@article {pmid40367854,
year = {2025},
author = {Ahmad, W and Coffman, L and Ray, R and Woldesenbet, S and Singh, G and Khan, AL},
title = {Flooding episodes and seed treatment influence the microbiome diversity and function in the soybean root and rhizosphere.},
journal = {The Science of the total environment},
volume = {982},
number = {},
pages = {179554},
doi = {10.1016/j.scitotenv.2025.179554},
pmid = {40367854},
issn = {1879-1026},
abstract = {Climate change-related events such as flooding have threatened crop productivity, agricultural sustainability, and global food security by causing hypoxic conditions. Such conditions impaire root development and nutrient acquisition, and alter root rhizospheric microbial communities that are vital for plant health and productivity. Seed treatment with pathogen protection have been key to maintaining early seed germination and plant productivity in field conditions. Still, their role in flooding stress and microbiome diversity and functionality in soybeans is poorly understood. Here, we performed field-based investigations to understand the impact of flooding episodes (0, 3, and 7 days after floodings; DAF) and seed treatment (Cruiser MAXX) on soybean plant growth and rhizosphere microbiome diversity and functionality. Flooding episodes significantly reduced seed yield (746 kg ha[-1]) compared to untreated control. However, the seed treatment increased plant height and pods per plant (3-DAF) and reduced flood injury by 33 % (7-DAF). The shotgun metagenomic analysis showed that seed treatment significantly enhanced the microbial community in rhizospheric soil. Flooding episodes impacted the microbial communities with higher abundance at 3-DAF than at 7-DAF. Flooding stress reduced the microbial diversity, although Proteobacteria increased as root endophytes. Seed treatment and flooding combinations decreased microbiome functionality and reduced gene counts for phytohormone biosynthesis, fermentation, nitrogen, symbiosis, and degradation pathways. Similarly, flooding stress shifted the carbohydrate synthesis to a more specialized substrate. These findings enhance understanding of soybean root and rhizosphere microbiome diversity and functionality dynamics during flooding stress and provide a platform to develop sustainable agricultural practices for enhancing soybean stress tolerance to flooding.},
}

@article {pmid40367785,
year = {2025},
author = {Wang, Y and Huang, S and He, J and Feng, Z and Wu, W and Guo, C and He, J},
title = {Unveiling the dynamic viral landscape across developmental stages of cold seep ecosystems: Implications for global marine biogeochemistry.},
journal = {Journal of hazardous materials},
volume = {494},
number = {},
pages = {138594},
doi = {10.1016/j.jhazmat.2025.138594},
pmid = {40367785},
issn = {1873-3336},
abstract = {Cold seeps are methane-rich ecosystems playing pivotal roles in global biogeochemical cycling, yet their viral communities remain underexplored. We present the first comprehensive viral metagenomic analysis across developmental stages of the Haima Cold Seep. Characterizing viral assemblages from chemoautotrophic, mature, and extinct seep sediments revealed 4272 viral operational taxonomic units, with 77 % representing novel lineages, highlighting cold seeps' unique viral diversity. Viral community structure and diversity varied significantly by seep stage, with highest diversity in the chemoautotrophic stage. While Siphoviridae and Microviridae dominated, their relative abundances shifted with maturity. Gammaproteobacteria emerged as predominant viral hosts, exhibiting distinct interaction patterns across stages. Notably, the chemoautotrophic stage harbored the highest abundance and diversity of virus-encoded auxiliary metabolic genes (AMGs; ∼450 AMGs), with significantly enriched carbohydrate metabolism and central carbon pathway genes (2.2-fold and 1.8-fold higher respectively, p < 0.005), amino acid metabolism (1.9-fold, p = 0.003), and sulfur relay system genes (2.0-fold, p = 0.002). In contrast, the mature stage exhibited distinct enrichment in energy metabolism genes (up to 3.9-fold difference between sites, p < 0.001) and xenobiotics degradation pathways, suggesting stage-specific viral impacts on biogeochemical cycling. Lytic lifestyles prevailed across stages, indicating dynamic virus-host interactions during seep development. These findings unveil complex viral ecology in cold seeps, with potential influences on microbial community structure and biogeochemical processes. Providing a foundation for understanding viral roles in cold seep ecosystem functioning and biogeochemical cycles, this study has implications for marine microbial ecology and environmental biotechnology.},
}

@article {pmid40367670,
year = {2025},
author = {Yu, S and Cao, T and Xu, Z and Zhou, H and Li, Q},
title = {Metagenomic next-generation sequencing (mNGS) identified Clostridium perfringens infection presenting as acute hemolysis after surgery.},
journal = {Journal of infection and public health},
volume = {18},
number = {8},
pages = {102798},
doi = {10.1016/j.jiph.2025.102798},
pmid = {40367670},
issn = {1876-035X},
abstract = {Clostridium perfringens (C. perfringens) septicaemia is a rare, but rapidly fatal infection, characterized by massive hemolysis. In numerous documented instances, the patient was not diagnosed in time due to the absence of typical clinical features. In order to enhance diagnostic accuracy, metagenomic next-generation sequencing (mNGS) has been adopted as a novel approach to pathogen identification. CASE PRESENTATION: A 67-year-old male who had undergone transcatheter arterial chemoembolization (TACE) surgery four days earlier presented with severe anemia, and laboratory investigations disclosed intravascular hemolysis. Swift and accurate identification was imperative, resulting in the confirmation of mNGS analysis, his medical history, clinical symptoms, physical signs, additional tests, and C. perfringens as the causative pathogen of hemolysis. After successful treatment with effective antibiotics, the patient recovered and was discharged from the hospital after 19 days. CONCLUSIONS: mNGS achieves expedited diagnostic turnaround time through rapid pathogen identification, significantly surpassing conventional culture methods. This may enable the diagnosis of atypical cases of C. perfringens infection, which can cause rapid systemic shock, renal failure, intravascular hemolysis, and even death.},
}

@article {pmid40367615,
year = {2025},
author = {Guo, Y and Cheng, S and Fang, H and Geng, J and Shi, F and Wang, H and Chen, L and Pu, H and Liu, B and Zhou, Y},
title = {Water regime alters microbial mechanisms of N2O emission in metal-contaminated paddy soils.},
journal = {Ecotoxicology and environmental safety},
volume = {298},
number = {},
pages = {118304},
doi = {10.1016/j.ecoenv.2025.118304},
pmid = {40367615},
issn = {1090-2414},
abstract = {Microorganisms are essential for soil nitrous oxide (N2O) emissions through participating in key nitrogen (N)-related processes. However, the effect of water regimes on the interactions between N2O emissions and microbial processes in metal-contaminated soils is unclear. Here, we conducted a soil microcosm experiment with two water management strategies (non-flooding and flooding) and six metal addition treatments including low (2 and 200 mg kg[-1]) and high (10 and 1000 mg kg[-1]) levels of individual and combined Cd and Cu. The effects of high levels of individual Cd and Cu contamination on soil N2O emissions varied depending on water regimes, showing antagonistic effects under non-flooding conditions and synergistic effects under flooding conditions. High levels of co-contamination significantly inhibited nitrification under both water regimes, primarily due to reduced abundance of Nitrosospira. In contrast, this co-contamination decreased the abundance of Ramlibacter, thereby inhibiting denitrification and dissimilatory nitrate reduction to ammonium (DNRA) under flooding conditions. The inhibition of these key microorganisms and their mediated N-cycle processes reduced soil N2O emissions under both water regimes. This reduction was greater under flooding conditions because more N-related processes were inhibited. Metagenomic binning further indicated that Nitrosospira carried nitrifying genes, while Ramlibacter contained genes involved in denitrification, assimilatory nitrate reduction to ammonium (ANRA), and DNRA. These findings implied that both microorganisms had potential to produce N2O. Overall, water management strategies and metal contamination altered the microbial processes of N2O emissions, highlighting the importance of appropriate water management in mitigating greenhouse gas emissions from metal-contaminated paddy soils in southern China.},
}

@article {pmid40367351,
year = {2025},
author = {Heo, H and Nguyen-Dinh, T and Jung, MY and Greening, C and Yoon, S},
title = {Hydrogen-dependent dissimilatory nitrate reduction to ammonium enables growth of Campylobacterota isolates.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf092},
pmid = {40367351},
issn = {1751-7370},
abstract = {Dissimilatory nitrate reduction to ammonium (DNRA) is a key process used by diverse microorganisms in the global nitrogen cycle. For long, DNRA has been considered primarily as an organotrophic reaction, despite evidence that oxidation of inorganic electron donors also supports DNRA. Evidence of DNRA coupling with molecular hydrogen (H2) oxidation has been reported for several microbial isolates; however, the underlying physiology of the microbial process remains understudied. In this study, we report the isolation of two Campylobacterotastrains, Aliarcobacter butzlerihDNRA1 and Sulfurospirillumsp. hDNRA2, which grow using H2as the sole electron donor for DNRA, and physiological insights gained from a close examination of hydrogenotrophic DNRA in these isolates. In both batch and continuous cultures, DNRA sensu stricto(i.e. NO3-reduction that includes stoichiometric NO2--to-NH4+reduction) was strictly dependent on the presence of H2and exhibited stoichiometric coupling with H2oxidation, indicating that electrons required for NO2-reduction were unequivocally derived from H2. Successful chemostat incubation further demonstrated that hydrogenotrophic DNRA is viable under NO3-limiting, H2-excess conditions. Genomic and transcriptomic analyses identified group 1b [NiFe]-hydrogenase and cytochrome c552nitrite reductase as the key enzymes catalyzing hydrogenotrophic DNRA. Additionally, metagenomic surveys revealed that bacteria capable of hydrogenotrophic DNRA are taxonomically diverse and abundant in various ecosystems, particularly in the vicinity of deep-sea hydrothermal vents. These findings, integrating physiological, genomic, and transcriptomic analyses, clarify that H2can solely serve as a growth-supporting electron donor for DNRA and suggest potential significance of this microbial process in nitrogen- and hydrogen-related environmental biogeochemical cycles.},
}

@article {pmid40366862,
year = {2025},
author = {Wang, L and Chen, X and Pollock, NR and Villafuerte Gálvez, JA and Alonso, CD and Wang, D and Daugherty, K and Xu, H and Yao, J and Chen, Y and Kelly, CP and Cao, Y},
title = {Metagenomic analysis reveals distinct patterns of gut microbiota features with diversified functions in C. difficile infection (CDI), asymptomatic carriage and non-CDI diarrhea.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2505269},
doi = {10.1080/19490976.2025.2505269},
pmid = {40366862},
issn = {1949-0984},
abstract = {Clostridioides difficile infection (CDI) has been recognized as a leading cause of healthcare-associated infections and a considerable threat to public health globally. Increasing evidence suggests that the gut microbiota plays a key role in the pathogenesis of CDI. The taxonomic composition and functional capacity of the gut microbiota associated with CDI have not been studied systematically. Here, we performed a comprehensive shotgun metagenomic sequencing in a well-characterized human cohort to reveal distinct patterns of gut microbiota and potential functional features associated with CDI. Fecal samples were collected from 104 inpatients, including : (1) patients with clinically significant diarrhea and positive nucleic acid amplification testing (NAAT) and received CDI treatment (CDI, n = 47); (2) patients with positive stool NAAT but without diarrhea (Carrier, n = 17); (3) patients with negative stool NAAT but with diarrhea (Diarrhea, n = 14); and (4) patients with negative stool NAAT and without diarrhea (Control, n = 26). Downstream statistical analyses (including alpha and beta diversity analysis, differential abundance analysis, correlation network analysis, and potential functional analysis) were then performed. The gut microbiota in the Control group showed higher Chao1 index (p < 0.05), while Shannon index at KEGG module level was higher in CDI than in Carrier and Control (p < 0.05). Beta diversity for species composition differed significantly between CDI vs Carrier/Control cohorts (p < 0.05). Microbial Linear discriminant analysis Effect Size and ANCOM analysis both identified 8 species (unclassified_f_Enterobacteriaceae, Veillonella_parvula, unclassified_g_Klebsiella and etc.) were enriched in CDI, Enterobacter_aerogenes was enriched in Diarrhea, Collinsella_aerofaciens, Collinsella_sp_4_8_47FAA, Collinsella_tanakaei and Collinsella_sp_CAG_166 were enriched in Control (LDA >3.0, adjusted p < 0.05). Correlation network complexity was higher in CDI with more negative correlations than in other three cohorts. Modules involved in iron complex transport system (M00240) was enriched in CDI, ABC-2 type transport system (M00254), aminoacyl-tRNA biosynthesis (M00359), histidine biosynthesis (M00026) and inosine monophosphate biosynthesis (M00048) were enriched in Carrier, ribosome (M00178 and M00179) was enriched in Diarrhea, fluoroquinolone resistance (M00729) and aminoacyl-tRNA biosynthesis (M00360) were enriched in Control (LDA > 2.5, adjusted p < 0.05). Resistance functions of acriflavine and glycylcycline were enriched in CDI, while resistance function of bacitracin was enriched in Carrier (LDA > 3.0, adjusted p < 0.05), and the contributions of phylum and species to resistance functions differed among the four groups. Our results reveal alterations of gut microbiota composition and potential functions among four groups of differential colonization/infection status of Clostridioides difficile. These findings support the potential roles of gut microbiota and their potential functions in the pathogenesis of CDI.},
}

@article {pmid40366770,
year = {2025},
author = {Baba, Y and Tsuge, D and Aoki, R},
title = {Enhancement of carbohydrate metabolism by probiotic and prebiotic intake promotes short-chain fatty acid production in the gut microbiome: A randomized, double-blind, placebo-controlled crossover trial.},
journal = {Bioscience, biotechnology, and biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1093/bbb/zbaf071},
pmid = {40366770},
issn = {1347-6947},
abstract = {Short-chain fatty acids (SCFAs) are thought to be a key factor in the health benefits of prebiotics and probiotics. This study investigated the effect of Bifidobacterium animalis subsp. lactis GCL2505 and inulin (BL+IN) on fecal SCFAs and gut microbial composition and function. A placebo-controlled, randomized, double-blind, crossover study was conducted with 120 participants. Two weeks of BL+IN intake significantly increased acetate, propionate, and butyrate concentrations and Bifidobacterium abundance compared to placebo. Functional analysis of the gut metagenome showed enrichment of genes associated with carbohydrate and amino acid metabolism, suggesting an enhanced capacity for SCFA production. A responder was defined as a participant with increased fecal SCFAs after BL+IN consumption. Responder metagenomes exhibited greater enrichment of genes involved in SCFA production and carbohydrate metabolism. In conclusion, short-term BL+IN ingestion may benefit healthy adults by increasing fecal SCFAs through influencing the composition and functional activation of SCFA-associated pathways in the gut microbiome.},
}

@article {pmid40366182,
year = {2025},
author = {Martin Říhová, J and Vodička, R and Hypša, V},
title = {An obligate symbiont of Haematomyzus elephantis with a strongly reduced genome resembles symbiotic bacteria in sucking lice.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0022025},
doi = {10.1128/aem.00220-25},
pmid = {40366182},
issn = {1098-5336},
abstract = {The parvorder Rhynchophthirina with a single genus Haematomyzus is a small group of ectoparasites of unclear phylogenetic position, related to sucking and chewing lice. Previous screening based on the 16S rRNA gene indicated that Haematomyzus harbors a symbiotic bacterium whose DNA exhibits a strong shift in nucleotide composition typical of obligate mutualistic symbionts in insects. Within Phthiraptera, the smallest known genomes are found in the symbionts associated with sucking lice, which feed exclusively on mammal blood, compared to the generally larger genomes of the symbionts inhabiting chewing lice, which feed on skin derivatives. In this study, we investigate the genome characteristics of the symbiont associated with Haematomyzus elephantis. We sequenced and assembled the H. elephantis metagenome, extracted a genome draft of its symbiotic bacterium, and showed that the symbiont has a significantly reduced genome, which is with 0.39 Mbp the smallest genome among the symbionts known from Phthiraptera. Multigenic phylogenetic analysis places the symbiont into one of three clusters composed of long-branched symbionts from other insects. More specifically, it clusters together with symbionts from several other sucking lice and also with Wigglesworthia glossinidia, an obligate symbiont of tsetse flies. Consistent with the dramatic reduction of its genome, the H. elephantis symbiont lost many metabolic capacities. However, it retained functional pathways for four B vitamins, a trait typical for symbionts in blood-feeding insects. Considering genomic, metabolic, and phylogenetic characteristics, the new symbiont closely resembles those known from several sucking lice rather than chewing lice.IMPORTANCERhynchophthirina is a unique small group of permanent ectoparasites that is closely related to both sucking and chewing lice. These two groups of lice differ in their morphology, ecology, and feeding strategies. As a consequence of their different dietary sources, i.e., mammals' blood vs vertebrate skin derivatives, they also exhibit distinct patterns of symbiosis with obligate bacterial symbionts. While Rhynchophthirina shares certain traits with sucking and chewing lice, the nature of its obligate symbiotic bacterium and its metabolic role is not known. In this study, we assemble the genome of symbiotic bacterium from Haematomyzus elephantis (Rhynchophthirina), demonstrating its close similarity and phylogenetic proximity to several symbionts of sucking lice. The genome is highly reduced (representing the smallest genome among louse-associated symbionts) and exhibits a significant loss of metabolic pathways. However, similar to other sucking louse symbionts, it retains essential pathways for the synthesis of several B vitamins.},
}

@article {pmid40366158,
year = {2025},
author = {Geonczy, SE and Hillary, LS and Santos-Medellín, C and Sorensen, JW and Emerson, JB},
title = {Patchy burn severity explains heterogeneous soil viral and prokaryotic responses to fire in a mixed conifer forest.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0174924},
doi = {10.1128/msystems.01749-24},
pmid = {40366158},
issn = {2379-5077},
abstract = {UNLABELLED: Effects of fire on soil viruses and virus-host dynamics are largely unexplored, despite known microbial contributions to biogeochemical processes and ecosystem recovery. Here, we assessed how viral and prokaryotic communities responded to a prescribed burn in a mixed conifer forest. We sequenced 91 viral-size fraction metagenomes (viromes) and 115 16S rRNA gene amplicon libraries from 120 samples: four samples at five timepoints (two before fire and three after fire) at six sites (four treatment, two control). We hypothesized that compositional differences would be most significant between burned and unburned soils, but instead, plot location best distinguished viral communities, more than treatment (burned or not), depth (0-3 or 3-6 cm), or timepoint. For both viruses and prokaryotes, some burned communities resembled unburned controls, while others were significantly different, revealing heterogeneous responses to fire. These patterns were explained by burn severity, here defined by soil chemistry. Viral but not prokaryotic richness decreased significantly with burn severity, and low viromic DNA yields indicated substantial loss of viral biomass at higher severity. The relative abundances of Firmicutes, Actinobacteriota, and the viruses predicted to infect them increased significantly with burn severity, suggesting survival and viral infection of these fire-responsive and potentially spore-forming taxa. The degree of burn severity experienced by each patch of soil, rather than burn status alone, differed over mere meters in the same fire. Therefore, our analyses highlight the importance of high-resolution, paired biogeochemical data to explain soil community responses to fire.

IMPORTANCE: The impact of fire on the soil microbiome, particularly on understudied soil viral communities, warrants investigation, given known microbial contributions to biogeochemical processes and ecosystem recovery. Here, we collected 120 soil samples before and after a prescribed burn in a mixed conifer forest to assess the impacts of this disturbance on soil viral and prokaryotic communities. We show that simple categorical comparisons of burned and unburned areas were insufficient to reveal the underlying community response patterns. The patchy nature of the fire (indicated by soil chemistry data) led to significant changes in viral and prokaryotic community composition in areas of high burn severity, while communities that experienced lower burn severity were indistinguishable from those in unburned controls. Our results highlight the importance of considering highly resolved burn severity and biogeochemical measurements, even in nearby soils after the same fire, in order to understand soil microbial responses to prescribed burns.},
}

@article {pmid40366141,
year = {2025},
author = {Li, J and Zheng, K and Ding, W and Lu, L and Liang, Y and Xiong, Y and Wei, Z and Gao, C and Su, Y and Wang, Z and Chen, X and Bao, Z and Hu, X and McMinn, A and Wang, M},
title = {Healthy and moribund Zhikong scallops (Chlamys farreri) developed different viral communities during a mass mortality event.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0034225},
doi = {10.1128/msystems.00342-25},
pmid = {40366141},
issn = {2379-5077},
abstract = {UNLABELLED: Viral assemblages of scallops are still relatively unknown. Here, metagenomic analysis was used to study virus communities in the gut of scallops to establish the first scallop virome data set (SVD); this contains 7,447 viral operational taxonomic units. Protein-sharing networks and phylogenetic analyses demonstrated the high diversity and novelty of the SVD, which is very different from viromes from other habitats. Potentially pathogenic viruses are prevalent in the gut of scallops. In particular, the novel smacoviruses were identified, indicating that scallops may be a potential hotspot for this viral group. Inference of virus-host associations found extensive interactions between viruses and major prokaryotic lineages. Intriguingly, moribund scallops showed a higher diversity of auxiliary metabolic genes (AMGs) related to amino acid metabolism and cofactor and vitamin genes, while healthy scallops had fewer AMGs, with those present focusing on secondary metabolite biosynthesis and carbohydrate metabolism. These findings provide the first landscape of scallop gut viruses based on metagenomes and highlight the potential roles of diverse and unique gut viruses for the health of filter-feeding bivalves.

IMPORTANCE: This study uses metagenome sequencing to establish the first scallop virome database. The study reveals previously unknown diversity of scallop-associated viruses and provides insights into links between disease status and viral diversity and genome content. The study will interest many aquatic virologists and could have important implications in managing marine resources.},
}

@article {pmid40366139,
year = {2025},
author = {Crouch, AL and Severance, BM and Creary, S and Hood, D and Bailey, M and Mejias, A and Ramilo, O and Gillespie, M and Ebelt, S and Sheehan, V and Kopp, BT and Anderson, MZ},
title = {Altered nasal and oral microbiomes define pediatric sickle cell disease.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0013725},
doi = {10.1128/msphere.00137-25},
pmid = {40366139},
issn = {2379-5042},
abstract = {UNLABELLED: Sickle cell disease (SCD) is a chronic blood disorder that disrupts multiple organ systems and can lead to severe morbidity. Persistent and acute symptoms caused by immune system dysregulation in individuals with SCD could contribute to disease either directly or indirectly via dysbiosis of commensal microbes and increased susceptibility to infection. Here, we explored the nasal and oral microbiomes of children with SCD (cwSCD) to uncover potential dysbiotic associations with the blood disorder. Microbiota collected from nasal and oral swabs of 40 cwSCD were compared to eight healthy siblings using shotgun metagenomic sequencing. Commensal taxa were present at similar levels in the nasal and oral microbiome of both groups. However, the nasal microbiomes of cwSCD contained a higher prevalence of Pseudomonadota species, including pathobionts such as Yersinia enterocolitica and Klebsiella pneumoniae. Furthermore, the oral microbiome of cwSCD displayed lower α-diversity and fewer commensal and pathobiont species compared to the healthy siblings. Thus, subtle but notable shifts seem to exist in the nasal and oral microbiomes of cwSCD, suggesting an interaction between SCD and the microbiome that may influence health outcomes.

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

@article {pmid40366134,
year = {2025},
author = {Gilbert, NE and Kimbrel, JA and Samo, TJ and Siccardi, AJ and Stuart, RK and Mayali, X},
title = {A bloom of a single bacterium shapes the microbiome during outdoor diatom cultivation collapse.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0037525},
doi = {10.1128/msystems.00375-25},
pmid = {40366134},
issn = {2379-5077},
abstract = {Algae-dominated ecosystems are fundamentally influenced by their microbiome. We lack information on the identity and function of bacteria that specialize in consuming algal-derived dissolved organic matter in high algal density ecosystems such as outdoor algal ponds used for biofuel production. Here, we describe the metagenomic and metaproteomic signatures of a single bacterial strain that bloomed during a population-wide crash of the diatom, Phaeodactylum tricornutum, grown in outdoor ponds. 16S rRNA gene data indicated that a single Kordia sp. strain (family Flavobacteriaceae) contributed up to 93% of the bacterial community during P. tricornutum demise. Kordia sp. expressed proteins linked to microbial antagonism and biopolymer breakdown, which likely contributed to its dominance over other microbial taxa during diatom demise. Analysis of accompanying downstream microbiota (primarily of the Rhodobacteraceae family) provided evidence that cross-feeding may be a pathway supporting microbial diversity during diatom demise. In situ and laboratory data with a different strain suggested that Kordia was a primary degrader of biopolymers during algal demise, and co-occurring Rhodobacteraceae exploited degradation molecules for carbon. An analysis of 30 Rhodobacteraceae metagenome assembled genomes suggested that algal pond Rhodobacteraceae commonly harbored pathways to use diverse carbon and energy sources, including carbon monoxide, which may have contributed to the prevalence of this taxonomic group within the ponds. These observations further constrain the roles of functionally distinct heterotrophic bacteria in algal microbiomes, demonstrating how a single dominant bacterium, specialized in processing senescing or dead algal biomass, shapes the microbial community of outdoor algal biofuel ponds.IMPORTANCEAquatic biogeochemical cycles are dictated by the activity of diverse microbes inhabiting the algal microbiome. Outdoor biofuel ponds provide a setting analogous to aquatic algal blooms, where monocultures of fast-growing algae reach high cellular densities. Information on the microbial ecology of this setting is lacking, and so we employed metagenomics and metaproteomics to understand the metabolic roles of bacteria present within four replicated outdoor ponds inoculated with the diatom Phaeodactylum tricornutum. Unexpectedly, after 29 days of cultivation, all four ponds crashed concurrently with a "bloom" of a single taxon assigned to the Kordia bacterial genus. We assessed how this dominant taxon influenced the chemical and microbial fate of the ponds following the crash, with the hypothesis that it was primarily responsible for processing senescent/dead algal biomass and providing the surrounding microbiota with carbon. Overall, these findings provide insight into the roles of microbes specialized in processing algal organic matter and enhance our understanding of biofuel pond microbial ecology.},
}

@article {pmid40366096,
year = {2025},
author = {Ragupathy, V and Kelley, K and Hewlett, I},
title = {Near-complete torque teno virus (TTV) genome identified in a blood donor infected with hepatitis B virus (HBV).},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0117824},
doi = {10.1128/mra.01178-24},
pmid = {40366096},
issn = {2576-098X},
abstract = {We have identified a near full-length torque teno virus (TTV) genome sequence in plasma from a blood donor infected with hepatitis B virus. The consensus sequence of TTV was extracted from Nanopore metagenomic sequencing. The identified TTV open reading frame 1 is 3,062 nucleotides (nt) long and shares 90%-100% identity with other human TTVs.},
}

@article {pmid40365535,
year = {2025},
author = {Li, M and Chen, J and Zhang, L and Chen, X and Zhou, J and Liu, F and Zhou, X and Xiao, J and Yang, K and Qi, L and Han, X and Liu, T and Zhao, H and Zhou, Z and Chen, X and Sun, L},
title = {Clinicopathological characteristics and diagnostic performance of metagenomic pathogen detection technology in mycobacterial infections among HIV patients.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1584189},
pmid = {40365535},
issn = {2235-2988},
mesh = {Humans ; Male ; Female ; *HIV Infections/complications ; Adult ; Middle Aged ; Mycobacterium tuberculosis/isolation & purification/genetics ; *Metagenomics/methods ; Sputum/microbiology ; *Mycobacterium Infections/diagnosis/microbiology/pathology ; Sensitivity and Specificity ; *Molecular Diagnostic Techniques/methods ; Mycobacterium Infections, Nontuberculous/diagnosis/microbiology ; Biopsy ; },
abstract = {BACKGROUND: Mycobacterial infections represent a major cause of morbidity and mortality in HIV-infected individuals. This study evaluated diagnostic techniques for mycobacterial identification and compared clinicopathological features between HIV-positive and HIV-negative patients.

