@article {pmid41601066,
year = {2026},
author = {Chen, Y and Cai, S and Zhang, P and Sun, C and Huang, D and Zhang, M and Tian, S},
title = {Effects of soil covering on bacterial communities and C/N functional genes during phytoremediation of copper tailings.},
journal = {Ecotoxicology and environmental safety},
volume = {309},
number = {},
pages = {119639},
doi = {10.1016/j.ecoenv.2025.119639},
pmid = {41601066},
issn = {1090-2414},
mesh = {*Copper/metabolism ; Biodegradation, Environmental ; *Soil Pollutants/metabolism/analysis ; *Soil Microbiology ; *Soil/chemistry ; Mining ; Nitrogen/metabolism ; Carbon/metabolism ; *Bacteria/genetics/metabolism ; China ; Metals, Heavy/analysis ; Genes, Bacterial ; },
abstract = {Copper tailings, a mining waste, pose environmental threats, and phytoremediation commonly employs soil covering to improve substrate properties and promote vegetation recovery. This study was conducted at the Yangshanchong Tailings Reservoir in Tongling City, Anhui Province, to comprehensively evaluate changes in soil physicochemical properties, bacterial community structure, and carbon/nitrogen functional genes during copper tailings remediation. We compared areas with and without soil covering, which were vegetated by two dominant species, Imperata cylindrica and Miscanthus floridulus, across profile depths of 0-20 cm, 20-40 cm, and 40-60 cm. Results indicated that: (i) soil covering significantly modified substrate pH, elevated levels of organic matter, organic carbon, and ammonium nitrogen, decreased surface total nitrogen, total phosphorus, and selected heavy metals, and altered the depth-dependent distribution of copper, manganese, and cadmium, (ii) soil covering reduced bacterial richness and diversity in I. cylindrica areas, increased the relative abundance of phyla such as Deinococcota, and significantly enriched genera including Brevundimonas, Acidisoma, and Acinetobacter, while enhancing the influence of heavy metals on dominant genera, (iii) soil covering reduced the abundance of genes related to nitrogen cycling (nifH, amoA, nosZ) and methane metabolism (pmoA1), and altered their correlations with specific bacterial genera. Overall, soil covering shapes bacterial community structure and the dynamics of carbon/nitrogen functional genes by altering the physicochemical properties and heavy metal distribution in tailings substrates, thereby playing a key regulatory role in microbial ecology during copper tailings revegetation. This study provides valuable insights for the restoration management of mining areas.},
}

*Copper/metabolism
Biodegradation, Environmental
*Soil Pollutants/metabolism/analysis
*Soil Microbiology
*Soil/chemistry
Mining
Nitrogen/metabolism
Carbon/metabolism
*Bacteria/genetics/metabolism
China
Metals, Heavy/analysis
Genes, Bacterial

@article {pmid41601011,
year = {2026},
author = {Staley, BT and DeWitt, ME and Wenner, JJ and Sanders, JW and Wierzba, TF and Poehling, K},
title = {Trusted Sources of COVID-19 Vaccine Information by County Characteristics in North Carolina.},
journal = {Vaccines},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/vaccines14010096},
pmid = {41601011},
issn = {2076-393X},
support = {49927//NC Department of Health and Human Services/ ; },
abstract = {BACKGROUND/OBJECTIVES: The COVID-19 pandemic disproportionately impacted rural areas across the United States, including rural North Carolina (NC). Consistent with national patterns, COVID-19 vaccination coverage as of December 2022 was higher for non-rural (72%) than rural (58%) NC counties. The role of trusted sources of vaccine information used by rural and non-rural residents is unknown.

METHODS: Using data from two surveys distributed by the COVID-19 Community Research Partnership from 8 June 2021 through 21 December 2021, we compared self-reported sources of trusted COVID-19 vaccine information by non-rural and rural counties and by county-level predominant political vote in the 2020 Presidential election.

RESULTS: While NC respondents were highly vaccinated (94%), fewer residents from rural counties self-reported COVID-19 vaccination than those from non-rural counties (91% versus 95%). The most common reported source of trusted vaccine information was federal health agencies. The proportion citing a federal health agency was higher for respondents from non-rural (80%) than rural (72%) counties and was higher for vaccinated (75%) than unvaccinated (42%) rural respondents. The next two most trusted sources of vaccine information were state/local health officials (48%) and health care providers (42%). Among trusted resources reported by 10-15% of respondents, those from rural counties were less likely to use hospital websites, employers, or news sources than those from non-rural counties. More respondents from counties with >60% vote for the 2020 Democratic Presidential candidate cited federal health agencies, state and local officials, and new sources than respondents from counties with >60% vote for the 2020 Republican Presidential candidate.

CONCLUSIONS: By identifying the trusted sources of vaccine information for residents in non-rural and rural NC counties, future vaccine implementation efforts can tailor communication efforts to increase vaccine uptake and potentially reduce the rates of hospitalizations and death from vaccine-preventable diseases such as COVID-19 or other future pandemics.},
}

@article {pmid41600663,
year = {2025},
author = {Polyorach, S and Suphalucksana, W and Klompanya, A and Yuangklang, C and Wanapat, M and Cheas, S and Cherdthong, A and Kang, S and Gunun, P and Gunun, N and Foiklang, S and Kongmun, P and Montri, N and Srikijkasemwat, K},
title = {Ensiling Time and Mixed Microbe Fermented Liquid Modulate In Vitro Digestibility and Rumen Fermentation of Fermented Total Mixed Rations.},
journal = {Veterinary sciences},
volume = {13},
number = {1},
pages = {},
doi = {10.3390/vetsci13010006},
pmid = {41600663},
issn = {2306-7381},
support = {Grant No. 2561-01-04-006//Faculty of Agricultural Technology, King Mongkut's Institute of Technology Ladkrabang, Bangkok, Thailand/ ; },
abstract = {This study investigated how varying the ensiling period and the level of mixed microbes fermented liquid (MMFL) influences the chemical composition, in vitro degradability, rumen fermentation profile, and microbial ecology of fermented total mixed rations (FTMR). A completely randomized 4 × 4 factorial design was used, incorporating four fermentation durations (0, 7, 14, and 21 days) and four MMFL inclusion rates (0, 0.5, 1.0, and 1.5% of DM). Both factors exerted significant effects on FTMR quality (p < 0.05). The combination of a 14-day fermentation period with 0.5% MMFL consistently produced the most desirable outcomes. Under these conditions, crude protein concentration rose from 12.0% to 14.3% of DM, while neutral-detergent fiber declined from 54.2% to 49.1%. Improvements were also observed in in vitro digestibility, with DM and OM increasing by 9-12% relative to the untreated control (p < 0.05). Fermentation end-products were enhanced, as total volatile fatty acids increased by 15% (92.4 vs. 80.1 mmol/L), and the molar proportion of propionate increased from 24.5 to 29.2 mol/100 mol, thereby lowering the acetate-to-propionate ratio (2.4 vs. 3.0; p < 0.05). Estimated methane production declined by 18% (p < 0.01). Microbial counts reflected a shift toward a more efficient fermentative community, with bacterial and fungal populations increasing by 21% and 18%, and protozoa decreasing by 25% (p < 0.05). Overall, moderate MMFL supplementation during a 14-day ensiling phase enhanced nutrient conservation and fermentation efficiency, suggesting practical value for improving FTMR utilization in ruminant systems. Further in vivo and economic evaluations remain necessary.},
}

