@article {pmid40573435,
year = {2025},
author = {Ajileye, TG and Akinleye, TE and Faleye, TOC and De Coninck, L and George, UE and Onoja, AB and Agbaje, ST and Ifeorah, IM and Olayinka, OA and Oni, EI and Oragwa, AO and Popoola, BO and Olayinka, OT and Osasona, OG and George, OA and Ajayi, PG and Suleiman, AA and Muhammad, AI and Komolafe, I and Adeniji, AJ and Matthijnssens, J and Adewumi, MO},
title = {Ten Previously Unassigned Human Cosavirus Genotypes Detected in Feces of Children with Non-Polio Acute Flaccid Paralysis in Nigeria in 2020.},
journal = {Viruses},
volume = {17},
number = {6},
pages = {},
doi = {10.3390/v17060844},
pmid = {40573435},
issn = {1999-4915},
mesh = {Humans ; *Feces/virology ; Nigeria/epidemiology ; Phylogeny ; *Genotype ; Child ; Child, Preschool ; *Picornaviridae/genetics/classification/isolation & purification ; Genome, Viral ; Infant ; *Picornaviridae Infections/virology/epidemiology ; Genetic Variation ; Adolescent ; Female ; Male ; Metagenomics ; *Paralysis/virology ; },
abstract = {Since its discovery via metagenomics in 2008, human cosavirus (HCoSV) has been detected in the cerebrospinal fluid (CSF) and feces of humans with meningitis, acute flaccid paralysis (AFP), and acute gastroenteritis. To date, 34 HCoSV genotypes have been documented by the Picornaviridae study group. However, the documented genetic diversity of HCoSV in Nigeria is limited. Here we describe the genetic diversity of HCoSV in Nigeria using a metagenomics approach. Archived and anonymized fecal specimens from children (under 15 years old) diagnosed with non-polio AFP from five states in Nigeria were analyzed. Virus-like particles were purified from 55 pools (made from 254 samples) using the NetoVIR protocol. Pools were subjected to nucleic acid extraction and metagenomic sequencing. Reads were trimmed and assembled, and contigs classified as HCoSV were subjected to phylogenetic, pairwise identity, recombination analysis, and, when necessary, immuno-informatics and capsid structure prediction. Fifteen pools yielded 23 genomes of HCoSV. Phylogenetic and pairwise identity analysis showed that all belonged to four species (eleven, three, three, and six members of Cosavirus asiani, Cosavirus bepakis, Cosavirus depakis, and Cosavirus eaustrali, respectively) and seventeen genotypes. Ten genomes belong to seven (HCoSV-A3/A10, A15, A17, A19, A24, D3, and E1) previously assigned genotypes, while the remaining thirteen genomes belonged to ten newly proposed genotypes across the four HCoSV species, based on the near-complete VP1 region (VP1*) of the cosavirus genome. Our analysis suggests the existence of at least seven and eight Cosavirus bepakis and Cosavirus eaustrali genotypes, respectively (including those described here). We report the first near-complete genomes of Cosavirus bepakis and Cosavirus depakis from Nigeria, which contributes to the increasing knowledge of the diversity of HCoSV, raising the number of tentative genotypes from 34 to over 40. Our findings suggest that the genetic diversity of HCoSV might be broader than is currently documented, highlighting the need for enhanced surveillance.},
}

Humans
*Feces/virology
Nigeria/epidemiology
Phylogeny
*Genotype
Child
Child, Preschool
*Picornaviridae/genetics/classification/isolation & purification
Genome, Viral
Infant
*Picornaviridae Infections/virology/epidemiology
Genetic Variation
Adolescent
Female
Male
Metagenomics
*Paralysis/virology

@article {pmid40573403,
year = {2025},
author = {Zhang, X and Fan, IX and Xu, Y and Rule, J and Tse, LPV and Pourkarim, MR and Lee, WM and Di Bisceglie, AM and Fan, X},
title = {Novel Viral Sequences in a Patient with Cryptogenic Liver Cirrhosis Revealed by Serum Virome Sequencing.},
journal = {Viruses},
volume = {17},
number = {6},
pages = {},
doi = {10.3390/v17060812},
pmid = {40573403},
issn = {1999-4915},
support = {1R21AI175438-24/NH/NIH HHS/United States ; },
mesh = {Humans ; *Liver Cirrhosis/virology ; *Virome/genetics ; Male ; Middle Aged ; Female ; *Viruses/genetics/classification/isolation & purification ; Genome, Viral ; Metagenomics ; Aged ; Sequence Analysis, DNA ; Adult ; *Serum/virology ; },
abstract = {Clinical studies indicate the etiology of liver disease to be unknown in 5% to 30% of patients. A long-standing hypothesis is the existence of unknown viruses beyond hepatitis A through E virus. We conducted serum virome sequencing in nine patients with cryptogenic liver disease and identified eight contigs that could not be annotated. One was determined to be a contaminant, while two of seven contigs from an individual (Patient 3) were validated by reverse transcription and polymerase chain reaction (RT-PCR) and Sanger sequencing. The possibility of contamination was completely excluded through PCR, with templates extracted using different methods from samples taken at different time points. One of the contigs, Seq260, was characterized as negative-sense single-stranded DNA via enzymatic digestion and genome walking. Digital-droplet PCR revealed the copy number of Seq260 to be low: 343 copies/mL. Seq260-based nested PCR screening was negative in 200 blood donors and 225 patients with liver disease with/without known etiologies. None of the seven contigs from Patient 3 was mapped onto 118,713 viral metagenomic data. Conclusively, we discovered seven unknown contigs from a patient with cryptogenic liver cirrhosis. These sequences are likely from a novel human virus with a negative-sense, linear single-stranded DNA genome.},
}

Humans
*Liver Cirrhosis/virology
*Virome/genetics
Male
Middle Aged
Female
*Viruses/genetics/classification/isolation & purification
Genome, Viral
Metagenomics
Aged
Sequence Analysis, DNA
Adult
*Serum/virology

@article {pmid40573397,
year = {2025},
author = {Wang, W and Wang, Q and Cao, R and Li, Y and Liu, Z and Xue, Z and Wang, X and Liu, Z},
title = {Metagenomic Investigation of Pathogenic RNA Viruses Causing Diarrhea in Sika Deer Fawns.},
journal = {Viruses},
volume = {17},
number = {6},
pages = {},
doi = {10.3390/v17060803},
pmid = {40573397},
issn = {1999-4915},
support = {CAAS-ASTIP-2021-ISAPS//Science and Technology Innovation Project of the Chinese Academy of Agricultural Sciences/ ; 2023YFD1800704//National Key Research and Development Program of China/ ; },
mesh = {Animals ; *Deer/virology ; *Diarrhea/virology/veterinary ; Metagenomics ; Feces/virology ; *RNA Viruses/genetics/classification/isolation & purification ; Phylogeny ; Genome, Viral ; China/epidemiology ; Rotavirus/genetics ; Metagenome ; Cattle ; },
abstract = {Diarrhea is a common disease in sika deer. The causes of diarrhea in sika deer are complex and involve a variety of pathogens. Additionally, new virulent pathogens are continuously emerging, which poses a serious threat to deer's health and particularly affects fawns' survival rate. In the present study, feces samples were collected from fawns with diarrhea in Jilin Province, in the northeast of China. The viral communities were investigated using the metagenomic method. Viral metagenome data revealed that the viruses in the fecal samples were mainly from 21 families in 14 orders. The major viruses in high abundance were astrovirus, rotavirus, coronavirus, and bovine viral diarrhea virus. In addition, a large number of phages, which mainly belonged to the family Siphoviridae, were identified. Then, the known causative virus species were investigated via RT-qPCR. The results showed that the infection rates of bovine coronavirus, bovine rotavirus, and bovine viral diarrhea virus were 59.44%, 58.89%, and 21.67%, respectively, and mixed infections were commonly seen in the samples. A bovine rotavirus strain was successfully isolated from the positive samples. Whole-genome sequencing revealed that the genotype of the strain was G6-P[1]-I2-R2-C2-M2-A3-N2-T6-E2-H3, indicating the recombination of rotavirus. This study revealed the profiles and characteristics of viruses that cause sika deer diarrhea, which will be helpful for understanding diarrhea diseases in sika deer.},
}

Animals
*Deer/virology
*Diarrhea/virology/veterinary
Metagenomics
Feces/virology
*RNA Viruses/genetics/classification/isolation & purification
Phylogeny
Genome, Viral
China/epidemiology
Rotavirus/genetics
Metagenome
Cattle

@article {pmid40573349,
year = {2025},
author = {Hernández-Villegas, EN and Castelán-Sánchez, HG and Moreira-Soto, A and Vigueras-Galván, AL and Jiménez-Rico, MA and Rico-Chávez, O and Rodríguez-González, S and Tolsá-García, MJ and Roiz, D and Martínez-Duque, P and Arana-Guardía, R and García-Súarez, O and Jiménez, MZ and Falcón, LI and Roche, B and Sarmiento-Silva, RE and Arnal, A and Drexler, JF and Suzán, G},
title = {Characterization of the Virome in Mosquitoes Across Distinct Habitats in the Yucatán Peninsula, Mexico.},
journal = {Viruses},
volume = {17},
number = {6},
pages = {},
doi = {10.3390/v17060758},
pmid = {40573349},
issn = {1999-4915},
mesh = {Animals ; Mexico ; *Culicidae/virology ; *Ecosystem ; *Virome ; *Mosquito Vectors/virology ; *Viruses/classification/genetics/isolation & purification ; High-Throughput Nucleotide Sequencing ; Phylogeny ; Genome, Viral ; Biodiversity ; },
abstract = {Human activities and land use changes have a major impact on the distribution and diversity of mosquito vectors and their associated viruses. This study describes the diversity and differential abundance of viruses associated with mosquito species from four habitats of the Yucatan Peninsula, Mexico. Using next-generation sequencing (NGS), we analyzed 61 genomic libraries belonging to 20 mosquito species to characterize the viral community. A total of 16 viral species were identified, representing 14 different viral families. Most identified viruses were associated with insects, plants, and fungi. Additionally, vertebrate associated viral families, including Herpesviridae, Peribunyaviridae, Nairoviridae, and Arenaviridae, were detected in mosquitoes from urban habitats. Notably, insect-associated viruses like Hubei mosquito virus 4 and Hubei virga-like virus 2 were identified, along with the first report of Mercadeo virus in Mexico. Variations in viral community composition were primarily driven by mosquito species, with species of the same genus maintaining similar viromes despite occupying different habitats. These findings reinforce that intrinsic traits of mosquito species play a key role in shaping viral community composition. To our knowledge, this is the first study that describes the viral community in mosquitoes in Yucatan Peninsula, Mexico. This study provides essential baseline data for the surveillance of mosquitoes and associated viruses from a biodiverse tropical region that faces strong land use modifications.},
}

Animals
Mexico
*Culicidae/virology
*Ecosystem
*Virome
*Mosquito Vectors/virology
*Viruses/classification/genetics/isolation & purification
High-Throughput Nucleotide Sequencing
Phylogeny
Genome, Viral
Biodiversity

@article {pmid40573347,
year = {2025},
author = {Pardo, I and Finamor, LPS and Marra, PS and Ferreira, JMG and Gutfreund, MC and Hsieh, MK and Li, Y and Pinho, JRR and Rizzo, LV and Kobayashi, T and Diekema, DJ and Edmond, MB and Bispo, PJM and Marra, AR},
title = {Metagenomic Next-Generation Sequencing for the Diagnosis of Infectious Uveitis: A Comprehensive Systematic Review.},
journal = {Viruses},
volume = {17},
number = {6},
pages = {},
doi = {10.3390/v17060757},
pmid = {40573347},
issn = {1999-4915},
mesh = {Humans ; *Metagenomics/methods ; *Uveitis/diagnosis/virology/microbiology/parasitology ; *High-Throughput Nucleotide Sequencing/methods ; Sensitivity and Specificity ; Toxoplasma/genetics ; },
abstract = {Background: Infectious uveitis is a potentially sight-threatening condition that requires timely and accurate pathogen identification to guide effective therapy. However, conventional microbiological tests (CMTs) often lack sensitivity and the inclusiveness of pathogen detection. Metagenomic next-generation sequencing (mNGS) offers an unbiased approach to detecting a broad range of pathogens. This review evaluates its diagnostic performance in detecting infectious uveitis. Methods: A systematic search across multiple databases identified studies assessing the use of mNGS for diagnosing infectious uveitis. The included studies compared mNGS to CMTs, including polymerase chain reaction (PCR), culture, serology, and the IGRA (Interferon-Gamma Release Assay). The study characteristics; the detection rates; and the sensitivity, specificity, and predictive values were extracted. The sensitivity and specificity of mNGS were calculated using CMTs as a reference. Results: Twelve studies comprising 859 patients were included. The sensitivity of mNGS compared to that of CMTs ranged from 38.4% to 100%, while specificity varied between 15.8% and 100%. The commonly detected pathogens included varicella-zoster virus, cytomegalovirus, Toxoplasma gondii, and herpes simplex virus. In some cases, mNGS outperformed PCR in viral detection, aiding diagnosis when the standard methods failed. However, contamination risks and inconsistent diagnostic thresholds were noted. Conclusions: mNGS enables the diagnosis of infectious uveitis, particularly for viral causes, but its variable performance and standardization challenges warrant further investigation.},
}

Humans
*Metagenomics/methods
*Uveitis/diagnosis/virology/microbiology/parasitology
*High-Throughput Nucleotide Sequencing/methods
Sensitivity and Specificity
Toxoplasma/genetics

@article {pmid40573336,
year = {2025},
author = {Žuštra, A and Howard, A and Schwartz, K and Day, R and Dietrich, J and Sobotyk, C and Kraberger, S and Varsani, A},
title = {Three Distinct Circovirids Identified in a Tapeworm Recovered from a Bobcat (Lynx rufus).},
journal = {Viruses},
volume = {17},
number = {6},
pages = {},
doi = {10.3390/v17060745},
pmid = {40573336},
issn = {1999-4915},
mesh = {Animals ; Phylogeny ; *Cestoda/virology ; Genome, Mitochondrial ; Genome, Viral ; Metagenomics ; Feces/virology ; },
abstract = {Bobcats (Lynx rufus) are an iconic North American predator; however, there is limited knowledge regarding their associated parasites. In this case study, we used a metagenomic approach to identify associated viruses and helminth species from a deceased bobcat. We determined the full mitochondrial genome of the bobcat and three helminths, i.e., tapeworm (Taenia sp.), stomach worm (Physaloptera sp.), and lung worm (Metathelazia sp.). Furthermore, we identified four circovirids; two (identified in a tapeworm and fecal swab) are members of the genus Circovirus and share 96.7% genome-wide identity between isolates and 87.4-88.6% identity with members of the species Circovirus miztontli. These appear to infect vertebrate species common to the Sonoran Desert, which could be a rodent preyed upon by the bobcat, and/or bobcat itself. The other two circovirids are novel members of the genus Cyclovirus (both identified in a tapeworm), one sharing 99.8% with those in the species Cyclovirus misi from a rodent and the other <67.3% with all other Cycloviruses. Our data support that these two Cycloviruses are likely tapeworm-infecting; however, more studies are needed to confirm the host. These findings enhance our understanding of viruses and helminths in bobcats, emphasizing the need for further research to unravel the ecology of parasites in these elusive predators.},
}

Animals
Phylogeny
*Cestoda/virology
Genome, Mitochondrial
Genome, Viral
Metagenomics
Feces/virology

@article {pmid40573190,
year = {2025},
author = {Ruiz-Álvarez, BE and Cattero, V and Desjardins, Y},
title = {Prebiotic-like Effects of Proanthocyanidin-Rich Aronia Extract Supplementation on Gut Microbiota Composition and Function in the Twin-M-SHIME[®] Model.},
journal = {Pharmaceuticals (Basel, Switzerland)},
volume = {18},
number = {6},
pages = {},
doi = {10.3390/ph18060793},
pmid = {40573190},
issn = {1424-8247},
support = {NSERC-Symrise Industrial Chair on prebiotic Effects of Fruits and Vegetables//Symrise/ ; },
abstract = {Background: Phenolic compounds, particularly anthocyanins and proanthocyanidins (PACs), are poorly absorbed in the upper digestive tract and reach the colon largely intact, where they may influence gut microbiota (GM) composition and, in turn, impact host health. We hypothesized that a PAC-rich aronia extract would beneficially modulate the GM, promote the growth of health-associated bacteria, and enhance short-chain fatty acid (SCFA) production across different colon sections, with partial reversion effects after supplementation ends. Methods: The Twin-M-SHIME[®] system was used to simulate the digestion and colonic fermentation in two donors with contrasting microbiota profiles. The experimental design included four phases: stabilization (14 days), control (7 days), treatment with 500 mg/day PAC-rich aronia extract (21 days), and wash-out (10 days). SCFA production was monitored, and changes in microbiome composition were assessed using 16S rRNA gene sequencing. Results: PAC-rich aronia extract significantly modulated SCFA levels, increasing butyrate and reducing acetate, with some inter-donor variability. SCFA concentrations tended to return to baseline after the wash-out (WO) period. Metagenomic analysis revealed a decrease in Collinsella, Sutterella, Selenomonas, and Parabacteroides-genera linked to low-fiber diets and gut inflammation-while promoting Proteobacteria (e.g., Escherichia-Shigella, Klebsiella) and butyrate-associated Firmicutes such as Lactiplantibacillus. Although some microbial shifts partially reverted during the wash-out (e.g., Akkermansia, Bacteroides, and Bifidobacterium), other changes persisted. Conclusions: These findings suggest that PAC-rich aronia extract beneficially modulates GM and SCFA production, but continuous intake may be necessary to maintain these effects over time.},
}

@article {pmid40572226,
year = {2025},
author = {Cho, HE and Kim, MJ and Choi, J and Sohn, YH and Lee, JJ and Park, KS and Cho, SY and Park, KH and Kim, YJ},
title = {Shotgun Metagenomic Sequencing Analysis as a Diagnostic Strategy for Patients with Lower Respiratory Tract Infections.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572226},
issn = {2076-2607},
support = {RS-2023-00246999//National Research Foundation of Korea/ ; },
abstract = {Conventional diagnostic methods (CDMs) for lower respiratory infections (LRIs) have limitations in detecting causative pathogens. This study evaluates the utility of shotgun metagenomic sequencing (SMS) as a complementary diagnostic tool using bronchoalveolar lavage (BAL) fluid. Sixteen BAL fluid samples from pneumonia patients with positive CDM results-including bacterial/fungal cultures; PCR for Mycobacterium tuberculosis or cytomegalovirus; and the BioFire[®] FilmArray[®] Pneumonia Panel (BioFire Diagnostics LLC, Salt Lake City, UT, USA)-underwent 10 Gb SMS on the Illumina NovaSeq 6000 platform (Illumina, San Diego, CA, USA). Reads were aligned to the NCBI RefSeq database; with fungal identification further supported by internal transcribed spacer (ITS) analysis. Antibiotic resistance genes (ARGs) were annotated using the Comprehensive Antibiotic Resistance Database. Microbial reads accounted for 0.00002-0.04971% per sample. SMS detected corresponding bacteria in 63% of cases, increasing to 69% when subdominant taxa were included. Fungal reads were low; however, Candida species were identified in four samples via ITS. No viral reads were detected. ARGs meeting perfect match criteria were found in two cases. This is the first real-world study comparing SMS with CDMs, including semiquantitative PCR, in BAL fluid for LRI. SMS shows promise as a supplementary diagnostic method, with further research needed to optimize its performance and cost-effectiveness.},
}

@article {pmid40572225,
year = {2025},
author = {Jiang, Y and Li, W and Li, J and Hu, J and Wei, Y and Wang, Y and Yang, H and Zhou, Y and Wu, Y and Zhang, S},
title = {Co-Inoculating Burkholderia vietnamiensis B418 and Trichoderma harzianum T11W Reduced Meloidogyne incognita Infestation of Tomato Plants.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572225},
issn = {2076-2607},
support = {ZR2021MC085//Shandong Provincial Natural Science Foundation/ ; 2022TSGC2370//Shandong Provincial Innovation Capability Promotion Project for Sci-tech Small and Medium-sized Enterprises/ ; 2024GH15//Innovation Pilot Project of Integration of Science, Education, and Industry of Shandong Academy of Sciences (International Scientific and Technology Cooperation)/ ; },
abstract = {Root-knot nematodes (RKNs; Meloidogyne incognita) pose a significant threat to tomato crops, necessitating sustainable control methods. This study investigated the inoculation efficacy of co-cultured Burkholderia vietnamiensis B418 and Trichoderma harzianum T11W compared with single-strain treatments for RKNs suppression and their influence on the structure and function of the rhizosphere microbiome. Co-inoculation with B418 + T11W achieved a 71.42% reduction in the disease index, significantly outperforming single inoculations of B418 (54.46%) and T11W (58.93%). Co-inoculation also increased plant height by 38.51% and fresh weight by 76.02% compared to the RKNs infested plants control, promoting robust tomato growth. Metagenomic analysis reveals that co-inoculation enhanced bacterial diversity, with 378 unique bacterial species and a high Shannon index, while fungal diversity decreased with Trichoderma dominance (83.31% abundance). Actinomycetota (46.42%) and Ascomycota (97.92%) were enriched in the co-inoculated rhizosphere, showing negative correlations with RKNs severity. Functional analysis indicates enriched metabolic pathways, including streptomycin and unsaturated fatty acid biosynthesis, enhancing microbial antagonism. Single inoculations altered pathways like steroid degradation (B418) and terpenoid biosynthesis (T11W), but co-inoculation uniquely optimized the rhizosphere microenvironment. These findings highlight co-inoculation with B418 + T11W effectively suppressing RKNs and fostering plant health by reshaping microbial communities and functions, offering a promising approach for sustainable agriculture.},
}

@article {pmid40572188,
year = {2025},
author = {Asao, K and Hashida, N},
title = {Overview of Microorganisms: Bacterial Microbiome, Mycobiome, Virome Identified Using Next-Generation Sequencing, and Their Application to Ophthalmic Diseases.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572188},
issn = {2076-2607},
support = {23K15906 [to K.A.]//the Japan Society for the Promotion of Science/ ; 21K09695 [to N.H.]//the Japan Society for the Promotion of Science/ ; },
abstract = {This review outlines technological advances in pathogen identification and describes the development and evolution of next-generation sequencers that can be applied to the ocular microbiome. Traditional methods such as culture and PCR have limitations in detecting the full spectrum of resident microorganisms, prompting a transition toward metagenomic analysis. As microbiome research expands across body systems, the comprehensive identification of ocular bacteria, fungi, and viruses has become possible. The commensal ocular microbiome may influence disease development through changes in the immune system and ocular environment. Next-generation sequencing enables detailed microbial profiling, aiding in disease diagnosis and treatment selection. Alterations in the microbiome may also induce metabolic changes, offering insights into novel treatment methods. This review outlines the evolution of next-generation sequencing technology, summarizes current knowledge of microorganisms found on the ocular surface and in intraocular fluid, and discusses future challenges and prospects. However, the large volume of microbiome data obtained must be interpreted with caution due to possible analytical biases. Furthermore, determining whether the microbiome is truly pathogenic requires comprehensive interpretation beyond the clinical findings and results of traditional identification methods.},
}

@article {pmid40572136,
year = {2025},
author = {Shi, M and Zhang, L and Sun, H and Ji, S and Cui, H and Wan, W and Liu, X and Tian, A and Yang, W and Wang, X and Yang, F and Jin, S},
title = {The Plant Growth-Promoting Bacterium Bacillus cereus LpBc-47 Can Alleviate the Damage of Saline-Alkali Stress to Lilium pumilum.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572136},
issn = {2076-2607},
support = {([2023] 1197)//Heilongjiang Province Agriculture Research System-Ecological Agriculture/ ; [LJGXCG2023-036]//Heilongjiang Province "Double First Class" Discipline Collaborative Innovation Achievement Project/ ; },
abstract = {Soil salinization severely impacts plant cultivation. Lilium pumilum (L. pumilum) exhibits tolerance to saline-alkali stresses. One Bacillus cereus strain, LpBc-47, possesses the ability of growth promotion and saline-alkali tolerance. The microbial diversity of L. pumilum was assessed through metagenomic sequencing. LpBC-47 obtained from L. pumilum was subjected to physiological and biochemical analyses and whole-genome sequencing. The effects of endophytic bacteria on plants were evaluated by measuring growth parameters, physiological indices, antioxidant enzyme activities, and ROS content. Microbial diversity analysis revealed that the abundance of endophytic bacteria in L. pumilum decreased under saline-alkali conditions, whereas the abundance of Bacillus cereus increased. Physiological and biochemical analysis showed that LpBC-47 has the characteristics of promoting growth and reducing plant damage caused by salt-alkali stress, such as phosphorus solubilization, nitrogen fixation, siderophore production, IAA, and ACC deaminase synthesis. Genomic analysis revealed that LpBC-47 contains growth-associated and stress-alleviation genes. GFP indicated the colonization of LpBc-47 in the roots and bulbs of L. pumilum. The LpBc-47 inoculant plant increased leaf length and dry weight, elevated proline and chlorophyll levels, enhanced antioxidant enzyme activity, and reduced oxidative damage. This study highlights the potential of LpBc-47 for improving plant growth under saline-alkali conditions.},
}

@article {pmid40572128,
year = {2025},
author = {Strike, W and Faleye, TOC and Lubega, B and Rockward, A and Torabi, S and Noble, A and Banadaki, MD and Keck, J and Mugerwa, H and Scotch, M and Berry, S},
title = {Implementing Wastewater-Based Epidemiology for Long-Read Metagenomic Sequencing of Antimicrobial Resistance in Kampala, Uganda.},
journal = {Microorganisms},
volume = {13},
number = {6},
pages = {},
pmid = {40572128},
issn = {2076-2607},
support = {1U01DA053903-01/NH/NIH HHS/United States ; 1P30ES026529-01/NH/NIH HHS/United States ; BAA 75D301-20-R-68024/CC/CDC HHS/United States ; 2154934//U.S. National Science Foundation/ ; 2412446//U.S. National Science Foundation/ ; },
abstract = {Antimicrobial resistance (AMR) is an emerging global threat that is expanding in many areas of the world. Wastewater-based epidemiology (WBE) is uniquely suited for use in areas of the world where clinical surveillance is limited or logistically slow to identify emerging threats, such as in Sub-Saharan Africa (SSA). Wastewater was analyzed from three urban areas of Kampala, including a local HIV research clinic and two informal settlements. Wastewater extraction was performed using a low-cost, magnetic bead-based protocol that minimizes consumable plastic consumption followed by sequencing on the Oxford Nanopore Technology MinION platform. The majority of the analysis was performed using cloud-based services to identify AMR biomarkers and bacterial pathogens. Assemblies containing AMR pathogens were isolated from all locations. As one example, clinically relevant AMR biomarkers for multiple drug classes were found within Acinetobacter baumannii genomic fragments. This work presents a metagenomic WBE workflow that is compatible with areas of the world without robust water treatment infrastructure. This study was able to identify various bacterial pathogens and AMR biomarkers without shipping water samples internationally or relying on complex concentration methods. Due to the time-dependent nature of wastewater surveillance data, this work involved cross-training researchers in Uganda to collect and analyze wastewater for future efforts in public health development.},
}

@article {pmid40572043,
year = {2025},
author = {Yang, C and Sun, J and Li, L and Zheng, J and Wang, C and Zhao, Y and Yun, D and Jia, M and Wu, Z and Liang, H and Li, W and Hu, T and Guo, R and Xiao, L and Zou, Y and Liu, Z},
title = {Synbiotics of Lactobacillus suilingensis and inulin alleviates cognitive impairment via regulating gut microbiota indole-3-lactic acid metabolism in female AD mice.},
journal = {Alzheimer's & dementia : the journal of the Alzheimer's Association},
volume = {21},
number = {7},
pages = {e70406},
doi = {10.1002/alz.70406},
pmid = {40572043},
issn = {1552-5279},
support = {2022ZD0208100//National Science and Technology Innovation 2030-Major Program of Brain Science and Brain-Like Research/ ; 32241012//National Natural Science Foundation of China/ ; 32472351//National Natural Science Foundation of China/ ; JCYJ20220818102810022//Shenzhen Science and Technology Program/ ; XMHT20220104017//Shenzhen Municipal Government of China/ ; 2022A1515110717//Regional Consolidated Fund-Youth Fund Project in Guangdong Province/ ; BGIRSZ20220009//open project of BGI-shenzhen/ ; //China Biotechnology Development Center/ ; //Shenzhen Science and Technology Innovation Commission/ ; //Shenzhen Municipal Government/ ; //Guangdong Basic and Applied Basic Research Foundation/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Inulin/pharmacology/administration & dosage ; Female ; *Cognitive Dysfunction/metabolism ; Mice ; *Synbiotics/administration & dosage ; *Indoles/metabolism ; *Alzheimer Disease/metabolism ; Humans ; Tryptophan/metabolism ; Disease Models, Animal ; Receptors, Aryl Hydrocarbon/metabolism ; Probiotics ; },
abstract = {INTRODUCTION: Recent studies have found that gut microbial tryptophan metabolism is altered in Alzheimer's disease (AD) patients. However, the functional consequences of these changes and their therapeutic potential remain unclear.

