@article {pmid39900713,
year = {2025},
author = {Zhang, L and Zheng, C and Sun, Y and Chen, X and Wang, Y and Xiang, H and Liang, Y and Wei, F and Zhang, Y},
title = {Diagnostic tests performance in detecting Pneumocystis jirovecii: A systematic review and meta-analysis.},
journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology},
volume = {},
number = {},
pages = {},
pmid = {39900713},
issn = {1435-4373},
support = {BRWEP2024W042180101//Beijing Research Ward Excellence Program, BRWEP/ ; },
abstract = {BACKGROUND AND OBJECTIVE: Pneumocystis jirovecii (Pj) pneumonia (PJP) is a life-threatening opportunistic infection primarily affecting immunocompromised individuals. Detecting Pj is challenging, particularly in distinguishing between Pj colonization (PJC) and infection. We aimed to systematically evaluate the diagnostic accuracy of various tests in differentiating Pj colonization from infection.

METHODS: Systematic reviews and meta-analyses were performed. Searches were conducted in PubMed, Embase, and Web of Science. Original clinical studies reporting sensitivity and specificity data for diagnostic tests such as quantitative polymerase chain reaction (qPCR), nested PCR, (1,3)-Beta-D glucan (BDG), metagenomic next-generation sequencing (mNGS), and digital PCR (ddPCR) to differentiate PJC from PJP were included. Quality assessment was performed using QUADAS-2 tool, and data processing followed Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Diagnostic performance was evaluated using either a random-effects or fixed-effects model.

RESULTS: Twenty-eight studies (2,550 patients, 1,445 with PJP) were included, with moderate methodological quality. The pooled sensitivity of these diagnostic tests was 0.80 (95% CI 0.77-0.82) and specificity was 0.83 (95% CI 0.81-0.85), with a diagnostic odds ratio (DOR) of 23.12. Among the individual tests, BDG (5 studies) showed high pooled sensitivity (0.83, 95% CI 0.77-0.88) but lower specificity (0.78, 95% CI 0.69-0.85). mNGS (3 studies) had the highest performance, with pooled sensitivity and specificity both at 0.87 (95% CI 0.80-0.92 and 95% CI 0.77-0.94, respectively), and the highest DOR of 41.57. qPCR (19 studies) demonstrated adequate pooled sensitivity (0.78, 95% CI 0.76-0.81) and high specificity (0.83, 95% CI 0.81-0.86), with a DOR of 20.44.

CONCLUSION: While BDG has low specificity and mNGS is costly with no standardized interpretation, along with the limited number of relevant studies in BDG and mNGS, this meta-analysis concluded that qPCR remains valuable for distinguishing P. jirovecii infection from colonization. A well-designed randomized clinical trial that standardizes the technical aspects of the qPCR protocol is needed to assess its effectiveness and provide a solid basis for clinical diagnosis.},
}

@article {pmid39900569,
year = {2025},
author = {Priest, T and Oldenburg, E and Popa, O and Dede, B and Metfies, K and von Appen, WJ and Torres-Valdés, S and Bienhold, C and Fuchs, BM and Amann, R and Boetius, A and Wietz, M},
title = {Seasonal recurrence and modular assembly of an Arctic pelagic marine microbiome.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {1326},
pmid = {39900569},
issn = {2041-1723},
mesh = {Arctic Regions ; *Seasons ; *Microbiota/genetics ; *Seawater/microbiology ; *Oceans and Seas ; Metagenomics/methods ; Bacteria/genetics/classification/metabolism ; RNA, Ribosomal, 16S/genetics ; Ecosystem ; DNA Barcoding, Taxonomic ; Metagenome ; Phylogeny ; },
abstract = {Deciphering how microbial communities are shaped by environmental variability is fundamental for understanding the structure and function of ocean ecosystems. While seasonal environmental gradients have been shown to structure the taxonomic dynamics of microbiomes over time, little is known about their impact on functional dynamics and the coupling between taxonomy and function. Here, we demonstrate annually recurrent, seasonal structuring of taxonomic and functional dynamics in a pelagic Arctic Ocean microbiome by combining autonomous samplers and in situ sensors with long-read metagenomics and SSU ribosomal metabarcoding. Specifically, we identified five temporal microbiome modules whose succession within each annual cycle represents a transition across different ecological states. For instance, Cand. Nitrosopumilus, Syndiniales, and the machinery to oxidise ammonia and reduce nitrite are signatures of early polar night, while late summer is characterised by Amylibacter and sulfur compound metabolism. Leveraging metatranscriptomes from Tara Oceans, we also demonstrate the consistency in functional dynamics across the wider Arctic Ocean during similar temporal periods. Furthermore, the structuring of genetic diversity within functions over time indicates that environmental selection pressure acts heterogeneously on microbiomes across seasons. By integrating taxonomic, functional and environmental information, our study provides fundamental insights into how microbiomes are structured under pronounced seasonal changes in understudied, yet rapidly changing polar marine ecosystems.},
}

Arctic Regions
*Seasons
*Microbiota/genetics
*Seawater/microbiology
*Oceans and Seas
Metagenomics/methods
Bacteria/genetics/classification/metabolism
RNA, Ribosomal, 16S/genetics
Ecosystem
DNA Barcoding, Taxonomic
Metagenome
Phylogeny

@article {pmid39900484,
year = {2025},
author = {Van Etten, J and Stephens, TG and Bhattacharya, D},
title = {Genetic Transfer in Action: Uncovering DNA Flow in an Extremophilic Microbial Community.},
journal = {Environmental microbiology},
volume = {27},
number = {2},
pages = {e70048},
doi = {10.1111/1462-2920.70048},
pmid = {39900484},
issn = {1462-2920},
support = {//U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231/ ; 10.46936/10.25585/60000481//Joint Genome Institute/ ; NJ01180//National Institute of Food and Agriculture/ ; 80NSSC19K1542/NASA/NASA/United States ; NASA (80NSSC19K0462)/NASA/NASA/United States ; },
mesh = {*Gene Transfer, Horizontal ; *Bacteria/genetics/classification ; Extremophiles/genetics ; Microbiota/genetics ; DNA, Bacterial/genetics ; Genome, Bacterial ; },
abstract = {Horizontal genetic transfer (HGT) is a significant driver of genomic novelty in all domains of life. HGT has been investigated in many studies however, the focus has been on conspicuous protein-coding DNA transfers that often prove to be adaptive in recipient organisms and are therefore fixed longer-term in lineages. These results comprise a subclass of HGTs and do not represent exhaustive (coding and non-coding) DNA transfer and its impact on ecology. Uncovering exhaustive HGT can provide key insights into the connectivity of genomes in communities and how these transfers may occur. In this study, we use the term frequency-inverse document frequency (TF-IDF) technique, that has been used successfully to mine DNA transfers within real and simulated high-quality prokaryote genomes, to search for exhaustive HGTs within an extremophilic microbial community. We establish a pipeline for validating transfers identified using this approach. We find that most DNA transfers are within-domain and involve non-coding DNA. A relatively high proportion of the predicted protein-coding HGTs appear to encode transposase activity, restriction-modification system components, and biofilm formation functions. Our study demonstrates the utility of the TF-IDF approach for HGT detection and provides insights into the mechanisms of recent DNA transfer.},
}

*Gene Transfer, Horizontal
*Bacteria/genetics/classification
Extremophiles/genetics
Microbiota/genetics
DNA, Bacterial/genetics
Genome, Bacterial

@article {pmid39900123,
year = {2025},
author = {Soto-Rodriguez, SA and Quiroz-Guzman, E and Gomez-Gil, B and Lozano-Olvera, R and Aguilar-Rendon, KG and Serrano-Hernández, JM and González-Gómez, JP and Chaidez, C},
title = {Phage cocktail against Vibrio parahaemolyticus causing acute hepatopancreatic necrosis disease (AHPND) in Penaeus vannamei: genomic, biological, and pathological characterization.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {107354},
doi = {10.1016/j.micpath.2025.107354},
pmid = {39900123},
issn = {1096-1208},
abstract = {Phages vB_Pd_PDCC-1, vB_Vc_SrVc9, and vB_Vp_PvVp11 were found to be lytic against Vibrio parahaemolyticus acute hepatopancreatic necrosis disease (AHPND) and other pathogenic vibrios. The complete genomic and biological characterization of phage vB_Vp_PvVp1 was conducted, and a cocktail of these three phages was applied to juvenile Penaeus vannamei infected with V. parahaemolyticus AHPND. Water samples collected during the challenges were analyzed using metagenomics. At the end of the experimental infection, the phage cocktail did not improve shrimp survival compared to the positive control group (infected only with bacteria). This suggests the emergence of phage-resistant V. parahaemolyticus strains. However, a significantly lower mortality rate was observed 12 hours post-infection, along with a shortening of the disease course in the phage therapy treatment. A phage-resistant strain of V. parahaemolyticus AHPND was in vitro isolated. For the first time, we report the identification of nucleotide variants in the glycosyltransferase gene of this mutant strain through genome sequencing. Although the phage cocktail was ineffective in controlling AHPND, some protective benefits of phage therapy were noted in P. vannamei during the acute phase-the most critical stage-compared to the positive control. Phage therapy decreased alpha diversity and altered the microbiota composition during the challenge, increasing V. parahaemolyticus. The Vibrio AHPND pathogen produces a potent PirAB toxin, making this disease difficult to manage. Further studies are needed to explore synergistic approaches as effective therapeutic tools.},
}

@article {pmid39899931,
year = {2025},
author = {Wang, Y and Chen, C and Zhou, B and Zhang, Y and Qin, J and Huang, J and Li, X},
title = {Presence of high-risk ARGs with greater diversity and abundance in the rare resistome in wastewater across China.},
journal = {Journal of hazardous materials},
volume = {488},
number = {},
pages = {137435},
doi = {10.1016/j.jhazmat.2025.137435},
pmid = {39899931},
issn = {1873-3336},
abstract = {Antibiotic resistance genes (ARGs) are widely recognized as hazardous materials that pose risks to public health. The core resistome, with its low ARG diversity yet accounting for the majority of the total ARG abundance, dominating the profile of antibiotic resistance. In this study, nationwide wastewater surveillance in China using metagenomic sequencing also identified a core resistome of 117 ARGs that accounted for 69.6 % of the total abundance. The emphasis of the work was to examine the rare resistome that included 1503 ARGs outside the core resistome. The abundances of clinically relevant ARG types (e.g., β-lactams and quinolones) were significantly higher in the rare resistome compared to the core resistome. Human pathogen-related ARGs were much greater in subtype number (96 vs. 34) and significantly higher in abundance (67.0 % vs. 33.0 %) in the rare relative to the core resistome, indicating that the rare resistome was the major contributor to the human pathogen resistome. The majority of ARG types accounting for the highest proportions of the rare resistome were plasmid-originated (65.5 %-100 %). In addition, human pathogen-related ARGs also had a significantly higher proportion of plasmid sources than non-pathogen ARGs, further highlighting their importance in wastewater-based surveillance.},
}

@article {pmid39900940,
year = {2025},
author = {Prabhaharan, D and Go, YW and Kim, H and Kang, S and Sang, BI},
title = {Representative Metagenomes of Mesophilic Biogas Reactor Across South Korea.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {198},
pmid = {39900940},
issn = {2052-4463},
support = {MOE; 2022003480001//MOE | Korea Environmental Industry and Technology Institute (KEITI)/ ; MOE; 2022003480001//MOE | Korea Environmental Industry and Technology Institute (KEITI)/ ; MOE; 2022003480001//MOE | Korea Environmental Industry and Technology Institute (KEITI)/ ; MOE; 2022003480001//MOE | Korea Environmental Industry and Technology Institute (KEITI)/ ; },
mesh = {Republic of Korea ; *Biofuels ; *Metagenome ; *Bioreactors ; Microbiota ; Anaerobiosis ; },
abstract = {Biogas production through the anaerobic digestion (AD) of organic waste plays a crucial role in promoting sustainability and closing the carbon cycle. Over the past decade, this has driven global research on biogas-producing microbiomes, leading to significant advances in our understanding of microbial diversity and metabolic pathways within AD plants. However, substantial knowledge gaps persist, particularly in understanding the specific microbial communities involved in biogas production in countries such as South Korea. The present dataset addresses one of these gaps by providing comprehensive information on the metagenomes of five full-scale mesophilic biogas reactors in South Korea. From 110 GB of raw DNA sequences, 401 metagenome-assembled genomes (MAGs) were created, which include 42,301 annotated genes. Of these, 187 MAGs (46.7%) were classified as high-quality based on Minimum Information about Metagenome-Assembled Genome (MIMAG) standards. The data presented here contribute to a broader understanding of biogas-specific microbial communities and offers a significant resource for future studies and advancements in sustainable biogas production.},
}

Republic of Korea
*Biofuels
*Metagenome
*Bioreactors
Microbiota
Anaerobiosis

@article {pmid39899597,
year = {2024},
author = {Tibiri, EB and Boua, PR and Soulama, I and Dubreuil-Tranchant, C and Tando, N and Tollenaere, C and Brugidou, C and Nanema, RK and Tiendrebeogo, F},
title = {Challenges and opportunities of developing bioinformatics platforms in Africa: the case of BurkinaBioinfo at Joseph Ki-Zerbo University, Burkina Faso.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {1},
pages = {},
doi = {10.1093/bib/bbaf040},
pmid = {39899597},
issn = {1477-4054},
support = {2012PASS019//Green Revolution in Africa/ ; },
mesh = {Burkina Faso ; *Computational Biology/methods/education ; Universities ; Humans ; },
abstract = {Bioinformatics, an interdisciplinary field combining biology and computer science, enables meaningful information to be extracted from complex biological data. The exponential growth of biological data, driven by high-throughput omics technologies and advanced sequencing methods, requires robust computational resources. Worldwide, bioinformatics skills and computational clusters are essential for managing and analysing large-scale biological datasets across health, agriculture, and environmental science, which are crucial for the African continent. In Burkina Faso, the establishment of bioinformatics infrastructure has been a gradual process. Initial training initiatives between 2015-2016, including bioinformatics courses and the establishment of the BurkinaBioinfo (BBi) platform, marked significant progress. Over 250 scientists have been trained at diverse levels in bioinformatics, 105 user accounts have been created for high-performance computing access. Operational since 2019, this platform has significantly facilitated training programs for scientists and system administrators in west Africa, covering data production, introductory bioinformatics, phylogenetic analysis, and metagenomics. Financial and technical support from various sources has facilitated the rapid development of the platform to meet the growing need for bioinformatics analysis, particularly in conjunction with local 'wet labs'. Establishing a bioinformatics cluster in Burkina Faso involved identifying the needs of researchers, selecting appropriate hardware and installing the necessary bioinformatics tools. At present, the main challenges for the BBi platform include ongoing staff training in bioinformatics skills and high-level IT infrastructure management in the face of growing infrastructure demands. Despite these challenges, the establishment of a bioinformatics platform in Burkina Faso offers significant opportunities for scientific research and economic development in the country.},
}

Burkina Faso
*Computational Biology/methods/education
Universities
Humans

@article {pmid39898908,
year = {2025},
author = {Navia, JC and Alfonso, A and Miller, D and Maestre-Mesa, J and Durkee, H and Sepulveda-Beltran, PA and Echeverri-Tribin, F and Merikansky, S and Martinez, JD and Flynn, HW and Alfonso, EC and Parel, JM and Amescua, G},
title = {Prevalence of HSV Genomic Signatures Among Acanthamoeba Hosts and Contaminated Lens Cases: A Molecular and Clinical Study.},
journal = {Investigative ophthalmology & visual science},
volume = {66},
number = {2},
pages = {4},
doi = {10.1167/iovs.66.2.4},
pmid = {39898908},
issn = {1552-5783},
mesh = {Humans ; Male ; *Acanthamoeba/genetics/isolation & purification ; Female ; Adult ; *Acanthamoeba Keratitis/epidemiology/diagnosis/parasitology ; Prevalence ; Middle Aged ; DNA, Viral/genetics/analysis ; Young Adult ; Polymerase Chain Reaction ; Genome, Viral/genetics ; Contact Lenses/parasitology ; Keratitis, Herpetic/epidemiology/virology/diagnosis ; Adolescent ; Herpesvirus 1, Human/genetics/isolation & purification ; Visual Acuity ; Metagenomics ; Simplexvirus/genetics ; Aged ; },
abstract = {PURPOSE: To document the presence of herpes simplex virus (HSV) genomic signatures among Acanthamoeba hosts recovered from patients with Acanthamoeba keratitis (AK) and in contaminated lens cases.

METHODS: We used a combination of PCR sequencing and shotgun metagenomics to detect and confirm the presence of HSV genomic signatures in Acanthamoeba hosts and lens cases. Clinical outcomes were correlated with the prevalence of host HSV signatures.

RESULTS: HSV genomic signatures were detected in 26% (n = 6) of Acanthamoeba hosts recovered from patients with culture confirmed AK. HSV-1 and HSV-2 or both were identified in 33%, 50%, and 17% of isolates, respectively. Fifty-two percent of patients (12/23) were misdiagnosed initially as presenting with HSV keratitis. Patients with HSV-positive Acanthamoeba isolates had a mean best-corrected visual acuity of 1.43 LogMAR at diagnosis and 0.53 LogMAR at follow-up, compared with 1.85 and 0.92 LogMAR, respectively, in HSV-negative cases. Contact lens use was identified as a risk factor in 83% of 18 patients. We detected 46,597 viral signatures in 5 of 14 contaminated lens cases (35.7%). Distribution included 33% bacteriophages, 8.2% giant viruses, 4.1% nonhuman Herpesviridae, and 0.39% human Herpesviridae. Among the 184 human Herpesviridae genomic signatures, HSV types 1 or 2 or both were documented in 5.7%, VZV in 39.7%, HHV7 in 38.6%, HHV6 in 15.0%, and Epstein-Barr virus in 0.5%.

CONCLUSIONS: This study is the first to identify HSV-positive genomic signatures in clinical AK isolates and/or contact lens cases. Taken together, the high prevalence of HSV genomic signatures in both amebic hosts and lens cases, might signal an unrecognized Acanthamoeba-HSV association and the need for reassessing current management.},
}

Humans
Male
*Acanthamoeba/genetics/isolation & purification
Female
Adult
*Acanthamoeba Keratitis/epidemiology/diagnosis/parasitology
Prevalence
Middle Aged
DNA, Viral/genetics/analysis
Young Adult
Polymerase Chain Reaction
Genome, Viral/genetics
Contact Lenses/parasitology
Keratitis, Herpetic/epidemiology/virology/diagnosis
Adolescent
Herpesvirus 1, Human/genetics/isolation & purification
Visual Acuity
Metagenomics
Simplexvirus/genetics
Aged

@article {pmid39898315,
year = {2025},
author = {Walker, JR and Bente, DA and Burch, MT and Cerqueira, FM and Ren, P and Labonté, JM},
title = {Molecular assessment of oyster microbiomes and viromes reveals their potential as pathogen and ecological sentinels.},
journal = {One health (Amsterdam, Netherlands)},
volume = {20},
number = {},
pages = {100973},
pmid = {39898315},
issn = {2352-7714},
abstract = {Oyster aquaculture world-wide is a booming industry that can provide many benefits to coastal habitats, including economic, ecosystem-level, and cultural benefits. Oysters present several risks for human consumption, including transmission of parasites, and bacterial and viral pathogens. Oyster microbiomes are well-defined, but their connection to the incidence of pathogens, humans or others, is unclear. Furthermore, viruses associated with oysters are largely unknown, and their connection to humans, animals, and ecosystem health has not been explored. Here, we employed a One Health framework and modern molecular techniques, including 16S rRNA amplicon and metagenomic sequencing, to identify links between changes in the microbial and viral communities associated with oysters and the incidence of pathogens detected in oyster tissues and their surrounding environments. In addition, we adapted the BioFire® FilmArray®, commonly used in hospitals, to determine the presence of human pathogens within the sampled oysters. We detected known human pathogens in 50 % of the oysters tested. Within the genomic datasets, we noted that pathogens of humans, animals, and plants in oysters were shared with the nearby water and sediments, suggesting a sink-source dynamic between the oysters and their surroundings. 16S rRNA gene analysis revealed that while oysters share common microbial constituents with their surrounding environments, they enrich for certain bacteria such as Mycoplasmatales, Fusobacteriales, and Spirochaetales. On the contrary, we found that oyster viromes harbored the same viruses in near equal relative abundances as their surrounding environments. Our results show how oysters could be used not only to determine the risk of human pathogens within coastal estuaries but also how oyster viruses could be used as ecosystem-level sentinels.},
}

@article {pmid39897886,
year = {2025},
author = {Qayyum, H and Talib, MS and Ali, A and Kayani, MUR},
title = {Evaluating the potential of assembler-binner combinations in recovering low-abundance and strain-resolved genomes from human metagenomes.},
journal = {Heliyon},
volume = {11},
number = {2},
pages = {e41938},
pmid = {39897886},
issn = {2405-8440},
abstract = {Human-associated microbial communities are a complex mixture of bacterial species and diverse strains prevalent at varying abundances. Due to the inherent limitations of metagenomic assemblers and genome binning tools in recovering low-abundance species (<1 %) and strains, we lack comprehensive insight into these communities. Although many bioinformatics approaches are available for recovering metagenome-assembled genomes, their effectiveness in recovering low-abundance species and strains is often questioned. Moreover, each tool has its trade-offs, making selecting the right tools challenging. In this study, we investigated the combinatory effect of various assemblers and binning tools on the recovery of low-abundance species and strain-resolved genomes from real and simulated human metagenomes. We evaluated the performance of nine combinations of metagenome assemblers and genome binning tools for their potential to recover genomes of useable quality. Our results revealed that the metaSPAdes-MetaBAT2 combination is highly effective in recovering low-abundance species, while MEGAHIT-MetaBAT2 excels in recovering strain-resolved genomes. These findings highlight the significant variation in the performance of different combinations, even when aiming for the same objective. This suggests the profound impact of selecting the right assembler-binner combination for metagenome analyses. We believe this study will be a cornerstone for the scientific community, guiding the choice of tools by highlighting their complementary effects. Furthermore, it underscores the potential of existing tools to address the current challenges in the field improving the recovery of information from metagenomes.},
}

@article {pmid39897789,
year = {2025},
author = {Schmidt, JE and Lewis, CA and Firl, AJ and Umaharan, P},
title = {Microbial bioindicators associated with cadmium uptake in sixteen genotypes of Theobroma cacao.},
journal = {Heliyon},
volume = {11},
number = {2},
pages = {e41890},
pmid = {39897789},
issn = {2405-8440},
abstract = {Recent regulatory limits on concentrations of cadmium (Cd), an element of concern for human health, have made Cd reduction a key issue in the global chocolate industry. Research into Cd minimization has investigated soil management, cacao genetic variation, and postharvest processing, but has overlooked the cacao-associated microbiome despite promising evidence in other crops that root-associated microorganisms could help reduce Cd uptake. A novel approach combining both amplicon and metagenomic sequencing identified microbial bioindicators associated with leaf and stem Cd accumulation in sixteen field-grown genotypes of Theobroma cacao. Sequencing highlighted over 200 amplicon sequence variants (ASVs) whose relative abundance was related to cacao leaf and stem Cd content or concentration. The two highest-accumulating genotypes, PA 32 and TRD 94, showed enrichment of four ASVs belonging to the genus Haliangium, the family Gemmataceae, and the order Polyporales. ASVs whose relative abundance was most negatively associated with plant Cd were identified as Paenibacillus sp. (β = -2.21), Candidatus Koribacter (β = -2.17), and Candidatus Solibacter (β = -2.03) for prokaryotes, and Eurotiomycetes (β = -4.58) and two unidentified ASVs (β = -4.32, β = -3.43) for fungi. Only two ASVs were associated with both leaf and stem Cd, both belonging to the Ktedonobacterales. Of 5543 C d-associated gene families, 478 could be assigned to GO terms, including 68 genes related to binding and transport of divalent heavy metals. Screening for Cd-related bioindicators prior to planting or developing microbial bioamendments could complement existing strategies to minimize the presence of Cd in the global cacao supply.},
}

@article {pmid39897560,
year = {2025},
author = {Zhang, P and Guo, R and Ma, S and Jiang, H and Yan, Q and Li, S and Wang, K and Deng, J and Zhang, Y and Zhang, Y and Wang, G and Chen, L and Li, L and Guo, X and Zhao, G and Yang, L and Wang, Y and Kang, J and Sha, S and Fan, S and Cheng, L and Meng, J and Yu, H and Chen, F and He, D and Wang, J and Liu, S and Shi, H},
title = {A metagenome-wide study of the gut virome in chronic kidney disease.},
journal = {Theranostics},
volume = {15},
number = {5},
pages = {1642-1661},
pmid = {39897560},
issn = {1838-7640},
mesh = {Humans ; *Renal Insufficiency, Chronic/virology ; *Virome/genetics ; *Gastrointestinal Microbiome/genetics ; *Metagenome/genetics ; *Feces/virology/microbiology ; Middle Aged ; Male ; Female ; Aged ; Dysbiosis/virology/microbiology ; Adult ; Viruses/genetics/classification/isolation & purification ; Bacteria/genetics/classification/isolation & purification ; },
abstract = {Rationale: Chronic kidney disease (CKD) is a progressively debilitating condition leading to kidney dysfunction and severe complications. While dysbiosis of the gut bacteriome has been linked to CKD, the alteration in the gut viral community and its role in CKD remain poorly understood. Methods: Here, we characterize the gut virome in CKD using metagenome-wide analyses of faecal samples from 425 patients and 290 healthy individuals. Results: CKD is associated with a remarkable shift in the gut viral profile that occurs regardless of host properties, disease stage, and underlying diseases. We identify 4,649 differentially abundant viral operational taxonomic units (vOTUs) and reveal that some CKD-enriched viruses are closely related to gut bacterial taxa such as Bacteroides, [Ruminococcus], Erysipelatoclostridium, and Enterocloster spp. In contrast, CKD-depleted viruses include more crAss-like viruses and often target Faecalibacterium, Ruminococcus, and Prevotella species. Functional annotation of the vOTUs reveals numerous viral functional signatures associated with CKD, notably a marked reduction in nicotinamide adenine dinucleotide (NAD[+]) synthesis capacity within the CKD-associated virome. Furthermore, most CKD viral signatures are reproducible in the gut viromes of diabetic kidney disease and several other common diseases, highlighting the considerable universality of disease-associated viromes. Conclusions: This research provides comprehensive resources and novel insights into the CKD-associated gut virome, offering valuable guidance for future mechanistic and therapeutic investigations.},
}