@article {pmid41600038,
year = {2026},
author = {Shen, H and Liu, Z and Wang, C and Chu, Y and Zhang, C and Yu, Y and Yang, S},
title = {EDDS-Enhanced Phytoremediation of Cd-Zn Co-Contaminated Soil by Sedum lineare: Mechanisms of Metal Uptake, Soil Improvement, and Microbial Community Modulation.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {2},
pages = {},
doi = {10.3390/plants15020231},
pmid = {41600038},
issn = {2223-7747},
support = {32271705//National Natural Science Foundation of China/ ; },
abstract = {Soil co-contamination with cadmium (Cd) and zinc (Zn) poses serious threats to environmental safety and public health. This study investigates the enhancement effect and underlying mechanism of the biodegradable chelator Ethylenediamine-N,N'-disuccinic acid (EDDS) on phytoremediation of Cd-Zn contaminated soil using Sedum lineare. The results demonstrate that EDDS application (3.65 g·L[-1]) effectively alleviated metal-induced phytotoxicity by enhancing chlorophyll synthesis, activating antioxidant enzymes (catalase and dismutase), regulating S-nitrosoglutathione reductase activity, and promoting leaf protein synthesis, thereby improving photosynthetic performance and cellular integrity. The combined treatment significantly increased the bioavailability of Cd and Zn in soil, promoted their transformation into exchangeable fraction, and resulted in removal rates of 30.8% and 28.9%, respectively. EDDS also modified the interaction patterns between heavy metals and essential nutrients, particularly the competitive relationships through selective chelation between Cd/Zn and Fe/Mn during plant uptake. Soil health was substantially improved, as evidenced by reduced electrical conductivity, enhanced cation exchange capacity, and enriched beneficial microbial communities including Sphingomonadaceae. Based on the observed ion antagonism during metal uptake and translocation, this study proposes a novel "Nutrient Regulation Assisted Remediation" strategy to optimize heavy metal accumulation and improve remediation efficiency through rhizosphere nutrient management. These findings confirm the EDDS-S. lineare system as an efficient and sustainable solution for remediation of Cd-Zn co-contaminated soils.},
}

@article {pmid41599027,
year = {2025},
author = {Maçin, S and Özden, Ö and Samadzade, R and Saylam, E and Çiftçi, N and Arslan, U and Yormaz, S},
title = {Oral Microbiota Alterations and Potential Salivary Biomarkers in Colorectal Cancer: A Next-Generation Sequencing Study.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {1},
pages = {},
doi = {10.3390/pathogens15010043},
pmid = {41599027},
issn = {2076-0817},
support = {23401136//Selçuk University/ ; },
mesh = {Humans ; *Colorectal Neoplasms/microbiology/diagnosis ; Male ; Female ; *Saliva/microbiology ; Middle Aged ; *Microbiota/genetics ; High-Throughput Nucleotide Sequencing ; Aged ; RNA, Ribosomal, 16S/genetics ; Pilot Projects ; *Biomarkers, Tumor ; Phylogeny ; Bacteria/classification/genetics/isolation & purification ; *Mouth/microbiology ; Biomarkers ; Case-Control Studies ; Gastrointestinal Microbiome ; },
abstract = {Colorectal cancer (CRC) has a high mortality rate worldwide. Oral and intestinal microbiota members may have an effect on gastrointestinal tumors' pathogenesis, particularly in CRC. Designed as a pilot study, this study's aim was to investigate the relationship between CRC and oral microbiota and to identify potential biomarkers for CRC diagnosis. Saliva samples were collected from recently diagnosed CRC patients (n = 14) and healthy controls (n = 14) between March 2023 and December 2023. Microbiota (16S rRNA) analyses were conducted on these saliva samples using a next-generation sequencing method. Phylogenetic analyses, including alpha diversity, principal component analysis (PCA), principal coordinate analysis (PCoA), beta diversity, biomarker, and phenotype analyses, were conducted using the Qiime2 (Quantitative Insights Into Microbial Ecology) platform. Alpha diversity indices (Shannon: p = 0.78, Cho1: p = 0.28, Simpson: p = 0.81) showed no significant difference between CRC and control groups. Beta diversity analysis using Bray-Curtis PCoA indicated significant differences in the microbial community between the two groups (p = 0.003). Examination of OTU distributions revealed that the Mycoplasmatota phylum was undetectable in the oral microbiota of healthy controls but was significantly elevated in CRC patients (CRC: 0.13 ± 0.30, Control: 0.00 ± 0.00, p < 0.05). Additionally, Metamycoplasma salivarium, Bacteroides intestinalis, and Pseudoprevotella muciniphila were undetectable in healthy controls but significantly more prevalent in CRC patients (p < 0.05 for all three species). LEfSe analysis identified eight species with an LDA score > 2, Granulicatella adiacens, Streptococcus thermophilus, Streptococcus gwangjuense, Capnocytophaga sp. FDAARGOS_737, Capnocytophaga gingivalis, Granulicatella elegans, Bacteroides intestinalis, and Pseudoprevotella muciniphila, as potential biomarkers. The results of this study contribute critical evidence of the role of oral microbiota in the pathogenesis of colorectal cancer. Alterations in the microbiota suggest potential biomarkers in understanding the biological mechanisms underlying CRC and developing diagnostic and therapeutic strategies.},
}

Humans
*Colorectal Neoplasms/microbiology/diagnosis
Male
Female
*Saliva/microbiology
Middle Aged
*Microbiota/genetics
High-Throughput Nucleotide Sequencing
Aged
RNA, Ribosomal, 16S/genetics
Pilot Projects
*Biomarkers, Tumor
Phylogeny
Bacteria/classification/genetics/isolation & purification
*Mouth/microbiology
Biomarkers
Case-Control Studies
Gastrointestinal Microbiome