METHODS: The metagenomic data of 49 preclinical AD patients and 115 healthy controls were analyzed. A synbiotic with targeted metabolic functions was formulated based on in vitro testing, and its effect on AD was evaluated using female 5×FAD mice.

RESULTS: Indole lactic acid (ILA) synthesis was downregulated in AD patients. Synbiotic treatment combining Lactobacillus suilingensis and inulin outperformed probiotic treatment alone in enhancing tryptophan metabolism, and increasing ILA biosynthesis. Increased ILA could reduce Aβ accumulation and significantly alleviate cognitive impairment in female AD mice by inhibiting neuroinflammation through activation of the aryl hydrocarbon receptor (AhR) signaling pathway.

DISCUSSION: This study highlights the therapeutic potential of targeting gut microbial tryptophan metabolism in AD and provides a rationale for future precision strategies aimed at modulating microbiota-derived metabolic pathways.

HIGHLIGHTS: Gut metagenomic analysis reveals reduced indole lactic acid (ILA) biosynthesis genes in preclinical AD patients. Screening and formulating ILA-producing synbiotic by using whole-genome analysis. Synbiotic treatment alleviates cognitive impairment and promotes ILA synthesis in female 5×FAD mice. ILA alleviates neuroinflammation in female 5×FAD mice by activating aryl hydrocarbon receptor (AhR) in the brain. Synbiotic targeting tryptophan metabolism provides a novel approach for Alzheimer's intervention.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Inulin/pharmacology/administration & dosage
Female
*Cognitive Dysfunction/metabolism
Mice
*Synbiotics/administration & dosage
*Indoles/metabolism
*Alzheimer Disease/metabolism
Humans
Tryptophan/metabolism
Disease Models, Animal
Receptors, Aryl Hydrocarbon/metabolism
Probiotics

@article {pmid40571109,
year = {2025},
author = {Chen, H and Qiu, X and Lei, S and Zhao, Y and Zhang, M and Gao, M and Guo, R and Di, H and Huang, J and Yu, Z},
title = {Gut vs. Vaginal Microbiome in Diabetes Progression: Key Microbial Shifts and Implications.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {107833},
doi = {10.1016/j.micpath.2025.107833},
pmid = {40571109},
issn = {1096-1208},
abstract = {BACKGROUND: Dysiosis in gut and vaginal microbiome is implicated in type 2 diabetes (T2D) pathogenesis, but their contributions remain unclear. This study aims to compare their alterations and clinical relevance in diabetes development.

METHODS: Metagenomic sequencing was performed on vaginal and fecal samples from T2D patients. Differential feature selection and correlation model were used to dissect microbial contributions to diabetic markers.

RESULTS: Gut microbiota exhibited reduced diversity in T2D patients, with enrichment of Desulfovibrio desulfuricans and Adlercreutzia equolifaciens validated in public cohorts. Vaginal microbiota diversity remained unaffected. Furthermore, structural equation modeling revealed stronger gut microbiota associations with blood glucose and HbA1c. Notably, Romboutsia ilealis-derived pgm was enriched in the diabetes group, which could catalyze the production of glucose, suggesting that it may be involved in the progression of T2D.

CONCLUSION: Our findings establish the gut microbiome as the dominant driver of T2D progression, with R. ilealis emerging as a potential therapeutic target. This highlights the priority of gut-centric microbiota interventions in diabetes management.},
}

@article {pmid40571107,
year = {2025},
author = {Chen, J and Chen, Z and Xu, B and Huang, Z and Zhang, C},
title = {Skin microbiome of Asian elephants with skin diseases during seasonal transitions.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {107832},
doi = {10.1016/j.micpath.2025.107832},
pmid = {40571107},
issn = {1096-1208},
abstract = {INTRODUCTION: Wild Asian elephants (Elephas maximus), which are an endangered species, often suffer from skin diseases during seasonal transitions, which seriously affect their health. Understanding the pathogenesis of such skin diseases is critical for their prevention and treatment. It is known that skin microorganisms are closely related to host skin health.

OBJECTIVE: To compare the microbiotas and microbiomes of diseased and healthy skin of Asian elephants.

METHODS: DNA was extracted from skin swab samples from diseased and healthy Asian elephants for metagenomic sequencing. Various bioinformatic tools were used to process the raw sequencing data and identify gene sequences for functional annotation and species identification as well as to determine species abundance. Antibiotic resistance genes and virulence factors were also identified using DIAMOND.

RESULTS: Staphylococcus was highly enriched in the microbiota of diseased skin, whereas Leuconostoc predominated in that of healthy skin. Moreover, substantial differences existed between the two elephant skin groups in terms of metabolic pathways related to ATP-binding cassette transporters and TCSs and the abundance of antibiotic resistance genes and Staphylococcus-associated toxins. The substantial difference in Staphylococcus-related virulence factors was likely due to the significant enrichment of Staphylococcus in the diseased skin samples, suggesting that this bacterial genus is the causative agent of skin diseases in Asian elephants. Additionally, Leuconostoc mesenteroides, which was enriched in the healthy skin samples, has anti-inflammatory, antimicrobial, and other beneficial effects that have promising applications in the prevention, diagnosis, and treatment of skin diseases.

CONCLUSION: This study reveals the cause of skin diseases in Asian elephants and provides a theoretical basis for improving the skin health of wild animals and expanding wildlife conservation methods and technologies.},
}

@article {pmid40570964,
year = {2025},
author = {Fishman, JA and El Khoury, J and Kawai, T and Riella, LV and Elias, N and Williams, W and Crisalli, KA and Hashimoto, D and Bercovici, S and Lindner, M and Noll, N and Balasundaram, G and Getchell, K and Low, S and Scales, B and Chhangawala, S and Marett, A and Curtis, M and Yeung, V},
title = {Infectious Disease Surveillance and Management in Clinical Xenotransplantation: Experience with the First Human Porcine Kidney Transplant.},
journal = {American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajt.2025.06.016},
pmid = {40570964},
issn = {1600-6143},
abstract = {The success and safety of clinical xenotransplantation are determined by technical aspects of surgery, the nature and intensity of immunosuppression, xenograft function, and the ability to avoid immunologic, hematologic, infectious and malignant complications. In clinical xenotransplantation from swine, infectious challenges relate to the potential spread of pig pathogens to immunosuppressed humans as well as manifestations of infections of the recipient from prior exposures to common human organisms. Robust strategies are required for donor screening, recipient monitoring, and infection prevention. This report outlines the comprehensive infectious disease management strategy deployed in the first living human recipient of a genetically modified pig kidney, including (1) donor screening and pathogen mitigation, (2) pre- and post-transplant infection monitoring of the recipient, (3) infectious complications and management, with (4) implications for future xenotransplantation protocols.},
}

@article {pmid40570762,
year = {2025},
author = {Pateriya, D and Malwe, AS and Sharma, VK},
title = {CRCpred: An AI-ML tool for colorectal cancer prediction using gut microbiome.},
journal = {Computers in biology and medicine},
volume = {195},
number = {},
pages = {110592},
doi = {10.1016/j.compbiomed.2025.110592},
pmid = {40570762},
issn = {1879-0534},
abstract = {Colorectal cancer (CRC) is a leading cause of death worldwide. A plethora of research shows the alteration of the gut microbiome and the association of bacterial taxa with CRC. Gaining insights into the health status through microbiome-based diagnosis is a rapidly growing area of research. Many studies have utilized machine learning (ML) to leverage gut microbial dysbiosis for CRC screening, yet most have been limited by their training data and algorithms. Here, using 1728 publicly available metagenomic samples from 11 studies across eight countries, we developed a web-based tool, "CRCpred," employing ML and deep learning-based hybrid algorithms for CRC prediction. The XGBoost algorithm demonstrated the highest performance, achieving an average area under the curve (AUC) of 0.90 on the test and 0.91 on the validation datasets. Our results highlight the utility of CRCpred in predicting CRC and healthy status using gut bacterial species relative abundance profile. CRCpred is publicly available at https://metabiosys.iiserb.ac.in/crcpred.},
}

@article {pmid40570628,
year = {2025},
author = {Hu, F and Zhang, W and Chen, P and Yuan, Z and Ye, J and Xu, Z},
title = {Glucose as a dual-functional co-substrate in intimately coupled photocatalysis and biodegradation systems: Synergistic enhancement of refractory organics mineralization and nitrate removal.},
journal = {Journal of hazardous materials},
volume = {495},
number = {},
pages = {138975},
doi = {10.1016/j.jhazmat.2025.138975},
pmid = {40570628},
issn = {1873-3336},
abstract = {Nitrate contamination threatens water quality and human health; however, conventional denitrification treatment strategies struggle in complex wastewater due to the low bioavailability of refractory organics. The intimately coupled photocatalysis and biodegradation (ICPB) system addresses this by transforming recalcitrant compounds into usable electron donors, enabling simultaneous nitrate and organic pollutant removal. This study demonstrates that adding a small dose of glucose (50 mg/L chemical oxygen demand) to the ICPB system enhanced performance by increasing organic mineralization from 53 % to 81 % and total nitrate and nitrite removal from 40 % to 93 %. Supplementing the ICPB system with glucose significantly stimulated microbial activity. The heightened activity accelerated the mineralization of photocatalytically-derived intermediates, preventing toxic byproduct accumulation. Microbial inhibition was reduced from 68 % to 20 %, further enhancing the pollutant removal efficiency of the ICPB system. Additionally, glucose functioned as an auxiliary electron donor, concurrently enhancing denitrification. Metagenomic analysis suggested that riboflavin biosynthesis upregulation may have promoted electron transfer, potentially boosting system efficiency. This strategy offers a simple and effective means to optimize the synergistic removal of refractory organics and nitrate during wastewater treatment.},
}

@article {pmid40570627,
year = {2025},
author = {Li, YQ and Zhang, CM and Ma, H and Shao, KJ and Yuan, PH and Jiang, HY},
title = {Antiallergic drugs drive the alteration of microbial community and antibiotic resistome in surface waters: A metagenomic perspective.},
journal = {Journal of hazardous materials},
volume = {495},
number = {},
pages = {139028},
doi = {10.1016/j.jhazmat.2025.139028},
pmid = {40570627},
issn = {1873-3336},
abstract = {Antiallergic drugs (AADs) are emerging contaminants of global concern due to their environmental persistence and potential ecological impacts. This study investigated the effects of seven AADs (chlorpheniramine, diphenhydramine, cetirizine, loratadine, desloratadine, sodium cromoglicate and calcium gluconate) at environmentally relevant concentrations on antibiotic resistome and bacterial community structures in water using microcosm experiments and metagenomic sequencing. The results showed that AADs increased the abundance of antibiotic-resistant bacteria (ARB) by 1.24- to 7.78-fold. Community structure shifts indicated that chlorpheniramine, diphenhydramine, and cetirizine promoted Actinobacteria (e.g., Aurantimicrobium), while the other four AADs favored Proteobacteria (e.g., Limnohabitans). AADs also significantly altered the relative abundance of antibiotic resistance genes (ARGs), with Actinobacteria and Proteobacteria identified as key ARB components and potential hosts of ARGs (e.g., evgS, mtrA, RanA). Host analysis showed ARGs were primarily carried by Actinobacteria (e.g., Aurantimicrobium) under chlorpheniramine, diphenhydramine, and cetirizine exposure, but by Proteobacteria (e.g., Limnohabitans) under the other four AADs. Furthermore, AADs facilitated the horizontal transfer of ARGs (e.g., evgS) within microbial communities, contributing to antibiotic resistance dissemination. This study highlights the ecological risks of AADs in promoting antibiotic resistance spread and provides new insights into their impact on microbial communities and resistome dynamics in aquatic environments.},
}

@article {pmid40570498,
year = {2025},
author = {Zhang, X and Jiao, P and Li, B and Zhang, XX and Ma, L},
title = {Phage lysis-mediated reduction of antibiotic-resistant bacteria alleviates micro/nanoplastic-driven antimicrobial resistance dissemination in anaerobic digestion.},
journal = {Water research},
volume = {285},
number = {},
pages = {124046},
doi = {10.1016/j.watres.2025.124046},
pmid = {40570498},
issn = {1879-2448},
abstract = {Micro/nanoplastics (MPs/NPs) prevalent in anaerobic digestion (AD) have posed escalating threats to antimicrobial resistance (AMR) dissemination, yet mechanistic insights remain insufficient. Here we investigated polypropylene (PP)-MPs (200 μm) and PP-NPs (100 nm) at environmentally relevant concentrations (10, 50, and 100 mg/g TS) on antibiotic resistance gene (ARG) dynamics and transfer mechanisms using metagenomics and bioinformatic modeling. PP-MPs/NPs significantly elevated (6.4-17.8 %, p < 0.05) ARG abundance through selective enrichment of aminoglycoside, mupirocin, multidrug, polymyxin, sulfonamide, tetracycline, and novobiocin ARGs. Metagenomic assembly revealed the particle-induced ecological niche specialization of antibiotic-resistant bacteria (ARB), notably the multi-resistant ESKAPE pathogen Enterobacter hormaechei (53.4-69.4 % enrichment, p < 0.05), which harbored mobile aadA, qacEdelta1, and sul1 via conjugative plasmids. Mechanistically, MPs/NPs facilitated horizontal gene transfer (HGT) through synergism of plasmids and phages. The enhanced abundance of conjugation elements, enriched plasmid-borne ARGs, and extensive HGT events promoted plasmid-conjugative transfer, while the strongly correlated ARG-carrying lysogenic phage-host pairs highlighted phage-mediated transfer under MPs/NPs. The significant increase of phage-to-host-ratio (1.0-1.2 folds) revealed the underestimated role of phages lysing ARB under MPs/NPs stress, thereby contributing to ARG load reduction. A novel risk assessment framework prioritizing prevalence, enrichment, mobility, and host pathogenicity identified dfrA3, mefB, OXA-347, and tet44 as high-risk biomarkers and quantified 1.5-9.9 % increased health risks in digestate-exposed scenarios. These findings reveal the neglected role of phage lysis driving ARG reduction, providing actionable targets for mitigating plastic-driven resistance in AD.},
}

@article {pmid40570497,
year = {2025},
author = {Thornton, M and Eder, G and Amman, F and Pantielieieva, A and Vierheilig, J and Bergthaler, A},
title = {Comparative wastewater virome analysis with different enrichment methods.},
journal = {Water research},
volume = {285},
number = {},
pages = {123985},
doi = {10.1016/j.watres.2025.123985},
pmid = {40570497},
issn = {1879-2448},
abstract = {Wastewater-based epidemiology (WBE) has proven its value for public health. Physical concentration of virus particles is a crucial step for WBE to permit a sensitive and unbiased characterization of the catchment virome. Here we evaluate five different virion concentration techniques, including polyethylene glycol precipitation (PEG), vacuum-based direct capture (VDC), ultrafiltration (UF), NanoTrap® (NT), and membrane adsorption (MEM) for their suitability to concentrate a wide variety of viral taxa from raw wastewater for PCR detection and sequencing-based metagenomic readouts. We found that to capture a taxonomically diverse virome from wastewater, PEG and VDC outperform all other methods tested in enrichment rates, reproducibility, species detection, and captured nucleotide diversity. We observed that different methods exhibit variable concentration efficiencies across taxonomic groups in a reproducible manner, though we could not identify common physiochemical attributes driving this difference. We conclude that both PEG and VDC are equally capable at detecting and enriching a broad range of viral taxa, boosting the genomic information potential and reducing blind spots relative to other tested methods. These results advance WBE towards capturing the complex wastewater virome and help guide protocol choices for potential future viral threats.},
}

@article {pmid40570415,
year = {2025},
author = {Yin, Z and Cao, K and Duan, N and Zhang, Z},
title = {Microbial community dynamics and functional potential during the natural fermentation of rose: A metagenomic and volatile compound analysis.},
journal = {Enzyme and microbial technology},
volume = {190},
number = {},
pages = {110703},
doi = {10.1016/j.enzmictec.2025.110703},
pmid = {40570415},
issn = {1879-0909},
abstract = {This study investigates the dynamics of microbial communities and their functional characteristics during the natural fermentation of roses. Utilizing metagenomic sequencing and volatile compound analysis, the research elucidates the succession of microbial communities and their relationship with the flavor compound production. The findings indicate that Klebsiella and Pichia are predominant in the early stages of fermentation, while Acetobacter and Cyberlindnera become more abundant in the middle and later stages. The glycosyltransferase (GT) family is identified as the primary carbohydrate-active enzyme (CAZy) family involved in fermentation, with GT1 and GT2 exhibiting a higher gene abundance. Functional genes are predominantly associated with the carbohydrate and amino acid metabolism. Analysis of volatile compounds reveals that substances such as phenethyl acetate and (S,S)-2,3-Butanediol are closely related to the structure of the microbial community. These findings contribute to a deeper understanding of the mechanisms underlying rose fermentation and offer a theoretical foundation for technological advancements in the rose product industry.},
}

@article {pmid40570391,
year = {2025},
author = {Holm, RH and Chigwechokha, P and Strike, WD and Nyirenda, RL and Tandwe, C and Noble, A and Keck, J and Berry, S},
title = {Multi-pathogen wastewater surveillance in Malawi: An assessment of culture-based, RT-PCR, and long-read metagenomics methods with multiple ongoing outbreaks.},
journal = {The Science of the total environment},
volume = {992},
number = {},
pages = {179946},
doi = {10.1016/j.scitotenv.2025.179946},
pmid = {40570391},
issn = {1879-1026},
abstract = {There is little infrastructure for human disease testing apart from rapid malaria diagnostic tests in many low- and middle-income countries of sub-Saharan Africa outside major referral hospitals, and animal testing is also limited. Eight pathogens were studied in wastewater and environmental surveillance (WES) sites in Malawi with identified locally relevant disease prevalence: influenza A virus, influenza B virus, measles virus, respiratory syncytial virus, Salmonella Typhi, SARS-CoV-2, Vibrio cholerae, and yellow fever virus. Culture-based inoculation onto plates, single-plex RT-PCR, and/or Oxford Nanopore Technologies MinION genomics methods were used for a real-world assessment. This analysis included 20 grab samples from three locations over 4-weeks. Three samples tested positive for V. cholerae using culture-based methods, the only pathogen analyzed using this method. In 14 of the 20 samples, at least one pathogen was detected using PCR. Genomic analysis was conducted on 12 samples; V. cholerae was detected in eight samples, but Salmonella Typhi was not detected. V. cholerae was a clear case of disconnection between methods for the same sample during an outbreak period: 3/20 detected by culture, 1/20 detected by PCR (ctxAB), 3/20 detected by PCR (hlyA), and 8/12 detected by genomics. S. Typhi was the most frequently detected pathogen via PCR (10/20 detections) but was not detected by genomics. Influenza B, measles, SARS-CoV-2, and yellow fever viruses were determined to not be detected (Ct > 40) in the samples studied. This study demonstrated discrepancies in multi-pathogen WES detection across the three methods and highlights the need for further investigation into the limitations of their portability in local, low-resource, laboratories. This presents a valuable learning opportunity in regions experiencing ongoing outbreaks.},
}

@article {pmid40570246,
year = {2025},
author = {Ma, C and Bao, Y and Hereid, S and Zhang, H and Bai, X and Bai, Q and Zhao, L and Zhang, X and Lian, H and Dai, L and Bao, X and Bao, L},
title = {Mechanistic Elucidation of Tricholoma mongolicum Polysaccharides in Treating MAFLD via Regulation of the Gut Microbiota-Metabolite-Ferroptosis Axis: A Multi-Omics Perspective.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c05877},
pmid = {40570246},
issn = {1520-5118},
abstract = {This study aimed to elucidate the modulatory effects and underlying molecular mechanisms of Tricholoma mongolicum polysaccharide (TMP) in the context of metabolic dysfunction-associated fatty liver disease (MAFLD). High-performance gel permeation chromatography (HPGPC) analysis indicated a bimodal molecular weight distribution. Monosaccharide composition profiling revealed a predominance of glucose and galactose among other constituents. Scanning electron microscopy (SEM) illustrated a porous, aggregated colloidal microstructure. In a model of MAFLD, TMP intervention significantly attenuated serum levels of TC, TG, and AST, ALT, accompanied by notable histological improvements, including reduced hepatic steatosis and inflammatory cell infiltration. Metagenomic analysis demonstrated that TMP substantially enhanced gut microbial α-diversity, restructured microbial community composition, decreased the Firmicutes/Bacteroidetes ratio, enriched SCFAs-producing genera, and suppressed the excessive proliferation of pro-inflammatory bacterial genera. Integrated proteomic and lipidomic analyses revealed that TMP inhibited hepatic immune-inflammatory responses and ferroptosis pathways, enhanced pathways associated with metabolic homeostasis. Furthermore, TMP modulated hepatic iron metabolism by upregulating the Nrf2/GPx4 antioxidant axis and FPN1 while downregulating TFR1, thereby alleviating oxidative stress and iron overload. These findings demonstrate that TMP exerts therapeutic efficacy through a bidirectional gut-liver regulatory mechanism involving microbial modulation, ferroptosis inhibition, metabolic reprogramming, and activation of antioxidant defenses. This research provides novel insights and molecular targets for the development of natural polysaccharide-based interventions for MAFLD.},
}

@article {pmid40570071,
year = {2025},
author = {Savelieva, EI and Shachneva, MD},
title = {Problems and prospects of metabolomic studies in the alteration of the gut microbiome.},
journal = {Biomeditsinskaia khimiia},
volume = {71},
number = {3},
pages = {195-208},
doi = {10.18097/PBMCR1556},
pmid = {40570071},
issn = {2310-6972},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Metabolomics/methods ; *Metabolome ; Animals ; Bile Acids and Salts/metabolism ; *Renal Insufficiency, Chronic/microbiology/metabolism ; Fatty Acids, Volatile/metabolism ; },
abstract = {The review summarizes existing knowledge on the relationship between certain diseases and alteration (degeneration) of the intestinal microbiome. We consider major microbial metabolites firmly recognized as signaling molecules acting in communication between the microbiome and the host organism. These include short-chain fatty acids, bile acids, amines, amino acids, and their metabolites. Special attention is paid to metabolomic studies of the microbiome in chronic kidney diseases, in particular, immunoglobulin A nephropathy. The arguments supporting a concept of the microbiome of blood, previously considered an exclusively sterile environment in healthy humans, are considered. Metagenomic methods plays a key role in characterization of both the composition and potential physiological effects of microbial communities. The advantages and limitations of metabolomic analysis of blood serum/plasma and feces have been analyzed. Since the potential of clinical studies of the mutual impact of the microbiome-metabolome is limited by genetic and external factors, preclinical studies still employ both germ-free models and models based on the effects of antibiotics. The review considers the problems and prospects of metabolomics in studying the nature and mechanisms of the mutual impact of the microbiome and metabolome.},
}

Humans
*Gastrointestinal Microbiome
*Metabolomics/methods
*Metabolome
Animals
Bile Acids and Salts/metabolism
*Renal Insufficiency, Chronic/microbiology/metabolism
Fatty Acids, Volatile/metabolism

@article {pmid40569902,
year = {2025},
author = {Belheouane, M and Kalsdorf, B and Niemann, S and Gaede, KI and Lange, C and Heyckendorf, J and Merker, M},
title = {Serratia sp. traits distinguish the lung microbiome of patients with tuberculosis and non-tuberculous mycobacterial lung diseases.},
journal = {PloS one},
volume = {20},
number = {6},
pages = {e0325362},
pmid = {40569902},
issn = {1932-6203},
mesh = {Humans ; *Microbiota/genetics ; Male ; Middle Aged ; *Lung/microbiology ; RNA, Ribosomal, 16S/genetics ; Female ; Adult ; *Serratia/genetics/isolation & purification/classification ; Bronchoalveolar Lavage Fluid/microbiology ; Aged ; *Mycobacterium Infections, Nontuberculous/microbiology ; Nontuberculous Mycobacteria/genetics ; *Tuberculosis, Pulmonary/microbiology ; *Lung Diseases/microbiology ; },
abstract = {BACKGROUND: Pathogenic mycobacteria, such as Mycobacterium tuberculosis complex (Mtbc), and non-tuberculous mycobacteria (NTMs) can cause severe chronic pulmonary infections. However, not all infected patients develop active disease, and it remains unclear whether key lung microbiome taxa play a role in the pathogenesis of tuberculosis (TB) and NTM lung diseases (LD). Here, we aim to further define the lung microbiome composition in TB, and NTM-LD prior to the initiation of therapy.