METHODS: We analyzed 88 tissue samples (with 41 matched blood and 28 sputum samples) using histopathology (HE and acid-fast staining), bacterial culture, MTB-PCR (sputum/biopsy), PCR-reverse dot blot hybridization (RDBH), and metagenomic pathogen detection technology (MetaPath™). Logistic regression analyses were performed to identify factors affecting detection rates.

RESULTS: Mycobacterial infection was detected in 95.5% (84/88) of patients. Among HIV-positive patients (n=63), 46% (29/63) had Mycobacterium tuberculosis (MTB) infections, and 44% (28/63) had non-tuberculous mycobacteria (NTM) infections, significantly higher than the 20% (5/25) NTM rate in HIV-negative patients. Univariate analysis identified HIV-positive status (p=0.009), lymph node involvement (p=0.020), and positive MetaPath™ results (p=0.002) as significant predictors of detection, while multivariate analysis confirmed these as independent factors (p=0.036; p=0.042; p=0.006). Lymph nodes were the most common infection site in HIV-positive patients (42.9%, 27/63), while lung tissue predominated in HIV-negative patients (48%, 12/25). MetaPath™ demonstrated superior sensitivity and specificity for detecting both MTB and NTM. Biopsy samples provided higher diagnostic accuracy than sputum or blood for lung and lymph node infections, but not for brain. In HIV-positive patients, NTM infections showed significantly more granuloma formation (p=0.032) and foam cells (p=0.005), but less necrosis (p=0.0005) compared to MTB infections. No significant differences were observed in HIV-negative patients.

CONCLUSIONS: MetaPath™ is a highly effective diagnostic tool for mycobacterial infections, particularly in tissue biopsies. HIV-positive status, lymph node involvement, and MetaPath™ positivity independently predict mycobacterial detection. HIV-positive patients exhibit distinct clinicopathological features, emphasizing the need for tailored diagnostic and therapeutic approaches based on immune status.},
}

Humans
Male
Female
*HIV Infections/complications
Adult
Middle Aged
Mycobacterium tuberculosis/isolation & purification/genetics
*Metagenomics/methods
Sputum/microbiology
*Mycobacterium Infections/diagnosis/microbiology/pathology
Sensitivity and Specificity
*Molecular Diagnostic Techniques/methods
Mycobacterium Infections, Nontuberculous/diagnosis/microbiology
Biopsy

@article {pmid40365473,
year = {2025},
author = {Pu, T and Tan, Y and Zhao, Y and Zhao, Z and Zhang, N and Li, C and Song, Y},
title = {Effect of Seasonal Variations on Soil Microbial, Extracellular Enzymes, and Ecological Stoichiometry in Tea Plantations.},
journal = {Ecology and evolution},
volume = {15},
number = {5},
pages = {e71362},
pmid = {40365473},
issn = {2045-7758},
abstract = {Tea plantations are important agricultural ecosystems in karst areas, yet the seasonal dynamics of soil microbial communities, functional genes, and extracellular enzyme activities (EEA) under different management practices remain poorly understood. This study investigated organic (HY), pollution-free (TS), and conventional (XY) tea plantations in Weng'an County, Southwest China, during the spring (April) and autumn (August) tea seasons via metagenomics and stoichiometric analyses. Seasonal variations significantly altered the soil physicochemical properties (e.g., SOC, TN, and TP) and EEA (p < 0.05), with higher C-acquiring enzyme activity in autumn and elevated soil C:N:P ratios in spring. The soil extracellular enzyme stoichiometry (EES C:N:P) deviated from the theoretical 1:1:1 ratio, indicating that microbial metabolism was constrained by soil resource availability rather than homeostasis. Phosphorus limitation (vector angle > 45°) persisted across seasons, contradicting initial hypotheses, with acid phosphatase (ACP) activity and EES C:P identified as critical drivers. Random forest (RF) and structural equation modeling (SEM) revealed that the spring season had stronger impacts on microbial communities and functional genes, with the soil TN, C:N, NAG, ACP, and EES C:P ratios as key predictors. Compared with conventional practices, organic management enhances microbial diversity and functional redundancy, buffering seasonal fluctuations. These findings highlight the interplay between seasonal climatic shifts and agricultural practices regulating soil nutrient cycling and microbial adaptation. Strategic interventions-such as spring carbon supplementation, autumn organic phosphorus fertilization, and intercropping-are proposed to optimize microbial resilience and ecosystem stability in fragile karst tea plantations. This study provides novel insights into soil ecological stoichiometry and microbial metabolic strategies, offering a reference for the sustainable management of agroecosystems in karst areas.},
}

@article {pmid40365061,
year = {2025},
author = {Liu, L and Wang, Z and Luo, C and Deng, Y and Wu, W and Jin, Y and Wang, Y and Huang, H and Wei, Z and Zhu, Y and He, X and Guo, L},
title = {Beneficial soil microbiome profiles assembled using tetramycin to alleviate root rot disease in Panax notoginseng.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1571684},
pmid = {40365061},
issn = {1664-302X},
abstract = {BACKGROUND: Root rot disease is a major threat to the sustainable production of Panax notoginseng. Tetramycin has a broad-spectrum fungicidal efficacy, low toxicity, and high efficiency, However, the prevention and control of root rot disease of P. notoginseng and the specific mechanism of action are still unclear.

METHODS: In this paper, a combination of indoor and pot experiments was used to assess the effectiveness of tetramycin at alleviating root rot disease challenges encountered by P. notoginseng. Amplicon sequencing, metagenomic analysis with microbial verification were used to investigate the microecological mechanisms underlying tetramycin's ability to reduce soil biological barriers.

RESULTS: We found that tetramycin significantly inhibited mycelial growth and spore germination of pathogenic fungi. Tetramycin, T2 (1000×) and T3 (500×), applied to continuous cropping soil, increased the seedling survival rates of P. notoginseng. Additionally, tetramycin reduced fungal α-diversity and shifted the fungal community assembly from deterministic to stochastic process. The microbial functions influenced by tetramycin were primarily associated with antibiotic synthesis and siderophore synthesis. Antibiotic efflux and inactivation have also been identified as the main resistance mechanisms. Microbial verification results showed that the artificially assembled tetramycin-regulated microbial community could indeed alleviate the occurrence of diseases. Furthermore, the cross-kingdom synthetic community assembled by the three key strains (Pseudomonas aeruginosa, Variovorax boronicumulans, and Cladosporium cycadicola) significantly improved the control of root rot disease and promoted plant growth.

DISCUSSION: This study provides novel insights into developing efficient biological control strategies and elucidates the role and mechanism of tetramycin in modulating soil microflora assembly to strengthen host disease resistance.},
}

@article {pmid40364394,
year = {2025},
author = {Cao, K and Shi, P and Xu, X and Wang, J},
title = {Self-Inhibition Effects of Litter-Mediated Plant-Phyllosphere Feedback on Seedling Growth in Invasive and Native Congeneric Species.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/plants14091355},
pmid = {40364394},
issn = {2223-7747},
abstract = {Plant-phyllosphere feedback (PPF) is an ecological process in which phyllosphere microbiota, originating from plant litter, are transmitted via aerosols and subsequently influence the growth of conspecific or heterospecific plants. However, the cross-species generality of this mechanism and its role in invasive plant success remain to be fully elucidated. This study systematically examined PPF effects using three invasive/native congeneric plant pairs from distinct families (Phytolaccaceae, Asteraceae, and Amaranthaceae) in Jiangxi Province, China. Key findings include the following: (1) Wide conspecific negative feedback across families, with four of six species exhibiting 6.2-12.7% biomass reduction under their own litter treatments (p < 0.05). (2) Comparable feedback intensity between invasive and native species, as indicated by average pairwise indices (invasive I = -0.05 vs. native I = -0.04; p = 0.15). Notably, the invasive species Phytolacca americana uniquely showed a positive biomass response (+7.1%), though underlying mechanisms (phytochemical or microbial) were not investigated. (3) Lack of correlation between PPF strength and plant functional traits or phylogenetic distance, as indicated by Mantel tests (p > 0.8), in contrast to the trait/phylogeny associations commonly observed in soil feedback systems. This study provided the first evidence of PPF universality across multiple plant families-previously documented only within Asteraceae-and highlights the potential microbial-mediated advantages in plant invasions. Future research should integrate spatiotemporal metagenomic and metabolomic approaches to decipher the dynamic pathogen/microbe networks and their phytochemical interactions.},
}

@article {pmid40363788,
year = {2025},
author = {Zhou, L and Li, J and Ding, C and Zhou, Y and Xiao, Z},
title = {Mechanistic Advances in Hypoglycemic Effects of Natural Polysaccharides: Multi-Target Regulation of Glycometabolism and Gut Microbiota Crosstalk.},
journal = {Molecules (Basel, Switzerland)},
volume = {30},
number = {9},
pages = {},
doi = {10.3390/molecules30091980},
pmid = {40363788},
issn = {1420-3049},
support = {2024JJ8163//Hunan Natural Science Foundation/ ; C2023005//Key Project of Hunan Provincial Administration of Traditional Chinese Medicine/ ; 201923//Key Project of Hunan Provincial Administration of Traditional Chinese Medicine/ ; 2022ZYYGN06//2022 Annual Natural Drug Resources and Function Development Fund Project/ ; },
mesh = {*Gastrointestinal Microbiome/drug effects ; Humans ; *Polysaccharides/pharmacology/chemistry/therapeutic use ; Animals ; *Hypoglycemic Agents/pharmacology/chemistry/therapeutic use ; Signal Transduction/drug effects ; Insulin Resistance ; Glucose/metabolism ; },
abstract = {Natural polysaccharides (NPs), as a class of bioactive macromolecules with multitarget synergistic regulatory potential, exhibit significant advantages in diabetes intervention. This review systematically summarizes the core hypoglycemic mechanisms of NPs, covering structure-activity relationships, integration of the gut microbiota-metabolism-immunity axis, and regulation of key signaling pathways. Studies demonstrate that the molecular weight, branch complexity, and chemical modifications of NPs mediate their hypoglycemic activity by influencing bioavailability and target specificity. NPs improve glucose metabolism through multiple pathways: activating insulin signaling, improving insulin resistance (IR), enhancing glycogen synthesis, inhibiting gluconeogenesis, and regulating gut microbiota homeostasis. Additionally, NPs protect pancreatic β-cell function via the nuclear factor E2-related factor 2 (Nrf2)/Antioxidant Response Element (ARE) antioxidant pathway and Toll-like receptor 4 (TLR4)/nuclear factor-κB (NF-κB) anti-inflammatory pathway. Clinical application of NPs still requires overcoming challenges such as resolving complex structure-activity relationships and dynamically integrating cross-organ signaling. Future research should focus on integrating multi-omics technologies (e.g., metagenomics, metabolomics) and organoid models to decipher the cross-organ synergistic action networks of NPs, and promote their translation from basic research to clinical applications.},
}

*Gastrointestinal Microbiome/drug effects
Humans
*Polysaccharides/pharmacology/chemistry/therapeutic use
Animals
*Hypoglycemic Agents/pharmacology/chemistry/therapeutic use
Signal Transduction/drug effects
Insulin Resistance
Glucose/metabolism

@article {pmid40362493,
year = {2025},
author = {Žukienė, G and Narutytė, R and Rudaitis, V},
title = {Association Between Vaginal Microbiota and Cervical Dysplasia Due to Persistent Human Papillomavirus Infection: A Systematic Review of Evidence from Shotgun Metagenomic Sequencing Studies.},
journal = {International journal of molecular sciences},
volume = {26},
number = {9},
pages = {},
doi = {10.3390/ijms26094258},
pmid = {40362493},
issn = {1422-0067},
mesh = {Humans ; Female ; *Papillomavirus Infections/complications/microbiology/virology ; *Vagina/microbiology/virology ; *Microbiota/genetics ; Metagenomics/methods ; *Uterine Cervical Dysplasia/microbiology/virology/etiology ; Papillomaviridae ; Dysbiosis/microbiology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The role of vaginal dysbiosis in the progression of human papilloma virus (HPV) associated cervical lesions has gained attention in recent years. While many studies use 16S rRNA gene sequencing for microbiota analysis, shotgun metagenomic sequencing offers higher taxonomic resolution and insights into microbial gene functions and pathways. This systematic review evaluates the relationship between compositional and functional changes in the vaginal microbiome during HPV infection and cervical lesion progression. A literature search was performed according to PRISMA guidelines in PubMed, Web of Science, Scopus, and ScienceDirect databases. Seven studies utilizing metagenomic sequencing in patients with HPV infection or HPV-associated cervical lesions were included. Progression from HPV infection to cervical lesions and cancer was associated with a reduction in Lactobacillus species (particularly Lactobacillus crispatus) and an enrichment of anaerobic and pathogenic species, especially Gardnerella vaginalis. Heterogeneous enriched metabolic pathways were also identified, indicating functional shifts during lesion progression. As most studies were conducted in Asia, further research in diverse regions is needed to improve the generalizability of findings. Future studies employing metagenomic sequencing may help identify biomarkers for early pre-cancerous lesions and clarify the role of vaginal microbiota in persistent HPV infection and cervical dysplasia.},
}

Humans
Female
*Papillomavirus Infections/complications/microbiology/virology
*Vagina/microbiology/virology
*Microbiota/genetics
Metagenomics/methods
*Uterine Cervical Dysplasia/microbiology/virology/etiology
Papillomaviridae
Dysbiosis/microbiology
RNA, Ribosomal, 16S/genetics

@article {pmid40362462,
year = {2025},
author = {Chakraborty, N and Holmes-Hampton, G and Rusling, M and Kumar, VP and Hoke, A and Lawrence, AB and Gautam, A and Ghosh, SP and Hammamieh, R},
title = {Delayed Impact of Ionizing Radiation Depends on Sex: Integrative Metagenomics and Metabolomics Analysis of Rodent Colon Content.},
journal = {International journal of molecular sciences},
volume = {26},
number = {9},
pages = {},
doi = {10.3390/ijms26094227},
pmid = {40362462},
issn = {1422-0067},
support = {xxxxx//AFRRI/ ; },
mesh = {Animals ; Male ; Female ; Mice ; *Metabolomics/methods ; *Metagenomics/methods ; *Radiation, Ionizing ; *Colon/radiation effects/metabolism/microbiology ; *Gastrointestinal Microbiome/radiation effects ; Sex Factors ; Whole-Body Irradiation/adverse effects ; Mice, Inbred C57BL ; },
abstract = {There is an escalating need to comprehend the long-term impacts of nuclear radiation exposure since the permeation of ionizing radiation has been frequent in our current societal framework. A system evaluation of the microbes that reside inside a host's colon could meet this knowledge gap since the microbes play major roles in a host's response to stress. Indeed, our past study suggested that these microbes might break their symbiotic association with moribund hosts to form a pro-survival condition exclusive to themselves. In this study, we undertook metagenomics and metabolomics assays regarding the descending colon content (DCC) of adult mice. DCCs were collected 1 month and 6 months after 7 Gy or 7.5 Gy total body irradiation (TBI). The assessment of the metagenomic diversity profile in DCC found a significant sex bias caused by TBI. Six months after 7.5 Gy TBI, decreased Bacteroidetes were replaced by increased Firmicutes in males, and these alterations were reflected in the functional analysis. For instance, a larger number of networks linked to small chain fatty acid (SCFA) synthesis and metabolism were inhibited in males than in females. Additionally, bioenergy networks showed regression dynamics in females at 6 months post-TBI. Increased accumulation of glucose and pyruvate, which are typical precursors of beneficial SCFAs coupled with the activated networks linked to the production of reactive oxygen species, suggest a cross-sex energy-deprived state. Overall, there was a major chronic adverse implication in male mice that supported the previous literature in suggesting females are more radioresistant than males. The sex-biased chronic effects of TBI should be taken into consideration in designing the pertinent therapeutics.},
}

Animals
Male
Female
Mice
*Metabolomics/methods
*Metagenomics/methods
*Radiation, Ionizing
*Colon/radiation effects/metabolism/microbiology
*Gastrointestinal Microbiome/radiation effects
Sex Factors
Whole-Body Irradiation/adverse effects
Mice, Inbred C57BL

@article {pmid40362406,
year = {2025},
author = {Krivonos, DV and Fedorov, DE and Konanov, DN and Vvedensky, AV and Sonets, IV and Korneenko, EV and Speranskaya, AS and Ilina, EN},
title = {Pike: OTU-Level Analysis for Oxford Nanopore Amplicon Metagenomics.},
journal = {International journal of molecular sciences},
volume = {26},
number = {9},
pages = {},
doi = {10.3390/ijms26094168},
pmid = {40362406},
issn = {1422-0067},
support = {24-15-00419//Russian Science Foundation/ ; },
mesh = {*Metagenomics/methods ; Fungi/genetics/classification ; *Nanopore Sequencing/methods ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification ; Algorithms ; Metagenome ; *Nanopores ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; *Software ; },
abstract = {The Oxford Nanopore platform and nanopore sequencing are gaining increasing popularity in modern metagenomic research. However, there is a limited set of dedicated tools for analyzing this type of data. The tools used for nanopore amplicon sequencing data analysis often provide only taxonomy annotation without OTU sequence assembly. Conversely, tools that facilitate OTU assembly are constrained in their analysis to long reads, such as the V1-V9 regions of 16S rRNA for bacterial community studies or the full-length ITS cluster (ITS1-5.8S-ITS2) for fungal community studies. In other cases, researchers propose their own solutions without dedicated tools. In this paper, we present Pike, a novel tool for analyzing Oxford Nanopore amplicon sequencing data. Pike allows analysis without amplicon size limitations and allows de novo assembly of OTU sequences. In our research, we created mock communities of fungi and bacteria, which we then used to demonstrate the efficiency of our algorithm. Furthermore, we validated the algorithm using externally available data. We also compared our approach with similar ones to show its applicability.},
}

*Metagenomics/methods
Fungi/genetics/classification
*Nanopore Sequencing/methods
RNA, Ribosomal, 16S/genetics
Bacteria/genetics/classification
Algorithms
Metagenome
*Nanopores
High-Throughput Nucleotide Sequencing/methods
Sequence Analysis, DNA/methods
*Software

@article {pmid40361215,
year = {2025},
author = {Ma, Y and Jiang, J and Yang, Z and Li, Y and Bai, H and Liu, Z and Zhang, S and Zhi, Z and Yang, Q},
title = {Changes of gastric microflora and metabolites in patients with chronic atrophic gastritis.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {537},
pmid = {40361215},
issn = {1479-5876},
support = {No.21377724D//Hebei Provincial Department of Science and Technology/ ; No. 18//National Administration of Traditional Chinese Medicine Science and Technology/ ; 246W7701D//Provincial Science and Technology Plan of Hebei Province/ ; },
mesh = {Humans ; *Gastritis, Atrophic/microbiology/metabolism ; Chronic Disease ; Middle Aged ; Female ; Male ; RNA, Ribosomal, 16S/genetics ; Metabolome ; *Stomach/microbiology ; Metabolomics ; *Microbiota ; Bacteria/genetics/metabolism ; Adult ; Aged ; *Gastrointestinal Microbiome ; },
abstract = {BACKGROUND: Chronic atrophic gastritis (CAG) is related to the body's microbial and metabolic systems. Combined studies of microbiome and metabolomics can clarify the mechanisms of disease occurrence and progression. We used 16S rRNA sequencing, metagenomics sequencing and metabolomics sequencing to depict the landscapes of bacterium and metabolites, construct correlation networks of different bacterium and metabolites describe potential pathogenic mechanisms of chronic atrophic gastritis.

METHODS: The gastric juices of 30 non-atrophic gastritis (NAG) patients and 30 CAG patients were collected. Gastric microflora was analyzed by 16S rRNA sequencing and metagenomics sequencing. Gastric metabolites were analyzed by LC-MS analysis. Different bioinformatics methods were used to analyze the data of microbiome and metabolome, and to analyze the relationship between them.

RESULTS: In atrophic gastritis, bacteria diversity decreased. The genera with a mean decrease in Gini greater than 1.5 included peptostreptococcus, fusobacterium, prevotella, sphingomonas and bacteroides. KEGG pathway included renal cell carcinoma, proximal tubule bicarbonate reclamation, citrate cycle and aldosterone synthesis and secretion with significant enrichment of differential metabolites. Peptostreptococcus, fusobacterium, prevotella and sphingomonas were in pivot positions of the correlation network of differential metabolites and differential bacterium. Viral carcinogenesis, glycine serine and threonine metabolism, RNA polymerase, galactose metabolism and retinol metabolism were enriched in chronic atrophic gastritis based on the metagenomic sequencing data.

CONCLUSION: Peptostreptococcus, fusobacterium, prevotella, sphingomonas and bacteroides were the essential features that distinguish atrophic gastritis from non-atrophic gastritis, and caused disease by altering various metabolic pathways. Viral carcinogenesis, glycine serine and threonine metabolism, RNA polymerase, galactose metabolism and retinol metabolism may be related to the occurrence and progression of CAG.},
}

Humans
*Gastritis, Atrophic/microbiology/metabolism
Chronic Disease
Middle Aged
Female
Male
RNA, Ribosomal, 16S/genetics
Metabolome
*Stomach/microbiology
Metabolomics
*Microbiota
Bacteria/genetics/metabolism
Adult
Aged
*Gastrointestinal Microbiome

@article {pmid40360994,
year = {2025},
author = {Zhai, R and Zhao, C and Chang, L and Liu, J and Zhao, T and Jiang, J and Zhu, W},
title = {The gut-liver axis plays a limited role in mediating the liver's heat susceptibility of Chinese giant salamander.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {475},
pmid = {40360994},
issn = {1471-2164},
support = {31900327//National Natural Science Foundation of China/ ; 2023NSFSC1153//Natural Science Foundation of Sichuan Province of China/ ; },
mesh = {Animals ; *Liver/metabolism ; *Gastrointestinal Microbiome ; *Caudata/physiology/genetics/microbiology ; Heat-Shock Response ; Transcriptome ; Gene Expression Profiling ; Energy Metabolism ; Larva ; },
abstract = {The Chinese giant salamander (CGS, Andrias davidianus), a flagship amphibian species, is highly vulnerable to high temperatures, posing a significant threat under future climate change. Previous research linked this susceptibility to liver energy deficiency, accompanied by shifts in gut microbiota and reduced food conversion rates, raising questions about the role of the gut-liver axis in mediating heat sensitivity. This study investigated the responses of Chinese giant salamander larvae to a temperature gradient (10-30 °C), assessing physiological changes alongside histological, gut metagenomic, and tissue transcriptomic analyses. Temperatures above 20 °C led to mortality, which resulted in delayed growth. Histological and transcriptomic data revealed metabolic exhaustion and liver fibrosis in heat-stressed salamanders, underscoring the liver's critical role in heat sensitivity. While heat stress altered the gut microbiota's community structure, their functional profiles, especially in nutrient absorption and transformation, remained stable. Both gut and liver showed temperature-dependent transcriptional changes, sharing some common variations in actins, heat shock proteins, and genes related to transcription and translation. However, their energy metabolism exhibited opposite trends: it was downregulated in the liver but upregulated in the gut, with the gut showing increased activity in the pentose phosphate pathway and oxidative phosphorylation, potentially countering metabolic exhaustion. Our findings reveal that the liver of the larvae exhibits greater thermal sensitivity than the gut, and the gut-liver axis plays a limited role in mediating thermal intolerance. This study enhances mechanistic understanding of CGS heat susceptibility, providing a foundation for targeted conservation strategies in the face of climate change.},
}

Animals
*Liver/metabolism
*Gastrointestinal Microbiome
*Caudata/physiology/genetics/microbiology
Heat-Shock Response
Transcriptome
Gene Expression Profiling
Energy Metabolism
Larva

@article {pmid40360555,
year = {2025},
author = {Baek, JW and Lim, S and Park, N and Song, B and Kirtipal, N and Nielsen, J and Mardinoglu, A and Shoaie, S and Kim, JI and Son, JW and Koh, A and Lee, S},
title = {Extensively acquired antimicrobial-resistant bacteria restructure the individual microbial community in post-antibiotic conditions.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {78},
pmid = {40360555},
issn = {2055-5008},
support = {2021R1C1C1006336, 2021M3A9G8022959, RS-2024-00419699//National Research Foundation of Korea/ ; 2021R1C1C1006336, 2021M3A9G8022959, RS-2024-00419699//National Research Foundation of Korea/ ; 2021R1C1C1006336, 2021M3A9G8022959, RS-2024-00419699//National Research Foundation of Korea/ ; 2021R1C1C1006336, 2021M3A9G8022959, RS-2024-00419699//National Research Foundation of Korea/ ; 2021R1C1C1006336, 2021M3A9G8022959, RS-2024-00419699//National Research Foundation of Korea/ ; 2021R1C1C1006336, 2021M3A9G8022959, RS-2024-00419699//National Research Foundation of Korea/ ; HR22C141105//the Korea Health Industry Development Institute/ ; HR22C141105//the Korea Health Industry Development Institute/ ; HR22C141105//the Korea Health Industry Development Institute/ ; HR22C141105//the Korea Health Industry Development Institute/ ; HR22C141105//the Korea Health Industry Development Institute/ ; HR22C141105//the Korea Health Industry Development Institute/ ; 2024-ER2108-00, 2024-ER0608-00//Korea National Institute of Health/ ; 2024-ER2108-00, 2024-ER0608-00//Korea National Institute of Health/ ; 2024-ER2108-00, 2024-ER0608-00//Korea National Institute of Health/ ; 2024-ER2108-00, 2024-ER0608-00//Korea National Institute of Health/ ; 2024-ER2108-00, 2024-ER0608-00//Korea National Institute of Health/ ; 2024-ER2108-00, 2024-ER0608-00//Korea National Institute of Health/ ; 2024-ER2108-00, 2024-ER0608-00//Korea National Institute of Health/ ; GIST-MIT research Collaboration grant//GIST Research Institute/ ; GIST-MIT research Collaboration grant//GIST Research Institute/ ; GIST-MIT research Collaboration grant//GIST Research Institute/ ; GIST-MIT research Collaboration grant//GIST Research Institute/ ; GIST-MIT research Collaboration grant//GIST Research Institute/ ; GIST-MIT research Collaboration grant//GIST Research Institute/ ; },
mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; *Bacteria/drug effects/genetics/classification/isolation & purification ; *Gastrointestinal Microbiome/drug effects/genetics ; *Drug Resistance, Bacterial ; Metagenome ; *Microbiota/drug effects ; Microbial Sensitivity Tests ; Metagenomics ; },
abstract = {In recent years, the overuse of antibiotics has led to the emergence of antimicrobial-resistant (AMR) bacteria. To evaluate the spread of AMR bacteria, the reservoir of AMR genes (resistome) has been identified in environmental samples, hospital environments, and human populations, but the functional role of AMR bacteria and their persistence within individuals has not been fully investigated. Here, we performed a strain-resolved in-depth analysis of the resistome changes by reconstructing a large number of metagenome-assembled genomes from the gut microbiome of an antibiotic-treated individual. Interestingly, we identified two bacterial populations with different resistome profiles: extensively acquired antimicrobial-resistant bacteria (EARB) and sporadically acquired antimicrobial-resistant bacteria, and found that EARB showed broader drug resistance and a significant functional role in shaping individual microbiome composition after antibiotic treatment. Our findings of AMR bacteria would provide a new avenue for controlling the spread of AMR bacteria in the human community.},
}