@article {pmid41597698,
year = {2026},
author = {Mohammed, A and Negm, E and Amarin, N and Sayed, S and Soliman, A and Askar, H and Yusuf, S and Rayan, AA},
title = {Impact of Dietary Supplementation of Probiotics on Cecal Microbial Ecology, Immune Response, and Meat Quality of Muscovy Ducks.},
journal = {Microorganisms},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/microorganisms14010182},
pmid = {41597698},
issn = {2076-2607},
support = {United Animal Health//United Animal Health (United States)/ ; },
abstract = {Probiotics represent a beneficial approach to boost the welfare, health, and meat quality of poultry. One hundred and twenty one-day-old male Muscovy ducklings were divided among 24 floor pens (five ducklings per pen). The pens were randomly distributed among one of four dietary treatments with six replicates (G-C) without any supplementation of probiotics; (G-A) was supplemented with 0.4 g/kg of Amnil[®]; (G-M) was supplemented with 0.5 g/kg of M-Mobilize[®]; and (G-A-M) was supplemented with 0.4 g/kg of Amnil[®] (1-30 day) and 0.5 g/kg of M-Mobilize[®] (31-60 day), respectively. The results indicated that BW at day 60 was improved in (G-A) birds compared with (G-C) ones, IL-6 was decreased in (G-A) and (G-A-M) in liver and spleen in comparison with (G-C) (p < 0.05), but no differences were observed between (G-C) and (G-M) (p > 0.05); IL-10 was decreased in all the probiotic-fed ducklings compared with (G-C) birds in the spleen (p < 0.05), and IL-10 was decreased in the (G-A) birds compared with the other treatments in the liver (p < 0.05). Probiotic-fed birds showed a higher enumeration of Lactobacillus spp. compared to (G-C) group (p < 0.05). In addition, the (G-M) group showed improved breast meat flavor, general acceptability, and water-holding capacity (WHC%) compared to (G-C) group (p < 0.05). These results suggest that the probiotic supplement (G-A), could be a good management tool for improving Muscovy ducks' health and production and further research is needed to improve meat quality traits.},
}

@article {pmid41597665,
year = {2026},
author = {Khachatryan, A and Vardanyan, A and Zhang, R and Zhang, Y and Shi, X and Willscher, S and Nguyen, NHA and Vardanyan, N},
title = {Metagenome Insights into Armenian Acid Mine Drainage: A Novel Thermoacidophilic Iron-Oxidizing Bacterium with Perspectives for Copper Bioleaching.},
journal = {Microorganisms},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/microorganisms14010146},
pmid = {41597665},
issn = {2076-2607},
support = {22rl-031//Higher Education Science Committee of Armenia/ ; 23-YSIP-012//Higher Education Science Committee of Armenia/ ; },
abstract = {The microbial ecology of acid mine drainage (AMD) systems in Armenia, with a long mining history, remains unexplored. This study aimed to characterize the microbial diversity and functional potential of AMD in the Syunik region and to isolate novel microorganisms with biotechnological value. A comprehensive analysis of the microbial communities' structure of Kavart abandoned, Kapan exploring mines effluent, and Artsvanik tailing was conducted. Metagenomics revealed bacterial-dominated communities, comprising Pseudomonadota (previously "Proteobacteria") (68-72%), with site-specific variations in genus abundance. A high abundance and diversity of metal resistance genes (MRGs), particularly for copper and arsenic, were identified. Carbohydrate-active enzyme (CAZy) analysis showed a dominance of GT2 and GT4 genes, suggesting a high potential for extracellular polymeric substances (EPS) production and biofilm formation. A novel strain of iron-oxidizing bacteria Arm-12 was isolated that shares only ~90% similarity with known Leptospirillum type species, indicating it may represent a new genus without culturable representatives. The strain exhibits enhanced copper extraction from concentrate. This study provides the first metagenomic insights into Armenian AMD systems and tailing, revealing a unique community rich in metal resistance and biofilm-forming genes. The isolation of a novel highly effective iron-oxidizer Arm-12 highlights the potential of AMD environments as a source of novel taxa with significant applications in biomining and bioremediation processes.},
}

@article {pmid41597639,
year = {2026},
author = {Yin, Y and Xu, W and Xu, M and Wang, Y and Liu, H and Cao, H and Wang, F},
title = {Prokaryotic Microbial Diversity and Community Assembly in Reclaimed Coastal Agricultural Soils.},
journal = {Microorganisms},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/microorganisms14010120},
pmid = {41597639},
issn = {2076-2607},
support = {32471725//National Natural Science Foundation of China/ ; 2021S018//Ningbo Municipal Bureau of Science and Technology/ ; 2022Z169//Ningbo Municipal Bureau of Science and Technology/ ; },
abstract = {Coastal reclamation profoundly alters soil physicochemical conditions and strongly influences soil microbial ecology; however, the millennial-scale successional patterns and assembly mechanisms of prokaryotic communities under such long-term disturbance remain insufficiently understood. In this study, we investigated archaeal and bacterial communities in the plow layer along a 0-1000-year coastal reclamation chronosequence on the southern shore of Hangzhou Bay. We analyzed community abundance, diversity, composition and assembly processes, and quantified the relative contributions of geographic distance, environmental factors and reclamation years to microbial biogeographic patterns. The results showed that reclamation markedly drove continuous soil desalination, acidification, nutrient accumulation, and particle-size refinement. Bacterial abundance exhibited a sharp decline during the early stages of reclamation, whereas archaeal abundance remained relatively stable. The α-diversity of both archaea and bacteria peaked at approximately 210-230 years of reclamation. Community assembly processes differed substantially between the two microbial domains: the archaeal communities were dominated by stochastic processes (77.78%) identified as undominated processes and dispersal limitation, whereas bacterial communities were primarily shaped by deterministic processes (70.75%) driven as variable selection. Distance-decay analysis indicated that bacterial communities were more sensitive to environmental gradients. Multiple regression and variance partitioning further demonstrated that soil pH and electrical conductivity were the key drivers of community structure. Overall, this study reveals the millennial-scale community dynamics and assembly mechanisms of archaea and bacteria in response to coastal reclamation, providing mechanistic insights into long-term microbial ecological succession and offering valuable guidance for sustainable agricultural management and ecological restoration in reclaimed coastal regions.},
}