STUDY DESIGN: We employed 16S rRNA amplicon sequencing to characterize the baseline microbiome in bronchoalveolar lavage fluid (BALF) from patients diagnosed with TB (n = 23), NTM-LD (n = 19), or non-infectious inflammatory disease (n = 4). We applied depletion of human cells, removal of extracellular DNA, implementation of a decontamination strategy, and exploratory whole-metagenome sequencing (WMS) of selected specimens.

RESULTS: Genera Serratia and unclassified Yersiniaceae dominated the lung microbiome of most patients with a mean relative abundance of >15% and >70%, respectively. However, at the sub-genus level, as determined by amplicon sequence variants (ASVs), TB-patients exhibited increased community diversity, and distinct signatures of ASV_7, ASV_21 abundances which resulted in a significant association with disease state. Exploratory WMS, and ASV similarity analyses suggested the presence of Serratia liquefaciens, Serratia grimesii, Serratia myotis and/or Serratia quinivorans in TB and NTM-LD patients.

CONCLUSIONS: The lung microbiome of TB-patients harbored a distinct, and heterogenous structure, with specific occurrences of certain Serratia traits. Some of these traits may play a role in understanding the microbial interactions in the lung microbiome of patients infected with Mtbc.},
}

Humans
*Microbiota/genetics
Male
Middle Aged
*Lung/microbiology
RNA, Ribosomal, 16S/genetics
Female
Adult
*Serratia/genetics/isolation & purification/classification
Bronchoalveolar Lavage Fluid/microbiology
Aged
*Mycobacterium Infections, Nontuberculous/microbiology
Nontuberculous Mycobacteria/genetics
*Tuberculosis, Pulmonary/microbiology
*Lung Diseases/microbiology

@article {pmid40569694,
year = {2025},
author = {Kasmanas, JC and Magnúsdóttir, S and Zhang, J and Smalla, K and Schloter, M and Stadler, PF and de Leon Ferreira de Carvalho, ACP and Rocha, U},
title = {Integrating comparative genomics and risk classification by assessing virulence, antimicrobial resistance, and plasmid spread in microbial communities with gSpreadComp.},
journal = {GigaScience},
volume = {14},
number = {},
pages = {},
pmid = {40569694},
issn = {2047-217X},
support = {2019/03,396-9//São Paulo Research Foundation/ ; 2022/03,534-5//São Paulo Research Foundation/ ; //Deutsche Forschungsgemeinschaft/ ; //International Development Research Centre/ ; },
mesh = {*Plasmids/genetics ; Humans ; *Genomics/methods ; Virulence/genetics ; *Drug Resistance, Bacterial/genetics ; Gastrointestinal Microbiome/genetics ; Virulence Factors/genetics ; Computational Biology/methods ; Software ; Genome, Bacterial ; *Bacteria/genetics/pathogenicity/drug effects ; },
abstract = {BACKGROUND: Comparative genomics, genetic spread analysis, and context-aware ranking are crucial in understanding microbial dynamics' impact on public health. gSpreadComp streamlines the path from in silico analysis to hypothesis generation. By integrating comparative genomics, genome annotation, normalization, plasmid-mediated gene transfer, and microbial resistance-virulence risk-ranking into a unified workflow, gSpreadComp facilitates hypothesis generation from complex microbial datasets.

FINDINGS: The gSpreadComp workflow works through 6 modular steps: taxonomy assignment, genome quality estimation, antimicrobial resistance (AMR) gene annotation, plasmid/chromosome classification, virulence factor annotation, and downstream analysis. Our workflow calculates gene spread using normalized weighted average prevalence and ranks potential resistance-virulence risk by integrating microbial resistance, virulence, and plasmid transmissibility data and producing an HTML report. As a use case, we analyzed 3,566 metagenome-assembled genomes recovered from human gut microbiomes across diets. Our findings indicated consistent AMR across diets, with diet-specific resistance patterns, such as increased bacitracin in vegans and tetracycline in omnivores. Notably, ketogenic diets showed a slightly higher resistance-virulence rank, while vegan and vegetarian diets encompassed more plasmid-mediated gene transfer.

CONCLUSIONS: The gSpreadComp workflow aims to facilitate hypothesis generation for targeted experimental validations by the identification of concerning resistant hotspots in complex microbial datasets. Our study raises attention to a more thorough study of the critical role of diet in microbial community dynamics and the spread of AMR. This research underscores the importance of integrating genomic data into public health strategies to combat AMR. The gSpreadComp workflow is available at https://github.com/mdsufz/gSpreadComp/.},
}

*Plasmids/genetics
Humans
*Genomics/methods
Virulence/genetics
*Drug Resistance, Bacterial/genetics
Gastrointestinal Microbiome/genetics
Virulence Factors/genetics
Computational Biology/methods
Software
Genome, Bacterial
*Bacteria/genetics/pathogenicity/drug effects

@article {pmid40569093,
year = {2025},
author = {Brown, L and Hoa, NT and Ly, VT and Li, L and Cao, C and Youngchim, S and Chayakulkeeree, M and Bicanic, T and Chan, JF and Yuen, KY and Le, T},
title = {Recent Advances in the Diagnosis of Talaromycosis.},
journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America},
volume = {},
number = {},
pages = {},
doi = {10.1093/cid/ciaf253},
pmid = {40569093},
issn = {1537-6591},
support = {//National Institute for Health Research/ ; //Federation of European Microbiological Societies/ ; //Dowager Countess Eleanor Peel Trust/ ; //British Society for Medical Mycology/ ; //Wingate Foundation/ ; R01 AI181764-01//National Institutes of Allergy and Infectious Diseases/ ; R01AI177098-02//National Institutes of Allergy and Infectious Diseases/ ; R01-AI143409-05//National Institutes of Allergy and Infectious Diseases/ ; U01AI169358-03//National Institutes of Allergy and Infectious Diseases/ ; },
abstract = {Talaromycosis is an invasive fungal disease endemic to Southeast Asia. While culture is essential in identification, susceptibility testing, and typing, the low sensitivity and long turnaround times limit its clinical utility. Several promising monoclonal antibody-based (MAb) antigen-detection assays have been evaluated in large patient cohorts. This includes the MAb-Mp1p and MAb-4D1 enzyme immunoassays and their point-of-care platforms. Quantitative polymerase chain reaction (qPCR) assays targeting the 5.8S or 18S region of ribosomal RNA have been developed. These antigen and qPCR assays are highly specific and more sensitive than blood culture, making them excellent rapid rule-in tests for talaromycosis in people with a compatible clinical syndrome. Metagenomic next-generation sequencing is emerging as a promising tool for non-bias detection of talaromycosis. Host-based diagnostics targeting antibodies, interferon-gamma release, and transcriptomics are being actively developed. This review summarizes recent advances in the diagnosis of talaromycosis and provides expert recommendations on the application of these novel tests to improve the diagnostic algorithm and management of talaromycosis.},
}

@article {pmid40568985,
year = {2025},
author = {Zhao, J and Brandt, G and Gronniger, JL and Wang, Z and Li, J and Hunt, DE and Rodriguez-R, LM and Hatt, JK and Konstantinidis, KT},
title = {Quantifying the contribution of the rare biosphere to natural disturbances.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf129},
pmid = {40568985},
issn = {1751-7370},
abstract = {Understanding how populations respond to disturbances represents a major goal for microbial ecology. While several hypotheses have been advanced to explain microbial community compositional changes in response to disturbance, appropriate data to test these hypotheses is scarce, due to the challenges in delineating rare vs. abundant taxa and generalists vs. specialists, a prerequisite for testing the theories. Here, we operationally define these two key concepts by employing the patterns of coverage of a (target) genome by a metagenome to identify rare populations, and by borrowing the proportional similarity index (PS index) from macroecology to identify generalists. We applied these concepts to time-series (field) metagenomes from the Piver's Island Coastal Observatory (PICO) to establish that coastal microbial communities are resilient to major perturbations such as tropical cyclones and (uncommon) cold or warm temperature events, in part due to the response of rare populations. Therefore, these results provide support for the insurance hypothesis [i.e., the rare biosphere has the buffering capacity to mitigate the effects of disturbance]. Additionally, generalists appear to contribute proportionally more than specialists to community adaptation to perturbations like warming, supporting the disturbance-specialization hypothesis [i.e., disturbance favors generalists]. Several of these findings were also observed in replicated laboratory mesocosms that aimed to simulate disturbances such as a rain-driven washout of microbial cells and a labile organic matter release from a phytoplankton bloom. Taken together, our results advance understanding of the mechanisms governing microbial population dynamics under changing environmental conditions and have implications for ecosystem modeling.},
}

@article {pmid40568706,
year = {2025},
author = {Mu, X and Luo, H and Li, H and Chen, S and Han, Y and Zhang, L and Liu, W and Qiao, W and Zheng, S and Huang, Z},
title = {Pathogen detection and antibiotic use in granulomatous lobular mastitis: a comparison of mNGS and culture.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1570776},
pmid = {40568706},
issn = {2235-2988},
mesh = {Humans ; Female ; Retrospective Studies ; *Anti-Bacterial Agents/therapeutic use ; Adult ; *Granulomatous Mastitis/microbiology/drug therapy/diagnosis ; Corynebacterium/isolation & purification/genetics ; High-Throughput Nucleotide Sequencing/methods ; Middle Aged ; Sensitivity and Specificity ; Young Adult ; Metagenomics/methods ; Bacteriological Techniques/methods ; *Bacteria/isolation & purification/genetics/classification ; Corynebacterium Infections/diagnosis/drug therapy/microbiology ; },
abstract = {OBJECTIVE: This study aimed to evaluate the clinical microbial profile of patients with granulomatous lobular mastitis (GLM) and compare various detection methods to identify the most effective approach for pathogen detection, which could help enhance clinical diagnosis and treatment.

METHODS: We retrospectively analyzed data from 84 patients diagnosed with GLM, assessed the composition of pathogenic microorganisms in these patients, and compared the effectiveness of different sampling methods and detection techniques.

RESULTS: Corynebacterium kroppenstedtii (C. kroppenstedtii) was identified as the predominant microorganism among GLM patients. The positivity rate was low in skin swabs (10%) but similar in pus (40%) and tissue samples (37%). After antibiotic treatment, the pathogen detection rate of metagenomic next-generation sequencing (mNGS) (54.55%) was found to be higher than that of culture-based methods (27.27%). Among the GLM cases with pathogenic infection, although mNGS demonstrated higher sensitivity (75.0%) than culture tests (50.0%), both methods exhibited 100.0% specificity. However, the time for obtaining results with mNGS was significantly shorter (1.2 ± 0.41 days) compared to bacterial culture (5.5 ± 0.64 days) (P < 0.05).

CONCLUSIONS: Our findings indicate that pus was the most suitable sample type for microbial evidence collection in patients with GLM. mNGS demonstrated superior performance compared to culture in distinguishing infectious from non-infectious cases, with reduced antibiotic interference, faster turnaround time, and higher accuracy. Based on our single-center experience, empirical cephalosporin treatment may be appropriate for these patients. Additionally, surgical intervention remains the most efficient approach for rapid and complete resolution.},
}

Humans
Female
Retrospective Studies
*Anti-Bacterial Agents/therapeutic use
Adult
*Granulomatous Mastitis/microbiology/drug therapy/diagnosis
Corynebacterium/isolation & purification/genetics
High-Throughput Nucleotide Sequencing/methods
Middle Aged
Sensitivity and Specificity
Young Adult
Metagenomics/methods
Bacteriological Techniques/methods
*Bacteria/isolation & purification/genetics/classification
Corynebacterium Infections/diagnosis/drug therapy/microbiology

@article {pmid40568699,
year = {2025},
author = {Hu, H and Li, K and Jin, Z and Wang, K and Liu, B},
title = {Rapidly progressive pulmonary abscess initially misdiagnosed as lung cancer: the role of Peptostreptococcus stomatis and Parvimonas micra.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1590220},
pmid = {40568699},
issn = {2235-2988},
mesh = {Humans ; *Peptostreptococcus/isolation & purification/genetics ; *Lung Abscess/microbiology/diagnosis/pathology/drug therapy ; *Lung Neoplasms/diagnosis ; *Gram-Positive Bacterial Infections/diagnosis/microbiology/pathology/drug therapy ; *Diagnostic Errors ; *Firmicutes/isolation & purification/genetics ; Male ; High-Throughput Nucleotide Sequencing ; Anti-Bacterial Agents/therapeutic use ; Middle Aged ; },
abstract = {Pulmonary abscess is a serious infectious disease characterized by localized lung tissue necrosis, primarily caused by anaerobic or facultative anaerobic bacterial infections. While the Streptococcus anginosus group (SAG) is a well-established pathogen in pulmonary abscess formation, recent findings suggest that strict anaerobes such as Peptostreptococcus stomatis and Parvimonas micra can also contribute to deep-seated infections. However, their role in rapidly progressive pulmonary abscesses has not been previously documented. Here, we present a case of a rapidly progressive pulmonary abscess caused by Peptostreptococcus stomatis and Parvimonas micra in an immunocompetent patient, initially misdiagnosed as lung cancer. This case highlights the importance of differentiating infectious lung lesions from malignancies and underscores the clinical utility of metagenomic next-generation sequencing (mNGS) in diagnosing rare anaerobic infections, offering valuable insights for precise diagnostic and therapeutic strategies.},
}

Humans
*Peptostreptococcus/isolation & purification/genetics
*Lung Abscess/microbiology/diagnosis/pathology/drug therapy
*Lung Neoplasms/diagnosis
*Gram-Positive Bacterial Infections/diagnosis/microbiology/pathology/drug therapy
*Diagnostic Errors
*Firmicutes/isolation & purification/genetics
Male
High-Throughput Nucleotide Sequencing
Anti-Bacterial Agents/therapeutic use
Middle Aged

@article {pmid40568670,
year = {2025},
author = {Iqbal, NT and Sawatzki, K and Ahmed, K and Tisoncik-Go, J and Smith, E and Voss, K and Cornelius, J and Wang, L and Spaulding, AB and Serebryannyy, L and Douek, DC and Syed, MA and Mahmood, SF and Khan, E and Van Voorhis, WC and Gale, M},
title = {Metagenomic investigation of febrile illness in Pakistan reveals global transmission and co-circulation of Zika and Dengue viruses.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.03.10.25322803},
pmid = {40568670},
abstract = {We report the first identification of Zika virus in Pakistan following genomic and serological analyses of blood samples from 20 patients with febrile illness. In November 2021, an outbreak of dengue-like illness occurred in the metropolitan city of Karachi. Viral genome capture and sequencing of seven patients revealed six cases of dengue virus serotype 2 and two Zika virus infections, including one dengue and Zika virus co-infection. The next year, following severe flooding, 13 suspected dengue patients were screened by real time qRT-PCR and serology, and 92% (12/13) had evidence of current or recent Zika virus infection. Phylogenetic analyses revealed the Zika viruses originated from Brazil. The most recent observed ancestor dates to 2016, suggesting a prior importation event and ongoing circulation. Our results suggest that Zika virus may be circulating and contributing to disease burden during seasonal Dengue outbreak.},
}

@article {pmid40568302,
year = {2025},
author = {Ostrzinski, A and Kunath, BJ and Soares, AR and Laczny, CC and Halder, R and Kallmeyer, J and di Primio, R and Wilmes, P and Probst, AJ and Trautwein-Schult, A and Becher, D},
title = {Systematic evaluation of protein extraction for metaproteomic analysis of marine sediment with high clay content.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf074},
pmid = {40568302},
issn = {2730-6151},
abstract = {Marine sediments harbor extremely diverse microbial communities that contribute to global biodiversity and play an essential role in the functioning of ecosystems. However, the metaproteome of marine sediments is still poorly understood. The extraction of proteins from environmental samples is still a challenge, especially from marine sediments, due to the complexity of the matrix. Therefore, methods for protein extraction from marine sediments need to be improved. To develop an effective workflow for protein extraction for clayey sediments, we compared, combined and enhanced different protein extraction methods. The workflow presented here includes blocking of protein binding sites on sediment particles with high concentrations of amino acids, effective cell lysis by ultrasonic capture, electro-elution, and simultaneous fractionation of proteins. To test the protocol's efficacy, we added Escherichia coli cells to sediment samples before protein extraction. By using our refined workflow, we were able to identify a comparable number of E. coli proteins from the supplemented sediment to those from pure E. coli cultures. This new protocol will enable future studies to identify active players in clay-rich marine sediments and accurately determine functional biodiversity based on their respective protein complements.},
}

@article {pmid40568210,
year = {2025},
author = {Chen, M and Zeng, SY and Lu, SJ and Shi, M and Zhang, QQ},
title = {Early re-examination of chest CT may be unnecessary when patients with psittaci pneumonia at low and intermediate risk on Pneumonia Severity Index present with response to initial treatment.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1574706},
pmid = {40568210},
issn = {2296-858X},
abstract = {BACKGROUND: Chlamydia parrot pneumonia (CPS) is a rare community-acquired pneumonia (CAP) caused by Chlamydia parrot infection. With the development of metagenomic second-generation sequencing technology (mNGS), its diagnostic rate has improved in recent years. However, there are few clinical studies on Chlamydia parrot pneumonia, especially for patients with low and intermediate pneumonia severity index (PSI), and the necessity of early review of chest computed tomography (CT) is not clear. This study aimed to explore the clinical significance of early review of chest CT in patients with low and intermediate risk of Chlamydia parrot pneumonia with PSI after initial treatment was effective.

METHODS: Retrospective analysis of 8 patients with Chlamydia psittaci pneumonia diagnosed by metagenomic next-generation sequencing (mNGS) admitted to Zhejiang Provincial Tongde Hospital from January 2020 to December 2022 (PSI score ≤ 130 points). All patients had improved clinical symptoms and inflammatory markers after receiving antibiotic treatment, and chest CT was reexamined within 5-12 days. Evaluate the correlation between imaging changes before and after treatment and clinical symptoms and inflammatory indicators (CRP, PCT, WBC, etc.).

RESULTS: After treatment, the patient's body temperature, CRP, PCT and other indicators decreased significantly (P < 0.05). However, early CT reexamination showed that imaging progressed in 5 cases (62.5%), was stable in 2 cases (25%), and only 1 case (12.5%) showed partial improvement (P > 0.05). Nevertheless, none of the patients had a deterioration in their condition later on and finally achieved imaging recovery. Clinicians did not adjust the treatment plan when imaging progressed, and only 1 case was given glucocorticoid additionally.

CONCLUSION: For patients with low- intermediate risk Chlamydia psittaci pneumonia with low PSI, if clinical symptoms and inflammatory markers improve, early reexamination of chest CT may have no additional clinical value and does not affect treatment decisions. Therefore, it is not recommended to routinely perform early CT re-examination for such patients to reduce unnecessary consumption of medical resources. Larger sample studies are needed in the future for further verification.

CLINICAL TRIAL REGISTRATION: https://www.medicalresearch.org.cn/login, identifier MR-33-25003507.},
}

@article {pmid40567259,
year = {2025},
author = {Li, Q and Jiang, J and Li, J and Zhang, W and Xin, Y and He, B and He, S and Tu, C and Guo, Y and Gong, W},
title = {Complexity of Diarrhea-Associated Viruses in Stunted Pigs Identified by Viral Metagenomics.},
journal = {Transboundary and emerging diseases},
volume = {2025},
number = {},
pages = {1974716},
pmid = {40567259},
issn = {1865-1682},
mesh = {Animals ; Swine ; *Swine Diseases/virology/epidemiology ; *Diarrhea/veterinary/virology/epidemiology ; Metagenomics ; Phylogeny ; China/epidemiology ; },
abstract = {Viral diarrhea poses a severe threat to the health and growth of piglets, especially when caused by co-infection with multiple diarrhea-associated viruses. In this study anal swabs were collected from pigs older than 3 months from a farm in Gansu province, China, and subjected to viral metagenomic analysis. They had been suffering from diarrhea and their growth was significantly retarded. A total of 18 viruses were identified by high-throughput sequencing (HTS) in pooled samples from 22 stunted pigs and (separately) three healthy pigs. They included 15 diarrhea-associated RNA viruses with five porcine rotaviruses (PoRVs), porcine epidemic diarrhea virus (PEDV), a torovirus, and a sapelovirus present only in the stunted pigs. Among the identified PoRVs, PoRVBs showed a much greater genetic diversity than other PoRVs with multiple variant gene sequences identified in segments VP1 (2), VP2 (3), VP3 (4), VP4 (5), VP7 (5), NSP1 (2), NSP3 (3), NSP4 (2), and NSP5 (4), with 1-3 new genotypes being defined within each segment except NSP5. Unexpectedly, PoRVF was identified for the first time in pigs, with all gene segments exhibiting low nucleotide (56.5%-79.4%) and amino acid sequence identities (46.2%-92.0%) with previously identified avian RVF reference strains. Phylogenetic analysis showed that multiple variant strains of PAstV2 (6) and PAstV4 (13) were found in stunted pigs, and other enteric viruses were highly homologous with reference strains. Overall, the findings indicate that the stunted pigs may serve as a hotbed for the propagation of diarrhea-associated viruses and that they should be isolated and treated as early as possible.},
}

Animals
Swine
*Swine Diseases/virology/epidemiology
*Diarrhea/veterinary/virology/epidemiology
Metagenomics
Phylogeny
China/epidemiology

@article {pmid40566942,
year = {2025},
author = {Kara, K and Yilmaz Öztaş, S and Baytok, E},
title = {In Vitro Ruminal Metagenomic Profiles and Ruminal Fermentation Variables of Aromatic Plant Pulps.},
journal = {Veterinary medicine and science},
volume = {11},
number = {4},
pages = {e70447},
doi = {10.1002/vms3.70447},
pmid = {40566942},
issn = {2053-1095},
support = {TSA-2023-13007//Erciyes University Scientific Research Projects Unit/ ; },
mesh = {*Fermentation ; *Rumen/microbiology/metabolism/physiology ; Animals ; Cattle ; Metagenomics ; Animal Feed/analysis ; *Metagenome ; Gastrointestinal Microbiome ; Digestion ; },
abstract = {BACKGROUND: Aromatic plant residues remaining after aromatic oil extraction represent a promising alternative feed source due to their rich bioactive compound content and fibrous structure. However, their fermentative behaviour and microbial degradability in the rumen require evaluation.

OBJECTIVE: This study aimed to determine the nutrient composition, in vitro ruminal gas production, digestibility characteristics and fermentation end-products of aromatic plant pulps (sage, thyme, lavender and yarrow) obtained via hydrodistillation.

METHODS: Dried pulps were analysed for nutrient contents and subjected to in vitro ruminal fermentation for 24 h. Gas production estimated metabolizable energy (ME), net energy for lactation (NEL), organic matter digestibility (OMd), ammonia nitrogen (NH3-N) and short-chain fatty acid (SCFA) profiles were evaluated. Microbial community composition was assessed via 16S rRNA-based metagenomics.

RESULTS: Yarrow pulp had the highest gas production, ME, NEL, OMd and SCFA concentrations (AA, BA, IVA, T-SCFA) (p < 0.05). Thyme pulp exhibited the highest NH3-N levels (75.14 mg/L), suggesting high rumen-degradable protein content. Sage pulp had the lowest NH3-N levels (60.93 mg/L). Microbial composition shifted with fibre content; higher lignin (in lavender) was associated with lower Bacteroidota and higher Firmicutes abundance. Methanogenic archaea (Methanobrevibacter) were least abundant in thyme pulp (p < 0.05).

