@article {pmid40723361,
year = {2025},
author = {Jiang, J and Zhang, H and Hussain, M and Abdullah, and Feng, F and Guan, R and Zhong, H},
title = {Novel Approaches in Glucose and Lipid Metabolism Disorder Therapy: Targeting the Gut Microbiota-Bile Acid Axis.},
journal = {Biology},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/biology14070802},
pmid = {40723361},
issn = {2079-7737},
support = {32402088//National Natural Science Foundation of China/ ; 2024C04012//"Pioneer" and "Leading Goose" R&D Program of Zhejiang Province/ ; LQ23C200011//Zhejiang Provincial Natural Science Foundation of China/ ; KYY-HX-20230084, KYY-HX-20240810//Zhejiang University of Technology - Company Crosswise Project/ ; },
abstract = {Metabolic dysregulation involving glucose and lipids is closely associated with chronic diseases such as type 2 diabetes mellitus. Emerging evidence highlights the regulatory role of bile acid (BA)-gut microbiota interactions in these metabolic disorders. The gut microbiota orchestrates the biotransformation of primary BAs into bioactive secondary BAs, which function as endocrine signaling molecules by activating the nuclear farnesoid X receptor (FXR) and G protein-coupled membrane receptor (TGR5), forming a communication network essential for metabolic homeostasis. BAs also reciprocally modulate gut microbiota composition. This BA-gut microbiota co-metabolism has emerged as a promising therapeutic target for lipid metabolism disorders. This comprehensive review examines the bidirectional interplay between gut microbiota and BA metabolism, focusing on microbial transformation of BAs, host-microbial co-regulatory pathways and mechanisms of BA metabolism, and the therapeutic implications of modulating the gut microbiota-BA axis in addressing glucose and lipid metabolism disorders. The synthesis of current evidence aims to elucidate the intricate crosstalk between microbial ecology and host metabolism mediated by BA signaling pathways, thereby exploring novel therapeutic intervention strategies.},
}

@article {pmid40722002,
year = {2025},
author = {Jordan, S and Pothier, JF and de Maayer, P and Broders, K and Kvitko, BH and Coutinho, TA and Smits, THM},
title = {Design of genus-specific semi-nested primers for simple and accurate identification of Enterobacter strains.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {456},
doi = {10.1186/s12866-025-04175-1},
pmid = {40722002},
issn = {1471-2180},
support = {310030L_204333//Swiss National Science Foundation (SNSF)- South-African National Research Foundation (NRF) Lead Agency project/ ; 2019-51181-30013//USDA NIFA SCRI/ ; },
mesh = {*Enterobacter/genetics/classification/isolation & purification ; *Polymerase Chain Reaction/methods ; *DNA Primers/genetics ; DNA, Bacterial/genetics ; Phylogeny ; },
abstract = {BACKGROUND: The genus Enterobacter, in the family Enterobacteriaceae, is of both clinical and environmental importance. This genus has undergone frequent taxonomic changes, making it challenging to identify taxa even at genus level. This study aimed to design Enterobacter genus-specific primers that can be used for simple PCR identification of large sets of putative Enterobacter isolates.

RESULTS: Comparative genomic approaches were employed to identify genes that were universally present on Enterobacter genomes but absent from the genomes of other members of the family Enterobacteriaceae, based on an initial set of 89 genomes. The presence of these genes was further confirmed in 4,276 Enterobacter RefSeq genomes. While no strictly genus-specific genes were identified, the hpaB gene demonstrated a restricted distribution outside of the genus Enterobacter. Semi-nested primers were designed for hpaB and its flanking gene hpaC (hpaBC) and evaluated on 123 strains in single-tube PCR reactions. All taxa showing positive reactions belonged to the genus Enterobacter. For Enterobacter strains the PCR yielded two amplicons at 110 bp and at 370 bp, while strains only displaying the 110 bp amplicon were classified as Leclercia pneumoniae. A blind-test on 120 strains accessioned as Enterobacter sp. from the USDA-ARS culture collection (NRRL), revealed that one third of the strains had an incorrect genus assignment. Comparison of gene trees of the hpaBC fragment sequences with marker genes frequently used for single-gene barcoding or multi-locus sequence analysis (MLSA) further demonstrated its potential for preliminary species identification.

CONCLUSIONS: The nested PCR assay represents a rapid and cost-effective approach for preliminary identification of Enterobacter species. As the primer design was based on large-scale genomic comparison, including currently undescribed species clades, it will remain valid even after taxonomic changes within the genus.},
}

*Enterobacter/genetics/classification/isolation & purification
*Polymerase Chain Reaction/methods
*DNA Primers/genetics
DNA, Bacterial/genetics
Phylogeny

@article {pmid40721486,
year = {2025},
author = {de Aviz, RO and Campos, JR and Silva, DEO and Barbosa, LMP and Costa, RM and Borges, JF and Leite, MRL and Rocha, SMB and Morais, PGC and Dauala, GA and Pereira, APA and de Medeiros, EV and Araujo, ASF},
title = {Microbial biomass and enzymatic activity in the rhizosphere of prickly-pear cactus genotypes inoculated with Bacillus subtilis and Paenibacillus Sp.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {27415},
pmid = {40721486},
issn = {2045-2322},
mesh = {*Rhizosphere ; *Paenibacillus/physiology ; *Bacillus subtilis/physiology ; Biomass ; Genotype ; Soil Microbiology ; *Cactaceae/microbiology/genetics ; },
abstract = {Some bacterial taxa, such as Bacillus and Paenibacillus, are known to colonize the rhizosphere and promote plant growth. However, little is known about their effect on microbial biomass and enzymatic activity in the rhizosphere of plants under semi-arid conditions. This field study assessed the effects of B. subtilis and Paenibacillus sp. in the rhizosphere of two prickly-pear cactus genotypes on microbial biomass of C, N, and P, and on enzymatic activity during early and late growth stages. The analysis of variance showed that microbial biomass and enzymatic activity were significantly influenced by the interaction between PGPB taxa (B. subtilis and Paenibacillus sp.), prickly-pear cactus genotypes ('Baiana' and 'Doce'), and plant growth stage (90 and 270 days). Specifically, PGPB inoculation increased microbial biomass P, β-glucosidase, and acid phosphatase, while microbial biomass of C and N were primarily driven by differences between cactus genotypes 'Baiana' and 'Doce'. At the early growth stage (90 days), the highest values of microbial biomass C, P, and acid phosphatase were observed, whereas N biomass was higher at the later stage (270 days). B. subtilis increased microbial biomass P in the 'Doce' genotype and acid phosphatase in 'Baiana,' while Paenibacillus sp. increased β-glucosidase in 'Baiana.' The combination of the 'Doce' genotype with B. subtilis enhanced phosphorus availability, suggesting that specific plant-microbe interactions may benefit nutrient acquisition in arid, nutrient-poor soils; however, further research is needed to confirm whether this effect extends to other genotypes.},
}

*Rhizosphere
*Paenibacillus/physiology
*Bacillus subtilis/physiology
Biomass
Genotype
Soil Microbiology
*Cactaceae/microbiology/genetics

@article {pmid40719475,
year = {2025},
author = {Fan, X and Guo, X and Qi, Q and Gui, H and Li, Y and Yang, Y and He, J-S and Wu, L},
title = {Long-term elevated precipitation promotes an acid metabolic preference in soil microbial communities in a Tibetan alpine grassland.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0047025},
doi = {10.1128/msystems.00470-25},
pmid = {40719475},
issn = {2379-5077},
abstract = {Alpine ecosystems store vast amounts of soil organic carbon but are highly sensitive to climate change. Despite this, the response of in situ soil microbial metabolic processes, especially carbon substrate utilization, to climatic shifts remains underexplored. Here, we assessed microbial activity by metatranscriptomics in a Tibetan alpine grassland after a decade of experimental warming (+2°C) and altered precipitation (+50% and -50% of ambient precipitation). The experiment revealed that altered precipitation, rather than warming, shaped the active microbial community. Altered precipitation and warming had significant interactions: warming combined with increased precipitation generally suppressed microbial carbohydrate metabolism and methane oxidation, while warming with decreased precipitation enhanced these processes. Notably, increased precipitation induced a shift in microbial communities towards acid metabolism over sugar metabolism, predominantly driven by taxa such as Betaproteobacteria. This metabolic shift corresponded with an increased emission ratio of methane (CH4) to carbon dioxide (CO2), a change primarily driven by CH4, underscoring the critical role of microbial carbon metabolic preferences in regulating greenhouse gas emissions. Our findings highlight the necessity of integrating microbial carbon metabolic preferences and their interactions with climatic factors into models to accurately predict carbon-climate feedbacks.IMPORTANCEMicrobes have specific preferences for different carbon substrates, but their responses to climate change remain unclear. Our study, conducted through a long-term climate manipulation experiment in a Tibetan alpine grassland, reveals that increased precipitation leads soil microbial communities to favor acid metabolism over sugar metabolism. This shift significantly affects greenhouse gas emissions by increasing the CH4/CO2 ratio, which has important implications for global warming. These findings are crucial for accurately forecasting carbon-climate feedbacks and managing alpine ecosystems as climate change progresses.},
}

@article {pmid40715283,
year = {2025},
author = {Tan, JH and Liew, KJ and Sani, RK and Samanta, D and Pointing, SB and Chan, KG and Goh, KM},
title = {Microbial diversity and metabolic predictions of high-temperature streamer biofilms using metagenome-assembled genomes.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {27297},
pmid = {40715283},
issn = {2045-2322},
mesh = {*Biofilms/growth & development ; *Hot Springs/microbiology ; *Metagenome ; Hot Temperature ; *Bacteria/genetics/metabolism/classification ; Microbiota ; Phylogeny ; Biodiversity ; Genome, Bacterial ; Metagenomics/methods ; Malaysia ; },
abstract = {High-temperature streamer biofilm communities (SBCs) are often dominated by Aquificota, which can comprise over 90% of the microbial population in shallow water channels, such as those found at Mammoth hot springs of Yellowstone National Park and the Rehai hot springs in China. This study examines SBCs from the Dusun Tua (DT) hot spring in Malaysia (75 °C, pH 7.6), where Aquificota accounted for only ~ 35% of the total amplicon sequence variants. Amplicon and hybrid metagenomic sequencing revealed a more balanced microbial community, co-dominated by Aquificota, Chloroflexota, Desulfobacterota, Bacteroidota, Deinococcota, and Candidatus Hydrothermae, along with Thermoproteota and Micrarchaeota. To our knowledge, the co-dominance of Aquificota and Chloroflexota in SBCs has not been previously reported. The unexpected abundance of Chloroflexota may stem from dispersal from upstream Cyanobacteriota-Chloroflexota biofilms, contributing to community diversification. Genome-resolved analyses identified more than 60 medium- to high-quality metagenome-assembled genomes (MAGs), suggesting that biofilm formation was initially driven by chemoautotrophic sulfur oxidation and CO2 fixation, followed by the gradual integration of heterotrophic taxa. Nitrogen cycling and hydrogen oxidation are likely to contribute additional sources of energy. The presence of diverse CAZymes suggests that plant litter may serve as an additional carbon source. Genome-centric analyses across multiple phyla indicated that extracellular polymeric substances (EPS), curli fibers, and other matrix components contribute to the biofilm matrix, enhancing structural resilience and supporting persistence under harsh conditions. Overall, this study highlights the distinct microbial ecology of the DT SBC and broader metabolic roles beyond Aquificota dominance. The genes identified in this study may hold biotechnological potential and serve as a valuable resource for future enzyme discovery and functional screening.},
}

*Biofilms/growth & development
*Hot Springs/microbiology
*Metagenome
Hot Temperature
*Bacteria/genetics/metabolism/classification
Microbiota
Phylogeny
Biodiversity
Genome, Bacterial
Metagenomics/methods
Malaysia

@article {pmid40713799,
year = {2025},
author = {Soleimani Samarkhazan, H and Nouri, S and Maleknia, M and Aghaei, M},
title = {"The microbiome in graft-versus-host disease: a tale of two ecosystems".},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {832},
pmid = {40713799},
issn = {1479-5876},
mesh = {*Graft vs Host Disease/microbiology/therapy ; Humans ; *Microbiota ; Hematopoietic Stem Cell Transplantation ; Animals ; *Ecosystem ; Fecal Microbiota Transplantation ; Dysbiosis ; },
abstract = {Graft-versus-host disease (GVHD), a life-threatening complication of allogeneic hematopoietic stem cell transplantation (HSCT), is shaped by a dynamic interplay between two microbial ecosystems: the recipient's disrupted microbiome and the donor's transplanted microbiota. This narrative review unravels the "tale of two ecosystems," exploring how pre-transplant chemotherapy, radiation, and antibiotics induce recipient dysbiosis-marked by loss of beneficial taxa (Clostridia, Faecalibacterium) and dominance of pathobionts (Enterococcus). These shifts impair barrier integrity, fuel systemic inflammation, and skew immune responses toward pro-inflammatory T-cell subsets, exacerbating GVHD. Conversely, emerging evidence implicates donor microbiota in modulating post-transplant immune reconstitution, though its role remains underexplored. Therapeutic strategies, including probiotics, prebiotics, and fecal microbiota transplantation (FMT), demonstrate promise in restoring microbial balance, enhancing short-chain fatty acid (SCFA)-driven immune regulation, and reducing GVHD severity. However, challenges such as strain-specific efficacy, safety in immunocompromised hosts, and protocol standardization persist. By bridging microbial ecology and immunology, this review underscores the microbiome's transformative potential in redefining GVHD management and advocates for personalized, microbiome-targeted interventions to improve HSCT outcomes.},
}

*Graft vs Host Disease/microbiology/therapy
Humans
*Microbiota
Hematopoietic Stem Cell Transplantation
Animals
*Ecosystem
Fecal Microbiota Transplantation
Dysbiosis

@article {pmid40711892,
year = {2025},
author = {Turner, D and Adriaenssens, EM and Amann, RI and Bardy, P and Bartlau, N and Barylski, J and Błażejak, S and Bouzari, M and Briegel, A and Briers, Y and Carrillo, D and Chen, X and Claessen, D and Cook, R and Crisci, MA and Dechesne, A and Deptula, P and Dutilh, BE and Ely, B and Fieseler, L and Fogg, PCM and Fukudome, A and Ganjoor, MS and Gientka, I and Holmfeldt, K and Kalatzis, PG and Kauffman, KM and Kempff, A and Knezevic, P and Koonin, EV and Kropinski, AM and Krupovic, M and Kurtböke, I and Lambon, K and Lavigne, R and Lehman, SM and Liu, HT and Lood, C and Lurz, R and Mäntynen, S and Matrishin, CB and Middelboe, M and Millard, AD and Moraru, C and Nielsen, DS and Nobrega, FL and Nunoura, T and Oksanen, HM and Ongenae, V and Parra, B and Pas, C and Pogliano, J and Poranen, MM and Potipimpanon, S and Prichard, A and Pye, HV and Rothschild-Rodriguez, D and Rozen, DE and Santini, JM and Sha, Y and Shymialevich, D and Sokołowska, B and Soleimani-Delfan, A and Średnicka, P and Tavares, P and Telatin, A and Tolstoy, I and Urayama, SI and van Neer, V and Vogensen, FK and Wen, Q and Wichels, A and Wójcicki, M and Ictv Taxonomy Summary Consortium, and , },
title = {Summary of taxonomy changes ratified by the International Committee on Taxonomy of Viruses (ICTV) from the Bacterial Viruses Subcommittee, 2025.},
journal = {The Journal of general virology},
volume = {106},
number = {7},
pages = {},
doi = {10.1099/jgv.0.002111},
pmid = {40711892},
issn = {1465-2099},
mesh = {*Viruses/classification/genetics ; *Bacteria/virology ; Phylogeny ; *Classification/methods ; },
abstract = {This article summarises the activities of the International Committee on Taxonomy of Viruses Bacterial Viruses Subcommittee, detailing developments in the classification of bacterial viruses. We provide here an overview of all new, abolished, moved and renamed taxa proposed in 2024, approved by the Executive Committee, and ratified by membership vote in 2025. Through the collective efforts of 74 international contributors of taxonomy proposals in this round, 43 ratified proposals have led to the creation of one new phylum, one class, four orders, 33 families, 14 subfamilies, 194 genera and 995 species. These proposals mark significant progress in refining the taxonomy of bacterial viruses. Key updates include the creation of new orders and families that include existing taxa to better reflect genomic and evolutionary relationships. As sequencing and bioinformatics approaches continue to advance, further expansion and refinements in viral taxonomy can be anticipated in the coming years.},
}

*Viruses/classification/genetics
*Bacteria/virology
Phylogeny
*Classification/methods

@article {pmid40711674,
year = {2025},
author = {Xiong, Q and Wang, R and Lai, D and Cai, S and Wang, H and Zhou, N},
title = {Metagenomic Insights into the Root‒Soil Response Mechanisms of Indica and Japonica Rice Under Nitrogen Deficiency and High-Efficiency Nitrogen Compensation.},
journal = {Rice (New York, N.Y.)},
volume = {18},
number = {1},
pages = {72},
pmid = {40711674},
issn = {1939-8425},
support = {32101816//National Natural Science Foundation of China/ ; 2021M702768//China Postdoctoral Science Foundation/ ; 2021K292B//Jiangsu Province Postdoctoral Research Funding/ ; 2021KY47//Jiangxi Province Postdoctoral Scientific Research Funding/ ; 202425YBKT17//Jiangxi Provincial Water Resources Department Science and Technology Project/ ; 20242BAB20263//Natural Science Foundation of Jiangxi Province/ ; PAPD//Priority Academic Program Development of Jiangsu Higher Education Institutions/ ; },
abstract = {Nitrogen (N) dynamics critically regulate rice productivity through root-mediated absorption and assimilation processes. This study investigates the differential responses of japonica (Suxiu 867) and indica (Yangxianyou 918) rice to N deficiency and subsequent high-efficiency compensation, integrating metagenomic analysis with physiological assessments of N metabolism. Building on an established high-efficiency N compensation period (18 days after tillering for japonica and 12 days for indica), we demonstrate that optimized N compensation significantly enhances dry matter accumulation and yield in both subspecies through distinct biological mechanisms. Compensation treatment elevated key metabolic indicators including soluble protein content (Cpr), glutamine synthetase (GDH) activity, soil urease (S-UE) activity, glutamate synthase (GOGAT) activity, and glutamine synthetase (GS) activity, collectively enhancing N assimilation efficiency. Rhizosphere microbiome restructuring showed subspecies-specific patterns, with Chloroflexi and Betaproteobacteria abundance positively correlating with N metabolic enzymes in indica, versus Actinomycetia, Deltaproteobacteria associations in japonica. Functional microbial analysis revealed divergent keystone taxa, with Noviherbaspirillum (indica) and Bacillus (japonica) driving N conversion efficiencies through niche-specific community synergies. Notably, indica rice presented a relatively high N absorption capacity and conversion efficiency, while japonica rice presented relatively stable N absorption and distribution mechanisms, and relatively high N fertilizer application significantly increased the abundance of specific microbial communities in japonica rice. These findings elucidate how subspecies-specific root physiology coordinates with rhizosphere microbial ecology to optimize N utilization, providing actionable insights for precision N management strategies tailored to rice genetic types.},
}

@article {pmid40711470,
year = {2025},
author = {Lera-Lozano, D and Ruiz-Toquica, JS and Kratman, SA and Holt, MW and McIntyre, CA and Jones, EK and Lopez-Victoria, M and Ritchie, KB and Medina, M and González-Pech, RA},
title = {Genomic potential of crustose coralline algae-associated bacteria for the biosynthesis of novel antimicrobials.},
journal = {Microbial genomics},
volume = {11},
number = {7},
pages = {},
doi = {10.1099/mgen.0.001456},
pmid = {40711470},
issn = {2057-5858},
mesh = {*Bacteria/genetics/metabolism/isolation & purification/classification ; *Rhodophyta/microbiology ; Biosynthetic Pathways/genetics ; *Anti-Bacterial Agents/biosynthesis ; Multigene Family ; *Anti-Infective Agents/metabolism ; Genome, Bacterial ; Animals ; *Anthozoa/microbiology ; Genomics ; Microbiota/genetics ; Phylogeny ; },
abstract = {The global rise of antimicrobial resistance has intensified efforts in bioprospecting, with researchers increasingly exploring unique marine environments for novel antimicrobials. In line with this trend, our study focused on bacteria isolated from the unique microbiome of crustose coralline algae (CCA), which has yet to be investigated for antimicrobial discovery. In the present work, bacteria were isolated from a CCA collected from Varadero Reef located in Cartagena Bay, Colombia. After performing antimicrobial assays against antibiotic-resistant human and marine pathogens, three isolates were selected for genome sequencing using the Oxford Nanopore technology. Genome mining of the high-quality assemblies revealed 115 putative biosynthetic gene clusters (BGCs) and identified genes in relevant biosynthetic pathways across the three genomes. Nonetheless, we hypothesize that the biosynthesis of antimicrobial compounds results from the expression of undescribed BGCs. Further analysis revealed the absence of genes pertaining to the synthesis of coral larvae settling molecule tetrabromopyrrole, commonly produced by CCA-associated bacteria. We also discuss how differential representation of gene functions between the three isolates may be attributed to the distinct ecological niches they occupy within the CCA. This study provides valuable resources for future research aimed at the discovery of novel antimicrobials, particularly in the face of the antibiotic-resistance global crisis, and highlights the potential of specialized marine environments like CCA.},
}

*Bacteria/genetics/metabolism/isolation & purification/classification
*Rhodophyta/microbiology
Biosynthetic Pathways/genetics
*Anti-Bacterial Agents/biosynthesis
Multigene Family
*Anti-Infective Agents/metabolism
Genome, Bacterial
Animals
*Anthozoa/microbiology
Genomics
Microbiota/genetics
Phylogeny

@article {pmid40709922,
year = {2025},
author = {Li, H and Li, W and Liu, X and Zhang, J and Lin, C and Ji, S and Jiang, H and Wang, T and Su, Z},
title = {The gut microbiota features and the application value in predicting recurrent risks for gallstone patients who underwent laparoscopic cholecystectomy.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0176024},
doi = {10.1128/msystems.01760-24},
pmid = {40709922},
issn = {2379-5077},
abstract = {Gut microbiota is associated with gallstone occurrence and recurrence. But whether they can predict post-cholecystectomy choledocholithiasis recurrence needs to be investigated. From September 2020 to June 2021, a total of 100 symptomatic gallstone patients scheduled for laparoscopic cholecystectomy were enrolled in the Disease group in the Department of Hepatobiliary Surgery at Quanzhou First Hospital. Meanwhile, a total of 50 age- and sex-matched healthy controls were included in the Control group. Fecal specimens were collected from both groups and subjected to 16S rDNA sequencing (V3V4 region) for microbiologic analysis. After laparoscopic cholecystectomy, patients were followed up, and recurrent cases were recorded. Finally, a nomogram for predicting recurrent risks was built. The gut microbial diversity in the Disease group was significantly lower than that of the Control group (all P < 0.05). The Chao1 index of the recurrent group was remarkably lower than the control group (P < 0.05). Linear discriminant analysis (LDA) effect size (LEfSe) analysis showed that Phocaeicola dorei (LDA score = 4.2, P < 0.05) was the feature microbiota in the recurrent group. Logistic regression analysis showed that the composition of stones, the high abundances of P. dorei and Fusobacterium necrogenes were potential risk factors for recurrent choledocholithiasis, and a nomogram based on these factors demonstrated high accuracy and excellent calibration. This study has identified potential risk factors for recurrent choledocholithiasis and built a nomogram that can well predict recurrent risks for patients who undergo cholecystectomy, which might serve as a useful tool for patients' stratification and post-surgery management.IMPORTANCEThis study identifies specific gut microbiome signatures of gallstone patients and indicates that reduced diversity and high abundances of Phocaeicola dorei and Fusobacterium necrogenes might be potential predictors for choledocholithiasis recurrence after cholecystectomy. By demonstrating a link between gut microbiota composition and post-surgical recurrence risk, it advances our understanding beyond simple association with predictive capability. The development of a nomogram incorporating these microbial markers provides a novel, clinically applicable tool for accurate risk stratification of patients undergoing cholecystectomy, therefore bridging the gap between microbial ecology and clinical practice. The significance of this study lies in that it aims to address a critical unmet need in gallstone disease management by offering a more cost-effective and non-invasive tool to improve long-term patient outcomes and pave the way for microbiome-targeted interventions.CLINICAL TRIALSThis study is registered with Chinese Clinical Trial Registry Center as ChiCTR2400090232.},
}

@article {pmid40708948,
year = {2025},
author = {Zai, X and Zhu, F and Zhao, M and Diao, X and Zhang, F and Dini-Andreote, F and Melkonian, C and Medema, MH and Raaijmakers, JM and Cordovez, V and Song, C},
title = {Harnessing the phyllosphere microbiota of wild foxtail millet for designing beneficial cross-kingdom synthetic communities.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf066},
pmid = {40708948},
issn = {2730-6151},
abstract = {Understanding the interplay between mechanisms in plant microbiome assembly and functioning of wild ancestors has led to the proposal of a novel strategy to enhance resilience to the (a)biotic stresses of domesticated crops. The challenge is determining how to harness the diverse microbiota of wild crop ancestors in their natural habitats in order to design effective synthetic microbial communities (SynComs) that reconstitute specific microbiome-associated plant phenotypes. In this study, we profiled the phyllosphere microbiota of wild green foxtail collected from seven geographically diverse natural ecosystems and showed that variations in soil parameters and climatic conditions as well as plant genetic distance significantly correlated with bacterial and fungal community compositions. Environmental selection and dispersal limitation differently governed the assembly of bacterial and fungal communities with distinct habitat niche breadth. Specific bacterial and yeast genera were identified as core phyllosphere taxa of wild green foxtail millet on the basis of their abundance and prevalence across the seven sampling sites. Moreover, several genera of bacteria (Bacillus, Pantoea, Methylobacterium) and yeast (Vishniacozyma, Filobasidium, Sporobolomyces) displayed significant correlations with the abundances of one or more foliar pathogenic fungi, in particular fungi of the genus Alternaria. Subsequent isolation and characterization of these bacterial and yeast genera allowed the design of cross-kingdom SynComs that protected domesticated foxtail millet from leaf infections by Alternaria alternata. These results provide fundamental insight into the mechanisms governing the phyllosphere microbiota assembly of a wild crop ancestor across large geographic scales and a practical framework to leverage this fundamental knowledge for the design of SynComs that mitigate the biotic stress of the domesticated crop.},
}

