identifying responsible complex pathogens, especially with the gradual ease of COVID-19 control policies in China since 2022. A total of 327 patients with suspected Aspergillus infection in non-neutropenic populations were enrolled in the current study. The diagnostic efficacy with mNGS and conventional microbial tests (CMTs) in suspected IPA patients was assessed, and the incidence and risk factors for Aspergillus infection were also investigated. mNGS exhibited excellent performance in detecting Aspergillus. The sensitivity of mNGS (80.58%) was superior to that of CMTs, as demonstrated by comparisons with smears (22.30%, P < 0.001), culture (30.94%, P < 0.001), serum GM (22.62%, P < 0.001), BALF GM (55.40%, P < 0.001), and combined CMTs (61.87%, P < 0.001). The results of mNGS caused a direct shift in the management of 212 (64.8%) positive effect patients, making a clear diagnosis and instructing antifungal therapy. Notably, in addition to the common risk factors, the patients with a history of COVID-19 infection were more prone to IPA. The occurrence of IPA increased significantly with the gradual ease of COVID-19 control policies (47.62% vs 30.21%, P = 0.004). Meanwhile, mixed infections were commonly observed in IPA patients, with Human gammaherpesvirus and Acinetobacter baumannii being the most common co-pathogens. Our study demonstrated that mNGS might present a feasible and remarkably sensitive approach for detecting Aspergillus, thereby serving as a valuable auxiliary tool for CMTs.

IMPORTANCE: Our study is the first to focus on Aspergillus infection after the COVID-19 pandemic and find that (i) mNGS is a feasible and highly sensitive method for detecting Aspergillus post-COVID-19 pandemic, thereby serving as a valuable auxiliary tool for CMTs. (ii) mNGS has the potential to revolutionize the management of fungal infections. (iii) The history of COVID-19 infection is an independent risk factor for IPA. Identification of this risk factor for IPA may raise clinical attention and require careful follow-up of high-risk individuals post-COVID-19 infection. (iv) Mixed infections were commonly observed in IPA patients, with Human gammaherpesvirus and Acinetobacter baumannii being the most common co-pathogens.},
}

@article {pmid40488469,
year = {2025},
author = {Rissanen, AJ and Mangayil, R and Tveit, AT and Maanoja, ST and Khanongnuch, R},
title = {Dissolved organic matter and sulfide enhance the CH4 consumption of a psychrophilic lake methanotroph, Methylobacter sp. S3L5C.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0313324},
doi = {10.1128/spectrum.03133-24},
pmid = {40488469},
issn = {2165-0497},
abstract = {Gammaproteobacterial methanotrophic bacteria (gMOB) are dominant methanotrophs in the water column of oxygen-stratified boreal and subarctic lakes and ponds. (Meta)genomic data suggest that, besides methane (CH4), gMOB potentially use dissolved organic matter (DOM) and reduced sulfur compounds (e.g., sulfide) as electron sources. To study the DOM and sulfide metabolism of lake gMOB, we subjected a psychrophilic lake water strain, Methylobacter sp. S3L5C, first to different sulfide levels (Na2S, 0-5 mM) to test the toxicity, and subsequently, to freshwater DOM (60 mg L[-1]) either alone or with sulfide (0.05 mM) at 1 and 20% CH4 levels. The growth, CH4 and O2 consumption, CO2 production, and mRNA expression patterns of S3L5C were analyzed. Sulfide concentrations of 0-0.5 mM had no effect, while 1 and 5 mM concentrations inhibited the strain's growth. At 20% CH4, DOM addition enhanced CH4 consumption, CO2 production, and growth of S3L5C, while the addition of sulfide+DOM led to further increases in these variables. The addition of sulfide+DOM enhanced CH4 consumption even at 1% CH4. The effect of DOM on the S3L5C's metabolism was accompanied by enhanced expression of the cyc2 gene, which has been suggested to mediate the extracellular electron transfer from DOM. Furthermore, the addition of sulfide+DOM enhanced the expression of the sqr and soxB genes encoding dissimilatory sulfide and thiosulfate oxidation, respectively. Together with previous metagenomic data, these results suggest that the usage of DOM and reduced sulfur compounds as electron sources is a trait that enhances methanotrophy among gMOB of boreal and subarctic lakes and ponds.IMPORTANCEGammaproteobacterial methanotrophic bacteria (gMOB) are crucial mitigators of methane emissions of many ecosystems, like boreal and subarctic lakes and ponds. Metagenomic data suggest that besides using methane, gMOB have genetic potential to use dissolved organic matter (DOM) and sulfide, typically present in lakes and ponds, as electron donors. To test the effect of DOM and sulfide on the methane metabolism of gMOB of oxygen-stratified boreal lakes, we subjected our recently isolated lake gMOB strain, Methylobacter sp. S3L5C, to additions of freshwater DOM and sulfide. We show that DOM and sulfide enhance methane consumption and growth of S3L5C. Furthermore, the expression of genes mediating the electron transfer from DOM and sulfide is enhanced. Our results suggest that the usage of DOM and reduced sulfur compounds as electron sources is a trait that enhances methanotrophy among gMOB and adds significantly to the growing body of literature highlighting the enormous metabolic versatility of gMOB.},
}

@article {pmid40488467,
year = {2025},
author = {Liu, Y and Qiu, Q and Chen, Y and Deng, Y and Huang, W and Sun, C and Shang, X and Chen, X and Wang, C and Han, L and Chen, S and Yuan, J and Xu, F and Yang, Z and Fang, X and Huang, L},
title = {Integrated multi-omics analysis reveals the functional signature of microbes and metabolomics in pre-diabetes individuals.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0145924},
doi = {10.1128/spectrum.01459-24},
pmid = {40488467},
issn = {2165-0497},
abstract = {Pre-diabetes (PD) represents a critical stage in the progression toward type 2 diabetes, with significant alterations observed in the human microbial community among pre-diabetic individuals in observational studies. However, understanding the interaction between human microbiota and the host during pre-diabetes remains limited. Therefore, this study aims to understand the alterations in the human microbial community during pre-diabetes, a critical stage toward type 2 diabetes. Using an integrated analysis of human microbiota and metabolomics data, we seek to identify the functional signature associated with PD and gain insights into potential mechanisms driving its progression to type 2 diabetes. These findings could inform the development of early intervention strategies for those at high risk. Samples were collected from pre-diabetes, diabetes, and healthy control groups. Through metagenome and 16S rRNA sequencing, we analyzed the gut microbial and tongue coating compositions, respectively. Untargeted metabolomics techniques were also applied for comprehensive plasma data. Using integrated multi-omics analysis, we aim to understand the metabolic potentials of the human microbiome, its molecular links with host targets, and their effects on pre-diabetes, thereby deepening our understanding of microbiome-host interactions in this context. The pre-diabetes group exhibited distinct clinical characteristics, particularly in blood glucose levels and a higher average level of γ-glutamyl transferase. We identified 509 intestinal bacterial species, with Megamonas funiformis and Parabacteroides merdae showing higher abundance in the PD group. In tongue coating samples, we found 1,122 bacterial genera, with the PD group showing altered levels of Corynebacterium and Johnsonella. Furthermore, we detected 795 metabolites, primarily involved in carbohydrate and lipid metabolism. Importantly, our integrated multi-omics analysis suggested Flavonifractor plautii's role in modulating blood glucose through influencing carbohydrate metabolism. Our integrated multi-omics analysis revealed significant alterations in several regulatory pathways associated with pre-diabetes, particularly emphasizing the impact of gut bacterium Flavonifractor plautii on blood glucose levels through its influence on carbohydrate metabolism. These intricate relationships among gut microbiota, metabolites, and blood glucose levels underscore the significance of personalized treatment approaches and preventive strategies for pre-diabetes. The insights gained from this research hold considerable promise for advancing our understanding and management of pre-diabetes.IMPORTANCEThis study investigates alterations in the human microbial community during PD, a critical stage leading to type 2 diabetes. Through integrated analysis of metagenomic and metabolomics data from pre-diabetes, diabetes, and healthy control groups, we identified distinct clinical characteristics in the PD group, including elevated blood glucose levels and γ-glutamyl transferase. A total of 509 intestinal bacterial species were identified, with Flavonifractor plautii playing a key role in modulating blood glucose levels via its influence on carbohydrate metabolism. Our findings underscore the complex interactions among gut microbiota, metabolites, and blood glucose levels, highlighting the potential for personalized treatment approaches and early intervention strategies for individuals at high risk of developing type 2 diabetes.},
}

@article {pmid40488405,
year = {2025},
author = {Ricci, F and Leung, PM and Hutchinson, T and Nguyen-Dinh, T and Frank, AH and Hood, AVS and Salazar, VW and Eate, V and Wong, WW and Cook, PLM and Greening, C and McClelland, H},
title = {Chemosynthesis enhances net primary production and nutrient cycling in a hypersaline microbial mat.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf117},
pmid = {40488405},
issn = {1751-7370},
abstract = {Photosynthetic microbial mats are macroscopic microbial ecosystems consisting of a wide array of functional groups and microenvironments arranged along variable redox gradients. Light energy ultimately drives primary production and a cascade of daisy-chained metabolisms. Heterotrophic members of these communities remineralise organic material, decreasing net primary production, and returning nutrients to the aqueous phase. However, reduced inorganic and one-carbon substrates such as trace gases and those released as metabolic byproducts in deeper anoxic regions of the mat, could theoretically also fuel carbon fixation, mitigating carbon loss from heterotrophy and enhancing net primary production. Here, we investigated the intricate metabolic synergies that sustain community nutrient webs in a biomineralising microbial mat from a hypersaline lake. We recovered 331 genomes spanning 40 bacterial and archaeal phyla that influence the biogeochemistry of these ecosystems. Phototrophy is a major metabolic potential found in 17% of the genomes, but over 50% encode enzymes to harness energy from inorganic substrates and 12% co-encode chemosynthetic carbon fixation pathways that use sulfide and hydrogen as electron donors. We experimentally demonstrated that the microbial community oxidises ferrous iron, ammonia, sulfide, and reduced trace gas substrates aerobically and anaerobically. Furthermore, carbon isotope assays revealed that diverse chemosynthetic pathways contribute significantly to carbon fixation and organic matter production alongside photosynthesis. Chemosynthesis in microbial mats results from a complex suite of spatially organised metabolic interactions and continuous nutrient cycling, which decouples carbon fixation from the diurnal cycle, and enhances the net primary production of these highly efficient ecosystems.},
}

@article {pmid40488306,
year = {2025},
author = {Yoshimura, E and Hamada, Y and Hatamoto, Y and Nakagata, T and Nanri, H and Nakayama, Y and Iwasaka, C and Hayashi, T and Suzuki, I and Ando, T and Ishikawa-Takata, K and Tanaka, S and Ono, R and Araki, M and Kawashima, H and Chen, YA and Park, J and Hosomi, K and Mizuguchi, K and Kunisawa, J and Miyachi, M},
title = {Effect of short-term dietary intervention on fecal serotonin, gut microbiome-derived tryptophanase, and energy absorption in a randomized crossover trial: an exploratory analysis.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2514137},
doi = {10.1080/19490976.2025.2514137},
pmid = {40488306},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Feces/chemistry/microbiology ; Cross-Over Studies ; Male ; *Serotonin/analysis/metabolism ; Adult ; Female ; Young Adult ; *Tryptophanase/metabolism/analysis/genetics ; Energy Metabolism ; *Diet ; Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; },
abstract = {In this study, we investigated the effects of short-term energy loads on changes in gut microbiome-derived tryptophanase and fecal serotonin levels and their association with variations in energy absorption. This randomized crossover energy-load intervention study included 15 healthy participants subjected to three dietary conditions - overfeeding, control, and underfeeding - for eight days. The effects of the dietary conditions on energy absorption (digestible and metabolizable energy) were assessed using a bomb calorimeter. Fecal serotonin levels were assessed using LC-MS/MS, and the gut microbiota was analyzed using the 16S rRNA gene and metagenomic shotgun analysis. Significant differences were observed in digestible energy (p < 0.001), with higher values in the overfeeding than in the control (p = 0.032) conditions. Furthermore, significant differences were noted in metabolizable energy and gut transit time (p < 0.001), both of which were higher in the overfeeding than in the control (metabolizable energy: p = 0.001; gut transit time: p = 0.014) and underfeeding (metabolizable energy: p < 0.001; gut transit time: p = 0.004) conditions. Fecal serotonin levels differed significantly (p < 0.001), with significantly lower levels in the overfeeding than in the control (p = 0.005) and underfeeding (p < 0.001) conditions. Tryptophanase exhibited significant differences (p = 0.0019), with lower gene abundance in the overfeeding than in the underfeeding (p = 0.001) condition. Tryptophanase positively correlated with Bacteroides abundance under all conditions (correlation coefficient: 0.696-0.896). Intra-individual variability in fecal serotonin levels was significantly negatively associated with digestible energy (β = -0.077, p = 0.019). The findings suggest that short-term energy loads dynamically alter fecal serotonin, Bacteroides, and tryptophanase levels. Moreover, changes in fecal serotonin levels might be indirectly associated with energy absorption.},
}

Humans
*Gastrointestinal Microbiome
*Feces/chemistry/microbiology
Cross-Over Studies
Male
*Serotonin/analysis/metabolism
Adult
Female
Young Adult
*Tryptophanase/metabolism/analysis/genetics
Energy Metabolism
*Diet
Bacteria/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics

@article {pmid40487918,
year = {2025},
author = {Boak, EN and Bowen, BP and Louie, KB and Northen, TR and Kroeger, ME},
title = {Bacterial and fungal composition and exometabolites control the development and persistence of soil water repellency.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf084},
pmid = {40487918},
issn = {2730-6151},
abstract = {Soil water repellency (SWR), the reduced affinity of soil for water, is a phenomenon that affects soils globally. With worsening climate change, SWR is expected to increase emphasizing the need to understand the mechanisms driving SWR development and persistence. The importance of the soil microbes in SWR has been postulated for decades, but limited research has been conducted into whole-community interactions and the role of community metabolic activity. To address this gap in knowledge, we investigated the direct effect of microbial community composition, activity, and diversity, as well as their associated metabolites on the development and persistence of SWR by inoculating microcosms containing model soils with 15 different microbial communities and quantified respiration and SWR over time. Six communities that consistently produced either a hydrophobic or hydrophilic phenotype were characterized using metagenomics and metabolomics to determine the impact of microbial and metabolite composition and diversity on SWR. We identified several bacterial genera with significant changes in abundance between SWR phenotypes including Nocardiopsis and Kocuria in hydrophilic and Streptomyces and Cutibacterium in hydrophobic. We discovered that hydrophilic communities were more positively connected when compared to hydrophobic communities, which could be due to an increase in defense mechanism genes. Additionally, we identified specific metabolites associated with hydrophilic and hydrophobic phenotypes including an increase in the osmolyte ectoine in hydrophilic and an increase in plant-derived decomposition products in hydrophobic communities. Finally, our research suggests that fungi, previously thought to cause hydrophobicity, may actually contribute to hydrophilicity through their preferential consumption of hydrophobic compounds.},
}

@article {pmid40487916,
year = {2025},
author = {Okazaki, Y and Nishikawa, Y and Wagatsuma, R and Takeyama, H and Nakano, SI},
title = {Contrasting defense strategies of oligotrophs and copiotrophs revealed by single-cell-resolved virus-host pairing of freshwater bacteria.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf086},
pmid = {40487916},
issn = {2730-6151},
abstract = {Characterizing virus-host pairs and the infection state of individual cells is the major technical challenge in microbial ecology. We addressed these challenges using state-of-the-art single-cell genome technology (SAG-gel) combined with extensive metagenomic datasets targeting the bacterial and viral communities in Lake Biwa. From two water layers and two seasons, we obtained 862 single-cell amplified genomes (SAGs), including 176 viral (double-stranded DNA phage) contigs, which identified novel virus-host pairs involving dominant freshwater lineages. The viral infection rate, estimated by mapping the individual SAG's raw reads to viral contigs, showed little variation among samples (12.1%-18.1%) but significant variation in host taxonomy (4.2%-65.3%), with copiotrophs showing higher values than oligotrophs. The high infection rates of copiotrophs were attributed to collective infection by diverse viruses, suggesting weak density-dependent virus-host selection, presumably due to their nonpersistent interactions with viruses resulting from fluctuating abundance. In contrast, the low infection rates of oligotrophs supported the idea that their codominance with viruses is achieved by genomic microdiversification, which diversifies the virus-host specificity, sustained by their large population size and persistent density-dependent fluctuating selection. Notably, we discovered viruses infecting CL500-11, the dominant bacterioplankton lineage in deep freshwater lakes worldwide. These viruses showed extremely high read coverages in cellular and virion metagenomes but were detected in <1% of host cells, suggesting a low infection rate and high burst size. Overall, we revealed highly diverse virus-host interactions within and between host lineages that were overlooked at the metagenomic resolution.},
}

@article {pmid40487915,
year = {2025},
author = {Wu, X and Liu, Y and He, Z and Zhou, X and Liesack, W and Peng, J},
title = {Coevolution and cross-infection patterns between viruses and their host methanogens in paddy soils.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf088},
pmid = {40487915},
issn = {2730-6151},
abstract = {Methanogens play a critical role in global methane (CH4) emissions from rice paddy ecosystems. Through the integration of metagenomic analysis and meta-analysis, we constructed a CRISPR spacer database comprising 14 475 spacers derived from 351 methanogenic genomes. This enabled the identification of viruses targeting key methanogenic families prevalent in rice paddies, including Methanosarcinaceae, Methanotrichaceae, Methanobacteriaceae, Methanocellaceae, and Methanomassiliicoccaceae. We identified 419 virus-host linkages involving 56 methanogenic host species and 189 viruses, spanning the families Straboviridae, Salasmaviridae, Kyanoviridae, Herelleviridae, and Demerecviridae, along with 126 unclassified viral entities. These findings highlight a virome composition that is markedly distinct from those observed in gut environments. Cross-infection patterns were supported by the presence of specific viruses predicted to infect multiple closely related methanogenic species. Evidence for potential virus-host coevolution was observed in 24 viruses encoding anti-CRISPR proteins, likely facilitating evasion of host CRISPR-mediated immunity. Collectively, this study reveals a complex and dynamic network of virus-host interactions shaping methanogen communities in rice paddy ecosystems.},
}

@article {pmid40487637,
year = {2025},
author = {Chen, M and Peng, Y and Hu, Y and Kang, Z and Chen, T and Zhang, Y and Chen, X and Li, Q and Yuan, Z and Wu, Y and Xu, H and Zhou, G and Liu, T and Zhou, H and Yuan, C and Huang, W and Zhang, W},
title = {A critical role for Phocaeicola vulgatus in negatively impacting metformin response in diabetes.},
journal = {Acta pharmaceutica Sinica. B},
volume = {15},
number = {5},
pages = {2511-2528},
pmid = {40487637},
issn = {2211-3835},
abstract = {Metformin has been demonstrated to attenuate hyperglycaemia by modulating the gut microbiota. However, the mechanisms through which the microbiome mediates metformin monotherapy failure (MMF) are unclear. Herein, in a prospective clinical cohort study of newly diagnosed type 2 diabetes mellitus (T2DM) patients treated with metformin monotherapy, metagenomic sequencing of faecal samples revealed that Phocaeicola vulgatus abundance was approximately 12 times higher in nonresponders than in responders. P. vulgatus rapidly hydrolysed taurine-conjugated bile acids, leading to ceramide accumulation and reversing the improvements in glucose intolerance conferred by metformin in high-fat diet-fed mice. Interestingly, C22:0 ceramide bound to mitochondrial fission factor to induce mitochondrial fragmentation and impair hepatic oxidative phosphorylation in P. vulgatus-colonized hyperglycaemic mice, which could be exacerbated by metformin. This work suggests that metformin may be unsuitable for P. vulgatus-rich T2DM patients and that clinicians should be aware of metformin toxicity to mitochondria. Suppressing P. vulgatus growth with cefaclor or improving mitochondrial function using adenosylcobalamin may represent simple, safe, effective therapeutic strategies for addressing MMF.},
}