CONCLUSION: Due to their fermentability and favourable microbial responses, aromatic plant pulps, particularly yarrow, show promise as functional ruminant feed ingredients. These byproducts may enhance ruminal fibre utilization while modulating microbial ecology and reducing methane-associated archaea.},
}

*Fermentation
*Rumen/microbiology/metabolism/physiology
Animals
Cattle
Metagenomics
Animal Feed/analysis
*Metagenome
Gastrointestinal Microbiome
Digestion

@article {pmid40566543,
year = {2025},
author = {von Känel, G and Steinmann, LY and Mauz, B and Lukesch, R and Küenzi, P},
title = {It Is Useless to Resist: Biofilms in Metalworking Fluid Systems.},
journal = {Life (Basel, Switzerland)},
volume = {15},
number = {6},
pages = {},
doi = {10.3390/life15060890},
pmid = {40566543},
issn = {2075-1729},
support = {n.a.//Blaser Swisslube AG/ ; },
abstract = {Biofouling, the undesirable deposition of microorganisms on surfaces, is ubiquitous in aqueous systems. This is no different for systems running with water-miscible metalworking fluids (MWFs), which additionally contain many organic chemicals that create favorable conditions for growth and metabolism. Biofilm formation is thus inevitable, as there is no shortage of wetted surfaces in metalworking systems. MWF manufacturers tried in vain to offer resistance by using biocides and biostatic compounds as ingredients in concentrates and as tank-side additives. We report here that such elements, alone or as components of MWFs, did not prevent biofilm formation and had negligible effects on pre-established laboratory biofilms. Moreover, biofilms in metalworking systems are interwoven with residues, sediments, and metal swarfs generated during machining. Again, co-incubation of such "real" biofilms with MWFs had no significant effect on population size-but on population composition! The implications of this finding are unclear but could provide a starting point for the treatment of biofouling, as biofilm population structure might be of importance. Finally, we show that bacteria gain function in biofilms and that they were able to degrade a toxic amine in MWFs, which the same bacteria were unable to do in planktonic form.},
}

@article {pmid40565719,
year = {2025},
author = {Landi, N and Scognamiglio, M and Muscariello, L and Marasco, R and Palazzo, A and De Chiara, I and Ragucci, S and Pedone, PV and Fiorentino, A and Di Maro, A},
title = {Chemical Traits and Microbial Population Characterization of 'Asprinio' Grape Must, a Local Vine Cultivated in Campania Region (Italy).},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {12},
pages = {},
doi = {10.3390/foods14122110},
pmid = {40565719},
issn = {2304-8158},
support = {CUP B53C22001790006//"ITACA.SB" (Project No. IR0000009) funded by the European Union's NextGenerationEU under the MUR call 3264/2021 PNRR M4/C2/L3.1.1./ ; CUP E25I22000010007//'Rigenerazione culturale e sociale dei borghi storici del Matese - Castello del Matese e Letino', (Unione europea - NextGenerationEU)/ ; },
abstract = {'Asprinio' grape is used to produce a white wine from the Campania region, known as 'Asprinio' (DOC since 1993). A plethora of approaches was adopted to characterize the organic compounds (e.g., free amino acids and other metabolites) and microbial population (bacteria and fungi) in 'Asprinio' grape must by collecting samples from three different vineyards cultivated with the 'alberata' training system. The average free amino acid content of 'Asprinio' grape must showed quantitative variations, but no significant statistical differences were found. On average, proline was the most abundant free amino acid (~282 mg/L; 47.9%), followed by arginine (~66 mg/L; 11.5%) and glutamine (~25.2 mg/L; 4.2%). On the other hand, the total polyphenol content (TPC) of 'Asprinio' grape must was different, like their antioxidant activity, which increased when the TPC content was higher. Moreover, 1D and 2D NMR spectra highlighted the presence of high sugars amount (in particular glucose) as well as trans-caftaric acid, trans-coutaric acid, trans-fertaric acid, and the cis-isomers of these cinnamate esters. Finally, the evaluation of the microbial communities in the 'Asprinio' grape must revealed the presence of several representative bacterial phyla-mainly Bacteroidota, Proteobacteria, and Actinobacteriota-as well as various fungal genera, including Cladosporium, Hanseniaspora, Aspergillus, and Saccharomyces. Notably, these microorganisms, which contribute to the fermentation process and influence the final wine flavor, have been found in different proportions in the grape musts analyzed. Our results contribute to increasing knowledge of the 'Asprinio' grape, an indigenous vine of Southern Italy.},
}

@article {pmid40565014,
year = {2025},
author = {Monareng, NJ and Ncube, KT and van Rooi, C and Modiba, MC and Mtileni, B},
title = {A Systematic Review on Microbial Profiling Techniques in Goat Milk: Implications for Probiotics and Shelf-Life.},
journal = {International journal of molecular sciences},
volume = {26},
number = {12},
pages = {},
doi = {10.3390/ijms26125551},
pmid = {40565014},
issn = {1422-0067},
support = {PMDS240528221992//National Research Foundation/ ; },
mesh = {Goats ; Animals ; *Milk/microbiology ; *Probiotics ; *Microbiota ; *Food Microbiology ; Humans ; },
abstract = {Due to its high digestibility, rich nutrient profile, and potential probiotic content, goat milk is an essential nutritional resource, particularly for individuals with cow milk allergies. This review summarises the current state of microbial diversity in goat milk, emphasising the implications for quality, safety, and probiotic potential. This systematic review adhered to PRISMA guidelines, conducting a comprehensive literature search across PubMed, ScienceDirect, and Google Scholar using keywords related to microbial profiling in goat milk. The inclusion criteria targeted English-language studies from 2000 to 2025 that utilised high-throughput or next-generation sequencing methods. Out of 126 articles screened, 84 met the eligibility criteria. The extracted data focused on microbial diversity, profiling techniques, and their respective strengths and limitations in evaluating probiotic potential and spoilage risks. The review addresses the challenges linked to microbial spoilage and the composition and functional roles of microbial communities in goat milk. With species such as Bacillus and Pseudomonas playing crucial roles in fermentation and spoilage, key findings emphasise the prevalence of microbial phyla, including Proteobacteria, Firmicutes, and Actinobacteria in goat milk. The review also explores the probiotic potential of the goat milk microbiota, highlighting the health benefits associated with strains such as Lactobacillus and Bifidobacterium. Significant discoveries underline the necessity for advanced multi-omics techniques to thoroughly define microbial ecosystems and the substantial gaps in breed-specific microbiota research. Important findings illustrate the need for enhanced multi-omics techniques, given the challenges of host RNA and protein interference, low microbial biomass, and limited goat-specific reference databases, for optimising probiotic development, spoilage prevention strategies, and integrating metagenomics, metabolomics, metaproteomics, and metatranscriptomics to improve milk quality and safety as some of the future research objectives. This study emphasises the importance of understanding goat milk microbiology to advance dairy science and enhance human health.},
}

Goats
Animals
*Milk/microbiology
*Probiotics
*Microbiota
*Food Microbiology
Humans

@article {pmid40564305,
year = {2025},
author = {Rodriguez, AE and Britez, JD and Pisón-Martínez, ML and Delgado, FO and Balbiani, F and Berardo, CC and Gramaglia, C and Cuba, F and Poklepovich, TJ and Moreno, C and Francinelli, G and Morici, G and Arias, M and Schapiro, J and Barbano, P and Tomazic, ML},
title = {Evaluating Good Husbandry Practices and Organic Fermented Additives for Coccidiosis Control in a Pilot Study Using Slow-Growing Broilers.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {12},
pages = {},
doi = {10.3390/ani15121752},
pmid = {40564305},
issn = {2076-2615},
support = {FONTAGRO ATN/RF 18136 RG//Inter-American Development Bank/ ; PNSA PDL01-I113 and PE-I078//INSTITUTO NACIONAL DE TECNOLOGÍA AGROPECUARIA/ ; },
abstract = {The Argentine Campero-INTA slow-growing chicken, a widely used breed in family poultry farming, faces high coccidiosis prevalence, impairing productivity. Control often relies on management and drugs due to vaccination costs. This pilot study assessed the breed's susceptibility to local Eimeria and the impact of good animal welfare practices (AWPs) and an organic fermented additive, locally produced, combined with AWPs (OF-AWPs). Two trials evaluated productive (body weight gain and feed conversion), infection (oocyst excretion and lesion score), and histopathological parameters (villus height and crypt depth). The productivity (PI) and anticoccidial (ACI) indexes were calculated. Metagenomic analysis of the additive was also conducted. Mild to moderate coccidiosis significantly reduced PI (7.99-16.83 vs. 29.29 in unchallenged controls). In the second trial, AWPs showed good anticoccidial efficacy (ACI 173.9), while OF-AWPs demonstrated high efficacy, especially in birds of 28 days (ACI 180.6), improving productive parameters, reducing oocyst shedding, and enhancing the villus height to crypt depth ratio. Over a 75-day cycle, the OF-AWP increased the PI by 24.44% compared to untreated chickens (108.8 vs. 87.43). Lactic acid bacteria were the main component of the organic fermented additive. This research highlights the potential of an agroecological strategy to manage coccidiosis in Campero-INTA chickens.},
}

@article {pmid40564077,
year = {2025},
author = {Theis, BF and Park, JS and Kim, JSA and Zeydabadinejad, S and Vijay-Kumar, M and Yeoh, BS and Saha, P},
title = {Gut Feelings: How Microbes, Diet, and Host Immunity Shape Disease.},
journal = {Biomedicines},
volume = {13},
number = {6},
pages = {},
doi = {10.3390/biomedicines13061357},
pmid = {40564077},
issn = {2227-9059},
abstract = {The human gut microbiome is intricately linked to systemic and organ-specific immune responses and is highly responsive to dietary modulation. As metagenomic techniques enable in-depth study of an ever-growing number of gut microbial species, it has become increasingly feasible to decipher the specific functions of the gut microbiome and how they may be modulated by diet. Diet exerts both supportive and selective pressures on the gut microbiome by regulating a multitude of factors, including energy density, macronutrient and micronutrient content, and circadian rhythm. The microbiome, in turn, contributes to local and systemic immune responses by providing colonization resistance against pathogens, shaping immune cell activity and differentiation, and facilitating the production of bioactive metabolites. Emerging research has strengthened the connections between the gut microbiome and cardiometabolic disorders (e.g., cardiovascular disease, obesity, type-2 diabetes), autoimmune conditions (e.g., type-1 diabetes, rheumatoid arthritis, celiac disease), respiratory disease, chronic kidney and liver disease, inflammatory bowel disease, and neurological disorders (e.g., Alzheimer's, Parkinson's disease, depressive disorders). Here, we outline ways in which dietary factors impact host response in diseases through alterations of gut microbiome functionality and composition. Consideration of diet-mediated microbial effects within the context of the diseases discussed highlights the potential of microbiome-targeted treatment strategies as alternative or adjunct therapies to improve patient outcomes.},
}

@article {pmid40563973,
year = {2025},
author = {Qumsani, AT},
title = {Gut Microbiome Engineering for Diabetic Kidney Disease Prevention: A Lactobacillus rhamnosus GG Intervention Study.},
journal = {Biology},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/biology14060723},
pmid = {40563973},
issn = {2079-7737},
abstract = {The gut microbiota has emerged as a critical modulator in metabolic diseases, with substantial evidence supporting its role in attenuating diabetes-related nephropathy. Recent investigations demonstrate that strategic manipulation of intestinal microflora offers novel therapeutic avenues for safeguarding renal function against diabetic complications. This investigation sought to determine the nephroprotective potential of Lactobacillus rhamnosus GG (LGG) administration in diabetic nephropathy models. Six experimental cohorts were evaluated: control, probiotic-supplemented control, diabetic, diabetic receiving probiotic therapy, diabetic with antibiotics, and diabetic treated with both antibiotics and probiotics. Diabetic conditions were established via intraperitoneal administration of streptozotocin (50 mg/kg) following overnight fasting, according to validated protocols for experimental diabetes induction. Probiotic therapy (3 × 10[9] CFU/kg, bi-daily) began one month before diabetes induction and continued throughout the study duration. Glycemic indices were monitored at bi-weekly intervals, inflammatory biomarkers, renal function indices, and urinary albumin excretion. The metabolic profile was evaluated through the determination of HOMA-IR and the computation of metabolic syndrome scores. Microbiome characterization employed 16S rRNA gene sequencing alongside metagenomic shotgun sequencing for comprehensive microbial community mapping. L. rhamnosus GG supplementation substantially augmented microbiome richness and evenness metrics. Principal component analysis revealed distinct clustering of microbial populations between treatment groups. The Prevotella/Bacteroides ratio, an emerging marker of metabolic dysfunction, normalized following probiotic intervention in diabetic subjects. Results: L. rhamnosus GG administration markedly attenuated diabetic progression, achieving glycated hemoglobin reduction of 32% compared to untreated controls. Pro-inflammatory cytokine levels (IL-6, TNF-α) decreased significantly, while anti-inflammatory mediators (IL-10, TGF-β) exhibited enhanced expression. The renal morphometric analysis demonstrated preservation of glomerular architecture and reduced interstitial fibrosis. Additionally, transmission electron microscopy confirmed the maintenance of podocyte foot process integrity in probiotic-treated groups. Conclusions: The administration of Lactobacillus rhamnosus GG demonstrated profound renoprotective efficacy through multifaceted mechanisms, including microbiome reconstitution, metabolic amelioration, and inflammation modulation. Therapeutic effects suggest the potential of a combined probiotic and pharmacological approach to attenuate diabetic-induced renal pathology with enhanced efficacy.},
}

@article {pmid40563865,
year = {2025},
author = {Zhao, L and Dong, XN and Cui, H and Sun, LY and Mu, R and Nie, M and Kang, JM and Bu, N and Zhang, YS and Qi, ZH and Li, ZX and Zhang, ZL and Zhang, XY and Ding, YL and Wang, R and Wang, Y and Liu, YH},
title = {Comparative Analysis of Microbial Communities in Each Developmental Stage of Dermacentor nuttalli in Two Regions in Inner Mongolia, China.},
journal = {Biology},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/biology14060613},
pmid = {40563865},
issn = {2079-7737},
support = {32260887//National Natural Science Foundation of China/ ; },
abstract = {Dermacentor is the most widely distributed tick genus in China. Dermacentor nuttalli, a predominant tick species in Inner Mongolia, can carry and transmit pathogenic microorganisms. Here, D. nuttalli were collected from Ordos (O-D) and Hinggan League (H-D) in the Inner Mongolia. D. nuttalli specimens at different developmental stages were subsequently reared under identical laboratory conditions. Sample processing, nucleic acid extraction, high-throughput sequencing, and microbial community analyses were conducted. Bacterial communities in O-D and H-D were annotated to 8 phyla, 145 genera and 16 phyla, 141 genera, respectively, with Proteobacteria showing the highest relative abundance. Differences in dominant bacterial genera were observed across developmental stages between the two regions. The most abundant bacterial species were Arsenophonus_uncultured_bacterium in O-D and Rickettsia japonica in H-D. Viral communities were annotated to 4 orders, 25 families, 61 genera, and 126 species in O-D and 6 orders, 28 families, 49 genera, 135 species in H-D. Notable difference in the viral genera with >1% abundance were identified at different developmental stages in the two regions. To our knowledge, this is the first study to compare microbial community compositions of D. nuttalli across developmental stages in two Inner Mongolian regions under under identical rearing conditions and to report the presence of R. japonica, Tacheng Tick Virus-2, and bovine viral diarrhea virus in D. nuttalli.},
}

@article {pmid40563782,
year = {2025},
author = {Hong, SH and Roh, HW and Nam, YJ and Kim, TW and Cho, YH and Son, SJ and Hong, CH},
title = {Age- and Sex-Specific Gut Microbiota Signatures Associated with Dementia-Related Brain Pathologies: An LEfSe-Based Metagenomic Study.},
journal = {Brain sciences},
volume = {15},
number = {6},
pages = {},
doi = {10.3390/brainsci15060611},
pmid = {40563782},
issn = {2076-3425},
support = {2024-ER0505-00//Korea National Institute of Health (KNIH)/ ; GRRCAjou2023-B02//Gyeonggi-do Regional Research Center program of Gyeonggi province/ ; RS-2022-KH130309//Korea Health Technology R&D Project through the Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health & Welfare, Republic of Korea/ ; RS-2021-KH113821//Korea Health Technology R&D Project through the Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health & Welfare, Republic of Korea/ ; },
abstract = {BACKGROUND/OBJECTIVES: Emerging evidence suggests that gut microbiota composition is influenced by both age and sex and may contribute to dementia-related brain pathologies. However, comprehensive microbiome-based biomarker discovery stratified by these factors remains limited.

METHODS: We performed a metagenomic analysis of the gut microbiota of participants stratified by sex (female vs. male) and age (<75 vs. ≥75 years). Alpha diversity (observed operational taxonomic unit, Chao1, Shannon, and Simpson) and linear discriminant analysis effect size analyses were conducted to identify dominant taxa associated with Alzheimer's pathology, vascular pathology, and dementia-related structural brain changes.

RESULTS: Females and non-elderly participants (aged < 75 years) exhibited higher gut microbial diversity, characterized by an increased abundance of Bifidobacterium spp. and Blautia spp., whereas males and elderly participants (aged ≥ 75 years) exhibited increased levels of Bacteroides spp. and Bacteroidia, which have been associated with inflammation and dysbiosis. Several taxa, including Bifidobacterium spp. were consistently identified as potential protective biomarkers, while Bacteroides spp. was linked to a higher risk of dementia-related brain pathologies.

CONCLUSIONS: Our findings demonstrate distinct age- and sex-specific differences in gut microbiota composition that may be closely associated with the pathophysiology of dementia-related brain pathologies. These results demonstrate that gut microbiota may serve as potential biomarkers for monitoring cerebrovascular conditions, potentially contributing to the development of personalized therapeutic strategies.},
}

@article {pmid40563710,
year = {2025},
author = {Kazen, AB and Umfleet, LG and Aboulalazm, FA and Cohen, AD and Terhune, S and Mason, L and Obarski, S and Franczak, M and Kindel, TL and Wang, Y and Kirby, JR},
title = {Gut Microbiota and Neurovascular Patterns in Amnestic Mild Cognitive Impairment.},
journal = {Brain sciences},
volume = {15},
number = {6},
pages = {},
doi = {10.3390/brainsci15060538},
pmid = {40563710},
issn = {2076-3425},
support = {1R21AG075501-24A1/NH/NIH HHS/United States ; },
abstract = {Background/Objectives: The interplay between the gut microbiome (GMB) and neurovascular function in neurodegeneration is unclear. The goal of this proof-of-concept, cross-sectional study is to identify relationships between the GMB, neurovascular functioning, and cognition in amnestic mild cognitive impairment (aMCI), the prototypical prodromal symptomatic stage of Alzheimer's disease (AD). Methods: Participants (n = 14 aMCI and 10 controls) provided fecal samples for GMB sequencing (16S and shotgun metagenomics), underwent MRI, and completed cognitive testing. Cerebral vascular reactivity (CVR), cerebral blood flow (CBF), and arterial transit time (ATT) were assessed. Statistical analyses evaluated the relationships between discriminatory taxa, cerebrovascular metrics, and cognition. Results: Sequencing revealed differentially abundant bacterial and viral taxa distinguishing aMCI from controls. Spearman correlations revealed that bacteria known to induce inflammation were negatively associated with CVR, CBF, and cognition, and positively associated with ATT. A reciprocal pattern emerged for the association of taxa with gut health. Conclusions: Our results provide preliminary evidence that pro-inflammatory gut bacterial and viral taxa are associated with neurovascular dysfunction and cognitive impairment in prodromal AD, highlighting their potential as candidate microbial biomarkers and targets for early intervention.},
}

@article {pmid40563261,
year = {2025},
author = {Gao, J and Zhu, H and Gao, J and Xu, G},
title = {Characteristics of Intestinal Microbiota and Host Gene Regulation in Coilia nasus Responding to Stress.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/antiox14060626},
pmid = {40563261},
issn = {2076-3921},
support = {32302976//the National Natural Science Foundation of China/ ; BK20230179//the Natural Science Foundation of Jiangsu Province/ ; 2022YFD2400904//the National Key Research and Development Program of China/ ; JSGS [2021]134//the Jiangsu Province seed industry revitalization "revealing-list" project/ ; },
abstract = {Transport stress in aquaculture poses significant challenges to fish health by inducing oxidative stress and intestinal damage. This study investigated the effects of transport stress on intestinal microbiota, host gene regulation, and metabolic responses in Coilia nasus. The fish were subjected to simulated transport conditions, followed by an analysis of their intestinal antioxidant capacity, inflammatory factors, transcriptome sequencing, metagenomic profiling, and metabolomic assays. The results revealed that transport stress significantly suppressed antioxidant enzyme activities (e.g., catalase, superoxide dismutase, glutathione peroxidase) and elevated oxidative damage (malondialdehyde, lipid peroxidation) alongside upregulating pro-inflammatory cytokines. The transcriptomic analysis identified differentially expressed genes enriched in the lipid metabolism and ferroptosis pathways, with the increased lipid peroxidation and iron overload activating ferroptosis. The metagenomic data showed an altered gut microbiota composition, including increased Aeromonas and reduced beneficial metabolites (e.g., propionic acid, bile acids). Correlation analyses linked the microbial shifts and metabolite changes to ferroptosis and barrier dysfunction. These findings demonstrate that transport stress disrupts intestinal redox balance, induces ferroptosis, and reshapes gut microbiota, collectively compromising intestinal integrity and health in C. nasus.},
}

@article {pmid40563104,
year = {2025},
author = {Trutschel, L and Kruger, B and Czaja, A and Brueck, M and Sackett, J and Druschel, G and Rowe, A},
title = {Sulfide Oxidation Products Support Microbial Metabolism at Interface Environments in a Marine-Like Serpentinizing Spring in Northern California.},
journal = {Geobiology},
volume = {23},
number = {4},
pages = {e70026},
pmid = {40563104},
issn = {1472-4669},
support = {80NSSC21K0482/NASA/NASA/United States ; },
mesh = {Oxidation-Reduction ; California ; *Sulfides/metabolism ; *Bacteria/metabolism/classification/genetics ; *Natural Springs/microbiology/chemistry ; Microbiota ; },
abstract = {Interface environments between extreme and neutrophilic conditions are often hotspots of metabolic activity and taxonomic diversity. In serpentinizing systems, the mixing of high pH fluids with meteoric water, and/or the exposure of these fluids to the atmosphere can create interface environments with distinct but related metabolic activities and species. Investigating these systems can provide insights into the factors that stimulate microbial growth, and/or what attributes may be limiting microbial physiologies in native serpentinized fluids. To this aim, changes in geochemistry and microbial communities were investigated for different interface environments at Ney Springs-a marine-like terrestrial serpentinization system where the main serpentinized fluids have been well characterized geochemically and microbially. We found that reduced sulfur species from Ney Springs had large impacts on the community changes observed at interface environments. Oxygen availability at outflow environments resulted in a relative increase in the taxa observed that were capable of sulfur oxidation, and in some cases light-driven sulfur oxidation. A combination of cultivation work and metagenomics suggests these groups seem to predominantly target sulfur intermediates like polysulfide, elemental sulfur, and thiosulfate as electron donors, which are present and abundant to various degrees throughout the Ney system. Fluid mixing with meteoric water results in more neutral pH systems which in turn select for different sulfur-oxidizing taxa. Specifically, we see blooms of taxa that are not typically observed in the primary Ney fluids, such as Halothiobacillus in zones where fluids mix underground with meteoric water (~pH 10) or the introduction of Thiothrix into the nearby creek as fluids enter at the surface (~pH 8). This work points to the potential importance of oxidants for stimulating microbial respiration at Ney Springs, and the observation that these serpentinized fluids act as an important source of reduced sulfur, supporting diverse taxa around the Ney Springs system.},
}

Oxidation-Reduction
California
*Sulfides/metabolism
*Bacteria/metabolism/classification/genetics
*Natural Springs/microbiology/chemistry
Microbiota

@article {pmid40562730,
year = {2025},
author = {Vetterli, D and Zennaro, M and Tacchini, V and Lobrinus, JA and Prendki, V and Lazarevic, V and Schrenzel, J},
title = {Next-Generation Sequencing Techniques to Diagnose Culture-Negative Subacute Native Aortic Endocarditis.},
journal = {Emerging infectious diseases},
volume = {31},
number = {7},
pages = {1478-1481},
doi = {10.3201/eid3107.241739},
pmid = {40562730},
issn = {1080-6059},
mesh = {Humans ; Male ; *Aortic Valve/microbiology ; *Endocarditis/diagnosis/microbiology ; *Endocarditis, Bacterial/diagnosis/microbiology ; *High-Throughput Nucleotide Sequencing/methods ; Streptococcus gordonii/genetics/isolation & purification ; Aged, 80 and over ; },
abstract = {Next-generation sequencing might improve diagnosis of infective endocarditis. A case in Switzerland was initially attributed to Solobacterium moorei bacteria. Metagenomic analysis of the affected heart valve detected Streptococcus gordonii, but not S. moorei, illustrating that the results of molecular detection can vary depending on sampling time and anatomic site.},
}

Humans
Male
*Aortic Valve/microbiology
*Endocarditis/diagnosis/microbiology
*Endocarditis, Bacterial/diagnosis/microbiology
*High-Throughput Nucleotide Sequencing/methods
Streptococcus gordonii/genetics/isolation & purification
Aged, 80 and over

@article {pmid40562294,
year = {2025},
author = {Zhang, J and Zhan, H and Xu, H and Wang, R and Li, Z and Feng, F and Wu, H and Xu, Z and Wang, S and Guo, Y and Li, Y},
title = {Infectious agents in dilated cardiomyopathy: Genetic interactions, autoimmunity, mechanisms, and therapeutic approaches.},
journal = {Autoimmunity reviews},
volume = {},
number = {},
pages = {103860},
doi = {10.1016/j.autrev.2025.103860},
pmid = {40562294},
issn = {1873-0183},
abstract = {Dilated cardiomyopathy (DCM) is a heterogeneous myocardial disorder characterized by left ventricular dilation and systolic dysfunction in the absence of ischemic, hypertensive, or valvular heart disease. Although its precise etiology remains unclear, it is widely recognized as a multifactorial disease arising from complex interactions between genetic predisposition and environmental triggers. Among these, infectious agents have been implicated in the pathogenesis of various subtypes, particularly inflammatory and idiopathic DCM. These agents can contribute to disease onset and progression through direct cardiomyocyte injury, immune-mediated chronic inflammation, and other yet-to-be-defined mechanisms. Infection-driven autoimmune activation is another potential key contributor to DCM, potentially linking infectious exposure to sustained myocardial damage. However, the precise role of various infectious agents in DCM initiation and progression, as well as their interactions with genetic predisposition and autoimmune activation, is inadequately understood. Improving understanding of infection-related etiologies could facilitate development of targeted therapeutic strategies; however, significant challenges persist in identifying causative and novel pathogens, and translating this into clinical practice. Therefore, this review explores the complex interactions between infectious agents, genetic predisposition, and autoimmune responses in DCM pathogenesis. We summarize current evidence on the role of infectious agents in DCM and emerging therapeutic strategies aimed at treating infection-related DCM. Finally, we outline future research directions to advance understanding of infection-associated DCM and improve patient outcomes. We reveal that a deeper understanding of host-microbe interactions, immune pathways, and genetic predisposition is essential for advancing DCM research. Furthermore, integrating genomics, metagenomics, and antibody and immunological profiling is crucial for developing personalized therapeutic strategies for this complex disease.},
}

@article {pmid40562247,
year = {2025},
author = {Yang, X and Wang, W and Liu, X and Xie, S and Feng, J and Lv, J},
title = {Nitrogen metabolism functional shifts of indigenous bacteria and effect on nitrogen removal in microalgae-based municipal wastewater treatment system across aeration modes.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132881},
doi = {10.1016/j.biortech.2025.132881},
pmid = {40562247},
issn = {1873-2976},
abstract = {Although the effect of aeration intensity on the performance of microalgae-based wastewater treatment systems has been widely studied, the impact of aeration mode has received less attention. This study explored how different aeration modes influence nitrogen metabolism in microalgae-based wastewater systems using metagenomic analysis. Both continuous aeration (CA) and intermittent aeration (IA) supported rapid bacterial growth and effective pollutant removal. Compared to CA, IA and no-aeration modes significantly enhanced bacterial nitrification and denitrification. Key nitrogen-metabolizing genera such as Paracoccus, Acidovorax, and Rhizobium played major roles in nitrogen cycling. Their abundances were closely associated with NH4[+]-N, NO3[-]-N, NO2[-]-N, total phosphorus, chemical oxygen demand, dissolved oxygen, bacterial number, and total biomass. Overall, environmental changes induced by different aeration modes significantly shaped indigenous bacterial communities involved in nitrogen metabolism, thereby influencing the abundances of nitrogen metabolism-related genes and, ultimately, nitrogen removal performance.},
}