@article {pmid41597573,
year = {2025},
author = {Si, W and Zhang, J and Zhang, Y and Ji, Y and Khan, MZ and Chen, Y and Cheng, Z and Zhuang, J and Zhao, X and Liu, W},
title = {Characterization of Bacterial Communities in Air and Bedding Materials of Intensive Donkey Farms During Summer.},
journal = {Microorganisms},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/microorganisms14010053},
pmid = {41597573},
issn = {2076-2607},
support = {SDAIT-27-11//Shandong Donkey Industry Technology System Fund/ ; },
abstract = {This study investigated the bacterial community composition and diversity in air and exercise yard bedding samples from large-scale donkey farms in Liaocheng, China, during summer using 16S rRNA high-throughput sequencing. Air samples were collected from five functional areas of donkey barns, while bedding samples were obtained from eight farms housing Dezhou donkeys. Sequencing analysis revealed 894 operational taxonomic units (OTUs) in air samples and 3127 OTUs in bedding samples. Alpha diversity indices indicated that the mare barn exhibited the highest microbial diversity in air, while the foal barn showed the lowest. Actinobacteriota, Proteobacteria, and Firmicutes were the dominant phyla across different functional areas. Rhodococcus was identified as the predominant airborne genus, representing a potential pneumonia risk in foals. In bedding materials, Firmicutes, Actinobacteriota, and Proteobacteria predominated, with Corynebacterium, Salinicoccus, and Solibacillus as dominant genera. Several potentially pathogenic bacteria were detected, including Rhodococcus, Corynebacterium, Clostridium, Streptococcus, and Escherichia-Shigella. These findings provide critical insights into the microbial ecology of intensive donkey farming environments and offer scientific evidence for developing targeted biosecurity strategies to safeguard animal health and promote sustainable livestock production.},
}

@article {pmid41597522,
year = {2025},
author = {Tamahara, T and Kouketsu, A and Fukase, S and Sripodok, P and Saito, T and Ito, A and Li, B and Kumada, K and Shimada, M and Iikubo, M and Shimizu, R and Yamauchi, K and Sugiura, T},
title = {Ecological and Functional Landscape of the Oral Microbiome: A Multi-Site Analysis of Saliva, Dental Plaque and Tongue Coating.},
journal = {Microorganisms},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/microorganisms14010002},
pmid = {41597522},
issn = {2076-2607},
support = {JP24K1310 and JP22K17150//JSPS KAKENHI/ ; },
abstract = {The oral cavity contains several microbial niches, including saliva, dental plaque and tongue coating, each shaped by distinct local environments and host factors. This study compared the ecological and functional characteristics of the microbiomes of these three oral sites within the same individuals and examined host conditions associated with their variation. Saliva, supragingival plaque and tongue coating samples were collected simultaneously from 31 adults without clinical oral lesions. The bacterial 16S rRNA gene (V3-V4 region) was sequenced using the Illumina MiSeq platform, and analyses included α and β diversity, Mantel correlations, differential abundance tests, network analysis and functional prediction. The three sites displayed a clear ecological gradient. Saliva and tongue coating were taxonomically similar but were influenced by different host factors, whereas plaque maintained a distinct, biofilm-like structure with limited systemic influence. Functional divergence was most pronounced on the tongue coating despite its taxonomic similarity to saliva, whereas functional differences between saliva and plaque were modest despite larger taxonomic separation. These findings indicate that microbial composition and function vary independently across oral niches and support the need for multi-site sampling to more accurately characterize oral microbial ecology.},
}

@article {pmid41596857,
year = {2026},
author = {Tsouggou, N and Korozi, E and Pemaj, V and Drosinos, EH and Kapolos, J and Papadelli, M and Skandamis, PN and Papadimitriou, K},
title = {Advances in Shotgun Metagenomics for Cheese Microbiology: From Microbial Dynamics to Functional Insights.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {2},
pages = {},
doi = {10.3390/foods15020259},
pmid = {41596857},
issn = {2304-8158},
abstract = {The cheese microbiome is a complex ecosystem strongly influenced by both technological practices and the processing environment. Moving beyond traditional cultured-based methods, the integration of shotgun metagenomics into cheese microbiology has enabled in-depth resolution of microbial communities at the species and strain levels. The aim of the present study was to review recent applications of shotgun metagenomics in cheese research, underscoring its role in tracking microbial dynamics during production and in discovering genes of technological importance. In addition, the review highlights how shotgun metagenomics enables the identification of key metabolic pathways, including amino acid catabolism, lipid metabolism, and citrate degradation, among others, which are central to flavor formation and ripening. Results of the discussed literature demonstrate how microbial composition, functional traits, and overall quality of cheese are determined by factors such as raw materials, the cheesemaking environment, and artisanal practices. Moreover, it highlights the analytical potentials of shotgun metagenomics, including metagenome-assembled genomes (MAGs) reconstruction, characterization of various genes contributing to flavor-related biosynthetic pathways, bacteriocin production, antimicrobial resistance, and virulence, as well as the identification of phages and CRISPR-Cas systems. These insights obtained are crucial for ensuring product's authenticity, enabling traceability, and improving the assessment of safety and quality. Despite shotgun metagenomics' advantages, there are still analytical restrictions concerning data handling and interpretation, which need to be addressed by importing standardization steps and moving towards integrating multi-omics approaches. Such strategies will lead to more accurate and reproducible results across studies and improved resolution of active ecosystems. Ultimately, shotgun metagenomics has shifted the field from descriptive surveys to a more detailed understanding of the underlying mechanisms shaping the overall quality and safety of cheese, thus bringing innovation in modern dairy microbiology.},
}

@article {pmid41595487,
year = {2026},
author = {Ucero-Carretón, A and Puente, H and Ithurbide, M and Estellé, J and Carvajal, A and Argüello, H},
title = {Factors Involved in Host Resilience to Enteric Infections in Pigs: Current Knowledge in Genetic, Immune, and Microbiota Determinants of Infection Resistance.},
journal = {Genes},
volume = {17},
number = {1},
pages = {},
doi = {10.3390/genes17010067},
pmid = {41595487},
issn = {2073-4425},
support = {PID2024-160714OB-I00//Ministerio de Ciencia, Innovación y Universidades/ ; MICIU/AEI/10.13039/501100011033//Ministerio de Ciencia, Innovación y Universidades/ ; LE088P23//Junta de Castilla y León/ ; JDC2023-051122-I//Ministerio de Ciencia, Innovación y Universidades/ ; ULE-Predoc/2024//Universidad de León/ ; },
mesh = {Animals ; Swine/genetics ; *Gastrointestinal Microbiome/genetics/immunology ; *Disease Resistance/genetics ; *Swine Diseases/microbiology/genetics/immunology/virology ; *Host-Pathogen Interactions/genetics/immunology ; Quantitative Trait Loci ; },
abstract = {Enteric infections remain a major health and economic challenge in swine production, with outcomes determined not only by pathogen virulence but also by the complex interplay between host genetics, immune competence, and the intestinal microbiota. This review synthesises current knowledge on host-pathogen genomic interactions in pigs, with a focus on resilience mechanisms against enteric diseases in swine. For this purpose, 103 articles were used as information sources, retrieved through structured keyword searches in PubMed. The review first addresses host genetic factors, highlighting genomic variants and quantitative trait loci associated with resistance or resilience to viral and bacterial pathogens such as porcine epidemic diarrhoea virus (PEDV) or Escherichia coli. Next, the key factors of the immune system to confer protection are also reviewed, emphasising the role of innate and adaptive responses in controlling each pathogen and disclosing the contribution of regulatory networks that balance pathogen clearance. Finally, the last section of the review is devoted to exploring current knowledge in the involvement of the microbiota in resilience against enteric pathogens, mostly, but not exclusively, enteric bacteria. In this sense, competitive exclusion is a concept which has gained attention in recent years. The review pinpoints and discusses the state of the art about how the microbial community provides colonisation resistance, shapes immune development, and influences pathogen fitness within the intestinal niche. As final perspectives, the review explores future drivers in the genetic immune and microbiota resistance. By bridging host genomic data with functional insights into immunity and microbial ecology, this review underscores the potential of multi-omics approaches to enhance resilience against enteric infections in pigs and advance sustainable swine health management.},
}