@article {pmid40708946,
year = {2025},
author = {Liu, ZQ and Yang, XY and Chen, JH and Ge, SC and Dai, SX and Zhu, SH and Xian, ZY},
title = {From dysbiosis to precision therapy: decoding the gut-bladder axis in bladder carcinogenesis.},
journal = {Frontiers in oncology},
volume = {15},
number = {},
pages = {1630726},
pmid = {40708946},
issn = {2234-943X},
abstract = {The gut-bladder axis (GBA), a bidirectional network connecting gastrointestinal and urinary systems, has recently emerged as a pivotal focus in bladder cancer research. Beyond conventional risk factors, gut dysbiosis, aberrant microbial metabolites, and neuro-immune pathway disruptions have been implicated in tumorigenesis and progression. Short-chain fatty acids (SCFAs), microbial-derived metabolites, are shown to indirectly modulate tumor behavior through immune microenvironment regulation and inflammatory response attenuation. Cross-organ crosstalk is further mediated by neural pathways (e.g., vagal signaling) and shared receptors, including the Farnesoid X Receptor (FXR) and Toll-like Receptor 4 (TLR4). Novel therapies leveraging microbial ecology principles demonstrate potential, including immune checkpoint inhibitors combined with microbiota modulation (e.g., Parabacteroides distasonis-enhanced PD-1 efficacy), probiotics to reverse chemoresistance, and microbiota reprogramming for SCFA-targeted strategies. However, molecular mechanisms underlying GBA-host interactions remain poorly characterized. Clinical translation is hindered by limited cohort sizes and interindividual heterogeneity. Current studies, while revealing partial pathways, face methodological inconsistencies, particularly in urinary microbiome profiling, and a lack of longitudinal human data. Future breakthroughs will require multi-omics integration, organoid-based models, and interdisciplinary collaboration to address these gaps.},
}

@article {pmid40708752,
year = {2025},
author = {Zhang, Y},
title = {Fucoidan as a therapeutic agent for ulcerative colitis: mechanisms of action and modulation of the gut microbiota.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1626614},
pmid = {40708752},
issn = {2235-2988},
mesh = {*Polysaccharides/pharmacology/therapeutic use ; Humans ; *Gastrointestinal Microbiome/drug effects ; *Colitis, Ulcerative/drug therapy/microbiology ; Animals ; Cytokines/metabolism ; *Anti-Inflammatory Agents/pharmacology/therapeutic use ; NF-kappa B/metabolism ; Signal Transduction/drug effects ; },
abstract = {Ulcerative colitis (UC), a chronic inflammatory bowel disease driven by gut dysbiosis, immune dysregulation, and oxidative stress, lacks universally effective therapies. Fucoidan (FCD), a sulfated polysaccharide derived from brown algae, has emerged as a multifaceted therapeutic candidate due to its anti-inflammatory, antioxidant, and immunomodulatory properties. This review synthesizes FCD's mechanisms in UC pathogenesis, emphasizing its suppression of NF-κB and MAPK signaling pathways to reduce proinflammatory cytokines (e.g., IL-6, TNF-α) and regulate TLR-mediated macrophage polarization. FCD enhances intestinal barrier integrity via upregulation of tight junction proteins (Claudin-1, ZO-1) and mucin MUC2 expression, while remodeling gut microbial ecology through enrichment of SCFAs-producing bacteria (e.g., Ruminococcaceae) and suppression of pathogens (Escherichia coli, Candida albicans). Preclinical studies highlight LMWF as a superior candidate, demonstrating enhanced bioavailability and efficacy in mitigating DSS-induced colitis. Despite its promise, challenges persist in structural heterogeneity (source- and extraction-dependent), scalable production of LMWF, and insufficient pharmacokinetic data. Emerging strategies-including nanoparticle-based delivery systems and structural modifications (cross-linking, covalent bonding)-aim to overcome bioavailability limitations. This review underscores FCD's potential as a functional food or adjuvant therapy for UC, while advocating for rigorous clinical validation to bridge translational gaps, Enrichment of SCFAs-producing taxa and suppression of pathobionts (Escherichia coli, Candida albicans), mediated through prebiotic fermentation. Suppression of NF-κB activation via IκBα stabilization and inhibition of p65 nuclear translocation, and downregulation of MAPK phosphorylation (ERK1/2, JNK, p38), reducing proinflammatory cytokines (IL-6, TNF-α, IL-1β). FCD can be used as a potential treatment for UC.},
}

*Polysaccharides/pharmacology/therapeutic use
Humans
*Gastrointestinal Microbiome/drug effects
*Colitis, Ulcerative/drug therapy/microbiology
Animals
Cytokines/metabolism
*Anti-Inflammatory Agents/pharmacology/therapeutic use
NF-kappa B/metabolism
Signal Transduction/drug effects

@article {pmid40708120,
year = {2025},
author = {Perkins, AK and Grossart, HP and Rojas-Jimenez, K and Retter, A and Oakes, JM},
title = {The Functional Role of Fungi and Bacteria in Sulfur Cycling During Kelp (Ecklonia Radiata) Degradation: Unconventional Use of PiCrust2.},
journal = {Environmental microbiology reports},
volume = {17},
number = {4},
pages = {e70140},
doi = {10.1111/1758-2229.70140},
pmid = {40708120},
issn = {1758-2229},
support = {RRF-2.3.1-21-2022-00008//National Laboratory for Water Science and Water Security, HUN-REN Balaton Limnological Research Institute/ ; DFG GR1540/47-1//Deutsche Forschungsgemeinschaft/ ; },
mesh = {*Sulfur/metabolism ; *Bacteria/metabolism/genetics/classification ; *Fungi/metabolism/genetics/classification ; *Kelp/microbiology/metabolism ; Metabolic Networks and Pathways ; Ecosystem ; High-Throughput Nucleotide Sequencing ; },
abstract = {Macroalgae is a major source of detritus in coastal ecosystems, contributing approximately 1521 ± 732 Tg C year[-1] to global net primary production. Fungal remineralisation of Ecklonia radiata detritus produces substantial amounts of dimethylsulfoniopropionate, total alkalinity, and dissolved inorganic carbon, supporting coastal biogeochemical cycles. To expand on the role of fungi during E. radiata degradation, we examined changes in fungal and bacterial communities at the start and after 21 days in a mesocosm, comparing microbial functional roles between blades and stipes. We employed next-generation sequencing to evaluate the potential contributions of fungi and bacteria, and additionally utilized FUNGuild, FungalTraits, and PiCrust2 databases. We cross-referenced the metabolic pathways predicted by PiCrust2 with the literature to determine whether these pathways have been documented in fungi. Of the 423 metabolic pathways identified, 342 have also been reported in fungi, including 281 redox-related pathways, 220 associated with nicotinamide adenine dinucleotide, and 194 linked to sulfur metabolism. These overlaps suggest that bacteria and fungi could play complementary roles in kelp degradation, contributing distinct yet interconnected functions. Our results highlight that these metabolic pathways cannot be attributed to bacteria alone and fungi are essential to kelp remineralisation.},
}

*Sulfur/metabolism
*Bacteria/metabolism/genetics/classification
*Fungi/metabolism/genetics/classification
*Kelp/microbiology/metabolism
Metabolic Networks and Pathways
Ecosystem
High-Throughput Nucleotide Sequencing

@article {pmid40707845,
year = {2025},
author = {Jürisoo, L and Agan, A and Tedersoo, L and Witzell, J and Selikhovkin, A and Drenkhan, R},
title = {Fungal Assemblages in Northern Elms-Impacts of Host Identity and Health, Growth Environment, and Presence of Dutch Elm Disease.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {82},
pmid = {40707845},
issn = {1432-184X},
support = {PRG1615//Estonian Research Competency Council/ ; TEMTA22//the European Union and Ministry of Education and Research/ ; },
mesh = {*Plant Diseases/microbiology ; *Ulmus/microbiology/growth & development/genetics ; Estonia ; Endophytes/genetics/classification/isolation & purification ; *Mycobiome ; *Ophiostoma/genetics/isolation & purification ; Russia ; *Fungi/classification/genetics/isolation & purification ; },
abstract = {Dutch elm disease (DED), caused by the pathogenic ascomycete Ophiostoma novo-ulmi, has devastated natural elm (Ulmus spp.) populations in Europe and North America. Elm species vary in their susceptibility to this vascular disease, which may partly reflect differences in their associated mycobiomes. To investigate the diversity and composition of fungal endophyte communities in relation to host genotype, health status, and environment, we analyzed twig-associated fungi in symptomatic and asymptomatic individuals of highly susceptible U. glabra, less susceptible U. laevis, and hybrid elms growing in Estonia and Russia. Fungal communities were analyzed using PacBio long-read amplicon sequencing of the ITS1-5.8S-ITS2 gene region. Tree species exhibited distinct fungal community profiles. Ophiostoma novo-ulmi was detected exclusively in symptomatic trees and was dominant in U. glabra; it was absent in symptomatic hybrid elms. In contrast, the canker-associated pathogen Sphaeropsis ulmicola occurred in both symptomatic and asymptomatic trees, was dominant in symptomatic U. laevis, and common in symptomatic and healthy U. glabra, though less prevalent in symptomatic hybrid elms. Remarkably, S. ulmicola was associated with the highest level of damage in U. laevis while being present also in hybrid elms. While O. novo-ulmi's presence did not affect overall fungal richness, S. ulmicola was linked to higher fungal diversity. Additionally, fungal species richness was significantly greater in urban compared to rural environments. This was the first comparable analysis of fungal diversity and composition on three different Ulmus species shoots.},
}

*Plant Diseases/microbiology
*Ulmus/microbiology/growth & development/genetics
Estonia
Endophytes/genetics/classification/isolation & purification
*Mycobiome
*Ophiostoma/genetics/isolation & purification
Russia
*Fungi/classification/genetics/isolation & purification

@article {pmid40707215,
year = {2025},
author = {Li-Hau, F and Nakagawa, M and Kakegawa, T and Ward, LM and Ueno, Y and McGlynn, SE},
title = {Metabolic Potential and Microbial Diversity of Late Archean to Early Proterozoic Ocean Analog Hot Springs of Japan.},
journal = {Microbes and environments},
volume = {40},
number = {3},
pages = {},
doi = {10.1264/jsme2.ME24067},
pmid = {40707215},
issn = {1347-4405},
mesh = {*Hot Springs/microbiology/chemistry ; Japan ; *Bacteria/classification/metabolism/genetics/isolation & purification ; *Archaea/classification/metabolism/genetics/isolation & purification ; Oxidation-Reduction ; Phylogeny ; Nitrogen Fixation ; Oceans and Seas ; Iron/metabolism ; *Biodiversity ; Carbon Cycle ; RNA, Ribosomal, 16S/genetics ; Nitrogen Cycle ; Hydrogen/metabolism ; },
abstract = {Circumneutral iron-rich hot springs may represent analogues of Neoarchean to Paleoproterozoic oceans of early Earth, potentially providing windows into ancient microbial ecology. Here we sampled five Japanese hot springs to gain insights into functional processes and taxonomic diversity in these analog environments. Amplicon and metagenomic sequencing confirm a hypothesis where taxonomy is distinct between sites and linked to the geochemical setting. Metabolic functions shared among the springs include carbon fixation via the reductive pentose phosphate cycle, nitrogen fixation, and dissimilatory iron oxidation/reduction. Among the sites, Kowakubi was unique in that it was dominated by Hydrogenophilaceae, a group known for performing hydrogen oxidation, motivating a hypothesis that H2 as an electron donor may shape community composition even in the presence of abundant ferrous iron. Evidence for nitrogen cycling across the springs included N2 fixation, dissimilatory nitrate reduction to ammonia (DNRA), and denitrification. The low-salinity springs Furutobe and OHK lacked evidence for ammonium oxidation by ammonia monooxygenase, but evidence for complete nitrification existed at Kowakubi, Jinata, and Tsubakiyama. In most sites, the microaerophilic iron-oxidizing bacteria from the Zetaproteobacteria or Gammaproteobacteria classes had higher relative abundances than Cyanobacteria. Microaerophilic iron oxidizers may outcompete abiotic Fe oxidation, while being fueled by oxy-phototrophic Cyanobacteria. Our data provide a foundation for considering which factors may have controlled productivity and elemental cycling as Earth's oceans became oxygenated at the onset of the Great Oxidation Event.},
}

*Hot Springs/microbiology/chemistry
Japan
*Bacteria/classification/metabolism/genetics/isolation & purification
*Archaea/classification/metabolism/genetics/isolation & purification
Oxidation-Reduction
Phylogeny
Nitrogen Fixation
Oceans and Seas
Iron/metabolism
*Biodiversity
Carbon Cycle
RNA, Ribosomal, 16S/genetics
Nitrogen Cycle
Hydrogen/metabolism

@article {pmid40705368,
year = {2025},
author = {Duff, AM and Giles, M and Ganasamurthy, S and Santos, A and Morales, SE and Brennan, F},
title = {Counting soil microbial communities: the impact of qPCR platform and mastermix on accuracy and precision.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf073},
pmid = {40705368},
issn = {1574-6941},
abstract = {Quantitative PCR (qPCR) is widely used in soil microbial ecology to quantify microbial communities, but its accuracy can be compromised by co-extracted inhibitors. Furthermore, large scale international studies involving multiple laboratories or meta-analyses studies can introduce variation in qPCR results when data generated from different sources are compared. This study evaluated the performance of four commercial mastermixes across different soil types, a mock community, and a positive template control against three targets on three widely used platforms. Sensitivity to inhibitors was tested, with one mastermix affected, although this was mitigated by adding 1 mg ml-1 BSA. Amplification success varied by mastermix, platform, gene, and sample matrix. Most mastermix-platform combinations showed low accuracy emphasising the need for careful pairing. Precision was primarily influenced by gene target, followed by platform, sample matrix, and mastermix, and was reduced at lower template concentrations. Only 64.67% of intra-assay (within an assay) measurements meet accepted thresholds. Inter-assay (between platforms) quantification was unreliable due to significant variability, which increased the risk of inaccurate data interpretation. The study highlights the necessity of considering inter and intra assay variation, assay accuracy and inhibitors that may impact sample amplification when utilising qPCR for quantification of microbial communities in environmental samples.},
}

@article {pmid40705167,
year = {2025},
author = {Gdanetz, K and Noel, ZA and Saville, K and Marsh, T and Scribner, KT and Trail, F},
title = {Eukaryotic Microbiome of Lake Sturgeon Eggs, and Identification of Chemical Thresholds for Infection Control.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {80},
pmid = {40705167},
issn = {1432-184X},
mesh = {Animals ; *Fishes/microbiology ; *Microbiota/drug effects ; Lakes/microbiology ; *Fish Diseases/microbiology/prevention & control/parasitology ; *Ovum/microbiology ; *Fungi/isolation & purification/classification/drug effects/genetics ; Oomycetes/drug effects/isolation & purification ; Aquaculture ; *Eukaryota/isolation & purification/classification/drug effects/genetics ; },
abstract = {Eukaryotic microorganisms are an important, but understudied, component of freshwater aquatic ecosystems, and are significant sources of mortality in early life stages of fishes in natural and aquaculture systems. The eukaryotic microbiome colonizing egg surfaces of the lake sturgeon (Acipenser fulvescens) was characterized from eggs collected in natural stream habitats and a streamside hatchery in the Cheboygan River watershed in MI, USA. The taxonomic diversity of members of the Kingdoms Fungi and Stramenopile associated with infections of lake sturgeon eggs during spawning is contributing to lake sturgeon mortality in the hatchery. Characterization of the microbial communities from deposited eggs demonstrated heavy influence of spawning location on the diversity of Pythium, an Oomycete predominating in the microbiome. The Ascomycota also had a strong and distinguishing presence, with members of the Dothidiales found only on eggs from the streamside hatchery. Aureobasidium pullulans, a ubiquitous pigmented yeast, was present in the greatest numbers of egg samples, and Helotiales were found only on samples from the Black River. Independent isolates were collected from egg surfaces and tested for chemical sensitivity to the oomicides ethaboxam and mefenoxam, which are used for control of Oomycete agricultural pathogens. Ethaboxam inhibited mycelial growth almost completely for all Saprolegnia strains tested, while mefenoxam, at 20 × strength, was largely ineffective. Water prevents the natural inactivation of mefenoxam by light, thus is not advisable in aquatic systems, where it could accumulate. Alternatively, ethaboxam may be a nonpersistent, welcome control option for these fish pathogens.},
}

Animals
*Fishes/microbiology
*Microbiota/drug effects
Lakes/microbiology
*Fish Diseases/microbiology/prevention & control/parasitology
*Ovum/microbiology
*Fungi/isolation & purification/classification/drug effects/genetics
Oomycetes/drug effects/isolation & purification
Aquaculture
*Eukaryota/isolation & purification/classification/drug effects/genetics

@article {pmid40705121,
year = {2025},
author = {Martin-Pozas, T and Ghezzi, D and D'Angeli, IM and Madonia, G and Chiarini, V and Vattano, M and De Waele, J and Cappelletti, M and Saiz-Jimenez, C and Jurado, V},
title = {Microbial and Geochemical Variability in Sediments and Biofilms from Italian Gypsum Caves.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {81},
pmid = {40705121},
issn = {1432-184X},
support = {JDC2023-051909-I//Ministerio de Ciencia e Innovación/ ; PID2020-114978GB-I00 and PDI2023-146299OB-C22//Ministerio de Ciencia e Innovación/ ; PID2020-114978GB-I00 and PDI2023-146299OB-C22//Ministerio de Ciencia e Innovación/ ; Europlanet 2020 7-EPN3-021//European Commission/ ; },
mesh = {*Biofilms/growth & development ; *Geologic Sediments/microbiology/chemistry ; *Calcium Sulfate/analysis ; *Caves/microbiology/chemistry ; *Bacteria/classification/genetics/isolation & purification ; Italy ; *Archaea/classification/isolation & purification/genetics ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; },
abstract = {In Europe, several gypsum karst regions occur among which the gypsum karsts located in Emilia-Romagna (UNESCO World Heritage Site since 2023) and Sicily are notable. The sediments, spring water microbial aggregates, and wall biofilms from three caves, Re Tiberio, Befana (Emilia-Romagna), and the Sicilian Santa Ninfa, have been studied from a microbiological and geochemical point of view. The samples of wall biofilms from gypsum caves were exclusively composed of Bacteria, while the sediments showed negligible abundances of Archaea. The two most abundant phyla in most sediments and biofilms were Actinomycetota and Pseudomonadota, whereas the microbial aggregates floating in the spring waters of Befana Cave showed a deviation from the typical abundance pattern as Campylobacterota replaced Actinomycetota, and the abundances of Bacteroidota and Desulfobacterota were high. The most abundant genus in the wall biofilms was Crossiella (Actinomycetota), but it was absent in the water aggregates collected in Befana Cave. The abundances of Crossiella in the cave sediments were very low. The dominant genera in Befana microbial aggregates showed different abundances and microbial composition when compared with the previously studied Frasassi and Fetida thermal sulfuric acid caves, located in Central and South Italy, respectively, suggesting that the community composition of the microbial aggregates is specific for each cave and related to the geochemistry of the sulfidic spring. Also, a different microbial community composition was found in Befana water aggregates with respect to the wall biofilms from Befana and Santa Ninfa caves. In the case of sediments, they significantly clustered together indicating that the microbial communities associated with sediments are similar, independently from the cave and possible other environmental parameters.},
}

*Biofilms/growth & development
*Geologic Sediments/microbiology/chemistry
*Calcium Sulfate/analysis
*Caves/microbiology/chemistry
*Bacteria/classification/genetics/isolation & purification
Italy
*Archaea/classification/isolation & purification/genetics
RNA, Ribosomal, 16S/genetics
Phylogeny

@article {pmid40704825,
year = {2025},
author = {Fang, J and Deng, Y and Liu, Z and Adams, JM},
title = {Is Everything Everywhere? Dispersal Limitation Impacts Methanotroph Community Functioning.},
journal = {Environmental microbiology},
volume = {27},
number = {7},
pages = {e70158},
doi = {10.1111/1462-2920.70158},
pmid = {40704825},
issn = {1462-2920},
support = {SBX2020010098//The Provincial Policy Guidance Program-Jiangsu "100 Foreign Experts Program"/ ; 42371135//The National Natural Science Foundation of China/ ; 41971077//The National Natural Science Foundation of China/ ; },
mesh = {*Methane/metabolism ; *Geologic Sediments/microbiology ; *Methylococcaceae/metabolism/genetics/classification/isolation & purification ; Salinity ; Rivers/microbiology ; Ecosystem ; Lakes/microbiology ; China ; Oxidation-Reduction ; },
abstract = {The significance of dispersal limitation in microbial ecology and biogeography remains debated. We aimed to clarify the role of dispersal limitation in the adaptation of methanotroph communities to salt-stress, essentially testing the 'everything is everywhere' hypothesis in functional terms. Riparian sediments along the Yangtze River and lakeshore sediments at varying geographical distances inland from the river were collected. Microcosms were incubated with ~5% CH4 under three conditions: 50 g/L salinity, 50 g/L salinity plus a methanotroph community inoculum, and a control. We observed a significant delay in methane oxidation at increased salinity, but salt-tolerant methanotrophic activity persisted in riparian sediments. Using DNA-SIP, we identified halotolerant Methylobacter-taxa that possibly dispersed from the saline estuary. By contrast, in lakes/ponds inland away from the Yangtze, progressively fewer samples oxidised methane under high salinity without inoculation, until at 130 km distance, no samples could adapt. Methanotrophy was restored in every case by inoculation with propagules from the saline Yangtze Delta, confirming the impact of dispersal limitation of halotolerant Methylobacter-propagules in constraining ecosystem functional adaptation. By focusing on ecosystem functions rather than just taxonomic communities, this study uniquely tests a key paradigm in microbial ecology, suggesting that broad-scale microbial dispersal limitation can constrain ecosystem adaptation.},
}

*Methane/metabolism
*Geologic Sediments/microbiology
*Methylococcaceae/metabolism/genetics/classification/isolation & purification
Salinity
Rivers/microbiology
Ecosystem
Lakes/microbiology
China
Oxidation-Reduction

@article {pmid40704813,
year = {2025},
author = {Zeng, Q and Jian, L and Shi, S and Guo, Q and Quadri, SR and Long, L and Tian, X},
title = {Identified Neptunicella plasticusilytica sp. nov. and its novel PET-degrading enzyme derived from mangrove plastic debris.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0113625},
doi = {10.1128/aem.01136-25},
pmid = {40704813},
issn = {1098-5336},
abstract = {Mangrove ecosystems are critical for coastal protection and biodiversity but are increasingly threatened by plastic pollution, particularly polyethylene terephthalate (PET). In this study, a novel marine bacterium, strain SCSIO 80796[T], was isolated from PET debris collected from the mangrove in QiAo Island, Zhuhai, China. Using a polyphasic taxonomic approach, including 16S rRNA gene sequencing, genome-based comparisons (average nucleotide identity [ANI] 72.2%, digital DNA-DNA hybridization [dDDH] 19.0%, average amino acid identity [AAI] 70.6%), and phenotypic and chemotaxonomic analyses, the strain was classified as a novel species within the genus Neptunicella. It is proposed as Neptunicella plasticusilytica sp. nov. (type strain SCSIO 80796ᵀ = MCCC 1K08369[T] = KCTC 92826[T]). Genomic analysis revealed that strain SCSIO 80796ᵀ encodes a novel PET-degrading enzyme, NmCut, which degrades PET and yields 105-120 µM of degradation products [terephthalic acid (TPA), mono(2-hydroxyethyl) terephthalate (MHET), bis(2-hydroxyethyl) terephthalate (BHET)] within 48 h at 60°C. NmCut exhibits both structural and evolutionary novelty, featuring a unique PET-binding module (PBM) absent in known PETases. PBM is characterized by a long, positively charged α-helix enriched in aromatic residues, forming a distinct substrate-interacting surface with potential as a transferable domain to enhance the efficiency of other plastic-degrading enzymes. This study not only expands the known diversity within Neptunicella but also highlights the potential of marine-derived microbes in addressing plastic pollution through biotechnological applications.IMPORTANCEThe discovery of Neptunicella plasticusilytica sp. nov. advances marine microbial ecology by revealing a novel species in the scarcely studied genus Neptunicella, which previously contained only one cultured representative. Isolated from plastic-polluted mangroves, this bacterium exemplifies microbial adaptation to anthropogenic habitats. Its functional uniqueness is underscored by a phylogenetically distinct polyethylene terephthalate (PET)-degrading enzyme (NmCut), forming an evolutionary clade separate from all known plastic-degrading enzymes. By integrating taxonomic discovery with functional genomics, this study bridges the gap between microbial diversity and biotechnological potential. The dual novelty of N. plasticusilytica-as a taxonomic addition and a source of evolutionarily unique enzymes-highlights the importance of exploring understudied environments to address global challenges like plastic pollution.},
}

@article {pmid40704792,
year = {2025},
author = {Zhang, M and Zhang, C and Ramos, A and Whitaker, RJ and Whiteley, M},
title = {Conserved cross-domain protein-to-mRNA ratios enable proteome prediction in microbes.},
journal = {mBio},
volume = {},
number = {},
pages = {e0141125},
doi = {10.1128/mbio.01411-25},
pmid = {40704792},
issn = {2150-7511},
abstract = {UNLABELLED: Microbial communities are often studied by measuring gene expression (mRNA levels), but translating these data into functional insights is challenging because mRNA abundance does not always predict protein levels. Here, we present a strategy to bridge this gap by deriving gene-specific RNA-to-protein conversion factors that improve the prediction of protein abundance from transcriptomic data. Using paired mRNA-protein data sets from seven bacteria and one archaeon, we identified orthologous genes where mRNA levels poorly predicted protein abundance, yet each gene's protein-to-RNA ratio was consistent across these diverse organisms. Applying the resulting conversion factors to mRNA levels dramatically improved protein abundance predictions, even when the conversion factors were obtained from distantly related species. Remarkably, conversion factors derived from bacteria also enhanced protein prediction in an archaeon, demonstrating the robustness of this approach. This cross-domain framework enables more accurate functional inference in microbiomes without requiring organism-specific proteomic data, offering a powerful new tool for microbial ecology, systems biology, and functional genomics.

