@article {pmid40603374,
year = {2025},
author = {Guta, M and Van Eenooghe, B and Bacha, K and Cools, P},
title = {Bacterial community profile of three Ethiopian hot springs based on 16S rRNA gene nanopore sequencing.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {23491},
pmid = {40603374},
issn = {2045-2322},
mesh = {*RNA, Ribosomal, 16S/genetics ; *Hot Springs/microbiology ; Ethiopia ; *Bacteria/genetics/classification/isolation & purification ; Phylogeny ; *Nanopore Sequencing/methods ; Biodiversity ; },
abstract = {Ethiopia harbors a number of hot springs not yet well explored or studied using a metagenomic approach to reveal their bacterial diversity. Understanding the bacterial diversity of these ecosystems is valuable for uncovering their ecological roles and potential for biotechnological applications. The aim of this study was, therefore, to perform the first full-length 16S rRNA gene nanopore sequencing on the three Ethiopian hot springs, namely Shalla, Woliso and Wondo Genet. The bacterial community composition of the three hot springs, whose temperatures ranged from 45 to 96 °C, was effectively assessed using the ONT MinION sequencer. It was found that Shalla hot spring had the highest species richness and accounted for 323 species, followed by 116 species from Woliso and 54 species from Wondo Genet hot springs. Pseudomonadota and Bacillota were the most dominant phyla recovered from the three hot springs, whereas Acinetobacter and Paracoccus were the most abundant bacterial genera. The most abundant species were Alkalihalobacterium elongatum from Shalla hot spring, and Acinetobacter junii and Acinetobacter johnsonii from Wondo Genet hot spring. Our study provided the first insight into the bacterial diversity of three Ethiopian hot springs and may serve as a basis for further functional analysis of these hot springs.},
}

*RNA, Ribosomal, 16S/genetics
*Hot Springs/microbiology
Ethiopia
*Bacteria/genetics/classification/isolation & purification
Phylogeny
*Nanopore Sequencing/methods
Biodiversity

@article {pmid40603287,
year = {2025},
author = {Samarra, A and Alcañiz, AJ and Martínez-Costa, C and Marina, A and Comas, I and Segata, N and Quijada, NM and Collado, MC},
title = {Breastfeeding and early Bifidobacterium-driven microbial colonization shape the infant gut resistome.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {6099},
pmid = {40603287},
issn = {2041-1723},
support = {MAMI-639226 project//EC | EU Framework Programme for Research and Innovation H2020 | H2020 European Institute of Innovation and Technology (H2020 The European Institute of Innovation and Technology)/ ; PROMETEO2020/12//Generalitat Valenciana (Regional Government of Valencia)/ ; CIPROM2023/030//Generalitat Valenciana (Regional Government of Valencia)/ ; },
mesh = {Humans ; *Breast Feeding ; *Bifidobacterium/physiology/genetics ; *Gastrointestinal Microbiome/genetics/drug effects ; Infant ; Female ; Infant, Newborn ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Cesarean Section ; Metagenome ; Adult ; Male ; Milk, Human/microbiology ; Feces/microbiology ; },
abstract = {The assembly of the gut resistome in early life is key to infant health. Specific perinatal factors such as cesarean section (C-section), antibiotic exposure and lack of breastfeeding practices are detrimental to proper microbial development and increase the antimicrobial resistance genes (ARGs). Using 265 gut longitudinal metagenomes from 66 mother-infant pairs, we investigated how perinatal factors influence the acquisition and dynamics of ARGs during the first year of life. Our findings reveal that Bifidobacterium plays a crucial role in modulating the infant resistome, with its high relative abundance being associated with a lower ARG load. Exclusive breastfeeding during the first month of life accelerates the reduction of ARGs and ensures a lower resistome burden at six months. Moreover, early breastfeeding cessation correlates with a higher ARG load, underscoring its long-term influence on microbial resilience. Importantly, we identify exclusive breastfeeding as a key strategy to mitigate the impact of C-section delivery on the infant gut resistome, counteracting the early-life antibiotic exposure associated with this procedure and the resulting resistance acquisition. By promoting a microbiome enriched in Bifidobacterium, breastfeeding may help suppress ARG-carrying taxa, reducing the risk of resistance dissemination. Our findings underscore the importance of breastfeeding as a natural intervention to shape the infant microbiome and resistome. Supporting breastfeeding through public health policies could help limit the spread of antimicrobial resistance in early life.},
}

Humans
*Breast Feeding
*Bifidobacterium/physiology/genetics
*Gastrointestinal Microbiome/genetics/drug effects
Infant
Female
Infant, Newborn
Anti-Bacterial Agents/pharmacology
*Drug Resistance, Bacterial/genetics
Cesarean Section
Metagenome
Adult
Male
Milk, Human/microbiology
Feces/microbiology

@article {pmid40602621,
year = {2025},
author = {Zhang, Z and Yuan, G and Turgun, X and Turgun, Z and Hou, L and Ye, M and Wang, Y and Xu, X},
title = {Biogeographic Patterns and Ecological Roles of Microorganisms in Sediments Along an Estuarine Salinity Gradient.},
journal = {Environmental microbiology reports},
volume = {17},
number = {4},
pages = {e70139},
doi = {10.1111/1758-2229.70139},
pmid = {40602621},
issn = {1758-2229},
support = {2023A1515110368//Guangdong Basic and Applied Basic Research Foundation/ ; XJNUZBS2423//Doctoral Research Foundation of Xinjiang Normal University/ ; 42361144846 and 42461006//National Natural Science Foundation of China/ ; //Tianchi Talents (Xinjiang) Plan Project (Young Doctor)/ ; },
mesh = {*Geologic Sediments/microbiology/chemistry ; *Salinity ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Estuaries ; China ; Biodiversity ; Microbiota ; Ecosystem ; Metagenome ; Phylogeny ; },
abstract = {The distribution patterns and driving mechanisms of microbial biogeographic patterns are fundamental questions in microbiology. This study analysed and compared the bacterial biogeographic patterns in the coastal environment, focusing on the Yangtze Estuary and its adjacent coastal zone. The purpose is to explore the driving mechanisms under spatial distribution, the community assembly processes and potential functions. Our results revealed that the sediment bacterial community structure exhibited a distinct geographical pattern and was significantly influenced by environmental factors. The microbial community displayed a non-random co-occurrence pattern, and the biogeographic patterns were shaped not only by environmental constraints (deterministic processes) but also by stochastic processes resulting from dispersal limitation. The metagenome sequencing analysis revealed a pronounced salinity gradient in the nitrogen-cycling function of the bacterial community. This functional difference appears to be driven by microbial diversity changes from the estuarine region to the ocean, highlighting the key role of microbial ecological characteristics. The findings of this study contribute to a deeper understanding of microbial ecology in estuarine environments, emphasizing the complex interplay between environmental factors and microbial community dynamics in shaping the function of estuarine sediment bacterial communities.},
}

*Geologic Sediments/microbiology/chemistry
*Salinity
*Bacteria/classification/genetics/isolation & purification/metabolism
Estuaries
China
Biodiversity
Microbiota
Ecosystem
Metagenome
Phylogeny

@article {pmid40601719,
year = {2025},
author = {Wanjiru, T and Bulimo, W and Langat, S and Kinyua, J and Odemba, N and Yalwala, S and Oullo, D and Ochieng, R and Ngere, F and Kerich, G and Ambale, J and Achieng, E and Abuom, D and Egbo, T and Johnson, J and Ojwang, E and Eads, J and Garges, E and Eyase, F},
title = {Vertical transmission of Dengue virus type-3 and metagenomic virome profiles of Aedes aegypti mosquitoes collected in Kisumu, Kenya.},
journal = {PloS one},
volume = {20},
number = {7},
pages = {e0315492},
doi = {10.1371/journal.pone.0315492},
pmid = {40601719},
issn = {1932-6203},
mesh = {Animals ; *Aedes/virology ; Kenya ; *Dengue Virus/genetics/isolation & purification/classification ; *Virome/genetics ; *Mosquito Vectors/virology ; *Infectious Disease Transmission, Vertical ; Metagenomics ; High-Throughput Nucleotide Sequencing ; Phylogeny ; Dengue/transmission/virology ; Metagenome ; Female ; },
abstract = {Aedes aegypti is the main vector of several arboviruses including chikungunya, dengue, yellow fever and Zika. Beyond arboviruses, Aedes aegypti harbours insect-specific viruses (ISVs), which can modulate mosquito's ability to transmit diseases by interfering with viral processes and triggering immune responses. Both arboviruses and ISVs can be transmitted vertically, where viruses are passed from parent to offspring. The lack of systematic molecular and entomological surveillance, has left the diversity of viruses in local Aedes aegypti populations largely unexplored. This study aimed to characterize the viromes of Aedes aegypti mosquitoes from Kisumu, Kenya, focusing on viral diversity. Immature larvae and pupae were collected from Jua Kali area in Kisumu, reared into adults, and subjected to viral isolation by cell culture and metagenomic next-generation sequencing. RNA extraction, library preparation, and Illumina MiSeq sequencing were performed on CPE positive pools and metagenomic superpools. Initial data analysis was conducted using the CZ-ID platform, with quality control applied using PrinseqLite v0.20.4 to filter low-quality reads and remove adapters. De novo sequence assembly was performed with MEGAHIT v1.2.9, followed by BLAST analysis. Phylogenetic relationships were analyzed using the Maximum Likelihood method. A total of 2,142 female Aedes aegypti, grouped into 86 pools and 4 superpools, were analyzed using cell culture and metagenomic next-generation sequencing respectively. Dengue virus type-3 was detected in one of the 86 pool. Additionally, a variety of ISVs were identified, including Iflaviruses related to Tesano Aedes Iflavirus (TeAV), Armigeres Iflavirus, and Negeviruses related to Rabai Virus. An unclassified virus closely related to Korle-Bu Aedes virus was also detected. Our study provides insights into the viral diversity within Aedes aegypti mosquitoes in Kisumu and evidence of natural vertical transmission, specifically transovarial transmission of dengue virus type-3. Ongoing research is imperative to unravel vertical transmission mechanisms and subtleties governing ISV-arbovirus interactions across diverse environmental settings.},
}

Animals
*Aedes/virology
Kenya
*Dengue Virus/genetics/isolation & purification/classification
*Virome/genetics
*Mosquito Vectors/virology
*Infectious Disease Transmission, Vertical
Metagenomics
High-Throughput Nucleotide Sequencing
Phylogeny
Dengue/transmission/virology
Metagenome
Female

@article {pmid40601568,
year = {2025},
author = {Manavalan, S and Pradeep, D and Dharmalingam, D and Semalaiyappan, J and Sivarasan, T and Venkatesan, S and Thirumal, S and Kuttiatt, VS},
title = {Comparative analysis of skin microbiome of patients with filarial lymphedema and healthy individuals.},
journal = {PloS one},
volume = {20},
number = {7},
pages = {e0325380},
doi = {10.1371/journal.pone.0325380},
pmid = {40601568},
issn = {1932-6203},
mesh = {Humans ; *Microbiota/genetics ; Male ; *Skin/microbiology ; *Elephantiasis, Filarial/microbiology ; Adult ; Female ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Case-Control Studies ; *Lymphedema/microbiology ; Pilot Projects ; Skin Microbiome ; },
abstract = {BACKGROUND: Lymphatic filariasis, a vector borne parasitic disease is a public health problem in the tropical region. Recurrent skin and soft tissue infections termed adenolymphangitis (ADL) is a major complication of filarial lymphedema. Understanding the changes in skin microbiome associated with this disease may provide novel insights on ADL attacks and lymphedema progression. This study investigates the changes in skin microbial flora in patients affected with filarial lymphedema.

METHODS: We employed 16S rRNA gene amplicon-based metagenomic technique to profile the skin microbiome of patients with filarial lymphedema in comparison with healthy volunteers.

RESULTS: There were notable differences in the bacterial flora between patients and healthy controls. Actinobacteria were under-represented in the patient group. Staphylococcus dominated both the groups, 63% in patients and 44% in controls. Samples from a few patients showed the presence of certain rare bacteria like Eremococcus and Facklamia.

CONCLUSION: This pilot study applying advanced molecular tools provides insight on the changes in skin microflora associated with filarial lymphedema for the first time. Further studies are necessary for a better understanding of the role of the altered skin microbiome in frequent episodes of adenolymphangitis in patients with filarial lymphedema.},
}

Humans
*Microbiota/genetics
Male
*Skin/microbiology
*Elephantiasis, Filarial/microbiology
Adult
Female
Middle Aged
RNA, Ribosomal, 16S/genetics
Case-Control Studies
*Lymphedema/microbiology
Pilot Projects
Skin Microbiome

@article {pmid40599650,
year = {2025},
author = {Zhang, H and Zheng, X and Huang, Y and Zou, Y and Zhang, T and Repo, MA and Yin, M and You, Y and Jie, Z and Xu, WA},
title = {Novel potential biomarkers for predicting childhood caries via metagenomic analysis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1522970},
pmid = {40599650},
issn = {2235-2988},
mesh = {Humans ; *Dental Caries/diagnosis/microbiology ; Child ; *Biomarkers/analysis ; *Metagenomics/methods ; Saliva/microbiology ; Female ; Male ; *Microbiota/genetics ; Bacteria/classification/genetics/isolation & purification ; Metagenome ; },
abstract = {BACKGROUND: Dental caries is a prevalent global health issue, particularly among children, with significant oral and overall health implications. The oral microbiome is considered a critical factor in caries development, with various microbial species implicated in the disease process.

OBJECTIVES: This study aims to explore the changes and interactions of oral microbiota in childhood caries using metagenomic analysis, and identify potential biomarkers for early caries detection and treatment.

METHODS: Saliva samples were collected from 241 children aged 6 to 9 years, categorized into caries-free (CF), low-caries (CL), and caries-severe (CS) groups. Metagenomic sequencing was performed to analyze the oral microbiome, followed by a series of statistical and functional analyses to characterize microbial diversity and function.

RESULTS: The study revealed significant differences in the microbial community composition among the groups, with the CS group exhibiting higher alpha and beta diversity than that of the CF group. Numerous unclassified microorganisms, such as Campylobacter SGB19347 and Catonella SGB4501, are intimately linked to dental caries and display intricate interaction networks, suggesting the potential formation of a distinct ecological network. In functional assessment, we identified a possible link between pectin and caries, suggesting that microorganisms that produce pectinase enzymes might play a role in the advancement of severe dental caries. Additionally, we identified 16 species as the best marker for severe dental caries, achieving an impressive AUC of 0.91.

CONCLUSION: The role of microbiota in dental caries is multifaceted, involving a complex interplay of microbial species and functions. Our findings enhance the understanding of the microbial basis of dental caries and offer potential diagnostic and therapeutic targets. The predictive capacity of the identified biomarkers warrants further investigation for early caries detection and intervention.

CLINICAL SIGNIFICANCE: The identification of novel biomarkers through metagenomic analysis enables early detection and targeted intervention for childhood caries, potentially transforming children dental care and significantly improving long-term oral health outcomes.},
}

Humans
*Dental Caries/diagnosis/microbiology
Child
*Biomarkers/analysis
*Metagenomics/methods
Saliva/microbiology
Female
Male
*Microbiota/genetics
Bacteria/classification/genetics/isolation & purification
Metagenome

@article {pmid40598608,
year = {2025},
author = {Liu, F and McNally, J and Flemming, D and Ingham, AB and Hunt, PW and Li, RW},
title = {Escherichia coli is implicated in the development and manifestation of host susceptibility to the roundworm Trichostrongylus colubriformis infections in sheep.},
journal = {Veterinary research},
volume = {56},
number = {1},
pages = {133},
pmid = {40598608},
issn = {1297-9716},
support = {58-8042-3-022-F//Agricultural Research Service/ ; 242102311161//Henan Provincial Science and Technology Research Project/ ; },
mesh = {Animals ; *Sheep Diseases/parasitology/microbiology/immunology ; Sheep ; *Trichostrongylosis/veterinary/parasitology/immunology ; *Trichostrongylus/physiology ; *Escherichia coli/physiology ; *Gastrointestinal Microbiome ; Disease Susceptibility/veterinary/parasitology/microbiology ; RNA, Ribosomal, 16S/genetics/analysis ; },
abstract = {Applied breeding for host resistance to gastrointestinal nematodes represents a cost-effective strategy for parasitic control. While resistance is under moderate genetic influences, gut microbial components involved in the development of resistance or susceptibility remain largely unknown. Here we characterize the structure and metabolic potential of the proximal colon microbiota in unique ovine populations bred for resistance and susceptibility using a full-length 16S rRNA gene sequencing-based microbiome approach. The resistant lambs produced significantly fewer parasite eggs than susceptible animals grazing on the same pasture. Further, the resistant lambs displayed a significant reduction in worm establishment in response to a Trichostrongylus colubriformis challenge infection (P < 0.0001; N = 20 per group). Among 32 bacterial species or strains displaying a significant difference in relative abundance between the resistant and susceptible group, E. coli was more abundant in susceptible lambs. E. coli was also ranked as the most important species in distinguishing the resistant and susceptible status. Moreover, a microbial signature or balance consisting of E. coli (Numerator) and Parabacteroides distasonis and Bacteroides thetaiotaomicron (Denominator) predicted the resistance status with high accuracy. The metagenome function prediction also revealed that several pathways related to infectious diseases, such as Shigellosis and pathogenic E. coli infection, were significantly altered between the two phenotypes. Our findings demonstrated that microbial signatures with a high predictive power for the resistance status can be developed as biomarkers to facilitate the selection for host resistance in sheep.},
}

Animals
*Sheep Diseases/parasitology/microbiology/immunology
Sheep
*Trichostrongylosis/veterinary/parasitology/immunology
*Trichostrongylus/physiology
*Escherichia coli/physiology
*Gastrointestinal Microbiome
Disease Susceptibility/veterinary/parasitology/microbiology
RNA, Ribosomal, 16S/genetics/analysis

@article {pmid40598319,
year = {2025},
author = {Maeke, MD and Yin, X and Wunder, LC and Vanni, C and Richter-Heitmann, T and Miravet-Verde, S and Ruscheweyh, HJ and Sunagawa, S and Fabian, J and Piontek, J and Friedrich, MW and Hassenrück, C},
title = {Extensive data mining uncovers novel diversity among members of the rare biosphere within the Thermoplasmatota.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {155},
pmid = {40598319},
issn = {2049-2618},
support = {EXC-2077-390741603//Deutsche Forschungsgemeinschaft/ ; EXC-2077-390741603//Deutsche Forschungsgemeinschaft/ ; XJ2300006031//Start-up research fund of Hainan University, China/ ; LT0050/2023-L//Human Frontier Science Program/ ; 205320_215395//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; 03F0814//German Federal Ministry of Education and Research (BMBF)/ ; 03F0848A//German Federal Ministry of Education and Research (BMBF)/ ; },
mesh = {Phylogeny ; *Geologic Sediments/microbiology ; *Archaea/classification/genetics/isolation & purification ; Metagenomics/methods ; *Data Mining/methods ; Metagenome ; Biodiversity ; RNA, Ribosomal, 16S/genetics ; Ecosystem ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: Rare species, especially of the marine sedimentary biosphere, have long been overlooked owing to the complexity of sediment microbial communities, their sporadic temporal and patchy spatial abundance, and challenges in cultivating environmental microorganisms. In this study, we combined enrichments, targeted metagenomic sequencing, and extensive data mining to uncover uncultivated members of the archaeal rare biosphere in marine sediments.

RESULTS: In protein-amended enrichments, we detected the ecologically and metabolically uncharacterized class Candidatus Penumbrarchaeia within the phylum Thermoplasmatota. By screening more than 8000 metagenomic runs and 11,479 published genome assemblies, we expanded the phylogeny of Ca. Penumbrarchaeia by 3 novel orders. All six identified families of this class show low abundance in environmental samples characteristic of rare biosphere members. Members of the class Ca. Penumbrarchaeia were predicted to be involved in organic matter degradation in anoxic, carbon-rich habitats. All Ca. Penumbrarchaeia families contain high numbers of taxon-specific orthologous genes, highlighting their environmental adaptations and habitat specificity. Besides, members of this group exhibit the highest proportion of unknown genes within the entire phylum Thermoplasmatota, suggesting a high degree of functional novelty in this class.

CONCLUSIONS: In this study, we emphasize the necessity of targeted, data-integrative approaches to deepen our understanding of the rare biosphere and uncover the functions and metabolic potential hidden within these understudied taxa. Video Abstract.},
}

Phylogeny
*Geologic Sediments/microbiology
*Archaea/classification/genetics/isolation & purification
Metagenomics/methods
*Data Mining/methods
Metagenome
Biodiversity
RNA, Ribosomal, 16S/genetics
Ecosystem
Sequence Analysis, DNA

@article {pmid40597620,
year = {2025},
author = {Yang, L and Yan, Y and Shen, J and Xia, Y and Lang, F and Chen, C and Zou, W},
title = {Metagenomic insights into microbial community succession and its functional changes during the stage of acetic acid fermentation of shanxi aged vinegar.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {374},
pmid = {40597620},
issn = {1471-2180},
support = {20220401931002//Open Project Program of Shanxi Provincial Key Laboratory for Vinegar Fermentation Science and Engineering/ ; 20220401931002//Open Project Program of Shanxi Provincial Key Laboratory for Vinegar Fermentation Science and Engineering/ ; 20220401931002//Open Project Program of Shanxi Provincial Key Laboratory for Vinegar Fermentation Science and Engineering/ ; 20220401931002//Open Project Program of Shanxi Provincial Key Laboratory for Vinegar Fermentation Science and Engineering/ ; 20220401931002//Open Project Program of Shanxi Provincial Key Laboratory for Vinegar Fermentation Science and Engineering/ ; 20220401931002//Open Project Program of Shanxi Provincial Key Laboratory for Vinegar Fermentation Science and Engineering/ ; 20220401931002//Open Project Program of Shanxi Provincial Key Laboratory for Vinegar Fermentation Science and Engineering/ ; 202202140601018; 202102130501008//Key Research and Development Program Projects in Shanxi Province/ ; 202202140601018; 202102130501008//Key Research and Development Program Projects in Shanxi Province/ ; 202202140601018; 202102130501008//Key Research and Development Program Projects in Shanxi Province/ ; 202202140601018; 202102130501008//Key Research and Development Program Projects in Shanxi Province/ ; 202202140601018; 202102130501008//Key Research and Development Program Projects in Shanxi Province/ ; 202202140601018; 202102130501008//Key Research and Development Program Projects in Shanxi Province/ ; 202202140601018; 202102130501008//Key Research and Development Program Projects in Shanxi Province/ ; 2023NSFSC0184//Sichuan Natural Science Foundation General Project/ ; 2023NSFSC0184//Sichuan Natural Science Foundation General Project/ ; 2023NSFSC0184//Sichuan Natural Science Foundation General Project/ ; 2023NSFSC0184//Sichuan Natural Science Foundation General Project/ ; 2023NSFSC0184//Sichuan Natural Science Foundation General Project/ ; 2023NSFSC0184//Sichuan Natural Science Foundation General Project/ ; 2023NSFSC0184//Sichuan Natural Science Foundation General Project/ ; },
mesh = {*Acetic Acid/metabolism ; Fermentation ; *Metagenomics/methods ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Acetobacter/metabolism/genetics ; Metabolic Networks and Pathways ; *Microbiota/genetics ; Food Microbiology ; Metagenome ; },
abstract = {Traditional fermentation of Shanxi aged vinegar involves complex microbial interactions driving flavor synthesis, but the mechanisms underpinning metabolic adaptation and community succession remain poorly characterized. This study aimed to unravel stage-specific microbial dynamics and their functional contributions to flavor formation during Cupei fermentation. Metagenomic sequencing analyzed microbial communities and metabolic pathways at three fermentation stages (D3, D6, D9). Functional annotation (KEGG, CAZy) and species-level contribution assessments identified key taxa and genes linked to flavor biosynthesis. Microbial succession shifted from Lactobacillus dominance (64.68% at D3) to Acetobacter prevalence (48.04% at D9), with Lactobacillus acetotolerans persisting throughout (17.15-26.23%). Early-stage carbohydrate metabolism (GHs-driven: 60.38% at D3) transitioned to late-stage amino acid (15.62%) and cofactor synthesis (12.17%), activating valine, leucine, and histidine pathways critical for flavor compounds. Acetobacter oryzoeni and Acetobacter pomorum drove acetate (ALDH: 27.07-41.52%), valine (ilvE: 53.21-20.22%), and histidine (hisD: 41.83-33.30%) metabolism at D9. Low abundance species (Weissella confusa, 0.51%) and uncultured Limosilactobacillus sp. contributed via multi-gene networks (e.g., dat, ldh), which revealed an important functional contribution by overlooked low-abundance species. The study uncovers ecological coupling between microbial succession and metabolic adaptation, where dominant taxa and rare species synergistically govern flavor formation. These insights enable targeted microbial community design for flavor optimization in traditional fermented foods.},
}

