@article {pmid41249177,
year = {2025},
author = {Zhang, D and Hu, Q and Zhou, Y and Yu, H and Cong, W and Cheng, M and Wang, J and Liu, X and Zou, K and Long, S and Zhao, C and Jiang, J and Zhang, Y},
title = {Multi-omic profiling reveals distinct gut microbial and metabolic landscapes in golden snub-nosed monkeys under contrasting conservation strategies.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {209},
pmid = {41249177},
issn = {2055-5008},
support = {2020BCA081//Key Research and Development Project of Hubei Province/ ; 2013BAD03B02//National Key Technology R&D Program of China/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology/chemistry ; Metagenomics/methods ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Conservation of Natural Resources/methods ; Metabolomics/methods ; Metabolome ; *Colobinae/microbiology ; Endangered Species ; Multiomics ; },
abstract = {Gut microbiota are crucial for the fitness of endangered wildlife, yet how different conservation strategies affect these microbial ecosystems and their metabolic activities remains insufficiently understood. This study employed integrated metagenomic and metabolomic analyses to compare the gut microbial communities and fecal metabolomes of endangered golden snub-nosed monkeys (Rhinopithecus roxellana) under three distinct conservation scenarios: natural wild, food provisioning, and captivity. We established a comprehensive species-specific gut microbial gene catalog and observed significant microbial and metabolic divergence associated with each conservation strategy. Monkeys in managed settings (captive and provisioned) exhibited larger gut microbial gene catalogs than wild individuals. While alpha diversity was highest in the provisioned group, both captive and provisioned groups showed notably altered microbial community structures and co-occurrence networks compared to the wild baseline. Captivity was linked to the most pronounced shifts, including a microbiome assembly more strongly governed by deterministic processes, reduced network stability, and an enrichment of habitat specialists, alongside an increased abundance of antibiotic resistance genes (ARGs) and virulence factors (VFs), and distinct alterations in microbiota-metabolite co-variation patterns, particularly concerning amino acid metabolism. These findings highlight that food provisioning, when managed to emulate natural conditions, is associated with a less disruptive microbial and metabolic profile than intensive captivity, offering crucial insights for developing microbiome-informed conservation practices to enhance the health and long-term viability of this endangered primate.},
}

Animals
*Gastrointestinal Microbiome/genetics
Feces/microbiology/chemistry
Metagenomics/methods
*Bacteria/classification/genetics/metabolism/isolation & purification
*Conservation of Natural Resources/methods
Metabolomics/methods
Metabolome
*Colobinae/microbiology
Endangered Species
Multiomics

@article {pmid41248761,
year = {2025},
author = {Wang, X and Liu, L and Fan, W and Liu, R and Yuan, H and Li, X},
title = {Enhanced anaerobic digestion performance of food waste by Fe-Mn MOF-derived carbon composite: Methane production, microbial response, and intrinsic mechanisms.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133667},
doi = {10.1016/j.biortech.2025.133667},
pmid = {41248761},
issn = {1873-2976},
abstract = {This study investigated the effects of Fe-Mn MOF-derived carbon composite (Fe-Mn MDC) on anaerobic digestion (AD) performance of food waste (FW) and elucidated the underlying mechanisms. The methane yield increased to 457.44 ± 14.21 mL/g VS under 0.05 g/g TS Fe-Mn MDC addition, representing a 36.47 % increase compared to the control group. Metagenomics analysis indicated that Fe-Mn MDC altered the microbial community structure, enriched the abundance and mutualism of exoelectrogenic bacteria (Geobacter) and electroactive methanogenic microorganisms (Methanothrix) involved in direct interspecies electron transfer. The metabolic activity of hydrogenotrophic methanogens was enhanced under Fe-Mn MDC addition, and the content of dehydrogenase and coenzyme F420 was also stimulated, thereby accelerating substrate consumption and methane production. The physicochemical characterization results of Fe-Mn MDC demonstrated that it could act as an electron shuttle and facilitate proton transfer. Besides, AD system exhibited not only an increase in e-pili and c-type genes abundance, but also an enhanced representation of gene modules linked to the biosynthesis of V/A-type ATPases (M00159) and F-type (M00157), which further indicated that Fe-Mn MDC enhanced the proton-coupled electron transfer in AD system. These results provided potential applications in FW management and new insights into the mechanism of renewable energy recovery from AD.},
}

@article {pmid41248576,
year = {2025},
author = {Zhou, Y and Chang, L and Sun, H and Li, W and Ao, T and Lin, J},
title = {Evaluation of reclaimed treated wastewater on soil quality, microbial community and function in urban greening irrigation.},
journal = {Journal of environmental management},
volume = {395},
number = {},
pages = {127958},
doi = {10.1016/j.jenvman.2025.127958},
pmid = {41248576},
issn = {1095-8630},
abstract = {Reclaimed treated wastewater (TWW) offers a sustainable irrigation alternative for urban greening amid freshwater scarcity. However, its impact on soil quality and microbial ecology in urban landscapes remains underexplored. This study assessed the effects of three TWW types and one TWW-purified water mixture on soil properties, heavy metal accumulation, enzyme activity and microbial community dynamics in Common Nandina (Nandina domestica Thunb.) systems over three- and five-month in Nanjing, China, using a metagenomic approach. The results showed that TWW irrigation significantly increased soil nitrogen, phosphorus content and pH (P < 0.05), with stronger effects observed at three-month (P < 0.05). Soil heavy metal content varied, with Cr and As exhibiting potential accumulation. Enzyme activity (N-acetyl-glucosaminidase and phosphatase) was positively influenced by TWW irrigation at three-month. Metagenomic analysis revealed significant shifts in microbial community composition, particularly fungi, with Mucoromycota increasing and Ascomycota decreasing under TWW. The Normalized Stochasticity Ratio indicated increased stochasticity in microbial assembly under TWW irrigation (P < 0.05). Functionally, TWW increased abundance of functional genes related to amino acid metabolism and peroxisomes (P < 0.05), but decreased degradation genes for aromatic compounds. TWW also increased the abundance of antibiotic resistance genes (ARGs), particularly those related to triclosan and glycopeptide, and plant pathogenic genera like Aspergillus and Fusarium. The findings suggest that while TWW irrigation improves certain soil properties and microbial functions in the short term, it may pose ecological risks from heavy metal and microbial contamination, offering key insights for sustainable urban irrigation strategies.},
}

@article {pmid41249156,
year = {2025},
author = {Liu, L and Wang, Z and Zhang, W and Lin, W},
title = {Recovery of 1,773 microbial genomes and 2,060 viral genomes from the Mars-analog Qaidam Basin desert.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1795},
pmid = {41249156},
issn = {2052-4463},
support = {T2225011//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Genome, Viral ; Desert Climate ; *Soil Microbiology ; *Mars ; *Genome, Microbial ; Metagenome ; Metagenomics ; Tibet ; },
abstract = {The Qaidam Basin on the northern Tibetan Plateau represents a terrestrial Mars-analog desert characterized by hyperaridity, low temperatures, intense ultraviolet radiation, and high-salinity soils. To unveil the largely unexplored genomic diversity of microbes and viruses in this extreme environment, we collected 58 soil samples from various landforms and depths for metagenomic sequencing and analysis. We reconstructed 1,773 microbial metagenome-assembled genomes (mMAGs) and 2,060 viral MAGs (vMAGs), the vast majority (>94%) of which represent novel taxa. Among these, 327 mMAGs (completeness ≥ 90% and contamination ≤ 5%) and 325 vMAGs (completeness ≥ 90%) were classified as high-quality genomes. Taxonomic classification revealed that the bacterial, archaeal, and viral phyla with the largest numbers of genomes were Actinomycetota (n = 565), Halobacteriota (n = 111), and Uroviricota (n = 836), respectively. This metagenomic and genomic dataset provides valuable reference data for advancing our understanding of the diversity and function of microbial and viral communities across global desert ecosystems. Furthermore, these data offer astrobiological insights for research on life in Mars-analog extreme environments.},
}

*Genome, Viral
Desert Climate
*Soil Microbiology
*Mars
*Genome, Microbial
Metagenome
Metagenomics
Tibet

@article {pmid41248707,
year = {2025},
author = {Mizuno, S and Horiba, K and Nakahashi, T and Atsumi, Y and Takahara, T and Hashino, M and Ito, Y and Kamimura, K},
title = {A 1-year-old boy presenting with roseola accompanied by bilateral eyelid oedema and acute infectious mononucleosis syndrome caused by human herpesuvirus-6B: a case report.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {108213},
doi = {10.1016/j.ijid.2025.108213},
pmid = {41248707},
issn = {1878-3511},
abstract = {Bilateral eyelid oedema, also known as Hoagland sign, is a specific physical sign of infectious mononucleosis (IM) syndrome caused by Epstein-Barr virus (EBV) infection in older children and adolescents. IM syndrome, which is mainly caused by EBV or cytomegalovirus infection, has milder symptoms in young children than in older children and adolescents. The human herpesvirus 6B (HHV-6B) causes roseola infantum (sixth disease) and various complications in children younger than 2 years; however, bilateral eyelid oedema and IM syndrome are rarely reported. We report the case of a 1-year-old boy with bilateral upper eyelid oedema and severe IM syndrome, including pancytopenia with an increased atypical lymphocyte count, purpura due to thrombocytopenia, and elevated liver enzyme and ferritin levels. Metagenomic next-generation sequencing indicated active HHV-6B infection. The patient improved within 1 week without any specific treatment. Our experience with this case suggests that the presentations observed should be considered rare complications of HHV-6B infection.},
}

@article {pmid41247052,
year = {2025},
author = {Huang, X and Zeng, J and Yang, F and Liu, Y and Chen, J and Wang, H and Li, S and Li, C and Zhang, S},
title = {Microbial succession in human tissues postmortem: insights from 2bRAD-M sequencing.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0266624},
doi = {10.1128/spectrum.02666-24},
pmid = {41247052},
issn = {2165-0497},
abstract = {Microbial communities play a crucial role in decomposition, yet their patterns in human tissues remain underexplored. Most previous research has often focused on animal models such as mice and swine, with limited studies on human samples, primarily targeting specific environments like the gut and skin. Consequently, gaps persist in understanding postmortem microbial dynamics within internal human organs. The 2bRAD-M sequencing technology offers a powerful approach for human thanatomicrobiome research, overcoming key limitations of 16S rRNA and metagenomic sequencing methods. In this study, we used 2bRAD-M to profile microbial succession across seven human tissues-heart, liver, spleen, lung, kidney, calf muscle, and gut-at various postmortem intervals (PMIs). Significant variations in microbial community composition were observed across organs and decomposition stages, with Proteobacteria dominating early and Firmicutes later. A comparison of frozen and unfrozen cadavers (PMI 1-7 days) revealed divergent microbial shifts in the liver and spleen, while other tissues exhibited limited variation. These findings highlight complex, organ-specific microbial trajectories and suggest that microbial signatures could serve as biomarkers for PMI estimation. This research deepens our understanding of the microbial succession within internal human organs postmortem and contributes to elucidating the identity and role of microorganisms in human decomposition.IMPORTANCEHumans host a diverse array of microbial communities that play a crucial role in the decomposition process after death. Understanding these postmortem microbial dynamics is essential, as they offer valuable insights into the progression of decomposition with significant implications for forensic science. The role of microorganisms in corpse decomposition has gained increasing attention in both forensic and ecological research, but studies in this area remain in their early stages, requiring further in-depth exploration. This work pioneers the use of 2bRAD-M sequencing to investigate microbial changes across various human organs over increasing postmortem intervals. By enhancing knowledge of postmortem microbiota dynamics, the study contributes to refining and improving the accuracy of forensic methodologies.},
}

@article {pmid41247049,
year = {2025},
author = {Ma, J and Yu, L and Zhao, K and Qiao, Q and Zhu, X and Wu, T and Rong, H and Ning, S and Guo, J and Ding, Y and Chi, Y and Cui, L and Ge, Y},
title = {A novel targeted hybrid capture-NGS assay for sensitive detection of multiplex respiratory pathogens.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0290825},
doi = {10.1128/spectrum.02908-25},
pmid = {41247049},
issn = {2165-0497},
abstract = {UNLABELLED: Emerging respiratory infectious diseases represented by COVID-19, along with traditional respiratory infections, pose a serious threat to human health. High-throughput sequencing (NGS), with its high sensitivity and ultra-high throughput, is particularly suitable for the detection of respiratory pathogens (RP) that are extremely diverse in types and frequently involved in mixed infections. In this study, by integrating a Micro-Targets Hybrid Capture (MT-Capture) system, we developed previously with NGS, we developed a novel assay (termed RP-MT-Capture NGS) for the detection of multiple respiratory pathogens (more than 300 species/types). By optimizing probe design and hybridization capture procedures, RP-MT-Capture NGS achieved high detection sensitivity for different types of pathogens. For influenza viruses, this assay could acquire full-length sequences of hemagglutinin (HA) and neuraminidase (NA) genes for samples with CT values < 32, offering a robust tool for viral mutation surveillance and recombination analysis. The results of clinical sample detection showed that RP-MT-Capture NGS exhibited superior accuracy and sensitivity compared to TaqMan array and metagenomic NGS (mNGS) technologies for respiratory pathogen detection. Compared with traditional probe hybridization-based targeted NGS (tNGS), RP-MT-Capture NGS significantly shortens the wet lab experiment time to within 6 h. In summary, the RP-MT-Capture NGS assay developed in this study offers a novel tool for detecting multiple respiratory pathogens, with substantial clinical and public health relevance.

IMPORTANCE: Emerging and traditional respiratory infections pose threats to human health. These diseases are caused by a variety of pathogens, which often lead to co-infections and, thus, make detection difficult. This study combines a novel probe hybridization capture system with high-throughput sequencing to develop a new detection tool (RP-MT-Capture NGS), which can identify over 300 types of respiratory pathogens. For influenza viruses, it can reveal complete details of key viral genes, facilitating the tracking of viral mutations. Compared with existing detection methods, this new tool is more accurate, more sensitive, and has a higher throughput. It provides great value for clinical practice and public health in respiratory pathogen detection.},
}

@article {pmid41246284,
year = {2025},
author = {Yang, C and Lv, M and Li, Y and He, Y and Zhang, S and Zhang, G and Lan, J and Guo, Z and Cheng, Y and Yang, Y and Sun, J and Ma, L and Zhang, L},
title = {The interactions between psychological stress, gut microbiota, and fecal metabolites: A longitudinal multi-omics study in Chinese adolescents.},
journal = {Current research in microbial sciences},
volume = {9},
number = {},
pages = {100498},
doi = {10.1016/j.crmicr.2025.100498},
pmid = {41246284},
issn = {2666-5174},
abstract = {OBJECTIVES: This study investigated the bidirectional associations between psychological stress, gut microbiota, and fecal metabolites in a cohort of Chinese adolescents using a multi-omics approach.

METHODS: Baseline fecal samples from 124 adolescents were subjected to 16S rRNA gene amplicon sequencing, with 51 participants providing samples for metagenomic sequencing and untargeted metabolomics at baseline and follow-up. Psychological stress was assessed via the Adolescent Self-Rating Life Events Checklist.

RESULTS: After covariates adjustment, baseline total stress was associated with depleted alpha- and beta-diversity and abundances of the genera Lachnospiraceae NK4A136 group and unclassified Muribaculaceae.In longitudinal analyses, with the same covariates, baseline total stress was associated with six follow-up microbial species (Pfdr < 0.1; Actinomyces spp. HMSC035G02, Actinomyces sp. ICM58, Actinomyces sp. oral taxon 172, Schaalia odontolytica, Blautia sp. AF17-9LB, and Blautia sp. AM47-4) and 83 metabolites, predominantly lipids. These metabolites were primarily enriched in Kyoto Encyclopedia of Genes and Genomes pathways of lipid metabolism. Schaalia odontolytica, Actinomyces sp. ICM58, and Actinomyces spp. HMSC035G02 mediated associations between the total stress score and five lipids, with Schaalia odontolytica demonstrating the strongest effect (26.3 % mediated). Seven baseline metabolites but no microbial species were predictive of follow-up total stress. These metabolites exhibited an area under the curve of 0.72 for differentiating adolescents with high versus low stress, with 5-oxo-eicosatetraenoic acid being the strongest predictor.

CONCLUSIONS: This study suggests that psychological stress is associated with specific gut microbes and lipid metabolites change, and in turn, specific metabolites contribute to psychological stress change. These findings provide insights into bidirectional interactions between psychological stress and gut microbiota in adolescents.},
}

@article {pmid41246108,
year = {2025},
author = {Benghanem, S and Pérot, P and Rodriguez, C and Fourgeaud, J and Bouguerra, M and Mathon, B and Seilhean, DD and Bielle, F and Plu, I and Jamet, A and Weiss, N and Marois, C and Rohaut, B and Eloit, M and Demeret, S},
title = {Diagnostic Yield of Next-Generation Sequencing in CSF or Brain Biopsy for Severe Encephalitis Requiring Intensive Care.},
journal = {Neurology. Clinical practice},
volume = {15},
number = {6},
pages = {e200558},
doi = {10.1212/CPJ.0000000000200558},
pmid = {41246108},
issn = {2163-0402},
abstract = {OBJECTIVES: The aim of this study was to evaluate the contribution of metagenomic next-generation sequencing (mNGS) in critically ill patients with encephalitis of unknown etiology.

METHODS: This retrospective study (2016-2023) was conducted in a tertiary care referral neuro-ICU at La Pitié-Salpêtrière Hospital (Paris, France). The inclusion criteria were encephalitis with unknown etiology and mNGS performed on CSF, brain biopsy, and/or autopsy. We assessed the yield of mNGS and whether specific treatments were initiated. Neurologic outcome at 1 year was assessed using the Glasgow Outcome Scale-Extended (GOSE-1: death; GOSE-8: upper good recovery).

RESULTS: A total of 49 patients were included, of whom 44.9% were immunosuppressed. At 1 year, 38.8% had a GOSE score 4-8 and 47.7% died. mNGS was performed on the CSF of 40 of 49 patients (81.6%) and on brain biopsy of 19 of 49 patients (38.8%), including 12 patients who underwent both CSF and biopsy testing. Among the 40 mNGS analyses performed on the CSF, 7 (17.5%) yielded positive results but only 1 (2.5%) was likely causative. Conversely, 7 of 19 mNGS analyses (36.8%) on biopsies were positive and causative. Regarding the yield of mNGS in the entire cohort, 15 of 49 patients (30.6%) had a positive result but only 7 of 49 (14.3%) were causative (dengue virus, measles virus, rubella virus, Nocardia spp, HHV6, astrovirus, and orthobunyavirus), all from brain biopsies of immunocompromised patients. Conversely, 8 of 49 mNGS analyses (16.3%) were noncausative (polyomavirus, HHV8, HHV7, EBV, 2 pegiviruses, and 2 rhinoviruses). Specific treatments were initiated in 4 of 7 patients (57%). Among the 34 patients with a negative mNGS result, 5 (14.7%) were diagnosed with infectious encephalitis using conventional methods.

CONCLUSION: In critically ill patients with encephalitis of unknown etiology, mNGS performed on brain biopsy could reduce diagnostic uncertainty.},
}

@article {pmid41245671,
year = {2025},
author = {Orbea, M and Fortini, M and Amerson-Brown, MH and Palazzi, DL and Dunn, JJ},
title = {Mycetohabitans rhizoxinica bacteremia in the setting of invasive fungal disease in an immunocompromised patient.},
journal = {ASM case reports},
volume = {1},
number = {4},
pages = {},
doi = {10.1128/asmcr.00014-24},
pmid = {41245671},
issn = {2996-2684},
abstract = {BACKGROUND: Mycetohabitans [Burkholderia] rhizoxinica is an endosymbiotic bacteria of Rhizopus microsporus that normally causes rice seedling blight. In our case report, we present one of the first known cases of concomitant bacteremia with M. rhizoxinica and invasive mold infection due to Rhizopus spp. in an immunocompromised child.

CASE SUMMARY: A 3 year old male recently diagnosed with B-cell acute lymphoblastic leukemia developed febrile neutropenia. His workup was significant for invasive fungal sinusitis due to Exserohilum spp. based on histopathology and culture, a right middle lobe infiltrate, and a blood culture positive for gram-negative coccobacilli, later identified as M. rhizoxinica. Additionally, metagenomics next-generation sequencing was positive for R. microsporus as was broad-range fungal PCR testing of a lung biopsy sample. His surgical treatments included sinus debridement and a near total right pneumonectomy, and his antimicrobial treatment included 10 days of cefepime for his bacteremia, 4 weeks of liposomal amphotericin B, 4 weeks of micafungin following his pneumonectomy, and approximately 12 months of posaconazole.

CONCLUSION: This case highlights the association of M. rhizoxinica with Rhizopus spp., wherein the isolation of M. rhizoxinica led to a high index of suspicion of Rhizopus infection in an immunocompromised patient who developed bacteremia with a slow-growing, oxidase positive, gram-negative bacteria not able to be identified by traditional identification methods.},
}

@article {pmid41245635,
year = {2025},
author = {Wongwattanarat, S and Schorn, A and Klose, L and Carré, C and Malvis Romero, A and Liese, A and Pérez-García, P and Streit, WR},
title = {A combined chemo-enzymatic treatment for the oxidation of epoxy-based carbon fiber-reinforced polymers (CFRPs).},
journal = {Frontiers in bioengineering and biotechnology},
volume = {13},
number = {},
pages = {1670548},
doi = {10.3389/fbioe.2025.1670548},
pmid = {41245635},
issn = {2296-4185},
abstract = {Carbon fiber-reinforced polymers (CFRPs), particularly epoxy-based composites, have become essential in the aerospace, automotive, and wind energy industries due to their robust mechanical properties, and lightweight nature. However, there is a lack of recycling technologies that are environmentally sustainable while also ensuring the recovery of carbon fibers in their original state. Although certain bacterial and fungal strains can colonize epoxy polymers, enzymes capable of efficiently degrading these materials have not yet been reported. Consequently, there is an urgent need for an effective, sustainable, and biologically inspired solution for CFRP recycling. Here, a chemo-enzymatic two-step oxidation process was developed. A chemical pre-treatment with propionic acid and hydrogen peroxide was used to recover imbedded carbon fibers. Additionally, three novel bacterial laccases isolated from a European spruce bark beetle gut metagenome (Ips typographus) demonstrated the ability to oxidize three epoxy resin scaffolds derived from TGMDA-based epoxy resin system, a high-performance material commonly used in aerospace applications. The sequential combination of both oxidative steps enabled the retrieval of clean carbon fibers and showed the potential of the laccase to partially further modify the pre-treated cured epoxy. This bio-inspired approach marks an initial step toward developing a bio-based recycling method for epoxy CFRPs.},
}

@article {pmid41245257,
year = {2025},
author = {Devarajalu, P and Attri, SV and Kumar, J and Dutta, S and Kabeerdoss, J},
title = {Correction: Characterization of gut microbiota signatures in Indian preterm infants with necrotizing enterocolitis: a shotgun metagenomic approach.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1706582},
doi = {10.3389/fcimb.2025.1706582},
pmid = {41245257},
issn = {2235-2988},
abstract = {[This corrects the article DOI: 10.3389/fcimb.2025.1649384.].},
}

@article {pmid41244979,
year = {2025},
author = {Ladines-Lim, JB and Yang, WT and Tebas, P and O'Donnell, J and Koenig, H and Kreider, E and Dyer, K and Anwar, M and Rodriguez, E and Patel, S and Rodino, K and Glaser, L and Richterman, A},
title = {Delayed diagnosis of disseminated Mycobacterium intracellulare subsp. chimaera infective endocarditis via cell-free metagenomic next-generation sequencing: a case report.},
journal = {ASM case reports},
volume = {1},
number = {5},
pages = {},
doi = {10.1128/asmcr.00003-25},
pmid = {41244979},
issn = {2996-2684},
abstract = {BACKGROUND: Mycobacterium intracellulare subsp. chimaera infective endocarditis associated with contaminated heater-cooler units has been well documented, leading to the discontinuation of these devices in most hospitals by 2018. The rarity of this infection and its nonspecific symptoms often result in delayed diagnosis.

CASE SUMMARY: We describe a 56-year-old female diagnosed with M. intracellulare subsp. chimaera infective endocarditis with disseminated intracranial abscess 7 years after aortic and mitral valve replacement. Diagnosis was achieved using cell-free microbial DNA next-generation sequencing (cfmNGS). She underwent left temporal craniotomy for abscess drainage and aortic and mitral valve replacement. Diagnosis was confirmed via mycobacterial culture from blood, brain tissue, and explanted valve tissue. Treatment included rifabutin, ethambutol, azithromycin, and amikacin, alongside a prednisone taper prescribed for a previously diagnosed undifferentiated inflammatory process. Amikacin was discontinued 6 weeks after valve surgery because of unilateral hearing loss. She remained clinically stable 5 months after valve surgery.