@article {pmid40487313,
year = {2025},
author = {Wei, H and Thammasit, P and Amsri, A and Pruksaphon, K and Deng, F and Nosanchuk, JD and Youngchim, S},
title = {An overview of rapid non-culture-based techniques in various clinical specimens for the laboratory diagnosis of Talaromyces marneffei.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1591429},
pmid = {40487313},
issn = {2235-2988},
mesh = {*Talaromyces/isolation & purification/genetics ; Humans ; *Mycoses/diagnosis/microbiology ; Sensitivity and Specificity ; Molecular Diagnostic Techniques/methods ; High-Throughput Nucleotide Sequencing ; },
abstract = {Talaromyces marneffei (T. marneffei) is a temperature-dependent biphasic deep opportunistic infectious fungus that primarily affects individuals with advanced HIV disease and other immunocompromised populations. Traditional diagnostic methods rely on fungal culture, but this process, although sensitive, is time-consuming and susceptible to contamination. Therefore, non-culture techniques serve as important complementary and alternative methods for diagnosing talaromycosis. They enable faster and more convenient pathogen identification, improving diagnostic efficiency and facilitating earlier initiation of treatment. Patients with talaromycosis can present with a wide range of clinical symptoms, and different clinical samples require different detection techniques. Blood samples are the most versatile, as laboratory technologists can utilize a wide range of diagnostic methods to obtain accurate results, particularly in the setting of a suspected disseminated infection. In contrast, urine diagnosis relies primarily on immunological methods that detect an antigen abundantly secreted during an infection. Moreover, for invasive samples like bronchoalveolar lavage fluid or cerebrospinal fluid, metagenomic next-generation sequencing is likely to be of significant importance for the early diagnosis due to its high sensitivity and specificity, though this approach is not yet standardized or widely available. For tissue samples, histopathology for light microscopy analysis is a well-established basic method, but it relies on experienced laboratory personnel, is time-consuming, and the histological appearance of other fungi can overlap with T. marneffei. Recent advances in rapid non-culture-based methods diagnostics underscore the growing importance of these tools in clinical settings, particularly for resource-limited areas where culture facilities are inadequate or unavailable. These methods improve diagnostic turnaround time and may lead to better clinical outcomes, especially for vulnerable patient populations. This review emphasizes the need for ongoing development and validation of non-culture diagnostics, with a focus on standardization, accessibility, and integration of rapid molecular and immunological tools to improve early detection and patient management in endemic regions.},
}

*Talaromyces/isolation & purification/genetics
Humans
*Mycoses/diagnosis/microbiology
Sensitivity and Specificity
Molecular Diagnostic Techniques/methods
High-Throughput Nucleotide Sequencing

@article {pmid40487152,
year = {2025},
author = {Leys, SP and Hentschel, U and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Erpenbeck, D and Niu, H and McKenna, V and , and , and , and , and , },
title = {The chromosome-level genome sequences of the freshwater sponge, Spongilla lacustris (Linnaeus, 1759) and the chlorophyte cobiont Choricystis sp., and the associated microbial metagenome sequences.},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {222},
pmid = {40487152},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual Spongilla lacustris (freshwater sponge; Porifera; Demospongiae; Spongillida; Spongillidae). The genome sequence is 248.7 megabases in span. Most of the assembly is scaffolded into 23 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 28.04 kilobases in length. A 14.6-megabase genome assembly of the green algal cobiont Choricystis sp. (Chlorophyta; Trebouxiophyceae) was scaffolded into 16 chromosomal pseudomolecules. Additionally, three bacterial metagenome bins were recovered from the same sample. Gene annotation of this assembly at Ensembl identified 30,435 protein coding genes.},
}

@article {pmid40486693,
year = {2025},
author = {Witonsky, JI and Elhawary, JR and Eng, C and Oh, SS and Salazar, S and Contreras, MG and Medina, V and Secor, EA and Zhang, P and Everman, JL and Fairbanks-Mahnke, A and Pruesse, E and Sajuthi, SP and Chang, CH and Guerrero, TR and Fuentes, KC and Lopez, N and Montañez-López, CA and Morales, EV and Morales, NV and Otero, RA and Rivera, RC and Rodriguez, L and Vazquez, G and Hu, D and Huntsman, S and Jackson, ND and Li, Y and Morin, A and Nieves, NA and Rios, C and Serrano, G and Williams, BJM and Ziv, E and Moore, CM and Sheppard, D and Burchard, EG and Seibold, MA and Rodríguez-Santana, JR},
title = {The PRIMERO birth cohort: Design and baseline characteristics.},
journal = {The journal of allergy and clinical immunology. Global},
volume = {4},
number = {3},
pages = {100470},
pmid = {40486693},
issn = {2772-8293},
abstract = {BACKGROUND: Although early-life respiratory illnesses (RIs) are linked to childhood asthma, it is unclear whether children are predisposed to both conditions or if RIs induce alterations that lead to asthma. Puerto Rican children, who bear a disproportionate burden of early-life RIs and asthma, are an important population for studying this relationship.

OBJECTIVE: We sought to describe the design and baseline characteristics of the Puerto Rican Infant Metagenomic and Epidemiologic Study of Respiratory Outcomes (PRIMERO) birth cohort.

METHODS: PRIMERO is designed to examine the role of respiratory viruses on the development of RIs and asthma. Pregnant women were recruited at Hospital Interamericano de Medicina Avanzada-San Pablo in Caguas, Puerto Rico. Questionnaires at birth and annual follow-ups gather clinical, social, and environmental data. Collected samples include postterm maternal blood; infant cord blood; the child's blood at year 2; and the child's nasal airway epithelium at birth, during RIs over the first 2 years, and annually until age 5.

RESULTS: We enrolled 2,100 mother-child dyads into the PRIMERO study between February 2020 and June 2023, representing 59% of births at Hospital Interamericano de Medicina Avanzada. As of April 29, 2024, 2,069 participants remain active, with high rates of biospecimen collection and annual visit participation. Illness surveillance detected 6,076 RIs, with 38.4% involving the lower respiratory tract.

CONCLUSION: The PRIMERO birth cohort study, with its comprehensive data on viral exposures, respiratory outcomes, and airway molecular phenotypes in a high-risk population of Puerto Rican children, is uniquely positioned to address long-standing questions about the early-life determinants and mechanisms underlying virus-related asthma development.},
}

@article {pmid40486234,
year = {2025},
author = {Shilov, S and Korotetskiy, I and Kuznetsova, T and Zubenko, N and Ivanova, L and Solodova, E and Tugeyeva, A and Kaziyev, A and Korotetskaya, N and Izmailov, T},
title = {The chicken gut resistome data from different regions of Kazakhstan.},
journal = {Data in brief},
volume = {60},
number = {},
pages = {111608},
pmid = {40486234},
issn = {2352-3409},
abstract = {Antibiotic resistance (AR) is a serious global health problem affecting both human medicine and animal agriculture. The poultry farming, especially industrial poultry, antibiotics are widely used for disease prevention and growth promotion, leading to the accumulation and dissemination of antibiotic resistance genes (ARGs) within the intestinal microbiomes of birds. Poultry, which often have close contact with humans, can serve as reservoirs for resistant microorganisms, posing potential public health risks. Determination of avian intestinal resistomes through metagenomic sequencing and bioinformatics analysis enables the identification of diversity and transmission dynamics of ARGs, and to evaluate the influence of environmental factors and conditions of poultry on resistance gene distribution. The article presents data of resistome analysis of gut microbiota in populations of chickens from different regions of Kazakhstan. The data obtained will allow to develop a strategy to reduce the spread of antibiotic-resistant pathogens and improve safety in poultry farming, as well as to predict the risk of transmission of resistant microorganisms between animals and humans.},
}

@article {pmid40485833,
year = {2025},
author = {Sibalekile, A and Araya, T and Castillo Hernandez, J and Kotzé, E},
title = {Glyphosate-microbial interactions: metagenomic insights and future directions.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1570235},
pmid = {40485833},
issn = {1664-302X},
abstract = {Glyphosate [N-(phosphonomethyl) glycine] is the most widely used systematic non-selective herbicide worldwide. However, there is increasing concern about its potential impacts on soil microbial communities, which play crucial roles in maintaining soil functions, plant health, and crop productivity. While glyphosate can be inactivated in soil through strong sorption, desorption remains a significant challenge as glyphosate residues and metabolites can exert toxicity effects on agroecosystems, particularly by altering microbial diversity and functionality. This review synthesizes current knowledge on glyphosate's behavior in soils and advancements in metagenomics approaches (including their limitations) to better understand the complex interactions between glyphosate and microbial communities in genetically modified (GM) cropping systems. Glyphosate has demonstrated antimicrobial properties, inhibiting the growth of various bacteria and fungi. Conversely, other studies suggest that glyphosate may enhance microbial richness, promoting the proliferation of potential glyphosate degraders (e.g., Bacillus, Stenetrophomonas, Pseudomonas, Sphingomonas, and Phenylobacterium) and N2 fixing bacteria (e.g., Bradyrhizobium, Rhizobium, and Devosia) in the bulk soil and rhizosphere of GM crops. These contrasting findings are influenced by factors such as soil types, glyphosate rates, and crop varieties. Moreover, the review highlights that methodological discrepancies, including variations in next-generation sequencing (NGS) platforms and reference databases, contribute significantly to inconsistencies in the literature. These differences stem from varying levels of accuracy or annotation standards in the databases and NGS technologies used. To address these challenges, this study underscores the need for standardized molecular and bioinformatics approaches. Integrating advanced long-read sequencing technologies, such as Oxford Nanopore and PacBio, with compatible reference databases could provide more accurate and consistent analyses of microbial community composition at finer taxonomic levels. Such advancements could improve our understanding of how glyphosate influences the balance between pathogenic microorganisms and plant-growth-promoting microbes in GM cropping systems, ultimately informing sustainable agricultural practices.},
}

@article {pmid40484974,
year = {2025},
author = {Smith, ME and Kavamura, VN and Hughes, D and Mendes, R and Lund, G and Clark, I and Mauchline, TH},
title = {Uncovering functional deterioration in the rhizosphere microbiome associated with post-green revolution wheat cultivars.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {64},
pmid = {40484974},
issn = {2524-6372},
support = {FR2021-02017//Svenska Forskningsrådet Formas/ ; BB/N016246/1//Bilateral BBSRC-Embrapa gran/ ; BBS/E/C/00005196//Bilateral BBSRC-Embrapa grant/ ; BB/X010953/1//Growing Health Institute Strategic Programme/ ; },
abstract = {BACKGROUND: During the Green Revolution, one of the biggest developments of wheat domestication was the development of new cultivars that respond well to fertilisers and produce higher yields on shorter stems to prevent lodging. Consequently, this change has also impacted the wheat microbiome, often resulting in reduced selection of taxa and a loss of network complexity in the rhizospheres of modern cultivars. Given the importance of rhizosphere microbiomes for plant health and performance, it is imperative that we understand if and how these changes have affected their function. Here, we use shotgun metagenomics to classify the functional potential of prokaryote communities from the rhizospheres of pre-green revolution (heritage) cultivars to compare the impact of modern wheat breeding on rhizosphere microbiome functions.

RESULTS: We found distinct taxonomic and functional differences between heritage and modern wheat rhizosphere communities and identified that modern wheat microbiomes were less distinct from the communities in the surrounding soil. Of the 113 functional genes that were differentially abundant between heritage and modern cultivars, 95% were depleted in modern cultivars and 65% of differentially abundant reads best mapped to genes involved in staurosporine biosynthesis (antibiotic product), plant cell wall degradation (microbial mediation of plant root architecture, overwintering energy source for microbes) and sphingolipid metabolism (signal bioactive molecules).

CONCLUSIONS: Overall, our findings indicate that green revolution breeding has developed wheat cultivars with a reduced rhizosphere effect. The consequences of this are likely detrimental to the development of microbiome-assisted agriculture which will require a strong rhizosphere selective environment for the establishment of a beneficial plant root microbiome. We believe our results are of striking importance and highlight that implementation of microbiome facilitated agriculture will benefit from deliberately incorporating the development of beneficial plant-microbiome interactions, alongside traditional yield traits, to advance sustainable wheat production.},
}

@article {pmid40484531,
year = {2025},
author = {Hu, Q and Cheng, S and Qian, D and Wang, Y and Xie, G and Peng, Q},
title = {Identification of core microbial communities and their influence on flavor-oriented traditional fermented sour cucumbers.},
journal = {Food microbiology},
volume = {131},
number = {},
pages = {104810},
doi = {10.1016/j.fm.2025.104810},
pmid = {40484531},
issn = {1095-9998},
mesh = {Volatile Organic Compounds/metabolism/analysis ; Fermentation ; *Cucumis sativus/microbiology/chemistry ; *Fermented Foods/microbiology/analysis ; Taste ; *Bacteria/metabolism/classification/genetics/isolation & purification ; *Flavoring Agents/metabolism ; Humans ; *Microbial Consortia ; Food Microbiology ; *Microbiota ; },
abstract = {Sour cucumber is a traditional fermented vegetable with global popularity, yet its fermentation process often leads to inconsistencies in quality and flavor due to the reliance on natural fermentation. This study identifies 12 core volatile organic compounds (VOCs) contributing to its unique flavor and investigates the key microbial species involved in the fermentation process. Using a synthetic microbial consortium constructed from core microbial species, we successfully replicated the flavor profile of naturally fermented sour cucumbers while enhancing safety by reducing nitrite levels. This approach also reduced bitterness and astringency, while improving sourness and umami, providing a robust framework for standardized production of high-quality fermented vegetables. These findings offer practical solutions for improving flavor quality and ensuring the safety of fermented foods.},
}

Volatile Organic Compounds/metabolism/analysis
Fermentation
*Cucumis sativus/microbiology/chemistry
*Fermented Foods/microbiology/analysis
Taste
*Bacteria/metabolism/classification/genetics/isolation & purification
*Flavoring Agents/metabolism
Humans
*Microbial Consortia
Food Microbiology
*Microbiota

@article {pmid40484397,
year = {2025},
author = {Adachi, A and Dominguez, JJ and Utami, YD and Fuji, M and Kirita, S and Imai, S and Murakami, T and Hongoh, Y and Shinjo, R and Kamiya, T and Fujiwara, T and Minamisawa, K and Ono, N and Kanaya, S and Saijo, Y},
title = {Field Dynamics of the Root Endosphere Microbiome Assembly in Paddy Rice Cultivated under No Fertilizer Input.},
journal = {Plant & cell physiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/pcp/pcaf045},
pmid = {40484397},
issn = {1471-9053},
abstract = {Plants accommodate diverse microbial communities, termed the microbiome, which can change dynamically during plant adaptation to varying environmental conditions. However, the direction of these changes and the underlying mechanisms driving them, particularly in crops adapting to the field conditions, are not well understood. Here, we investigate the root endosphere microbiome of rice (Oryza sativa ssp. japonica) across four consecutive cultivation seasons in a high-yield, non-fertilized, and pesticide-free paddy field, compared to a neighboring fertilized and pesticide-treated field. Using 16S rRNA amplicon and metagenome sequencing, we analyzed three Japonica cultivars-Nipponbare, Hinohikari, and Kinmaze. Our findings reveal that the root endosphere microbiomes diverge based on fertilization regime and plant developmental stages, while the effects of cultivar variation are less significant. Machine learning model and metagenomic analysis of nitrogenase (nif) genes suggest enhanced nitrogen fixation activity in the non-fertilized field-grown roots, highlighting a potential role of diazotrophic, iron-reducing bacteria Telmatospirillum. These results provide valuable insights into the assembly of the rice root microbiome in nutrient-poor soil, which can aid in managing microbial homeostasis for sustainable agriculture.},
}

@article {pmid40483623,
year = {2025},
author = {Chi, Y and Luo, M and Ding, C},
title = {The role of microbiota in fish spoilage: biochemical mechanisms and innovative preservation strategies.},
journal = {Antonie van Leeuwenhoek},
volume = {118},
number = {7},
pages = {89},
pmid = {40483623},
issn = {1572-9699},
support = {202411049301XJ//National College Student Innovation and Entrepreneurship Training Program Funding Project/ ; },
mesh = {*Fishes/microbiology ; *Microbiota ; Animals ; *Food Preservation/methods ; *Food Microbiology ; *Seafood/microbiology ; *Bacteria/metabolism/classification/genetics ; },
abstract = {Fish spoilage is a microbially-mediated biochemical process resulting in quality deterioration, economic losses, and food safety risks. Studies have indicated that spoilage microbiota are phylogenetically diverse, with Gram-negative bacteria (Pseudomonas, Shewanella, Photobacterium) representing primary spoilage organisms, and Gram-positive bacteria (Lactobacillus, Brochothrix) causing spoilage only under specific conditions. Microorganisms cause spoilage through the utilization of three main metabolic processes: (i) proteolytic degradation of muscle proteins, (ii) lipolytic breakdown of triglycerides, and (iii) production of volatile bioactive organic compounds and biogenic amines. By combining high-throughput sequencing with metabolomics, researchers have been uncovering strain-specific metabolic networks and how they are influenced by environmental factors such as temperature, pH, and packaging. This review systematically examines: (1) patterns of taxonomic succession in spoilage microbiota, (2) enzymatic and biochemical pathways involved in spoilage, and (3) innovative preservation strategies targeting spoilage consortia. Emerging technologies, such as bacteriocin-mediated biopreservation, phage therapy, and modified atmosphere packaging, show considerable promise in inhibiting spoilage organisms while maintaining the sensory qualities of the fish. Microbiome-directed interventions combined with predictive modeling and precision storage systems also represent a novel approach to fish preservation. There is a critical need to integrate traditional microbiology with the use of multi-omic technologies for the development of sustainable, microbiota-based preservation strategies that address global seafood security challenges.},
}

*Fishes/microbiology
*Microbiota
Animals
*Food Preservation/methods
*Food Microbiology
*Seafood/microbiology
*Bacteria/metabolism/classification/genetics

@article {pmid40483486,
year = {2025},
author = {Bergholm, J and Tessema, TS and Blomström, AL and Berg, M},
title = {Metagenomic insights into the complex viral composition of the enteric RNA virome in healthy and diarrheic calves from Ethiopia.},
journal = {Virology journal},
volume = {22},
number = {1},
pages = {188},
pmid = {40483486},
issn = {1743-422X},
support = {2021-04343//Vetenskapsrådet/ ; 2021-04343//Vetenskapsrådet/ ; 2021-04343//Vetenskapsrådet/ ; 2021-04343//Vetenskapsrådet/ ; },
mesh = {Animals ; Cattle ; Ethiopia/epidemiology ; *Diarrhea/veterinary/virology ; *Virome ; Metagenomics ; *Cattle Diseases/virology ; Feces/virology ; *RNA Viruses/genetics/classification/isolation & purification ; Phylogeny ; Genome, Viral ; RNA, Viral/genetics ; High-Throughput Nucleotide Sequencing ; },
abstract = {BACKGROUND: Viruses and the virome have received increased attention in the context of calf diarrhea and with the advancement of high-throughput sequencing the detection and discovery of viruses has been improved. Calf diarrhea, being the main contributor to calf morbidity and mortality, is a major issue within the livestock sector in Ethiopia. However, studies on viruses and the virome in calves is lacking in the country. Therefore, we utilized viral metagenomics to investigate the diversity of RNA viruses in healthy and diarrheic calves from central Ethiopia.

METHODS: Fecal material from 47 calves were collected, pooled, and sequenced using Illumina. Following sequencing, the virome composition and individual viral sequences were investigated using bioinformatic analysis.

RESULTS: The metagenomic analysis revealed the presence of several RNA viruses, including rotavirus and bovine coronavirus, known causative agents in calf diarrhea. In addition, several enteric RNA viruses that have not been detected in cattle in Ethiopia previously, such as norovirus, nebovirus, astrovirus, torovirus, kobuvirus, enterovirus, boosepivirus and hunnivirus were identified. Furthermore, a highly divergent viral sequence, which we gave the working name suluvirus, was found. Suluvirus showed a similar genome structure to viruses within the Picornaviridae family and phylogenetic analysis showed that it clusters with crohiviruses. However, due to its very divergent amino acid sequence, we propose that suluvirus represent either a new genus within the Picornaviridae or a new species within crohiviruses.