Humans
*Renal Insufficiency, Chronic/virology
*Virome/genetics
*Gastrointestinal Microbiome/genetics
*Metagenome/genetics
*Feces/virology/microbiology
Middle Aged
Male
Female
Aged
Dysbiosis/virology/microbiology
Adult
Viruses/genetics/classification/isolation & purification
Bacteria/genetics/classification/isolation & purification

@article {pmid39897495,
year = {2025},
author = {Solymosi, N and Tóth, AG and Nagy, SÁ and Csabai, I and Feczkó, C and Reibling, T and Németh, T},
title = {Clinical considerations on antimicrobial resistance potential of complex microbiological samples.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e18802},
pmid = {39897495},
issn = {2167-8359},
mesh = {*Escherichia coli/drug effects/genetics ; *Anti-Bacterial Agents/pharmacology ; Humans ; *Drug Resistance, Bacterial/genetics ; *Microbial Sensitivity Tests ; Genotype ; Metagenomics/methods ; Phenotype ; Genes, Bacterial/genetics ; },
abstract = {Antimicrobial resistance (AMR) is one of our greatest public health challenges. Targeted use of antibiotics (ABs) can reduce the occurrence and spread of AMR and boost the effectiveness of treatment. This requires knowledge of the AB susceptibility of the pathogens involved in the disease. Therapeutic recommendations based on classical AB susceptibility testing (AST) are based on the analysis of only a fraction of the bacteria present in the disease process. Next and third generation sequencing technologies allow the identification of antimicrobial resistance genes (ARGs) present in a bacterial community. Using this metagenomic approach, we can map the antimicrobial resistance potential (AMRP) of a complex, multi-bacterial microbial sample. To understand the interpretiveness of AMRP, the concordance between phenotypic AMR properties and ARGs was investigated by analyzing data from 574 Escherichia coli strains of five different studies. The overall results show that for 44% of the studied ABs, phenotypically resistant strains are genotypically associated with a 90% probability of resistance, while for 92% of the ABs, the phenotypically susceptible strains are genotypically susceptible with a 90% probability. ARG detection showed a phenotypic prediction with at least 90% confidence in 67% of ABs. The probability of detecting a phenotypically susceptible strain as resistant based on genotype is below 5% for 92% of ABs. While the probability of detecting a phenotypically resistant strain as susceptible based on genotype is below 5% for 44% of ABs. We can assume that these strain-by-strain concordance results are also true for bacteria in complex microbial samples, and conclude that AMRP obtained from metagenomic ARG analysis can help choose efficient ABs. This is illustrated using AMRP by a canine external otitis sample.},
}

*Escherichia coli/drug effects/genetics
*Anti-Bacterial Agents/pharmacology
Humans
*Drug Resistance, Bacterial/genetics
*Microbial Sensitivity Tests
Genotype
Metagenomics/methods
Phenotype
Genes, Bacterial/genetics

@article {pmid39896983,
year = {2025},
author = {Sayyad, LE and Smith, KL and Sadigh, KS and Cossaboom, CM and Choi, MJ and Whitmer, S and Cannon, D and Krapiunaya, I and Morales-Betoulle, M and Annambhotla, P and Basavaraju, SV and Ruberto, I and Kretschmer, M and Gutierrez, N and Zabel, K and Austin, C and Sandoval, E and Servellita, V and Foresythe, A and Sumimoto, N and Aqel, BA and Khamash, HA and Jadlowiec, CC and Grys, TE and Jaramillo, A and Grill, MF and Montgomery, JM and Shoemaker, T and Klena, JD and Chiu, CY and Vikram, HR},
title = {Severe Non-Donor-Derived Lymphocytic Choriomeningitis Virus Infection in 2 Solid Organ Transplant Recipients.},
journal = {Open forum infectious diseases},
volume = {12},
number = {2},
pages = {ofaf002},
pmid = {39896983},
issn = {2328-8957},
abstract = {BACKGROUND: Lymphocytic choriomeningitis virus (LCMV) infection in immunocompromised hosts can result in disseminated disease, meningoencephalitis, and death. Published cases in transplant recipients have been traced to transmission from infected donors. We report 2 cases of serious, non-donor-derived LCMV infection in solid organ transplant recipients.

METHODS: Initial identification of LCMV infection was done by using metagenomic next-generation sequencing (mNGS). Subsequent evaluations and confirmatory testing involved molecular diagnostics, serology, and phylogenetic analysis. A detailed epidemiologic investigation was conducted.

RESULTS: LCMV was detected by mNGS in 2 solid organ transplant recipients from distinct donors. A heart transplant recipient (from donor 1) died of progressive, disseminated LCMV infection, while a kidney transplant recipient (from donor 2) with LCMV meningoencephalitis survived. A multistate laboratory and epidemiologic investigation of both donors and all their organ recipients was initiated. Postmortem samples were obtained from both donors, and pretransplant and/or posttransplant samples were obtained from 5 of the 6 organ recipients. mNGS, serologic, and real-time reverse-transcription polymerase chain reaction testing confirmed LCMV infection in both solid organ transplant recipients. Epidemiologic investigation revealed significant pretransplant rodent exposures for both LCMV-infected recipients. Laboratory studies for the other organ recipients from both donors were negative for LCMV infection.

CONCLUSIONS: Our investigations suggest that LCMV infection in 2 solid organ transplant recipients originated from rodent exposure preceding transplantation and were not donor derived. Although uncommon, healthcare providers should be aware of LCMV-associated serious and life-threatening illness in immunocompromised hosts. Diagnostic modalities are limited to reference laboratories.},
}

@article {pmid39896720,
year = {2024},
author = {Coltro, EP and Cafferati Beltrame, L and da Cunha, CR and Zamparette, CP and Feltrin, C and Benetti Filho, V and Vanny, PA and Beduschi Filho, S and Klein, TCR and Scheffer, MC and Palmeiro, JK and Wagner, G and Sincero, TCM and Zárate-Bladés, CR},
title = {Evaluation of the resistome and gut microbiome composition of hospitalized patients in a health unit of southern Brazil coming from a high animal husbandry production region.},
journal = {Frontiers in antibiotics},
volume = {3},
number = {},
pages = {1489356},
pmid = {39896720},
issn = {2813-2467},
abstract = {INTRODUCTION: Antimicrobial resistance (AMR) poses a significant threat to global public health. The One Health approach, which integrates human, animal, and environmental health, highlights the roles of agricultural and hospital settings in the propagation of AMR. This study aimed to analyze the resistome and gut microbiome composition of individuals from a high-intensity animal husbandry area in the western region of Santa Catarina, Southern Brazil, who were subsequently admitted to the University Hospital in the city of Florianopolis, located in the eastern part of the same state.

METHODS: Rectal swab samples were collected upon admission and discharge. Metagenomic sequencing and resistome analysis were employed to identify antimicrobial resistance genes (ARGs) and their associated bacterial taxa. Additionally, the impact of the hospital environment on the resistome and microbiome profiles of these patients was assessed.

RESULTS: A total of 247 genetic elements related to AMR were identified, with 66.4% of these elements present in both admission and discharge samples. Aminoglycoside resistance genes were the most prevalent, followed by resistance genes for tetracyclines and lincosamides. Notably, unique resistance genes, including dfrF and mutations in gyrB, were identified at discharge. ARGs were associated with 55 bacterial species, with Lactobacillus fermentum, harboring the ermB gene. (MLSB), detected in both admission and discharge samples. The most prevalent bacterial families included Mycobacteriaceae, Enterobacteriaceae, and Bacteroidaceae. Among these, Mycobacteriaceae was the most abundant, with ARGs primarily associated with mutations in the 16S rRNA gene, RNA polymerase subunits, and gyrases.

DISCUSSION: The study revealed a high prevalence of genes related to aminoglycoside and tetracycline resistance, with a notable increase in certain resistance determinants at discharge, likely influenced by extended antimicrobial use. The presence of mcr genes, associated with colistin resistance, in both admission and discharge samples from a single patient highlights a concerning trend in AMR, particularly in relation to animal husbandry. These findings underscore the substantial impact of antimicrobial use on resistance development and the complex dynamics of the resistome in hospital settings. They also emphasize the influence of local factors, such as intensive animal production, on resistance patterns and advocate for ongoing surveillance and policy development to manage multidrug-resistant bacteria eVectively.},
}

@article {pmid39896099,
year = {2025},
author = {Iwami, N and Komiya, S and Asada, Y and Tatsumi, K and Habara, T and Kuramoto, T and Seki, M and Yoshida, H and Takeuchi, K and Shiotani, M and Mukaida, T and Odawara, Y and Mio, Y and Kamiya, H},
title = {"Shortening time to pregnancy in infertile women by personalizing treatment of microbial imbalance through Emma & Alice: A multicenter prospective study".},
journal = {Reproductive medicine and biology},
volume = {24},
number = {1},
pages = {e12634},
pmid = {39896099},
issn = {1445-5781},
abstract = {PURPOSE: To evaluate the impact of Endometrial Microbiome Metagenomic Analysis and Analysis of Infectious Chronic Endometritis (EMMA & ALICE) on pregnancy outcomes following recommended treatments in women with recurrent implantation failure (RIF) or recurrent pregnancy loss (RPL).

METHODS: This prospective, multicenter cohort study included 527 women under 42 years old with RIF or RPL across 14 IVF centers in Japan. Endometrial samples were analyzed using EMMA & ALICE, and patients received antibiotics, probiotics, or no treatment based on test results. Pregnancy outcomes were assessed using Kaplan-Meier survival analysis and multivariate generalized linear models.

RESULTS: Amongst participants, 43.4% had a normal Lactobacillus-dominated microbiota, 20.9% had dysbiosis, and 35.7% had mild dysbiosis or ultralow biomass. Kaplan-Meier analysis revealed significantly higher ongoing pregnancy rates in the dysbiosis group treated with antibiotics and probiotics compared to other groups (p = 0.031). Post-treatment, ongoing pregnancy rates in the dysbiosis and mild dysbiosis groups were comparable to the normal group.

CONCLUSIONS: EMMA & ALICE-guided antimicrobial and probiotic treatments improved pregnancy outcomes, enabling the dysbiosis group to achieve pregnancy earlier than the normal group. Addressing uterine dysbiosis may reduce the time to pregnancy in patients with RIF and RPL.

TRIAL REGISTRATION: University Hospital Medical Information Network (UMIN), UMIN000036917.},
}

@article {pmid39895875,
year = {2025},
author = {Esparteiro, D and Fouquet, G and Courtois, A and Naassila, M and Nguyen-Khac, E and Marcq, I},
title = {Shotgun Metagenomics Reveals Bacteroides stercoris as a Fecal Biomarker Depleted in Late-Stage Hepatocellular Carcinoma.},
journal = {Gastro hep advances},
volume = {4},
number = {1},
pages = {100539},
pmid = {39895875},
issn = {2772-5723},
}

@article {pmid39895797,
year = {2025},
author = {Gao, Y and Zheng, H and Ye, M and Zhou, G and Chen, J and Qiang, X and Bai, J and Lu, X and Tang, Q},
title = {Characteristics and function of the gut microbiota in patients with rectal neuroendocrine tumors.},
journal = {Journal of Cancer},
volume = {16},
number = {4},
pages = {1040-1050},
pmid = {39895797},
issn = {1837-9664},
abstract = {The gut microbiota plays a significant role in the initiation and progression of tumors, but its role in rectal neuroendocrine tumors (rNETs) remains unclear. Fecal samples were collected from 19 healthy individuals and 21 rNET patients,with the rNET cohort further divided into metastatic (rNETs-M) and non-metastatic (rNETs-nM) groups. Using metagenomic high-throughput sequencing, we analyzed the diversity, species composition, and functional characteristics of the gut microbiota. We applied a random forest model to identify potential microbial biomarkers for predicting rNET and specifically distinguishing rNETs-M cases. Alpha diversity analysis revealed that species diversity was lower in the rNETs group than in the control group. In contrast, the rNETs-M group exhibited higher species diversity than the rNETs-nM group. Beta diversity analysis demonstrated significant differences in community structure between the rNETs and control groups between the rNET-M and rNETs-nM groups. Notably, in the rNETs group, the abundance of potential pathogens such as Escherichia coli and Shigella was elevated.Furthermore, the rNETs-M group exhibited an increased abundance of potential pathogens such as Alistipes. KEGG enrichment analysis indicated that these distinct microbiota play a significant role in environmental information processing, genetic information processing, and metabolic pathways. Random forest analysis and ROC curve results identified Lachnospira pectinoschiza (AUC=0.885), Parasutterella muris (AUC=0.862), Sodaliphilus pleomorphus(AUC=0.956), Methylobacterium iners (AUC=0.971) as biomarkers with significant discriminatory value.},
}

@article {pmid39895693,
year = {2025},
author = {Zhou, CY and Dai, K and Lin, YP and Huang, XC and Hu, YL and Chen, XX and Yang, XF and Sun, QY and Zhang, Y and van Loosdrecht, MCM and Zeng, RJ and Zhang, F},
title = {Elucidating the complex hydrolysis and conversion network of xanthan-like extracellular heteropolysaccharides in waste activated sludge fermentation.},
journal = {Water research X},
volume = {27},
number = {},
pages = {100303},
pmid = {39895693},
issn = {2589-9147},
abstract = {The hydrolysis of structural extracellular polymeric substances (St-EPS) is considered a major limiting step in the anaerobic fermentation of waste activated sludge (WAS). However, the degradation of heteropolysaccharides, characterized by complex monomers of uronic acids and neutral saccharides in St-EPS, has rarely been reported. In this study, microbial-produced xanthan-like heteropolysaccharides, characterized by a blue filamentary film, were identified. The xanthan-producing bacteria comprised ∼7.2% of total genera present in WAS. An xanthan-degrading consortium (XDC) was enriched in an anaerobic batch reactor. This consortium could degrade Xanthan for over 90% and disrupt the gel structure of xanthan while promoting methane production from WAS by 29%. The xanthan degradation network consisting of extracellular enzymes and bacteria was elucidated by combining high-throughput sequencing, metagenomic, and metaproteomic analyses. Five enzymes were identified as responsible for hydrolyzing xanthan to monomers, including xanthan lyase, β-d-glucosidase, β-d-glucanase, α-d-mannosidase, and unsaturated glucuronyl hydrolase. Seven genera, including Paenibacillus (0.2%) and Clostridium (3.1%), were identified as key bacteria excreting one to five of the aforementioned enzymes. This study thus provides insights into the complex conversions in anaerobic digestion of WAS and gives a foundation for future optimization of this process.},
}

@article {pmid39895114,
year = {2025},
author = {Di Simone, SK and Forster, SC},
title = {Sputum Metagenomics Reveals Multidrug-Resistant Pseudomonas-Dominant Communities in Severe Asthma.},
journal = {Respirology (Carlton, Vic.)},
volume = {},
number = {},
pages = {},
doi = {10.1111/resp.14890},
pmid = {39895114},
issn = {1440-1843},
support = {//CSL Centenary Fellowship/ ; },
}

@article {pmid39895074,
year = {2025},
author = {Lee, KA and Ul-Haq, A and Seo, H and Jo, S and Kim, S and Song, HY and Kim, HS},
title = {Characteristics of skin microbiome associated with disease severity in systemic sclerosis.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {63},
number = {1},
pages = {e.2409018},
doi = {10.71150/jm.2409018},
pmid = {39895074},
issn = {1976-3794},
support = {//Korea Health Industry Development Institute/ ; HI21C1888//Ministry of Health and Welfare/ ; //National Research Foundation of Korea/ ; RS-2023-00219563//Ministry of Science and ICT/ ; //Soonchunhyang University Research Fund/ ; },
mesh = {Humans ; *Scleroderma, Systemic/microbiology ; *Skin/microbiology/pathology ; *Microbiota ; Female ; Middle Aged ; Male ; *RNA, Ribosomal, 16S/genetics ; Adult ; *Bacteria/classification/genetics/isolation & purification ; Severity of Illness Index ; Aged ; Biomarkers ; Metagenomics ; },
abstract = {Systemic sclerosis (SSc) is a chronic autoimmune disorder characterised by skin fibrosis and internal organ involvement. Disruptions in the microbial communities on the skin may contribute to the onset of autoimmune diseases that affect the skin. However, current research on the skin microbiome in SSc is lacking. This study aimed to investigate skin microbiome associated with disease severity in SSc. Skin swabs were collected from the upper limbs of 46 healthy controls (HCs) and 36 patients with SSc. Metagenomic analysis based on the 16S rRNA gene was conducted and stratified by cutaneous subtype and modified Rodnan skin score (mRSS) severity. Significant differences in skin bacterial communities were observed between the HCs and patients with SSc, with further significant variations based on subtype and mRSS severity. The identified biomarkers were Bacteroides and Faecalibacterium for patients with diffuse cutaneous SSc with high mRSS (≥ 10) and Mycobacterium and Parabacteroides for those with low mRSS (< 10). Gardnerella, Abies, Lactobacillus, and Roseburia were the biomarkers in patients with limited cutaneous SSc (lcSS) and high mRSS, whereas Coprococcus predominated in patients with lcSS and low mRSS. Cutaneous subtype analysis identified Pediococcus as a biomarker in the HCs, whereas mRSS analysis revealed the presence of Pseudomonas in conjunction with Pediococcus. In conclusion, patients with SSc exhibit distinct skin microbiota compared with healthy controls. Bacterial composition varies by systemic sclerosis cutaneous subtype and skin thickness.},
}

Humans
*Scleroderma, Systemic/microbiology
*Skin/microbiology/pathology
*Microbiota
Female
Middle Aged
Male
*RNA, Ribosomal, 16S/genetics
Adult
*Bacteria/classification/genetics/isolation & purification
Severity of Illness Index
Aged
Biomarkers
Metagenomics

@article {pmid39894814,
year = {2025},
author = {El Leithy, AA and Youssef, ASE and Nassar, A and Aziz, RK and Khaled, NM and Mahrous, MT and Farahat, GN and Mohamed, AH and Bakr, YM},
title = {Long-read 16S rRNA amplicon sequencing reveals microbial characteristics in patients with colorectal adenomas and carcinoma lesions in Egypt.},
journal = {Gut pathogens},
volume = {17},
number = {1},
pages = {8},
doi = {10.1186/s13099-025-00681-9},
pmid = {39894814},
issn = {1757-4749},
abstract = {BACKGROUND: Colorectal cancer (CRC) is among the five leading causes of cancer incidence and mortality. During the past decade, the role of the gut microbiota and its dysbiosis in colorectal tumorigenesis has been emphasized. Metagenomics and amplicon-based microbiome profiling provided insights into the potential role of microbial dysbiosis in the development of CRC.

AIM: To address the scarcity of information on differential microbiome composition of tumor tissue in comparison to adenomas and the lack of such data from Egyptian patients with CRC.

MATERIALS AND METHODS: Long-read nanopore sequencing of 16S rRNA amplicons was used to profile the colonic microbiota from fresh colonoscopic biopsy samples of Egyptian patients with CRC and patients with colonic polyps.

RESULTS: Species richness of CRC lesions was significantly higher than that in colonic polyps (p-value = 0.0078), while evenness of the CRC group was significantly lower than the colonic polyps group (p-value = 0.0055). Both species richness and Shannon diversity index of the late onset CRC samples were significantly higher than those of the early onset ones. The Firmicutes-to-Bacteroidetes (F/B) ratio was significantly higher in the CRC group than in the colonic polyps group (p-value = 0.0054), and significantly higher in samples from early-onset CRC. The Enterococcus spp. were significantly overabundant in patients with rectal cancer and early-onset CRC, while Staphylococcus spp. were significantly higher in patients with sigmoid cancer and late-onset CRC. In addition, the relative abundance of Fusobacterium nucleatum was significantly higher in CRC patients.

CONCLUSION: Differentiating trends were identified at phylum, genus, and species levels, despite the inter-individual differences. In summary, this study addressed the microbial dysbiosis associated with CRC and colonic polyps groups, paving the way for a better understanding of the pathogenesis of early and late-onset CRC in Egyptian patients.},
}

@article {pmid39894607,
year = {2025},
author = {Gong, JC and Li, BH and Liu, CY and Li, PF and Hu, JW and Yang, GP},
title = {Impact of salinity gradients on nitric oxide emissions and functional microbes in estuarine wetland sediments.},
journal = {Water research},
volume = {273},
number = {},
pages = {123046},
doi = {10.1016/j.watres.2024.123046},
pmid = {39894607},
issn = {1879-2448},
mesh = {*Wetlands ; *Salinity ; *Nitric Oxide/metabolism ; *Geologic Sediments/microbiology ; Estuaries ; China ; },
abstract = {Estuarine wetland sediments are hotspots for nitrogen cycling and critical sources of atmospheric nitric oxide (NO). Yet studies on the impact of sediment salinity gradients on NO emissions and associated functional microbes at the land-ocean interface remain limited. Here, we measured sediment NO emission rates from incubated sediment samples that were collected from an estuarine wetland in Qingdao, China. Our findings indicate that sediment salinity is a pivotal factor shaping NO emission rates, by altering the community composition and gene abundance of functional microbes involved in NO emissions, with rates ranging from 0.04 to 0.25 μg N kg[-1] dry soil h[-1]. Metagenomic analysis of the sediment samples reveals that greater NO emission rates (+486 %) under salinity changes are linked to a higher abundance of the nirS gene (+26 %) responsible for NO formation and a lower abundance of norBC genes (-23 %) responsible for NO consumption. Accordingly, the increase of NO emissions may be attributed to the accumulation of denitrifying NO, which could improve plant salt tolerance through co-evolutionary interactions between plants and sediment-dwelling microbes. Taken together, these findings contribute to a richer understanding of how biochemical NO emissions in estuarine wetland sediments respond to salinity gradients.},
}

*Wetlands
*Salinity
*Nitric Oxide/metabolism
*Geologic Sediments/microbiology
Estuaries
China

@article {pmid39894448,
year = {2025},
author = {Zhu, Y and Miao, H and Zhang, J and Jiang, Z and Chu, X and Xu, Y and Tian, W and Gao, H and Zhu, Y and Li, L and Yang, Q},
title = {Role of plasma and blood-cell co-metagenomic sequencing in precise diagnosis and severity evaluation of sepsis, a prospective cohort study in sepsis patients.},
journal = {The Journal of infection},
volume = {},
number = {},
pages = {106434},
doi = {10.1016/j.jinf.2025.106434},
pmid = {39894448},
issn = {1532-2742},
abstract = {PURPOSES: Sepsis caused great clinical burden all over the world. This study clarified the value of plasma metagenomic next-generation sequencing (p-mNGS) and blood cell mNGS (bc-mNGS) in sepsis diagnosis and evaluation.

METHODS: One hundred and fourty-seven blood samples were collected from sepsis patients who met sepsis 3.0 criteria. Blood culture (BC), qPCR, p-mNGS, bc-mNGS and necessary routine assays were conducted. Taking BC and qPCR as reference, diagnosis performance of p-mNGS and bc-mNGS was analyzed. Blood transcriptome was conducted to evaluate the immunological response of patients in groups with different p/bc-mNGS results. Impact of antibiotic use on different methods was also analyzed.

RESULTS: The p-mNGS demonstrated a sensitivity of 100% for bacteria/fungi and 97% for viruses, which was higher than bc-mNGS (88% for bacteria and fungi, 71% for viruses). However, bc-mNGS showed higher concordance with BC results, which indicated that co-mNGS (p-mNGS plus bc-mNGS) protocol increase sensitivity and helpful to justify viable blood pathogens in sepsis patients. This study showed that p-mNGS(+) & bc-mNGS(+) samples represented more activated immunity response (low expression of interferon-induced genes and high expression of JAK-STAT pathway genes), poorer clinical laboratory indicators (higher Sequential Organ Failure Assessment, higher procalcitonin and higher C-reactive protein) and lower survival rate. This study also proved that the use of broad-spectrum antibiotics affected much less on p/bc-mNGS diagnostic ability than on BC.

CONCLUSIONS: This research highlighted the potential value of plasma and blood-cell co-metagenomic sequencing in precise diagnosis and severity evaluation of sepsis patients, which will benefit the management of sepsis patients.},
}

@article {pmid39894225,
year = {2025},
author = {Kim, SY and Woo, SY and Kim, HL and Chang, YS and Ryu, S and Kim, HN},
title = {A shotgun metagenomic study identified short-chain fatty acid-producing species and their functions in the gut microbiome of adults with depressive symptoms: Large-scale shotgun sequencing data of the gut microbiota using a cross-sectional design.},
journal = {Journal of affective disorders},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jad.2025.01.149},
pmid = {39894225},
issn = {1573-2517},
abstract = {BACKGROUND: The gut-brain axis is emerging as a novel mechanism to explain depressive disorders.

METHODS: We performed shotgun metagenomic sequencing of stool samples obtained from 133 individuals with depression and 532 without depression. This study examined the taxonomy, functional pathways, and predicted metabolites profiles associated with depressive symptoms, using generalized linear models. To explore links between the taxonomic and functional pathway results, we compared the relative abundance of specific species contributing to pathways significantly associated with depressive symptoms.

RESULTS: Taxonomic composition suggested a disruption in short-chain fatty acid (SCFA)-producing capacity of the gut microbiome in the depressed group. Pathways related to SCFA biosynthesis were also depleted in this group. Faecalibacterium prausnitzii, a well-known SCFA-producing bacterium, was significantly decreased in the depressed group and was identified as a major contributor to the depleted pathways. When inferring the metabolites related to depression from metagenomic data, higher levels of docosapentaenoic acid, stearoyl ethanolamide, putrescine, and bilirubin were more likely to be found in the depressed group.