*Acetic Acid/metabolism
Fermentation
*Metagenomics/methods
*Bacteria/genetics/classification/metabolism/isolation & purification
Acetobacter/metabolism/genetics
Metabolic Networks and Pathways
*Microbiota/genetics
Food Microbiology
Metagenome

@article {pmid40597414,
year = {2025},
author = {Kadyan, S and Park, G and Singh, TP and Patoine, C and Singar, S and Heise, T and Domeier, C and Ray, C and Kumar, M and Behare, PV and Chakrabarty, P and Efron, P and Sheffler, J and Nagpal, R},
title = {Microbiome-based therapeutics towards healthier aging and longevity.},
journal = {Genome medicine},
volume = {17},
number = {1},
pages = {75},
pmid = {40597414},
issn = {1756-994X},
mesh = {Humans ; *Longevity ; *Gastrointestinal Microbiome ; *Healthy Aging ; *Aging ; *Microbiota ; Animals ; },
abstract = {The gut microbiome is our lifetime companion, regulating our health from birth throughout the lifespan. The gut microbiome composition changes continually with age, influencing both physiological and immunological development. Emerging evidence highlights the close association, and thus implication, of the microbiome with healthy disease-free aging and longevity. Accordingly, targeting the gut microbiome is emerging as a promising avenue to prevent, alleviate, and ameliorate aging-related disorders. Herein, we provide a prospective and inclusive framework of the close connection of the gut microbiome with human aging, while contemplating how this association is intertwined with age-related diseases. We delve into recently emerging and potential microbiome-based therapeutics that are projected to aid in alleviating myriad aging-related diseases, thereby enhancing the health and well-being of the aging population. Finally, we present a foundation and perspective underlining the prospects of microbiome-based therapeutics developed and tailored precisely for the elderly, with the overarching goal of promoting health and longevity.},
}

Humans
*Longevity
*Gastrointestinal Microbiome
*Healthy Aging
*Aging
*Microbiota
Animals

@article {pmid40597307,
year = {2025},
author = {Wang, Z and Wang, W and Wang, Y and Hu, H and Wang, B and Zhu, W and Li, X and Hou, X and Sun, W and Liu, Z and Lu, S and Chen, X},
title = {Mapping gut microbiota and metabolite alterations in patients with postmenopausal osteoporosis in the Beijing Community of China.},
journal = {European journal of medical research},
volume = {30},
number = {1},
pages = {539},
pmid = {40597307},
issn = {2047-783X},
support = {No.2020YFC2004900//National Key Research and Development Program of China/ ; H0608//National Natural Science Foundation of China/ ; No.81672201, 81871794//Natural Science Foundation of China/ ; No.7242065//Beijing Natural Science Foundation/ ; },
mesh = {Humans ; Female ; *Gastrointestinal Microbiome ; *Osteoporosis, Postmenopausal/microbiology/metabolism/epidemiology ; Middle Aged ; Aged ; Bone Density ; Beijing ; China ; Feces/microbiology ; },
abstract = {INTRODUCTION: Postmenopausal osteoporosis (PMO) is a chronic disease in the elderly women, which has been shown to be related to the gut microbiota (GM) alternation in recent studies. Few studies have investigated which specific bacterial species and metabolites have an impact on postmenopausal osteoporosis patients, especially in urban communities.

METHODS: With the aim of comprehending GM features and metabolite variation in women suffering from PMO in the Beijing Community of China, we divided the 76 eligible participants into osteoporosis (OP) and health control (HC) groups taking into account the bone mineral density (BMD), and adopted 16 S rRNA gene sequencing and metagenomic sequencing to examine the GM compositions in the respective groups. Besides, the study adopted liquid chromatography and mass spectrometry (LC-MS) for the fecal metabolite analysis.

RESULTS: The OP group presented obviously changed bacterial α-diversity and β-diversity versus the HC group. GM at the genus level was differentially enriched in the OP or HC groups. Megamonas genus exhibited the strongest positive relevance to BMD and OC. Bacteroides genus had the strongest negative relevance to BMD and positive relevance to β-CTX. GM at the species level was also differentially enriched in OP or HC groups. After multiple linear regression analysis, Roseburia_intestinalis and Glycoursodeoxycholic acid were positively associated with BMD, hinting their beneficial effect in BMD. Corresponding signaling pathways also exhibited an obvious change, particularly in up-regulation Glycerol Phosphate Shuttle and down-regulation Malate-Aspartate Shuttle pathways.

CONCLUSIONS: According to the results of this study, GM and metabolites in women with PMO in the Beijing Community changed dramatically, which were significantly associated with BMD and bone turnover markers. Roseburia_intestinalis and Glycoursodeoxycholic acid levels were the most positively associated with BMD. All these assist in understanding the development mechanism of PMO from new perspectives and in developing novel therapeutic methods for improving bone health.},
}

Humans
Female
*Gastrointestinal Microbiome
*Osteoporosis, Postmenopausal/microbiology/metabolism/epidemiology
Middle Aged
Aged
Bone Density
Beijing
China
Feces/microbiology

@article {pmid40596882,
year = {2025},
author = {Hekker, MD and Platteel, TN and Venekamp, RP and Top, J and Geerlings, SE and Schultsz, C and de Vos, MGJ and van de Wijgert, JHHM},
title = {Urinary tract infections in postmenopausal women revisited (UTIr): a prospective observational cohort study to explore the urobiomes of postmenopausal women with and without recurrent urinary tract infections.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {822},
pmid = {40596882},
issn = {1471-2334},
support = {OCENW.XL21.XL21.088//The Dutch Research Council (NWO)/ ; OCENW.XL21.XL21.088//The Dutch Research Council (NWO)/ ; OCENW.XL21.XL21.088//The Dutch Research Council (NWO)/ ; OCENW.XL21.XL21.088//The Dutch Research Council (NWO)/ ; OCENW.XL21.XL21.088//The Dutch Research Council (NWO)/ ; OCENW.XL21.XL21.088//The Dutch Research Council (NWO)/ ; OCENW.XL21.XL21.088//The Dutch Research Council (NWO)/ ; OCENW.XL21.XL21.088//The Dutch Research Council (NWO)/ ; },
mesh = {Humans ; Female ; *Urinary Tract Infections/microbiology/epidemiology ; *Postmenopause ; Prospective Studies ; Middle Aged ; Recurrence ; Vagina/microbiology ; *Microbiota ; Aged ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; },
abstract = {BACKGROUND: Recurrent urinary tract infections (RUTI) are prevalent, particularly among postmenopausal women, and place a significant burden on the affected individuals and the healthcare system. While Escherichia coli is the primary cause of most UTIs in premenopausal women, this may not hold true for postmenopausal women. To facilitate development of novel diagnostics, preventive interventions, and clinical management of RUTI in postmenopausal women, it is essential to strengthen the biological evidence base.

METHODS: This observational prospective cohort study will enrol 20 postmenopausal women without RUTI (controls) and approximately 30 with RUTI (cases), aiming to sample at least 50 UTI episodes. Questionnaires are completed, samples (urine, vulvoperineal and vaginal swabs, and faeces) are collected by participants or study staff at five scheduled time points over one year of follow-up, as well as during and after each UTI episode. All samples will undergo 16S rRNA amplicon sequencing, with selected urine samples also subjected to bacterial culturing, metagenomic sequencing, and metabolomics. Various urobiome comparisons will be conducted, such as between women with and without RUTI in the absence of a UTI, and over time during UTIs. Urobiomes will also be compared to vaginal, vulvoperineal, and gut microbiomes in the same women at the same time points. Finally, urine samples will be cultured to obtain bacterial isolates, which will be characterised and used for co-culture and urothelium organoid experiments.

DISCUSSION: The UTIr cohort study is an exploratory, hypothesis-generating study designed to improve understanding of the ecological mechanisms driving UTI onset, response to antibiotic treatment, and UTI recurrence in postmenopausal women. The data collected from each individual woman is longitudinal and comprehensive, which is instrumental for advancing the field. The study population consists of women over the age of 50 and the study procedures are demanding. Flexibility with protocol procedures has proven to be essential to maximise retention and minimise missing data. We recommend employing a sufficiently large recruitment team and/or planning for a sufficiently long recruitment period to accommodate the demanding nature of these types of in-depth studies with vulnerable populations.

TRIAL REGISTRATION: Not applicable.},
}

Humans
Female
*Urinary Tract Infections/microbiology/epidemiology
*Postmenopause
Prospective Studies
Middle Aged
Recurrence
Vagina/microbiology
*Microbiota
Aged
RNA, Ribosomal, 16S/genetics
Feces/microbiology

@article {pmid40596159,
year = {2025},
author = {Bayatian, M and Pourbabaee, AA and Amoozegar, MA},
title = {Revealing the composition of bacterial communities in various oil-contaminated soils and investigating their intrinsic traits in hydrocarbon degradation.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {22016},
pmid = {40596159},
issn = {2045-2322},
mesh = {*Soil Microbiology ; *Hydrocarbons/metabolism ; Biodegradation, Environmental ; *Bacteria/genetics/classification/metabolism ; *Soil Pollutants/metabolism ; RNA, Ribosomal, 16S/genetics ; *Petroleum/metabolism ; Soil/chemistry ; *Microbiota ; Petroleum Pollution ; Iran ; High-Throughput Nucleotide Sequencing ; Phylogeny ; },
abstract = {This study explores prokaryotic diversity and oil biodegradation potential in soils from three evaporation ponds in the Ahvaz and Maroon oil fields, Iran. Despite prior studies on prokaryotic diversity in contaminated soils, systematic comparisons within the same region remain limited. The analysis identified distinct physicochemical differences across sites. Ahvaz 1 soil, with a loamy silty clay texture, had the highest salinity (15.4%) and total petroleum hydrocarbons (TPH, 3.5%). Ahvaz 4 soil, loamy silty in texture, showed 7.49% salinity and 1% TPH, while Maroon 3 soil exhibited the lowest salinity (5.06%) and TPH (0.5%). Prokaryotic diversity and biodegradation traits were assessed using 16S rRNA next-generation sequencing (NGS) and qPCR, respectively. NGS revealed reduced prokaryotic diversity in all contaminated soils, with Bacillota dominating, whereas Pseudomonadota prevailed in all control samples. Maroon 3 soils had higher diversity, but Cyanobacteria and Actinomycetota, dominant in controls, were replaced by Chloroflexota, Gemmatimonadota, and Acidobacteriota in polluted soils. At the genus level, Bacillus, Lysinibacillus, Virgibacillus, Brevibacillus, and Paenibacillus showed increased abundance in contaminated soils. Real-time PCR of alkB and C23DO genes indicated enhanced hydrocarbon degradation potential. FAPROTAX and PICRUSt2 analyses revealed enhanced microbial capacity for hydrocarbon degradation in polluted soils, with enriched functions related to chemoheterotrophy, aromatic compound degradation, and increased levels of alkane 1-monooxygenase, alcohol dehydrogenase, and protocatechuate 4,5-dioxygenase subunits. The findings highlight crude oil's impact on microbial community structure, reducing archaea and emphasizing bacterial dominance while underscoring shifts in microbial responses and functional gene expression in hydrocarbon degradation.},
}

*Soil Microbiology
*Hydrocarbons/metabolism
Biodegradation, Environmental
*Bacteria/genetics/classification/metabolism
*Soil Pollutants/metabolism
RNA, Ribosomal, 16S/genetics
*Petroleum/metabolism
Soil/chemistry
*Microbiota
Petroleum Pollution
Iran
High-Throughput Nucleotide Sequencing
Phylogeny

@article {pmid40595658,
year = {2025},
author = {Zhang, Z and Liu, Y and Zhao, W and Liu, K and Chen, Y and Wang, F and Mao, G and Ji, M},
title = {Distinct genes and microbial communities involved in nitrogen cycling between monsoon- and westerlies-dominated Tibetan glaciers.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {5926},
pmid = {40595658},
issn = {2041-1723},
support = {42421001//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42330410//National Natural Science Foundation of China (National Science Foundation of China)/ ; U21A20176//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Tibet ; *Nitrogen Cycle/genetics ; *Ice Cover/microbiology ; *Microbiota/genetics ; Nitrogen/metabolism ; Metagenome/genetics ; Climate Change ; Bacteria/genetics/metabolism/classification ; Temperature ; Nitrous Oxide/metabolism ; Nitrogen Fixation/genetics ; Transcriptome ; },
abstract = {The Tibetan Plateau (TP) glaciers are influenced by monsoon and westerlies. They are highly sensitive to climate change, with atmospheric nitrogen deposition significantly impacting microbial communities and functions. However, key uncertainties persist regarding biogeography and drivers of genes and microbial communities involved in nitrogen cycling. Here, we investigate the diversity and transcriptional activity of microbial communities and nitrogen-cycling genes using 85 metagenomes and 28 metatranscriptomes from the ablation zone of 21 TP glaciers. Our results show that over 90% of the glacial taxa possess the potential for nitrogen metabolism, with ~33% exhibiting transcriptional activity. Moreover, monsoon-dominated glaciers present greater microbial diversity and higher prevalence of nitrogen-fixing genes than westerlies-dominated glaciers, linked to higher temperatures. Comparatively, the latter show elevated genomic potential for nitrous oxide emissions, likely due to higher nitrate concentrations. These findings establish temperature-nitrogen co-regulation of microbial nitrogen transformations, critical for predicting climate feedback in the extreme environment.},
}

Tibet
*Nitrogen Cycle/genetics
*Ice Cover/microbiology
*Microbiota/genetics
Nitrogen/metabolism
Metagenome/genetics
Climate Change
Bacteria/genetics/metabolism/classification
Temperature
Nitrous Oxide/metabolism
Nitrogen Fixation/genetics
Transcriptome

@article {pmid40595444,
year = {2025},
author = {Minabou Ndjite, G and Jiang, AK and Ravel, CT and Grant, MR and Jiang, X and Hall, B},
title = {Gut microbial utilization of the alternative sweetener, D-allulose, via AlsE.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {970},
pmid = {40595444},
issn = {2399-3642},
support = {1R35GM155208-01//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; },
mesh = {*Gastrointestinal Microbiome ; Humans ; *Sweetening Agents/metabolism ; *Fructose/metabolism ; Adult ; *Clostridium/genetics/enzymology/metabolism ; },
abstract = {D-allulose, a rare sugar with emerging potential as a low-calorie sweetener, has garnered attention as an alternative to other commercially available alternative sweeteners, such as sugar alcohols, which often cause severe gastrointestinal discomfort. D-allulose-6-phosphate 3-epimerase (AlsE) is a prokaryotic enzyme that converts D-allulose-6-phosphate into D-fructose-6-phosphate, enabling its use as a carbon source. However, the taxonomic breadth of AlsE across gut bacteria remains poorly understood, hindering insights into the utilization of D-allulose by microbial communities. In this study, we provide experimental evidence showing that Clostridium innocuum is capable of D-allulose metabolism via a homologous AlsE. A bioinformatics search of 85,202 bacterial genomes identified 116 bacterial species with AlsE homologs, suggesting a limited distribution of AlsE in bacteria. Additionally, Escherichia coli contains a copy of alsE, but it does not grow on D-allulose as a sole carbon source unless alsE is heterologously expressed. A metagenomic analysis revealed that 15.8% of 3079 adult healthy human metagenomic samples that we analyzed contained alsE, suggesting a limited prevalence of the enzyme in the gut microbiome. These results suggest that the gut microbiome has limited capacity to metabolize D-allulose via alsE, supporting its use as an alternative sweetener with minimal impact on microbial composition and gastrointestinal symptoms. This finding also enables personalized nutrition, allowing diabetic individuals to assess their gut microbiota for alsE, and manage glycemic response while reducing gastrointestinal distress.},
}

*Gastrointestinal Microbiome
Humans
*Sweetening Agents/metabolism
*Fructose/metabolism
Adult
*Clostridium/genetics/enzymology/metabolism

@article {pmid40595004,
year = {2025},
author = {Raina, TK and Gupta, M and Salgotra, RK},
title = {Metagenomic analysis to identify unique microbes in the rhizosphere of basmati rice (Oryza sativa L.) accessions.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {22864},
pmid = {40595004},
issn = {2045-2322},
mesh = {*Oryza/microbiology/genetics ; *Rhizosphere ; *Metagenomics/methods ; Soil Microbiology ; *Bacteria/genetics/classification/isolation & purification ; Odorants/analysis ; Microbiota ; },
abstract = {The captivating aroma of basmati rice is highly favoured by consumers across the globe. Unfortunately, the aroma of basmati rice has been gradually diminishing over time due to the excessive use of inorganic fertilizers and the impact of climate change. To understand the microbial community that plays a significant role in aroma enhancement in basmati rice accessions, a systematic study is required. A unique rhizobacteria of basmati rice associated with basmati rice were Actinobacteria, Bacillus subtilis, Burkholderia, Enterobacter, Klebsiella, Lactobacillus, Micrococcus, Pseudomonas, and Sinomonas. The biosynthesis of potential precursors (ornithine, putrescine, proline, and polyamines) of aroma in basmati rice involved various enzymes such as acetylornithine aminotransferase, acetylornithine deacetylase, N-acetylornithine carbomyltransferase, acetylornithine/succinyldiaminopimelate aminotransferase, and ornithine cyclodeaminase. These findings significantly contribute to the existing understanding of the rhizobacteria associated with basmati rice that play a crucial role in enhancing the aroma. The introduction of these cultures into the basmati rice growing areas has the potential to augment the plant growth and enhances the aroma. The present study explored the functional potential of the microbial community associated with aroma improvement in basmati rice. This will also enhance the export potential of the basmati rice in the region on sustainable basis.},
}

*Oryza/microbiology/genetics
*Rhizosphere
*Metagenomics/methods
Soil Microbiology
*Bacteria/genetics/classification/isolation & purification
Odorants/analysis
Microbiota

@article {pmid40594354,
year = {2025},
author = {Flores, SS and Cordovez, V and Arias Giraldo, LM and Leon-Reyes, A and van 't Hof, P and Raaijmakers, JM and Oyserman, BO},
title = {Unveiling diversity and adaptations of the wild tomato Microbiome in their center of origin in the Ecuadorian Andes.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {22448},
pmid = {40594354},
issn = {2045-2322},
support = {CZ07-000440-2018//SENESCYT scholarship/ ; 10093//Chancellor Grant and COCIBA-USFQ/ ; 10093//Chancellor Grant and COCIBA-USFQ/ ; 024.004.014/NWO_/Dutch Research Council/Netherlands ; 024.004.014/NWO_/Dutch Research Council/Netherlands ; },
mesh = {*Solanum lycopersicum/microbiology/genetics ; *Microbiota/genetics ; Soil Microbiology ; Rhizosphere ; Ecuador ; Plant Roots/microbiology ; Biodiversity ; *Adaptation, Physiological ; Phylogeny ; },
abstract = {Microbiome assembly has been studied for many plant species and is recognized as a key driver of plant growth and plant tolerance to (a)biotic stresses. To date, assembly of the tomato rhizosphere microbiome has been investigated primarily for commercial varieties and field soils subjected to agricultural management practices, whereas the microbiome of wild tomato genotypes in their native habitats remains largely unexplored. This research focused on distinct populations of Solanum pimpinellifolium in three natural habitats in the Ecuadorian Andes to identify the taxonomic and functional diversity of their rhizosphere microbiome. The results showed that, despite genotypic differences among the wild tomato populations, different soil types and soil microbiome compositions, the rhizosphere microbiome showed strikingly compositional similarity across the three habitats. Proteobacteria, in particular taxa classified as Enterobacteriaceae, and specific unclassified fungal taxa were highly represented in the rhizosphere of S. pimpinellifolum. Metagenomic analyses suggested that the prevalence of Enterobacteriaceae on wild tomato roots may be explained by several traits, in particular nutrient competition, motility, iron acquisition, membrane transport, stress response, and plant hormone biosynthesis. These results reveal a conserved microbiome signature associated with wild tomato rhizosphere in their center of origin. Just as the genomes of wild crop ancestors provide a valuable source of beneficial traits for breeding cultivated varieties, exploring their microbiome in native environments could uncover microbial taxa and traits that similarly contribute to crop growth and health.},
}

*Solanum lycopersicum/microbiology/genetics
*Microbiota/genetics
Soil Microbiology
Rhizosphere
Ecuador
Plant Roots/microbiology
Biodiversity
*Adaptation, Physiological
Phylogeny

@article {pmid40594317,
year = {2025},
author = {Song, X and Li, JN and Wang, D and Han, ZY and Yan, XX and Yang, ZH and Xu, J and Wang, Q and Wu, D},
title = {Metagenomics reveals functional profiles of gut microbiota during the recovery phase of acute pancreatitis.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {20549},
pmid = {40594317},
issn = {2045-2322},
support = {32170788//National Natural Science Foundation of China/ ; 2022-PUMCH-B-023//National High Level Hospital Clinical Research Funding/ ; ZK108000//National Key Clinical Specialty Construction Project/ ; 7232123//Natural Science Foundation of Beijing/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; *Pancreatitis/microbiology ; Male ; Female ; Middle Aged ; Adult ; Aged ; Acute Disease ; Bacteria/genetics/classification ; },
abstract = {Gut microbiota play a critical pathogenic role in acute pancreatitis (AP). This study aimed to investigate the composition and function of gut microbiota during the recovery phase of AP. Rectal swab samples obtained from 12 AP patients of varying severity during both the acute and recovery phases were sequenced using shotgun metagenomic sequencing. We analysed α-diversity, enterotypes, and the dominant microbiome composition, and performed differential analysis of gut microbiota composition and functional enrichment. During the recovery phase of AP, microbial diversity remained decreased, and minimal difference were observed in the structural diversity of the microbiome. There was an increasing tendency of beneficial bacteria (Bacteroidales) and a decreasing tendency of harmful bacteria (Firmicutes) in the recovery phase of mild AP (MAP). However, in the recovery phase of moderately severe AP (MSAP) and severe AP, Enterococcus abundance increased compared with that in the acute phase. Some signalling pathways showed opposite trends in the recovery phase of MAP and MSAP compared to the acute phase. These results suggested that gut microbiome composition and function are associated with AP recovery, which may inform strategies for the treatment and prognosis of AP.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Metagenomics/methods
*Pancreatitis/microbiology
Male
Female
Middle Aged
Adult
Aged
Acute Disease
Bacteria/genetics/classification