IMPORTANCE: Deciphering the biology of natural microbial communities is limited by the lack of functional data. While transcriptomics enables gene expression profiling, mRNA levels often fail to predict protein abundance, the primary indicator of microbial function. Prior studies addressed this by calculating RNA-to-protein (RTP) conversion factors using conserved protein-to-RNA (ptr) ratios across bacterial strains, but their cross-species and cross-domain utility remained unknown. We generated comprehensive transcriptomic and proteomic data sets from seven bacteria and one archaeon spanning diverse metabolisms and ecological niches. We identified orthologous genes with conserved ptr ratios, enabling the discovery of RTP conversion factors that significantly improved protein prediction from mRNA, even between distant species and domains. This reveals previously unrecognized conservation in ptr ratios across domains and eliminates the need for paired proteomic data in many cases. Our approach offers a broadly applicable framework to enhance functional prediction in microbiomes using only transcriptomic data.},
}

@article {pmid40704791,
year = {2025},
author = {Reasoner, SA and Francis, J and Hadjifrangiskou, M},
title = {The urinary microbiome: the next frontier of bacterial ecology.},
journal = {Journal of bacteriology},
volume = {},
number = {},
pages = {e0010525},
doi = {10.1128/jb.00105-25},
pmid = {40704791},
issn = {1098-5530},
abstract = {The human urinary tract, once presumed to be sterile, has emerged as a new frontier of microbial ecology. Recent advancements in high-throughput sequencing technologies have revealed the complexity and diversity of microbial communities that reside within the urinary tract. This mini-review discusses the prominent bacteria identified in the urinary microbiome and their correlations with various urologic conditions. This review serves to summarize the current state of urobiome research and chart a path for ongoing discovery. Additionally, we address the methodological challenges in urinary microbiome research, emphasizing the need for standardization in study protocols and the refinement of bioinformatics tools. We highlight that although differences in urobiome composition have been described for various urologic diseases. Similarly, the pathophysiologic source and consequences of those differences remain uncertain. We outline the steps to move urobiome research from descriptive to mechanistic studies, emphasizing rigorous study design, integrating multi-omics approaches, and developing robust model systems for experimental investigation. Finally, we outline critical questions for future investigation aimed at elucidating the intricate connections between the urinary microbiome and host health.},
}

@article {pmid40704790,
year = {2025},
author = {Best, MB and Kazemi Motlagh, Z and McLemore, VT and Jones, DS},
title = {Historic mine waste contains diverse microbial communities that reflect waste type and geochemistry.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0043425},
doi = {10.1128/aem.00434-25},
pmid = {40704790},
issn = {1098-5336},
abstract = {UNLABELLED: Waste rock and tailings left behind by historic mining operations can contain substantial critical mineral resources. However, over the decades and centuries, since these deposits were emplaced, microbial communities developed that can catalyze rock weathering and elemental cycling, which could have impacted the economic resources but also might be harnessed for future biomining or other metal recovery efforts. Here, we combined microbial cell counting, rRNA gene and transcript sequencing, and whole rock geochemistry to compare the composition and abundance of microbial communities from five inactive mine sites in south-central New Mexico that contain critical minerals. While acidic seeps and adits at the sites contained organisms commonly found in acid rock drainage and bioleaching operations, these organisms were only present at very low abundance in the waste rock and tailings, which were instead dominated by bacteria and archaea that are related to inorganic nitrogen- and organic carbon-oxidizing taxa. Generally, rRNA transcript libraries contain many of the same organisms as rRNA gene libraries, indicating that most of these populations are active. Differences among total and active microbial communities correspond to waste rock geochemistry, including concentrations of sulfur, iron, and other variables such as copper, lead, and rare earth elements. Nevertheless, many of the rRNA gene and transcript sequences in these deposits were from groups without cultured representatives, and these unknown microorganisms are likely important for biogeochemical cycling over the long lifetime of these waste deposits. We also discuss recommendations for microbiological assessment of similar large historic mine waste deposits.

IMPORTANCE: New Mexico has a long history of mining, with hundreds of mining districts across the state, many of which contain inactive operations with historic tailings and waste rock. Because metallurgical processing was in its infancy when most of these mines were active, they contain substantial metal resources in tailings and waste rock that could be used to support domestic demand for critical minerals. We found that microbial communities associated with these deposits do not represent typical bioleaching communities, and instead are dominated by taxa not typically associated with mine waste. However, the deposits did contain rare iron and sulfur-cycling taxa that could catalyze metal mobilization, as well as active populations of novel microorganisms that are likely important for biogeochemical cycling. These microbial communities could represent important resources for bioremediation and other biotechnological applications to recover valuable elements from these and other historic mine wastes.},
}

@article {pmid40703236,
year = {2025},
author = {Žilić, DJ and Naletilić, Š and Mihaljević, Ž and Gagović, E and Špičić, S and Reil, I and Duvnjak, S and Tuk, MZ and Hodžić, A and Beck, R},
title = {Hemotropic pathogens in aborted fetuses of domestic ruminants: transplacental transmission and implications for reproductive loss.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1632135},
pmid = {40703236},
issn = {1664-302X},
abstract = {OBJECTIVE: Hemotropic pathogens of the genera Anaplasma, Babesia, Theileria, and hemotropic Mycoplasma are significant infectious agents in domestic ruminants, most commonly associated with vector-borne transmission. However, their potential for transplacental transmission and their contribution to reproductive disorders remains poorly understood. This study aimed to investigate the presence of hemopathogens in aborted fetuses of cattle, sheep, and goats in Croatia, and to evaluate their potential role in transplacental transmission.

METHODS: Molecular analyses were conducted on tissue samples from 651 aborted fetuses collected between 2016 and 2019 as part of national abortion surveillance programs. PCR screening followed by sequencing were used to detect Anaplasmataceae, Babesia, Theileria, and hemotropic Mycoplasma.

RESULTS: Thirteen hemopathogens were detected in 94 of 651 fetuses (14.44%), including Anaplasma marginale, Anaplasma ovis, Anaplasma phagocytophilum, Theileria orientalis, Theileria ovis, Theileria sp. OT3, Babesia ovis, Babesia canis, Babesia vulpes, Mycoplasma wenyonii, Mycoplasma haemobos, Mycoplasma ovis, and Mycoplasma haemominutum. The highest infection rates were observed in cattle (17.27%) and sheep (15.85%), while goats showed significantly lower prevalence (5.3%). A. marginale and A. ovis were the most frequently detected pathogens in bovine and ovine fetuses, respectively. Hemotropic mycoplasmas were reported for the first time in Croatia, with the first Western Balkan record of 'Candidatus M. haemobos'. Our study represents the first molecular documentation of a wide array of hemopathogens in aborted ruminant fetuses in Croatia, strongly indicating the possibility of transplacental transmission. The detection of species-specific patterns and the unexpected identification of protozoan species typically associated with canines highlight complex epidemiological dynamics.

CONCLUSION: Vertical transmission of the detected pathogens may play a role in abortion in endemic regions and should be integrated into differential diagnostic protocols for reproductive failure investigations.},
}

@article {pmid40701356,
year = {2025},
author = {Hu, L and Ye, Y and Li, Y and Tan, X and Liu, X and Zhang, T and Wang, J and Du, Z and Ye, M},
title = {Bacteria-algae synergy in carbon sequestration: Molecular mechanisms, ecological dynamics, and biotechnological innovations.},
journal = {Biotechnology advances},
volume = {},
number = {},
pages = {108655},
doi = {10.1016/j.biotechadv.2025.108655},
pmid = {40701356},
issn = {1873-1899},
abstract = {Rising atmospheric CO2 levels require innovative strategies to increase carbon sequestration. Bacteria-algae interactions, as pivotal yet underexplored drivers of marine and freshwater carbon sinks, involve multiple mechanisms that amplify CO2 fixation and long-term storage. This review systematically describes the synergistic effects of bacteria-algae consortia spanning both microalgae (e.g., Chlorella vulgaris and Phaeodactylum tricornutum) and macroalgae (e.g., Macrocystis and Laminaria) on carbon sequestration. These effects include (1) molecular-level regulation (e.g., signal transduction via N-acyl-homoserine lactones (AHLs), and horizontal gene transfer), (2) ecological facilitation of recalcitrant dissolved organic carbon (RDOC) formation, and (3) biotechnological applications in wastewater treatment and bioenergy production. We highlight that microbial crosstalk increases algal photosynthesis by 20-40 % and contributes to 18.9 % of kelp-derived RDOC storage. Furthermore, engineered systems integrating algal-bacterial symbiosis achieve greater than 80 % nutrient removal and a 22-35 % increase in CO2 fixation efficiency (compared with axenic algal systems), demonstrating their dual role in climate mitigation and a circular economy. This review is the first to integrate molecular mechanisms (e.g., quorum sensing), ecological carbon transformation processes (e.g., the formation of RDOC), and applications in synthetic biology (e.g., CRISPR-engineered consortia) into a unified framework. Moreover, the novel strategy "microbial interaction network optimization" for enhancing carbon sinks is proposed. However, scalability challenges persist, including light limitations in photobioreactors and the ecological risks of synthetic consortia. By bridging microbial ecology with synthetic biology, this work provides a roadmap for harnessing bacteria-algae synergy to achieve carbon neutrality.},
}

@article {pmid40699317,
year = {2025},
author = {Mairi, A and Ibrahim, NA and Idres, T and Basher, NS and Smaili, A and Idres, T and Toutati, A},
title = {Emerging antimicrobial resistance and high prevalence of genital Mycoplasma hominis and Ureaplasma urealyticum infections among infertile women in Algeria : Implications for reproductive health.},
journal = {Wiener klinische Wochenschrift},
volume = {},
number = {},
pages = {},
pmid = {40699317},
issn = {1613-7671},
support = {IMSIU-DDRSP2501//Deanship of Scientific Research at Imam Mohammad Ibn Saud Islamic University (IMSIU)./ ; },
abstract = {BACKGROUND: Genital infections caused by Mycoplasma hominis and Ureaplasma urealyticum are increasingly linked to female infertility, yet their epidemiology and resistance patterns remain poorly characterized in low-resource settings.

OBJECTIVE: This study aimed to determine the prevalence, antimicrobial resistance (AMR) profiles, and risk factors of M. hominis and U. urealyticum infections among infertile women in Akbou, Algeria.

METHODS: In this cross-sectional analysis (February-July 2024), cervicovaginal swabs from 79 infertile women were tested using the MYCOFAST® RevolutioN 2 system. Demographic, clinical, and reproductive data were collected via structured questionnaires. Statistical analyses included χ[2]-testsand logistic regression.

RESULTS: The overall infection prevalence was 37.9% (n = 30), with U. urealyticum (17.7%), M. hominis (13.9%), and co-infections (6.3%) predominating. Infections peaked in women aged 31-35 years (63.3%). Resistance to tetracycline was high (U. urealyticum: 71.4%; M. hominis: 54.5%), while doxycycline and clindamycin retained full efficacy. Significant risk factors included prior abortion (adjusted odds ratio, OR = 4.2, p < 0.001), STI history (OR = 3.8, p < 0.001), and artificial insemination (OR = 2.9, p = 0.018).

CONCLUSION: The high prevalence of genital Mycoplasma infections and emerging AMR in Algeria underscores the need for routine screening, updated treatment guidelines, and targeted antimicrobial stewardship programs to safeguard reproductive health.},
}

@article {pmid40699244,
year = {2025},
author = {Bei, Q and Zhang, J and Huang, Q and Yang, C and Li, Y and Mu, R and Shu, D and Dai, Y and Megharaj, M and He, W and Tian, H},
title = {Rhizosphere Microbiome-Root Exudate Synergy in Pteris vittata: Coordinated Arsenic Speciation and Multielement Metabolic Coupling Drive Hyperaccumulation Efficiency.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {79},
pmid = {40699244},
issn = {1432-184X},
support = {2023YFD1700102//the National Key R&D Program of China/ ; 2024NC-ZDCYL-02-14//the Key R&D Program of Shaanxi Province/ ; 2025JC-QYCX-034//Frontier Exploration Project (Innovative Exploration Category)/ ; },
mesh = {*Arsenic/metabolism ; *Rhizosphere ; *Pteris/microbiology/metabolism ; *Plant Roots/microbiology/metabolism ; *Microbiota ; Soil Microbiology ; Bacteria/metabolism/classification/genetics/isolation & purification ; *Soil Pollutants/metabolism ; Biodegradation, Environmental ; Fungi/metabolism/classification/genetics/isolation & purification ; *Plant Exudates/metabolism ; Soil/chemistry ; },
abstract = {Rhizosphere microorganisms play a pivotal role in enhancing the arsenic (As) remediation efficiency of Pteris vittata. However, the interactions among rhizosphere microorganisms, root exudates, and As, as well as their influence on As uptake by Pteris vittata at different As concentrations, remain poorly understood. This study systematically elucidates the molecular-ecological mechanisms through which Pteris vittata facilitates arsenic (As) remediation within a multidimensional interaction network. It was found that the rhizosphere microbial community was dominated by Proteobacteria, Acidobacteriota, and Ascomycota, with 44 bacterial and 10 fungal genera identified as genetically conserved core microorganisms. Microbial-mediated arsenic (As) methylation and reduction processes, coupled with metabolic pathways such as carbon fixation, sulfur oxidation, and phosphorus mineralization, contribute to the formation of an "As-multielement cycling" synergy. This synergy drives As speciation transformation and enhances plant uptake. Root exudates, such as L-phenylalanine and citric acid, enhance arsenic (As) activation and detoxification by selectively recruiting functional microbes, including Sphingomonas carrying arsC. The resulting metabolite profiles exhibit soil-specific response patterns. High As stress shifted microbial community assembly from stochastic to deterministic processes while maintaining remediation efficiency through enhanced fungal network stability (increased average connectivity). These findings reveal the dual "genetic conservation-environmental adaptation" regulatory strategy of Pteris vittata, providing both theoretical and practical foundations for designing targeted rhizosphere microecological technologies to enhance the phytoremediation of arsenic (As)-contaminated soils.},
}

*Arsenic/metabolism
*Rhizosphere
*Pteris/microbiology/metabolism
*Plant Roots/microbiology/metabolism
*Microbiota
Soil Microbiology
Bacteria/metabolism/classification/genetics/isolation & purification
*Soil Pollutants/metabolism
Biodegradation, Environmental
Fungi/metabolism/classification/genetics/isolation & purification
*Plant Exudates/metabolism
Soil/chemistry

@article {pmid40699006,
year = {2025},
author = {Nauwynck, W and Faust, K and Boon, N},
title = {Droplet microfluidics for single-cell studies: a frontier in ecological understanding of microbiomes.},
journal = {FEMS microbiology reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsre/fuaf032},
pmid = {40699006},
issn = {1574-6976},
abstract = {Recent advances in single-cell technologies have profoundly impacted our understanding of microbial communities-shedding light on cell-to-cell variability in gene expression, regulatory dynamics and metabolic potential. These approaches have shown that microbial populations are more heterogeneous and functionally complex than previously thought. However, direct probing of single-cell physiology-arguably more ecologically relevant by focusing on functional traits such as growth, metabolic activity, and enzymatic activity-remains underexplored. Droplet microfluidics provides a practical and high-throughput approach to address this gap, allowing functional characterization of individual microbial cells within complex communities and offering new opportunities to study ecological processes at high resolution. In this review we look at the state of droplet microfluidics for single-cell microbial ecology. We revisit the fundamentals of microbial droplet workflows, we overview the current capabilities of droplet microfluidics that exist for microbial ecology and we look at the phenomena these workflows have uncovered and understanding they have generated. Finally, we integrate these capabilities to envision future droplet workflows that could enhance our understanding of single-cell physiology and discuss the fundamental limitations that go together with the droplet format.},
}

@article {pmid40698177,
year = {2025},
author = {Roy, A and Ghosh, A and Yash, and Mehra, P and Roy, S and Bhadury, P},
title = {Insights into the genome of Azotobacter sp. strain CWF10, isolated from an agricultural field in Central India.},
journal = {Access microbiology},
volume = {7},
number = {1},
pages = {},
pmid = {40698177},
issn = {2516-8290},
abstract = {Azotobacter sp. strain CWF10, an aerobic gram-negative, oval-shaped and motile bacterium, was isolated from the lateritic agricultural soil of Madhya Pradesh, India. The draft genome of the isolate is 5.7 Mb in size, consisting of 14 contigs with 65.09% G+C content. Average nucleotide identity (94.66%) and digital DNA-DNA hybridization (62%) calculation with the closest reference strains underpin the bacterium as a potential novel species. The bacterium has a plethora of plant growth-promoting genes that point towards the potential ability to enhance available nitrogen and biosynthesis of folic acid, among others. Siderophores such as vibrioferrin and crochelin A are also present in the genome and are known to regulate iron uptake. Overall, mining the genome of Azotobacter sp. strain CWF10 has revealed the potential of this strain for application in regenerative agriculture and sustaining soil health.},
}

@article {pmid40696151,
year = {2025},
author = {Laso-Pérez, R},
title = {Anaerobic oxidation of methane: it takes two to tango.},
journal = {Nature reviews. Microbiology},
volume = {},
number = {},
pages = {},
pmid = {40696151},
issn = {1740-1534},
}

@article {pmid40695133,
year = {2025},
author = {Shi, F and Fang, H and Cheng, S and Guo, Y and Wang, H and Chen, L and Pu, H and Liu, B},
title = {Cadmium accumulation suppresses rice nitrogen use efficiency by inhibiting rhizosphere nitrification and promoting nitrate reduction.},
journal = {Journal of hazardous materials},
volume = {496},
number = {},
pages = {139298},
doi = {10.1016/j.jhazmat.2025.139298},
pmid = {40695133},
issn = {1873-3336},
abstract = {Cadmium (Cd) pollution significantly disrupts paddy soil nitrogen (N) availability and impairs rice nitrogen use efficiency (NUE). However, most existing studies rely on microcosm or pot experiments, with limited field-based manipulative studies involving Cd addition. The regulatory mechanisms by which N transformation processes influence rice N utilization under Cd stress remain poorly understood. In this study, a field experiment incorporating multiple levels of Cd addition was conducted to address this gap. Plant traits, nutrient content, and microbial community characteristics in rhizosphere and bulk soils were examined through soil chemical analysis, metagenomic sequencing, and bioinformatics approaches. The results demonstrated that microbial communities, soil N transformation potential, and rice NUE responded to Cd addition in a dose-dependent manner, with rhizosphere soils exhibiting greater sensitivity than bulk soils. Cd addition reduced dissolved organic carbon (DOC), NH4[+]-N, and NO3[-]-N in rhizosphere soil, while increasing total and available phosphorus (P) contents in both rhizosphere and bulk soils. Although Cd addition enhanced aboveground biomass and total N uptake, it led to a decline in plant N concentration and NUE. Moreover, Cd accumulation markedly suppressed the abundance of nitrification genes while promoting genes involved in dissimilatory nitrate reduction to ammonium (DNRA) and denitrification. Overall, Cd stress altered microbial community structure and soil N and P availability, thereby impairing rice N uptake and NUE. These findings suggest that acute Cd exposure rapidly disrupts microbial ecology, decouples the soil N cycle, and reduces N supply potential of paddy soils and rice NUE, ultimately threatening agroecosystem stability in southern China. These impacts warrant greater consideration in future farmland management strategies.},
}

@article {pmid40694412,
year = {2025},
author = {Benz, BR and Lopez-Echartea, E and Whitaker, BK and Baldwin, T and Geddes, BA},
title = {Improved efficiency of two-step amplicon PCR using an acoustic liquid handler.},
journal = {Microbiology (Reading, England)},
volume = {171},
number = {7},
pages = {},
doi = {10.1099/mic.0.001579},
pmid = {40694412},
issn = {1465-2080},
mesh = {*Polymerase Chain Reaction/methods/instrumentation/economics ; *High-Throughput Nucleotide Sequencing/methods ; Humans ; *Bacteria/genetics/classification/isolation & purification ; Microbiota/genetics ; Gene Library ; *Acoustics/instrumentation ; DNA, Bacterial/genetics ; },
abstract = {The improvement in next-generation sequencing technologies has reduced the costs of sequencing significantly. However, library preparation costs for amplicon sequencing have remained largely unchanged - which is ultimately the cost-limiting step in processing large numbers of microbiome samples. Acoustic liquid handlers can transfer volumes as low as 2.5 nl and have been used to miniaturize several different molecular and cellular assays, including single-step PCR amplicon library preparations. However, there are no current methods available for a two-step library preparation process using an acoustic liquid handler. In this study, we tested the efficiency of an acoustic liquid handler to automate the PCRs and library quantification while also incorporating automated library bead cleanup. We compared the material usage and costs for library preparation and sequencing results of this automated method to the standard, manual method. The automated protocol was able to reduce both PCR reaction volumes fivefold and increased efficiency for library preparation by ~32% without affecting bacterial community compositions. The associated increase in the efficiency of our automated method will allow for greater throughput in sequencing hundreds of microbiome samples without affecting the quality of those sequences.},
}

*Polymerase Chain Reaction/methods/instrumentation/economics
*High-Throughput Nucleotide Sequencing/methods
Humans
*Bacteria/genetics/classification/isolation & purification
Microbiota/genetics
Gene Library
*Acoustics/instrumentation
DNA, Bacterial/genetics

@article {pmid40694117,
year = {2025},
author = {Adam, MAC and Cailleau, G and Junier, P and Benrey, B},
title = {Host Diet and Species Interact to Shape the Bacterial and Fungal Microbiome in the Regurgitant of Four Spodoptera Species.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {78},
pmid = {40694117},
issn = {1432-184X},
support = {162860/SNSF_/Swiss National Science Foundation/Switzerland ; 162860/SNSF_/Swiss National Science Foundation/Switzerland ; 162860/SNSF_/Swiss National Science Foundation/Switzerland ; 162860/SNSF_/Swiss National Science Foundation/Switzerland ; },
mesh = {Animals ; *Spodoptera/microbiology/physiology/classification ; *Bacteria/classification/genetics/isolation & purification ; *Fungi/classification/genetics/isolation & purification ; *Diet ; *Gastrointestinal Microbiome ; Herbivory ; Phylogeny ; *Mycobiome ; Microbiota ; },
abstract = {The gut microbiome of Lepidopteran insects is highly dynamic, influenced by both host diet and phylogeny. While microbial communities are thought to facilitate host adaptation to diverse diets and environments, the existence of a core microbiome shared among closely related herbivores remains largely untested. In this study, we examined the microbial communities in the regurgitant of four Spodoptera species (S. exigua, S. frugiperda, S. latifascia, and S. littoralis) across different diets (artificial diet, cotton, maize, and squash). Using a high-throughput sequencing, we characterized bacterial and fungal community composition and diversity. Bacterial communities were shaped by both diet and host species, indicating species-specific bacterial selection. In contrast, fungal communities were exclusively structured by diet, with lower diversity and dominance of a few key taxa. Notably, no operational taxonomic units were consistently shared across all species or diets, challenging the concept of a conserved core microbiome in these generalist herbivores. Understanding how microbial communities shape generalist herbivores' ability to feed on diverse plants may offer potential strategies for microbiome-based pest management.},
}

Animals
*Spodoptera/microbiology/physiology/classification
*Bacteria/classification/genetics/isolation & purification
*Fungi/classification/genetics/isolation & purification
*Diet
*Gastrointestinal Microbiome
Herbivory
Phylogeny
*Mycobiome
Microbiota

@article {pmid40693737,
year = {2025},
author = {F M Kop, L and Koch, H and Speth, D and Lüke, C and Spieck, E and S M Jetten, M and Daims, H and Lücker, S},
title = {Comparative genome analysis reveals broad phylogenetic and functional diversity within the order Nitrospirales.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf151},
pmid = {40693737},
issn = {1751-7370},
abstract = {Nitrification, a key process in the nitrogen cycle, involves the oxidation of ammonia to nitrite and nitrate by a diverse group of chemolithoautotrophic microorganisms. The order Nitrospirales (referred to in literature as the genus Nitrospira), which includes both nitrite-oxidizing and complete ammonia-oxidizing bacteria, plays a central role in this process. We sequenced the genomes of nine Nitrospirales members, incorporating genomes from previously unsequenced taxonomic Nitrospirales lineages. A comprehensive genomic analysis of these new Nitrospirales was conducted, which included an examination of their habitat distribution, phylogenetic diversity, and functional capabilities. This was complemented by the construction of and comparison to a database of 446 non-redundant, high-quality Nitrospirales genomes. Our phylogenomic analysis uncovered the presence of additional unclassified lineages and provided a comparison between genome-based and 16S rRNA gene-based taxonomies. Whereas some Nitrospirales lineages seem to exhibit habitat preferences, others are found across a wide variety of ecosystems, suggesting a broad niche spectrum. This capacity to adapt to different environmental conditions is also reflected in the high variability and modularity of the respiratory chain and nitrogen assimilation mechanisms. Additionally, we found evidence of quorum sensing systems in species beyond lineage II, implying a broader ecological role for this communication mechanism within the Nitrospirales. Finally, we identified a set of conserved genes unique to nitrite oxidoreductase-containing Nitrospirales, providing insights into the emergence of this functional group. In conclusion, our study emphasizes the adaptability of the various nitrifying classes of the order Nitrospirales to diverse environments and reveals the presence of new taxonomic lineages.},
}

@article {pmid40693139,
year = {2025},
author = {Nankova, BB and Hu, F and LaGamma, EF},
title = {Early life microbiome disbalance impacts neuroendocrine outcomes in pre-pubertal mice in a sexually dimorphic manner.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1504513},
pmid = {40693139},
issn = {1664-302X},
abstract = {INTRODUCTION: Adverse exposures during perinatal development disrupt the emerging gut microbial ecology that in turn negatively influences long term health. How gut dysbiosis affects complex neurobehavioral functions or even simple reflex arcs (e.g. the amplitude of sympathoadrenal adaptive responses to hypoglycemia) in the extrauterine environment is not well understood.