Humans
*Anti-Bacterial Agents/pharmacology
*Bacteria/drug effects/genetics/classification/isolation & purification
*Gastrointestinal Microbiome/drug effects/genetics
*Drug Resistance, Bacterial
Metagenome
*Microbiota/drug effects
Microbial Sensitivity Tests
Metagenomics

@article {pmid40360028,
year = {2025},
author = {Fang, B and Liu, YF and Wei, HX and Zhou, L and Yang, SZ and Gu, JD and Mu, BZ},
title = {Enhancing methanogenesis from long-chain fatty acids (LCFA) and enrichment of novel bacteria with resuscitation-promoting factors.},
journal = {Bioresource technology},
volume = {432},
number = {},
pages = {132663},
doi = {10.1016/j.biortech.2025.132663},
pmid = {40360028},
issn = {1873-2976},
abstract = {Long-chain fatty acids (LCFA) are important intermediate metabolites in lipid hydrolysis during anaerobic digestion for biogas production. High LCFA loads inhibit microbial activity by toxicity, impairing the coupling of β-oxidation and methanogenesis, thus reducing LCFA degradation efficiency. This study employed and tested seven stimulants, including the resuscitation-promoting factors (Rpf and YeaZ), the quorum-sensing molecules (cAMP, and AHLs), the chemical stimulants (pyruvate), the growth promoter (fumarate), and yeast extract + peptone (YP) for enhancement of methanogenic degradation of LCFA. The results indicate that the chemical stimulants and resuscitation-promoting factors enhanced maximum methane-production rate 1.58 to 2.20 fold versus the NS, reducing the lag phase by 1.46-9.76 days. Analysis of the microbial community composition revealed that the quorum sensing factors only increased species richness, while Rpf, YeaZ fumarate, and YP stimulated the growth of core members of the communities. Metagenomic analysis detected three previously unreported LCFA-degrading bacterial taxa, Marinisomatota, Thermoanaerobaculaceae and Pelomonas. Particularly, Rpf and YeaZ significantly enriched LCFA-degrading bacteria such as Syntrophomonadaceae, Leptospiraceae, and Marine Group B within the core species, while YeaZ also stimulated methanogenic bacteria, possibly due to resuscitating dormant microbes from unfavorable conditions. Syntrophic interactions between LCFA degraders and non-degraders, rather than methanogen abundance, govern methanogenic LCFA degradation. These results demonstrate that the use of stimulants is an effective approach to enhance LCFA degradation and provide a new pathway for energy recovery.},
}

@article {pmid40359864,
year = {2025},
author = {Fan, M and Li, H and Liu, C and Du, L and Xu, Y and Chen, Y},
title = {Insights into the molecular mechanism on high salt tolerance of electroactive microorganisms collaborated by biochar supported cerium dioxide.},
journal = {Journal of environmental management},
volume = {386},
number = {},
pages = {125679},
doi = {10.1016/j.jenvman.2025.125679},
pmid = {40359864},
issn = {1095-8630},
abstract = {Electroactive microorganisms are a promising approach for treating high-salinity organic wastewater, however, they are highly susceptible to salt stress, which can compromise their metabolic activity. In this paper, biochar supported nano-cerium dioxide catalyst (BC-CeO2) was prepared to strengthen electroactive microorganisms in high salt environment. It was found that BC-CeO2 significantly improved the bioelectrochemical and metabolic activity of microorganisms in high salt environment (600 mM NaCl) compared with the Control. At the initial stage of the reaction, the maximum power density of microbial fuel cells (MFCs) reached 343.21 mW/m[2], and the degradation efficiency of norfloxacin (NOR) was 64.8 %, which was 1.7 times that of the Control. The analysis of microbial antioxidant properties demonstrated that BC-CeO2 could significantly increase the activities of superoxide dismutase (SOD) and catalase (CAT), effectively enhancing the ability of microorganisms to scavenge reactive oxygen species produced by salt stress. Metagenomic analysis revealed that the abundance of KEGG pathways conducive to microbial growth and metabolism under BC-CeO2 was relatively high, such as biosynthesis of amino acids (ko01230), microbial metabolism in diverse environments (ko01120) and so on. The enrichment of salt tolerant genes further illustrated the strengthening effect of BC-CeO2 on microbial adaptation to high salt environment, including genes related to NADH ubiquinone oxidoreductase, Na[+]/H[+] antiporter, intracellular small molecule compatible substance synthesis and transport related enzyme system and K[+] transporter related genes. Furthermore, the activity changes of Na[+]/K[+]-ATPase, which regulates cell permeability, in different environments also confirmed this point. This paper provides an effective strategy for enhancing the treatment of high-salt organic wastewater by electroactive microorganisms.},
}

@article {pmid40359746,
year = {2025},
author = {Bansal, M and Santhiya, D and Sharma, JG},
title = {Simulated dump yard microbes drive significant biodegradation of polypropylene and polyvinyl chloride microplastics.},
journal = {Journal of hazardous materials},
volume = {494},
number = {},
pages = {138545},
doi = {10.1016/j.jhazmat.2025.138545},
pmid = {40359746},
issn = {1873-3336},
abstract = {Bacterial culture isolates were used to demonstrate the breakdown of polypropylene (PPs) and polyvinyl chloride (PVCs) microplastics for the first time. Using metagenomics and phylogenetic analysis, bacterial isolates were discovered from a simulated dump yard. PPs and PVCs were broken down using bacterial isolates found to be Acinetobacter baumannii and mixed culture species with a Bacillus sp. dominance. After 50 days of activity, the dry weight of microplastics decreased by 33.3 % (PPs) and 27.1 % (PVCs) due to the breakdown process aided by Acinetobacter baumannii. Weight reductions of 20.3 % for PPs and 18.2 % for PVCs have been observed in mixed bacterial cultures, respectively. Microplastics' thermal stability and transition properties changed, according to experiments like DTG NMR, Raman, and WCA. FTIR analysis captured the structural changes in PPs and PVCs. SEM, TEM, and cell hydrophobicity tests showed that microplastics were biodegrading. GC-MS identified the released byproducts, which included carboxylic acids, alkanes, esters, and aromatic chemicals. Based on these findings, it can be concluded that bacterial isolates are effective in degrading PPs and PVCs and may help create sustainable methods of handling plastic trash.},
}

@article {pmid40359745,
year = {2025},
author = {Yang, T and Gong, X and Xu, A and Wang, B and Huang, Z and Wang, C and Gao, D},
title = {Integrated evaluation for advanced removal of nitrate using novel solid carbon biochar/corncob/PHBV composite: Insight into electron transfer and metabolic pathways.},
journal = {Journal of hazardous materials},
volume = {494},
number = {},
pages = {138549},
doi = {10.1016/j.jhazmat.2025.138549},
pmid = {40359745},
issn = {1873-3336},
abstract = {This study developed a novel Biochar/Corncob/PHBV (BCP) composite material, integrating the electron transfer capability of biochar, the cost-effectiveness of corncob, and the sustained carbon release performance of PHBV. The BCP system achieved a maximum nitrate removal efficiency of 97.3 %, significantly outperforming the single PHBV system (91.05 %), while effectively reducing nitrous oxide and other greenhouse gas emissions. It also demonstrated stable carbon release and enhanced electron transfer capabilities, contributing to a more sustainable denitrification process. The physical and chemical characterization of BCP confirmed that its superior performance is attributed to the uniformly distributed functional groups (e.g., CO and -COOH) on the surface and its porous structure, which facilitated electron transfer and microbial adhesion. Metagenomic and microbial analyses further revealed that BCP enriched functional genera such as Cellulomonas and Chryseobacterium and significantly increased the abundance of key functional genes related to nitrate reduction (e.g., NaR and NiR), enhancing organic matter decomposition and microbial nitrogen transformation. Beyond improving nitrate removal efficiency compared to PHBV, the BCP material offers practical engineering value by addressing carbon source limitations in long-term wastewater treatment applications. Its enhanced electron transfer and microbial enrichment suggest strong potential for application in constructed wetlands, biofilters, and other decentralized wastewater treatment systems. The study demonstrates that the BCP composite is not only a viable alternative to traditional PHBV but also a cost-effective and environmentally friendly material with broad applicability in nitrogen pollution control.},
}

@article {pmid40359589,
year = {2025},
author = {Silva, MKP and Nicoleti, VYU and Rodrigues, BDPP and Araujo, ASF and Ellwanger, JH and de Almeida, JM and Lemos, LN},
title = {Exploring deep learning in phage discovery and characterization.},
journal = {Virology},
volume = {609},
number = {},
pages = {110559},
doi = {10.1016/j.virol.2025.110559},
pmid = {40359589},
issn = {1096-0341},
abstract = {Bacteriophages, or bacterial viruses, play diverse ecological roles by shaping bacterial populations and also hold significant biotechnological and medical potential, including the treatment of infections caused by multidrug-resistant bacteria. The discovery of novel bacteriophages using large-scale metagenomic data has been accelerated by the accessibility of deep learning (Artificial Intelligence), the increased computing power of graphical processing units (GPUs), and new bioinformatics tools. This review addresses the recent revolution in bacteriophage research, ranging from the adoption of neural network algorithms applied to metagenomic data to the use of pre-trained language models, such as BERT, which have improved the reconstruction of viral metagenome-assembled genomes (vMAGs). This article also discusses the main aspects of bacteriophage biology using deep learning, highlighting the advances and limitations of this approach. Finally, prospects of deep-learning-based metagenomic algorithms and recommendations for future investigations are described.},
}

@article {pmid40359177,
year = {2025},
author = {, },
title = {Editorial Note: Extensive culturomics of 8 healthy samples enhances metagenomics efficiency.},
journal = {PloS one},
volume = {20},
number = {5},
pages = {e0324350},
doi = {10.1371/journal.pone.0324350},
pmid = {40359177},
issn = {1932-6203},
}

@article {pmid40359062,
year = {2025},
author = {Jules, E and Decker, C and Bixler, BJ and Ahmed, A and Zhou, ZC and Arora, I and Tafesse, H and Dakanay, H and Bombin, A and Wang, E and Ingersoll, J and Bifulco, K and Frediani, JK and Parsons, R and Sullivan, J and Greenleaf, M and Waggoner, JJ and Martin, GS and Lam, WA and Piantadosi, A},
title = {Respiratory Virus Detection and Sequencing from SARS-CoV-2-Negative Rapid Antigen Tests.},
journal = {Emerging infectious diseases},
volume = {31},
number = {13},
pages = {39-44},
doi = {10.3201/eid3113.241191},
pmid = {40359062},
issn = {1080-6059},
mesh = {Humans ; *SARS-CoV-2/genetics ; Genome, Viral ; COVID-19/diagnosis/virology ; *Respiratory Tract Infections/virology/diagnosis ; Phylogeny ; Antigens, Viral ; *Viruses/genetics/isolation & purification/classification ; },
abstract = {Genomic epidemiology offers insight into the transmission and evolution of respiratory viruses. We used metagenomic sequencing from negative SARS-CoV-2 rapid antigen tests to identify a wide range of respiratory viruses and generate full genome sequences. This process offers a streamlined mechanism for broad respiratory virus genomic surveillance.},
}

Humans
*SARS-CoV-2/genetics
Genome, Viral
COVID-19/diagnosis/virology
*Respiratory Tract Infections/virology/diagnosis
Phylogeny
Antigens, Viral
*Viruses/genetics/isolation & purification/classification

@article {pmid40358997,
year = {2025},
author = {Connan, C and Fromentin, S and Benallaoua, M and Alvarez, AS and Pons, N and Quinquis, B and Morabito, C and Nazare, JA and Borezée-Durant, E and , and Haimet, F and Ehrlich, SD and Valeille, K and Cavezza, A and Blottière, H and Veiga, P and Almeida, M and Doré, J and Benamouzig, R},
title = {Associations Among Diet, Health, Lifestyle, and Gut Microbiota Composition in the General French Population: Protocol for the Le French Gut - Le Microbiote Français Study.},
journal = {JMIR research protocols},
volume = {14},
number = {},
pages = {e64894},
doi = {10.2196/64894},
pmid = {40358997},
issn = {1929-0748},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology/genetics ; France ; *Life Style ; Feces/microbiology ; *Diet ; Adult ; Prospective Studies ; *Health Status ; Female ; Male ; Metagenomics/methods ; },
abstract = {BACKGROUND: Over the past 2 decades, the gut microbiota has emerged as a key player in human health, being involved in many different clinical contexts. Yet, many aspects of the relationship with its host are poorly documented. One obstacle is the substantial variability in wet-laboratory procedures and data processing implemented during gut microbiota studies, which poses a challenge of comparability and potential meta-analysis.

OBJECTIVE: The study protocol described here aimed to better understand the relationship between health, dietary habits, and the observed heterogeneity of gut microbiota composition in the general population. "Le French Gut - Le microbiote français" aimed to collect, sequence, and analyze 100,000 fecal samples from French residents using a high-quality shotgun metagenomic pipeline, complemented with comprehensive health, lifestyle, and dietary metadata.

METHODS: "Le French Gut - Le microbiote français" is a prospective, noninterventional French national study involving individuals, the creation of a biological collection (feces), and the exploitation of data from questionnaires and the National Health Data System (Système National des Données de Santé). This national study is open to all metropolitan French adult residents, excluding those who have undergone a colectomy or digestive stoma, or who have had a colonoscopy or taken antibiotics in the last 3 months. This is a home-based trial in which volunteers complete a questionnaire with insights about their health and habits, and in which stool samples are self-collected. Data analysis is structured into 6 work packages, each focusing on a specific aspect of the gut microbiome, including its composition and associations with lifestyle, quality of life, and health.

RESULTS: This paper outlines the study protocol, with recruitment having started in September 2022 and expected to continue until the end of December 2025. As of January 2025, a total of 20,000 participants have been enrolled. The first scientific publications based on the data analysis are expected by mid-2025.

CONCLUSIONS: "Le French Gut" aims to provide a reference database and new ecosystem tools for understanding the relationship between the gut microbiota, its host, and diet. We expect to be able to find new signatures or targets and promote the design of innovative preventive strategies, personalized nutrition, and precision medicine.

TRIAL REGISTRATION: ClinicalTrials.gov NCT05758961; https://clinicaltrials.gov/study/NCT05758961.

DERR1-10.2196/64894.},
}

Humans
*Gastrointestinal Microbiome/physiology/genetics
France
*Life Style
Feces/microbiology
*Diet
Adult
Prospective Studies
*Health Status
Female
Male
Metagenomics/methods

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

@article {pmid40357419,
year = {2025},
author = {Liu, H and Xu, T and Fu, H and Dai, B and Xie, Y},
title = {Application of Metagenomic Next-Generation Sequencing in HIV-Infected Patients with Bloodstream Infections.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {2389-2399},
pmid = {40357419},
issn = {1178-6973},
abstract = {BACKGROUND: Bloodstream infections (BSI) are common complications in HIV-infected patients and are prone to septic shock and death. This study aimed to analyze the application of blood metagenomic next-generation sequencing (mNGS) in HIV-infected patients with BSI.

METHODS: Fifty-four HIV-infected patients with suspected BSI were hospitalized at the First Affiliated Hospital of the Zhejiang University School of Medicine between August 2020 and June 2023. Blood mNGS and blood culture (BC) results were retrospectively reviewed and compared to the application value of BSI.

RESULTS: The mNGS was more sensitive for detecting pathogens (82.4% versus 35.3%; P < 0.05), and when combining blood mNGS with culture results, the sensitivity increased to 88.2%. The detection rate of mNGS for blood-mixed infection was significantly higher than that of BC (P < 0.05). Among the positive results for fungi and bacteria detected by mNGS, 13.5% of the pathogenic microorganisms were consistent with the results of BC.

CONCLUSION: The mNGS combined with BC can improve pathogen detection sensitivity and the comprehensive identification of pathogenic microorganisms in HIV-infected patients with BSI.},
}

@article {pmid40357399,
year = {2025},
author = {Xing, ZC and Guo, HZ and Zhen, P and Ao, T and Hu, M},
title = {Clinical application of metagenomic next-generation sequencing in etiologic diagnosis of severe pneumonia in adults.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1561468},
pmid = {40357399},
issn = {2235-2988},
mesh = {Humans ; Male ; Female ; Aged ; Middle Aged ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Adult ; COVID-19/diagnosis/virology ; Risk Factors ; *Pneumonia/diagnosis/microbiology/mortality ; Aged, 80 and over ; Bacteria/genetics/isolation & purification/classification ; SARS-CoV-2/isolation & purification ; Bronchoalveolar Lavage Fluid/microbiology/virology ; },
abstract = {OBJECTIVE: To analyze the clinical characteristics and risk factors for death of severe pneumonia (SP) in adults and explore the application value of metagenomic next-generation sequencing in the detection of pathogens.

METHODS: A total of 132 adult patients with SP admitted from May 2021 to October 2023 were selected. Data on gender, age, smoking, underlying diseases, laboratory tests and prognosis were collected. BALF samples were sent for mNGS, smear-stained microscopy and culture. Meanwhile, conventional methods were used for pathogen detection of blood, urine and throat swab specimens. The detection efficiencies of different methods were compared and the associated pathogen profiles were analyzed.

RESULTS: Among the 132 patients, there were 92 males and 40 females, with a total of 52 deaths. Age≥65 years, heart failure, renal insufficiency, positive of COVID-19, use of vasoactive drugs, use of mechanical ventilation and use of CRRT were statistically different between the survivors and non-survivors. Heart failure (OR=4.751) and use of mechanical ventilation (OR=11.914) were risk factors of SP mortality. The bacteria detected were mainly Klebsiella pneumoniae, Acinetobacter baumannii and Pseudomonas aeruginosa. The fungi detected were mainly Candida and Aspergillus. The viruses detected were mainly COVID-19 and influenza virus. The positive rate of mNGS was higher than conventional methods in both bacteria, fungus and virus (82.58% vs 63.64%, 50.76% vs 37.88% and 67.42% vs 37.88%, respectively) (P<0.05). The sensitivity and accuracy of mNGS in bacterial detection were significantly higher than traditional methods (P<0.05). Compared to culture, mNGS detected more Staphylococcus aureus, Streptococcus pneumoniae, Haemophilus influenzae and Escherichia coli, and had a significant advantage in the detection of Mycobacterium tuberculosis complex, Nontuberculous mycobacterial, Legionella pneumophila, Chlamydia psittaci, Pneumocystis jirovecii and Aspergillus. Moreover, mNGS can better indicate mixed infections of bacteria, viruses, or fungi.

CONCLUSION: Elderly people with chronic diseases were the main group of severe pneumonia in adults. The pathogenic microorganisms that caused SP are complex, and mixed infection is common. mNGS enhanced the effectiveness of pathogen detection, makes up for the shortcomings of conventional methods, especially in identifying unexpected pathogens, and provides a new means for early targeted anti-infection treatment.},
}

Humans
Male
Female
Aged
Middle Aged
*High-Throughput Nucleotide Sequencing/methods
*Metagenomics/methods
Adult
COVID-19/diagnosis/virology
Risk Factors
*Pneumonia/diagnosis/microbiology/mortality
Aged, 80 and over
Bacteria/genetics/isolation & purification/classification
SARS-CoV-2/isolation & purification
Bronchoalveolar Lavage Fluid/microbiology/virology

@article {pmid40357303,
year = {2025},
author = {Fu, C and Sun, Y and Chen, C},
title = {First reported Tannerella forsythia infection in a patient with extensive bronchiectasis: a case report.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1571506},
pmid = {40357303},
issn = {2296-858X},
abstract = {Tannerella forsythia infection was common in oral diseases but less reported in lung diseases. This report presents a patient with bronchiectasis who was infected by Tannerella forsythia and subsequently hospitalized with symptoms including fever, progressive cough, sputum production, and shortness of breath. A chest computed tomography (CT) scan revealed multiple bilateral pulmonary bronchiectasis with signs of infection. Metagenomic next-generation sequencing (mNGS) of the bronchoalveolar lavage fluid primarily detected Tannerella forsythia. Treatment with Piperacillin-tazobactam and ornidazole resulted in a favorable outcome. This case first reported a patient with extensive bronchiectasis infected by Tannerella forsythia and provided an effective treatment.},
}

@article {pmid40357282,
year = {2025},
author = {Wu, A and Gai, W and Guo, Y and Zhou, C and Xu, Y and Zhang, X and Wang, H},
title = {Clinical features of Talaromyces marneffei infection and colonization in HIV-negative patients: the role of mNGS in diagnosis.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1579522},
pmid = {40357282},
issn = {2296-858X},
abstract = {BACKGROUND: Talaromycosis, caused by Talaromyces marneffei (T. marneffei), has become more common in HIV-negative and immunocompetent patients. The fungus colonizes the body through dormant spores, causing opportunistic infections. Early diagnosis is challenging. This study aims to analyze the clinical features, diagnosis, treatment, and prognosis of T. marneffei infections.

METHODS: Patients diagnosed with T. marneffei infection or colonization at the People's Hospital of Ningbo University between August 2022 and July 2024 were included. Demographic characteristics, clinical data, diagnostic approaches, and treatment outcomes were analyzed.

RESULTS: Seven patients were diagnosed with T. marneffei infection, and three with colonization. Productive cough and fever were the predominant symptoms in all patients. Nodules, cavitary lesions, and pleural effusions on chest imaging were observed exclusively in infected patients. The positivity rates for metagenomic next-generation sequencing (mNGS) and conventional microbiological testing were 100 and 10%, respectively. Of the seven infected patients, three had a single infection with T. marneffei, and four had co-infection with T. marneffei and Mycobacterium avium complex. All patients were treated with monotherapy or combination therapy using voriconazole. All but one recovered.

CONCLUSION: Early diagnosis and combination therapy are critical for T. marneffei infection. mNGS complements traditional methods, facilitating accurate diagnosis and guiding targeted treatment.},
}

@article {pmid40356662,
year = {2025},
author = {Vallejo-Espín, D and Galarza-Mayorga, J and Lalaleo, L and Calero-Cáceres, W},
title = {Beyond clinical genomics: addressing critical gaps in One Health AMR surveillance.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1596720},
pmid = {40356662},
issn = {1664-302X},
abstract = {Antimicrobial resistance (AMR) poses an escalating global threat that demands comprehensive surveillance approaches beyond traditional clinical contexts. Although next-generation sequencing (NGS), particularly whole-genome sequencing (WGS), has revolutionized AMR surveillance, current implementation predominantly targets clinical isolates, largely neglecting critical environmental and animal reservoirs. Consequently, significant gaps persist in our understanding of AMR dynamics across diverse ecosystems. This Perspective emphasizes the urgent need to adopt an integrated genomic framework, combining isolate-based WGS with shotgun metagenomics within a cohesive One Health strategy. Such an integrated approach would significantly enhance the detection, tracking, and containment of resistance determinants, facilitating proactive rather than reactive AMR management. Achieving this vision requires global standardization of sequencing methods, harmonization of bioinformatics pipelines, and strengthened cross-sectoral collaboration to ensure timely interventions against AMR threats worldwide.},
}

@article {pmid40356641,
year = {2025},
author = {Xing, Y and Xie, Y and Wang, X},
title = {Enhancing soil health through balanced fertilization: a pathway to sustainable agriculture and food security.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1536524},
pmid = {40356641},
issn = {1664-302X},
abstract = {Sustainable soil health management is pivotal for advancing agricultural productivity and ensuring global food security. This review comprehensively evaluates the effects of mineral-organic fertilizer ratios on soil microbial communities, enzymatic dynamics, functional gene abundance, and holistic soil health. By integrating bioinformatics, enzyme activity assays, and metagenomic analyses, we demonstrate that balanced fertilization significantly enhances microbial diversity, community stability, and functional resilience against environmental stressors. Specifically, the synergistic application of mineral and organic fertilizers elevates β-glucosidase and urease activities, accelerating organic matter decomposition and nutrient cycling while modulating microbial taxa critical for nutrient transformation and pathogen suppression. Notably, replacing 20-40% of mineral fertilizers with organic alternatives mitigates environmental risks such as greenhouse gas emissions and nutrient leaching while sustaining crop yields. This dual approach improves soil structure, boosts water and nutrient retention capacity, and increases microbial biomass by 20-30%, fostering long-term soil fertility. Field trials reveal yield increases of 25-40% in crops like rice and maize under combined fertilization, alongside enhanced soil organic carbon (110.6%) and nitrogen content (59.2%). The findings underscore the necessity of adopting region-specific, balanced fertilization strategies to optimize ecological sustainability and agricultural productivity. Future research should prioritize refining fertilization frameworks through interdisciplinary approaches, addressing soil-crop-climate interactions, and scaling these practices to diverse agroecosystems. By aligning agricultural policies with ecological principles, stakeholders can safeguard soil health-a cornerstone of environmental sustainability and human wellbeing-while securing resilient food systems for future generations.},
}

@article {pmid40356191,
year = {2025},
author = {Charalambous, H and Brown, C and Vogazianos, P and Katsaounou, K and Nikolaou, E and Stylianou, I and Papageorgiou, E and Vraxnos, D and Aristodimou, A and Chi, J and Costeas, P and Shammas, C and Apidianakis, Y and Antoniades, A},
title = {Dysbiosis in the Gut Microbiome of Pembrolizumab-Treated Non-Small Lung Cancer Patients Compared to Healthy Controls Characterized Through Opportunistic Sampling.},
journal = {Thoracic cancer},
volume = {16},
number = {9},
pages = {e70075},
pmid = {40356191},
issn = {1759-7714},
support = {//Investigator-Initiated Studies Program of Merck Sharp & Dohme Corp/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Dysbiosis/chemically induced/microbiology/pathology ; Male ; *Carcinoma, Non-Small-Cell Lung/drug therapy/pathology/microbiology ; Female ; *Lung Neoplasms/drug therapy/pathology/microbiology ; *Antibodies, Monoclonal, Humanized/therapeutic use/pharmacology/adverse effects ; Middle Aged ; Aged ; Prospective Studies ; Case-Control Studies ; *Antineoplastic Agents, Immunological/therapeutic use ; },
abstract = {BACKGROUND: The gut microbiome influences the host immune system, cancer development and progression, as well as the response to immunotherapy during cancer treatment. Here, we analyse the composition of the gut bacteriome in metastatic Non-Small Cell Lung Cancer (NSCLC) patients receiving Pembrolizumab immunotherapy within a prospective maintenance trial through opportunistic sampling during treatment.

METHODS: The gut microbiome profiles of NSCLC patients were obtained from stool samples collected during Pembrolizumab treatment and analysed with 16S rRNA metagenomics sequencing. Patient profiles were compared to a group of healthy individuals of matching ethnic group, age, sex, BMI and comorbidities.