CONCLUSION: This case highlights that M. intracellulare subsp. chimaera infections may continue to emerge years after heater-cool unit discontinuation, suggesting that the time window for case incidence may still be active. cfmNGS may serve as a valuable diagnostic tool for disseminated M. intracellulare subsp. chimaera. Finally, we discuss pharmacotherapeutic factors, including the need for multiple agents over long durations, in this case with specific considerations given to the dissemination of infection into the central nervous system and potential drug-drug interactions, including steroids.},
}

@article {pmid41244776,
year = {2025},
author = {Tan, J and Liu, L and Wang, L and Qu, Y and Sun, Z and Wang, Q and Liu, Y},
title = {Case Report: First pulmonary infection caused by Mycobacterium colombiense in a non-immunosuppressed host with bronchiectasis: diagnosis facilitated by synergistic mNGS and culture.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1671968},
doi = {10.3389/fmed.2025.1671968},
pmid = {41244776},
issn = {2296-858X},
abstract = {Mycobacterium colombiense, a rare slow-growing mycobacterium within the Mycobacterium avium complex (MAC), causes disseminated disease almost exclusively in immunocompromised hosts, with no prior reports of localized pulmonary infection in non-immunosuppressed individuals. A 47-year-old non-immunosuppressed male with bronchiectasis presented with progressive cough, night sweats, and fatigue. Computed tomography (CT) revealed bronchiectasis with nodules in the right middle and lower lobes. Empirical β-lactam therapy failed, and conventional bronchoalveolar lavage fluid (BALF) tests (smears, cultures, PCR) yielded no pathogens at 48 h. Although metagenomic next-generation sequencing (mNGS) of BALF detected a low number of M. colombiense sequences (eight reads), definitive confirmation was achieved through extended culture, which is considered the gold standard for the diagnosis of nontuberculous mycobacteria. This culture revealed acid-fast bacilli within 12 days (160 CFU), confirming the presence of viable M. colombiense. Subsequent mNGS of the isolated colonies further confirmed the species identity with high sequence reads (25,787 reads). Guideline-based triple therapy (guided by drug susceptibility testing and guidelines) with clarithromycin, rifampicin, and ethambutol achieved significant radiographic resolution at 24 weeks. This case demonstrates that M. colombiense pulmonary infection is diagnostically elusive and mimics non-specific respiratory syndromes. It defines the clinical features of this pathogen in non-immunosuppressed hosts and highlights the need for heightened surveillance for nontuberculous mycobacteria (NTM) in bronchiectasis patients, given the likelihood of underdiagnosis.},
}

@article {pmid41244772,
year = {2025},
author = {Li, Q and Song, XC and Li, K and Wang, J},
title = {Gut-lung immunometabolic crosstalk in sepsis: from microbiota to respiratory failure.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1685044},
doi = {10.3389/fmed.2025.1685044},
pmid = {41244772},
issn = {2296-858X},
abstract = {Sepsis is a systemic immune-metabolic disorder syndrome caused by infection, in which gut microbiota dysbiosis plays a central role in the occurrence and development of multi-organ dysfunction. This paper systematically elaborates on the bidirectional regulatory mechanism of the "gut-lung axis" in sepsis. Gut microbiota dysregulation damages the gut barrier function, reduces the production of short-chain fatty acids (SCFAs), and increases endotoxin translocation. Subsequently, it activates alveolar macrophage polarization, promotes the formation of neutrophil extracellular traps (NETs), and leads to an imbalance in the Treg/Th17 cell ratio, ultimately exacerbating the pathological process of acute lung injury (ALI) or acute respiratory distress syndrome (ARDS). Conversely, the pulmonary inflammatory response can also aggravate gut barrier damage through circulating inflammatory mediators, forming a vicious cycle. Mechanistically, HIF-1α, mTOR, and Sirtuins do not act in isolation. Instead, they jointly regulate the metabolic fate of immune cells through spatiotemporally dynamic interactions. During the evolution of sepsis, these signals exhibit opposite regulatory polarities during the hyper-inflammatory phase and the immunosuppressive phase, and mitochondrial dysfunction and oxidative stress further amplify the inflammatory cascade reaction. Preclinical research evidence shows that microbiota-based intervention measures (including probiotic preparations, fecal microbiota transplantation, and SCFA supplementation) and vagus nerve electrical stimulation can effectively alleviate sepsis-related lung injury and improve prognosis, but there is significant individual heterogeneity in their therapeutic effects. Future research should not be restricted to descriptive associations. Instead, it is essential to conduct in-depth analyses of the specific logic of the aforementioned signaling networks in terms of cell types, subcellular compartments, and disease course timings, and clarify their context-dependent controversies to promote the transformation of mechanistic understanding into precision treatment. Meanwhile, research efforts should focus on constructing a multi-omics dynamic biomarker system integrating metagenomics, metabolomics, and immunophenotyping analysis and designing clinical trials through precise patient stratification to facilitate the clinical translation of individualized treatment strategies based on gut-lung axis regulation.},
}

@article {pmid41244681,
year = {2025},
author = {Ru, J and Jiang, Z and Li, J and Li, X and Su, Z and Li, T and Xu, M},
title = {Screening of microbial consortium with high efficiency of lignin-degrading and its synergistic metabolic mechanism.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1709019},
doi = {10.3389/fmicb.2025.1709019},
pmid = {41244681},
issn = {1664-302X},
abstract = {INTRODUCTION: Lignin is difficult to degrade, which makes its high-value utilization a challenge. So finding an efficient method to degrade lignin is very important. At present, microbial degradation is considered to be one of the most effective and environmentally friendly degradation methods that is widely accepted.

METHODS: This study enriched three lignin-degrading microbial consortia R0, R1 and R2 using alkali lignin as the sole carbon source under 15 °C conditions. Using the methods of 16S rRNA sequencing, metagenomics, and metabolomics, the degradation mechanism of these three microbial consortia were systematically analyzed.

RESULTS: The microbial consortium R0, which has the best degradation efficiency, can degrade more than 80% within 6 days, with dominant genera being Achromobacter and Pseudomonas. The dominant genera in other two microbial consortia R1 and R2 are Pseudomonas and Achromobacter in R1, Pseudomonas and Sphingobacterium in R2. Protocatechuic acid is a central intermediate in the degradation of lignin, its degradation pathway was fully annotated in microbial consortia R0 and R1. Microbial consortium R0 has the most abundant of AA (Auxiliary Activities) family genes annotated as carbohydrate annotation enzymes. The dominant genera in the microbial consortium R0 based on AA family gene abundance were Pseudomonas and Achromobacter.

DISCUSSION: Our results indicated that Pseudomonas is the dominant genus in lignin degradation, the metabolic potential of other abundant genera suggests a possible complementary role in the lignin degradation process. In the lignin degradation system with Pseudomonas as the dominant genera, the degradation of protocatechuic acid is the core of the degradation process. This study could enrich the mechanism of efficient and stable lignin degradation by microbial consortium, and could provide theoretical guidance for the development of lignin biodegradation technology in industry.},
}

@article {pmid41244617,
year = {2025},
author = {Ma, ZS},
title = {Microbial Biomarkers of Breast Tumor and Mastitis: Deciphering the Delicate Balance between Potentially "Evil" and "Benign" Alliances in Mammary Microbiomes.},
journal = {Breast care (Basel, Switzerland)},
volume = {},
number = {},
pages = {},
doi = {10.1159/000548037},
pmid = {41244617},
issn = {1661-3791},
abstract = {INTRODUCTION: Breast cancer and mastitis significantly impact women's health and their infants' wellbeing. The advent of metagenomic sequencing technology has opened new avenues to explore the relationships between mammary microbiomes and these diseases. Despite recent extensive studies, detailed understanding of the mammary microbiome-disease relationships remains incomplete.

METHODS AND RESULTS: Here, we apply the Specificity and Specificity Diversity framework (Ma 2024, BMC Biology) to identify unique/enriched species (US/ES) associated with mastitis, breast cancer, or their healthy controls. The US/ES lists contain potential biomarkers and offer fresh insights into the intricacies of mastitis etiology and the relationship between breast tissue microbiomes and breast cancer.

CONCLUSIONS: (i) The dynamic balance between coexisting alliances of beneficial microbes and harmful microbes (including opportunistic pathogens) holds key to understanding mastitis etiology. (ii) Intra-tumor microbes may serve multiple roles - as oncogenic microbes, neutral bystanders, or tumor suppressors, and their dynamic balance can influence breast cancer onset and progression. (iii) Significant challenges remain in developing effective probiotics, prebiotics and infant formulas due to complex entanglements between beneficial and harmful microbes. This complexity suggests that broad-spectrum or one-size-fits-all probiotic approaches may prove inadequate, pointing instead to the need for personalized prebiotic/probiotic/infant-formula solutions to restore and maintain healthy mammary microbiomes.},
}

@article {pmid41244590,
year = {2025},
author = {An, Z and Cha, JH and Lee, KH and Lee, I},
title = {Metagenome-assembled genomes enhance bacterial read decontamination and variant calling in oral samples.},
journal = {iScience},
volume = {28},
number = {11},
pages = {113772},
doi = {10.1016/j.isci.2025.113772},
pmid = {41244590},
issn = {2589-0042},
abstract = {Whole genome sequencing (WGS) offers advantages over DNA chip-based genotyping, typically using blood-derived DNA. However, saliva and buccal samples-popular in direct-to-consumer tests-suffer reduced accuracy because of oral bacterial contamination. Decontamination strategies using decoy bacterial genomes yielded limited improvements, likely because they cover only a subset of oral bacteria with available isolate genomes. To overcome this, we developed a decontamination pipeline leveraging metagenome-assembled genomes (MAGs). Concordance analysis of variant calling between blood and matched oral samples confirmed the superiority of MAG-augmented decontamination over conventional methods relying mainly on isolate genomes. Although the underlying mechanism remains unclear, it particularly improves variant calls in GC-rich regions, recovering many likely pathogenic variants. Additionally, we demonstrate that certain bacterial genomic regions mimic human regions with clinically relevant variants, potentially confounding genotyping. These results highlight the need for MAG-based bacterial read decontamination to achieve accurate personal genotyping from non-invasive, self-collected oral samples.},
}

@article {pmid41244294,
year = {2025},
author = {Fuller, R and Petersen, BE and Hussein, S and Salib, C and Duffield, A and Gaglia, R and Gabrilove, JL and Hernández, C and Ramirez, JD and Jacobs, SE and Paniz-Mondolfi, A},
title = {Expedited diagnosis of disseminated Mycobacterium kansasii infection using targeted (amplicon-based) next-generation sequencing in an immunocompromised patient.},
journal = {ASM case reports},
volume = {1},
number = {6},
pages = {},
doi = {10.1128/asmcr.00110-24},
pmid = {41244294},
issn = {2996-2684},
abstract = {BACKGROUND: Mycobacterium kansasii is typically associated with pulmonary disease and is an uncommon cause of disseminated infection and thus can be challenging to diagnose and treat.

CASE SUMMARY: We present a 59-year-old female with a history of renal cell carcinoma (RCC) and T-cell large granular lymphocytic leukemia (T-LGLL) who developed disseminated Mycobacterium kansasii infection. Targeted next-generation sequencing (tNGS) facilitated the rapid detection of M. kansasii from formalin-fixed, paraffin-embedded (FFPE) tissue, aiding in clinical decision-making prior to culture confirmation.

CONCLUSION: The case highlights the diagnostic challenges posed by overlapping clinical features and chronic granulomatous inflammation in immunocompromised patients, as well as the utility of amplicon-based sequencing in expediting diagnostic turnaround and guiding therapeutic interventions.},
}

@article {pmid41244270,
year = {2025},
author = {Rabinowitz, PM and Walia, R and Pottinger, P and Lieberman, JA},
title = {Tropheryma whipplei native valve endocarditis diagnosed by sequencing of microbial cell-free DNA in plasma.},
journal = {ASM case reports},
volume = {1},
number = {6},
pages = {},
doi = {10.1128/asmcr.00070-25},
pmid = {41244270},
issn = {2996-2684},
abstract = {BACKGROUND: Endocarditis is an important manifestation of extra-intestinal Whipple's disease. The etiologic agent, the bacterium Tropheryma whipplei, cannot be cultivated in clinical laboratories, making the diagnosis of this culture-negative infection challenging. Molecular methods have emerged as useful adjuncts for the diagnosis of culture-negative endocarditis.

CASE SUMMARY: A 67-year-old male was seen in an infectious disease clinic for evaluation of a possible infectious etiology of chronic musculoskeletal pain with exercise intolerance. He had a history of an embolic stroke 2 years earlier, echocardiographic evidence of aortic valve thickening, and multiple negative blood cultures. Following an evaluation that included serology and extended incubation blood culture, plasma was sent for metagenomic sequencing of microbial cell-free DNA, which was positive for Tropheryma whipplei.

CONCLUSION: The patient's musculoskeletal complaints and his exercise intolerance resolved after treatment with ceftriaxone and trimethoprim-sulfamethoxazole. To our knowledge, this is the first report of T. whipplei native valve endocarditis diagnosed by metagenomic sequencing.},
}

@article {pmid41244037,
year = {2025},
author = {Leys, SP and Hentschel, U and Easson, CG and Stimson, D and Lopez, JV and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , },
title = {The chromosomal genome sequence of the fragile freshwater sponge, Eunapius fragilis (Leidy, 1851) and its associated microbial metagenome sequences.},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {268},
doi = {10.12688/wellcomeopenres.24165.1},
pmid = {41244037},
issn = {2398-502X},
abstract = {We present a genome assembly from a specimen of Eunapius fragilis (fragile freshwater sponge; Porifera; Demospongiae; Spongillida; Spongillidae). The genome sequence has a total length of 218.91 megabases. Most of the assembly (99.98%) is scaffolded into 23 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 28.5 kilobases in length. Gene annotation of this assembly on Ensembl identified 26,614 protein-coding genes. Additionally, eight high-quality bacterial metagenomes belonging to the Bacteroidota and Pseudomonadota phyla were assembled.},
}

@article {pmid41243980,
year = {2025},
author = {Aguilar, C and Fontove-Herrera, F and Pashkov, A and García-Estrada, DA and Contreras-Peruyero, H and Guerrero-Flores, S and Ramírez-Sánchez, O and Sélem-Mojica, N},
title = {MicroAgroBiome: a toolkit for exploring specialized metabolism and ecological interactions in rhizosphere microbiomes of cultivated crops.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkaf1083},
pmid = {41243980},
issn = {1362-4962},
support = {320237//Secretaría de Ciencia, Innovación, Tecnología e Innovación (SECIHTI)/ ; //Secretaría de Ciencia, Innovación, Tecnología e Innovación (SECIHTI) Postdoctoral Fellowship 2025/ ; IN114323//Universidad Nacional Autónoma de México/ ; },
abstract = {The microbiome is crucial to agroecosystems, as it influences plant nutrition, resilience, and overall health. Recent advances in metagenomics have expanded our understanding of plant-microbe interactions, yet curated, high-resolution data capturing the global diversity of crop-associated microbiomes remain scarce. To fill this gap, we developed MicroAgroBiome, a publicly accessible platform that offers standardized taxonomic and functional data, mainly from the rhizosphere microbiomes of agriculturally important crops. The platform integrates 554 metagenomes from 28 crops and soil sample health, advancing microbiome-informed agricultural strategies. It also underscores Latin America's growing leadership in agricultural microbiome research. MicroAgroBiome is available at https://agrobiom.matmor.unam.mx.},
}

@article {pmid41243635,
year = {2025},
author = {Wu, S and Wei, Z and He, Z and Li, M and Zeng, W},
title = {Clinical characteristics of tracheobronchial mucormycosis: a retrospective analysis of twenty cases.},
journal = {Annals of medicine},
volume = {57},
number = {1},
pages = {2584286},
doi = {10.1080/07853890.2025.2584286},
pmid = {41243635},
issn = {1365-2060},
mesh = {Humans ; *Mucormycosis/diagnosis/drug therapy ; Middle Aged ; Male ; Female ; Retrospective Studies ; Aged ; *Antifungal Agents/therapeutic use/administration & dosage ; Adult ; Amphotericin B/therapeutic use/administration & dosage ; Bronchoscopy ; Tomography, X-Ray Computed ; *Bronchial Diseases/diagnosis/microbiology/drug therapy ; Immunocompromised Host ; Treatment Outcome ; },
abstract = {BACKGROUND: Tracheobronchial mucormycosis (TM) is a rare and potentially fatal disease commonly occurred in immunocompromised individuals, with death risk from massive hemoptysis or asphyxia.To enhance clinical understanding, we retrospectively analyzed the clinical features, therapeutic regimen, and outcomes of TM patients.

METHODS: We conducted a comprehensive analysis of hospitalized patients diagnosed with TM between January 1, 2010, and April 30, 2025, systematically collecting and evaluating data on clinical manifestations, treatment strategies, and clinical outcomes.

RESULTS: Twenty patients were included in this study, with a median age of 56 years. Most patients had diabetes mellitus, followed by those with hematological malignancies. Common symptoms included cough, expectoration, hemoptysis, and fever. Chest CT revealed pulmonary infiltrates, bronchial stenosis or occlusion, obstructive pneumonia, and pleural effusion, while bronchoscopy revealed neoplasms, purulent secretions, and bronchial obstruction or stenosis.Metagenomic next-generation sequencing demonstrated a higher positive diagnostic rate and shorter time to diagnosis compared to histopathology and culture. Three patients received intravenous amphotericin B (AmB) monotherapy, eight patients were treated with a combination of intravenous and intratracheal AmB, one patient was treated with intravenous triazole drug alone, two patients received a regimen consisting of intravenous triazole drugs combined with intratracheal AmB, and five patients underwent triple therapy involving both intravenous triazole drugs and concurrent intravenous and intratracheal AmB administration. Additionally, one patient underwent bronchoscopic intervention, and two patients underwent lobectomy. Fourteen patients demonstrated clinical improvement, whereas six died. Massive hemoptysis was the leading cause of mortality.

CONCLUSIONS: TM is a highly lethal disease that is often underdiagnosed. Bronchoscopy plays an essential role in both diagnosis and management. Systemic antifungal therapy, combined with intratracheal administration of AmB, has shown favorable therapeutic outcomes.},
}

Humans
*Mucormycosis/diagnosis/drug therapy
Middle Aged
Male
Female
Retrospective Studies
Aged
*Antifungal Agents/therapeutic use/administration & dosage
Adult
Amphotericin B/therapeutic use/administration & dosage
Bronchoscopy
Tomography, X-Ray Computed
*Bronchial Diseases/diagnosis/microbiology/drug therapy
Immunocompromised Host
Treatment Outcome

@article {pmid41243436,
year = {2025},
author = {Cen, Q and Cui, Y and Jin, J and Feng, J and Xin, Y and Zhang, Z and Li, J and Wang, J and Zhang, A},
title = {Unraveling multiple sclerosis: a hidden interaction between intestinal microbiota and host lipid metabolism.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2576657},
doi = {10.1080/19490976.2025.2576657},
pmid = {41243436},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Multiple Sclerosis/metabolism/microbiology/therapy ; *Lipid Metabolism ; Animals ; },
abstract = {Dysregulation of the structure of the gut microbiota is closely linked to the risk of onset and progression of multiple sclerosis. The intricate interaction between the gut microbiota and lipid metabolism likely serves as a crucial pathway mediating this relationship: the gut microbiota directly or indirectly modifies lipid metabolism (including cholesterol, sphingolipids, phospholipids, and fatty acids) by controlling the production of specific metabolites (such as short-chain fatty acids, tryptophan metabolites, bile acids, trimethylamine-N-oxide, and lipopolysaccharides), thereby impacting core pathological processes in multiple sclerosis. Therefore, elucidating the specific roles and mechanisms of the gut microbiota in modulating lipid metabolism in multiple sclerosis will accelerate the development of precision therapeutic strategies. In this review, we conduct an in-depth exploration of the interaction between the gut microbiota and lipid metabolism in the context of multiple sclerosis and provide a comprehensive summary of existing strategies targeting the gut microbiota and lipid metabolism for treating multiple sclerosis (including microbiota-based therapies, pharmacotherapy, and lifestyle modifications). Finally, we outline the present challenges in this field and offer an in-depth prospect for future directions.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Multiple Sclerosis/metabolism/microbiology/therapy
*Lipid Metabolism
Animals

@article {pmid41243097,
year = {2025},
author = {Hang, WJ and Yin, R and Kang, XW and He, L and Cao, X and Chen, J},
title = {Berberine ameliorates high-fat diet-induced metabolic disorders through promoting gut Akkermansia and modulating bile acid metabolism.},
journal = {Chinese medicine},
volume = {20},
number = {1},
pages = {190},
pmid = {41243097},
issn = {1749-8546},
support = {82100402//National Natural Science Foundation of China/ ; 82370837//National Natural Science Foundation of China/ ; 2022CFB201//Bureau of Science and Technology of Hubei Province/ ; 2022YFE0209900//National Key Research and Development Program of China/ ; WZ21A02//Wuhan Municipal Health Commission's Scientific Research/ ; },
abstract = {BACKGROUND: Coptidis Rhizoma, the rhizome of Coptis chinensis Franch., has long been employed in the treatment of diabetes. Its active component, berberine, has been utilized in clinical practice; however, the underlying mechanisms of its protective effects remain to be fully elucidated.

METHODS: Metabolomics and lipidomics analyzed plasma metabolite and lipid changes in mice fed a high-fat diet and treated with 25 mg/kg/day berberine for three months. Metagenomics and microbiota transplantation identified gut microbiota responding to berberine. Co-administration of berberine and Akkermansia was studied for metabolic effects, analyzing plasma and fecal metabolomics.

RESULTS: Berberine reduced triglycerides and cholesterol, showing metabolic protective effects. Metagenomics identified Akkermansia as key to berberine's benefits, validated by microbiota transplantation. Berberine enhanced Akkermansia growth, preserving intestinal mucus and tight junctions. It promotes the conversion of cholesterol to bile acids by inhibiting adenosine 5 '-monophosphate -activated protein kinase (AMPK), which promotes the expression of cholesterol 7-alpha hydroxylase (CYP7A1). Co-administration of berberine and Akkermansia amplified these effects. Potential metabolites, including linoleic acid and N-acetylputrescine, contributed to the observed benefits.

CONCLUSION: Berberine, through Akkermansia, maintains intestinal integrity and reduces cholesterol, highlighting its potential as a therapeutic agent for metabolic disorders. Combining berberine with Akkermansia enhances its efficacy against hyperlipidemia.},
}

@article {pmid41243094,
year = {2025},
author = {Andreani-Gerard, CM and Jiménez, NE and Palma, R and Muller, C and Hamon-Giraud, P and Le Cunff, Y and Cambiazo, V and González, M and Siegel, A and Frioux, C and Maass, A},
title = {Modeling the emergent metabolic potential of soil microbiomes in Atacama landscapes.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {142},
pmid = {41243094},
issn = {2524-6372},
support = {Associated Team "SymBioDiversity"//Institut national de recherche en informatique et en automatique (INRIA)/ ; Associated Team "SymBioDiversity"//Institut national de recherche en informatique et en automatique (INRIA)/ ; Associated Team "SymBioDiversity"//Institut national de recherche en informatique et en automatique (INRIA)/ ; Associated Team "SymBioDiversity"//Institut national de recherche en informatique et en automatique (INRIA)/ ; Associated Team "SymBioDiversity"//Institut national de recherche en informatique et en automatique (INRIA)/ ; FB210005//Centro de Modelamiento Matemático, Facultad de Ciencias Físicas y Matemáticas/ ; FB210005//Centro de Modelamiento Matemático, Facultad de Ciencias Físicas y Matemáticas/ ; FB210005//Centro de Modelamiento Matemático, Facultad de Ciencias Físicas y Matemáticas/ ; FB210005//Centro de Modelamiento Matemático, Facultad de Ciencias Físicas y Matemáticas/ ; ANID-MILENIO-ICN2021_044//Millennium Institute Center for Genome Regulation/ ; ANID-MILENIO-ICN2021_044//Millennium Institute Center for Genome Regulation/ ; ANID-MILENIO-ICN2021_044//Millennium Institute Center for Genome Regulation/ ; ANID-MILENIO-ICN2021_044//Millennium Institute Center for Genome Regulation/ ; Exploración 13220002//Agencia Nacional de Investigación y Desarrollo/ ; Exploración 13220002//Agencia Nacional de Investigación y Desarrollo/ ; Exploración 13220002//Agencia Nacional de Investigación y Desarrollo/ ; Exploración 13220002//Agencia Nacional de Investigación y Desarrollo/ ; ANR-22-PEAE-0011//Agence Nationale de la Recherche/ ; ANR-22-PEAE-0011//Agence Nationale de la Recherche/ ; },
abstract = {BACKGROUND: Soil microbiomes harbor complex communities from which diverse ecological roles unfold, shaped by syntrophic interactions. Unraveling the mechanisms and consequences of such interactions and the underlying biochemical transformations remains challenging due to niche multidimensionality. The Atacama Desert is an extreme environment that includes unique combinations of stressful abiotic factors affecting microbial life. In particular, the Talabre Lejía transect is a natural laboratory for understanding microbiome composition, functioning, and adaptation.

RESULTS: We propose a computational framework for the simulation of the metabolic potential of microbiomes, as a proxy of how communities are prepared to respond to the environment. Through the coupling of taxonomic and functional profiling, community-wide and genome-resolved metabolic modeling, and regression analyses, we identify key metabolites and species from six contrasting soil samples across the Talabre Lejía transect. We highlight the functional redundancy of whole metagenomes, which act as a gene reservoir, from which site-specific adaptations emerge at the species level. We also link the physicochemistry from the puna and the lagoon samples to metabolic machineries that are likely crucial for sustaining microbial life in these unique environmental conditions. We further provide an abstraction of community composition and structure for each site that allowed us to describe microbiomes as resilient or sensitive to environmental shifts, through putative cooperation events.