Animals
Swine/genetics
*Gastrointestinal Microbiome/genetics/immunology
*Disease Resistance/genetics
*Swine Diseases/microbiology/genetics/immunology/virology
*Host-Pathogen Interactions/genetics/immunology
Quantitative Trait Loci

@article {pmid41593721,
year = {2026},
author = {Xi, J and Tao, H and Zhang, Z and Lian, B and Sun, W and Zhang, Y and Bu, S and Yang, X and Qian, X},
title = {Captive breeding of specialty animals represents an overlooked yet critical reservoir for spreading antibiotic resistance genes.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag009},
pmid = {41593721},
issn = {1751-7370},
abstract = {Driven by wildlife conservation and economic demands, captive breeding has expanded globally, intensifying wildlife-human interactions. In specialty animal breeding, particularly for species with short domestication histories and underdeveloped breeding protocols, clinically important antibiotics are commonly misused, posing potential ecological and health risks that remain largely unexplored. We collected fecal samples from three groups of musk deer (Moschus berezovskii): those exposed to clinically important antibiotics, those not exposed for six months, and wild musk deer, and analyzed their microbiomes and resistomes using metagenomic and culture-based methods. We found that captivity significantly expanded and reshaped the fecal resistome of musk deer. The antibiotic-exposed musk deer harbored a significantly higher diversity and abundance of antibiotic resistance genes (ARGs) compared to those non-exposed to antibiotics and wild deer. We observed a higher abundance of clinically important ARGs within Enterobacteriaceae in fecal samples of captive musk deer. This observation was further supported by the antibiotic susceptibility profiles of 124 Escherichia coli strains isolated from antibiotic-exposed musk deer. Seven identical mobile genetic element-associated ARGs were detected in distinct bacterial hosts across fecal samples from musk deer and farm workers, indicating potential conjugative transfer between the two groups. Our results suggest that captive breeding of specialty animals is an overlooked but significant reservoir for disseminating clinically important ARGs, and underscore the transmission risk at the animal-human interface.},
}

@article {pmid41592901,
year = {2026},
author = {Pedreira, A and Vázquez, JA and García, MR},
title = {The mini revolution: application of mini-bioreactors in adaptive laboratory evolution.},
journal = {Critical reviews in biotechnology},
volume = {},
number = {},
pages = {1-19},
doi = {10.1080/07388551.2025.2608012},
pmid = {41592901},
issn = {1549-7801},
abstract = {Adaptive laboratory evolution (ALE) is a powerful tool for understanding and controlling the evolutionary trajectories of microorganisms. The scope of applications extends widely, including areas such as: biotechnology, synthetic biology, microbial ecology, and fundamental evolutionary research. In this work, we systematically explore the implementation and advantages of mini-bioreactors, defined as reactors with working volumes below 0.5 L, in ALE experiments. Mini-bioreactors offer substantial improvements over traditional large-scale reactors, including: reduced costs, enhanced parallelization capabilities, customizable configurations, and ease of automation. Through the utilization of illustrative case studies, which facilitate a comparative and critical evaluation of: batch, chemostat, turbidostat, and morbidostat operational modes, this review underscores the distinct capabilities of mini-bioreactors in enabling precise, dynamic control of evolutionary pressures. The novelty of this review lies in its comprehensive synthesis of recent advancements in mini-bioreactor technologies and operational strategies, particularly emphasizing innovations, such as: integrated automation, advanced sensors, and novel control algorithms adapted or specially designed for ALE. The ultimate objective is to provide both novices and experienced researchers with an updated, in-depth resource that addresses current technological limitations and future directions of mini-bioreactors in ALE.},
}

@article {pmid41592403,
year = {2026},
author = {Zhang, B and Wang, M and Zheng, J and Yu, C and Wei, C and Ren, J and Sun, S and Wang, G and Wang, J and Lu, Y and Lin, L and Zhang, C},
title = {Strain-specific impacts of Pichia kudriavzevii on metabolite profiles and microbial community dynamics in Chinese Baijiu fermentation: Integrated metabolomics and metagenomics analysis.},
journal = {International journal of food microbiology},
volume = {450},
number = {},
pages = {111660},
doi = {10.1016/j.ijfoodmicro.2026.111660},
pmid = {41592403},
issn = {1879-3460},
abstract = {Pichia kudriavzevii is a dominant yeast species in Chinese baijiu fermentation, yet its intraspecific diversity remains underexplored. This study used metabolomics and metagenomics analysis to investigate the impact of four distinct P. kudriavzevii strains (PK12, PK25, PK97, and PK360) on the metabolite profiles and microbial community structure in a controlled baijiu solid-state fermentation. Metabolomics analysis identified 49 key volatile compounds and 2792 non-volatile metabolites. Strain PK97 exhibited exceptional capacity for butanoic acid metabolism, inducing a 55.27-fold increase in butanoic acid and a 30.54-fold enhancement in ethyl butanoate production. Strain PK25 specialized in acetoin biosynthesis, while PK360 maximized 2-phenylethanol production. Metagenomic analysis uncovered that strains PK12, PK25, and PK360 promoted Lactobacillus acetotolerans population, increasing its relative abundance to 67.39%, 58.57%, and 71.79%, respectively. In contrast, strain PK97 orchestrated a dramatic ecological shift, elevating Enterobacter mori abundance from 0.56% to 17.60%, transforming the community from Lactobacillus-dominated to Enterobacteriaceae-enriched. Integration of metabolomic and metagenomic data revealed that strain PK97's promotion of Enterobacter mori correlated with significant upregulation of key enzymes including α-amylase (EC 3.2.1.1), enoyl-CoA hydratase (EC 4.2.1.17), and succinyl-CoA synthetase (EC 6.2.1.5), creating a metabolic environment favoring enhanced starch hydrolysis, altered TCA cycle flux, and butanoic acid accumulation. Strain PK25 specifically upregulated acetyl-CoA hydrolase (EC 3.1.2.1), facilitating acetic acid and acetoin formation. Strain PK360 enhanced glucose pyrophosphorylase (EC 2.7.7.9) and asparagine synthetase (EC 6.3.1.1) activities, accelerating galactose metabolism and amino acid transformations. These findings illustrate the impact of P. kudriavzevii intraspecific diversity on reshaping microbial ecology and flavor chemistry in Chinese baijiu, offering novel insights for targeted fermentation control and quality enhancement strategies in baijiu production.},
}