CONCLUSION: The present findings highlight the altered gut microbiota and associated SCFA-related pathways in individuals with depression. The depletion of F. prausnitzii and its contribution to SCFA production suggest that it is a potential therapeutic target for depression.},
}

@article {pmid39894202,
year = {2025},
author = {Ladjouzi, R and Taminiau, B and Daube, G and Lucau-Danila, A and Drider, D},
title = {The efficacy of the bacteriocinogenic Enterococcus faecalis 14 in the control of induced necrotic enteritis in broilers.},
journal = {Microbes and infection},
volume = {},
number = {},
pages = {105477},
doi = {10.1016/j.micinf.2025.105477},
pmid = {39894202},
issn = {1769-714X},
abstract = {PURPOSE: To demonstrate the efficacy of the bacteriocinogenic Enterococcus faecalis 14 (E. faecalis 14) in the control of induced necrotic enteritis (NE) in broilers.

METHODS: Six groups of 504 broilers consisting of an infected untreated control (IUC) group, an infected and amoxicillin treated control (ITC) group, and groups receiving prophylactically (2 groups) or therapeutically (2 groups) E. faecalis 14 or its Δbac mutant were used. All groups were challenged with Clostridium perfringens 56 to induce NE. To predispose the boilers to develop subclinical NE, a high protein grower diet containing 15% fishmeal and a coccidial inoculum were administered.

RESULTS: NE lesions were observed on D26 in all groups except ITC and those receiving prophylactically and therapeutically E. faecalis 14. On D27, only ITC and the group prophylactically treated with E. faecalis 14 (T03 T03) were without lesions. Average body weight and daily weight gain remained lower in the treated groups compared to the ITC group, but there was a clear improvement in the period between D21 to D27, especially in the group prophylactically treated with E. faecalis 14. Specifically, the daily weight gain (DWG) in this period for group T03, was second highest after the group ITC. Metataxonomic analyses showed a positive effect of E. faecalis 14 in maintaining the diversity and richness of the intestinal microbiota, in contrast to ITC group and other conditions.

CONCLUSIONS: The results of this in vivo study demonstrated the efficacy of the prophylactic administration of the bacteriocinogenic E. faecalis 14 in preventing of the NE lesions caused by C. perfringens.},
}

@article {pmid39893935,
year = {2025},
author = {Luo, Y and Gao, J and Su, X and Li, H and Li, Y and Qi, W and Han, X and Han, J and Zhao, Y and Zhang, A and Zheng, Y and Qian, F and He, H},
title = {Unraveling the immunological landscape and gut microbiome in sepsis: a comprehensive approach to diagnosis and prognosis.},
journal = {EBioMedicine},
volume = {113},
number = {},
pages = {105586},
doi = {10.1016/j.ebiom.2025.105586},
pmid = {39893935},
issn = {2352-3964},
abstract = {BACKGROUND: Comprehensive and in-depth research on the immunophenotype of septic patients remains limited, and effective biomarkers for the diagnosis and treatment of sepsis are urgently needed in clinical practice.

METHODS: Blood samples from 31 septic patients in the Intensive Care Unit (ICU), 25 non-septic ICU patients, and 18 healthy controls were analyzed using flow cytometry for deep immunophenotyping. Metagenomic sequencing was performed in 41 fecal samples, including 13 septic patients, 10 non-septic ICU patients, and 18 healthy controls. Immunophenotype shifts were evaluated using differential expression sliding window analysis, and random forest models were developed for sepsis diagnosis or prognosis prediction.

FINDINGS: Septic patients exhibited decreased proportions of natural killer (NK) cells and plasmacytoid dendritic cells (pDCs) in CD45[+] leukocytes compared with non-septic ICU patients and healthy controls. These changes statistically mediated the association of Bacteroides salyersiae with sepsis, suggesting a potential underlying mechanism. A combined diagnostic model incorporating B.salyersia, NK cells in CD45[+] leukocytes, and C-reactive protein (CRP) demonstrated high accuracy in distinguishing sepsis from non-sepsis (area under the receiver operating characteristic curve, AUC = 0.950, 95% CI: 0.811-1.000). Immunophenotyping and disease severity analysis identified an Acute Physiology and Chronic Health Evaluation (APACHE) II score threshold of 21, effectively distinguishing mild (n = 19) from severe (n = 12) sepsis. A prognostic model based on the proportion of total lymphocytes, Helper T (Th) 17 cells, CD4[+] effector memory T (TEM) cells, and Th1 cells in CD45[+] leukocytes achieved robust outcome prediction (AUC = 0.906, 95% CI: 0.732-1.000), with further accuracy improvement when combined with clinical scores (AUC = 0.938, 95% CI: 0.796-1.000).

INTERPRETATION: NK cell subsets within innate immunity exhibit significant diagnostic value for sepsis, particularly when combined with B. salyersiae and CRP. In addition, T cell phenotypes within adaptive immunity are correlated with sepsis severity and may serve as reliable prognostic markers.

FUNDING: This project was supported by the National Key R&D Program of China (2023YFC2307600, 2021YFA1301000), Shanghai Municipal Science and Technology Major Project (2023SHZDZX02, 2017SHZDZX01), Shanghai Municipal Technology Standards Project (23DZ2202600).},
}

@article {pmid39893934,
year = {2025},
author = {Zeng, S and Mo, S and Wu, X and Meng, C and Peng, P and Kashif, M and Li, J and He, S and Jiang, C},
title = {Microbial-mediated carbon metabolism in the subtropical marine mangroves affected by shrimp pond discharge.},
journal = {Marine environmental research},
volume = {205},
number = {},
pages = {106980},
doi = {10.1016/j.marenvres.2025.106980},
pmid = {39893934},
issn = {1879-0291},
abstract = {Mangrove ecosystems exhibit high efficiency in carbon (C) sequestering within the global ecosystem. However, the rapid expansion of the shrimp farming industry poses a significant threat to these delicate ecosystems. The microbial mechanisms driving C metabolism in shrimp-affected sediments remain poorly understood. This study investigates the spatiotemporal dynamics of C metabolism-related microbial communities in shrimp pond and natural mangrove sediments in a subtropical region. Shrimp pond discharge altered soil properties, microbial diversity, and microbial stability, driven by factors such as salinity, sulfide, and total organic C (TOC). Metagenomic analyses reveals shifts in C degradation and oxidation, with a reduction in genes for cellulose and hemicellulose degradation. Microbial markers like Prolixibacteraceae and Nitrosopumilaceae reflect these changes. Co-occurrence network analysis indicates higher connectivity within shrimp pond groups, suggesting nutrient-driven changes in symbiotic relationships. PLS-PM analysis further confirms the interplay between microbial composition, nutrient levels, and C metabolism, with higher 16S rRNA operon copy numbers linked to increased C fixation. These findings demonstrate how shrimp pond discharge alters microbial networks and C metabolism, with implications for ecosystem resilience.},
}

@article {pmid39893982,
year = {2025},
author = {Zhong, YQ and He, XL and Li, YH and Zhu, H and Li, JW and Xu, H and Liu, C and Lin, LC and Wang, JF},
title = {Enhancing antibiotic removal in constructed wetlands: A MgFe-LDHs-based strategy for optimizing microbial communities and metabolic functions.},
journal = {Journal of hazardous materials},
volume = {488},
number = {},
pages = {137412},
doi = {10.1016/j.jhazmat.2025.137412},
pmid = {39893982},
issn = {1873-3336},
abstract = {To efficiently remove antibiotics from domestic and livestock wastewater in southern China, vertical flow constructed wetlands (CWs) were designed with and without magnesium-iron layered double hydroxides (MgFe-LDHs). Their removal efficiencies for three typical antibiotics (tetracycline, oxytetracycline, and ofloxacin) were evaluated. Results showed that MgFe-LDHs significantly improved nitrogen and phosphorus removal (18.7 %-25.6 %) and enhanced the degradation of tetracycline, oxytetracycline, and ofloxacin (13.1 %-17.8 %). High-resolution LC-MS analysis indicated significant biodegradation through various pathways, such as oxidation, hydrolysis, and dealkylation. Analysis of the Shannon diversity index demonstrated that the introduction of novel MgFe-LDHs enhanced microbial diversity and evenness at the phylum, class, and genus levels. The introduction of MgFe-LDHs increased microbial diversity and enriched antibiotic-degrading genera like Xanthobacter, Ochrobactrum, and Stenotrophomonas. Moreover, MgFe-LDHs may have enhanced the metabolic pathways of glycolysis and the tricarboxylic acid cycle, thereby improving the microbial degradation of organic matter. In summary, MgFe-LDHs exhibited a multifaceted role in enhancing antibiotic removal in CWs by inducing the enrichment of antibiotic-degrading bacteria and regulating the metabolic functions of the microbial community, while also ensuring higher nitrogen and phosphorus removal efficiency.},
}

@article {pmid39893570,
year = {2025},
author = {Zampieri, G and Santinello, D and Palù, M and Orellana, E and Costantini, P and Favaro, L and Campanaro, S and Treu, L},
title = {Core cooperative metabolism in low-complexity CO2-fixing anaerobic microbiota.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf017},
pmid = {39893570},
issn = {1751-7370},
abstract = {Biological conversion of carbon dioxide into methane has a crucial role in global carbon cycling and is operated by a specialised set of anaerobic archaea. Although it is known that this conversion is strictly linked with cooperative bacterial activity, such as through syntrophic acetate oxidation, there is also a limited understanding on how this cooperation is regulated and metabolically realised. In this work, we investigate the activity in a microbial community evolved to efficiently convert carbon dioxide into methane and predominantly populated by Methanothermobacter wolfeii. Through multi-omics, biochemical analysis and constraint-based modelling, we identify a potential formate cross-feeding from an uncharacterised Limnochordia species to M. wolfeii, driven by the recently discovered reductive glycine pathway and upregulated when hydrogen and carbon dioxide are limited. The quantitative consistency of this metabolic exchange with experimental data is shown by metagenome-scale metabolic models integrating condition-specific metatranscriptomics, which also indicate a broader three-way interaction involving M. wolfeii, the Limnochordia species, and Sphaerobacter thermophilus. Under limited hydrogen and carbon dioxide, aspartate released by M. wolfeii is fermented by S. thermophilus into acetate, which in turn is convertible into formate by Limnochordia, possibly forming a cooperative loop sustaining hydrogenotrophic methanogenesis. These findings expand our knowledge on the modes of carbon dioxide reduction into methane within natural microbial communities and provide an example of cooperative plasticity surrounding this process.},
}

@article {pmid39893166,
year = {2025},
author = {Bourquin, M and Peter, H and Michoud, G and Busi, SB and Kohler, TJ and Robison, AL and Styllas, M and Ezzat, L and Geers, AU and Huss, M and Fodelianakis, S and , and Battin, TJ},
title = {Predicting climate-change impacts on the global glacier-fed stream microbiome.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {1264},
pmid = {39893166},
issn = {2041-1723},
mesh = {*Microbiota/genetics ; *Ice Cover/microbiology ; *Climate Change ; *Phylogeny ; *Bacteria/genetics/classification ; *Rivers/microbiology ; Metagenome ; Biodiversity ; Ecosystem ; },
abstract = {The shrinkage of glaciers and the vanishing of glacier-fed streams (GFSs) are emblematic of climate change. However, forecasts of how GFS microbiome structure and function will change under projected climate change scenarios are lacking. Combining 2,333 prokaryotic metagenome-assembled genomes with climatic, glaciological, and environmental data collected by the Vanishing Glaciers project from 164 GFSs draining Earth's major mountain ranges, we here predict the future of the GFS microbiome until the end of the century under various climate change scenarios. Our model framework is rooted in a space-for-time substitution design and leverages statistical learning approaches. We predict that declining environmental selection promotes primary production in GFSs, stimulating both bacterial biomass and biodiversity. Concomitantly, predictions suggest that the phylogenetic structure of the GFS microbiome will change and entire bacterial clades are at risk. Furthermore, genomic projections reveal that microbiome functions will shift, with intensified solar energy acquisition pathways, heterotrophy and algal-bacterial interactions. Altogether, we project a 'greener' future of the world's GFSs accompanied by a loss of clades that have adapted to environmental harshness, with consequences for ecosystem functioning.},
}

*Microbiota/genetics
*Ice Cover/microbiology
*Climate Change
*Phylogeny
*Bacteria/genetics/classification
*Rivers/microbiology
Metagenome
Biodiversity
Ecosystem

@article {pmid39893159,
year = {2025},
author = {Sampson, TR and Wallen, ZD and Won, WJ and Standaert, DG and Payami, H and Harms, AS},
title = {Alpha synuclein overexpression can drive microbiome dysbiosis in mice.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {4014},
pmid = {39893159},
issn = {2045-2322},
support = {ASAP-020527//Aligning Science Across Parkinson's/ ; ASAP-020527//Aligning Science Across Parkinson's/ ; ASAP-020527//Aligning Science Across Parkinson's/ ; ASAP-000375//Aligning Science Across Parkinson's/ ; },
mesh = {Animals ; *alpha-Synuclein/metabolism/genetics ; *Dysbiosis/microbiology ; *Gastrointestinal Microbiome ; Mice ; *Mice, Transgenic ; *Parkinson Disease/microbiology/metabolism/genetics ; Disease Models, Animal ; Humans ; Aging ; Male ; },
abstract = {Growing evidence indicates that persons with Parkinson disease (PD), have a unique composition of indigenous gut microbes. Given the long prodromal or pre-diagnosed period, longitudinal studies of the human and rodent gut microbiome before symptomatic onset and for the duration of the disease are currently lacking. PD is partially characterized by the accumulation of the protein α-synuclein (α-syn) into insoluble aggregates, in both the central and enteric nervous systems. As such, several experimental rodent and non-human primate models of α-syn overexpression recapitulate some of the hallmark pathophysiologies of PD. These animal models provide an opportunity to assess how the gut microbiome changes with age under disease-relevant conditions. Here, we used a transgenic mouse strain, which overexpress wild-type human α-syn to test how the gut microbiome composition responds in this model of PD pathology during aging. Using shotgun metagenomics, we find significant, age and genotype-dependent bacterial taxa whose abundance becomes altered with age. We reveal that α-syn overexpression can drive alterations to the gut microbiome composition and suggest that it limits diversity through age. Taxa that were most affected by genotype-age interaction were Lactobacillus and Bifidobacteria. In a mouse model, we showed direct link between alpha synuclein geneotype (hallmark of PD), a dysbiotic and low-diversity gut microbiome, and dysbiotic levels of Bifidobacteria and Lactobacillus (most robust features of PD microbiome). Given emerging data on the potential contributions of the gut microbiome to PD pathologies, our data provide an experimental foundation to understand how the PD-associated microbiome may arise as a trigger or co-pathology to disease.},
}

Animals
*alpha-Synuclein/metabolism/genetics
*Dysbiosis/microbiology
*Gastrointestinal Microbiome
Mice
*Mice, Transgenic
*Parkinson Disease/microbiology/metabolism/genetics
Disease Models, Animal
Humans
Aging
Male

@article {pmid39892935,
year = {2025},
author = {Hannaford, A and Hernandez-Acosta, RA and Little, JS and Campbell, JI and Weiss, ZF and Sherman, AC},
title = {Molecular Diagnostics for Invasive Molds: From Lab to Bedside.},
journal = {Clinics in laboratory medicine},
volume = {45},
number = {1},
pages = {27-40},
doi = {10.1016/j.cll.2024.10.009},
pmid = {39892935},
issn = {1557-9832},
mesh = {Humans ; *Invasive Fungal Infections/diagnosis ; *Molecular Diagnostic Techniques ; Fungi/isolation & purification ; Immunocompromised Host ; Mycoses/diagnosis ; },
abstract = {This review highlights the current state of molecular diagnostic modalities to detect invasive fungal infections, with a focus on molds in immunocompromised children and adults. Molecular diagnostics may also be utilized to detect antifungal drug resistance. Although both pathogen-specific and pathogen-agnostic assays may be beneficial in more rapidly identifying fungal infection with less invasive sampling in high-risk populations, the clinical implementation and interpretation of these tests must consider several important factors, including anatomic site and type of specimen, host characteristics, use of antifungal prophylaxis, and timing of specimen collection.},
}

Humans
*Invasive Fungal Infections/diagnosis
*Molecular Diagnostic Techniques
Fungi/isolation & purification
Immunocompromised Host
Mycoses/diagnosis

@article {pmid39892320,
year = {2025},
author = {Huang, L and Dai, W and Sun, X and Pu, Y and Feng, J and Jin, L and Sun, K},
title = {Diet-driven diversity of antibiotic resistance genes in wild bats: implications for public health.},
journal = {Microbiological research},
volume = {293},
number = {},
pages = {128086},
doi = {10.1016/j.micres.2025.128086},
pmid = {39892320},
issn = {1618-0623},
abstract = {Wild bats may serve as reservoirs for antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria, potentially contributing to antibiotic resistance and pathogen transmission. However, current assessments of bats' antibiotic resistance potential are limited to culture-dependent bacterial snapshots. In this study, we present metagenomic evidence supporting a strong association between diet, gut microbiota, and the resistome, highlighting bats as significant vectors for ARG propagation. We characterized gut microbiota, ARGs, and mobile genetic elements (MGEs) in bats with five distinct diets: frugivory, insectivory, piscivory, carnivory, and sanguivory. Our analysis revealed high levels of ARGs in bat guts, with limited potential for horizontal transfer, encompassing 1106 ARGs conferring resistance to 26 antibiotics. Multidrug-resistant and polymyxin-resistant genes were particularly prevalent among identified ARG types. The abundance and diversity of ARGs/MGEs varied significantly among bats with different dietary habits, possibly due to diet-related differences in microbial composition. Additionally, genetic linkage between high-risk ARGs and multiple MGEs was observed on the genomes of various zoonotic pathogens, indicating a potential threat to human health from wild bats. Overall, our study provides a comprehensive analysis of the resistome in wild bats and underscores the role of dietary habits in wildlife-associated public health risks.},
}

@article {pmid39892190,
year = {2025},
author = {Su, R and Shi, L and Wei, Y and Ma, B},
title = {Comammox and AOA responses to ammonia loading rate in oligotrophic environments.},
journal = {Water research},
volume = {275},
number = {},
pages = {123191},
doi = {10.1016/j.watres.2025.123191},
pmid = {39892190},
issn = {1879-2448},
abstract = {Nitrification is a central process in the global nitrogen cycle, yet the ecological niches and growth strategies of ammonia-oxidizing microorganisms in oligotrophic environments remain poorly understood. To investigate the ecological responses of complete ammonia oxidizers (Comammox) and ammonia-oxidizing archaea (AOA), a membrane bioreactor (MBR) system with two distinct ammonia loading rates (ALRs) was employed in this study. Metagenomic and meta-transcriptomic analyses showed that Comammox species-including Candidatus Nitrospira nitrosa and Candidatus Nitrospira inopinata-underwent a pronounced "bloom" only at high ALR, where their DNA and mRNA relative abundances reached 4.7 % and 5.63 %, respectively. Meanwhile, AOA steadily increased under both high and low ALR in oligotrophic environments. Network analysis further indicated stronger cooperative interactions between Comammox and AOA in higher ALR, highlighting distinct ecological strategies that underpin ammonia oxidation in oligotrophic environments. These findings not only support the development of low-carbon nitrogen removal processes in wastewater treatment but also clarify the impact of nitrogen loading on the distribution of ammonia-oxidizing microorganisms in natural ecosystems and provide insights into the origin and evolutionary pathways of these essential microbes.},
}

@article {pmid39891257,
year = {2025},
author = {Elrashedy, A and Mousa, W and Nayel, M and Salama, A and Zaghawa, A and Elsify, A and Hasan, ME},
title = {Advances in bioinformatics and multi-omics integration: transforming viral infectious disease research in veterinary medicine.},
journal = {Virology journal},
volume = {22},
number = {1},
pages = {22},
pmid = {39891257},
issn = {1743-422X},
mesh = {Animals ; *Computational Biology/methods ; *Veterinary Medicine/methods ; *Virus Diseases/veterinary/virology ; Genomics/methods ; Proteomics ; Multiomics ; },
abstract = {The world is changing due to factors like bioterrorism, massive environmental changes, globalization of trade and commerce, growing urbanization, changing climate, and pollution. Numerous diseases have emerged because of these factors, especially in companion and food-producing animals. Numerous pathogens have established themselves in naïve populations, harming reproduction, productivity, and health. Bioinformatics is considered a valuable tool in infectious disease research, as it provides a comprehensive overview of the identification of pathogens, their genetic makeup, and their evolutionary relationship. Therefore, there is an urgent need for a novel bioinformatics approach to help decipher and model viral epidemiology and informatics on domestic animals and livestock. With significant advancements in bioinformatics and NGS, researchers can now identify contigs, which are contiguous sequences of DNA that are assembled from overlapping fragments, assemble a complete genome, perform phylogenetic analysis to diagnose, investigate the risk of viral diseases in animals, handle and share large biological datasets across various species. Additionally, multi-omics data integration further deepens our understanding of homology, divergence, mutations, and evolutionary relationships, providing a comprehensive perspective on the molecular mechanisms driving animal pathogens infections. This review aims to reveal the importance of utilizing the multidisciplinary areas of bioinformatics, genomics, proteomics, transcriptomics, metabolomics, and metagenomics and their roles in studying viral infectious diseases in veterinary medicine that will eventually improve the health of animals.},
}

Animals
*Computational Biology/methods
*Veterinary Medicine/methods
*Virus Diseases/veterinary/virology
Genomics/methods
Proteomics
Multiomics

@article {pmid39891205,
year = {2025},
author = {Huang, D and Liao, J and Balcazar, JL and Ye, M and Wu, R and Wang, D and Alvarez, PJJ and Yu, P},
title = {Adaptive modification of antiviral defense systems in microbial community under Cr-induced stress.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {34},
pmid = {39891205},
issn = {2049-2618},
support = {42177113//National Natural Science Foundation of China/ ; 42277418//National Natural Science Foundation of China/ ; Y2022084//the Youth Innovation Promotion Association, Chinese Academy of Sciences/ ; 2022YFC3704700//National Key Research and Development Program of China/ ; },
mesh = {*Chromium/pharmacology ; *Soil Microbiology ; *Stress, Physiological ; *Bacteria/genetics/classification/drug effects ; *Microbiota/drug effects ; Soil Pollutants ; Metagenomics/methods ; Viruses/genetics/drug effects/classification ; Soil/chemistry ; },
abstract = {BACKGROUND: The prokaryotic antiviral defense systems are crucial for mediating prokaryote-virus interactions that influence microbiome functioning and evolutionary dynamics. Despite the prevalence and significance of prokaryotic antiviral defense systems, their responses to abiotic stress and ecological consequences remain poorly understood in soil ecosystems. We established microcosm systems with varying concentrations of hexavalent chromium (Cr(VI)) to investigate the adaptive modifications of prokaryotic antiviral defense systems under abiotic stress.

RESULTS: Utilizing hybrid metagenomic assembly with long-read and short-read sequencing, we discovered that antiviral defense systems were more diverse and prevalent in heavily polluted soils, which was corroborated by meta-analyses of public datasets from various heavy metal-contaminated sites. As the Cr(VI) concentration increased, prokaryotes with defense systems favoring prokaryote-virus mutualism gradually supplanted those with defense systems incurring high adaptive costs. Additionally, as Cr(VI) concentrations increased, enriched antiviral defense systems exhibited synchronization with microbial heavy metal resistance genes. Furthermore, the proportion of antiviral defense systems carried by mobile genetic elements (MGEs), including plasmids and viruses, increased by approximately 43% and 39%, respectively, with rising Cr concentrations. This trend is conducive to strengthening the dissemination and sharing of defense resources within microbial communities.

CONCLUSIONS: Overall, our study reveals the adaptive modification of prokaryotic antiviral defense systems in soil ecosystems under abiotic stress, as well as their positive contributions to establishing prokaryote-virus mutualism and the evolution of microbial heavy metal resistance. These findings advance our understanding of microbial adaptation in stressful environments and may inspire novel approaches for microbiome manipulation and bioremediation. Video Abstract.},
}

*Chromium/pharmacology
*Soil Microbiology
*Stress, Physiological
*Bacteria/genetics/classification/drug effects
*Microbiota/drug effects
Soil Pollutants
Metagenomics/methods
Viruses/genetics/drug effects/classification
Soil/chemistry

@article {pmid39891076,
year = {2025},
author = {Jia, Q and Sun, J and Wang, D and Xu, J and Li, X and Zhang, S and Wang, L and Liu, S and Tong, X and Fan, H},
title = {Clinical features and prognostic predictors of C. Psittaci Pneumonia: a systematic review and individual patient meta-analysis.},
journal = {BMC pulmonary medicine},
volume = {25},
number = {1},
pages = {55},
pmid = {39891076},
issn = {1471-2466},
mesh = {Humans ; *Psittacosis/diagnosis ; Prognosis ; *Chlamydophila psittaci/isolation & purification ; Risk Factors ; Pneumonia/diagnosis ; Severity of Illness Index ; },
abstract = {BACKGROUND: The clinical presentations and prognostic indicators of C. psittaci pneumonia are inadequately investigated currently. The objective of the study was to assess the clinical presentation of C. psittaci pneumonia and the risk factors for severe pneumonia, within a systematic review and individual patient meta-analysis.

METHODS: We searched PubMed, CNKI, and Wanfang databases for case reports/series of proven/probable psittacosis published between 1st January 2000 and 28th February 2023, including all hospitalized individuals aged ≥ 18 years. Patient demographics, manifestations, diagnostic methods, and outcomes were summarized descriptively. Patients were divided into severe or non-severe pneumonia groups mainly according to the ATS/IDSA 2007 criteria. Prognostic predictors for severe C. psittaci pneumonia were identified using multivariate logistic regression.