@article {pmid40562089,
year = {2025},
author = {Gu, P and Xu, Y and Li, X},
title = {Chronic Low-Dose Cadmium Exposure Disrupts Gut Microbiota and Lipid Metabolism to Induce Liver Injury.},
journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association},
volume = {},
number = {},
pages = {115603},
doi = {10.1016/j.fct.2025.115603},
pmid = {40562089},
issn = {1873-6351},
abstract = {Cadmium (Cd) is a widespread environmental pollutant linked to liver injury and metabolic dysfunction, yet the gut-liver axis mechanisms remain unclear. We investigated chronic low-dose Cd exposure (100 nM CdCl2, 12 weeks) in mice using integrated metagenomic and metabolomic profiling. Despite intact intestinal morphology, Cd exposure induced hepatic inflammation, steatosis, and elevated transaminases. Shotgun metagenomics revealed gut microbiota shifts, with enrichment of Prevotella and depletion of Turicibacter. Fecal metabolomics showed disrupted bile acid detoxification and lipid remodeling. Functional analysis indicated upregulation of microbial fatty acid metabolism genes, suggesting compensatory but dysregulated responses. These findings demonstrate that chronic Cd exposure perturbs gut microbiota and metabolic outputs, driving liver injury via microbiota-mediated mechanisms. Our study highlights the gut-liver axis as a key target of Cd toxicity and points to microbiota-based interventions as potential therapies.},
}

@article {pmid40561629,
year = {2025},
author = {Deng, Z and Xie, Y and Yu, H and Zhang, X and Tan, T and Kuang, W and Han, Z and Li, Y and Wang, H and Zhang, N and Zhang, C},
title = {Harnessing deep-sea cold seep microbiomes for reductive dehalogenation: from culturomics and genomics insights.},
journal = {Water research},
volume = {285},
number = {},
pages = {124072},
doi = {10.1016/j.watres.2025.124072},
pmid = {40561629},
issn = {1879-2448},
abstract = {Deep-sea cold seeps harbor a rich and diverse repertoire of reductive dehalogenase-encoding genes (rdhA), yet their potential for reductive dehalogenation remains largely unexplored. In this study, we investigated the microbial debromination of 2,4,6-tribromophenol (TBP) in cold seep sediment microcosms. By optimizing culture conditions with different nutrient sources and substrate concentrations, we established a highly efficient debrominating microbial consortium capable of completely degrading 50 μM TBP within 72 h. Metagenomic analysis revealed Bin3, a novel bacterium affiliated with Peptococcaceae, as a key dehalogenator harboring multiple rdhA genes. Microbial community analysis demonstrated that nutrient availability significantly influenced beta diversity (community composition) but had only a minor effect on alpha diversity. Through degradation kinetics, co-occurrence network analysis, normalized stochasticity ratio analysis, and metagenomic quantification, we found that supplementing lactate along with 0.05 % yeast extract significantly enhanced TBP degradation efficiency and facilitated the targeted enrichment of key dehalogenating microbes (with relative abundance increasing from <1 % to 32 %). Comparative genomic analysis indicated that Bin3 has undergone specific adaptations through expansion of gene families involved in pili formation, cell motility, nutrient acquisition, and diverse metabolic pathways, potentially enhancing its competitiveness in deep-sea cold seep environments. This study advances our understanding of deep-sea dehalogenating microbiomes and their adaptation to extreme environments, providing insights into their ecological significance and potential applications in pollutant bioremediation.},
}

@article {pmid40561623,
year = {2025},
author = {Zhang, Y and Wang, M and Wu, H and Cheng, W and Zhao, L and Yu, G and Ren, J},
title = {Hydroperiodic dynamics of microbial-mediated nitrogen cycling and its multi-element coupling effect in the Weihe River.},
journal = {Water research},
volume = {285},
number = {},
pages = {124057},
doi = {10.1016/j.watres.2025.124057},
pmid = {40561623},
issn = {1879-2448},
abstract = {The aquatic ecosystem is affected by both human activities and climate change, and the excessive input and imbalance of nitrogen (N) have become an environmental issue of global concern. In this study, based on metagenomic sequencing, network analysis, random forest and structural equation model were used to investigate the hydroperiod dynamics, driving mechanisms of N cycling and the coupling effects of N, carbon (C) and sulfur (S) cycling in the Weihe River. The results showed that the nitrogen concentration and pathways exhibited heterogeneity during the high, normal and low water periods. Nitrogen fixation and organic nitrogen mineralization were abundant during the high water period, and nitrification, anammox were dominant during the low water period. The co-occurrence network of bacteria and nitrogen cycling genes was dominated by positive correlations, and Limnohabitans, Flavobacterium, and Polynucleobacter showed diverse metabolic potentials. Redundancy analysis showed that nitrogen cycling genes were more sensitive to substrate changes in the high and low water periods, and dependent on basic physicochemical conditions during the normal water period. A structural equation model revealed that climatic conditions, water properties, and microbial communities had positive effects on nitrogen cycling genes (standard effects of 0.154, 0.347, 0.603), with microbial-gene collaboration driving core functionality. The strong positive correlation of the co-occurrence network of C, N, and S functional genes revealed the elemental synergies. The multi-element coupled cycling networks showed more complex and stronger interactions during the normal water periods, and the efficiency of cross-element metabolism was reduced during low water periods. This study holds significance in understanding the ecological effects of microbial-mediated nitrogen cycling and multi-element coupled cycling in rivers, and provides a theoretical basis for nutrient control in micro-polluted rivers.},
}

@article {pmid40560512,
year = {2025},
author = {Pramanik, K and Sen, A and Dutta, S and Mandal, GS and Paramanik, B and Das, A and Chatterjee, N and Ghorai, AK and Ali, MN},
title = {Microbial populations under fluoride stress: a metagenomic exploration from Indian soil.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {7},
pages = {221},
pmid = {40560512},
issn = {1573-0972},
mesh = {*Soil Microbiology ; *Fluorides/analysis ; India ; Metagenomics ; *Bacteria/genetics/classification/drug effects/isolation & purification ; Soil/chemistry ; Fungi/genetics/classification/drug effects/isolation & purification ; Archaea/genetics/classification/drug effects/isolation & purification ; Metagenome ; Phylogeny ; Microbiota/drug effects ; },
abstract = {Fluoride exposure, even at a low concentration, significantly impairs crop growth and productivity by inhibiting metabolic enzymes and disrupting photosynthesis. Addressing this challenge, microbial de-fluoridation emerges as a vital strategy to improve soil health, enhance crop growth, and ensure agricultural sustainability. This study analyzed topsoil samples (0-0.2 m depth) from rice fields in three blocks of Purulia district, West Bengal-Arsha, Jhalda-I, and Joypur. Fluoride content in the samples ranged from 58.76 ± 0.76 mg/kg to 282.9 ± 4.9 mg/kg (total) and 1.57 ± 0.02 mg/kg to 2.97 ± 0.03 mg/kg (available). The metagenomic analysis of the collected soil samples revealed diverse microbial communities comprising archaea, bacteria, fungi, and viruses, with Actinobacteria (phylum), Hyphomicrobiales (order), and Nocardioidaceae (family) being the dominant prokaryotes. Arsha soil with comparatively low fluoride contamination exhibited the highest microbial diversity (11,891 taxa), followed by Joypur (11,528 taxa) and Jhalda-I (11,358 taxa), with Arsha showing nearly double the unique microbial taxa compared to the other locations. Clusters of orthologous groups of proteins functional analysis identified 60,898 genes in Arsha, 63,403 genes in Jhalda-I, and 73,334 genes in Joypur, while Kyoto encyclopedia of genes and genomes analysis revealed 9,385, 9,104, and 10,633 genes, respectively. Key genes associated with fluoride metabolism-inorganic pyrophosphatase, divalent metal cation transporter mntH, and putative fluoride ion transporter crcB-were abundant across all sites, highlighting the influence of fluoride on microbial community structure. This study provides the first comprehensive report on soil microbial communities in fluoride-rich areas, highlighting the potential of native fluoride-tolerant microbes to mitigate fluoride toxicity in agricultural soils and offer sustainable, microbe-based solutions to fluoride contamination.},
}

*Soil Microbiology
*Fluorides/analysis
India
Metagenomics
*Bacteria/genetics/classification/drug effects/isolation & purification
Soil/chemistry
Fungi/genetics/classification/drug effects/isolation & purification
Archaea/genetics/classification/drug effects/isolation & purification
Metagenome
Phylogeny
Microbiota/drug effects

@article {pmid40559797,
year = {2025},
author = {Hai, C and Gong, H and Xu, Y and Liu, X and Bai, C and Su, G and Yang, L and Li, G},
title = {Loss of Myostatin Alters Gut Microbiota and Carbohydrate Metabolism to Influence the Gut-Muscle Axis in Cattle.},
journal = {Veterinary sciences},
volume = {12},
number = {6},
pages = {},
pmid = {40559797},
issn = {2306-7381},
support = {2023ZD0404803//Scientific and Technological Innovation 2030/ ; 32360837, 32341052//National Natural Science Foundation of China/ ; 2022JBGS0025//Inner Mongolia Open Competition Projects/ ; 2022LJRC0006//Inner Mongolia Science and Technology Leading Team/ ; 2021ZD0009, 2021ZD0008, 2022ZD0008, 2023KJHZ0028//Inner Mongolia Science and Technology Major Projects/ ; NJYT23138//Inner Mongolia Young Talents Projects/ ; 2023MS03004//Inner Mongolia Natural Science Foundation/ ; 2022ZY0212//Central Government Guides Development/ ; NK2022130203//National Agricultural Science and Technology Project/ ; XTCX2023-06//Collaborative Innovation among Universities in Hohhot/ ; JYBGCSYS2022//Ministry of Education Engineering Centre Project/ ; 2023A02011-1//Xinjiang Uygur Science and Technology Major Project/ ; },
abstract = {The gut-muscle axis plays a vital role in host metabolism and health. Although the MSTN gene is a well-known negative regulator of muscle growth, its role in intestinal function and metabolism remains unclear. Understanding this connection is crucial for revealing the systemic impact of MSTN gene editing and its potential to improve metabolic efficiency in livestock. In this study, we investigated the influence of MSTN deletion on gut microbiota composition and carbohydrate metabolism in the cecum and colon of cattle. Using integrated metagenomic, metabolomic, serum biochemical, and muscle transcriptomic analyses, we found significant alterations in microbial communities and key metabolic pathways. Hallella and Escherichia in the colon, as well as Alishewanella in the cecum, were closely linked to carbohydrate metabolism. Differential microbes and metabolites influenced key metabolic pathways, including glycolysis/gluconeogenesis and lipopolysaccharide biosynthesis. Functional gene analysis identified Bacteroides as the most critical bacterium affecting glycolysis/gluconeogenesis. Additionally, genes related to carbohydrate esterases were upregulated. These changes correlated with reduced serum glucose and insulin levels while increasing muscle gene expression related to glucose-to-lactose conversion. Overall, MSTN gene editing alters gut microbiota composition and carbohydrate metabolism in the cecum and colon, thereby influencing host glucose metabolism and energy homeostasis.},
}

@article {pmid40559651,
year = {2025},
author = {Wimmer, BC and Dwan, C and De Medts, J and Duysburgh, C and Rotsaert, C and Marzorati, M},
title = {Undaria pinnatifida Fucoidan Enhances Gut Microbiome, Butyrate Production, and Exerts Anti-Inflammatory Effects in an In Vitro Short-Term SHIME[®] Coupled to a Caco-2/THP-1 Co-Culture Model.},
journal = {Marine drugs},
volume = {23},
number = {6},
pages = {},
pmid = {40559651},
issn = {1660-3397},
support = {n.a.//Marinova Pty Ltd., 249 Kennedy Drive, Cambridge, TAS 7170, Australia/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Polysaccharides/pharmacology/isolation & purification ; *Undaria/chemistry ; *Anti-Inflammatory Agents/pharmacology ; Caco-2 Cells ; Coculture Techniques ; *Butyrates/metabolism ; THP-1 Cells ; Colon/microbiology/drug effects ; Feces/microbiology ; Cytokines/metabolism ; Adult ; Fatty Acids, Volatile/metabolism ; Edible Seaweeds ; },
abstract = {Fucoidans have demonstrated a wide range of bioactivities including immune modulation and benefits in gut health. To gain a deeper understanding on the effects of fucoidan from Undaria pinnatifida (UPF) on the colonic microbiome, the short-term Simulator of the Human Intestinal Microbial Ecosystem[®], a validated in vitro gut model, was applied. Following a three-week intervention period on adult faecal samples from three healthy donors, microbial community activity of the colonic microbiota was assessed by quantifying short-chain fatty acids while composition was analysed utilising 16S-targeted Illumina sequencing. Metagenomic data were used to describe changes in community structure. To assess the secretion of cytokines, co-culture experiments using Caco-2 and THP1-Blue™ cells were performed. UPF supplementation over a three-week period had a profound butyrogenic effect while also enriching colonic microbial diversity, consistently stimulating saccharolytic genera, and reducing genera linked with potentially negative health effects in both regions of the colon. Mild immune modulatory effects of UPF were also observed. Colonic fermentation of UPF showed anti-inflammatory properties by inducing the secretion of the anti-inflammatory cytokines IL-6 and IL-10 in two out of three donors in the proximal and distal colon. In conclusion, UPF supplementation may provide significant gut health benefits.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Polysaccharides/pharmacology/isolation & purification
*Undaria/chemistry
*Anti-Inflammatory Agents/pharmacology
Caco-2 Cells
Coculture Techniques
*Butyrates/metabolism
THP-1 Cells
Colon/microbiology/drug effects
Feces/microbiology
Cytokines/metabolism
Adult
Fatty Acids, Volatile/metabolism
Edible Seaweeds

@article {pmid40559609,
year = {2025},
author = {Mziray, SR and Githinji, G and de Laurent, ZR and Mbelele, PM and Mohammed, KS and Wadugu, BD and Grundy, BS and Heysell, SK and Mpagama, SG and Chilongola, JO},
title = {Deploying Metagenomics to Characterize Microbial Pathogens During Outbreak of Acute Febrile Illness Among Children in Tanzania.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {6},
pages = {},
pmid = {40559609},
issn = {2076-0817},
support = {TMA2016SF-1463-REMODELTZ//European & Developing Countries Clinical Trials Partnership/ ; },
mesh = {Humans ; Tanzania/epidemiology ; Child ; *Metagenomics/methods ; Male ; Female ; *Disease Outbreaks ; *Fever/microbiology/epidemiology ; Cross-Sectional Studies ; *Bacteria/genetics/classification/isolation & purification ; Child, Preschool ; Adolescent ; High-Throughput Nucleotide Sequencing ; Acute Disease ; },
abstract = {Outbreaks of infectious diseases contribute significantly to morbidity and mortality in resource-limited settings, yet the capacity to identify their etiology remains limited. We aimed to characterize microbes and antimicrobial resistance (AMR) genes in Tanzanian children affected by an acute febrile illness (AFI) outbreak using metagenomic next-generation sequencing (mNGS). A cross-sectional study was conducted on archived blood samples from children who presented with AFI between 2018 and 2019. Total nucleic acids were extracted from 200 µL of blood, and complementary DNA (cDNA), along with enriched pathogenic DNA, was sequenced using the Illumina MiSeq platform. mNGS data were analyzed using CZ-ID Illumina mNGS bioinformatics pipeline v7.0. Results were obtained from 25 participants (mean age: 11.6 years; SD ± 5), of whom 36% had a moderate to high-grade fever. The following five potential microbial causes of AFI were identified: Escherichia coli (n = 19), Paraclostridium bifermentans (n = 2), Pegivirus C (n = 2), Shigella flexneri (n = 1) and Pseudomonas fluorescens (n = 1), with E. coli being the most prevalent. Twelve AMR genes were detected, including mdtC, acrF, mdtF, and emrB. E. coli harbored most of the AMR genes previously associated with resistance to commonly used antibiotics. mNGS offers a promising complementary approach to conventional diagnostics for identifying pathogens and AMR profiles in vulnerable populations.},
}

Humans
Tanzania/epidemiology
Child
*Metagenomics/methods
Male
Female
*Disease Outbreaks
*Fever/microbiology/epidemiology
Cross-Sectional Studies
*Bacteria/genetics/classification/isolation & purification
Child, Preschool
Adolescent
High-Throughput Nucleotide Sequencing
Acute Disease

@article {pmid40559526,
year = {2025},
author = {Kim, M and Fida, M and Abu Saleh, OM and Ranganath, N},
title = {From Culture-Negative to DNA-Positive: The Molecular Revolution in Infective Endocarditis Diagnosis.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {6},
pages = {},
pmid = {40559526},
issn = {2076-0817},
mesh = {Humans ; *Endocarditis/diagnosis/microbiology ; *Molecular Diagnostic Techniques/methods ; DNA, Bacterial/genetics ; Metagenomics/methods ; },
abstract = {Infective endocarditis (IE) remains a diagnostic challenge, particularly in cases where microbiological diagnosis is not established. Advances in molecular diagnostics have expanded the ability to identify causative pathogens beyond traditional culture-based methods. This review explores the role of molecular assays, including pathogen-specific PCR, multiplex PCR, broad-range PCR, and shotgun metagenomic sequencing, in diagnosing IE. These molecular techniques enhance pathogen detection, especially in patients with prior antibiotic exposure, and improve diagnostic accuracy in culture-negative IE. Broad-range PCR assays and metagenomic sequencing offer the untargeted detection of a wide spectrum of organisms. Despite their advantages, limitations such as availability, interpretation challenges, and a lack of antimicrobial susceptibility testing remain. A multimodal approach integrating molecular diagnostics with conventional methods is essential to optimize patient management. Further research is needed to refine diagnostic algorithms and improve cost-effectiveness in clinical practice.},
}

Humans
*Endocarditis/diagnosis/microbiology
*Molecular Diagnostic Techniques/methods
DNA, Bacterial/genetics
Metagenomics/methods

@article {pmid40559436,
year = {2025},
author = {Domilescu, I and Miutescu, B and Horhat, FG and Popescu, A and Nica, C and Ghiuchici, AM and Gadour, E and Sîrbu, I and Hutanu, D},
title = {Gut-Microbiome Signatures Predicting Response to Neoadjuvant Chemoradiotherapy in Locally Advanced Rectal Cancer: A Systematic Review.},
journal = {Metabolites},
volume = {15},
number = {6},
pages = {},
pmid = {40559436},
issn = {2218-1989},
abstract = {BACKGROUND AND OBJECTIVES: Rectal cancer management increasingly relies on watch-and-wait strategies after neoadjuvant chemoradiotherapy (nCRT). Accurate, non-invasive prediction of pathological complete response (pCR) remains elusive. Emerging evidence suggests that gut-microbiome composition modulates radio-chemosensitivity. We systematically reviewed primary studies that correlated baseline or on-treatment gut-microbiome features with nCRT response in locally advanced rectal cancer (LARC).

METHODS: MEDLINE, Embase and PubMed were searched from inception to 30 April 2025. Eligibility required (i) prospective or retrospective human studies of LARC, (ii) faecal or mucosal microbiome profiling by 16S, metagenomics, or metatranscriptomics, and (iii) response assessment using tumour-regression grade or pCR. Narrative synthesis and random-effects proportion meta-analysis were performed where data were homogeneous.

RESULTS: Twelve studies (n = 1354 unique patients, median sample = 73, range 22-735) met inclusion. Four independent machine-learning models achieved an Area Under the Receiver Operating Characteristic curve AUROC ≥ 0.85 for pCR prediction. Consistently enriched taxa in responders included Lachnospiraceae bacterium, Blautia wexlerae, Roseburia spp., and Intestinimonas butyriciproducens. Non-responders showed over-representation of Fusobacterium nucleatum, Bacteroides fragilis, and Prevotella spp. Two studies linked butyrate-producing modules to radiosensitivity, whereas nucleotide-biosynthesis pathways conferred resistance. Pooled pCR rate in patients with a "butyrate-rich" baseline profile was 44% (95% CI 35-54) versus 21% (95% CI 15-29) in controls (I[2] = 18%).

CONCLUSIONS: Despite heterogeneity, convergent functional and taxonomic signals underpin a microbiome-based radiosensitivity axis in LARC. Multi-centre validation cohorts and intervention trials manipulating these taxa, such as prebiotics or live-biotherapeutics, are warranted before clinical deployment.},
}

@article {pmid40559193,
year = {2025},
author = {Anselmo, A and Rizzo, F and Gervasi, E and Corrent, L and Ciammaruconi, A and Fillo, S and Fortunato, A and Marella, AM and Costantini, S and Baldassari, L and Lista, F and Ciervo, A},
title = {Tropheryma whipplei and Giardia intestinalis Co-Infection: Metagenomic Analysis During Infection and the Recovery Follow-Up.},
journal = {Infectious disease reports},
volume = {17},
number = {3},
pages = {},
pmid = {40559193},
issn = {2036-7430},
support = {B1519 ESM4 GP//Italian General Secretariat of Defense and the National Armaments Directorate within the "Eu-ropean Biodefence Laboratory Network 2 (EBLN2) project",/ ; },
abstract = {BACKGROUND: Whipple's disease (WD) is a rare infection caused by Tropheryma whipplei. Diagnosis is challenging and requires a combination of several data sets, such as patient history, clinical and laboratory investigations, and endoscopy with histology analyses. While persistent diarrhea is a common symptom, WD can affect multiple organs.

CASE DESCRIPTION: We present the case of a 66-year-old immunocompetent patient with WD and a history of Helicobacter pylori infection who developed chronic diarrhea. Colonoscopy and histopathological analysis revealed the presence of foamy macrophages with periodic acid-Schiff-positive particles. Subsequently, molecular methods confirmed the clinical WD diagnosis and metagenomic analyses further identified a co-infection with Giardia intestinalis. The patient fully recovered after 14 months of antibiotic therapy. During pharmacological treatment, clinical and laboratory follow-ups were conducted at 6 and 12 months, and microbiome profiles were also analyzed to identify the most abundant species in the samples.

CONCLUSION: The metagenomic analyses showed the eradication of the two pathogens and a progressive restoration to a healthy/balanced status after antibiotic therapy.},
}

@article {pmid40559130,
year = {2025},
author = {Chaple-Gil, AM and Santiesteban-Velázquez, M and Urbizo Vélez, JJ},
title = {Association Between Oral Microbiota Dysbiosis and the Risk of Dementia: A Systematic Review.},
journal = {Dentistry journal},
volume = {13},
number = {6},
pages = {},
pmid = {40559130},
issn = {2304-6767},
abstract = {Background/Objectives: Growing evidence suggests that oral microbiota dysbiosis may contribute to the development of systemic conditions, including neurodegenerative diseases. This dysregulation promotes immunoinflammatory responses that are increasingly associated with dementia. This systematic review aimed to evaluate the association between oral microbiota dysbiosis and the risk of dementia in older adults. Methods: Eligible studies evaluated oral microbial composition using validated methods such as genetic sequencing, bacterial culture, or metagenomic analysis. Following PRISMA guidelines and a PICO framework, the review included cohort, case-control, and cross-sectional studies. Searches were conducted across PubMed, Scopus, Web of Science, Embase, and Cochrane Library. Two independent reviewers screened and selected studies, resolving disagreements through a third evaluator. Results: This systematic review revealed that Tannerella forsythia, Fusobacterium nucleatum, Porphyromonas, Prevotella, Leptotrichia, Fusobacteriota, Peptostreptococcaceae, and Candida spp. were consistently associated with Alzheimer's disease and mild cognitive impairment, indicating their potential role in neurodegeneration. In contrast, Streptococcus gordonii, Gemella haemolysans, Rothia, Neisseria, and Haemophilus were reduced in cognitively impaired individuals, suggesting a link with healthy cognition. Studies also showed decreased microbial diversity in Alzheimer's disease and the possible modifying effect of the APOE4 allele. Oral health interventions improved microbial composition and slowed cognitive decline, supporting the diagnostic and therapeutic potential of oral microbiota modulation. Conclusions: The findings suggest that oral microbiota dysbiosis may not only result from cognitive decline but also contribute to its pathogenesis. Future studies with larger and more diverse cohorts are recommended to validate these associations.},
}

@article {pmid40558984,
year = {2025},
author = {Crane, YM and Crane, CF and Subramanyam, S and Schemerhorn, BJ},
title = {Shotgun Metagenome Analysis of Two Schizaphis graminum Biotypes over Time With and Without Carried Cereal Yellow Dwarf Virus.},
journal = {Insects},
volume = {16},
number = {6},
pages = {},
pmid = {40558984},
issn = {2075-4450},
support = {5020-21000-000-D//USDA-ARS Research Project/ ; },
abstract = {The greenbug aphid (Schizaphis graminum (Rondani)) is a major pest of wheat and an important vector of wheat viruses. An RNA-seq study was conducted to investigate the microbial effects of two greenbug genotypes, the presence or absence of cereal yellow dwarf virus, and the condition of the wheat host over a 20-day time course of unrestricted greenbug feeding. Messenger RNA reads were mapped to ca. 47,000 bacterial, 1218 archaeal, 14,165 viral, 571 fungal, and 94 protozoan reference or representative genomes, plus greenbug itself and its wheat host. Taxon counts were analyzed with QIIME2 and DESeq2. Distinct early (days 1 through 10) and late (days 15 and 20) communities differed in the abundance of typical enteric genera (Shigella, Escherichia, Citrobacter), which declined in the late community, while the ratio of microbial to greenbug read counts declined 50% and diversity measures increased. The nearly universal aphid endosymbiont, Buchnera aphidicola, accounted for less than 25% of the read counts in both communities. There were 302 differentially expressed (populated) genera with respect to early and late dates, while 25 genera differed between the greenbug genotypes and nine differed between carrier and virus-free greenbugs. The late community was likely responding to starvation as the wheat host succumbed to aphid feeding. Our results add to basic knowledge about aphid microbiomes and offer an attractive alternative method to assess insect microbiomes.},
}