RESULTS: A significant decrease in the treated patients was observed in two prominent bacterial families of the phylum Firmicutes, Lachnospiraceae and Ruminoccocaceae, which comprised 31.6% and 21.8% of the bacteriome in the healthy group but only 10.9% and 14.2% in the treated patient group, respectively. Species within the Lachnospiraceae and Ruminococcaceae families are known to break down undigested carbohydrates generating short chain fatty acids (SCFA), such as butyrate, acetate and propionate as their major fermentation end-products, which have been implicated in modifying host immune responses. In addition, a significant increase of the Bacteroidacaeae family (Bacteroidetes phylum) was observed from 10.7% in the healthy group to 23.3% in the treated patient group. Moreover, and in agreement with previous studies, a decrease in the Firmicutes to Bacteroidetes ratio in the metastatic NSCLC Pembrolizumab-treated patients was observed.

CONCLUSION: The observed differences indicate dysbiosis and a compromised intestinal health status in the metastatic NSCLC Pembrolizumab-treated patients. This data could inform future studies of immunotherapy treatment responses and modulation of the gut microbiome to minimise dysbiosis prior or concurrent to treatment.

TRIAL REGISTRATION: SWIPE Trial (NCT02705820).},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Dysbiosis/chemically induced/microbiology/pathology
Male
*Carcinoma, Non-Small-Cell Lung/drug therapy/pathology/microbiology
Female
*Lung Neoplasms/drug therapy/pathology/microbiology
*Antibodies, Monoclonal, Humanized/therapeutic use/pharmacology/adverse effects
Middle Aged
Aged
Prospective Studies
Case-Control Studies
*Antineoplastic Agents, Immunological/therapeutic use

@article {pmid40356165,
year = {2025},
author = {Park, C and Park, J and Chang, D and Kim, S},
title = {Development of reference-based model for improved analysis of bacterial community.},
journal = {Food research international (Ottawa, Ont.)},
volume = {211},
number = {},
pages = {116380},
doi = {10.1016/j.foodres.2025.116380},
pmid = {40356165},
issn = {1873-7145},
mesh = {RNA, Ribosomal, 16S/genetics ; *Probiotics ; High-Throughput Nucleotide Sequencing/methods ; *Bacteria/genetics/classification ; *Gastrointestinal Microbiome/genetics ; DNA, Bacterial/genetics ; Polymerase Chain Reaction/methods ; },
abstract = {Probiotic bacteria play a vital role in maintaining gut microbial homeostasis and are widely used in various commercial products. Although 16S rRNA amplicon-based next-generation sequencing (NGS) is commonly used to analyze probiotic products, biases can arise from various 16S rRNA amplification regions, sequencing platforms, and library kits. In this study, a reference-based bias correction model was developed to correct sequencing biases. The model was validated using eight mock communities and 12 commercial products, which were analyzed across multiple NGS platforms and various 16S rRNA regions. Specific primer-probe assays were developed for accurate bacterial quantification, and their specificity was validated and used in conjunction with droplet digital PCR (ddPCR) to establish initial bacterial ratios within communities. Analysis of the mock communities revealed platform- and region-specific biases, with specific species consistently over- or under-represented. Similarly, commercial product analyses have shown biased outcomes owing to varying sequencing protocols. The correction model, based on PCR efficiencies from the reference communities, successfully corrected biased ratios across different amplification regions and platforms to achieve results that closely matched the proportions predicted by ddPCR. The model effectively corrected the biases arising from the different polymerases. Notably, partial references containing approximately 40 % of the species achieved correction results that were comparable to those of the complete references. This approach demonstrates the potential for improving microbiome analysis accuracy within predictable ranges, and could serve as a model for addressing sequencing bias in metagenomic research.},
}

RNA, Ribosomal, 16S/genetics
*Probiotics
High-Throughput Nucleotide Sequencing/methods
*Bacteria/genetics/classification
*Gastrointestinal Microbiome/genetics
DNA, Bacterial/genetics
Polymerase Chain Reaction/methods

@article {pmid40356145,
year = {2025},
author = {Wang, S and Zheng, C and Bu, C and Guo, D and Zhang, C and Xie, Q and Pan, J and Sun, J and Chen, W and Jiang, S and Zhai, Q},
title = {Role of sn-2 palmitate on the development of the infant gut microbiome: A metagenomic insight.},
journal = {Food research international (Ottawa, Ont.)},
volume = {211},
number = {},
pages = {116488},
doi = {10.1016/j.foodres.2025.116488},
pmid = {40356145},
issn = {1873-7145},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/genetics ; *Infant Formula/chemistry ; Infant ; Feces/microbiology ; *Metagenomics/methods ; Milk, Human/chemistry ; Female ; Male ; Breast Feeding ; *Palmitates/pharmacology ; Infant, Newborn ; Phylogeny ; },
abstract = {The infant gut microbiome, which develops from birth, has profound and lasting effects on human health. Its establishment in early life is influenced by events such as delivery mode and feeding type. This study examined the effects of formula milk enriched with sn-2 palmitate on the gut microbiota of healthy term infants. We conducted a 16-week comparative analysis of three feeding groups: infants receiving high sn-2 palmitate formula (n = 30), regular vegetable oil formula (n = 32), and breast milk (n = 30). Using shotgun metagenomic sequencing of fecal samples, we performed a comprehensive assessment of the gut microbiota. While overall microbial composition and diversity were comparable across groups, the functional profile of the microbiome in infants receiving sn-2 palmitate-enriched formula more closely resembled that of breastfed infants compared to the control formula group. This similarity extended to microbial species interactions, virulence gene abundance, and metabolic pathway expression patterns. In addition, sn-2 palmitate promoted the proliferation of Bifidobacterium breve and enhanced the robustness of the gut microbial ecology. Notably, the phylogenetic analysis of B. breve strains in the sn-2 palmitate group showed closer alignment with the breastfed group compared to the control group. These findings suggest that sn-2 palmitate-enriched formula may confer gut microbiota functional benefits that more closely resemble those of breast milk compared to control formula milk. This study provides scientific evidence for the development of future functional infant formulas.},
}

Humans
*Gastrointestinal Microbiome/drug effects/genetics
*Infant Formula/chemistry
Infant
Feces/microbiology
*Metagenomics/methods
Milk, Human/chemistry
Female
Male
Breast Feeding
*Palmitates/pharmacology
Infant, Newborn
Phylogeny

@article {pmid40356136,
year = {2025},
author = {Luo, Y and Tang, R and Huang, Y},
title = {Differences in structure, antioxidant capacity and gut microbiota modulation of red raspberry pectic polysaccharides extracted by different methods.},
journal = {Food research international (Ottawa, Ont.)},
volume = {211},
number = {},
pages = {116474},
doi = {10.1016/j.foodres.2025.116474},
pmid = {40356136},
issn = {1873-7145},
mesh = {*Gastrointestinal Microbiome/drug effects ; *Rubus/chemistry ; *Antioxidants/pharmacology/chemistry ; *Pectins/chemistry/pharmacology ; Prebiotics/analysis ; *Polysaccharides/chemistry/pharmacology ; *Fruit/chemistry ; Humans ; *Plant Extracts/chemistry/pharmacology ; },
abstract = {Red raspberries are associated with various health benefits, with pectic polysaccharides as their primary component and potential key contributor to these effects. This study aimed to evaluate the antioxidant and prebiotic potential of four red raspberry pectic polysaccharides (RP)-EN-RP (enzyme-assisted extraction), AC-RP (acid-assisted extraction), AL-RP (alkali-assisted extraction), and US-RP (ultrasound-assisted extraction)-and to elucidate the relationship between their structure and function. AC-RP and US-RP contained higher proportions of homogalacturonan (HG) at 50.92 % and 53.10 %, respectively, while EN-RP and AL-RP exhibited higher proportions of rhamnogalacturonan-I (RG-I) at 63.89 % and 43.37 %, respectively. All four polysaccharides demonstrated significant antioxidant and prebiotic properties. AL-RP exhibited the strongest DPPH radical scavenging activity, while US-RP showed the highest hydroxyl radical scavenging ability. These pectic polysaccharides were highly fermentable, significantly modulating gut microbiota composition and promoting the production of propionic acid, particularly EN-RP and AL-RP. Compared to the blank group, RP intervention significantly enriched Bacteroides, Phocaeicola, Bifidobacterium, Limosilactobacillus, and Paraprevotella. Carbohydrate-active enzyme genes in metagenomes revealed that glycoside hydrolases played a vital role in the degradation and utilization of red raspberry polysaccharides. Furthermore, correlation analysis indicated that a higher RG-I proportion and an elevated Rha/GalA ratio enhanced the abundance of certain beneficial microbial species and increased propionic acid production. These findings advance the understanding of the structure-function relationship of natural pectic polysaccharides and highlight their potential for tailoring gut microbiota and promoting health through precise dietary interventions.},
}

*Gastrointestinal Microbiome/drug effects
*Rubus/chemistry
*Antioxidants/pharmacology/chemistry
*Pectins/chemistry/pharmacology
Prebiotics/analysis
*Polysaccharides/chemistry/pharmacology
*Fruit/chemistry
Humans
*Plant Extracts/chemistry/pharmacology

@article {pmid40355758,
year = {2025},
author = {Saeedi Saravi, SS and Pugin, B and Constancias, F and Shabanian, K and Spalinger, M and Thomas, A and Le Gludic, S and Shabanian, T and Karsai, G and Colucci, M and Menni, C and Attaye, I and Zhang, X and Allemann, MS and Lee, P and Visconti, A and Falchi, M and Alimonti, A and Ruschitzka, F and Paneni, F and Beer, JH},
title = {Gut microbiota-dependent increase in phenylacetic acid induces endothelial cell senescence during aging.},
journal = {Nature aging},
volume = {},
number = {},
pages = {},
pmid = {40355758},
issn = {2662-8465},
support = {#310030_21A053//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; #CRSK-3_229134//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; #21A053//Novartis Stiftung für Medizinisch-Biologische Forschung (Novartis Foundation for Medical-Biological Research)/ ; },
abstract = {Endothelial cell senescence is a key driver of cardiovascular aging, yet little is known about the mechanisms by which it is induced in vivo. Here we show that the gut bacterial metabolite phenylacetic acid (PAA) and its byproduct, phenylacetylglutamine (PAGln), are elevated in aged humans and mice. Metagenomic analyses reveal an age-related increase in PAA-producing microbial pathways, positively linked to the bacterium Clostridium sp. ASF356 (Clos). We demonstrate that colonization of young mice with Clos increases blood PAA levels and induces endothelial senescence and angiogenic incompetence. Mechanistically, we find that PAA triggers senescence through mitochondrial H2O2 production, exacerbating the senescence-associated secretory phenotype. By contrast, we demonstrate that fecal acetate levels are reduced with age, compromising its function as a Sirt1-dependent senomorphic, regulating proinflammatory secretion and redox homeostasis. These findings define PAA as a mediator of gut-vascular crosstalk in aging and identify sodium acetate as a potential microbiome-based senotherapy to promote healthy aging.},
}

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

@article {pmid40355385,
year = {2025},
author = {Wang, L and Chen, Y and Wang, Q and Wang, F},
title = {Microbial imbalances linked to early pregnancy loss: a comparative analysis of vaginal microbiota.},
journal = {The journal of maternal-fetal & neonatal medicine : the official journal of the European Association of Perinatal Medicine, the Federation of Asia and Oceania Perinatal Societies, the International Society of Perinatal Obstetricians},
volume = {38},
number = {1},
pages = {2496787},
doi = {10.1080/14767058.2025.2496787},
pmid = {40355385},
issn = {1476-4954},
mesh = {Humans ; Female ; Pregnancy ; *Vagina/microbiology ; Case-Control Studies ; *Abortion, Spontaneous/microbiology ; Adult ; *Microbiota ; Young Adult ; },
abstract = {OBJECTIVE: To explore the role and related functions of vaginal microbiota in early pregnancy loss.

METHODS: This study was a case-control study with a comparison group (reference group). We recruited 178 women, including 73 who had experienced at least one early clinical pregnancy loss and 105 patients with one live birth and no history of pregnancy loss. Data on demographics, disease history, menstrual and reproductive history was collected. The case group patients were sampled immediately upon presenting with pregnancy loss at their first visit. The reference group patients underwent samples when they chose to participate voluntarily. All vaginal discharge was performed DNA Preparation and Metagenomics Sequencing. DNA extraction was performed using the phenol/trichloromethane method and the DNA fragments were then size-selected to 300-700 bp using magnetic beads. The selected fragments were repaired and ligated with indexed adaptors. The captured DNA was amplified again by PCR and circularized to create a single-stranded circular (ssCir) library. The ssCir library was subsequently amplified through rolling circle amplification (RCA) to produce DNA nanoballs (DNBs). The DNBs were then loaded onto a flow cell and sequenced using the DNBSEQ Platform. Nonparametric tests, including Kruskal-Wallis and Wilcoxon tests, were employed. Relative abundance between groups was compared, and differential species selection was performed using the LEfSe software with linear discriminant analysis.

RESULTS: 1. PCoA analysis based on Bray-Curtis distances at the species level revealed a difference between the groups (p = 0.011). At the genus level, α-diversity, assessed using the Shannon, Simpson, and Inverse Simpson indices, indicated higher bacterial richness and diversity in the control group (Shannon: mean 0.554 vs. 0.383, p = 0.0044; Simpson: mean 0.254 vs. 0.179, p = 0.0043; Inverse Simpson: mean 1.636 vs. 1.414, p = 0.0043); At the genus level, 107 microbial genera were identified, 18 of which displayed statistically significant differences. At the species level, 23 microbial species showed significant differences between the two groups. 2. We analyzed the differences in the most abundant phyla, genera, and species, with a particular focus on the top 20 most abundant genera and species. Firmicutes and Proteobacteria were significantly more prevalent among patients with pregnancy loss (PL). Among the top 20 most abundant genera, Streptococcus and Porphyromonas were significantly more abundant in patients with PL, whereas Bifidobacterium was significantly more prevalent in the reference group. Among the 20 most abundant species, Lactobacillus crispatus was significantly more prevalent in patients with PL, whereas common in the control group. 3. Principal Coordinates Analysis (PCoA) of Bray-Curtis distances, highlight their distinct clustering patterns, suggesting a notable difference between the metabolic pathways of the two groups. Key pathways with a negative correlation to PL include those related to amino acid biosynthesis, lipid metabolism, and nucleotide biosynthesis.

CONCLUSION: Our study highlights the association between vaginal microbiota dysbiosis and EPL, identifying specific microbial taxa that may contribute to pregnancy loss. These findings underscore the importance of the vaginal microbiome in reproductive health and open up new avenues for research into microbiome-based diagnostics and therapies. By integrating microbial, immune, and environmental data, future research has the potential to uncover the mechanisms underlying EPL and develop targeted interventions to improve pregnancy outcomes.},
}

Humans
Female
Pregnancy
*Vagina/microbiology
Case-Control Studies
*Abortion, Spontaneous/microbiology
Adult
*Microbiota
Young Adult

@article {pmid40355358,
year = {2025},
author = {Zhang, WL and Zu, YL and Huang, ZH and Li, Z and Gui, RR and Wang, J and Wang, XJ and Wang, HL and Fan, XX and Song, YP and Fang, BJ and Zhou, J},
title = {[BK virus nephropathy after allogeneic hematopoietic stem cell transplantation: a case report and literature review].},
journal = {Zhonghua xue ye xue za zhi = Zhonghua xueyexue zazhi},
volume = {46},
number = {3},
pages = {273-275},
doi = {10.3760/cma.j.121090-20240810-00298},
pmid = {40355358},
issn = {0253-2727},
mesh = {Humans ; Male ; *Hematopoietic Stem Cell Transplantation/adverse effects ; BK Virus ; Young Adult ; *Polyomavirus Infections ; *Kidney Diseases/virology/etiology ; *Tumor Virus Infections ; Transplantation, Homologous ; },
abstract = {A 20-year-old male patient with T-lymphoblastic lymphoma/leukemia received 9/10 human leukocyte antigen-compatible unrelated peripheral blood stem cell transplantation. He was transplanted with 5.91×10(8) mononuclear cells/kg and 2.88×10(6) CD34(+) cells/kg, and neutrophil engraftment was obtained at +11 days and platelet engraftment at +9 days. After transplantation, he presented with repeatedly increased serum creatinine levels, BK virus (BKV) -associated hemorrhagic cystitis, and BKV viremia. BK virus nephropathy was diagnosed based on renal biopsy and metagenomic next-generation sequencing. After adjusting the immunosuppressant, intravenous immunoglobulin, and donor lymphocyte infusion treatment, the patient's renal function deteriorated progressively, and he eventually died of multiple organ failure at +289 days.},
}

Humans
Male
*Hematopoietic Stem Cell Transplantation/adverse effects
BK Virus
Young Adult
*Polyomavirus Infections
*Kidney Diseases/virology/etiology
*Tumor Virus Infections
Transplantation, Homologous

@article {pmid40354774,
year = {2025},
author = {Hu, T and He, S and Gao, Z and Feng, L and Jiang, J and Zhao, Q and Wei, L},
title = {Micro-mechanism of rhamnolipid promoting acid production during anaerobic digestion: protein structures, metagenomics and molecular dynamics simulations.},
journal = {Water research},
volume = {283},
number = {},
pages = {123795},
doi = {10.1016/j.watres.2025.123795},
pmid = {40354774},
issn = {1879-2448},
abstract = {The addition of rhamnolipid (RL) is a promising strategy to enhance volatile fatty acids (VFAs) production in anaerobic digestion (AD) systems. However, the microscopic mechanisms underlying this enhancement remain poorly understood. This study investigates the micro-mechanisms by which RL promotes VFAs production, integrating protein structural analysis, metagenomics, and molecular dynamics simulations. Experimental results revealed that adding RL at 0.08 g/g TS significantly increased VFAs production to 11,441.8 mg COD/L. Protein structural analysis revealed disruption of amide I-related C = O groups and amide II-related CN and NH bonds, indicating the release or structural alteration of sludge proteins. Metagenomic analysis indicated an increase in the abundance of microbial communities and related genes, suggesting that RL enhanced the activity of acid-producing microorganisms and related metabolic pathways. Furthermore, molecular docking and molecular dynamics simulations indicated that RL spontaneously aggregated and absorbed acetate kinase (AK), altering its conformation and reducing structural compactness, which made acetyl phosphate (AcP) more accessible to the binding site of AK. RL reduced the energy barrier associated with the polar solvation interactions, increasing the contributions of key residues (LYS176 and GLU234) to the binding free energy, which enhanced the binding affinity of AK-AcP complex. This study provides a comprehensive molecular basis for how RL promotes VFAs production in AD, offering a promising strategy for optimizing acid production.},
}

@article {pmid40354675,
year = {2025},
author = {Zhi, N and Chang, X and Zha, L and Zhang, K and Wang, J and Gui, S},
title = {Platycodonis radix polysaccharides suppress progression of high-fat-induced obesity through modulation of intestinal microbiota and metabolites.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {142},
number = {},
pages = {156653},
doi = {10.1016/j.phymed.2025.156653},
pmid = {40354675},
issn = {1618-095X},
abstract = {BACKGROUND: Obesity is a prevalent chronic condition worldwide, posing a significant risk to public health. Polysaccharides derived from Platycodonis Radix (PR) have been identified as the primary bioactive compounds in combating obesity, although the underlying molecular mechanisms remain inadequately understood.

PURPOSE: The purpose of the research is to analyze the potential anti-obesity influnces within PR polysaccharides (PG: PG1 and PG2) by analyzing their impact on gut microbiota (GM) composition, SCFA and BA metabolism, and the regulation of associated gene and protein expression.

STUDY DESIGN AND METHODS: In this research, 7-week-old male C57BL/6 mice were assigned to a HFD or a control chow diet for 90 days to evaluate the therapeutic effects of PG intervention. Metagenomic analysis was performed to assess GM alterations, while GC-MS and LC-MS were used to quantify SCFA and BA concentrations in cecal contents, respectively. Furthermore, the effects of PG on SCFA- and BA-associated metabolic pathways were examined through qRT-PCR and WB.

RESULTS: PG1 demonstrated superior efficacy compared to PG2 in reducing HFD-induced obesity and associated metabolic disturbances. High-dose PG1 treatment effectively inhibited weight gain, dyslipidemia, inflammation, liver damage, and fat deposition caused by the HFD. Additionally, PG1 treatment primarily promoted the abundance of SCFA-producing bacteria, enhanced the expression of GPR41 and GPR43 genes, significantly elevated levels of GLP-1 and PYY, and improved circulating leptin and adiponectin levels. The intervention with PG1 notably enhanced the relative abundances of bacteria involved in the production of secondary BAs, such as Lachnospiraceae_NK4A136 and Eubacterium coprostanoligenes. This augmentation facilitated the transformation of primary BAs into secondary forms, diminished the relative expression of intestinal FXR and FGF15, and reduced FGFR4 levels. Consequently, this led to an upregulation of hepatic CYP7A1, accelerating liver cholesterol metabolism and the synthesis of new BAs.

CONCLUSION: Supplementation with PG1 protects mice from obesity induced by an HFD. The observed protective effects of PG1 appear to be primarily mediated through the activation of the GM-SCFA-GPR pathway and the inhibition of the GM-BA-FXR-FGF15 signaling pathway.},
}

@article {pmid40354439,
year = {2025},
author = {Llarena, AK and Haverkamp, THA and Gulliksen, WS and Herstad, K and Holst-Jensen, A and Skjerve, E and Rannem, L and Rodriguez-Campos, S and Øines, Ø},
title = {DNA extraction protocols for animal fecal material on blood spot cards.},
journal = {PloS one},
volume = {20},
number = {5},
pages = {e0313808},
doi = {10.1371/journal.pone.0313808},
pmid = {40354439},
issn = {1932-6203},
mesh = {Animals ; *Feces/microbiology/chemistry ; Dogs ; Cattle ; Metagenomics/methods ; Horses ; Swine ; Sheep ; *DNA/isolation & purification ; *DNA, Bacterial/isolation & purification/genetics ; High-Throughput Nucleotide Sequencing ; },
abstract = {BACKGROUND: Collecting fecal samples using dry preservatives is an attractive option in large epidemiological studies as they are easy to use, cheap and independent of cold chain logistics. Here, we test four DNA extraction methods with the aim of identifying an efficient procedure to extract high-quality DNA from fecal material of canine, sheep, equine, bovine, and pig collected on dry blood spot cards, with the goal of generating good quality shotgun metagenomics datasets. Further, the suitability of Illumina shotgun metagenomic sequencing at 20 million paired-end (PE) read depth per sample was assessed on its ability to successfully characterize the taxonomic and functional aspects of the resulting fecal microbiome.

METHODS: DNA was extracted from pig feces and mock communities collected on blood spot cards using four DNA extraction methods; two different methods of the QIAsymphony® PowerFecal® Pro DNA Kit, the ZymoBIOMICS™ DNA Miniprep Kit, and the MagNA Pure 96 DNA and Viral NA Small Volume Kit. Possible extraction bias was controlled by amplicon sequencing of mock communities. Fecal samples from canine, sheep, equine, bovine, and pig were thereafter subjected to the best performing DNA extraction method and shotgun metagenomic sequencing to determine sequencing efforts for functional and taxonomic analysis.

RESULTS: The four DNA extraction methods demonstrated similar community composition in the sequenced bacterial mock community. The QIAsymphony® PowerFecal® Pro DNA Kit was identified as the DNA extraction method of choice, and the resulting DNA was subjected to shotgun metagenomic sequencing with 20million PE reads. We found that higher number of reads increased the richness of observed genera between 100,000 and 5 million reads, after which higher sequencing effort did not increase the richness of the metagenomes. As for functional analysis, the number of low abundance functions in the metagenomes of the animals' feces increased with sequencing depth above 20 million PE reads.

CONCLUSION: Our experiments identified several methods suitable for extracting DNA from feces collected on blood spot cards. The QIAGEN's Blood and Tissue kit on the QiaSymphony platform fulfilled the criteria of high yield, quality, and unbiased DNA, while maintaining high throughput for shotgun metagenomic sequencing. A sequencing depth of 20 million PE reads proved adequate for taxonomic estimations and identifying common functional pathways. Detecting rarer traits, however, requires more sequencing effort.},
}

Animals
*Feces/microbiology/chemistry
Dogs
Cattle
Metagenomics/methods
Horses
Swine
Sheep
*DNA/isolation & purification
*DNA, Bacterial/isolation & purification/genetics
High-Throughput Nucleotide Sequencing

@article {pmid40353658,
year = {2025},
author = {Laso-Pérez, R and Rivas-Santisteban, J and Fernandez-Gonzalez, N and Mundy, CJ and Tamames, J and Pedrós-Alió, C},
title = {Nitrogen cycling during an Arctic bloom: from chemolithotrophy to nitrogen assimilation.},
journal = {mBio},
volume = {},
number = {},
pages = {e0074925},
doi = {10.1128/mbio.00749-25},
pmid = {40353658},
issn = {2150-7511},
abstract = {In the Arctic, phytoplankton blooms are recurring phenomena occurring during the spring-summer seasons and influenced by the strong polar seasonality. Bloom dynamics are affected by nutrient availability, especially nitrogen, which is the main limiting nutrient in the Arctic. This study aimed to investigate the changes in an Arctic microbial community using omics approaches during a phytoplankton bloom focusing on the nitrogen cycle. Using metagenomic and metatranscriptomic samples from the Dease Strait (Canada) from March to July (2014), we reconstructed 176 metagenome-assembled genomes. Bacteria dominated the microbial community, although archaea reached up to 25% of metagenomic abundance in early spring, when Nitrososphaeria archaea actively expressed genes associated with ammonia oxidation to nitrite (amt, amo, nirK). The resulting nitrite was presumably further oxidized to nitrate by a Nitrospinota bacterium that highly expressed a nitrite oxidoreductase gene (nxr). Since May, the constant increase in chlorophyll a indicated the occurrence of a phytoplankton bloom, promoting the successive proliferation of different groups of chemoorganotrophic bacteria (Bacteroidota, Alphaproteobacteria, Gammaproteobacteria). These bacteria showed different strategies to obtain nitrogen, whether it be from organic or inorganic sources, according to the expression patterns of genes encoding transporters for nitrogen compounds. In contrast, during summer, the chemolithotrophic organisms thriving during winter reduced their relative abundance and the expression of their catabolic genes. Based on our functional analysis, we see a transition from a community where nitrogen-based chemolitotrophy plays a relevant role to a chemoorganotrophic community based on the carbohydrates released during the phytoplankton bloom, where different groups seem to specialize in different nitrogen sources.IMPORTANCEThe Arctic is one of the environments most affected by anthropogenic climate change. It is expected that the rise in temperature and change in ice cover will impact the marine microbial communities and the associated biogeochemical cycles. In this regard, nitrogen is the main nutrient limiting Arctic phytoplankton blooms. In this study, we combine genetic and expression data to study the nitrogen cycle at the community level over a time series covering from March to July. Our results indicate the importance of different taxa (from archaea to bacteria) and processes (from chemolithoautotrophy to incorporation of different nitrogen sources) in the cycling of nitrogen during this period. This study provides a baseline for future research that should include additional methodologies like biogeochemical analysis to fully understand the changes occurring on these communities due to global change.},
}

@article {pmid40352947,
year = {2025},
author = {Zhong, QL and Xiong, JQ},
title = {A Globally Distributed Cyanobacterial Nitroreductase Capable of Conferring Biodegradation of Chloramphenicol.},
journal = {Research (Washington, D.C.)},
volume = {8},
number = {},
pages = {0692},
pmid = {40352947},
issn = {2639-5274},
abstract = {Cyanobacteria play pivotal roles in global biogeochemical cycles and aquatic ecosystems due to their widespread distribution and significant contributions to primary production. Yet, the interactions between cyanobacteria and antibiotics remain unclear. This study revealed that Synechocystis sp., a cyanobacterial species, removed 94.27% of 0.1 mg l[-1] chloramphenicol (CAP) through enzyme-mediated degradation. While cytochrome P450 enzymes (CYP450s) were found unnecessary for CAP removal, a gene encoding cyanobacterial nitroreductase was significantly up-regulated (7.85-fold) under CAP exposure. The purified nitroreductase exhibited strong binding affinity to CAP (K d = 2.9 nM) and a Michaelis constant (K m) of 104.0 μM. By engineering a bacterial strain with nitroreductase, 94.43% of 0.1 mg l[-1] CAP was removed within 2 h. Metagenomic and metatranscriptomic analyses showed that nitroreductase genes and transcripts are globally distributed across diverse microbial phyla. These findings uncover a novel enzyme for CAP degradation and advance sustainable biotechnologies to mitigate antibiotic pollution, addressing critical environmental challenges in aquaculture and other industries globally.},
}

@article {pmid40351504,
year = {2025},
author = {Wilkhoo, HS and Islam, AW and Wilkhoo, HS and Hussain, S and Singh, B and Kadam, SR},
title = {Clinical Insights and Advancements in Human Metapneumovirus Management and Prognosis.},
journal = {Discoveries (Craiova, Romania)},
volume = {13},
number = {1},
pages = {e204},
pmid = {40351504},
issn = {2359-7232},
abstract = {Human metapneumovirus is a respiratory pathogen that infects children, the elderly, and immunocompromised individuals. Despite its global prevalence, underdiagnosis persists because of clinical overlap with other respiratory viruses. The current approach is mostly supportive, with oxygen therapy and hydration being crucial interventions. Ribavirin contains antiviral properties but has little clinical application. Vaccine development is moving forward, with prospects including live-attenuated, subunit-based, and virus-like particle vaccines. Molecular diagnostics, such as RT-PCR and metagenomic sequencing, have increased detection rates, which aids epidemiological monitoring. Monoclonal antibodies targeting the fusion (F) protein are being studied for passive immunity, while immunomodulatory treatments such as corticosteroids and intravenous immunoglobulins may help treat severe cases. Emerging treatments include fusion inhibitors and pan-pneumovirus vaccinations that protect against HMPV and RSV. Future research should concentrate on optimizing antiviral methods, increasing vaccination trials, and improving surveillance to detect outbreaks. A multidisciplinary approach that combines virology, immunology, and epidemiology is required to reduce HMPV's effect and improve patient outcomes. This review serves as a comprehensive literature about HMPV which provides all the crucial clinical perspectives and the latest advancements in management, antivirals, patient prognosis as well and diagnostic modalities.},
}

@article {pmid40351315,
year = {2025},
author = {Li, S and Sun, Y and Cao, S and Guo, T and Tong, X and Zhang, Z and Sun, J and Yang, Y and Wang, Q and Li, D and Min, L},
title = {Asparagopsis taxiformis mitigates ruminant methane emissions via microbial modulation and inhibition of methyl-coenzyme M reductase.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1586456},
pmid = {40351315},
issn = {1664-302X},
abstract = {INTRODUCTION: Asparagopsis taxiformis (A. taxiformis) has shown great potential to mitigate methane (CH4) emissions in recent years. This study aims to evaluate the impact of A. taxiformis on methane emissions and to fill the knowledge gap regarding its mechanisms of action in affecting CH4 metabolism and rumen fermentation.