RESULTS: 3062 articles of 196 (566 individual patient cases) were included in the final analysis. Patients with chronic cardiovascular disease face a significantly elevated risk of developing severe C. psittaci pneumonia (adjusted odds ratio (aOR) 2.63; 95% confidence interval (CI) 1.05-6.59; P = 0.039). Symptoms including dyspnea (aOR 4.88; 95% CI 3.19-7.46; P < 0.001), neuropsychiatric symptoms (aOR 3.58; 95% CI 2.05-6.28; P < 0.001), gastrointestinal symptoms (aOR 1.76; 95% CI 1.10-2.80; P = 0.018), or the presence of multilobar infiltrates on imaging (aOR 3.27; 95% CI 2.11-5.06; P < 0.001) upon admission frequently serve as indicators of severe pneumonia.

CONCLUSIONS: Chronic cardiovascular disease increases susceptibility to severe C. psittaci pneumonia. The presence of dyspnea, neuropsychiatric symptoms, gastrointestinal symptoms, and multilobar infiltrates upon admission merits clinicians' attention, advocating for timely sample submission for metagenomic next-generation sequencing (mNGS) to ascertain the etiology.},
}

Humans
*Psittacosis/diagnosis
Prognosis
*Chlamydophila psittaci/isolation & purification
Risk Factors
Pneumonia/diagnosis
Severity of Illness Index

@article {pmid39890997,
year = {2025},
author = {Marter, P and Freese, HM and Ringel, V and Brinkmann, H and Pradella, S and Rohde, M and Jarek, M and Spröer, C and Wagner-Döbler, I and Overmann, J and Bunk, B and Petersen, J},
title = {Superior Resolution Profiling of the Coleofasciculus Microbiome by Amplicon Sequencing of the Complete 16S rRNA Gene and ITS Region.},
journal = {Environmental microbiology reports},
volume = {17},
number = {1},
pages = {e70066},
doi = {10.1111/1758-2229.70066},
pmid = {39890997},
issn = {1758-2229},
support = {34509606-TRR 51//Deutsche Forschungsgemeinschaft/ ; //Collaborative Research Center Roseobacter (TRR51)/ ; },
mesh = {*RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Cyanobacteria/genetics/classification/isolation & purification ; Sequence Analysis, DNA ; Phylogeny ; DNA, Ribosomal Spacer/genetics ; DNA, Bacterial/genetics ; Bacteria/genetics/classification/isolation & purification ; Metagenomics ; },
abstract = {The filamentous cyanobacterium Coleofasciculus chthonoplastes is the key primary producer of marine microbial mats. We elucidated the microbiomes of 32 non-axenic Coleofasciculus isolates using PacBio-based amplicon sequencing of the complete 16S rRNA gene and the internally transcribed spacer (16S-ITS). The length of authentic amplicon sequence variants (ASVs) ranged from 1827 to 3044 nucleotides (median: 2267 nt). The results, which were complemented by metagenome analyses and cultivation approaches, revealed the presence of more than 70 associated heterotrophs in the culture of Coleofasciculus sp. WW12. The great bacterial diversity in the cyanosphere is dominated by Pseudomonadota (59%) and Bacteroidota (23%). Allelic ribosomal operon variants were detected in 18 Coleofasciculus strains and our analyses proposed the presence of at least four different species. A comparative analysis of cyanobacterial microbiomes documented complementary advantages of amplicon sequencing versus metagenomics with an individual strength of the 16S-ITS approach in terms of (i) ribosomal target sequence quality, (ii) contaminant detection and (iii) identification of rare bacteria. The characterisation of the Coleofasciculus microbiome showed that long-read amplicon sequencing of the 16S-ITS region is the method of choice for rapid profiling of non-axenic cyanobacteria. Its superior resolution allows a reliable differentiation of even very closely related strains.},
}

*RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
*Cyanobacteria/genetics/classification/isolation & purification
Sequence Analysis, DNA
Phylogeny
DNA, Ribosomal Spacer/genetics
DNA, Bacterial/genetics
Bacteria/genetics/classification/isolation & purification
Metagenomics

@article {pmid39890137,
year = {2025},
author = {Kennedy, EC and Ross, FC and O'Shea, CA and Lavelle, A and Ross, P and Dempsey, E and Stanton, C and Hawkes, CP},
title = {Observational study protocol: the faecal microbiome in the acute stage of new-onset paediatric type 1 diabetes in an Irish cohort.},
journal = {BMJ open},
volume = {15},
number = {1},
pages = {e089206},
doi = {10.1136/bmjopen-2024-089206},
pmid = {39890137},
issn = {2044-6055},
mesh = {Humans ; *Diabetes Mellitus, Type 1/microbiology ; *Feces/microbiology ; Child ; *Gastrointestinal Microbiome ; Male ; Female ; Prospective Studies ; Ireland ; Child, Preschool ; Adolescent ; Metabolome ; },
abstract = {INTRODUCTION: Type 1 diabetes (T1D) is an autoimmune-mediated disorder caused by the destruction of pancreatic beta cells. Although there is an underlying genetic predisposition to developing T1D, the trigger is multifactorial and likely includes environmental factors. The intestinal microbiome has been identified as one such factor. Previous studies have illustrated differences in the microbiota of people with T1D compared with healthy controls. This study aims to describe the evolution of the microbiome and metabolome during the first year of clinical T1D, or stage 3 T1D diagnosis, and investigate whether there are differences in the microbiome and metabolome of children who present with and without diabetic ketoacidosis. The study will also explore possible associations between the microbiome, metabolome, glycaemic control and beta cell reserve.

METHODS AND ANALYSIS: This prospective cohort study will include children with newly diagnosed T1D and sibling controls (n=100, males and females) and their faecal microbiome will be characterised using shotgun metagenomic sequencing at multiple time points during the first year of diagnosis. We will develop a microbial culture biobank based on culturomic studies of stool samples from the healthy controls that will support future investigation. Metabolomic analysis will aim to identify additional biomarkers which may be involved in disease presentation and progression. Through this initial exploratory study, we aim to identify specific microbial biomarkers which may be used as future interventional targets throughout the various stages of T1D progression.

ETHICS AND DISSEMINATION: This study has been approved by the Clinical Research Ethics Committee of the Cork Teaching Hospitals. Study results will be available to patients with T1D and their families, carers, support networks and microbiome societies and other researchers.

TRIAL REGISTRATION NUMBER: The clinicaltrials.gov registration number for this trial is NCT06157736.},
}

Humans
*Diabetes Mellitus, Type 1/microbiology
*Feces/microbiology
Child
*Gastrointestinal Microbiome
Male
Female
Prospective Studies
Ireland
Child, Preschool
Adolescent
Metabolome

@article {pmid39889699,
year = {2025},
author = {Tagirdzhanova, G and Scharnagl, K and Sahu, N and Yan, X and Bucknell, A and Bentham, AR and Jégousse, C and Ament-Velásquez, SL and Onuț-Brännström, I and Johannesson, H and MacLean, D and Talbot, NJ},
title = {Complexity of the lichen symbiosis revealed by metagenome and transcriptome analysis of Xanthoria parietina.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2024.12.041},
pmid = {39889699},
issn = {1879-0445},
abstract = {Lichens are composite, symbiotic associations of fungi, algae, and bacteria that result in large, anatomically complex organisms adapted to many of the world's most challenging environments. How such intricate, self-replicating lichen architectures develop from simple microbial components remains unknown because of their recalcitrance to experimental manipulation. Here, we report a metagenomic and metatranscriptomic analysis of the lichen Xanthoria parietina at different developmental stages. We identified 168 genomes of symbionts and lichen-associated microbes across the sampled thalli, including representatives of green algae, three different classes of fungi, and 14 bacterial phyla. By analyzing the occurrence of individual species across lichen thalli from diverse environments, we defined both substrate-specific and core microbial components of the lichen. Metatranscriptomic analysis of the principal fungal symbiont from three different developmental stages of a lichen, compared with axenically grown fungus, revealed differential gene expression profiles indicative of lichen-specific transporter functions, specific cell signaling, transcriptional regulation, and secondary metabolic capacity. Putative immunity-related proteins and lichen-specific structurally conserved secreted proteins resembling fungal pathogen effectors were also identified, consistent with a role for immunity modulation in lichen morphogenesis.},
}

@article {pmid39889605,
year = {2025},
author = {Gong, X and Peng, Q and Jiang, R and Yang, N and Xing, C and Wang, R},
title = {Mn-oxidizing microalgae and woodchip-denitrifying bioreactor system for recovering manganese and removing nitrogen from electrolytic manganese metal industrial tailwater.},
journal = {Journal of hazardous materials},
volume = {488},
number = {},
pages = {137383},
doi = {10.1016/j.jhazmat.2025.137383},
pmid = {39889605},
issn = {1873-3336},
abstract = {Excess manganese (Mn) and NH4[+]-N emissions from electrolytic manganese metal industrial tailwater may harm the environment. However, previous studies have not combined Mn-oxidizing microalgae to reclaim Mn with woodchip substrates for nitrogen removal from tailwater. Here, a two-stage bioreactor system was constructed to recover Mn by microalgal-mediated bio-oxidation in an algae reactor (AR) and remove nitrogen by denitrification in a woodchip reactor (WR). The results showed that up to 100 % of Mn[2+] in the tailwater was removed after a 3-day incubation period. The maximum amount of biogenerated Mn oxide nanoparticles reached 13.34 mg/L with Mn[4+] as the main Mn valence. Mn recovery reached 65.69 % through precipitate collection, and the NH4[+]-N removal efficiency reached 97 % in the AR. Mn oxidation by algae might promote oxidative removal of NH4[+]-N. NO3[-]-N and total nitrogen removal efficiencies in the WR reached 82-90 % and 65-87 %, respectively, which was attributed to denitrification. The predominance of the denitrification gene narG in the WR may have driven the efficient nitrate removal. Flavobacterium, Acidovora, Massilia, Arcticibacter, and Acinetobacter were the most abundant genera in the WR and represented dominant denitrifying bacteria in the woodchip microbiome, indicating their important contribution to denitrification. Overall, the combined application of Mn-oxidizing algae and woodchip-denitrifying bioreactors may represent an efficient treatment technology for electrolytic manganese wastewater remediation.},
}

@article {pmid39889194,
year = {2025},
author = {Zhong, Y and Cai, ZY and Wang, JR and Qi, QG and Hao, J},
title = {Peritoneal dialysis-associated peritonitis caused by Coxiella Burnetii: A case report.},
journal = {Medicine},
volume = {104},
number = {5},
pages = {e41407},
doi = {10.1097/MD.0000000000041407},
pmid = {39889194},
issn = {1536-5964},
support = {2022MS08036//Inner Mongolia Natural Science Foundation/ ; NJYT- 23-068//Program for Young Talents of Science and Technology in Universities of Inner Mongolia Autonomous Region/ ; 202201253//Medical and Health Science and Technology Plan of Health Commission of Inner Mongolia Autonomous Region/ ; YKD2021MS034//Inner Mongolia Medical University General program/ ; },
mesh = {Female ; Humans ; *Peritonitis/microbiology/drug therapy/diagnosis ; Middle Aged ; *Coxiella burnetii/isolation & purification ; *Peritoneal Dialysis/adverse effects ; *Q Fever/diagnosis/drug therapy/microbiology ; *Anti-Bacterial Agents/therapeutic use ; Kidney Failure, Chronic/therapy ; Animals ; China ; },
abstract = {RATIONALE: Peritoneal dialysis (PD)-associated peritonitis (PDAP) is the leading cause of PD failure and discontinuation of PD. Several zoonotic pathogens could lead to the development of PDAP. Coxiella burnetii (C. burnetii) was a zoonotic pathogen and the cause of Q fever. However, reports of PDAP caused by C. burnetii are rare. We herein report the first case of PDAP caused by C. burnetii in mainland China.

PATIENTS CONCERNS: A 45-year-old woman was admitted to our hospital with chief complaint of yellow and cloudy PD effluent for 2 days. She had undergone PD for 5 years due to end-stage renal disease. She was engaged in cattle and sheep breeding. The culture of PD effluent was negative, even for specific species, such as Mycobacteria and fungi.

DIAGNOSES: The culture from the PD effluent tested positive for C. burnetii by adopting metagenomic next-generation sequencing on day 37. We diagnosed her as PDAP caused by C. burnetii.

INTERVENTIONS: Empirical treatment with multiple broad-spectrum antibiotics (including vancomycin, etimicin, piperacillin) was initially adopted. After identifying C. burnetii as the culprint as the PDAP, the regimen was changed to doxycycline (100 mg twice daily) and moxifloxacin (400 mg once daily) orally, leading to clinical improvement.

OUTCOMES: The white blood cell count of the PD effluent decreased to within the normal range and the culture of PD effluent was negative for C. burnetii at the visit of 4 months after discharge. Also, there was no sign for recurrence.

LESSONS: Vigilance should be heightened for PDAP cases with negative culture of PD fluid and poor response to standard broad-spectrum antibiotic treatment, along with a history of cattle and sheep breeding. In such conditions, PD effluent should be tested to detect possible peritonitis caused by C. burnetii, even in patients without symptoms of fever. Prompt pathogen identification and appropriate treatment are crucial for clinical improvement of such cases.},
}

Female
Humans
*Peritonitis/microbiology/drug therapy/diagnosis
Middle Aged
*Coxiella burnetii/isolation & purification
*Peritoneal Dialysis/adverse effects
*Q Fever/diagnosis/drug therapy/microbiology
*Anti-Bacterial Agents/therapeutic use
Kidney Failure, Chronic/therapy
Animals
China

@article {pmid39888330,
year = {2025},
author = {Thompson, JR and Canto, T and Carr, JP and Pallás, V and Šafářová, D},
title = {ICTV Virus Taxonomy Profile: Bromoviridae 2025.},
journal = {The Journal of general virology},
volume = {106},
number = {1},
pages = {},
doi = {10.1099/jgv.0.002069},
pmid = {39888330},
issn = {1465-2099},
mesh = {*Genome, Viral ; *Plant Diseases/virology ; *Bromoviridae/genetics/classification ; RNA, Viral/genetics ; Virion/ultrastructure/genetics ; Phylogeny ; },
abstract = {Bromoviridae is a family of plant viruses with tripartite, positive-sense RNA genomes of about 8 kb in total. Genomic RNAs are packaged in separate virions that may also contain sub-genomic, defective or satellite RNAs. Virions are variable in morphology (spherical or bacilliform) and may be transmitted between hosts mechanically, via pollen, or non-persistently by insect vectors. Members of the family are responsible for major disease epidemics in fruit, vegetable and fodder crops such as tomatoes, cucurbits, bananas, fruit trees, common beans and alfalfa. Since the adoption of metagenomic high-throughput sequencing methodologies, there has been a notable increase in the number of species in the genus Ilarvirus. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Bromoviridae, which is available at ictv.global/report/bromoviridae.},
}

*Genome, Viral
*Plant Diseases/virology
*Bromoviridae/genetics/classification
RNA, Viral/genetics
Virion/ultrastructure/genetics
Phylogeny

@article {pmid39887801,
year = {2025},
author = {Tonoli, A and Anselmi, S and Ward, JM and Hailes, HC and Jeffries, J},
title = {Expanding the Enzymatic Toolbox for Carboligation: Increasing the Diversity of the 'Split' Transketolase Sequence Space.},
journal = {Chembiochem : a European journal of chemical biology},
volume = {},
number = {},
pages = {e202401028},
doi = {10.1002/cbic.202401028},
pmid = {39887801},
issn = {1439-7633},
abstract = {Transketolases (TKs) are thiamine diphosphate (ThDP)-dependent enzymes that catalyze the transfer of two-carbon units in a stereoselective manner, making them valuable biocatalysts for sustainable processes. Most known TKs are about 650 amino acids long; however, a second type found in Archaea and many Bacteria consists of two proteins, each of about 300 amino acids. Exploring the unique features and differences of split TKs may help in assessing their potential use in biocatalysis and for uncovering new reactivities. Additionally, it could provide valuable information on how their structure relates to their function, especially compared to full-length TKs. In this study, we significantly expanded the known repertoire of split TKs approximately 14-fold to the best of our knowledge, by identifying and providing accessions of nearly 500 putative split-TK subunit pairs. Moreover, we doubled the number of experimentally produced and tested split TKs by cloning, purifying, and testing ten candidates retrieved from genomes and in-house metagenomes. Interestingly, pQR2809 and pQR2812, derived from hyperthermophilic organisms, showed enhanced thermostability compared to other TK examples in the literature, maintaining partial activity after heating at 90 °C or 100 °C for 1 hour, respectively.},
}

@article {pmid39887373,
year = {2025},
author = {Byrd, DA and Damerell, V and Gomez Morales, MF and Hogue, SR and Lin, T and Ose, J and Himbert, C and Ilozumba, MN and Kahlert, C and Shibata, D and Toriola, AT and Li, CI and Figueiredo, J and Stephens, WZ and Warby, CA and Hardikar, S and Siegel, EM and Round, J and Ulrich, CM and Gigic, B},
title = {The gut microbiome is associated with disease-free survival in stage I-III colorectal cancer patients.},
journal = {International journal of cancer},
volume = {},
number = {},
pages = {},
doi = {10.1002/ijc.35342},
pmid = {39887373},
issn = {1097-0215},
support = {//ERA-NET on Translational Cancer Research (TRANSCAN)/ ; //Heidelberger Stiftung Chirurgie, Heidelberg University Hospital/ ; //Medizinische Fakultät Heidelberg, Universität Heidelberg/ ; //Matthias-Lackas Foundations/ ; //Stiftung LebensBlicke/ ; R01 CA189184/NH/NIH HHS/United States ; U01 CA206110/NH/NIH HHS/United States ; //Rahel Goitein-Straus-Program/ ; 01KD2101D//German Federal Ministry of Education and Research/ ; 01KT1503//German Federal Ministry of Education and Research/ ; },
abstract = {Colorectal cancer (CRC) is the second overall leading cause of cancer death in the United States, with recurrence being a frequent cause of mortality. Approaches to improve disease-free survival (DFS) are urgently needed. The gut microbiome, reflected in fecal samples, is likely mechanistically linked to CRC progression and may serve as a non-invasive biomarker. Accordingly, we leveraged baseline fecal samples from N = 166 stage I-III CRC patients in the ColoCare Study, a prospective cohort of newly diagnosed CRC patients. We sequenced the V3 and V4 regions of the 16S rRNA gene to characterize fecal bacteria. We calculated estimates of alpha diversity, beta diversity, and a priori- and exploratory-selected bacterial presence/absence and relative abundance. Associations of microbial metrics with DFS were estimated using multivariable Cox proportional hazards models. We found that alpha diversity was strongly associated with improved DFS, most strongly among rectal cancer patients (Shannon HRrectum = 0.40 95% CI = 0.19, 0.87; p = .02). Overall microbiome composition differences (beta diversity), as characterized by principal coordinate axes, were statistically significantly associated with DFS. Peptostreptococcus was statistically significantly associated with worse DFS (HR = 1.62, 95% CI = 1.13, 2.31; p = .01 per 1-SD) and Order Clostridiales was associated with improved DFS (HR = 0.62, 95% CI = 0.43-0.88; p = .01 per 1-SD). In exploratory analyses, Coprococcus and Roseburia were strongly associated with improved DFS. Overall, higher bacterial diversity and multiple bacteria were strongly associated with DFS. Metagenomic sequencing to elucidate species, gene, and functional level details among larger, diverse patient populations are critically needed to support the microbiome as a biomarker of CRC outcomes.},
}

@article {pmid39887237,
year = {2025},
author = {Stewart, AG and Fishman, JA},
title = {Surveillance and prevention of infection in clinical xenotransplantation.},
journal = {Clinical microbiology reviews},
volume = {},
number = {},
pages = {e0015023},
doi = {10.1128/cmr.00150-23},
pmid = {39887237},
issn = {1098-6618},
abstract = {SUMMARYXenotransplantation, the transplantation of living organs, tissues, or cells between species, carries the potential to address the global shortage of human organs for patients with end-stage organ failure. Recent advances in genetic engineering have improved prospects for clinical xenotransplantation by reducing immune and inflammatory responses to grafts, controlling coagulation on endothelial surfaces, and modifying viral risks, including the porcine endogenous retrovirus (PERV). Management of infectious risks posed by clinical xenotransplantation requires meticulous attention to the biosecure breeding and microbiological surveillance of source animals and recipients and consideration of novel infection control requirements. Infectious risks in xenotransplantation stem from both known human pathogens in immunosuppressed transplant recipients and from porcine organisms for which the clinical manifestations, microbial assays, and therapies are generally limited. Both known and unknown zoonoses may be transmitted from pigs to humans. Some pig-specific pathogens do not infect human cells but have systemic manifestations when active within the xenograft, including porcine cytomegalovirus/porcine roseolovirus (PCMV/PRV), which contributes to graft rejection and consumptive coagulopathy. The role of porcine endogenous retrovirus (PERV) in humans remains uncertain despite the absence of documented transmissions and the availability of swine with inactivated genomic PERV. New technologies, such as metagenomic sequencing and multi-omics approaches, will be essential for detection of novel infections and for understanding interactions between the xenograft, the host's immune system, and potential pathogens. These approaches will allow development of infection control protocols, pathogen surveillance requirements, and tailored antimicrobial therapies to enhance the safety and success of clinical xenotransplantation.},
}

@article {pmid39887086,
year = {2025},
author = {Breton, J and Tu, V and Tanes, C and Wilson, N and Quinn, R and Kachelries, K and Friedman, ES and Bittinger, K and Baldassano, RN and Compher, C and Albenberg, L},
title = {A pro-inflammatory diet is associated with growth and virulence of Escherichia coli in pediatric Crohn's disease.},
journal = {Journal of Crohn's & colitis},
volume = {},
number = {},
pages = {},
doi = {10.1093/ecco-jcc/jjaf018},
pmid = {39887086},
issn = {1876-4479},
abstract = {BACKGROUND & AIMS: Epidemiological studies have suggested an association between the inflammatory potential of dietary patterns and Crohn's disease (CD). However, relationships of these inflammatory dietary determinants with the microbiome remain largely unknown. In this cross-sectional study, we evaluate the association between the inflammatory potential of habitual diet, as assessed by the modified Children-Dietary Inflammatory Index (mC-DII), and the fecal microbiome and metabolome of children with CD in comparison to healthy children.

METHODS: A cross-sectional study including 51 children with CD between 6 and 18 years of age and 50 healthy controls was conducted. Dietary inflammatory potential was measured using the modified Children-Dietary Inflammatory Index (mC-DII) and diet quality assessed by the Healthy Eating Index (HEI)-2015 and alternate Mediterranean eating index (aMed). Microbiome was analysed using shotgun metagenomic sequencing and untargeted metabolomic analysis.

RESULTS: A poor-quality, pro-inflammatory diet with similar mC-DII, HEI-2015 and aMed scores was found across healthy children and children with CD. In children with active disease, a pro-inflammatory diet was associated with decreased diversity, increased virulence potential and expansion of the Proteobacteria phylum dominated by Escherichia coli (E. coli) spp. Positive correlation between E. coli relative abundance and mC-DII was associated with a low intake of a cluster composed of fibers, vitamins and minerals with anti-inflammatory potential. A negative association between metabolites of fatty acid metabolism and HEI was found.