@article {pmid40593979,
year = {2025},
author = {Chen, L and Chen, H and Lv, T and Guo, X and Wu, W and Zhao, D and Liu, F},
title = {Differences of the respiratory microbiota between children suffering from community acquired pneumonia with presence or absence of asthma.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {20458},
pmid = {40593979},
issn = {2045-2322},
mesh = {Humans ; *Asthma/microbiology/complications ; *Community-Acquired Infections/microbiology/complications ; *Microbiota ; Male ; Female ; Child ; Child, Preschool ; *Pneumonia/microbiology/complications ; Infant ; High-Throughput Nucleotide Sequencing ; Metagenomics ; Adolescent ; Community-Acquired Pneumonia ; },
abstract = {Recent advancements in respiratory microbiota research have progressively elucidated their pivotal role in pediatric respiratory pathologies. Alterations in airway microbial communities are intricately associated with diverse respiratory conditions and distinct disease states. This study conducted a comparative analysis of respiratory microecological profiles in pediatric cohorts diagnosed with community-acquired pneumonia (CAP), stratified by the presence or absence of comorbid bronchial asthma, from whom nasopharyngeal aspirates were obtained for metagenomic next-generation sequencing (mNGS). Analyses revealed comparable alpha-diversity indices between groups; however, beta-diversity metrics demonstrated marked compositional divergence. In the asthma-CAP cohort, Streptococcus pneumoniae and Rothia mucilaginosa emerged as predominant taxa, whereas Mycoplasmoides pneumoniae and Trichoderma citrinoviride dominated microbial profiles in uncomplicated CAP patients.},
}

Humans
*Asthma/microbiology/complications
*Community-Acquired Infections/microbiology/complications
*Microbiota
Male
Female
Child
Child, Preschool
*Pneumonia/microbiology/complications
Infant
High-Throughput Nucleotide Sequencing
Metagenomics
Adolescent
Community-Acquired Pneumonia

@article {pmid40593735,
year = {2025},
author = {Flores Ventura, E and Esteban-Torres, M and Gueimonde, M and van Sinderen, D and Koren, O and Hall, LJ and Segata, N and Valles-Colomer, M and Collado, MC},
title = {Mother-to-infant vertical transmission in early life: a systematic review and proportional meta-analysis of Bifidobacterium strain transmissibility.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {121},
pmid = {40593735},
issn = {2055-5008},
support = {CEX2021-001189-S-20-1//Ministerio de Ciencia e Innovación/ ; CEX2021-001189-S/ MCIN/AEI / 10.13039/501100011033//Ministerio de Ciencia e Innovación/ ; PID2022-139328OA-I00//Ministerio de Ciencia e Innovación/ ; CEX2021-001189-S/ MCIN/AEI / 10.13039/501100011033//Ministerio de Ciencia e Innovación/ ; 898088//European Union's Horizon 2020/ ; SFI/12/RC/2273-P1 and SFI/12/RC/2273-P2/SFI_/Science Foundation Ireland/Ireland ; 220876/Z/20/Z//Wellcome Trust Investigator/ ; Beatriz Galindo Junior Fellowship BG22/00172//Ministerio de Universidades/ ; 639226/ERC_/European Research Council/International ; },
mesh = {Female ; Humans ; Infant ; Infant, Newborn ; Pregnancy ; *Bifidobacteriales Infections/transmission/microbiology ; *Bifidobacterium/classification/genetics/isolation & purification ; Gastrointestinal Microbiome ; *Infectious Disease Transmission, Vertical ; Metagenomics ; Mothers ; Vagina/microbiology ; },
abstract = {Early-life colonization is a critical developmental process influencing infant biological programming, with bifidobacteria playing a key role. This systematic review examines the transmissibility of Bifidobacterium strains from mothers to infants. Adhering to Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) guidelines, 31 articles from 2009 to 2024 were selected from 2825 screened titles and abstracts. Using a narrative synthesis and meta-analysis, the review focuses on studies employing strain-level metagenomic approaches (Protocol registry CRD: CRD42023490507). Ten studies using shotgun metagenomic sequencing identified specific strains of B. adolescentis, B. angulatum, B. bifidum, B. breve, B. pseudocatenulatum, B. catenulatum, and B. longum shared between mothers and infants. A meta-analysis of 810 mother-infant pairs revealed an overall species transmissibility estimate of 30% (95% CI: 0.17; 0.44), with B. longum strains persisting in infants' guts for up to 6 months. Strain transmissibility was higher in vaginally delivered infants compared to those delivered by caesarean section. This review highlights the high transmission rates of maternal Bifidobacterium strains in early-life gut seeding, particularly B. bifidum and B. longum. Despite ongoing research, uncertainties remain regarding the precise characteristics, transmission routes, and mechanisms of transmitted strains. Comprehensive approaches, including metagenomic sequencing and longitudinal studies, are needed to understand the role of vertical transmission in infant gut microbiome engraftment and its functional implications.},
}

Female
Humans
Infant
Infant, Newborn
Pregnancy
*Bifidobacteriales Infections/transmission/microbiology
*Bifidobacterium/classification/genetics/isolation & purification
Gastrointestinal Microbiome
*Infectious Disease Transmission, Vertical
Metagenomics
Mothers
Vagina/microbiology

@article {pmid40593262,
year = {2025},
author = {Liu, L and Li, M and Qin, Y and Liu, Y and Li, M and Lian, B and Guo, R and Xiao, Y and Yin, C},
title = {Childhood obesity and insulin resistance is correlated with gut microbiome serum protein: an integrated metagenomic and proteomic analysis.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {21436},
pmid = {40593262},
issn = {2045-2322},
support = {81903340//National Natural Science Foundation of China/ ; },
mesh = {Child ; Female ; Humans ; Male ; *Blood Proteins/metabolism ; Feces/microbiology ; *Gastrointestinal Microbiome ; *Insulin Resistance ; Metagenomics/methods ; *Pediatric Obesity/microbiology/blood/metabolism ; Proteomics/methods ; },
abstract = {The aim of this study was to investigate the changes in the gut microbiota and proteins related to metabolism and immunity caused by childhood obesity and insulin resistance (IR) and to assess the underlying relationship between the gut microbiota and IR in children. Nineteen children with obesity and sixteen healthy children were recruited. Children with obesity were divided into two groups: obese with IR and obese without IR. All of the obese children participated in a 1-month lifestyle-based weight loss program. Faecal metagenomics and serum Olink proteomics combined with clinical parameters were used to identify the metabolic alterations associated with childhood obesity and IR. The gut microbiota and serum protein were significantly altered in obese children with IR. The relative abundances of Akkermansia muciniphila, IGFBP1 and GP6 were decreased in obese children with IR. Butyricicoccus sp. AM29-23AC, DLK1, CD163, CCL16 and CTSD levels were recovered after IR improved. TNFR1 had a significant indirect effect on the interaction between s-Citrobacter.freundii and fasting insulin. In conclusion, obese children with IR have abnormal gut microbiota and serum proteins related to metabolism and immunity, which can be improved after weight loss. The gut microbiome of children with obesity may contribute to the development of IR by triggering metabolic inflammation.Clinical Trial Registration: This study was registered with the Chinese Clinical Trial Registry (Registration number: ChiCTR2300072179).},
}

Child
Female
Humans
Male
*Blood Proteins/metabolism
Feces/microbiology
*Gastrointestinal Microbiome
*Insulin Resistance
Metagenomics/methods
*Pediatric Obesity/microbiology/blood/metabolism
Proteomics/methods

@article {pmid40593012,
year = {2025},
author = {Sitko, K and Piotrowska, E and Podlacha, M and Zagórska, N and Starke, MD and Trzeciak, M and Tukaj, S},
title = {Topical application of the HSP90 inhibitor 17-AAG reduces skin inflammation and partially restores microbial balance: implications for atopic dermatitis therapy.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {21245},
pmid = {40593012},
issn = {2045-2322},
support = {2020/39/B/NZ6/00357//Polish National Science Centre (NCN)/ ; 2020/39/B/NZ6/00357//Polish National Science Centre (NCN)/ ; 2020/39/B/NZ6/00357//Polish National Science Centre (NCN)/ ; 2020/39/B/NZ6/00357//Polish National Science Centre (NCN)/ ; 2020/39/B/NZ6/00357//Polish National Science Centre (NCN)/ ; },
mesh = {*Benzoquinones/administration & dosage/pharmacology ; *Lactams, Macrocyclic/administration & dosage/pharmacology ; Animals ; *Dermatitis, Atopic/drug therapy/pathology/chemically induced/microbiology/metabolism ; *HSP90 Heat-Shock Proteins/antagonists & inhibitors/metabolism ; Mice ; Humans ; Disease Models, Animal ; Administration, Topical ; *Skin/drug effects/pathology/microbiology ; Female ; Cytokines/metabolism ; Eosinophils/drug effects/metabolism ; Gastrointestinal Microbiome/drug effects ; Staphylococcus aureus/drug effects ; Inflammation/drug therapy ; Keratinocytes/drug effects/metabolism ; },
abstract = {Heat shock proteins belonging to the HSP90 family promote inflammation and are potential therapeutic targets in inflammatory and autoimmune diseases. Here the effects of the HSP90 inhibitor 17-AAG applied topically were evaluated in a DNCB-induced murine model of atopic dermatitis (AD). The use of 17-AAG improved clinical disease activity without causing toxicity in the animals. Topical application of 17-AAG resulted in reduced epidermal hyperplasia, decreased expression of TSLP, IL-5, and IL-6, as well as reduced activation of NF-κB in the skin. In addition, the eosinophil proportion in the blood and eosinophil peroxidase (EPX) activity in the skin were significantly reduced in 17-AAG-treated AD mice. The inhibitory effects of 17-AAG on the production of epidermal alarmins, T-helper cell-associated cytokines, and ROS release were demonstrated in cultures of activated human keratinocytes, CD4[+] T lymphocytes, and eosinophils, respectively. Finally, next-generation sequencing metagenomic approaches revealed that topical application of 17-AAG partially restored the normal gut microbiome in AD mice. Moreover, 17-AAG inhibited Staphylococcus aureus biofilm formation in vitro. The findings of this study, combined with the observed increase in HSP90 and EPX activity in the leukocytes of the analyzed cohort of AD patients, support the potential therapeutic use of HSP90 inhibitors in individuals with AD.},
}

*Benzoquinones/administration & dosage/pharmacology
*Lactams, Macrocyclic/administration & dosage/pharmacology
Animals
*Dermatitis, Atopic/drug therapy/pathology/chemically induced/microbiology/metabolism
*HSP90 Heat-Shock Proteins/antagonists & inhibitors/metabolism
Mice
Humans
Disease Models, Animal
Administration, Topical
*Skin/drug effects/pathology/microbiology
Female
Cytokines/metabolism
Eosinophils/drug effects/metabolism
Gastrointestinal Microbiome/drug effects
Staphylococcus aureus/drug effects
Inflammation/drug therapy
Keratinocytes/drug effects/metabolism

@article {pmid40592825,
year = {2025},
author = {Mali, N and Mali, S and Zhang, L and Fu, P},
title = {Interplay between gut microbiota and acute kidney injury: a review of their mutual influence and causation.},
journal = {Renal failure},
volume = {47},
number = {1},
pages = {2522976},
pmid = {40592825},
issn = {1525-6049},
mesh = {Humans ; *Acute Kidney Injury/microbiology/immunology/physiopathology ; *Gastrointestinal Microbiome/immunology/physiology ; Kidney/physiopathology/microbiology ; Animals ; },
abstract = {It is unclear, therefore, exactly how gut microbes and renal processes communicate. Recent developments in the field of microbiome research present chances to enhance our comprehension and management of acute kidney injury (AKI). This review highlights important ideas and suggests more research while giving a general summary of the microbiome's influence on kidney function and AKI. AKI is a complex condition that develops through a variety of pathways. Recent experimental research has highlighted the important role that the gut microbiota plays in the course of AKI. Our understanding of human biology has been completely transformed by the current increase in gut microbiota research. Amazing progress in DNA sequencing analysis, especially in the areas of metagenomics and metatranscriptomics, has greatly increased our ability to measure and track complex microbial populations. As such, we are now in a better position to look at how these communities affect human health and illness. As a result, the relationships between renal physiology and pathophysiology and the gut microbiota are now better understood. Both experimental AKI and chronic renal illness have been linked to changes in the intestinal microbiome. This succinct review attempts to examine our present knowledge of the immune-modulatory effects of the gut microbiota, how kidney disorders are influenced by it, and the possible reciprocal interaction between kidney diseases and the microbiota. Subsequent investigations ought to concentrate on delving deeper into the function of the gut microbiota in renal disorders and finding possible therapeutic strategies for adjusting it.},
}

Humans
*Acute Kidney Injury/microbiology/immunology/physiopathology
*Gastrointestinal Microbiome/immunology/physiology
Kidney/physiopathology/microbiology
Animals

@article {pmid40497681,
year = {2025},
author = {Fan, Y and Li, Y and Wang, L and Zhao, D and Zhou, Y and Houpt, ER and Liu, J},
title = {Fecal microbiome profiling of children with Shigella diarrhea from low- and middle-income countries.},
journal = {Microbiology spectrum},
volume = {13},
number = {7},
pages = {e0057325},
pmid = {40497681},
issn = {2165-0497},
support = {OPP1019093//Bill and Melinda Gates Foundation/ ; },
mesh = {Humans ; *Feces/microbiology ; *Shigella/genetics/isolation & purification/pathogenicity/classification ; *Dysentery, Bacillary/microbiology/diagnosis ; Child, Preschool ; *Diarrhea/microbiology ; Infant ; Virulence Factors/genetics ; Female ; Male ; *Gastrointestinal Microbiome ; Child ; Developing Countries ; },
abstract = {Shigella is one of the leading pathogens causing diarrhea in children globally. Stool culture remains the standard for diagnosing Shigella infections; however, quantitative PCR (qPCR) offers greater sensitivity. In this study, we evaluated the fecal microbiomes of 27 diarrheal children with and without Shigella identified by culture and quantitative PCR, respectively, aiming to characterize the fecal microbiome profiles of children with Shigella diarrhea and to explore the differences in microbiome and the mechanisms associated with the culturability of Shigella. Our results showed that Shigella qPCR positive cases were characterized by a significantly higher abundance of Shigella and other Proteobacteria, alongside a lower abundance of the probiotic genus Bifidobacterium. This profile was associated with specific virulence factors (VFGs) and antimicrobial resistance genes (ARGs), indicating a unique pathogenic module related to Shigella infection. While no significant difference in Shigella abundance was found between the Shigella culture positive and culture negative groups, genera Bifidobacterium and Ligilactobacillus were enriched in the culture positive group. Interestingly, the culture positive group also possessed a higher abundance of virulence factors associated with pathogenicity, likely resulting from the higher copy number of pINV plasmid. The fecal metagenomic analyses from diarrheal children suggested a potentially distinct intestinal microbial profile associated with Shigella infection and a possible correlation between increased pathogenicity and the Shigella culturability. These findings might contribute to a more comprehensive understanding of Shigella pathogenicity and improving diagnostic methods for Shigella.IMPORTANCEDiarrhea represents the fifth leading cause of mortality among children under the age of five, with Shigella representing the second most common pathogen responsible for diarrhea-related mortality. In the current study, we employed metagenomics to comprehensively characterize the fecal microbiome profiles of children infected with Shigella and to investigate the factors affecting Shigella culturability. We identified a distinct intestinal microbial profile associated with Shigella-infected diarrheal children, observed a correlation between increased pathogenicity and the Shigella culturability, and also proposed some potential factors that might promote the in vitro growth of Shigella strains. These findings might provide evidence for improving diagnostic methods for Shigella.},
}

Humans
*Feces/microbiology
*Shigella/genetics/isolation & purification/pathogenicity/classification
*Dysentery, Bacillary/microbiology/diagnosis
Child, Preschool
*Diarrhea/microbiology
Infant
Virulence Factors/genetics
Female
Male
*Gastrointestinal Microbiome
Child
Developing Countries

@article {pmid40494644,
year = {2025},
author = {Ma, R and Shi, Y and Wu, W and Huang, C and Xue, F and Hou, R and Zhou, Y and Gu, J and Feng, F and Yu, X and Liu, J and Li, Z and Zhang, L and Lan, G and Chen, C and Bi, W and Song, X and Fu, M and Yang, H and Gu, H and Yang, J and Qi, D},
title = {The bacterial diversity and potential pathogenic risks of giant panda-infesting ticks.},
journal = {Microbiology spectrum},
volume = {13},
number = {7},
pages = {e0219724},
pmid = {40494644},
issn = {2165-0497},
support = {U21A20193//National Natural Science Foundation of China/ ; 32400405//National Natural Science Foundation of China/ ; 2023NSFSC1156//Sichuan Science and Technology Program/ ; 2024NSFSC0023//Sichuan Science and Technology Program/ ; 2023-YF09-00017-SN//Chengdu Science and Technology Bureau/ ; 2024CPB-A23, 2024CPB-Y05, CAZG2025C13//Chengdu Giant Panda Breeding Research Foundation/ ; },
mesh = {Animals ; *Ursidae/parasitology/microbiology ; Female ; *Bacteria/genetics/classification/isolation & purification/pathogenicity/drug effects ; RNA, Ribosomal, 16S/genetics ; Male ; *Ticks/microbiology ; *Tick Infestations/veterinary/parasitology/microbiology ; Seasons ; Metagenomics ; Anti-Bacterial Agents/pharmacology ; Microbiota ; },
abstract = {UNLABELLED: As common parasites in the wild, ticks significantly limit the population growth of wild giant pandas and hinder the process of reintroducing captive giant pandas into their natural habitats. Research on microbial communities and pathogens in ticks infesting giant pandas is limited, emphasizing the need for a comprehensive investigation. To thoroughly investigate the microbial communities in giant panda-infesting ticks, particularly potential pathogens, we analyzed 246 ticks collected from the ears of wild-living giant pandas using 16S rRNA and metagenomic sequencing. We found that the microbial diversity in female ticks was significantly enriched in summer. The microbial community structure carried by ticks is more significantly influenced by seasonal changes than by sex. Metagenomic results indicated that giant pandas have a higher risk of Coxiella burnetii infection in summer and a higher risk of Anaplasma phagocytophilum, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Rickettsia amblyommatis infections in autumn. Over 90% of the ticks carried pathogens, with 82.54% harboring a single potentially pathogenic symbiont and the remaining 17.46% carrying multiple pathogens, all involving Coxiella burnetii. Using the CARD database, we identified a total of 121 antibiotic resistance genes (ARGs), with 76% exhibiting antibiotic efflux mechanisms. Based on the significantly associated ARGs, we provided antibiotic treatment recommendations for infections potentially caused by pathogenic symbionts. This study provides a clear answer to the potential microbial pathogen risks of ticks infesting giant pandas and offers a framework for tick-borne diseases in reintroduced wild panda populations.

IMPORTANCE: Importance: The emergence of tick-borne bacterial diseases poses a serious threat to the population health of wild-living giant pandas. Ticks are obligate hematophagous ectoparasites that survive by feeding on the blood of various animal hosts and spreading pathogens. Although some previous studies have confirmed that wild ticks carried various viruses, the role of wild giant panda-infesting ticks in the bacterial community remains unknown. Here, the identification of the microbial community and antibiotic resistome in giant panda-infesting ticks revealed that most Ixodes ovatus ticks are potentially pathogenic symbionts, including Anaplasma phagocytophilum, Coxiella burnetii, and Rickettsia amblyommatis. Tick-borne disease control also needs to take into account the effects of season, sex, and antibiotic efflux resistance genes. Our findings highlight the contribution of the scientific management of tick-borne diseases in the giant panda population.},
}

Animals
*Ursidae/parasitology/microbiology
Female
*Bacteria/genetics/classification/isolation & purification/pathogenicity/drug effects
RNA, Ribosomal, 16S/genetics
Male
*Ticks/microbiology
*Tick Infestations/veterinary/parasitology/microbiology
Seasons
Metagenomics
Anti-Bacterial Agents/pharmacology
Microbiota

@article {pmid40488467,
year = {2025},
author = {Liu, Y and Qiu, Q and Chen, Y and Deng, Y and Huang, W and Sun, C and Shang, X and Chen, X and Wang, C and Han, L and Chen, S and Yuan, J and Xu, F and Yang, Z and Fang, X and Huang, L},
title = {Integrated multi-omics analysis reveals the functional signature of microbes and metabolomics in pre-diabetes individuals.},
journal = {Microbiology spectrum},
volume = {13},
number = {7},
pages = {e0145924},
pmid = {40488467},
issn = {2165-0497},
support = {2024YFC3506300, 2024YFC3506303//National Key R&D Program of China/ ; },
mesh = {Humans ; *Prediabetic State/microbiology/metabolism ; *Metabolomics/methods ; *Gastrointestinal Microbiome/genetics ; Male ; Diabetes Mellitus, Type 2/microbiology/metabolism ; Female ; Middle Aged ; Adult ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Metagenome ; Blood Glucose ; Multiomics ; },
abstract = {Pre-diabetes (PD) represents a critical stage in the progression toward type 2 diabetes, with significant alterations observed in the human microbial community among pre-diabetic individuals in observational studies. However, understanding the interaction between human microbiota and the host during pre-diabetes remains limited. Therefore, this study aims to understand the alterations in the human microbial community during pre-diabetes, a critical stage toward type 2 diabetes. Using an integrated analysis of human microbiota and metabolomics data, we seek to identify the functional signature associated with PD and gain insights into potential mechanisms driving its progression to type 2 diabetes. These findings could inform the development of early intervention strategies for those at high risk. Samples were collected from pre-diabetes, diabetes, and healthy control groups. Through metagenome and 16S rRNA sequencing, we analyzed the gut microbial and tongue coating compositions, respectively. Untargeted metabolomics techniques were also applied for comprehensive plasma data. Using integrated multi-omics analysis, we aim to understand the metabolic potentials of the human microbiome, its molecular links with host targets, and their effects on pre-diabetes, thereby deepening our understanding of microbiome-host interactions in this context. The pre-diabetes group exhibited distinct clinical characteristics, particularly in blood glucose levels and a higher average level of γ-glutamyl transferase. We identified 509 intestinal bacterial species, with Megamonas funiformis and Parabacteroides merdae showing higher abundance in the PD group. In tongue coating samples, we found 1,122 bacterial genera, with the PD group showing altered levels of Corynebacterium and Johnsonella. Furthermore, we detected 795 metabolites, primarily involved in carbohydrate and lipid metabolism. Importantly, our integrated multi-omics analysis suggested Flavonifractor plautii's role in modulating blood glucose through influencing carbohydrate metabolism. Our integrated multi-omics analysis revealed significant alterations in several regulatory pathways associated with pre-diabetes, particularly emphasizing the impact of gut bacterium Flavonifractor plautii on blood glucose levels through its influence on carbohydrate metabolism. These intricate relationships among gut microbiota, metabolites, and blood glucose levels underscore the significance of personalized treatment approaches and preventive strategies for pre-diabetes. The insights gained from this research hold considerable promise for advancing our understanding and management of pre-diabetes.IMPORTANCEThis study investigates alterations in the human microbial community during PD, a critical stage leading to type 2 diabetes. Through integrated analysis of metagenomic and metabolomics data from pre-diabetes, diabetes, and healthy control groups, we identified distinct clinical characteristics in the PD group, including elevated blood glucose levels and γ-glutamyl transferase. A total of 509 intestinal bacterial species were identified, with Flavonifractor plautii playing a key role in modulating blood glucose levels via its influence on carbohydrate metabolism. Our findings underscore the complex interactions among gut microbiota, metabolites, and blood glucose levels, highlighting the potential for personalized treatment approaches and early intervention strategies for individuals at high risk of developing type 2 diabetes.},
}

Humans
*Prediabetic State/microbiology/metabolism
*Metabolomics/methods
*Gastrointestinal Microbiome/genetics
Male
Diabetes Mellitus, Type 2/microbiology/metabolism
Female
Middle Aged
Adult
RNA, Ribosomal, 16S/genetics
*Bacteria/classification/genetics/metabolism/isolation & purification
Metagenome
Blood Glucose
Multiomics