CONCLUSION: Our results show that the study of multi-scale metabolic potential, together with targeted modeling, contributes to elucidating the role of metabolism in the adaptation of microbial communities. Our framework was designed to handle non-model microorganisms, making it suitable for any (meta)genomic dataset that includes high-quality environmental data for enough samples.},
}

@article {pmid41243090,
year = {2025},
author = {Liu, Z and Xiao, L and Tang, X and He, Y and Nan, X and Wang, H and Guo, Y and Xiong, B},
title = {Salvianolic acid C inhibits methane emissions in dairy cows by targeting MCR and reshaping the rumen microbial community.},
journal = {Journal of animal science and biotechnology},
volume = {16},
number = {1},
pages = {151},
pmid = {41243090},
issn = {1674-9782},
support = {2022YFD1301100//Integrated Demonstration of Scalable and Efficient Healthy Breeding for Cattle and Sheep/ ; 2024-YWF-ZYSQ-10//State Key Laboratory for Diagnosis and Treatment of Infectious Diseases/ ; },
abstract = {BACKGROUND: Methane (CH4) emissions from ruminants significantly contribute to greenhouse gas effects and energy loss in livestock production. Methyl-coenzyme M reductase (MCR) is the key enzyme in methanogenesis, making it a promising target for CH4 mitigation. This study aimed to identify and validate plant-derived inhibitors by using molecular docking to screen compounds with strong binding affinity to the F430 active site of MCR and assessing their efficacy in reducing CH4 emissions.

RESULTS: Molecular docking analysis identified salvianolic acid C (SAC) as a potent inhibitor of MCR, showing a strong binding affinity to the F430 active site (binding energy: -8.2 kcal/mol). Enzymatic inhibition assays confirmed its inhibitory effect, with a half-maximal inhibitory concentration (IC50) of 692.3 µmol/L. In vitro rumen fermentation experiments demonstrated that SAC supplementation (1.5 mg/g DM) significantly reduced CH4 production (P < 0.01) without negatively affecting major fermentation parameters. Microbial community analysis using 16S rRNA sequencing and metagenomics revealed that SAC selectively altered the rumen microbiota, increasing the relative abundance of Bacteroidota while significantly reducing Methanobrevibacter (P = 0.04). Moreover, metagenomic analysis showed the downregulation of key methanogenesis-related genes (mcrA and rnfC), suggesting a dual mechanism involving direct enzymatic inhibition and microbial community modulation.

CONCLUSIONS: These findings indicate that SAC effectively reduces CH4 production by inhibiting MCR activity and reshaping the rumen microbial community. As a plant-derived compound with strong inhibitory effects on methanogenesis, SAC presents a promising and sustainable alternative to synthetic CH4 inhibitors, offering potential applications for mitigating CH4 emissions in livestock production.},
}

@article {pmid41242690,
year = {2025},
author = {Li, X and Pan, L and Li, Z and Li, Y and Yang, L and Ye, X and Wubuli, A and Ye, Q and Yang, F and Yi, H and Maitusong, R and Liang, Y and Cai, Y and Chen, Z},
title = {Etiology and Clinical Characteristics of Pathogen Co-detection in Pediatric Mycoplasma pneumoniae Pneumonia: A Multicenter Retrospective Study.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {108230},
doi = {10.1016/j.ijid.2025.108230},
pmid = {41242690},
issn = {1878-3511},
abstract = {OBJECTIVES: Co-detection are frequent in pediatric Mycoplasma pneumoniae pneumonia (MPP), yet their full pathogen spectrum and clinical impact remain incompletely characterized. This study aimed to characterize co-detection etiology and clinical impacts of MPP in hospitalized children.

METHODS: A multicenter retrospective cohort study was conducted among hospitalized children under 14 years with MPP, diagnosed by metagenomic or targeted next-generation sequencing of bronchoalveolar lavage fluid, from June 2023 to July 2024. Multivariate logistic regression models were used to assess differences in clinical characteristics among various Mycoplasma pneumoniae (MP) co-detection patterns.

RESULTS: Among 570 MPP cases, co-detection occurred in 338 (59.3%) cases: viral-only (29.3%), bacterial-only (30.2%), and viral-bacterial (40.5%). The main bacteria were Streptococcus pneumoniae and Haemophilus influenzae, while human adenovirus and Epstein-Barr virus were the most common viruses. Co-detection rates inversely correlated with age, decreasing from 91.1% in infants to 48.1% in adolescents. Younger age (36-72mo vs 72-168mo, OR: 1.57), non-summer seasons (Spring, OR: 2.44; Autumn, OR: 1.93; Winter, OR: 2.77), and elevated white blood cell count (OR: 1.18) were associated with higher risk of co-detection, whereas higher fibrinogen and pleural effusion reduced risk (all P < 0.01).

CONCLUSIONS: The high prevalence of co-detection in pediatric MPP, notably viral-bacterial, exhibits distinct age and seasonal patterns essential for informing targeted control strategies. Study limitations include its retrospective design and potential heterogeneity from multicenter differences in NGS methodologies.},
}

@article {pmid41242396,
year = {2025},
author = {Sharma, R and Walia, A and Lakhanpal, D},
title = {Human metapneumovirus: an underdiagnosed public health threat.},
journal = {Infectious diseases now},
volume = {},
number = {},
pages = {105189},
doi = {10.1016/j.idnow.2025.105189},
pmid = {41242396},
issn = {2666-9919},
abstract = {Human metapneumovirus (hMPV), a negative-sense RNA virus in the Pneumoviridae family, has emerged as a major yet under-recognized cause of acute respiratory infections worldwide. Since its identification in 2001, hMPV has shown steady genetic evolution into genotypes A and B, with newer sublineages such as A2.2.1, A2.2.2, and B2 currently detected across continents. A recent global rise in hMPV detections, detailed in reports from China, Europe, and the USA, likely reflects both expanded testing and the re-establishment of seasonal circulation following the COVID-19 pandemic. Co-infections with respiratory viruses, including RSV and influenza, contribute to severe clinical outcomes and hospital burden. Multiplex RT-PCR remains the most sensitive and widely used diagnostic method for detection of hMPV, outperforming conventional PCR approaches, while metagenomic sequencing and CRISPR-based assays are primarily research tools. Diagnostic sensitivity also varies with sample source, and access to advanced technologies remains globally uneven. Despite its growing clinical impact, no approved antiviral is available. Promising candidates, including monoclonal antibodies against the fusion protein, siRNA therapies, and mRNA-based vaccines, are in the early stages of development. This review encompasses recent evidence on hMPV epidemiology, molecular evolution, diagnostic approaches, and therapeutic and vaccine development, underscoring a need for sustained surveillance, equitable diagnostic capacity, and proactive vaccine research more effectively addressing a largely overlooked respiratory pathogen.},
}

@article {pmid41242241,
year = {2025},
author = {Yang, L and Chen, J and Chen, Z and Gao, Y and Su, Y and Zeng, S and He, Q and Qiu, Q},
title = {Integrated metagenomic and metabolomic analyses reveal that nitrogen fertilizer reduction combined with biochar application improves the soil microenvironment of Phoebe bournei seedlings.},
journal = {Journal of environmental management},
volume = {395},
number = {},
pages = {127954},
doi = {10.1016/j.jenvman.2025.127954},
pmid = {41242241},
issn = {1095-8630},
abstract = {Biochar has emerged as a globally recognized soil amendment, yet its synergistic effects with nitrogen fertilization on rhizosphere ecosystems remain underexplored. This study employed non-targeted metabolomics and metagenomic analyses to investigate the soil microenvironment of Phoebe bournei seedlings under four treatments: control (CK), optimum nitrogen application (F1), 20 % nitrogen fertilizer reduction with biochar application (F2B1), and 40 % nitrogen fertilizer reduction with biochar application (F3B2). A total of 842 (421 up-/421 down-regulated) and 789 (415 up-/374 down-regulated) differential metabolites were identified in the F2B1 and F3B2 treatments, respectively. Nitrogen fertilizer reduction combined with biochar application significantly reshaped soil metabolomic profiles, with pronounced enrichment in eight key metabolic pathways, including ascorbate and aldarate metabolism pathways and arachidonic acid metabolism pathways. Streptomyces, Pseudomonas, and Afipia exhibited higher relative abundance levels in both F2B1 and F3B2 treatments. Redundancy analysis indicated that soil pH was the dominant influence on the variation of microbial communities. The topological complexity and stability of bacterial co-occurrence networks were significantly improved by F3B2. An upregulation of functional genes involved in soil nitrification (amoAB, hao, and nxrAB) resulted from F3B2. Furthermore, network analysis revealed significant correlations between microbial taxa and differential metabolites, with a preponderance of positive correlations. Our results indicate that nitrogen fertilizer reduction combined with biochar application significantly influences soil microbial metabolism, establishing a theoretical foundation for enhancing soil quality in Phoebe bournei woodlands and for the judicious use of nitrogen fertilizer and biochar in forestry.},
}

@article {pmid41242205,
year = {2025},
author = {Li, X and Gao, X and Yu, S and Du, F and Liu, J and Kan, X and Liu, X and Yao, D},
title = {Rhizosphere microbiota diversity and salt stress-alleviating functional genes in coastal wild salt-tolerant plants.},
journal = {Microbiological research},
volume = {303},
number = {},
pages = {128397},
doi = {10.1016/j.micres.2025.128397},
pmid = {41242205},
issn = {1618-0623},
abstract = {Saline-alkali land significantly threatens global food security and ecological safety, and root-associated microorganisms help plants survive salt-alkali stress. However, the ecological functions and factors that influence the rhizosphere microbiomes of salt-tolerant plants remain poorly understood. In this study, we used high-throughput sequencing and metagenomics to reveal the microbial communities and functional traits of bulk and rhizosphere soil from salt-tolerant species (Suaeda glauca, Phragmites australis, and Spartina alterniflora) growing in saline soil. Bacterial and fungal taxa were significantly enriched in the rhizosphere soil compared to the non-rhizosphere soil. Metagenomic analyses revealed that metabolic pathways, including glycolysis and ABC transporters, were highly enriched in the rhizosphere. Functional profiling indicated that salt stress-related pathways were more abundant in the core genera Pseudomonas and Woeseia. The abundance of functional genes related to plant growth-promoting traits, including phosphate solubilization and salt adaptation pathways, was higher in the rhizosphere soil than in the non-rhizosphere soil, which was mainly driven by soil salinity, total nitrogen content, and total carbon content. Additionally, P. aeruginosa obtained from the rhizosphere of S. alterniflora exhibited high phosphorus solubilization efficiency (908.38 μg/mL), nitrogen fixation activity (2.84 μg/mL) and salt tolerance (≦ 5 % NaCl). These findings demonstrate that salt-tolerant plants shape microbial activities by controlling the rhizosphere microenvironment, mitigating salt stress, providing a scientific and practical foundation for the development of targeted microbial inoculants for saline-alkali land reclamation.},
}

@article {pmid41241245,
year = {2025},
author = {Li, L and Yu, X and Wang, M and Sun, H and Zhu, J and Wang, X and Chen, S and Hu, S},
title = {Salicylic acid as a pathway inducer for improved bioremediation of oil-polluted saline-alkali soils by chemotactic S. Stutzeri M3.},
journal = {Bioresource technology},
volume = {441},
number = {},
pages = {133647},
doi = {10.1016/j.biortech.2025.133647},
pmid = {41241245},
issn = {1873-2976},
abstract = {The bioremediation would be inhibited by low-efficiency of mass transfer and persistent high-molecular weight polycyclic aromatic hydrocarbons (PAHs). In this study, chemotactic strain named as Stutzerimonas stutzeri M3 and salicylic acid were employed for enhancing biodegradation of petroleum hydrocarbon. The addition of salicylic acid significantly enhanced the activities of alkane hydroxylase and catechol 1,2-dioxygenase, as well as the biodegradation rate of petroleum hydrocarbons. Moreover, the inputs of salicylic acid reshaped microbial community, and obviously affected their cooperative metabolic process by increasing relative abundance of petroleum-degrading bacteria, such as Stutzerimonas, Pontibacillus, Halobacillus and Virgibacillus. Metagenomic analysis furtherly confirmed that overall metabolic pathways of microbial communities and expression of functional genes associated with petroleum degradation (e.g., fad, cat and nah) were enhanced. Furthermore, chemotactic gene expression in strain M3 was significantly increased, thereby facilitating petroleum hydrocarbons degradation. These findings provide a new regulating strategy for effective bioremediation in oil-contaminated sites.},
}

@article {pmid41241073,
year = {2025},
author = {Du, JY and Qin, FL and Yang, RN and Chen, YL and Tan, GF and Li, WJ and Yang, L and Cai, J and Shen, DL and Zhu, HR and Yuan, ML and Zhang, W},
title = {Metagenomic analysis of the gut microbiota in major depressive disorder with different antidepressant efficacy: A prospective cohort study.},
journal = {Journal of affective disorders},
volume = {},
number = {},
pages = {120709},
doi = {10.1016/j.jad.2025.120709},
pmid = {41241073},
issn = {1573-2517},
abstract = {BACKGROUND: Major depressive disorder (MDD) is globally prevalent, with Selective Serotonin Reuptake Inhibitors (SSRIs) and Serotonin-Norepinephrine Reuptake Inhibitors (SNRIs) as first-line treatment. However, 30 %-40 % of patients have inadequate response, and early identification is difficult. Gut microbiota contributes to MDD pathogenesis through the gut-brain axis, but baseline differences between responders and non-responders to SSRIs or SNRIs remain unclear.

METHODS: 82 MDD individuals were initially screened. However, due to issues with the drug administration and fecal sample availability, a total of 43 people were eventually included. Based on 3-month Hamilton Depression Rating Scale (HAMD-17) changes, 29 patients were responders (39.12 ± 15.79 years, 8 males), while 14 were non-responders (40.14 ± 17.28 years, 5 males). Baseline assessments encompassed Depression Anxiety scales, demographics, and fecal metagenomic analysis (taxonomic/functional annotation, and differential analysis of microbial species and pathways).

RESULTS: Baseline demographic characteristics, lifestyle factors, and anxiety/depression scores were comparable. Non-responders had higher relative abundances of Bacteroidaceae and Bacteroide; LEfSe showed responders enriched Hungatella, Ligilactobacillus_ruminis, and non-responders enriched Anaerostipes, Bacteroides_faecis. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analysis identified 246 differentially expressed KEGG Orthologies and 13 pathways, with the steroid biosynthesis pathway (map00100) being enriched in non-responders and the D-amino acid metabolism pathway (map00470) enriched in responders. The study has limitations: small sample size and it lacks direct mechanism validation.

CONCLUSIONS: The composition and functional pathways of gut microbiota exhibit significant differences between responders and non-responders to SSRIs or SNRIs among MDD patients, providing clues for the development of new treatment strategies.},
}

@article {pmid41240828,
year = {2025},
author = {Liu, J and Xie, S and Ji, Y and Fan, X and Luo, S and Xu, X and Wang, C and Zhu, L},
title = {Dual suppression of methanogenesis by dichloromethane and salinity: Competitive methyltransferase inhibition and energy-coupling disruption.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140408},
doi = {10.1016/j.jhazmat.2025.140408},
pmid = {41240828},
issn = {1873-3336},
abstract = {The pervasive co-occurrence of dichloromethane (DCM), a prevalent chlorinated solvent, with high salinity in industrial wastewater poses a poorly understood combined ecological stress on anaerobic microbial ecosystems. This study deciphered the molecular mechanisms underlying the dual inhibition of methanogenesis under such combined stress. Metagenomic analysis revealed that methanogens (particularly Methanobacterium and Methanothrix) were more sensitive to DCM and salinity stress, while fermentative bacteria and acetogens exhibited better resilience. Under salinity stress, methanogens primarily expelled extra Na[+] was via the Na[+] pump coupled with methyltransferase (Mtr). However, density functional theory (DFT) calculations demonstrated that DCM competitively bound to the cobamide cofactor in Mtr (ΔG = -10.5 kcal/mol for DCM vs. +14.6 kcal/mol for methylated carrier), thereby impairing sodium extrusion (58 % downregulation in mtrH gene abundance) and subsequent ATP synthesis. Concurrently, elevated Na[+] levels forced a metabolic shift towards energy-intensive sodium extrusion pathways, as evidenced by the upregulation of mrpA (Na[+]/H[+] antiporter, +20 %) and natA/natB (ABC sodium transporters, +162 %). These disruptions culminated in a severe bioenergetic crisis, indicated by decreased coenzyme F420 activity (31.11 ± 1.58 vs. 48.66 ± 2.09 U/L in control) and suppression of methane yield (22.31 ± 3.63 CH4/g COD vs. 178.91 ± 1.28 mL CH4/g COD in control). Our findings uncovered a novel dual inhibition mechanism, combining molecular-level competitive enzyme inhibition with cellular-scale energy uncoupling, providing critical insights into the microbial toxicological effects of co-occurring chlorinated solvents and salinity.},
}

@article {pmid41240707,
year = {2025},
author = {Fonseca, A and Kenney, S and Boney, J and Ganda, E},
title = {Mycobiome temporal and functional dynamics in broilers: Ecological perspective on bacterial-fungal correlations and the effect of feed additives.},
journal = {Poultry science},
volume = {104},
number = {12},
pages = {106092},
doi = {10.1016/j.psj.2025.106092},
pmid = {41240707},
issn = {1525-3171},
abstract = {The gut mycobiome (the fungal component of the microbiome) of chickens, though less abundant than bacterial populations, plays a vital role in gut ecology, yet remains underexplored. This study investigated the temporal, dietary, and ecological factors shaping the broiler chicken excreta-associated fungal communities and their correlation with bacterial microbiota. A total of 320 Cobb 500 (1-day-old) chicks were raised for 21 days in 32 randomly allocated cages. Treatments consisted of four experimental diets: a Basal Diet, a Basal Diet with an Antibiotic (bacitracin methylene disalicylate), an Essential oils blend (oregano oil, rosemary, and red pepper), or a Probiotic (Bacillus subtilis). Shotgun metagenomic sequencing was performed on excreta samples collected at days 1, 10, and 21 to evaluate fungal diversity, composition, cross-kingdom correlation and functional profiling. The fungal community was dominated by Ascomycota and Basidiomycota across all treatments and time points. While alpha diversity metrics did not differ significantly between treatments (P > 0.05), fungal richness and evenness increased significantly over time (P < 0.05), indicating age-driven ecological succession. Beta diversity analysis revealed distinct age-related clustering patterns, with early dominance by Candida albicans and later shifts toward genera such as Fusarium and Malassezia. Feed additives exerted limited influence on fungal composition or diversity metrics, although clustering patterns suggested subtle treatment-specific effects over time. Cross-kingdom correlation analysis identified co-occurring temporal dynamics between the two microbial communities. Candida was positively correlated with Streptococcus and Escherichia/Shigella but negatively associated with beneficial genera like Bifidobacterium and Faecalibacterium. Additionally, microbial functional characteristics were observed in each treatment exhibiting metabolic features. Overall, this study demonstrates that excreta fungal succession in the broiler gut is primarily driven by host age and highlights the temporal plasticity of concurrent changes in fungal and bacteria communities. The findings underscore the importance of multi-kingdom ecological approaches to better understand gut health in poultry production.},
}

@article {pmid39617895,
year = {2024},
author = {Perrin, AJ and Dorrell, RG},
title = {Protists and protistology in the Anthropocene: challenges for a climate and ecological crisis.},
journal = {BMC biology},
volume = {22},
number = {1},
pages = {279},
pmid = {39617895},
issn = {1741-7007},
mesh = {*Climate Change ; *Eukaryota/physiology ; *Ecosystem ; Biodiversity ; },
abstract = {Eukaryotic microorganisms, or "protists," while often inconspicuous, play fundamental roles in the Earth ecosystem, ranging from primary production and nutrient cycling to interactions with human health and society. In the backdrop of accelerating climate dysregulation, alongside anthropogenic disruption of natural ecosystems, understanding changes to protist functional and ecological diversity is of critical importance. In this review, we outline why protists matter to our understanding of the global ecosystem and challenges of predicting protist species resilience and fragility to climate change. Finally, we reflect on how protistology may adapt and evolve in a present and future characterized by rapid ecological change.},
}

*Climate Change
*Eukaryota/physiology
*Ecosystem
Biodiversity

@article {pmid34286093,
year = {2021},
author = {Cheng, CT and Jeng, ML and Tsai, JF and Li, CL and Wu, LW},
title = {Two mitochondrial genomes of Taiwanese rhinoceros beetles, Oryctes rhinoceros and Eophileurus chinensis (Coleoptera: Scarabaeidae).},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {6},
number = {8},
pages = {2260-2262},
pmid = {34286093},
issn = {2380-2359},
abstract = {Two mitochondrial genomes of the dynastine beetles, Oryctes rhinoceros (Linnaeus, 1758) and Eophileurus chinensis (Faldermann, 1835), were assembled via high-throughput sequencing (HTS). Each of the mitogenomes has 37 genes, showing standard gene order and annotation as the other insects, except for the transfer genes, presenting tQ-tI-tM order. To examine their phylogenetic positions, 118 public mitogenomes of Scarabaeidae were used to infer a ML tree. Overall, our scarabaeid phylogeny reveals clear relationships with high nodal supports, and the two rhinoceros beetles are both grouped with the subfamily Dynastinae. The feeding habit of the two clades seems to represent coprophagous and phytophagous types. However, polyphyletic relationships were observed in the subfamily Melolothinae and in the tribes of Onthophagini and Oniticellini. Further systematic revision is needed.},
}

@article {pmid33898751,
year = {2021},
author = {Jeng, ML and Chen, MY and Wu, LW},
title = {Two complete mitochondrial genomes of Papilio butterflies obtained from historical specimens (Lepidoptera: Papilionidae).},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {6},
number = {4},
pages = {1341-1343},
pmid = {33898751},
issn = {2380-2359},
abstract = {Museum specimens are collected for education, exhibition, and various multiple scientific purposes. However, millions of specimens remain in their collection boxes for years without being analyzed. Historical specimens have been known to contain low-quality DNA; hence, it is difficult to utilize their sequence information in phylogenetic studies. However, recent advances in high-throughput sequencing (HTS) make these collections amenable to phylogenomic studies. In this study, two historical specimens (Papilio xuthus Linnaeus, 1767, and Papilio thoas Linnaeus, 1771) were sampled and DNA extracted for HTS via the Miseq platform. Two complete mitogenomes were assembled, even though the DNA quality of those specimens was highly fragmented, below 250 bp in length. The 37 genes of 60 mitogenomes were aligned and used for inferring the phylogenetic relationships of Papilioninae. These two newly sequenced mitogenomes are correctly grouped in the genus Papilio, and this result indicates that historical specimens show great potential for phylogenetic studies with HTS technology.},
}

@article {pmid32019036,
year = {2020},
author = {Brandon, TA and Stamps, BW and Cummings, A and Zhang, T and Wang, X and Jiang, D},
title = {Poised potential is not an effective strategy to enhance bio-electrochemical denitrification under cyclic substrate limitations.},
journal = {The Science of the total environment},
volume = {713},
number = {},
pages = {136698},
doi = {10.1016/j.scitotenv.2020.136698},
pmid = {32019036},
issn = {1879-1026},
mesh = {Biofilms ; Bioreactors ; *Denitrification ; Nitrates ; Thiobacillus ; },
abstract = {Bio-electrochemical denitrification (BED) is a promising organic carbon-free nitrate remediation technology. However, the relationship between engineering conditions, biofilm community composition, and resultant functions in BED remains under-explored. This study used deep sequencing and variation partitioning analysis to investigate the compositional shifts in biofilm communities under varied poised potentials in the batch mode, and correlated these shifts to reactor-level functional differences. Interestingly, the results suggest that the proliferation of a key species, Thiobacillus denitrificans, and community diversity (the Shannon index), were almost equally important in explaining the reactor-to-reactor functional variability (e.g. variability in denitrification rates was 51% and 38% attributable to key species and community diversity respectively, with a 30% overlap), but neither was heavily impacted by the poised potential. The findings suggest that while enriching the key species may be critical in improving the functional efficiency of BED, poised potentials may not be an effective strategy to achieve the desired level of enrichment in substrate-limited real-world conditions.},
}