@article {pmid40558870,
year = {2025},
author = {Abreu, CM and Carneiro, GHF and Costa, MRD and Barroso, GM and Duque, TS and Silva, JMS and Santos, JBD},
title = {Avena sativa as a Multifunctional Tool for Phytoremediation and Bioenergy Production in Sulfentrazone Contaminated Soils.},
journal = {Journal of xenobiotics},
volume = {15},
number = {3},
pages = {},
pmid = {40558870},
issn = {2039-4713},
support = {APQ 01151-23; APQ 00694-23 and, APQ 004955-23//Fundação de Amparo à Pesquisa do Estado de Minas Gerais/ ; 001//National Council for Scientific and Technological Development/ ; },
abstract = {Phytoremediation using Avena sativa offers a sustainable strategy for mitigating sulfentrazone contamination while integrating bioenergy production. This study proposes an analysis of the bioenergy potential and the microbial metagenomic profile associated with Avena sativa in the presence and absence of sulfentrazone, aiming at the synergistic bioprospecting of microbial communities capable of biodegradation and remediation of contaminated environments. Using a randomized block design, we evaluated the bioenergy potential and rhizospheric microbial dynamics of A. sativa in soils with and without sulfentrazone (600 g ha[-1]). Herbicide residues were quantified via UHPLC-MS/MS, and metagenomic profiles were obtained through 16S rRNA gene and ITS region sequencing to assess shifts in rhizospheric microbiota. Microbial diversity was analyzed using the Shannon and Gini-Simpson Indices, complemented by Principal Component Analysis (PCA). Bioenergy yields (biogas and ethanol) were estimated based on plant biomass. Over 80 days, the cultivation of A. sativa promoted a 19.7% dissipation of sulfentrazone, associated with rhizospheric enrichment of plant growth-promoting taxa (Bradyrhizobium, Rhodococcus, and Trichoderma), which increased by 68% compared to uncontaminated soils. Contaminated soils exhibited reduced microbial diversity (Gini-Simpson Index = 0.7), with a predominance of Actinobacteria and Ascomycota, suggesting adaptive specialization. Despite herbicide-induced stress (39.3% reduction in plant height and 60% reduction in grain yield), the biomass demonstrated considerable bioenergy potential: 340.6 m[3] ha[-1] of biogas and 284.4 L ha[-1] of ethanol. The findings highlight the dual role of A. sativa in soil rehabilitation and renewable energy systems, supported by plant-microbe synergies. Scalability challenges and regulatory gaps in ecotoxicological assessments were identified, reinforcing the need to optimize microbial consortia and implement region-specific management strategies. These results support the integration of phytoremediation into circular bioeconomy models, balancing ecological recovery with agricultural productivity. Future research should focus on microbial genetic pathways, field-scale validation, and the development of regulatory frameworks to advance this green technology in global soil remediation efforts.},
}

@article {pmid40558084,
year = {2025},
author = {Brumfield, KD and Enke, S and Swan, BK and Carrasquilla, L and Lee, MD and Stern, DB and Gieser, L and Hasan, NA and Usmani, M and Jutla, AS and Huq, A and Caviness, K and Goodrich, JS and Bull, R and Colwell, RR},
title = {Hybridization capture sequencing for Vibrio spp. and associated virulence factors.},
journal = {mBio},
volume = {},
number = {},
pages = {e0051625},
doi = {10.1128/mbio.00516-25},
pmid = {40558084},
issn = {2150-7511},
abstract = {Proliferation of Vibrio spp. in aquatic ecosystems is associated with climate change and, concomitantly, increased incidence of vibriosis. They are autochthonous to aquatic environments globally, but traditional metagenomic methods for detecting and typing pathogenic Vibrio spp. are challenged by their presence in relatively low abundance and ability to persist in a viable but nonculturable state. In the study reported here, hybridization capture sequencing (HCS) was employed to profile low-abundance Vibrio spp. in environmental samples. The HCS panel targeted a family of molecular chaperones (CPN60) specific to 69 Vibrio spp. and 162 Vibrio-specific virulence factors. This approach was evaluated in parallel with traditional whole-community shotgun sequencing in a metagenomic analysis of water and oyster samples collected from the Chesapeake Bay. In addition, Vibrio parahaemolyticus and Vibrio vulnificus strains isolated from the samples were subjected to whole-genome sequencing to determine the genetic characteristics of pathogenic Vibrio spp. circulating in an aquatic environment. HCS, employed to determine the incidence and characterization of specific Vibrio spp., yielded significantly greater metagenomic insight, notably a variety of other Vibrio spp., including detection of Vibrio cholerae, Vibrio fluvialis, and Vibrio aestuarianus, in addition to Vibrio parahaemolyticus and Vibrio vulnificus, and also important virulence factors not detectable using traditional molecular methods. Thus, pathogenic Vibrio spp. in aquatic ecosystems may be far more common than currently understood. It is concluded that environmental surveillance should include HCS, a valuable tool for the detection and characterization of pathogenic agents in aquatic ecosystems, notably vibrios.IMPORTANCEThe increasing prevalence of pathogenic Vibrio spp. in aquatic ecosystems, driven by climate change, is closely linked to a rise in cholera and vibriosis cases, emphasizing the need for improved environmental surveillance. Vibrios are naturally occurring in aquatic environments globally, but traditional metagenomic methods for detecting and typing pathogenic Vibrio spp. are challenged by their presence in relatively low abundance and ability to persist in a viable but nonculturable state. In the study reported here, hybridization capture sequencing was employed to profile low-abundance Vibrio spp. in metagenomic samples, namely water and oysters collected from the Chesapeake Bay. This approach was evaluated in parallel with traditional whole-community shotgun sequencing and whole-genome sequencing of Vibrio parahaemolyticus and Vibrio vulnificus strains isolated from the samples. Results suggest pathogenic Vibrio spp. in aquatic ecosystems may be far more common than currently understood, when multiple methods are considered for environmental surveillance.},
}

@article {pmid40558050,
year = {2025},
author = {Phan, J and Jain, S and Nijkamp, JF and Sasidharan, R and Agarwal, A and Bird, JK and Spooren, A and Wittwer Schegg, J and Ver Loren van Themaat, E and Mak, TN},
title = {Gut health predictive indices linking gut microbiota dysbiosis with healthy state, mild gut discomfort, and inflammatory bowel disease phenotypes using gut microbiome profiling.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0027125},
doi = {10.1128/spectrum.00271-25},
pmid = {40558050},
issn = {2165-0497},
abstract = {Despite the complexity of the gut microbiome, several scores that use taxonomic characteristics exist that attempt to identify a healthy gut or gastrointestinal disease. Two systems in use are the metagenomic aerotolerant predominance index (MAPI) and keystone scores. The aim of this analysis was to compare different gut microbiome scores, specifically MAPI and a keystone species score, on two cross-sectional data sets and to investigate correlations of these scores with self-reported gut discomfort and gastrointestinal disease. The first data set is a commercial data set (Sun Genomics data set) with whole-genome shotgun sequencing samples from 5,372 customers. The second data set is curated from publicly available data (public data set) with 2,415 samples from participants in human studies with gut-related taxonomic profiles. MAPI scores and keystone species scores were calculated using standard methodology. The MAPI score was significantly lower in men for the public data set. There was a graded response for both the MAPI and keystone scores between healthy subjects, subjects with mild gastrointestinal discomfort, and patients with gastrointestinal disease: the MAPI score was higher, and the keystone score was lower in subjects with gastrointestinal discomfort or with inflammatory bowel disease patients. The keystone and MAPI scores have the potential to help identify factors associated with gut microbial dysbiosis and gastrointestinal discomfort or disease. Furthermore, given the functional link of the MAPI score to oxidative stress in the microbiome, the scores can help to identify conditions where oxidative stress is one of the hallmarks of dysbiosis.IMPORTANCEGut bacteria play a role in both mild gastrointestinal discomfort, which includes bloating and constipation, and inflammatory bowel disease. There are many different types of bacteria in the gut, and gut microbiome composition differs greatly between different people. Therefore, it is difficult to predict who has a gut microbiome associated with a healthy gut and who might develop disease or experience gut discomfort. Several scoring systems have been developed to categorize gut health states. This analysis compared two different scoring systems using data from two different sources to see how well they could identify people with gastrointestinal disease, gastrointestinal complaints, or a healthy gut. The scoring systems showed similar trends according to gut health status: groups of people with gut bacteria imbalance or gut disease had a different score than groups of people with healthy gut bacteria.},
}

@article {pmid40557789,
year = {2025},
author = {Jones, KS and Pilliod, DS and Aunins, AW},
title = {Metabarcoding Analysis of Arthropod Pollinator Diversity: A Methodological Comparison of eDNA Derived From Flowers and DNA Derived From Bulk Samples of Insects.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e70003},
doi = {10.1111/mec.70003},
pmid = {40557789},
issn = {1365-294X},
support = {//U.S. Bureau of Land Management/ ; //U.S. Geological Survey/ ; },
abstract = {Limitations of traditional insect sampling methods have motivated the development and optimisation of new non-lethal methods capable of quantifying diverse arthropod communities. Environmental DNA (eDNA) metabarcoding using arthropod-specific primers has recently been investigated as a novel way to characterise arthropod communities from the DNA they deposit on the surface of plants. This sampling method has had demonstrated success, but pollinators-especially bees-are oddly underrepresented in these studies. To evaluate this inconsistency, we investigated the limitations of eDNA metabarcoding for bees and other pollinators. We compared pollinator diversity derived from eDNA extracted from flowers and DNA extracted from pulverised bulk samples of insects collected from vane traps deployed at the same sites using three metabarcoding primers, two of which target arthropods generally (COI-Jusino and 16S-Marquina) and one that targets bumblebees (Bombus spp., COI-Milam). Across methods, we detected 77 insect families from 9 orders. The COI-Jusino marker amplified the highest taxonomic diversity compared to 16S-Marquina and COI-Milam. More amplicon sequence variants (ASVs) were recovered from vane traps (blue: 1357, yellow: 1542) than flowers (245), but only 23% of families and 13% of genera were shared among methods, indicating that flowers and blue and yellow vane traps may each sample different parts of the available arthropod community. Of 29 flower samples with known bee visitations, only 10 samples had bee detections from eDNA, and incomplete reference databases hindered assignment to species. Although our study provides additional evidence for the usefulness of eDNA metabarcoding for characterising arthropod communities, significant challenges remain when using eDNA metabarcoding methods to identify and quantify pollinator communities, especially bees.},
}

@article {pmid40557508,
year = {2025},
author = {Schroeder, TH and Vanwynsberghe, M and Dervishi, A and Stäudle, H},
title = {Detection of pathogenic microorganisms using metagenomic next generation sequencing for patients with suspected infection presenting in the emergency department.},
journal = {European journal of emergency medicine : official journal of the European Society for Emergency Medicine},
volume = {32},
number = {4},
pages = {288-290},
doi = {10.1097/MEJ.0000000000001239},
pmid = {40557508},
issn = {1473-5695},
}

@article {pmid40557420,
year = {2025},
author = {Girard, M and Vandamme, L and Cazaux, B and Limasset, A},
title = {OReO: optimizing read order for practical compression.},
journal = {Bioinformatics advances},
volume = {5},
number = {1},
pages = {vbaf128},
pmid = {40557420},
issn = {2635-0041},
abstract = {MOTIVATION: Recent advances in high-throughput and third-generation sequencing technologies have created significant challenges in storing and managing the rapidly growing volume of read datasets. Although more than 50 specialized compression tools have been developed, employing methods such as reference-based approaches, customized generic compressors, and read reordering, many users still rely on common generic compressors (e.g. gzip, zstd, xz) for convenience, portability, and reliability, despite their low compression ratios. Here, we introduce Optimizing Read Order (OReO), a simple read-reordering framework that achieves high compression performance without requiring specialized software for decompression. By grouping overlapping reads together before applying generic compressors, OReO exploits inherent redundancies in sequencing data and achieves compression ratios on par with state-of-the-art tools. Moreover, because it relies only on standard decompressors, OReO avoids the need for dedicated installations and maintenance, removing a key barrier to practical adoption.

RESULTS: We evaluated OReO on both Oxford Nanopore Technologies (ONT) and HiFi genomic and metagenomic datasets of varying sizes and complexities. Our results demonstrate that OReO provides substantial compression gains with comparable resource usage and outperforms dedicated methods in decompression speed. We propose that future compression strategies should focus on reordering as a means to let generic compression tools fully exploit data redundancy, offering an efficient, sustainable, and user-friendly solution to the growing challenges of sequencing data storage.

The OReO code is open source and available at github.com/girunivlille/oreo.},
}

@article {pmid40557317,
year = {2025},
author = {Ding, Y and Jing, C and Wei, J and Wang, D and Li, W and Wang, M and Zhou, J and Qian, Q and Sun, W},
title = {Comparison of the diagnostic capabilities of tNGS and mNGS for pathogens causing lower respiratory tract infections: a prospective observational study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1578939},
pmid = {40557317},
issn = {2235-2988},
mesh = {Humans ; *Respiratory Tract Infections/diagnosis/microbiology ; Male ; Prospective Studies ; Female ; Middle Aged ; Bronchoalveolar Lavage Fluid/microbiology/virology ; Sensitivity and Specificity ; Aged ; Adult ; China ; *High-Throughput Nucleotide Sequencing/methods ; Bacteria/isolation & purification/genetics/classification ; Fungi/isolation & purification/genetics ; *Molecular Diagnostic Techniques/methods ; },
abstract = {AIMS: Pathogens in lower respiratory tract infections(LRTI) are complex. Conventional microbiological testings(CMTs) are time-consuming and inaccurate. mNGS is widely used to overcome these issues. tNGS, as an emerging NGS technology, has uncertain diagnostic efficacy.

MATERIALS AND METHODS: 136 suspected LRTI patients were included from January 2022 to February 2024 from the Department of Respiratory and Critical Care Medicine at Jiangsu Province People's Hospital,China.We simultaneously submitted the bronchoalveolar lavage fluids (BALFs) for mNGS, tNGS and conventional microbial testing (CMTs) and compared the pathogen diagnostic efficacy of mNGS, and tNGS.

RESULTS: A total of 136 patients were included, and there was no statistically significant difference in the detection sensitivity(74.75% VS 78.64%, p>0,05) and specificity(81.82% vs 93,94%,p>0.05) between mNGS and tNGS. However, tNGS has a higher sensitivity(27.94% vs 17.65%,p=0.043)and specificity(88.78% vs 84.82%,p=0.048) for fungi. According to our diagnostic criteria, tNGS successfully identified 3 cases of Pneumocystis jirovecii(P. jirovecii) individually. In addition, both tNGS and mNGS detected chlamydia psittaci whereas CMTs were unable to detect it.

CONCLUSIONS: tNGS demonstrates diagnostic efficacy for pathogens in lower respiratory tract infections that is comparable to mNGS. However, tNGS has specific advantages in the detection of fungi. Considering the cost-effectiveness of tNGS, it is recommended to implement tNGS clinically for patients with lower respiratory tract infections.},
}

Humans
*Respiratory Tract Infections/diagnosis/microbiology
Male
Prospective Studies
Female
Middle Aged
Bronchoalveolar Lavage Fluid/microbiology/virology
Sensitivity and Specificity
Aged
Adult
China
*High-Throughput Nucleotide Sequencing/methods
Bacteria/isolation & purification/genetics/classification
Fungi/isolation & purification/genetics
*Molecular Diagnostic Techniques/methods

@article {pmid40557154,
year = {2025},
author = {Bai, X and Raju, SC and Knudsen, AD and Thudium, RF and Arentoft, NS and Gelpi, M and Heidari, SL and Kunisaki, KM and Kristiansen, K and Hov, JR and Nielsen, SD and Trøseid, M},
title = {Microbiome profiling reveals gut bacterial species associated with rapid lung function decline in people with HIV.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1555441},
pmid = {40557154},
issn = {1664-3224},
mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; Female ; *HIV Infections/microbiology/complications/physiopathology ; Middle Aged ; Dysbiosis ; *Lung/physiopathology ; *Bacteria/genetics/classification ; Adult ; *Lung Diseases/microbiology ; Respiratory Function Tests ; Aged ; },
abstract = {BACKGROUND: People with HIV (PWH) have an increased risk of pulmonary comorbidities compared to people without HIV. The gut microbiome regulates host immunity and is altered in PWH. This study aims to determine potential associations between gut microbiome, lung function decline, and airflow limitation in PWH.

METHODS: PWH from the Copenhagen Comorbidity in HIV Infection (COCOMO) Study with available lung function testing and microbiome data were included (n=385). The gut microbiome was characterized using shotgun metagenomic sequencing. Associations between gut microbiome, rapid lung function decline, and airflow limitation were analysed in multivariable logistic regressions adjusted for traditional and HIV-associated risk factors for lung disease.

RESULTS: Several bacterial species were significantly enriched in PWH with rapid lung function decline, including opportunistic pathogenic bacterial species Bacteroides coprophilus, Klebsiella michiganensis, and Clostridium perfringens. A gut microbial dysbiosis index based on compositional changes was associated with rapid lung function decline (adjusted odds ratio (aOR) 1.18, 95% confidence interval (CI) [1.11-1.27], p<0.001), and airflow limitation (aOR 1.16, 95% CI [1.04-1.29], p=0.007) in adjusted multivariable logistic regression analyses.

CONCLUSION: Associations between the gut dysbiosis index and rapid lung function decline and airflow limitation suggest a potential role of certain gut bacterial species in the pathogenesis of pulmonary comorbidities in PWH.},
}

Humans
*Gastrointestinal Microbiome
Male
Female
*HIV Infections/microbiology/complications/physiopathology
Middle Aged
Dysbiosis
*Lung/physiopathology
*Bacteria/genetics/classification
Adult
*Lung Diseases/microbiology
Respiratory Function Tests
Aged

@article {pmid40556944,
year = {2025},
author = {Chen, Y and Fan, B and Zeng, J and Zou, Y and Tao, C and Chen, C and Zhang, P and Liang, J and Qi, F and Tang, H and Lu, L},
title = {Single-Cell RNA Transcriptomics and Multi-omics Analyses Reveal the Clinical Effects of Acupuncture on Methadone Reduction.},
journal = {Research (Washington, D.C.)},
volume = {8},
number = {},
pages = {0741},
pmid = {40556944},
issn = {2639-5274},
abstract = {Opioid use disorders (OUDs) pose a substantial global health burden, with methadone maintenance treatment (MMT) widely adopted as an intervention; however, MMT is associated with immunosuppression, metabolic disturbances, and dysbiosis of the gut microbiota. Despite the potential of acupuncture in reducing methadone dosages and opioid addiction, the underlying biological mechanisms remain unclear. Therefore, we aimed to integrate clinical trial data with multi-omics analysis, including single-cell sequencing, transcriptomics, metabolomics, and metagenomics, to evaluate the effects of acupuncture in patients undergoing MMT. We collected peripheral blood mononuclear cells, plasma, and fecal samples from 48 MMT participants in a randomized, placebo-controlled trial. Participants were divided into acupuncture (n = 25) and sham-acupuncture (n = 23) groups. After 8 weeks of intervention, 84% of patients in the acupuncture group achieved ≥20% reduction in methadone dosage, compared to 39% in the sham-acupuncture group (P < 0.01). Our findings revealed that acupuncture may activate the defense response to viruses, with altered immune cell functions in classical monocytes correlating with clinical responses to reduced methadone doses. Acupuncture might ameliorate intestinal microbial disruptions caused by OUD by up-regulating Bilophila and modulating bile acid metabolism. Furthermore, acupuncture up-regulated galectin-9 (LGALS9)-mediated intercellular communication between classical monocytes and other immune subsets. To further validate the mechanistic link between bile acid metabolism and immune regulation, we conducted in vitro experiments using THP-1 monocytes treated with cholic acid. The results showed that bile acid exposure suppressed galectin-9 and IFN-γ expression, while low-dose bile acid (simulating acupuncture effects) partially reversed this effect. These findings support a bile acid-galectin-interferon axis that may be modulated by acupuncture in OUD. Collectively, our results provide clinical and mechanistic evidence supporting acupuncture as a potential adjunct therapy to mitigate the adverse effects of long-term opioid use.},
}

@article {pmid40556900,
year = {2025},
author = {Zhang, Q and Wang, X and Cheng, P and Huo, S and Liu, C and Yu, Z},
title = {Editorial: Recent advances in agricultural waste recycling by microorganisms and their symbiosis.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1631828},
doi = {10.3389/fmicb.2025.1631828},
pmid = {40556900},
issn = {1664-302X},
}

@article {pmid40556899,
year = {2025},
author = {Ning, T and Zheng, X and Liang, J and Wang, W and Zhang, G and Wei, X and Tan, L},
title = {Effect of different bulking agents on the quality, microbial community structure and metabolic functions during human feces composting in foam composting device.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1556537},
pmid = {40556899},
issn = {1664-302X},
abstract = {Aerobic composting represents an efficacious strategy for the disposal of human feces, yet investigations into the effects of different bulking agents on this process remain limited. This study investigated the effects of composting human feces with four types of bulking agents-wheat straw, corn straw, millet straw, and sawdust-in a foam composting device, as well as the impacts of the process on the microbial community structure and metabolic functions adopting sequencing data analysis and metagenomic analysis. The results demonstrate that aerobic composting can safely treat human feces, resulting in a mature compost product. Comparative assessments of compost quality and microbial profiles with various bulking agents indicated superior performance of corn straw compost, surpassing those produced with wheat straw, millet straw, and sawdust in terms of humification level (HA/FA = 2.9), peak temperature reached (71.2°C), composting duration (20 days), and nutrient composition (TN 42.87 g/kg). Additionally, the diversity and dominance of certain microbial colonies (Firmicutes, Actinobacteria, Proteobacteria, and Bacteroidota) were significantly higher in composts formulated with corn straw. The metagenomic data analysis reveals significant differences in the abundance of "carbon metabolism" and "microbial metabolism" among different groups, further indicating that the addition of different bulking agents affects the utilization of metabolic products, amino acids, and carbohydrates as carbon sources by microbes in human feces compost. Consequently, leveraging corn straw as a bulking agent, given its abundant availability, could potentially improve the efficiency and outcome of the human feces composting process.},
}

@article {pmid40556897,
year = {2025},
author = {Lu, L and Huang, X and Zheng, P and Wei, S and Jiao, N and Zhang, R and Li, X and Yang, Y},
title = {Two novel phages infecting Erythrobacter isolated from the epipelagic ocean.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1592355},
pmid = {40556897},
issn = {1664-302X},
abstract = {Erythrobacter, an aerobic anoxygenic photoheterotrophic bacterial genus, plays a vital role in carbon and energy cycling in marine environments. However, their phage predators remain poorly understood, with only two strains previously reported. This study isolated and characterized a novel Erythrobacter phage, vB_EauS-R34L1 (R34L1), and its sub-strain vB_EauS-R34L2 (R34L2), from coastal seawater. Both phages exhibit long-tailed, icosahedral morphologies and relatively narrow but slightly different host ranges. One-step growth curve analysis revealed a 160-min latent period and burst sizes of 81 and 91 PFU/cell for R34L1 and R34L2, respectively. Genomic analysis showed that the phages possess dsDNA genomes of 56,415 bp (R34L1) and 54,924 bp (R34L2), with G + C contents of 61.60 and 61.19%, respectively. Both phages harbor a suite of unique genes, including GapR and GH19, which are crucial for host interaction and ecological functionality. Blastn analysis indicated a 99.73% genome similarity between them. Taxonomic and phylogenetic analyses positioned them in a novel viral genus cluster, Eausmariqdvirus, under the family Casjensviridae, indicating a distant evolutionary relationship with known phages. Metagenomic queries suggested that R34L1- and R34L2-like phages are exclusively abundant in temperate and tropical epipelagic zones. This study expands our understanding of Erythrobacter phages and provides insights into their ecological roles in marine ecosystems.},
}

@article {pmid40556523,
year = {2025},
author = {Huang, J and Liang, W and Zhang, R and Zhao, Y and Shi, R and Chen, X and Zheng, Y and Li, X and Liu, D and Wang, H and Liu, J and Liao, Y and Zhang, X and Jiang, Z and Fu, C and Huang, T and Shan, X and Wang, W and Bu, J and Peng, T and Shen, E},
title = {Pou2af1 Deficiency Aggravates DSS-Induced Colitis via Impaired Germinal Center Responses and Altered Gut Microbiota.},
journal = {Inflammatory bowel diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/ibd/izaf089},
pmid = {40556523},
issn = {1536-4844},
support = {//The Affiliated Qingyuan Hospital/ ; 202301-316//Guangzhou Medical University/ ; JCXKJS2021C11//Discipline from School of Basic Medicine of Guangzhou Medical University/ ; 2021KTSCX090//Department of Education of Guangdong Province/ ; //Guangzhou Medical University 2022 Student Innovation Ability Improvement Program/ ; },
abstract = {BACKGROUND: Bob1 plays a critical role in immune system regulation, particularly in the function of B cells. Its deficiency in the context of colitis remains underexplored. This study investigates the effects of Bob1 (Pou2af1) deficiency on colitis, particularly focusing on immune responses and gut microbiota alterations in a murine model.

METHODS: In this study, we employed Pou2af1 knockout (KO) and wild-type (WT) mice to investigate the role of Bob1 in dextran sodium sulfate (DSS)-induced colitis. Colitis was induced by administering 2.5% DSS in drinking water for 7 days. Mice were monitored daily for weight loss, stool consistency, and rectal bleeding to calculate the disease activity index (DAI). Colon length was measured, and colon tissues were collected for histological analysis using hematoxylin and eosin (H&E) staining. Flow cytometry was performed to assess germinal center responses as well as the proportion of T helper (Th)1 and Th17 cells in the colonic lamina propria. Metagenomic sequencing was conducted on fecal samples to evaluate gut microbiota composition.

RESULTS: Pou2af1-deficient mice exhibited significantly exacerbated colitis compared to WT mice. This was evidenced by greater weight loss, elevated disease activity index, reduced colon length, and more severe pathological changes. Immune analysis revealed an impaired germinal center response, diminished generation of IgA⁺ plasma cells, and decreased Th17 cells in the colonic lamina propria in Pou2af1-deficient mice. Additionally, microbiota analysis indicated dysbiosis in the Pou2af1-deficient group, with a notable decrease in Bacteroides species and an increase in pro-inflammatory microbes.