CONCLUSIONS: In total, our results suggest that a pro-inflammatory diet may potentiate hallmarks of the inflammation-associated dysbiosis in CD and highlight the need for microbiome-targeted dietary interventions optimizing the anti-inflammatory potential of habitual diet in the management of pediatric CD.},
}

@article {pmid39886930,
year = {2025},
author = {Zhang, W and Feng, J and Tan, K and Jiang, J and Deng, J},
title = {Bordetella pertussis Detected in Blood Samples From Neonatal Twins via Metagenomic Next-generation Sequencing.},
journal = {The Pediatric infectious disease journal},
volume = {44},
number = {2},
pages = {e71-e72},
doi = {10.1097/INF.0000000000004615},
pmid = {39886930},
issn = {1532-0987},
}

@article {pmid39885140,
year = {2025},
author = {Shao, B and Xie, YG and Zhang, L and Ruan, Y and Liang, B and Zhang, R and Xu, X and Wang, W and Lin, Z and Pei, X and Wang, X and Zhao, L and Zhou, X and Wu, X and Xing, D and Wang, A and Lee, DJ and Ren, N and Canfield, DE and Hedlund, BP and Hua, ZS and Chen, C},
title = {Versatile nitrate-respiring heterotrophs are previously concealed contributors to sulfur cycle.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {1202},
pmid = {39885140},
issn = {2041-1723},
support = {52076063//National Natural Science Foundation of China (National Science Foundation of China)/ ; 52100035//National Natural Science Foundation of China (National Science Foundation of China)/ ; 52400025//National Natural Science Foundation of China (National Science Foundation of China)/ ; 52300155//National Natural Science Foundation of China (National Science Foundation of China)/ ; 52321005//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32170014//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2023DX04//State Key Laboratory of Urban Water Resource and Environment (SKLUWRE)/ ; 2024M754204//China Postdoctoral Science Foundation/ ; 2023M740917//China Postdoctoral Science Foundation/ ; },
mesh = {*Sulfur/metabolism ; *Nitrates/metabolism ; *Heterotrophic Processes ; *Denitrification ; *Oxidation-Reduction ; Bacteria/metabolism/genetics ; Geologic Sediments/microbiology ; Nitrous Oxide/metabolism ; Microbiota ; Sulfides/metabolism ; Metagenomics ; Greenhouse Gases/metabolism ; },
abstract = {Heterotrophic denitrifiers play crucial roles in global carbon and nitrogen cycling. However, their inability to oxidize sulfide renders them vulnerable to this toxic molecule, which inhibits the key enzymatic reaction responsible for reducing nitrous oxide (N2O), thereby raising greenhouse gas emissions. Here, we applied microcosm incubations, community-isotope-corrected DNA stable-isotope probing, and metagenomics to characterize a cohort of heterotrophic denitrifiers in estuarine sediments that thrive by coupling sulfur oxidation with denitrification through chemolithoheterotrophic metabolism. Remarkably, ecophysiology experiments from enrichments demonstrate that such heterotrophs expedite denitrification with sulfur acting as alternative electron sources and substantially curtail N2O emissions in both organic-rich and organic-limited environments. Their flexible, non-sulfur-dependent physiology may confer competitive advantages over conventional heterotrophic denitrifiers in detoxifying sulfide, adapting to organic matter fluctuations, and mitigating greenhouse gas emissions. Our study provides insights into the ecological role of heterotrophic denitrifiers in microbial communities with implications for sulfur cycling and climate change.},
}

*Sulfur/metabolism
*Nitrates/metabolism
*Heterotrophic Processes
*Denitrification
*Oxidation-Reduction
Bacteria/metabolism/genetics
Geologic Sediments/microbiology
Nitrous Oxide/metabolism
Microbiota
Sulfides/metabolism
Metagenomics
Greenhouse Gases/metabolism

@article {pmid37480259,
year = {2024},
author = {Ahmad, V and Jamal, A and Khan, MI and Alzahrani, FA and Albiheyri, R and Jamal, QMS},
title = {Cefoperazone targets D-alanyl-D-alanine carboxypeptidase (DAC) to control Morganella morganii-mediated infection: a subtractive genomic and molecular dynamics approach.},
journal = {Journal of biomolecular structure & dynamics},
volume = {42},
number = {13},
pages = {6799-6812},
doi = {10.1080/07391102.2023.2238088},
pmid = {37480259},
issn = {1538-0254},
mesh = {*Morganella morganii/drug effects/enzymology ; *Enterobacteriaceae Infections/drug therapy ; *Cefoperazone/pharmacology ; Humans ; *Serine-Type D-Ala-D-Ala Carboxypeptidase/chemistry/metabolism ; *Metagenome ; Gastrointestinal Microbiome ; Escherichia coli Proteins/chemistry/metabolism ; Penicillin-Binding Proteins/chemistry/metabolism ; Escherichia coli/enzymology ; *Molecular Dynamics Simulation ; Molecular Conformation ; },
abstract = {Morganella morganii is a Gram-negative bacterial pathogen that causes bacteremia, urinary tract infections, intra-abdominal infections, chorioamnionitis, neonatal sepsis, and newborn meningitis. To control this bacterial pathogen a total of 3565 putative proteins targets in Morganella morganii were screened using comparative subtractive analysis of biochemical pathways annotated by the KEGG that did not share any similarities with human proteins. One of the targets, D-alanyl-D-alanine carboxypeptidase DacB [Morganella] was observed to be implicated in the majority of cell wall synthesis pathways, leading to its selection as a novel pharmacological target. The drug that interacted optimally with the identified target was observed to be Cefoperazone (DB01329) with the estimated free energy of binding -8.9 Kcal/mol. During molecular dynamics simulations; it was observed that DB01328-2exb and DB01329-2exb complexes showed similar values as the control FMX-2exb complex near 0.2 nm with better stability. Furthermore, MMPBSA total free energy calculation showed better binding energy than the control complex for DB01329-2exb interaction i.e. -31.50 (±0.93) kcal/mol. Our presented research suggested that D-alanyl-D-alanine carboxypeptidase DacB could be a therapeutic target and cefoperazone could be a promising ligand to inhibit the D-alanyl-D-alanine carboxypeptidase DacB protein of Morganella morganii. To identify prospective therapeutic and vaccine targets in Morganella morganii, this is the first computational and subtractive genomics investigation of various metabolic pathways exploring other therapeutic targets of Morganella morganii. In vitro/in vivo experimental validation of the identified target D-alanyl-D-alanine carboxypeptidase and the design of its inhibitors is suggested to figure out the best dose, the drug's effectiveness, and its toxicity.Communicated by Ramaswamy H. Sarma.},
}

*Morganella morganii/drug effects/enzymology
*Enterobacteriaceae Infections/drug therapy
*Cefoperazone/pharmacology
Humans
*Serine-Type D-Ala-D-Ala Carboxypeptidase/chemistry/metabolism
*Metagenome
Gastrointestinal Microbiome
Escherichia coli Proteins/chemistry/metabolism
Penicillin-Binding Proteins/chemistry/metabolism
Escherichia coli/enzymology
*Molecular Dynamics Simulation
Molecular Conformation

@article {pmid39885121,
year = {2025},
author = {Nooij, S and Plomp, N and Sanders, IMJG and Schout, L and van der Meulen, AE and Terveer, EM and Norman, JM and Karcher, N and Larralde, MF and Vossen, RHAM and Kloet, SL and Faber, KN and Harmsen, HJM and Zeller, GF and Kuijper, EJ and Smits, WK and Ducarmon, QR},
title = {Metagenomic global survey and in-depth genomic analyses of Ruminococcus gnavus reveal differences across host lifestyle and health status.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {1182},
pmid = {39885121},
issn = {2041-1723},
mesh = {Humans ; *Crohn Disease/microbiology/genetics ; *Metagenomics/methods ; *Genome, Bacterial/genetics ; *Gastrointestinal Microbiome/genetics ; Metagenome/genetics ; Health Status ; Genome-Wide Association Study ; Clostridiales/genetics/isolation & purification ; Life Style ; Phylogeny ; Infant, Newborn ; Genomics ; Female ; Male ; Adult ; Virulence Factors/genetics ; },
abstract = {Ruminococcus gnavus is a gut bacterium found in > 90% of healthy individuals, but its increased abundance is also associated with chronic inflammatory diseases, particularly Crohn's disease. Nevertheless, its global distribution and intraspecies genomic variation remain understudied. By surveying 12,791 gut metagenomes, we recapitulated known associations with metabolic diseases and inflammatory bowel disease. We uncovered a higher prevalence and abundance of R. gnavus in Westernized populations and observed bacterial relative abundances up to 83% in newborns. Next, we built a resource of R. gnavus isolates (N = 45) from healthy individuals and Crohn's disease patients and generated complete R. gnavus genomes using PacBio circular consensus sequencing. Analysis of these genomes and publicly available high-quality draft genomes (N = 333 genomes) revealed multiple clades which separated Crohn's-derived isolates from healthy-derived isolates. Presumed R. gnavus virulence factors could not explain this separation. Bacterial genome-wide association study revealed that Crohn's-derived isolates were enriched in genes related to mobile elements and mucin foraging. Together, we present a large R. gnavus resource that will be available to the scientific community and provide novel biological insights into the global distribution and genomic variation of R. gnavus.},
}

Humans
*Crohn Disease/microbiology/genetics
*Metagenomics/methods
*Genome, Bacterial/genetics
*Gastrointestinal Microbiome/genetics
Metagenome/genetics
Health Status
Genome-Wide Association Study
Clostridiales/genetics/isolation & purification
Life Style
Phylogeny
Infant, Newborn
Genomics
Female
Male
Adult
Virulence Factors/genetics

@article {pmid39884534,
year = {2025},
author = {Zhou, M and Luo, C and Zhang, J and Li, R and Chen, J and Ren, P and Tang, Y and Suo, Z and Chen, K},
title = {Potential risk of microplastics in plateau karst lakes: Insights from metagenomic analysis.},
journal = {Environmental research},
volume = {},
number = {},
pages = {120984},
doi = {10.1016/j.envres.2025.120984},
pmid = {39884534},
issn = {1096-0953},
abstract = {Microplastic (MP) pollution has become one of global concern. While MP pollution in lakes has been well studied, research on MP sources, distribution, and ecological risks in the Tibetan Plateau is limited. We systematically investigated the MP abundance and distribution in alpine travertine lakes in Jiuzhai nature reserve located in east edge of Qinghai-Tibetan Plateau and assessed the distributions of microbiomes, antibiotic resistance genes (ARGs), and virulence factor genes (VFGs) in water, sediments, and MPs, using macrogenomics. MP abundance was 20.27-58.80 n/L in water and 583.33-996.67 n/kg in sediments. MPs were dominantly fibrous and transparent. The particle size distribution was 0.1-0.5 mm for MPs in water, and 0.5-1 mm in sediments. MPs were mainly composed of polyethylene and polyethylene terephthalate. The microbial community of MP biofilms differed from that in the surrounding environmental medium, and Proteobacteria were more abundant in biofilm than in water and sediment. MP biofilms exhibited more cooperative behavior with microorganisms in water than with those in sediments. MPs were selectively enriched for ARGs and VFGs, and MP biofilms had a higher diversity of ARGs, the most abundant isoform being msbA, which is a multidrug resistance gene. VFGs were more abundant in MP biofilms than in water and sediment. The study results are useful for understanding MP sources and ecological risks in plateau karst lakes and provide a valuable dataset and theoretical basis for studies on MP pollution in other alpine calcareous lakes.},
}

@article {pmid39884152,
year = {2025},
author = {Maphosa, S and Steyn, M and Lebre, PH and Gokul, JK and Convey, P and Marais, E and Maggs-Kölling, G and Cowan, DA},
title = {Rhizosphere bacterial communities of Namib Desert plant species: Evidence of specialised plant-microbe associations.},
journal = {Microbiological research},
volume = {293},
number = {},
pages = {128076},
doi = {10.1016/j.micres.2025.128076},
pmid = {39884152},
issn = {1618-0623},
abstract = {Rhizosphere microbial communities are intimately associated with plant root surfaces. The rhizosphere microbiome is recruited from the surrounding soil and is known to impact positively on the plant host via enhanced resistance to pathogens, increased nutrient availability, growth stimulation and increased resistance to desiccation. Desert ecosystems harbour a diversity of perennial and annual plant species, generally exhibiting considerable physiological adaptation to the low-water environment. In this study, we explored the rhizosphere bacterial microbiomes associated with selected desert plant species. The rhizosphere bacterial communities of 11 plant species from the central Namib Desert were assessed using 16S rRNA gene-dependent phylogenetic analyses. The rhizosphere microbial community of each host plant species was compared with control soils collected from their immediate vicinity, and with those of all other host plants. Rhizosphere and control soil bacterial communities differed significantly and were influenced by both location and plant species. Rhizosphere-associated genera included 67 known plant growth-promoting taxa, including Rhizobium, Bacillus, Microvirga, Kocuria and Paenibacillus. Other than Kocuria, these genera constituted the 'core' rhizosphere bacterial microbiome, defined as being present in > 90 % of the rhizosphere communities. Nine of the 11 desert plant species harboured varying numbers and proportions of species-specific microbial taxa. Predictive analyses of functional pathways linked to rhizosphere microbial taxa showed that these were significantly enriched in the biosynthesis or degradation of a variety of substances such as sugars, secondary metabolites, phenolic compounds and antimicrobials. Overall, our data suggest that plant species in the Namib Desert recruit unique taxa to their rhizosphere bacterial microbiomes that may contribute to their resilience in this extreme environment.},
}

@article {pmid39884010,
year = {2025},
author = {Peng, Y and Lu, J and Fan, L and Zhou, J and Dong, W and Jiang, M},
title = {Enzymes offer a promising avenue for enhancing the competitiveness of biodegradable plastics in environmental restoration and the circular economy.},
journal = {Waste management (New York, N.Y.)},
volume = {195},
number = {},
pages = {32-43},
doi = {10.1016/j.wasman.2025.01.040},
pmid = {39884010},
issn = {1879-2456},
abstract = {As a promising alternative to traditional plastics, the widespread application of biodegradable plastic (BP) will help solve worsening environmental problems. Enzymes such as cutinase, lipase, protease and esterase produced by bacteria and fungi in the environment play a crucial role in the degradation, recycling and valorization of BP by degrading them into low-molecular-weight oligomers or small monomers. These enzymes offering advantages such as high efficiency, cleanliness, safety and environmental friendliness, making them more competitive in environmental restoration and circular economy. This review describes in detail the occurrence and distribution of enzymes involved in the degradation of BPs (represented by PHB, PLA and PCL). Omics methods (metagenomic and proteomic) combined with high-throughput platforms can screen out BP-degrading enzymes in different environments, and then use protein engineering to optimize the degrading enzymes to improve enzymatic degradation efficiency. Finally, we focus on the methods and strategies for the commercialization of degrading enzymes, future research prospects and challenges are also discussed. This review highlights the importance of BP-degrading enzymes in the bio-cycling of BP, and expected to drive the widespread use of BP.},
}

@article {pmid39883852,
year = {2025},
author = {Monpierre, L and Angebault, C and Hua, C and Merio, L and Ortonne, N and Lafont, E and Foulet, F and Botterel, F},
title = {Contribution of shotgun metagenomics in the diagnosis of a subcutaneous phaeohyphomycosis caused by Parathyridaria percutanea.},
journal = {The British journal of dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1093/bjd/ljaf018},
pmid = {39883852},
issn = {1365-2133},
}

@article {pmid39883300,
year = {2024},
author = {Zhang, D and Yu, H and Yu, X and Yang, Y and Wang, C and Wu, K and Niu, M and He, J and He, Z and Yan, Q},
title = {Mechanisms underlying the interactions and adaptability of nitrogen removal microorganisms in freshwater sediments.},
journal = {Advanced biotechnology},
volume = {2},
number = {3},
pages = {21},
pmid = {39883300},
issn = {2948-2801},
support = {SML2023SP237//Southern Marine Science and Engineering Guangdong Laboratory/ ; SML2021SP203//Southern Marine Science and Engineering Guangdong Laboratory/ ; SML2023SP205//Southern Marine Science and Engineering Guangdong Laboratory/ ; },
abstract = {Microorganisms in eutrophic water play a vital role in nitrogen (N) removal, which contributes significantly to the nutrient cycling and sustainability of eutrophic ecosystems. However, the mechanisms underlying the interactions and adaptation strategies of the N removal microorganisms in eutrophic ecosystems remain unclear. We thus analyzed field sediments collected from a eutrophic freshwater ecosystem, enriched the N removal microorganisms, examined their function and adaptability through amplicon, metagenome and metatranscriptome sequencing. We found that the N removal activities could be affected through potential competition and inhibition among microbial metabolic pathways. High-diversity microbial communities generally increased the abundance and expression of N removal functional genes. Further enrichment experiments showed that the enrichment of N removal microorganisms led to a development of simplified but more stable microbial communities, characterized by similar evolutionary patterns among N removal microorganisms, tighter interactions, and increased adaptability. Notably, the sustained provision of NH4[+] and NO2[-] during the enrichment could potentially strengthen the interconnections among denitrification, anaerobic ammonium oxidation (anammox) and dissimilatory nitrate reduction to ammonium (DNRA) processes. Moreover, the identification of shared metabolic traits among denitrification, anammox and DNRA implies important cooperative associations and adaptability of N removal microorganisms. Our findings highlight the microbial interactions affect the adaptive strategies of key microbial taxa involved in N removal.},
}

@article {pmid39882903,
year = {2025},
author = {Huang, X and Yao, X and Song, W and Zhao, M and Zhu, Z and Liu, H and Song, X and Huang, J and Chen, Y and Wang, Z and Peng, C and Wu, W and Yang, H and Hua, L and Chen, H and Wu, B and Peng, Z},
title = {Discovery of viruses and bacteria associated with swine respiratory disease on farms at a nationwide scale in China using metatranscriptomic and metagenomic sequencing.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0002525},
doi = {10.1128/msystems.00025-25},
pmid = {39882903},
issn = {2379-5077},
abstract = {Respiratory disease (RD) is a worldwide leading threat to the pig industry, but there is still limited understanding of the pathogens associated with swine RD. In this study, we conducted a nationwide genomic surveillance on identifying viruses, bacteria, and antimicrobial resistance genes (ARGs) from the lungs of pigs with RD in China. By performing metatranscriptomic sequencing combined with metagenomic sequencing, we identified 21 viral species belonging to 12 viral families. Among them, porcine reproductive and respiratory syndrome virus, influenza A virus, herpes virus, adenovirus, and parvovirus were commonly identified. However, emerging viruses, such as Getah virus and porcine respiratory coronaviruses, were also characterized. Apart from viruses, a total of 164 bacterial species were identified, with Streptococcus suis, Mycoplasma hyorhinis, Mycoplasma hyopneumoniae, Glaesserella parasuis, and Pasteurella multocida being frequently detected in high abundances. Notably, Escherichia coli, Enterococcus faecalis, Staphylococcus aureus, and Klebsiella pneumoniae were also highly detected. Our further analysis revealed a complex interaction between the identified pathogens in swine RD. We also conducted retrospectively analyses to demonstrate the prevalent viral genotypes or bacterial serotypes associated with swine RD in China. Finally, we identified 48 ARGs, which conferred resistance to 13 predicted antimicrobial classes, and many of these ARGs were significantly associated with a substantial number of mobile genetic elements, including transposons (e.g., tnpAIS1, tnpA1353, int3, and ISCau1) and plasmids (e.g., Col(BS512), Col(YC)]. These findings will contribute to further understanding the etiology, epidemiology, and microbial interactions in swine RD, and may also shed a light on the development of effective vaccines.IMPORTANCEIn this study, we identified viruses and bacteria from the lungs of pigs with RD in China at a nationwide farm scale by performing metatranscriptomic sequencing combined with metagenomic sequencing. We also demonstrated the complex interactions between different viral and/or bacterial species in swine RD. Our work provides a comprehensive knowledge about the etiology, epidemiology, and microbial interactions in swine RD and data reference for the research and development of effective vaccines against the disease.},
}

@article {pmid39882902,
year = {2025},
author = {Zhu, D and Wozniak, KJ and Midani, F and Wang, S and Sun, X and Britton, RA},
title = {Control of Clostridioides difficile virulence and physiology by the flagellin homeostasis checkpoint FliC-FliW-CsrA in the absence of motility.},
journal = {mBio},
volume = {},
number = {},
pages = {e0380124},
doi = {10.1128/mbio.03801-24},
pmid = {39882902},
issn = {2150-7511},
abstract = {UNLABELLED: Mutations affecting Clostridioides difficile flagellin (FliC) have been shown to be hypervirulent in animal models and display increased toxin production and alterations in central metabolism. The regulation of flagellin levels in bacteria is governed by a tripartite regulatory network involving fliC, fliW, and csrA, which creates a feedback system to regulate flagella production. Through genomic analysis of C. difficile clade 5 strains (non-motile), we identified they have jettisoned many of the genes required for flagellum biosynthesis yet retain the major flagellin gene fliC and regulatory gene fliW. We therefore investigated the roles of fliC, fliW, and csrA in the clade 5 ribotype 078 strain C. difficile 1015, which lacks flagella and is non-motile. Analysis of mutations in fliC, fliW, and csrA (and all combinations) on C. difficile pathogenesis indicated that FliW plays a central role in C. difficile virulence as animals infected with strains carrying a deletion of fliW showed decreased survival and increased disease severity. These in vivo findings were supported by in vitro studies showing that mutations impacting the activity of FliW showed increased toxin production. We further identified that FliW can interact with the toxin-positive regulator TcdR, indicating that modulation of toxin production via FliW occurs by sequestering TcdR from activating toxin transcription. Furthermore, disruption of the fliC-fliW-csrA network results in significant changes in carbon source utilization and sporulation. This work highlights that key proteins involved in flagellar biosynthesis retain their regulatory roles in C. difficile pathogenesis and physiology independent of their functions in motility.

IMPORTANCE: Clostridioides difficile is a leading cause of nosocomial antibiotic-associated diarrhea in developed countries with many known virulence factors. In several pathogens, motility and virulence are intimately linked by regulatory networks that allow coordination of these processes in pathogenesis and physiology. Regulation of C. difficile toxin production by FliC has been demonstrated in vitro and in vivo and has been proposed to link motility and virulence. Here, we show that clinically important, non-motile C. difficile strains have conserved FliC and regulatory partners FliW and CsrA, despite lacking the rest of the machinery to produce functional flagella. Our work highlights a novel role for flagellin outside of its role in motility and FliW in the pathogenesis and physiology of C. difficile.},
}

@article {pmid39882857,
year = {2025},
author = {Grettenberger, C and Gold, DA and Brown, CT},
title = {Distribution of early-branching Cyanobacteriia and the potential habitats that gave rise to the earliest oxygenic phototrophs.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0101324},
doi = {10.1128/msphere.01013-24},
pmid = {39882857},
issn = {2379-5042},
abstract = {The evolution of oxygenic photosynthesis in the Cyanobacteria was one of the most transformative events in Earth history, eventually leading to the oxygenation of Earth's atmosphere. However, it is difficult to understand how the earliest Cyanobacteria functioned or evolved on early Earth in part because we do not understand their ecology, including the environments in which they lived. Here, we use a cutting-edge bioinformatics tool to survey nearly 500,000 metagenomes for relatives of the taxa that likely bookended the evolution of oxygenic photosynthesis to identify the modern environments in which these organisms live. Ancestral state reconstruction suggests that the common ancestors of these organisms lived in terrestrial (soil and/or freshwater) environments. This restricted distribution may have increased the lag between the evolution of oxygenic photosynthesis and the oxygenation of Earth's atmosphere.IMPORTANCECyanobacteria generate oxygen as part of their metabolism and are responsible for the rise of oxygen in Earth's atmosphere over two billion years ago. However, we do not know how long this process may have taken. To help constrain how long this process would have taken, it is necessary to understand where the earliest Cyanobacteria may have lived. Here, we use a cutting-edge bioinformatics tool called branch water to examine the environments where modern Cyanobacteria and their relatives live to constrain those inhabited by the earliest Cyanobacteria. We find that these species likely lived in non-marine environments. This indicates that the rise of oxygen may have taken longer than previously believed.},
}

@article {pmid39882224,
year = {2025},
author = {Takamaru, H and Tsay, C and Shiba, S and Yachida, S and Saito, Y},
title = {Microbiome and Colorectal Cancer in Humans: A Review of Recent Studies.},
journal = {Journal of the anus, rectum and colon},
volume = {9},
number = {1},
pages = {20-24},
pmid = {39882224},
issn = {2432-3853},
abstract = {The tumor microenvironment has recently been well-studied in various gastrointestinal cancers, including colorectal cancer (CRC). The gut microbiota, a collection of microorganisms in the human gastrointestinal tract, is one of the microenvironments associated with colon carcinogenesis. It has been challenging to elucidate the mechanisms by which gut microbiota contributes to carcinogenesis and cancer progression due to complex interactions with the host, including its metabolites and immune and inflammatory responses. Various studies described the influence of diet on reported changes in the composition and microbiota of gut bacteria and its association with CRC. In recent years, metagenomic techniques such as shotgun sequencing and genome-wide association studies focused on understanding the role of the microbiota and the metabolome on early CRCs and colon carcinogenesis to determine if there are modifiable or intervenable targets for CRC. In this review, we will attempt to provide an overview of gut microbiota related to CRC, with particular attention to the findings of recent studies.},
}

@article {pmid39881980,
year = {2024},
author = {Renk, H and Schoppmeier, U and Müller, J and Kuger, V and Neunhoeffer, F and Gille, C and Peter, S},
title = {Oxygenation and intestinal perfusion and its association with perturbations of the early life gut microbiota composition of children with congenital heart disease.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1468842},
pmid = {39881980},
issn = {1664-302X},
abstract = {BACKGROUND: Early life gut microbiota is known to shape the immune system and has a crucial role in immune homeostasis. Only little is known about composition and dynamics of the intestinal microbiota in infants with congenital heart disease (CHD) and potential influencing factors.

METHODS: We evaluated the intestinal microbial composition of neonates with CHD (n = 13) compared to healthy controls (HC, n = 30). Fecal samples were analyzed by shotgun metagenomics. Different approaches of statistical modeling were applied to assess the impact of influencing factors on variation in species composition. Unsupervised hierarchical clustering of the microbial composition of neonates with CHD was used to detect associations of distinct clusters with intestinal tissue oxygenation and perfusion parameters, obtained by the "oxygen to see" (O2C) method.

RESULTS: Overall, neonates with CHD showed an intestinal core microbiota dominated by the genera Enterococcus (27%) and Staphylococcus (20%). Furthermore, a lower abundance of the genera Bacteroides (8% vs. 14%), Parabacteroides (1% vs. 3%), Bifidobacterium (4% vs. 12%), and Escherichia (8% vs. 23%) was observed in CHD compared to HCs. CHD patients that were born by vaginal delivery showed a lower fraction of the genera Bacteroides (15% vs. 21%) and Bifidobacterium (7% vs. 22%) compared to HCs and in those born by cesarean section, these genera were not found at all. In infants with CHD, we found a significant impact of oxygen saturation (SpO2) on relative abundances of the intestinal core microbiota by multivariate analysis of variance (F[8,2] = 24.9, p = 0.04). Statistical modeling suggested a large proportional shift from a microbiota dominated by the genus Streptococcus (50%) in conditions with low SpO2 towards the genus Enterococcus (61%) in conditions with high SpO2. We identified three distinct compositional microbial clusters, corresponding neonates differed significantly in intestinal blood flow and global gut perfusion.

CONCLUSION: Early life differences in gut microbiota of CHD neonates versus HCs are possibly linked to oxygen levels. Delivery method may affect microbiota stability. However, further studies are needed to assess the effect of potential interventions including probiotics or fecal transplants on early life microbiota perturbations in neonates with CHD.},
}

@article {pmid39881594,
year = {2025},
author = {Kaur, I and Shaw, B and Multani, A and Pham, C and Malhotra, S and Smith, E and Adachi, K and Allyn, P and Bango, Z and Beaird, OE and Caldera, JR and Chandrasekaran, S and Chan, L and Cheema, R and Daouk, S and Deville, J and Dong, HV and Fan, A and Garner, O and Gaynor, P and Gray, H and Gorin, A and Kalava, S and Kanatani, M and Karnaze, A and Saleh, T and Sharma, Y and Stauber, S and Vargas, M and Veral, M and Winston, D and Yanagimoto-Ogawa, L and Aldrovandi, G and Nielsen-Saines, K and Fuller, T and Jackson, N and Uslan, D and Schaenman, J and Vijayan, T and Sakona, A and Yang, S},
title = {Real-world clinical impact of plasma cell-free DNA metagenomic next-generation sequencing assay.},
journal = {Infection control and hospital epidemiology},
volume = {},
number = {},
pages = {1-8},
doi = {10.1017/ice.2024.242},
pmid = {39881594},
issn = {1559-6834},
abstract = {OBJECTIVE: To describe the real-world clinical impact of a commercially available plasma cell-free DNA metagenomic next-generation sequencing assay, the Karius test (KT).