METHODS: The experimental design consisted of a control group (CON) and test groups supplemented with 2% (Low), 5% (Mid), and 10% (High) of dried and freeze-dried treatment A. taxiformis, respectively, for 48 h of in vitro rumen fermentation. The optimal combination strategy for mitigating CH4 emissions was confirmed by analyzing nutrient degradation, CH4 production and rumen fermentation parameters, and the mechanism of action was analyzed by metagenomic and metabolomic approaches.

RESULTS AND DISCUSSION: The results showed that freeze-dried treatment had better potential to mitigate CH4 emissions than dried treatment, and supplementation of freeze-dried treatments at Low, Mid, and High groups significantly reduced CH4 production by 32.44%, 98.53%, and 99.33%, respectively. However, the High group exhibited a huge negative impact on rumen fermentation. Therefore, subsequent analyses focused on the Low and Mid groups to explore the underlying mechanisms. Metagenomics analyses showed that supplementation of freeze-dried treatment with the Mid-level supplementation significantly increased the relative abundance of propionate-producing bacteria such as Prevotella, Ruminobacter, and Succinivibrio, while inhibited acetate-producing bacteria such as Ruminococcus, altered the pattern of volatile fatty acid (VFA) synthesis in the rumen, and reduced H2 availability for methanogenesis and promoted propionate production, indirectly alleviating CH4 production. Moreover, by suppressing the relative abundance of Methanobrevibacter, CH4 production in the rumen was directly suppressed. Furthermore, KEGG pathway analysis showed that A. taxiformis significantly inhibited the abundance of K00399, methyl-coenzyme M reductase alpha subunit, which directly inhibited CH4 synthesis. Metabolomics analysis of A. taxiformis supplementation significantly enriched ketoglutarate, malate, isocitrate, and melatonin, which may have reduced the release of rumen fermented H2, thereby mitigating CH4 emissions. In summary, freeze-dried treatment A. taxiformis at the 5% supplementation level achieved the optimal balance between CH4 mitigation and rumen fermentation efficiency.},
}

@article {pmid40350519,
year = {2025},
author = {Schultz, J and Jamil, T and Sengupta, P and Sivabalan, SKM and Rawat, A and Patel, N and Krishnamurthi, S and Alam, I and Singh, NK and Raman, K and Rosado, AS and Venkateswaran, K},
title = {Genomic insights into novel extremotolerant bacteria isolated from the NASA Phoenix mission spacecraft assembly cleanrooms.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {117},
pmid = {40350519},
issn = {2049-2618},
support = {BAS/1/1096-01-01//KAUST Baseline Grant/ ; PPR-ROSES-2006//National Aeronautical and Space Administration/ ; },
mesh = {*Spacecraft ; United States National Aeronautics and Space Administration ; *Bacteria/genetics/isolation & purification/classification ; United States ; Biofilms/growth & development ; Space Flight ; *Extremophiles/genetics/isolation & purification/classification ; *Genome, Bacterial ; Humans ; Microbiota/genetics ; Genomics ; Metagenome ; Phylogeny ; },
abstract = {BACKGROUND: Human-designed oligotrophic environments, such as cleanrooms, harbor unique microbial communities shaped by selective pressures like temperature, humidity, nutrient availability, cleaning reagents, and radiation. Maintaining the biological cleanliness of NASA's mission-associated cleanrooms, where spacecraft are assembled and tested, is critical for planetary protection. Even with stringent controls such as regulated airflow, temperature management, and rigorous cleaning, resilient microorganisms can persist in these environments, posing potential risks for space missions.

RESULTS: During the Phoenix spacecraft mission, genomes of 215 bacterial isolates were sequenced and based on overall genome-related indices, 53 strains belonging to 26 novel species were recognized. Metagenome mapping indicated less than 0.1% of the reads associated with novel species, suggesting their rarity. Genes responsible for biofilm formation, such as BolA (COG0271) and CvpA (COG1286), were predominantly found in proteobacterial members but were absent in other non-spore-forming and spore-forming species. YqgA (COG1811) was detected in most spore-forming members but was absent in Paenibacillus and non-spore-forming species. Cell fate regulators, COG1774 (YaaT), COG3679 (YlbF, YheA/YmcA), and COG4550 (YmcA, YheA/YmcA), controlling sporulation, competence, and biofilm development processes, were observed in all spore-formers but were missing in non-spore-forming species. COG analyses further revealed resistance-conferring proteins in all spore-formers (n = 13 species) and eight actinobacterial species, responsible for enhanced membrane transport and signaling under radiation (COG3253), transcription regulation under radiation stress (COG1108), and DNA repair and stress responses (COG2318). Additional functional analysis revealed that Agrococcus phoenicis, Microbacterium canaveralium, and Microbacterium jpeli contained biosynthetic gene clusters (BGCs) for ε-poly-L-lysine, beneficial in food preservation and biomedical applications. Two novel Sphingomonas species exhibited for zeaxanthin, an antioxidant beneficial for eye health. Paenibacillus canaveralius harbored genes for bacillibactin, crucial for iron acquisition. Georgenia phoenicis had BGCs for alkylresorcinols, compounds with antimicrobial and anticancer properties used in food preservation and pharmaceuticals.

CONCLUSION: Despite stringent decontamination and controlled environmental conditions, cleanrooms harbor unique bacterial species that form biofilms, resist various stressors, and produce valuable biotechnological compounds. The reduced microbial competition in these environments enhances the discovery of novel microbial diversity, contributing to the mitigation of microbial contamination and fostering biotechnological innovation. Video Abstract.},
}

*Spacecraft
United States National Aeronautics and Space Administration
*Bacteria/genetics/isolation & purification/classification
United States
Biofilms/growth & development
Space Flight
*Extremophiles/genetics/isolation & purification/classification
*Genome, Bacterial
Humans
Microbiota/genetics
Genomics
Metagenome
Phylogeny

@article {pmid40350492,
year = {2025},
author = {Ding, Y and Ke, J and Hong, T and Zhang, A and Wu, X and Jiang, X and Shao, S and Gong, M and Zhao, S and Shen, L and Chen, S},
title = {Microbial diversity and ecological roles of halophilic microorganisms in Dingbian (Shaanxi, China) saline-alkali soils and salt lakes.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {287},
pmid = {40350492},
issn = {1471-2180},
support = {STEP 2024QZKK02010//Supported by the Second Tibetan Plateau Scientific Expedition and Research Program/ ; 2208085MC39//Natural Science Foundation of Anhui Province, China/ ; },
mesh = {China ; *Lakes/microbiology/chemistry ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; *Archaea/classification/genetics/isolation & purification ; Phylogeny ; DNA, Archaeal/genetics ; Salinity ; *Biodiversity ; Alkalies/analysis ; Soil/chemistry ; High-Throughput Nucleotide Sequencing ; Sodium Chloride ; Sequence Analysis, DNA ; Bacteria/classification/genetics ; },
abstract = {Halophilic microorganisms abound in numerous hypersaline environments, such as salt lakes, salt mines, solar salterns, and salted seafood. In the northwest of Dingbian county (Shaanxi province, China), there exists a belt of hypersaline habitats extending from the west to the north consisting of saline-alkali soil and salt lakes. Theoretically, such a hypersaline environment has a high probability of containing abundant halophilic archaea communities. Nevertheless, there is nearly no systematic research on halophilic archaea in this area. Here, we employed a combination of culture-dependent and culture-independent methods to analyze the collected samples. The high-throughput sequencing results of the archaeal 16S rRNA gene indicated that the richness of halophilic archaea in saline-alkali soils was significantly higher than that in salt lakes. In saline-alkali soils, the Natronomonas genus of archaea was more predominant compared to other genera, while in salt lakes, the Halonotius, Halorubrum, and Haloarcula genera of archaea had relatively higher abundances. However, the dominant families of halophilic archaea in both environments were mainly Haloferacaceae (30.96-72%), Halomicrobiaceae (17-53.19%) and Nanosalinaceae (1-19.08%). Based on the outcomes of pure culture experiments, a total of 26 genera and 98 strains were identified. Among the identified halophilic microorganisms, the predominant species were Halorubrum and Fodinibius, accounting for 33.67% and 13.27%, respectively. The remainder were mostly low-abundance groups within the community, and 22 potential novel taxa were discovered. Additionally, metagenomic technology was employed in our research. The analysis results demonstrated that the microorganisms in this area possess metabolic pathways capable of degrading various pollutants such as atrazine, methane, and dioxins, suggesting that some microorganisms in this area play a positive role in environmental remediation. This study roughly reveals the diversity composition and dominant species of halophilic archaea in these hypersaline environments and provides a scientific basis for the possible ecological functions of microorganisms in this area during long-term survival. It also offers scientific evidence for the development and utilization of halophilic microbial resources and ecological protection.},
}

China
*Lakes/microbiology/chemistry
RNA, Ribosomal, 16S/genetics
*Soil Microbiology
*Archaea/classification/genetics/isolation & purification
Phylogeny
DNA, Archaeal/genetics
Salinity
*Biodiversity
Alkalies/analysis
Soil/chemistry
High-Throughput Nucleotide Sequencing
Sodium Chloride
Sequence Analysis, DNA
Bacteria/classification/genetics

@article {pmid40350460,
year = {2025},
author = {Zhang, X and Zhong, R and Wu, J and Tan, Z and Jiao, J},
title = {Dietary selection of distinct gastrointestinal microorganisms drives fiber utilization dynamics in goats.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {118},
pmid = {40350460},
issn = {2049-2618},
support = {32372829, 31972992//National Natural Science Foundation of China/ ; 2023JJ10047//Hunan Provincial Natural Science Foundation of China/ ; 2022RC1158//The Science and Technology innovation Program of Hunan Province/ ; 2023382//Youth Innovation Promotion Association CAS/ ; },
mesh = {Animals ; *Goats/microbiology ; *Dietary Fiber/metabolism ; *Gastrointestinal Microbiome ; Rumen/microbiology/metabolism ; Animal Feed/analysis ; Metagenomics/methods ; Fermentation ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Fibrobacter/metabolism/genetics/isolation & purification ; Ruminococcus/metabolism/genetics/isolation & purification ; Diet/veterinary ; Cecum/microbiology/metabolism ; Cellulose/metabolism ; Fatty Acids, Volatile/metabolism ; Polysaccharides/metabolism ; *Gastrointestinal Tract/microbiology ; },
abstract = {BACKGROUND: Dietary fiber is crucial to animal productivity and health, and its dynamic utilization process is shaped by the gastrointestinal microorganisms in ruminants. However, we lack a holistic understanding of the metabolic interactions and mediators of intestinal microbes under different fiber component interventions compared with that of their rumen counterparts. Here, we applied nutritional, amplicon, metagenomic, and metabolomic approaches to compare characteristic microbiome and metabolic strategies using goat models with fast-fermentation fiber (FF) and slow-fermentation fiber (SF) dietary interventions from a whole gastrointestinal perspective.

RESULTS: The SF diet selected fibrolytic bacteria Fibrobacter and Ruminococcus spp. and enriched for genes encoding for xylosidase, endoglucanase, and galactosidase in the rumen and cecum to enhance cellulose and hemicellulose utilization, which might be mediated by the enhanced microbial ATP production and cobalamin biosynthesis potentials in the rumen. The FF diet favors pectin-degrading bacteria Prevotella spp. and enriched for genes encoding for pectases (PL1, GH28, and CE8) to improve animal growth. Subsequent SCFA patterns and metabolic pathways unveiled the favor of acetate production in the rumen and butyrate production in the cecum for SF goats. Metagenomic binning verified this distinct selection of gastrointestinal microorganisms and metabolic pathways of different fiber types (fiber content and polysaccharide chemistry).

CONCLUSIONS: These findings provide novel insights into the key metabolic pathways and distinctive mechanisms through which dietary fiber types benefit the host animals from the whole gastrointestinal perspective. Video Abstract.},
}

Animals
*Goats/microbiology
*Dietary Fiber/metabolism
*Gastrointestinal Microbiome
Rumen/microbiology/metabolism
Animal Feed/analysis
Metagenomics/methods
Fermentation
*Bacteria/classification/genetics/metabolism/isolation & purification
Fibrobacter/metabolism/genetics/isolation & purification
Ruminococcus/metabolism/genetics/isolation & purification
Diet/veterinary
Cecum/microbiology/metabolism
Cellulose/metabolism
Fatty Acids, Volatile/metabolism
Polysaccharides/metabolism
*Gastrointestinal Tract/microbiology

@article {pmid40350266,
year = {2025},
author = {Ohyama, Y and Miura, T and Furukawa, M and Shimamura, M and Asami, Y and Yamazoe, A and Uchino, Y and Kawasaki, H},
title = {A HPLC-based Method for Counting the Genome Copy Number of Cells Allows the Production of a High-quality Mock Community of Bacterial Cells.},
journal = {Microbes and environments},
volume = {40},
number = {2},
pages = {},
doi = {10.1264/jsme2.ME24076},
pmid = {40350266},
issn = {1347-4405},
mesh = {Chromatography, High Pressure Liquid/methods ; *Bacteria/genetics/isolation & purification/classification ; Humans ; *Microbiota/genetics ; *Genome, Bacterial ; Metagenomics/methods ; Reproducibility of Results ; },
abstract = {Improving the reliability of a metagenomic sequencing ana-lysis requires the use of control samples, known as mock communities. Therefore, mock communities must be prepared with high accuracy and reproducibility, which is particularly challenging for cellular mock communities. In the present study, we prepared a cellular mock community consisting of bacterial strains representative of the human and surrounding environmental microbiomes to demonstrate the suitability of a HPLC-based method that measures the genome number of cells. This method proved to be more accurate and reproducible for preparing cellular mock communities than traditional cell counting-based enumeration methods.},
}

Chromatography, High Pressure Liquid/methods
*Bacteria/genetics/isolation & purification/classification
Humans
*Microbiota/genetics
*Genome, Bacterial
Metagenomics/methods
Reproducibility of Results

@article {pmid40350102,
year = {2025},
author = {El-Son, MAM and Elbahnaswy, S and Khormi, MA and Aborasain, AM and Abdelhaffez, HH and Zahran, E},
title = {Harnessing the Fish Gut Microbiome and Immune System to Enhance Disease Resistance in Aquaculture.},
journal = {Fish & shellfish immunology},
volume = {},
number = {},
pages = {110394},
doi = {10.1016/j.fsi.2025.110394},
pmid = {40350102},
issn = {1095-9947},
abstract = {The increasing global reliance on aquaculture is challenged by disease outbreaks, exacerbated by antibiotic resistance, and environmental stressors. Traditional strategies, such as antibiotic treatments and chemical interventions, are becoming less effective, necessitating a shift toward microbiota-based disease control. The fish gut microbiome is a key determinant of immune homeostasis and pathogen resistance. However, previous reviews lack integration of microbiome engineering, machine learning, and next-generation sequencing in fish health strategies. This review encompasses recent advancements in microbiome research, including dietary strategies such as prebiotics, probiotics, synbiotics, and phytogenic feed additives. It synthesizes the latest metagenomic insights, microbiota modulation techniques, and AI-driven disease prediction models. It presents a novel conceptual framework for disease control using microbiome-based approaches in aquaculture. Additionally, we explore emerging methodologies, including microbiota transplantation and synthetic probiotics, to develop precision microbiome interventions. By bridging existing knowledge gaps, this review provides actionable insights into sustainable aquaculture practices through microbiome-driven disease resistance.},
}

@article {pmid40349998,
year = {2025},
author = {Patel, M and Patel, K},
title = {Emerging Insights of Staphylococcus spp. in Human mastitis.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {107685},
doi = {10.1016/j.micpath.2025.107685},
pmid = {40349998},
issn = {1096-1208},
abstract = {Human mastitis represents a prevalent and intricate condition that significantly challenges breastfeeding women, often exacerbated by pathogenic bacteria such as Staphylococcus aureus. A deep understanding of the interplay between human mastitis, the breast milk microbiome, and causative agents is imperative. This understanding must focus on the bacterium's virulence and resistance genes, which critically influence the severity and persistence of mastitis. Current methods for detecting these genes, including Polymerase Chain Reaction (PCR), 16S rRNA gene sequencing, shotgun metagenomic sequencing, multiplex PCR, whole genome sequencing (WGS), loop-mediated isothermal amplification (LAMP), CRISPR-based assays, and microarray technology, are vital in elucidating bacterial pathogenicity and resistance profiles. However, advanced attention is required to refine diagnostic techniques, enabling earlier detection and more effective therapeutic approaches for human mastitis. The involvement of Staphylococcus aureus in human infection should be a prime focus, especially in women's health, which deals directly with neonates. Essential virulence genes in Staphylococcus species are instrumental in infection mechanisms and antibiotic resistance, serving as potential targets for personalized treatments. Thus, this review focuses on Staphylococcus aureus induced mastitis, examining its virulence factors and detection techniques to advance diagnostic and therapeutic strategies.},
}

@article {pmid40349794,
year = {2025},
author = {Dai, Y and Wang, B and Zhang, M and Li, W and Wang, L and Zou, Y and Peng, Y},
title = {Thermal activation of peroxymonosulfate for enhanced volatile fatty acids production and phosphorus release during anaerobic fermentation of iron-rich sludge.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132653},
doi = {10.1016/j.biortech.2025.132653},
pmid = {40349794},
issn = {1873-2976},
abstract = {Heat-peroxymonosulfate (PMS) pre-treatment was simultaneously used for phosphorus (P) release and volatile fatty acids (VFAs) production in this study. Maximum P concentrations increased from 10.3 ± 0.4 mg/L in PMS-0 to 246.1 ± 1.6 mg/L in PMS-0.8, with 41.4 % of total P released. VFAs production on day 5 increased from 2409.1 ± 30.8 mg chemical oxygen demand (COD)/L in PMS-0 to 2995.4 ± 86.5 mg COD/L in PMS-0.8. Metagenomic analysis showed that an increase in PMS dosage was detrimental to P release during polyphosphate hydrolysis by polyphosphate-accumulating organisms; functional genes involved in S cycling increased, suggesting that sulfate reduction was a critical cause of P release from iron-rich sludge during anaerobic fermentation (AF). These results provide important insights for the improvement of P release efficiency and acid production during AF, enhancing the potential for resource recovery from iron-rich sludge.},
}

@article {pmid40349588,
year = {2025},
author = {Zhang, S and Li, X and Li, X and Fu, Y and Chen, L and Wang, W and Lin, Q and Lou, H and Yao, Y and Chen, W and Zhong, C and Ye, J and Yao, Y and Guo, H and Yu, Y and Zhou, H},
title = {Optimisation and clinical validation of a metagenomic third-generation sequencing approach for aetiological diagnosis in bronchoalveolar lavage fluid of patients with pneumonia.},
journal = {EBioMedicine},
volume = {116},
number = {},
pages = {105752},
doi = {10.1016/j.ebiom.2025.105752},
pmid = {40349588},
issn = {2352-3964},
abstract = {BACKGROUND: Metagenomic Third Generation Sequencing (mTGS), based on nanopore technology, has emerged as a promising tool for the rapid diagnosis of pneumonia pathogens. However, this technology currently lacks standardised technical protocols, quality control measures, and comprehensive performance evaluations for the simultaneous detection of bacteria, fungi, and viruses in clinical settings.

METHODS: We optimised the mTGS workflow by refining key parameters (cell wall lysis, fragment size selection, host DNA depletion, and sequencing depth) using reference samples and bronchoalveolar lavage fluid (BALF) from eight patients with pneumonia. These optimisations formed the basis for a standardised mTGS protocol. To assess the clinical diagnostic value of the optimised mTGS, a multicentre prospective cohort study involving 313 pneumonia-suspected patients was conducted. Each BALF sample was tested using conventional microbiological testing (CMTs), metagenomic next-generation sequencing (mNGS), pre-optimised mTGS, and optimised mTGS.

FINDINGS: The optimised mTGS protocol, based on the refined cell wall lysis, fragment size selection, no host DNA depletion, and 800 MB sequencing depth, achieved a tenfold increase in sensitivity compared with pre-optimised mTGS for detecting the species of Bacillus subtilis, Mycobacterium tuberculosis, Mycobacterium avium, Cryptococcus neoformans, and Human papillomavirus in reference samples. In the prospective cohort, 274 patients with a confirmed diagnosis of pneumonia were identified, yielding 376 distinct microbes. The mTGS identified more microbes than CMTs (314 vs. 115), with a 45.30% increase in sensitivity (84.70% vs. 39.40%, P < 0.01, Chi-square test/Fisher's exact test). Compared with pre-optimised mTGS, the sensitivity of optimised mTGS increased by 32.51% (84.70% vs. 52.19%, P < 0.01, Chi-square test/Fisher's exact test). mTGS showed comparable performance to mNGS (84.70% vs. 79.90%, P = 0.14,Chi-square test/Fisher's exact test), both significantly outperforming CMTs. mNGS was more sensitive for detecting Non-tuberculous mycobacteria, Pneumocystis jirovecii, and Aspergillus spp., while mTGS demonstrated higher sensitivity for M. tuberculosis, Chlamydia psittaci, and Streptococcus pneumoniae. The overall diagnostic agreement between mTGS and clinical diagnosis was 81.80%.

INTERPRETATION: We optimised and validated a standardised mTGS protocol that significantly improved the ability to detect pathogens in the BALF of patients with pneumonia. Optimised mTGS demonstrated comparable performance to mNGS, making it a promising tool for the aetiological diagnosis of pneumonia.