METHODS: The C57Bl6 dams were given broad-spectrum antibiotics in the drinking water at parturition until weaning of their litter to perturb the normal seeding and maturation of the postnatal microbiome, control animals received sterile water. To evaluate the impact of altered postnatal flora the offspring were subjected to behavioral tests or sacrificed after exposure to insulin-induced hypoglycemia. Fecal samples were collected for microbial whole genome shotgun taxonomic profiling and predictive functionality. As an index of host sympathoadrenal capacity, individual adrenal medulla samples from each group were subjected to RNA sequencing to identify differentially expressed genes between the groups and gain insights into molecular pathways contributing to the observed outcomes. Given that several neurodevelopmental disorders in humans are biased by sex we also included it as variable in this report.

RESULTS: The offspring of control dams displayed sex-specific differences in microbiome composition, exploratory behavior, adrenal transcriptome profiles and basal urinary epinephrine levels. Maternal antibiotics during nursing caused: (1) microbial dysbiosis in the offspring as evident by markedly enlarged ceca, no detectable by-products of bacterial fermentation (sp. SCFA) and dramatic changes in microbial composition, diversity (reduced - alpha Chao1and beta Bray-Curtis, as compared to their respective controls) and predictive metabolic activity; (2) alteration in the transcriptional signature of the adrenal medullae and attenuated peripheral stress responses in male offspring, associated with gap junction signaling pathways; (3) increased anxiety-like testing metrics, and decreased locomotor activity; all in a sexually dimorphic manner.

DISCUSSION: We speculate that the observed sex differences in the gut microbiome may contribute to neurodevelopmental disorders known to have sex-related disparities and in the capacity for successful adaptation to stress. A better understanding of how microbial communities and their hosts interact during critical portions of postnatal neurobehavioral development may help personalize nutritional and therapeutic strategies to promote long term health.},
}

@article {pmid40691348,
year = {2025},
author = {Almario, J},
title = {Blurred lines in the mycorrhiza world.},
journal = {Nature reviews. Microbiology},
volume = {},
number = {},
pages = {},
pmid = {40691348},
issn = {1740-1534},
}

@article {pmid40689185,
year = {2025},
author = {Li, K and Xu, J and Chen, S and Du, A and Feng, S and Yuan, S and Wu, B},
title = {Dose-dependent effects of capsaicin on intestinal morphology and microbiota composition in mice: Structural, immunohistochemical, and microbial insights.},
journal = {Veterinary world},
volume = {18},
number = {6},
pages = {1703-1714},
pmid = {40689185},
issn = {0972-8988},
abstract = {BACKGROUND AND AIM: Capsaicin (CAP), the pungent component of chili peppers, possesses diverse bioactive properties, including antioxidant, anti-inflammatory, and antimicrobial effects. However, its impact on gastrointestinal integrity and microbial ecology remains dose-dependent and incompletely understood. This study aimed to investigate the effects of varying CAP doses on intestinal morphology, tight junction protein expression, goblet cell density, mucosal injury markers, and gut microbiota composition in mice.

MATERIALS AND METHODS: Seventy-five male Kunming mice were randomly assigned to five groups (n = 15/group): Normal control, vehicle control (dimethyl sulfoxide), low-dose CAP (5 mg/kg), medium-dose (15 mg/kg), and high-dose (20 mg/kg). Mice received oral gavage every other day for 14 days. Histological assessments (H&E and Alcian Blue-Periodic Acid-Schiff staining), enzyme-linked immunosorbent assays for diamine oxidase, fatty acid-binding protein 2, and plasma endotoxin as well as immunohistochemistry for ZO-1, Claudin-1, and Occludin, and 16S rRNA sequencing were employed to evaluate structural and microbial changes.

RESULTS: Low-dose CAP significantly enhanced villus height, reduced crypt depth, and elevated the villus-to-crypt ratio across all intestinal segments (p < 0.05). Tight junction protein expression and goblet cell counts were highest in the low-dose group, suggesting mucosal protection. In contrast, medium and high-dose CAP induced epithelial damage, villus atrophy, and downregulation of junctional proteins. Microbiota analysis revealed the suppression of Proteobacteria and the expansion of Firmicutes in the medium- and high-dose groups. All CAP doses stimulated microbial biosynthesis of cofactors, vitamins, and electron carriers, with enhanced alpha diversity at higher doses.

CONCLUSION: CAP exhibits a biphasic effect on intestinal physiology. While low-dose administration supports mucosal integrity and promotes beneficial microbial functions, higher doses disrupt epithelial architecture and induce dysbiosis. These findings underscore the importance of dose consideration in CAP's dietary and therapeutic applications, providing mechanistic insights into its gut-mediated effects.},
}

@article {pmid40688383,
year = {2025},
author = {Liu, S and Rodriguez, JS and Munteanu, V and Ronkowski, C and Sharma, NK and Alser, M and Andreace, F and Blekhman, R and Błaszczyk, D and Chikhi, R and Crandall, KA and Della Libera, K and Francis, D and Frolova, A and Gancz, AS and Huntley, NE and Jaiswal, P and Kosciolek, T and Łabaj, PP and Łabaj, W and Luan, T and Mason, C and Moustafa, AM and Muralidharan, HS and Mutlu, O and Mansouri Ghiasi, N and Rahnavard, A and Sun, F and Tian, S and Tierney, BT and Van Syoc, E and Vicedomini, R and Zackular, JP and Zelikovsky, A and Zielińska, K and Ganda, E and Davenport, ER and Pop, M and Koslicki, D and Mangul, S},
title = {Analysis of metagenomic data.},
journal = {Nature reviews. Methods primers},
volume = {5},
number = {},
pages = {},
pmid = {40688383},
issn = {2662-8449},
support = {R35 GM146980/GM/NIGMS NIH HHS/United States ; },
abstract = {Metagenomics has revolutionized our understanding of microbial communities, offering unprecedented insights into their genetic and functional diversity across Earth's diverse ecosystems. Beyond their roles as environmental constituents, microbiomes act as symbionts, profoundly influencing the health and function of their host organisms. Given the inherent complexity of these communities and the diverse environments where they reside, the components of a metagenomics study must be carefully tailored to yield accurate results that are representative of the populations of interest. This Primer article examines the methodological advancements and current practices that have shaped the field, from initial stages of sample collection and DNA extraction to the advanced bioinformatics tools employed for data analysis, with a particular focus on the profound impact of next-generation sequencing (NGS) on the scale and accuracy of metagenomics studies. We critically assess the challenges and limitations inherent in metagenomics experimentation, available technologies and computational analysis methods. Beyond technical methodologies, we explore the application of metagenomics across various domains, including human health, agriculture and environmental monitoring. Looking ahead, we advocate for the development of more robust computational frameworks and enhanced interdisciplinary collaborations. This Primer serves as a comprehensive guide for advancing the precision and applicability of metagenomic studies, positioning them to address the complexities of microbial ecology and their broader implications for human health and environmental sustainability.},
}

@article {pmid40685652,
year = {2025},
author = {Hedjem, A and Kouchkar, A and Ladjeroud, A and Zerrouki, N and Benaissa, F and Ibrahim, NA and Aleissa, MS and Basher, NS and Derguini, A and Idres, T and Houali, K},
title = {Androgen receptor expression in triple negative breast cancer: an Algerian population study.},
journal = {The Libyan journal of medicine},
volume = {20},
number = {1},
pages = {2535778},
pmid = {40685652},
issn = {1819-6357},
mesh = {Humans ; *Receptors, Androgen/metabolism ; *Triple Negative Breast Neoplasms/pathology/mortality/metabolism/genetics ; Female ; Middle Aged ; Algeria/epidemiology ; Adult ; Aged ; Biomarkers, Tumor/metabolism ; Survival Rate ; Ki-67 Antigen/metabolism ; },
abstract = {Triple-negative breast cancer (TNBC) is a molecular subtype of breast cancer characterized by the absence of estrogen and progesterone receptors and the lack of HER2 overexpression. TNBC is highly heterogeneous, complicating the identification of new therapeutic targets. However, the expression of the androgen receptor (AR) in the luminal androgen receptor (LAR TNBC) subgroup has opened the door to alternative therapeutic approaches. This study aimed to assess AR expression and correlate it with clinicopathological factors in 160 early-stage TNBC patients treated from February 2015 to February 2017. Our findings reveal that AR expression is observed in 16.87% (27/160) of ≥1% AR positivity cases. Moreover, a significant 12.5% (20/160) was found in ≥10% AR positive cases. Positive AR expression was inversely correlated with a high Ki-67 proliferation index and with the basal immunophenotype. The five-year survival rate for our cohort was 83.12%, and no significant association between AR expression and overall survival was observed (p = 0.77). The study highlights the potential role of AR expression in TNBC and its implications for therapeutic strategies, although no significant association with overall survival was found.},
}

Humans
*Receptors, Androgen/metabolism
*Triple Negative Breast Neoplasms/pathology/mortality/metabolism/genetics
Female
Middle Aged
Algeria/epidemiology
Adult
Aged
Biomarkers, Tumor/metabolism
Survival Rate
Ki-67 Antigen/metabolism

@article {pmid40681538,
year = {2025},
author = {Sedláček, I and Holochová, P and Sedlář, K and Staňková, E and Šedo, O and Kralova, S and Umair, M and Koublová, V and Švec, P},
title = {Two new psychrotolerant Massilia species inhibit plant pathogens Clavibacter and Curtobacterium.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {26134},
pmid = {40681538},
issn = {2045-2322},
support = {LM2023069//MEYS CR/ ; LM2023042//MEYS CR/ ; 101020356//Horizon 2020/ ; },
mesh = {Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Clavibacter/pathogenicity ; Antarctic Regions ; *Plant Diseases/microbiology ; },
abstract = {Three bacterial strains producing blue-violet pigmented colonies on R2A agar were isolated from a wet rock wall and lakes in the deglaciated northern part of James Ross Island, Antarctica. The isolated strains inhibited phytopathogenic Gram-positive bacteria Clavibacter spp., Curtobacterium flacumfaciens, and Paenarthrobacter ilicis. Phylogenetic analysis based on the 16S rRNA gene indicated that the isolates belonged to the genus Massilia and the closest relatives were Massilia violaceinigra B2[T], Massilia rubra CCM 8692[T], Massilia frigida CCM 8695[T], Massilia antarctica CCM 8941[T], and Massilia aquatica CCM 8693[T]. A polyphasic taxonomic study based on lepA genes sequencing, automated ribotyping, MALDI-TOF MS, chemotaxonomy analyses, extensive biotyping, average nucleotide identity, and digital DNA-DNA hybridization calculations based on whole-genome sequences proved that the isolates represent a novel Massilia species for which the names Massilia pseudoviolaceinigra sp. nov. and Massilia scottii sp. nov. are suggested, with the type strains P3689[T] (= CCM 9206[T] = LMG 33568[T]) and P5043[T] (= CCM 9029[T] = LMG 32502[T]), respectively. These two bioactive metabolite-producing species may play an important role in shaping the composition of fresh-water Antarctic microbiomes due to the inhibition of various Gram-positive bacteria.},
}

Phylogeny
RNA, Ribosomal, 16S/genetics
*Clavibacter/pathogenicity
Antarctic Regions
*Plant Diseases/microbiology

@article {pmid40681451,
year = {2025},
author = {Nichols, HL and Coon, KL},
title = {Leveraging microbial ecology for mosquito-borne disease control.},
journal = {Trends in parasitology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.pt.2025.06.010},
pmid = {40681451},
issn = {1471-5007},
abstract = {Mosquitoes transmit pathogens causing 700 000 deaths annually. Microbe-based vector control, which reduces vector populations or blocks pathogen development within vectors, offers an innovative way to lower global morbidity and mortality due to vector-borne disease. This review addresses challenges hindering the widespread adoption of microbe-based vector control in mosquitoes. We consider understudied transmission routes of mosquito-associated microbiota, factors affecting colonization and persistence of candidate microbial control agents in mosquito hosts, and the need for robust tools and methodologies to validate that observations in laboratory populations can be reliably extended to field populations. We highlight how understanding the microbial ecology underlying interactions between mosquitoes and their native microbiota can guide successful vector control efforts in these and other arthropod disease vectors.},
}

@article {pmid40679638,
year = {2025},
author = {Fulke, AB and Sharma, N and Nadekar, J},
title = {Darkness to Discovery: A Comprehensive Mini-Review on Culturable and Non-Culturable Microbial Diversity from Deep Sea.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {77},
pmid = {40679638},
issn = {1432-184X},
support = {OLP2009//National Institute of Oceanography, India/ ; OLP2009//National Institute of Oceanography, India/ ; OLP2009//National Institute of Oceanography, India/ ; },
mesh = {*Seawater/microbiology ; *Bacteria/genetics/classification/isolation & purification/growth & development ; *Microbiota ; *Biodiversity ; Metagenomics/methods ; Ecosystem ; Hydrothermal Vents/microbiology ; Oceans and Seas ; },
abstract = {Microorganisms are essential players in Earth's ecosystems, demonstrating remarkable adaptability to harsh conditions including arctic ice caps, deep-sea hydrothermal vents, and high-pressure oceanic zones. While the study of these extremophiles has long been constrained by challenges in culturing, recent advances in metagenomic techniques have enabled a deeper understanding of microbial diversity in these extreme habitats. This review explores both culturable and non-culturable microbial communities, focusing on the diverse strategies employed by microorganisms to thrive in harsh conditions, including high pressure, temperature, salinity, and nutrient limitations. Traditional cultivation methods often fail to capture the full spectrum of deep-sea microbiota due to the unique growth requirements of many organisms. In the omic era, however, microbial cultivation and the function of microbial resources are important. Non-culturable methods, like metagenomic studies and environmental DNA sequencing, have uncovered hitherto unknown microbial taxa and metabolic pathways, offering important new information on microbial ecology and biogeochemistry. The complex microbial interactions and adaptive methods that support these ecosystems are highlighted by case studies, including as studies on hydrothermal plumes and hadal deposits. The expanding significance of non-culturable techniques in microbial research is highlighted in this review, which also highlights how they might help us better understand microbial life in harsh conditions and how they may be used in biotechnology and environmental management.},
}

*Seawater/microbiology
*Bacteria/genetics/classification/isolation & purification/growth & development
*Microbiota
*Biodiversity
Metagenomics/methods
Ecosystem
Hydrothermal Vents/microbiology
Oceans and Seas

@article {pmid40678115,
year = {2025},
author = {Tankova, H},
title = {Association between the severity of gingival inflammation and microbial findings in children.},
journal = {Frontiers in dental medicine},
volume = {6},
number = {},
pages = {1638435},
pmid = {40678115},
issn = {2673-4915},
abstract = {INTRODUCTION: The oral cavity is home to hundreds of distinct microbial species, and specific periodontal pathogens are isolated from different ecological niches. Present study aimed to investigate the relationship between the severity of gingival inflammation and the presence of subgingival microorganisms in children with dental biofilm induced gingivitis.

MATERIAL AND METHODS: The study included 30 children aged 12-14 years, divided into two groups based on the extent of gingival inflammation: Group I-16 children with BOP up to 30%; Group II-14 children with BOP over 30%. All children were interviewed to assess oral hygiene habits. Clinical examination was performed using an electronic periodontal probe, and the following were recorded: oral hygiene status (FMPS) and gingival status through BOP and SBI. For quantitative assessment of subgingival periodontopathogens, a genetic method - PCR-Real Time was used, and the following microorganisms were examined: Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis, Treponema denticola, Tannerella forsythia, Prevotella intermedia, Peptostreptococcus micros, Fusobacterim nucleatum, Eubacterium nodatum, Capnocytophaga gingivalis. The critical significance level for testing the null hypothesis was set at α = 0.05, corresponding to a 95% confidence level.

RESULTS: The majority of children showed improper oral hygiene habits. Children with generalized gingival inflammation had significantly higher plaque accumulation index values compared to those with localized inflammation. In children with generalized gingival inflammation, the quantities of all isolated periodontopathogens were higher compared to those with localized inflammation, which was also confirmed regarding the overall microbial load. A. actinomycetemcomitans was not isolated in children with localized gingival inflammation, while T. denticola was isolated in significantly lower quantities compared to generalized inflammation. P. intermedia and P. micros were isolated in significantly higher quantities in more severe gingival inflammation. In children with localized gingival inflammation, combinations of an average of 2 microorganisms were found in microbial complexes, while in children with generalized inflammation, microorganisms were twice as many and in more complex combinations.

CONCLUSION: The microbial diversity within the subgingival biofilm significantly increases with disease severity, providing further evidence for the critical role of microbial ecology in the pathogenesis of gingival inflammation in children.},
}

@article {pmid40676356,
year = {2025},
author = {Sibanyoni, NR and Piater, LA and Kerchev, P and Madala, NE and Mhlongo, MI},
title = {Metabolomic Insights into Cross-Feeding Interactions Between Priestia megaterium PM and Pseudomonas fluorescens NO4: Unveiling Microbial Communication in Plant Growth-Promoting Rhizobacteria.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {76},
pmid = {40676356},
issn = {1432-184X},
support = {TTK2404507217709//National Research Foundation/ ; },
mesh = {*Pseudomonas fluorescens/metabolism/physiology/growth & development ; Metabolomics ; Rhizosphere ; *Microbial Interactions ; Soil Microbiology ; Quorum Sensing ; Plant Development ; Metabolome ; Volatile Organic Compounds/metabolism ; },
abstract = {Plant growth-promoting rhizobacteria (PGPR) engage in complex chemical exchange and signalling processes to enhance their survival, rhizosphere colonisation, and plant-beneficial roles. These microbial interactions are mediated by various chemical cues, including quorum sensing (QS) molecules, cyclic peptides, lipopeptides, nutrients, volatile organic compounds (VOC), and phytohormones. Cross-feeding, where one microorganism consumes metabolites produced by another, exemplifies direct chemical communication that shapes community dynamics and metabolic cooperation. However, the effects of cross-feeding among different PGPR strains remain insufficiently characterised. In this study, an LC-MS-based metabolomics approach, combined with multivariate statistical analysis, was employed to investigate metabolic perturbations induced by cross-feeding among PGPR strains. Growth curve analysis revealed that cross-fed PGPR exhibited growth patterns comparable to controls, with a slight reduction in biomass. Metabolic profiling indicated time-dependent shifts in the metabolic state of the cross-fed organisms, suggesting adaptive metabolic reprogramming in response to the donor-conditioned media. Multivariate analysis identified distinct metabolite alterations between cross-fed and control groups across different time points, highlighting the influence of nutrient availability on microbial growth dynamics. Notably, cross-fed groups showed decreased levels of primary metabolites such as amino acids and sugars alongside increased production of secondary metabolites, including surfactins, salicylic acid, and carboxylic acids. These secondary metabolites are implicated in plant growth promotion and defence, indicating their potential as natural biostimulants. The findings advance the understanding of PGPR interactions and chemical communication in the rhizosphere, supporting the development of sustainable agricultural practices by leveraging beneficial microbial interactions. Future research should explore these interactions within more complex microbial communities.},
}

*Pseudomonas fluorescens/metabolism/physiology/growth & development
Metabolomics
Rhizosphere
*Microbial Interactions
Soil Microbiology
Quorum Sensing
Plant Development
Metabolome
Volatile Organic Compounds/metabolism

@article {pmid40671255,
year = {2025},
author = {Bartsch, S and Kreutz, C and Scholz, KJ and Kohnert, E and Hertel, J and Wolf, M and Jakubovics, N and Al-Ahmad, A and Cieplik, F},
title = {Culturomics: Deciphering the Microbial Dark Matter in the Oral Cavity.},
journal = {Journal of dental research},
volume = {},
number = {},
pages = {220345251346781},
doi = {10.1177/00220345251346781},
pmid = {40671255},
issn = {1544-0591},
abstract = {The idea of the tree of life originated in the 19th century and has steadily evolved since then. In the last 20 y, high-throughput sequencing methods have revolutionized microbial ecology and expanded our understanding of this tree of life tremendously. However, this has led to a sharp increase in what is known as microbial dark matter, consisting of bacterial and archaeal taxa that are only known by sequencing and have not yet been cultivated. The lack of ecologic information about these species poses a major challenge. This has led to the need for other approaches to supplement the DNA sequence-based findings. The term "culturomics"-which describes the large-scale isolation, culture, and identification of species from an environment-was introduced in 2012 with a focus on the human gut microbiota. The cultivation of new species, which had been neglected for many years, is now firmly back in the spotlight since strains are required for experimental studies to complement the knowledge obtained from microbial DNA sequences. Laboratory culture is essential to gain knowledge of microbial physiology, assign functions to novel genes and proteins, identify resistance profiles, and better understand the impact of different microorganisms on human health. While many culturomics studies have focused on gut microbiota, significant progress has been made in oral microbiology, with the enrichment of Candidatus Nanosynbacter lyticus representing one of the greatest achievements. This review gives a comprehensive overview of the oral microbial community regarding the microbial dark matter and summarizes the work carried out to date on the oral microbiota using culturomics. The capability and challenges of metagenomics and culturomics and the potential use of artificial intelligence are examined, with insights from extensive culturomics research on gut microbiota, which promises applicability to the field of oral microbiology.},
}

@article {pmid40670676,
year = {2025},
author = {Su, J and Su, Y and Weng, Y and Ayub, G and She, C and Xiao, Y},
title = {Insights Into Proliferation Effects of Low-Dose Glyphosate on Phytoplankton Communities.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {75},
pmid = {40670676},
issn = {1432-184X},
support = {FJ2025MGCA019//Fujian Province Social Science Fund Project/ ; 2024R016//Fujian Environmental Protection Science and Technology Program/ ; DH1408//Enterprise and Public Institution Commissioned Science and Technology Project/ ; },
mesh = {Glyphosate ; *Glycine/analogs & derivatives/pharmacology/toxicity ; *Phytoplankton/drug effects/growth & development ; *Herbicides/pharmacology/toxicity ; Biomass ; Cyanobacteria/drug effects/growth & development ; Phosphorus/metabolism ; Microcystis/drug effects/growth & development ; Harmful Algal Bloom/drug effects ; Microalgae/drug effects/growth & development ; *Water Pollutants, Chemical/toxicity ; Ecosystem ; },
abstract = {Glyphosate-based herbicides are among the most widely used agricultural chemicals globally, and their widespread application presents risks to environmental health and aquatic ecosystems. Continuous glyphosate inputs disrupt phytoplankton communities, potentially triggering harmful algal blooms. This study examines the proliferation of microalgal species exposed to low glyphosate concentrations (0.05 mg/L) and various phosphorus sources, with a particular focus on C-P and C-O-P bond phosphonates, which have been insufficiently studied in previous research. We hypothesized that cyanobacteria might exhibit a competitive growth advantage over other algal species when exposed to C-P bond glyphosate, especially under phosphorus-limited conditions. In monoculture experiments, Microcystis aeruginosa and Peridinium umbonatum var. inaequale significantly increased their biomass when cultured with C-P bond phosphonates, whereas Scenedesmus bijuga failed to thrive under similar conditions. Peridinium umbonatum var. inaequale also displayed increased soluble protein content in response to glyphosate stress, indicating an adaptive stress response. In co-culture experiments, M. aeruginosa demonstrated greater tolerance to glyphosate than P. umbonatum var. inaequale, though biomass increases were not significantly correlated with soluble protein or APA. Sediment-water interface experiments revealed that glyphosate exposure significantly promoted cyanobacterial biomass, which was approximately five times greater than that of the inorganic phosphorus group. Notably, when cyanobacterial biomass exceeded 20% of the total, Cyanophyta replaced Chlorophyta as the dominant group, suggesting a potential competitive advantage under low-dose glyphosate exposure. These findings highlight that glyphosate may promote cyanobacterial dominance by altering phytoplankton community composition, potentially contributing to the increased frequency of harmful algal blooms in nutrient-limited aquatic environments.},
}

Glyphosate
*Glycine/analogs & derivatives/pharmacology/toxicity
*Phytoplankton/drug effects/growth & development
*Herbicides/pharmacology/toxicity
Biomass
Cyanobacteria/drug effects/growth & development
Phosphorus/metabolism
Microcystis/drug effects/growth & development
Harmful Algal Bloom/drug effects
Microalgae/drug effects/growth & development
*Water Pollutants, Chemical/toxicity
Ecosystem