@article {pmid40488405,
year = {2025},
author = {Ricci, F and Leung, PM and Hutchinson, T and Nguyen-Dinh, T and Frank, AH and Hood, AVS and Salazar, VW and Eate, V and Wong, WW and Cook, PLM and Greening, C and McClelland, H},
title = {Chemosynthesis enhances net primary production and nutrient cycling in a hypersaline microbial mat.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
pmid = {40488405},
issn = {1751-7370},
mesh = {*Archaea/metabolism/genetics/classification ; *Bacteria/metabolism/genetics/classification ; Carbon Cycle ; *Lakes/microbiology ; Photosynthesis ; Oxidation-Reduction ; Hydrogen/metabolism ; *Microbiota ; Phototrophic Processes ; *Nutrients/metabolism ; },
abstract = {Photosynthetic microbial mats are macroscopic microbial ecosystems consisting of a wide array of functional groups and microenvironments arranged along variable redox gradients. Light energy ultimately drives primary production and a cascade of daisy-chained metabolisms. Heterotrophic members of these communities remineralise organic material, decreasing net primary production, and returning nutrients to the aqueous phase. However, reduced inorganic and one-carbon substrates such as trace gases and those released as metabolic byproducts in deeper anoxic regions of the mat, could theoretically also fuel carbon fixation, mitigating carbon loss from heterotrophy and enhancing net primary production. Here, we investigated the intricate metabolic synergies that sustain community nutrient webs in a biomineralising microbial mat from a hypersaline lake. We recovered 331 genomes spanning 40 bacterial and archaeal phyla that influence the biogeochemistry of these ecosystems. Phototrophy is a major metabolism found in 17% of the genomes, but over 50% encode enzymes to harness energy from inorganic substrates and 12% co-encode chemosynthetic carbon fixation pathways that use sulfide and hydrogen as electron donors. We experimentally demonstrated that the microbial community oxidises ferrous iron, ammonia, sulfide, and reduced trace gas substrates aerobically and anaerobically. Furthermore, carbon isotope assays revealed that diverse chemosynthetic pathways contribute significantly to carbon fixation and organic matter production alongside photosynthesis. Chemosynthesis in microbial mats results from a complex suite of spatially organised metabolic interactions and continuous nutrient cycling, which decouples carbon fixation from the diurnal cycle, and enhances the net primary production of these highly efficient ecosystems.},
}

*Archaea/metabolism/genetics/classification
*Bacteria/metabolism/genetics/classification
Carbon Cycle
*Lakes/microbiology
Photosynthesis
Oxidation-Reduction
Hydrogen/metabolism
*Microbiota
Phototrophic Processes
*Nutrients/metabolism

@article {pmid40407311,
year = {2025},
author = {Li, H and Wang, Z and He, S and Zhao, X and Wu, Q and Sun, Y and Fan, Y and Hu, X and Tian, Z and Zhang, S},
title = {Unraveling gut microbiome alterations and metabolic signatures in hereditary transthyretin amyloidosis.},
journal = {Microbiology spectrum},
volume = {13},
number = {7},
pages = {e0230224},
pmid = {40407311},
issn = {2165-0497},
support = {20220484031//Beijing Nova Program/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Cross-Sectional Studies ; Male ; Female ; Middle Aged ; *Amyloid Neuropathies, Familial/microbiology/metabolism ; Aged ; *Metabolome ; Taurine/blood/metabolism ; gamma-Aminobutyric Acid/blood ; Bacteria/classification/genetics/metabolism/isolation & purification ; Glutamic Acid/metabolism ; Adult ; Metagenomics ; },
abstract = {UNLABELLED: Hereditary transthyretin amyloidosis (hATTR) is a rare, often fatal disease characterized by the abnormal aggregation of atypical transthyretin fibrils. Given the variability in the penetrance and clinical manifestations of hATTR, the role of nongenetic factors, particularly those related to the gut microbiota, warrants investigation. We conducted a cross-sectional study, examining the untargeted serum metabolome and gut metagenome in 13 patients with hATTR and 22 healthy controls. Significant disparities were observed in both the serum metabolome and gut microbiome of individuals with hATTR when compared to healthy controls. Notably, the serum levels of gamma-aminobutyric acid (GABA) and taurine were markedly decreased in the hATTR group, with the most pronounced reduction in those exhibiting hATTR-related cardiac amyloidosis. Additionally, commensals such as Bifidobacterium pseudocatenulatum, Lactobacillus rogosae, and Hungatella hathewayi were significantly diminished in hATTR patients and were positively correlated with the metabolite module containing GABA and taurine. Metagenomic and metabolomic pathway enrichment analyses collectively revealed disruptions in glutamate and taurine metabolism in hATTR. Our findings imply that patients with hATTR may exhibit metabolic irregularities in glutamate and taurine, potentially associated with an imbalance in the gut microbiota.

IMPORTANCE: Hereditary transthyretin amyloidosis (hATTR) is influenced not only by genetic factors but also by environmental or host factors during its onset and progression. Previous studies have independently examined the metabolome or gut microbiome in hATTR, but the interplay between the microbiota and metabolism under this condition remains largely unknown. Our cross-sectional study represents the first comprehensive integration of gut metagenome and serum metabolome analyses in hATTR patients. We observed disturbances in glutamate and taurine metabolism among these patients, which correlated with distinctive shifts in the gut microbiota. This study offers insights into the intricate dynamics among gut dysbiosis, metabolic imbalances, and the progression of hATTR, suggesting directions for future research into the underlying mechanisms and therapeutic strategies.},
}

Humans
*Gastrointestinal Microbiome
Cross-Sectional Studies
Male
Female
Middle Aged
*Amyloid Neuropathies, Familial/microbiology/metabolism
Aged
*Metabolome
Taurine/blood/metabolism
gamma-Aminobutyric Acid/blood
Bacteria/classification/genetics/metabolism/isolation & purification
Glutamic Acid/metabolism
Adult
Metagenomics

@article {pmid40151093,
year = {2025},
author = {Liu, D and Zhang, W and Zhu, L and Gong, J and Huang, Y and Li, Z and He, J},
title = {Autoinducer-2 Quorum Sensing Is an Active Universal Signaling System in Sociomicrobiology.},
journal = {Journal of basic microbiology},
volume = {65},
number = {7},
pages = {e70024},
doi = {10.1002/jobm.70024},
pmid = {40151093},
issn = {1521-4028},
support = {//This study was supported by National Natural Science Foundation of China (grants 32371495 and 32171424), Hubei Province Technology Innovation Plan Project (2024BCB028), and Wuhan Science and Technology Major Project (grant 2023020302020708)./ ; },
mesh = {*Quorum Sensing/physiology ; *Homoserine/analogs & derivatives/metabolism ; *Lactones/metabolism ; Humans ; *Signal Transduction ; Bacterial Proteins/metabolism/genetics ; *Bacteria/metabolism/genetics/classification ; Gastrointestinal Microbiome ; Metagenomics ; },
abstract = {Autoinducer-2 (AI-2) is a bacterial quorum sensing (QS) signaling molecule that regulates inter-specific and intraspecific bacterial communication in complex ecological environments. Here, we systematically analyzed the distribution of AI-2 QS-related proteins (synthases and receptors) in the domain bacteria, explored the evolution and development of AI-2 receptors, and analyzed the AI-2 regulatory networks using human intestinal metagenomic data. The results show that AI-2 QS-related proteins are distributed in 17 bacterial phyla, accounting for approximately 36.80% of the total genomes. Based on the ability of bacteria to synthesize and receive AI-2 signals, we divided bacteria into four major categories, namely Prosumer, Producer, Monitor, and Immunizer. The Gram-positive bacteria are mainly responsible for producing the AI-2 signals, while Gram-negative bacteria are more likely to respond to AI-2. Evolutionary analysis shows that the AI-2 receptor CahR is mainly derived from the methyl-accepting chemotaxis protein (MCP). Based on the length difference of the ligand-binding domains, we further speculate that AI-2 binding activates CahR through either allostery or aggregation mode. Using human intestinal metagenomic data, we found a strong correlation between AI-2 signaling and c-di-GMP signaling. These findings will have an important impact on the AI-2 QS research and accelerate its development.},
}

*Quorum Sensing/physiology
*Homoserine/analogs & derivatives/metabolism
*Lactones/metabolism
Humans
*Signal Transduction
Bacterial Proteins/metabolism/genetics
*Bacteria/metabolism/genetics/classification
Gastrointestinal Microbiome
Metagenomics

@article {pmid40015361,
year = {2025},
author = {Liu, W and Geng, Y and Wang, Y and Zhao, J and Fan, Y and Zhang, X and Xie, W and Zhang, L and Zhang, Z},
title = {Evolution of gut microbiota in psoriatic arthritis treated with IL-17 inhibitor revealed by metagenomics.},
journal = {Joint bone spine},
volume = {92},
number = {4},
pages = {105868},
doi = {10.1016/j.jbspin.2025.105868},
pmid = {40015361},
issn = {1778-7254},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/genetics ; Male ; *Metagenomics/methods ; Female ; Middle Aged ; *Arthritis, Psoriatic/drug therapy/microbiology/diagnosis ; *Interleukin-17/antagonists & inhibitors ; *Antibodies, Monoclonal, Humanized/therapeutic use ; Feces/microbiology ; Treatment Outcome ; Adult ; Aged ; },
abstract = {OBJECTIVES: To explore the evolution of gut microbiota in taxonomy and function in PsA patients during IL-17i treatment.

METHODS: Twenty PsA patients treated with secukizumab were included. Fecal samples were collected before treatment (0 mo.), first month (1 mo.) and third month (3 mo.) after treatment, and a total of 60 samples were collected. Shotgun metagenomic sequencing was used to detect all fecal samples.

RESULTS: In the 1 mo. and 3 mo. after IL-17i treatment, the disease activity in PsA patients decreased significantly. Compared with 0 mo., α-diversity calculated by Shannon index and Pielou index increased significantly at 1 mo. and 3 mo. after treatment. Microbial genes encoding Carbohydrate-Active enZymes (CAZymes) tended to be upregulated after treatment. After treatment, Bacteroidota phylum expanded, especially the abundance of Phocaeicola genus increased gradually with the treatment time (P<0.05). The abundance of Phocaeicola genus was positively correlated with the α-diversity. The Polysaccharide Lyases and Carbohydrate Esterases in CAZymes were significantly positively correlated with most of species in Phocaeicola genus.

CONCLUSIONS: Treatment with IL-17i induces gut microbiota evolution in PsA patients. The key features of this evolution include increased α-diversity, expansion of the Phocaeicola genus, and upregulation of CAZymes. Species within the Phocaeicola genus may be the critical bacteria driving this evolution.},
}

Humans
*Gastrointestinal Microbiome/drug effects/genetics
Male
*Metagenomics/methods
Female
Middle Aged
*Arthritis, Psoriatic/drug therapy/microbiology/diagnosis
*Interleukin-17/antagonists & inhibitors
*Antibodies, Monoclonal, Humanized/therapeutic use
Feces/microbiology
Treatment Outcome
Adult
Aged

@article {pmid40591379,
year = {2025},
author = {Orenburkina, OI and Rezbaeva, GN and Dudurich, VV and Babushkin, AE and Sogomonian, KS and Danilova, AA and Danilov, LG},
title = {[Microbiota of the ocular surface in children with myopia].},
journal = {Vestnik oftalmologii},
volume = {141},
number = {3},
pages = {5-12},
doi = {10.17116/oftalma20251410315},
pmid = {40591379},
issn = {0042-465X},
mesh = {Humans ; Child ; *Myopia/diagnosis/microbiology/physiopathology ; Male ; Female ; Adolescent ; *Microbiota ; *Conjunctiva/microbiology ; *Bacteria/genetics/isolation & purification/classification ; RNA, Ribosomal, 16S/genetics ; Disease Progression ; },
abstract = {UNLABELLED: A healthy ocular surface is characterized by relatively stable and comparatively low microbial diversity. However, pathological conditions can provoke shifts in the composition of bacterial taxa, which may be associated, among other factors, with the progression of myopia.

PURPOSE: This study compared the taxonomic diversity of the conjunctival microbiota in children with varying degrees of myopia and those without clinically confirmed myopia.

MATERIAL AND METHODS: Ocular surface samples were obtained from 29 children aged 6-17 years with myopia (58 eyes) and from 12 children of the control group aged 9-17 years (24 eyes). The taxonomic composition of the conjunctival microbiota was analyzed using 16S ribosomal RNA gene (rRNA) sequencing, followed by microbiome profiling through bioinformatics and statistical tools.

RESULTS: The ocular surface microbiota in children with myopia demonstrated higher alpha diversity compared to the control group. This was confirmed by values of the Chao (reflecting low-abundance taxa) and Shannon (reflecting overall bacterial diversity - higher diversity means higher index; optimal value; 3.1-4.2) indices. The results revealed a clear trend toward differentiation in bacterial composition between myopic and control groups. These differences were associated with changes in the relative abundance of opportunistic bacteria depending on the degree of myopia.

CONCLUSION: The taxonomic diversity of the ocular microbiota at the genus level in patients with varying degrees of myopia was characterized by a higher number of taxonomic units compared to the control group. The general trend is an increase in the biodiversity of the bacterial composition due to an increase in the relative representation of opportunistic microorganisms. Further research on the influence of the ocular microbiota on the progression of myopia is needed.},
}

Humans
Child
*Myopia/diagnosis/microbiology/physiopathology
Male
Female
Adolescent
*Microbiota
*Conjunctiva/microbiology
*Bacteria/genetics/isolation & purification/classification
RNA, Ribosomal, 16S/genetics
Disease Progression

@article {pmid40589860,
year = {2025},
author = {Nimnoi, P and Pongsilp, N},
title = {Insights into the metagenomic and metabolomic compositions of the bacterial communities in Thai traditional fermented foods as well as the relationships between food nutrition and food microbiomes.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19606},
pmid = {40589860},
issn = {2167-8359},
mesh = {*Fermented Foods/microbiology ; Thailand ; *Food Microbiology ; *Bacteria/genetics/classification/metabolism ; *Microbiota ; Metagenomics ; Metabolomics ; Fermentation ; },
abstract = {Five Thai traditional fermented foods, including khao-mak (sweet fermented sticky rice), pak-kard-dong (sour salt-fermented mustard greens), nor-mai-dong (sour salt-fermented bamboo sprouts), moo-som (sour salt-fermented pork), and pla-som (sour salt-fermented fish), were analyzed for their food nutrition and bacterial community structures. Sour salt-fermented bamboo sprouts possessed the highest unique amplicon sequence variables (ASVs), which were 3,476, as well as the highest bacterial diversity and richness, while in contrast, sweet fermented sticky rice possessed the lowest such indices. The phylum Firmicutes accounted for the largest proportions in both sour salt-fermented meats and sweet fermented sticky rice whereas the Proteobacteria occupied the largest proportions in both sour salt-fermented vegetables. The bacterial community structures of both sour salt-fermented meats were similar in terms of composition at class level, while the dominant genera compositions were totally different among all foods. Gene functions, enzymes, and metabolic pathways annotated from the bacterial communities in all foods were those involved in growth metabolisms, genetic information processing, environmental information processing, and cellular signaling. Sour salt-fermented bamboo sprouts had the highest numbers of unique annotated genes, enzymes, and metabolic pathways.},
}

*Fermented Foods/microbiology
Thailand
*Food Microbiology
*Bacteria/genetics/classification/metabolism
*Microbiota
Metagenomics
Metabolomics
Fermentation

@article {pmid40586794,
year = {2025},
author = {Chadd, EF and Ergunay, K and Kumsa, B and Bourke, BP and Broomfield, BS and Long, LS and Linton, YM},
title = {Nanopore sequencing reveals a diversity of microorganisms in ticks from Ethiopia.},
journal = {Parasitology research},
volume = {124},
number = {7},
pages = {73},
pmid = {40586794},
issn = {1432-1955},
support = {FY23 Award # 23-101//Deployed Warfighter Protection (DWFP) Program/ ; Award # P0031_21_WR//Armed Forces Health Surveillance Division/ ; },
mesh = {Animals ; Ethiopia ; *Nanopore Sequencing ; Metagenomics ; *Bacteria/genetics/classification/isolation & purification ; *Ticks/microbiology ; Rickettsia/genetics/isolation & purification ; *Viruses/classification/genetics/isolation & purification ; Metagenome ; Phylogeny ; *Biodiversity ; },
abstract = {Ethiopia is home to a diverse group of ixodid ticks that are known to transmit disease to both animals and humans. Recent advances in metagenome sequencing show there is more microorganism diversity found in ticks than previously known. Compared to amplicon-based gene identification methods, agnostic metagenomic sequencing provides broader insights into the diversity of microorganisms in ticks, providing knowledge that will better enable public health measures in preventing the spread of zoonotic disease. In the present study, metagenomic sequencing was used to look at the microbial diversity of ticks collected from livestock in Ethiopia. This study identified six bacterial genera (Coxiella, Francisella, spotted-fever group (SFG) Rickettsia, Spiroplasma, Ehrlichia, and Borrelia), one genus of eukaryotic parasite (Babesia sp.), and one virus species (Parapoxvirus bovinestomatitis) from 154 tick pools representing 22 species of ticks among four genera (Amblyomma, Haemaphysalis, Hyalomma, and Rhipicephalus). We were able to differentiate between pathogenic and nonpathogenic microorganisms, highlighting concerns among traditional gene-targeted screening methods. Among all pooled samples, the predominant microorganisms included Coxiella-like endosymbionts (55.2%), SFG Rickettsia (38.3%), and nonpathogenic Francisella spp. (26.0%). Rickettsia africae was the predominant pathogenic agent detected, and phylogenetic analysis of two samples from A. gemma and A. variegatum confirmed the presence of R. africae. This study highlights the power of metagenomics applied to potential vectors of zoonotic disease, and it expands the knowledge on tick-pathogen associations in Ethiopia.},
}

Animals
Ethiopia
*Nanopore Sequencing
Metagenomics
*Bacteria/genetics/classification/isolation & purification
*Ticks/microbiology
Rickettsia/genetics/isolation & purification
*Viruses/classification/genetics/isolation & purification
Metagenome
Phylogeny
*Biodiversity

@article {pmid40523415,
year = {2025},
author = {Xu, Y and Ontita, NC and Zeng, W and Huang, J and Jiang, L and Huang, X and Li, Q and Hu, P},
title = {High-efficiency nitrogen removal by cold-tolerant bacteria consortium at low temperatures.},
journal = {Bioresource technology},
volume = {434},
number = {},
pages = {132816},
doi = {10.1016/j.biortech.2025.132816},
pmid = {40523415},
issn = {1873-2976},
mesh = {*Nitrogen/isolation & purification/metabolism ; *Cold Temperature ; Wastewater/chemistry ; *Bacteria/metabolism/genetics ; *Microbial Consortia/physiology ; Water Purification/methods ; },
abstract = {A cold-tolerant bacteria consortium (M2) was developed to enhance nitrogen removal efficiency in wastewater treatment processes operating at low temperatures (below 15 ℃). Bacteria consortium M2 demonstrated high removal efficiencies for nitrogen (NH4[+]-N, 97.34 %; NO3[-]-N, 97.13 %; NO2[-]-N, 59.92 %). Dominated by genera including Comamonas, Pseudomonas, and Acinetobacter, M2 produced substantial extracellular polymeric substances (EPS) and unsaturated fatty acids, which mitigated cold-induced stress. Metagenomic analysis revealed the presence of cold-shock responsive genes, including unsaturated fatty acid synthase, and cpsA, which contribute to its resilience under low-temperature conditions. Moreover, M2 enhanced both nitrogen assimilation and nitrate reduction under cold stress. These findings highlight the potential of M2 as an effective and practical strategy for improving nitrogen removal in wastewater treatment facilities during winter, thereby addressing a critical operational limitation in cold-climate regions.},
}

*Nitrogen/isolation & purification/metabolism
*Cold Temperature
Wastewater/chemistry
*Bacteria/metabolism/genetics
*Microbial Consortia/physiology
Water Purification/methods

@article {pmid40435904,
year = {2025},
author = {Liu, Z and Yan, K and Li, J and Zhang, C and Xu, D and Wang, Y and Xie, X and Li, H and Qie, J and Li, J and Dong, X and Dong, L and Cui, H},
title = {Acute appendicitis in children: Two microbial states associated with clinical indicators and severity.},
journal = {Diagnostic microbiology and infectious disease},
volume = {113},
number = {2},
pages = {116925},
doi = {10.1016/j.diagmicrobio.2025.116925},
pmid = {40435904},
issn = {1879-0070},
mesh = {Humans ; *Appendicitis/microbiology/pathology ; Child ; Male ; Female ; Child, Preschool ; Adolescent ; *Bacteria/classification/isolation & purification/genetics ; Acute Disease ; Severity of Illness Index ; C-Reactive Protein/analysis ; *Microbiota ; Appendectomy ; Metagenomics ; Dysbiosis/microbiology ; },
abstract = {BACKGROUND: Acute appendicitis (AA) is one of the most common abdominal emergencies worldwide. It is associated with dysbiosis and is usually classified clinically as either simple appendicitis (SA) or complicated appendicitis (CA) . The etiology and pathogenesis of AA remain incompletely understood.

METHODS: A total of 74 pediatric intra-abdominal pus samples from appendectomy cases (aged 3-15) were collected for AA at Tianjin Children's Hospital (Feb 2022-Sep 2023). The samples were categorised into two groups based on pathological findings: SA (n = 27) and CA (n = 47). Metagenomic profiling was employed to characterized the microbial composition and function in both groups. Additionally, clinical parameters associated with the microbiota were analysed.

RESULTS: The SA group exhibited higher levels of Burkholderia, Mycobacterium, and Klebsiella, while the CA group demonstrated higher levels of Porphyromonas, Bacteroides, Fusobacterium, Prevotella, and Tannerella. Additionaly, there were significant differences in clinical parameters, including C-reactive protein (CRP), procalcitonin (PCT), fibrinogen, sodium, potassium, phosphorus, complement C3, and chloride, between two groups. Furthermore, functional profiling revealed alterations in microbial metabolism and antibiotic resistance, highlighting the complex interplay between microbial communities and host inflammatory responses in appendicitis.