CONCLUSIONS: To our knowledge, this is the first characterization of the RNA virome in Ethiopian cattle and the study revealed multiple RNA viruses circulating in both diarrheic and healthy calves, as well as a putative novel virus, suluvirus. Our study highlights that viral metagenomics is a powerful tool in understanding the divergence of viruses and their possible association to calf diarrhea, enabling characterization of known viruses as well as discovery of novel viruses.},
}

Animals
Cattle
Ethiopia/epidemiology
*Diarrhea/veterinary/virology
*Virome
Metagenomics
*Cattle Diseases/virology
Feces/virology
*RNA Viruses/genetics/classification/isolation & purification
Phylogeny
Genome, Viral
RNA, Viral/genetics
High-Throughput Nucleotide Sequencing

@article {pmid40483351,
year = {2025},
author = {Koblitz, J and Reimer, LC and Pukall, R and Overmann, J},
title = {Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {897},
pmid = {40483351},
issn = {2399-3642},
support = {K280/2019//Leibniz-Gemeinschaft (Leibniz Association)/ ; },
mesh = {*Machine Learning ; *Bacteria/genetics ; Phenotype ; Software ; Computational Biology/methods ; },
abstract = {Predicting prokaryotic phenotypes-observable traits that govern functionality, adaptability, and interactions-holds significant potential for fields such as biotechnology, environmental sciences, and evolutionary biology. In this study, we leverage machine learning to explore the relationship between prokaryotic genotypes and phenotypes. Utilizing the highly standardized datasets in the BacDive database, we model eight physiological properties based on protein family inventories, evaluate model performance using multiple metrics, and examine the biological implications of our predictions. The high confidence values achieved underscore the importance of data quality and quantity for reliably inferring bacterial phenotypes. Our approach generates 50,396 completely new datapoints for 15,938 strains, now openly available in the BacDive database, thereby enriching existing phenotypic resources and enabling further research. The open-source software we provide can be readily applied to other datasets, such as those from metagenomic studies, and to various applications, including assessing the potential of soil bacteria for bioremediation.},
}

*Machine Learning
*Bacteria/genetics
Phenotype
Software
Computational Biology/methods

@article {pmid40483244,
year = {2025},
author = {Duong, JT and Hayden, HS and Verster, AJ and Pope, CE and Miller, C and Kelsi Penewit, and Salipante, SJ and Rowe, SM and Solomon, GM and Nichols, D and Kelly, A and Schwarzenberg, SJ and Freedman, SD and Hoffman, LR},
title = {Fecal microbiota changes in people with cystic fibrosis after 6 months of elexacaftor/tezacaftor/ivacaftor: Findings from the promise study.},
journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jcf.2025.05.006},
pmid = {40483244},
issn = {1873-5010},
abstract = {BACKGROUND: People with cystic fibrosis (PwCF) often have fecal dysbioses relative to those without CF, characterized by increased pro-inflammatory microbiota and gastrointestinal (GI) inflammation as measured by fecal calprotectin, suggesting that inflammation contributes to CF GI disease. The multicenter observational PROMISE study (NCT04038047) found that calprotectin decreased in PwCF treated with elexacaftor/tezacaftor/ivacaftor (ETI). To better understand the dynamics between fecal dysbiosis and GI inflammation, we characterized the microbiomes of fecal samples from PROMISE and the relationships with calprotectin before, 1-month post, and 6-months post ETI.

METHODS: Fecal microbiota from participants ≥12 y/o were determined by shotgun metagenomic sequencing with random forest modeling and multivariate linear regression analysis to define relationships between microbiota, calprotectin, and deltaF508 genotype before and after ETI.

RESULTS: We analyzed 345 samples from 124 participants. At baseline, we observed community-level differences in the fecal microbiota among participants with abnormal compared to normal calprotectin. With ETI, the relative abundances of 7 bacterial species - Escherichia coli, Staphylococcus aureus, Clostridium scindens, Enterocloster clostridioformis, Clostridium butyricum, Anaeroglobus geminatus, and Ruminococcus gnavus - decreased significantly, correlating with calprotectin decrease. We detected community-level differences in the fecal microbiota based on CFTR genotype and a distinct pattern of microbiota change in F508del homozygous compared to heterozygous participants after ETI.

CONCLUSIONS: We identified 7 species for which fecal abundances decreased with ETI and correlated with calprotectin decrease, supporting a close relationship between fecal microbiota and inflammation in PwCF. Future work will define these relationships with metabolites and GI symptoms during long-term ETI therapy.},
}

@article {pmid40482930,
year = {2025},
author = {Adiningrat, A and Maulana, I and Fadhlurrahman, AG and Yumoto, H},
title = {Probiotic bacteria from asymptomatic necrotic tooth can regulate the microbiome homeostasis.},
journal = {Microbial pathogenesis},
volume = {206},
number = {},
pages = {107791},
doi = {10.1016/j.micpath.2025.107791},
pmid = {40482930},
issn = {1096-1208},
abstract = {OBJECTIVE: This study was performed to identify and isolate the dominant bacteria from a chronic asymptomatic necrotic root canal and investigate in vitro its potential postbiotics effect at the biofilm maturation maintaining root canal microbiome homeostasis.

METHODS: For bacterial identification of an in vivo root canal sample, metagenomic analysis was applied, followed by single colony isolation and PCR analysis. Cell free supernatant (CFS) was then cultivated through serial L paracasei culture procedures prior antibiofilm analysis. Antibiofilm effects of the CFS product were evaluated using in vitro biofilm analysis against S. mutans and E. faecalis. Biofilm mass analysis was measured by using colorimetric approach with cresyl-vast violet staining, morphological appearance was observed using both phase-contrast and scanning electron microscope (SEM). Shapiro-Wilk analysis was applied for normality test, followed by the ANOVA to compare multiple groups or a student t-test for independent two groups mean comparisons.

RESULTS: The isolated root canal bacteria produced biofilm mass that was similar to the Enterococcus faecalis control pathogenic biofilm. From the morphological analysis suggested that population of the isolated bacteria were predominantly occupied by rod-shaped rather than cocci-shaped inhabitants. Further metagenomic analysis indicated that the isolated dominant bacteria in the mixed culture were mainly identified as probiotic bacteria, Lacticaseibacillus paracasei. Moreover, the functional analysis revealed that the L. paracasei cell free supernatant product (CFS) exhibited a promising positive effect in biofilm structure integrity disturbances of S. mutans and E. faecalis.

CONCLUSIONS: The isolated Lacticaseibacillus paracasei from the root canal of a chronic asymptomatic necrotic tooth, produces potential postbiotic products that demonstrated a disruptive ability against Streptococcus mutans and Enterococcus faecalis biofilm integrity.},
}

@article {pmid40482668,
year = {2025},
author = {Garcia-Mauriño, C and Shao, Y and Miltz, A and Lawley, TD and Rodger, A and Field, N},
title = {Investigation of associations between the neonatal gut microbiota and severe viral lower respiratory tract infections in the first 2 years of life: a birth cohort study with metagenomics.},
journal = {The Lancet. Microbe},
volume = {},
number = {},
pages = {101072},
doi = {10.1016/j.lanmic.2024.101072},
pmid = {40482668},
issn = {2666-5247},
abstract = {BACKGROUND: Early-life gut microbiota affects immune system development, including the lung immune response (gut-lung axis). We aimed to investigate whether gut microbiota composition in neonates in the first week of life is associated with hospital admissions for viral lower respiratory tract infections (vLRTIs).

METHODS: The Baby Biome Study (BBS) is a prospective birth cohort, which enrolled mother-baby pairs between Jan 1, 2016, and Dec 31, 2017, at three UK hospitals. In the present study, we only included BBS babies with a sequenced first-week stool sample and successful data linkage. Stool was collected in the first week of life for shotgun-metagenomic sequencing. We examined the following microbiota features: alpha diversity (Chao1, Shannon, and Simpson indices) and community structures (cluster-partitioning against medoids method). The participants were followed up through linkage to the Hospital Episode Statistics-Admitted Patient Care (HES-APC) database to determine vLRTI hospital admission incidence in the first 2 years of life. We used Poisson mixed-effects models for univariable and multivariable analyses to evaluate the association between microbiota features and vLRTI hospital admission incidence, adjusting for confounders identified through direct acyclic graphs.

FINDINGS: 3305 (95%) of the 3476 BBS-enrolled babies for whom consent to data linkage was obtained were included in the present study. 1111 (34%) babies had a first-week sequenced stool sample, of whom 1082 (97%; 564 born vaginally and 518 born by caesarean section) were successfully linked to HES-APC, and had median follow-up of 2·0 years (IQR 1·4-2·9). Most babies were born at term (996 [92%] ≥37 weeks gestational age and 1070 [99%] >35 weeks gestational age) and healthy (1050 [97%] had no comorbidities), and 520 (48%) were female and 562 (52%) were male. Higher first-week gut microbiota alpha diversity was associated with reduced rates of vLRTI hospital admission (Chao1 Index adjusted hazard ratio [HR] 0·92 [95% CI 0·85-0·99]; Shannon Index adjusted HR 0·57 [0·33-0·98]; and Simpson Index adjusted HR 0·36 [0·11-1·20]). Three microbiota clusters were identified. Cluster 1 had a mixed composition and cluster 2 was dominated by Bifidobacterium breve, with both clusters observed in babies born vaginally and by caesarean section. Cluster 3 was found only in vaginally born babies and was dominated by Bifidobacterium longum. Having cluster 1 (mixed) or cluster 2 (B breve dominated) was independently associated with increased rates of vLRTI hospital admission compared with cluster 3 (B longum dominated; cluster 1 [mixed] 3·05 [1·25-7·41] and cluster 2 [B breve dominated] 2·80 [1·06-7·44]).

INTERPRETATION: We report observational evidence that first-week gut microbiota differences are associated with clinically severe vLRTI in young children. This study identified bacterial species that could be of interest for vLRTI prevention. This finding has important implications for the design of future research and intervention strategies.

FUNDING: The Wellcome Trust and Wellcome Sanger Institute core funding.},
}

@article {pmid40482531,
year = {2025},
author = {Yan, R and Manjunatha, V and Thomas, A and Shankar, V and Lumpkins, B and Hoerr, FJ and Greene, A and Jiang, X},
title = {Comparative effects of vegetarian diet and rendered animal by-product on the chicken gut health.},
journal = {Poultry science},
volume = {104},
number = {9},
pages = {105360},
doi = {10.1016/j.psj.2025.105360},
pmid = {40482531},
issn = {1525-3171},
abstract = {Rendered animal proteins and fats can provide vital nutrients for poultry at affordable prices. With growing interest in reintroducing rendered animal by-products into poultry diets, this study investigated the effects of replacing a portion of soybean meal and vegetable fat with rendered animal proteins and fats in a standard vegetarian chicken diet. The study focused on the changes in gut and liver histopathology, and gut microbiome composition and functions. Five diet treatments were formulated to be isocaloric and isonitrogenous and balanced for amino acids, including a standard vegetarian control diet and four diets containing rendered animal by-products. A total of 15 pens with 50 chickens each were assigned one of the five diets from hatch to 42 days of age, with three replicate pens per treatment. On days 28 and 42, six birds were randomly selected from two pens per treatment and humanely euthanized by cervical dislocation. Cecal samples were collected for microbial enumeration and DNA extraction, while gut and liver histopathology analyses were conducted on day 42. Enumeration of Clostridium perfringens was performed under anaerobic conditions using selective media and metagenomic sequencing was used to assess taxonomic and functional profiles of the microbiome. Statistical analysis included data transformation, permutational multivariate analysis of variance, and differential abundance testing. No significant differences were observed between the vegetarian control and rendered animal by-product diets in gut or liver histopathology, C. perfringens levels, or microbiome composition, indicating that inclusion of animal by-products did not significantly affect broiler intestinal health or microbial functions over a 42-day period. These findings suggest that partially replacing soybean meal and vegetable fat with rendered animal by-products can be a safe and cost-effective alternative to plant-based ingredients in poultry diets.},
}

@article {pmid40482428,
year = {2025},
author = {Roy, S and King, GM and Hernández, M},
title = {Classification of MAGs associated with trace gas metabolism in volcanic soils named following SeqCode rules.},
journal = {Systematic and applied microbiology},
volume = {48},
number = {4},
pages = {126622},
doi = {10.1016/j.syapm.2025.126622},
pmid = {40482428},
issn = {1618-0984},
abstract = {Trace gas metabolism is important for nutrient flow in all ecosystems, particularly volcanic ecosystems. Microbes in volcanic ecosystems are among the early colonisers and can play key roles in ecological succession. Here, we describe the taxonomic and functional characteristics of two new metagenome-assembled genomes (MAGs), one belonging to Bacteria (MAG_1957-2.1) and one to Archaea (MAG_C2-3), retrieved from soils in volcanoes located in Chile (Llaima) and the USA (Kilauea), respectively. MAG_1957-2.1 has a genome size of 6.36Mb with 96.21 % completeness. MAG_C2-3 has a genome size of 3.02Mb with 97.57 % completeness. Phylogenetic analyses of the bacterial MAGs placed MAG_1957-2.1 in the class Ktedonobacteria, while the archaeal MAG_C2-3 was placed in the class Nitrososphaeria. Functional characterisation for potential trace gas metabolism showed that MAG_1957-2.1 contains a coxL gene encoding the large subunit of form I carbon monoxide dehydrogenase (CoxL), which is associated with the oxidation of carbon monoxide (CO). It also contains the form I cox gene cluster with a coxMSL arrangement. On the other hand, MAG_C2-3 contains gene subunit A (amoA) as well as subunit B (amoB), which encode for ammonia monooxygenase, the enzyme that catalyses the oxidation of ammonia. Based on the sequence characteristics and phylogenomic analyses we propose the names Paraktedonobacter carboxidivorans sp. nov for MAG_1957-2.1 and Nitrososphaera maunauluensis sp. nov for MAG_C2-3. The names are proposed following the rules of the published Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode).},
}

@article {pmid40482427,
year = {2025},
author = {Mao, YL and Tan, S and Wang, BB and Yang, XY and Hou, J and Cui, HL},
title = {Halosimplex amylolyticum sp. nov., Halosimplex halobium sp. nov., Halosimplex marinum sp. nov., Halosimplex rarum sp. nov., Halovenus amylolytica sp. nov., Halovenus halobia sp. nov., and Halovenus marina sp. nov., halophilic archaea isolated from a marine tidal flat, a marine solar saltern, three coarse sea salts, and two saline lakes.},
journal = {Systematic and applied microbiology},
volume = {48},
number = {4},
pages = {126626},
doi = {10.1016/j.syapm.2025.126626},
pmid = {40482427},
issn = {1618-0984},
abstract = {Seven novel halophilic archaeal strains DYHT-AS-1[T], GDY60[T], TS25[T], XH63[T], SHR40[T], SYNS179[T], and ZY30[T] were isolated from tidal flat, saline lakes, marine solar saltern and coarse sea salts from different regions of China. Metagenomic and amplicon analyses indicated that the abundance of these seven strains in respective habitats was low. Phylogenetic and comparative genomic analyses indicated that strains DYHT-AS-1[T], GDY60[T], TS25[T], and XH63[T] formed a tight cluster with Halosimplex species, exhibiting high 16S rRNA gene sequence similarity (90.4-99.4 %). The ANI, dDDH, and AAI values among these four strains and current Halosimplex species were 80.8-92.3 %, 24.5-53.3 %, and 77.8-91.5 %, respectively. Strains SHR40[T], SYNS179[T], and ZY30[T] were related to Halovenus species, with 16S rRNA gene sequence similarities ranging from 88.8 % to 98.4 %. The ANI, dDDH, and AAI values among these three strains and current Halovenus species were 69.9-77.8 %, 19.4-21.5 %, and 62.1-78.1 %, respectively. These values are significantly lower than the thresholds for species demarcation. The optimal growth conditions for these seven strains in terms of NaCl, MgCl2, temperature, and pH were 3.1-3.4 M, 0.05-0.5 M, 35-40 °C, and 6.5-7.5, respectively. According to phenotypic differences in nutrition, biochemical activity, and antibiotic sensitivity, these seven strains can be distinguished from their related species. Based on the above results, strains DYHT-AS-1[T], GDY60[T], TS25[T], and XH63[T] represent four new species of the genus Halosimplex, and strains SHR40[T], SYNS179[T], and ZY30[T] represent three novel species of the genus Halovenus.},
}

@article {pmid40482059,
year = {2025},
author = {Rendina, M and Turnbaugh, PJ and Bradley, PH},
title = {Human xenobiotic metabolism proteins have full-length and split homologs in the gut microbiome.},
journal = {G3 (Bethesda, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1093/g3journal/jkaf131},
pmid = {40482059},
issn = {2160-1836},
abstract = {Xenobiotics, including pharmaceutical drugs, can be metabolized by both host and microbiota, in some cases by homologous enzymes. We conducted a systematic search for all known human proteins with gut microbial homologs. Because gene fusion and fission can obscure homology detection, we built a pipeline to identify not only full-length homologs, but also cases where microbial homologs were split across multiple adjacent genes in the same neighborhood or operon ("split homologs"). We found that human proteins with full-length gut microbial homologs disproportionately participate in xenobiotic metabolism. While this included many different enzyme classes, short-chain and aldo-keto reductases were the most frequently detected, especially in prevalent gut microbes, while cytochrome P450 homologs were largely restricted to lower-prevalence facultative anaerobes. In contrast, human proteins with split homologs tended to play roles in central metabolism, especially of nucleobase-containing compounds. We identify twelve specific drugs that gut microbial split homologs may metabolize; two of these, 6-mercaptopurine by xanthine dehydrogenase (XDH) and 5-fluorouracil by dihydropyrimidine dehydrogenase (DPYD), have been recently confirmed in mouse models. This work provides a comprehensive map of homology between the human and gut microbial proteomes, indicates which human xenobiotic enzyme classes are most likely to be shared by gut microorganisms, and finally demonstrates that split homology may be an underappreciated explanation for microbial contributions to drug metabolism.},
}

@article {pmid40481853,
year = {2025},
author = {Chaverri, P and Escudero-Leyva, E and Mora-Rojas, D and Calvo-Obando, A and González, M and Escalante-Campos, E and Mesén-Porras, E and Wicki-Emmenegger, D and Rojas-Gätjens, D and Avey-Arroyo, J and Campos-Hernández, M and Castellón, E and Moreira-Soto, A and Drexler, JF and Chavarría, M},
title = {Differential Microbial Composition and Fiber Degradation in Two Sloth Species (Bradypus variegatus and Choloepus hoffmanni).},
journal = {Current microbiology},
volume = {82},
number = {7},
pages = {327},
pmid = {40481853},
issn = {1432-0991},
support = {VI 809-C3-102//Vicerrectoría de Investigación, Universidad de Costa Rica/ ; 57592642//Deutscher Akademischer Austauschdienst/ ; },
mesh = {Animals ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Gastrointestinal Microbiome ; Cellulose/metabolism ; *Dietary Fiber/metabolism ; *Fungi/classification/metabolism/genetics/isolation & purification ; Metagenomics ; },
abstract = {Sloths have the slowest digestion among mammals, requiring 5-20 times longer to digest food than other herbivores, which suggests differences in their gut microbiota, particularly in plant-fiber-degrading microorganisms. Bradypus variegatus has a lower metabolic rate and moves less than Choloepus hoffmanni. However, no comprehensive studies have compared the microbiota (e.g., fungi) of these species. We hypothesized that differences in digestion and metabolism between the two species would be reflected in their microbiota composition and functionality, which we characterized using metagenomics, metabarcoding, and cellulose degradation. Results revealed significant differences in microbiota composition and functionality. Both species are dominated by bacteria; fungi comprised only 0.06-0.5% of metagenomic reads. Neocallimastigomycota, an anaerobic fungus involved in fiber breakdown in other herbivores, was found in low abundance, especially in B. variegatus. Bacterial communities showed subtle differences: C. hoffmanni was dominated by Bacillota and Bacteroidota, while B. variegatus showed higher Actinomycetota. Expected herbivore bacterial taxa (e.g., Fibrobacter and Prevotella) were scarce. Functional analysis showed a low abundance of carbohydrate-active enzymes essential for polysaccharide breakdown. Cellulose degradation assays confirmed that sloths digest only ~ 3-30% of ingested plant material. This research sheds light on the potential multidirectional links between the gut microbiota, metabolism, and digestion.},
}