@article {pmid41592132,
year = {2026},
author = {Rathod, DR and Silverman, JD},
title = {PCR bias impacts microbiome ecological analyses.},
journal = {PLoS computational biology},
volume = {22},
number = {1},
pages = {e1013908},
doi = {10.1371/journal.pcbi.1013908},
pmid = {41592132},
issn = {1553-7358},
abstract = {Polymerase Chain Reaction (PCR) is a critical step in amplicon-based microbial community profiling, allowing the selective amplification of marker genes such as 16S rRNA from environmental or host-associated samples. Despite its widespread use, PCR is known to introduce amplification bias, where some DNA sequences are preferentially amplified over others due to factors such as primer-template mismatches, sequence GC content, and secondary structures. Although these biases are known to affect transcript abundance, their implications for ecological metrics remain poorly understood. In this study, we conduct a comprehensive evaluation of how PCR-bias influences both within-samples (α-diversity) and between-sample (β-diversity) analyses. We show that perturbation-invariant diversity measures remain unaffected by PCR bias, but widely used metrics such as Shannon diversity and Weighted-Unifrac are sensitive. To address this, we provide theoretical and empirical insight into how PCR-induced bias varies across ecological analyses and community structures, and we offer practical guidance on when bias-correction methods should be applied. Our findings highlight the importance of selecting appropriate diversity metrics for PCR-based microbial ecology workflows and offer guidance for improving the reliability of diversity analyses.},
}

@article {pmid41591842,
year = {2026},
author = {Islam, H and Sharma, A and Blair, J and Lopatkin, AJ},
title = {PlasAnn: a curated plasmid-specific database and annotation pipeline for standardized gene and function analysis.},
journal = {Nucleic acids research},
volume = {54},
number = {3},
pages = {},
doi = {10.1093/nar/gkaf1507},
pmid = {41591842},
issn = {1362-4962},
support = {1R35GM150871-01/NH/NIH HHS/United States ; //Pew Charitable Trusts Foundation/ ; 2440082//National Science Foundation/ ; //Edward Mallinckrodt Jr. Foundation/ ; },
mesh = {*Plasmids/genetics ; *Molecular Sequence Annotation/methods ; *Databases, Genetic ; Genome, Bacterial ; Software ; DNA Transposable Elements ; Genes, Bacterial ; Bacteria/genetics ; },
abstract = {Conjugative plasmids are key drivers of bacterial adaptation, enabling the horizontal transfer of accessory genes within and across diverse microbial populations, yet annotating them remains challenging due to their highly mosaic genetic architectures and inconsistent gene naming conventions that complicate functional predictions and comparative analyses. To address this, we developed PlasAnn, a database designed specifically for genes encoded on natural plasmids, paired with a dedicated annotation pipeline (available via Bioconda or through the URL https://plasann.rochester.edu/). The curated database provides highly accurate, plasmid-type-specific gene names with standardized functional annotations, enabling direct comparison across plasmids without manual curation or specialized expertise, while the integrated annotation tool incorporates other common plasmid features for a fast, one-stop solution that outperforms broad prokaryotic genome annotation pipelines in both accuracy and efficiency. We demonstrate PlasAnn's utility by showing that plasmid accessory genes from different groups often share conserved repertoires, suggesting dynamic, modular networks of interconnected genes, and by revealing that plasmid-encoded transposable elements frequently carry genes related to bacterial adaptation beyond antibiotic resistance, including metabolism, virulence, and stress responses, emphasizing their broader contributions to fitness and adaptability. These insights, not captured by current field-standard tools, highlight how PlasAnn improves plasmid annotation and advances our understanding of plasmid biology, microbial ecology, and evolution.},
}

*Plasmids/genetics
*Molecular Sequence Annotation/methods
*Databases, Genetic
Genome, Bacterial
Software
DNA Transposable Elements
Genes, Bacterial
Bacteria/genetics

@article {pmid41590453,
year = {2026},
author = {Zhang, K and Cai, Y and Shi, X and Yan, Z and Huang, Q and Perez-Moreno, J and Liu, D and Yang, Z and Yang, C and Yu, F and Liu, W},
title = {Symbiosis Among Naematelia aurantialba, Stereum hirsutum, and Their Associated Microbiome in the Composition of a Cultivated Mushroom Complex JinEr.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {12},
number = {1},
pages = {},
doi = {10.3390/jof12010041},
pmid = {41590453},
issn = {2309-608X},
support = {202205AD160036//Fuqiang Yu/ ; Yunnan Revitalization Talent Support Program//Jesús Pérez-Moreno, Xinhua He/ ; },
abstract = {The JinEr mushroom ("Golden Ear"), a globally rare edible and medicinal macrofungus, comprises a symbiotic complex formed by the symbiotic association of Naematelia aurantialba (Tremellomycetes) and Stereum hirsutum (Agaricomycetes). However, the interactions between these fungi and their associated microbiome remain poorly understood. This study employed high-throughput amplicon sequencing, in situ microbial isolation and culture, and microbial confrontation assays to analyze microbial diversity, community structure, and potential functional roles of the endomycotic bacterial community within JinEr basidiomata and its cultivation substrate. Molecular analysis confirmed the heterogenous composition of the basidiomata, revealing N. aurantialba constitutes less than 20% of the fungal biomass, while S. hirsutum predominates, accounting for approximately 80%. Endomycotic fungi accounted for 0.33% (relative abundance) of the fungal community. Prokaryotic analysis identified Delftia and Sphingomonas as the dominant endomycotic bacterial genera within basidiomata, comprising 85.42% of prokaryotic sequences. Endomycotic bacterial diversity differed significantly (p < 0.05) between basidiomata and substrate, indicating host-specific selection. Cultivation-based approaches yielded 140 culturable bacterial isolates (spanning four families and seven genera) from basidiomata core tissues. In vitro co-culture experiments demonstrated that eight representative bacterial strains exhibited compatible growth with both hosts, while one Enterobacteriaceae strain displayed antagonism towards them. These findings confirm that the heterogeneous JinEr basidiomata harbor a specific prokaryotic assemblage potentially engaged in putative symbiotic or commensal associations with the host fungi. This research advances the understanding of microbial ecology in this unique fungal complex and establishes a culture repository of associated bacteria. This collection facilitates subsequent screening for beneficial bacterial strains to enhance the JinEr cultivation system through the provision of symbiotic microorganisms.},
}