FUNDING: The Research and Development Programme of Zhejiang Province (2023C03068, 2024C03187), the National Natural Science Foundation of China (82272338), the Key R&D Plan of the Ministry of Science and Technology (China) of China (2022YFC2504502).},
}

@article {pmid40349412,
year = {2025},
author = {Ren, P and You, C and Chen, P and Mei, X and Yang, T and Xu, Y and Wang, X and Shen, Q and Wei, Z},
title = {Organic amendments derived from Chinese herb residues enhance soil ecosystem multifunctionality by enriching key microorganisms.},
journal = {Microbiological research},
volume = {298},
number = {},
pages = {128213},
doi = {10.1016/j.micres.2025.128213},
pmid = {40349412},
issn = {1618-0623},
abstract = {Ecosystem multifunctionality (EMF), a key metric reflecting soil health, has been proven to be positively influenced by organic amendments. Chinese herb residues (CHR), rich in bioactive compounds and with lower ecological risks, are regarded as a promising source for organic amendments. Therefore, we conducted a greenhouse experiment with four treatments: no fertilizer (CK), chemical fertilizer (CF), single application of CHR-OA (OA), and partially replacing chemical fertilizers with CHR-OA (OA-CF), aiming to explore the regulatory mechanism of CHR-OA addition to EMF. A total of 19 ecosystem functions, covering plant growth, pathogen suppression, soil physicochemical properties, and microbial diversity, were used to calculate EMF. The results showed that most of the above ecosystem functions were improved by adding CHR-OA, with the OA-CF possessing the highest EMF, followed by OA. Additionally, Lysobacter was enriched as a key genus. Further analysis revealed that Lysobacter drove EMF by influencing bacterial Simpson index, plant height, and root length, and this conclusion was confirmed in greenhouse verification experiments. Through this study, we have gained a clearer understanding of the prominent ecosystem functions provided by CHR-OA and the regulatory mechanism of EMF.},
}

@article {pmid40349120,
year = {2025},
author = {Jiang, S and Huang, S and Zhang, Z and Ma, W and Han, Z and Song, Y and Huo, D and Cui, W and Zhang, J},
title = {Gut microbiota drives structural variation of exogenous probiotics to enhance colonization.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2503371},
doi = {10.1080/19490976.2025.2503371},
pmid = {40349120},
issn = {1949-0984},
mesh = {*Probiotics/pharmacology ; *Gastrointestinal Microbiome/genetics ; Animals ; Mice ; *Lactobacillus plantarum/genetics/growth & development ; Gastrointestinal Tract/microbiology ; Bile Acids and Salts ; Metagenomics ; },
abstract = {Probiotics encounter colonization resistance from native gut microbiomes, affecting their effectiveness. Genetic engineering of probiotics lacks universal applicability, as gut microbiotas are highly individualized. Here, we employed probiotic Lactiplantibacillus plantarum HNU082 (Lp082) to test whether Lp082 gut-adapted mutants can resolve colonization resistance in a new gut environment. Relying on culture-based methods and metagenomics, two distinct evolutionary clades of Lp082 in mice gut were observed, where one clade, which acquired more mutations, exhibited a longer survival time. However, these Lp082 isolates carrying many single nucleotide variants (SNVs) still exhibited phenotypic inconsistencies, with 13 strains of enhanced acid resistance. Thus, nanopore sequencing was proposed to identify structural variations (SVs). Among them, 12 strains had the Cro/C1-type HTH DNA-binding domain insertion, which enhanced growth and reproduction under bile salt stress, thereby increasing colonization time and quantity in the gut. The gut domestication process can drive probiotics to undergo many SNVs and SVs, thereby enhancing their colonization ability, which provides new insights into the colonization mechanisms and offers an ecology-based strategy.},
}

*Probiotics/pharmacology
*Gastrointestinal Microbiome/genetics
Animals
Mice
*Lactobacillus plantarum/genetics/growth & development
Gastrointestinal Tract/microbiology
Bile Acids and Salts
Metagenomics

@article {pmid40348945,
year = {2025},
author = {Chen, J and Liu, J and Liu, S and Li, Z and Gao, C and Wang, Z and Huang, S and Jiang, Z and Yang, H},
title = {Multiomics reveals the synergistic response of gut microbiota and spider A. ventricosus to lead and cadmium toxicity.},
journal = {Bulletin of environmental contamination and toxicology},
volume = {114},
number = {5},
pages = {77},
pmid = {40348945},
issn = {1432-0800},
support = {32001205//National Natural Science Foundation of China/ ; 2023JJ30299//Natural Science Foundation of Hunan Province/ ; 2019JJ50236//Natural Science Foundation of Hunan Province/ ; },
mesh = {Animals ; *Cadmium/toxicity ; *Gastrointestinal Microbiome/drug effects ; *Lead/toxicity ; *Spiders/physiology/drug effects ; Metagenomics ; Multiomics ; },
abstract = {The potential crosstalk between the host and gut microbiota (GM) under heavy metal compound pollution remains unexplored. Herein, using comprehensive analysis of metagenomics, metabolomics, behavioral analysis, and cell morphology to investigate the causal relationship between GM and host responses to cadmium (Cd) and lead (Pb) toxicities. Results indicate that Pb and Cd pollution, alone or together, hinder spider predatory behavior and change the composition and function of GM. Combined exposure reduces protein and exogenous compound metabolism, while single exposure affects energy and lipid metabolism. Gut microbiota helps spider antioxidant activity by increasing glutathione, lipoic acid, and L-cysteine. Oxidative damage, increased Enterobacteriaceae (Salmonella), and lipopolysaccharide (LPS) may harm the midgut barrier. Upregulation of choline and acetylcholine, and downregulation of spermidine, may initiate neurotoxicity. Inhibiting actinomycetes might boost sodium gallate for detoxifying single contaminants. Combined pollution detoxification may involve downregulation of indole synthesis metabolic bacteria, tryptophan, indole metabolites, cytochrome P450 (CYP450), and an increase in Desulfobulbia could remove heavy metals and reduce oxidative stress. Combined pollution has a synergistic effect, making the toxicity of multiple pollutants greater than their individual effects, impacting metal resistance genes (MRGs), and antibiotic resistance ontology (AROs) which used for classifying and describing antibiotic resistance, midgut barrier integrity, oxidative stress, and detoxification. The results help to elucidate the interplay of GM and host's reactions, and aid in monitoring and bioremediation of heavy metal pollution.},
}

Animals
*Cadmium/toxicity
*Gastrointestinal Microbiome/drug effects
*Lead/toxicity
*Spiders/physiology/drug effects
Metagenomics
Multiomics

@article {pmid40348632,
year = {2025},
author = {Lotankar, M and Houttu, N and Benchraka, C and Lahti, L and Laitinen, K},
title = {Links between gut microbiota with specific serum metabolite groups in pregnant women with overweight or obesity.},
journal = {Nutrition, metabolism, and cardiovascular diseases : NMCD},
volume = {},
number = {},
pages = {104095},
doi = {10.1016/j.numecd.2025.104095},
pmid = {40348632},
issn = {1590-3729},
abstract = {BACKGROUND AND AIM: Gut microbiota may regulate metabolism but is incompletely characterized in pregnancy. Our objective was to investigate the relations using omics techniques.

METHODS AND RESULTS: In a cross-sectional setting, fecal and serum samples of 361 healthy pregnant women with overweight or obesity were analyzed with a combinatorial approach of metagenomics and targeted NMR-based metabolomics, with statistical and machine learning techniques to identify and analyze the extent to which the gut microbiota composition and predicted functions would be reflected in the serum metabolome. We identified five biclusters, each of which consisted of a set of gut microbial species and serum metabolites with correlated abundance profiles. Two of the biclusters included metabolites that have been linked to the cardiovascular health; one was linked with factors known to increase the risk i.e., various sizes of lipoprotein subclasses (VLDL and LDL), subclasses of relative lipoprotein lipid concentrations (VLDL, IDL, and LDL), apolipoprotein B, and an inflammation marker, glycoprotein acetylation. These metabolites were associated with abundances of species such as, Enterocloster bolteae and Ruminococcus gnavus. The second bicluster included metabolites linked with a reduced cardiovascular risk, such as different sizes of HDL (high-density lipoprotein), subclasses for relative lipoprotein lipid concentrations and mean diameter for HDL particles, and fatty acid ratios. These metabolites were associated with abundances of species, such as Bacteroides cellulosilyticus and Alistipes finegoldii. We did not observe any biclusters between predicted pathways and serum metabolites.

CONCLUSION: Overall, we identified five biclusters of co-abundant gut bacteria and serum metabolites , of which two were linked to pro-atherogenic and anti-atherogenic properties.

TRIAL REGISTRATION: www.

CLINICALTRIALS: Gov: NCT01922791.},
}

@article {pmid40348492,
year = {2025},
author = {Quigley, EMM},
title = {Microbial Influences on Irritable Bowel Syndrome.},
journal = {Gastroenterology clinics of North America},
volume = {54},
number = {2},
pages = {351-365},
doi = {10.1016/j.gtc.2024.12.003},
pmid = {40348492},
issn = {1558-1942},
mesh = {*Irritable Bowel Syndrome/microbiology ; Humans ; *Gastrointestinal Microbiome ; Feces/microbiology ; Metabolomics ; Metagenomics ; Dysbiosis ; },
abstract = {Since the description of postinfection irritable bowel syndrome (IBS), a role for gut microbes in the pathogenesis of IBS has been proposed. Molecular microbiological tools have now been applied to IBS, though data are largely derived from fecal samples with attendant limitations. Metagenomics, metabolomics, and other 'omics facilitate a comprehensive picture of the microbiome and its metabolic activity. Has a microbial signature characteristic of IBS been identified? The answer is no; this should not be a surprise given the heterogeneity of the phenotype and each individual's microbiome profile.},
}

*Irritable Bowel Syndrome/microbiology
Humans
*Gastrointestinal Microbiome
Feces/microbiology
Metabolomics
Metagenomics
Dysbiosis

@article {pmid40348264,
year = {2025},
author = {Hu, Z and Li, Z and Xu, Y and He, F and Zhang, J and Li, T},
title = {MgFe-LDHs/Vallisneria natans combined system for simultaneous elimination of endogenous N and P pollution in eutrophic water: Performance, synergetic mechanism, and metagenomics analysis.},
journal = {Environmental research},
volume = {},
number = {},
pages = {121798},
doi = {10.1016/j.envres.2025.121798},
pmid = {40348264},
issn = {1096-0953},
abstract = {Eutrophication is the main factor for the degradation of lake ecosystems. More than exogenous input, endogenous N and P nutrients are responsible for it. Although the P passivation technology with functional materials is common for alleviating endogenous P pollution, will it have the same effect for endogenous N removal? In this study, a novel MgFe-LDHs/Vallisneria natans (V. natans) combined system was established for effective eliminating endogenous N and P simultaneously. During remediation periods, MgFe-LDHs/V. natans combined system with the most obvious improvement for overlying water quality that was reflected by DO, ORP, and SS, and TP, TN, and NH4[+]-N removal efficiency were up to 99%. In sediments, TP and TN removal rate was approximately 68% and 63%, where the reduction of Org-P and NH4[+]-N accounted for the majority of it, respectively. Under stimulation of MgFe-LDHs, NH4[+]-N assimilation in V. natans could be promoted through improving the metabolizing enzymes activity. In turn, V. natans contributed to Org-P mineralization by secreting organic acid, further facilitating IP enrichment on MgFe-LDHs. Additionally, owing to the synergism between V. natans allelopathy and MgFe-LDHs, the symbiotic relationship between microbial communities was much closer and more stable, the expression of functional genes that relate to denitrification, assimilatory nitrate reduction, phosphorylation and organophosphorus mineralization processes were up-regulated prominently. That is, microorganisms acted synergistically were important for endogenous N and P elimination performance. This study proposed a high-efficiency and environmentally friendly materials/plants combined remediation technology for eutrophication, especially those where with much high endogenous N and P loading.},
}

@article {pmid40348210,
year = {2025},
author = {Lin, Z and Zhang, P and Shi, D and Zhang, Y and Wu, W and Tang, Q and Wang, Q and Wang, S},
title = {Association between the gut microbiota and cystitis: A two-sample mendelian randomization study combined with the GEO database.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {107683},
doi = {10.1016/j.micpath.2025.107683},
pmid = {40348210},
issn = {1096-1208},
abstract = {BACKGROUND: Disturbances within the intestinal microbiota have emerged as a significant factor contributing to systemic inflammation, thereby rendering distant anatomical sites more vulnerable to various illnesses, including inflammatory conditions in the urinary tract such as cystitis. However, the causal relationship between dysbiosis of the gut microbiota and cystitis remains unclear. We sought to elucidate the causal relationship between the intestinal microbiota and cystitis employing Mendelian randomization (MR), offering insights into novel preventive and therapeutic strategies for managing cystitis.

METHOD: Summary statistics for the Genome-Wide Association Study (GWAS) of cystitis were sourced from the R5 release dataset provided by the FinnGen consortium, which included 8,081 cystitis cases and 195,140 controls. Single Nucleotide Polymorphisms (SNPs) that showed strong associations with 196 microbial taxa (encompassing 18,340 individuals) were selected as instrumental variables. To analyse the causal relationships between cystitis and gut microbiota, we employed four MR analysis methods: random effects, inverse variance weighting, weighted medians, and MR-Egger regression. Sensitivity analyses were performed using the Cochran's Q test, funnel plots, leave-one-out analyses, and the MR-Egger intercept test. We conducted metagenomic analysis of fecal samples from 7 patients with cystitis and 7 healthy controls to validate the findings from our MR results. To further elucidate the biological mechanisms, we conducted positional mapping of the extracted SNPs associated with the significant taxa. Additionally, we curated differentially expressed genes (DEGs) from three datasets about cystitis obtained from the Gene Expression Omnibus (GEO). Finally, we intersected the DEGs with the mapped genes to identify common genes of cystitis.

RESULTS: Our analysis revealed significant associations between specific gut microbiota and cystitis. IVW results revealed that four gut microorganisms, specifically, the genus RuminococcaceaeUCG011, genus Sutterella, family Porphyromonadaceae, and family Veillonellaceae (P < 0.05), contributed to a reduction in the incidence of cystitis. Similarly, four cystitis-related bacteria, namely, the genus Marvinbryantia, the genus Odoribacter, the genus Ruminiclostridium6, and the genus Sellimonas, are thought to play a significant role in elevating the risk of cystitis (P < 0.05). The metagenomic analysis revealed significant differences in the abundance of the genera Sutterella and Odoribacter in patients with cystitis compared to healthy controls. Additionally, we mapped causal SNPs to genes and identified 62 genes. Bioinformatics analysis reveals 161 common DEGs in cystitis. Through MR and bioinformatics analysis, we identified two common genes-ICAM1 and HP-as potential targets for cystitis.

CONCLUSION: Our research identified genetic connections between eight components of gut microbiota and two genes related to cystitis. These results offer important insights for subsequent studies into the complex relationship between gut microbiota and cystitis.},
}

@article {pmid40347608,
year = {2025},
author = {Ahmed, I and Zhuang, Z and Zhang, D and Li, P and Zhang, B},
title = {Temperature-driven dynamics of intracellular and extracellular antibiotic resistance genes during aerobic composting: Insights from qPCR and metagenomic analysis.},
journal = {Journal of hazardous materials},
volume = {494},
number = {},
pages = {138519},
doi = {10.1016/j.jhazmat.2025.138519},
pmid = {40347608},
issn = {1873-3336},
abstract = {The widespread use of antibiotics in animal farming has accelerated the dissemination of antibiotic resistance genes (ARGs). Aerobic composting is an effective method for managing animal manure, yet its effects on intracellular (iARGs) and extracellular ARGs (eARGs) under different temperature regimes including control (LT), gradual increase temperature (GT), and initially enriched temperature (HT) remain unclear. This study investigated the dynamics of iARGs and eARGs across these temperature gradients during composting. Initial composting substrate harbored higher levels of iARGs than eARGs. After composting, ARG rebound was primarily driven by eARG enrichment. On day 40, iARGs decreased by 3.1 logs in HT, 1.2 logs in LT, and 1 log in GT, while eARGs decreased by 0.9 log only in HT but increased in LT and GT. Initially phyla Firmicutes and Proteobacteria were dominated, the microbial community shifted to Bacteroidetes in LT, Actinobacteria in GT, and retained Firmicutes dominance in HT on day 40. Metagenomic analysis revealed that 68 % ARG reduction was associated with plasmid-borne ARGs, with reductions of 83.4 % in HT, 68.2 % in GT, and 51.6 % in LT, whereas non-plasmid ARGs were reduced by up to 75 % across all treatments. Notably, plasmid conjugation was significantly inhibited under HT and GT conditions.},
}

@article {pmid40347566,
year = {2025},
author = {Jiang, J and Wu, H and Yuan, Y},
title = {Comparative analysis of different Phyllostachys species on gut microbiome and fecal metabolome in giant pandas (Ailuropoda melanoleuca).},
journal = {Comparative biochemistry and physiology. Part D, Genomics & proteomics},
volume = {55},
number = {},
pages = {101529},
doi = {10.1016/j.cbd.2025.101529},
pmid = {40347566},
issn = {1878-0407},
abstract = {The influences of different bamboo species on the microbiome and metabolome of giant pandas (Ailuropoda melanoleuca) remain understudied. The aim of this study was to investigate the effects of different Phyllostachys species on the gut microbial communities and fecal metabolite profiles in giant pandas. Metagenome and metabolome were performed on the feces of giant pandas fed with different Phyllostachys species (P. edulis, P. iridescens, P. glauca, and P. violascens). The results of metagenome showed that dietary with P. glauca could notably decrease the microbial Shannon index. The relative abundances of both Cellulosilyticum and Pseudomonas were enhanced after dietary with P. iridescens, suggesting P. iridescens could enhance the cellulose-degrading function in giant pandas. However, dietary with P. glauca or P. violascens could increase the relative abundances of certain pathogenic bacteria (Escherichia, Shigella, and Klebsiella). Metabolomics analysis further revealed that all experimental groups exhibited notably elevated levels of fecal flavonoids and fatty acids. In addition, the correlation analysis showed that certain nutrients of bamboo leaves (mainly crude protein and Cu) were significantly correlated with several differential gut bacteria and fecal metabolites. Based on the present results, P. iridescens might be a substitute for the routinely used Phyllostachys species (P. edulis) in the captive management of giant pandas. The results have revealed that bamboo species is an important factor affecting the gut microbiota and fecal metabolites in giant pandas. Our results could provide important information about bamboo species-induced alterations on the microbiome and metabolome in giant pandas.},
}

@article {pmid40347421,
year = {2025},
author = {Akinbi, GO and Lin, Q and Fiola, TE and Rathore, RS and Badisa, VLD and Mwashote, B and Chen, G and Ibeanusi, V},
title = {Ecosystem assessment to support innovative advancements in soil sustainability in the major land resource areas of Mississippi through geochemical and metagenomics studies.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {40347421},
issn = {1614-7499},
support = {NR204423XXXXC125-F1-SA1-21//U.S. Department of Agriculture/ ; },
abstract = {In the present study, the ecosystem of Roebuck (RF) and Nesbit blueberry plantation (NBP) farms in Mississippi state, USA that differed by type of fertilizer treatment was assessed using soil samples through geophysical-chemical parameters and metagenomics studies. Soil geophysical-chemical parameters such as pH, moisture, organic content, nutrients, and toxic metal concentrations were measured. Metagenomic analysis was performed to identify the bacterial communities in the soil samples. The results revealed that the pH of the NBP farm (organic fertilizer) was lower than that of the RF farm (chemical fertilizer). The NBP soil samples exhibited higher moisture and organic contents than the RF soil samples. The tested heavy metal concentrations in both farm soil samples were within the limits recommended by the EPA (United States Environmental Protection Agency). Different concentrations of nutrients were observed between these two farms soil samples. RF soil indicated greater species richness and a more balanced distribution of species abundances. Proteobacteria, Bacteroidota, and Actinobacteriota were the most abundant phyla observed in RF soil, whereas Proteobacteria, Acidobacteriota, and Actinobacteriota were the most abundant phyla observed in NBP soil. This study clearly demonstrated the effects of fertilizer type on the soil through variations in geophysical-chemical parameters, which subsequently changed the microbial communities. This study suggests that organic fertilizer application could be an effective method for sustainable soil quality as the organic fertilized soils exhibited higher moisture and organic content that promotes plant growth.},
}

@article {pmid40347034,
year = {2025},
author = {Song, L and He, W and Lu, H and Jiang, J and Ding, PH and He, F},
title = {Submucosal Microbiome in Peri-Implantitis: A Comparative Metagenomic Analysis.},
journal = {Journal of periodontal research},
volume = {},
number = {},
pages = {},
doi = {10.1111/jre.13407},
pmid = {40347034},
issn = {1600-0765},
support = {82470973;82271026;82170953//the National Natural Science Foundation of China/ ; 2024M762880//the Postdoctoral Science Foundation of China/ ; },
abstract = {Through metagenomic sequencing, this study reveals significant microbial and functional differences between peri-implant health and peri-implantitis, identifying pathogenic species, virulence genes, and antibiotic resistance markers that may contribute to disease progression.},
}

@article {pmid40346812,
year = {2025},
author = {Pryor, JC and Nieva, C and Talley, NJ and Eslick, GD and Duncanson, K and Burns, GL and Hoedt, EC and Keely, S},
title = {Microbial-derived peptidases are altered in celiac disease, non-celiac gluten sensitivity, and functional dyspepsia: a systematic review and re-analysis of the duodenal microbiome.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2500063},
doi = {10.1080/19490976.2025.2500063},
pmid = {40346812},
issn = {1949-0984},
mesh = {Humans ; *Celiac Disease/microbiology/enzymology ; *Gastrointestinal Microbiome ; *Glutens/metabolism ; *Duodenum/microbiology ; *Dyspepsia/microbiology ; *Peptide Hydrolases/metabolism/genetics ; *Bacteria/enzymology/genetics/classification/isolation & purification ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Dietary gluten triggers symptoms in patients with gluten-related disorders (GRDs) including celiac disease (CeD), non-celiac gluten sensitivity (NCGS), and subsets of patients with functional dyspepsia (FD). The gastrointestinal microbiota is altered in these patients when compared to healthy individuals. As the microbiota is crucial for the hydrolysis of gluten, we hypothesized that the capacity of the microbiota to digest gluten is reduced in these conditions. We systematically reviewed and re-analyzed published datasets to compare gastrointestinal microbiomes of GRD patients and identify signals explaining gluten responses. A systematic search of five databases was conducted to identify studies where the microbiota of CeD, NCGS, or FD patients was analyzed by 16S rRNA amplicon or shotgun metagenomic sequencing and compared to control populations. Where available, raw duodenal microbiota sequence data were re-analyzed with a consistent bioinformatic pipeline. Thirty articles met the inclusion criteria for this systematic review. Microbiota diversity metrics were not impacted by the diseases; however, genera including Streptococcus, Neisseria, and Lactobacillus were commonly altered in GRD patients. Re-analysis of duodenal 16S rRNA data was possible for five included articles but did not identify any consistent differentially abundant taxa. Predicted functional analysis of the microbiome revealed that peptidases including aminopeptidase, proline iminopeptidase, and Xaa-Pro dipeptidase are altered in CeD, NCGS, and FD, respectively. These microbial-derived peptidases hydrolyze bonds in proline-rich gluten peptides. While the gastrointestinal microbiota in patients with GRDs differ from controls, no distinct phenotype links them. However, alterations to the predicted functional capacity of the microbiome to produce gluten-hydrolyzing enzymes suggest that inappropriate digestion of gluten by the microbiome impacts host responses to dietary gluten in these conditions. These findings have implications for therapeutic management of GRDs, as treatment with gluten-degrading enzymes or tailored probiotics could improve disease outcomes by enhancing gluten digestion into non-reactive peptides.},
}

Humans
*Celiac Disease/microbiology/enzymology
*Gastrointestinal Microbiome
*Glutens/metabolism
*Duodenum/microbiology
*Dyspepsia/microbiology
*Peptide Hydrolases/metabolism/genetics
*Bacteria/enzymology/genetics/classification/isolation & purification
RNA, Ribosomal, 16S/genetics

@article {pmid40346542,
year = {2025},
author = {Gao, H and Xu, L and Liu, Y and Wang, X and Zhu, S and Lin, H and Gao, Y and Mao, D and Lu, X and Luo, Y},
title = {Whole genome comparisons reveal gut-to-lung translocation of Escherichia coli and Burkholderia cenocepacia in two cases of ventilator-associated pneumonia in ICU patients.},
journal = {Respiratory research},
volume = {26},
number = {1},
pages = {178},
pmid = {40346542},
issn = {1465-993X},
support = {2022BKY015//the Tianjin Graduate Research and Innovation Projects/ ; 42377426//the National Natural Science Foundation of China/ ; 18ZXDBSY00100//the Tianjin Science and Technology Plan Project/ ; 21JCYBJC01200//the Tianjin Municipal Natural Science Foundation/ ; 2023220//the Research Project on Integrated Traditional Chinese and Western Medicine of Tianjin Municipal Health Commission/ ; 2020YFC1806904//the National Key R&D Program of China/ ; 41831287//the Key Projects of the National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Escherichia coli/genetics/isolation & purification/pathogenicity ; Animals ; *Pneumonia, Ventilator-Associated/microbiology/diagnosis/genetics ; Mice ; *Burkholderia cenocepacia/genetics/isolation & purification/pathogenicity ; *Gastrointestinal Microbiome/genetics ; Male ; *Intensive Care Units/trends ; Female ; *Bacterial Translocation/physiology/genetics ; *Lung/microbiology ; Middle Aged ; Aged ; *Whole Genome Sequencing/methods ; *Genome, Bacterial ; Mice, Inbred C57BL ; },
abstract = {BACKGROUND: Identifying the sources of pathogenic bacteria causing ventilator-associated pneumonia (VAP) in intensive care unit (ICU) patients is crucial for developing effective prevention and treatment strategies. However, the scarcity of reported cases with confirmed sources limits the ability to evaluate and manage VAP, which remains a major challenge for healthcare systems globally.

METHODS: Pathogens were isolated from endotracheal aspirate (ETA) samples of VAP patients using conventional culture techniques. Whole-genome comparisons, based on average nucleotide identity (ANI), were performed to identify genetically identical strains by comparing pulmonary isolate genomes with gut metagenome-derived bacterial genomes. Mouse models of pneumonia and colitis were used to validate the translocation of pathogenic bacteria from the gut to the lungs. Metagenomic analysis was performed to characterize the gut microbiome and resistome.

RESULTS: Pathogenic isolates were obtained from the ETA samples of seven VAP patients, with one isolate per sample. Among these, Escherichia coli (Ec1) and Burkholderia cenocepacia (Bc1) from two patients were genetically identical to strains in their respective gut microbiota, with ANI values above 99%, indicating gut-to-lung translocation. The Ec1 strain demonstrated increased resistance to cefazolin while remaining susceptible to gentamicin, amikacin, and kanamycin, compared to previously reported pneumonia-associated E. coli strains. The Bc1 strain showed elevated resistance to macrolides, chloramphenicols, and tetracyclines relative to pneumonia-associated B. cenocepacia strains. Metagenomic analysis revealed a highly individualized gut microbiota composition among VAP patients. Notably, the translocated bacteria were not dominant within their gut microbiota. Additionally, these patients showed a marked increase in the total abundance of antibiotic resistance genes (ARGs) in their gut microbiota. The translocation ability of the Ec1 strain was validated in a mouse pneumonia model, where it caused more severe lung damage. Furthermore, elevated levels of Escherichia-Shigella were detected in the lung tissues of colitis mice, suggesting that gut-to-lung bacterial translocation may occur in a severely inflamed host, potentially leading to pneumonia.

CONCLUSIONS: This study demonstrates the gut-to-lung translocation of E. coli and B. cenocepacia, highlighting their role in the development and progression of VAP in ICU patients. These findings provide valuable insights for implementing targeted prevention and treatment strategies for VAP in ICU settings.},
}

Humans
*Escherichia coli/genetics/isolation & purification/pathogenicity
Animals
*Pneumonia, Ventilator-Associated/microbiology/diagnosis/genetics
Mice
*Burkholderia cenocepacia/genetics/isolation & purification/pathogenicity
*Gastrointestinal Microbiome/genetics
Male
*Intensive Care Units/trends
Female
*Bacterial Translocation/physiology/genetics
*Lung/microbiology
Middle Aged
Aged
*Whole Genome Sequencing/methods
*Genome, Bacterial
Mice, Inbred C57BL

@article {pmid40346475,
year = {2025},
author = {Yuan, T and Ren, W and Zhang, J and Mahmood, M and Jia, Z and Zhang, S and Wang, M and Liang, S and Yuan, F and Liu, Y},
title = {Synergistic effect of grassland plants and beneficial rhizosphere bacteria helps plants cope with overgrazing stress.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {614},
pmid = {40346475},
issn = {1471-2229},
support = {32060407//Natural Science Foundation of China/ ; 2021ZD00804//Major Special Foundation of Science and Technology Plan of Inner Mongolia/ ; },
mesh = {*Rhizosphere ; Soil Microbiology ; *Grassland ; Plant Roots/microbiology ; *Poaceae/microbiology/physiology/growth & development ; Stress, Physiological ; Plant Growth Regulators/metabolism ; },
abstract = {BACKGROUND: Overgrazing (OG) is an important driver of grassland degradation and productivity decline. Highly effective synergy between plants and rhizosphere growth-promoting rhizobacteria (PGPR) may be a major way for grassland plants to effectively cope with OG stress. There have been few reports providing solid evidence on how this synergy occurs.