CONCLUSIONS: This study identifies unique microbial and serum biomarkers and their correlates in varying severities of acute appendicitis, highlighting the role of the microbiome in the aetiology of acute appendicitis.},
}

Humans
*Appendicitis/microbiology/pathology
Child
Male
Female
Child, Preschool
Adolescent
*Bacteria/classification/isolation & purification/genetics
Acute Disease
Severity of Illness Index
C-Reactive Protein/analysis
*Microbiota
Appendectomy
Metagenomics
Dysbiosis/microbiology

@article {pmid40403370,
year = {2025},
author = {Liang, X and Li, B and Dong, X and Zhao, X and Li, H and Ye, Y and Ma, H and Ran, S and Li, J},
title = {Impact of microplastics exposure on the reconfiguration of viral community structure and disruption of ecological functions in the digestive gland of Mytilus coruscus.},
journal = {Journal of hazardous materials},
volume = {494},
number = {},
pages = {138692},
doi = {10.1016/j.jhazmat.2025.138692},
pmid = {40403370},
issn = {1873-3336},
mesh = {*Microplastics/toxicity ; *Mytilus/virology/drug effects ; Animals ; Biofilms/drug effects ; *Water Pollutants, Chemical/toxicity ; Digestive System/virology/drug effects ; *Virome/drug effects ; *Viruses/genetics/drug effects ; },
abstract = {Microplastics (MPs) pose ecological risks by serving as viral vectors and disrupting host microbiomes. This study investigated the impact of MPs on the digestive gland virome of Mytilus coruscus through an in situ exposure experiment on Xixuan Island, Zhoushan, China, using polyethylene MPs and metagenomic sequencing. MPs biofilms were dominated by lytic viruses (> 99 %) with low diversity (Shannon index = 4.10 ± 0.39), whereas digestive glands harbored a more diverse virome (Shannon index = 7.26 ± 1.26). MPs ingestion significantly reduced virome diversity and altered viral community composition. Functional analysis showed that MPs biofilms were enriched in genes related to genetic processing, carbohydrate metabolism and membrane biogenesis, while transcription- and replication-related genes declined (P < 0.05) in digestive glands post-ingestion. MPs biofilms carried abundant antibiotic resistance genes (ARGs) and virulence factors, selectively enriching multidrug resistance genes (efrA, patB) while reducing functional viral gene abundance. Metal (Zn, Hg, As) and biocide resistance genes were prevalent in MPs biofilms but declined post-ingestion. Additionally, MPs ingestion weakened microbial network stability, potentially impairing immune regulation and metabolic homeostasis. These findings underscore MPs' role in shaping viral communities and spreading resistance genes, heightening ecological risks in marine environments.},
}

*Microplastics/toxicity
*Mytilus/virology/drug effects
Animals
Biofilms/drug effects
*Water Pollutants, Chemical/toxicity
Digestive System/virology/drug effects
*Virome/drug effects
*Viruses/genetics/drug effects

@article {pmid40378749,
year = {2025},
author = {Yu, YL and Lin, WH and Surampalli, RY and Chen, SC and Kao, CM},
title = {Adaptive fluoride removal across concentration scales: Potential roles of microbial and acicular gypsum interactions in nitrogen and phosphate cycling.},
journal = {Journal of hazardous materials},
volume = {494},
number = {},
pages = {138628},
doi = {10.1016/j.jhazmat.2025.138628},
pmid = {40378749},
issn = {1873-3336},
mesh = {*Calcium Sulfate/chemistry ; *Fluorides/chemistry ; *Phosphates/metabolism/chemistry ; *Nitrogen/metabolism/chemistry ; *Water Pollutants, Chemical/chemistry/metabolism ; Groundwater/chemistry ; Microbiota ; Bacteria/metabolism/genetics ; },
abstract = {Fluoride contamination in groundwater is a critical environmental and public health concern. Traditional remediation methods, including chemical precipitation and adsorption, are hindered by low nucleation efficiency at low fluoride concentrations and severe microbial inhibition under high fluoride stress. This study introduces an adaptive two-stage remediation system that synergistically integrates abiotic and biotic mechanisms to achieve effective fluoride removal across concentration scales. In Stage I, under elevated fluoride stress (100 mg/L), acicular gypsum (AG) facilitated abiotic calcium precipitation, effectively reducing fluoride toxicity and creating favorable conditions for microbial activity. Residual calcium released from AG further supported microbial-induced calcium precipitation (MICP) in Stage II under lower fluoride stress (10 mg/L). The system achieved a fluoride removal efficiency of 98.85 % under high fluoride conditions and demonstrated consistent performance across a broad concentration range. This integrated approach, combining abiotic and biotic mechanisms, offers a promising strategy for addressing diverse fluoride contamination scenarios. Here, phosphate (P)-mediated mineralization and microbial denitrification drive pH modulation, stabilizing fluoride as fluorapatite [Ca5(PO4)3F]. Microbial community and network analysis revealed key taxa, including Cupriavidus and Ralstonia, which facilitated P cycling and fluorapatite formation. Additionally, Bradyrhizobium enhanced nitrogen (N) cycling and supported early microbial adaptation, emphasizing the interplay of microbial interactions in driving system functionality. Functional predictions using PICRUSt2 identified genes associated with N and P cycling, highlighting the capacity of the system for nutrient adaptation under complex environmental conditions.},
}

*Calcium Sulfate/chemistry
*Fluorides/chemistry
*Phosphates/metabolism/chemistry
*Nitrogen/metabolism/chemistry
*Water Pollutants, Chemical/chemistry/metabolism
Groundwater/chemistry
Microbiota
Bacteria/metabolism/genetics

@article {pmid40378468,
year = {2025},
author = {Siddiquee, M and Cornelius, S and Seo, Y and Bullerjahn, GS and Bridgeman, TB and Sudman, M and Kang, DW},
title = {Uncovering microbial interactions in a persistent Planktothrix bloom: Towards early biomarker identification in hypereutrophic lakes.},
journal = {Water research},
volume = {283},
number = {},
pages = {123683},
doi = {10.1016/j.watres.2025.123683},
pmid = {40378468},
issn = {1879-2448},
mesh = {*Lakes/microbiology ; *Planktothrix ; Biomarkers ; Microbiota ; Nitrogen/metabolism ; Cyanobacteria ; *Harmful Algal Bloom ; RNA, Ribosomal, 16S ; },
abstract = {Cyanobacterial harmful algal blooms pose significant threats to global water supplies, ecosystems, and economies. Among the harmful cyanobacteria, Planktothrix, a resilient and toxin-producing filamentous cyanobacterium, has garnered increasing attention. However, an understanding of the entire microbiome, particularly the phycosphere surrounding Planktothrix blooms, remains largely unexplored. To the best of our knowledge, this is the first comprehensive study combining 16S rDNA and fungal internal transcribed spacer amplicon sequencing and shotgun metagenomics to elucidate Planktothrix bloom microbiomes and identify potential microbial or functional biomarkers for CyanoHABs. Our observations revealed that a summer bloom in Grand Lake St. Marys was initiated with Dolichospermum and then shifted to Planktothrix dominance. This transition was associated with nitrogen metabolism genes, suggesting that nitrogen plays a key role in bloom persistence through interactions among nitrogen-fixing bacteria, ammonia-oxidizing archaea, anammox bacteria, and denitrifiers. Additionally, metagenomic data revealed a strong positive correlation of toxin concentration with carbohydrate-nitrogen-sulfur-fatty acid associated metabolic pathways and a strong negative correlation with pollutant degradation pathways. Intriguingly, diazotrophic methane-related microbes were detected, which opens discussion on potential symbiosis that couples nitrogen and carbon metabolism. Toxin-degrading bacteria, such as Polynucleobacter and Acidovorax, were positively correlated with fungi like Vishniacozyma, proposing their cooperative roles during bloom events. Notably, Rhodobacter, a photosynthetic purple non-sulfur bacterium, showed strong negative correlations with both Planktothrix and the toxin-producing gene mcyE, positioning it as a promising biomarker for early bloom detection. Overall, this study advances the understanding of Planktothrix-dominated bloom ecology and highlights microbial signatures for proactive CyanoHAB management in freshwater systems.},
}

*Lakes/microbiology
*Planktothrix
Biomarkers
Microbiota
Nitrogen/metabolism
Cyanobacteria
*Harmful Algal Bloom
RNA, Ribosomal, 16S

@article {pmid40339368,
year = {2025},
author = {Zhang, X and Liu, T and Sun, W and Zhang, C and Jiang, X and You, X and Wang, X},
title = {The fate and ecological risk of typical diamide insecticides in soil ecosystems under repeated application.},
journal = {Journal of hazardous materials},
volume = {494},
number = {},
pages = {138440},
doi = {10.1016/j.jhazmat.2025.138440},
pmid = {40339368},
issn = {1873-3336},
mesh = {*Insecticides/toxicity ; *Soil Microbiology ; *Soil Pollutants/toxicity/analysis ; *ortho-Aminobenzoates/toxicity ; Ecosystem ; Soil/chemistry ; Nitrogen/metabolism ; Bacteria/drug effects/genetics ; Microbiota/drug effects ; },
abstract = {Diamide insecticides are the third most widely used class of pesticides worldwide. However, the long-term impacts of repeated diamide applications on soil ecosystems remain unclear. This study investigated chlorantraniliprole (CLP) and cyantraniliprole (CYP) effects on soil ecosystems through simulated repeated exposures. Results showed both exhibited slow degradation in the soil, with repeated applications extending their persistence, particularly for CLP. Both significantly inhibited soil alkaline nitrogen and organic matter accumulation, while reducing urease and sucrase activities, with CLP exerting stronger inhibitory effects. Metagenomic analysis indicated that CLP and CYP notably reduced soil microbial diversity. Additionally, the two insecticides altered the soil microbial community structure and inhibited carbon-nitrogen metabolic pathways. Further analysis revealed that CLP treatment significantly decreased the relative abundances of Mesorhizobium and Marmoricola, whereas CYP treatment primarily reduced Clostridium_sensu_stricto_1. All of these genera exhibited significant positive correlations with key metabolic pathways in soil carbon and nitrogen cycling. Notably, the relative abundance of Sphingomonas increased significantly following CLP and CYP treatments, demonstrating potential degradation capabilities. Overall, both CLP and CYP posed ecological risks to soil ecosystems, with CLP exhibiting more severe impacts. These findings revealed the need for strengthened scientific management in actual production.},
}

*Insecticides/toxicity
*Soil Microbiology
*Soil Pollutants/toxicity/analysis
*ortho-Aminobenzoates/toxicity
Ecosystem
Soil/chemistry
Nitrogen/metabolism
Bacteria/drug effects/genetics
Microbiota/drug effects

@article {pmid40304704,
year = {2025},
author = {Burnside, M and Tang, J and Baker, JL and Merritt, J and Kreth, J},
title = {Shining Light on Oral Biofilm Fluorescence In Situ Hybridization (FISH): Probing the Accuracy of In Situ Biogeography Studies.},
journal = {Molecular oral microbiology},
volume = {40},
number = {4},
pages = {137-146},
pmid = {40304704},
issn = {2041-1014},
support = {DE029612//NIH-NIDCR/ ; DE029492//NIH-NIDCR/ ; DE029228//NIH-NIDCR/ ; DE028252//NIH-NIDCR/ ; },
mesh = {*Biofilms ; *In Situ Hybridization, Fluorescence/methods ; *Mouth/microbiology ; Humans ; Microbiota/genetics ; Streptococcus/genetics/classification ; Species Specificity ; *Bacteria/classification/genetics ; },
abstract = {The oral biofilm has been instrumental in advancing microbial research and enhancing our understanding of oral health and disease. Recent developments in next-generation sequencing have provided detailed insights into the microbial composition of the oral microbiome, enabling species-level analyses of biofilm interactions. Fluorescence in situ hybridization (FISH) has been especially valuable for studying the spatial organization of these microbes, revealing intricate arrangements such as "corncob" structures that highlight close bacterial interactions. As more genetic sequence data become available, the specificity and accuracy of existing FISH probes used in biogeographical studies require reevaluation. This study examines the performance of commonly used species-specific FISH probes, designed to differentiate oral microbes within in situ oral biofilms, when applied in vitro to an expanded set of bacterial strains. Our findings reveal that the specificity of several FISH probes is compromised, with cross-species hybridization being more common than previously assumed. Notably, we demonstrate that biogeographical associations within in situ oral biofilms, particularly involving Streptococcus and Corynebacterium, may need to be reassessed to align with the latest metagenomic data.},
}

*Biofilms
*In Situ Hybridization, Fluorescence/methods
*Mouth/microbiology
Humans
Microbiota/genetics
Streptococcus/genetics/classification
Species Specificity
*Bacteria/classification/genetics

@article {pmid40156536,
year = {2025},
author = {Sarker, S and Klukowski, N and Talukder, S and Athukorala, A and Uddin, MJ},
title = {Opportunistic sampling from the near-threatened Alexandrine parakeet uncovers genomes of a novel parvovirus and beak and feather disease virus.},
journal = {Australian veterinary journal},
volume = {103},
number = {7},
pages = {416-421},
doi = {10.1111/avj.13442},
pmid = {40156536},
issn = {1751-0813},
support = {DE200100367//Australian Research Council/ ; },
mesh = {Animals ; *Circovirus/genetics/isolation & purification ; *Genome, Viral ; *Bird Diseases/virology ; Phylogeny ; *Circoviridae Infections/veterinary/virology ; *Parakeets/virology ; *Parvovirus/genetics/isolation & purification ; Endangered Species ; Feces/virology ; *Parvoviridae Infections/veterinary/virology ; },
abstract = {Birds are known to harbour a wide range of pathogenic viruses, including the beak and feather disease virus (BFDV; species, Circovirus parrot), which poses a significant threat to the conservation of endangered avian species. This study reports the genomic identification and characterisation of a novel psittaciform chaphamaparvovirus (PsChPV-6) and BFDV, sequenced from the faecal samples of healthy Alexandrine parakeets (Psittacula eupatria). PsChPV-6 is a linear, single-stranded DNA virus consisting of 4232 nucleotides (nt) with a high A + T content and five predicted open reading frames (ORFs). Key proteins encoded by PsChPV-6, such as the nonstructural protein 1 (NS1) and major capsid protein VP1, demonstrate strong sequence similarities to other avian parvoviruses, with conserved motifs in NS1 crucial for viral replication. The presence of a previously uncharacterised ORF1 region suggests strain-specific viral features that warrant further exploration. BFDV is a circular single-stranded DNA virus in the Circoviridae family and was also identified in the samples. Phylogenetic analysis positioned PsChPV-6 within the Chaphamaparvovirus genus, closely related to parvoviruses from diverse avian species, whereas BFDV was grouped with strains from Australian cockatoos and other nonpsittacine birds, suggesting potential cross-species transmission. These findings contribute to a deeper understanding of the genetic diversity and evolutionary dynamics of these viral pathogens in bird populations, underscoring the importance of ongoing surveillance to evaluate their ecological and veterinary impacts.},
}

Animals
*Circovirus/genetics/isolation & purification
*Genome, Viral
*Bird Diseases/virology
Phylogeny
*Circoviridae Infections/veterinary/virology
*Parakeets/virology
*Parvovirus/genetics/isolation & purification
Endangered Species
Feces/virology
*Parvoviridae Infections/veterinary/virology

@article {pmid40585302,
year = {2025},
author = {Louca, S},
title = {Machine learning models for delineating marine microbial taxa.},
journal = {NAR genomics and bioinformatics},
volume = {7},
number = {2},
pages = {lqaf090},
doi = {10.1093/nargab/lqaf090},
pmid = {40585302},
issn = {2631-9268},
mesh = {*Machine Learning ; *Archaea/genetics/classification ; *Bacteria/genetics/classification ; Metagenome ; Phylogeny ; Genome, Bacterial ; *Aquatic Organisms/genetics/classification ; },
abstract = {The relationship between gene content differences and microbial taxonomic divergence remains poorly understood, and algorithms for delineating novel microbial taxa above genus level based on multiple genome similarity metrics are lacking. Addressing these gaps is important for macroevolutionary theory, biodiversity assessments, and discovery of novel taxa in metagenomes. Here, I develop machine learning classifier models, based on multiple genome similarity metrics, to determine whether any two marine bacterial and archaeal (prokaryotic) metagenome-assembled genomes (MAGs) belong to the same taxon, from the genus up to the phylum levels. Metrics include average amino acid and nucleotide identities, and fractions of shared genes within various categories, applied to 14 390 previously published non-redundant MAGs. At all taxonomic levels, the balanced accuracy (average of the true-positive and true-negative rate) of classifiers exceeded 92%, suggesting that simple genome similarity metrics serve as good taxon differentiators. Predictor selection and sensitivity analyses revealed gene categories, e.g. those involved in metabolism of cofactors and vitamins, particularly correlated to taxon divergence. Predicted taxon delineations were further used to de novo enumerate marine prokaryotic taxa. Statistical analyses of those enumerations suggest that over half of extant marine prokaryotic phyla, classes, and orders have already been recovered by genome-resolved metagenomic surveys.},
}

*Machine Learning
*Archaea/genetics/classification
*Bacteria/genetics/classification
Metagenome
Phylogeny
Genome, Bacterial
*Aquatic Organisms/genetics/classification

@article {pmid40580323,
year = {2025},
author = {Callejas, C and Guerrero, L and Erijman, L and López, I and Borzacconi, L},
title = {Microbiota and methanogenic activities in an anaerobic internal circulation reactor: insights into biogas production from brewery wastewater.},
journal = {Biodegradation},
volume = {36},
number = {4},
pages = {56},
pmid = {40580323},
issn = {1572-9729},
support = {2019//Comisión Sectorial de Investigación Científica/ ; 2019//Comisión Sectorial de Investigación Científica/ ; 2019//Comisión Sectorial de Investigación Científica/ ; },
mesh = {*Bioreactors/microbiology ; *Methane/metabolism ; *Microbiota ; *Biofuels/microbiology ; *Wastewater/microbiology ; Anaerobiosis ; Archaea/metabolism/genetics/classification ; Bacteria/metabolism/genetics/classification ; RNA, Ribosomal, 16S/genetics ; Sewage/microbiology ; },
abstract = {In this study, we analyzed the prokaryotic community and methanogenic activities in sludge samples collected from a full-scale internal circulation (IC) reactor used to treat brewery wastewater. The reactor performance was monitored over 15 months, and specific methanogenic activities were periodically measured in fresh sludge samples using CO2/H2 or acetate as substrates. The maximum hydrogenotrophic activities were consistently higher than maximum acetoclastic activities, suggesting the relevance of hydrogenotrophic methanogens in the sludge. Over six months, the prokaryotic community present in four sludge samples was analyzed using amplicon libraries and metagenomics. V4-16S rRNA amplicon libraries revealed the presence of a diverse microbial community dominated by Firmicutes and Bacteroidetes among bacterial phyla, and Halobacterota and Euryarchaeota among archaea. Furthermore, the 16S libraries constructed with cDNA were consistent with the methanogenic activity assays. A genome-centric metagenomics approach was used to assemble 42 high-quality metagenome-assembled genomes (MAGs), among which Methanothrix and Methanobacterium were the dominant archaeal members, and Acidobacteriota, Synergistota, Krumholzibacteriota, and Nitrospirota phyla were among the bacteria. Potential acetogenic members were explored via the fths gene; 15 MAGs contained this marker gene. A combination of methanogenic activity tests, amplicon libraries, and MAG analysis was used to gain insights into the prokaryotic structure and functional potential of the microbial community driving methane production in the reactor.},
}

*Bioreactors/microbiology
*Methane/metabolism
*Microbiota
*Biofuels/microbiology
*Wastewater/microbiology
Anaerobiosis
Archaea/metabolism/genetics/classification
Bacteria/metabolism/genetics/classification
RNA, Ribosomal, 16S/genetics
Sewage/microbiology

@article {pmid40580234,
year = {2025},
author = {Biessy, L and Sissons, J and Kihika, JK and Wood, SA and Pearman, JK},
title = {Microbial adaptations to acidic, nutrient- and metal-rich lakes in Aotearoa New Zealand.},
journal = {Extremophiles : life under extreme conditions},
volume = {29},
number = {2},
pages = {24},
pmid = {40580234},
issn = {1433-4909},
mesh = {*Lakes/microbiology/chemistry ; New Zealand ; *Microbiota ; *Adaptation, Physiological ; Geologic Sediments/microbiology ; *Metals/analysis ; Nutrients/analysis ; Bacteria/genetics/metabolism ; },
abstract = {Four lakes in the same region of Aotearoa New Zealand were investigated to characterize sediment microbial communities and functions under contrasting environmental conditions. Two lakes, an acidic lake (Rototai) and a lake with elevated metals and nutrients (Killarney) were impacted by extreme stressors, while the lowland mesotrophic lake (Kaihoka East) and an alpine lake (Peel) were used as reference lakes. Using metabarcoding and metagenomics analysis, we profiled community composition, functional pathways, and resistance mechanisms in the lake sediments. Rototai contained high abundances of genes involved in sulfur cycling (assimilatory and dissimilatory sulfate reduction, sulfur oxidation) and acid tolerance (kdp potassium-transport system, ClcA antiporters). In contrast, Killarney had elevated abundances of genes involved in methanogenesis, however despite high metal concentrations, no enrichment of metal-resistance genes was detected. Kaihoka East contained the highest prokaryotic diversity and an elevated abundance of genes involved in nitrification. Although community taxonomic differences were modest across lakes, functional analyses revealed distinct metabolic adaptations. These findings highlight the utility of using metagenomic approaches to identify biogeochemical processes and stress-response strategies in lakes. Improved understanding of microbial functional diversity in surface sediments has implications for lake management, particularly in systems impacted by acidification, high nutrient loading, and metal contamination.},
}

*Lakes/microbiology/chemistry
New Zealand
*Microbiota
*Adaptation, Physiological
Geologic Sediments/microbiology
*Metals/analysis
Nutrients/analysis
Bacteria/genetics/metabolism

@article {pmid40575481,
year = {2025},
author = {Chen, L and Li, Z and Yuan, D and Chen, Y and Xu, Y and Tang, W and Liu, C},
title = {Microorganism changes in the gut of Apis mellifera surviving for the long term in Camellia oleifera forests.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1608835},
pmid = {40575481},
issn = {2235-2988},
mesh = {Animals ; Bees/microbiology ; *Camellia ; *Gastrointestinal Microbiome ; Oligosaccharides/metabolism ; Forests ; Metabolomics ; Metagenomics ; *Gastrointestinal Tract/microbiology ; *Bacteria/classification/genetics/isolation & purification/metabolism ; },
abstract = {Alpha-galactosides (oligosaccharides) in C. oleifera nectar and pollen cause honey bee larval rot and worker bloats. Honey bee colonies surviving in C. oleifera forests for a long period have low rates of larval rot and worker bloats; however, the mechanism of oligosaccharide metabolism is unclear. In this study, we used metagenomics and metabolomics to investigate the structure and function of the gut flora and the digestion characteristics of oligosaccharides in the gut of A. mellifera foragers (CN group) that had been in the C. oleifera forest for a long period (continuously for 14 years), and those that had not been pollinated with C. oleifera (N group) after 24 h of consumption of C. oleifera honey. The results revealed that the abundance of Gilliamella apicola up to 24.08%, which can metabolize α-galactoside (α-Gal), was significantly higher (P < 0.05) in the gut of foragers in the CN group than in the N group. Additionally, the gut flora of foragers in the CN group carried a significantly higher (P < 0.05) abundance of genes encoding α-galactosidase (Glycoside hydrolase family 4, GH4) than the N group. Similarly, metabolomic results indicated that the three toxic oligosaccharides in C. oleifera honey were lower in the gut of CN group foragers. These results suggest that the gut flora of A. mellifera, which inhabits oil tea forests for long periods of time, changes and adapts to the predominant ecological niche, enhancing the host's ability to metabolize toxic oligosaccharides. This important discovery provides positive guidance for the subsequent directions for breeding of A. mellifera (G. apicola enrichment and GH4 upregulation), specialized in pollinating C. oleifera.},
}

Animals
Bees/microbiology
*Camellia
*Gastrointestinal Microbiome
Oligosaccharides/metabolism
Forests
Metabolomics
Metagenomics
*Gastrointestinal Tract/microbiology
*Bacteria/classification/genetics/isolation & purification/metabolism

@article {pmid40573768,
year = {2025},
author = {Giménez-Valero, C and Maciá-Vázquez, AA and Núñez-Gómez, D and Conesa, A and Lidón, V and Melgarejo, P},
title = {Evolution of the Soil Bacterial Community as a Function of Crop Management: A Metagenomic Study in Orange Tree (Citrus sinensis) Plantations.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {12},
pages = {},
doi = {10.3390/plants14121781},
pmid = {40573768},
issn = {2223-7747},
support = {AGROALNEXT program (AGROALNEXT 2022/013, SIRIS Project)//European Union/ ; },
abstract = {Soil management significantly influences the structure and diversity of soil bacterial communities, affecting biodiversity and ecosystem functions. In semi-arid regions, water efficiency strategies like anti-weed netting are implemented, but their impact on soil microbial communities remains underexplored. This study evaluates the temporal evolution of soil bacterial communities in orange tree (Citrus sinensis (L.) Osbeck) plantations under two conditions: with and without anti-weed netting. Soil samples were collected at three time points over a period of 18 months since the establishment of the crop and analyzed using high-throughput 16S rRNA sequencing, assessing alpha and beta diversity, taxonomic composition, and functional pathways via KEGG analysis. The results indicate that weed control netting contributes to stabilizing bacterial diversity over time and increases the relative abundance of dominant phyla such as Planctomycetota, Proteobacteria, Bacteroidota, and Acidobacteriota. Functional predictions revealed significant differences in metabolic pathways, including those associated with nitrogen fixation and organic matter degradation. These findings suggest that anti-weed netting not only influences the taxonomic composition of soil bacterial communities but also modulates their functional potential, with implications for sustainable agriculture in semi-arid environments. This study provides new insights into the interaction between soil management and soil bacterial communities, offering valuable information for optimizing agricultural practices and soil conservation strategies.},
}