Biofilms
Bioreactors
*Denitrification
Nitrates
Thiobacillus

@article {pmid31974023,
year = {2020},
author = {Gladding, PA and Legget, M and Fatkin, D and Larsen, P and Doughty, R},
title = {Polygenic Risk Scores in Coronary Artery Disease and Atrial Fibrillation.},
journal = {Heart, lung & circulation},
volume = {29},
number = {4},
pages = {634-640},
doi = {10.1016/j.hlc.2019.12.004},
pmid = {31974023},
issn = {1444-2892},
mesh = {*Atrial Fibrillation/genetics/physiopathology/therapy ; *Coronary Artery Disease/genetics/physiopathology/therapy ; *Genetic Predisposition to Disease ; Genome-Wide Association Study ; Humans ; *Multifactorial Inheritance ; *Polymorphism, Single Nucleotide ; Risk Factors ; },
abstract = {Coronary artery disease (CAD) and atrial fibrillation (AF) are two highly prevalent cardiovascular disorders that are associated with substantial morbidity and mortality. Conventional clinical risk factors for these disorders may not be identified prior to mid-adult life when pathophysiological processes are already established. A better understanding of the genetic underpinnings of disease should facilitate early detection of individuals at risk and preventative intervention. Single rare variants of large effect size that are causative for CAD, AF, or predisposing factors such as hypertension or hyperlipidaemia, may give rise to familial forms of disease. However, in most individuals, CAD and AF are complex traits in which combinations of genetic and acquired factors play a role. Common genetic variants that affect disease susceptibility have been identified by genome-wide association studies, but the predictive value of any single variant is limited. To address this issue, polygenic risk scores (PRS), comprised of suites of disease-associated common variants have been devised. In CAD and AF, incorporation of PRS into risk stratification algorithms has provided incremental prognostic information to clinical factors alone. The long-term health and economic benefits of PRS-guided clinical management remain to be determined however, and further evidence-based data are required.},
}

*Atrial Fibrillation/genetics/physiopathology/therapy
*Coronary Artery Disease/genetics/physiopathology/therapy
*Genetic Predisposition to Disease
Genome-Wide Association Study
Humans
*Multifactorial Inheritance
*Polymorphism, Single Nucleotide
Risk Factors

@article {pmid31942825,
year = {2020},
author = {Ho, J and Yeoh, YK and Barua, N and Chen, Z and Lui, G and Wong, SH and Yang, X and Chan, MC and Chan, PK and Hawkey, PM and Ip, M},
title = {Systematic review of human gut resistome studies revealed variable definitions and approaches.},
journal = {Gut microbes},
volume = {12},
number = {1},
pages = {1700755},
pmid = {31942825},
issn = {1949-0984},
mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/classification/*drug effects/*genetics ; Drug Resistance, Bacterial/*genetics ; Gastrointestinal Microbiome/*drug effects/*genetics ; Gastrointestinal Tract/microbiology ; Genes, Bacterial ; Humans ; },
abstract = {In this review, we highlight the variations of gut resistome studies, which may preclude comparisons and translational interpretations. Of 22 included studies, a range of 12 to 2000 antibiotic resistance (AR) genes were profiled. Overall, studies defined a healthy gut resistome as subjects who had not taken antibiotics in the last three to 12 months prior to sampling. In studies with de novo assembly, AR genes were identified based on variable nucleotide or amino acid sequence similarities. Different marker genes were used for defining resistance to a given antibiotic class. Validation of phenotypic resistance in the laboratory is frequently lacking. Cryptic resistance, collateral sensitivity and the interaction with repressors or promotors were not investigated. International consensus is needed for selecting marker genes to define resistance to a given antibiotic class in addition to uniformity in phenotypic validation and bioinformatics pipelines.},
}

Anti-Bacterial Agents/pharmacology
Bacteria/classification/*drug effects/*genetics
Drug Resistance, Bacterial/*genetics
Gastrointestinal Microbiome/*drug effects/*genetics
Gastrointestinal Tract/microbiology
Genes, Bacterial
Humans

@article {pmid31248111,
year = {2019},
author = {Richardson, E and Dacks, JB},
title = {Microbial Eukaryotes in Oil Sands Environments: Heterotrophs in the Spotlight.},
journal = {Microorganisms},
volume = {7},
number = {6},
pages = {},
pmid = {31248111},
issn = {2076-2607},
support = {RES0021028, RES0043758, RES0046091//Natural Sciences and Engineering Research Council of Canada/ ; },
abstract = {Hydrocarbon extraction and exploitation is a global, trillion-dollar industry. However, for decades it has also been known that fossil fuel usage is environmentally detrimental; the burning of hydrocarbons results in climate change, and environmental damage during extraction and transport can also occur. Substantial global efforts into mitigating this environmental disruption are underway. The global petroleum industry is moving more and more into exploiting unconventional oil reserves, such as oil sands and shale oil. The Albertan oil sands are one example of unconventional oil reserves; this mixture of sand and heavy bitumen lying under the boreal forest of Northern Alberta represent one of the world's largest hydrocarbon reserves, but extraction also requires the disturbance of a delicate northern ecosystem. Considerable effort is being made by various stakeholders to mitigate environmental impact and reclaim anthropogenically disturbed environments associated with oil sand extraction. In this review, we discuss the eukaryotic microbial communities associated with the boreal ecosystem and how this is affected by hydrocarbon extraction, with a particular emphasis on the reclamation of tailings ponds, where oil sands extraction waste is stored. Microbial eukaryotes, or protists, are an essential part of every global ecosystem, but our understanding of how they affect reclamation is limited due to our fledgling understanding of these organisms in anthropogenically hydrocarbon-associated environments and the difficulties of studying them. We advocate for an environmental DNA sequencing-based approach to determine the microbial communities of oil sands associated environments, and the importance of studying the heterotrophic components of these environments to gain a full understanding of how these environments operate and thus how they can be integrated with the natural watersheds of the region.},
}

@article {pmid31226241,
year = {2019},
author = {Roth, H and Gallo, S and Badger, P and Hillwig, M},
title = {Changes in microbial communities of a passive coal mine drainage bioremediation system.},
journal = {Canadian journal of microbiology},
volume = {65},
number = {10},
pages = {775-782},
doi = {10.1139/cjm-2018-0612},
pmid = {31226241},
issn = {1480-3275},
mesh = {Bacteria/genetics ; Biodegradation, Environmental ; *Coal Mining ; *Microbiota ; *Wetlands ; },
abstract = {Drainage from abandoned mines is one factor greatly affecting the streams and vegetation in and around Pittsburgh and the Appalachian Mountains where coal mining occurred. This drainage may be more acidic, alkaline, or metal based. Different methods for remediation exist. Passive remediation is one method used to naturally allow the metals to precipitate out and aid in cleaning up the water. The goal of this study is to sample different holding ponds in a sequential passive remediation system and determine microbial communities present at each site of an abandoned coal mine drainage site. Sequencing of the 16S rRNA gene of the sediment indicated the most abundant phyla at each of the 5 ponds and wetland area included Proteobacteria (36%-43%), Bacteroidetes (12%-37%), Firmicutes (3%-11%), and Verrucomicrobia (6%-11%). Analysis of genera between the first, and most polluted, pond included Solitalea, Pedosphaera, and Rhodocyclus, whereas the microbial community from the wetland site at the end of the remediation system included Ignavibacterium, Pelotomaculum, and Petrimonas. The results of our microbial community composition study of sediment from a passive treatment system are in line with organisms commonly found in sediment regardless of iron oxide precipitation, while others are preferentially found in the less polluted wetland site.},
}

Bacteria/genetics
Biodegradation, Environmental
*Coal Mining
*Microbiota
*Wetlands

@article {pmid30769763,
year = {2019},
author = {, and Singh, BR and Gupta, VK and Deeba, F and Bajpai, R and Pandey, V and Naqvi, AH and Upreti, DK and Gathergood, N and Jiang, Y and El Enshasy, HA and Sholkamy, EN and Mostafa, AA and Hesham, AE and Singh, BN},
title = {Non-Toxic and Ultra-Small Biosilver Nanoclusters Trigger Apoptotic Cell Death in Fluconazole-Resistant Candida albicans via Ras Signaling.},
journal = {Biomolecules},
volume = {9},
number = {2},
pages = {},
pmid = {30769763},
issn = {2218-273X},
mesh = {Antifungal Agents/chemistry/*pharmacology ; Candida albicans/cytology/*drug effects ; Cell Death ; Cell Survival/drug effects ; Drug Resistance, Fungal/*drug effects ; Fluconazole/chemistry/*pharmacology ; Lichens/chemistry/metabolism ; Metal Nanoparticles/*chemistry ; Particle Size ; Proto-Oncogene Proteins p21(ras)/*antagonists & inhibitors/metabolism ; Reactive Oxygen Species/metabolism ; Signal Transduction/drug effects ; Silver/chemistry/*metabolism ; Surface Properties ; },
abstract = {Silver-based nanostructures are suitable for many biomedical applications, but to be useful therapeutic agents, the high toxicity of these nanomaterials must be eliminated. Here, we biosynthesize nontoxic and ultra-small silver nanoclusters (rsAg@NCs) using metabolites of usnioid lichen (a symbiotic association of algae and fungi) that exhibit excellent antimicrobial activity against fluconazole (FCZ)-resistant Candida albicans that is many times higher than chemically synthesized silver nanoparticles (AgNPs) and FCZ. The rsAg@NCs trigger apoptosis via reactive oxygen species accumulation that leads to the loss of mitochondrial membrane potential, DNA fragmentation, chromosomal condensation, and the activation of metacaspases. The proteomic analysis clearly demonstrates that rsAg@NCs exposure significantly alters protein expression. Most remarkable among the down-regulated proteins are those related to glycolysis, metabolism, free radical scavenging, anti-apoptosis, and mitochondrial function. In contrast, proteins involved in plasma membrane function, oxidative stress, cell death, and apoptosis were upregulated. Eventually, we also established that the apoptosis-inducing potential of rsAg@NCs is due to the activation of Ras signaling, which confirms their application in combating FCZ-resistant C. albicans infections.},
}

Antifungal Agents/chemistry/*pharmacology
Candida albicans/cytology/*drug effects
Cell Death
Cell Survival/drug effects
Drug Resistance, Fungal/*drug effects
Fluconazole/chemistry/*pharmacology
Lichens/chemistry/metabolism
Metal Nanoparticles/*chemistry
Particle Size
Proto-Oncogene Proteins p21(ras)/*antagonists & inhibitors/metabolism
Reactive Oxygen Species/metabolism
Signal Transduction/drug effects
Silver/chemistry/*metabolism
Surface Properties

@article {pmid30278254,
year = {2019},
author = {Wu, LW and Chiba, H and Lees, DC and Ohshima, Y and Jeng, ML},
title = {Unravelling relationships among the shared stripes of sailors: Mitogenomic phylogeny of Limenitidini butterflies (Lepidoptera, Nymphalidae, Limenitidinae), focusing on the genera Athyma and Limenitis.},
journal = {Molecular phylogenetics and evolution},
volume = {130},
number = {},
pages = {60-66},
doi = {10.1016/j.ympev.2018.09.020},
pmid = {30278254},
issn = {1095-9513},
mesh = {Animals ; Asia ; Butterflies/*classification/*genetics ; Genome, Insect/*genetics ; Genome, Mitochondrial/*genetics ; *Phylogeny ; },
abstract = {The phylogenetic relationships of the nymphalid butterfly tribe Limenitidini are best known for the genera Limenitis and Adelpha, model taxa for evolutionary processes such as Batesian mimicry and rapid adaptive radiations. Whereas these American limenitidines have received the most attention, phylogenetic relationships of their Asian relatives are still controversial and largely unexplored. Even one of the largest genera in Asia, Athyma, is polyphyletic. To clarify the phylogenetic relationships of these Asian Limenitidini, a total of 53 representatives were sampled; 37 have their mitogenomes sequenced for the first time. Our phylogenetic results confirm that mitogenomic data provides well-resolved relationships at most major levels of the phylogeny, even using different partition schemes or different inference methods. Interestingly, our results show that some Athyma taxa are embedded within the genus Limenitis, whereas the genus Tacola, previously considered to be a synonym of Athyma, needs to be recognized as a valid clade. Additionally, the other Limenitidini genera in Asia (namely Tarattia, Litinga, Sumalia, Pandita and Patsuia) are now grouped either within Athyma or Limenitis, so these genera need to be sunk. Importantly, we also show that the mainly Old World Limenitis and entirely New World Adelpha are sister groups, confirming the relevance of Asian lineages to global studies of Limenitis evolution.},
}

Animals
Asia
Butterflies/*classification/*genetics
Genome, Insect/*genetics
Genome, Mitochondrial/*genetics
*Phylogeny

@article {pmid28105307,
year = {2016},
author = {Ankenbrand, MJ and Terhoeven, N and Hohlfeld, S and Förster, F and Keller, A},
title = {biojs-io-biom, a BioJS component for handling data in Biological Observation Matrix (BIOM) format.},
journal = {F1000Research},
volume = {5},
number = {},
pages = {2348},
pmid = {28105307},
issn = {2046-1402},
abstract = {The Biological Observation Matrix (BIOM) format is widely used to store data from high-throughput studies. It aims at increasing interoperability of bioinformatic tools that process this data. However, due to multiple versions and implementation details, working with this format can be tricky. Currently, libraries in Python, R and Perl are available, whilst such for JavaScript are lacking. Here, we present a BioJS component for parsing BIOM data in all format versions. It supports import, modification, and export via a unified interface. This module aims to facilitate the development of web applications that use BIOM data. Finally, we demonstrate its usefulness by two applications that already use this component. Availability: https://github.com/molbiodiv/biojs-io-biom, https://dx.doi.org/10.5281/zenodo.218277.},
}

@article {pmid41240515,
year = {2025},
author = {Wang, S and Xu, R and Xiao, M and Yu, J and Yu, L and Heng, Z and Li, Z and Du, Q and Zhou, Y and Li, Y and Zhu, G},
title = {Comammox ammonia oxidization and N2O production in vadose and saturated zone soils.},
journal = {Water research},
volume = {289},
number = {Pt B},
pages = {124899},
doi = {10.1016/j.watres.2025.124899},
pmid = {41240515},
issn = {1879-2448},
abstract = {Riparian zones are biogeochemical hotspots of N2O emission. The important role of ammonia oxidation in N2O production has been reported in rivers, even higher than heterotrophic denitrification, however, the mechanisms controlling riparian N2O production remain unknown. Here, we found that complete ammonia oxidation (comammox) process significantly contributes to ammonia oxidation and N2O production in subsurface riparian zone. The contribution of comammox to ammonia oxidation in surface soils (38.7 ± 6.5 %) is equivalent to that of bacterial ammonia oxidation (49.4 ± 6.9 %), and both processes are significantly more important than archaeal ammonia oxidation (11.9 ± 4.1 %). Moreover, comammox dominates ammonia oxidation in both vadose and saturated zone soils, especially in summer with the average contributions of over 67.9 %. However, as a biotic N2O production pathway, comammox produces more N2O in vadose (up to 72 %) and saturated zone (up to 100.0 %) soils, significantly higher than that produced by archaeal ammonia oxidation (32.0 ± 4.0 %) and bacterial ammonia oxidation (18.0 ± 5.7 %). We obtained the first metagenome-assembled genomes (MAGs) of comammox bacteria in a riparian profile, and metagenomic binning analysis revealed that the wide niche of comammox may attribute to its diverse metabolic pathways, which not only perform ammonia oxidation but also nitrate reduction to ammonia. This research enhances the understanding of the biogeochemical ammonia cycle in riparian zone systems and provides new insights for the control of nitrogen pollution in riparian zones.},
}

@article {pmid41240423,
year = {2025},
author = {Alzeer, S and Almaghrabi, RS and Magrashi, A and Alzahrani, T and Bakheet, R and Alqasabi, A and Tayeb, H},
title = {Revealing co-infections in pneumonia: A case report on advancing diagnosis with metagenomic sequencing technologies.},
journal = {Journal of infection and public health},
volume = {19},
number = {1},
pages = {103036},
doi = {10.1016/j.jiph.2025.103036},
pmid = {41240423},
issn = {1876-035X},
abstract = {Pneumonia, a frequent and serious complication in kidney transplant recipients, is significantly increased by long-term immunosuppressive medication. This case report details a patient with lung cavitation, in which conventional microbiological methods revealed Escherichia coli as the principal pathogen. Metagenomic long-read sequencing also identified Klebsiella pneumoniae as a co-pathogen, underscoring the shortcomings of traditional diagnostic techniques. In identifying infectious pathogens, this case illustrates the superior diagnostic accuracy of long-read sequencing, offering crucial information that conventional methods might miss. The implementation of sophisticated sequencing technologies may overcome these diagnostic deficiencies, improving infection care in challenging and immunocompromised patients.},
}

@article {pmid41240163,
year = {2025},
author = {Perez-Hernandez, C and Aldaroub, J and Barth, ZK and Aylward, FO},
title = {A novel lineage of large aquatic bacteriophages identified through metagenomics.},
journal = {Archives of virology},
volume = {170},
number = {12},
pages = {253},
pmid = {41240163},
issn = {1432-8798},
support = {#2141862//National Science Foundation/ ; },
mesh = {*Metagenomics ; *Bacteriophages/genetics/classification/isolation & purification ; *Genome, Viral ; Phylogeny ; },
abstract = {"Jumbo phages" are tailed phages with genome sizes >200 kbp and physical dimensions reaching up to 0.45 μm. Although jumbo phages represent only a small fraction of the isolated phages to date, metagenomic surveys have shown that they are broadly distributed in a wide range of environments. In this study, we surveyed metagenomic data from aquatic systems and identified 25 genomes from a heretofore-undescribed lineage of jumbo phages with genomes reaching up to 307 kbp. We refer to these phages as "moraphages", from the Gaelic word 'mór', for large. Moraphages represent a diverse lineage with inter-genome average amino acid identity (AAI) ranging from 39 to 95%, and our pan-genomic analysis identified only 26 viral orthologous groups (VOGs) found in at least 80% of the genomes. Our phylogenomic analysis suggests that moraphages are distant relatives of a recently described lineage of huge phages from marine sediment. Moraphages lack much of the genetic machinery found in other lineages of large phages, but they have a range of genes that may be used to take over host cellular machinery and subvert host defenses, such as glutamine synthetases, antitoxin genes, and chaperones. The predicted hosts of most moraphages are members of the phylum Bacteroidota, and some encode homologs of the chaperones DnaK and DnaJ that bear evidence of recent gene transfer from members of the order Flavobacteriales. Our work sheds light on the emerging diversity of large phages that are found across the biosphere.},
}

*Metagenomics
*Bacteriophages/genetics/classification/isolation & purification
*Genome, Viral
Phylogeny

@article {pmid41240088,
year = {2025},
author = {V, C and Lal, SB and Mishra, DC and Sharma, A and Kumar, S and Chaturvedi, KK and Behera, BK},
title = {In Silico Identification of Enzymes Involved in Bioremediation from Metagenomic Sequence of River Ganga.},
journal = {Bulletin of environmental contamination and toxicology},
volume = {115},
number = {6},
pages = {64},
pmid = {41240088},
issn = {1432-0800},
mesh = {Biodegradation, Environmental ; *Rivers/chemistry/microbiology ; *Water Pollutants, Chemical/metabolism/analysis ; Metagenomics ; Computer Simulation ; Environmental Monitoring ; Metagenome ; },
abstract = {Environmental pollution, particularly in aquatic ecosystems, poses a major global threat. The Ganga River, vital to millions, suffers from severe contamination despite multiple remediation efforts. Bioremediation, especially enzyme-mediated approaches, offers an eco-friendly and efficient alternative to conventional methods. This study utilizes metagenomic reads to identify bioremediating enzymes, their host microorganisms, target pollutants, and enzyme abundance at two Ganga sites: Nawabganj, Kanpur (highly polluted), and Below Farakka Bridge, West Bengal (less polluted). In-silico analysis was conducted using RemeDB for enzyme identification and MG-RAST for microbial abundance. Enzyme abundance was determined by integrating microbial profiles with the RemeDB enzyme database. Key enzymes identified include Phenylacetaldehyde dehydrogenase (plastic), Biphenyl dioxygenase (hydrocarbons), and Catechol 1,2-dioxygenase (dyes). Results indicate higher bioremediating enzyme diversity in the more polluted Nawabganj site. The findings highlight the potential of native enzymes for pollutant degradation and support further exploration for environmental cleanup strategies.},
}

Biodegradation, Environmental
*Rivers/chemistry/microbiology
*Water Pollutants, Chemical/metabolism/analysis
Metagenomics
Computer Simulation
Environmental Monitoring
Metagenome

@article {pmid41239457,
year = {2025},
author = {Kaczmarczyk, M and Kędzierska-Kapuza, K and Skonieczna-Żydecka, K and Surówka, A and Drożdżal, S and Lechowicz, K and Buszman, M and Szkudlarek, U and Cembrowska-Lech, D and Podsiadło, K and Samborowska, E and Łoniewski, I and Ciechanowski, K},
title = {Modulating effects of microbiota on synbiotic intervention outcomes for microbiota-derived trimethylamine, trimethylamine N-oxide and indoxyl sulfate in healthy young medical students: insights from a 12-week randomized clinical trial.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {1287},
pmid = {41239457},
issn = {1479-5876},
mesh = {Humans ; *Methylamines/blood ; *Synbiotics ; *Indican/blood ; Female ; Male ; Young Adult ; *Students, Medical ; *Microbiota ; Adult ; Gastrointestinal Microbiome ; *Healthy Volunteers ; },
abstract = {BACKGROUND: Microbiota-derived metabolites, trimethylamine-N-oxide (TMAO) and indoxyl sulfate (IS), have been implicated in cardiovascular, renal, and metabolic diseases. Synbiotic interventions are a promising strategy to modulate these metabolites, but their efficacy may vary depending on host-microbial characteristics. This study investigated whether a multi-strain synbiotic could reduce serum concentrations of trimethylamine (TMA), TMAO, and IS in healthy young adults, and whether baseline characteristics of the gut microbiota influence individual responses to the intervention.

METHODS: In a 12-week, double-blind, randomized, placebo-controlled trial, 38 healthy young medical students received either a synbiotic or placebo. Serum levels of TMA, TMAO, and IS were measured at baseline, 6 weeks, and week 12, two hours after consuming two eggs. Gut microbiota composition and function were assessed using 16 S rRNA gene sequencing and predicted through metagenomic profiling (PICRUSt2). Weighted Gene Co-expression Network Analysis (WGCNA) was applied to identify groups of co-occurring bacterial taxa (ASVs) and functional orthologous groups - KEGG Orthologs (KOs).

RESULTS: The synbiotic intervention did not produce significant changes in TMA, TMAO, or IS levels across the entire study population. There were no significant changes in alpha diversity or microbiota composition during the intervention. However, baseline microbiota-related factors influenced individual responses to synbiotic therapy. Two taxonomic WGCNA modules, containing Lachnospiraceae and Ruminococcaceae, were associated with greater reductions in IS levels in participants receiving synbiotics. Also, a module containing Lachnospirales and Oscillospirales showed a potential modulatory effect on TMA levels. A KO module enriched in genes involved in bacterial secretion systems, sulfur metabolism, and methanogenesis pathways - including K14083 (mttB) and K14084 (mttC), both implicated in the conversion of TMA to methane - was significantly associated with reductions in TMA.

CONCLUSIONS: In this randomized, placebo-controlled trial in healthy young adults, the synbiotic did not produce a significant arm-wide effect on post-challenge serum TMA, TMAO, or indoxyl sulfate over 12 weeks. Exploratory moderation analyses suggest that baseline gut-microbiota features, taxonomic and functional, may modulate individual responses, particularly for IS and TMA, supporting a precision-nutrition framework. The translational significance of this study stems from the observation that primary prevention, which is particularly important in metabolic diseases, should be individualised based on the function of the microbiota.},
}

Humans
*Methylamines/blood
*Synbiotics
*Indican/blood
Female
Male
Young Adult
*Students, Medical
*Microbiota
Adult
Gastrointestinal Microbiome
*Healthy Volunteers

@article {pmid41239428,
year = {2025},
author = {Chen, W and Zhang, Y and Gong, H and Cao, Z and Yang, K and Mi, J},
title = {Exploring diversity and distribution patterns of chicken gut bacteriophage community.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {119},
pmid = {41239428},
issn = {2524-4671},
}

@article {pmid41239203,
year = {2025},
author = {Wen, S and Sun, J and Zeng, W and Xiang, H and Zhao, M and Xiang, D},
title = {Effects of different arbuscular mycorrhizal fungi on tobacco seedling growth and their rhizosphere microecological mechanisms.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {1578},
pmid = {41239203},
issn = {1471-2229},
}

@article {pmid41239201,
year = {2025},
author = {Akanmu, AM and Lawal, IB and Ibrahim, SL and Marle-Köster, EV and Hassen, A},
title = {Metagenomic data from the rumen of South African Mutton Merino sheep supplemented with crude or encapsulated Acacia tannin extracts.},
journal = {BMC genomic data},
volume = {26},
number = {1},
pages = {86},
pmid = {41239201},
issn = {2730-6844},
support = {SRUG2204254606//National Research Foundation/ ; },
mesh = {Animals ; *Rumen/microbiology ; *Tannins/pharmacology/administration & dosage ; *Acacia/chemistry ; Sheep/microbiology ; *Metagenomics ; Gastrointestinal Microbiome ; *Plant Extracts/pharmacology ; Animal Feed ; Dietary Supplements ; },
abstract = {OBJECTIVES: This dataset was generated as part of a study investigating the impact of crude and encapsulated Acacia mearnsii tannin extracts on the rumen microbiota of South African Mutton Merino sheep. The aim was to provide high-quality metagenomic data to support methane mitigation strategies through dietary interventions targeting rumen microbial communities.