Animals
*Bacteria/classification/genetics/metabolism/isolation & purification
*Gastrointestinal Microbiome
Cellulose/metabolism
*Dietary Fiber/metabolism
*Fungi/classification/metabolism/genetics/isolation & purification
Metagenomics

@article {pmid40481811,
year = {2025},
author = {Baeza, JA and Rosales, SM},
title = {The complete mitochondrial genome of the 'maze' coral Meandrina meandrites (Scleractinia: Vacatina: Meandrinidae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {},
number = {},
pages = {1-8},
doi = {10.1080/24701394.2025.2504422},
pmid = {40481811},
issn = {2470-1408},
abstract = {The shallow water reef-building 'maze' or 'brain' stony coral Meandrina meandrites (fam. Meandrinidae) is currently experiencing major environmental problems in the Caribbean Sea. In this study, we assembled the mitochondrial genome of M. meandrites to support future conservation of this imperiled coral. We also explored the phylogenetic position of this coral in the Class Scleractinia utilizing the phylogenetic signal provided by translated mitochondrial protein-coding genes (PCGs). A complete mitochondrial genome of M. meandrites, 17,196 bp in length, was assembled using short-reads next-generation sequencing (NGS) sequencing with the target-restricted-assembly pipeline GetOrganelle. The newly assembled mitochondrial genome of M. meandrites encoded 13 PCGs, two ribosomal genes (ribosomal RNA), and two transfer genes (tRNAs). It also contains two relatively long non-coding regions 400 and 1,877 bp long. A group I intron bisected the nad5 PCG. Each of the two tRNAs exhibited a canonical 'cloverleaf' secondary structure. The mitochondrial genome of M. meandrites is identical to that of a conspecific assembled using HiFi PacBio long reads (available in GenBank with accession number OY855917 but without a companion paper) with the exception of four single nucleotide variants. The aforementioned comparison indicates that the mitochondrial genome assembled from a short-read NGS dataset is reliable (complete and accurate). A maximum-likelihood phylomitogenomic analysis based on PCGs (translated) supported the monophyly of the order Scleractinia and placed M. meandrites in a moderately to well-supported clade with Astrangia sp. (family Astrangidae). This newly assembled mitochondrial genome can be used as a reference to support conservation planning, including biomonitoring of this stony coral using environmental DNA.},
}

@article {pmid40481438,
year = {2025},
author = {Babalola, OO and Osuji, IE and Akanmu, AO},
title = {Amplicon-based metagenomic survey of microbes associated with the organic and inorganic rhizosphere soil of Glycine max L.},
journal = {BMC genomic data},
volume = {26},
number = {1},
pages = {40},
pmid = {40481438},
issn = {2730-6844},
}

@article {pmid40481394,
year = {2025},
author = {Lu, X and Chen, J and Miao, S and Xie, Y},
title = {Two cases of Talaromyces marneffei tracheobronchial infection in HIV-negative patients.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {800},
pmid = {40481394},
issn = {1471-2334},
abstract = {OBJECTIVES: In recent years, the incidence and prevalence of Talaromyces marneffei (TM) have been on the rise. This infection predominantly affects immunocompromised or immunodeficient individuals, especially those with acquired immunodeficiency syndrome (AIDS). There has been a notable increase in the incidence of TM and its associated infections. The majority of cases occur within immunocompromised or immunodeficient populations, with a high prevalence among AIDS patients. However, cases are also occasionally detected in HIV - negative individuals. Due to the insidious and slow - growing nature of TM, the disease can be misdiagnosed as other conditions such as tuberculosis, bacterial pneumonia, and lung cancer, particularly in non - endemic regions. Such misdiagnosis significantly impacts the patient’s prognosis.

METHODS: Two HIV-negative patients with TM infection from non - endemic areas were hospitalized with a high suspicion of co-infection with lung cancer and poor symptomatic treatment response. These patients underwent a comprehensive diagnostic workup, including lung puncture biopsy, sputum, blood, pleural, and peritoneal fluid cultures, as well as Metagenomics Next Generation Sequencing (mNGS) analysis. Eventually, both patients were diagnosed with TM tracheobronchial infection.

RESULTS: The patients were treated with voriconazole antifungal therapy, combined with methylprednisolone (used for reducing inflammation, relieving spasms, and treating asthma) and acyclovir (used for treating viral infections). The 49 - year - old patient was cured and discharged from the hospital, while the 79 - year - old male patient’s condition continued to deteriorate, and he ultimately died.

CONCLUSION: It has been determined that TM infection, presenting primarily with respiratory symptoms, is highly susceptible to misdiagnosis in the early stages of the disease. This can lead to treatment delays and a negative impact on the prognosis. It is crucial for medical professionals to be more aware of the possibility of TM infection in non - HIV - infected and non - endemic populations. Collecting respiratory and lung tissue specimens from the infection sites at the earliest possible stage is essential for diagnosing TM infection. Integrating mNGS and mass spectrometry results is crucial for improving the detection and early diagnosis of TM infection, which is of great value for enhancing the efficacy of clinical treatment and the prognosis of patients.

CLINICAL TRIAL NUMBER: Not applicable.},
}

@article {pmid40480048,
year = {2025},
author = {Yang, J and Liu, J and Gu, H and Song, W and Zhang, H and Wang, J and Yang, P},
title = {Gut microbiota, metabolites, and pulmonary hypertension: Mutual regulation and potential therapies.},
journal = {Microbiological research},
volume = {299},
number = {},
pages = {128245},
doi = {10.1016/j.micres.2025.128245},
pmid = {40480048},
issn = {1618-0623},
abstract = {Pulmonary hypertension is a progressive condition characterized by increased pulmonary vascular pressure and resistance, ultimately leading to right heart failure and death. Increasing evidence has underscored the importance of the gut-lung axis in the development of respiratory and cardiovascular diseases. Notably, significant changes in the gut microbiota, including altered microbial composition and function, have been observed in pulmonary hypertension. Specifically, microbiota-derived metabolites, including short chain fatty acids, trimethylamine N-oxide, bile acids and tryptophan, play a significant role in the development of pulmonary hypertension. The identification of key bacteria and metabolites, along with recent advances in gut microbiota-targeting technologies and metabolic pathway-targeting inhibitors/agonists, holds potential for developing diagnostic, prognostic, and therapeutic strategies for pulmonary hypertension. Emerging research directions include metagenomic analysis of viruses and fungi, artificial intelligence-aided prediction models, novel metabolites and their associated enzymes, drug-microbiota interactions, selective antibiotics, and advanced microbiota transplantation. This review synthesizes clinical and experimental evidence linking the gut microbiota to pulmonary hypertension, highlighting their interplay as a promising avenue for further investigation and translational applications.},
}

@article {pmid40478725,
year = {2025},
author = {Wang, J and den Bakker, HC and Denes, TG},
title = {A critical review of metagenomic approaches for foodborne pathogen surveillance.},
journal = {Critical reviews in food science and nutrition},
volume = {},
number = {},
pages = {1-14},
doi = {10.1080/10408398.2025.2503453},
pmid = {40478725},
issn = {1549-7852},
abstract = {High-throughput sequencing methods (e.g., whole-genome sequencing and metagenomics) are rapidly changing multiple fields of microbiology, including food safety and pathogen surveillance. Current foodborne pathogen surveillance relies heavily on resource-intensive, isolate-based approaches, limiting large-scale implementation. To facilitate more efficient public health responses, innovative technologies that can rapidly and accurately identify diverse foodborne pathogens are essential. Metagenomics-based approaches represent a potential transformative advancement in food safety diagnostics. These techniques enable unbiased and comprehensive analysis of foodborne pathogen genetic material from clinical, food product, processing facility, and environmental samples, positioning metagenomics as a promising strategy for foodborne pathogen surveillance. Here, we explore how metagenomics can be applied to foodborne pathogen surveillance and outbreak detection, focusing on recent advances in both short- and long-read sequencing technologies. The challenges limiting potential applications are reviewed, including the detection and characterization of low-abundance pathogens, the complexity of assembly-based analysis, and the identification of antimicrobial resistance genes. Finally, we discuss a future outlook for metagenomics impacting public health response to foodborne pathogens. It is anticipated that through continuous improvements in sequencing and analytical technologies, that metagenomic approaches to foodborne pathogen detection and characterization will become routine, with the potential to reduce the foodborne illness burden.},
}

@article {pmid40478660,
year = {2025},
author = {Nicolas, M and Lemaitre, C and Vicedomini, R and Frioux, C},
title = {Mapler: A pipeline for assessing assembly quality in taxonomically rich metagenomes sequenced with HiFi reads.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btaf334},
pmid = {40478660},
issn = {1367-4811},
abstract = {SUMMARY: Metagenome assembly seeks to reconstruct the most high-quality genomes from sequencing data of microbial ecosystems. Despite technological advancements that facilitate assembly, such as Hi-Fi long reads, the process remains challenging in complex environmental samples consisting of hundreds to thousands of populations. Mapler is a metagenome assembly and evaluation pipeline with a focus on evaluating the quality of Hi-Fi long read metagenome assemblies. It incorporates several state-of-the-art metrics, as well as novel metrics assessing the diversity that remains uncaptured by the assembly process. Mapler facilitates the comparison of assembly strategies and helps identify methodological bottlenecks that hinder genome reconstruction.

Mapler is open source and publicly available under the AGPL-3.0 licence at https://github.com/Nimauric/Mapler. Source code is implemented in Python and Bash as a Snakemake pipeline. A snapshot of the code is available on Software Heritage at swh:1:snp:df4f5f02e22ebbab285ec14af58d4d88436ee5d6.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}

@article {pmid40478429,
year = {2025},
author = {Ogola, HJO and Ijoma, GN and Edokpayi, JN},
title = {Hydrological regime and niche partitioning drive fungal community structure and function in arid wetlands sediments of South Africa.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {40478429},
issn = {1614-7499},
support = {DST/CON0197/2017//Department of Science and Innovation, South Africa/ ; },
abstract = {Arid wetlands are ecologically significant yet understudied ecosystems shaped by extreme conditions and hydrological variability. However, the structure and ecological functional of fungal communities in these habitats remain poorly understood, especially in southern Africa. This study integrated shotgun metagenomics, FUNGuild functional profiling, and multivariate analyses to examine fungal diversity, functional composition, and environmental drivers in seasonal and permanent arid wetlands of South Africa. Distinct fungal assemblages emerged, primarily shaped by hydrological regimes and ionic stress. Seasonal wetlands were dominated by Mucoromycota (79%), particularly arbuscular mycorrhizal (AM) fungus (Rhizophagus, 62%), while permanent wetlands had higher Ascomycota (54%), with Aspergillus (50%) prevalent in oxygen-limited sediments. Although alpha diversity showed no significant difference, beta diversity confirmed significant mycobiome differentiation. Total dissolved solids (TDS), electrical conductivity (EC), and salinity were key predictors of fungal composition, with TDS the strongest determinant (p < 0.01). Functional guild analysis highlighted niche differentiation, with saprotrophs dominating permanent wetlands (59.7% vs. 21.5%; p < 0.05), while symbiotrophs, particularly AM fungi, were enriched in seasonal wetlands (69.3% vs. 36.1%; p < 0.001). Indicator taxa identified via LefSe (LDA > 3, p < 0.05) and random forest modeling included Rhizophagus, Trichoderma, Fusarium, and Entomophthora in seasonal wetlands, and Aspergillus in permanent wetlands. This study provides the first integrative insight into fungal ecology in South Africa's arid wetlands, demonstrating that hydrological regime shapes fungal structure and function through environmental filtering and niche specialization, with implications for guiding conservation and adaptive management of these fragile ecosystems.},
}

@article {pmid40478395,
year = {2025},
author = {Zhang, T and Liu, Y and Li, J and Yuan, M and Qiao, C and Huang, X and Yang, X and Gao, B and Lou, C and Yang, Y and Cao, Y},
title = {Toad's survivability and soil microbiome alterations impacted via individual abundance.},
journal = {Biologia futura},
volume = {},
number = {},
pages = {},
pmid = {40478395},
issn = {2676-8607},
support = {CI2021A04012//CACMS Innovation Fund/ ; ZZ16-YQ-04//Fundamental Research Funds of CACMS/ ; H2023406026//Hebei Natural Science Foundation/ ; QN2024119//Science Research Project of Hebei Education Department/ ; },
abstract = {Artificial breeding is a valid strategy for the reverse of current extinction tendency in wild population of amphibian like toads. Considering public health, an alternative to antibiotics is demanded for ameliorating survival of toads during the culture period. Relying on the cognition of probiotics or antagonistic bacteria, the present work investigated viability and soil microorganism variations induced by distribution characteristic on toads using high-throughput sequencing technology. Comparison and analysis of soil metagenome from clustered and depopulated groups distinguished by toad behavior showed differences of bacterial community composition (e.g., Proteobacteria bacterium TMED72 and Nannocystis exedens) and antibiotic resistance genes involving antibiotic efflux and inactivation (e.g., mdtB and acrF). There were 18 and 10 distribution-typical genes independently enriched in Proteobacteria bacterium TMED72 and bacterium TMED88 of clustered group and Nannocystis exedens of depopulated group. In Nannocystis exedens, one of the distribution-typical genes was annotated as 6-phosphogluconate dehydrogenase acting role on bacterial growth restriction. It implied that, compared with the group emerging rare traces, the reduction of soil bacteria which possess genes retarding bacterial growth putatively impairs competitiveness to pathogenic bacteria and results in poor survivability of toads under clustering behavior. With the co-occurrence of virulence genes, more evidences are needed on the antagonistic bacteria Nannocystis exedens as antibiotic substitute.},
}

@article {pmid40476734,
year = {2025},
author = {Marcos-Zambrano, LJ and Lacruz-Pleguezuelos, B and Aguilar-Aguilar, E and Marcos-Pasero, H and Valdés, A and Loria-Kohen, V and Cifuentes, A and Ramirez de Molina, A and Diaz-Ruiz, A and Pancaldi, V and Carrillo de Santa Pau, E},
title = {Microbiome gut community structure and functionality are associated with symptom severity in non-responsive celiac disease patients undergoing a gluten-free diet.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0014325},
doi = {10.1128/msystems.00143-25},
pmid = {40476734},
issn = {2379-5077},
abstract = {UNLABELLED: Non-responsive celiac disease (NRCD) challenges clinicians due to persistent symptoms despite a gluten-free diet (GFD). We present a cross-sectional pilot study including 39 NRCD patients to describe the underlying mechanisms contributing to symptom persistence by integrating different levels of data (fecal shotgun metagenomics, mucosal integrity markers, and metabolomic profiles) and using microbial networks to unravel the community structure of the patient's microbiome. Two distinct clusters of patients were identified based on clinical and demographic variables not influenced by gluten consumption. Cluster 1, labeled "Low-grade symptoms," displayed milder symptoms and lower inflammatory markers and a fragmented microbial network characterized by high modularity and a reliance on localized hubs, suggesting a microbial community under stress but capable of maintaining limited functionality. Cluster 2, named "High-grade symptoms," exhibited more severe symptoms, elevated inflammatory markers, and a more connected but antagonistic microbial network with a greater number of keystone taxa, including taxa associated with Th17 activation and inflammation. In contrast, the control network, representing asymptomatic treated celiac disease (tCD) patients, was highly interconnected, resilient, and cooperative, with a robust structure maintained even under simulated disruptions. Metabolomic analysis revealed differential metabolites between clusters, particularly those involved in amino acid metabolism pathways and microbial-derived metabolites such as indolelactic acid and mannitol, which were associated with symptom severity. This study identifies NRCD subgroups based on the gut microbiome and metabolic signatures associated with clinical manifestations, highlighting variations in microbial network stability and metabolite profiles as contributors to symptom persistence and potential therapeutic targets.

IMPORTANCE: Celiac disease (CD) is a chronic immune-mediated systemic disorder caused by consuming gluten in genetically susceptible individuals. There is currently no cure for CD, and the most effective treatment is maintaining a strict, lifelong gluten-free diet (GFD). This nutritional therapy aims to prevent the immune reaction triggered by gluten and promote the healing of the intestinal lining, resolving the clinical, serological, and histological abnormalities within 6-12 months. However, up to 30% of patients may continue to experience symptoms or exhibit laboratory abnormalities or intestinal inflammation suggestive of active CD, despite following a GFD. This challenge, which encompasses various diagnoses, is known as nonresponsive celiac disease (NRCD). In this study, we explored the role of intestinal microbiota in causing NRCD, finding an association between the persistence of symptoms and changes in mucosal integrity biomarkers, with different gut microbiome structures among NRCD patients, indicating a significant role of the microbiome in NRCD.},
}

@article {pmid40475999,
year = {2025},
author = {Hwang, D and Chong, E and Li, Y and Li, Y and Roh, K},
title = {Deciphering the gut microbiome's metabolic code: pathways to bone health and novel therapeutic avenues.},
journal = {Frontiers in endocrinology},
volume = {16},
number = {},
pages = {1553655},
pmid = {40475999},
issn = {1664-2392},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Bone and Bones/metabolism ; Animals ; Probiotics/therapeutic use ; *Bone Remodeling/physiology ; *Osteoporosis/metabolism/microbiology/therapy ; Prebiotics ; Fecal Microbiota Transplantation ; Bone Diseases/metabolism/microbiology/therapy ; },
abstract = {The gut microbiome plays an important role in the protection against various systemic diseases. Its metabolic products profoundly influence a wide range of pathophysiological events, including the regulation of bone health. This review discusses the recently established connections between the gut microbiome and bone metabolism, focusing on the impact of microbiome-derived metabolites such as SCFAs, Bile Acids, and tryptophan to the control of bone remodeling and immunoreactions. Recent advances in metagenomics and microbiome profiling have unveiled new exciting therapeutic opportunities, ranging from the use of probiotics, prebiotics, engineered microbes, and to fecal microbiota transplantation. Understanding of the interplay among diet, microbiota, and bone health provides new avenues for tailored interventions aimed at reducing disease risk in osteoporosis and other related disorders. By drawing knowledge from microbiology, metabolism, and bone biology, this review highlights the potential of microbiome-targeted therapies to transform skeletal health and the management of bone diseases.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Bone and Bones/metabolism
Animals
Probiotics/therapeutic use
*Bone Remodeling/physiology
*Osteoporosis/metabolism/microbiology/therapy
Prebiotics
Fecal Microbiota Transplantation
Bone Diseases/metabolism/microbiology/therapy

@article {pmid40475488,
year = {2025},
author = {Price, A and Rasolofomanana-Rajery, S and Manpearl, K and Robertson, CE and Krebs, NF and Frank, DN and Krishnan, A and Hendricks, AE and Tang, M},
title = {Network-based representation learning reveals the impact of age and diet on the gut microbial and metabolomic environment of U.S. infants in a randomized controlled feeding trial.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.11.01.621627},
pmid = {40475488},
issn = {2692-8205},
abstract = {While studies have explored differences in gut microbiome development for infant liquid diets (breastmilk, formula), little is known about the impact of complementary foods on infant gut microbiome development. Here, we investigated how different protein-rich foods (i.e., meat vs. dairy) affect fecal metagenomics and metabolomics during early complementary feeding from 5-12 months in U.S. formula-fed infants from a randomized controlled feeding trial. We used a network representation learning approach to model the time-dependent, complex interactions between microbiome features, metabolite compounds, and diet. We then used the embedded space to detect features associated with age and diet type and found the meat diet group was enriched with microbial genes encoding amino acid, nucleic acid, and carbohydrate metabolism. Compared to a more traditional differential abundance analysis, which analyzes features independently and found no significant diet associations, network node embedding represents the infant samples, microbiome features, and metabolites in a single transformed space revealing otherwise undetected associations between infant diet and the gut microbiome.},
}

@article {pmid40475394,
year = {2025},
author = {Ebadi, M and Gem, H and Sebastian, G and Abasaeed, R and Lloid, M and Tseng, YD and Mian, OY and Minot, S and Dean, DR and Rashidi, A},
title = {Different Patterns of Oral Mucositis and Microbiota Injury After Total Body Irradiation- Versus Chemotherapy-Based Myeloablative Allogeneic Hematopoietic Cell Transplantation.},
journal = {Advances in radiation oncology},
volume = {10},
number = {6},
pages = {101787},
pmid = {40475394},
issn = {2452-1094},
abstract = {PURPOSE: Oral mucositis (OM) is a common complication of allogeneic hematopoietic cell transplantation, causing pain, infections, swallowing/speech impairment, and poor quality of life. We hypothesized that patterns (severity and dynamics) of OM and oral microbiota disruptions may be different after high-dose total body irradiation (TBI)- versus chemotherapy-based myeloablative conditioning.