METHODS: We retrospectively evaluated the clinical impact of KT by clinical panel adjudication. Descriptive statistics were used to study associations of diagnostic indications, host characteristics, and KT-generated microbiologic patterns with the clinical impact of KT. Multivariable logistic regression modeling was used to further characterize predictors of higher positive clinical impact.

RESULTS: We evaluated 1000 unique clinical cases of KT from 941 patients between January 1, 2017-August 31, 2023. The cohort included adult (70%) and pediatric (30%) patients. The overall clinical impact of KT was positive in 16%, negative in 2%, and no clinical impact in 82% of the cases. Among adult patients, multivariable logistic regression modeling showed that culture-negative endocarditis (OR 2.3; 95% CI, 1.11-4.53; P .022) and concern for fastidious/zoonotic/vector-borne pathogens (OR 2.1; 95% CI, 1.11-3.76; P .019) were associated with positive clinical impact of KT. Host immunocompromised status was not reliably associated with a positive clinical impact of KT (OR 1.03; 95% CI, 0.83-1.29; P .7806). No significant predictors of KT clinical impact were found in pediatric patients. Microbiologic result pattern was also a significant predictor of impact.

CONCLUSIONS: Our study highlights that despite the positive clinical impact of KT in select situations, most testing results had no clinical impact. We also confirm diagnostic indications where KT may have the highest yield, thereby generating tools for diagnostic stewardship.},
}

@article {pmid39881417,
year = {2025},
author = {Ye, GC and Peng, H and Xiang, JC and Miao, LT and Liu, CZ and Wang, SG and Xia, QD},
title = {Comprehensive analysis of the interaction microbiome and prostate cancer: an initial exploration from multi-cohort metagenome and GWAS studies.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {130},
pmid = {39881417},
issn = {1479-5876},
mesh = {Humans ; Male ; *Prostatic Neoplasms/microbiology/genetics/pathology ; *Metagenome/genetics ; *Genome-Wide Association Study ; *Gastrointestinal Microbiome/genetics ; Cohort Studies ; Neoplasm Metastasis ; Mendelian Randomization Analysis ; },
abstract = {INTRODUCTION: Prostate cancer is one of the most common cancers in the United States with a high mortality rate. In recent years, the traditional opinion about prostate microbiome was challenged. Although there still are some arguments, an escalating number of researchers are shifting their focus toward the microbiome within the prostate tumor environment.

METHODS: We mined the data of the microbiome extracted from the metagenome, and it offers a broader taxonomic coverage and accurate functional profiling. We used Kraken2, a mapping tool, to mine the gut microbiota of prostate cancer patients. A two-sample Mendelian Randomization was conducted to reflect the association between gut microbiome and cancer.

RESULTS: In the study, we found the consistency of the special intratumor microbiome of both non-metastatic tumors and metastatic tumors. And we dig the gut microbiome in patients with different treatments. We found that some microbiotas may be associated with prostate cancer progression and a special microbiome in metastatic prostate cancer may exist. The anti-androgen therapy can significantly change both the intratumor and gut microbiome.

CONCLUSION: With the progression and metastasis of prostate cancer, some intratumor microbiome changes. And anti-androgen influences both the intratumor and gut microbiome. Our discovery may help researchers further understand the progression, metastasis, and resistance of prostate cancer from the perspective of microbiome level.},
}

Humans
Male
*Prostatic Neoplasms/microbiology/genetics/pathology
*Metagenome/genetics
*Genome-Wide Association Study
*Gastrointestinal Microbiome/genetics
Cohort Studies
Neoplasm Metastasis
Mendelian Randomization Analysis

@article {pmid39881387,
year = {2025},
author = {Pangga, GM and Star-Shirko, B and Psifidi, A and Xia, D and Corcionivoschi, N and Kelly, C and Hughes, C and Lavery, U and Richmond, A and Ijaz, UZ and Gundogdu, O},
title = {Impact of commercial gut health interventions on caecal metagenome and broiler performance.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {30},
pmid = {39881387},
issn = {2049-2618},
support = {BB/T008709/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; EP/V030515/1//Engineering and Physical Sciences Research Council/ ; },
abstract = {BACKGROUND: Maintaining gut health is a persistent and unresolved challenge in the poultry industry. Given the critical role of gut health in chicken performance and welfare, there is a pressing need to identify effective gut health intervention (GHI) strategies to ensure optimal outcomes in poultry farming. In this study, across three broiler production cycles, we compared the metagenomes and performance of broilers provided with ionophores (as the control group) against birds subjected to five different GHI combinations involving vaccination, probiotics, prebiotics, essential oils, and reduction of ionophore use.

RESULTS: Using a binning strategy, 84 (≥ 75% completeness, ≤ 5% contamination) metagenome-assembled genomes (MAGs) from 118 caecal samples were recovered and annotated for their metabolic potential. The majority of these (n = 52, 61%) had a differential response across all cohorts and are associated with the performance parameter - European poultry efficiency factor (EPEF). The control group exhibited the highest EPEF, followed closely by the cohort where probiotics are used in conjunction with vaccination. The use of probiotics B, a commercial Bacillus strain-based formulation, was determined to contribute to the superior performance of birds. GHI supplementation generally affected the abundance of microbial enzymes relating to carbohydrate and protein digestion and metabolic pathways relating to energy, nucleotide synthesis, short-chain fatty acid synthesis, and drug-transport systems. These shifts are hypothesised to differentiate performance among groups and cycles, highlighting the beneficial role of several bacteria, including Rikenella microfusus and UBA7160 species.

CONCLUSIONS: All GHIs are shown to be effective methods for gut microbial modulation, with varying influences on MAG diversity, composition, and microbial functions. These metagenomic insights greatly enhance our understanding of microbiota-related metabolic pathways, enabling us to devise strategies against enteric pathogens related to poultry products and presenting new opportunities to improve overall poultry performance and health. Video Abstract.},
}

@article {pmid39881253,
year = {2025},
author = {Garcia, I and Riis, RK and Moen, LV and Rohringer, A and Madslien, EH and Bragstad, K},
title = {Unsupervised detection of novel SARS-CoV-2 mutations and lineages in wastewater samples using long-read sequencing.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {87},
pmid = {39881253},
issn = {1471-2164},
mesh = {*Wastewater/virology ; *SARS-CoV-2/genetics/isolation & purification ; *COVID-19/virology/epidemiology ; Humans ; *Mutation ; *High-Throughput Nucleotide Sequencing/methods ; Spike Glycoprotein, Coronavirus/genetics ; Wastewater-Based Epidemiological Monitoring ; },
abstract = {The COVID-19 pandemic has underscored the importance of virus surveillance in public health and wastewater-based epidemiology (WBE) has emerged as a non-invasive, cost-effective method for monitoring SARS-CoV-2 and its variants at the community level. Unfortunately, current variant surveillance methods depend heavily on updated genomic databases with data derived from clinical samples, which can become less sensitive and representative as clinical testing and sequencing efforts decline.In this paper, we introduce HERCULES (High-throughput Epidemiological Reconstruction and Clustering for Uncovering Lineages from Environmental SARS-CoV-2), an unsupervised method that uses long-read sequencing of a single 1 Kb fragment of the Spike gene. HERCULES identifies and quantifies mutations and lineages without requiring database-guided deconvolution, enhancing the detection of novel variants.We evaluated HERCULES on Norwegian wastewater samples collected from July 2022 to October 2023 as part of a national pilot on WBE of SARS-CoV-2. Strong correlations were observed between wastewater and clinical sample data in terms of prevalence of mutations and lineages. Furthermore, we found that SARS-CoV-2 trends in wastewater samples were identified one week earlier than in clinical data.Our results demonstrate HERCULES' capability to identify new lineages before their detection in clinical samples, providing early warnings of potential outbreaks. The methodology described in this paper is easily adaptable to other pathogens, offering a versatile tool for environmental surveillance of new emerging pathogens.},
}

*Wastewater/virology
*SARS-CoV-2/genetics/isolation & purification
*COVID-19/virology/epidemiology
Humans
*Mutation
*High-Throughput Nucleotide Sequencing/methods
Spike Glycoprotein, Coronavirus/genetics
Wastewater-Based Epidemiological Monitoring

@article {pmid39881163,
year = {2025},
author = {Dash, M and Thiyageshwari, S and Selvi, D and Johnson, HKV and Ariyan, M and Rajan, K and Anandham, R},
title = {Unveiling microbial diversity in slightly and moderately magnesium deficient acidic soils.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {3696},
pmid = {39881163},
issn = {2045-2322},
mesh = {*Soil Microbiology ; *Soil/chemistry ; *Magnesium/metabolism/analysis ; *RNA, Ribosomal, 16S/genetics ; India ; Bacteria/genetics/classification/metabolism ; Metagenomics/methods ; Biodiversity ; Magnesium Deficiency/genetics ; Phosphorus/deficiency/metabolism ; Microbiota/genetics ; },
abstract = {Magnesium (Mg) an essential plant nutrient is widespread deficient in the acidic soils of Nilgiris of Tamil nadu, India. The vegetable yield and quality is especially affected due to deficiency of nutrients like Mg. This study investigates soil characteristics and bacterial diversity in the Nilgiris district of Tamil Nadu, India, with respect to Mg deficiency. The soil samples were collected from different vegetable growing regions of the Nilgiris to assess soil physiocochemical parameters, soil enzymes and soil Mg status. 16S rRNA gene-based metagenomic analysis used to investigate the functional potential and structural diversity of the bacterial communities in high Mg and low Mg deficiency soil. Results indicated mildly acidic soils with a sandy loam texture and high organic carbon content. While nitrogen (N), phosphorus (P), and potassium (K) levels were adequate, Mg deficiency was consistent. Soil enzymes such as dehydrogenase, acid phosphatase, urease and aryl sulfatase, varied across the soil samples. Additionally, 16S rRNA gene-based metagenomics analysis revealed the bacterial diversity and functional pathways in soils with high and low Mg deficiency. Low Mg levels were associated with increased bacterial richness, dominated by Proteobacteria, Gemmatimonadetes, Actinobacteria, Bacteroidetes, and Acidobacteria. Functional pathways related to carbon metabolism, amino acid biosynthesis, and various metabolic processes were more abundant in low Mg deficient soils. This research highlights the significant influence of Mg levels on bacterial diversity and functional potentials in acidic soils, providing insights into soil management strategies in Mg-deficient regions.},
}

*Soil Microbiology
*Soil/chemistry
*Magnesium/metabolism/analysis
*RNA, Ribosomal, 16S/genetics
India
Bacteria/genetics/classification/metabolism
Metagenomics/methods
Biodiversity
Magnesium Deficiency/genetics
Phosphorus/deficiency/metabolism
Microbiota/genetics

@article {pmid39880818,
year = {2025},
author = {Jiang, ZJ and Hong, JC and Lin, BW and Zhang, WQ and Fan, QC and Yang, BH and Yao, XP},
title = {Comparison of mNGS with conventional methods for diagnosis of cryptococcal meningitis: a retrospective study.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {3656},
pmid = {39880818},
issn = {2045-2322},
support = {2019XQ1079//Startup Fund for Scientific Research of Fujian Medical University/ ; 82171841//National Natural Science Foundation of China/ ; 2020Y93010140//Joint Funds for the Innovation of Science and Technology, Fujian Province/ ; },
mesh = {*Meningitis, Cryptococcal/diagnosis/cerebrospinal fluid/microbiology ; Humans ; Retrospective Studies ; Male ; Female ; Middle Aged ; Adult ; *High-Throughput Nucleotide Sequencing/methods ; Aged ; Sensitivity and Specificity ; Metagenomics/methods ; Antigens, Fungal/cerebrospinal fluid/analysis ; Young Adult ; },
abstract = {The application of metagenomic next-generation sequencing (mNGS) in the diagnosis of cryptococcal meningitis is relatively under characterized. Here, we retrospectively evaluated data from cryptococcal meningitis patients who were tested using mNGS and/or routine testing, including fungal culture, India ink staining, and cryptococcal antigen (CrAg) testing. The performance of mNGS was then assessed. Initial cerebrospinal fluid (CSF) samples were collected from 65 patients with suspected central nervous system (CNS) infection and tested using conventional tests and/or mNGS. mNGS offers a culture-independent approach, facilitating a rapid and unbiased detection of a broad spectrum of pathogens. Patients with bacterial tuberculous or viral meningitis were used as mNGS-positive controls and one autoimmune encephalitis patient was used as an mNGS-negative control. In the 45 patients diagnosed with cryptococcal meningitis, the sensitivity, specificity, positive predictive value, negative predictive value, and concordance rate of mNGS were 92%, 100%, 100%, 90.9%, and 95.6%, respectively. Compared to conventional methods, the sensitivity of mNGS was slightly lower than CrAg tests (96.7%) but higher than India ink (79.5%) and culturing (63.4%). Of the two negative mNGS cases (2/25, 8.0%), one was positive by India ink staining, culture, and CrAg testing, while the other was positive only by CrAg testing. A combination of mNGS and conventional methods enhanced the detection rate to 100%. Our study demonstrates that both CrAg and mNGS offer excellent diagnostic accuracy for cryptococcal meningitis, and utilizing both tests can enhance clinical assessment and patient management.},
}

*Meningitis, Cryptococcal/diagnosis/cerebrospinal fluid/microbiology
Humans
Retrospective Studies
Male
Female
Middle Aged
Adult
*High-Throughput Nucleotide Sequencing/methods
Aged
Sensitivity and Specificity
Metagenomics/methods
Antigens, Fungal/cerebrospinal fluid/analysis
Young Adult

@article {pmid39879766,
year = {2025},
author = {Liu, X and Li, H and Yang, J and Yan, S and Zhou, Y and Jiang, R and Li, R and Wang, M and Ren, P},
title = {Different effects of bio/non-degradable microplastics on sewage sludge compost performance: Focusing on antibiotic resistance genes, virulence factors and key metabolic functions.},
journal = {Journal of hazardous materials},
volume = {488},
number = {},
pages = {137329},
doi = {10.1016/j.jhazmat.2025.137329},
pmid = {39879766},
issn = {1873-3336},
abstract = {Microplastics (MP) have aroused increasing concern due to the negative environmental impact. However, the impact of bio/non-biodegradable MPs on the sludge composting process has not been thoroughly investigated. This study examined antibiotic resistance genes (ARGs), virulence factors (VFs), and microbial community functions in sludge compost with the application of polylactic acid (PLA) and polypropylene (PP), using metagenomic sequencing. The findings indicated that both types of MPs could extend the thermophilic phase, enhance microbial activity, and inhibit the formation of humic acids. Compared to CK, the subtypes of ARGs decreased 4.22 % and 13.11 % in PLA and PP groups, respectively. But new ARGs emerged, particularly in the PLA group. The proportions of ARGs related to efflux and VFs associated with the adhesion system increased 1.62 %-2.27 % and 55.56 %-60.00 %, respectively, in MPs-added composts. The relative abundance of potential bacterial hosts (e.g., Psychrobacter) carrying multiple ARGs and VFs was much higher in PLA-added compost than in the other two. Moreover, PP facilitated denitrification process and PLA enhanced dissimilatory nitrate reduction to ammonium. Both types of MPs inhibited assimilatory nitrate reduction to ammonia but promoted inorganic nitrogen assimilation. This study broadens our understanding of the potential environmental risks posed by biodegradable and non-biodegradable microplastics on sludge compost and offers valuable insights for the management and application of compost products.},
}

@article {pmid39880958,
year = {2025},
author = {Maghini, DG and Oduaran, OH and Olubayo, LAI and Cook, JA and Smyth, N and Mathema, T and Belger, CW and Agongo, G and Boua, PR and Choma, SSR and Gómez-Olivé, FX and Kisiangani, I and Mashaba, GR and Micklesfield, L and Mohamed, SF and Nonterah, EA and Norris, S and Sorgho, H and Tollman, S and Wafawanaka, F and Tluway, F and Ramsay, M and Wirbel, J and , and Bhatt, AS and Hazelhurst, S},
title = {Expanding the human gut microbiome atlas of Africa.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {39880958},
issn = {1476-4687},
abstract = {Population studies provide insights into the interplay between the gut microbiome and geographical, lifestyle, genetic and environmental factors. However, low- and middle-income countries, in which approximately 84% of the world's population lives[1], are not equitably represented in large-scale gut microbiome research[2-4]. Here we present the AWI-Gen 2 Microbiome Project, a cross-sectional gut microbiome study sampling 1,801 women from Burkina Faso, Ghana, Kenya and South Africa. By engaging with communities that range from rural and horticultural to post-industrial and urban informal settlements, we capture a far greater breadth of the world's population diversity. Using shotgun metagenomic sequencing, we identify taxa with geographic and lifestyle associations, including Treponema and Cryptobacteroides species loss and Bifidobacterium species gain in urban populations. We uncover 1,005 bacterial metagenome-assembled genomes, and we identify antibiotic susceptibility as a factor that might drive Treponema succinifaciens absence in urban populations. Finally, we find an HIV infection signature defined by several taxa not previously associated with HIV, including Dysosmobacter welbionis and Enterocloster sp. This study represents the largest population-representative survey of gut metagenomes of African individuals so far, and paired with extensive clinical biomarkers and demographic data, provides extensive opportunity for microbiome-related discovery.},
}

@article {pmid39880110,
year = {2025},
author = {Chen, N and Wang, L and Zhao, Z and Zhu, M and Li, Y},
title = {Impacts of aquaculture on nitrogen cycling and microbial community dynamics in coastal tidal flats.},
journal = {Environmental research},
volume = {},
number = {},
pages = {120973},
doi = {10.1016/j.envres.2025.120973},
pmid = {39880110},
issn = {1096-0953},
abstract = {The expansion of aquaculture areas has encroached upon vast areas of coastal wetlands and introduced excessive nitrogen inputs, disrupting microbial communities and contributing to various environmental issues. However, investigations on how aquaculture affects microbial communities and nitrogen metabolism mechanisms in coastal tidal flats remain scarce. Hence, we explored the composition, diversity, and assembly processes of nitrogen-cycling (N-cycling) microbial communities in tidal flats in Jiangsu using metagenomic assembly methods. Our study further delved into the seasonal variations of these microbial characteristics to better explore the effects of seasonal changes in aquaculture areas on microbial community. Nitrogen metabolism-related processes and functional genes were identified through the KEGG and NCyc databases. The results revealed significant seasonal variation in the relative abundance and composition of microbial communities. Higher diversity was observed in winter, while the co-occurrence network of microbial communities was more complex in summer. Pseudomonadota emerged as the most abundant phylum in the N-cycling community. Furthermore, pH and NO3-N were identified as the primary factors influencing bacterial community composition, whereas NO2-N was more strongly associated with the N-cycling community. Regarding the nitrogen metabolism processes, nitrogen mineralization and nitrification were predominant in the tidal flat regions. NO2-N and NO3-N exhibited significant effects on several N-cycling functional genes (e.g., nirB, hao, and narG). Finally, neutral and null modeling analyses indicated that bacterial communities were predominantly shaped by stochastic processes, whereas N-cycling communities were largely driven by deterministic processes. These findings highlighted the significant role that aquaculture pollution plays in shaping the N-cycling communities in tidal flats. This underscored the importance of understanding microbial community dynamics and nitrogen metabolism in tidal flats to improve environmental management in coastal aquaculture areas.},
}

@article {pmid39879767,
year = {2025},
author = {Li, S and Bai, Y and Li, Z and Wang, A and Ren, NQ and Ho, SH},
title = {Overlooked role of extracellular polymeric substances in antibiotic-resistance gene transfer within microalgae-bacteria system.},
journal = {Journal of hazardous materials},
volume = {488},
number = {},
pages = {137206},
doi = {10.1016/j.jhazmat.2025.137206},
pmid = {39879767},
issn = {1873-3336},
abstract = {Controlling the spread of antibiotic-resistance genes (ARGs) under antibiotic stress has become an increasingly urgent issue. Microalgae possess the capability to remove antibiotics while concurrently inhibiting ARGs. Microalgae-bacteria systems can produce significant quantities of extracellular polymeric substances (EPS). However, the roles of EPS in the spread of ARGs have not been sufficiently explored, resulting in an insufficient understanding of the contribution of each EPS component and a lack of analysis on the complex interactions between EPS and ARGs. This study systematically explored the overlooked role of EPS in the transmission of ARGs within microalgae-bacteria systems. The current results showed that the potential of the microalgae-bacteria system for treating antibiotic wastewater. The tightly bound-EPS (TB-EPS) can acquire the higher absolute abundances of ARGs compared with the loosely bound-EPS (LB-EPS). The correlation coefficient between polysaccharides and TB-EPS ARGs was higher than that between polysaccharides and LB-EPS ARGs. The gene patterns of LB-EPS closely clustered with those of TB-EPS, while intracellular ARG gene patterns differed from both TB-EPS and LB-EPS. Metagenomic analyses indicated that the relative abundances of sul1 and sul2 were considerably higher at the beginning stage compared to the end stage. The abundance of Achromobacter, increased by the end stage, aligning with its potential to produce exopolysaccharide. Additionally, the absolute abundance of genes encoding exopolysaccharides (nagB and galE) and conjugative transfer transcription regulator (traF), increased over time. These findings enhanced our comprehension of the significance of EPS on the fate of ARGs in microalgae-bacteria systems during the treatment of antibiotic-contaminated wastewater.},
}

@article {pmid39879090,
year = {2025},
author = {McReynolds, E and Elshahed, MS and Youssef, NH},
title = {An ecological-evolutionary perspective on the genomic diversity and habitat preferences of the Acidobacteriota.},
journal = {Microbial genomics},
volume = {11},
number = {1},
pages = {},
doi = {10.1099/mgen.0.001344},
pmid = {39879090},
issn = {2057-5858},
mesh = {*Phylogeny ; *Ecosystem ; *Soil Microbiology ; *Acidobacteria/genetics/classification ; Genome, Bacterial ; Evolution, Molecular ; Metagenomics ; Genetic Variation ; },
abstract = {Members of the phylum Acidobacteriota inhabit a wide range of ecosystems including soils. We analysed the global patterns of distribution and habitat preferences of various Acidobacteriota lineages across major ecosystems (soil, engineered, host-associated, marine, non-marine saline and alkaline and terrestrial non-soil ecosystems) in 248 559 publicly available metagenomic datasets. Classes Terriglobia, Vicinamibacteria, Blastocatellia and Thermoanaerobaculia were highly ubiquitous and showed a clear preference to soil over non-soil habitats, while classes Aminicenantia and Holophagae showed preferences to non-soil habitats. However, while specific preferences were observed, most Acidobacteriota lineages were habitat generalists rather than specialists, with genomic and/or metagenomic fragments recovered from soil and non-soil habitats at various levels of taxonomic resolution. Comparative analysis of 1930 genomes strongly indicates that phylogenetic affiliation plays a more important role than the habitat from which the genome was recovered in shaping the genomic characteristics and metabolic capacities of the Acidobacteriota. The observed lack of strong habitat specialization and habitat-transition-driven lineage evolution in the Acidobacteriota suggest ready cross-colonization between soil and non-soil habitats. We posit that such capacity is key to the successful establishment of Acidobacteriota as a major component in soil microbiomes post-ecosystem disturbance events or during pedogenesis.},
}

*Phylogeny
*Ecosystem
*Soil Microbiology
*Acidobacteria/genetics/classification
Genome, Bacterial
Evolution, Molecular
Metagenomics
Genetic Variation

@article {pmid39878481,
year = {2025},
author = {Ragupathy, V and Kelley, K and Hewlett, I},
title = {Identification of near full-length human pegivirus type 2 (HPgV-2) genomes in blood donor samples co-infected with hepatitis C virus (HCV).},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0117924},
doi = {10.1128/mra.01179-24},
pmid = {39878481},
issn = {2576-098X},
abstract = {Human pegivirus (HPgV) identified from an HCV-infected plasma sample through nanopore metagenomics. The analysis revealed a nearly complete HPgV-2 genome. Phylogenetic analysis confirmed its classification within the HPgV-2 genotype, providing insights into viral co-infection dynamics. The metagenomics approach advances the understanding of viral diversity and supports the development of accurate diagnostics.},
}

@article {pmid39878462,
year = {2025},
author = {Ho, JY and Hu, D and Case, RJ and Boucher, YF},
title = {Metagenome-assembled genomes (MAGs) of the emerging pathogen Shewanella algae from enrichment of coastal seawater, sediment, and algae at St. John's Island, Singapore.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0084624},
doi = {10.1128/mra.00846-24},
pmid = {39878462},
issn = {2576-098X},
abstract = {Coastal water, sediment, and algae samples were collected from St. John's Island, Singapore, and enriched in either broth or agar. Metagenomic sequencing was carried out on DNA from these enrichments and analyzed. A total of 29 metagenome-assembled genomes had been successfully asserted to be a close representation of Shewanella algae.},
}

@article {pmid39877883,
year = {2024},
author = {Takano, Y and Takekoshi, S and Takano, K and Matoba, Y and Mukumoto, M and Sowa, K and Kitazumi, Y and Shirai, O},
title = {A suitable solvent for adsorption of poorly water-soluble substances onto silica gel in a ready biodegradability test.},
journal = {Journal of pesticide science},
volume = {49},
number = {4},
pages = {271-276},
pmid = {39877883},
issn = {1348-589X},
abstract = {When a test substance is poorly water-soluble, it can be adsorbed onto silica gel to facilitate dispersibility in a ready biodegradability test. To uniformly adsorb the test substance onto silica gel, the substance is dissolved in a solvent and then mixed with the silica gel. It is desirable for the solvent to completely evaporate afterward. In this study, we identified n-hexane as a suitable solvent for this purpose. Furthermore, through fluorescence observation, we revealed that the test substance adsorbed onto the silica gel adhered to activated sludge flocs. This is thought to improve contact between the test substance and microorganisms, thereby accelerating biodegradation.},
}