@article {pmid41589897,
year = {2026},
author = {Huang, J and Cai, M and Han, M and Fang, B and Dong, L and Zhang, G and Han, J-R and Li, S and Rustamova, N and Liu, Y and Li, W-J and Jiang, H},
title = {Habitat heterogeneity drives microbial community assembly and functional specialization in extremely arid ecosystems.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0258825},
doi = {10.1128/aem.02588-25},
pmid = {41589897},
issn = {1098-5336},
abstract = {UNLABELLED: Extreme arid ecosystems present significant environmental challenges, yet the mechanisms by which habitat heterogeneity (e.g., salinity gradients, soil-sediment contrasts) shapes microbial community assembly and functional specialization remain poorly understood. This study integrated culture-dependent and culture-independent approaches to investigate microbial diversity, assembly processes, and metabolic potential across wasteland soils, desert soils, and saline lake sediments in the Turpan-Hami Basin. High-throughput sequencing revealed habitat-specific patterns, with lake sediments exhibiting significantly greater OTU richness and Shannon diversity than wasteland and desert soils (P < 0.05). These shifts were driven by salinity-dependent taxonomic succession, notably the dominance of Gammaproteobacteria, Halobacteria, and Desulfobacteria in hypersaline lakes. Ecological assembly processes diverged across habitats, with deterministic processes (heterogeneous/homogeneous selection) dominated in deserts and moderate saline lakes, whereas stochastic processes (dispersal limitation, drift) prevailed in wastelands and hypersaline systems. Metabolic profiling highlighted habitat-specific functional specialization: terrestrial systems were characterized by nitrogen-cycling, while saline lakes displayed partitioned sulfur metabolism (e.g., sulfate respiration in high-salinity sediments). Co-occurrence network analyses revealed greater topological complexity in freshwater lakes than in extreme environments, reflecting contrasting resilience strategies. Cultivation strategies informed by sequencing results recovered 4.02% to 21.76% of the sequence-detected genera, significantly improving access to the uncultured majority. These findings demonstrate that habitat heterogeneity drives microbial community assembly and functional evolution in extremely arid ecosystems, underscoring the value of integrating omics with cultivation to uncover microbial dark matter.

IMPORTANCE: Understanding microbial adaptation in hyperarid environments is crucial for predicting ecosystem responses to extreme stressors. This study provides an integrative framework linking environmental heterogeneity to microbial community assembly and metabolic specialization across diverse habitats in one of Earth's driest basins. Our findings demonstrate that deterministic environmental filtering dominates community assembly in deserts and moderately saline lakes, whereas stochastic processes prevail in wastelands and hypersaline systems. Habitat‑specific metabolic specialization is evident, with nitrogen cycling being key in terrestrial soils and sulfur metabolism central to saline lakes. By significantly improving the recovery of uncultured diversity through targeted strategies, this study bridges a major gap between molecular surveys and cultivable microorganisms. These findings advance ecological theory on community assembly and offer a model for studying microbial resilience and functional evolution under extreme aridity.},
}

@article {pmid41589889,
year = {2026},
author = {Wang, S and Su, Y},
title = {Challenging the paradigm of metabolic exclusivity: coexistence of methanogenesis and sulfate reduction in oil reservoirs.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0217225},
doi = {10.1128/aem.02172-25},
pmid = {41589889},
issn = {1098-5336},
abstract = {The prevailing dogma in microbial ecology holds that sulfate-reducing microorganisms (SRMs) outcompete methanogenic archaea for common substrates (e.g., H2/formate and acetate), leading to the mutual exclusion of sulfate reduction and methanogenesis in sulfate-rich anaerobic environments. This principle underpins models of organic carbon flow to sulfate-respiration-derived CO2 in ecosystems like oil reservoirs, where seawater injection introduces high concentrations of sulfate. In an Applied and Environmental Microbiology article by S. Beilig, L. Voskuhl, I. Geydirici, L. K. Tintrop, T. C. Schmidt, and R. U. Meckenstock (91:e00141-25, 2025, https://doi.org/10.1128/aem.00141-25), the authors challenge this view by demonstrating coexistence of methanogenesis and sulfate reduction in a sulfate-adapted enrichment culture from an oil reservoir. The authors employ incubation experiments and microbial activity assessment via the reverse stable isotope labeling (RSIL) method to argue for metabolic coexistence, even under conditions thought to favor complete competitive exclusion. This commentary discusses the mechanistic reasons underlying the coexistence and explores the broader implications for predicting microbial activities and interactions. The study compellingly argues that thermodynamic and kinetic arguments alone are insufficient to predict microbial community function, necessitating a more nuanced understanding of microbial interactions in complex environments.},
}

@article {pmid41588828,
year = {2026},
author = {Shaw, D and Gentekaki, E and Tsaousis, AD},
title = {The Microbiome Within a Microbe: Rethinking Blastocystis Biology.},
journal = {The Journal of eukaryotic microbiology},
volume = {73},
number = {1},
pages = {e70056},
doi = {10.1111/jeu.70056},
pmid = {41588828},
issn = {1550-7408},
support = {CA21105//COST/ ; //University of Kent/ ; },
mesh = {*Blastocystis/physiology/microbiology/virology ; Humans ; *Microbiota ; Blastocystis Infections/parasitology ; *Gastrointestinal Microbiome ; },
abstract = {Blastocystis spp., one of the most prevalent microeukaryotes in the human gut, has long puzzled researchers with its ambiguous role in health and disease. Decades-old microscopy studies reported bacterial- and viral-like particles within Blastocystis spp. cells, but these findings have been mainly overlooked. Comparable associations in other protozoa, such as those between Trichomonas vaginalis and Mycoplasma, as well as protozoan-virus interactions, are known to influence metabolism, immune evasion, and ecological fitness. Here, we revisit these neglected observations in Blastocystis spp., framing them within the holobiont concept and proposing that this protist may host its own microbial consortium. We also propose potential mechanisms, ecological implications, and modern experimental strategies-from organ-on-a-chip to single-cell multi-omics-to rigorously test this hypothesis. Recognizing Blastocystis spp. as a possible "microbiome within a microbe" could transform our understanding of its biology and its place in gut microbial ecology.},
}

*Blastocystis/physiology/microbiology/virology
Humans
*Microbiota
Blastocystis Infections/parasitology
*Gastrointestinal Microbiome

@article {pmid41588461,
year = {2026},
author = {Zheng, H and Payne, L and He, W and Mestre, MR and Yang, L and Dechesne, A and Pinilla-Redondo, R and Nesme, J and Sørensen, SJ},
title = {Plasmids as persistent genetic reservoirs of bacterial defense systems in wastewater treatment.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02297-2},
pmid = {41588461},
issn = {2049-2618},
abstract = {BACKGROUND: Bacterial antiphage defense systems play essential roles in microbial ecology, yet their dynamics within urban wastewater systems (UWS) remain poorly characterized.