DATA DESCRIPTION: Rumen fluid was collected from 24 rams (six per treatment) fed a total mixed ration (TMR) supplemented with either distilled water (control), monensin (positive control), crude tannin, or microencapsulated tannin. However, one sample did not yield sufficient sequencing depth, resulting in 23 usable datasets. DNA was extracted and subjected to shotgun metagenomic sequencing on the Illumina NovaSeq 6000 platform. The dataset comprises paired-end reads deposited in the NCBI SRA under accession SRP480487. Taxonomic profiling reveals dominant phyla such as Bacteroidetes and Firmicutes, and the presence of archaeal genera such as Methanobrevibacter. This dataset provides insights into the structural and functional composition of the rumen microbiome and may be useful for comparative studies and biotechnology applications.},
}

Animals
*Rumen/microbiology
*Tannins/pharmacology/administration & dosage
*Acacia/chemistry
Sheep/microbiology
*Metagenomics
Gastrointestinal Microbiome
*Plant Extracts/pharmacology
Animal Feed
Dietary Supplements

@article {pmid41239026,
year = {2025},
author = {Cao, D and Huang, W and Pang, M and Li, J and Huang, H and Ma, H and Li, D and Qin, Y and Peng, X and Fan, H},
title = {Investigation of the Alterations in the Gut Microbiota and Intestinal Mucosa in Mice Infected with Echinococcus multilocularis.},
journal = {Acta parasitologica},
volume = {70},
number = {6},
pages = {211},
pmid = {41239026},
issn = {1896-1851},
support = {No. 2020-ZJ-Y01//Key Laboratory Project of the Science and Technology Department of Qinghai Province/ ; Qinghai[2023]-125//The National Clinical Key Specialty Construction Project of Hepatobiliary Surgery (Hydatidosis) at Qinghai University Affiliated Hospital/ ; Qinghai Research Key Laboratory for Echinococcosis//The 2022 Science and Technology Plan Project of Qinghai Department of Science and Technology/ ; },
abstract = {PURPOSE: Alveolar echinococcosis (AE), a zoonotic parasitic disease caused by the larval metacestode of Echinococcus multilocularis (E. multilocularis), primarily affects the liver and can invide other organs. Given its extremely poor prognsis, witha 10-year mortality rate exceeding 90% in untreated cases, this study aimed to investigate the characteristics and compositional alterations of the intestinal microbiota in AE-infected hosts and evaluate associated intestinal mucosal damage.

METHODS: We established a mouse model of AE for analysis. Fecal samples were collected from 12 AE-infected mice and 12 age-matched healthy controls at 3 and 6 months post-infection. Gut microbiota composition was assessed by 16S rRNA gene sequencing. Intestinal tissues were subjected to histopathological exnamination using hematoxylin-eosin staining (H&E staining), Alcian blue-glucogen staining (AB-PAS staining), and Lendrum's fluorescent peach red staining, to evaluate mucosal structural integrity and quantify the Paneth and goblet cells.

RESULTS: The analysis revealed significant alterations in intestinal microbiota diversity and composition in AE-infected mice compared with controls, with changes becoming more pronounced as the infection progressed. Minimal disruption in microbial ecology was observed at 3 months, whereas substantial reductions in alpha diversity and distinct shifts in beta diversity emerged after 6 months of chronic infection. Phylum-level analysis showed an early increase in Verrucomicrobiota, Bacteroidota, and Campylobacterota at 3 months, followed by a marked enrichment of Verrucomicrobiota and Actinobacteriota at 6 months when compared with controls. At the genus level, AE infection led to a rapid depletion of Ligilactobacillus and Lactobacillus between 3 and 6 months, while Akkermansia abundance significantly increased. Histopathological examination of intestinal tissue further demonstrated severe mucosal damage, including villous atrophy, reduced crypt depth, a pronounced decrease in Paneth cell density (P < 0.01), and reduced goblet cell counts (P < 0.05), collectively indicating compromised intestinal barrier integrity.

CONCLUSION: AE infection induces progressive gut microbiota dysbiosis and compromises intestinal barrier integrity. The specific microbial shifts, particularly the depletion of Ligilactobacillus and enrichment of Akkermansia, represent promising diagnostic biomarkers and potential targets for probiotic supplementation or microbial modulation. To further clarify their roles, future research should incorporate multi-omics strategies, including metagenomics and metabolomics, within larger cohorts to better characterize microbiota-host metabolic interactions and to validate stage-specific microbial biomarkers in AE.},
}

@article {pmid41238915,
year = {2025},
author = {Morad, G and Damania, AV and Melendez, B and Singh, BB and Veguilla, FJ and Soto, RA and Hoballah, YM and Sahasrabhojane, PV and Wong, MC and Ahmed, MM and Rico, RN and Lewis, KN and Wani, K and Shamsutdinova, DD and Lazcano Segura, RN and Ingram, DR and Goethe, EA and Day, A and Flores, II and McDaniel, LK and Chelvanambi, M and Johnson, SB and Dimitriou, F and Gupta, P and Oberai, S and Zal, MA and Doss, P and Jamal, MA and Hayase, E and Wathoo, C and Norberg, LM and Jenkins, SL and Nass, S and Gumin, J and Long, L and Yang, J and Bradley, GR and Bekal, MP and Dono, AG and Pichardo-Rojas, PS and Andrewes, SW and Ballester, LY and Losh, JS and Liang, J and Huo, L and Nielsen, DC and Parker Kerrigan, BC and Brastianos, PK and Fowlkes, NW and Chang, CC and Jenq, RR and Gomez-Manzano, C and Huse, JT and Davies, MA and Lazar, AJ and Bhat, KP and Tandon, N and Esquenazi, Y and Peterson, CB and Puduvalli, VK and Lang, FF and Johnston, CD and Bullman, S and Ajami, NJ and Ferguson, SD and Wargo, JA},
title = {Microbial signals in primary and metastatic brain tumors.},
journal = {Nature medicine},
volume = {31},
number = {11},
pages = {3675-3688},
pmid = {41238915},
issn = {1546-170X},
support = {R21 NS130323/NS/NINDS NIH HHS/United States ; F32 CA260769/CA/NCI NIH HHS/United States ; 1R01 CA227156-01//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; P50 CA221703/CA/NCI NIH HHS/United States ; },
mesh = {Humans ; *Brain Neoplasms/microbiology/pathology ; RNA, Ribosomal, 16S/genetics ; Tumor Microenvironment ; Female ; *Glioma/microbiology/pathology ; Male ; Prospective Studies ; Middle Aged ; *Microbiota/genetics ; In Situ Hybridization, Fluorescence ; Aged ; Adult ; Bacteria/genetics ; },
abstract = {Gliomas and brain metastases are associated with poor prognosis, necessitating a deeper understanding of brain tumor biology and the development of effective therapeutic strategies. Although our group and others have demonstrated microbial presence in various tumors, recent controversies regarding cancer-type-specific intratumoral microbiota emphasize the importance of rigorous, orthogonal validation. This prospective, multi-institutional study included a total of 243 samples from 221 patients, comprising 168 glioma and brain metastases samples and 75 non-cancerous or tumor-adjacent tissues. Using stringent fluorescence in situ hybridization, immunohistochemistry and high-resolution spatial imaging, we detected intracellular bacterial 16S rRNA and lipopolysaccharides in both glioma and brain metastases samples, localized to tumor, immune and stromal cells. Custom 16S and metagenomic sequencing workflows identified taxa associated with intratumoral bacterial signals in the tumor microenvironment; however, standard culture methods did not yield readily cultivable microbiota. Spatial analyses revealed significant correlations between bacterial 16S signals and antimicrobial and immunometabolic signatures at regional, neighborhood and cellular levels. Furthermore, intratumoral 16S bacterial signals showed sequence overlap with matched oral and gut microbiota, suggesting a possible connection with distant communities. Together, these findings introduce microbial elements as a component of the brain tumor microenvironment and lay the foundation for future mechanistic and translational studies.},
}

Humans
*Brain Neoplasms/microbiology/pathology
RNA, Ribosomal, 16S/genetics
Tumor Microenvironment
Female
*Glioma/microbiology/pathology
Male
Prospective Studies
Middle Aged
*Microbiota/genetics
In Situ Hybridization, Fluorescence
Aged
Adult
Bacteria/genetics

@article {pmid41238729,
year = {2025},
author = {Lee, KY and Shin, SH and Park, G and Kang, SH and Kang, HJ and Kim, J and Lee, JJ and Son, GH and Hong, JY},
title = {Shotgun metagenomics of the vaginal microbiome in cervical shortening and preterm birth risk.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {39988},
pmid = {41238729},
issn = {2045-2322},
support = {HI21C1624//Korea Health Industry Development Institute (KHIDI)/ ; HI21C1624//Korea Health Industry Development Institute (KHIDI)/ ; RS-2023-00252948//Korea government (the Ministry of Science and ICT, the Ministry of Trade, Industry and Energy, the Ministry of Health & Welfare, the Ministry of Food and Drug Safety)/ ; },
mesh = {Female ; Humans ; *Vagina/microbiology ; *Premature Birth/microbiology ; *Microbiota/genetics ; Pregnancy ; *Metagenomics/methods ; Adult ; *Cervix Uteri/microbiology/pathology ; Risk Factors ; },
abstract = {Preterm birth (PTB), a leading cause of neonatal morbidity and mortality, is frequently associated with premature cervical remodeling and vaginal microbiome dysbiosis. Cervical shortening in mid-pregnancy is a well-established risk factor for spontaneous PTB (sPTB), yet the microbial signatures underlying this condition remain underexplored, especially in Asian populations. In this study, we conducted shotgun metagenomic analysis of vaginal samples from 35 East Asian pregnant women with a short cervix and 12 with normal cervical length. Species-level taxonomic profiling and functional pathway analysis revealed reduced Lactobacillus dominance, increased microbial diversity, and enrichment of non-optimal CST IV species, such as Fannyhessea vaginae, Bifidobacterium breve, and Mycobacterium canetti in the short cervix group. Functional profiling showed group differences in pathways related to folate biosynthesis, carbohydrate metabolism, and epithelial barrier regulation. Among women with a short cervix, those who delivered preterm had vaginal microbiomes enriched in opportunistic pathogens, including Peptoniphilus equinus, Treponema spp., and Staphylococcus hominis. Conversely, B. breve, Lactobacillus gasseri, and Lactobacillus paragasseri were associated with full-term delivery. Functions related to glycosylation, structural stability, and degradation of cervical mucin were enriched in the sPTB group. Network analysis identified distinct microbial interactions between Lactobacillus-dominated clusters and CST IV-associated taxa, providing ecological insights that may reflect competitive dynamics and potential influences on cervicovaginal barrier integrity. These findings enhance our understanding of the taxonomic and functional profiles of the vaginal microbiome linked to cervical shortening and sPTB, contributing to improved risk stratification and management strategies for PTB, particularly in women with cervical shortening.},
}

Female
Humans
*Vagina/microbiology
*Premature Birth/microbiology
*Microbiota/genetics
Pregnancy
*Metagenomics/methods
Adult
*Cervix Uteri/microbiology/pathology
Risk Factors

@article {pmid41238615,
year = {2025},
author = {Wang, R and Wang, H and Jiang, J and Xu, S and Dong, M},
title = {Diagnostic value of metagenomic next-generation sequencing in the etiological diagnosis of lower respiratory tract infection.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {39987},
pmid = {41238615},
issn = {2045-2322},
support = {GXLIRMMKL-201916//Guangxi Key Laboratory of Molecular Medicine in Liver Injury and Repair/ ; },
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; Female ; Male ; *Respiratory Tract Infections/diagnosis/microbiology/drug therapy ; Middle Aged ; *Metagenomics/methods ; Aged ; Adult ; Bronchoalveolar Lavage Fluid/microbiology ; Aged, 80 and over ; },
abstract = {Metagenomic next-generation sequencing (mNGS) has been widely used in infectious diseases. However, reports on mNGS for lower respiratory tract infection (LRTI) diagnosis remain limited, potentially offering significant value for improving pathogen identification. This study evaluates the diagnostic performance and clinical value of mNGS compared to traditional methods in LRTI. We analyzed traditional and mNGS detection results from 165 patients with suspected LRTI using different specimens including bronchoalveolar lavage fluid (BALF), blood, tissue samples, and pleural effusion. We compared diagnostic differences and characteristics between mNGS and traditional methods, and evaluated the effect of mNGS results on antibiotic treatment.Among 165 cases, 146 (88.48%) patients with LRTI had microbial etiology finally identified. Compared with traditional diagnostic methods, mNGS showed significantly higher positive rate (143/165, 86.7% vs 69/165, 41.8%, P < 0.05). The diagnostic performance of mNGS was not affected by sample types. mNGS demonstrated significant advantage in detecting poly-microbial infections and rare pathogens. Twenty-nine kinds of pathogens were detected only by mNGS, including non-tuberculous mycobacteria (NTM), Prevotella, anaerobic bacteria, Legionella gresilensis, Orientia tsugamushi, and viruses. The pathogen spectrum differed between immunocompetent and immunocompromised individuals. mNGS resulted in treatment changes in 119 patients (72.13%), with 54 patients (32.73%) having reduced antibiotics. mNGS has obvious advantages over traditional detection methods with results unaffected by sample types. mNGS demonstrates significant value for pathogen detection and may provide guidance in clinical practice.},
}

Humans
*High-Throughput Nucleotide Sequencing/methods
Female
Male
*Respiratory Tract Infections/diagnosis/microbiology/drug therapy
Middle Aged
*Metagenomics/methods
Aged
Adult
Bronchoalveolar Lavage Fluid/microbiology
Aged, 80 and over

@article {pmid41238538,
year = {2025},
author = {Bilcke, G and Campese, L and Annunziata, R and Amadei Martínez, L and Borgonuovo, C and Rijsdijk, N and Chaerle, P and Van den Berge, K and D'hondt, S and Iudicone, D and Montresor, M and Ferrante, MI and Vandepoele, K and Vyverman, W},
title = {Conserved genetic markers reveal widespread diatom sexual reproduction in the global ocean.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10029},
pmid = {41238538},
issn = {2041-1723},
support = {1228423N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; 11L2323N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; MARCO-BOLO (101082021)//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; AtlantECO (862923)//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; },
mesh = {*Diatoms/genetics/physiology ; Reproduction/genetics ; Genetic Markers/genetics ; Oceans and Seas ; Transcriptome ; Phytoplankton/genetics ; Gene Expression Profiling ; Salinity ; Metagenome ; Seawater ; },
abstract = {Sexual reproduction is a nearly universal characteristic of the eukaryotic life cycle, yet it is rarely observed in natural populations of micro-eukaryotes. Sex is particularly relevant for diatoms, a key group of marine and freshwater phytoplankton, where sexual reproduction counters a progressive cell size reduction due to cellular division. Here, we leveraged controlled sex transcriptome experiments of four diatom species to develop a robust method for in situ monitoring of sexual reproduction events. The resulting panel of conserved marker genes was validated for specificity and sensitivity using metatranscriptomic profiling of a natural estuarine community undergoing massive sexual reproduction of multiple species in response to increased salinity. Analysis of metatranscriptomic data linked with Metagenome-Assembled Genomes from the Tara Oceans expedition revealed widespread and coordinated expression of these markers across nine diatom genera, complemented by observations of sexual stages in automated imaging resources. Our results reveal that diatom sexual reproduction is more widespread in the global ocean than previously thought, encompassing both dominant bloom-forming species and rare taxa. Our panel of markers to detect sexual reproduction in natural environments paves the road to better understand the interplay between endogenous and environmental controls of this pivotal process, essential for the diatoms' evolutionary success.},
}

*Diatoms/genetics/physiology
Reproduction/genetics
Genetic Markers/genetics
Oceans and Seas
Transcriptome
Phytoplankton/genetics
Gene Expression Profiling
Salinity
Metagenome
Seawater

@article {pmid41238046,
year = {2025},
author = {Oliveira, RDS and Oliveira Alves Filho, NC and Gomes Netto, WB and Silva, DC and Oliveira, MS and Oliveira, ACFM and Baraúna, RA and Graças, DAD and Silva, A and Oliveira Veras, AA},
title = {ContigPolishing: A User-Friendly Java GUI for contig extension and refinement in prokaryotic genomes.},
journal = {Gene},
volume = {},
number = {},
pages = {149893},
doi = {10.1016/j.gene.2025.149893},
pmid = {41238046},
issn = {1879-0038},
abstract = {To determine the gene content of an organism, the reads generated by the sequencing process must be assembled using an assembly strategy, either by reference or de novo. However, this process often results in multiple sequences called contigs, which, after the sorting steps, are grouped into scaffolds. The completion stage aims to obtain a single genomic sequence, called a complete genome, which is not a trivial task. Various analytical strategies have been developed to help in this process, many of which have been implemented in computer tools to obtain complete genomes or as close to this as possible, the so-called drafts. The manuscript presents ContigPolishing, a computational tool with a simple and intuitive graphical interface, developed to improve the assembly of prokaryotic genomes, such as bacteria and metagenomes. Despite existing software, there is a gap for solutions that combine simplicity and robustness. ContigPolishing addresses this need, featuring an integrated database that allows processing to be resumed at any time. The tool was validated with 90 NCBI datasets from genera such as Escherichia coli, Corynebacterium, and Nocardia, as well as raw reads from the SRA database to simulate real-world situations. The results showed improvement in the contiguity of the assemblies, with an increase in N50 and improvement in L50, and a reduction in the number of contigs, by extending the contigs using the similarity between their flanks. In some cases, the software was able to elevate the status of genomes from draft to complete, proving its efficiency. ContigPolishing is available at: https://github.com/allanverasce/contigpolishing.},
}

@article {pmid41237940,
year = {2025},
author = {Borroni, D and Lo Monaco, F and Silvia, F and Mazzotta, C and Settino, M and Gabrielli, F and Papa, FT and Alfonsi, C and Di Pietro, F and Rizzuto, V and Stroffolini, G and Bonzano, C and Laganovska, G and Vanags, J and Rechichi, M and Rocha-de-Lossada, C and Ballesteros-Sánchez, A and Zeppieri, M and Gagliano, C},
title = {Ocular Surface Microbiota in Primary Open Angle Glaucoma.},
journal = {Experimental eye research},
volume = {},
number = {},
pages = {110734},
doi = {10.1016/j.exer.2025.110734},
pmid = {41237940},
issn = {1096-0007},
abstract = {Primary open-angle glaucoma (POAG) is a leading cause of irreversible blindness, yet the contribution of the ocular-surface (OS) microbiota remains poorly defined. We conducted a cross-sectional study including 27 POAG patients on chronic hypotensive therapy and 119 healthy Italian controls, profiled by 16S rRNA amplicon sequencing (Ion GeneStudio S5) and analyzed with QIIME2/phyloseq. POAG samples showed higher α-diversity (Shannon 4.23 vs 2.77; Observed richness 407 vs 154; Wilcoxon q < 1×10[-9]) and a distinct β-diversity profile (PERMANOVA p = 0.001; R[2] = 0.104). Compositional shifts included depletion of Firmicutes with loss of Staphylococcus in controls' place, and enrichment of Proteobacteria (e.g., Pseudomonas) together with unclassified Enterobacterales and a larger unclassified fraction. Differential-abundance testing identified numerous significant taxa separating groups, consistent with a more diverse yet less defined microbiota in POAG. These findings indicate an ocular-surface dysbiosis associated with POAG in a treatment-exposed cohort, supporting the relevance of host-microbe interactions and motivating longitudinal, treatment-naïve and functional studies before causal or translational inferences.},
}

@article {pmid41237902,
year = {2025},
author = {Pitarch, A and Arribas, V and Gil, C},
title = {Omics and Multiomics-Based Diagnostics for Invasive Candidiasis: Toward Precision Medicine.},
journal = {Molecular & cellular proteomics : MCP},
volume = {},
number = {},
pages = {101463},
doi = {10.1016/j.mcpro.2025.101463},
pmid = {41237902},
issn = {1535-9484},
abstract = {Invasive candidiasis (IC) is a serious, life-threatening, and costly fungal infection if not diagnosed early and treated appropriately. However, this healthcare-associated mycosis caused by Candida spp. is difficult to diagnose because of its nonspecific clinical signs and symptoms, and the lack of early and accurate detection methods. IC is also difficult to treat due to its late diagnosis, the limited antifungal arsenal, and the rapid emergence and spread of (multi)drug-resistant Candida strains. Therefore, early and accurate innovative methods for species and resistance identification in IC (candidemia and deep-seated candidiasis) are urgently needed to initiate timely and appropriate antifungal therapy, and reduce its high morbidity, mortality, and healthcare costs in hospitalized patients (in particular, severely immunocompromised or critically ill patients). The availability of the complete genome sequences of the most clinically relevant Candida species coupled with recent advances in high-throughput omics technologies have spurred an unprecedented era in the discovery and development of IC diagnostics at different levels of molecular complexity. Here we review the contribution of current and emerging omics technologies, including genomics, transcriptomics, proteomics, peptidomics, metabolomics, lipidomics, glycomics, immunomics (immunoproteomics, immunopeptidomics, and immunoglycomics), imiomics (imaging-omics), and microbiomics (metagenomics, metatranscriptomics, metaproteomics, and metabonomics), to the process of biomarker development for early diagnosis, antifungal susceptibility, prognosis, follow-up, and therapeutic monitoring in IC. We highlight the potential of integrating multiple omic data (through integromics, multiomics or panomics, together with systems biology and artificial intelligence) for the discovery of multidimensional biomarker signatures and computational algorithms for IC diagnosis. Finally, we discuss future challenges and prospects for their clinical implementation. These next-generation IC diagnostics promise to revolutionize medical practice by unraveling the complexity of biological systems at multiple levels. In addition, these could help clinicians make more precise and personalized clinical decisions through multiomics or panomics-based precision medicine approaches, rather than traditional one-size-fits-all approaches.},
}

@article {pmid41237728,
year = {2025},
author = {Meng, Q and Wang, J and Li, K and Zhang, Y and Hu, Z and Wang, F and Pan, F and Fu, J and Dang, C},
title = {Low-dose chlorine disinfection poses a greater potential risk of antibiotic resistance genes and their pathogenic hosts.},
journal = {Water research},
volume = {289},
number = {Pt B},
pages = {124895},
doi = {10.1016/j.watres.2025.124895},
pmid = {41237728},
issn = {1879-2448},
abstract = {Identifying the responses of antibiotic resistance genes (ARGs) and their hosts to chlorine disinfection is necessary because it has been paradoxically reported to both amplify and suppress antibiotic resistance in water treatment processes. In this study, our integrated metagenomic and metatranscriptomic analysis of sequencing batch reactors under different chlorine disinfection conditions (0, 2, 6, and 10 mg/L) in activated sludge reveals that low-dose chlorine obviously increases ARG abundance, diversity, and transcriptional activity, particularly for multidrug, β-lactam, and tetracycline types, while higher doses reduce transcriptional diversity and activity. Acinetobacter johnsonii, a pathogen abundant and active under chlorine-addition conditions, poses a high risk of ARG transmission due to its multiple mobile genetic elements and potential involvement in horizontal gene transfer with non-pathogens. Notably, chlorine disinfection may simultaneously promote the co-transfer of chlorine resistance and antibiotic resistance genes, such as the qacE gene, with the involvement of plasmids and integrons. Overall, this study demonstrates that low-dose chlorine may promote greater ARG enrichment, mobility, and pathogenic potential in activated sludge. The findings highlight overlooked risks of low-concentration residual chlorine, urging reconsideration of disinfection strategies to protect public health.},
}

@article {pmid41237727,
year = {2025},
author = {Zhao, Z and Zhao, Y and Hua, M and Yao, X and Hu, B},
title = {Deep metagenomic insights into the formation characteristics of the resistome in Pristine Saline Lakes.},
journal = {Water research},
volume = {289},
number = {Pt B},
pages = {124937},
doi = {10.1016/j.watres.2025.124937},
pmid = {41237727},
issn = {1879-2448},
abstract = {Pristine and isolated ecosystems remain underexplored in resistome research, leaving a major gap in understanding how antibiotic resistance genes (ARGs) persist and spread outside human influence. To address this, we performed the first long-term, systematic, ultra-deep metagenomic survey of four high-altitude pristine saline lakes in the Altun Shan National Nature Reserve-an uninhabited region of the Qinghai-Tibet Plateau-generating 1.8 terabases of sequencing data. We identified a total of 756 ARG subtypes spanning 28 ARG types in all sampled lakes, with the clinically relevant polymyxin resistance gene, ugd, accounting for 30.5 % of the total ARG abundance. Moreover, ugd showed high mobility potential, with 183 horizontal gene transfer (HGT) events identified across 18 genera, and was widely associated with mobile genetic elements (MGEs). Similarity analyses revealed that the ARG profiles of pristine saline lakes were most comparable to those of marine environments, suggesting that salinity is a key ecological driver shaping the prevalence of polymyxin resistance genes. These findings indicate that pristine saline lakes can act as previously underexplored reservoirs and exchange hubs for clinically important resistance genes. Our results reveal the abundance and dissemination potential of ugd in isolated ecosystems and provide new insights into how natural environmental factors independently shape the resistome, with implications for One Health antimicrobial resistance surveillance.},
}