@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 {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 {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 {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 {pmid40445833,
year = {2025},
author = {Li, W and Huang, B and Guo, M and Zeng, Z and Cai, T and Feng, L and Zhang, X and Guo, L and Jiang, X and Yin, Y and Wang, E and Huang, X and Zheng, J},
title = {Unveiling the evolution of antimicrobial peptides in gut microbes via foundation-model-powered framework.},
journal = {Cell reports},
volume = {44},
number = {6},
pages = {115773},
doi = {10.1016/j.celrep.2025.115773},
pmid = {40445833},
issn = {2211-1247},
mesh = {*Antimicrobial Peptides/genetics/chemistry/pharmacology ; *Gastrointestinal Microbiome/genetics ; Humans ; *Evolution, Molecular ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Antimicrobial resistance poses a major threat to public health, prompting the development of alternative therapies such as antimicrobial peptides (AMPs). Protein language models (PLMs) have advanced protein structure and function predictions, facilitating AMP discovery. We developed antimicrobial peptide structural evolution miner (AMP-SEMiner), an AI-driven framework that integrates PLMs, structural clustering, and evolutionary analysis to systematically identify AMPs encoded by small open reading frames and AMP-containing proteins in metagenome-assembled genomes. AMP-SEMiner identified over 1.6 million AMP candidates across diverse environments. Experimental validation showed antimicrobial activity in 9 of the 20 tested candidates, with 5 surpassing antibiotic effectiveness; variant peptides derived from these candidates similarly demonstrated strong antimicrobial efficacy. AMPs from human gut microbiomes revealed both conserved and adaptive evolutionary strategies, reflecting their dynamic ecological roles. AMP-SEMiner thus represents a valuable tool for expanding AMP discovery and has significant potential to inform the development of alternative antimicrobial treatments.},
}

*Antimicrobial Peptides/genetics/chemistry/pharmacology
*Gastrointestinal Microbiome/genetics
Humans
*Evolution, Molecular
Anti-Bacterial Agents/pharmacology

@article {pmid40313234,
year = {2025},
author = {Leibovitzh, H and Fliss Isakov, N and Werner, L and Thurm, T and Hirsch, A and Cohen, NA and Maharshak, N},
title = {A Mushroom Based Prebiotic Supplement Pilot Study Among Patients with Crohn's Disease.},
journal = {Journal of dietary supplements},
volume = {22},
number = {4},
pages = {511-524},
doi = {10.1080/19390211.2025.2498127},
pmid = {40313234},
issn = {1939-022X},
mesh = {Humans ; *Prebiotics/administration & dosage ; *Crohn Disease/microbiology/therapy/drug therapy ; Pilot Projects ; Female ; Male ; Feces/microbiology/chemistry ; Double-Blind Method ; Adult ; *Dietary Supplements ; *Agaricales/chemistry ; Gastrointestinal Microbiome ; Middle Aged ; Leukocyte L1 Antigen Complex/analysis ; C-Reactive Protein/analysis ; Treatment Outcome ; Young Adult ; },
abstract = {Data on a mushroom based prebiotic supplementation in patients with Crohn's disease (CD) in western population is scarce. In this pilot trial, we aimed to assess the clinical efficacy and fecal microbial compositional and functional alterations associated with 'Mycodigest,' a commercial prebiotic supplement composed of three mushroom extracts. Patients with mild to moderate CD were recruited to a single center, randomized, double-blind, placebo-controlled pilot induction trial. Clinical efficacy using the Harvey-Bradshaw index and biochemical response using C-reactive protein and fecal calprotectin were assessed at week 8 post-intervention. Fecal samples were assessed by DNA shotgun metagenomic sequencing. A multivariable linear mixed effects model was used to assess alteration in fecal microbiome composition and function pre- and post-'Mycodigest' intervention. Clinical response was higher in the 'Mycodigest' intervention (N = 10) compared to the placebo (N = 6) group (80 vs. 16.7%, respectively, p = 0.035). There were no differences in terms of biochemical response within each group pre- and post-intervention. Post-'Mycodigest' intervention, 25 species were found to be differentially abundant compared to baseline, including increase in short chain fatty acid producing bacteria, such as Parabacteroides distasonis (Beta coefficient 0.92, 95% Confidence interval [CI] 0.36-1.47) and Faecalimonas umbilicata (Beta coefficient 0.57, 95% CI 0.23-0.90). Two microbial pathways related to the metabolism of isoprenoid compounds were increased post-'Mycodigest' intervention. Mushroom based prebiotic supplementation in subjects with CD resulted in clinical improvement which may be related to post-intervention favorable compositional and functional microbial alterations.},
}

Humans
*Prebiotics/administration & dosage
*Crohn Disease/microbiology/therapy/drug therapy
Pilot Projects
Female
Male
Feces/microbiology/chemistry
Double-Blind Method
Adult
*Dietary Supplements
*Agaricales/chemistry
Gastrointestinal Microbiome
Middle Aged
Leukocyte L1 Antigen Complex/analysis
C-Reactive Protein/analysis
Treatment Outcome
Young Adult

@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},
doi = {10.1371/journal.pone.0325362},
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 = {},
doi = {10.1093/gigascience/giaf072},
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 {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 {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 {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 {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 {pmid40478429,
year = {2025},
author = {Ogola, HJO and Ijoma, GN and Edokpayi, JN},
title = {Hydrological regime and niche partitioning drive fungal community structure and function in arid wetlands sediments of South Africa.},
journal = {Environmental science and pollution research international},
volume = {32},
number = {25},
pages = {15217-15231},
pmid = {40478429},
issn = {1614-7499},
support = {DST/CON0197/2017//Department of Science and Innovation, South Africa/ ; },
mesh = {*Wetlands ; South Africa ; *Fungi ; *Geologic Sediments/microbiology ; Hydrology ; Mycobiome ; Mycorrhizae ; Ecosystem ; Biodiversity ; },
abstract = {Arid wetlands are ecologically significant yet understudied ecosystems shaped by extreme conditions and hydrological variability. However, the structure and ecological functional of fungal communities in these habitats remain poorly understood, especially in southern Africa. This study integrated shotgun metagenomics, FUNGuild functional profiling, and multivariate analyses to examine fungal diversity, functional composition, and environmental drivers in seasonal and permanent arid wetlands of South Africa. Distinct fungal assemblages emerged, primarily shaped by hydrological regimes and ionic stress. Seasonal wetlands were dominated by Mucoromycota (79%), particularly arbuscular mycorrhizal (AM) fungus (Rhizophagus, 62%), while permanent wetlands had higher Ascomycota (54%), with Aspergillus (50%) prevalent in oxygen-limited sediments. Although alpha diversity showed no significant difference, beta diversity confirmed significant mycobiome differentiation. Total dissolved solids (TDS), electrical conductivity (EC), and salinity were key predictors of fungal composition, with TDS the strongest determinant (p < 0.01). Functional guild analysis highlighted niche differentiation, with saprotrophs dominating permanent wetlands (59.7% vs. 21.5%; p < 0.05), while symbiotrophs, particularly AM fungi, were enriched in seasonal wetlands (69.3% vs. 36.1%; p < 0.001). Indicator taxa identified via LefSe (LDA > 3, p < 0.05) and random forest modeling included Rhizophagus, Trichoderma, Fusarium, and Entomophthora in seasonal wetlands, and Aspergillus in permanent wetlands. This study provides the first integrative insight into fungal ecology in South Africa's arid wetlands, demonstrating that hydrological regime shapes fungal structure and function through environmental filtering and niche specialization, with implications for guiding conservation and adaptive management of these fragile ecosystems.},
}

*Wetlands
South Africa
*Fungi
*Geologic Sediments/microbiology
Hydrology
Mycobiome
Mycorrhizae
Ecosystem
Biodiversity

@article {pmid40310938,
year = {2025},
author = {Ma, WJ and Wang, C and Kothandapani, J and Luzentales-Simpson, M and Menzies, SC and Bescucci, DM and Lange, ME and Fraser, ASC and Gusse, JF and House, KE and Moote, PE and Xing, X and Grondin, JM and Hui, BW and Clarke, ST and Shelton, TG and Haskey, N and Gibson, DL and Martens, EC and Abbott, DW and Inglis, GD and Sly, LM and Brumer, H},
title = {Bespoke plant glycoconjugates for gut microbiota-mediated drug targeting.},
journal = {Science (New York, N.Y.)},
volume = {388},
number = {6754},
pages = {1410-1416},
doi = {10.1126/science.adk7633},
pmid = {40310938},
issn = {1095-9203},
mesh = {Animals ; *Gastrointestinal Microbiome ; Humans ; Mice ; *Glycoconjugates/chemistry/administration & dosage ; *Drug Delivery Systems/methods ; *Inflammatory Bowel Diseases/drug therapy/microbiology ; Glycoside Hydrolases/metabolism ; *Anti-Inflammatory Agents/administration & dosage ; *Oligosaccharides/chemistry ; Dietary Fiber/metabolism ; Bacteria/enzymology/metabolism ; },
abstract = {The gut microbiota of mammals possess distinctive metabolic pathways with untapped therapeutic potential. Using molecular insights into dietary fiber metabolism by the human gut microbiota, we designed a targeted drug delivery system, called GlycoCaging, that is based on bespoke glycoconjugates of a complex plant oligosaccharide. GlycoCaging of exemplar anti-inflammatory drugs enabled release of active molecules triggered by specific glycosidases of autochthonous gut bacteria. GlycoCaging ensured that drug efficacy was potentiated, and off-target effects were eliminated in murine models of inflammatory bowel disease. Biochemical and metagenomic analyses of gut microbiota of individual humans confirmed the broad applicability of this strategy.},
}

Animals
*Gastrointestinal Microbiome
Humans
Mice
*Glycoconjugates/chemistry/administration & dosage
*Drug Delivery Systems/methods
*Inflammatory Bowel Diseases/drug therapy/microbiology
Glycoside Hydrolases/metabolism
*Anti-Inflammatory Agents/administration & dosage
*Oligosaccharides/chemistry
Dietary Fiber/metabolism
Bacteria/enzymology/metabolism

@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 {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 = {},
doi = {10.3390/md23060242},
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 {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 = {},
doi = {10.3390/jox15030087},
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 {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 {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 {pmid40396729,
year = {2025},
author = {Cunningham, AL and Zhbannikov, IY and Myers, R and Tran, TH and Gao, W and Lemon, KP and Aquino, JN and Hurst, JH and Yoon, JW and Seed, PC and Kelly, MS},
title = {Genome mining identifies a diversity of natural product biosynthetic capacity in human respiratory Corynebacterium strains.},
journal = {mSphere},
volume = {10},
number = {6},
pages = {e0025825},
doi = {10.1128/msphere.00258-25},
pmid = {40396729},
issn = {2379-5042},
mesh = {*Corynebacterium/genetics/metabolism/classification ; Humans ; *Genome, Bacterial ; *Biological Products/metabolism ; Multigene Family ; *Biosynthetic Pathways/genetics ; Genomics ; *Respiratory System/microbiology ; Microbiota ; Phylogeny ; },
abstract = {Corynebacterium species, integral to the healthy human upper respiratory tract (URT) microbiota, remain underexplored in microbial genomics for their potential to promote respiratory health and exclude pathobionts. This genomic study investigated the diversity and capacity for natural product synthesis within these species, as indicated by their biosynthetic gene clusters (BGCs). We aimed to map and quantify the BGC diversity in a contemporary collection of Corynebacterium strains, representative of their prevalence in the respiratory microbiota, and to elucidate intra- and interspecies variation in BGC content. The outcomes of this research could reveal key factors in maintaining the ecological balance of the upper respiratory tract and identify novel antimicrobial agents targeting respiratory pathobionts. Employing an in silico approach, we analyzed the biosynthetic potential of respiratory strains of non-diphtheriae Corynebacterium species and their reference genomes through genome sequencing and antiSMASH6 analysis. Among 161 genomes, we identified 672 BGCs, 495 of which were unique, including polyketide synthase, non-ribosomal peptide synthetase, ribosomally synthesized and post-translationally modified peptide, and siderophore families. To understand how this biosynthetic capacity compared to other respiratory bacteria, we then downloaded genomes from eight species that are associated with the URT and conducted BGC searches. We found that despite their compact genomes, Corynebacterium species possess a multitude of predicted BGCs, exceeding the diversity of natural product BGCs identified in multiple other respiratory bacteria. This research lays the foundation for future functional genomics studies on the role of Corynebacterium species in the respiratory microbiome and the discovery of novel therapeutics derived from this bacterial genus.IMPORTANCEBacterial secondary metabolites, produced by enzymes encoded by biosynthetic gene clusters, are ecologically important for bacterial communication and competition in nutrient-scarce environments and are a historically rich source of antibiotics and other medications. Human-associated Corynebacterium species, abundant in the healthy upper respiratory tract, are understudied despite evidence of their roles in promoting human health and preventing pathobiont colonization. Through genome mining of a large collection of Corynebacterium strains isolated from the human respiratory tract and publicly available genomes of other respiratory bacteria, our study suggests that Corynebacterium species have a high biosynthetic capacity and are predicted to harbor a wide range of biosynthetic gene cluster families. These findings substantially expand current knowledge regarding the production of secondary metabolites by human-associated Corynebacterium species. Our study also lays the foundations for understanding how Corynebacterium species interact in the healthy human upper respiratory tract and the potential for discovering novel biotherapeutics.},
}

*Corynebacterium/genetics/metabolism/classification
Humans
*Genome, Bacterial
*Biological Products/metabolism
Multigene Family
*Biosynthetic Pathways/genetics
Genomics
*Respiratory System/microbiology
Microbiota
Phylogeny

@article {pmid40372056,
year = {2025},
author = {Kok, CR and Thissen, JB and Cerroni, M and Tribble, DR and Cancio, A and Tran, S and Schofield, C and Colombo, RE and Troth, T and Joya, C and Lalani, T and Be, NA},
title = {Field expedient stool collection methods for gut microbiome analysis in deployed military environments.},
journal = {mSphere},
volume = {10},
number = {6},
pages = {e0081824},
doi = {10.1128/msphere.00818-24},
pmid = {40372056},
issn = {2379-5042},
support = {//Lawrence Livermore National Laboratory/ ; },
mesh = {Humans ; *Feces/microbiology ; *Gastrointestinal Microbiome ; *Specimen Handling/methods ; *Military Personnel ; Adult ; Male ; Female ; *Bacteria/classification/genetics/isolation & purification ; Metagenomics ; Young Adult ; Diarrhea/microbiology ; Middle Aged ; Travel ; },
abstract = {Field expedient devices and protocols for the collection, storage, and shipment of stool samples in deployed settings are needed for the advancement of microbiome research in military health. Relevant assessments include the evaluation of microbiome signatures associated with susceptibility to travelers' diarrhea and recovery of gut function following infection. However, inherent biases in microbial measurements due to preservatives and sampling methods are unclear and should be assessed for an accurate evaluation of the microbiome. We performed shotgun metagenomic sequencing and compared the microbiome composition in paired fecal samples collected using Flinters Technology Associates (FTA) cards and OMNIgene (OG) Gut tubes, prior to and during international travel, from 49 adult participants, 39 of whom remained asymptomatic and 10 experienced travelers' diarrhea. Higher concentrations of nucleic acid and sequencing libraries were observed in OG samples. A majority of genera (82.9%) were detected with both methods, and detections of genera limited to one collection method were not highly prevalent across samples and were present in extremely low relative abundances (<0.01%). Differences in beta diversity were largely explained by inter-individuality of microbiome composition, followed by the effect of collection method and timepoint-disease states. Differential abundance analysis indicated that Corynebacterium and Blautia were consistently higher in abundance across all groups with FTA and OG collection, respectively. The observed differences in microbiome composition between methods suggest the need for consistent and standardized protocols within a study. Overall, the data presented here could help guide the future design of fecal microbiome study protocols in field and military deployment settings.IMPORTANCEThe assessment of field-deployable methods for fecal sample collection and storage is required to reliably capture samples collected in remote and austere locations. This study describes a comparative metagenomics analysis between samples collected by two different commercially available methods in a military-deployed setting. The results presented here are foundational for the future design of fecal microbiome study protocols in an operational context.},
}

Humans
*Feces/microbiology
*Gastrointestinal Microbiome
*Specimen Handling/methods
*Military Personnel
Adult
Male
Female
*Bacteria/classification/genetics/isolation & purification
Metagenomics
Young Adult
Diarrhea/microbiology
Middle Aged
Travel

@article {pmid40366139,
year = {2025},
author = {Crouch, AL and Severance, BM and Creary, S and Hood, D and Bailey, M and Mejias, A and Ramilo, O and Gillespie, M and Ebelt, S and Sheehan, V and Kopp, BT and Anderson, MZ},
title = {Altered nasal and oral microbiomes define pediatric sickle cell disease.},
journal = {mSphere},
volume = {10},
number = {6},
pages = {e0013725},
doi = {10.1128/msphere.00137-25},
pmid = {40366139},
issn = {2379-5042},
support = {Advancing Research in Infection and Immunity//The Ohio State University/ ; Science Diversity Leadership Award//Chan Zuckerberg Initiative (CZI)/ ; T32 Interdisciplinary Program in Microbe-Host Biology//The Ohio State University/ ; NIAIDR21AI174000/NH/NIH HHS/United States ; Center for Ethnic Studies research grant//The Ohio State University/ ; },
mesh = {Humans ; *Anemia, Sickle Cell/microbiology ; *Microbiota ; Child ; Male ; Female ; *Mouth/microbiology ; Dysbiosis/microbiology ; Bacteria/classification/genetics/isolation & purification ; Adolescent ; Child, Preschool ; Metagenomics ; *Nose/microbiology ; },
abstract = {UNLABELLED: Sickle cell disease (SCD) is a chronic blood disorder that disrupts multiple organ systems and can lead to severe morbidity. Persistent and acute symptoms caused by immune system dysregulation in individuals with SCD could contribute to disease either directly or indirectly via dysbiosis of commensal microbes and increased susceptibility to infection. Here, we explored the nasal and oral microbiomes of children with SCD (cwSCD) to uncover potential dysbiotic associations with the blood disorder. Microbiota collected from nasal and oral swabs of 40 cwSCD were compared to eight healthy siblings using shotgun metagenomic sequencing. Commensal taxa were present at similar levels in the nasal and oral microbiome of both groups. However, the nasal microbiomes of cwSCD contained a higher prevalence of Pseudomonadota species, including pathobionts such as Yersinia enterocolitica and Klebsiella pneumoniae. Furthermore, the oral microbiome of cwSCD displayed lower α-diversity and fewer commensal and pathobiont species compared to the healthy siblings. Thus, subtle but notable shifts seem to exist in the nasal and oral microbiomes of cwSCD, suggesting an interaction between SCD and the microbiome that may influence health outcomes.

IMPORTANCE: The oral and nasal cavities are susceptible to environmental exposures including pathogenic microbes. In individuals with systemic disorders, antibiotic exposure, changes to the immune system, or changes to organ function could influence the composition of the microbes at these sites and the overall health of individuals. Children with sickle cell disease (SCD) commonly experience respiratory infections, such as pneumonia or sinusitis, and may have increased susceptibility to infection because of disrupted microbiota at these body sites. We found that children with SCD (cwSCD) had more pathobiont bacteria in the nasal cavity and reduced bacterial diversity in the oral cavity compared to their healthy siblings. Defining when, why, and how these changes occur in cwSCD could help identify specific microbial signatures associated with susceptibility to infection or adverse outcomes, providing insights into personalized treatment strategies and preventive measures.},
}

Humans
*Anemia, Sickle Cell/microbiology
*Microbiota
Child
Male
Female
*Mouth/microbiology
Dysbiosis/microbiology
Bacteria/classification/genetics/isolation & purification
Adolescent
Child, Preschool
Metagenomics
*Nose/microbiology

@article {pmid40358144,
year = {2025},
author = {Mukherjee, SD and Suryavanshi, M and Knight, J and Lange, D and Miller, AW},
title = {Metagenomic and phylogenetic analyses reveal gene-level selection constrained by bacterial phylogeny, surrounding oxalate metabolism in the gut microbiota.},
journal = {mSphere},
volume = {10},
number = {6},
pages = {e0091324},
doi = {10.1128/msphere.00913-24},
pmid = {40358144},
issn = {2379-5042},
mesh = {*Oxalates/metabolism ; *Phylogeny ; *Gastrointestinal Microbiome/genetics ; Humans ; *Metagenomics ; *Bacteria/genetics/classification/metabolism ; *Selection, Genetic ; },
abstract = {The gut microbiota is critical for neutralizing dietary toxins. Oxalate is a toxin commonly produced by plants to deter herbivory and is widely consumed in the human diet. Excess levels of systemic or urinary oxalate increase risk of multiple urologic and cardiometabolic diseases. The current study employed multiple amplicon-based and shotgun metagenomic methodologies, alongside comparative phylogenetic analyses, to interrogate evolutionary radiation surrounding microbial oxalate degradation within the human gut microbiome. In conservative genome-based estimates, over 30% of gut microbial species harbored at least one oxalate-handling gene, with the specific pathways used dependent on bacterial phylum. Co-occurrence analyses revealed interactions between specialist genes that can metabolize oxalate or its by-products, but not multi-functional genes that can act in more than one oxalate-related pathway. Specialization was rare at the genome level. Amplicon-based metagenomic sequencing of the oxalate-degrading gene, formyl-CoA transferase (frc), coupled with molecular clock phylogenetic analyses are indicative of rapid evolutionary divergence, constrained by phylum. This was corroborated by paired analyses of non-synonymous to synonymous substitutions (dN/dS ratios), which pointed toward neutral to positive selection. Sequence similarity network analyses of frc sequences suggest extensive horizontal gene transferring has occurred with the frc gene, which may have facilitated rapid divergence. The frc gene was primarily allocated to the Pseudomonodota phylum, particularly the Bradyrhizobium genus, which is a species capable of utilizing oxalate as a sole carbon and energy source. Collectively evidence provides strong support that, for oxalate metabolism, evolutionary selection occurs at the gene level, through horizontal gene transfer, rather than at the species level.IMPORTANCEA critical function of the gut microbiota is to neutralize dietary toxins, such as oxalate, which is highly prevalent in plant-based foods and is not degraded by host enzymes. However, little is known about the co-evolutionary patterns of plant toxins and the mammalian gut microbiota, which are expected to exhibit features of an evolutionary arms race. In the current work, we present molecular evidence that microbial genes for oxalate degradation are highly prevalent in humans, potentially driven by extensive horizontal gene transfer events. Phylogenetic analyses reveal that oxalate-degrading genes are under a positive selection pressure and have historically undergone rapid diversification events, which has led to diverse ecological strategies for handling oxalate by gut bacteria. Collectively, data shed light on potential evolutionary relationships between the diet and the gut microbiota that occur relatively independently of the mammalian host.},
}

*Oxalates/metabolism
*Phylogeny
*Gastrointestinal Microbiome/genetics
Humans
*Metagenomics
*Bacteria/genetics/classification/metabolism
*Selection, Genetic