DISCUSSION: The findings suggest that Pou2af1 deficiency exacerbates DSS-induced colitis by impairing immune responses, particularly the germinal center reaction, and altering gut microbiota composition. These alterations contribute to increased disease severity, highlighting the importance of Pou2af1 in maintaining intestinal immune homeostasis.},
}

@article {pmid40556381,
year = {2025},
author = {Zhao, S and Xu, Q and Li, M and Chen, J and Francis, F and Dai, X and Tan, J and Kong, Z},
title = {Exploring the Impact of Dinotefuran Residue on Microbial Community and Flavor Generation in Huangjiu Fermentation.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c02308},
pmid = {40556381},
issn = {1520-5118},
abstract = {Pesticide residues create food safety hazards while negatively affecting the quality of fermented foods, but the mechanisms of the deterioration response have been a mystery. In this study, headspace solid-phase microextraction gas chromatography-mass spectrometry (HS-SPME-GC-MS) and metagenomics sequencing analyses were employed to investigate the effect of dinotefuran residue on the aroma profile and microbial community of Huangjiu. The presence of dinotefuran led to a reduction in the overall concentration of volatile compounds, and some floral, fruity, and sweet aromas such as piperitenol, citronellyl isobutyrate, and trans-2-decenal were no longer detected. Meanwhile, the levels of certain acidic volatiles, including formic acid, propionic acid, and heptanoic acid, increased and contributed to off-flavors. Dinotefuran affected the Huangjiu flavor by modifying the abundance and structure of key genera such as Saccharomyces, Lactococcus, and Cyberlindnera. These changes were associated with disturbances in 16 KEGG tertiary metabolic pathways, including glycolysis, pyruvate metabolism, and amino acid biosynthesis. These results provided some reference for further studies on how pesticide residues affect the flavor and microbial characteristics of traditional fermented beverages like Huangjiu.},
}

@article {pmid40555957,
year = {2025},
author = {Gonçalves, OS and Fernandes, AS and de Sousa, TGG and Santana, MF and Barreto, CC},
title = {From cultivation challenges of Acidobacteriota to biotechnological promises - unveiling what is needed to fully harness their potential.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {7},
pages = {208},
pmid = {40555957},
issn = {1573-0972},
support = {00//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; 5.10/2022//Fundação de Amparo à Pesquisa do Estado de Minas Gerais/ ; 402644/2021-2//Fundação de Amparo à Pesquisa do Estado de Minas Gerais/ ; APQ-02381-21//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; },
mesh = {*Biotechnology/methods ; Biodegradation, Environmental ; Genome, Bacterial ; Industrial Microbiology ; Genomics ; },
abstract = {Acidobacteriota are currently well-known for their ubiquity and metabolic versatility. Their environmental importance is the subject of many studies, but their biotechnological applications still need to be explored. Although they are considered hard-to-culture bacteria, many genomes are available, which reveals promising biotechnological potential. Despite these promising features, the application of Acidobacteriota in biotechnology remains underexplored. In this context, we review key findings regarding the potential applications of Acidobacteriota, emphasizing advancements derived from genomic, metagenomic, and culture-based studies. We specifically focus on their ability to produce enzymes and other bioactive molecules, their antimicrobial properties, and their potential applications in agriculture and bioremediation. Furthermore, we discuss strategies to overcome the challenges associated with culturing and manipulating these bacteria, such as heterologous expression and other emerging techniques related to -omics and computational approaches. These strategies could provide deeper insights into Acidobacteriota's metabolism, including their biosynthetic pathways and interactions within microbial consortia. Ultimately, this understanding could lead to broader applications of Acidobacteriota in environmental and industrial biotechnology.},
}

*Biotechnology/methods
Biodegradation, Environmental
Genome, Bacterial
Industrial Microbiology
Genomics

@article {pmid40555791,
year = {2025},
author = {Lin, S and Sun, Z and Zhu, X and Wang, M and Zhang, Q and Qian, J and Zhang, H and Mei, Z and Pu, Y and Kong, M and Guo, P and Zhou, X and Li, J and Sun, X and Ma, L and Zhang, X and Zhao, F and Nie, J and Hong, S and Chen, J and Wang, X and Li, X and Zheng, Y},
title = {Segatella copri and gut microbial ammonia metabolism contribute to chronic kidney disease pathogenesis.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {40555791},
issn = {2058-5276},
abstract = {Alterations in gut microbiota have been linked to chronic kidney disease (CKD), but large-scale studies and mechanistic insights are limited. Here we analysed gut metagenome data from 1,550 older individuals (aged 65-93 years) with comprehensive kidney function measurements. Segatella copri was positively associated with kidney function through microbial ammonia metabolism-related pathways and the asnA gene, which encodes an ammonia-assimilating enzyme. These associations were replicated in two external studies. In mice, ammonia supplementation increased serum levels of creatinine and blood urea nitrogen, accelerating CKD progression. In vitro cultures of S. copri or asnA-overexpressing Escherichia coli reduced ammonia concentrations, which was markedly attenuated in asnA-knockout S. copri. Gavage of either S. copri or asnA-overexpressing E. coli, but not asnA-knockout S. copri, mitigated ammonia-induced CKD progression in mice. These findings highlight the role of gut microbial ammonia metabolism in CKD pathogenesis and underscore the therapeutic potential of microbial-based interventions.},
}

@article {pmid40555747,
year = {2025},
author = {Jarman, JB and Torres, PJ and Stromberg, S and Sato, H and Stack, C and Ladrillono, A and Pace, S and Jimenez, NL and Haselbeck, RJ and Insel, R and Van Dien, S and Culler, SJ},
title = {Bifidobacterium deficit in United States infants drives prevalent gut dysbiosis.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {867},
pmid = {40555747},
issn = {2399-3642},
mesh = {Humans ; *Bifidobacterium/isolation & purification/genetics ; *Gastrointestinal Microbiome ; *Dysbiosis/epidemiology/microbiology ; Infant ; United States/epidemiology ; Female ; Male ; Infant, Newborn ; Metagenomics ; },
abstract = {The composition of the infant gut microbiome is critical to immune development and noncommunicable disease (NCD) trajectory. However, a comprehensive evaluation of the infant gut microbiome in the United States is lacking. The My Baby Biome study, designed to address this knowledge gap, evaluated the gut microbiomes of 412 infants (representative of U.S. demographic diversity) using metagenomics and metabolomics. Regardless of birth mode and/or feeding method, widespread Bifidobacterium deficit was observed, with approximately 25% of U.S. infants lacking detectable Bifidobacterium. Bifidobacterium-dominant microbiomes exhibit distinct features when compared to microbiomes with other dominant microbial compositions including reduced antimicrobial resistance and virulence factor genes, altered carbohydrate utilization pathways, and altered metabolic signatures. In C-section birth infants, Bifidobacterium tended to be replaced in the human milk oligosaccharide utilization niche with potentially pathogenic species. Longitudinal health outcomes from these infants suggest that the disappearance of key Bifidobacterium may contribute to the development of atopy.},
}

Humans
*Bifidobacterium/isolation & purification/genetics
*Gastrointestinal Microbiome
*Dysbiosis/epidemiology/microbiology
Infant
United States/epidemiology
Female
Male
Infant, Newborn
Metagenomics

@article {pmid40555322,
year = {2025},
author = {Ying, S and Zhang, Z and Xiang, R},
title = {Metagenomic and Whole-Genome Characterization of Carbapenem-Resistant Acinetobacter baumannii Carrying blaOXA-23 Gene within the Tn2006 Transposon Among ICU Patients.},
journal = {Journal of global antimicrobial resistance},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jgar.2025.06.009},
pmid = {40555322},
issn = {2213-7173},
abstract = {PURPOSE: To characterize carbapenem-resistant Acinetobacter baumannii carrying blaOXA-23 genes within the Tn2006 transposon using metagenomic and whole-genome sequencing, focusing on their genetic features, antimicrobial resistance, and potential for clonal spread and horizontal gene transfer among ICU patients.

METHODS: Bronchoalveolar lavage fluid samples from 28 ICU patients were analyzed using mNGS to detect pathogens and resistance genes. A. baumannii isolates underwent whole-genome sequencing for genetic diversity assessment. Antimicrobial susceptibility testing and comparative genomic analysis were performed.

RESULTS: mNGS revealed mixed infections in 71.4% of patients, identifying multiple bacteria, viruses, fungi, and mycoplasma species. A. baumannii was detected in 25 samples, often alongside other pathogens. All isolates harbored blaOXA-23 within Tn2006 on the chromosome and belonged to sequence type ST2, indicating clonal dissemination despite significant genetic diversity (up to 2,969 SNP differences). The isolates were highly resistant to multiple antibiotics but remained susceptible to tigecycline and colistin. Comparative genomic analysis with 238 global CRAB genomes confirmed the prevalence of the Tn2006 transposon carrying blaOXA-23 in ST2 strains, emphasizing the potential for rapid spread of this resistance mechanism.

CONCLUSION: The widespread presence of multidrug-resistant A. baumannii carrying blaOXA-23 within Tn2006 among ICU patients poses a significant public health concern. The high rate of mixed infections and the potential for horizontal gene transfer complicate infection management in critically ill patients. Enhanced infection control measures, continuous surveillance, and targeted interventions are urgently needed to prevent further dissemination of these resistant strains in hospital settings.},
}

@article {pmid40555025,
year = {2025},
author = {Lin, Z and Pang, S and Wu, Y and Xu, T and Zhou, YL and Li, H and Zhang, C and Qian, PY and Zhang, S},
title = {Biodiversity and nitrogen metabolism in the plastisphere impacted by urban nitrogen loading from a coastal mega-city.},
journal = {Journal of hazardous materials},
volume = {495},
number = {},
pages = {139012},
doi = {10.1016/j.jhazmat.2025.139012},
pmid = {40555025},
issn = {1873-3336},
abstract = {The plastisphere, recognized for vast biomass and critical role in nitrogen cycling, is becoming a pertinent component of marine ecosystems. The relationship between plastisphere and increased nitrogen inputs from urban wastewater in coastal zones remains poorly understood. Through metagenomics, metatranscriptomics and metabolomics, this research sought to elucidate the plastisphere's reaction to elevated nitrogen loading and pinpoint key microbial resources that can be harnessed. Although the archaeal community composition within the plastisphere remains largely unchanged by nitrogen loading, bacterial diversity experiences a substantial boost, which is inversely correlated with fungal diversity. Furthermore, such conditions are associated with reduced intricate microbial interactions. Moreover, the plastisphere subjected to nitrogen loading shows an enrichment of genera and genes implicated in ammonium assimilation, denitrification and dissimilatory nitrate reduction to ammonium (DNRA). Metabolomics analysis highlighted the plastisphere's accumulation of L-glutathione oxidized (GSSG) in response to nitrogen loading. The research further highlighted a quartet of microbial phyla-Actinomycetota, Bacteroidota, Cyanobacteriota, and Pseudomonadota-that not only thrive but also constitute pivotal microbial resources within the plastisphere when confronted with strong nitrogen loading. In essence, this investigation illuminates the plastisphere's biodiversity dynamics and nitrogen metabolic adjustments during augmented nitrogen loading and offers novel perspectives on taking advantage of the plastisphere's untapped microbial potential.},
}

@article {pmid40554894,
year = {2025},
author = {Zheng, SJ and Gao, XY and Diao, XH and Chen, ND},
title = {Dendrobium huoshanense improves atherosclerosis in high-fat-induced ApoE mice by regulating gut microbiota and serum metabolite profiles.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {145},
number = {},
pages = {156964},
doi = {10.1016/j.phymed.2025.156964},
pmid = {40554894},
issn = {1618-095X},
abstract = {BACKGROUND: Cardiovascular diseases, particularly atherosclerosis (AS), remain leading causes of mortality, with limited effective treatments available. Dendrobium huoshanense, a traditional medicinal herb, has shown promising anti-inflammatory and antioxidant effects, but its cardiovascular protective potential remains underexplored.

PURPOSE: This study aimed to explore the protective effects of Dendrobium huoshanense polysaccharides (DHP) against AS and elucidate the underlying mechanisms involved.

METHODS: An ApoE(-/-) mice model of AS was established, and DHP was administered at different concentrations via gavage. After 14 weeks, serum and fecal samples were collected. The effects of DHP on lipid profiles, aortic plaques, matrix metalloproteinases (MMP-2 and MMP-9), and the Nrf2/HO-1 pathway were assessed. Additionally, metagenomic sequencing of fecal samples and untargeted metabolomics of serum were conducted and correlations between these findings were explored.

RESULTS: DHP improved lipid profiles, reduced reactive oxygen species (ROS) and malondialdehyde (MDA) levels, and enhanced superoxide dismutase (SOD) activity. It stabilized aortic plaques, suppressed MMP-2 and MMP-9 overexpression, and activated the Nrf2/HO-1 pathway. DHP also promoted gut microbiota balance, increasing Mucispirillum, Bifidobacterium, and Faecalibaculum while decreasing Desulfovibrionaceae and Eubacterium. Metabolomics revealed alterations in metabolites, including taurochenodeoxycholic acid and ursocolic acid, influencing amino acid, glycerophospholipid, and bile acid metabolism.

CONCLUSIONS: DHP effectively lowers lipid levels, stabilizes aortic plaques, restores gut microbiota balance, and corrects metabolic disturbances, thereby inhibiting the progression of atherosclerosis. These findings provide a scientific basis for the clinical use of DHP in AS prevention and treatment.},
}

@article {pmid40554566,
year = {2025},
author = {Calderón-Ezquerro, MC and Brunner-Mendoza, C and Guerrero-Guerra, C and Sanchez-Flores A, A and Salinas-Peralta, I and Toriello, C and Ponce-de León, A and Ortega-Rosas C I, CI},
title = {Genetic sequencing of the airborne fungal spectrum and air quality at a public hospital in Mexico City.},
journal = {PLOS global public health},
volume = {5},
number = {6},
pages = {e0004784},
pmid = {40554566},
issn = {2767-3375},
abstract = {Hospital bioaerosols represent significant risks for nosocomial infections, contributing to patient morbidity and mortality. Exposure to these particles, particularly airborne fungal spores or propagules, can trigger adverse effects on the immune system and cause respiratory diseases. This study evaluated the airborne fungal community in a public hospital in Mexico City using a metagenomic approach, two types of aerobiological samplers as well as temperature, humidity, and suspended particle analysis. Sampling was carried out in three areas within the hospital: and outside the hospital. Airborne sampling was performed for three consecutive days, except in the EU. The results showed that using two different samplers revealed fungal diversity and composition variations. Specifically, the Cμ-Sampler captured a higher abundance and diversity of fungi than the AVPS, with Total Taxonomy Annotations at a Genus level of 626 in F1, 632 in F2, 485 in EU and 617 in OH). In the analysis of fungal presence, Ascomycota and Basidiomycota were identified as dominant phyla. Using the AVPS sampler, Ascomycota showed an overwhelming presence of 90% to 100% inside and outside the hospital, while Basidiomycota was found in a range of 1% to 10%. Using the CμS-Sampler, Ascomycota was observed to vary between 39% and 72% in areas F1 and F2 of the hospital and from 73% to 82% outside it. On the other hand, Basidiomycota presented values between 54% and 61% in F1 and from 18% to 27% outside the hospital. The predominant genera were Aspergillus, Penicillium, Cladosporium and Alternaria. The identification of twenty-seven fungal species, including opportunistic pathogens such as Aspergillus fumigatus, Penicillium chrysogenum, P. expansum, Cladosporium and Alternaria alternata, is a significant result of this study. The results revealed the diversity of fungi in the hospital environment. The proposed complementary use of different samplers could significantly optimise current surveillance methods.},
}

@article {pmid40554279,
year = {2025},
author = {Zhang, Z and Liu, C and Chen, T and Liu, F and Luo, S and Ye, J},
title = {Microorganisms and characteristic volatile flavor compounds in Luocheng fermented rice noodles.},
journal = {Food chemistry},
volume = {490},
number = {},
pages = {145133},
doi = {10.1016/j.foodchem.2025.145133},
pmid = {40554279},
issn = {1873-7072},
abstract = {The association between the appealing flavors of Luocheng fermented rice noodles (LCFN) and microbial succession during long-term fermentation is poorly understood. This study aims to elucidate the mechanism of flavor formation in LCFN during fermentation over a 30-day period. The electronic nose results showed that the LCFN underwent a flavor shift in 7-10 days with maturation in 15-30 days. This transformation was associated with the formation of characteristic flavors of (E)-2-decenal, 2-undecenal, (E, E)-2,4-decadienal, (E)-2-octenal, (E)-2-heptenal, hexanal, nonanal, and 2-pentyl furan, which had significant positive correlation with palmitic acid, oleic acid, and linoleic acid. Changes in lipase activity and the analysis of metagenomics, suggested that the characteristic flavors may be produced by Lactobacillaceae and Geotrichum via lipid metabolism. This study provides theoretical guidance for the screening of safe and efficient microorganisms for the production of flavorful rice noodles.},
}

@article {pmid40554148,
year = {2025},
author = {Xiang, J and Zhou, Z and Liu, Z and Ren, C and Xu, Y},
title = {Constructing simplified microbial consortia that couple lactic acid and ethanol utilization to highly produce caproic acid from liquor-making wastewater.},
journal = {Water research},
volume = {284},
number = {},
pages = {123973},
doi = {10.1016/j.watres.2025.123973},
pmid = {40554148},
issn = {1879-2448},
abstract = {Converting biodegradable carbon in wastewater into medium-chain fatty acids (MCFAs) through stable microbiota is highly attractive. In this study, we utilized a top-down approach for constructing MCFA-producing microbial consortia. Specifically, an enrichment and plating-screening strategy employing lactic acid and ethanol as selective carbon sources was applied to isolate simplified caproic acid-producing microbial consortia from liquor-making pit mud. The representative microbial consortium SimpCom3 demonstrated high level of caproic acid production (14.62 ± 0.48 g/L) in a semi-synthetic medium, significantly outperforming consortium SimpCom1 (5.96 ± 0.11 g/L) and consortium SimpCom2 (9.63 ± 0.16 g/L). This performance of microbial consortium SimpCom3 was attributed to its ability to co-utilize lactic acid and ethanol, produce fewer odd-chain fatty acids byproducts, and maintain pH self-regulation between 6.45 and 8.29. Metagenomic analyses revealed the dominance of Clostridium kluyveri (30.69 %-50.46 %), C. butyricum (6.71 %-13.98 %) and C. tyrobutyricum (37.11 %-58.07 %) in consortium SimpCom3, which synergistically converted lactic acid and ethanol to caproic acid via reverse β-oxidation. Stable performance over 56 days of cyclic-batch fermentation processes confirmed the robustness of consortium SimpCom3. When applying consortium SimpCom3 to unsterilized liquor-making wastewater in a fermenter with a fed-batch approach, 22.13 g/L caproic acid was produced with 66.38 % selectivity, and microbial dynamics analysis demonstrated the consortium's high adaptability to real wastewater. Metabolic analysis based on high-quality assembly metagenomes (HQ-MAGs) revealed a novel cooperative metabolism: cross-feeding between Clostridium kluyveri (which utilizes ethanol and produces caproic acid) and lactate-utilizing butyrate producers maintained consortium stability and enhanced caproic acid production. Crucially, the decarboxylation of lactic acid counteracted acidification caused by ethanol-driven caproic acid synthesis, enabling self-regulated pH stability within the simplified microbiome system. Together, this study presents a simplified microbial consortium construction method for caproic acid production from liquor-making wastewater, overcoming the limitations of synthetic co-cultures and enhancing the viability of chain-elongation biorefineries in wastewater treatment.},
}

@article {pmid40554092,
year = {2025},
author = {Choi, BS and Holm, JB and Brejnrod, A and Fjære, E and Xia, Z and Allingbjerg, ML and Larsen, IS and Kristensen, DM and Dall, M and Myrmel, LS and Koch, J and Danneskiold-Samsøe, NB and Kalliokoski, O and Treebak, JT and Xiao, L and Hansen, AK and Sørensen, H and Madsen, L and Arumugam, M and Kristiansen, K and Jensen, BAH},
title = {Housing matters: experimental variables shaping metabolism in obese mice.},
journal = {Molecular metabolism},
volume = {},
number = {},
pages = {102190},
doi = {10.1016/j.molmet.2025.102190},
pmid = {40554092},
issn = {2212-8778},
abstract = {Diet-induced obesity in mice is an important model for investigating host-diet interactions as well as dietary and pharmacological treatments of metabolic diseases. Experimental reproducibility is, however, a recurrent challenge. To determine key controllable experimental drivers of mouse metabolism, we distributed 338 C57BL/6JBomTac mice (males and females) into six research units across two countries, divided them into a variety of housing conditions (i.e., diets, cage types, temperatures, group-housing vs. single-housing) and kept 26 reference mice at the vendor. We applied linear mixed models to rank the influence of each variable on metabolic phenotype (i.e., body weight gain, glucose intolerance, liver, and visceral adipose tissue weight). Group-housing was the most potent driver of metabolic dysfunction apart from sex and diet. Accordingly, single-housed mice exhibited reduced weight gain (∼50%), increased energy expenditure, and diminished respiratory exchange ratio concomitant with improved glucose tolerance (∼20%) compared to their group-housed counterparts. Our results may aid in clarifying the impact of experimental design and promote rational, transparent reporting to increase reproducibility.},
}

@article {pmid40554085,
year = {2025},
author = {Chen, H and Ruan, F and Wu, W and Liu, J and Wang, Z and Xu, X and Liu, Y and Wu, S and Zhou, J and Ma, J},
title = {Pulmonary fungal infection caused by Rhizopus microsporus in type II diabetic patient:A case report.},
journal = {Diagnostic microbiology and infectious disease},
volume = {113},
number = {2},
pages = {116953},
doi = {10.1016/j.diagmicrobio.2025.116953},
pmid = {40554085},
issn = {1879-0070},
abstract = {Pulmonary fungal infections are invasive fungal diseases with high mortality, particularly in immunocompromised patients. This case report describes a patient with type II diabetes mellitus who developed a pulmonary fungal infection. The patient presented with a one-week history of paroxysmal cough and expectoration of yellowish-white, purulent sputum following exposure to cold temperatures. Initial empirical antiviral therapy failed to yield any clinical improvement Subsequent chest computed tomography (CT) scans revealed irregular areas of increased density in the left lower lung, while metagenomic next-generation sequencing (mNGS) identified the infection as caused by Rhizopus microspores. The patient was treated with intravenous amphotericin B and showed clinical improvement without side effects during follow-up. This case highlighted the potential of mNGS as an adjunctive diagnostic tool for rare pathogen infections, especially in immunocompromised patients where conventional microbiological methods may be inconclusive.},
}

@article {pmid40554061,
year = {2025},
author = {Yang, W and Zou, P and He, S and Cui, H and Yang, Z and An, H and Chen, Q and Huang, W and Guo, H and Liu, J and Ling, X and Cao, J and Ao, L},
title = {Perfluorooctane sulfonic acid impairs spermatogenesis via the liver-gut microbiota-testis axis: a central role of chenodeoxycholic acid metabolism.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2025.06.037},
pmid = {40554061},
issn = {2090-1224},
abstract = {INTRODUCTION: Perfluorooctane sulfonic acid (PFOS) as a global contaminant is ubiquitously presented in the environmental media and human body. The association between PFOS exposure and reduced male fertility has been recently discovered. However, the relevant mechanism remains unexplored.

OBJECTIVES: Our study aimed to investigate the effect and mechanism of PFOS exposure on male reproductive function.

METHODS: In a murine PFOS exposure model, single-nucleus transcriptome sequencing was performed to delineate the transcriptomic landscape of mouse testes at the single-cell resolution. We examined the serum metabolomic profile and conducted in-depth analysis of hepatic transcriptome datasets to explore the metabolic connections between liver and testis under PFOS exposure. Through integrating chenodeoxycholic acid intervention, fecal microbiota transplantation (FMT), metagenomic sequencing, testicular metabolome, Ligilactobacillus murinus (L. murinus) metabolome, and administration of L. murinus, we confirmed the role of the liver-gut microbiota-testis axis and screened the critical gut microbiota involved in PFOS-mediated spermatogenic disorders.

RESULTS: The results showed that PFOS exposure led to spermatogenic arrest and abnormal spermatogenic microenvironment in the mouse testis. The PFOS-repressed hepatic chenodeoxycholic acid (CDCA) synthesis contributed to the reduced serum/testicular levels of essential fatty acid (linoleic acid) and lipid-soluble vitamins (retinol, vitamin D3), which was responsible for the spermatogenic arrest. Beyond this, PFOS-mediated impaired CDCA production decreased the abundance of gut L. murinus, which affected spermatogenesis through the potential involvement of aspartic acid metabolism. For the first time to our knowledge, we comprehensively assessed the effects of PFOS exposure on the spermatogenic process and elucidated the unrecognized role of liver-gut microbiota-testis axis in PFOS-induced abnormal spermatogenesis.

CONCLUSIONS: The unveiled organ crosstalks provide new insights into the metabolism-disrupting properties, hepatotoxicity, and reproductive toxicity of PFOS, which may facilitate the development of molecule-, metabolite-, and microbe-based strategies for PFOS-induced metabolic diseases and reproductive disorders.},
}

@article {pmid40553742,
year = {2025},
author = {Frutkoff, YA and Plotkin, L and Pollak, D and Livovsky, J and Focht, G and Lev-Tzion, R and Ledder, O and Assa, A and Yogev, D and Orlanski-Meyer, E and Broide, E and Kierkuś, J and Kang, B and Weiss, B and Aloi, M and Schwerd, T and Shouval, DS and Bramuzzo, M and Griffiths, AM and Yassour, M and Turner, D},
title = {Whole food diet induces remission in children and young adults with mild-moderate Crohn's disease and is more tolerable than exclusive enteral nutrition: a randomized controlled trial.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2025.06.011},
pmid = {40553742},
issn = {1528-0012},
abstract = {BACKGROUND: Tasty&Healthy (T&H) is a whole-food diet for Crohn's disease (CD), which excludes processed food, gluten, red meat, and dairy, without requiring formula or mandatory ingredients. TASTI-MM was a clinician-blinded, randomized-controlled trial comparing tolerability and effectiveness of T&H vs. exclusive enteral nutrition (EEN).