@article {pmid40668425,
year = {2025},
author = {Mnguni, FC and Shin, GY and du Toit, LJ and Derie, ML and Coutinho, TA},
title = {Ewingella allii sp. nov. isolated from a diseased onion plant in the Columbia Basin of Washington State, USA.},
journal = {Antonie van Leeuwenhoek},
volume = {118},
number = {8},
pages = {115},
pmid = {40668425},
issn = {1572-9699},
support = {2019-51181-3//USDA NIFA SCRI/ ; 2019-51181-3//USDA NIFA SCRI/ ; 2019-51181-3//USDA NIFA SCRI/ ; 2019-51181-3//USDA NIFA SCRI/ ; 2019-51181-3//USDA NIFA SCRI/ ; },
mesh = {Phylogeny ; Washington ; RNA, Ribosomal, 16S/genetics ; *Onions/microbiology ; *Plant Diseases/microbiology ; DNA, Bacterial/genetics ; Base Composition ; Genome, Bacterial ; Bacterial Typing Techniques ; },
abstract = {Isolation of strain 20WA0182[T] from a diseased onion plant grown in the Columbia Basin of Washington State, USA, led to preliminary identification as a member of the genus Ewingella. The strain was characterised as a Gram-stain-negative, facultative anaerobe that is rod-shaped, motile with polar flagella, catalase positive, and oxidase negative. The strain 20WA0182[T] isolated was pathogenic to yellow onion bulbs, weakly pathogenic on onion leaves of the cv. Ranchero, and caused a pathogenic response using the red onion bulb scale necrosis assay. Phylogenetic analyses using the 16S rRNA gene and four housekeeping genes, atpD, gyrB, infB, and rpoB, showed that strain 20WA0182[T] formed a branch that clustered with E. americana strains, but on a separate node, indicating it is a novel species of this genus. Whole-genome sequencing of strain 20WA0182[T] revealed a genome size of 4,604,541 nt, with 25 contigs and a G + C content of 53.8%, strain 20WA0182[T] was 99.2% complete. The average nucleotide identity of strain 20WA0182[T] compared with E. americana strains scores ranged from 92.85 to 93.96%, below the 95% threshold to classify strains as the same species. Similarly, dDDH scores were 56.0 to 56.2%, less than the 70% threshold required to delineate prokaryotes as the same species. Strain 20WA0182[T] and Ewingella sp. CoE-038-23 shared the ANI score above 97.59% and 81.0% dDDH score to be classified as a novel species of Ewingella. As the type strain 20WA0182[T] (= BD 3290[ T] = LMG 33618[ T]) was pathogenic to onion bulbs and leaves, the name Ewingella allii is proposed. GenBank accession number = JAWUDN000000000.},
}

Phylogeny
Washington
RNA, Ribosomal, 16S/genetics
*Onions/microbiology
*Plant Diseases/microbiology
DNA, Bacterial/genetics
Base Composition
Genome, Bacterial
Bacterial Typing Techniques

@article {pmid40667995,
year = {2025},
author = {Garin, T and Brault, A and Marais, C and Briand, M and Préveaux, A and Bonneau, S and Simonin, M and Barret, M and Sarniguet, A},
title = {T6SS-mediated competition by Stenotrophomonas rhizophila shapes seed-borne bacterial communities and seed-to-seedling transmission dynamics.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0045725},
doi = {10.1128/msystems.00457-25},
pmid = {40667995},
issn = {2379-5077},
abstract = {UNLABELLED: Seeds harbor diverse microbial communities important for plant growth and health. During germination, seed exudation triggers intense microbial competition, shaping the communities transmitted to seedlings. This study explores the role of the bacterial type VI secretion system (T6SS)-mediated interference competition in seed microbiota transmission to seedlings. The analysis of T6SS distribution within 180 genome sequences of seed-borne bacterial strains enabled the construction of synthetic communities (SynCom) with different levels of phylogenetic diversity and T6SS richness. These SynComs were inoculated with Stenotrophomonas rhizophila CFBP13503, a bacterial strain possessing an active T6SS in vitro and in planta. The impact of the T6SS on SynCom composition was assessed in vitro by comparing the CFBP13503 wild-type strain or its isogenic T6SS-deficient mutant co-inoculation. Additionally, the effects of the T6SS on bacterial community dynamics during seed-to-seedling transmission were examined following seed inoculation. The T6SS of S. rhizophila CFBP13503 targets a broad range of bacteria belonging to five different orders. The susceptibility of competing bacteria was partly explained by their phylogenetic proximity and metabolic overlap with CFBP13503. Furthermore, the T6SS modulates the relative abundance of specific bacterial taxa during seed-to-seedling transmission depending on the initial seed inoculum and plant developmental stage. Depending on the sensitivity of the co-inoculated competitors, the T6SS can provide a competitive advantage to CFBP13503, resulting in an increase in population size.

IMPORTANCE: The high prevalence of the type VI secretion system (T6SS) in seed-borne bacteria supports the importance of T6SS-mediated competition for seed microbiota assembly. In vitro, S. rhizophila CFBP13503 T6SS exerts a strong impact on bacterial community dynamics. The susceptibility to the T6SS increases with the phylogenetic and metabolic proximities of bacteria to CFBP13503, suggesting the influence of interspecies trophic patterns in T6SS-mediated competitions. In planta and in soil, CFBP13503 T6SS influences specific bacterial taxa, leading to shifts in bacterial interactions and distinct community dynamics. T6SS-mediated competition plays a pivotal role in shaping seed bacterial communities and the dynamics of seed-to-seedling transitions.},
}

@article {pmid40666882,
year = {2025},
author = {Orkin, JD and Fournier, A and Young, D and Webb, SE and Cheves Hernandez, SE and Jack, KM and Campos, FA and Dufour, A and Melin, AD},
title = {Fecal proteomics of wild capuchins reveals impacts of season, diet, age, and, sex on gut physiology.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.06.16.659980},
pmid = {40666882},
issn = {2692-8205},
abstract = {Understanding how the physiology of free-ranging mammals is impacted by environmental stressors is a major focus of ecological research. However, the constraints of non-invasive sampling pose serious challenges to the acquisition of physiological data from most species of primates. As a result, little is known about how the gut responds to ecological stimuli at the cellular level in wild populations. Recent research has demonstrated that proteomics could fill this knowledge gap by sequencing and quantifying proteins directly from primate feces. In order to ascertain how the gut of free-ranging white-faced capuchin monkeys (C. imitator) is influenced by environmental heterogeneity, diet, age, and sex, we sequenced 45 fecal proteomes from 24 individuals from the Sector Santa Rosa population in Costa Rica, using liquid chromatography-tandem mass spectrometry with label-free quantification. Fecal proteins assigned to C. imitator were strongly localized to gut tissues and functionally enriched for digestive and immune functions. We identified 41 capuchin candidate proteins linked to seasonality, age, sex, and diet. We also quantified abundances of dietary fruit, dietary insects, helminth gut parasites, and gut microbes. Our results demonstrate the viability of using quantitative fecal proteomics in free-ranging populations of mammals to integrate host physiology, diet, and microbial ecology through non-invasive means.},
}

@article {pmid40662685,
year = {2025},
author = {Verstraete, W and Strubbe, L and Pikaar, I and Vinestock, TW and Lee, PH and Matassa, S and Chong, J and Zhou, J and Daigger, GT and Guo, M},
title = {Escaping Historical Lock-in─Redesigning Wastewater Treatment Plants and Their Microbiomes for the 21st Century.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c06208},
pmid = {40662685},
issn = {1520-5851},
abstract = {Wastewater treatment plants (WWTPs) have gradually, over the last hundred years, been designed and extended to deal with a sequence of problems, including a) odor, b) suspended solids, c) organics, d) ammonia, e) nitrate and phosphate, and f) recalcitrant pollutants. The line of historical developments was piecemeal rather than holistic and did not focus on sustainability, resource recovery, and water reuse. On the contrary, microbial processes that accelerated the removal of nitrogen were incorporated and heralded as a positive part of the "cleanup" agenda, despite their relatively large energy consumption and substantial production of nitrous oxide, a potent greenhouse gas. The time has come to examine the historical, technological, and microbiological lock-in present in today's WWTPs, so that a more coherent integrated system can be developed for future generations. Some disruptive strategies are outlined, and a categorization of processes in terms of their potential for the future is formulated.},
}

@article {pmid40660619,
year = {2025},
author = {Armstrong, R},
title = {Microbes as Teachers: Rethinking Knowledge in the Anthropocene.},
journal = {Microbial biotechnology},
volume = {18},
number = {7},
pages = {e70195},
pmid = {40660619},
issn = {1751-7915},
support = {101114746//European Innovation Council (EIC), Pathfinder Challenges/ ; },
mesh = {Humans ; Ecosystem ; *Microbiology/education ; },
abstract = {This opinion piece proposes that the environmental crises of our time arise from a failure to recognise the vital role of microbes in sustaining life on Earth, where ecosystems have been shaped for billions of years by microbial processes, including oxygen production, nutrient cycling and climate regulation. Yet the idea that microbes can 'teach' us how to navigate complexity, adapt across scales, and sustain planetary systems is still marginalised in science, policy, and education. A paradigm shift is proposed: microbes must be reframed as active collaborators in solving global challenges. This perspective is grounded in microbial ecology, Indigenous knowledge, and ethical philosophy, advocating for 'learning' through and with microbial life. To institutionalise this transition, policy and educational reforms are urged, centring microbial literacy as a foundation for ecological understanding. By integrating microbial agency into human knowledge systems, societal actions could be realigned with the biochemical and evolutionary logics that have sustained life for millennia. Ultimately, a deeper engagement with microbial knowledge is called for-one that informs a more sustainable future.},
}

Humans
Ecosystem
*Microbiology/education

@article {pmid40657876,
year = {2025},
author = {Strachan, CR and Bowers, CM and Kim, BC and Movsesijan, T and Neubauer, V and Mueller, AJ and Yu, XA and Pereira, FC and Nagl, V and Faas, J and Wagner, M and Zebeli, Q and Weimer, PJ and Candry, P and Polz, MF and Lawson, CE and Selberherr, E},
title = {Distinct lactate utilization strategies drive niche differentiation between two co-existing Megasphaera species in the rumen microbiome.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf147},
pmid = {40657876},
issn = {1751-7370},
abstract = {Lactate utilization mitigates rumen acidosis and is associated with decreased methane production in the rumen. While several lactate utilization pathways exist across different microbial species in the rumen, how they are metabolically differentiated remains unclear. Here, we show that the key lactate-utilizing species Megasphaera hexanoica and Megasphaera elsdenii display distinct growth strategies based on their fermentative end products. This allows them to co-exist and play distinct metabolic roles, which appear particularly relevant in the early stages of rumen development, as both species are highly enriched in the calf. Specifically, M. hexanoica is more strongly associated with rumen microbiome states that involve increased lactate utilization and preferentially runs reverse beta-oxidation (termed chain elongation) to produce butyrate and medium-chain fatty acids from lactate. As M. elsdenii instead utilizes lactate via the acrylate pathway to produce propionate, we leverage Enzyme Cost Minimization to predict how this pathway relates to a distinct growth strategy. We find that M. elsdenii maximizes growth rate when lactate transiently accumulates, which contrasts M. hexanoica's invariably high-yield strategy. This trade-off, which is supported by the analysis of growth kinetics, metabolic flux, and bioreactors simulating the rumen microbiome, ultimately contributes to co-existence on lactate and may have driven niche differentiation. Lastly, we demonstrate how lactate utilization in the Megasphaera is threatened by toxins widespread in feed, which points to dietary interventions to support calf health.},
}

@article {pmid40657038,
year = {2025},
author = {Ronin, D and Hansen, MF and Flaig, ML and Dahl Dueholm, MK and Hostrup Daugberg, AO and Nesme, J and Kot, W and Burmølle, M},
title = {Unfolding the collective functional potential of a synergistic multispecies community through genotypic and phenotypic analyses.},
journal = {Biofilm},
volume = {10},
number = {},
pages = {100290},
pmid = {40657038},
issn = {2590-2075},
abstract = {By studying model multispecies biofilm systems, we can further our knowledge regarding why some properties emerge solely in a multispecies setting. In this study, the model system under investigation is composed of four bacterial species: Paenibacillus amylolyticus, Microbacterium oxydans, Stenotrophomonas rhizophila and Stenotrophomonas maltophilia. This community was isolated from soil and has previously shown synergistic biofilm formation capabilities in vitro, along with other intrinsic properties, some of which could lead to potential industrial and agricultural applications. In this study, we conducted the first complete genome assemblies for these four strains and performed a manually curated annotation of the genomes to identify genomic features that could guide the selection of relevant phenotypic assays. In all four strains, we identified genes linked to interspecies communication, biofilm formation, secondary metabolite production, antibiotic resistance, enzymatic activity and metabolism of toxic xenobiotics. With metabolism being the largest gene function category identified, we then conducted growth assays on various carbon sources and relevant polysaccharides. This revealed interesting emergent behaviors - regarding growth and enzymatic activity - in the four-species community which were not seen in the monocultures. Overall, analysis of the complete genomes of this model community uncovered gene functions which could play a role in the previously observed community intrinsic properties, as well as provided insight to the positive social interactions observed in vitro.},
}

@article {pmid40655931,
year = {2025},
author = {Redondo, MA and Jones, CM and Legendre, P and Guénard, G and Hallin, S},
title = {Predicting gene distribution in ammonia-oxidizing archaea using phylogenetic signals.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf087},
pmid = {40655931},
issn = {2730-6151},
abstract = {Phylogenetic conservatism of microbial traits has paved the way for phylogeny-based predictions, allowing us to move from descriptive to predictive functional microbial ecology. Here, we applied phylogenetic eigenvector mapping to predict the presence of genes indicating potential functions of ammonia-oxidizing archaea (AOA), which are important players in nitrogen cycling. Using 160 nearly complete AOA genomes and metagenome assembled genomes from public databases, we predicted the distribution of 18 ecologically relevant genes across an updated amoA gene phylogeny, including a novel variant of an ammonia transporter found in this study. All selected genes displayed a significant phylogenetic signal and gene presence was predicted with an average of >88% accuracy, >85% sensitivity, and >80% specificity. The phylogenetic eigenvector approach performed equally well as ancestral state reconstruction of gene presence. We implemented the predictive models on an amoA sequencing dataset of AOA soil communities and showed key ecological predictions, e.g. that AOA communities in nitrogen-rich soils were predicted to have capacity for ureolytic metabolism while those adapted to low-pH soils were predicted to have the high-affinity ammonia transporter (amt2). Predicting gene presence can shed light on the potential functions that microorganisms perform in the environment, further contributing to a better mechanistic understanding of their community assembly.},
}

@article {pmid40654884,
year = {2025},
author = {Wirbel, J and Hickey, AS and Chang, D and Enright, NJ and Dvorak, M and Chanin, RB and Schmidtke, DT and Bhatt, AS},
title = {Discovering Broader Host Ranges and an IS-bound Prophage Class Through Long-Read Metagenomics.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.09.652943},
pmid = {40654884},
issn = {2692-8205},
abstract = {Gut bacteriophages profoundly impact microbial ecology and human health, yet they are greatly understudied. Using deep, long-read bulk metagenomic sequencing, a technique that overcomes fundamental limitations of short-read approaches, we tracked prophage integration dynamics in 12 longitudinal stool samples from six healthy individuals, spanning a two-year timescale. While most prophages remain stably integrated into their host over two years, we discover that ∼5% of phages are dynamically gained or lost from persistent bacterial hosts. Within the same sample, we find evidence of population heterogeneity in which identical bacterial hosts with and without a given integrated prophage coexist simultaneously. Furthermore, we demonstrate that phage induction, when detected, occurs predominantly at low levels (1-3x coverage compared to the host region). Interestingly, we identify multiple instances of integration of the same phage into bacteria of different taxonomic families, challenging the dogma that phage are specific to a host of a given species or strain. Lastly, we describe a new class of phages, which we name "IScream phages". These phages co-opt bacterial IS30 transposases to mediate their integration, representing a previously unrecognized form of phage domestication of selfish bacterial elements. Taken together, these findings illuminate fundamental aspects of phage-bacterial dynamics in the human gut microbiome and expand our understanding of the evolutionary mechanisms that drive horizontal gene transfer and microbial genome plasticity in this ecosystem.},
}

@article {pmid40650753,
year = {2025},
author = {Pascual, A and Calabresi, F and de la Fuente, D and Catalano, MI and Brentassi, ME},
title = {Transcriptome Analysis of the Fat Body of the Maize Pest Delphacodes kuscheli (Hemiptera: Delphacidae) Reveals Essential Roles of Fungal Endosymbionts.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {74},
pmid = {40650753},
issn = {1432-184X},
support = {PICT 2021- 00914//Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CICPBA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de La Plata (UNLP), and Agencia Nacional de Promoción Científica y Tecnológica (ANPCyT) (PICT 2021- 00914)./ ; PICT 2021- 00914//Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CICPBA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de La Plata (UNLP), and Agencia Nacional de Promoción Científica y Tecnológica (ANPCyT) (PICT 2021- 00914)./ ; PICT 2021- 00914//Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CICPBA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de La Plata (UNLP), and Agencia Nacional de Promoción Científica y Tecnológica (ANPCyT) (PICT 2021- 00914)./ ; PICT 2021- 00914//Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CICPBA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de La Plata (UNLP), and Agencia Nacional de Promoción Científica y Tecnológica (ANPCyT) (PICT 2021- 00914)./ ; PICT 2021- 00914//Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CICPBA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de La Plata (UNLP), and Agencia Nacional de Promoción Científica y Tecnológica (ANPCyT) (PICT 2021- 00914)./ ; },
mesh = {Animals ; *Symbiosis ; *Hemiptera/microbiology/genetics ; Gene Expression Profiling ; Zea mays/parasitology ; *Fat Body/microbiology/metabolism ; *Transcriptome ; *Hypocreales/genetics/physiology ; Phylogeny ; },
abstract = {The fat body of certain insects, in addition to performing essential biosynthetic and metabolic functions, harbors endosymbionts that play critical roles for their host. While knowledge of the diversity and functions of fungal endosymbionts harbored in the fat body of planthoppers is mostly limited to rice pests of Asia, our study presents a comprehensive transcriptomic analysis of the fat body of Delphacodes kuscheli (Hemiptera: Delphacidae), an important agricultural pest of maize in Argentina. The dominant fungal endosymbionts, identified as yeast-like symbionts (YLS), include members of the genera Ophiocordyceps, Cordyceps, Hirsutella, and Tolypocladium (Ascomycota: Hypocreales). Transcriptomic data reveal that the fungal endosymbionts encode genes involved in vital metabolic processes for the host, such as essential amino acid biosynthesis, nitrogen recycling, and steroid biosynthesis. The genetic contribution of these endosymbionts to nutrient provision and metabolism supports a mutualistic obligate relationship with D. kuscheli. The results presented here provide insights into the evolutionary dynamics of endosymbiosis in the Delphacidae. Furthermore, this study highlights the potential of YLS as promising targets for innovative pest control strategies.},
}

Animals
*Symbiosis
*Hemiptera/microbiology/genetics
Gene Expression Profiling
Zea mays/parasitology
*Fat Body/microbiology/metabolism
*Transcriptome
*Hypocreales/genetics/physiology
Phylogeny

@article {pmid40650575,
year = {2025},
author = {Guigard, L and Nazaret, F and Almario, J and Bertolla, F and Boubakri, H and Cantarel, AAM and Cournoyer, B and Favre-Bonté, S and Florio, A and Galia, W and Hazard, C and Henry, G and Belaroussi, AH and Chong, SKTF and Lavire, C and Lobreau, C and Luis, P and Maréchal, M and Meyer, T and Pozzi, ACM and Minard, G and Nazaret, S and Nicol, GW and Prigent-Combaret, C and Richaume, A and Rodriguez, V and Sanchez-Cid, C and Moro, CV and Vial, L and Vigneron, A and Wisniewski-Dye, F and Shade, A},
title = {The connections of climate change with microbial ecology and their consequences for ecosystem, human, and plant health.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf168},
pmid = {40650575},
issn = {1365-2672},
abstract = {The climate crisis presents an urgent challenge for Earth's living creatures and the habitats in which they have been adapted to thrive. Climate-related stress presents risks to microorganisms, the stability of the functions they provide, and their maintenance of beneficial interactions with their hosts and ecosystems. Microbes move across the continuum of anthropogenic influence on Earth's ecosystems, from pristine to human-managed to fully urbanized environments. Because microbial feedback within and across this continuum exists at multiple, connected scales from molecules to ecosystem-level processes, predicting microbial responses to climate stress and their potentially wide-ranging consequences remains difficult. Here, we discuss the broad implications of microbial and microbiome responses to climate change as they interface with human, plant, and ecosystem health. For each section on human, plant and ecosystem health, we briefly discuss the state of knowledge for each and follow with proposed future research, including some directions that are promising but require more work to evaluate. We end by considering overarching microbial ecology research needs across these systems and microbial solutions under investigation as possible climate-resilient interventions to maintain human, plant, and ecosystem health. This work draws on diverse expertise to identify broad research directions across typically separated disciplines and builds a holistic framework for considering their interrelationships.},
}

@article {pmid40650408,
year = {2025},
author = {Beau, A and Natividad, J and Benoit, B and Delerive, P and Duboux, S and Feng, Y and Jammes, M and Barnel, C and Sequino, G and Pinteur, C and Glorieux, G and Fouque, D and Vidal, H and Koppe, L},
title = {A specifically designed multi-biotic reduces uremic toxin generation and improves kidney function.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2531202},
pmid = {40650408},
issn = {1949-0984},
mesh = {Humans ; *Uremic Toxins/metabolism ; *Renal Insufficiency, Chronic/microbiology/therapy ; Animals ; *Probiotics/administration & dosage ; Feces/microbiology/chemistry ; *Gastrointestinal Microbiome ; Male ; Cresols/metabolism ; *Kidney/physiology ; Prebiotics/administration & dosage ; Female ; Middle Aged ; Lactobacillus/metabolism/growth & development ; *Uremia ; Cellobiose/metabolism ; Rats ; Indican ; Bacteria/metabolism/genetics/classification ; Disease Models, Animal ; },
abstract = {Chronic kidney disease (CKD) is characterized by accumulation of uremic toxins (UTs), such as p-cresyl sulfate and indoxyl sulfate, generated through the transformation of tyrosine and tryptophan by the gut microbiota. Using an ex vivo Simulator of the Human Intestinal Microbial Ecosystem (SHIME) colonized with fecal samples from eight CKD patients or nine healthy volunteers, a higher bacterial generation of p-cresol and indoles post-amino acid enrichment, as well lower basal butyrate levels, in the feces of CKD patients were found. Through in silico data mining, we selected a probiotic strain lacking the capacity to produce UT, i.e. without genes for tryptophanase, tyrosinase and urease. In vitro, we confirmed the potential of cellobiose as a prebiotic supporting the growth of this strain. We further designed a novel specific multi-biotic for CKD (SynCKD) [containing a probiotic Lactobacillus johnsonii NCC533, a prebiotic (1% cellobiose), and a postbiotic (1% short and medium chain triglycerides C4-C8, a source of butyrate)]. SynCKD effectively curtailed UT precursor generation ex vivo. The in vivo efficacy of SynCKD (and the synergic effect) was established in two uremic rodent models, demonstrating lower plasma levels of UTs and enhancing kidney function after 6-8 weeks of treatment. These effects were linked to better gut microbial ecology. Metagenomic analysis revealed reduced microbial genes for tryptophan/tyrosine degradation. This study lays the foundation for SynCKD as a potential therapy to mitigate CKD progression.},
}

Humans
*Uremic Toxins/metabolism
*Renal Insufficiency, Chronic/microbiology/therapy
Animals
*Probiotics/administration & dosage
Feces/microbiology/chemistry
*Gastrointestinal Microbiome
Male
Cresols/metabolism
*Kidney/physiology
Prebiotics/administration & dosage
Female
Middle Aged
Lactobacillus/metabolism/growth & development
*Uremia
Cellobiose/metabolism
Rats
Indican
Bacteria/metabolism/genetics/classification
Disease Models, Animal

@article {pmid40649758,
year = {2025},
author = {Hu, Q and Huang, T and Zhu, A and Anglés, A and Abdelghany, O and Ahmed, A and Fernández-Remolar, DC},
title = {Comparing Protein Stability in Modern and Ancient Sabkha Environments: Implications for Molecular Remnants on Ancient Mars.},
journal = {International journal of molecular sciences},
volume = {26},
number = {13},
pages = {},
pmid = {40649758},
issn = {1422-0067},
support = {2021YFA0716100//National Key Research and Development Program of China/ ; 2022YFF0504000//National Key Research and Development Program of China/ ; 2024YFF0807702//National Key Research and Development Program of China/ ; 0005/2020/A1//Fundo para o Desenvolvimento das Ciências e da Tecnologia/ ; 0052/2024/RIA1//Fundo para o Desenvolvimento das Ciências e da Tecnologia/ ; 42441801//National Natural Science Foundation of China/ ; },
mesh = {*Mars ; Protein Stability ; Proteomics/methods ; *Extraterrestrial Environment/chemistry ; Archaea/metabolism/genetics ; Geologic Sediments/chemistry ; *Archaeal Proteins/chemistry ; Tandem Mass Spectrometry ; Chromatography, Liquid ; },
abstract = {Understanding the mechanisms of protein preservation in extreme environments is essential for identifying potential molecular biosignatures on Mars. In this study, we investigated five sabkha sedimentary samples from the Abu Dhabi coast, spanning from the present day to ~11,000 years before present (BP), to assess how mineralogy and environmental conditions influence long-term protein stability. Using LC-MS/MS and direct Data-independent Acquisition (DIA) proteomic analysis, we identified 722 protein groups and 1300 peptides, revealing a strong correlation between preservation and matrix composition. Carbonate- and silica-rich samples favored the retention of DNA-binding and metal-coordinating proteins via mineral-protein interactions, while halite- and gypsum-dominated facies showed lower recovery due to extreme salinity and reduced biomass input. Functional profiling revealed a shift from metabolic dominance in modern samples to genome maintenance strategies in ancient ones, indicating microbial adaptation to prolonged environmental stress. Contrary to expectations, some ancient samples preserved large, multi-domain proteins, suggesting that early mineral encapsulation can stabilize structurally complex biomolecules over millennial timescales. Taxonomic reconstruction based on preserved proteins showed broad archaeal diversity, including Thaumarchaeota and thermophilic lineages, expanding our understanding of microbial ecology in hypersaline systems. These findings highlight sabkhas as valuable analogs for Martian evaporitic environments and suggest that carbonate-silica matrices on Mars may offer optimal conditions for preserving ancient molecular traces of life.},
}