METHODS AND MATERIALS: We conducted an exploratory study including comprehensive, longitudinal mucositis assessment, paired with supragingival plaque and saliva collection. OM was assessed at baseline and days +7, +14, +21, +28, and +84. Total mucositis score at each timepoint was calculated from objective findings in 2 domains and 9 oral sites using a validated scoring system. Plaque and saliva samples (baseline and days +14, +28, and +84) were profiled using shotgun metagenomic sequencing.

RESULTS: A total of 249 OM assessments were performed and 342 samples were collected from 47 patients (27 chemotherapy-based, 20 TBI-based). Salivary flow rate remained stable in the chemotherapy-based cohort, but steadily declined in the TBI-based cohort, reaching a significantly lower level in the TBI-based cohort at day +84 both compared to baseline and the chemotherapy-based cohort. OM severity peaked at day +7 in the TBI-based cohort versus day +14 in the chemotherapy-based cohort. Day +14 OM was significantly more severe in the chemotherapy-based cohort; other timepoints were not different. Although the cohorts were similar in plaque microbiota composition at baseline, they became significantly different at all post- hematopoietic cell transplantation timepoints. Salivary microbiota composition was not significantly different between the 2 cohorts. Day +84 plaque microbiota diversity was significantly higher in the TBI-based cohort.

CONCLUSIONS: We demonstrated different patterns of OM, microbiota injury, and salivary flow rate after TBI- versus chemotherapy-based conditioning. If validated in future studies, our findings could enhance evidence-based pretransplant counseling on oral toxicity and have implications for short- and long-term oral health in transplant survivors.},
}

@article {pmid40475346,
year = {2025},
author = {Wang, Z and Wei, X and Piao, L and Zhang, X and Wang, H},
title = {Gut microbiota dysbiosis and metabolic shifts in pediatric norovirus infection: a metagenomic study in Northeast China.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1600470},
pmid = {40475346},
issn = {2235-2988},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Dysbiosis/microbiology ; China/epidemiology ; *Caliciviridae Infections/microbiology/virology ; *Norovirus ; Metagenomics ; Feces/microbiology ; Male ; Female ; *Gastroenteritis/virology/microbiology ; Child, Preschool ; Child ; Infant ; Bacteria/classification/genetics/isolation & purification ; Longitudinal Studies ; High-Throughput Nucleotide Sequencing ; },
abstract = {BACKGROUND: Norovirus (NoV) is a leading cause of acute gastroenteritis in pediatric populations worldwide. However, the role of gut microbiota in NoV pathogenesis remains poorly understood.

METHODS: We conducted a longitudinal metagenomic analysis of fecal samples from 12 NoV-infected children and 13 age-matched healthy controls in Northeast China. Microbial composition and functional pathways were assessed using high-throughput shotgun sequencing and bioinformatic profiling.

RESULTS: NoV infection was associated with significant gut microbial dysbiosis, including increased alpha diversity and distinct taxonomic shifts. Notably, Bacteroides uniformis, Veillonella spp., and Carjivirus communis were enriched in infected individuals. Functional analysis revealed upregulation of metabolic pathways involved in carbohydrate and lipid processing. These microbial and functional alterations persisted over time and correlated with disease severity.

CONCLUSIONS: Our findings reveal novel associations between NoV infection and gut microbiota dysbiosis, particularly the enrichment of Bacteroides uniformis, which may influence host-pathogen interactions via metabolic or immune mechanisms. The identified microbial and metabolic signatures offer potential biomarkers for diagnosis and targets for microbiota-based therapeutic strategies in pediatric NoV infection.},
}

Humans
*Gastrointestinal Microbiome
*Dysbiosis/microbiology
China/epidemiology
*Caliciviridae Infections/microbiology/virology
*Norovirus
Metagenomics
Feces/microbiology
Male
Female
*Gastroenteritis/virology/microbiology
Child, Preschool
Child
Infant
Bacteria/classification/genetics/isolation & purification
Longitudinal Studies
High-Throughput Nucleotide Sequencing

@article {pmid40475274,
year = {2025},
author = {Lv, Y and Peng, S and Liu, Y and Yang, H and Li, G and Peng, Y},
title = {Cross-omics analysis reveals microbe-metabolism interactions characteristic of gingival enlargement associated with fixed orthodontic in adolescents.},
journal = {Journal of oral microbiology},
volume = {17},
number = {1},
pages = {2513739},
pmid = {40475274},
issn = {2000-2297},
abstract = {OBJECTIVES: To investigate the oral microbiome and metabolome longitudinal changes associated with orthodontic treatment-induced gingival enlargement (OT-GE).

METHODS: Twenty-six subjects were divided into case and control groups based on the gingival overgrowth index (GOi). The OT-GE group was divided into the no gingival enlargement (OT-GE0, n = 5) and persistent gingival enlargement (OT-GE1, n = 11). The control group included orthodontic treatment periodontal health (OT-GH, n = 5), and no orthodontic treatment periodontal health (NOT-GH, n = 5). Microbial composition and metabolites in saliva were investigated using cross-omics.

RESULTS: Longitudinal analysis linked orthodontic treatment-induced gingival enlargement to distinct oral microbiome and metabolome shifts. The OT-GE group showed significantly higher bleeding on probing (BOP), plaque scores (p < 0.001), probing depth, GOi, and ligature wire differences (p < 0.05) versus controls. Microbial diversity and species richness were elevated in OT-GE (p < 0.05), though no differences emerged between OT-GE0 and OT-GE1) subgroup (p > 0.05). Cross-omics identified specific periodontal pathogens and metabolites linked to gingival enlargement. Disrupted amino acid biosynthesis pathways, particularly citrulline metabolism, correlated with functional gene dysregulation and microbial imbalance. Aberrant citrulline intake appeared to drive dysbiosis, potentially contributing to gingival overgrowth.

CONCLUSIONS: OT-GE pathogenesis involves functional gene-regulated metabolite metabolism influencing periodontal pathogens.},
}

@article {pmid40475154,
year = {2025},
author = {Cotto, I and Durán-Viseras, A and Jesser, KJ and Zhou, NA and Hemlock, C and Albán, V and Ballard, AM and Fagnant-Sperati, CS and Lee, GO and Hatt, JK and Royer, C and Eisenberg, JNS and Trueba, G and Konstantinidis, KT and Levy, K and Fuhrmeister, ER},
title = {Environmental Exposures and the Human Gut Resistome in Northwest Ecuador.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.23.25327954},
pmid = {40475154},
abstract = {Inadequate water, sanitation, and hygiene (WASH) infrastructure may increase exposure to antimicrobial resistance (AMR). In addition, close human-animal interactions and unregulated antibiotic use in livestock facilitate the spread of resistant bacteria. We used metagenomic sequence data and multivariate models to assess how animal exposure and WASH conditions affect the gut resistome and microbiome in 53 pregnant women and 84 children in Ecuador. Escherichia coli , Klebsiella pneumoniae, and clinically relevant antimicrobial resistance genes (ARGs) were detected across all age groups, but the highest abundance was found in children compared to mothers. In mothers, higher animal exposure trended towards a higher number of unique ARGs compared to low animal exposure (β= -5.58 [95% CI: -11.46, 0.29]) and was significantly associated with greater taxonomic diversity (β= -1.29 [-1.96, -0.63]). In addition, mothers with sewer systems or septic tanks and piped drinking water had fewer unique ARGs (β= -3.52 [-6.74, -0.30]) compared to those without, and mothers with longer duration of drinking water access had lower total ARG abundance (β= -0.05 [-0.1, -0.01]). In contrast, few associations were observed in children, likely due to the dynamic nature of the gut microbiome during early childhood. Improving WASH infrastructure and managing animal exposure may be important in reducing AMR but could also reduce taxonomic diversity in the gut.},
}

@article {pmid40474246,
year = {2025},
author = {Denison, ER and Pound, HL and Gann, ER and Gilbert, NE and Weston, DJ and Pelletier, DA and Wilhelm, SW},
title = {Identification of shared viral sequences in peat moss metagenomes reveals elements of a possible Sphagnum core virome.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {62},
pmid = {40474246},
issn = {2524-6372},
support = {DE-SC0020362//US Department of Energy, Office of Science, Office of Biological and Environmental Research, Genomic Science Program/ ; DE-SC0020362//US Department of Energy, Office of Science, Office of Biological and Environmental Research, Genomic Science Program/ ; DE-SC0020362//US Department of Energy, Office of Science, Office of Biological and Environmental Research, Genomic Science Program/ ; DE-SC0020362//US Department of Energy, Office of Science, Office of Biological and Environmental Research, Genomic Science Program/ ; DE-AC05-00OR22725//U.S. Department of Energy/ ; DE-AC05-00OR22725//U.S. Department of Energy/ ; },
abstract = {BACKGROUND: Viruses are an understudied component of plant microbiomes. Identifying viruses that are shared between individual plants, or members of the “core virome”, could reveal stable viral populations with the potential to modulate the composition and function of the microbiome. Here, we examined the virome associated with Sphagnum mosses, a keystone species that has direct influence over the fate of peatland carbon stores. We analyzed bulk metagenomes and metatranscriptomes generated from Sphagnum field samples collected over a ten-month period to identify virus-like sequences shared among plants.

RESULTS: Individual Sphagnum samples harbored distinct DNA and RNA viromes where only a small percentage (< 1%) of the total number of identified viral contigs were shared among all samples. Based on taxonomic classification, the shared viral contigs represent bacterial viruses, or phage (Caudoviricetes), as well as viruses of eukaryotes, namely nucleocytoplasmic large DNA viruses (Nucleocytoviricota) and RNA viruses (Riboviria). We linked the shared phage-like contigs to viral regions within sequenced genomes of bacterial taxa that are members of the Sphagnum core microbiome, suggesting that these contigs represent temperate phage or degraded prophage. The putative nucleocytoplasmic large DNA viruses and RNA viruses were phylogenetically diverse and showed sequence similarity to viruses associated with a broad range of hosts and environmental sources.

CONCLUSIONS: The identification of shared viral contigs suggested that, despite the compositional heterogeneity between samples, Sphagnum mosses may harbor a core virome. Future work validating the presence of the core virome is warranted as it may aid in understanding how persistent viruses impact microbiome ecology and symbiont evolution within this climatically relevant keystone species.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s40793-025-00719-0.},
}

@article {pmid40474206,
year = {2025},
author = {Tubbesing, T and Schlüter, A and Sczyrba, A},
title = {subMG automates data submission for metagenomics studies.},
journal = {BioData mining},
volume = {18},
number = {1},
pages = {38},
pmid = {40474206},
issn = {1756-0381},
support = {101081957//HORIZON EUROPE European Research Council/ ; 460129525 (NFDI4Microbiota)//Deutsche Forschungsgemeinschaft/ ; NNF200C0062223//Novo Nordisk Fonden/ ; },
abstract = {BACKGROUND: Publicly available metagenomics datasets are crucial for ensuring the reproducibility of scientific findings and supporting contemporary large-scale studies. However, submitting a comprehensive metagenomics dataset is both cumbersome and time-consuming. It requires including sample information, sequencing reads, assemblies, binned contigs, metagenome-assembled genomes (MAGs), and appropriate metadata. As a result, metagenomics studies are often published with incomplete datasets or, in some cases, without any data at all. subMG addresses this challenge by simplifying and automating the data submission process, thereby encouraging broader and more consistent data sharing.

RESULTS: subMG streamlines the process of submitting metagenomics study results to the European Nucleotide Archive (ENA) by allowing researchers to input files and metadata from their studies in a single form and automating downstream tasks that otherwise require extensive manual effort and expertise. The tool comes with comprehensive documentation as well as example data tailored for different use cases and can be operated via the command-line or a graphical user interface (GUI), making it easily deployable to a wide range of potential users.

CONCLUSIONS: By simplifying the submission of genome-resolved metagenomics study datasets, subMG significantly reduces the time, effort, and expertise required from researchers, thus paving the way for more numerous and comprehensive data submissions in the future. An increased availability of well-documented and FAIR data can benefit future research, particularly in meta-analyses and comparative studies.},
}

@article {pmid40477893,
year = {2023},
author = {Yu, Y and Zhang, Q and Zhang, Z and Xu, N and Li, Y and Jin, M and Feng, G and Qian, H and Lu, T},
title = {Assessment of residual chlorine in soil microbial community using metagenomics.},
journal = {Soil ecology letters},
volume = {5},
number = {1},
pages = {66-78},
pmid = {40477893},
issn = {2662-2297},
abstract = {Chlorine-containing disinfectants have been widely used around the world for the prevention and control of the COVID-19 pandemic. However, at present, little is known about the impact of residual chlorine on the soil micro-ecological environment. Herein, we treated an experimental soil-plant-microbiome microcosm system by continuous irrigation with a low concentration of chlorine-containing water, and then analyzed the influence on the soil microbial community using metagenomics. After 14-d continuous chlorine treatment, there were no significant lasting effect on soil microbial community diversity and composition either in the rhizosphere or in bulk soil. Although metabolic functions of the rhizosphere microbial community were affected slightly by continuous chlorine treatment, it recovered to the original status. The abundance of several resistance genes changed by 7 d and recovered by 14 d. According to our results, the chlorine residue resulting from daily disinfection may present a slight long-term effect on plant growth (shoot length and fresh weight) and soil micro-ecology. In general, our study assisted with environmental risk assessments relating to the application ofchlorine-containing disinfectants and minimization of risks to the environment during disease control, such as COVID-19.},
}

@article {pmid40473843,
year = {2025},
author = {Wu, S and Wang, S and Wu, Z and Chen, M and Chen, X and Lei, D and Peng, C},
title = {Comparative analysis of the clinical characteristic and lung microbiota in adult and elderly patients with pulmonary tuberculosis.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {19777},
pmid = {40473843},
issn = {2045-2322},
support = {2023K146//Quzhou City science and technology plan project/ ; },
mesh = {Humans ; Middle Aged ; Male ; Female ; *Tuberculosis, Pulmonary/microbiology/diagnosis/diagnostic imaging ; Aged ; Adult ; *Lung/microbiology/diagnostic imaging ; *Microbiota/genetics ; Retrospective Studies ; Age Factors ; High-Throughput Nucleotide Sequencing ; Young Adult ; Aged, 80 and over ; },
abstract = {The proportion of elderly people infected with tuberculosis (TB) is increasing, and misdiagnosis and missed diagnosis are common. This study aimed to explore the diagnostic value of metagenomic next-generation sequencing (mNGS) for pulmonary TB (PTB) and to investigate age-related differences in lung microbial composition, clinical characteristics and imaging findings among PTB patients. We retrospectively recruited 162 suspected PTB patients, and finally 143 patients were used in this analysis. Patients were classified into two groups: adult (18 ≤ age < 60, n = 66) and elderly (Age ≥ 60, n = 77). Differences and associations in clinical characteristics, imaging findings, and lung microbiota were analyzed. Compared to adult patients, elderly patients had a higher prevalence of hypertension (31.17% vs. 9.09%, P = 0.0012), fever (20.78% vs. 4.55%, P = 0.0044) and chest tightness (24.68% vs. 10.61%, P = 0.0297), but a lower prevalence of chest pain (7.58% vs. 0%, P = 0.0139). For TB identification, mNGS had the highest positive rate (100%), followed by T-spot (74.75%), GeneXpert (37.80%) and acid-fast staining (AFS) (7.30%), and all the conventional methods showed slight higher positive rates in the elderly group compared to the adult group (P > 0.05). Bilateral lung infection was more common in elderly patients (79.22% vs. 60.61%, P = 0.0148), with infiltration (32.17%, 46/143), shadows (26.57%, 38/143), nodules (20.28%, 29/143), and bronchiectasis (20.28%, 29/143) being the most common imaging features. The diversity of the lung microbial communities was significantly lower in elderly patients compared to adults (P < 0.05). Clinical characteristics, imaging findings, and the top 20 most abundant species in lung microbiota showed significantly positive correlation. This study demonstrates that mNGS has excellent diagnostic value for PTB in both adult and elderly patients. Significant differences in clinical characteristics, imaging, and lung microbial composition were observed between the two groups. Understanding these differences may aid in the diagnosis and treatment of tuberculosis in elderly patients.},
}

Humans
Middle Aged
Male
Female
*Tuberculosis, Pulmonary/microbiology/diagnosis/diagnostic imaging
Aged
Adult
*Lung/microbiology/diagnostic imaging
*Microbiota/genetics
Retrospective Studies
Age Factors
High-Throughput Nucleotide Sequencing
Young Adult
Aged, 80 and over

@article {pmid40473402,
year = {2025},
author = {Barnich, N and Arthur, JC and Buisson, A and Campbell, BJ and Carbonnel, F and Chassaing, B and Coombes, BK and Denizot, J and Dogan, B and Faith, J and Kamada, N and Longman, RS and Martinez-Medina, M and O'Brien, CL and Sartor, RB and Zhang, S and , and Colombel, JF and Simpson, KW and , },
title = {Adherent-invasive Escherichia coli in Crohn's disease: the 25th anniversary.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-335331},
pmid = {40473402},
issn = {1468-3288},
abstract = {In 1998, Arlette Darfeuille-Michaud, Christel Neut and Jean-Frederic Colombel discovered a novel pathovar of Escherichia coli, adherent and invasive Escherichia coli (AIEC), in the ileum of patients with Crohn's disease (CD), that was genetically distinct from diarrheagenic E. coli, could adhere to and invade intestinal epithelial cells and survive in macrophages. The consistent association between AIEC and CD (approximately 30% across the world), their ability to exploit CD-associated genetic traits, and virulence in preclinical colitis models but not healthy hosts spurred global research to elucidate their pathogenicity. Research focused on integrating AIEC with the microbiome, metabolome, metagenome, host response and the impact of diet and antimicrobials has linked the luminal microenvironment and AIEC metabolism to health and disease. This deeper understanding has led to therapeutic trials and precision medicine targeting AIEC-colonised patients. In November 2023, prominent members of the AIEC research community met to present and discuss the many facets of basic, translational and clinical AIEC fields at 'AIEC: past, present and future' in NYC. This review is a summary of this international meeting highlighting the history of AIEC, knowledge accumulated over the past 25 years about its pathogenic properties and proposes a standardised approach for screening patients for AIEC.},
}