METHODS: Patients with biologic-naive mild-moderate CD aged 6-25 years were randomized to either T&H or EEN for 8 weeks, receiving weekly dietary support. Tolerability was evaluated by weekly interviews, questionnaires and intake diaries. Other outcomes included symptomatic remission, Mucosal-Inflammation Non-Invasive (MINI) index, calprotectin, C-reactive protein (CRP) and erythrocyte sedimentation rate (ESR). Fecal microbiome was analyzed by metagenomics at baseline, week-4 and week-8. Data were analyzed by the intention-to-treat approach unless specified otherwise.

RESULTS: Among 83 included patients (41 T&H, 42 EEN; mean age 14.5±3.7 years), 88% tolerated T&H vs. 52% for EEN (aOR 7.7 [95%CI 2.4-25]; p<0.001). Calprotectin, CRP and ESR decreased significantly in both groups, with no between-group differences. Symptomatic remission was achieved in 56% of T&H group vs. 38% of the EEN group (aOR 2.5 [0.98-6.3], p=0.1; per-protocol: 67% vs. 76%; p=0.47). Calprotectin <250μg/g was achieved in 34% vs. 33% (aOR 0.97 [0.37-2.6], p=0.84) and MINI<8 in 44% vs. 31% (aOR 1.8 [0.7-4.5]; p=0.33). Microbiome α-diversity improved in the T&H arm and declined in the EEN arm, showing superior species richness at both week-4 and week-8. Species associated with bowel inflammation, such as Ruminococcus gnavus, decreased in T&H and increased in EEN (q<0.001).

CONCLUSIONS: T&H demonstrated better tolerability than EEN for inducing remission in mild-to-moderate CD, while positively affecting the microbiome (TASTI-MM, NCT#04239248).},
}

@article {pmid40553325,
year = {2025},
author = {Mukhopadhyay, S and Ulaganathan, N and Dumpuri, P and Aich, P},
title = {Integrative AI-Based Approaches to Connect the Multiome to Use Microbiome-Metabolome Interactive Outcome as Precision Medicine.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2952},
number = {},
pages = {15-37},
pmid = {40553325},
issn = {1940-6029},
mesh = {Humans ; *Precision Medicine/methods ; *Metabolomics/methods ; *Metabolome ; Metagenomics/methods ; *Microbiota ; *Artificial Intelligence ; Computational Biology/methods ; Gastrointestinal Microbiome ; },
abstract = {In the era of Genome-Wide Association Studies (GWAS), biologists have unprecedented access to vast datasets, mirrored in the wealth of information from various omics studies, including genomics, transcriptomics, proteomics, metabolomics, and metagenomics. Integrating diverse data sources has emerged as crucial in unravelling the intricacies of biological processes. This chapter delves into our method for merging various omics methodologies, emphasizing metabolomics and metagenomics data. A powerful strategy addresses data processing challenges and opens new avenues for personalized microbiome-based interventions. The combined analysis of host and microbial metabolomics and metagenomics data has significantly advanced our understanding in diagnosing and treating conditions such as inflammatory bowel disease and irritable bowel syndrome. Metabolic signatures in biological fluids and their microbial counterparts serve as indicators, differentiating health from disease. The sheer volume of data demands sophisticated automated tools for processing and interpretation. Recognizing this need, integrating artificial intelligence (AI) and data science has become increasingly prominent. In this chapter, we combine microbiome and metabolome analyses through publicly available models to elucidate the correlations between microbial and metabolic profiles. By harnessing AI models across various omics data sources, this chapter bridges the gap between data acquisition and clinical applications, paving the way for personalized interventions and optimizing individual health.},
}

Humans
*Precision Medicine/methods
*Metabolomics/methods
*Metabolome
Metagenomics/methods
*Microbiota
*Artificial Intelligence
Computational Biology/methods
Gastrointestinal Microbiome

@article {pmid40552763,
year = {2025},
author = {Claypool, J and Lindved, G and Myers, PN and Ward, T and Nielsen, HB and Blount, KF},
title = {Microbiome compositional changes and clonal engraftment in a phase 3 trial of fecal microbiota, live-jslm for recurrent Clostridioides difficile infection.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2520412},
doi = {10.1080/19490976.2025.2520412},
pmid = {40552763},
issn = {1949-0984},
mesh = {Humans ; *Clostridium Infections/therapy/microbiology ; *Fecal Microbiota Transplantation ; *Gastrointestinal Microbiome ; *Feces/microbiology ; Male ; *Clostridioides difficile/physiology ; Female ; Middle Aged ; *Bacteria/classification/genetics/isolation & purification ; Adult ; Recurrence ; Aged ; },
abstract = {Live microbiota therapies have shown promise in many gastrointestinal diseases, including in the prevention of recurrent Clostridioides difficile infections (rCDI); however, frameworks for their pharmacokinetic and pharmacodynamic analysis are not fully established. Fecal microbiota, live-jslm (RBL) is the first microbiota-based product approved by the US Food and Drug Administration for the prevention of rCDI and was superior to placebo in the PUNCH™ CD3 phase 3 clinical trial (NCT03244644). In this analysis, deep shotgun metagenomic sequencing was used to assess changes in gut microbiome compositions of participants and engraftment of bacterial clonal populations (i.e. strains) from RBL to recipients. Among RBL responders, gut microbiota shifted toward compositions that resembled healthy donors as early as 1 week after RBL administration; the resulting microbiota compositions included clonal populations that engrafted from RBL to recipients. Engraftment was higher in RBL responders compared with non-responders, and many clonally engrafted populations persisted for ≥ 6 months. Bacteroidia species were among the most effectively engrafted species from RBL. This study utilizes data from a large clinical trial to establish a method with high specificity for exploring clonal engraftment from microbiota-based treatments to facilitate future pharmacokinetic and pharmacodynamic analyses.Clinicaltrials Registration: NCT03244644.},
}

Humans
*Clostridium Infections/therapy/microbiology
*Fecal Microbiota Transplantation
*Gastrointestinal Microbiome
*Feces/microbiology
Male
*Clostridioides difficile/physiology
Female
Middle Aged
*Bacteria/classification/genetics/isolation & purification
Adult
Recurrence
Aged

@article {pmid40552317,
year = {2025},
author = {Jafari, E and Azizian, R and Tabasi, M and Banakar, M and Bagheri Lankarani, K},
title = {Human Gut Bacteriophageome: Insights Into Drug Resistance Mechanisms in Tuberculosis.},
journal = {Interdisciplinary perspectives on infectious diseases},
volume = {2025},
number = {},
pages = {8811027},
pmid = {40552317},
issn = {1687-708X},
abstract = {Tuberculosis (TB), caused by Mycobacterium tuberculosis, remains a major global health burden. The emergence of drug-resistant strains presents a critical challenge in TB management. The recent research has explored the interaction between TB and the human gut bacteriophage community (phageome). The gut phageome plays a crucial role in regulating microbial diversity and functionality, and its composition and function have been linked to various health conditions. Examining the gut phageome through metagenomic analysis provides insights into its composition, role in health, and interactions with the host immune system. Exploring the interaction between the gut phageome and M. tuberculosis may reveal how phages affect the bacterium's pathogenicity, survival, and mechanisms of drug resistance. Understanding the gut phageome's impact on TB drug resistance could inform novel therapeutic strategies, such as phage therapy, and highlight the importance of microbiome-based interventions in combating drug-resistant TB strains. This review explores the role of the gut phageome in influencing drug resistance in TB, focusing on interaction mechanisms and potential therapeutic implications, synthesizing current research findings, and identifying knowledge gaps in this emerging field. This review also synthesizes the current evidence on the gut phageome's role in TB drug resistance, focusing on phage-mediated horizontal gene transfer (e.g., rpoB, katG), immune modulation, and preclinical efficacy of mycobacteriophage therapies. Key findings highlight phage cocktails (e.g., DS6A, D29 LysB) as promising adjuncts to antibiotics, reducing M. tuberculosis burden in murine models. These insights advocate for phage therapy as a complementary strategy against drug-resistant TB, urging clinical validation to bridge the existing knowledge gaps.},
}

@article {pmid40551486,
year = {2025},
author = {Yan, F and Wu, SM and Yuan, WQ and Yang, YH and Zhu, H and Cui, DJ},
title = {Thermophiles, Thick-Walled Bacteria, and Pseudomonads in High-Altitude Gut Microbiota.},
journal = {Journal of gastroenterology and hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jgh.17032},
pmid = {40551486},
issn = {1440-1746},
support = {qiankehe2018-5764-11//Cultivation Fund of National Natural Science Foundation/ ; gzwkj2025-268//Science and Technology Fund of Guizhou provincial health committee/ ; },
abstract = {BACKGROUND AND AIM: High-altitude environments are characterized by low oxygen and reduced low pressure, which impose significant physiological challenges on organisms. Among various adaptive systems, the intestinal flora plays a crucial role in maintaining gut health and barrier integrity function under such conditions. This study aimed to elucidate the regulatory mechanisms of intestinal flora in high-altitude environments, focusing on downregulating intracellular Bone Morphogenetic Protein 4 (BMP4) to influence glycolysis metabolism, thereby affecting intercellular communication of the intestinal mucosal barrier and matrix remodeling.

METHODS: High-altitude mouse intestinal flora composition and function were analyzed using 16S rRNA and metagenomic sequencing. Additionally, single-cell sequencing was employed to examine cell population communication and gene expression differences between normal and high-altitude mouse intestinal tissues.

RESULTS: Single-cell sequencing showed significantly reduced interactions between intestinal fibroblasts and epithelial cells in high-altitude mice, accompanied by a marked increase in BMP4 expression. Overexpression of BMP4 was found to activate the glycolysis pathway. Gut microbiota metabolites, including secondary bile acids, lactic acid, and butyrate, exhibited protective effects on hypoxia-induced intestinal mucosal barrier injury, with butyrate showing the most prominent effect. Under hypoxic conditions, butyrate suppressed the BMP4/glycolysis pathway, thereby alleviating hypoxia-induced intestinal mucosal barrier damage.

CONCLUSION: This study uncovered a novel mechanism by which the gut microbiota in high-altitude environments modulate glycolysis metabolism through BMP4 downregulation, thereby affecting intercellular communication and matrix remodeling within the intestinal mucosal barrier.},
}

@article {pmid40551155,
year = {2025},
author = {Mizsei, E and Sos, T and Móré, A and Wenner, B and Rák, G and Mebert, K},
title = {Restriction times on the rise: mechanistic modelling of activity time of grassland vipers (Vipera spp.) in the face of climate change.},
journal = {Frontiers in zoology},
volume = {22},
number = {1},
pages = {10},
pmid = {40551155},
issn = {1742-9994},
support = {LIFE18 NAT/HU/000799//LIFE programme/ ; },
abstract = {Climate change threatens species adapted to cool alpine environments, particularly ectotherms like reptiles. Small-sized grassland specialist vipers inhabit such environments in Eurasia and are highly susceptible to overheating and dehydration as global temperature rises. This study modelled activity restriction times, defined as hours when environmental temperatures exceed the thermal tolerance (i.e. not available for essential activities) of the species, for 20 grassland viper taxa to assess climate change impacts. Under future conditions, hours of activity restriction are projected to increase by 21% by the SSP1-2.6 scenario, and by 52.1% by the SSP5-8.5 scenario. Elevation and latitude significantly influenced restriction time changes, with high-altitude and northern populations predicted to be most affected. The taxa Vipera graeca and Vipera ursinii moldavica are expected to experience the greatest increase in restriction times. Despite warmer conditions potentially increasing hours within preferred thermal ranges, vipers are unlikely to exploit lower-elevation habitats due to competition and ecological constraints. These findings emphasise the urgent need for conservation strategies, including habitat preservation and connectivity, to mitigate the adverse effects of climate change on grassland vipers, particularly the most vulnerable populations.},
}

@article {pmid40550680,
year = {2025},
author = {Lin, M and Hu, L and Hao, L and Wang, Z},
title = {[Microbiome and its genetic potential for carbon fixation in small urban wetlands].},
journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology},
volume = {41},
number = {6},
pages = {2415-2431},
doi = {10.13345/j.cjb.240399},
pmid = {40550680},
issn = {1872-2075},
mesh = {*Wetlands ; *Microbiota/genetics ; *Carbon Cycle/genetics ; *Bacteria/genetics/metabolism/classification ; RNA, Ribosomal, 16S/genetics ; China ; Cities ; Geologic Sediments/microbiology ; Archaea/genetics/metabolism/classification ; Metagenomics ; Metagenome ; },
abstract = {Small urban wetlands are widely distributed and susceptible to human activities, serving as important sources and sinks of carbon. Microorganisms play a crucial role in carbon cycle, while limited studies have been conducted on the microbial diversity in small urban wetlands and the functions of microbiome in carbon fixation and metabolism. To probe into the microbiome-driven carbon cycling in small urban wetlands and dissect the composition and functional groups of microbiome, we analyzed the relationships between the microbiome structure, element metabolism pathways, and habitat physicochemical properties in sediment samples across three small wetlands in Huzhou City, and compared them with natural wetlands in the Zoige wetland. High-throughput sequencing of 16S rRNA gene amplicons and metagenomics was employed to determine the species and functional groups. Sixty medium to high-quality metagenome-assembled genomes (MAGs) were constructed, including 55 bacterial and 5 archaeal taxa, and their potential in driving elemental cycles were analyzed, with a focus on carbon fixation. Several bacterial species were found to encode a nearly complete carbon fixation pathway, including the Calvin cycle, the reductive tricarboxylic acid cycle, the Wood-Ljungdahl pathway, and the reductive glycine pathway. There were several potential novel carbon-fixing bacterial members, such as those belonging to Syntrophorhabdus (Desulfobacterota) and UBA4417 (Bacteroidetes), which had high relative abundance in the wetland microbiome. Unveiling the genetic potential of these functional groups to facilitate element cycling is of great scientific importance for enhancing the carbon sequestration capacity of small urban wetlands.},
}

*Wetlands
*Microbiota/genetics
*Carbon Cycle/genetics
*Bacteria/genetics/metabolism/classification
RNA, Ribosomal, 16S/genetics
China
Cities
Geologic Sediments/microbiology
Archaea/genetics/metabolism/classification
Metagenomics
Metagenome

@article {pmid40550672,
year = {2025},
author = {Wang, X and Wang, S and Yang, K and Tang, Y and Xu, Y and Shen, Q and Wei, Z},
title = {[Methodological breakthroughs and challenges in research of soil phage microecology].},
journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology},
volume = {41},
number = {6},
pages = {2310-2323},
doi = {10.13345/j.cjb.250258},
pmid = {40550672},
issn = {1872-2075},
mesh = {*Bacteriophages/genetics/isolation & purification/physiology ; *Soil Microbiology ; Ecosystem ; Microbiota ; Metagenomics/methods ; },
abstract = {Phages, as obligate bacterial and archaeal parasites, constitute a virus group of paramount ecological significance due to their exceptional abundance and genetic diversity. These biological entities serve as critical regulators in Earth's ecosystems, driving biogeochemical cycles, energy fluxes, and ecosystem services across terrestrial and marine environments. Within soil microbiomes, phages function as microbial "dark matter," maintaining the soil-plant system balance through precise modulation of the microbial community structure and functional dynamics. Despite the growing research interests in soil phages in recent years, the proportion of such studies in environmental virology remains disproportionately low, which is primarily attributed to researchers' limited familiarity with the research methodologies for phage microecology, incomplete technical frameworks, and inherent challenges posed by soil environmental complexity. To address these challenges, this review synthesizes cutting-edge methodologies for soil phage investigation from four aspects: (1) tangential flow filtration (TFF)-based phage enrichment strategies; (2) integrated quantification approaches combining double-layer agar plating, epifluorescence microscopy, and flow cytometry; (3) multi-omics analytical pipelines leveraging metagenomics and viromics datasets; and (4) computational frameworks merging machine learning algorithms with eco-evolutionary theory for deciphering phage-host interaction networks. Through comparative analysis of methodological principles, technical merits, and application scopes, we establish a comprehensive workflow for soil phage research. Future research in this field should prioritize: (1) construction of soil phage resource libraries, (2) exploration of RNA phages based on transcriptomes, (3) functional characterization of unknown genes, and (4) deep integration and interaction validation of multi-omics data. This systematic methodological synthesis provides critical technical references for addressing fundamental challenges in characterizing soil phages regarding the community structure, functional potential, and interaction mechanisms with hosts.},
}

*Bacteriophages/genetics/isolation & purification/physiology
*Soil Microbiology
Ecosystem
Microbiota
Metagenomics/methods

@article {pmid40550235,
year = {2025},
author = {Howard-Jones, AR and Mahar, JE and Proudmore, K and Butel-Simoes, GI and Eden, JS and Neave, MJ and Mileto, P and Hueston, L and Freeman, K and Ellem, J and Caly, L and Sikazwe, C and Levy, A and Thomas, A and Taylor, C and Kurucz, N and Smyth, K and Jennison, A and Moore, P and Wright, R and Mee, PT and Brischetto, A and Feldman, R and Dwyer, DE and O'Sullivan, MV and Mahony, AA and Warner, MS and Papanicolas, LE and Schlebusch, S and Lim, CK and Baird, R and Speers, D and Williams, DT and Currie, BJ and Kok, J},
title = {Diagnostic and phylogenetic perspectives of the 2023 Murray Valley encephalitis virus outbreak in Australia: an observational study.},
journal = {The Lancet. Microbe},
volume = {},
number = {},
pages = {101089},
doi = {10.1016/j.lanmic.2025.101089},
pmid = {40550235},
issn = {2666-5247},
abstract = {BACKGROUND: An outbreak of Murray Valley encephalitis virus (MVEV), the largest since 1974, was observed in Australia between Jan 1 and July 31, 2023. This study aims to characterise the utility of diagnostic platforms, testing algorithms, and genomic characteristics of MVEV to facilitate a comprehensive framework for MVEV testing and surveillance in the outbreak setting.

METHODS: In this observational study, we assessed flavivirus diagnostics for all patients with suspected Murray Valley encephalitis in Australia from Jan 1 to July 31, 2023. We included all patients with confirmed Murray Valley encephalitis, probable Murray Valley encephalitis, or acute unspecified flavivirus infection using the Communicable Diseases Network Australia case definition. Cases were excluded if an alternative diagnosis was identified. We collected blood, serum, cerebrospinal fluid, brain tissue, urine, or a combination of these samples, as appropriate and at the discretion of the treating clinician. We conducted multimodal diagnostic testing, which included flavivirus-specific serological and nucleic acid amplification testing. Metagenomic next-generation sequencing, including next-generation deep sequencing, target-enrichment, and targeted amplification, was conducted on human and representative mosquito-derived samples obtained from established mosquito population surveillance programmes for phylogenetic analysis.

FINDINGS: 27 patients with encephalitis were assessed for MVEV between Jan 1, 2023, and July 31, 2023, 23 (85%) of whom fulfilled national case definitions for confirmed Murray Valley encephalitis. Patient ages ranged from 6 weeks to 83 years (median 62·0 years [IQR 31·0-67·5]) and patients were mostly male (21 [78%] male patients and six [22%] female patients). Incidence varied widely by geographical region and was highest in the Northern Territory (32·0 per 1 000 000 population). Diagnostic specimen collection generally occurred promptly (median 6·0 days [IQR 4·0-14·5] from symptom onset to diagnostic specimen collection). In seven patients, case assignation relied on convalescent serum samples to assess for seroconversion or an appropriate rise in antibody titre (to four times the initial value or greater), or both. MVEV-specific IgM was detectable in serum samples of 17 (81%) of 21 patients tested by day 7 and MVEV IgG or total antibody (TAb) were detected in 18 (100%) of 18 patients tested by day 30. MVEV-specific IgM (or TAb) and MVEV RNA were detected in cerebrospinal fluid collected within 14 days of symptom onset in nine (39%) of 23 patients and seven (28%) of 25 patients, respectively. Phylogenetic analysis revealed two circulating MVEV genotypes, G1A and G2, in mosquitoes and humans in 2023. In southeast Australia, only G1A was detected and probably introduced from enzootic foci in northern Australia.

INTERPRETATION: This study provides a comprehensive overview of the diagnostic workflows and phylogenetic evaluations used during the 2023 MVEV outbreak in Australia, emphasising the importance of a multimodal approach for accurate and timely confirmation of flavivirus infection. Further One Health surveillance for MVEV and other zoonotic flaviviruses is key, given potential expanded ecological niches in the context of episodic climatic events.

FUNDING: None.},
}

@article {pmid40549455,
year = {2025},
author = {Goryanin, I and Sorokin, A and Seitov, M and Emilov, B and Iskakov, M and Goryanin, I and Osmonov, B},
title = {Metagenome and metabolome study on inhaled corticosteroids in asthma patients with side effects.},
journal = {Journal of integrative bioinformatics},
volume = {},
number = {},
pages = {},
pmid = {40549455},
issn = {1613-4516},
abstract = {This study investigates the gut microbiome and metabolome of asthma patients treated with inhaled corticosteroids (ICS), some of whom experience adverse side effects. We analyzed stool samples from 24 participants, divided into three cohorts: asthma patients with side effects, those without, and healthy controls. Using next-generation sequencing and LC-MS/MS metabolomics, we identified significant differences in bacterial species and metabolites. Multi-Omics Factor Analysis (MOFA) and Global Sensitivity Analysis-Partial Rank Correlation Coefficient (GSA-PRCC) provided insights into key contributors to side effects, such as tryptophan depletion and altered linolenate and glucose-1-phosphate levels. The study proposes dietary or probiotic interventions to mitigate side effects. Despite the limited sample size, these findings provide a basis for personalized asthma management approaches. Further studies are required to confirm initial fundings.},
}

@article {pmid40549420,
year = {2025},
author = {Podowski, JC and Forrester, S and Yaqub, T and Aqel, A and Abu Lubad, M and Mukhtar, N and Waqar Aziz, M and Sardar, N and Bin Aslam, H and Pervaiz, H and Wolfe, AJ and Schabacker, DS},
title = {Genomic reconstruction of Bacillus anthracis from complex environmental samples enables high-throughput identification and lineage assignment in Pakistan.},
journal = {Microbial genomics},
volume = {11},
number = {6},
pages = {},
doi = {10.1099/mgen.0.001422},
pmid = {40549420},
issn = {2057-5858},
mesh = {*Bacillus anthracis/genetics/classification/isolation & purification ; Pakistan ; *Anthrax/microbiology/epidemiology ; Animals ; *Genome, Bacterial ; Humans ; Genomics/methods ; Phylogeny ; Computational Biology/methods ; High-Throughput Nucleotide Sequencing ; },
abstract = {Bacillus anthracis, the causative agent of anthrax, is a highly virulent zoonotic pathogen primarily affecting domesticated and wild herbivores. Human exposure to B. anthracis is primarily through contact with infected animals or contaminated animal products. In Pakistan, where livestock vaccines are largely unavailable and infected carcasses are often disposed of improperly, the risk to humans, wildlife and livestock is significant. Currently, the diagnosis of anthrax infections and outbreak tracing necessitates the isolation and culturing of B. anthracis, a process that requires BSL-3 facilities. In this study, we show that positive identification, genome reconstruction and lineage assignment can be accomplished using bioinformatic analysis of DNA extracted directly from environmental samples that would otherwise provide the starting material for isolation and culturing. This approach does not require laboratory target enrichment as is necessary for other pathogens, due in part to the extremely high bacterial load in the bloodstream in the deceased animals. Using these methods, we greatly expand the knowledge of endemic B. anthracis in Pakistan. We provide the first reference B. anthracis genomes from Pakistan since the 1970s and identify A.Br.014 Aust94 as a minor circulating sublineage alongside the dominant A.Br.047 Vollum. Future work will focus on the limits of detection and will determine if this bioinformatic method can be expanded more broadly for B. anthracis or other pathogens to replace typical culture-based methods.},
}

*Bacillus anthracis/genetics/classification/isolation & purification
Pakistan
*Anthrax/microbiology/epidemiology
Animals
*Genome, Bacterial
Humans
Genomics/methods
Phylogeny
Computational Biology/methods
High-Throughput Nucleotide Sequencing

@article {pmid40548737,
year = {2025},
author = {Ren, G and Ma, L and Yan, C and Xue, Q and Zhang, H and Wang, W and Ren, X and Lei, Y and Li, S and Liu, Y and Zheng, Q and Wei, S and Zhang, Y and Wang, X},
title = {Application of targeted metagenomic next-generation sequencing in pneumonia patients.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0171324},
doi = {10.1128/spectrum.01713-24},
pmid = {40548737},
issn = {2165-0497},
abstract = {After the coronavirus disease 2019 (COVID-19) pandemic, the incidence rate of mixed infections, especially in critically ill patients with severe pneumonia, increases due to the immunity gap and has also been proven to be associated with mortality, increasing the difficulty in accurate and rapid diagnoses. Here, we evaluated the performance of targeted metagenomic next-generation sequencing (mNGS), including capture hybridization-based mNGS (chNGS) and multiplex PCR-based targeted mNGS (tNGS), in diagnosing pneumonia. Patients admitted to the Pulmonary and Critical Care Medicine, Beijing Aerospace General Hospital, and diagnosed as suspected pulmonary infections from April 2022 to March 2024 were retrospectively evaluated, and 110 patients were finally enrolled. According to the final comprehensive clinical diagnoses, there were 99 patients diagnosed with definite infectious diseases. Single infections accounted for 58.6% of these patients (58/99), while mixed infections occurred in about half of these patients (41.4%, 41/99) and were found in most of the death cases. Pseudomonas aeruginosa (n = 22), Pneumocystis jirovecii (n = 15), and severe acute respiratory syndrome coronavirus 2 (n = 13) were found to be the most common bacterial, fungal, and viral pathogens, respectively. Taking final comprehensive clinical diagnoses as the reference standard, the total coincidence rate (TCR) of chNGS can reach up to 64.1% (95% confidence interval [CI], 54.8%-73.3%), while the TCR of conventional methods was only 39.8% (95% CI, 30.4%-49.3%). The performance of tNGS was slightly superior to that of chNGS, while chNGS yielded more false-negative results, especially for viral detection. Additionally, chNGS combined with tNGS can improve the TCR to 81.3% (95% CI, 62.1%-100.0%).IMPORTANCEThis is the first report on evaluating the performance of capture hybridization-based metagenomicnext-generation sequencing (chNGS), multiplex PCR-based targeted mNGS (tNGS), and conventional methods in diagnosing pneumonia. Our findings emphasized the importance of chNGS and tNGS in diagnosing, managing, and ruling out infections, and an era of widespread application of regional tNGS in monitoring and diagnosing infections with high sensitivity and low economic burden on patients can be expected.},
}