@article {pmid40355744,
year = {2025},
author = {Schreiber, S and Waetzig, GH and López-Agudelo, VA and Geisler, C and Schlicht, K and Franzenburg, S and di Giuseppe, R and Pape, D and Bahmer, T and Krawczak, M and Kokott, E and Penninger, JM and Harzer, O and Kramer, J and von Schrenck, T and Sommer, F and Zacharias, HU and , and Millet Pascual-Leone, B and Forslund, SK and Heyckendorf, J and Aden, K and Hollweck, R and Laudes, M and Rosenstiel, P},
title = {Nicotinamide modulates gut microbial metabolic potential and accelerates recovery in mild-to-moderate COVID-19.},
journal = {Nature metabolism},
volume = {7},
number = {6},
pages = {1136-1149},
pmid = {40355744},
issn = {2522-5812},
support = {EXC 2167: CD-1, CD-2, TI-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; EXC 2167//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; EXC 2167: RTF-VI//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; miTARGET (RU5042)//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SO1141/10-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SFB1470, SFB1449//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; EXC 2167: CD-2, RTF-VI, TI-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; e:Med Juniorverbund "Try-IBD" 01ZX1915A and 01ZX2215, e:Med Network iTREAT 01ZX2202A//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; e:Med CKDNapp 01ZX1912A//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; K126408//Christian-Albrechts-Universität zu Kiel (Christian-Albrechts-University Kiel)/ ; },
mesh = {Humans ; *Niacinamide/therapeutic use/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Male ; Double-Blind Method ; *COVID-19/metabolism ; Female ; Middle Aged ; SARS-CoV-2 ; *COVID-19 Drug Treatment ; Adult ; Feces/microbiology ; Prospective Studies ; Aged ; Dysbiosis ; Tryptophan/metabolism ; },
abstract = {Cellular NAD[+] depletion, altered tryptophan metabolism and gut microbiome dysbiosis are associated with disease progression and unfavourable clinical outcomes in COVID-19. Here, we show that supplementing tryptophan metabolism with nicotinamide alleviates COVID-19 symptoms. We evaluate a 4-week intervention with a novel nicotinamide formulation (1,000 mg) in a prospective, double-blind, randomized, placebo-controlled trial in 900 symptomatic outpatients with PCR-proven COVID-19. In the primary analysis population of participants at risk for severe COVID-19, 57.6% of those receiving nicotinamide and 42.6% receiving placebo recover from their performance drop at week 2 (P = 0.004). Nicotinamide is also beneficial for returning to normal activities (P = 0.009). Effects on gut metagenomic signatures parallel clinical efficacy, suggesting that nicotinamide influences COVID-19-associated faecal microbiome changes. After 6 months, responders to nicotinamide in acute COVID-19 show fewer post-COVID symptoms than placebo responders (P = 0.010). No relevant safety signals are observed. Overall, our results show that nicotinamide leads to faster recovery of physical performance and modulates COVID-19-associated faecal microbiome changes.},
}

Humans
*Niacinamide/therapeutic use/pharmacology
*Gastrointestinal Microbiome/drug effects
Male
Double-Blind Method
*COVID-19/metabolism
Female
Middle Aged
SARS-CoV-2
*COVID-19 Drug Treatment
Adult
Feces/microbiology
Prospective Studies
Aged
Dysbiosis
Tryptophan/metabolism

@article {pmid40340458,
year = {2025},
author = {Bay, L and Barnes, CJ and Fritz, BG and Ravnborg, N and Ruge, IF and Halling-Sønderby, A-S and Søeborg, SR and Langhoff, KH and Lex, C and Hansen, AJ and Thyssen, JP and Bjarnsholt, T},
title = {Unique dermal bacterial signature differentiates atopic dermatitis skin from healthy.},
journal = {mSphere},
volume = {10},
number = {6},
pages = {e0015625},
doi = {10.1128/msphere.00156-25},
pmid = {40340458},
issn = {2379-5042},
support = {LF-OC-19-0003//LEO Fondet (LEO Foundation)/ ; LF17067//LEO Fondet (LEO Foundation)/ ; LF17067//LEO Fondet (LEO Foundation)/ ; },
mesh = {Humans ; *Dermatitis, Atopic/microbiology ; Adult ; *Microbiota ; Female ; Male ; *Skin/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Middle Aged ; Metagenomics ; Young Adult ; Epidermis/microbiology ; Case-Control Studies ; *Dermis/microbiology ; },
abstract = {UNLABELLED: Gaining a deeper understanding of the variation in skin microbiota across habitats and layers provides critical insights into the complex host-microbial interactions that drive inflammatory skin diseases. Our study investigated dermal versus epidermal microbiota in lesional and non-lesional skin of 37 adult atopic dermatitis (AD) patients and 37 healthy controls. Skin biopsies were partitioned into epidermal and dermal compartments, while serial tape strips collected the superficial epidermis. Bacterial communities were analyzed by cultivation, matrix-assisted laser desorption ionization time-of-flight mass spectrometry, confocal laser scanning microscopy, and metagenomic sequencing. We found that the effects of AD were evident across skin layers. The natural variation between skin layers and habitats diminishes in AD-affected skin, intensifying the impact of the microenvironment and host factors. A remarkably distinct dermal bacterial community was discovered among AD patients, being more conserved and providing a clearer difference between skin habitats, while the epidermis varied substantially. Importantly, comparisons between AD patients and controls revealed more genera differed when studying the dermal samples than the epidermal ones. Staphylococcus, Corynebacterium, and Cutibacterium genera differed with AD status across all samples, but Prevotella and Mitsuokella only differed in the dermis. In the dry and moist dermis, this translated into 14 and 61 gene pathways significantly varying with AD status, including many related to the biosynthesis of menaquinones (vitamin K2). These results suggest dermal sampling would allow for the role of the skin microbiome within AD pathogenesis to be better resolved since these communities are simpler and less prone to environmental contamination.

IMPORTANCE: This study sheds light on the profound impact of skin microbiota's complex composition and distribution in atopic dermatitis (AD). The distinctive bacterial profile and activity, especially within the dermal skin compartment, vividly mirrored the cutaneous conditions in this inflamed microenvironment. The striking similarity in bacterial communities across different skin habitats in atopic skin underscores the high influence of atopic dermatitis-the genetic predisposition to an amplified immune response. This finding suggests that the dermal bacterial profile could be a valuable tool for longitudinally monitoring changes during the disease's relapsing phases, allowing for a precise categorization of patients into specific AD endotypes. Broadening the focus throughout the entire eczema-affected skin paves the way for treatments capable of modulating dermal biological factors, offering more effective management of AD. By further centering the interest in host-microbial interactions, we can refine personalized treatments, ultimately improving the lives of millions suffering from atopic dermatitis.},
}

Humans
*Dermatitis, Atopic/microbiology
Adult
*Microbiota
Female
Male
*Skin/microbiology
*Bacteria/classification/genetics/isolation & purification
Middle Aged
Metagenomics
Young Adult
Epidermis/microbiology
Case-Control Studies
*Dermis/microbiology

@article {pmid40320901,
year = {2025},
author = {Gervasoni, KN and Iacia, MVMS and Silva, KO and Franco, LG and Mendes, MEF and Neves, TJDC and Sanches, WS and Oliveira, LB and Saito, EA and Vieira, KCO and Pereira, VC and Nai, GA and Winkelstroter, LK},
title = {Protective Effect of Piperine on Indomethacin-Induced Intestinal Damage.},
journal = {Molecular nutrition & food research},
volume = {69},
number = {12},
pages = {e70097},
doi = {10.1002/mnfr.70097},
pmid = {40320901},
issn = {1613-4133},
mesh = {Animals ; *Polyunsaturated Alkamides/pharmacology ; *Piperidines/pharmacology ; *Alkaloids/pharmacology ; *Benzodioxoles/pharmacology ; Male ; *Indomethacin/adverse effects/toxicity ; Mice ; Gastrointestinal Microbiome/drug effects ; *Anti-Inflammatory Agents, Non-Steroidal/adverse effects ; Intestine, Small/drug effects/pathology ; Intestinal Mucosa/drug effects/pathology ; Aspartate Aminotransferases/blood ; Protective Agents/pharmacology ; Intestines/drug effects/pathology ; },
abstract = {Nonsteroidal antiinflammatory drugs (NSAIDs) are widely prescribed for the treatment of inflammation and chronic pain. Chronic use of NSAIDs is associated with adverse events and organ damage, especially to the gastric mucosa and small intestine. This study evaluates the protective effect of piperine on indomethacin-induced intestinal damage. Eighteen male Mus musculus mice, aged 6-8 weeks, were used. Intestinal damage was induced with indomethacin (10 mg/mL) and cotreatment with piperine (20 mg/mL), both administered orally. After 14 days, the animals were euthanized. Biochemical serological analysis was performed. Intestinal inflammation was assessed based on macroscopic, histopathological, and metagenomic analyses. Histopathological analysis showed a reduction in small intestine inflammation (p < 0.05) and the disappearance of necrosis in the intestinal wall of the large intestine. Crypt and villus measurements showed increased values in the piperine-treated group (p < 0.05). An approximately six-fold increase in aspartate aminotransferase (AST) was observed in the Indomethacin group (p < 0.05). Regarding the intestinal microbiota, an increase in genus diversity was observed in the piperine-treated group (p < 0.05). There was a 50% reduction in micronucleus formation with the administration of piperine 20 mg/kg (p < 0.05). It was concluded that cotreatment with piperine has great potential in mitigating the side effects caused by NSAIDs.},
}

Animals
*Polyunsaturated Alkamides/pharmacology
*Piperidines/pharmacology
*Alkaloids/pharmacology
*Benzodioxoles/pharmacology
Male
*Indomethacin/adverse effects/toxicity
Mice
Gastrointestinal Microbiome/drug effects
*Anti-Inflammatory Agents, Non-Steroidal/adverse effects
Intestine, Small/drug effects/pathology
Intestinal Mucosa/drug effects/pathology
Aspartate Aminotransferases/blood
Protective Agents/pharmacology
Intestines/drug effects/pathology

@article {pmid40172109,
year = {2025},
author = {Tarracchini, C and Lordan, C and Milani, C and Moreira, LPD and Alabedallat, QM and de Moreno de LeBlanc, A and Turroni, F and Lugli, GA and Mancabelli, L and Longhi, G and Brennan, L and Mahony, J and LeBlanc, JG and Nilaweera, KN and Cotter, PD and van Sinderen, D and Ventura, M},
title = {Vitamin biosynthesis in the gut: interplay between mammalian host and its resident microbiota.},
journal = {Microbiology and molecular biology reviews : MMBR},
volume = {89},
number = {2},
pages = {e0018423},
doi = {10.1128/mmbr.00184-23},
pmid = {40172109},
issn = {1098-5557},
support = {12/RC/2273/SFI_/Science Foundation Ireland/Ireland ; 16/SP/3827/SFI_/Science Foundation Ireland/Ireland ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Animals ; *Vitamins/biosynthesis ; *Bacteria/metabolism/genetics ; *Gastrointestinal Tract/microbiology/metabolism ; Mammals/microbiology ; *Host Microbial Interactions ; },
abstract = {SUMMARYIn recent years, exhaustive efforts have been made to dissect the composition of gut-associated microbial communities and associated interactions with their human host, which are thought to play a crucial role in host development, physiology, and metabolic functions. Although such studies were initially focused on the description of the compositional shifts in the microbiota that occur between different health conditions, more recently, they have provided key insights into the functional and metabolic contributions of the gut microbiota to overall host physiology. In this context, an important metabolic activity of the human gut microbiota is believed to be represented by the synthesis of various vitamins that may elicit considerable benefits to human health. A growing body of scientific literature is now available relating to (predicted) bacterial vitamin biosynthetic abilities, with ever-growing information concerning the prevalence of these biosynthetic abilities among members of the human microbiota. This review is aimed at disentangling if and how cooperative trophic interactions of human microbiota members contribute to vitamin production, and if such, gut microbiota-mediated vitamin production varies according to different life stages. Moreover, it offers a brief exploration of how different diets may influence vitamin production by shaping the overall composition and metabolic activity of the human gut microbiota while also providing preliminary insights into potential correlations between human microbiota-associated vitamin production and the occurrence of human diseases and/or metabolic disorders.},
}

Humans
*Gastrointestinal Microbiome/physiology
Animals
*Vitamins/biosynthesis
*Bacteria/metabolism/genetics
*Gastrointestinal Tract/microbiology/metabolism
Mammals/microbiology
*Host Microbial Interactions

@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 {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 {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 {pmid40548332,
year = {2025},
author = {Pita, L and Maldonado, M and Koutsouveli, V and Riesgo, A and Hentschel, U and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , },
title = {The chromosomal genome sequence of the kidney sponge, Chondrosia reniformis Nardo, 1847, and its associated microbial metagenome sequences.},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {283},
pmid = {40548332},
issn = {2398-502X},
abstract = {We present a genome assembly from a specimen of Chondrosia reniformis (kidney sponge; Porifera; Demospongiae; Chondrillida; Chondrillidae). The genome sequence has a total length of 117.37 megabases. Most of the assembly (99.98%) is scaffolded into 14 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 17.45 kilobases in length. Several symbiotic bacterial genomes were assembled as MAGs. Gene annotation of the host organism assembly on Ensembl identified 17,340 protein-coding genes. The metagenome of the specimen was also assembled and 53 binned bacterial genomes were identified, including 40 high-quality MAGs that were representative of a typical high microbial abundance sponge and included three candiate phyla (Poribacteria, Latescibacteria, Binatota).},
}

@article {pmid40544519,
year = {2025},
author = {Yu, X and Liang, J and Yang, R and Gai, W and Zheng, Y},
title = {Clinical Features and Value of Tracheal Aspirate Metagenomic Next-Generation Sequencing for Severe Pneumonia in Children in Pediatric Intensive Care Unit.},
journal = {Polish journal of microbiology},
volume = {74},
number = {2},
pages = {192-205},
doi = {10.33073/pjm-2025-016},
pmid = {40544519},
issn = {2544-4646},
mesh = {Humans ; Infant ; *High-Throughput Nucleotide Sequencing ; Male ; Child, Preschool ; Female ; *Metagenomics/methods ; Child ; Intensive Care Units, Pediatric ; *Trachea/microbiology ; *Pneumonia/microbiology/diagnosis/virology ; Microbiota/genetics ; Bacteria/genetics/classification/isolation & purification ; Coinfection/microbiology ; },
abstract = {Pneumonia is a leading cause of mortality in children. While metagenomic next-generation sequencing (mNGS) has the potential to detect all the microorganisms in pneumonia patients, the relationship between these microorganisms and the patients' clinical characteristics remains to be established. Fifty-five children, diagnosed with severe pneumonia and undergoing tracheal aspirate (TA) mNGS for pathogen detection at The Heilongjiang Hospital of Beijing Children's Hospital between July 2021 and November 2022, were included in this study. The clinical characteristics, pathogen distribution, and microbiome features of these children were analyzed. Results showed that the rate of mixed infections was notably high (80%, 44/55), with bacterial-viral infections being the most common. Streptococcus pneumoniae, Mycoplasma pneumoniae (MP), Candida albicans, and Respiratory syncytial virus (RSV) were the most common pathogens in this cohort. Furthermore, RSV and S. pneumoniae were the most prevalent pathogens in children younger than 12 months (infants), while MP and Haemophilus influenzae were more commonly identified in children between 12 and 144 months. Increased richness and diversity of the microbiota were observed in the TA of the older children. Linear discriminant analysis (LDA) effect size (LEfSe) analysis identified that RSV and Streptococcus mitis were the specific species associated with infants. In contrast, Human bocaparvovirus 1 and Prevotella histicola were significantly enriched in the older children. In addition, the top 20 most abundant species exhibited correlations with neutrophil count and C-reactive protein. This study emphasizes the significance of employing mNGS to understand better the clinical characteristics and microbial diversity in pediatric patients with severe pneumonia.},
}

Humans
Infant
*High-Throughput Nucleotide Sequencing
Male
Child, Preschool
Female
*Metagenomics/methods
Child
Intensive Care Units, Pediatric
*Trachea/microbiology
*Pneumonia/microbiology/diagnosis/virology
Microbiota/genetics
Bacteria/genetics/classification/isolation & purification
Coinfection/microbiology

@article {pmid40542451,
year = {2025},
author = {Ji, S and Ahmad, F and Peng, B and Yang, Y and Su, M and Zhao, X and Vatanen, T},
title = {Engrafting gut bacteriophages have potential to modulate microbial metabolism in fecal microbiota transplantation.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {149},
pmid = {40542451},
issn = {2049-2618},
support = {U22A20365//Joint Funds of National Natural Science Foundation of China/ ; T2341019//National Natural Science Foundation of China/ ; 2023A1515012429//Natural Science Foundation of Guangdong Province/ ; 2024B03J1343//Guangzhou Science and Technology Plan Project/ ; },
mesh = {*Fecal Microbiota Transplantation/methods ; Humans ; *Bacteriophages/genetics/classification/physiology/isolation & purification ; *Gastrointestinal Microbiome ; Feces/microbiology/virology ; *Clostridium Infections/therapy/microbiology ; Clostridioides difficile/virology ; Bacteria/metabolism/virology/genetics/classification ; Metagenome ; },
abstract = {BACKGROUND: Fecal microbiota transplantation (FMT) is widely used to treat severe infections and investigated for the treatment of complex diseases. The therapeutic efficacy of FMT is related to the successful engraftment of bacteriophages from healthy donors to recipients. However, gut bacteriophage contributions to FMT engraftment and treatment outcomes remain unclear.

METHODS: The gut phageome from previously published metagenomes of donors and recipients across 23 FMT studies was assembled and functionally annotated for a meta-analysis.

RESULTS: Gut phageome profiles of FMT recipients, especially those with recurrent Clostridioides difficile infection (rCDI), shifted toward donor phageomes, accompanied by increased phageome alpha diversity. Engraftment of donor phages varied between recipient conditions with the highest engraftment rate, overrepresented by putative temperate phage, in patients with rCDI. Consistently, a higher proportion of auxiliary metabolic genes (AMGs), with the potential to support and modulate bacterial metabolism, were annotated on putative temperate phages.

CONCLUSIONS: FMT leads to significant taxonomic, functional, and lifestyle shifts in recipient phageome composition. Future FMT studies should include gut phageome characterization and consider it as a potential factor in microbial community shifts and treatment outcomes. Video Abstract.},
}

*Fecal Microbiota Transplantation/methods
Humans
*Bacteriophages/genetics/classification/physiology/isolation & purification
*Gastrointestinal Microbiome
Feces/microbiology/virology
*Clostridium Infections/therapy/microbiology
Clostridioides difficile/virology
Bacteria/metabolism/virology/genetics/classification
Metagenome

@article {pmid40542420,
year = {2025},
author = {Yu, M and Chu, Y and Wang, Y and Mo, L and Tan, X and Guo, S and Yuan, S and Ma, Y},
title = {Metagenomic analysis reveals gut phage diversity across three mammalian models.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {146},
pmid = {40542420},
issn = {2049-2618},
support = {2024YFA0919400//National Key Research and Development Program of China/ ; 2024YFA0919400//National Key Research and Development Program of China/ ; 2024YFA0919400//National Key Research and Development Program of China/ ; B2302023//Shenzhen Medical Research Fund/ ; B2302023//Shenzhen Medical Research Fund/ ; KJZD20230923115859008//Shenzhen Science and Technology Program/ ; KJZD20230923115859008//Shenzhen Science and Technology Program/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; Swine ; *Bacteriophages/genetics/classification/isolation & purification ; Mice ; Humans ; Macaca fascicularis/virology ; Metagenome ; Virome ; Phylogeny ; Models, Animal ; Feces/virology ; },
abstract = {BACKGROUND: The gut virome plays a pivotal role in shaping the host's microbiota. However, gut viruses across different mammalian models, and their connections with the human gut microbiota remain largely unknown.

RESULTS: We identified 977 high-confidence species-level viral operational taxonomic units (vOTUs) in mice (hcMGV), 12,896 in pigs (hcPGV), and 1480 in cynomolgus macaques (hcCMGV) from metagenomes, respectively. Clustering these vOTUs at approximately genus level uncovered novel clades with high prevalence across animal guts (> = 60%). In particular, crAss-like phages and cas-harboring jumbophages were characterized. Comparative analysis revealed that hcCMGV had a closer relationship with hcPGV than hcMGV, despite the animal-specific characteristics, and that 55.88% hcCMGV had connections with the human microbiota.

CONCLUSIONS: Our findings shed light on the diversity of gut viruses across these three animals, contributing to future gut microbial studies using model animals. Video Abstract.},
}

Animals
*Gastrointestinal Microbiome/genetics
*Metagenomics/methods
Swine
*Bacteriophages/genetics/classification/isolation & purification
Mice
Humans
Macaca fascicularis/virology
Metagenome
Virome
Phylogeny
Models, Animal
Feces/virology

@article {pmid40537892,
year = {2025},
author = {Kang, J and Choi, Y and Keum, GB and Doo, H and Kwak, J and Kim, H and Chae, Y and Lee, S and Yang, H and Kim, S and Sun, X and Kim, HB and Yoo, SJ},
title = {Effect of Diet and Lifestyle Changes on Gut Microbial Diversity in Healthy Adolescents.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e2503018},
doi = {10.4014/jmb.2503.03018},
pmid = {40537892},
issn = {1738-8872},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics/physiology ; Adolescent ; RNA, Ribosomal, 16S/genetics ; *Life Style ; Feces/microbiology ; *Diet ; *Bacteria/classification/genetics/isolation & purification ; Male ; Female ; Biodiversity ; DNA, Bacterial/genetics ; Exercise ; Sequence Analysis, DNA ; },
abstract = {The human gut microbiome is a complex ecosystem shaped by both intrinsic and extrinsic factors, with external elements such as diet and exercise significantly influencing its diversity and composition. In this study, we evaluated gut microbiome shifts in adolescents participating in a four-week camp with controlled diets, lifestyle, and a healthy living environment. Stool samples were collected before and after the camp period and analyzed through 16S rRNA gene sequencing to assess changes in microbial composition and diversity. Post-intervention, gut microbiome diversity increased significantly, with notable changes in the relative abundance of taxa such as Lachnospira, Alistipes, and Barnesiella, which are associated with enhanced immune function and gut health. Additionally, functional prediction using PICRUSt indicated an increase in genes associated with energy production and metabolism, suggesting a broader functional impact of lifestyle modifications on gut microbial functionalities. These findings revealed the potential causal relationships between lifestyle modifications and gut microbiome shifts, providing valuable insights into the interactions between environment, diet, and the gut microbiota.},
}

Humans
*Gastrointestinal Microbiome/genetics/physiology
Adolescent
RNA, Ribosomal, 16S/genetics
*Life Style
Feces/microbiology
*Diet
*Bacteria/classification/genetics/isolation & purification
Male
Female
Biodiversity
DNA, Bacterial/genetics
Exercise
Sequence Analysis, DNA

@article {pmid40537448,
year = {2025},
author = {Rudi, K and Nilsen, T and Pettersen, R and Keeley, NB and Ray, JL and Majaneva, S and Stokkan, M and Hervik, A and Angell, IL and Philip, M and Martin, J and Sundt, MØ and Snipen, LG},
title = {The Coastal Seafloor Microbiota Is Structured by Local Selection of Cosmopolitan Taxa.},
journal = {Environmental microbiology reports},
volume = {17},
number = {3},
pages = {e70123},
pmid = {40537448},
issn = {1758-2229},
support = {320076//Norges Forskningsråd/ ; },
mesh = {*Microbiota ; *Seawater/microbiology ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Iceland ; Norway ; *Archaea/genetics/classification/isolation & purification/metabolism ; Metagenome ; Phylogeny ; Nitrates/metabolism ; Ecosystem ; },
abstract = {Understanding the assembly processes of the coastal seafloor microbiota is crucial for gaining insights into how ocean ecosystems work. In our study, we addressed the question about how local selection affects the global distribution of coastal seafloor microorganisms. We identified two main clusters of samples by examining the geographical distribution of 356 high-quality prokaryote metagenome-assembled genomes (MAGs) from 94 coastal samples collected along the Norwegian and Icelandic coasts. There was no identifiable correlation between the abundance of MAGs and the geographic distance between them central to the identified clusters (no distance decay). In contrast, noncentral MAGs demonstrate a pronounced distance decay. We also observed significant functional differences between the two sample clusters. One cluster showed enrichment in functions such as dissimilatory nitrate reduction to ammonium (DNRA), acetoclastic methanogenesis, thiosulphate conversion and acetate and butyrate metabolism. The other cluster was enriched in propionate metabolism, nitrite oxidation to nitrate and cobalamin-dependent carbon fixation. These results suggest that localised environmental selection acts on cosmopolitan taxa to shape seafloor microbiota. Our findings therefore profoundly impact the understanding of seafloor ecological processes and their management.},
}