@article {pmid41237724,
year = {2025},
author = {Huang, P and Zhou, Y},
title = {Enhance H2 production by regulating acetyl-CoA supply and reducing equivalent diversion in an enriched purple phototrophic bacteria culture.},
journal = {Water research},
volume = {289},
number = {Pt B},
pages = {124910},
doi = {10.1016/j.watres.2025.124910},
pmid = {41237724},
issn = {1879-2448},
abstract = {Short-chain volatile fatty acids (VFAs) are promising carbon sources for biohydrogen production by purple phototrophic bacteria (PPB), given their high hydrogen conversion potential and low cost. However, most existing studies used a single VFA as the carbon source, providing only partial insights for practical applications, as VFAs in waste streams typically exist in mixtures. Furthermore, the metabolic responses of PPB to VFA mixtures, which determine H2 yield, and the metabolic mechanisms, remain largely unexplored. This study investigated the effects of co-feeding propionate with acetate or butyrate on PPB's hydrogen production and explored the associated metabolic responses through metagenomic and metatranscriptomic analyses. Results show that co-feeding butyrate with propionate (1:1 COD ratio) increased substrate conversion efficiency to 61 %, compared to 54 % from sole propionate. This improvement is linked to increased acetyl-CoA (Ac-CoA) availability, which, on one hand, activates the tricarboxylic acid (TCA) cycle and generates more electrons during carbon assimilation, and on the other hand, reduces the competitiveness of other electron sinks, thereby enhancing electron flow toward hydrogen. In contrast, co-feeding acetate with propionate results in a comparable conversion efficiency (∼50 %), where the increased Ac-CoA availability promotes carbon assimilation through the glyoxylate shunt instead. These findings reveal a synergistic metabolic impact from mixed VFAs and highlight the role of Ac-CoA in regulating carbon assimilation and electron dissipation. Understanding these interactions can guide the selection of waste streams and pretreatment processes to provide PPB with favorable VFA compositions, enabling more efficient and sustainable hydrogen production in practice.},
}

@article {pmid41237630,
year = {2025},
author = {Hemmat-Jou, MH and Li, F and Wang, D and Gao, R and Xiao-Xia, Z and Chen, Y and Fang, L},
title = {Metagenomic analysis reveals global landscape of viruses in biogeochemical cycles and microbial resistance in paddy soils and wetlands.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140469},
doi = {10.1016/j.jhazmat.2025.140469},
pmid = {41237630},
issn = {1873-3336},
abstract = {Paddy soils and wetlands form a critical soil-water interface that supports global crop production and biogeochemical cycling. Understanding the role of viruses in these ecosystems is vital for predicting ecosystem resilience. Considering the significance of viruses in microbial community structure and environmental pollution, we analyzed 163 metagenomes from 18 countries in Asia, Europe, America, and Australia. We characterized the global distribution and potential ecological functions of viruses through viral auxiliary metabolic genes (vAMGs), antibiotic resistance genes (vARGs), and metal(loid) resistance genes (vMRGs). We found viruses with globally consistent compositions and host profiles, characterized by high richness and a dominance of lysogenic families. We identified 497 vAMGs associated with carbon, phosphorus, nitrogen, and sulfur cycling, and detected 279 vARGs (conferring resistance to 10 antibiotic) and 141 vMRGs (against 7 metal(loids)). These genes exhibited strong co-localization and co-selection patterns, and their transduction can promote the emergence of multi-resistant microbes, reshaping microbial communities. Therefore, viruses are key mobile vectors for the environmental spread of these genes. By quantifying these pathways, we provide a crucial advancement for ecological risk identification and assessment. This meta-analysis provides a comprehensive overview of virus-mediated biogeochemical processes and resistance gene propagation. We demonstrate that viruses can disseminate antibiotic and metal(loid) resistance, a pollution-driven process that poses potential health risks. Furthermore, by regulating key metabolic pathways, viruses can influence greenhouse gas fluxes. Our findings underscore the necessity of integrating viruses into climate models, pollution mitigation strategies, and One Health policies to assess ecological risks and to protect ecosystem and public health.},
}

@article {pmid41237622,
year = {2025},
author = {Liu, B and Wang, S and Ren, J and Zhang, Z and Ma, J and Li, T and Zhou, Q and Sun, J},
title = {Impacts of non-spherical polyethylene nanoplastics on microbial communities and antibiotic resistance genes in the rhizosphere of pea (Pisum sativum L.): An integrated metagenomic and metabolomic analysis.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140425},
doi = {10.1016/j.jhazmat.2025.140425},
pmid = {41237622},
issn = {1873-3336},
abstract = {The ecological effects of nanoplastics (NPs) has become a growing concern; however, the influence of non-spherical NPs-which better represent real-world morphologies-remains poorly understood. This study investigated the impact of non-spherical polyethylene (PE) NPs on the growth of pea (Pisum sativum L.) and its rhizosphere microenvironment across different concentration levels (0, 20, and 200 mg/kg) using integrated metagenomics and metabolomics. Results showed that high-dose (200 mg/kg) exposure significantly inhibited plant growth. Although soil physicochemical properties remained unchanged, the rhizosphere microbial communities experienced significant restructuring, characterized by a marked enrichment of Pseudomonas and a reduction in beneficial Rhizobium populations. Metagenomic analysis revealed a concurrent increase in the abundance and diversity of antibiotic resistance genes (ARGs) under non-spherical PE-NP stress. This was accompanied by a shift in bacterial host composition, with a trend toward a higher prevalence of potentially pathogenic taxa such as Pseudomonas aeruginosa. Metabolomics analysis further revealed that non-spherical PE-NPs altered the rhizosphere metabolite profile, thereby significantly driving the succession of ARG hosts. Our integrated analysis enhances the understanding of how non-spherical PE-NPs disrupt microbial communities and elevate the risks of ARGs in rhizosphere soil, highlighting the significance of incorporating environmentally relevant NPs into environmental risk assessments.},
}

@article {pmid41236809,
year = {2025},
author = {Shuvo, MSH and Kim, S and Jo, S and Rahim, MA and Barman, I and Hossain, MS and Jeong, Y and Jeong, H and Kim, S and Seo, H and Song, HY},
title = {Characterization of Gut Microbiota of Honey Bees in Korea.},
journal = {Polish journal of microbiology},
volume = {},
number = {},
pages = {},
doi = {10.33073/pjm-2025-025},
pmid = {41236809},
issn = {2544-4646},
abstract = {Korea's unique climate and agricultural environment suggest that the gut microbiome of honey bees may possess distinctive compositions influenced by regional factors. With the decline in honey bee populations and rising health challenges, understanding the role of gut microbiomes is essential for enhancing honey bee health and their resilience to environmental stressors. To explore caste-specific gut microbiota and identify microbial signatures associated with honey bee health, this study examined the gut microbial composition of worker bees, queen bees, and drones of Apis mellifera using 16S rRNA gene amplicon sequencing. Analysis of beta diversity and species richness demonstrated significant differences between worker bees and both drones and queens, with no significant differences identified between drones and queens. Notably, Lactobacillus dominated all groups, comprising 98.6% of the drones, 95.4% of the queens, and 68.3% of the workers. Additionally, Bombella was prominent in queens (4%), whereas Gilliamella (23%) and Frischella (4.7%) were notably enriched in workers. Drones and queens exhibited similar gut microbiome profiles, while workers displayed distinctly different compositions. These findings underscore the variation in gut microbiota composition and potential functional roles across honey bee castes. Such microbial distinctions may reflect caste-specific roles and physiological demands within the colony. Future research should investigate the physiological roles of gut microbiota and their contributions to environmental resilience, paving the way for microbiome-based strategies to promote honey bee health. This study lays a crucial scientific foundation for conserving the honey bee ecosystem and promoting sustainable agriculture.},
}

@article {pmid41236788,
year = {2025},
author = {Artale, S and Filiali, F and Beretta, E and Arosio, F and Cazzaniga, F and Tersalvi, C and Sofia, M and Tagliabue, P and Pozzi, P and Colombo, A and Carbone, C and Pietrogiovanna, L and Verga, M and Nova, P and Calori, R and Renso, R and Rota, S and Aglione, S and Manfrida, I and Facendola, G and Trojani, A and Dazzani, MC and Basciani, S and Valsecchi, MG and Capitoli, G and Cocola, C and Consolandi, C},
title = {The Effects of a Modified Mediterranean Diet on Gut Microbiota and Chemotherapy Side Effects in Patients With Metastatic Colorectal Cancer Undergoing First-Line Chemotherapy With or Without Either Antiepidermal Growth Factor Receptor or Antivascular Endothelial Growth Factor Agent: Protocol for a Randomized Pilot Study in Italy.},
journal = {JMIR research protocols},
volume = {14},
number = {},
pages = {e72950},
doi = {10.2196/72950},
pmid = {41236788},
issn = {1929-0748},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Colorectal Neoplasms/drug therapy/pathology ; *Diet, Mediterranean ; Pilot Projects ; Italy ; Female ; Male ; Prospective Studies ; ErbB Receptors/antagonists & inhibitors ; *Antineoplastic Agents/adverse effects/therapeutic use ; Middle Aged ; Aged ; Randomized Controlled Trials as Topic ; Adult ; },
abstract = {BACKGROUND: The gut microbiota is attracting increasing interest as a factor possibly impacting colorectal cancer risk, therapy toxicity, and, as a consequence, patient's quality of life. It has been observed that microbial imbalance in the gut and in cancer tissue is facilitated by a Western type of diet, rich in meat, sugars, and refined grains, while a Mediterranean diet, rich in low saturated fat and fibers, promotes gut eubiosis, and results in reduced risk of developing colorectal cancer. Specifically, a high fiber content diet has been associated with a reduced incidence of therapy related adverse events in patients with malignant melanoma.

OBJECTIVE: This study aimed to analyze and compare the gut microbiota of patients with metastatic colorectal cancer undergoing first-line chemotherapy with or without a biological agent (antiepidermal growth factor receptor or antivascular endothelial growth factor), and receiving either a free standard Western diet, or a modified Mediterranean diet, and the impact of microbiota on chemotherapy toxicity.

METHODS: This is a pilot nondrug, interventional prospective, randomized, controlled, single-center (Italian), open-label trial. Patients (n=40) living in Italy, and with a local style of life, will be randomized 1:1 to either a modified Mediterranean diet or a free Western-type diet. Blood and fecal samples will be collected at baseline and control visits, for metagenomic and metabolomic analysis. The primary endpoint is the Firmicutes:Bacteroidetes ratio after completion of the third cycle of first-line chemotherapy (time T1). Secondary endpoints are (1) the percentage of patients experiencing gastrointestinal side effects at T1, (2) the percentage of patients experiencing grade 3/4 gastrointestinal side effects at T1, and (3) changes in the Firmicutes:Bacteroidetes ratio, overall microbiome composition, and metabolome at T1, and after the sixth chemotherapy cycle (T2) versus baseline.

RESULTS: This pilot trial received ethics approval on July 24, 2024. By July 2025, a total of 17 participants have been recruited. The study will conclude with the visit at T2 for the last enrolled patient. Results are expected to be published in October 2028.

CONCLUSIONS: This study has the potential to provide critical insights into the role of diet in modifying the gut microbiota, diminishing chemotherapy-related side effects, and possibly enhancing the therapeutic efficacy in metastatic colorectal cancer by improving tolerability. In addition, data may pave the way for future research in immunotherapy, potentially influencing both clinical practice and public health strategies.

TRIAL REGISTRATION: Clinicaltrial.gov NCT06794931; https://clinicaltrials.gov/search?term=NCT06794931.

DERR1-10.2196/72950.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Colorectal Neoplasms/drug therapy/pathology
*Diet, Mediterranean
Pilot Projects
Italy
Female
Male
Prospective Studies
ErbB Receptors/antagonists & inhibitors
*Antineoplastic Agents/adverse effects/therapeutic use
Middle Aged
Aged
Randomized Controlled Trials as Topic
Adult

@article {pmid41236769,
year = {2025},
author = {Lima Filho, CM and Santos, AA and Lima, DVN and Silva, LO and Paranhos, RR and Branco, S and Pacheco, ABF and Azevedo, SMFO},
title = {Combining Ludwigia leptocarpa with the dried biomass of Pontederia crassipes for mitigating cyanobacteria: a sustainable way to use macrophyte waste.},
journal = {International journal of phytoremediation},
volume = {},
number = {},
pages = {1-13},
doi = {10.1080/15226514.2025.2579148},
pmid = {41236769},
issn = {1549-7879},
abstract = {Constructed Floating Wetlands (CFWs) with emergent macrophytes offer a low-cost, sustainable strategy to mitigate eutrophication. We evaluated the combined use of Ludwigia leptocarpa, a native macrophyte from the Americas, and dried biomass of Pontederia crassipes (DB Pc) as substrate in small-scale CFWs to suppress a natural cyanobacterial bloom. Ex-situ mesocosm experiments (40 L) were conducted over 16 days with treatments: L. leptocarpa with DB Pc (S+), L. leptocarpa alone (S-), DB Pc alone, and living P. crassipes as positive control. L. leptocarpa (S-) and P. crassipes reduced Soluble Reactive Phosphorus by >85%, but L. leptocarpa produced 10 times less biomass. Treatments with DB Pc increased nutrient and phenol concentrations. All treatments led to reduced chlorophyll-a and phytoplankton density, especially cyanobacteria, along with pH reduction. 16S rRNA sequencing revealed higher bacterial diversity in the L. leptocarpa rhizosphere than in the water, suggesting a role in phytoremediation. The combination of L. leptocarpa and DB Pc in CFWs shows potential for cyanobacterial control through nutrient uptake, allelopathy, and pH modulation. This method supports sustainable water management by utilizing a native, slow-growing macrophyte and repurposing waste biomass that would otherwise harm aquatic ecosystems.},
}

@article {pmid41236031,
year = {2025},
author = {Kim, JR and Byun, JS and Jung, JK and Hong, SH and Lee, HJ},
title = {Altered oral microbiome diversity in patients with oral candidiasis.},
journal = {Archives of oral biology},
volume = {180},
number = {},
pages = {106430},
doi = {10.1016/j.archoralbio.2025.106430},
pmid = {41236031},
issn = {1879-1506},
mesh = {Humans ; *Candidiasis, Oral/microbiology/drug therapy ; *Microbiota/drug effects ; Male ; Saliva/microbiology ; Female ; *Fluconazole/therapeutic use/pharmacology ; Middle Aged ; *Antifungal Agents/therapeutic use/pharmacology ; RNA, Ribosomal, 16S/genetics ; *Mouth/microbiology ; Aged ; Adult ; Streptococcus salivarius/drug effects ; Real-Time Polymerase Chain Reaction ; },
abstract = {OBJECTIVE: Oral candidiasis is a common opportunistic infection caused by Candida albicans, particularly in individuals with local or systemic risk factors. This study aimed to investigate how antifungal therapy affects the composition of the oral bacterial microbiome.

DESIGN: Unstimulated saliva samples were collected from ten patients diagnosed with acute pseudomembranous oral candidiasis before and after fluconazole treatment. Microbiome profiles were assessed using 16S rRNA gene sequencing. Quantitative PCR was performed to validate changes in specific bacterial species.

RESULTS: Alpha diversity did not change significantly, whereas beta-diversity analyses indicated modest compositional shifts. Antifungal therapy was associated with an increase in Streptococcus salivarius, a commensal linked to mucosal health. The signal was confirmed by species-specific qPCR in paired samples.

CONCLUSIONS: Fluconazole treatment for oral candidiasis induces modest shifts in the oral bacterial community, particularly increasing the abundance of S. salivarius. These changes may reflect partial recovery of microbial homeostasis, supporting the role of microbiome monitoring and probiotic approaches in post-treatment care.},
}

Humans
*Candidiasis, Oral/microbiology/drug therapy
*Microbiota/drug effects
Male
Saliva/microbiology
Female
*Fluconazole/therapeutic use/pharmacology
Middle Aged
*Antifungal Agents/therapeutic use/pharmacology
RNA, Ribosomal, 16S/genetics
*Mouth/microbiology
Aged
Adult
Streptococcus salivarius/drug effects
Real-Time Polymerase Chain Reaction

@article {pmid41235937,
year = {2025},
author = {Mills, S and Collins, G and Ijaz, UZ and Lens, PNL},
title = {Metagenome-assembled genomes from microbial communities in lab-scale anaerobic bioreactors treating simulated dairy wastewater.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0048725},
doi = {10.1128/mra.00487-25},
pmid = {41235937},
issn = {2576-098X},
abstract = {This dataset describes metagenome-assembled genomes from three lab-scale (4L) expanded granular sludge bed bioreactors treating synthetic dairy wastewater. The resulting MAGs encompass 60 phyla with average genome completeness of 78.68% and average contamination of 2.29%. These genomes represent a valuable resource for studying anaerobic bioreactors used in wastewater treatment.},
}

@article {pmid41235136,
year = {2025},
author = {Wu, Y and Pan, S and Yin, C and Kong, Y and Huo, W and Wang, Q and Wu, J and Li, L and Wei, J and Lu, C and Han, L and Lu, Y},
title = {PSORI-CM02 Restores Epidermal Differentiation in Psoriasis via the Gut Microbiota-Sphingolipid Axis.},
journal = {Drug design, development and therapy},
volume = {19},
number = {},
pages = {9993-10010},
pmid = {41235136},
issn = {1177-8881},
mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; *Psoriasis/drug therapy/metabolism/pathology ; Mice ; Humans ; *Cell Differentiation/drug effects ; *Sphingolipids/metabolism ; *Epidermis/drug effects/pathology/metabolism ; Keratinocytes/drug effects/metabolism ; },
abstract = {BACKGROUND: Psoriasis is linked to gut dysbiosis and disturbed sphingolipid metabolism. PSORI-CM02 improves epidermal differentiation, yet its impact on the microbiota-sphingolipid axis remains unknown.

METHODS: Transcriptomics of patient keratinocytes, Carmofur inhibition in IMQ mice, and multi-omics (metabolomics, metagenomics) of skin, lymph nodes and gut were combined. SPF, PGF and GF mice underwent FMT to test microbiota dependency.

RESULTS: Psoriatic lesions showed sphingolipid pathway enrichment. Carmofur enhanced differentiation. PSORI-CM02 lowered PASI, spleen index, and tissue levels of ceramide, S1P, C1P and sphingomyelin while restoring Flg, Krt10 and Krt14. It reduced Turicibacter, Bacteroides, Bifidobacterium and Acetobacter. PSORI-CM02-derived microbiota reproduced therapeutic effects in all FMT settings.

CONCLUSION: PSORI-CM02 reshapes gut microbiota, normalizes sphingolipid metabolism and improves epidermal differentiation to treat psoriasis.},
}

*Gastrointestinal Microbiome/drug effects
Animals
*Psoriasis/drug therapy/metabolism/pathology
Mice
Humans
*Cell Differentiation/drug effects
*Sphingolipids/metabolism
*Epidermis/drug effects/pathology/metabolism
Keratinocytes/drug effects/metabolism

@article {pmid41234773,
year = {2025},
author = {Levé, M and Manghi, P and Bredon, M and Lefevre, A and Manara, S and Armanini, F and Emond, P and Planchais, J and Rolhion, N and Segata, N and Sokol, H},
title = {Metabolomics and metagenomics in mice reveal the role of the gut microbiota in tryptophan metabolism.},
journal = {iScience},
volume = {28},
number = {11},
pages = {113751},
pmid = {41234773},
issn = {2589-0042},
abstract = {Tryptophan metabolism plays a key role in host-microbiota interactions, producing a wide array of bioactive metabolites. However, our understanding of the interactions between tryptophan metabolites and the gut microbiota is still limited. Using targeted quantitative metabolomics and metagenomics in mice across various compartments, we showed that the cecal microbiota massively impacts tryptophan metabolism both in the gut and systemically. Grouping bacterial taxa in co-abundance guilds better reflected the links between gut microbes and tryptophan metabolites than single taxa taken individually and suggested the involvement of complex microbial interactions in tryptophan metabolism regulation. Finally, analyzing functional data, we shed light on the potential links between tryptophan metabolism and bacterial enzymes or metabolic pathways.},
}

@article {pmid41234739,
year = {2025},
author = {Jin, L and Chen, S and Kang, R and Li, C and Yang, S and Yang, Q and Zhao, K and Zou, L},
title = {Variation and spread of resistomes in swine manure, manure slurries, and long-term manure-fertilized soils.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1683394},
pmid = {41234739},
issn = {1664-302X},
abstract = {BACKGROUND: Application of swine manure to soils exacerbates environmental antimicrobial resistance (AMR). However, a comprehensive evaluation of anaerobic digestion's (AD) mitigation potential against AMR and its influencing factors in swine manure-to-soil systems remains lacking.

METHODS: We employed mass spectrometry, metagenomics, and whole-genome sequencing (WGS) to investigate the fate of antibiotics, metals, and antibiotic resistance genes (ARGs) across manures, slurries, and soils from eight pig farms.

RESULTS: Anaerobic digestion reduced antibiotic and metal (except ciprofloxacin) content and risks in manure, but had limited effects on total ARG abundance, while increasing ARG network modularity. High-risk ARG abundance significantly increased from 404.7 in manure to 843.2 in slurries, with health-risk scores rising 1.88-fold during anaerobic digestion. Metagenomic analysis showed metal resistance gene (MRG) diversity and abundance decreased during anaerobic digestion, along with reduced ARG-MRG co-occurrence frequency, whereas mobile genetic element (MGE) diversity and ARG-MGE co-occurrence frequency increased. Escherichia coli was identified as the dominant ARG host. WGS of E. coli strains confirmed horizontal gene transfer (HGT) of nine ARGs (e.g., sul3 and blaTEM-1), and metagenomics suggested HGT of four ARGs (e.g., tet(M)) across different pathogens. Chromium concentrations, bacterial communities and MGEs were significantly associated with ARG profiles. Long-term slurry application resulted in elevated antibiotic, metal, and ARG concentrations in soils, with concomitant increases in high-risk ARGs and health risks.

CONCLUSION: This study demonstrates AD's limited effect on mitigating overall ARG abundance and highlights MGEs as critical drivers of ARG maintenance and dissemination from manure to soil process, guiding manure treatment optimization to reduce agricultural AMR risks.},
}

@article {pmid41234344,
year = {2025},
author = {Yang, L and Zeng, J and Zhang, Y and Li, L},
title = {Purulent Meningitis Due to Porphyromonas endodontalis, Bacteroides heparinolyticus, Prevotella pleuritidis and Streptococcus constellatus from Oral and Maxillofacial Space Infection: A Case Report.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {5843-5851},
pmid = {41234344},
issn = {1178-6973},
abstract = {BACKGROUND: Purulent meningitis caused by polymicrobial oral anaerobes represents a rare but life-threatening clinical challenge, with Porphyromonas endodontalis, Bacteroides heparinolyticus, Prevotella pleuritidis, and Streptococcus constellatus being pfastidious organisms. Traditional diagnostic methods often fail to identify these fastidious organisms, leading to delayed or inappropriate therapy.

CASE PRESENTATION: We report a rare case of purulent meningitis resulting from a polymicrobial infection involving Porphyromonas endodontalis, Bacteroides heparinolyticus, Prevotella pleuritidis, and Streptococcus constellatus in a 76-year-old male patient who presented with a 40-day history of left facial pain. This case represents the first documented instance of these four oral anaerobes concurrently causing an infection of the central nervous system.

CONCLUSION: To the best of our knowledge, this case represents the first documented evidence of polymicrobial purulent meningitis caused by oral anaerobes, specifically Porphyromonas endodontalis, Bacteroides heparinolyticus, Prevotella pleuritidis, and Streptococcus constellatus. Our findings not only provide direct evidence for the oral-central nervous system (CNS) infection pathway but also validate that the valuable approach based on metagenomic next-generation sequencing (mNGS) offers significant clinical insights for diagnostic and therapeutic strategies.},
}

@article {pmid41233937,
year = {2025},
author = {Zhang, P and Roque, B and Romero, P and Shapiro, N and Eloe-Fadrosh, E and Kebreab, E and Diamond, S and Hess, M},
title = {Red seaweed supplementation suppresses methanogenesis in the rumen, revealing potentially advantageous traits among hydrogenotrophic bacteria.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {231},
pmid = {41233937},
issn = {2049-2618},
mesh = {Animals ; *Rumen/microbiology/metabolism ; *Methane/metabolism/biosynthesis ; Cattle ; *Seaweed ; *Dietary Supplements ; *Bacteria/genetics/metabolism/classification/isolation & purification ; Animal Feed/analysis ; *Gastrointestinal Microbiome ; Fermentation ; Metagenome ; Metagenomics ; Hydrogen/metabolism ; },
abstract = {BACKGROUND: Macroalgae belonging to the genus Asparagopsis have shown to reduce methane (CH4) production during rumen fermentation, while increasing feed efficiency when added to the feed of cattle. However, little is known about how the rumen microbiome responds to Asparagopsis supplementation, and how changes in the microbiome may contribute to changes in rumen function and host phenotype. Here, we generated and analyzed metagenomic and metatranscriptomic data from the rumen microbiome from cows receiving (treatment) and not receiving (control) an Asparagopsis armata supplemented diet.