@article {pmid40473141,
year = {2025},
author = {Luo, Y and Liao, H and Wu, L and Wu, M and Luo, Y and Yao, Y and Ji, W and Gao, L and Xia, X},
title = {Temperature adaptability drives functional diversity and horizontal gene transfer within microbial communities in Daqu solid-state fermentation.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132770},
doi = {10.1016/j.biortech.2025.132770},
pmid = {40473141},
issn = {1873-2976},
abstract = {The spontaneous solid-state fermentation of high-temperature Daqu (HTD) is a temperature-dependent stacking bioprocessing for enriching microbiota and enzymes to guarantee efficient substrate utilization and fermentation. However, there is a lack of clarity regarding how temperature adaptability affects HTD microbial assembly, domestication direction, and metabolic profile. Here, the flavor substances, microbial assembly, metabolic network, and horizontal gene transfer (HGT) events of three HTDs from Renshu (RS), Jiushang (JS), and Maoyuan (MY) were analyzed. 125 volatile compounds were identified, tetramethylpyrazine, 3-methyl-butanoic acid, phenylethyl alcohol, and trimethylpyrazine were clarified as the typical flavor substances. Bacillus and Kroppenstedtia were the shared dominant bacterial genera. Paecilomyces, Aspergillus, Rasamsonia, and Lichtheimia were dominant fungal genera. Differences in flavor metabolism, microbial structure, and key enzyme metabolism are strongly correlated with sample distance. As proximity decreases, the microbial structural and functional metabolic traits tend to exhibit greater similarity. The frequency of HGT events was analyzed using MetaCHIP, 49, 9 and 69 groups of HGT events occurred in RS, JS, and MY, respectively. HGT events occurred most abundantly in Bacillaceae, and the microbial taxa with a closer phylogenetic relationship possessed the highest incidence of HGT. Specifically, the occurrence of HGT was mainly associated with high-temperature adaptability. It was also linked to characteristic flavor metabolism. Our results revealed the effects of temperature stress on microbial regulation of HTD and adaptive transfer of relevant genes in stacked fermented HTDs. This work provides important insights into HTD quality classification and regulation of solid-state fermentation quality and efficiency through microbial domestication.},
}

@article {pmid40473125,
year = {2025},
author = {Darwiche, S and Gacesa, R and Ferraro, RB and Alwan, W and Oben, JA and Rashidghamat, E and Long, PF},
title = {Prevalence of skin fungi markedly declines in the lesions of two patients with moderate Hidradenitis Suppurativa.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {107778},
doi = {10.1016/j.micpath.2025.107778},
pmid = {40473125},
issn = {1096-1208},
abstract = {Hidradenitis suppurativa (HS) is a chronic inflammatory disorder affecting hair follicles in intertriginous regions, leading to painful nodules, sinus tracts, and scarring. The pathogenesis of HS is far from clear, but alterations in the bacterial community of the skin microbiome has been debated, yet the potential involvement of fungi - the mycobiome - has received almost no attention. Large areas of skin were sampled for amplicon metagenomics sequencing to negate the inference of low-sequence counts with the objective of examining the provenance of fungi between lesion and lesion-free skin from the same individuals. The DNA from skin swabs was isolated and the V4 region of the 18S rRNA gene was amplified and sequenced. Total fungal counts were inferred from taxonomic assignment of unique operational taxonomic units and absolute numbers then compared between skin sites. There were dramatically lower numbers of fungi in HS lesions with Malassezia dominance, as expected, across samples. This finding suggested, for the first time, that fungal depletion in lesions might be linked to HS pathology through disruption of normal skin barrier function and immunity, potentially due to reduced sebum production essential for fungal growth.},
}

@article {pmid40472755,
year = {2025},
author = {Chen, M and Xing, L and Gao, S and Guo, Y and Qiu, T and Wang, X and Gao, M},
title = {Metagenomic analysis deciphers airborne pathogens with enhanced antimicrobial resistance and virulence factors in composting facilities.},
journal = {Environment international},
volume = {201},
number = {},
pages = {109569},
doi = {10.1016/j.envint.2025.109569},
pmid = {40472755},
issn = {1873-6750},
abstract = {The composting process has been shown to effectively reduce antimicrobial resistance (AMR) in animal manure, but its influence on surrounding airborne AMR remains unknown, particularly with regard to human-pathogenic antibiotic-resistant bacteria (HPARB). In this study, air and paired compost samples were collected from a full-scale composting facility, and the antibiotic resistome, microbiome, and HPARB were systematically analyzed in both two habitats using metagenomic analysis. Current result uncovered the profiles of HPARB in air, showing that significantly more airborne HPARB were assembled than that in compost samples. Airborne pathogens harboredan increased abundance and diversity of antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) in comparison with compost-borne HPARB. The core antibiotic resistome represents 18.58% of overall ARG subtypes, contributing to 86.31% of ARG abundance. A higher number of enriched core ARGs (2.16- to 13.36-times higher), including mexF, tetW, and vanS, were observed in air samples compared to compost samples. As an important human pathogen, Mycobacterium tuberculosis was prevalent in the air and carried more ARG (6) and VFG (130) subtypes than those in compost. A significantly higher risk score was detected for airborne AMR in the composting facility compared to that in hospital and urban environments. This study revealed the enhanced airborne HPARB through comparative experiments between air and composting habitats. It highlighted the unrecognized AMR risks associated with air in composting site and provided a scientific basis for accurately assessing health outcomes caused by occupational exposure.},
}

@article {pmid40472476,
year = {2025},
author = {Wang, JZ and Wang, JB and Yuan, D and Sun, CH and Hou, LL and Zhang, Y and Yang, XH and Xie, HX and Gao, YX},
title = {Metagenomic next-generation sequencing-based diagnosis of Pneumocystis jirovecii pneumonia in patients without human immunodeficiency virus infection: A dual-center retrospective propensity matched study.},
journal = {Journal of infection and public health},
volume = {18},
number = {9},
pages = {102831},
doi = {10.1016/j.jiph.2025.102831},
pmid = {40472476},
issn = {1876-035X},
abstract = {BACKGROUND: Pneumocystis jirovecii pneumonia (PJP), caused by Pneumocystis jirovecii (PJ), is an opportunistic infection prevalent in clinical settings. However, large-scale studies on the efficacy of metagenomic next-generation sequencing (mNGS)-based diagnosis of PJP in patients without human immunodeficiency virus infection (HIV) are lacking.

METHODS: The study included 168 patients diagnosed with either PJP (84) or other pneumonia types (non-PJP patients; 84) who underwent mNGS-mediated bronchoalveolar lavage fluid (BALF) analysis, Gomori methenamine silver (GMS) staining and peripheral blood 1,3-beta-D-glucan (BDG) testing. Additionally, patients with PJP were categorized into survival (n = 55) and non-survival (n = 29) groups based on a 28-day in-hospital outcome to compare clinical characteristics, inflammatory markers, PJ sequence counts in BALF, and serum BDG levels.

RESULTS: Serum BDG levels, the proportion of patients with serum BDG of > 60 pg/mL and > 200 pg/mL were notably higher in the PJP group compared with that in the non-PJP group (all P< 0.05). The sensitivity and specificity of mNGS in diagnosing PJP were higher than those of serum BDG testing (sensitivity: 100 % vs. 63.0 %; specificity: 96.4 % vs. 90.4 %; both P< 0.05). The most common coinfection was viral (30.9 %), followed by bacterial-viral coinfections (13.0 %). Treatment regimens were altered for 83.3 % of patients based on the mNGS results. The patients in the non-survival group showed markedly higher serum BDG levels (142.5 [32.7, 277.7] vs. 123.0 [34.0, 164.0]) and a higher proportion of PJ sequence counts of > 1 × 10[5] (13.7 % vs. 0, P= 0.005) relative to those in the survival group.

CONCLUSION: The mNGS showed superior performance over serum BDG testing and GMS staining in diagnosing PJP in non-HIV patients and identified a broader range of coinfections.},
}

@article {pmid40472426,
year = {2025},
author = {Zhuang, X and Wu, J and Liu, X and Lin, J and Wang, Z and Wang, Y},
title = {The synergistic corrosion of carbon steel by sulfate-reducing bacteria and methanogenic archaea microbial communities.},
journal = {Bioelectrochemistry (Amsterdam, Netherlands)},
volume = {166},
number = {},
pages = {109015},
doi = {10.1016/j.bioelechem.2025.109015},
pmid = {40472426},
issn = {1878-562X},
abstract = {The impact of sulfate-reducing bacteria (SRB) and methanogenic archaea (MA) on the corrosion of carbon steel was examined through weight loss tests, electrochemical measurements, surface analyses, and metagenomic analyses. The findings indicated that SRB and MA exhibited a synergistic effect on the corrosion process. This resulted in a significant increase in corrosion weight loss in the SRB + MA group (16.05 mg/cm[2]), which was 8.64 times that of the SRB group (1.86 mg/cm[2]) and 1.58 times that of the MA group (10.14 mg/cm[2]). This synergistic effect can be attributed to the influence of SRB and MA on the formation of corrosion products, producing more corrosion products such as FeS in the mixed group. In addition, the corrosion of carbon steel is further enhanced by electron transfer process between carbon steel and microorganisms in the mixed group.},
}

@article {pmid40472396,
year = {2025},
author = {Zheng, F and Guo, X and Zhang, W and Wang, Y and Hu, E and Guo, X and Su, H and Deng, C},
title = {Insights into the functional characteristics of rhubarb (Rheum officinale Baill) treatment on experimental traumatic brain injury through network pharmacology with metagenomics.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {143},
number = {},
pages = {156853},
doi = {10.1016/j.phymed.2025.156853},
pmid = {40472396},
issn = {1618-095X},
abstract = {BACKGROUND: Traumatic brain injury (TBI) imposes a heavy burden on society and families owing to its high morbidity and mortality. Rhubarb has been noticed in the Chinese herb for treating TBI. The pharmacological effects include anti-inflammation, anti-bacterial, and purgative. But little is known about its potential mechanism when treating TBI.

PURPOSE: In this study, we profiled the pharmacological and intestinal functional characteristics of rhubarb in post-TBI mice.

METHODS: Fifty adult male C57BL/6 mice were randomly allocated into five groups, including sham, controlled cortical impact (CCI), and rhubarb extract administered at low, medium, and high doses. The impaired neurobehavioral function was assessed using the modified neurological severity score (mNSS) and the wire hang test. hematoxylin-eosin (HE) and Nissl staining, terminal deoxynucleotidyl transferase-mediated dUTP-nick-end labeling (TUNEL) and immunoglobulin-γ (IgG) staining, immunostaining for GFAP, TNF-α and IL-1β were applied to detect the histological damage, neuronal apoptosis and blood-brain barrier (BBB) permeability, respectively. Subsequently, the network pharmacology approaches was used to identify putative therapeutic targets and the relevant pathway of rhubarb on TBI. In addition, metagenomics and targeted metabolomics revealed the alterations in composition and functions of gut flora and gut-derived serum short-chain fatty acids (SCFAs). Finally, we depleted the gut microbiota with an antibiotic cocktail (ampicillin, metronidazole, neomycin, vancomycin) to uncover the critical role of gut microbiota on rhubarb function.

RESULTS: Rhubarb reduced brain IgG leakage and neuronal apoptosis after TBI. The network pharmacology analysis identified seven genes as key potential therapeutic targets of rhubarb, and the genes were related to inflammation, oxidant and apoptosis. The enrichment analysis showed that three of the top signal pathways were involved in anti-inflammation, anti-apoptosis and anti-oxidant. The metagenomics analysis showed that rhubarb reshaped the structure and abundance of gut microbiota in TBI. The altered function of gut microbiota was enriched in the improvement of carbohydrate metabolism, gut-derived serum SCFAs and microbial resistance. Finally, gut microbiota depletion confirmed the effects of rhubarb on post-TBI IgG leakage and neuronal apoptosis were depended on gut microbiota.

CONCLUSIONS: Rhubarb may treat TBI by effects of targeting inflammatory factors and oxidant factors to inhibit neuronal apoptosis and protect the BBB. The therapeutic effects of rhubarb are partly mediated by altering gut microbiota. Our findings not only highlight a holistic and microbial potential of rhubarb's therapeutic functional actions but also elucidate previously unrecognized therapeutic development of novel targets and strategies for TBI therapies by rhubarb.},
}

@article {pmid40472050,
year = {2025},
author = {Kawashima, A and Yanagawa, Y and Chikata, T and Shimogawara, R and Mizushima, D and Tsuchiya, K and Yagita, K and Gatanaga, H and Watanabe, K},
title = {Optimization of TaqMan-based quantitative PCR diagnosis for Entamoeba histolytica using droplet digital PCR.},
journal = {PLoS neglected tropical diseases},
volume = {19},
number = {6},
pages = {e0012935},
doi = {10.1371/journal.pntd.0012935},
pmid = {40472050},
issn = {1935-2735},
abstract = {BACKGROUND: TaqMan-probed quantitative PCR (qPCR) is highly valued for diagnosing Entamoeba histolytica infections (amebiasis). However, unclear cycle threshold (Ct) values often yield low-titer positive results, complicating interpretation. This study aimed to optimize qPCR primer-probe sets with logically determined cut-off Ct value using droplet digital PCR (ddPCR).

Amplification efficacy was evaluated using ddPCR by measuring absolute positive droplet counts (APD) and mean fluorescence intensity at different PCR cycles and annealing temperatures (AT). A primer-probe specific cut-off Ct value was determined from a standard curve by correlating Ct values with APD. Twenty primer-probe sets targeting small subunit rRNA gene regions (X64142) were designed from previous papers. Amplification efficacy remained consistent at high PCR cycles (50 cycles), but differed at lower PCR cycles (30 cycles), identifying five sets with higher amplification efficiency than other candidates. Of these, only two sets maintained efficiency at higher AT (62°C). Ct value was inversely proportional to the square of APD, defining the specific cut-off Ct value as 36 cycles. Selected primer-probe set with a cut-off effectively differentiated E. histolytica infection in clinical specimens. However, discordant results between Ct value and APD were seen in some cases with high Ct value. Shotgun metagenomic sequencing suggested microbial-independent false positive reactions contributed to these discrepancies, although specific reactants were unidentified.

CONCLUSIONS/SIGNIFICANCE: The combination use of ddPCR with qPCR revealed that false positive reactions of qPCR and/or ddPCR commonly happen in stool specimens. Also, this study emphasizes the value of ddPCR for establishing accurate cut-off values with efficient primer-probes.},
}

@article {pmid40471671,
year = {2025},
author = {Alam, AM and Houlihan, CF and Bharucha, T},
title = {Novel techniques for the diagnosis of neurological infections.},
journal = {Current opinion in neurology},
volume = {},
number = {},
pages = {},
doi = {10.1097/WCO.0000000000001395},
pmid = {40471671},
issn = {1473-6551},
abstract = {PURPOSE OF REVIEW: On World Encephalitis Day 19th February 2025, Encephalitis International launched the World Health Organization technical brief on encephalitis, highlighting the growing public health challenge and need for improved diagnostics. This review summarizes the published literature over the last 18 months on novel methods of identifying the aetiology of neurological infections and existing research gaps.

RECENT FINDINGS: There is an increased availability and sensitivity of multiplex polymerase chain reaction assays and untargeted metagenomic sequencing in clinical practice. This is contributing to increasing diagnostic yield in suspected neurological infections. Preliminary results suggest that novel serological methods such as phage immunoprecipitation sequencing (Phip-seq) may be useful where molecular approaches are negative.

SUMMARY: Significant progress in improving diagnostics has been made in the last decade. Going forward, multicentre studies and meta-analyses are needed to achieve adequate power in ascertaining the role of novel diagnostic methods in neurological infections. Studies need to investigate the impact on patient management and cost-effectiveness. The role of other omics methods in identifying host biomarkers for utilization in diagnostic algorithms needs further work.},
}

@article {pmid40470551,
year = {2025},
author = {Yang, L and Yang, Q and Li, J and Zhang, L and Liu, S and Lian, C},
title = {Pneumocystis jirovecii pneumonia in anti-MDA5-positive dermatomyositis: characterisation, risk factors and prognosis.},
journal = {Clinical and experimental rheumatology},
volume = {},
number = {},
pages = {},
doi = {10.55563/clinexprheumatol/hpx173},
pmid = {40470551},
issn = {0392-856X},
abstract = {OBJECTIVES: This study aimed to identify risk and prognostic factors of Pneumocystis jirovecii pneumonia (PJP) in patients with anti-melanoma differentiation-associated gene 5 antibody-positive dermatomyositis (anti-MDA5+DM).

METHODS: We conducted a retrospective cohort study of anti-MDA5+DM patients who underwent metagenomic next-generation sequencing analysis of bronchoalveolar lavage fluid or lung tissue at our center between January 2019 and February 2023. Eligible patients were stratified into PJP+ and PJP- groups based on PJP status. Potential risk factors and prognostic indicators for PJP were analysed using univariate and multivariate logistic regression analysis.

RESULTS: A total of 107 anti-MDA5+DM patients were enrolled, of whom 47 were assigned to the PJP+ group. Multivariate logistic regression analysis revealed older age and high cumulative dosage of glucocorticoids within 3 months preceding PJP diagnosis were independent risk factors for PJP development. Conversely, prophylactic-dose trimethoprim-sulfamethoxazole (TMP/SMZ) was associated with a significantly reduced risk of PJP (all p<0.05). The 30-day mortality rate in the PJP+ group was 55.3%. Short disease duration and immunosuppressive therapy exposure, severe hypoxia, extensive radiological interstitial lung disease, moderate to severe acute respiratory distress syndrome, mechanical ventilation were associated with unfavourable prognosis (all p<0.05). Glucocorticoids therapy was more frenquently administered in survivors (p<0.05).

CONCLUSIONS: PJP significantly increases early mortality of anti-MDA5+DM patients. Clinicians should identify high-risk patients early and administer prophylactic-dose TMP/SMZ for PJP prophylaxis.},
}

@article {pmid40469774,
year = {2025},
author = {Levy Karin, E and Steinegger, M},
title = {Cutting-edge deep-learning based tools for metagenomic research.},
journal = {National science review},
volume = {12},
number = {6},
pages = {nwaf056},
pmid = {40469774},
issn = {2053-714X},
abstract = {Recent years have seen incredible progress in the development of deep-learning (DL) tools for the analysis of biological data, with the most prominent example being AlphaFold2 for accurate protein structure prediction. DL-based tools are especially useful for identifying patterns and connections within sparsely labeled datasets. This makes them essential for the analysis of metagenomic data, which is mostly unannotated and bears little sequence similarity to known genes and proteins. In this review, we chose to present 12 tools which we deem as offering novel capabilities for metagenomic analysis by utilizing interesting DL techniques. This review is thus intended to be a solid starting point for any data scientist looking to apply advanced methods to explore metagenomic datasets. For each DL-based tool, we present its computational principles, followed by relevant examples of its application where possible and a note on its limitations.},
}

@article {pmid37732396,
year = {2025},
author = {Lajmi, A and Glinka, F and Privman, E},
title = {Optimizing ddRAD sequencing for population genomic studies with ddgRADer.},
journal = {Molecular ecology resources},
volume = {25},
number = {5},
pages = {e13870},
doi = {10.1111/1755-0998.13870},
pmid = {37732396},
issn = {1755-0998},
support = {2017319//US-Israel Binational Science Foundation/ ; },
mesh = {*Sequence Analysis, DNA/methods ; *Genetics, Population/methods ; *Software ; *Computational Biology/methods ; *Genomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; },
abstract = {Double-digest Restriction-site Associated DNA sequencing (ddRADseq) is widely used to generate genomic data for non-model organisms in evolutionary and ecological studies. Along with affordable paired-end sequencing, this method makes population genomic analyses more accessible. However, multiple factors should be considered when designing a ddRADseq experiment, which can be challenging for new users. The generated data often suffer from substantial read overlaps and adaptor contamination, severely reducing sequencing efficiency and affecting data quality. Here, we analyse diverse datasets from the literature and carry out controlled experiments to understand the effects of enzyme choice and size selection on sequencing efficiency. The empirical data reveal that size selection is imprecise and has limited efficacy. In certain scenarios, a substantial proportion of short fragments pass below the lower size-selection cut-off resulting in low sequencing efficiency. However, enzyme choice can considerably mitigate inadvertent inclusion of these shorter fragments. A simple model based on these experiments is implemented to predict the number of genomic fragments generated after digestion and size selection, number of SNPs genotyped, number of samples that can be multiplexed and the expected sequencing efficiency. We developed ddgRADer - http://ddgrader.haifa.ac.il/ - a user-friendly webtool and incorporated these calculations to aid in ddRADseq experimental design while optimizing sequencing efficiency. This tool can also be used for single enzyme protocols such as Genotyping-by-Sequencing. Given user-defined study goals, ddgRADer recommends enzyme pairs and allows users to compare and choose enzymes and size-selection criteria. ddgRADer improves the accessibility and ease of designing ddRADseq experiments and increases the probability of success of the first population genomic study conducted in labs with no prior experience in genomics.},
}

*Sequence Analysis, DNA/methods
*Genetics, Population/methods
*Software
*Computational Biology/methods
*Genomics/methods
*High-Throughput Nucleotide Sequencing/methods
*Metagenomics/methods

@article {pmid40469735,
year = {2025},
author = {Heisel, T and Gonia, S and Dillon, A and Hoops, SL and Al-Ghalith, GA and Gohl, D and Mukhopadhyay, S and Puopolo, K and Kennedy, P and Sadowsky, MJ and Knights, D and Johnson, AJ and Gerber, JS and Gale, CA},
title = {Gut mycobiome maturation and its determinants during early childhood: a comparison of ITS2 amplicon and shotgun metagenomic sequencing approaches.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1539750},
pmid = {40469735},
issn = {1664-302X},
abstract = {INTRODUCTION: Microbial colonization of the gut in early life is important for the development of metabolism, immunity, and the brain. Fungi and bacteria both colonize the human infant gut. The relatively smaller contribution of fungi to the gut microbiome, as compared to bacteria, has posed technical challenges for the precise characterization of fungal communities (mycobiomes) and limited the ability to longitudinally examine mycobiome development.