*Microbiota
*Seawater/microbiology
*Bacteria/classification/genetics/metabolism/isolation & purification
Iceland
Norway
*Archaea/genetics/classification/isolation & purification/metabolism
Metagenome
Phylogeny
Nitrates/metabolism
Ecosystem

@article {pmid40517714,
year = {2025},
author = {Huang, H and Xiao, K and Shen, T and Chu, D and Xie, Z and Bi, Y and Ning, K and Yan, Y},
title = {The impact of enclosure management on the conservation and restoration of microbial community in a typical urban lake.},
journal = {The Science of the total environment},
volume = {989},
number = {},
pages = {179827},
doi = {10.1016/j.scitotenv.2025.179827},
pmid = {40517714},
issn = {1879-1026},
mesh = {*Lakes/microbiology ; *Microbiota ; *Conservation of Natural Resources/methods ; *Environmental Restoration and Remediation/methods ; China ; Ecosystem ; *Environmental Monitoring ; *Water Microbiology ; },
abstract = {Urban lake freshwater ecosystems, as vital lifelines intricately connected to human well-being, hosted microbes vital for biosynthetic and global biochemical cycles. Despite their ecological importance, current research has yet to fully elucidate how urban lake restoration efforts influence microbial diversity, community structure, and functional dynamics, leaving a significant gap in our understanding of the ecological outcomes of such interventions. Donghu Lake's ongoing restoration project employs enclosure management as a conservation strategy. To evaluate the impact of enclosure management on protecting and restoring microbial communities, we analyzed 72 metagenomic samples from the restoration waterbody. It was found that enclosure management profoundly reshaped microbial communities, making them more stable and similar to natural conditions, and boosting their biosynthetic gene encoding potential. Furthermore, research revealed antibiotic resistance genes (ARGs) tended to be preferentially hosted by specific microbes, identifying Gammaproteobacteria as a critical target for managing ARGs proliferation. These findings provide not only a fresh perspective for the understanding, but also a robust foundation for the management of urban lake freshwater ecosystems. Our findings highlight that enclosure management promotes microbial community stability and functional resilience, which are critical for restoring ecosystem services in urban lakes. This study provides actionable insights for designing targeted conservation strategies to enhance the sustainability of freshwater ecosystems under anthropogenic pressure.},
}

*Lakes/microbiology
*Microbiota
*Conservation of Natural Resources/methods
*Environmental Restoration and Remediation/methods
China
Ecosystem
*Environmental Monitoring
*Water Microbiology

@article {pmid40517504,
year = {2025},
author = {Tang, X and Liu, Y and Yang, W and Wu, Y and Yong, T and Liu, W and Lv, F and Hussain, K and Wang, Y and Gao, X and Zhang, Y},
title = {Macroplastics in soybean cultivation: Neutral on plant growth but disruptive to nitrogen-fixing microbiome.},
journal = {Ecotoxicology and environmental safety},
volume = {301},
number = {},
pages = {118499},
doi = {10.1016/j.ecoenv.2025.118499},
pmid = {40517504},
issn = {1090-2414},
mesh = {*Glycine max/growth & development/drug effects/microbiology ; *Nitrogen Fixation/drug effects ; *Soil Microbiology ; *Microbiota/drug effects ; *Soil Pollutants/toxicity ; Soil/chemistry ; Nitrogen/metabolism ; Nitrates/analysis/metabolism ; Agriculture ; Bradyrhizobium/drug effects ; Nitrogen Cycle/drug effects ; },
abstract = {Macroplastics are an emerging yet underexplored pollutant in agricultural soils, with the potential to disrupt nitrogen (N) cycling through physical interference and microbial community shifts. While extensive studies have focused on microplastics, the effects of larger plastic debris (>2 cm) on soil-plant systems in legume cropping systems remain poorly understood. We conducted a 71-d mesocosm study utilizing [15]N isotopic tracing and metagenomic sequencing to demonstrate how macroplastics influence soybean growth and soil-soybean continuum N cycling. Soybean growth was not affected under macroplastics exposure (up to 200 kg ha[-][1]). However, macroplastics increased soil NO3[-] and NH4[+] concentrations, and elevated urease and ammonia monooxygenase activities, suggesting enhanced N availability. Paradoxically, macroplastics significantly disrupted the N-fixing microbial community, reducing the abundance of key bacteria such as Azorhizobium and Bradyrhizobium. Nitrogen fixation pathways (in log10-transformed TPM+1) were markedly suppressed in soils treated with 200 kg ha[-1] macroplastics compared to untreated soils (p < 0.001). Our findings highlight the potential risks of macroplastics posing to N cycling and microbial health in agricultural soils. This study addresses a critical knowledge gap by shifting the focus from micro- to macroplastic impacts on biogeochemical cycling.},
}

*Glycine max/growth & development/drug effects/microbiology
*Nitrogen Fixation/drug effects
*Soil Microbiology
*Microbiota/drug effects
*Soil Pollutants/toxicity
Soil/chemistry
Nitrogen/metabolism
Nitrates/analysis/metabolism
Agriculture
Bradyrhizobium/drug effects
Nitrogen Cycle/drug effects

@article {pmid40489603,
year = {2025},
author = {Cao, J and He, Q and Zhang, M and Zhou, R and Feng, C},
title = {Characteristics and Clinical Significance of Gut Microbiota in Patients with Invasive Pulmonary Aspergillosis.},
journal = {Polish journal of microbiology},
volume = {74},
number = {2},
pages = {131-142},
pmid = {40489603},
issn = {2544-4646},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Invasive Pulmonary Aspergillosis/microbiology/diagnosis ; Male ; Female ; Middle Aged ; Feces/microbiology ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Aged ; Adult ; Metagenomics ; Case-Control Studies ; High-Throughput Nucleotide Sequencing ; Clinical Relevance ; },
abstract = {Gut microbiota acts on the lungs through the gut-lung axis and play an important role in lung diseases. However, there are no reports on the gut microbiota characteristics in patients with invasive pulmonary aspergillosis (IPA). We aimed to analyze changes in gut microbiota in IPA patients, correlate these changes with clinical indicators and disease prognosis, and explore the application value of these characteristic changes in diagnosing IPA. The objective was to provide a theoretical basis for preventing and treating individual immunity. We conducted metagenomic next-generation sequencing of fecal samples from 43 patients with IPA and 31 healthy controls to analyze changes in the gut microbiota of these patients. We also built a random forest model for diagnosing IPA based on the gut microbiota. Compared to healthy controls, IPA patients showed a decrease in gut microbiota diversity and metabolic levels. Changes in the microbiota were characterized by a significant reduction in anti-inflammatory species that produce short-chain fatty acids, such as Faecalibacterium, Blautia, Roseburia, Phocaeicola, and Bacteroides. In contrast, opportunistic pathogens, such as Enterococcus, Corynebacterium, Escherichia, Staphylococcus, Haemophilus, and Finegoldia, were significantly enriched. The classification model based on Clostridium fessum, Blautia wexlerae, Streptococcus pseudopneumoniae, Corynebacterium striatum, and Faecalibacterium prausnitzii showed high value in distinguishing patients with IPA from healthy controls. Patients with IPA exhibit gut microbiota imbalance. The gut microbiota can serve as a biomarker that helps in diagnosing IPA. Our findings support the potential use of gut microbiota as a target for IPA prevention and treatment.},
}

Humans
*Gastrointestinal Microbiome
*Invasive Pulmonary Aspergillosis/microbiology/diagnosis
Male
Female
Middle Aged
Feces/microbiology
*Bacteria/classification/genetics/isolation & purification/metabolism
Aged
Adult
Metagenomics
Case-Control Studies
High-Throughput Nucleotide Sequencing
Clinical Relevance

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

*Composting
*Virulence Factors/genetics
*Air Microbiology
Metagenomics
*Bacteria/genetics
*Drug Resistance, Bacterial/genetics
Microbiota
*Drug Resistance, Microbial/genetics
Humans

@article {pmid40448586,
year = {2025},
author = {Jones, LM and El Aidy, S},
title = {Electroactive ecosystem insights from corrosion microbiomes inform gut microbiome modulation.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
doi = {10.1093/ismejo/wraf112},
pmid = {40448586},
issn = {1751-7370},
support = {ENPPS.IPP.019.004/NWO_/Dutch Research Council/Netherlands ; },
mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; Biofilms/growth & development ; Corrosion ; Oxidation-Reduction ; *Ecosystem ; Bacteria/metabolism ; Electron Transport ; Host Microbial Interactions ; },
abstract = {Electroactive microorganisms influence environmental and host-associated ecosystems through their ability to mediate extracellular electron transfer. This review explores parallels between electroactive microorganisms (EAM)-driven microbiologically influenced corrosion systems and the human gut microbiome. In corrosion, EAMs contribute to biofilm formation, redox cycling, and material degradation through mechanisms such as direct electron transfer and syntrophic interactions. Similarly, gut-associated EAMs regulate redox balance, drive short-chain fatty acid production, and shape host-microbe interactions. Despite differing contexts, both systems share traits like anoxic niches, biofilm formation, and metabolic adaptability. Insights from well-characterized corrosion microbiomes offer valuable frameworks to understand microbial resilience, electron transfer strategies, and interspecies cooperation in the gut. Bridging knowledge between these systems can inform microbiome engineering approaches aimed at promoting gut health, highlighting the need for further functional metagenomics and exploration of archaeal contributions to biofilm stability and redox modulation.},
}

*Gastrointestinal Microbiome/physiology
Humans
Biofilms/growth & development
Corrosion
Oxidation-Reduction
*Ecosystem
Bacteria/metabolism
Electron Transport
Host Microbial Interactions

@article {pmid40318224,
year = {2025},
author = {Maritan, AJ and Clements, CS and Pratte, ZA and Hay, ME and Stewart, FJ},
title = {Sea cucumber grazing linked to enrichment of anaerobic microbial metabolisms in coral reef sediments.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
doi = {10.1093/ismejo/wraf088},
pmid = {40318224},
issn = {1751-7370},
mesh = {Animals ; *Geologic Sediments/microbiology ; RNA, Ribosomal, 16S/genetics ; Anaerobiosis ; *Sea Cucumbers/physiology ; *Coral Reefs ; *Anthozoa/microbiology ; *Microbiota ; Polynesia ; Metagenomics ; Metagenome ; Bacteria/classification/genetics/metabolism ; },
abstract = {Sea cucumbers have been overharvested world-wide, making assessments of their ecological effects challenging, but recent research demonstrated that sea cucumbers increased coral survival via disease suppression and were therefore important for facilitating reef health. The mechanisms underpinning the sea cucumber-coral interaction are not well understood but are likely mediated through sea cucumber grazing of microbes from reef sediments. We explored how sea cucumber grazing alters the sediment microbiome by leveraging a healthy sea cucumber population on a reef in French Polynesia. We used quantitative PCR, 16S rRNA gene sequencing, and shotgun metagenomics to compare the sediment microbiome in cages placed in situ with or without sea cucumbers. We hypothesized that grazing would lower microbial biomass, change sediment microbiome composition, and deplete sediment metagenomes of anaerobic metabolisms, likely due to aeration of the sediments. Sea cucumber grazing resulted in a 75% reduction in 16S rRNA gene abundances and reshaped microbiome composition, causing a significant decrease of cyanobacteria and other phototrophs relative to ungrazed sediments. Grazing also resulted in a depletion of genes associated with cyanotoxin synthesis, suggesting a potential link to coral health. In contrast to expectations, grazed sediment metagenomes were enriched with marker genes of diverse anaerobic or microaerophilic metabolisms, including those encoding high oxygen affinity cytochrome oxidases. This enrichment differs from patterns linked to other bioturbating invertebrates. We hypothesize that grazing enriches anaerobic processes in sediment microbiomes through removal of oxygen-producing autotrophs, fecal deposition of sea cucumber gut-associated anaerobes, or modification of sediment diffusibility. These results suggest that sea cucumber harvesting influences biogeochemical processes in reef sediments, potentially mediating coral survival by altering the sediment microbiome and its production of coral-influencing metabolites.},
}

Animals
*Geologic Sediments/microbiology
RNA, Ribosomal, 16S/genetics
Anaerobiosis
*Sea Cucumbers/physiology
*Coral Reefs
*Anthozoa/microbiology
*Microbiota
Polynesia
Metagenomics
Metagenome
Bacteria/classification/genetics/metabolism

@article {pmid40162572,
year = {2025},
author = {Wu, H and Zhang, H and Dong, T and Li, Z and Guo, X and Chen, H and Yao, Y},
title = {Overcoming Extreme Ammonia Inhibition on Methanogenesis by Artificially Constructing a Synergistically Community with Acidogenic Bacteria and Hydrogenotrophic Archaea.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {12},
number = {23},
pages = {e2502743},
doi = {10.1002/advs.202502743},
pmid = {40162572},
issn = {2198-3844},
support = {2024YFD1700500//National Key R&D Program of China/ ; A279021901//Shaanxi Youth Thousand Talents/ ; 2024CY2-GJHX-74//Shaanxi Key R&D Program of China/ ; 2452021112//Chinese Universities Scientific Fund/ ; JCYJ20220530161408019//Shenzhen Natural Science Foundation/ ; 2023KCXTD038//Guangdong Provincial University Innovation Team Project/ ; 2022-K32//Foundation of State Key Laboratory of High-efficiency Utilization of Coal and Green Chemical Engineering/ ; Z111021902//Northwest A&F University Young Talent Project/ ; },
mesh = {*Ammonia/metabolism ; *Methane/metabolism ; *Archaea/metabolism ; *Bacteria/metabolism ; Hydrogen/metabolism ; Anaerobiosis ; Microbiota ; },
abstract = {High total ammonia nitrogen (TAN) inhibits anaerobic digestion (AD) and cannot be completely eliminated by merely enhancing a stage of AD. This study incorporates TAN-tolerant inoculum into substrates hydrolyzed by Rhizopus mixed agents to simultaneously enhance hydrolysis-acidogenesis-methanogenesis. The results show a 16.46-fold increase in CH4 production under TAN-inhibited (6870.97 mg L-1) conditions, even exceeding the AD without TAN by 21.10%. Model substrates sodium acetate and mixed H2 confirm hydrogenotrophic methanogenesis is the main pathway, with reduced TAN inhibition. Furthermore, a synergistic metabolic microbial community dominated by hydrolytic bacteria JAAYGG01 sp. and DTU014 sp., acidogenic bacteria DTU015 sp., DTU013 sp., and JAAYLO01 sp., and methanogens Methanosarcina mazei and an unclassified species in the Methanoculleus is reconstructed to resist TAN inhibition. Metagenomic combined with metatranscriptomic sequencing identifies that this microbial community carries xynD and bglB to regulate substrate hydrolysis, leading to acetate production through glycolysis, butyrate, and pyruvate metabolism with high acetate kinase activity, thereby CH4 produced primarily via hydrogenotrophic methanogenesis with high coenzyme F420 activity, facilitated by efficient mass transfer processes and quorum sensing regulation. This cleaner strategy obtains higher economic benefit (US$149.02) than conventional AD and can increase 154.64-fold energy production of a 24 000 m3 biogas plant, guided by machine learning.},
}

*Ammonia/metabolism
*Methane/metabolism
*Archaea/metabolism
*Bacteria/metabolism
Hydrogen/metabolism
Anaerobiosis
Microbiota

@article {pmid39270978,
year = {2025},
author = {Fang, Z and Zang, Q and Chen, J and Li, Z and Yang, D and Wu, C and Yang, H and Guo, N},
title = {Whole-body mass spectrometry imaging reveals the systemic metabolic disorder and catecholamines biosynthesis alteration on heart-gut axis in heart failure rat.},
journal = {Journal of advanced research},
volume = {73},
number = {},
pages = {411-426},
doi = {10.1016/j.jare.2024.09.001},
pmid = {39270978},
issn = {2090-1224},
mesh = {Animals ; *Heart Failure/metabolism/diagnostic imaging ; *Catecholamines/biosynthesis/metabolism ; Rats ; Gastrointestinal Microbiome ; Male ; Rats, Sprague-Dawley ; *Myocardium/metabolism ; *Metabolic Diseases/metabolism/diagnostic imaging ; Disease Models, Animal ; Mass Spectrometry/methods ; Dysbiosis/metabolism ; Heart ; Tandem Mass Spectrometry ; Tyrosine 3-Monooxygenase/metabolism ; Norepinephrine ; },
abstract = {INTRODUCTION: Heart failure (HF) is a systemic metabolic disorder disease, across multiorgan investigations advancing knowledge of progression and treatment of HF. Whole-body MSI provides spatiotemporal information of metabolites in multiorgan and is expected to be a potent tool to dig out the complex mechanism of HF.

OBJECTIVES: This study aimed at exploring the systemic metabolic disorder in multiorgan and catecholamines biosynthesis alteration on heart-gut axis after HF.

METHODS: Whole-body MSI was used to characterize metabolic disorder of the whole rat body after HF. An integrated method by MSI, LC-MS/MS and ELISA was utilized to analyze key metabolites and enzymes on heart, small intestine, cecum and colon tissues of rat. Gut microbiota dysbiosis was investigated by 16S rDNA sequencing and metagenomic sequencing. Validation experiments and in vitro experiments were performed to verify the effect of catecholamines biosynthesis alteration on heart-gut axis after HF.

RESULTS: Whole-body MSI exhibited varieties of metabolites alteration in multiple organs. Remarkably, catecholamine biosynthesis was significantly altered in the serum, heart and intestines of rats. Furthermore, catecholamines and tyrosine hydroxylase were obviously upregulated in heart and colon tissue. Turicibacter_sanguinis was relevant to catecholamines of heart and colon. Validation experiments demonstrated excessive norepinephrine induced cardio-intestinal injury, including significantly elevating the levels of BNP, pro-BNP, LPS, DAO, and increased the abundance of Turicibacter_sanguinis. These alterations could be reversed by metoprolol treatment blocking the effect of norepinephrine. Additionally, in vitro studies demonstrated that norepinephrine promoted the growth of Turicibacter_sanguinis and Turicibacter_sanguinis could import and metabolize norepinephrine. Collectively, excessive norepinephrine exerted bidirectional effects on cardio-intestinal function to participate in the progression of HF.

CONCLUSION: Our study provides a new approach to elucidate multiorgan metabolic disorder and proposes new insights into heart-gut axis in HF development.},
}

Animals
*Heart Failure/metabolism/diagnostic imaging
*Catecholamines/biosynthesis/metabolism
Rats
Gastrointestinal Microbiome
Male
Rats, Sprague-Dawley
*Myocardium/metabolism
*Metabolic Diseases/metabolism/diagnostic imaging
Disease Models, Animal
Mass Spectrometry/methods
Dysbiosis/metabolism
Heart
Tandem Mass Spectrometry
Tyrosine 3-Monooxygenase/metabolism
Norepinephrine

@article {pmid39147198,
year = {2025},
author = {Zeng, Y and Guo, M and Wu, Q and Tan, X and Jiang, C and Teng, F and Chen, J and Zhang, F and Ma, X and Li, X and Gu, J and Huang, W and Zhang, C and Yuen-Kwan Law, B and Long, Y and Xu, Y},
title = {Gut microbiota-derived indole-3-propionic acid alleviates diabetic kidney disease through its mitochondrial protective effect via reducing ubiquitination mediated-degradation of SIRT1.},
journal = {Journal of advanced research},
volume = {73},
number = {},
pages = {607-630},
doi = {10.1016/j.jare.2024.08.018},
pmid = {39147198},
issn = {2090-1224},
mesh = {Animals ; *Diabetic Nephropathies/metabolism/drug therapy/pathology ; *Gastrointestinal Microbiome/physiology ; Mice ; *Sirtuin 1/metabolism ; *Mitochondria/metabolism/drug effects ; Humans ; *Indoles/pharmacology/metabolism ; Ubiquitination/drug effects ; Male ; Mice, Inbred C57BL ; Female ; Endothelial Cells/metabolism/drug effects ; *Propionates/metabolism/pharmacology ; },
abstract = {INTRODUCTION: Gut microbes and their metabolites play crucial roles in the pathogenesis of diabetic kidney disease (DKD). However, which one and how specific gut-derived metabolites affect the progression of DKD remain largely unknown.

OBJECTIVES: This study aimed to investigate the potential roles of indole-3-propionic acid (IPA), a microbial metabolite of tryptophan, in DKD.

METHODS: Metagenomic sequencing was performed to analyze the microbiome structure in DKD. Metabolomics screening and validation were conducted to identify characteristic metabolites associated with DKD. The protective effect of IPA on DKD glomerular endothelial cells (GECs) was assessed through in vivo and in vitro experiments. Further validation via western blot, immunoprecipitation, gene knockout, and site-directed mutation elucidated the mechanism of IPA on mitochondrial injury.

RESULTS: Alterations in gut microbial community structure and dysregulated tryptophan metabolism were evident in DKD mice. Serum IPA levels were significantly reduced in DKD patients and correlated with fasting blood glucose, HbA1c, urine albumin-to-creatinine ratio (UACR), and estimated glomerular filtration rate (eGFR). IPA supplementation ameliorated albuminuria, bolstered the integrity of the glomerular filtration barrier, and mitigated mitochondrial impairments in GECs. Mechanistically, IPA hindered SIRT1 phosphorylation-mediated ubiquitin-proteasome degradation, restoring SIRT1's role in promoting PGC-1α deacetylation and nuclear translocation, thereby upregulating genes associated with mitochondrial biosynthesis and antioxidant defense.

CONCLUSION: Our findings underscore the potential of the microbial metabolite IPA to attenuate DKD progression, offering novel insights and potential therapeutic strategies for its management.},
}

Animals
*Diabetic Nephropathies/metabolism/drug therapy/pathology
*Gastrointestinal Microbiome/physiology
Mice
*Sirtuin 1/metabolism
*Mitochondria/metabolism/drug effects
Humans
*Indoles/pharmacology/metabolism
Ubiquitination/drug effects
Male
Mice, Inbred C57BL
Female
Endothelial Cells/metabolism/drug effects
*Propionates/metabolism/pharmacology

@article {pmid28732571,
year = {2017},
author = {Stefanaki, C and Peppa, M and Mastorakos, G and Chrousos, GP},
title = {Examining the gut bacteriome, virome, and mycobiome in glucose metabolism disorders: Are we on the right track?.},
journal = {Metabolism: clinical and experimental},
volume = {73},
number = {},
pages = {52-66},
doi = {10.1016/j.metabol.2017.04.014},
pmid = {28732571},
issn = {1532-8600},
mesh = {Animals ; Gastrointestinal Microbiome/*physiology ; *Glucose Metabolism Disorders ; Humans ; Hyperglycemia ; Microbiota/*physiology ; Mycobiome/*physiology ; },
abstract = {Human gut microbiome is defined as the gene complement of the gut microbial community, measured via laboratory metagenomic techniques. It includes bacteriome, virome and mycobiome, which represent, respectively, the assemblages of bacteria, viruses and fungi, living in the human gut. Gut microbiota function as a living "organ" that interacts with the gastro-intestinal environment, provides nutrients and vitamins to the organism and transduces hormonal messages, essentially influencing the main metabolic pathways, including drug metabolism. A clear association between gut, and glucose metabolism disorders has recently emerged. Medications acting on glucose absorption in the gut, or enhancing gut hormone activity are already extensively employed in the therapy of diabetes. Moreover, the gut is characterized by immune, and autonomous neuronal features, which play a critical role in maintaining glucose metabolism homeostasis. Gut microbes respond to neuroendocrine, and immune biochemical messages, affecting the health, and behavior of the host. There is vast heterogeneity in the studies included in this review, hence a meta-analysis, or a systematic review were not applicable. In this article, we attempt to reveal the interplay between human gut microbiota physiology, and hyperglycemic states, synthesizing, and interpreting findings from human studies.},
}