RESULT: This study combined with multi-omics analysis and the interaction effect of specific root exudate with PGPR B68, aiming to reveal the synergistic effect and regulatory mechanism of L. chinensis and PGPR under overgrazing stress. The results showed that Leymus chinensis plants with OG history can recruit the beneficial Phyllobacterium sp. B68 by regulating specific root exudate compounds(such as amino acid L-leucyl-L-alanine and alkaloid cordycepin). These compounds enhanced B68 rhizosphere colonization by promoting B68 chemotaxis and biofilm formation. The pot study experiments indicated that the bacterial isolates used as bio inoculants increased L. chinensis growth (mainly including plant height and biomass) by significantly increasing the chlorophyll content, RuBisCO activity, soluble sugar, plant hormones and nutrient content. Metagenomics results show that B68 inoculation significantly altered rhizosphere soil bacterial community composition and function. Additionally, B68 systemically upregulated the expression level of genes involved in plant hormone signaling, nutrient and sugar transporters, nitrogen metabolism, cell division, cell wall modification and photosynthesis to promote plant growth. The above results indicate that the PGPR B68 recruited by the root exudates of L. chinensis under OG helps the plant adapt to stress by promoting nutrient uptake and transport, maintaining hormone homeostasis, and enhancing the expression of genes related to plant growth and nutrient metabolism.

CONCLUSION: This study provides new insights into the positive interactions between grassland plants and rhizosphere bacteria under OG stress, offering valuable knowledge for developing new fertilizers and better management practices for degraded rangeland restoration and sustainable agriculture development.

CLINICAL TRIAL NUMBER: Not applicable.},
}

*Rhizosphere
Soil Microbiology
*Grassland
Plant Roots/microbiology
*Poaceae/microbiology/physiology/growth & development
Stress, Physiological
Plant Growth Regulators/metabolism

@article {pmid40346456,
year = {2025},
author = {Cao, M and Huang, L and Zhang, R},
title = {Community-acquired pneumonia associated with influenza co-infection caused by fusobacterium necrophorum: a case report and literature review.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {686},
pmid = {40346456},
issn = {1471-2334},
mesh = {Humans ; *Community-Acquired Infections/microbiology/drug therapy/diagnosis ; *Influenza, Human/complications/diagnosis/drug therapy/microbiology ; *Fusobacterium Infections/drug therapy/microbiology/diagnosis/complications ; Anti-Bacterial Agents/therapeutic use ; *Coinfection/microbiology/drug therapy/diagnosis ; *Fusobacterium necrophorum/isolation & purification/genetics/drug effects ; *Pneumonia, Bacterial/microbiology/drug therapy/diagnosis ; Male ; Adult ; Community-Acquired Pneumonia ; },
abstract = {BACKGROUND: Fusobacterium necrophorum is a rare pathogen associated with community-acquired pneumonia (CAP), particularly among healthy adults. This case report presents a rare documented case of CAP caused by F. necrophorum in a young individual, providing valuable insights for the diagnosis and treatment of similar cases.

CASE PRESENTATION: The patient was initially diagnosed with influenza, and subsequently developed CAP caused by F. necrophorum. Despite one week of outpatient treatment with moxifloxacin, the symptoms persisted, leading to hospitalisation. Treatment with piperacillin tazobactam/imipenem and doxycycline, which target atypical pathogens, did not result in improvement after admission. Conventional diagnostic methods failed to identify the causative pathogen; however, metagenomic next-generation sequencing of bronchoalveolar lavage fluid confirmed it to be F. necrophorum. The patient showed significant improvement after ten days of targeted treatment with ornidazole and imipenem/piperacillin tazobactam, and was discharged.

CONCLUSION: Uncommon pathogens, such as F. necrophorum, should be considered as potential culprits in young individuals with CAP when conventional cultures yield negative results but there is a strong suspicion of infection, especially if initial antibiotic therapy is ineffective.},
}

Humans
*Community-Acquired Infections/microbiology/drug therapy/diagnosis
*Influenza, Human/complications/diagnosis/drug therapy/microbiology
*Fusobacterium Infections/drug therapy/microbiology/diagnosis/complications
Anti-Bacterial Agents/therapeutic use
*Coinfection/microbiology/drug therapy/diagnosis
*Fusobacterium necrophorum/isolation & purification/genetics/drug effects
*Pneumonia, Bacterial/microbiology/drug therapy/diagnosis
Male
Adult
Community-Acquired Pneumonia

@article {pmid40346111,
year = {2025},
author = {Song, W and Yang, Q and Lv, H and Lv, Y and Jiang, Y and Qu, J and Li, Y},
title = {Prospective multicenter study identifying prognostic biomarkers and microbial profiles in severe CAP using BALF, blood mNGS, and PBMC transcriptomics.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {16252},
pmid = {40346111},
issn = {2045-2322},
support = {No. 82200005//National Natural Science Foundation of China/ ; No. 82470002//National Natural Science Foundation of China/ ; 2023ZD0506200//National Key Research and Development Program of China/ ; SHDC2020CR5010//the three-year action plan of Shanghai Shenkang Hospital Development Center/ ; shslczdzk02202//Shanghai Municipal Key Clinical Specialty/ ; 2017ZZ02014//Shanghai Top-Priority Clinical Key Disciplines Construction Project/ ; 20dz2261100//Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases/ ; },
mesh = {Humans ; Male ; Female ; *Bronchoalveolar Lavage Fluid/microbiology ; *Biomarkers/blood ; Prospective Studies ; Prognosis ; Middle Aged ; Aged ; *Transcriptome ; *Leukocytes, Mononuclear/metabolism/microbiology ; High-Throughput Nucleotide Sequencing ; *Pneumonia/microbiology/genetics ; Severity of Illness Index ; Metagenomics/methods ; Adult ; Gene Expression Profiling ; },
abstract = {To identify potential biomarkers associated with the prognosis and severity of severe community-acquired pneumonia (SCAP), we conducted a multi-center prospective study from January 1, 2022, to December 31, 2023, enrolling 14 mild CAP and 75 SCAP patients in Shanghai, China. Patients underwent bronchoalveolar lavage fluid (BALF) and blood metagenomic next-generation sequencing (mNGS) as well as peripheral blood mononuclear cell (PBMC) transcriptomics. Among the 75 SCAP patients, 32 died within 30 days, with older age, a history of allergies, and comorbidities like cerebrovascular disease linked to worse outcomes. BALF mNGS showed greater microbial diversity, revealing a higher prevalence of pathogens, including Acinetobacter baumannii, Klebsiella pneumoniae, and Candida albicans, compared to mild CAP patients. RNA sequencing identified 431 differentially expressed genes in deceased SCAP patients, with significant alterations in immune pathways. Notably, microbial markers such as Pneumocystis jirovecii and viral markers like Human cytomegalovirus were associated with poor outcomes. Transcriptomic biomarkers, including otoferlin (OTOF), MS4A4A, and SIGLEC1, were identified as potential prognostic indicators for SCAP severity. GSEA and traditional GO/KEGG analyses identified key immune and metabolic pathways in SCAP (death) patients, including upregulation of complement activation, oxidative phosphorylation, nitrogen metabolism, while downregulation of adaptive immune response, hematopoietic cell lineage, and antigen processing pathways. These findings underscore the superiority of BALF mNGS over blood mNGS for pathogen detection, revealing microbial differences and transcriptomic alterations between mild and severe cases while identifying prognostic markers for SCAP treatment strategies.},
}

Humans
Male
Female
*Bronchoalveolar Lavage Fluid/microbiology
*Biomarkers/blood
Prospective Studies
Prognosis
Middle Aged
Aged
*Transcriptome
*Leukocytes, Mononuclear/metabolism/microbiology
High-Throughput Nucleotide Sequencing
*Pneumonia/microbiology/genetics
Severity of Illness Index
Metagenomics/methods
Adult
Gene Expression Profiling

@article {pmid40345996,
year = {2025},
author = {Eyssautier-Chuine, S and Besaury, L and Vaillant-Gaveau, N and Villaume, S and Habrant, A and Franco Castillo, I and Rondeau, M and Aggad, D and Gommeaux, M and Fronteau, G and Mitchell, SG},
title = {Controlling Lampenflora in Heritage Sites: In Situ Testing of POM-ILs in the Pommery Champagne Cellar.},
journal = {ChemPlusChem},
volume = {},
number = {},
pages = {e202500043},
doi = {10.1002/cplu.202500043},
pmid = {40345996},
issn = {2192-6506},
abstract = {Artificial lighting, essential for geotouristic purposes in subterranean sites, has facilitated the growth of colored photosynthetic organisms (lampenflora) on two monumental 19th-century bas-reliefs of the Pommery Champagne cellar - a UNESCO-protected heritage site - causing significant aesthetic and physical deterioration. To sustainably preserve these stone artworks, biocidal polyoxometalate-ionic liquids (POM-ILs) were tested alongside the commercial biocide Preventol RI80® on three trial zones, cleaned and colonized areas of a wall, and clean stone samples positioned on a testing station within the cellar. After one year, untreated control areas exhibited growth/regrowth of green biofilms, whereas surfaces treated with POM-ILs or Preventol RI80® remained biofilm-free. Measurements of colorimetry and chlorophyll fluorescence confirmed the effectiveness of both biocides in controlling photosynthetic microorganisms. However, confocal fluorescence microscopy highlighted a reduced long-term inhibition by Preventol RI80® compared to POM-ILs, despite the latter being applied at lower concentrations. Metagenomic analysis validated the performance of POM-ILs, showing a notable decrease in microbial richness and diversity in treated areas. While both products effectively inhibited phototrophs and fungi, their efficacy against Pseudomonadota was limited, due to microbial adaptation via antibiotic resistance genes. This study underscores the potential of POM-ILs as a sustainable alternative for preserving cultural heritage against microbial colonization.},
}

@article {pmid40345059,
year = {2025},
author = {Yao, H and Romans-Casas, M and Vassilev, I and Rinta-Kanto, JM and Puig, S and Rissanen, AJ and Kokko, M},
title = {Selective butyrate production from CO2 and methanol in microbial electrosynthesis - influence of pH.},
journal = {Bioelectrochemistry (Amsterdam, Netherlands)},
volume = {165},
number = {},
pages = {109000},
doi = {10.1016/j.bioelechem.2025.109000},
pmid = {40345059},
issn = {1878-562X},
abstract = {Methanol assisted microbial electrosynthesis (MES) enables butyrate production from carbon dioxide and methanol using external electricity. However, the effects of operational parameters on butyrate formation remain unclear. By running three flat plate MES reactors with fed-batch mode at three controlled pH values (5.5, 6 and 7), the present study investigated the influence of pH on methanol assisted MES by comparing the process performance, microbial community structure, and genetic potential. The highest butyrate selectivity (87 % on carbon basis) and the highest butyrate production rate of 0.3 g L[-1] d[-1] were obtained at pH 6. At pH 7, a comparable butyrate production rate was achieved, yet with a lower selectivity (70 %) accompanied with acetate production. Butyrate production rate was considerably hindered at pH 5.5, reaching 0.1 g L[-1] d[-1], while the selectivity reached was up to 81 %. Methanol and CO2 consumption increased with pH, along with more negative cathodic potential and more negative redox potential. Furthermore, pH affected the thermodynamical feasibility of involved reactions. The results of metagenomic analyses suggest that Eubacterium callanderi dominated the microbial communities at all pH values, which was responsible for methanol and CO2 assimilation via the Wood-Ljungdahl pathway and was likely the main butyrate producer via the reverse β-oxidation pathway.},
}

@article {pmid40344981,
year = {2025},
author = {Lin, F and Tang, W and Zeng, L and Peng, L and Li, Z and Fang, Z},
title = {A rare case of severe pneumonia caused by leptospirosis complicated with Jarisch-Herxheimer reaction.},
journal = {Diagnostic microbiology and infectious disease},
volume = {113},
number = {1},
pages = {116891},
doi = {10.1016/j.diagmicrobio.2025.116891},
pmid = {40344981},
issn = {1879-0070},
abstract = {BACKGROUND: Leptospirosis, a zoonotic disease caused by Leptospira species, presents significant diagnostic challenges due to its diverse clinical manifestations. Jarisch-Herxheimer reaction (JHR), an acute inflammatory response triggered by antibiotic therapy, can complicates disease management. Reports of leptospirosis with JHR remain rare, emphasizing the need for early diagnosis and appropriate treatment.

CASE PRESENTATION: An 80-year-old male presented with severe pneumonia, septic shock, and acute respiratory distress syndrome (ARDS). Diagnosis of leptospirosis was confirmed through metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid, identifying Leptospira species. The patient was treated with piperacillin-tazobactam and supportive care, leading to full recovery.

CONCLUSIONS: This case highlights the importance of mNGS in diagnosing rare infections and the need for vigilance in managing JHR. Clinicians should consider leptospirosis in patients with unexplained severe pneumonia and systemic inflammation.},
}

@article {pmid40344830,
year = {2025},
author = {Hou, X and Gu, J and Chen, J and Ullah, H and Mamtimin, T and Wang, X and Li, X and Jiang, Y and Fan, J and Han, H and Li, X},
title = {Identification and functional characterization of a novel CaSrpA enzyme for selenite reduction and selenium nanoparticle formation.},
journal = {Journal of hazardous materials},
volume = {494},
number = {},
pages = {138486},
doi = {10.1016/j.jhazmat.2025.138486},
pmid = {40344830},
issn = {1873-3336},
abstract = {Selenite reductases are widely distributed across various oxidoreductase families (e.g., ThxR, OYE, and FccA enzymes) [1]. The ability of short-chain dehydrogenase/reductase (SDR) family enzymes for selenite reduction remains unknown. Using metagenomic and metatranscriptomic analyses, 40 putative selenite reductases were identified from selenium-rich regions based on catalytic domain homology and transcriptional upregulation. These enzymes mainly belong to the SDR family and metalloenzymes. Enzyme activity analysis indicated that CaSrpA possessed the ability (Vmax, 18.85 μM/min/g) to reduce selenite to selenium nanoparticles (SeNPs). Phylogenetic analysis showed that CaSrpA was clustered in the clade of SDR enzymes, with the typical Rossmann fold. CaSrpA also oxidized S-1-phenylethanol to phenylacetone (Vmax, 15.4 μM/min/mg), sharing 53 % sequence similarity with the alcohol dehydrogenase RasADH. Molecular docking and structural superposition identified sixteen key residues associated with CaSrpA activity. Site-directed mutagenesis revealed that over 14 mutants exhibited a 30-90 % reduction in relative activity. Mutant M206A enhanced catalytic efficiency towards selenite by 2.4-fold and S-1-phenylethanol by 5.4-fold via a lid-opening mechanism. Molecular dynamics simulation elucidated that the mutant M206A utilized lid opening mechanism to accommodate more substrate and co-factor for catalysis via altering the conformation of the α7-α8 loop. This study helps understand the intrinsic connection between the SDR family and selenite-reducing capability, broadening the repertoire of selenite reductases.},
}

@article {pmid40344797,
year = {2025},
author = {Chen, Y and Liu, Q and Xu, XW},
title = {Spatio-temporal variability of nitrogen-cycling potentials in particle-attached and free-living microbial communities in the Yangtze River estuary and adjacent regions.},
journal = {Marine pollution bulletin},
volume = {217},
number = {},
pages = {118121},
doi = {10.1016/j.marpolbul.2025.118121},
pmid = {40344797},
issn = {1879-3363},
abstract = {Particle-attached (PA) and free-living (FL) microorganisms regulate coastal biogeochemical cycles, yet their roles in nitrogen transformation remain unclear. To address this knowledge gap, we seasonally sampled PA and FL from seawater along salinity gradients in the Yangtze River estuary (YRE) and adjacent regions to investigate the spatio-temporal variability of microbial communities, abundances of nitrogen-cycling genes, and key microbial groups affiliated with the nitrogen cycle in PA and FL. Compared to FL, the composition, structure and diversity of PA exhibited more pronounced variations in response to salinity and [NO3[-]]. Metagenomic analyses indicated a predominant role of denitrification in both PA and FL, with greater abundances of genes involved in most nitrogen transformation processes observed in the estuarine region. The potential for the nitrogen cycle in PA was relatively lower in May, while greater in FL, potentially due to competition for nitrogen substrates between PA and phytoplankton during spring. PERMANOVA and Mantel tests showed that gene abundances exhibited spatio-temporal dynamics and were associated with species and environmental factors. Gene-affiliated taxa identification and the Weighted Correlation Network Analysis revealed that the differences in environmental factors and taxa responsible for the nitrogen transformation drove spatio-temporal variations of the nitrogen cycle between PA and FL, and implied the significance of their interaction in nitrogen fates in coastal ecosystem. Gammaproteobacteria and Betaproteobacteria were highly affiliated with nitrogen-cycling genes, while Nitrososphaeria played an important role in nitrification and denitrification. This study offered practical insights for mitigating eutrophication through targeted regulation of microbial-mediated nitrogen fluxes.},
}

@article {pmid40344252,
year = {2025},
author = {Crawford, MS and Ulu, A and Ramirez, BM and Santos, AN and Chatterjee, P and Canale, V and Manz, S and Lei, H and Soriano, SM and Nordgren, TM and McCole, DF},
title = {Respiratory Exposure to Agriculture Dust Extract Alters Gut Commensal Species and Key Metabolites in Mice.},
journal = {Journal of applied toxicology : JAT},
volume = {},
number = {},
pages = {},
doi = {10.1002/jat.4808},
pmid = {40344252},
issn = {1099-1263},
support = {2R01DK091281/NH/NIH HHS/United States ; 1R01AI153314/NH/NIH HHS/United States ; 1R01DK130373/NH/NIH HHS/United States ; R00ES025819/NH/NIH HHS/United States ; R01HL158926/NH/NIH HHS/United States ; T34GM062756/NH/NIH HHS/United States ; U54OH007550//The University of California, Davis-Western Center for Agricultural Health and Safety/ ; //University of California Presidential Postdoctoral Fellowship Program/ ; //National Institute of Diabetes, Digestive and Kidney Diseases (NIDDK)/ ; },
abstract = {Exposure to agricultural dust containing antimicrobial-resistant pathogens poses significant health risks for workers in animal agriculture production. Beyond causing severe airway inflammation, pollutants are linked to intestinal diseases. Swine farm dust is rich in ultrafine particles, gram-positive and gram-negative bacteria, and bacterial components such as lipopolysaccharides (LPS; endotoxins). In our previous study, we demonstrated that intranasal exposure of male and female C57BL/6J mice to 12.5% hog dust extract (HDE, containing 22.1-91.1 EU/mL) for 3 weeks resulted in elevated total cell and neutrophil counts in bronchoalveolar lavage fluid and increased intestinal permeability compared to saline controls. Now, we report that 16S and metagenomic analyses of Week 3 stool samples from HDE-treated mice indicate a reduced abundance of the beneficial species Akkermansia muciniphila and Clostridium sp. ASF356 and Lachnospiraceae bacterium. Bacterial alpha diversity showed increased species evenness in fecal samples from HDE-treated mice (Pielou's evenness, p = 0.047, n = 5-6/group). Metabolomic analysis also indicated significant reductions in key metabolites involved in energy metabolism, including riboflavin (p = 0.027, n = 11) and nicotinic acid (p = 0.049, n = 11), as well as essential amino acids, such as inosine (p = 0.043, n = 11) and leucine (p = 0.018, n = 11). While HDE exposure does not robustly alter overall microbial abundance or community structure, it leads to specific reductions in beneficial bacterial species and critical metabolites necessary for maintaining intestinal homeostasis by supporting energy metabolism, gut barrier function, microbiota balance, and immune regulation. The results of this study underscore the potential risks for gut health posed by inhalation of agricultural dust.},
}

@article {pmid40344212,
year = {2025},
author = {Zhao, Y and Song, L and Li, HY and Liu, SX and Mao, FF and Li, XJ and Ding, PH},
title = {Metagenomic Insights Into the Subgingival Microbiome in Periodontal Health and Different Grades of Periodontitis.},
journal = {Journal of periodontal research},
volume = {},
number = {},
pages = {},
doi = {10.1111/jre.13408},
pmid = {40344212},
issn = {1600-0765},
support = {//Postdoctoral Science Foundation of China/ ; //National Natural Science Foundation of China/ ; //the Science Fund for Distinguished Young Scholars of Zhejiang Province/ ; //National Key Research and Development Program of China/ ; //Key Research and Development Program of Zhejiang Province/ ; //Fundamental Research Funds for the Central Universities/ ; },
abstract = {AIM: This cross-sectional study compared the subgingival microbiome in periodontal health (PH) and periodontitis, focusing on distinguishing Stage III Grade B periodontitis (PD-S3gB) and Stage III Grade C periodontitis (PD-S3gC) as defined by the 2018 Classification of Periodontitis.

METHODS: Subgingival samples from subjects with PH, PD-S3gB, and PD-S3gC were analyzed using metagenomic sequencing. Taxonomic and functional annotations were performed, followed by analyses of microbial diversity, differential abundance, interspecies networks, predictive modeling, and functional pathway enrichment.

RESULTS: Significant differences in both alpha and beta diversity were observed between PH and periodontitis. Several periodontal pathogens were more abundant in disease states, with Capnocytophaga granulosa and Capnocytophaga sp. CM59 enriched in PD-S3gC compared to PD-S3gB. The PD-S3gC group also exhibited a more complex microbial network with increased interspecies connectivity. An 11-species diagnostic model effectively distinguished PH, PD-S3gB, and PD-S3gC. Furthermore, pathways related to motility, chemotaxis, and methane metabolism were significantly enriched in periodontitis.

CONCLUSION: Distinct structural and functional differences in the subgingival microbiome characterize periodontal health and periodontitis. Periodontitis with a rapid rate of progression is marked by specific pathogen overgrowth and enhanced microbial interactions, supporting the development of microbiome-based diagnostics and personalized therapies.

TRIAL REGISTRATION: Chinese Clinical Trial Registration: ChiCTR2000039426.},
}

@article {pmid40343892,
year = {2025},
author = {Kiige, JK and Kavoo, AM and Mwajita, MR and Mogire, D and Ogada, S and Wekesa, TB and Kiirika, LM},
title = {Metagenomic characterization of bacterial abundance and diversity in potato cyst nematode suppressive and conducive potato rhizosphere.},
journal = {PloS one},
volume = {20},
number = {5},
pages = {e0323382},
doi = {10.1371/journal.pone.0323382},
pmid = {40343892},
issn = {1932-6203},
abstract = {Potato (Solanum tuberosum L.) is an important food crop in Kenya, providing a source of nutrition and income for many farmers. However, potato cyst nematodes (PCN) cause significant damage to potato plants, leading to substantial economic losses and threatening the nation's food security. Understanding the composition and functional potential of bacterial communities in the soil is important for developing sustainable biological control strategies against PCN and improving soil health. This cross-sectional purposive study examined the bacterial communities associated with PCN-suppressive and conducive potato rhizosphere from two major potato-producing counties in Kenya. We analyzed 180 soil samples from symptomatic and asymptomatic potato plants using shotgun metagenomics, followed by functional analysis to identify genes and metabolic pathways relevant to soil and plant health. Taxonomic classification revealed Enterobacteriaceae and Pseudomonadaceae as the most dominant bacterial families present. Within these families, the genera Pseudomonas and Enterobacter were highly abundant, both known for their plant growth-promoting traits, including biological control of soil pathogens and nutrient solubilization. KEGG and Pfam database analysis revealed pathways associated with nutrient cycling, transport systems, and metabolic functions. The abundance of iron-acquisition, chemotaxis, and diverse transport genes across analyzed samples suggests the presence of beneficial bacterial communities. This study provides the first report on bacterial ecology in PCN-infested rhizosphere in Kenya and its implications for soil health and PCN management.},
}

@article {pmid40343328,
year = {2025},
author = {McLamb, F and Vazquez, A and Olander, N and Vasquez, MF and Feng, Z and Malhotra, N and Bozinovic, L and Najera Ruiz, K and O'Connell, K and Stagg, J and Bozinovic, G},
title = {Comparative Three-Barcode Phylogenetics and Soil Microbiomes of Planted and Wild Arbutus Strawberry Trees.},
journal = {Plant direct},
volume = {9},
number = {5},
pages = {e70078},
doi = {10.1002/pld3.70078},
pmid = {40343328},
issn = {2475-4455},
abstract = {Taxonomic identification of closely related plants can be challenging due to convergent evolution, hybridization, and overlapping geographic distribution. To derive taxonomic relationships among planted and wild Arbutus plants across a large geographic range, we complemented three standard plastid barcodes rbcL, matK, and trnH-psbA with soil and fruit chemistry, soil microbiome, and plant morphology analyses. Soil and plant sampling included planted Arbutus from manicured sites in Southern California, USA, wild plants from Southern and Northern California, and wild populations from Mediterranean island of Hvar, Croatia. We hypothesized that phenotypic variation within and between sites correlates with plants' genotype and geographic distribution. Similar fruit chemistry corresponds to geographical proximity and morphological resemblance, while bulk soil bacterial content defines three distinct clusters distinguishing planted versus wild trees and continent of origin. The soil microbiome of wild California Arbutus was characterized by an abundance of Nitrobacter, while the presence of Candidatus Xiphinematobacter was high in wild Hvar samples and most planted samples, but low in all wild California samples. Although all three barcodes resolved four main groups, the position of samples varies across barcodes. The rbcL phylogram is relatively unbalanced, suggesting slower diversification among wild California populations and exhibiting greater resolution than other barcodes among planted individuals. While our data demonstrate an overall agreement among standard plant barcodes relative to geo-distribution and plant morphology, sustained efforts on cost-effective global plant DNA barcode library standardization for closely related and geographically overlapping plants is recommended.},
}

@article {pmid40343031,
year = {2025},
author = {Tan, MH and Bangre, O and Rios-Teran, CA and Tiedje, KE and Deed, SL and Zhan, Q and Rasyidi, F and Pascual, M and Ansah, PO and Day, KP},
title = {Metagenomic analysis reveals extreme complexity of Plasmodium spp. infections in high transmission in West Africa.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.04.29.25326533},
pmid = {40343031},
abstract = {Mixed-species, mixed-strain Plasmodia infections are known to occur in humans in malaria endemic areas. To date, the true extent of this complexity has not been explored in high- burden countries of sub-Saharan Africa. Here we take a metagenomic lens to infections obtained by sampling variable blood volumes from residents living in high, seasonal transmission in northern Ghana. We identified significantly higher prevalence of Plasmodium spp. and inter-/intra-species complexity in larger blood volumes. Overall, malaria infections displayed high levels of metagenomic complexity comprising single-, double-, and triple- species infections with varying levels of complexity for P. falciparum, P. malariae, P. ovale curtisi, and P. ovale wallikeri. We present evidence of individuals with greater susceptibility to highly-complex infections that cannot be explained by age or location. The implications of these findings to malaria epidemiology and control are illustrated by a geographic scaling exercise to district and region levels in Ghana.},
}

@article {pmid40342956,
year = {2025},
author = {Yang, Z and Liu, Q and Hu, Y and Geng, S and Ni, JX},
title = {Application of Metagenomic and Targeted Next-Generation Sequencing in Diagnosis of Pulmonary Tuberculosis in Bronchoalveolar Lavage Fluid.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {2229-2241},
doi = {10.2147/IDR.S514090},
pmid = {40342956},
issn = {1178-6973},
abstract = {PURPOSE: To explore the application value of metagenomic next-generation sequencing (mNGS) and targeted next-generation sequencing (tNGS) in the diagnosis of pulmonary tuberculosis (PTB) in bronchoalveolar lavage fluid (BALF).

PATIENTS AND METHODS: Data from 202 patients with suspected PTB at Wuhan Central Hospital (Jan 2022 - Jan 2024) were retrospectively analyzed. BALF samples were collected and examined using mNGS and tNGS, comparing their sensitivity to traditional methods like acid-fast staining, TB culture, and TB-DNA. Mixed microbial species were identified from the BALF using mNGS and tNGS, and the pros and cons of tNGS were evaluated against mNGS.