RESULTS: Using a combination of metatranscriptome and metagenome analysis, we found that reduction of CH4 emission from animals receiving A. armata was coupled to a significant reduction in the transcription of methanogenesis pathways. Additionally, a significant decrease in the transcription of genes for carbon catabolism and a reorganization of carbon catabolic gene expression occurred at the species level within the rumen microbiome of animals that received red seaweed with their diet. Increased H2 production, a consequence of methanogenesis suppression, was coupled to a significant increase in the transcription of hydrogenases that mediate hydrogenotrophic metabolism in the treatment group. Metatranscriptome analysis identified a single metagenome assembled genome (MAG) of a Duodenibacillus sp., a hitherto uncultured hydrogenotrophic bacterial species, as the dominant driver of this transcriptional change.

CONCLUSIONS: Comparative genomic analysis between the Duodenibacillus sp. and other hydrogenotrophic rumen organisms revealed metabolic traits that may provide Duodenibacillus sp. with a competitive advantage in H2 scavenging. Our findings provide an initial understanding of how the rumen microbiome responds to a promising CH4 reducing feed additive and serve as a model for alternative stable rumen microbiome states that produce less methane and increase animal productivity. Ultimately, insights from the work presented here might enable the development of advanced microbiome-based strategies to reduce enteric methane production.},
}

Animals
*Rumen/microbiology/metabolism
*Methane/metabolism/biosynthesis
Cattle
*Seaweed
*Dietary Supplements
*Bacteria/genetics/metabolism/classification/isolation & purification
Animal Feed/analysis
*Gastrointestinal Microbiome
Fermentation
Metagenome
Metagenomics
Hydrogen/metabolism

@article {pmid41233936,
year = {2025},
author = {Modolon, F and N Garritano, A and J Hill, L and Duarte, G and Bendia, A and de Moura, R and Pellizari, V and Thomas, T and Peixoto, RS},
title = {Putative promiscuous symbionts in deep-sea corals and crinoids may contribute to nitrogen cycling.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {234},
pmid = {41233936},
issn = {2049-2618},
support = {141954/2019-1//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; ANP 21005-4//Shell, Brazil/ ; BAS/1/1095-01-01 and FCC/1/1976-40-01//KAUST/ ; },
mesh = {*Anthozoa/microbiology ; Animals ; *Symbiosis ; *Nitrogen Cycle ; Metagenomics/methods ; Microbiota ; Brazil ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; In Situ Hybridization, Fluorescence ; },
abstract = {BACKGROUND: Crinoids (feather stars) are frequently found in association with corals, yet the physiological and microbial interactions between these organisms remain poorly understood. Both corals and crinoids host symbiotic microorganisms, but the functional roles of these symbionts, particularly in deep-sea environments, are largely unexplored. This study characterizes the microbiomes of the deep-sea corals Desmophyllum pertusum and Solenosmilia variabilis and their associated crinoid Koehlermetra sp. (Thalassometridae) from the Campos Basin, Brazil, to investigate potential cross-host microbial interactions and their ecological implications. We used multiple approaches for this investigation, including amplicon sequencing surveys, genome-resolved metagenomics, and fluorescence in situ hybridization.

RESULTS: We found that the same endosymbiotic members of the families Endozoicomonadaceae and Nitrosopumilaceae inhabit both corals and the crinoids, suggesting promiscuity in host-symbiont relationships. Metagenomic analysis revealed a novel and dominant Endozoicomonas species (E. promiscua sp. nov.), whose genome encodes pathways for dissimilatory nitrate reduction to ammonia (DNRA). This metabolic capability could provide a substrate for ammonia-oxidizing archaea (Nitrosopumilaceae), indicating a potential cross-host nitrogen-cycling network. Shared microbial taxa between corals and crinoids further support the hypothesis of symbiont promiscuity, where metabolic redundancy may facilitate colonization across species.

CONCLUSIONS: Our findings suggest that nitrogen cycling plays a key role in structuring microbial symbioses in deep-sea coral-crinoid holobionts. The promiscuous distribution of symbionts across hosts implies that metabolic interactions, such as DNRA-driven ammonia provisioning, could underpin resilience in nutrient-limited environments. This study highlights the importance of microbial versatility in deep-sea ecosystems and provides new insights into how cross-host symbiosis may contribute to biogeochemical cycling in the ocean. Video Abstract.},
}

*Anthozoa/microbiology
Animals
*Symbiosis
*Nitrogen Cycle
Metagenomics/methods
Microbiota
Brazil
*Bacteria/classification/genetics/metabolism/isolation & purification
Phylogeny
RNA, Ribosomal, 16S/genetics
In Situ Hybridization, Fluorescence

@article {pmid41233919,
year = {2025},
author = {Vohsen, SA and Gruber-Vodicka, HR and Osman, EO and Saxton, MA and Joye, SB and Dubilier, N and Fisher, CR and Baums, IB},
title = {Deep-sea corals near cold seeps associate with sulfur-oxidizing chemoautotrophs in the family Ca. Thioglobaceae.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {232},
pmid = {41233919},
issn = {2049-2618},
support = {ECOGIG//Gulf of Mexico Research Initiative/ ; },
mesh = {Animals ; *Anthozoa/microbiology ; *Sulfur/metabolism ; Symbiosis ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Chemoautotrophic Growth ; Metagenomics/methods ; Seawater/microbiology ; },
abstract = {BACKGROUND: Corals are known for their symbiotic relationships, yet there is limited evidence of chemoautotrophic associations. This is despite some corals occurring near cold seeps where chemosymbiotic fauna abound including mussels that host sulfur-oxidizing chemoautotrophs from the SUP05 cluster (family Ca. Thioglobaceae). We investigated whether corals near cold seeps associate with related bacteria and report here that these associations are widespread.

RESULTS: We screened corals, water, and sediment for Thioglobaceae using 16S metabarcoding and found ASVs associated with corals at high relative abundance (10 - 91%). These ASVs were specific to coral hosts, absent in water samples, and rare or absent in sediment samples. Using metagenomics and transcriptomics, we assembled the genome of one phylotype associated with Paramuricea sp. B3 (ASV 4) which contained the genetic potential to oxidize sulfur and fix carbon, and confirmed that these pathways were transcriptionally active. Furthermore, its relative abundance was negatively correlated with the stable isotopic composition of its host coral's tissue suggesting some contribution of chemoautotrophy to the coral holobiont.

CONCLUSIONS: We propose that some lineages of Thioglobaceae may facultatively supplement the diet of their host corals through chemoautotrophy at seeps or may provide essential amino acids or vitamins. This is the first documented association between chemoautotrophic symbionts and corals at seeps and suggests that the footprint of chemosynthetic environments is wider than currently understood.},
}

Animals
*Anthozoa/microbiology
*Sulfur/metabolism
Symbiosis
Oxidation-Reduction
Phylogeny
RNA, Ribosomal, 16S/genetics
Chemoautotrophic Growth
Metagenomics/methods
Seawater/microbiology

@article {pmid41233799,
year = {2025},
author = {Orschanski, D and Rubén Dandeu, LN and Rivero, MN and Labovsky, V and Fernández, EA},
title = {Dermatological implications of alignment-based de-hosting and bioinformatics pipelines on shotgun microbiome analysis.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {1276},
pmid = {41233799},
issn = {1479-5876},
abstract = {BACKGROUND: The skin microbiome is a critical component of dermatological health, with its dysbiosis implicated in conditions ranging from atopic dermatitis to cancer. Shotgun metagenomics offers an unparalleled resolution for comprehensive taxonomic and functional profiling, yet its application in dermatology is hampered by the high proportion of host DNA and the lack of consensus on best-practice bioinformatic pipelines. While Illumina's proprietary DRAGEN platform is widely used, its closed-source nature and cost limitations necessitate the validation of robust, open-source alternatives to democratize access and enable customization.

METHODS: This study evaluates the performance of Kraken-based open-source pipeline as a viable alternative to the DRAGEN platform as well as the effect of currently available alignment-based de-hosting methods-Bowtie2, BWA, and Rsubread-to remove human DNA, assuring the use of highly-curated human reference genome thus avoiding the limitations of potentially incomplete or contaminated k-mer-based databases. By using shotgun metagenomic data from 83 healthy individuals we systematically compared the impact of these de-hosting procedures prior to Kraken2/DRAGEN taxonomic classification and functional profiling using HUMAnN 3.0 to assess the influence of methodological choices on skin microbial community composition and metabolic pathway abundance interpretation.

RESULTS: Our analysis revealed marked discrepancies arising from the choice of de-hosting tool and taxonomic classifier, leading to substantial variability in microbial and functional profiles that could compromise clinical interpretation. Among the pipelines tested, Bowtie2 de-hosting combined with Kraken2 taxonomic classification and HUMAN functional profiling efficiently recovered well-established sex- and age-related bacterial associations in healthy skin that were missed by all other methods, including DRAGEN. This superior performance, together with its customizable features, underscores the value of this workflow for robust and clinically relevant dermatological metagenomic studies.

CONCLUSIONS: Our findings underscore the decisive impact of bioinformatic pipeline selection on skin microbiome analysis and offer actionable guidance for reproducible and clinically meaningful research. We present a customizable workflow that enhances reproducibility and transparency while improving the translational value of metagenomic data. This approach strengthens the reliability of microbiome studies and supports the development of precision diagnostics and personalized therapeutic strategies in dermatology.},
}

@article {pmid41233543,
year = {2025},
author = {Aroney, STN and Newell, RJP and Tyson, GW and Woodcroft, BJ},
title = {Bin Chicken: targeted metagenomic coassembly for the efficient recovery of novel genomes.},
journal = {Nature methods},
volume = {},
number = {},
pages = {},
pmid = {41233543},
issn = {1548-7105},
support = {DP230101171//Department of Education and Training | Australian Research Council (ARC)/ ; FT210100521//Department of Education and Training | Australian Research Council (ARC)/ ; 2022070//National Science Foundation (NSF)/ ; 2022070//National Science Foundation (NSF)/ ; DE-SC0010580//U.S. Department of Energy (DOE)/ ; DE-SC0016440//U.S. Department of Energy (DOE)/ ; DE-SC0004632//U.S. Department of Energy (DOE)/ ; DE-SC0010580//U.S. Department of Energy (DOE)/ ; DE-SC0016440//U.S. Department of Energy (DOE)/ ; DE-SC0004632//U.S. Department of Energy (DOE)/ ; },
abstract = {The recovery of microbial genomes from metagenomic datasets has provided genomic representation for hundreds of thousands of species from diverse biomes. However, low-abundance microorganisms are often missed due to insufficient genomic coverage. Here we present Bin Chicken, an algorithm that substantially improves genome recovery through automated, targeted selection of metagenomes for coassembly based on shared marker gene sequences derived from raw reads. Marker gene sequences that are divergent from known reference genomes can be further prioritized, providing an efficient means of recovering highly novel genomes. Applying Bin Chicken to public metagenomes and coassembling 800 sample groups recovered 77,562 microbial genomes, including the first genomic representatives of 6 phyla, 41 classes and 24,028 species. These genomes expand the genomic tree of life and uncover a wealth of novel microbial lineages for further research.},
}

@article {pmid41233523,
year = {2025},
author = {Dell, M and Kogawa, M and Streiff, AB and Shiraishi, T and Lotti, A and Meier, CM and Schorn, MA and Field, C and Cahn, JKB and Yokoyama, H and Yamada, Y and Peters, E and Egami, Y and Nakashima, Y and Tan, KC and Rückert, C and Alanjary, M and Kalinowski, J and Kuzuyama, T and Cardenas, P and Pomponi, S and Sipkema, D and Wright, A and Takada, K and Abe, I and Wakimoto, T and Takeyama, H and Piel, J},
title = {Chemical richness and diversity of uncultivated 'Entotheonella' symbionts in marine sponges.},
journal = {Nature chemical biology},
volume = {},
number = {},
pages = {},
pmid = {41233523},
issn = {1552-4469},
support = {22H05120//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 16H06279//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP21H02635//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP22H05128//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; },
abstract = {Marine sponges are the source of numerous bioactive natural products that serve as chemical defenses and provide pharmaceutical leads for drug development. For some of the compounds, symbiotic bacteria have been established as the actual producers. Among the known sponge symbionts, 'Candidatus Entotheonella' members stand out because of their abundant and variable biosynthetic gene clusters (BGCs). Here, to obtain broader insights into this producer taxon, we conduct a comparative analysis on eight sponges through metagenomic and single-bacterial sequencing and biochemical studies. The data suggest sets of biosynthetic genes that are largely unique in 14 'Entotheonella' candidate species and a member of a sister lineage named 'Candidatus Proxinella'. Four biosynthetic loci were linked in silico or experimentally to cytotoxins, antibiotics and the terpene cembrene A from corals. The results support widespread and diverse bacterial roles in the chemistry of sponges and aid the development of sustainable production methods for sponge-derived therapeutics.},
}

@article {pmid41233350,
year = {2025},
author = {Kim, YJ and Kim, KE and Kim, HJ and Park, JS and Kim, MJ and Kim, SM and Lee, T and Jung, SW},
title = {Dynamics of the DNA Viral Community in Korean Coastal Waters.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1782},
pmid = {41233350},
issn = {2052-4463},
support = {RS-2021-KS211475//Korea Institute of Marine Science and Technology promotion (Korea Institute of Marine Science & Technology promotion)/ ; RS-2021-KS211475//Korea Institute of Marine Science and Technology promotion (Korea Institute of Marine Science & Technology promotion)/ ; RS-2021-KS211475//Korea Institute of Marine Science and Technology promotion (Korea Institute of Marine Science & Technology promotion)/ ; RS-2021-KS211475//Korea Institute of Marine Science and Technology promotion (Korea Institute of Marine Science & Technology promotion)/ ; RS-2021-KS211475//Korea Institute of Marine Science and Technology promotion (Korea Institute of Marine Science & Technology promotion)/ ; RS-2021-KS211475//Korea Institute of Marine Science and Technology promotion (Korea Institute of Marine Science & Technology promotion)/ ; RS-2021-KS211475//Korea Institute of Marine Science and Technology promotion (Korea Institute of Marine Science & Technology promotion)/ ; RS-2021-KS211475//Korea Institute of Marine Science and Technology promotion (Korea Institute of Marine Science & Technology promotion)/ ; },
mesh = {Republic of Korea ; *Seawater/virology ; *DNA Viruses/genetics/classification ; DNA, Viral ; *Virome ; Metagenomics ; Bacteriophages/genetics ; },
abstract = {Recent advances in metaviromics have revealed vast viral diversity across aquatic environments, yet coastal marine viromes remain underexplored compared to their open-ocean counterparts. In this study, we analyzed 49 surface water samples from 16 coastal sites around Korea, generating 265 gigabases of metagenomic sequence data. Following quality control, 754 DNA viral contigs of ≥10 kb (medium quality or higher) were recovered, with bacteriophages comprising 95% and nucleocytoplasmic large DNA viruses (NCLDVs) 5% of the total. Among these, Puniceispirillum phage HMO-2011 and Micromonas pusilla virus 12 T exhibited the highest relative abundance within their respective groups. In addition, we provided the dataset of environmental parameters such as water temperature, salinity, etc., as well as viral taxonomic profiling of contig-level metadata. This dataset provides a resource for the investigation of coastal DNA viral communities and supports comparative studies across marine environments.},
}

Republic of Korea
*Seawater/virology
*DNA Viruses/genetics/classification
DNA, Viral
*Virome
Metagenomics
Bacteriophages/genetics

@article {pmid41233343,
year = {2025},
author = {Lu, JN and Chao, Y and Tian, L and Zhong, X and Chen, Z and He, H and Huang, B and Li, M and Feng, Z and Feng, H and Hu, C and Zhou, S and Zhang, L and Yang, Y and Ruan, Z and Ding, K and Yang, Y and Yuan, K and Liu, W and Qi, H and Cao, Y and Fei, YH and Ling, N and Wang, S and Tang, YT and Luan, T and Xu, Z and Qiu, R},
title = {DNA viral community enhances microbial carbon fixation capacity via auxiliary metabolic genes in contaminated soils.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9984},
pmid = {41233343},
issn = {2041-1723},
mesh = {*Carbon Cycle/genetics ; *Soil Microbiology ; Carbon/metabolism ; Soil/chemistry ; China ; *DNA Viruses/genetics/metabolism ; Metagenomics ; *Soil Pollutants/metabolism ; *DNA, Viral/genetics ; Metagenome ; Mining ; },
abstract = {Soil is the largest organic matter repository on land and the virosphere is an essential component of soil carbon cycling. While a few carbon-related auxiliary metabolic genes (AMGs) in viruses are reported to potentially influence the hosts, the effects of virus-host interactions on soil carbon fixation, particularly in carbon-deficient contaminated soils, need further validation. Here, we explore the impact of viruses on carbon fixation in contaminated soils from 58 metal mining areas across eastern China. Eleven different functional categories of carbon fixation AMGs are identified via metagenomic analysis in 323 contaminated soil samples. Enzymatic activities of three key AMGs (i.e., rbcL, ppdK and TKT) are experimentally characterized, indicating the positive role of these genes in carbon fixation. Furthermore, transcriptomic sequencing reveals that after active virus inoculation the carbon fixation genes significantly up-regulate (~73%, p < 0.05). In mesocosms with stable isotope labeling, the accumulation of [13]C-labeled organic carbon significantly increases (~10%, p < 0.01). Our results provide theoretical and experimental evidence for incorporating viral contributions into the assessments of carbon fixation, and improve the understanding of viral roles within the processes of carbon cycling.},
}

*Carbon Cycle/genetics
*Soil Microbiology
Carbon/metabolism
Soil/chemistry
China
*DNA Viruses/genetics/metabolism
Metagenomics
*Soil Pollutants/metabolism
*DNA, Viral/genetics
Metagenome
Mining

@article {pmid41233306,
year = {2025},
author = {Wu, F and Wang, Y and Mai, Z and Xu, Z and Li, S and Li, Y and Yin, R and Li, J and Yu, Z and Wu, Y and Tian, X and Feng, X and Huo, X and Wang, C and Ma, X},
title = {Human intestinal fungus Clavispora lusitaniae attenuates colitis through Pyruvate decarboxylase-derived Indole-3-ethanol.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9980},
pmid = {41233306},
issn = {2041-1723},
support = {82225048//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82204594//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82474340//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2024-MS-147 and 2025-YQ-13//Natural Science Foundation of Liaoning Province (Liaoning Provincial Natural Science Foundation)/ ; },
mesh = {Animals ; *Colitis/chemically induced/microbiology ; Mice ; Humans ; *Indoles/metabolism/pharmacology ; Gastrointestinal Microbiome ; Receptors, Aryl Hydrocarbon/metabolism/agonists ; Mice, Inbred C57BL ; *Hypocreales/metabolism/genetics ; Inflammatory Bowel Diseases/microbiology ; Male ; Female ; Feces/microbiology ; Disease Models, Animal ; Colon/microbiology/pathology ; Probiotics ; },
abstract = {Gut mycobiome dysbiosis has been implicated in inflammatory bowel disease (IBD). However, it remains unknown whether specific fungal species identified by sequencing directly contribute to IBD pathogenesis. Here, based on analysis of three fecal metagenome datasets of IBD cohorts and a previously established cultivated gut fungi catalog, we identify an IBD-depleted intestinal fungus Clavispora lusitaniae strain P4013B. We show P4013B attenuates DSS-induced colitis in wild-type, antibiotics-treated, and germ-free mice through activation of aryl hydrocarbon receptor (AHR). Using an activity-guided isolation strategy, we identify the P4013B metabolite indole-3-ethanol (IEt) as the AHR agonist mediating the anti-colitis activity. We further validate the role of IEt via engineering strains that overexpress pyruvate decarboxylases producing high yields of IEt. Tea polysaccharide enhanced the anti-colitis activity of P4013B by promoting its proliferation and colonization in the colon. Together, these results suggest that C. lusitaniae P4013B may be explored as a potential probiotic for the treatment and prevention of IBD.},
}

Animals
*Colitis/chemically induced/microbiology
Mice
Humans
*Indoles/metabolism/pharmacology
Gastrointestinal Microbiome
Receptors, Aryl Hydrocarbon/metabolism/agonists
Mice, Inbred C57BL
*Hypocreales/metabolism/genetics
Inflammatory Bowel Diseases/microbiology
Male
Female
Feces/microbiology
Disease Models, Animal
Colon/microbiology/pathology
Probiotics

@article {pmid41232906,
year = {2025},
author = {Kumar, S and Matra, S and Rajput, V and Ghode, H and Rathore, D and Kumar, S and Kamble, S and Dastager, S and Bajaj, A and Qureshi, A and Kapley, A and Dharne, M},
title = {Deciphering the antimicrobial resistomes and microbiome landscape of open drain wastewater using metagenomics in a progressive Indian state.},
journal = {Environmental research},
volume = {},
number = {},
pages = {123287},
doi = {10.1016/j.envres.2025.123287},
pmid = {41232906},
issn = {1096-0953},
abstract = {Antimicrobial resistance (AMR) is a growing environmental and public health concern, with wastewater systems are acting as a critical reservoirs for resistant microorganisms and genes. Open drains in densely populated and industrialized regions can accelerate AMR dissemination into the environment. Despite Maharashtra's high urban density and industrial activity, comprehensive metagenomic surveillance of its wastewater resistome is lacking. This study applied high-throughput nanopore sequencing to 138 wastewater samples collected from 23 open-drain sites across three regions of Maharashtra (Western, Mumbai, and Central). Bioinformatic pipelines were used to characterize microbial communities, resistance genes, mobile genetic elements (MGEs), and resistome risk scores. Microbial composition varied significantly across regions, with Mumbai and Central regions explaining up to 13% of variance at the family level. Thirty indicator taxa were identified through LEfSe analysis. Resistome profiling revealed 28 drug classes and 808 ARGs, dominated by multidrug (40.49%), macrolide-lincosamide-streptogramin (15.84%), beta-lactam (7.95%), and tetracycline (6.52%). WHO-priority pathogens such as Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa harbored high-abundance ARGs including sul1, mdr(ABC), and acrB. Resistome risk scores were highest in Mumbai, indicating elevated ecological and human health risks. These findings underscore wastewater as a hotspot for AMR persistence and spread. Integrating wastewater-based surveillance within a One Health framework enables systematic tracking of resistance trends, comprehensive assessment of environmental risks, and evidence-driven regional interventions. This integrated approach supports the development of targeted mitigation strategies to curb the spread of antibiotic-resistant contaminants across ecosystems.},
}

@article {pmid41232839,
year = {2025},
author = {Fang, L and Jiaqi, L and Zhenwei, Z and Jingang, Z and Xiao, L and Yongdong, C},
title = {Remediation of soil contaminated by waste drilling slurry in oilfield with mixed bacteria immobilized by fly ash modified biochar.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133644},
doi = {10.1016/j.biortech.2025.133644},
pmid = {41232839},
issn = {1873-2976},
abstract = {Organic and heavy metal combined pollution from large-scale landfill of waste drilling slurry in oilfields poses a significant remediation challenge. This study innovatively combined fly ash doping with physicochemical modification to regulate the morphology and functionalize the surface of reed straw biochar, developing a low-cost modified biochar-based carrier material. This material, validated through leachate adsorption experiments and characterization (SEM, FT-IR, BET, XRD, TEM-EDS), exhibited both high-efficiency organic pollutant adsorption capacity and strong microbial immobilization performance. To simulate practical conditions, pot experiments were conducted, with ICP-OES and metagenomic analyses used to investigate pollutant transformation and fate. Key findings showed that unmodified biochar and fly ash formed a "glass phase-carbon matrix" structure, and under optimal conditions (biochar-fly ash mass ratio 5:1, NaOH-H2O2-assisted ultrasonic modification, 700℃ calcination), the specific surface area of modified material increased by 158.60 % compared to unmodified biochar, with an organic pollutant adsorption capacity of 32.56 mg·g[-1]. When immobilized with specific degrading bacteria, this material achieved 80.54 % COD removal in contaminated soil over 63 days, a rate significantly higher than that of free bacterial or biochar-based material groups, thereby demonstrating stable degradation advantages. Mechanistically, the synergistic integration of high-efficiency adsorption and biodegradation leveraging local oilfield wastes highlights this as an engineerable, efficient, and low-cost strategy for remediating waste drilling slurry-contaminated sites, with broad implications for addressing legacy composite pollution in energy industries.},
}

@article {pmid41232286,
year = {2025},
author = {Romero-Arguelles, R and Gómez-Govea, MA and Adame-Martinez, AE and Guzman-Velazco, A and Gonzalez-Rojas, JI and Ham-Dueñas, JG and Amezquita-Garcia, HJ and Rios-Del Toro, EE},
title = {Sulfammox in sediments of a natural wetland in northeastern Mexico: a sustainable approach to nitrogen and sulfur removal.},
journal = {The Science of the total environment},
volume = {1006},
number = {},
pages = {180920},
doi = {10.1016/j.scitotenv.2025.180920},
pmid = {41232286},
issn = {1879-1026},
abstract = {The simultaneous removal of nitrogenous and sulfate compounds in natural environments represents a major environmental challenge. The sulfammox process, a microbial pathway that couples anaerobic ammonium oxidation with sulfate reduction, has recently been proposed as a sustainable alternative for the removal of these pollutants. In this study, we evaluated for the first time the presence and activity of sulfammox microbial communities in sediments from a natural wetland in northeastern Mexico under controlled microcosm conditions. Physicochemical parameters, sediment composition, and ammonium dynamics were analyzed in two natural wetlands: Cachorritos pond (CHP) and Azul turqueza pond (AZP), during a four-week incubation period under controlled conditions. A decrease in ammonium concentration (up to 41.38 mM) was observed only in the CHP, with a stoichiometric NH4[+]/SO4[2-] ratio of 2.45 (92 %), confirming the activity of the sulfammox process. Metagenomic analysis revealed an enrichment of bacterial phylum associated with the sulfammox process, such as Chloroflexi, Chlorobi and Proteobacteria, which increased markedly in sulfate and ammonium treatments. This study represents the first report of sulfammox activity in a natural wetland in Mexico, highlighting the ecological potential of these ecosystems as natural treatment systems and supporting their consideration in sustainable bioremediation strategies.},
}