@article {pmid39877881,
year = {2024},
author = {Takano, Y and Takekoshi, S and Takano, K and Matoba, Y and Mukumoto, M and Sowa, K and Kitazumi, Y and Shirai, O},
title = {Comparative evaluation of trimethylated α-, β-, and γ-cyclodextrins as optimal dispersants for ready biodegradability testing of poorly water-soluble substances.},
journal = {Journal of pesticide science},
volume = {49},
number = {4},
pages = {210-223},
pmid = {39877881},
issn = {1348-589X},
abstract = {We investigated whether various modified cyclodextrins (CDs) and emulsifiers could be applied as dispersing agents in ready biodegradability tests of poorly water-soluble substances. Trimethylated α-, β-, and γ-CDs and partially methylated β-CD were not biodegraded in the test period but accelerated the biodegradation of octabenzone and anthraquinone. The process by which trimethylated α-, β-, and γ-CDs enhance the biodegradation of test substances has been partially uncovered. These CDs create inclusion complexes with the substances, which then coalesce into larger aggregates. These aggregates disperse throughout the testing medium and attach to clusters of activated sludge, known as flocs. This close contact with the sludge speeds up the breakdown of the hydrophobic substances being tested.},
}

@article {pmid39877811,
year = {2025},
author = {Latif, S and Kousar, R and Fatima, A and Khan, N and Fatimah, H},
title = {Internal transcribed spacer metagenomics data unravelling the core fungal community structure residing the wheat and maize rhizosphere.},
journal = {Data in brief},
volume = {58},
number = {},
pages = {111269},
pmid = {39877811},
issn = {2352-3409},
abstract = {Plants are colonized by a vast array of microorganisms that outstrip plant cell densities and genes, thus referred to as plant's second genome or extended genome. The microbial communities exert a significant influence on the vigor, growth, development and productivity of plants by supporting nutrient acquisition, organic matter decomposition and tolerance against biotic and abiotic stresses such as heat, high salt, drought and disease, by regulating plant defense responses. The rhizosphere is a complex micro-ecological zone in the direct vicinity of plant roots and is considered a hotspot of microbial diversity. The exploration and understanding of the rhizosphere microbes can be valuable in sustainable agriculture. The present dataset aimed to reveal the core fungal community residing in the rhizosphere of wheat (Triticum aestivum L.) and maize (Zea mays L.). The rhizosphere fungal communities were explored via amplicon sequencing of the Internal Transcribed Spacer (ITS) region using the IonS5[TM]XL sequencing platform. The data obtained were filtered and the high-quality reads were clustered into Microbial Operational Taxonomic Units (OTUs) at 97 % similarity. Further, the data were subjected to alpha and beta diversity analysis. The OTUs obtained from the wheat rhizosphere soils of Kallar Syedian (TA.KS), Islamabad (TA.ISB) and Mirpur Azad Kashmir (TA.MAK) were 603, 513 and 424, respectively, whereas 616 OTUs were found in the maize rhizosphere soil of Kallar Syedian (ZM.KS). The major fungal phyla inhabiting the rhizosphere soils were Ascomycota, accounting for 94 %, 97 %, 95 % and 90 % of the fungal community in ZM.KS, TA.KS, TA.MAK and TA.ISB, respectively. Alpha and beta diversity analysis depicted the presence of considerable variations in the relative abundance of fungal groups residing in the rhizosphere soils. The dataset obtained can be employed in meta-analysis studies that will pave the way toward understanding the core fungal community structure and will directly aid in enhancing crop productivity through rhizosphere engineering.},
}

@article {pmid39877399,
year = {2025},
author = {Park, SY and Goldman, JD and Levine, DJ and Haidar, G},
title = {A Systematic Literature Review to Determine Gaps in Diagnosing Suspected Infection in Solid Organ Transplant Recipients.},
journal = {Open forum infectious diseases},
volume = {12},
number = {1},
pages = {ofaf001},
pmid = {39877399},
issn = {2328-8957},
abstract = {BACKGROUND: Improved diagnostic testing (DT) of infections may optimize outcomes for solid organ transplant recipients (SOTR), but a comprehensive analysis is lacking.

METHODS: We conducted a systematic literature review across multiple databases, including EMBASE and MEDLINE(R), of studies published between 1 January 2012-11 June 2022, to examine the evidence behind DT in SOTR. Eligibility criteria included the use of conventional diagnostic methods (culture, biomarkers, directed-polymerase chain reaction [PCR]) or advanced molecular diagnostics (broad-range PCR, metagenomics) to diagnose infections in hospitalized SOTR. Bias was assessed using tools such as the Cochrane Handbook and PRISMA 2020.

RESULTS: Of 2362 studies, 72 were eligible and evaluated heterogeneous SOT populations, infections, biospecimens, DT, and outcomes. All studies exhibited bias, mainly in reporting quality. Median study sample size was 102 (range, 11-1307). Culture was the most common DT studied (N = 45 studies, 62.5%), with positive results in a median of 27.7% (range, 0%-88.3%). Biomarkers, PCR, and metagenomics were evaluated in 7, 19, and 3 studies, respectively; only 6 reported sensitivity, specificity, and positive/negative predictive values. Directed-PCR performed well for targeted pathogens, but only 1 study evaluated broad-range PCR. Metagenomics approaches detected numerous organisms but required clinical adjudication, with too few studies (N = 3) to draw conclusions. Turnaround time was shorter for PCR/metagenomics than conventional diagnostic methods (N = 4 studies, 5.6%). Only 6 studies reported the impact of DT on outcomes like antimicrobial use and length of stay.

CONCLUSIONS: We identified considerable evidence gaps in infection-related DT among SOT, particularly molecular DT, highlighting the need for further research.},
}

@article {pmid39877321,
year = {2025},
author = {Ito, E and Ohki, T and Toya, N and Emoto, T and Yamashita, T and Sugiyama, T and Yamada, T and Mori, H and Toyoda, A and Hirata, KI},
title = {Metagenomic Analysis of Gut Microbiota for Abdominal Aortic Aneurysm.},
journal = {Annals of vascular diseases},
volume = {18},
number = {1},
pages = {},
pmid = {39877321},
issn = {1881-641X},
abstract = {Objectives: The pathophysiological mechanism of abdominal aortic aneurysm (AAA) remains unclear. We previously reported that Bifidobacterium adolescentis levels were reduced in the feces of patients with AAA by 16S ribosomal ribonucleic acid (RNA) gene sequencing. In this study, we increased the number of cases and conducted metagenomic analyses to examine bacterial genes associated with the pathophysiology of AAA. Methods: For gut microbiota data, feces from 55 patients with AAA and 52 patients with no history of AAA, lower extremity artery disease, or coronary artery disease (control group) were collected. Metagenomic analysis was performed by collecting raw stool samples from patients. For intestinal microbiota analysis, metagenomic analysis of the fecal samples was performed. Results: Oral bacteria, including Actinomyces oris (p <0.0001), Streptococcus salivarius (p <0.001), Lactobacillus salivarius (p <0.001), and Streptococcus sp. (p <0.001), were increased in the feces of patients with AAA. In addition, bacterial genes related to alpha lipoic acid (ALA) biosynthesis (M00882, M00883, and M00884, p <0.0001) were decreased in patients with AAA. Conclusions: In the feces of patients with AAA, there was an increase in oral bacteria, and the expression of bacterial genes related to ALA biosynthesis was reduced. The results suggest the possibility of developing gut microbial drug treatments for AAA.},
}

@article {pmid39877152,
year = {2025},
author = {Plewka, J and Alibrandi, A and Bornemann, TLV and Esser, SP and Stach, TL and Sures, K and Becker, J and Moraru, C and Soares, A and di Primio, R and Kallmeyer, J and Probst, AJ},
title = {Metagenomic analysis of pristine oil sheds new light on the global distribution of microbial genetic repertoire in hydrocarbon-associated ecosystems.},
journal = {microLife},
volume = {6},
number = {},
pages = {uqae027},
pmid = {39877152},
issn = {2633-6693},
abstract = {Oil reservoirs are society's primary source of hydrocarbons. While microbial communities in industrially exploited oil reservoirs have been investigated in the past, pristine microbial communities in untapped oil reservoirs are little explored, as are distribution patterns of respective genetic signatures. Here, we show that a pristine oil sample contains a complex community consisting of bacteria and fungi for the degradation of hydrocarbons. We identified microorganisms and their pathways for the degradation of methane, n-alkanes, mono-aromatic, and polycyclic aromatic compounds in a metagenome retrieved from biodegraded petroleum encountered in a subsurface reservoir in the Barents Sea. Capitalizing on marker genes from metagenomes and public data mining, we compared the prokaryotes, putative viruses, and putative plasmids of the sampled site to those from 10 other hydrocarbon-associated sites, revealing a shared network of species and genetic elements across the globe. To test for the potential dispersal of the microbes and predicted elements via seawater, we compared our findings to the Tara Ocean dataset, resulting in a broad distribution of prokaryotic and viral signatures. Although frequently shared between hydrocarbon-associated sites, putative plasmids, however, showed little coverage in the Tara Oceans dataset, suggesting an undiscovered mode of transfer between hydrocarbon-affected ecosystems. Based on our analyses, genetic information is globally shared between oil reservoirs and hydrocarbon-associated sites, and we propose that currents and other physical occurrences within the ocean along with deep aquifers are major distributors of prokaryotes and viruses into these subsurface ecosystems.},
}

@article {pmid39876557,
year = {2025},
author = {Morsink, MC and van Schaik, EN and Bossers, K and Duijker, DA and Speksnijder, AGCL},
title = {Metagenomics education in a modular CURE format positively affects students' scientific discovery perception and data analytical skills.},
journal = {Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology},
volume = {},
number = {},
pages = {},
doi = {10.1002/bmb.21888},
pmid = {39876557},
issn = {1539-3429},
abstract = {Targeted metagenomics is a rapidly expanding technology to analyze complex biological samples and genetic monitoring of environmental samples. In this research field, data analytical aspects play a crucial role. In order to teach targeted metagenomics data analysis, we developed a 4-week inquiry-driven modular course-based undergraduate research experience (mCURE) using publicly available Australian coral microbiome DNA sequencing data and associated metadata. Since an enormous amount of metadata was provided alongside the DNA sequencing data, groups of students were able to develop their own authentic research questions. Throughout the course, the student groups worked on these research questions and were supported with bioinformatics and statistics lessons. Additionally, practical aspects of data collection and analysis were addressed during hands-on field work on a nearby Dutch beach. Evaluation of the course indicated that the majority of students (1) achieved the intended metagenomics-based learning outcomes and (2) experienced scientific discovery while working on their research projects. In conclusion, the huge amount of data and metadata available in the coral microbiome data set facilitated the development of a strongly inquiry-driven course. Different groups of students were able to develop and conduct their own distinct microbiome research projects and our current mCURE format positively affected students' metagenomics data analytical skills and scientific discovery perception.},
}

@article {pmid39876003,
year = {2025},
author = {Li, Q and Huo, J and Ni, G and Zhang, F and Zhang, S and Zhang, X and Wang, R and Jiao, J and Yu, Z and Pu, X and Yue, Y and Ungerfeld, EM and Zhang, X and Wu, J and Tan, Z and Greening, C and Wang, M},
title = {Reductive acetogenesis is a dominant process in the ruminant hindgut.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {28},
pmid = {39876003},
issn = {2049-2618},
mesh = {Animals ; *Rumen/microbiology ; *Goats/microbiology ; *Cecum/microbiology ; *Hydrogen/metabolism ; *Bacteria/classification/metabolism/genetics/isolation & purification ; *Gastrointestinal Microbiome ; *Fermentation ; *Acetates/metabolism ; *Fatty Acids, Volatile/metabolism ; Archaea/classification/metabolism/genetics ; Ruminants/microbiology ; Methane/metabolism ; },
abstract = {BACKGROUND: The microbes residing in ruminant gastrointestinal tracts play a crucial role in converting plant biomass to volatile fatty acids, which serve as the primary energy source for ruminants. This gastrointestinal tract comprises a foregut (rumen) and hindgut (cecum and colon), which differ in structures and functions, particularly with respect to feed digestion and fermentation. While the rumen microbiome has been extensively studied, the cecal microbiome remains much less investigated and understood, especially concerning the assembling microbial communities and overriding pathways of hydrogen metabolism.

RESULTS: To address this gap, we comparatively investigated the composition, capabilities, and activities of the rumen and the cecum microbiome using goats as an experimental ruminant model. In situ measurements showed significantly higher levels of dissolved hydrogen and acetate in the cecum than in the rumen. Increased dissolved hydrogen indicated distinct processes and reduced coupling between fermentative H2 production and utilization, whereas higher levels of acetate could be caused by slower VFA absorption through cecal papillae than through the rumen papillae. Microbial profiling indicated that the cecum harbors a greater abundance of mucin-degrading microbes and fermentative hydrogen producers, whereas the rumen contains a higher abundance of fibrolytic fermentative bacteria, hydrogenotrophic respiratory bacteria, and methanogenic archaea. Most strikingly, reductive acetogenic bacteria were 12-fold more abundant in the cecum. Genome-resolved metagenomic analysis unveiled that the cecum acetogens are both phylogenetically and functionally distinct from those found in the rumen. Further supporting these findings, two in vitro experiments demonstrated a marked difference in hydrogen metabolism pathways between the cecum and the rumen, with increased acetate production and reduced methanogenesis in the cecum. Moreover, comparative analysis across multiple ruminant species confirmed a strong enrichment of reductive acetogens in the hindguts, suggesting a conserved functional role.

CONCLUSIONS: These findings highlight an enrichment of acetogenesis in a key region of the gastrointestinal tract and reshape our understanding of ruminant hydrogen metabolism and how the H2 can be managed in accord to livestock methane mitigation efforts. Video Abstract.},
}

Animals
*Rumen/microbiology
*Goats/microbiology
*Cecum/microbiology
*Hydrogen/metabolism
*Bacteria/classification/metabolism/genetics/isolation & purification
*Gastrointestinal Microbiome
*Fermentation
*Acetates/metabolism
*Fatty Acids, Volatile/metabolism
Archaea/classification/metabolism/genetics
Ruminants/microbiology
Methane/metabolism

@article {pmid39875829,
year = {2025},
author = {Zhang, Z and Zong, X and Liu, Z and Dong, X and Bai, H and Fan, L and Li, T},
title = {Comprehensive analysis of vaginal microbiota in Chinese women with genital tuberculosis: implications for diagnosis and treatment.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {52},
pmid = {39875829},
issn = {1471-2180},
support = {2024-4-2119//Capital's Funds for Health Improvement and Research/ ; FCYY201916//Special Training Program for Young and Middle-aged Subject Backbone of Beijing Obstetrics and Gynecology Hospital, Capital Medical University/ ; YQRC201906//"Excellent young Talents" project of Beijing Obstetrics and Gynecology Hospital, Capital Medical University/ ; },
mesh = {Humans ; Female ; *Vagina/microbiology ; Adult ; *Tuberculosis, Female Genital/microbiology/diagnosis ; *Microbiota ; China ; Middle Aged ; Young Adult ; Antitubercular Agents/therapeutic use ; Lactobacillus/isolation & purification/genetics ; Bacteria/classification/genetics/isolation & purification ; Metagenomics/methods ; East Asian People ; },
abstract = {BACKGROUND: Tuberculosis remains an infectious disease of global concern, with potential impacts on respiratory and intestinal microbiota owing to prolonged broad-spectrum antibiotic therapy. Despite its potential to cause infertility, the vaginal microbiota of women with genital tuberculosis remains poorly understood. We comprehensively analyzed the vaginal microbiota in Chinese women with genital tuberculosis.

RESULTS: We recruited women with pelvic (n = 28), endometrial (n = 16), and pulmonary (n = 12) tuberculosis as the research group, and healthy women (n = 11) as the control group. Vaginal discharges were collected for metagenomic analysis of its microbiota. The alpha diversity of the vaginal microbiota in women with genital tuberculosis was slightly higher than that in healthy women, though the difference was not statistically significant (P = 0.23). Similarly, no significant differences in alpha diversity were observed between women with genital and pulmonary tuberculosis (P = 0.82) or between those with pelvic and endometrial tuberculosis (P = 0.82). Notably, the lowest alpha diversity was recorded six months to one year after initiating anti-tuberculosis treatment, with this decline being statistically significant (P = 0.023). The dominance of Lactobacillus iners in the vaginal microbiota was more common in women with genital tuberculosis than that of Lactobacillus crispatus. Furthermore, the abundance of short-chain fatty acid -producing anaerobes, such as Actinomycetes, Streptococcus, and Finegoldia, were significantly increased. Short-chain fatty acid precursor pathways, including the ko03010 ribosome pathway, ko00970 aminoacyl-tRNA synthesis, ko00230 purine metabolism, ko00240 pyrimidine metabolism, and ko00010 glycolysis gluconeogenesis pathway, were significantly upregulated in women with endometrial tuberculosis.

CONCLUSIONS: Extrapulmonary tuberculosis, particularly genital tuberculosis and its associated vaginal dysbiosis impacts female fecundity. Vaginal dysbiosis is more pronounced when M. tuberculosis invades the endometrium. Given the effect of antibiotics on vaginal flora, probiotic combined interventions could be used as a future research direction.

CLINICAL TRIAL NUMBER: Not applicable.},
}

Humans
Female
*Vagina/microbiology
Adult
*Tuberculosis, Female Genital/microbiology/diagnosis
*Microbiota
China
Middle Aged
Young Adult
Antitubercular Agents/therapeutic use
Lactobacillus/isolation & purification/genetics
Bacteria/classification/genetics/isolation & purification
Metagenomics/methods
East Asian People

@article {pmid39875797,
year = {2025},
author = {Sung, YH and Ju, YK and Lee, HJ and Park, SM and Suh, JW and Kim, JY and Sohn, JW and Yoon, YK},
title = {Clinical performance of real-time nanopore metagenomic sequencing for rapid identification of bacterial pathogens in cerebrospinal fluid: a pilot study.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {3493},
pmid = {39875797},
issn = {2045-2322},
support = {Q2021541//Yuhan/ ; HI23C1297//Ministry of Health and Welfare/ ; },
mesh = {Humans ; Pilot Projects ; Female ; Male ; *Meningitis, Bacterial/cerebrospinal fluid/diagnosis/microbiology ; *Metagenomics/methods ; Middle Aged ; *Nanopore Sequencing/methods ; *RNA, Ribosomal, 16S/genetics ; Adult ; *Bacteria/genetics/isolation & purification/classification ; Aged ; Nanopores ; Cerebrospinal Fluid/microbiology ; Young Adult ; Sensitivity and Specificity ; High-Throughput Nucleotide Sequencing/methods ; },
abstract = {This study aimed to evaluate the usefulness of amplicon-based real-time metagenomic sequencing applied to cerebrospinal fluid (CSF) for identifying the causative agents of bacterial meningitis. We conducted a 16S rRNA amplicon sequencing using a nanopore-based platform, alongside routine polymerase chain reaction (PCR) testing or bacterial culture, to compare its clinical performance in pathogen detection on CSF samples. Among 17 patients, nanopore-based sequencing, multiplex PCR, and bacterial culture detected potential bacterial pathogens in 47.1%, 0%, and 47.1% samples, respectively. Nanopore-based sequencing demonstrated a sensitivity of 50.0%, specificity of 55.6%, positive predictive value of 50.0%, negative predictive value of 55.6%, and overall accuracy of 47.1%, compared to the gold standard method for bacterial culture. In 44.4% (4/9) of culture-negative cases, nanopore-based sequencing detected potentially causative pathogens, whereas four (23.5%) patients were positive only in culture. Using nanopore-based sequencing alongside bacterial culture increased the positivity rate from 47.1 to 70.6%. However, these values may be overestimated due to challenges in distinguishing significant pathogens from background noise. Meanwhile, the bioinformatics module in EPI2ME reduced the turn-around time to 10 min. Nanopore-based metagenomic sequencing is expected to serve as a complementary tool for pathogen detection in CSF samples by facilitating rapid and accurate diagnosis.},
}

Humans
Pilot Projects
Female
Male
*Meningitis, Bacterial/cerebrospinal fluid/diagnosis/microbiology
*Metagenomics/methods
Middle Aged
*Nanopore Sequencing/methods
*RNA, Ribosomal, 16S/genetics
Adult
*Bacteria/genetics/isolation & purification/classification
Aged
Nanopores
Cerebrospinal Fluid/microbiology
Young Adult
Sensitivity and Specificity
High-Throughput Nucleotide Sequencing/methods

@article {pmid39875095,
year = {2025},
author = {Moeller, AH},
title = {Partner fidelity, not geography, drives co-diversification of gut microbiota with hominids.},
journal = {Biology letters},
volume = {21},
number = {1},
pages = {20240454},
doi = {10.1098/rsbl.2024.0454},
pmid = {39875095},
issn = {1744-957X},
support = {/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; *Phylogeny ; Hominidae/microbiology ; Bacteria/classification/genetics/isolation & purification ; Genome, Bacterial ; Geography ; },
abstract = {Bacterial strains that inhabit the gastrointestinal tracts of hominids have diversified in parallel (co-diversified) with their host species. The extent to which co-diversification has been mediated by partner fidelity between strains and hosts or by geographical distance between hosts is not clear due to a lack of strain-level data from clades of hosts with unconfounded phylogenetic relationships and geographical distributions. Here, I tested these competing hypotheses through meta-analyses of 7121 gut bacterial genomes assembled from wild-living ape species and subspecies sampled throughout their ranges in equatorial Africa. Across the gut bacterial phylogeny, strain diversification was more strongly associated with host phylogeny than with geography. In total, approximately 14% of the branch length of the gut bacterial phylogeny showed significant evidence of co-diversification independent of geography, whereas only approximately 4% showed significant evidence of diversification associated with geography independent of host phylogeny. Geographically co-occurring heterospecific hosts (Pan and Gorilla) universally maintained distinct co-diversified bacterial strains. Strains whose diversification was associated with geography independent of host phylogeny included clades of Proteobacteria known to adopt free-living lifestyles (e.g. Escherichia). These results show that co-diversification of gut bacterial strains with hominids has been driven primarily by fidelity of strains to host lineages rather than geography.},
}

Animals
*Gastrointestinal Microbiome
*Phylogeny
Hominidae/microbiology
Bacteria/classification/genetics/isolation & purification
Genome, Bacterial
Geography

@article {pmid39875062,
year = {2025},
author = {Zhan, M and Li, Z and Chen, J and Zhao, Y and Bai, Z and Lu, B and Chen, H and Liu, Y},
title = {Indoxyl sulfate (IS) mediates pro-inflammatory responses in severe pneumonia in patients with rheumatoid arthritis associated interstitial lung disease.},
journal = {Clinical immunology (Orlando, Fla.)},
volume = {},
number = {},
pages = {110430},
doi = {10.1016/j.clim.2025.110430},
pmid = {39875062},
issn = {1521-7035},
abstract = {OBJECT: Patients with rheumatoid arthritis-associated interstitial lung disease (RA-ILD) have a high risk of serious infection, in particular severe pneumonia. This study aimed to investigate the transcriptional landscape, lower respiratory tract (LRT) microbiome and metabolomic profiles in the lung of RA-ILD patients with pneumonia.

METHOD: A total of 10 RA-ILD with pneumonia were enrolled in this study. In addition, 11 patients with COVID-19-associated pneumonia and 6 patients with non-autoimmune and non-COVID-19-related ILD with pneumonia were included as controls. Bronchoalveolar lavage fluid (BALF) was collected and prepared for metagenomic next-generation sequencing (mNGS), non-targeted metabolomics and bulk RNA-seq.

RESULT: Neutrophil-related genes were shared in the BALF cells of RA-ILD patients with pneumonia and patients with COVID-19-associated pneumonia. Carnobacterium, Wujia, Intestinimonas, Apibacter, Anaerotignum and Parvimonas were enriched in the LRT microbiome of RA-ILD, while Wujia, Apibacter, Pseudocitrobacter, and Thermobacillus were enriched in the LRT microbiome of COVID-19. Metabolomics analysis of BALF revealed significant elevation of indoxyl sulfate (IS) in the BALF of RA-ILD patients in comparison to COVID-19. Mechanistically, IS exerts an pro-inflammatory effect on macrophages and bronchial epithelial cells for pro-inflammatory cytokine production and potentiated neutrophils for neutrophil extracellular traps (NETs) formation.