RESULTS: Of the 202 patients evaluated, 94 were diagnosed with PTB. The BALF mNGS and tNGS exhibited a sensitivity of 77.66% and a specificity of 100%, with positive and negative predictive values of 100% and 83.72%, respectively, outperforming conventional diagnostic methods. It was possible to compare the AUC values of the ROC curves of the BALF mNGS and tNGS with the corresponding values of the other three assay methods (0.89 vs 0.56, p < 0.05), MTB culture (0.89 vs 0.71, p < 0.05), and TB-DNA (0.89 vs 0.68, p < 0.05). Additionally, these techniques identified mixed microbial species in 52.13% of the BALF samples. Although both mNGS and tNGS demonstrated similar diagnostic rates, tNGS proved to be faster, more cost-effective, and incorporated a tuberculosis-specific wall-breaking technology, thereby suggesting greater clinical utility.

CONCLUSION: BALF mNGS and tNGS technologies quickly and accurately detect PTB patients with greater sensitivity and specificity than traditional MTB methods. While both mNGS and tNGS demonstrate enhanced capacity for polymicrobial detection, the clinical significance of co-detected microorganisms requires integration with clinical context to differentiate colonization from active infection. Compared to mNGS, tNGS provides distinct advantages in clinical utility.},
}

@article {pmid40342698,
year = {2025},
author = {Kang, X and Shao, M and Jiang, J and He, L and Lu, Y and Song, J and Xu, J and Fan, Z},
title = {The Gut Microbiome of the Asiatic Toad (Bufo gargarizans) Reflects Environmental Changes and Human Activities.},
journal = {Ecology and evolution},
volume = {15},
number = {5},
pages = {e71394},
doi = {10.1002/ece3.71394},
pmid = {40342698},
issn = {2045-7758},
abstract = {Amphibians are extremely sensitive to environmental changes, and their gut microbiome may have different responses to environmental changes. Here, metagenomic sequencing was used to investigate the intestinal microbiota of the Asiatic toad (Bufo gargarizans) from three different habitats (city areas, transition areas, and wild areas) of Sichuan Province, China. The results showed that Proteobacteria, Firmicutes, and Fusobacteria were the main bacteria in the gut of B. gargarizans. There were significant differences in the composition and function of the gut microbiome among the samples from the three different habitats. Enterobacteriaceae showed significant changes in the three habitats and occupied a high relative abundance in the city areas, especially for Citrobacter. Especially, antibiotic resistance genes (ARGs) and virulence factors (VFs) were significantly increased in city areas. We performed de novo assembly of the metagenome-assembled genomes (MAGs). In total, 322 nonredundant MAGs were reconstructed, 304 of which might be potential novel genomes. Among the 13 species-level genome bins (SGBs) belonging to Enterobacteriaceae, the one belonging to Citrobacter portucalensis annotated the most types of ARGs and VFs. Phylogenetic and functional analyses of the assembled C. portucalensis MAG and public genome data were carried out, suggesting that it may play a potential role in intestinal diseases in amphibians. Our study revealed the differences in the gut microbiome of B. gargarizans across different habitats and suggests that amphibian intestinal microbiota could serve as environmental indicators to reflect environmental changes and human activities. The reconstructed MAGs expanded our understanding of the gut microbiota in amphibians, which may serve as a substantial reservoir for microbiome resources.},
}

@article {pmid40342619,
year = {2025},
author = {Sakiyama, Y and Yuan, JH and Yoshimura, A and Takeuchi, M and Maki, Y and Mori, T and Takei, J and Ando, M and Hiramatsu, Y and Nozuma, S and Higuchi, Y and Yonezawa, H and Kirishima, M and Suzuki, M and Kano, T and Tarisawa, M and Hashiguchi, S and Kunii, M and Sato, S and Takahashi-Iwata, I and Hashiguchi, A and Matsuura, E and Izumo, S and Tanimoto, A and Takashima, H},
title = {Brain biopsy and metagenomic sequencing enhance aetiological diagnosis of encephalitis.},
journal = {Brain communications},
volume = {7},
number = {3},
pages = {fcaf165},
doi = {10.1093/braincomms/fcaf165},
pmid = {40342619},
issn = {2632-1297},
abstract = {Identifying the aetiology of CNS diseases, regardless of their infectious or non-infectious nature, is often intricate. Next-generation sequencing (NGS) has emerged as a powerful tool for sensitive and unbiased screening of tissue or body fluid specimens. This study aimed to investigate the underlying aetiology of patients with suspected infectious CNS diseases. Between April 2013 and October 2021, we collected brain tissue samples from 33 patients diagnosed with encephalitis or encephalitis-like CNS diseases, obtained via biopsy or autopsy, and underwent metagenomic NGS (mNGS) in conjunction with pathological evaluations. Moreover, we employed PCR-based assays and pathogen-specific immunostaining to corroborate the presence of pathogens within the tissue samples. Among the 33 patients, mNGS elucidated pathogen-specific genomic sequences in 7 cases (21.2%), including halobacteria (archaea), Balamuthia mandrillaris, Epstein-Barr virus, Toxoplasma gondii and herpes simplex virus. Additionally, brain tissue mNGS ruled out known pathogens, identifying 14 cases (42.4%) of non-infectious CNS diseases, which included neoplastic, autoimmune/inflammatory and amyloid angiopathy conditions. The adjustment of therapeutic strategies based on these findings led to improvements in clinical symptoms, imaging outcomes and patient prognosis. Brain biopsy serves as both a direct pathological research target and a valuable source of samples for unbiased high-throughput sequencing. Our study illustrates the reliability of mNGS on brain tissue, which significantly improves the diagnostic rate for suspected encephalitis or encephalitis-like diseases of unknown aetiology. These findings underscore the importance of mNGS in guiding more precise and effective therapeutic interventions for patients in clinical practice.},
}

@article {pmid40342595,
year = {2025},
author = {Sun, Y and Cai, Q and Li, T and Chen, J and Fang, Y},
title = {Genome assembly of Klebsiella michiganensis based on metagenomic next-generation sequencing reveals its genomic characteristics in population genetics and molecular epidemiology.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1546594},
doi = {10.3389/fmicb.2025.1546594},
pmid = {40342595},
issn = {1664-302X},
abstract = {INTRODUCTION: Klebsiella michiganensis, a significant member of the Klebsiella oxytoca complex, has emerged as a potential pathogen in clinical settings. Despite extensive research on the Klebsiella pneumoniae complex, the pathogenicity and drug resistance of the K. oxytoca complex remain understudied, particularly regarding the reconstruction of whole genomes from metagenomic next-generation sequencing (mNGS) data.

METHODS: In this study, bronchoalveolar lavage fluid (BALF) from a 55-year-old woman with a suspected right lung infection in Anhui Province, China, was analyzed using mNGS.

RESULTS: Three distinct assembly strategies were employed to reconstruct the genome of K. michiganensis, leading to the identification of a novel ST452 strain, KMLRT2206. Comprehensive genomic analysis of this strain and 206 clinical isolates (genomes downloaded from public databases) revealed the population structure, distribution of drug resistance genes, and virulence factors of K. michiganensis. The results demonstrated significant genetic diversity, with the species divided into three major clades, each exhibiting distinct patterns of drug resistance and virulence genes. Notably, 38.6% of the strains harbored the bla OXY-1-1 gene, highlighting a potential threat of drug resistance. While virulence gene distribution was not correlated with sequence type (ST), significant differences were observed among clades.

CONCLUSION: This study underscores the value of mNGS combined with optimized assembly strategies for accurate species identification within the K. oxytoca complex, providing critical insights for clinical pathogen detection and epidemiological surveillance.},
}

@article {pmid40341642,
year = {2025},
author = {Humińska-Lisowska, K and Michałowska-Sawczyn, M and Kosciolek, T and Łabaj, PP and Kochanowicz, A and Mieszkowski, J and Proia, P and Cięszczyk, P and Zielińska, K},
title = {Gut microbiome and blood biomarkers reveal differential responses to aerobic and anaerobic exercise in collegiate men of diverse training backgrounds.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {16061},
pmid = {40341642},
issn = {2045-2322},
support = {2018/29/N/NZ7/02800//Narodowe Centrum Nauki/ ; 2018/29/N/NZ7/02800//Narodowe Centrum Nauki/ ; },
mesh = {Humans ; Male ; *Gastrointestinal Microbiome/physiology ; *Biomarkers/blood ; *Exercise/physiology ; Young Adult ; Feces/microbiology ; Exercise Test ; Athletes ; Anaerobiosis ; Adult ; },
abstract = {The gut microbiome influences physiological responses to exercise by modulating inflammatory markers and metabolite production. Athletes typically exhibit greater microbial diversity, which may be associated with improved performance, but the mechanisms linking different exercise modalities to the gut microbiome are not fully understood. In this study, blood and stool samples were collected from endurance athletes, strength athletes, and non-athletic controls performing two maximal exercise tests (the anaerobic Wingate test and the aerobic Bruce Treadmill Test) to integrate serum biomarker data with gut bacterial metagenomic profiles. While most biochemical markers showed similar post-exercise trends across groups, SPARC (secreted protein acidic and rich in cysteine) and adiponectin levels showed modality-specific responses. Strength-trained participants showed unique microbiome-biomarker associations after the Wingate test. In addition, baseline enrichment of certain bacterial taxa, including Clostridium phoceensis and Catenibacterium spp., correlated with reduced Bruce Treadmill test response in strength-trained individuals. These findings, while requiring further validation, indicate the complex interplay between exercise type, training background, and the gut microbiome, and suggest that specific microbial species may help shape recovery and adaptation.},
}

Humans
Male
*Gastrointestinal Microbiome/physiology
*Biomarkers/blood
*Exercise/physiology
Young Adult
Feces/microbiology
Exercise Test
Athletes
Anaerobiosis
Adult

@article {pmid40341309,
year = {2025},
author = {Coimbra, A and D'arc, M and Moreira, FRR and Cosentino, MAC and Schiffler, FB and Miranda, TDS and Mouta, R and Girardi, DL and Wanderkoke, V and Medeiros, G and Francisco, TM and Soffiati, FL and Ferreira, SS and Ruiz-Miranda, CR and Soares, MA and Santos, AFD},
title = {Fecal Virome of Southeastern Maned Sloth (Bradypus crinitus) (Pilosa: Bradypodidae).},
journal = {Genetics and molecular biology},
volume = {48},
number = {2},
pages = {e20240183},
doi = {10.1590/1678-4685-GMB-2024-0183},
pmid = {40341309},
issn = {1415-4757},
abstract = {We report a viral metagenomic analysis of fecal samples from Bradypus crinitus (Pilosa: Bradypodidae), a recently described sloth species that occurs in the Atlantic Forest of Espírito Santo and Rio de Janeiro states, Southeast Brazil. Through Illumina sequencing, we generated a total of 2,065,344 raw reads, of which 945,386 reads (45.77%) passed the quality and size filter. The highest proportion of them was assigned to Eukarya, followed by Bacteria and only a small proportion to Virus. However, we identified 24 viral families using distinct taxonomic assignment tools, including phages and vertebrate viruses, such as retroviruses and papillomaviruses. Also, we identified four bacterial genus already associated with disease in sloths. Our study sheds light on the microbiome of a previously unexplored species, further contributing to the comprehension of metagenomic global diversity.},
}

@article {pmid40341174,
year = {2025},
author = {Kalwasińska, A and Królikiewicz, I and Tirkey, SR and Szabó, A and Kumar, SB},
title = {Enhanced understanding of nitrogen fixing bacteria through DNA extraction with polyvinylidene fluoride membrane.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {16079},
pmid = {40341174},
issn = {2045-2322},
support = {101038072//European Commission/ ; 101038072//European Commission/ ; },
mesh = {*Polyvinyls/chemistry ; Triticum/microbiology ; *DNA, Bacterial/isolation & purification/genetics ; Rhizosphere ; Soil Microbiology ; *Nitrogen-Fixing Bacteria/genetics/isolation & purification/classification ; Metagenomics/methods ; Nitrogen Fixation ; Fluorocarbon Polymers ; },
abstract = {The rhizobiota, particularly nitrogen-fixing bacteria, play a crucial role in plant functioning by providing essential nutrients and defense against pathogens. This study investigated the diversity of nitrogen-fixing bacteria in a relatively understudied habitat: technosoils developed from industrial soda production. To analyze the bacterial diversity in the rhizosphere soils of wheat (Triticum aestivum L.) and aster (Tripolium pannonicum Jacq.), regions of the nifH gene were amplified and sequenced from the resident bacterial communities. A polyvinylidene fluoride (PVDF) membrane was employed for metagenomic DNA extraction, enhancing the detection of nitrogen-fixing bacteria. Prior to standard DNA extraction, an enrichment step was conducted in nitrogen-free JMV medium at 26 °C for 24 h, with a modification that replaced soil with the PVDF membrane. This approach enabled a more comprehensive analysis of the rhizosphere bacterial community, revealing that unique amplicon sequence variants (ASVs) in aster and wheat membrane samples accounted for a notable proportion of all ASVs in the dataset (8.5% and 23%, respectively) that were not captured using the standard method. Additionally, our findings demonstrated higher alpha diversity of nitrogen-fixing bacteria in the wheat rhizosphere compared to the aster rhizosphere. In wheat, the dominant genus was Insolitispirillum (38.80%), followed by unclassified genera within Gammaproteobacteria (9.76%) and Rhodospirillaceae (4.74%). In contrast, the aster rhizosphere was predominantly occupied by Azotobacter (95.69%).},
}

*Polyvinyls/chemistry
Triticum/microbiology
*DNA, Bacterial/isolation & purification/genetics
Rhizosphere
Soil Microbiology
*Nitrogen-Fixing Bacteria/genetics/isolation & purification/classification
Metagenomics/methods
Nitrogen Fixation
Fluorocarbon Polymers

@article {pmid40340931,
year = {2025},
author = {Niu, BB and Xu, JJ and Li, JA and Zhu, LD},
title = {Case report: Cervical suppurative lymphadenitis caused by burkholderia multivorans in a healthy child.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {678},
pmid = {40340931},
issn = {1471-2334},
support = {ZR2024QH132//Natural Science Foundation of Shandong Province/ ; },
mesh = {Humans ; Male ; *Lymphadenitis/microbiology/diagnosis/drug therapy/pathology ; Child, Preschool ; Anti-Bacterial Agents/therapeutic use ; *Burkholderia Infections/diagnosis/microbiology/drug therapy ; Neck/pathology/microbiology ; Lymph Nodes/pathology/microbiology ; Meropenem/therapeutic use ; },
abstract = {BACKGROUND: Cervical suppurative lymphadenitis in children is commonly caused by Staphylococcus aureus or Streptococcus pyogenes. However, cases caused by Burkholderia multivorans (BM) are rare. The clinical presentation lacks specificity, making it difficult for clinicians to recognize, which may delay diagnosis and treatment.

CASE PRESENTATION: We report a case of a 5-year-old boy admitted with recurrent fever and neck swelling. Initial treatment with meropenem and linezolid was ineffective, and symptoms persisted after 24 days of conservative therapy. Aspiration of pus yielded negative culture results. Definitive diagnosis was achieved through surgical biopsy of cervical lymph nodes, pathological examination, and metagenomic next-generation sequencing (mNGS), which identified BM as the causative pathogen. The patient was successfully treated with a combination of trimethoprim-sulfamethoxazole and meropenem. The cervical lesion exhibited granulomatous inflammation and was managed with adjunctive vacuum-assisted closure (VAC) therapy, resulting in complete wound healing without recurrence.

CONCLUSIONS: This study aims to raise awareness among all specialists about BM as a potential causative agent in cervical suppurative lymphadenitis. Early recognition and timely intervention can reduce misdiagnosis and missed diagnoses, improving patient outcomes.},
}

Humans
Male
*Lymphadenitis/microbiology/diagnosis/drug therapy/pathology
Child, Preschool
Anti-Bacterial Agents/therapeutic use
*Burkholderia Infections/diagnosis/microbiology/drug therapy
Neck/pathology/microbiology
Lymph Nodes/pathology/microbiology
Meropenem/therapeutic use

@article {pmid40340823,
year = {2025},
author = {Shen, Y and An, Z and Gao, L and Gu, M and Xia, S and Ding, Q and Li, Y and Cao, S and Li, J and Huang, J and Zhong, J and Chen, K and Wang, X and Wang, H},
title = {Integrated multi-omics analysis and functional validation uncovers RPL26 roles in regulating growth traits of Asian water buffaloes (Bubalus bubalis).},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {456},
pmid = {40340823},
issn = {1471-2164},
support = {2021YFD1200404//National Key R & D Program of China/ ; ZR2023QC252//Shandong Provincial Natural Science Foundation/ ; },
mesh = {Animals ; *Buffaloes/genetics/growth & development/metabolism ; *Ribosomal Proteins/genetics/metabolism ; Quantitative Trait Loci ; Transcriptome ; Genomics ; Metabolomics ; Metabolome ; Multiomics ; },
abstract = {BACKGROUND: Asian water buffaloes (Bubalus bubalis) in the Yangtze River Basin of China are the important meat provider for local residents because of its outstanding body size. Several previous studies have highlighted their genetic basis of growth characteristics, but the crucial genes regulating growth traits via multi-layer omics are still rarely investigated.

RESULTS: We conducted a comprehensive multi-omics analysis integrating blood and muscle transcriptome, plasma metabolome, rumen fluid metagenome, and genome of Haizi water buffaloes. Of note, ribosomal protein L26 (RPL26) located in the evolutionary selection regions associated with body sizes is the top differentially expressed gene (DEG) in both blood and muscle tissues. Further metabolomics and metagenomics identified growth-related molecular biomarkers (myristicin and Bacteroidales) and microbiological composition (Bacteroides and Prevotella). Leveraging cattle quantitative trait loci (QTLs) and genotype-tissue expression (CattleGTEx) databases, we found the significant correlations of QTL_180979 on RPL26 and two identified cis-eQTLs in muscle tissue in the upstream of RPL26 with weight gain. The follow-up cell assay validations confirmed the regulation roles of RPL26 in cell cycle, apoptosis, and differentiation, where the low RPL26 expressions enhanced the antiapoptotic ability and promoted the differentiation of myoblasts into myotubes markedly.

CONCLUSIONS: Our study illustrates RPL26 roles in regulating growth traits via both integrated multi-omics analysis and functional validations that suggests the further applications of RPL26 for growth trait selection of water buffaloes.},
}

Animals
*Buffaloes/genetics/growth & development/metabolism
*Ribosomal Proteins/genetics/metabolism
Quantitative Trait Loci
Transcriptome
Genomics
Metabolomics
Metabolome
Multiomics

@article {pmid40340756,
year = {2025},
author = {Laue, HE and Willis, AD and Wang, F and MacDougall, MC and Xu, Y and Karagas, MR and Madan, JC and Fleisch, AF and Lanphear, BP and Cecil, KM and Yolton, K and Chen, A and Buckley, JP and Braun, JM},
title = {Early-life and concurrent predictors of the healthy adolescent microbiome in a cohort study.},
journal = {Genome medicine},
volume = {17},
number = {1},
pages = {50},
pmid = {40340756},
issn = {1756-994X},
support = {K99/R00ES034086 , P01ES011261, R01ES0272244, R01ES025214//National Institute of Environmental Health Sciences,United States/ ; K99/R00ES034086 , P01ES011261, R01ES0272244, R01ES025214//National Institute of Environmental Health Sciences,United States/ ; K99/R00ES034086 , P01ES011261, R01ES0272244, R01ES025214//National Institute of Environmental Health Sciences,United States/ ; K99/R00ES034086 , P01ES011261, R01ES0272244, R01ES025214//National Institute of Environmental Health Sciences,United States/ ; K99/R00ES034086 , P01ES011261, R01ES0272244, R01ES025214//National Institute of Environmental Health Sciences,United States/ ; K99/R00ES034086 , P01ES011261, R01ES0272244, R01ES025214//National Institute of Environmental Health Sciences,United States/ ; K99/R00ES034086 , P01ES011261, R01ES0272244, R01ES025214//National Institute of Environmental Health Sciences,United States/ ; K99/R00ES034086 , P01ES011261, R01ES0272244, R01ES025214//National Institute of Environmental Health Sciences,United States/ ; R35GM133420/GM/NIGMS NIH HHS/United States ; UL1TR001425/TR/NCATS NIH HHS/United States ; UL1TR001425/TR/NCATS NIH HHS/United States ; UL1TR001425/TR/NCATS NIH HHS/United States ; UL1TR001425/TR/NCATS NIH HHS/United States ; UL1TR001425/TR/NCATS NIH HHS/United States ; UL1TR001425/TR/NCATS NIH HHS/United States ; UL1TR001425/TR/NCATS NIH HHS/United States ; },
mesh = {Humans ; Adolescent ; Female ; Male ; Child ; *Gastrointestinal Microbiome ; Feces/microbiology ; Cohort Studies ; Metagenomics/methods ; },
abstract = {BACKGROUND: The microbiome of adolescents is poorly understood, as are factors influencing its composition. We aimed to describe the healthy adolescent microbiome and identify early-life and concurrent predictors of its composition.

METHODS: We performed metagenomic sequencing of 247 fecal specimens from 167 adolescents aged 11-14 years participating in the Health Outcomes and Measures of the Environment (HOME) Study, a longitudinal pregnancy and birth cohort (Cincinnati, OH). We described common features of the adolescent gut microbiome and applied self-organizing maps (SOMs)-a machine-learning approach-to identify distinct microbial profiles (n = 4). Using prospectively collected data on sociodemographic characteristics, lifestyle, diet, and sexual maturation, we identified early-life and concurrent factors associated with microbial diversity and phylum relative abundance with linear regression models and composition with Kruskal-Wallis and Fisher's exact tests.

RESULTS: We found that household income and other sociodemographic factors were consistent predictors of the microbiome, with higher income associated with lower diversity and differential relative abundances of Firmicutes (increased) and Actinobacteria (decreased). Sexual maturation, distinct from chronological age, was related to higher diversity in females and differences in phylum relative abundances and compositional profiles in both males and females.

CONCLUSIONS: Our study suggests that adolescence is a unique window for gut microbial composition and that it may be shaped by both early-life and concurrent exposures, highlighting its potential in future epidemiologic research.},
}

Humans
Adolescent
Female
Male
Child
*Gastrointestinal Microbiome
Feces/microbiology
Cohort Studies
Metagenomics/methods

@article {pmid40340623,
year = {2025},
author = {Deng, J and Zhang, J and Su, M and Li, J and Su, Y and Zhong, Q and Hu, J and Chen, Y and Liao, S and Lin, D and Guo, X},
title = {Fusobacterium mortiferum and its metabolite 5-aminovaleric acid promote the development of colorectal cancer in obese individuals through Wnt/β-catenin pathway by DKK2.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2502138},
doi = {10.1080/19490976.2025.2502138},
pmid = {40340623},
issn = {1949-0984},
mesh = {*Colorectal Neoplasms/metabolism/microbiology/genetics/pathology ; Animals ; Humans ; Mice ; Gastrointestinal Microbiome ; *Fusobacterium/metabolism ; *Wnt Signaling Pathway/drug effects ; *Obesity/microbiology/metabolism/complications ; *Intercellular Signaling Peptides and Proteins/metabolism/genetics ; Male ; Female ; Cell Line, Tumor ; Cell Proliferation ; Mice, Inbred C57BL ; },
abstract = {Colorectal cancer (CRC) is one of the most prevalent cancers worldwide, with high incidence and mortality rates. An increasing body of research suggests that obesity is a significant risk factor for the development of CRC. Moreover, recent findings have highlighted the close association between the gut microbiota and both obesity and CRC. Despite this, the specific mechanisms by which the gut microbiota influences obesity and CRC remain unclear. This study aims to explore the role of the gut bacterium Fusobacterium mortiferum and its metabolite 5-aminovaleric acid (5-AVA) in the development of obesity and CRC. Our study found that the metabolite 5-aminovaleric acid produced by Fusobacterium mortiferum significantly inhibits the expression of the tumor suppressor DKK2. This inhibition leads to enhanced proliferation of CRC cells. Furthermore, we discovered that Fusobacterium mortiferum and 5-AVA can activate the Wnt/β-catenin signaling pathway by inhibiting DKK2, thereby promoting tumor growth. This finding was validated in CRC mouse models and in vitro experiments. Additional mechanistic studies revealed that 5-AVA interacts with the demethylase KDM6B, affecting the demethylation process of DKK2 and subsequently activating the Wnt/β-catenin signaling pathway. Our study retrospectively collected fecal samples from patients who underwent gastrointestinal endoscopy at the Sixth Affiliated Hospital of Sun Yat-sen University over the past five years. Participants were stratified into a healthy control group and an adenoma group based on the outcomes of their colonoscopies. Following this, we conducted metagenomic analysis to identify differential bacteria, and based on the results, we performed bacterial cultivation and metabolomic profiling. The roles of the targeted bacteria and their metabolites were further validated through animal models and cellular assays, employing techniques such as Western Blot, qPCR, immunohistochemistry, molecular docking simulations, and gene overexpression studies. This study uncovers the potential carcinogenic effects of Fusobacterium mortiferum and 5-AVA in the development of obesity and CRC. Our research emphasizes the complex interplay between the gut microbiota and host metabolism and suggests new directions for future research to explore how modulation of the gut microbiota could prevent and treat CRC.},
}

*Colorectal Neoplasms/metabolism/microbiology/genetics/pathology
Animals
Humans
Mice
Gastrointestinal Microbiome
*Fusobacterium/metabolism
*Wnt Signaling Pathway/drug effects
*Obesity/microbiology/metabolism/complications
*Intercellular Signaling Peptides and Proteins/metabolism/genetics
Male
Female
Cell Line, Tumor
Cell Proliferation
Mice, Inbred C57BL

@article {pmid40340466,
year = {2025},
author = {Javornik Cregeen, S and Tisza, MJ and Hanson, B and Cook, M and Surathu, A and Schneider, R and Wu, J and Short, K and Domakonda, K and Hopkins, L and Ross, MC and Petrosino, JF and Deegan, J and Stadler, LB and Boerwinkle, E and Maresso, A},
title = {Sequencing-Based Detection of Measles in Wastewater: Texas, January 2025.},
journal = {American journal of public health},
volume = {},
number = {},
pages = {e1-e5},
doi = {10.2105/AJPH.2025.308146},
pmid = {40340466},
issn = {1541-0048},
abstract = {Measles is a potentially deadly viral infection spread via respiratory droplets from infected individuals. Outbreaks occur when vaccine coverage drops below the threshold of herd, or community, immunity. Using a sequencing-based approach, we report the prospective (January 7, 2025) detection of measles in nucleic acid extracts from 2 wastewater treatment plants in Houston, Texas, with a population of more than 218 000 residents. The sequencing data from 2 samples contained 53 unique reads mapping to 11 different regions of the measles virus genome with a 99.4% match to genotype B3. Importantly, no detections were observed from 821 previous samples from the same city spanning nearly 3 years of monitoring. The findings were confirmed using droplet digital polymerase chain reaction. A concomitant investigation identified 2 unvaccinated measles-positive travelers living within the same sewershed as the wastewater detection event. This work suggests that sequencing-based wastewater analysis is valuable as a comprehensive early detection warning system that facilitates more targeted epidemiological investigation. (Am J Public Health. Published online ahead of print May 8, 2025:e1-e5. https://doi.org/10.2105/AJPH.2025.308146).},
}