@article {pmid41232227,
year = {2025},
author = {Sharma, V and Goel, S and Bisht, K and Kaura, T and Verma, S and Mewara, A and Grover, GS and Biswal, M},
title = {Unveiling the Presence of Coxiella-like bacteria in Rhipicephalus microplus Ticks from Punjab, North India: A 16S rRNA metagenomic study.},
journal = {Veterinary microbiology},
volume = {312},
number = {},
pages = {110783},
doi = {10.1016/j.vetmic.2025.110783},
pmid = {41232227},
issn = {1873-2542},
abstract = {In this study, using 16S rRNA gene-based metagenomics, we aimed to determine the presence of infectious bacteria in the ticks collected from Punjab state in north India. Tick samples were collected from the domesticated animals from the Patiala, Ropar, and Mohali districts of Punjab, India from February 2022- April 2022. DNA was extracted, and the library was prepared by targeting the V3-V4 hypervariable region of the 16S rRNA gene. The sequencing was conducted in Illumina using the 300 bp paired-end chemistry. Eight tick samples were analyzed from the Patiala, Ropar and Mohali districts of Punjab, India, revealing a diverse range of bacterial species within the tick microbiome. Seven out of eight samples were found to harbour Coxiella-like bacteria (46-181,607 reads; closely related to C. burnetii based on 16S rRNA [V3-V4] sequence similarity), indicating their abundance in the tick population. Furthermore, the analysis uncovered the presence of other pathogenic bacterial genera, including Staphylococcus, Streptococcus, Corynebacterium, Enterococcus, Pseudomonas, Bordetella, and Micrococcus in the tick microbiome, highlighting the abundance and diversity of infectious organisms within ticks. 16S rRNA gene-based metagenomics enables valuable insights into infectious agents in disease-transmitting vectors. Coxiella-like bacteria were found to be predominant bacterial species in the tick microbiomes in this study. The public health significance of this finding in animals and humans needs to be explored in this region. However, as 16S rRNA sequencing offers limited resolution for distinguishing closely related taxa, further confirmation using additional loci or whole-genome sequencing is warranted.},
}

@article {pmid41231980,
year = {2025},
author = {Gelsinger, DR and Ronda, C and Ma, J and Kar, OB and Edwards, M and Huang, Y and Mavros, CF and Sun, Y and Perdue, T and Vo, PL and Ivanov, II and Sternberg, SH and Wang, HH},
title = {Metagenomic editing of commensal bacteria in vivo using CRISPR-associated transposases.},
journal = {Science (New York, N.Y.)},
volume = {390},
number = {6774},
pages = {eadx7604},
doi = {10.1126/science.adx7604},
pmid = {41231980},
issn = {1095-9203},
mesh = {Animals ; Mice ; *Gastrointestinal Microbiome/genetics ; *Gene Editing/methods ; *Bacteroides/genetics/growth & development ; Humans ; Metagenomics/methods ; *CRISPR-Cas Systems ; Symbiosis ; Mice, Inbred C57BL ; Metagenome ; Clustered Regularly Interspaced Short Palindromic Repeats ; },
abstract = {Although metagenomic sequencing has revealed a rich microbial biodiversity in the mammalian gut, methods to genetically alter specific species in the microbiome are highly limited. Here, we introduce Metagenomic Editing (MetaEdit) as a platform technology for microbiome engineering that uses optimized CRISPR-associated transposases delivered by a broadly conjugative vector to directly modify diverse native commensal bacteria from mice and humans with new pathways at single-nucleotide genomic resolution. Using MetaEdit, we achieved in vivo genetic capture of native murine Bacteroides by integrating a metabolic payload that enables tunable growth control in the mammalian gut with dietary inulin. We further show in vivo editing of segmented filamentous bacteria, an immunomodulatory small-intestinal microbial species recalcitrant to cultivation. Collectively, this work provides a paradigm to precisely manipulate individual bacteria in native communities across gigabases of their metagenomic repertoire.},
}

Animals
Mice
*Gastrointestinal Microbiome/genetics
*Gene Editing/methods
*Bacteroides/genetics/growth & development
Humans
Metagenomics/methods
*CRISPR-Cas Systems
Symbiosis
Mice, Inbred C57BL
Metagenome
Clustered Regularly Interspaced Short Palindromic Repeats

@article {pmid41231970,
year = {2025},
author = {Coelho, C and Taborda, A and Lorena, C and Frazão, T and Veríssimo, A and Borges, PT and Brissos, V and Tiago, I and Martins, LO},
title = {Shotgun metagenomic mining reveals a new FAD-dependent D-lactate dehydrogenase in an isopod gut microbiome.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0148025},
doi = {10.1128/aem.01480-25},
pmid = {41231970},
issn = {1098-5336},
abstract = {UNLABELLED: Shotgun metagenomic sequencing has emerged as a powerful tool for exploring microbial diversity and uncovering genes encoding novel biocatalysts from complex environments. Here, we report the discovery and characterization of a new FAD-dependent D-lactate dehydrogenase (PdG-D-LDH) from the gut microbiome of the isopod Porcellio dilatatus. The enzyme was identified through in silico screening using BLAST and AlphaFold3 and functionally characterized as a homodimeric, thermoactive, and thermostable protein, demonstrating the robustness required for biotechnological applications. PdG-D-LDH exhibits a strong catalytic preference toward D-lactate and preferentially reduces quinones over cytochrome c or molecular oxygen. X-ray crystallography revealed a VAO/PCMH-like fold with a solvent-accessible active site that harbors both a FAD cofactor and an Fe(II) ion. Molecular docking studies provided insights into the structural determinants of its stereoselective substrate recognition. Under mild conditions, the enzyme catalyzed the oxidation of D-lactate to pyruvate with a 90% yield after 24 h of reaction, using molecular oxygen as the electron acceptor.

IMPORTANCE: This study illustrates how metagenomics, structural biology, and computational tools can jointly drive the discovery of new enzymes with valuable biotechnological applications aligned with circular economic principles. The newly identified D-lactate dehydrogenase, PdG-D-LDH, exhibits thermostability, stereoselectivity, and high catalytic efficiency, providing new insights into the structure-function relationships of lactate-metabolizing enzymes.},
}

@article {pmid41231285,
year = {2025},
author = {Padur Sankaranarayanan, A and Dhanapal, S and Valliyappan, M and Shyu, DJH and Parthasarathy, TN},
title = {Intestinal microbiome diversity and disparity between wild and captive endangered Asian elephants (Elephas maximus indicus) in southern India.},
journal = {Antonie van Leeuwenhoek},
volume = {118},
number = {12},
pages = {191},
pmid = {41231285},
issn = {1572-9699},
support = {31950410559//National Natural Science Foundation [NSFC] of China/ ; },
mesh = {Animals ; *Elephants/microbiology ; *Gastrointestinal Microbiome/genetics ; India ; RNA, Ribosomal, 16S/genetics ; *Animals, Wild/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Endangered Species ; Biodiversity ; Phylogeny ; Animals, Zoo/microbiology ; Male ; DNA, Bacterial/genetics/chemistry ; Feces/microbiology ; Female ; },
abstract = {The gut microbiome affects the physical and mental wellbeing of an animal. Several factors, including diet, host physiology, age, sex, lifestyle, and environmental factors, influence the dynamic gut microbiome. We studied the gut microbiome composition of the endangered Asian elephants (Elephas maximus) kept under prolonged captive conditions (15.8 ± 3.9 years) and their wild counterparts, as both were exposed to two different environmental pressures. A total of 648,581 high-quality sequences were obtained, comprising 208 microbial families from 22 phyla and 97 orders, as determined by high-throughput 16S rRNA gene sequencing. Among them, 90% of the microbes belonged to the phyla Firmicutes, Proteobacteria and Bacteroidetes. Our analysis revealed a distinct variation in the gut microbiome between captive and wild elephants. The captive elephants had a higher abundance of the microbial phyla Kiritimatiellaeota, Tenericutes, Euryarchaeota, and Verrucomicrobia, which suggests that captivity alters the gut microbiome. These findings reveal distinct patterns of gut microbiome diversity between captive and wild elephants, underscoring the role of diet and environmental conditions in shaping the elephant gut microbiome.},
}

Animals
*Elephants/microbiology
*Gastrointestinal Microbiome/genetics
India
RNA, Ribosomal, 16S/genetics
*Animals, Wild/microbiology
*Bacteria/classification/genetics/isolation & purification
Endangered Species
Biodiversity
Phylogeny
Animals, Zoo/microbiology
Male
DNA, Bacterial/genetics/chemistry
Feces/microbiology
Female

@article {pmid41231233,
year = {2025},
author = {Absolon, DE and Jackson, VLN and Monier, A and Smith, AG and Helliwell, KE},
title = {Metagenomics of the MAST-3 stramenopile, Incisomonas, and its associated microbiome reveals unexpected metabolic attributes and extensive nutrient dependencies.},
journal = {Microbial genomics},
volume = {11},
number = {11},
pages = {},
doi = {10.1099/mgen.0.001510},
pmid = {41231233},
issn = {2057-5858},
mesh = {*Metagenomics/methods ; *Microbiota/genetics ; *Stramenopiles/genetics/metabolism/classification ; Bacteria/genetics/metabolism/classification ; Phylogeny ; },
abstract = {Protists are polyphyletic single-celled eukaryotes that underpin global ecosystem functioning, particularly in the oceans. Most remain uncultured, limiting the investigation of their physiology and cell biology. MArine STramenopiles (MASTs) are heterotrophic protists that, although related to well-characterized photosynthetic diatoms and parasitic oomycetes, are poorly studied. The Nanomonadea (MAST-3) species Incisomonas marina has been maintained in co-culture with a bacterial consortium, offering opportunities to investigate the metabolic attributes and nutritional dependencies of the community. Employing a metagenomics approach, the 68 Mbp haploid genome of I. marina was retrieved to an estimated completeness of 93%, representing the most complete MAST genome so far. We also characterized the diversity of, and assembled genomes for, 23 co-cultured bacteria. Auxotrophy of I. marina for B vitamins (B1, B2, B6, B7 and B12), but not vitamins C, B3, B5 and B9, was predicted. Several bacteria also lacked complete B-vitamin biosynthesis pathways, suggesting that vitamins and/or their precursors are exchanged in the consortium. Moreover, I. marina lacked the ability to synthesize half the protein amino acids, although genes encoding the complete urea cycle were identified, like diatoms; this may play a role in recycling organic nitrogen compounds. Unexpectedly, we also identified the gene DSYB for dimethylsulphoniopropionate biosynthesis. Biosynthesis of this important stress protectant and bacterial chemoattractant is typically found in photosynthetic eukaryotes and has not been identified before in heterotrophic stramenopiles. Together, our study reveals the metabolic attributes of a hitherto understudied organism, advancing knowledge of the evolution and adaptations of the stramenopiles and informing future culturing efforts.},
}

*Metagenomics/methods
*Microbiota/genetics
*Stramenopiles/genetics/metabolism/classification
Bacteria/genetics/metabolism/classification
Phylogeny

@article {pmid41231016,
year = {2025},
author = {Wang, YL and Aghdam, SA and Brown, AMV and Deonarine, A},
title = {Global Survey of Mercury Methylation and Demethylation Microbial Communities in Wastewater and Activated Sludge.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c11448},
pmid = {41231016},
issn = {1520-5851},
abstract = {Wastewater treatment plants (WWTPs) are an understudied source of mercury methylating and demethylating microbes to downstream aquatic and terrestrial environments, where methylmercury production and subsequent bioaccumulation in the food web occur. To identify methylators and demethylators and evaluate their occurrence in WWTPs, metagenomic and metatranscriptomic analyses of raw sewage, activated sludge, and effluent samples from WWTPs across the globe were conducted. Results indicated that hgcA- and merB-carriers were widespread in WWTPs, with higher abundance in raw sewage and sludge compared to treated effluent. Bdellovibrionota were identified as merB-carriers, linking them to demethylation for the first time. Novel conserved motifs of hgcB and fused hgcAB were also identified. 30% of hgcA genes were colocalized with arsenic-resistance operons on the same contig, while all merB-carriers contained arsenic resistance genes (ars), though merB and arsR were not colocated. Antibiotic resistance genes were also present in the genomes of multiple hgcA- amd merB-carriers, including one sample where hgcA and the antiseptic/antibiotic resistant gene (qacG) were colocated on the same contig, suggesting possible coselection in environments containing antibiotics. Mobile genetic element-mediated horizontal gene transfer was identified as a mechanism facilitating the genetic transfer of hgcA. Overall, these findings highlight WWTPs as reservoirs of genes involved in mercury methylation and demethylation, with potential implications for mercury cycling in downstream environments.},
}

@article {pmid41230645,
year = {2025},
author = {El-Mayet, FS and Moharam, I and El-Nahas, EM and El-Habbaa, AS and Najar, FZ and Stayton, E and El Nagar, EMS and Radi, M and Khalil, NW and Abaza, MA},
title = {First identification of concurrent infections with novel emerging duck astrovirus and duck hepatitis A virus type 3 (DHAV-3) in ducklings in Egypt using metagenomic next-generation sequencing (m-NGS).},
journal = {Avian pathology : journal of the W.V.P.A},
volume = {},
number = {},
pages = {1-17},
doi = {10.1080/03079457.2025.2581279},
pmid = {41230645},
issn = {1465-3338},
abstract = {First complete genome sequencing of a DHAV-3 strain from Egypt using m-NGS.Discovery of a novel duck astrovirus co-infecting with DHAV-3.Phylogenetic analysis reveals cross-border transmission links with Asian strains of both DHAV-3 and DAstV-5.},
}

@article {pmid41230492,
year = {2025},
author = {Rodriguez-Fernandez, IA and Santiago-Rodriguez, TM and Figueroa-Pratts, PG and Cintrón-Berríos, K and Rodriguez-Cornier, ND and Toranzos, GA},
title = {Gut microbial community structure of the adult citrus root weevil Diaprepes abbreviatus.},
journal = {Frontiers in insect science},
volume = {5},
number = {},
pages = {1676003},
pmid = {41230492},
issn = {2673-8600},
abstract = {Diaprepes abbreviatus is an agricultural pest known to affect around 270 plant species across the Caribbean and the United States, posing significant challenges to pest management. Chemical control dominates management, but environmental and health concerns motivate microbiome-informed alternatives. However, limited information exists on the gut anatomy, physicochemical environment, and microbial composition of D. abbreviatus. In this study, we provide the first comprehensive characterization of the gut morphology, pH, and microbiota of adult D. abbreviatus in both females and males collected in Puerto Rico. Using dye-based gut tracing, we identified foregut, midgut, and hindgut or posterior gut compartments, and confirmed the presence of a muscular, sclerotized gizzard. Colorimetric analysis revealed a mildly acidic gut environment (approximately pH 4-5, based on qualitative ranges), consistent across sexes and regions. Shotgun metagenomic sequencing of dissected guts from males and females revealed microbial communities distinct from the leaf samples microbiota. While alpha and beta diversity did not differ significantly between sexes, co-occurrence analyses identified sex-specific correlation patterns among bacterial taxa. Notably, Enterobacter cloacae, Pantoea vagans, Lactococcus lactis, and Pseudomonas monteilii were repeatedly detected across individuals and generated metagenomic datasets, and some were localized to the hindgut, suggesting possible niche specialization. The presence of taxa, such as Enterobacter cloacae, previously reported as symbionts in other phytophagous insects further supports the hypothesis that certain bacteria may contribute to host digestion or adaptation. These findings establish a framework for understanding the gut environment and microbial community of D. abbreviatus, and highlight candidate taxa for future functional studies. More broadly, this work supports further research into the potential roles of gut microbiota in the ecology and management of this pest.},
}

@article {pmid41230491,
year = {2025},
author = {Juhász, J and Ligeti-Nagy, N and Bodnár, B and Juhász, J and Pongor, S and Ligeti, B},
title = {ProkBERT PhaStyle: accurate phage lifestyle prediction with pretrained genomic language models.},
journal = {Bioinformatics advances},
volume = {5},
number = {1},
pages = {vbaf188},
pmid = {41230491},
issn = {2635-0041},
abstract = {MOTIVATION: Phage lifestyle prediction, i.e. classifying phage sequences as virulent or temperate, is crucial in biomedical and ecological applications. Phage sequences from metagenome or virome assemblies are often fragmented, and the diversity of environmental phages is not well known. Current computational approaches often rely on database comparisons that require significant effort and expertise to update. We propose using genomic language models (LMs) for phage lifestyle classification, allowing efficient direct analysis from nucleotide sequences without the need for sophisticated preprocessing pipelines or manually curated databases. We trained three genomic LMs (DNABERT-2, Nucleotide Transformer, and ProkBERT) on datasets of short, fragmented sequences. These models were then compared with dedicated phage lifestyle prediction methods in terms of accuracy, prediction speed, and generalization capability.

RESULTS: ProkBERT PhaStyle achieves accuracy comparable to, and in many cases higher than, state-of-the-art models across various scenarios. It demonstrates the ability to generalize to unseen data in our benchmarks, accurately classifies phages from extreme environments, and also demonstrates high inference speed.

Genomic LMs offer a simple and computationally efficient alternative for solving complex classification tasks, such as phage lifestyle prediction. ProkBERT PhaStyle's simplicity, speed, and performance suggest its utility in various ecological and clinical applications.},
}

@article {pmid41230489,
year = {2025},
author = {Scherz, V and Nassirnia, S and Chaabane, F and Castelo-Szekely, V and Greub, G and Pillonel, T and Bertelli, C},
title = {zAMP and zAMPExplorer: reproducible scalable amplicon-based metagenomics analysis and visualization.},
journal = {Bioinformatics advances},
volume = {5},
number = {1},
pages = {vbaf255},
pmid = {41230489},
issn = {2635-0041},
abstract = {SUMMARY: To enable flexible, scalable, and reproducible microbiota profiling, we have developed zAMP, an open-source bioinformatics pipeline for the analysis of amplicon sequence data, such as 16S rRNA gene for bacteria and archaea or ITS for fungi. zAMP is complemented by two modules: one to process databases to optimize taxonomy assignment, and the second to benchmark primers, databases and classifier performances. Coupled with zAMPExplorer, an interactive R Shiny application that provides an intuitive interface for quality control, diversity analysis, and statistical testing, this complete toolbox addresses both research and clinical needs in microbiota profiling.

Comprehensive documentation and tutorials are provided alongside the source code of zAMP and zAMPExplorer software to facilitate installation and use. zAMP is implemented as a Snakemake workflow, ensuring reproducibility by running within Singularity or Docker containers, and is also easily installable via Bioconda. The zAMPExplorer application, designed for visualization and statistical analysis, can be installed using either a Docker image or from R-universe.},
}

@article {pmid41230409,
year = {2025},
author = {Tian, Y and Xu, N and Chen, Y and Xu, Z and Zhou, JX and Zhang, L},
title = {Cost-effectiveness analysis of metagenomic next-generation sequencing versus traditional bacterial cultures for postoperative central nervous system infections in critical care settings: a prospective pilot study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1710412},
pmid = {41230409},
issn = {2235-2988},
mesh = {Humans ; *Cost-Benefit Analysis ; Pilot Projects ; Prospective Studies ; *High-Throughput Nucleotide Sequencing/economics/methods ; Female ; Male ; Middle Aged ; *Central Nervous System Infections/diagnosis/microbiology/economics ; *Metagenomics/economics/methods ; *Critical Care/economics ; Aged ; *Bacteria/genetics/isolation & purification/classification ; Adult ; *Postoperative Complications/microbiology/diagnosis ; Intensive Care Units ; China ; *Bacteriological Techniques/economics/methods ; Cost-Effectiveness Analysis ; },
abstract = {BACKGROUND: Early and accurate pathogen identification is crucial for managing central nervous system infections (CNSIs). While Metagenomic Next-Generation Sequencing (mNGS) offers rapid and sensitive pathogen detection, its cost-effectiveness in postoperative neurosurgical patients in critical care settings remains underexplored. Our study aims to investigate the clinical health economic value of mNGS in detecting pathogens of CNSIs after neurosurgery.

METHODS: In this prospective pilot study, 60 patients with CNSIs at Beijing Tiantan Hospital ICU (March 2023-January 2024) were randomized 1:1 to mNGS or conventional pathogen culture groups. A decision-tree model compared cost-effectiveness using incremental cost-effectiveness ratios (ICERs). A decision-tree model was used to compare the cost-effectiveness between mNGS and traditional pathogen culture methods using incremental cost-effectiveness ratios (ICERs).

RESULTS: From March 2023 to January 2024, 60 patients were included. mNGS demonstrated superior diagnostic efficiency with shorter turnaround time (1 vs 5 days; _P_<0.001) and lower anti-infective costs (¥18,000 vs ¥23,000; _P_=0.02). Despite higher detection costs (¥4,000 vs ¥2,000; _P_<0.001), the ICER of ¥36,700 per additional timely diagnosis suggested cost-effectiveness at China's GDP-based WTP threshold. No significant differences in hospitalization duration or total costs were observed (_P_>0.05).

CONCLUSION: mNGS improves diagnostic efficiency and reduces antimicrobial expenditure for postoperative CNSIs in critical care, demonstrating favorable cost-effectiveness when considering clinical outcome gains.},
}

Humans
*Cost-Benefit Analysis
Pilot Projects
Prospective Studies
*High-Throughput Nucleotide Sequencing/economics/methods
Female
Male
Middle Aged
*Central Nervous System Infections/diagnosis/microbiology/economics
*Metagenomics/economics/methods
*Critical Care/economics
Aged
*Bacteria/genetics/isolation & purification/classification
Adult
*Postoperative Complications/microbiology/diagnosis
Intensive Care Units
China
*Bacteriological Techniques/economics/methods
Cost-Effectiveness Analysis

@article {pmid41230408,
year = {2025},
author = {Lin, L and Li, X and Li, J and Wu, B and Lin, Y and Li, W and Li, H and Guo, Y and Huang, C and Huang, Z and Zhang, W and Fang, X},
title = {Microbial culture vs. mNGS: diagnostic variations in periprosthetic joint infection.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1611332},
pmid = {41230408},
issn = {2235-2988},
mesh = {Humans ; *Prosthesis-Related Infections/diagnosis/microbiology ; Male ; Female ; Aged ; Middle Aged ; *High-Throughput Nucleotide Sequencing/methods ; *Bacteria/isolation & purification/genetics/classification ; Aged, 80 and over ; *Metagenomics/methods ; *Microbiological Techniques/methods ; Retrospective Studies ; },
abstract = {OBJECTIVE: This study aimed to compare the diagnostic performance of conventional microbial culture and metagenomic next-generation sequencing (mNGS) in detecting pathogens in periprosthetic joint infection (PJI) and to identify factors contributing to discrepancies between these two methods.

METHODS: A total of 167 patients with suspected PJI (including PJI patients and aseptic failure patients) who underwent revision joint replacement at our center from September 2017 to April 2024 were enrolled. Demographic data, prior antibiotic use, and results of microbial culture and mNGS were documented. Joint fluid, periprosthetic tissue, or prosthetic ultrasonic fluid samples were collected, and at least one sample from each patient underwent both microbial culture and mNGS testing. In the light of the concordance between culture and mNGS results, patients were divided into the detection consistent and detection inconsistent groups. The differences in pathogen detection between the two models were compared, and factors contributing to discordant results were analyzed.

RESULTS: The prior antibiotic use (OR = 2.137, 95% CI = 1.069-4.272, P = 0.032), polymicrobial infections (OR = 3.245, 95% CI = 1.278-8.243, P = 0.013), infection caused by rare pathogens (OR = 2.735, 95% CI = 1.129-6.627, P = 0.026), and intraoperative tissue specimens (OR = 2.837, 95% CI = 1.007-7.994, P = 0.049) were identified as risk factors for discordance between microbial culture and mNGS results, particularly in cases with negative microbial culture but positive mNGS findings. Conversely, consistency in specimen type (OR = 0.471, 95%CI=0.254-0.875, P = 0.017) was identified as a protective factor against discordance.

CONCLUSION: Clinicians should optimize diagnostic strategies by tailoring microbial culture methods to the patient's clinical condition and integrating mNGS testing where appropriate. It is recommended to use tissue specimens from the same anatomical site across multiple tests while sampling from different regions when necessary. Although this approach may increase costs, it significantly enhances the accuracy of pathogen identification and facilitates more effective treatment.},
}

Humans
*Prosthesis-Related Infections/diagnosis/microbiology
Male
Female
Aged
Middle Aged
*High-Throughput Nucleotide Sequencing/methods
*Bacteria/isolation & purification/genetics/classification
Aged, 80 and over
*Metagenomics/methods
*Microbiological Techniques/methods
Retrospective Studies