*Mars
Protein Stability
Proteomics/methods
*Extraterrestrial Environment/chemistry
Archaea/metabolism/genetics
Geologic Sediments/chemistry
*Archaeal Proteins/chemistry
Tandem Mass Spectrometry
Chromatography, Liquid

@article {pmid40649719,
year = {2025},
author = {Popov, IV and Manakhov, AD and Gorobets, VE and Diakova, KB and Lukbanova, EA and Malinovkin, AV and Venema, K and Ermakov, AM and Popov, IV},
title = {Metagenomic Investigation of Intestinal Microbiota of Insectivorous Synanthropic Bats: Densoviruses, Antibiotic Resistance Genes, and Functional Profiling of Gut Microbial Communities.},
journal = {International journal of molecular sciences},
volume = {26},
number = {13},
pages = {},
pmid = {40649719},
issn = {1422-0067},
support = {23-14-00316//Russian Science Foundation/ ; 075-10-2025-017//Ministry of Science and Higher Education of the Russian Federation/ ; },
mesh = {Animals ; *Chiroptera/microbiology/virology ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; *Drug Resistance, Microbial/genetics ; Phylogeny ; *Metagenome ; },
abstract = {Bats serve as key ecological reservoirs of diverse microbial communities, including emerging viruses and antibiotic resistance genes. This study investigates the intestinal microbiota of two insectivorous bat species, Nyctalus noctula and Vespertilio murinus, at the Rostov Bat Rehabilitation Center in Southern Russia using whole metagenome shotgun sequencing. We analyzed taxonomic composition, functional pathways, antibiotic resistance genes, and virulence factors. Densoviruses, especially those closely related to Parus major densovirus, were the most dominant viral sequences identified. Metagenome-assembled densovirus genomes showed high sequence similarity with structural variations and clustered phylogenomically with viruses from mealworms and birds, reflecting both dietary origins and the potential for vertebrate infection. Functional profiling revealed microbial pathways associated with cell wall biosynthesis, energy metabolism, and biofilm formation. A total of 510 antibiotic resistance genes, representing 142 unique types, mainly efflux pumps and β-lactamases, were identified. Additionally, 870 virulence factor genes were detected, with a conserved set of iron acquisition systems and stress response regulators across all samples. These findings highlight the ecological complexity of bat-associated microbiota and viromes and suggest that synanthropic bats may contribute to the circulation of insect-associated viruses and antimicrobial resistance in urban settings.},
}

Animals
*Chiroptera/microbiology/virology
*Gastrointestinal Microbiome/genetics
*Metagenomics/methods
*Drug Resistance, Microbial/genetics
Phylogeny
*Metagenome

@article {pmid40647934,
year = {2025},
author = {Gao, X and Qian, H and Huang, R and He, W and Jiang, H and Shen, A and Li, Z and Hu, Y},
title = {Rhizosphere and Non-Rhizosphere Soil Microbial Communities in Alpine Desertified Grassland Affected by Vegetation Restoration.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {13},
pages = {},
pmid = {40647934},
issn = {2223-7747},
support = {41771552//National Natural Science Foundation of China/ ; 2022YFS0469//Sichuan Science and Technology Project/ ; },
abstract = {The rhizosphere serves as a critical interface for plant-soil-microorganism interactions. Rhizosphere soil refers to the soil directly adhering to root surfaces, while non-rhizosphere soil denotes the surrounding soil not in direct contact with roots. This study investigated the characteristics of soil microbial community structure, diversity, and enzyme activity dynamics in both rhizosphere and non-rhizosphere soils of Salix cupularis (shrub) across different restoration periods (4, 8, 16, and 24 years) in alpine sandy lands on the eastern Qinghai-Tibet Plateau, with unrestored sandy land as control (CK), while analyzing relationships between soil properties and microbial characteristics. Results demonstrated that with increasing restoration duration, activities of sucrase, urease, alkaline phosphatase, and catalase in Salix cupularis rhizosphere showed increasing trends across periods, with rhizosphere enzyme activities consistently exceeding non-rhizosphere levels. Bacterial Chao1 and Shannon indices followed similar patterns to enzyme activities, revealing statistically significant differences between rhizosphere and non-rhizosphere soils after 8 and 24 years of restoration, respectively. Dominant bacterial phyla ranked by relative abundance were Actinobacteria > Proteobacteria > Acidobacteria > Chloroflexi > Gemmatimonadetes. The relative abundance of Actinobacteria exhibited highly significant positive correlations with carbon, nitrogen, phosphorus, and enzyme activity indicators, indicating that Salix cupularis restoration promoted improvements in soil physicochemical properties and nutrient accumulation, thereby enhancing bacterial community diversity and increasing Actinobacteria abundance. These findings provide fundamental data for restoration ecology and microbial ecology in alpine ecosystems, offering a scientific basis for optimizing ecological restoration processes and improving recovery efficiency in alpine sandy ecosystems.},
}

@article {pmid40647139,
year = {2025},
author = {Bach, LG and Braga, GZA and Bedutti, MC and Dias, LMP and Dos Santos, EAR and Tadielo, LE and Silva, ECD and Schmiedt, JA and Alves, VF and De Martinis, ECP and Possebon, FS and Barcellos, VC and Bersot, LDS},
title = {Total Culturable Microbial Diversity of Food Contact Surfaces in Poultry and Fish Processing Industries After the Pre-Operational Cleaning Process.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {13},
pages = {},
pmid = {40647139},
issn = {2304-8158},
support = {001//Coordination for the Improvement of Higher Education - CAPES/ ; Proc.# 3069982022-0//National Council for Scientific and Technological Development/ ; },
abstract = {This study assessed the viable and culturable microbial diversity that remained on equipment surfaces after hygiene procedures in Brazilian poultry and fish slaughterhouses. Food-contact surface samples were collected using sterile swabs in poultry (n = 50) and fish (Oreochromis niloticus, n = 50) slaughterhouses. The swab samples were used to prepare culture plates to recover viable and culturable cells. The grown plates were washed, and the total DNA of the cell suspension was extracted with a commercial kit. Sequencing of the total DNA extracted from cultures was targeted at the V3 and V4 regions of the 16S rRNA. DNA reads were analyzed by QIIME2 software, with results expressed in relative frequency (%RF). Alpha and beta diversity indexes were analyzed considering the spots of sample collection, type of industry, surfaces (smooth or modular), and materials (polypropylene, stainless steel, or polyurethane). The results showed that in the poultry slaughterhouse, the most abundant genera were Acinetobacter (27.4%), Staphylococcus (7.7%), and Pseudomonas (5.3%), while for the fish slaughterhouse, there was a higher abundance of Staphylococcus (27.7%), Acinetobacter (17.2%), and Bacillus (12.5%). Surface characteristics influenced the microbial diversity, with Acinetobacter spp. dominating modular surfaces and Staphylococcus spp. prevailing on smooth surfaces. The results obtained indicate there is an important resident microbiota that persists even after hygiene processes, and surface-specific cleaning strategies should be developed.},
}

@article {pmid40647044,
year = {2025},
author = {Park, I and Mannaa, M},
title = {Fermented Foods as Functional Systems: Microbial Communities and Metabolites Influencing Gut Health and Systemic Outcomes.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {13},
pages = {},
doi = {10.3390/foods14132292},
pmid = {40647044},
issn = {2304-8158},
support = {2024//This work was supported by Youngsan University research fund of/ ; },
abstract = {Fermented foods represent an intricate ecosystem that delivers live microbes and numerous metabolites, influencing gut health. In this review, we explore how complex microbial communities and metabolites generated during food fermentation modulate the gut microbiome and affect human health. We discuss fermentation-induced biochemical transformations, including enhanced fiber fermentability; nutrient availability; and the synthesis of bioactive metabolites such as short-chain fatty acids, exopolysaccharides, bacteriocins, and modified polyphenols. We describe the dynamic microbial ecology of fermented foods, influenced by ingredient variations, highlighting its effect on health-related metabolic outcomes. Fermented products when consumed transiently introduce beneficial microbes and bioactive compounds into the gut, thereby boosting microbial diversity, resilience, and barrier function. We review clinical and preclinical studies to substantiate the roles of fermented foods in immune regulation, metabolic homeostasis, cognitive function, and inflammation mitigation. Individual variability in response to fermented foods has been emphasized, underscoring the potential for personalized nutrition strategies informed by advanced omics technologies. By integrating microbial ecology, metabolomics, and clinical evidence, this review positions fermented food intake as a strategic dietary intervention for microbiome modulation and health promotion.},
}

@article {pmid40643242,
year = {2025},
author = {Nguyen, A and Ustick, LJ and Larkin, AA and Martiny, AC},
title = {Global phylogeography and microdiversity of the marine diazotrophic photoautotrophs Trichodesmium and UCYN-A.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0024525},
doi = {10.1128/msphere.00245-25},
pmid = {40643242},
issn = {2379-5042},
abstract = {Photoautotrophic diazotrophs, specifically the genera Trichodesmium and UCYN-A, play a pivotal role in marine nitrogen cycling through their capacity for nitrogen fixation. Despite their global distribution, the microdiversity and environmental drivers of these diazotrophs remain underexplored. This study provides a comprehensive analysis of the global diversity and distribution of Trichodesmium and UCYN-A using the nitrogenase gene (nifH) as a genetic marker. We sequenced 954 samples from the Pacific, Atlantic, and Indian Oceans as part of the Bio-GO-SHIP project. Our results reveal significant phylogenetic and biogeographic differences between and within the two genera. Trichodesmium exhibited greater microdiversity compared to UCYN-A, with clades showing region-specific distribution. Trichodesmium clades were primarily influenced by temperature and nutrient availability. They were particularly frequent in regions of phosphorus stress. In contrast, UCYN-A was most frequently observed in regions experiencing iron stress. UCYN-A clades demonstrated more homogeneous distributions, with a single sequence variant within the UCYN-A1 clade dominating across varied environments. The biogeographic patterns and environmental correlations of Trichodesmium and UCYN-A highlight the role of microdiversity in their ecological adaptation and reflect their different ecological strategies. These findings underscore the importance of characterizing the global patterns of fine-scale genetic diversity to better understand the functional roles and distribution of marine nitrogen-fixing photoautotrophs.IMPORTANCEThis study provides insights into the global diversity and distribution of nitrogen-fixing photoautotrophs, specifically Trichodesmium and UCYN-A. We sequenced 954 oceanic samples of the nifH nitrogenase gene and uncovered significant differences in microdiversity and environmental associations between these genera. Trichodesmium showed high levels of sequence diversity and region-specific clades influenced by temperature and nutrient availability. In contrast, UCYN-A exhibited a more uniform distribution, thriving in iron-stressed regions. Quantifying these fine-scale genetic variations enhances our knowledge of their ecological roles and adaptations, emphasizing the need to characterize the genetic diversity of marine nitrogen-fixing prokaryotes.},
}

@article {pmid40640502,
year = {2025},
author = {Liu, L and Firrman, JA and Narrowe, AB and Mahalak, KK and Lemons, JMS and Marzorati, M and Duysburgh, C and Rotsaert, C and Van de Wiele, T},
title = {Structural and functional characterization of a porcine intestinal microbial ecosystem developed in vitro.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {24821},
pmid = {40640502},
issn = {2045-2322},
support = {8072-41000-108-00-D//USDA/ ; 8072-41000-108-00-D//USDA/ ; 8072-41000-108-00-D//USDA/ ; 8072-41000-108-00-D//USDA/ ; 8072-41000-108-00-D//USDA/ ; EOS-Homistasis project//FWO-FNR/ ; GOA-Microbes4Immunity//UGent-BOF/ ; },
mesh = {Animals ; Swine ; *Gastrointestinal Microbiome ; Metagenome ; Feces/microbiology ; *Bacteria/genetics/classification ; Metagenomics/methods ; Metabolomics ; *Intestines/microbiology ; Ecosystem ; },
abstract = {The mammalian digestive tract harbors a vast microbial community that has the potential to modulate numerous health-related processes. Multicompartment dynamic gut models have been developed to study microbial communities in a controlled environment. To verify the assumption that the experimental results produced in vitro in a mechanical device would be highly similar to those obtained from an in vivo study, in this study fecal samples from four pigs were inoculated in a simulator of the porcine intestinal microbial ecosystem (SPIME) and cultured until reaching steady state. The composition and structure of the resultant microbial communities, and the metabolites produced were compared with those harvested from the intestine of the same pigs. Taxonomic abundance identification based on shallow shotgun metagenomic sequencing revealed only 12.1% of species or 15% of metagenome-assembled genomes (MAGs) being shared across the colon compartments of the source pigs and the SPIME. Despite these overwhelming compositional shifts, higher functional conservation was indicated as measured by functional richness, MAG-level traits, CAZymes, and untargeted metabolomics. Environmental selection and bacterial functional redundancy were considered the two key elements in microbial compositional shifts and functional preservation.},
}

Animals
Swine
*Gastrointestinal Microbiome
Metagenome
Feces/microbiology
*Bacteria/genetics/classification
Metagenomics/methods
Metabolomics
*Intestines/microbiology
Ecosystem

@article {pmid40639195,
year = {2025},
author = {Estrada-Peña, A and Antunes, S and Domingos, A and Esser, H and Földvári, G and Fuehrer, HP and Gargili, A and van Gestel, M and Grandi, G and Kazimirova, M and Kiewra, D and Klemola, T and Kjær, LJ and Kjelland, V and Kubiak, K and de Meneghi, D and Mihalca, AD and Moutailler, S and Potkonjak, A and Prokop, P and Robert, K and Ranka, R and Sainz, A and Sormunen, J and Sotiraki, S and Strube, C and Stuen, S and Široký, P and Tomassone, L and Zintl, A},
title = {Living with ticks: Results of an online survey of the knowledge, attitudes and practices (KAP) regarding ticks and tick-borne pathogens in academic environments across Europe.},
journal = {Ticks and tick-borne diseases},
volume = {16},
number = {4},
pages = {102515},
doi = {10.1016/j.ttbdis.2025.102515},
pmid = {40639195},
issn = {1877-9603},
abstract = {We prepared a digital questionnaire to capture knowledge, attitudes and practices (KAP) regarding ticks and tick-borne pathogens (TBPs) in 20 languages. The questionnaire was distributed to 21 universities and research institutions in 22 European countries and 9401 valid responses were collected. Most survey participants identified ticks correctly and regarded ticks as a serious health risk. There was also a good level of knowledge regarding tick activity, habitats and the predominant TBPs in the country or region. Moreover, most respondents were familiar with effective tick protection and removal measures. Over 75 % of respondents had been bitten by ticks and up to 12 % of participants had been diagnosed with a tick-borne infection in the past. Respondents from northern and central European countries who reported engaging in outdoor activities more frequently, reported increased frequencies of tick bites and infection with TBPs compared to respondents from southern Europe. Awareness of national information campaigns on ticks and TBPs was also greater among respondents from northern and central European countries than among Mediterranean countries. This study identified knowledge gaps among respondents from some European countries where TBPs have not been prioritised historically. These knowledge gaps should be addressed by reputable bodies to encourage personal protective behaviours without causing alarm and to forestall the spreading of incorrect and unreliable information propagated by some social media sources.},
}

@article {pmid40638961,
year = {2025},
author = {Schröer, L and Balcaen, T and Folens, K and Boon, N and De Kock, T and Samari-Kermani, M and Kerckhofs, G and Cnudde, V},
title = {Contrast-Enhanced micro-computed tomography for 3D imaging of biofilms in opaque materials: Insights from water treatment plant sand filters.},
journal = {Water research},
volume = {285},
number = {},
pages = {124152},
doi = {10.1016/j.watres.2025.124152},
pmid = {40638961},
issn = {1879-2448},
abstract = {Microorganisms form biofilms in various environments, including porous media, where they alter substrate properties and fluid flow. Visualizing biofilms in 3D within the pore system is essential to understand their effect. Micro-computed tomography (µCT) is a powerful technique to visualize the pore system, but biofilms are usually invisible due to low contrast with water. Contrast-enhancing staining agents (CESAs) can improve their visibility by changing the attenuation of the biofilm or water phase. Traditional CESAs such as BaSO4, silver-coated microspheres or 1-chloronapthalene proved to be successful, but often stain the water phase and have drawbacks such as sedimentation or toxicity. After the successful use of isotonic Lugol and Hf-WD 1:2 POM on cyanobacteria at the surface, this study investigated the use of those CESAs to stain biofilms within opaque materials and, in particular, on biofilms colonizing field-derived sand filters of water treatment plants. Both CESAs increased the biofilms' visibility, including channels within the Hf-WD 1:2 POM stained biofilms and improved segmentation. Their visualization was consistent with Scanning Electron Microscopy (SEM). The CESAs quickly stained the biofilms, and their effect was stable. Isotonic Lugol enhanced the X-ray attenuation the most but might have caused shrinkage. The use of BaSO4 solution, added for comparison and positive control, was complicated due to its fast precipitation. BaSO4 was unable to visualize the isotonic Lugol-stained biofilms but corresponded with the Hf-WD 1:2 POM-stained biofilms. However, the stability and detail shown by isotonic Lugol and Hf-WD 1:2 POM make the latter two preferred. The study showed the potential of µCT and these CESAs for biofilm visualization and water research. Future research should apply these CESAs and focus on the CESA-biofilm interaction to understand the binding mechanisms and their effect on the structure.},
}

@article {pmid40638158,
year = {2025},
author = {Dhara, S and Majhi, J and Mandal, B and Bhadury, P and Bhattacharya, S and Ghorai, SK},
title = {Polydendrorhynchus amaleshii sp. nov., a New Species With Branched Proboscis (Nemertea: Heteronemertea) From the North-East Coastal Bay of Bengal.},
journal = {Zoological science},
volume = {42},
number = {3},
pages = {326-334},
doi = {10.2108/zs240093},
pmid = {40638158},
issn = {0289-0003},
mesh = {Animals ; Phylogeny ; India ; *Invertebrates/classification/anatomy & histology/genetics ; Bays ; Species Specificity ; Animal Distribution ; RNA, Ribosomal, 16S/genetics ; },
abstract = {A new lineid heteronemertean with a branched proboscis, Polydendrorhynchus amaleshii sp. nov., is described as the second member of the genus Polydendrorhynchus Yin and Zeng, 1986, following Polydendrorhynchus zhanjiangensis (Yin and Zeng, 1984). The description is based on specimens collected from the northeastern coastal Bay of Bengal, including the Subarnarekha Estuary and Frazerganj in the Indian Sundarbans mangrove ecosystem. The new species is distinguished from its congener by having up to 56 terminal branchlets of the proboscis and the absence of rhynchocoel compartments. In a maximum-likelihood phylogenetic analysis based on COI and 16S rRNA genes, P. amaleshii and P. zhanjiangensis formed a well-supported clade. Polydendrorhynchus amaleshii represents the ninth nemertean species recorded from India.},
}

Animals
Phylogeny
India
*Invertebrates/classification/anatomy & histology/genetics
Bays
Species Specificity
Animal Distribution
RNA, Ribosomal, 16S/genetics

@article {pmid40637783,
year = {2025},
author = {Philippe, C and Denis, LA and Fonville, M and Devriendt, B and Dufrasne, FE and Obregon, D and Maître, A and Skičková, Š and Cox, E and Sprong, H and Cruz, AC and Mori, M},
title = {Diversity of the Ixodes ricinus Microbiome Across Belgian Ecoregions and Its Association with Pathogen and Symbiont Presence.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {73},
pmid = {40637783},
issn = {1432-184X},
mesh = {*Ixodes/microbiology ; Animals ; *Microbiota ; Belgium ; *Symbiosis ; *Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Nymph/microbiology ; Anaplasma phagocytophilum/isolation & purification/genetics ; Biodiversity ; },
abstract = {Ticks are important vectors of zoonotic pathogens, and their presence can be influenced by the composition of the tick microbiome. In turn, this microbiome is shaped by environmental and ecological factors, as demonstrated in several studies conducted under controlled conditions. However, the extent of these influences under natural ecological conditions remains underexplored. In this study, we investigated the diversity of the microbiome and the prevalence of pathogens in Ixodes ricinus nymphs across three distinct Belgian ecoregions: Sandy Loam, Condroz, and Ardennes. Using real-time quantitative PCR (qPCR) and Oxford Nanopore 16S rRNA sequencing, we assessed how geography and pathogen presence influence tick-associated microbial communities. Our results revealed significant regional differences in microbiome composition and pathogen prevalence. Borrelia burgdorferi sensu lato (s.l.) was most prevalent in the Ardennes (9% (7.4-10.9) vs 3.8% (2.8-5.2) in the Condroz and 2.1% (1.4-3.2) in Sandy Loam) while Anaplasma phagocytophilum was more common in the Sandy Loam region (21.1% (18.7-23.8) vs 4% (3-5.4) in the Condroz and 3.2% (2.2-4.4) in the Ardennes). Endosymbionts such as Midichloria mitochondrii and Spiroplasma ixodetis also exhibited distinct geographic distributions. Network analysis identified potential pathogen-microbiota interactions, with certain bacterial taxa showing positive or negative associations with specific pathogens. Moreover, microbiome composition was influenced not only by ecoregion but also by microorganisms such as Rickettsia helvetica, suggesting that its colonization may actively shape microbial community structure, potentially through competition or facilitation mechanisms. Additionally, microbiome network robustness varied across ecoregions, highlighting the role of ecological context in shaping microbial interactions within ticks. These findings underscore the complex interplay between geography, pathogen presence, and microbial diversity in ticks, highlighting the importance of integrating these interactions to inform microbiome-based strategies for vector control and disease prevention.},
}

*Ixodes/microbiology
Animals
*Microbiota
Belgium
*Symbiosis
*Bacteria/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
Nymph/microbiology
Anaplasma phagocytophilum/isolation & purification/genetics
Biodiversity

@article {pmid40636495,
year = {2025},
author = {Chen, F and Cheng, M and Rong, D and Wang, Y and Liang, R and Irfan, M and Kang, Y and Cao, Y},
title = {Metagenomic insights into the microbial communities and functional traits of hot springs in Guizhou Province, China.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1615879},
pmid = {40636495},
issn = {1664-302X},
abstract = {INTRODUCTION: Hot springs were previously believed to be uninhabitable due to their hostile nature. However, recent studies have determined that hot springs not only have a rich microbiota but are also involved in various biogeochemical processes and possess unique characteristics that can be utilized for several biotechnological applications. This study aimed to determine the bacterial taxonomic diversity and functional profiles of 11 hot springs in the Guizhou Province, China.

METHODS: Illumina high-throughput sequencing was used to sequence the V3-V4 region of the 16S rRNA gene from microorganisms in samples collected from these hot springs. Software such as Mothur, the SILVA ribosomal RNA database, and Quantitative Insights into Microbial Ecology (QIIME) were utilized for taxonomic and operational taxonomic unit (OTU) analysis, while PICRUST2 was employed for functional predictions.

RESULTS: Guizhou Baili Rhododendron Hot Spring No.1 (BLDJA) had the highest diversity in terms of species richness, while Jianhe Hot Spring (YAS) had the lowest diversity. At the phylum level, the highest reported phyla included Pseudomonadota, Bacillota, Nitrospirota, Bacteroidota, and Actinomycetota, where Pseudomonadota had the highest abundance (92.094%) in Jianhe Hot Spring (YAS) and the lowest (41.238%) in Guizhou Baili Rhododendron Hot Spring No. 2 (BLDJB). Bacillota has the highest abundance (39.178%) in Guizhou Baili Rhododendron Hot Spring No. 2 (BLDJB) and the lowest (0.547%) in Jiutian Hot Spring (SNJT). The highest predicted functions were observed for amino acid metabolism, followed by carbohydrates. Predicted pathways for secondary metabolite and vitamin synthesis, along with stress-adaptation genes, underscore the biotechnological value of these habitats.