BACKGROUND: The aims of this study were to (1) characterize mycobiome maturation and identify clinical determinants of mycobiome compositional variation during the first 2 years of life and (2) compare two sequencing approaches (ITS2 amplicon and whole genome metagenomics) for characterizing mycobiome maturational features. Longitudinal fecal samples and associated clinical metadata were obtained from subjects enrolled as part of the MAGIC (Microbiome, Antibiotics and Growth Infant Cohort) study.

RESULTS: Overall, fungal richness increased and mycobiome composition changed in a similar ordered pattern during the first 2 years of life utilizing either amplicon or metagenomic sequencing approaches. Less resolution of taxa to species and genera levels was observed for the metagenomic dataset. The predominant taxa identified by both sequencing approaches, Candida albicans, Saccharomyces/S. cerevisiae, and Malassezia restricta, each exhibited similar dynamics in abundances and prevalences over the first 2 years of life, irrespective of sequencing approach. Antibiotic exposure and breastfeeding status contributed to time-specific mycobiome compositional variation, results that were consistent for both types of sequence datasets. Candida albicans exhibited altered abundance dynamics in association with perinatal antibiotic exposure and birth mode for both sequencing approaches. Post hoc analyses suggested that the birth mode association could be driven by exposure to perinatal antibiotics in children delivered by cesarean section rather than by birth mode itself.

DISCUSSION: In summary, amplicon and metagenomic sequencing approaches provide generally similar results with respect to mycobiome maturational dynamics and the contribution of clinical variables to variation. Differences in taxa identification by the two approaches likely due to sequence database differences, primer/genome sequence variation, and/or sequencing depth should be taken into consideration.},
}

@article {pmid40469725,
year = {2025},
author = {Moumi, NA and Ahmed, S and Brown, C and Pruden, A and Zhang, L},
title = {ARGContextProfiler: extracting and scoring the genomic contexts of antibiotic resistance genes using assembly graphs.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1604461},
pmid = {40469725},
issn = {1664-302X},
abstract = {Antibiotic resistance (AR) presents a global health challenge, necessitating an improved understanding of the ecology, evolution, and dissemination of antibiotic resistance genes (ARGs). Several tools, databases, and algorithms are now available to facilitate the identification of ARGs in metagenomic sequencing data; however, direct annotation of short-read data provides limited contextual information. Knowledge of whether an ARG is carried in the chromosome or on a specific mobile genetic element (MGE) is critical to understanding mobility, persistence, and potential for co-selection. Here we developed ARGContextProfiler, a pipeline designed to extract and visualize ARG genomic contexts. By leveraging the assembly graph for genomic neighborhood extraction and validating contexts through read mapping, ARGContextProfiler minimizes chimeric errors that are a common artifact of assembly outputs. Testing on real, synthetic, and semi-synthetic data, including long-read sequencing data from environmental samples, demonstrated that ARGContextProfiler offers superior accuracy, precision, and sensitivity compared to conventional assembly-based methods. ARGContextProfiler thus provides a powerful tool for uncovering the genomic context of ARGs in metagenomic sequencing data, which can be of value to both fundamental and applied research aimed at understanding and stemming the spread of AR. The source code of ARGContextProfiler is publicly available at GitHub.},
}

@article {pmid40469537,
year = {2025},
author = {Yu, X and Zou, Y and Li, M and Wang, L and Feng, W and Wei, L and Yang, L and He, J and Bu, H and Li, Y},
title = {Auto-Immune Glial Fibrillary Acidic Protein Astrocytopathy with Active Intrathecal Epstein-Barr Virus: A Single-Center Case Series Report.},
journal = {Neuropsychiatric disease and treatment},
volume = {21},
number = {},
pages = {1119-1130},
pmid = {40469537},
issn = {1176-6328},
abstract = {PURPOSE: Auto-immune glial fibrillary acidic protein (GFAP) astrocytopathy is a disease with unclear mechanisms and no diagnostic and treatment guidelines. Epstein-Barr virus (EBV) infection is reportedly involved in glial activities. However, the relationship between GFAP astrocytopathy and EBV infection is not clear. This study reports a case series of auto-immune GFAP astrocytosis with positive cerebrospinal fluid (CSF) EBV DNA, describing its clinical manifestations and treatment experience.

PATIENTS AND METHODS: In the serial case study, we reported six patients diagnosed with GFAP astrocytopathy having intrathecal EBV.

RESULTS: The significant signs included headache, fever and urination disorder, ataxia, limb weakness, numbness, consciousness disorder, psychological disorder, and blindness, among others. CSF analysis showed increased pressure, white blood cell count, abnormal biochemical components, positive GFAP antibody, and EBV. The positive results of metagenomic next-generation sequencing (mNGS) and PCR in CSF indicated that there might be active replication of EBV in the CSF of patients. The results of EBV-associated antibodies in blood suggest no evidence of acute primary EBV infection in six patients. Initial single antivirus therapy did not show satisfactory effects, but all patients showed improvement in clinical features and laboratory analysis after immunotherapy.

CONCLUSION: This study indicated that intrathecal EBV activity was closely related to auto-immune GFAP astrocytopathy, of which the mechanism remains to be further studied.},
}

@article {pmid40469517,
year = {2025},
author = {Zhang, F and Li, R and Liu, Y and Liang, J and Gong, Y and Xiao, C and Cai, J and Wang, T and You, Q and Zhang, J and Chen, H and Xiao, J and Zhang, Y and Yang, Y and Li, H and Yao, J and Zhang, Q and Zheng, J},
title = {Integrative cross-tissue analysis unveils complement-immunoglobulin augmentation and dysbiosis-related fatty acid metabolic remodeling during mammalian aging.},
journal = {iMeta},
volume = {4},
number = {3},
pages = {e70027},
pmid = {40469517},
issn = {2770-596X},
abstract = {Aging-related decline and adaptation are complex, multifaceted processes that affect various tissues and increase risk of chronic diseases. To characterize key changes in cross-tissue aging, we performed comprehensive proteomic and metabolomic analyses across 21 solid tissues and plasma samples, alongside shotgun metagenomic profiling of fecal microbial communities in young and aged mice. Our findings revealed widespread aging-rewired chronic inflammation, characterized by complement system activation in plasma and universal immunoglobulins accumulation across multiple solid tissues. This inflammatory remodeling significantly enhanced vulnerability to aging-related tissue injury. Moreover, we identified organ-specific and organ-enriched proteins with high functional specificity. Among these, aging-related proteins were closely linked to disorders arising from lipid metabolism dysfunction. Analysis of multi-tissue metabolomic and fecal metagenomic profiles revealed that aging significantly disrupted inter-tissue metabolic coupling, activities of polyunsaturated fatty acids metabolism, and gut microbiota homeostasis. Aged mice exhibited a marked decrease in Escherichia and an increase in Helicobacter, strongly correlating with alterations in omega-3 and omega-6 fatty acid abundances. Through multi-omics integration, we identified key molecular hubs driving organismal responses to aging. Collectively, our study uncovers extensive aging-associated alterations across tissues, emphasizing the interplay between systemic inflammation and dysbiosis-driven fatty acid remodeling. These findings provide deeper insights into the development of healthy aging from a cross-tissue perspective.},
}

@article {pmid40469508,
year = {2025},
author = {Zhao, S and Zhong, H and He, Y and Li, X and Zhu, L and Xiong, Z and Zhang, X and Zheng, N and Morgavi, DP and Wang, J},
title = {Leveraging core enzyme structures for microbiota targeted functional regulation: Urease as an example.},
journal = {iMeta},
volume = {4},
number = {3},
pages = {e70032},
pmid = {40469508},
issn = {2770-596X},
abstract = {Microbial communities play critical roles in various ecosystems. Despite extensive research on the taxonomic and functional diversity of microbial communities, effective approaches to regulate targeted microbial functions remain limited. Here, we present an innovative methodology that integrates core enzyme identification, protein structural characterization, regulator virtual screening, and functional validation to achieve precise microbiome functional regulation. As a proof of concept, we focused on the regulation of urea decomposition by the rumen microbiota in ruminants. Through metagenomic analysis, we identified the core urease gene and its corresponding microbial genome (MAG257) affiliated with the unclassified Succinivibrionaceae, and reconstructed its complete gene cluster. Structural analysis of the urease catalytic subunit (UreC) via cryo-electron microscopy (cryo-EM) revealed detailed features of its active site, guiding molecular docking studies that identified epiberberine, a natural compound with potent urease inhibitory activity. Validation in a rumen simulation system demonstrated that epiberberine significantly reduced urea decomposition and enhanced nitrogen utilization. This study establishes a robust framework that combines structural biology and computational screening to achieve targeted microbiome functional regulation, offering a promising tool for microbiome engineering and broader applications in animal productivity, human health, environmental improvement, and biotechnology.},
}

@article {pmid40469506,
year = {2025},
author = {Li, X and Wu, Y and Yi, B and Chen, M and Zhang, G and Shao, X and Jiang, X and Cui, Y and Chen, L and Dong, X and Zhang, S and Zhao, Y and Deng, Y and Li, X and Wang, Y and Wu, L and Fu, Y and Ran, D and Peng, C and Yang, X and Zhang, L and Wang, Y and Zhu, Y and Sun, D and Ran, Y and Zheng, D and Yin, X and Chen, Y and Long, Y and Wang, W and Zhao, X and Liu, E and Xu, T and Li, Q and Zhong, W},
title = {A multi-centered prospective birth cohort study in Western China.},
journal = {iMeta},
volume = {4},
number = {3},
pages = {e70049},
pmid = {40469506},
issn = {2770-596X},
abstract = {The Western China Birth Cohort (WCBC) is a large-scale, multi-centered, prospective birth cohort study designed to address critical gaps in maternal and child health research in Western China, a region with diverse altitudes, ethnic groups, and unique environmental exposures. WCBC had enrolled 15,093 pregnant women across eight clinical centers in five provinces (Qinghai, Gansu, Guizhou, Chongqing, and Sichuan), spanning from the high-altitude Qinghai-Tibet Plateau to lowland regions. WCBC has collected over 220,000 medical records, 80,000 questionnaires, and 12 different types of biological samples, including peripheral blood, cord blood, dried blood spots, placenta, umbilical cord, decidua, saliva, feces, throat and nasal swabs, vaginal swabs, and breast milk. By integrating advanced multi-omics measurement, including genomics, proteomics, exosome profiling, metabolomics, spatial transcriptomics, single-cell RNA sequencing, culturome, metagenomics, and virosome analysis, WCBC provides a valuable platform to explore gene-environment interplay, early-life determinants of health, and long-term disease risks in diverse populations in Western China.},
}

@article {pmid40468884,
year = {2025},
author = {Lee, Y and Ko, YM and Kwak, YS},
title = {Genetic and Nutritional Dynamics of SynCom in Suppressing Apple Fire Blight.},
journal = {The plant pathology journal},
volume = {41},
number = {3},
pages = {380-391},
doi = {10.5423/PPJ.OA.03.2025.0040},
pmid = {40468884},
issn = {1598-2254},
support = {RS-2020-RD009282//Rural Development Administration/ ; RS-2025-00516084//National Research Foundation of Korea/ ; },
abstract = {Fire blight disease, caused by Erwinia amylovora, occurs in apples and other Rosaceae plants and is known to cause significant economic damage. The pathogen usually infects flowers during the reproductive growth period of plants, colonizes, and penetrates by producing exopolysaccharides in the stigma. A synthetic microbial community (SynCom) is an artificial community of microorganisms designed to enhance host viability. To construct SynCom, we attempted to identify and utilize the microbial characteristics of apple trees that are not infected with the pathogen compared to those that are infected. In our previous study, we composed SynCom with strains expected to reduce the density of fire blight pathogens through microbiome analysis, strain isolation, and continuous replacement culture. We are able to observe the disease control effect of the constructed SynCom. However, no study has been conducted to clearly determine the genetic mechanism underlying this effect of the SynCom. Here, we present that potential secondary metabolite candidates and nutritional competition with the pathogen were confirmed as biochemical mechanisms through whole genome analysis of SynCom strains. Additionally, by co-cultivating SynCom with the pathogen in limited nutrient conditions, such as apple blossom extracts, which are susceptible to the pathogen, we confirmed the potential of SynCom treatment to reduce the pathogen densities. This study demonstrates that genetic selection using metagenomics can effectively identify microorganisms with potential functional capabilities.},
}

@article {pmid40468453,
year = {2025},
author = {Hu, F and Gebeyew, K and Wu, Z and Chen, B and Jiao, J and Tan, Z and Tian, D and He, Z},
title = {Fat-rich diet promotes microbiome-dependent ATP synthesis in sheep model.},
journal = {Journal of animal science and biotechnology},
volume = {16},
number = {1},
pages = {81},
pmid = {40468453},
issn = {1674-9782},
support = {XDA26040304//Strategic Priority Research Program/ ; XDA26050102//Strategic Priority Research Program/ ; 32072760//National Natural Science Foundation of China/ ; 2022JJ10054//Natural Science Foundation of Hunan Province of China/ ; },
abstract = {BACKGROUND: The ketogenic diet that forces adenosine triphosphate (ATP) production by beta-oxidation of fatty acids instead of carbohydrate glycolysis, has gained consensus on host metabolism. However, the mechanisms how a ketogenic diet alters gastrointestinal microbiome and its downstream consequences on microbial nutrient availability and energy metabolism remain to be elucidated. Here, we used the sheep model fed with fat-rich diet to evaluate the symbiotic microbiome across three regions of the gastrointestinal tract (rumen, ileum, and colon) to gain a comprehensive understanding of the microbial energy metabolism and microbe-mediated ATP biosynthesis.

RESULTS: Results showed that sheep fed a fat-rich diet had a greater ADG and increased reliance on fat oxidation for fuel utilization. Metagenomics analysis showed the loss of the specialized fiber-degrading bacteria (genus_Fibrobacter) in the rumen and enrichment of genera RUG420 and Eubacterium, which are involved in lipid metabolism and bile acid processing, in the ileum. A significant functional shift related to energy metabolism was shared across three regions of the gastrointestinal microbiomes. These shifts were dominated by glycolysis/gluconeogenesis and TCA cycle in the rumen and by fatty acid degradation and bile acid transformation in the ileum, indicating adaptation to nutrient availability and energy acquisition. Notably, the abundance of substrate-level phosphorylation (SLP) enzymes was significantly increased in the rumen, ileum and colon, while the ATP-producing capacity through electron transport phosphorylation (ETP) by family_Bacteroidaceae in rumen and Acutalibacteraceae in ileum of sheep with fat-rich diet.

CONCLUSIONS: Altogether, the ATP-related microbiome encoding SLP and ETP in rumen, ileum, and colon contributed 36.95% to the host's weight variation. Our study is the first one demonstrating the microbial potential in the ATP synthesis under the shift in dietary energy source, providing a new perspective on the energy metabolism and precise human macronutrients nutrition.},
}

@article {pmid40468444,
year = {2025},
author = {Tang, Q and Yin, X and Wen, G and Luo, Z and Zhang, L and Tan, S},
title = {Unraveling the composition and function of pig gut microbiome from metagenomics.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {60},
pmid = {40468444},
issn = {2524-4671},
support = {No. [2023] 211//2022 Hunan Province Vocational Education "Chuyi" Action High Level Teacher Team Construction Project/ ; No. [2023] 211//2022 Hunan Province Vocational Education "Chuyi" Action High Level Teacher Team Construction Project/ ; },
abstract = {The gut microbiome plays a crucial role in intestinal maturation, metabolism, and immunoregulation, significantly influencing the host's health and growth performance. This review highlights the use of metagenomic techniques to the composition, function, and dynamic changes of the pig gut microbiota. Research has revealed that environmental and host factors, particularly diet, drive significant variations in microbial composition, which in turn shape host epigenetics through microbial components and metabolites. Furthermore, the strong correlation between the gut microbiota and host health presents opportunities for improving growth performance in the livestock industry.},
}

@article {pmid40468439,
year = {2025},
author = {Ravelo, AD and Ruch, M and Suazo, M and Ferm, P and Su, R and Chen, C and Crooker, BA and Noyes, NR and Salfer, IJ and Caixeta, LS},
title = {Associations between hyperketonemia and the rumen metagenome and metabolome in Holstein cows during the first 2 weeks postpartum.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {59},
pmid = {40468439},
issn = {2524-4671},
support = {1025222//U.S. Department of Agriculture/ ; },
abstract = {Hyperketonemia (HYK) is characterized by elevated levels of blood ketone bodies in dairy cows. Despite previous research on the physiological events related to HYK, associations between the rumen metagenome, metabolome, and HYK have not been well described. Therefore, the objective of this study was to compare rumen metagenome and metabolome profiles of cows with naturally occurring HYK to those without HYK during the first two weeks postpartum. Blood beta-hydroxybutyrate (BHB) concentrations at d 5, 10 and 14 postpartum were used to classify 16 rumen cannulated Holstein cows as either hyperketonemic (+ HYK; ≥1.2 mmol/L BHB at any of the collection days) or non-hyperketonemic (-HYK). Five + HYK cows were identified and were paired with 5 -HYK cows based on parity and calving date. Microbial DNA was extracted from rumen fluid and sequenced using shotgun metagenomics with the Illumina platform. Kraken2 was used to map reads to microbial taxonomic groups and Humann3.8 was used to predict potential functions. Metabolome profiling of rumen fluid was conducted using high-resolution liquid chromatography-mass spectroscopy. MetaboAnalyst6.0 was used to identify potential changes in metabolic pathways. Metagenomes and metabolomes comparisons were conducted using mixed models that included the fixed effects of group, day, their interaction, and the random effect of cow. There was minimal difference detected in alpha diversity for the metagenome, but differences in the metabolome were detected by HYK status. The concentration of asparagine and p-cresol was greater in + HYK cows compared to -HYK, but citrulline was greater in -HYK cows throughout all days considered. On d5 the concentration of ornithine was greater in + HYK compared to-HYK cows, and on d10 acetate was greater in the -HYK cows. There were no differences detected in the pathway analysis from the metabolites quantified by HYK status. Overall, modest differences in rumen metabolome were observed between + HYK and -HYK cows in early lactation. Future studies should explore associations between the rumen environment and HYK as this could be informative for treatment and management practices.},
}

@article {pmid40468436,
year = {2025},
author = {Kilama, J and Islam, MS and Amat, S},
title = {Bovine ocular microbiome: the next frontier in managing Pinkeye in cattle.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {58},
pmid = {40468436},
issn = {2524-4671},
abstract = {Infectious bovine keratoconjunctivitis (IBK), or pinkeye, represents a significant economic challenge to dairy and beef cattle industries resulting in decreased productivity and increased treatment costs. The current IBK prevention and control strategies in cattle face challenges owing to the multifactorial nature of the disease, the rise of antibiotic resistance in IBK pathogens, and inconsistent efficacy of IBK vaccines. Recent efforts in metagenomic characterization of the eye microbiome in humans and animals, including cattle, have revealed that the ocular surface is colonized by relatively diverse and dynamic microbial community that is essential for maintaining ocular health and can be leveraged to enhance resistance against infectious ocular diseases. In this narrative review, we provide comprehensive insights into the ocular microbiota by summarizing the amplicon and metagenomic sequencing- and culture-based studies conducted in cattle, and by reviewing relevant findings from humans and other animal species. We also explore the potential of the ocular microbiome as a new frontier in managing IBK. Finally, we examine the gut-eye-microbiome axis and discuss its potential contribution in improving the resistance of cattle against IBK.},
}

@article {pmid40468430,
year = {2025},
author = {Khoiri, AN and Costa, NR and Crusciol, CAC and Pariz, CM and Costa, C and Calonego, JC and de Castilhos, AM and de Souza, DM and de Lima Meirelles, PR and Cru, IV and Moretti, LG and Bossolani, JW and Kuramae, EE},
title = {Pigeon pea-mediated soil microbial shifts improve agroecosystem multifunctionality in long-term maize-palisade grass intercropping.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {60},
pmid = {40468430},
issn = {2524-6372},
support = {#2014/21772-4 and #2014/14935-4//São Paulo Research Foundation (FAPESP)/ ; #458225/2014-2//National Council for Scientific and Technological Development (CNPq)/ ; 1378/14//Fundação Agrisus/ ; },
abstract = {BACKGROUND: Intercropping systems enhance agricultural sustainability by promoting ecosystem multifunctionality (EMF). This study examined the impact of adding pigeon pea (M + PG + PP) into a maize-palisade grass (M + PG) intercropping system under a no-till system (NTS) on soil microbial communities and ecosystem services. After five consecutive growing seasons, bulk soil samples from a soybean-based crop-livestock system were analyzed using metagenomics.