CONCLUSIONS: Our results demonstrated a significant differences in the LRT microbiome and BALF metabolites between RA-ILD and COVID-19 patients with pneumonia, although they displayed similar local immune responses against lung infection. Alterations of LRT microbiome and related metabolites may be implicated in the pathogenesis of pneumonia in RA-ILD.},
}

@article {pmid39874761,
year = {2025},
author = {Wang, R and Chen, J and Chen, H},
title = {Metagenomic insights into efficiency and mechanism of antibiotic resistome reduction by electronic mediators-enhanced microbial electrochemical system.},
journal = {Journal of hazardous materials},
volume = {488},
number = {},
pages = {137350},
doi = {10.1016/j.jhazmat.2025.137350},
pmid = {39874761},
issn = {1873-3336},
abstract = {Electronic mediators are an effective means of enhancing the efficiency of microbial electrochemical electron transfer; however, there are still gaps in understanding the strengthening mechanisms and the efficiency of removing antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB). This study systematically elucidates the effects of various electron mediators on bioelectrochemical processes, electron transfer efficiency, and the underlying mechanisms that inhibit ARG propagation within sediment microbial fuel cell systems (SMFCs). The results indicate that the addition of electron mediators significantly increased the output voltage (33.3 %-61.1 %) and maximum power density (14 %-106 %) of SMFCs, while also reducing ARB abundance and transmission risk. The enhancement effect follows the order of biochar, nanoscale zero-valent iron, graphene, and carbon nanotubes, with biochar emerging as the most economical and efficient choice for generating electricity and removing human pathogenic bacteria carrying ARGs. Procrustes analysis revealed that electron mediators facilitated the removal of ARGs by altering the structure of the microbiome, particularly the electricity-generating microorganisms (EGMs). Voltage and mobile genetic elements were the primary drivers of ARGs in the SMFCs. The network analysis results show that multiple carbohydrate-active enzymes, cluster of orthologous groups, and EGMs were negatively correlated with ARGs, indicating that the electron mediator-enhanced SMFCs mainly inhibit the spread of ARGs by promoting cell division, carbohydrate metabolism, and electricity generation. This study provides novel insights into how electron mediators affect ARG removal in microbial electrochemistry, which can inform economically viable strategies for sustainable environmental remediation.},
}

@article {pmid39874694,
year = {2025},
author = {Wang, H and Dai, H and Jiang, D and Cao, X and Wang, R and Dai, Z and Zhang, W and Abbasi, HN and Li, B and Zhu, G and Wang, X},
title = {Screening, identification, and application of anaerobic ammonia oxidizing bacteria in activated sludge systems: A comprehensive review.},
journal = {Journal of environmental management},
volume = {375},
number = {},
pages = {124272},
doi = {10.1016/j.jenvman.2025.124272},
pmid = {39874694},
issn = {1095-8630},
abstract = {Anaerobic ammonium oxidation (Anammox) has garnered significant attention due to its ability to eliminate the need for aeration and supplementary carbon sources in biological nitrogen removal process, relying on the capacity of anaerobic ammonium oxidizing bacteria (AnAOB) to directly convert ammonium and nitrite nitrogen into nitrogen gas. This review consolidates the latest advancements in AnAOB research, outlining the mechanisms and enzymatic processes of Anammox, and summarizing the molecular biological techniques used for studying AnAOB, such as 16s rRNA sequencing, qPCR, and metagenomic sequencing. Additionally, it also overviews the currently identified AnAOB species and their distinct metabolic traits, while consolidating strategies to improve their performance. It further delineates coupled processes that utilize Anammox technology, offering practical insights for process selection. Eventually, the review concludes by suggesting future research directions and highlighting critical areas for further investigation. This review serves as a theoretical reference for the enrichment and cultivation of AnAOB, environmental impact management, and the selection of effective treatment processes.},
}

@article {pmid39874239,
year = {2025},
author = {Zhou, H and Balint, D and Shi, Q and Vartanian, T and Kriegel, MA and Brito, I},
title = {Lupus and inflammatory bowel disease share a common set of microbiome features distinct from other autoimmune disorders.},
journal = {Annals of the rheumatic diseases},
volume = {84},
number = {1},
pages = {93-105},
doi = {10.1136/ard-2024-225829},
pmid = {39874239},
issn = {1468-2060},
mesh = {Humans ; *Inflammatory Bowel Diseases/microbiology/immunology ; *Lupus Erythematosus, Systemic/microbiology/immunology ; *Gastrointestinal Microbiome/genetics ; *Autoimmune Diseases/microbiology/immunology ; Biomarkers ; Female ; Metagenomics/methods ; Metagenome ; Male ; Receptors, Glucocorticoid/genetics ; },
abstract = {OBJECTIVES: This study aims to elucidate the microbial signatures associated with autoimmune diseases, particularly systemic lupus erythematosus (SLE) and inflammatory bowel disease (IBD), compared with colorectal cancer (CRC), to identify unique biomarkers and shared microbial mechanisms that could inform specific treatment protocols.

METHODS: We analysed metagenomic datasets from patient cohorts with six autoimmune conditions-SLE, IBD, multiple sclerosis, myasthenia gravis, Graves' disease and ankylosing spondylitis-contrasting these with CRC metagenomes to delineate disease-specific microbial profiles. The study focused on identifying predictive biomarkers from species profiles and functional genes, integrating protein-protein interaction analyses to explore effector-like proteins and their targets in key signalling pathways.

RESULTS: Distinct microbial signatures were identified across autoimmune disorders, with notable overlaps between SLE and IBD, suggesting shared microbial underpinnings. Significant predictive biomarkers highlighted the diverse microbial influences across these conditions. Protein-protein interaction analyses revealed interactions targeting glucocorticoid signalling, antigen presentation and interleukin-12 signalling pathways, offering insights into possible common disease mechanisms. Experimental validation confirmed interactions between the host protein glucocorticoid receptor (NR3C1) and specific gut bacteria-derived proteins, which may have therapeutic implications for inflammatory disorders like SLE and IBD.

CONCLUSIONS: Our findings underscore the gut microbiome's critical role in autoimmune diseases, offering insights into shared and distinct microbial signatures. The study highlights the potential importance of microbial biomarkers in understanding disease mechanisms and guiding treatment strategies, paving the way for novel therapeutic approaches based on microbial profiles.

TRIAL REGISTRATION NUMBER: NCT02394964.},
}

Humans
*Inflammatory Bowel Diseases/microbiology/immunology
*Lupus Erythematosus, Systemic/microbiology/immunology
*Gastrointestinal Microbiome/genetics
*Autoimmune Diseases/microbiology/immunology
Biomarkers
Female
Metagenomics/methods
Metagenome
Male
Receptors, Glucocorticoid/genetics

@article {pmid39873828,
year = {2025},
author = {Pal, S and Biswas, R and Sar, A and Misra, A and Dam, S and Dam, B},
title = {ABC-type salt tolerance transporter genes are abundant and mutually shared among the microorganisms of the hypersaline Sambhar Lake.},
journal = {Extremophiles : life under extreme conditions},
volume = {29},
number = {1},
pages = {14},
pmid = {39873828},
issn = {1433-4909},
mesh = {*Salt Tolerance ; *Lakes/microbiology ; *ATP-Binding Cassette Transporters/genetics/metabolism ; Metagenome ; India ; Bacterial Proteins/genetics/metabolism ; },
abstract = {To fish-out novel salt-tolerance genes, metagenomic DNA of moderately saline sediments of India's largest hypersaline Sambhar Lake was cloned in fosmid. Two functionally-picked clones helped the Escherichia coli host to tolerate 0.6 M NaCl. Deep sequencing of their fosmid DNA insert revealed 32-37% of genes to encode transporters, mostly belonging to ABC (ATP-Binding Cassette)-type, but none specific to channel Na[+]. The complete metagenome sequence of Sambhar Lake brines, and reanalysed data of twelve other hypersaline metagenome sequences, however, have only around 5% transporter genes, suggesting metagenomic DNA fragments being biasedly-cloned during functional screening. Almost half of the ~ 40 Kb inserts in the two clones was shared, and encode several transporters, and some transposase. This advocates that these transporter-loaded DNA lengths are shuttled among microorganisms of hypersaline environments. Interestingly, one clone showed retarded growth with prominent cell disruptions in scanning electron microscopic images, when fosmid copy number was increased or transporters were NaCl-induced. Its cloned insert exclusively has three genes, encoding a structurally functional ATP-binding protein and its efflux component, whose possible overexpression led to membrane crowding and cell rupture. Thus, microorganisms thriving in hypersaline lakes have plentiful ABC transporters that are mutually shared among themselves. These novel salt tolerance genes have future agricultural biotechnological potential.},
}

*Salt Tolerance
*Lakes/microbiology
*ATP-Binding Cassette Transporters/genetics/metabolism
Metagenome
India
Bacterial Proteins/genetics/metabolism

@article {pmid39873521,
year = {2025},
author = {Pu, G and Hou, L and Zhao, Q and Liu, G and Wang, Z and Zhou, W and Niu, P and Wu, C and Li, P and Huang, R},
title = {Interactions between gut microbes and host promote degradation of various fiber components in Meishan pigs.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0150024},
doi = {10.1128/msystems.01500-24},
pmid = {39873521},
issn = {2379-5077},
abstract = {UNLABELLED: Although metagenomic investigations into microbial fiber-degrading capabilities are currently prevalent, there is a notable gap in research concerning the regulatory mechanisms underpinning host-microbiota interactions that confer tolerance to high-fiber diets in pigs. In this study, 28 Meishan (MS) and 28 Large White (LW) pigs were subjected to feeding experiments involving various fiber levels. Subsequently, multi-omics was employed to investigate the influence of host-microbiota interactions on the fiber degradation of pigs. MS exhibited superior fiber digestibility compared with LW, particularly evident when fed a high-fiber diet. In MS, positive interactions among Treponema bryantii, Treponema sp., Rikenellaceae bacterium, and Bacteroidales bacterium WCE2004 facilitated the degradation of both cellulose and pectin. The reduced polymerization of polysaccharides and oligosaccharides observed in MS provides compelling evidence for their superior microbial fiber-degrading capability. The concentrations of propionate and butyrate retained in cecal lumen of MS was unchanged, whereas it was significantly increased in LW, indicating a strong absorption of short-chain fatty acids (SCFAs) in MS intestines. Correlation analysis using RNA-seq data revealed distinct patterns in LW and MS. In LW, microbial profiles along with GPR183 and GPR174 exhibited negative correlations with butyrate and propionate, respectively. Conversely, in MS, GPR174 and SLC2A4 were positively correlated with butyrate. Our findings underscore the dynamic collaboration among microbial species in degrading cellulose and pectin, coupled with the synergistic effects of SCFA transport-related genes, as crucial underpinnings for the heightened fiber digestibility observed in MS. These discoveries offer fresh perspectives into the intricate mechanisms governing host-microbiota interactions that influence fiber digestion in pigs.

IMPORTANCE: Studies on porcine intestinal microbiota have been widely conducted, and some microbial taxa with fiber degradation functions have been identified. However, the mechanisms of division among gut microbes in the degradation of complex fiber components are still unclear. In addition, the regulation of fiber digestion by host through absorption of short-chain fatty acids (SCFAs) needs to be further investigated. Our study used apparent total tract digestibility of dietary fiber to assess the utilization efficiency of dietary fiber between Meishan and Large White pigs. Subsequently, through metagenome sequencing and determination of fiber-degrading products, we found that in Meishan pigs, positive interactions among Treponema bryantii, Treponema sp., Rikenellaceae bacterium, and Bacteroidales bacterium WCE2004 facilitated the degradation of both cellulose and pectin. RNA-seq analysis elucidated breed-specific genes associated with SCFA absorption in cecum. By integrating multi-omics data, we constructed a framework outlining host-microbiota interactions that control dietary fiber utilization in pigs. Our data provide novel insights into host-microbiota interactions regulating fiber degradation and lay some theoretical foundations for improving the utilization efficiency of high-fiber cereal feed in pigs through targeted modulation of gut microbial function.},
}

@article {pmid39873074,
year = {2025},
author = {Yang, YH and Yu, JJ and Han, HY and Chang, WM and Wang, CW},
title = {Ex-vivo investigation of human salivary microbial growth with lysogeny broth for translational research-A pilot study.},
journal = {Journal of dental sciences},
volume = {20},
number = {1},
pages = {437-443},
pmid = {39873074},
issn = {2213-8862},
abstract = {BACKGROUND/PURPOSE: Salivary microbiome has become a surrogate indicator of oral disease due to its collective reservoirs and convenience in sampling. However, failed clinical trials often lead to wastes of resources, indicating a need for preclinical models. In this pilot study, we aimed to compare the salivary microbiome by metagenomics analysis before and after lysogeny broth culture for prospective translational studies.

MATERIALS AND METHODS: The study cohort included seven patients with severe periodontitis (Stage III/IV, Grade C), from whom unstimulated saliva was collected. The salivary microbiome was sequenced over the 16S rRNA gene V3-V4 hypervariable regions at baseline and after 6 hours of lysogeny broth culture.

RESULTS: The results revealed changes in salivary microbiome and reduced bacterial diversity after culture, mainly due to the expansion of genera Neisseria (Median (Mdn) 15.95% to 37.52%, P < 0.05), Rothia (Mdn 10.21% to 16.32%, P < 0.05), and Haemophilus (Mdn 5.88% to 13.25%, P < 0.05). Periodontitis-related pathogens such as phyla Bacteroidetes, Fusobacteria and Spirochaetes were identified, while genera Porphyromonas, Parvimonas, Peptostreptococcus, and Campylobacter showed a decrease after lysogeny broth culture. Caries-related pathogens, including genera Veillonella, Leptotrichia, and species Haemophilus parainfluenzae and Streptococcus salivarius, were also detected.

CONCLUSION: This pilot study revealed that periodontitis- and caries-related bacteria could be identified in the saliva at baseline and after 6 hours ex-vivo culture with lysogeny broth. Our findings also suggested that lysogeny broth favored the growth of specific genera and may serve as a reference to monitor short-term modulation of these bacteria in salivary microbiome.},
}

@article {pmid39872816,
year = {2024},
author = {Gu, G and Zeeshan Ul Haq, M and Sun, X and Zhou, J and Liu, Y and Yu, J and Yang, D and Yang, H and Wu, Y},
title = {Continuous cropping of Patchouli alters soil physiochemical properties and rhizosphere microecology revealed by metagenomic sequencing.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1482904},
pmid = {39872816},
issn = {1664-302X},
abstract = {Continuous cropping (CC) profoundly impacts soil ecosystems, including changes in soil factors and the structure and stability of microbial communities. These factors are interrelated and together affect soil health and plant growth. In this research, metagenomic sequencing was used to explore the effects of CC on physicochemical properties, enzyme activities, microbial community composition, and functional genes of the rhizosphere soil of patchouli. We found that this can lead to changes in various soil factors, including the continuous reduction of pH and NH 4 + -N and the unstable changes of many factors. In addition, S-PPO enzyme activity increased significantly with the cropping years, but S-NAG increased in the first 2 years and decreased in the third cropping year. Metagenomic sequencing results showed that CC significantly changed the diversity and composition of rhizosphere microbial communities. The relative abundance of Pseudomonas and Bacteroides decreased substantially from the phylum level. At the genus level, the number of microbial genera specific to the zero-year cropping (CK) and first (T1), second (T2), and third (T3) years decreased significantly, to 1798, 172, 42, and 44, respectively. The abundance of many functional genes changed, among which COG0823, a gene with the cellular process and signaling functions, significantly increased after CC. In addition, NH 4 + -N, S-CAT, S-LAP, and SOC were the main environmental factors affecting rhizosphere-dominant microbial communities at the phylum level, while pH, SOC, and AK were the key environmental factors affecting rhizosphere functional genes of Pogostemon cablin. In summary, this study showed the dynamic changes of soil factors and rhizosphere microorganisms during CC, providing a theoretical basis for understanding the formation mechanism and prevention of CC obstacles and contributing to the formulation of scientific soil management and fertilization strategies.},
}

@article {pmid39872134,
year = {2025},
author = {Li, Y and Ren, X and Wang, Q and Shen, S and Li, Y and Qian, X and Tang, Y and Jia, J and Zhang, H and Ding, J and Song, Y and Zhang, S and Wang, S and Xu, Y and Jiang, Y and He, X and Dai, M and Zhong, L and Xiong, Y and Pan, Y and Wang, M and Shao, H and Cai, H and Huang, L and Wang, H},
title = {A Predictive Model for Pulmonary Aspergillosis in ICU Patients: A Multicenter Retrospective Cohort Study.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {441-454},
pmid = {39872134},
issn = {1178-6973},
abstract = {BACKGROUND: Several predictive models for invasive pulmonary aspergillosis (IPA) based on clinical characteristics have been reported. Nevertheless, the significance of other concurrently detected microorganisms in IPA patients is equally noteworthy. This study aimed to develop a risk prediction model for IPA by integrating clinical and microbiological characteristics.

METHODS: This retrospective study was conducted in adult intensive care units (ICUs) of 17 medical centers in China. Clinical data were collected from patients with severe pneumonia who underwent clinical metagenomics of bronchoalveolar lavage fluid between January 1, 2019, and June 30, 2023. Subsequently, patients were randomly assigned to training and validation cohorts in a 7:3 ratio. In the training cohort, potential influencing factors were identified through univariate analysis, clinical practice, and existing literature, and a risk prediction model was constructed using multivariate logistic regression analysis. The performance of this model was then assessed and validated in the validation cohort.

RESULTS: Out of 1737 patients initially included in the study, 898 were ultimately analyzed, of which 100 (11%) were diagnosed with IPA. The risk prediction model for IPA, incorporating microbiological characteristics, identified six independent risk factors, namely age, immunosuppression, chronic kidney disease, connective tissue disease, liver failure, and cytomegalovirus positivity. The model demonstrated a superior discriminative ability, with area under the curve (AUC) values of 0.791 and 0.792 in the training and validation cohorts, respectively. Sensitivity and specificity reached 73.1% and 74.9%, respectively, and the model demonstrated good calibration.

CONCLUSION: This study developed a novel risk prediction model for IPA incorporating microbiological characteristics based on clinical metagenomics. The model exhibited good discriminative ability and calibration.},
}

@article {pmid39872133,
year = {2025},
author = {Liu, B and Bao, Z and Chen, W and Xi, X and Ge, X and Zhou, J and Zheng, X and Zhang, P and Deng, W and Ding, R and Zhou, M and Fang, J},
title = {Targeted Next-Generation Sequencing in Pneumonia: Applications in the Detection of Responsible Pathogens, Antimicrobial Resistance, and Virulence.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {407-418},
pmid = {39872133},
issn = {1178-6973},
abstract = {BACKGROUND: Targeted next-generation sequencing (tNGS) is a high-throughput and cost-effective diagnostic alternative for pneumonia, with the ability to simultaneously detect pathogens, antimicrobial resistance genes, and virulence genes. We aimed to explore the applicability of tNGS in the co-detection of the responsible pathogens, antimicrobial resistance (AMR) genes, and virulence genes in patients with pneumonia.

METHODS: A prospective study was conducted among patients with suspected pneumonia at Ruijin Hospital from March 1 to May 31, 2023. Bronchoalveolar lavage fluid (BALF) or sputum samples were collected and sent for tNGS, metagenomic next-generation sequencing (mNGS), and conventional microbiological tests (CMTs).

RESULTS: In total, 67 BALF and 11 sputum samples from 78 patients were included in the analyses. According to the composite reference standards, the accuracy of tNGS in the detection of responsible pathogens was 0.852 (95% confidence interval 0.786-0.918), which resembled that of mNGS and remarkably exceeded that of CMTs. In addition, 81 AMR genes associated with responsible pathogens were reported, and 75.8% (25/33) priority drug-resistant pathogens could be directly identified. A total of 144 virulence genes were detected for four common pathogens. And patients with virulence genes detected were of higher proportions of severe pneumonia (95.0% vs 42.9%, P = 0.009), acute respiratory distress syndrome (55.0% vs 0%, P = 0.022), and neutrophils (82.3% vs 62.2%, P = 0.026) than those not.

CONCLUSION: In patients with pneumonia, tNGS could detect the responsible pathogens, AMR genes, and virulence genes simultaneously, serving as an efficient and cost-effective tool for the diagnosis, treatment, and severity indication of pneumonia.},
}

@article {pmid39872132,
year = {2025},
author = {Jia, Q and Wang, L and Tong, X and Sun, J and Fan, H},
title = {Coexistence of Asymptomatic Allergic Bronchopulmonary Aspergillosis and Active Pulmonary Tuberculosis: Case Report.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {401-405},
pmid = {39872132},
issn = {1178-6973},
abstract = {We present a rare case of asymptomatic allergic bronchopulmonary aspergillosis (ABPA) concurrent with active pulmonary tuberculosis. Allergic bronchopulmonary aspergillosis is an immunological pulmonary disorder characterized by hypersensitivity to Aspergillus fumigatus, while pulmonary tuberculosis (PTB) is a complex infection caused by Mycobacterium tuberculosis (MTB). The association between pulmonary tuberculosis infections and Aspergillus infections remains a fascinating area of inquiry. A 26-year-old female patient exhibited no symptoms. However, her initial chest computed tomography revealed bronchiectasis with high-attenuation mucus plugs in the upper lobes, peripheral lung atelectasis, and a tree-in-bud pattern. To obtain a clear diagnosis, she visited multiple hospitals and incurred substantial time and financial costs. Active tuberculosis was initially confirmed using specialized detection methods, including metagenomic next-generation sequencing and Xpert MTB/RIF analysis of bronchoalveolar lavage fluid. Subsequent pathological biopsy and Aspergillus-specific antibody tests further confirmed the diagnosis of allergic bronchopulmonary aspergillosis combined with active tuberculosis. Following twelve months of antituberculosis therapy, an avoidable surgery, and three months of oral glucocorticoid treatment, the patient's lung lesions showed significant resolution. This case provides valuable insights into the clinical diagnosis and management of these two distinct infectious diseases.},
}

@article {pmid39871844,
year = {2024},
author = {Zhang, Y and Yin, M and Wen, H},
title = {VV-ECMO adjuvant therapy for Leptospira complicated with H1N1 infection: a case report.},
journal = {Frontiers in medicine},
volume = {11},
number = {},
pages = {1495324},
pmid = {39871844},
issn = {2296-858X},
abstract = {BACKGROUND: Leptospirosis is an acute infectious disease that occurs by infection, progresses rapidly, and has a high mortality rate, with an estimated 1.2 million new cases and nearly 59,000 deaths each year. Due to its diverse clinical manifestations, diagnosis is often delayed. Therefore, it is necessary to pay attention to its clinical manifestations, diagnostic techniques, and treatment methods.

CASE REPORT: A 51-year-old male patient from the Han ethnic group experienced fever, chills, headache, and overall fatigue after being exposed to rain, followed by yellowing of the skin and worsening of breathing difficulties. Metagenomic next-generation sequencing (mNGS) indicates infection with leptospirosis and influenza A. After 5 days of treatment with venovenous extracorporeal membrane oxygenation (VV-ECMO), Penicillium, and Oseltamivir, the condition improved.

CONCLUSION: Leptospirosis improves with VV-ECMO support and anti-infective treatment with penicillin and oseltamivir. VV-ECMO provides a therapeutic time window for rescue, and mNGS lays a foundation for early detection of etiology of leptospirosis.},
}

@article {pmid39871406,
year = {2025},
author = {Noell, SE and Abbaszadeh, J and Richards, H and Labat Saint Vincent, M and Lee, CK and Herbold, CW and Stott, MB and Cary, SC and McDonald, IR},
title = {Antarctic Geothermal Soils Exhibit an Absence of Regional Habitat Generalist Microorganisms.},
journal = {Environmental microbiology},
volume = {27},
number = {1},
pages = {e70032},
doi = {10.1111/1462-2920.70032},
pmid = {39871406},
issn = {1462-2920},
support = {18-UOW-028//Marsden Fund/ ; },
mesh = {Antarctic Regions ; *Soil Microbiology ; *Archaea/classification/genetics ; *Bacteria/classification/isolation & purification/genetics ; *Ecosystem ; Microbiota ; Phylogeny ; Hot Springs/microbiology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Active geothermal systems are relatively rare in Antarctica and represent metaphorical islands ideal to study microbial dispersal. In this study, we tested the macro-ecological concept that high dispersal rates result in communities being dominated by either habitat generalists or specialists by investigating the microbial communities on four geographically separated geothermal sites on three Antarctic volcanoes (Mts. Erebus, Melbourne, and Rittman). We found that the microbial communities at higher temperature (max 65°C) sites (Tramway Ridge on Erebus and Rittmann) were unique from each other and were dominated by a variety of novel Archaea from class Nitrososphaeria, while lower temperature (max 50°C) sites (Western Crater on Erebus and Melbourne) had characteristically mesophilic communities (Planctomycetes, Acidobacteriota, etc.) that were highly similar. We found that 97% of the detected microbial taxa were regional habitat specialists, with no generalists, with community assembly driven by high dispersal rates and drift (25% and 30% of community assembly, respectively), not environmental selection. Our results indicate that for microbial communities experiencing high dispersal rates between isolated communities, habitat specialists may tend to out-compete habitat generalists.},
}

Antarctic Regions
*Soil Microbiology
*Archaea/classification/genetics
*Bacteria/classification/isolation & purification/genetics
*Ecosystem
Microbiota
Phylogeny
Hot Springs/microbiology
RNA, Ribosomal, 16S/genetics

@article {pmid39871128,
year = {2025},
author = {Roy, S and Dawson, RA and Bradley, JA and Hernández, M},
title = {Prevalence and dynamics of antimicrobial resistance in pioneer and developing Arctic soils.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {50},
pmid = {39871128},
issn = {1471-2180},
support = {NE/X018180/1//Natural Environment Research Council/ ; NE/X018180/1//Natural Environment Research Council/ ; 730938//HORIZON EUROPE European Research Council/ ; RF\ERE\210050//Royal Society/ ; },
mesh = {*Soil Microbiology ; Arctic Regions ; *Bacteria/genetics/drug effects/classification/isolation & purification ; *Soil/chemistry ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Genes, Bacterial/genetics ; Interspersed Repetitive Sequences ; Ecosystem ; },
abstract = {Antimicrobial resistance (AMR) in soil is an ancient phenomenon with widespread spatial presence in terrestrial ecosystems. However, the natural processes shaping the temporal dissemination of AMR in soils are not well understood. We aimed to determine whether, how, and why AMR varies with soil age in recently deglaciated pioneer and developing Arctic soils using a space-for-time approach. Specifically, we assess how the magnitude and spread of AMR changes with soil development stages, including antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and antibiotic-resistant bacteria (ARB). We showed that ARGs, MGEs, and ARB are present, and exhibit a non-uniform distribution in the developing soils. Their abundance generally increases with soil age but at different rates overall and across different glacier forefields. Our analyses suggest a strong positive relationship between soil age and ARGs and ARB, which we attribute to increased competition between microbes in older soils. We also observed a strong negative relationship between soil age and ARG diversity mediated by soil organic matter - suggesting facilitation due to the alleviation of nutrient limitation. These contrasting results suggest that both competition and facilitation can regulate AMR spread through time in the Arctic, but competition might be the stronger determinant of AMR spread.},
}

*Soil Microbiology
Arctic Regions
*Bacteria/genetics/drug effects/classification/isolation & purification
*Soil/chemistry
*Anti-Bacterial Agents/pharmacology
*Drug Resistance, Bacterial/genetics
Genes, Bacterial/genetics
Interspersed Repetitive Sequences
Ecosystem