DISCUSSION: This study presents a preliminary survey of 11 hot springs in Guizhou Province, providing important insights into the origin and evolution of microorganisms. Furthermore, studying these microorganisms is crucial for understanding the adaptive mechanisms of life under extreme conditions, such as high temperatures, and for exploring the potential biotechnological applications of these microbes. An in-depth approach combining functional metagenomics and next-generation culturomics is required to fully understand the microbial flora and its potential biotechnological applications.},
}

@article {pmid40634370,
year = {2025},
author = {Crombez, E and Van de Peer, Y and Li, Z},
title = {The subordinate role of pseudogenization to recombinative deletion following polyploidization in angiosperms.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {6335},
pmid = {40634370},
issn = {2041-1723},
support = {G0ADO25N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; BOF.BAF.2024.0889.01//Universiteit Gent (UGent)/ ; BOF.MET.2021.0005.01//Universiteit Gent (UGent)/ ; No. 833522//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; },
mesh = {*Polyploidy ; *Pseudogenes/genetics ; Genome, Plant/genetics ; *Magnoliopsida/genetics ; *Gene Deletion ; Evolution, Molecular ; Gene Duplication ; *Recombination, Genetic ; },
abstract = {Extensive gene loss is a hallmark of rediploidization following polyploidization, but its molecular basis remains unclear: whether it occurs primarily through pseudogenization or DNA deletion. Here, we examine pseudogenization in collinear segments from ancient whole-genome multiplications (WGMs) across 12 angiosperms. Although total pseudogenes are abundant, we find far fewer WGM-derived pseudogenes than expected if pseudogenization and DNA deletion contribute equally to gene loss. Simulations of neutrally evolving pseudogenes indicate that, if DNA deletion is absent, pseudogenes should be detectable for far longer than observed in the paleo-polyploid genomes, suggesting gene loss driven by DNA deletion. Analyses of three neo-autopolyploid genomes confirm this pattern: among substantial gene loss, DNA deletions occur on average 1.5 times more frequently than pseudogenization. Our findings imply that gene loss post-polyploidization primarily takes place via DNA deletion, enabled by a genomic environment with an elevated recombination rate created by WGMs. In contrast, small-scale duplications yield scattered duplicated genes, which appear less exposed to deletion and hence result in a high number of pseudogenes. This model is further reinforced by an enrichment of WGM-derived pseudogenes in high recombination regions. Moreover, some pseudogenes may govern a function, as indicated by non-neutral Ka/Ks ratios and overlap with lncRNAs.},
}

*Polyploidy
*Pseudogenes/genetics
Genome, Plant/genetics
*Magnoliopsida/genetics
*Gene Deletion
Evolution, Molecular
Gene Duplication
*Recombination, Genetic

@article {pmid40633764,
year = {2025},
author = {Kovarova, A and Amadasun, M and Hooban, B and McDonagh, F and Tumeo, A and Ryan, K and Clarke, C and Cormican, M and Miliotis, G},
title = {Characterisation of Citrobacter freundii and Enterobacter cloacae complex isolates co-carrying blaNDM-1 and mcr-9 from three hospitals.},
journal = {Journal of global antimicrobial resistance},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jgar.2025.07.003},
pmid = {40633764},
issn = {2213-7173},
abstract = {OBJECTIVES: Antimicrobial resistance (AMR) is a global health concern related to antimicrobial use and the subsequent emergence of resistant organisms, including carbapenemase-producing Enterobacterales (CPE). CPE isolate co-carrying blaNDM-1 and mcr-9.1 have been scarcely reported internationally. The identification of 20 such isolates, including 16 of one species, within a group of three hospitals in one region indicated potential dissemination within and between healthcare facilities.

METHODS: Twenty isolates were pseudo-anonymised and identified via MALDI-ToF MS. Antimicrobial susceptibility testing was performed by disc diffusion and Minimal Inhibition Concentration for colistin was carried out using the UMIC system. Short-read sequencing was conducted using the Illumina MiSeq platform and genomic analysis identified antimicrobial resistance genes, virulence factors and plasmid contigs. Taxonomic classification of draft genomes was bioinformatically assessed using Kraken2.

RESULTS: This collection comprised of Enterobacter hormaechei (n=16) Citrobacter freundii (n=3) and Enterobacter cloacae (n=1) sourced from patient rectal swabs collected during routine screening (n=13) or from healthcare-associated environmental sites (n=7). The E. hormaechei isolates included four different ST types with one unassigned ST. Contig-based plasmid analysis identified 17 plasmid replicon types among the isolates. IncHI2A, IncHI2, and pKPC-CAV1321_1 were detected in all isolates. Linked blaNDM-1 and mcr-9.1 gene spread in hospitals likely occurred via plasmid-mediated transfer rather than spread of E. hormaechei.

CONCLUSIONS: This study represents the first documented instance of blaNDM-1/mcr-9.1 co-occurrence in Europe to date. It highlights the increasing public health threat posed by antimicrobial resistance and underscores the importance of genomic surveillance and clinical screening.},
}

@article {pmid40633699,
year = {2025},
author = {Sun, HJ and Zhao, X and Ding, J and Wang, YQ and Wang, WS and Feng, ZH and Zhao, S and Wang, L and Ren, NQ and Yang, SS},
title = {Unveiling dynamics of microbial communities, species interactions, and ecological assembly during low-temperature-induced sludge bulking in full-scale wastewater treatment systems.},
journal = {Bioresource technology},
volume = {435},
number = {},
pages = {132950},
doi = {10.1016/j.biortech.2025.132950},
pmid = {40633699},
issn = {1873-2976},
abstract = {This study investigated the microbial community characteristics and ecological mechanisms of floating sludge and suspended sludge in a full-scale wastewater treatment plant under low-temperature conditions. Floating sludge exhibited a lower proportion of positive correlations compared to suspended sludge (56.98 % vs. 61.03 %), indicating stronger competition within the microbial community. Null model analysis revealed the roles of deterministic and stochastic processes in shaping the microbial communities, with stochastic processes being dominant. However, deterministic selection played a larger role in floating sludge, highlighting stronger influence of species interactions and temperature fluctuations. Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathway analysis revealed stronger energy metabolism in floating sludge, while suspended sludge microbes were more active in material transport. This study reveals distinct microbial and ecological differences between floating and suspended sludge at low temperatures, providing theoretical support for optimizing wastewater treatment and controlling sludge bulking in cold climates.},
}

@article {pmid40632216,
year = {2025},
author = {Romano, F and John, U and Laval-Peuto, M and Pitta, P},
title = {Small Things that Make a Big Difference: Single-Cell Transcriptomic of Nanociliates Reveals Genes Potentially Involved in Mixotrophy.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {72},
pmid = {40632216},
issn = {1432-184X},
support = {766327//MixITiN/ ; 766327//MixITiN/ ; 766327//MixITiN/ ; },
mesh = {*Transcriptome ; Phylogeny ; *Haptophyta/genetics/classification ; Mediterranean Sea ; Photosynthesis/genetics ; Single-Cell Analysis ; Food Chain ; },
abstract = {Nanociliates play an important role in the microbial food web of oligotrophic marine systems as grazers of picoplankton on one side, and as prey for microplankton, on the other. However, knowledge on their taxonomy, phylogeny, and trophic strategies is very limited, as well as their potential role as mixotrophs. In the present study, we investigated the transcriptomes of five marine planktonic nanociliates isolated from the Eastern Mediterranean Sea. Our aim was the following: (i) to characterize the phylogenetic placement of these cells using concatenated phylotranscriptomic and (ii) to identify genes potentially involved in mixotrophy by focusing on both photosynthesis and digestion-related genes (phagosome, lysosome). Phylogenetic reconstruction revealed that two cells clustered with Tintinnida, while the other three clustered with Oligotrichida. Reciprocal best hits (RHBs) BlastP analysis indicated the presence of genes related to photosynthesis across all the transcriptomes, while the detection of genes associated with phagosome, lysosome, and generic metabolic pathways provided a more informative insight into the mechanism of mixotrophy. These findings suggest that photosynthesis-related genes alone may not be sufficient indicators of mixotrophic potential in nanociliates and highlight the importance of considering additional cellular pathways involved in phagotrophy. Moreover, these transcriptomes will help to establish a basis for the evaluation of differential gene expression in Oligotrichida, Choreotrichida, and Tintinnida, and a step stone for mixotrophic investigation.},
}

*Transcriptome
Phylogeny
*Haptophyta/genetics/classification
Mediterranean Sea
Photosynthesis/genetics
Single-Cell Analysis
Food Chain

@article {pmid40630186,
year = {2025},
author = {Ceretto, A and Weinig, C},
title = {A comparison of 16S rRNA-gene and 16S rRNA-transcript derived microbial communities in bulk and rhizosphere soils.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1608399},
pmid = {40630186},
issn = {1664-302X},
abstract = {Root exudates in a plant's rhizosphere alters microbial community membership and activity, which can in turn alter a plant's health and fitness. In this study we characterized bacterial community composition, using 16S rRNA-gene (DNA) sequencing to define total community membership and 16S rRNA-transcripts (RNA) to define protein synthesis potential (PSP) as a proxy of microbial activity in both rhizosphere and bulk soils of a Wyoming native plant Boechera stricta. Using PSP rather than total microbial membership reveals fine-scale differences in genera between the rhizosphere and control soil communities. This study found DNA community analysis alone disproportionately increased the importance of Saccharibacteria and Gemmatimonadetes phyla in the overall soil community profile, and underestimated the importance of several known root associates (Comamonadaceae, Rhizobacter, and Variovorax), which had elevated PSP in the rhizosphere soil. Thus, the use of DNA-vs. RNA-based community characterization reveals that community composition (DNA) may not completely capture community activity (RNA). Analysis of the PSP community profile also indicated elevated levels of proteins associated with carbohydrate and amino acid metabolism in the rhizosphere-associated bacteria, which may shed light on potential mechanisms by which root exudates shape the rhizosphere soil community.},
}

@article {pmid40626910,
year = {2025},
author = {Kust, A and Zorz, J and Paniker, CC and Bouma-Gregson, K and Krishnappa, N and Liu, W and Banfield, JF and Diamond, S},
title = {Model cyanobacterial consortia reveal a consistent core microbiome independent of inoculation source or cyanobacterial host species.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf142},
pmid = {40626910},
issn = {1751-7370},
abstract = {Cyanobacteria are integral to biogeochemical cycles, influence climate processes, and hold promise for commercial applications. In natural habitats, they form complex consortia with other microorganisms, where interspecies interactions shape their ecological roles. Although in vitro studies of these consortia have significantly advanced our understanding, they often lack the biological replication needed for robust statistical analysis of shared microbiome features and functions. Moreover, the microbiomes of many model cyanobacterial strains, which are central to our understanding of cyanobacterial biology, remain poorly characterized. Here, we expanded on existing in vitro approaches by co-culturing five well-characterized model cyanobacterial strains with microorganisms filtered from three distinct freshwater sources, generating 108 stable consortia. Metagenomic analyses revealed that, despite host and inoculum diversity, these consortia converged on a similar set of non-cyanobacterial taxa, forming a 25-species core microbiome. The large number of stable consortia in this study enabled statistical validation of both previously observed and newly identified core microbiome functionalities in micronutrient biosynthesis, metabolite transport, and anoxygenic photosynthesis. Furthermore, core species showed significant enrichment of plasmids, and functions encoded on plasmids suggested plasmid-mediated roles in symbiotic interactions. Overall, our findings uncover the potential microbiomes recruited by key model cyanobacteria, demonstrate that laboratory-enriched consortia retain many taxonomic and functional traits observed more broadly in phototroph-heterotroph assemblages, and show that model cyanobacteria can serve as robust hosts for uncovering functional roles underlying cyanobacterial community dynamics.},
}

@article {pmid40626735,
year = {2025},
author = {Kellom, M and Berg, M and Chen, I-MA and Chu, K and Clum, A and Huntemann, M and Ivanova, NN and Kyrpides, NC and Mukherjee, S and Reddy, TBK and Roux, S and Seshadri, R and Szabo, G and Varghese, NJ and Woyke, T and Eloe-Fadrosh, EA},
title = {Tetranucleotide frequencies differentiate genomic boundaries and metabolic strategies across environmental microbiomes.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0174424},
doi = {10.1128/msystems.01744-24},
pmid = {40626735},
issn = {2379-5077},
abstract = {UNLABELLED: Microbiomes are constrained by physicochemical conditions, nutrient regimes, and community interactions across diverse environments, yet genomic signatures of this adaptation remain unclear. Metagenome sequencing is a powerful technique to analyze genomic content in the context of natural environments, establishing concepts of microbial ecological trends. Here, we developed a data discovery tool-a tetranucleotide-informed metagenome stability diagram-that is publicly available in the integrated microbial genomes and microbiomes (IMG/M) platform for metagenome ecosystem analyses. We analyzed the tetranucleotide frequencies from quality-filtered and unassembled sequence data of over 12,000 metagenomes to assess ecosystem-specific microbial community composition and function. We found that tetranucleotide frequencies can differentiate communities across various natural environments and that specific functional and metabolic trends can be observed in this structuring. Our tool places metagenomes sampled from diverse environments into clusters and along gradients of tetranucleotide frequency similarity, suggesting microbiome community compositions specific to gradient conditions. Within the resulting metagenome clusters, we identify protein-coding gene identifiers that are most differentiated between ecosystem classifications. We plan for annual updates to the metagenome stability diagram in IMG/M with new data, allowing for refinement of the ecosystem classifications delineated here. This framework has the potential to inform future studies on microbiome engineering, bioremediation, and the prediction of microbial community responses to environmental change.

IMPORTANCE: Microbes adapt to diverse environments influenced by factors like temperature, acidity, and nutrient availability. We developed a new tool to analyze and visualize the genetic makeup of over 12,000 microbial communities, revealing patterns linked to specific functions and metabolic processes. This tool groups similar microbial communities and identifies characteristic genes within environments. By continually updating this tool, we aim to advance our understanding of microbial ecology, enabling applications like microbial engineering, bioremediation, and predicting responses to environmental change.},
}

@article {pmid40625615,
year = {2025},
author = {Goodall, T and Busi, SB and Griffiths, RI and Jones, B and Pywell, RF and Richards, A and Nowakowski, M and Read, DS},
title = {Soil properties in agricultural systems affect microbial genomic traits.},
journal = {FEMS microbes},
volume = {6},
number = {},
pages = {xtaf008},
pmid = {40625615},
issn = {2633-6685},
abstract = {Understanding the relationships between bacteria, their ecological and genomic traits, and their environment is important to elucidate microbial community dynamics and their roles in ecosystem functioning. Here, we examined the relationships between soil properties and bacterial traits within highly managed agricultural soil systems subjected to arable crop rotations or management as permanent grass. We assessed the bacterial communities using metabarcoding and assigned each amplicon trait scores for rRNA copy number, genome size, and guanine-cytosine (GC) content, which are classically associated with potential growth rates and specialization. We also calculated the niche breadth trait of each amplicon as a measure of social ubiquity within the examined samples. Within this soil system, we demonstrated that pH was the primary driver of bacterial traits. The weighted mean trait scores of the samples revealed that bacterial communities associated with soils at lower pH (<7) tended to have larger genomes (potential plasticity), have more rRNA (higher growth rate potential), and are more ubiquitous (have less niche specialization) than the bacterial communities from higher pH soils. Our findings highlight not only the association between pH and bacterial community composition but also the importance of pH in driving community functionality by directly influencing genomic and niche traits.},
}

@article {pmid40624251,
year = {2025},
author = {Karlsson, CJ and Gerlee, P and Rowlett, J},
title = {An adaptive dynamics framework for microbial ecology and evolution.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {24307},
pmid = {40624251},
issn = {2045-2322},
mesh = {*Biological Evolution ; Game Theory ; Models, Biological ; Biodiversity ; *Adaptation, Physiological ; },
abstract = {Adaptive dynamics describes a deterministic approximation of the evolution of scalar- and function-valued traits. We construct an evolutionary process for a game-theoretic model which may describe the evolution of microbes. In our analysis, we demonstrate the existence of solutions to the adaptive dynamics and determined their regularity. Moreover, we identify all stationary solutions and prove that these are precisely the Nash equilibria of the game theoretic model. Numerical examples are provided to highlight the main characteristics of the dynamics. The dynamics are unstable; non-stationary solutions oscillate and perturbations of the stationary solutions do not shrink. Instead, a linear type of branching may occur. This may explain the ever-increasing complexity in microbial biological systems and provide a mechanistic explanation for not only the tremendous biodiversity observed in microbe species but also for the extensive phenotypic variability within species.},
}

*Biological Evolution
Game Theory
Models, Biological
Biodiversity
*Adaptation, Physiological

@article {pmid40624015,
year = {2025},
author = {Wang, C and Zhang, L and Kan, C and He, J and Liang, W and Xia, R and Zhu, L and Yang, J and Jiang, X and Ma, W and Liang, Z and Xiao, Z and Zhang, J and Zhong, J and Sun, X and Chang, D and Wang, Z and Zhang, G and Li, M},
title = {Benefits and challenges of host depletion methods in profiling the upper and lower respiratory microbiome.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {130},
pmid = {40624015},
issn = {2055-5008},
support = {Z211100002121135//Beijing Nova Program/ ; 32100098//National Natural Science Foundation of China/ ; 2021097//Youth Innovation Promotion Association of the Chinese Academy of Sciences/ ; KCXFZ20211020163545004//Shenzhen Scientific and Technological Foundation/ ; SZZYSM202311009//Sanming Project of Medicine in Shenzen Municipality/ ; 2022YFA1304300//National Key Research and Development Program of China/ ; },
mesh = {Humans ; Bronchoalveolar Lavage Fluid/microbiology ; *Microbiota/genetics ; *Metagenomics/methods ; *Bacteria/genetics/classification/isolation & purification ; *Respiratory Tract Infections/microbiology/diagnosis ; Oropharynx/microbiology ; *Respiratory System/microbiology ; },
abstract = {Metagenomic sequencing for respiratory pathogen detection faces two challenges: efficient host DNA depletion and the representativeness of upper respiratory samples for lower tract infections. In this study, we benchmarked seven host depletion methods, including a new method (F_ase), using bronchoalveolar lavage fluid (BALF), oropharyngeal swab (OP), and mock samples. All methods significantly increased microbial reads, species richness, genes richness, and genome coverage while reduced bacterial biomass, introduced contamination, and altered microbial abundance. Some commensals and pathogens, including Prevotella spp. and Mycoplasma pneumoniae, were significantly diminished. F_ase demonstrated the most balanced performance. High-resolution microbiomes profiling revealed distinct microbial niche preferences and microbiome disparities between the upper and lower respiratory tract. In pneumonia patients, 16.7% of high-abundance species (>1%) in BALF were underrepresented (<0.1%) in OP, highlighting OP's limitations as lower respiratory proxies. This study underscores both the potential and challenges of metagenomic sequencing in advancing microbial ecology and clinical research.},
}

Humans
Bronchoalveolar Lavage Fluid/microbiology
*Microbiota/genetics
*Metagenomics/methods
*Bacteria/genetics/classification/isolation & purification
*Respiratory Tract Infections/microbiology/diagnosis
Oropharynx/microbiology
*Respiratory System/microbiology

@article {pmid40622379,
year = {2025},
author = {Mars Brisbin, M and Acord, M and Davitt, R and Bent, S and Van Mooy, BAS and Flaum, E and Norlin, A and Turner, J and Krinos, A and Alexander, H and Saito, M},
title = {Exploring the Phaeosphere: Characterizing the microbiomes of Phaeocystis antarctica colonies from the coastal Southern Ocean and laboratory culture.},
journal = {Journal of phycology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jpy.70051},
pmid = {40622379},
issn = {1529-8817},
support = {874439//Simons Foundation/ ; OPP-2224611//National Science Foundation/ ; },
abstract = {Interactions between phytoplankton and bacteria play critical roles in shaping marine ecosystems. However, the intricate relationships within these communities-particularly in rapidly changing polar environments-remain poorly understood. We use targeted methods to directly characterize the microbiomes of individual colonies of Phaeocystis antarctica, a keystone phytoplankton species in the Southern Ocean, and showed that colony microbiomes were consistent across individual colonies collected 108 nautical miles apart. These results suggest that hosting specific colony microbiomes is a shared trait across colony-forming Phaeocystis species, with different species hosting colony microbiomes suited to their respective environments. The bacterial orders Alteromonadales, Oceanospirillales, and Sphingomonadales dominated the microbiomes of all field-collected P. antarctica colonies. The relative abundances of bacterial taxa comprising the majority of field-collected colony microbiomes-for example, Paraglaciecola sp. (Alteromonadales) and Nitrincolaceae (Oceanospirillales)-correlated with Phaeocystis abundance in surface waters, highlighting their potential roles in bloom dynamics and carbon cycling. After a year of laboratory culture, we observed a reduction in colony microbiome diversity, and Caulobacterales, Cellvibrionales, and Rhodobacterales dominated the cultured colony microbiomes. Notably, abundant genera in field-collected colony microbiomes that were lost in culture were psychrophiles. The shift in microbiome structure emphasizes the importance of field-based studies to capture the complexity of microbial interactions, especially for species from polar environments that are difficult to replicate in laboratory conditions. This research provides valuable insights into the ecological significance of prokaryotic interactions with a key phytoplankton species and underscores the necessity of considering these dynamics in the context of climate-driven shifts in marine ecosystems.},
}

@article {pmid40622159,
year = {2025},
author = {Hernandez, JB and Hayer, SS and Alvarez, S and Fischer, A and Hassenstab, HR and Cooper, K and Alsafwani, ZW and Benson, AK and Suhr Van Haute, MJ and Izard, J and Song, H-S and Clayton, JB},
title = {Microbiome and metabolome association network analysis identifies Clostridium_sensu_stricto_1 as a stronger keystone genus candidate than Bifidobacterium in the gut of common marmosets.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0021425},
doi = {10.1128/msystems.00214-25},
pmid = {40622159},
issn = {2379-5077},
abstract = {The common marmoset (Callithrix jacchus), a nonhuman primate species, is a model organism of great interest due to its translational value in a variety of research settings, including the field of microbiomics. While the composition of the marmoset's gut microbiome has been somewhat described in captivity, little is known about how gut microbiota interact with each other over time and how they relate to metabolite production. To help answer this, we characterized interactions in the gut microbiome of the common marmoset by calculating the Spearman correlation coefficient between 16S rDNA-derived relative genera abundance data and targeted metabolomics data collected longitudinally from 10 captive marmosets. Association network graphs were used to visualize significant correlations and identify genera and metabolites that have high degree centrality, marking them as more influential within the microbiome. The genus Clostridium_sensu_stricto_1 engaged in the most metabolomic associations, indicating that it potentially plays a gatekeeping role over metabolites involved in microbial growth and signaling. Its associations with downregulated taurine and bile acids further suggest Clostridium_sensu_stricto_1 modifies bile acids to exert its influence. Flavonifractor and several Bacteroidales members had the most bacterial associations and were negatively associated with Bifidobacterium, indicating a potential competitive relationship. To further characterize microbiome interactions, we performed hierarchical clustering on significant within-dataset associations and developed a new "Keystone Candidate Score" metric that identified Clostridium_sensu_stricto_1 and Alloprevotella as the most influential bacteria (so-called candidate keystone genera) in the marmoset gut microbiome.IMPORTANCEPrevious studies have identified significant individuality within the gut microbiome of common marmosets. The reasons for this inter-subject variability and how it relates to health in captivity are poorly understood, owing to a lack of knowledge regarding dynamic interactions between specific microbiota. To that end, this study characterized significant temporal associations between the gut microbiome and metabolome of healthy captive marmosets. Our findings suggest that certain microbial taxa exert a stronger influence within the gut than others. Specifically, Bifidobacterium was the most abundant genus and primary driving force behind subject-specific microbiome differences, while Clostridium_sensu_stricto_1 and bacteria from the order Bacteroidales were the main sources, respectively, for significant bacteria-metabolite and bacteria-bacteria associations. Together, this suggests that Bifidobacterium may compete with the other taxa for resources and a metabolic niche in the marmoset microbiome.},
}

@article {pmid40621946,
year = {2025},
author = {Engelberts, JP and Ye, J and Parks, DH and McMaster, ES and McInnes, AS and Woodcroft, BJ and Volmer, JG and McIlroy, SJ and Tyson, GW},
title = {GenomeFISH: genome-based fluorescence in situ hybridisation for strain-level visualisation of microbial communities.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf138},
pmid = {40621946},
issn = {1751-7370},
abstract = {Fluorescence in situ hybridisation (FISH) is a powerful tool for visualising the spatial organisation of microbial communities. However, traditional FISH has several limitations, including limited phylogenetic resolution, difficulty visualising certain lineages, and the design and optimis ation of new probes is time consuming and does not scale to the known diversity of microbial life. Here, we present GenomeFISH, a high-throughput, genome-based FISH approach that can differentiate strains within complex communities. Fluorescent probes are generated from the genomes of single cells, which are obtained from environmental or clinical samples through fluorescence activated single-cell sorting (FACS). GenomeFISH can distinguish between strains with up to 99% average nucleotide identity and was successfully applied to visualise strains in mock communities and human faecal samples. Given the superior sensitivity and specificity of GenomeFISH, we envisage it will become widely used for the visualisation of complex microbial systems.},
}

@article {pmid40621919,
year = {2025},
author = {Reintjes, G and Giljan, G and Fuchs, BM and Arnosti, C and Amann, R},
title = {Using phenotyping to visualize and identify selfish bacteria: a methods guide.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0160224},
doi = {10.1128/spectrum.01602-24},
pmid = {40621919},
issn = {2165-0497},
abstract = {Polysaccharides are dominant components of plant and algal biomass, whose degradation is typically mediated by heterotrophic bacteria. These bacteria use extracellular enzymes to hydrolyze polysaccharides to oligosaccharides that are then also available to other bacteria. Recently, a new mechanism of polysaccharide processing-"selfish" uptake-has been recognized, initially among gut-derived bacteria. In "selfish" uptake, polysaccharides are bound at the outer membrane, partially hydrolyzed, and transported into the periplasmic space without loss of hydrolysis products, thus limiting the availability of smaller sugars to the surrounding environment. Selfish uptake is widespread in environments ranging from the ocean's cool, oxygen-rich, organic carbon-poor waters to the warm, carbon-rich, anoxic environment of the human gut. In this methods paper, we present a detailed guide to identifying selfish bacteria, including techniques for rapidly visualizing selfish uptake in complex bacterial communities, detecting selfish organisms, and distinguishing their activity from that of other community members.IMPORTANCEUnderstanding the role of heterotrophic bacteria in the degradation of organic matter is critical for comprehending carbon cycling and microbial ecology across different environments. This study highlights the significant prevalence of "selfish uptake" among bacteria-often overlooked by standard microbial activity assessments-and presents the method used to quantify and identify these "selfish" bacteria. Found in diverse habitats such as anoxic gut environments, oxygenated waters, sediments, and soils, their widespread presence underscores the necessity of revisiting current methodologies to include these crucial organisms. By identifying and studying selfish bacteria, we can gain detailed insights into how microbial communities function, how carbon flows through ecosystems, and how these processes impact global biogeochemical cycles.},
}