RESULTS: The inclusion of pigeon pea significantly improved the EMF index, with higher plant productivity and slightly enhanced outcomes in soil health, lamb meat productivity, and climate protection. The M + PG + PP treatment enriched Bradyrhizobium spp., which were positively correlated with soil health, plant productivity, and EMF index. Functional analysis indicated that M + PG + PP treatment enhanced nitrogen metabolism, biofilm formation, and exopolysaccharide (EPS) biosynthesis, improving soil fertility and microbial activity. Similarly, functional analysis of microbial plant growth-promoting traits revealed that the M + PG + PP treatment promoted microbial functions related to nitrogen and iron acquisition, sulfur assimilation, and plant colonization, all essential for plant growth and nutrient cycling. In contrast, the M + PG treatment primarily enhanced pathways related to competitive exclusion and phytohormone production.

CONCLUSIONS: These findings highlight the importance of incorporating legumes such as pigeon pea into intercropping systems to optimize ecosystem services, enhance soil health, and promote long-term agricultural productivity and sustainability.},
}

@article {pmid40468269,
year = {2025},
author = {Li, B and Yang, Y and Xu, B and Song, P and Jiang, F and Gao, H and Cai, Z and Gu, H and Zhang, T},
title = {Comparative macrogenomics reveal plateau adaptation of gut microbiome in cervids.},
journal = {BMC biology},
volume = {23},
number = {1},
pages = {154},
pmid = {40468269},
issn = {1741-7007},
mesh = {*Gastrointestinal Microbiome/genetics ; Animals ; *Deer/microbiology/genetics ; Phylogeny ; Metagenome ; Metagenomics ; *Adaptation, Physiological/genetics ; Energy Metabolism ; Biological Evolution ; },
abstract = {BACKGROUND: Diverse gut microbiota in animals significantly influences host physiology, ecological adaptation, and evolution. However, the specific functional roles of gut microbiota in facilitating host adaptation, as well as the coevolutionary dynamics between microbiota and their hosts, remain largely understudied.

RESULTS: A total of 41,847 metagenome-assembled genomes and 3193 high-quality species-level genome bins were generated, establishing a comprehensive gut microbiome catalog for cervids in this study. Phylogenetic analysis revealed a coevolutionary relationship between cervids and their gut microbiota. Comparative metagenomic analyses further indicated that the gut microbiota of plateau cervids have undergone genome-level adaptations related to energy metabolism. At the genus level, species-level genome bins from the genera Alistipes and Faecousia in plateau cervids exhibit enhanced energy metabolism capabilities. Structural variations analysis revealed that the insertion and duplications structural variations in the gut microbiota of plateau cervids were significantly enriched in energy metabolism pathways. In contrast, the deletions and contractions in structural variations were predominantly enriched with metabolic pathways involved in the biosynthesis of diverse biochemical molecules.

CONCLUSIONS: Our study provides a comprehensive gut microbiome catalog of the cervid gut microbiota, revealing the coevolutionary relationship between cervid gut microbiota and hosts. These findings highlight the adaptive genomic evolution of the gut microbiota in contributing to the plateau adaptability of cervids and offer new insights into the mechanisms by which the gut microbiota help hosts adapt to extreme environments.},
}

*Gastrointestinal Microbiome/genetics
Animals
*Deer/microbiology/genetics
Phylogeny
Metagenome
Metagenomics
*Adaptation, Physiological/genetics
Energy Metabolism
Biological Evolution

@article {pmid40468214,
year = {2025},
author = {Yang, X and Chen, H and Wu, L and Guo, X and Xue, D},
title = {Diversity and correlation analysis of microbiomes and metabolites of Sphagnum palustre in various microhabitats.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {761},
pmid = {40468214},
issn = {1471-2229},
support = {2019QZKK0304//Second Tibetan Plateau Scientific Expedition/ ; QNTS202201//Youth Innovation Program of CIB/ ; 2022376//Youth Innovation Promotion Association of the Chinese Academy of Sciences/ ; 2021JDTD011//Youth Science and Technology Innovation Team Program of Sichuan Province of China/ ; },
mesh = {*Microbiota ; *Sphagnopsida/microbiology/metabolism ; Ecosystem ; Soil Microbiology ; Bacteria/genetics/metabolism ; },
abstract = {BACKGROUND: Sphagnum peat mosses are crucial contributors to global carbon sequestration and are a dominant presence in many northern peatland environments. These mosses host a wide variety of microorganisms, which reside within their tissues and on their surfaces. Despite this close association, the connection between these microorganisms and the production of metabolites across different parts of Sphagnum remains unclear.

RESULTS: This research explored the connection between microbial diversity and metabolite production in various microhabitats of Sphagnum palustre by employing metagenomic and metabolomic techniques. Our results indicate that the S. palustre microbiome composition is more strongly influenced by microhabitat than by geographic location. Microbiome diversity microbiomes related to S. palustre showed a steady decrease from soil to near soil, from X to CAP, and from belowground to aboveground habitats. In contrast, network complexity increased. Species abundance analysis indicated that Proteobacteria was the most prevalent bacterial phylum across CAP, S, Z, and X. Additionally, Ascomycota emerged as the predominant fungal phylum. There were significant differences in nitrogen fixation activity, methane oxidation activity, total nitrogen, and total carbon among different microhabitats. The FAPROTAX analysis revealed differences in the metabolic potential of the carbon (C) and nitrogen (N) cycles across the four microhabitats. LC-MS/MS technology was employed to quantitatively assess metabolites across various S. palustre microhabitats. A total of 3,822 metabolites and 353 differential metabolites were detected, predominantly including lipids, organic acids, and carboxylic acids. The majority of these differential metabolites were associated with metabolic pathways such as carotenoid biosynthesis, steroid biosynthesis, secondary bile acid biosynthesis, as well as the biosynthesis of neomycin, kanamycin, and gentamicin. Correlation analysis revealed both positive and negative relationships between microorganisms and differential metabolites. Methylocystis, which was significantly enriched in X and T, showed a strong positive correlation with differential metabolites in S vs T and Z vs X, but a negative correlation with those in X vs T (p < 0.05).

CONCLUSION: In summary, our study demonstrates that Sphagnum palustre microbiomes are primarily influenced by microhabitats rather than specific environmental conditions at different sites. We identified significant variations in microbial community diversity across various S. palustre microhabitats. Correlation analysis revealed links between microorganisms and differential metabolic processes. This comprehensive investigation of aboveground and belowground microbiomes and metabolites in S. palustre provides new insights into the distribution of microbial communities and metabolites across different microhabitats.},
}

*Microbiota
*Sphagnopsida/microbiology/metabolism
Ecosystem
Soil Microbiology
Bacteria/genetics/metabolism

@article {pmid40468175,
year = {2025},
author = {Lin, Z and Chen, Y and Yu, Z and Zhang, Z and Lin, Y and Zhang, W and Li, W and Guo, Y and Fang, X},
title = {Early and Accurate Pathogen Identification Based on mNGS: Key to Timely Therapy for Mycoplasma Prosthetic Joint Infection.},
journal = {Orthopaedic surgery},
volume = {},
number = {},
pages = {},
doi = {10.1111/os.70069},
pmid = {40468175},
issn = {1757-7861},
support = {2023J01597,2023J01315//Natural Science Foundation of Fujian Province/ ; 2023CXA020//Fujian Medical Innovation Grant, China/ ; },
abstract = {OBJECTIVES: Prosthetic joint infection (PJI) caused by Mycoplasma infection is relatively rare in clinical practice; all cases are primarily reported as individual case reports, and the characteristics of PJI induced by Mycoplasma infection have not been clearly studied. This case-control study was designed to systematically compare demographic profiles, clinical histories, diagnostic modalities, and therapeutic outcomes between Mycoplasma PJI and conventional bacterial PJI through retrospective analysis.

METHODS: This retrospective single-center study included 6 cases of simplex Mycoplasma PJI, 4 cases of mixed Mycoplasma PJI, 33 cases of Staphylococcus aureus, and 21 cases of Staphylococcus epidermidis infection from January 1, 2017 to January 1, 2024. Perioperative inflammatory markers, pathogen cultures, metagenomic next-generation sequencing (mNGS) results, history of invasive urinary catheterization, clinical presentation, treatment, and rate of treatment success were recorded and analyzed for the four groups. Continuous variables were compared two-by-two between the four groups using independent t-tests or the Mann-Whitney U test based on the distribution of the data. The categorical variables were compared using the chi-square test or Fisher's exact test.

RESULTS: The proportion of invasive urinary catheterization history in the mixed versus simplex Mycoplasma group was significantly higher than that in the Staphylococcus aureus and Staphylococcus epidermidis control groups (p < 0.05). Routine microbial culture positivity was significantly lower in the mixed versus simplex Mycoplasma group than in the control group (p < 0.01), but positive results for Mycoplasma can be detected by mNGS. Of note, one patient in the simplex Mycoplasma group was cured with targeted antibiotic-only therapy and avoided surgery. There was no statistically significant difference in cure rates between the mixed and simplex Mycoplasma groups and the Staphylococcus aureus and Staphylococcus epidermidis control groups (p = 1.000).

CONCLUSION: Prior invasive urinary catheterization represents a significant risk factor for Mycoplasma PJI. The synergistic use of mNGS, optimized culture methods, and 16S rRNA PCR enables early detection of Mycoplasma. This multimodal diagnostic approach significantly enhances pathogen identification accuracy, minimizes diagnostic oversights, and provides essential guidance for effective therapeutic intervention.},
}

@article {pmid40468098,
year = {2025},
author = {Srivastava, A and Rai, PK and Agnihotri, VK and Choure, K and Vishvakarma, R},
title = {Metagenomic analysis of viral communities in the polluted Varuna River reveals site-specific diversity patterns associated with environmental aspects.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
pmid = {40468098},
issn = {1618-1905},
abstract = {Varuna River, which is native to Varanasi, is of great importance as a water reservoir for the people and is contaminated with heavy pollutants due to urbanization. In this study, four sites (VR1, VR2, VR3, and VR4) of Varuna River water were sampled to assess the viral diversity. The metagenomics approach was used to study the viral diversity and functional analysis, suggesting the overall quality of the water at the sampled location. The analysis shows that VR1 had the most species richness (3000 species), followed by VR3 (2500), VR2 (2000), and VR4 (1500). The PCA analysis revealed distinct spatial patterns and community differentiation where VR2 and VR4 clustered while VR1 and VR3 were distant.Diversity analysis showed that Negarnaviricota dominated all samples at the phylum level. Yunchangviricetes, a non-reported virus, and Insthoviricetes were the dominant classes. Pakpunavirus was the leading genus, followed by the human pathogen Mimivirus. The highest species abundance in VR1 and VR2 was Mimivirus, Megavirus, chilensis, while VR3 and VR4 had Hpunavirus and Pseudomonas phage O4, indicating human involvement. Functional analyses of enzymatic activity and KEGG Orthology in microbial communities from VR1 to VR4 samples showed that VR4 exhibited maximal enzymatic activity, genetic flexibility, and advanced regulatory control compared to the other samples. The increased presence of transporter genes alongside signal transduction proteins and metabolic enzymes in VR4 indicates enhanced functional diversity, which aids in coping with environmental stresses. On the basis of viral species, ecological, biotechnological aspects were also interpreted. This study concluded that the Negarnaviricota plays a key role in maintaining the overall water quality and there is an urgent need for remediation of the Varuna River especially at site VR4 (25° 19' 46.7″ N 83° 02' 38.3″ E).},
}

@article {pmid40468041,
year = {2025},
author = {Lin, D and Du, S and Zhao, Z and Zhang, T and Wang, L and Zhang, Q and Zhou, SY and Graham, DW and Tissue, DT and Zhu, D and Zhu, YG and Penuelas, J and Reich, PB},
title = {Climate warming fuels the global antibiotic resistome by altering soil bacterial traits.},
journal = {Nature ecology & evolution},
volume = {},
number = {},
pages = {},
pmid = {40468041},
issn = {2397-334X},
support = {2023321//Youth Innovation Promotion Association of the Chinese Academy of Sciences (Youth Innovation Promotion Association CAS)/ ; 42222701//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42090063//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Understanding the implications of global warming on the spread of antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) within soil ecosystems is crucial for safeguarding human well-being and sustaining ecosystem health. However, there is currently a lack of large-scale, systematic underpinning data needed to examine this issue. Here, using an integrative approach that combines field experiments, extensive global metagenomic data and microbial culturing, we show that warming enriches bacteria with ARGs and VFGs, increases metabolic complexity and adaptability in bacteria, and accelerates genetic alterations related to ARG and VFGs development. Our validation experiments confirm that the warming effect is more pronounced in colder regions. Machine learning predictions further suggest that warming will increase the soil ARG abundance, especially in some areas that rely heavily on fossil fuels. These results suggest another major negative consequence of global warming, highlighting the importance of developing and implementing sustainability policies that simultaneously combat climate change and antibiotic resistance.},
}

@article {pmid40467587,
year = {2025},
author = {Xiong, S and Xie, B and Yin, N and Zhu, H and Gao, H and Xu, X and Xiao, K and Cai, X and Sun, G and Sun, X and Cui, Y and Van de Wiele, T and Zhu, Y},
title = {Prenatal exposure to trace elements impacts mother-infant gut microbiome, metabolome and resistome during the first year of life.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {5186},
pmid = {40467587},
issn = {2041-1723},
support = {No. L232076//Natural Science Foundation of Beijing Municipality (Beijing Natural Science Foundation)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/genetics ; Female ; Pregnancy ; Infant ; *Trace Elements/adverse effects ; *Metabolome/drug effects ; Feces/microbiology ; *Prenatal Exposure Delayed Effects/microbiology/metabolism ; Adult ; Male ; Metagenomics ; Hair/chemistry ; *Maternal Exposure/adverse effects ; Infant, Newborn ; Bacteria/genetics/classification/drug effects ; Copper ; },
abstract = {Infancy is a critical window for the colonization of gut microbiome. However, xenobiotic impacts on gut microbiome development in early life remain poorly understood. Here, we recruit 146 mother-infant pairs and collect stool samples at 3, 6, and 12 months after delivery for amplicon sequencing (N = 353), metagenomics (N = 65), and metabolomics (N = 198). Trace elements in maternal hair samples (N = 119) affect diversity and composition of the infant gut microbiome. Shannon diversity in 3 month-old infants is correlated positively with selenium and negatively with copper, and relative abundance of Bifidobacterium increases under high exposure to aluminum and manganese. During the first year of life, infants and their paired mothers have distinct microbial diversity and composition, and their bacterial community structures gradually approach. here are 56 differential metabolites between the first and second visit and 515 differential metabolites between the second and third visit. The typical profile of antibiotic resistance genes (ARGs) significantly differs between infants and their mothers. High levels of copper and arsenic exposure may induce the enrichment of ARGs in the infant gut. Our findings highlight the dynamics of the gut microbiome, metabolites, and ARG profiles of mother-infant pairs after delivery, associated with prenatal exposure to trace elements.},
}

Humans
*Gastrointestinal Microbiome/drug effects/genetics
Female
Pregnancy
Infant
*Trace Elements/adverse effects
*Metabolome/drug effects
Feces/microbiology
*Prenatal Exposure Delayed Effects/microbiology/metabolism
Adult
Male
Metagenomics
Hair/chemistry
*Maternal Exposure/adverse effects
Infant, Newborn
Bacteria/genetics/classification/drug effects
Copper

@article {pmid40467492,
year = {2025},
author = {Tonomura, S and Hattori, Y and Ishibashi, T and Ikeda, S and Noda, K and Chiba, T and Kato, Y and Asano, R and Fukuma, K and Edamoto-Taira, Y and Motooka, D and Inagaki, T and Okazawa, M and Nakamura, S and Koga, M and Toyoda, K and Nomura, R and Nakano, K and Friedland, RP and Takeda, K and Takahashi, R and Ihara, M and Nakaoka, Y},
title = {Oral Pathobiont Streptococcus Anginosus Is Enriched in the Gut of Stroke Patients and Predicts 2-Year Cardiovascular Outcome.},
journal = {Circulation journal : official journal of the Japanese Circulation Society},
volume = {},
number = {},
pages = {},
doi = {10.1253/circj.CJ-24-0872},
pmid = {40467492},
issn = {1347-4820},
abstract = {BACKGROUND: Several cross-sectional studies have implicated gut dysbiosis caused by an abundance of oral commensals in stroke, but the effect on long-term prognosis is still unknown. Therefore, we longitudinally investigated oral pathobionts in the gut and their clinical relevance to stroke.

METHODS AND RESULTS: We analyzed the salivary and gut microbiomes collected from 189 acute stroke and 55 non-stroke subjects, and found that Streptococcus anginosus was significantly more abundant in both the saliva (median [IQR], 0.01 [0.00-0.14] vs. 0.00 [0.00-0.03], P=0.02) and gut (0.09 [0.00-0.28] vs. 0.00 [0.00-0.02], P<0.001) of the stroke patients compared with their non-stroke counterparts. Network analysis revealed S. anginosus as a central hub in gut dysbiosis. After adjusting for vascular risks, S. anginosus (odds ratio 1.20, 95% confidence interval 1.06-1.36, P<0.01), Anaerostipes hadrus (0.82, [0.73-0.93], P<0.01), and Bacteroides plebeius (0.86, [0.86-0.93], P=0.01) in the gut were independent predictors of stroke. Longitudinally, S. anginosus in the gut was significantly associated with increased rates of death and major cardiovascular events (P=0.04; log-rank test), whereas A. hadrus and B. plebeius were not (P=0.45 and P=0.19). After adjusting for vascular risks, S. anginosus in the gut was a residual risk for increased rates of death and major cardiovascular events (hazard ratio 4.78, 95% confidence interval 1.08-21.18, P=0.04)Conclusions: S. anginosus in the gut may increase the risk of stroke and a poor prognosis.},
}