@article {pmid40621498,
year = {2025},
author = {Chong, J and Zhou, Y and Li, Z and Li, X and Zhang, J and Cao, H and Ma, J and Ge, L and Zhong, H and Sun, J},
title = {Hyodeoxycholic acid modulates gut microbiota and bile acid metabolism to enhance intestinal barrier function in piglets.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1610956},
pmid = {40621498},
issn = {2297-1769},
abstract = {Oral bile acids, particularly hyodeoxycholic acid (HDCA), serve as critical drivers for gut microbial community maturation in mice. In the first study, Cy5-labeled HDCA combined with fluorescence imaging revealed rapid gastrointestinal transit of HDCA in piglets, contrasting with its delayed absorption observed in mice. In the second study, the effects of the oral HDCA supplementation on microbiota-host metabolic interactions were investigated using four piglet model groups: OPM-HDCA (naturally born, raised germ-free (GF), and orally administered HDCA), OPM-CON (naturally born, raised GF, and orally administered PBS), SPF-HDCA (naturally born, raised GF, and received fecal microbiota transplantation (FMT) and HDCA), and SPF-CON (naturally born, raised GF with FMT but no HDCA). The results demonstrated that HDCA administration at 0.2 mg/mL suppressed body weight gain in piglets, which was alleviated by FMT. HDCA significantly altered gut microbiota composition in SPF piglets, markedly increasing the Lactobacillus abundance (37.97% vs. 5.28% in SPF-CON) while decreasing the proportion of Streptococcus (28.34% vs. 38.65%) and pathogenic family Erysipelotrichaceae (0.35% vs. 17.15%). Concurrently, HDCA enhanced intestinal barrier integrity by upregulating tight junction proteins (ZO-1, Claudin, Occludin) and suppressing pro-inflammatory cytokines (TNF-α, IL-1β). Additionally, HDCA significantly upregulated ileal gene expression of CYP7A1 (cytochrome P450 family 7 subfamily A member 1) and TGR5 (G protein-coupled bile acid receptor 1) in both SPF-HDCA and OPM-HDCA groups compared to their respective controls (p < 0.05). These findings demonstrate that HDCA exerts microbiota-dependent effects on growth performance, intestinal barrier function, and bile acid metabolism in piglets. Although 0.2 mg/mL HDCA treatment suppressed body weight gain, it potentially enhanced intestinal barrier integrity by activating the TGR5 signaling pathway and increasing the abundance of beneficial bacteria such as Lactobacillus. These results also highlight the critical role of early-life gut microbiota in nutritional interventions, providing a basis for developing precision nutritional strategies targeting intestinal microbial ecology in piglets.},
}

@article {pmid40619451,
year = {2025},
author = {Yan, F and Niu, Z},
title = {Impacts of pollution on coral bacterial and metabolites diversity across Dapeng Cove of South China sea.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {24107},
pmid = {40619451},
issn = {2045-2322},
mesh = {*Anthozoa/microbiology/metabolism ; China ; Animals ; *Bacteria/metabolism/classification/genetics ; Seawater/microbiology/chemistry ; Biodiversity ; Environmental Monitoring ; Oceans and Seas ; },
abstract = {Coastal ecosystems are increasingly threatened by anthropogenic activities, including sewage discharge and tourism-related pollution, which alter microbial diversity and biochemical cycles. This study applied molecular techniques to examine the coral microbial diversity, and metabolite composition of seawater across five sites (A-E) in Dapeng Cove, South China Sea, to assess pollution impacts. Sites A and B, within the yacht tourism area, exhibited high microbial diversity, dominated by Synechococcus and Rhodobacteraceae, with minimal pollution effects. Site C, inside a domestic drainage channel, showed moderate pollution, with elevated nitrite (NO2) and nitrate (NO3) levels, microbial taxa linked to organic matter degradation, and increased hydroxy acids and indoles. Sites D and E, located in main sewage channels, experienced severe pollution, characterized by high salinity, low dissolved oxygen, and dominance of pollution-tolerant bacteria such as Exiguobacterium and Tepidibacter. Metabolite analysis revealed elevated fatty acyls, organonitrogen compounds, and amino acids at these sites, highlighting strong anthropogenic influence. Beta diversity analysis (NMDS and ANOSIM) confirmed distinct microbial community structures, while KEGG pathway analysis indicated shifts in metabolic functions, with enrichment in xenobiotic biodegradation and anaerobic respiration in sewage-impacted areas. These findings underscore the detrimental effects of wastewater discharge on microbial ecology and biochemical functions. Urgent interventions, including improved wastewater management and regular environmental monitoring, are recommended to mitigate pollution effects. Future research integrating multi-omics approaches is necessary to evaluate the long-term ecological consequences of pollution and climate variability on coastal microbial communities.},
}

*Anthozoa/microbiology/metabolism
China
Animals
*Bacteria/metabolism/classification/genetics
Seawater/microbiology/chemistry
Biodiversity
Environmental Monitoring
Oceans and Seas

@article {pmid40614873,
year = {2025},
author = {Lu, X and Gao, Y and Liu, X and Sun, Y and Zhen, G},
title = {Unlocking microbial community succession and key influencing factors during bioelectrocatalytically-driven simultaneous removal of ammonia nitrogen and sulfate from wastewater.},
journal = {Bioresource technology},
volume = {435},
number = {},
pages = {132934},
doi = {10.1016/j.biortech.2025.132934},
pmid = {40614873},
issn = {1873-2976},
abstract = {Ammonia nitrogen (NH4[+]-N) and sulfate (SO4[2][-]) removal by Anaerobic ammonium oxidation (Anammox) and sulfate-reducing bacteria (SRB) was studied in dual-chamber microbial electrolysis cells (MECs). Appropriate anode potential stimulation promoted biofilm formation and enhanced extracellular polymeric substances fluorescence, facilitating electron transfer. The highest NH4[+]-N removal (81.1 %) was achieved at the anode potential of 0.6 V vs. Ag/AgCl after 50 days, coinciding with the increase in electroactive Candidatus_Brocadia from 1.1 % to 27.4 %. Simultaneously, SO4[2][-] removal reached 77.0 %, supported by cathodic biofilms dominated by SRB (Desulfofustis, Desulfomicrobium, and Desulfatirhabdium). Automated machine learning and principal co-ordinates analysis identified the anode potential as the key factor shaping microbial ecology. The appropriate anode potential (0.4-0.6 V vs. Ag/AgCl) promoted cathodic sulfidogenesis, indirectly enhancing electron flow and supporting Anammox process at the anode. These findings demonstrate that MECs hold great promise for simultaneously enhancing anaerobic ammonia oxidation bacteria and SRB activities, enabling efficient NH4[+]-N and SO4[2][-] removal.},
}

@article {pmid40614496,
year = {2025},
author = {Brotto, AC and Kurt, H and Chandran, K},
title = {Impacts of intermittent and continuous aeration modes on performance, substrate dynamics, and microbial ecology of mainstream nitrification processes.},
journal = {Water research},
volume = {285},
number = {},
pages = {124123},
doi = {10.1016/j.watres.2025.124123},
pmid = {40614496},
issn = {1879-2448},
abstract = {Intermittent and continuous aeration strategies in combination with solids retention time (SRT) were investigated in terms of their impact on the performance and ecology of mainstream nitrification. Two lab-scale reactors (R1 and R2) were seeded with the same inoculum and subjected to intermittent aeration and continuous low aeration, respectively at statistically similar air-supply rates. For both reactors, SRT was progressively decreased from 8 d during Phase I to 4 and 2.5 d during Phases II and III, respectively. Compared to R2 (93 ± 4.8 %), R1 achieved more stable and higher ammonia oxidation (99 ± 0.13 %) averaged across SRTs. In R1, Nitrosospira were the dominant AOB, while in R2, AOB were a combination of Nitrosospira and Nitrosomonas. Among NOB, Nitrospira were more abundant than Nitrobacter for both R1 and R2 across SRTs. Intermittent aeration in R1 supported higher relative abundance of Comammox Nitrospira than R2. Notably, the enrichment patterns for nitrifying bacteria in the two reactors reflected distinct drivers (beyond microbial kinetics), including inoculum composition, extant oxygen or nitrogen concentrations or both. Overall, intermittent aeration strategies are integral to the design of biological nitrogen removal processes, although other considerations such as operational feasibility and process emissions might ultimately influence operating strategies.},
}

@article {pmid40614494,
year = {2025},
author = {Mol, Z and Waegenaar, F and Pluym, T and Vermeir, P and Van Langenhove, H and De Gusseme, B and Boon, N and Walgraeve, C and Demeestere, K},
title = {Effect of biofilm, temperature and type of source water on the formation of haloanisoles in a pilot drinking water distribution system.},
journal = {Water research},
volume = {285},
number = {},
pages = {124078},
doi = {10.1016/j.watres.2025.124078},
pmid = {40614494},
issn = {1879-2448},
abstract = {Taste and odor deviations in tap water affect many consumers and cause a preference for bottled water. However, since tap water is more sustainable than bottled water, these issues should be solved and prevented rapidly. Haloanisoles (HAs) have a very low odor threshold concentration (sub ng.L[-1]) and are of considerable concern since they are mainly formed in drinking water distribution systems (DWDS). Understanding their formation and influencing factors is a crucial aspect of addressing these odor problems. Therefore, this study uses a DWDS pilot to closely mimic the complex situation in real DWDS and investigates the (microbial) formation of six HAs regarding biofilm cell density and composition, temperature, and type of source water. Ten to thirty times higher formation was observed when a stable biofilm (5 months, 10 times more biomass) was present, compared to a young biofilm (2 weeks). With a spiked halophenol (HP) concentration of 0.1 mg.L[-1], the HA concentrations produced by a young biofilm were already within the OTC range. The mature biofilm contained a higher variety of HA-producing microorganisms and more O-methyltransferase genes to convert the precursors (HPs) into HAs. Higher temperatures (24 °C instead of 16 °C) increased the formation of each HA by a factor of 2 to 4, although still low HP-HA conversion ratios were observed (0.2 %). Regardless of the temperature and the type of source water, a clear pattern is observed in the type of HAs formed, with 2,3,4-trichloroanisole being the most abundant. This study finally investigated the effectiveness of flushing to mitigate these odorous compounds in DWDS and concludes that their partitioning between the biofilm and water phase affects the performance of flushing procedures.},
}

@article {pmid40614303,
year = {2025},
author = {Ferrocino, I and Buzzanca, D and Pagiati, L and Kazou, M and Georgalaki, M and Hatzopoulos, I and Tsakalidou, E},
title = {The microbial terroir of the Greek olive varieties.},
journal = {International journal of food microbiology},
volume = {441},
number = {},
pages = {111332},
doi = {10.1016/j.ijfoodmicro.2025.111332},
pmid = {40614303},
issn = {1879-3460},
abstract = {The microbial terroir of Greek olive varieties remains underexplored. In this study, 62 samples of olive fruits, collected across the harvest period 2019-2020, were analyzed by high-throughput sequencing. The samples represented 38 olive varieties collected from geographically well distributed regions of Greece. Analysis of the bacterial composition revealed that the geographical area was a significant factor in discriminating samples. The core microbiota included Erwinia, Pseudomonas, and members of the Enterobacteriaceae family. Furthermore, a notable variation in bacterial taxa abundances associated with the geographic location was observed. The sampling area was a key discriminant factor for the mycobiota, and the core mycobiota comprised Alternaria, Taphrina, Candida, Wickerhamomyces anomalus and Penicillium. Finally, Redundancy Analysis (RDA) revealed a notable association between environmental characteristics and microbial composition. Specifically, tree age was associated with certain bacterial and fungal taxa (Pearson's correlation p-value adj.[FDR] < 0.05).},
}

@article {pmid40613821,
year = {2025},
author = {Saini, N and Ghosh, A and Bhadury, P},
title = {Linking Plastic Degradation Potential and Resistance Gene Abundance in Bacterioplankton Community of the Sundarbans Estuarine Ecosystem.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnaf067},
pmid = {40613821},
issn = {1574-6968},
abstract = {Harnessing microbial capabilities offers a promising and sustainable approach to address the global challenge of plastic waste. However, the potential of mangrove microbiomes to degrade diverse plastic polymers remains largely unexplored. In this metagenomic-based study, surface water microbiomes were analysed from the Indian Sundarbans, part of the world's largest contiguous mangrove ecosystem, revealing 748.21 hits per billion nucleotides associated with plastic-degrading enzymes (PDEs) targeting 17 different polymer types. Of these, 72.9% corresponded to synthetic polymers and 27.1% to natural polymers. The highest number of hits (223) was associated with polyethylene glycol-degrading enzymes, representing 26.7% of the total PDEs hits. Taxonomic analysis revealed Deltaproteobacteria and Gammaproteobacteria as key degraders of diverse synthetic plastic polymers, with Deltaproteobacteria emerging as a previously unreported group. This suggests that surface sediments may serve as reservoirs for novel plastic-degrading microbes. Co-occurrence network analysis indicated possible emerging co-selection or complex associations between PDEs, antibiotic resistance genes (ARGs), and metal resistance genes (MRGs). Notably, zinc resistance genes and aminoglycoside-related ARGs showed more associations with PDEs. While the presence of PDEs offers a promising avenue for bioremediation, their application may be complicated by the concurrent rise of ARGs and MRGs within PDE-harbouring microbes. Thus, it highlights the need for careful assessment when employing microbes for plastic bioremediation.},
}

@article {pmid40610473,
year = {2025},
author = {Ivanova, EA and Suleymanov, AR and Nikitin, DA and Semenov, MV and Abakumov, EV},
title = {Machine learning-based mapping of Acidobacteriota and Planctomycetota using 16 S rRNA gene metabarcoding data across soils in Russia.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {23763},
pmid = {40610473},
issn = {2045-2322},
support = {24-44-00006//Russian Science Support Foundation/ ; 24-44-00006//Russian Science Support Foundation/ ; },
mesh = {*Machine Learning ; *Soil Microbiology ; *RNA, Ribosomal, 16S/genetics ; Russia ; *DNA Barcoding, Taxonomic/methods ; Soil/chemistry ; Microbiota/genetics ; *Acidobacteria/genetics/classification ; Ecosystem ; },
abstract = {The soil microbiome plays a crucial role in maintaining healthy ecosystems and supporting sustainable agriculture. Studying its biogeographical structure and distribution is essential for understanding the rates and mechanisms of microbially mediated soil ecosystem services. This study aimed to investigate the spatial distribution patterns of Acidobacteriota and Planctomycetota across soils in Russia, summarizing data from 16S rRNA gene metabarcoding of topsoils. A machine learning approach (Random Forest) was employed to generate digital distribution maps using climatic, topographic, vegetation, geological, and soil variables. Model interpration was performed using variable importance assessment and Shapley values. According to the error metrics, the Acidobacteriota model achieved a root mean squared error (RMSE) of 6.67% and an R[2] of 0.41, while the Planctomycetota model achieved an RMSE of 2.04% and an R[2] of 0.46. Both phyla exhibited similar spatial distribution patterns, with relative abundance decreasing from North to South. For Acidobacteriota, vegetation cover, surface temperature, and soil pH were significant predictors, whereas the relative abundance of Planctomycetota was mainly influenced by climatic variables. Specifically, Acidobacteriota were more abundant in areas with dense vegetation, stable surface temperatures, and acidic soils. In contrast, Planctomycetota showed reduced abundance in regions with higher levels of precipitable water vapor. These results highlight the potential of machine learning techniques to visualize predictive biogeographic patterns in soil microbial taxa abundance at the phylum level. Despite limitations related to the heterogeneous nature of source data, focusing on higher taxonomic ranks less sensitive to methodological variation enabled to identify preliminary large-scale distribution trends of microbial phyla in soils.},
}

*Machine Learning
*Soil Microbiology
*RNA, Ribosomal, 16S/genetics
Russia
*DNA Barcoding, Taxonomic/methods
Soil/chemistry
Microbiota/genetics
*Acidobacteria/genetics/classification
Ecosystem

@article {pmid40607773,
year = {2025},
author = {Tao, Y and Liu, D and Shi, Q and Sun, Q and Liu, C and Zeng, X},
title = {Lead exposure in relation to gut homeostasis, microbiota, and metabolites.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0037225},
doi = {10.1128/aem.00372-25},
pmid = {40607773},
issn = {1098-5336},
abstract = {Lead (Pb) is a hazardous heavy metal with no known safe threshold for exposure or consumption, posing significant risks to human health. Pb exposure can cause multiple system damage, depending on exposure levels, duration, and its high bioavailability and bioaccumulative potential. Gastrointestinal tract serves as a primary site for Pb absorption, making it particularly vulnerable to Pb-induced damage, including disruption of gut microbiota composition and metabolic function. This study briefly summarizes the detrimental effects of Pb gut homeostasis, microbial ecology, and host metabolism, which, in turn, further contribute to systemic toxicity. Notably, Pb exposure compromises intestinal barrier integrity, increasing gut permeability and facilitating the translocation of harmful biomolecules into systemic circulation, thereby exacerbating organ dysfunction. Importantly, we underscore that dietary and nutritional interventions such as fiber, probiotic, and vitamin C supplementation is a practicable and effective strategy for mitigating or preventing Pb toxicity.},
}

@article {pmid40606160,
year = {2025},
author = {Al-Khlifeh, E and Khadem, S and Hausmann, B and Berry, D},
title = {Corrigendum: Microclimate shapes the phylosymbiosis of rodent gut microbiota in Jordan's Great Rift Valley.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1639190},
doi = {10.3389/fmicb.2025.1639190},
pmid = {40606160},
issn = {1664-302X},
abstract = {[This corrects the article DOI: 10.3389/fmicb.2023.1258775.].},
}

@article {pmid40605266,
year = {2025},
author = {Herman, C and Barker, BM and Bartelli, TF and Chandra, V and Krajmalnik-Brown, R and Jewell, M and Li, L and Liao, C and McAllister, F and Nirmalkar, K and Xavier, JB and Caporaso, JG},
title = {A review of engraftment assessments following fecal microbiota transplant.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2525478},
doi = {10.1080/19490976.2025.2525478},
pmid = {40605266},
issn = {1949-0984},
mesh = {*Fecal Microbiota Transplantation ; Humans ; *Gastrointestinal Microbiome ; *Clostridium Infections/therapy/microbiology ; Clostridioides difficile/physiology ; Animals ; Feces/microbiology ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {Fecal Microbiota Transplant (FMT) is a treatment for recurrent Clostridium difficile infections and is being explored for other clinical applications, from alleviating digestive and neurological disorders, to restoring microbiomes impacted by cancer treatment. Quantifying the extent of engraftment following an FMT is important in understanding a recipient's response to treatment. Engraftment and clinical response need to be investigated independently to evaluate an FMT's role (or lack thereof) in achieving a clinical response. Standardized bioinformatics methodologies for quantifying engraftment extent would not only improve assessment and understanding of FMT outcomes, but also facilitate comparison of FMT results and protocols across studies. Here we review FMT studies, integrating three concepts from microbial ecology as framework to discuss how these studies approached assessing engraftment extent: 1) Community Coalescence investigates microbiome shifts following FMT engraftment, 2) Indicator Features tracks specific microbiome features as a signal of engraftment, and 3) Resilience examines how resistant post-FMT recipients' microbiomes are to reverting back to baseline. These concepts explore subtly different questions about the microbiome following FMT. Taken together, they provide holistic insight into how an FMT alters a recipient's microbiome composition and provide a clear framework for quantifying and communicating about microbiome engraftment.},
}

*Fecal Microbiota Transplantation
Humans
*Gastrointestinal Microbiome
*Clostridium Infections/therapy/microbiology
Clostridioides difficile/physiology
Animals
Feces/microbiology
Bacteria/classification/genetics/isolation & purification

@article {pmid40603778,
year = {2025},
author = {Brinck, JE and Sinha, AK and Laursen, MF and Dragsted, LO and Raes, J and Uribe, RV and Walter, J and Roager, HM and Licht, TR},
title = {Intestinal pH: a major driver of human gut microbiota composition and metabolism.},
journal = {Nature reviews. Gastroenterology & hepatology},
volume = {},
number = {},
pages = {},
pmid = {40603778},
issn = {1759-5053},
abstract = {In the human gastrointestinal tract, pH is a key factor in shaping gut microbial composition and activity, while also being influenced by microbial metabolism. pH varies substantially along the gastrointestinal tract within an individual and between different individuals due to a combination of host, diet, microbial and external factors. The importance of pH on microbiota composition and metabolic response has been widely explored over the past century. Here, we review the literature to explore the major physiological and dietary factors that influence pH along the gastrointestinal tract. From a microbial ecology perspective, we discuss how gastrointestinal pH affects microbiota composition and metabolism. We explore mechanisms by which pH can influence bacterial acid response systems, gene expression and the production of microbial metabolites important for health. Finally, we review the literature regarding the potential role of gastrointestinal pH in human diseases. We propose that we can advance our understanding of the gut microbiota in health and disease by considering gastrointestinal pH. We argue that pH-mediated gut microbial metabolic variation is highly important for predicting and manipulating metabolic output relevant to human health.},
}

@article {pmid40602916,
year = {2025},
author = {Puche, E and Roger, B and Vargas-Sánchez, M and Sánchez-Carrillo, S and Rodrigo, MA},
title = {Freshwater macrophyte type (macroalgae versus phanerogams) mainly determines detritus-derived greenhouse gases production: A microcosm experiment.},
journal = {Journal of environmental sciences (China)},
volume = {157},
number = {},
pages = {674-689},
doi = {10.1016/j.jes.2025.01.015},
pmid = {40602916},
issn = {1001-0742},
mesh = {*Greenhouse Gases/analysis/metabolism ; *Seaweed ; Ecosystem ; Methane/analysis ; Fresh Water ; Carbon Dioxide/analysis ; Eutrophication ; *Environmental Monitoring ; *Air Pollutants/analysis ; },
abstract = {Freshwater ecosystems are crucial in the global emissions of greenhouse gases (GHGs) such as CH4. Macrophytes are the main organic matter (i.e., detritus) supplier to the sediment of these systems, thus controlling CH4 production. However, species-specific differences (structure and composition) may determine contrasting patterns of detritus transformation into CH4. Furthermore, eutrophication can affect the degradation and, consequently, CH4 production. We performed a 64-day microcosm experiment with anoxic incubations of detritus from seven phylogenetically different macrophytes (two charophytes, filamentous algae -Spirogyra, Cladophora-, three submerged plants and an amphibious one), under two trophic conditions (oligo- versus eutrophic) and with/without sediment. We assessed the CH4 and CO2 production and the changes in the detritus quality at the end of the experiment. The ranking in the mean cumulative CH4 production was: Chara hispida > Nitella hyalina > Najas marina ≈ Teucrium scordium > Stuckenia pectinata ≈ Myriophyllum spicatum > filamentous algae, and it was related to the detritus quality. GHGs maximum production rates were 1.6 (N. marina)-1.2 (C. hispida) mmol CH4/(g OC·day) and 1.7 (N. marina)-1.5 (C. hispida) mmol CO2/(g OC·day). The CO2:CH4 ratio was biased towards CO2 during the first 10 days (average ratio of 200) and fell afterwards to about 1 for all macrophyte species and treatments. The sediment favored detritus decomposition (probably due to the "positive priming effect"), increasing GHGs production. The influence of nutrient enrichment was not evident. Delving into the macrophyte detritus quality-GHGs production relationship is needed to forecast the GHGs emissions in macrophyte-dominated systems.},
}

*Greenhouse Gases/analysis/metabolism
*Seaweed
Ecosystem
Methane/analysis
Fresh Water
Carbon Dioxide/analysis
Eutrophication
*Environmental Monitoring
*Air Pollutants/analysis

@article {pmid40602642,
year = {2025},
author = {Pieńkowska, A and Fleischmann, J and Drabesch, S and Merbach, I and Wang, G and Rocha, U and Reitz, T and Marie Muehe, E},
title = {Long-term organic fertilization shields soil prokaryotes from metal stress while mineral fertilization exacerbates it.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {382},
number = {},
pages = {126747},
doi = {10.1016/j.envpol.2025.126747},
pmid = {40602642},
issn = {1873-6424},
abstract = {Metal contamination in agricultural soils threatens prokaryote dynamics essential for soil health and crop productivity. Yet, whether fertilization in the long-run affects their resilience to metals remains unclear. This study examined the biogeochemical impacts of realistically low-dose applications of cadmium, zinc, and lead in soils subjected to 119 years of non-fertilization, mineral-fertilization (NPK), organic-fertilization (manure), or combined mineral-organic fertilization. Amended metals remained in the mobile fraction with the order: mineral < unfertilized < mineral + organic < organic, mirroring the effects on soil prokaryotes. In both unfertilized and mineral-fertilized soils, 16S rRNA gene copy numbers declined by 30 % upon metal addition, but recovery timing differed: in unfertilized soil, recovery began after three days, whereas in mineral-fertilized soil, numbers declined until day seven before recovering. This coincided with an increase in metal-resistant taxa, particularly in mineral-fertilized soil, with 10 significantly affected OTUs, and to a lesser extent in unfertilized soil, with 5 affected OTUs. Carbon-, nitrogen-, and phosphorus-mining enzyme activities increased 50-100 % in mineral-fertilized soils, suggesting enhanced nutrient acquisition to mitigate metal toxicity. In contrast, organic-fertilized soil hosted stable enzymatic activities and microbial copy numbers with minimal community shifts (1 affected OTU), indicating greater resistance to metal amendment. Combined mineral-organic fertilization stabilized copy numbers and enzymatic activity upon metal amendment, but 8 OTUs were affected, including specialized nutrient cyclers, suggesting increased availability of previously adsorbed NPK cations. Our findings indicate that organic fertilization shields prokaryotes from metal stress, while mineral fertilization exacerbates it, highlighting the benefits of organic practices for maintaining soil health and productivity.},
}

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

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