RESULTS: In this study, we performed comprehensive metagenomic and plasmidome analyses on 78 wastewater samples collected during two seasons and four sampling points across UWS from three European countries. We observed a significant reduction in the abundance, diversity, and mobility potential of defense systems during biological treatment. However, these reductions were not directly correlated with changes in microbial abundance. Defense systems were significantly enriched on plasmids, particularly conjugative plasmids, where their gene density was approximately twice as high as on chromosomes and remained relatively stable across compartments. In contrast to chromosomal defense systems, plasmid-borne systems exhibited more frequent co-localization with a wide range of mobile genetic elements (MGEs)-associated genes, thereby facilitating multilayered dissemination networks. Furthermore, we detected a strong correlation between phage abundance and host defense system profiles, indicating ongoing phage-host co-evolutionary dynamics in these environments.

CONCLUSIONS: In summary, our results demonstrate that UWS reduce the abundance and diversity of bacterial defense system genes. However, plasmid-associated defense systems can persist through shared mobile genetic reservoirs. These findings underscore the critical role of plasmids in bacterial immunity and provide new insights into defense system dynamics within urban wastewater environments.},
}

@article {pmid41588066,
year = {2026},
author = {Pániková, L and Ondreičková, K and Pánik, P and Janiga, M and Oxikbayev, B},
title = {Linkages Between Trace Elements and Bacterial Communities in Glacial Freshwater Systems of Zhongar Alatau National Park, Kazakhstan.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02674-2},
pmid = {41588066},
issn = {1432-184X},
abstract = {Glacial ecosystems of Central Asia represent extreme environments where microbial communities are shaped by both physicochemical conditions and hydrological dynamics. In this study, we analysed 21 surface and meltwater samples collected in September 2023 from a lake, river, glacier, glacial river, and sedimentary lake in the Zhongar Alatau National Park (Kazakhstan, 1 040-3 360 m a.s.l.). Bacterial community structure was assessed using ARISA profiling, while spectrometric methods determined concentrations of chemical elements. Alpha diversity indices revealed the highest richness and diversity in lake and sedimentary lake samples, moderate diversity in river samples, and the lowest values in glacier samples. The glacial river samples showed the strongest variability among the samples. Unique operational taxonomic units (OTUs) were most abundant in the lake, but the glacier exhibited the highest relative proportion of habitat-specific OTUs. Principal component analysis revealed that DNA yield, along with heavy metals and other elements (Rb, Fe, Mn, K, Ba), covaried along the major axes, primarily reflecting differences driven by habitat. Overall, our results demonstrate that glacial valley habitats host distinct bacterial assemblages and that the chemical environment is consistent with the observed spatial structuring of microbial communities. These findings highlight the vulnerability and sensitivity of mountain freshwater ecosystems to glacier retreat and associated changes in water chemistry.},
}

@article {pmid41587649,
year = {2026},
author = {Shi, J and Li, LK and Lin, LH and Li, DK and Lu, J and Saleh, SM and Zhang, TY and He, H and Dong, ZY and Xiao, Q and Xu, B and Zeng, C},
title = {Magnetic properties driving nitrogen removal improvement in magnetite-enhanced activated sludge: Mechanistic insights and process validation.},
journal = {Environmental research},
volume = {294},
number = {},
pages = {123870},
doi = {10.1016/j.envres.2026.123870},
pmid = {41587649},
issn = {1096-0953},
abstract = {The magnetite-enhanced activated sludge (MEAS) process offers a promising in situ strategy for upgrading wastewater treatment plants (WWTPs) to meet increasing treatment demands and stricter discharge regulations. Unlike conventional materials, magnetite possesses intrinsic magnetic properties, yet their influence on biological treatment efficiency and microbial ecology remains underexplored. This study systematically evaluated three types of magnetite particles with varying properties, focusing on their roles in denitrification, sludge settling, and microbial responses. Batch experiments under low carbon-to-nitrogen conditions (C/N = 4.4) demonstrated that magnetite with high saturation magnetization (65.9 emu/g) achieved 79.3 ± 10.2 % nitrate removal, 3.3 times higher than the control. It reduced the sludge volume index (SVI) from 84.7 to 28.4 mL/g by promoting compact floc formation through extracellular polymeric substance (EPS) protein conformational changes and enhanced microbe-particle interactions. It also increased bio-capacitance of the sludge and achieved a 77.0 % increase in electron transport system activity (ETSA). Surface analysis confirmed that magnetite served as a passive electron mediator rather than actively participating in redox cycling. Metagenomic sequencing further demonstrated the selective enrichment of denitrifying and magnetotactic bacteria and enrichment of key nitrogen metabolism genes (narG, nirK, narK, narH). Validation in an anaerobic-anoxic-aerobic (AAO) reactor treating real municipal wastewater achieved NH4[+]-N and total nitrogen removal efficiencies of 98.7 % and 73.6 %, respectively, meeting stringent discharge limits. These results identify saturation magnetization as a critical parameter for selecting or engineering magnetite materials and provide mechanistic insights and engineering guidance for deploying MEAS as an efficient, retrofit-friendly technology for WWTP upgrading.},
}

@article {pmid41586525,
year = {2026},
author = {Díaz-González, F and Rojas-Villalobos, C and Issotta, F and Reyes-Impellizzeri, S and Hedrich, S and Johnson, DB and Temporetti, P and Quatrini, R},
title = {Trait-based meta-analysis of microbial guilds in the iron redox cycle.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0148825},
doi = {10.1128/msystems.01488-25},
pmid = {41586525},
issn = {2379-5077},
abstract = {UNLABELLED: Microbial iron (Fe) redox cycling underpins key biogeochemical processes, yet the functional diversity, ecological roles, and trait architectures of iron-transforming microbes remain poorly synthesized across global environments. Here, we present a systematic review and trait-based meta-analysis of 387 microbial taxa spanning 314 studies and 76 years of research, integrating phenotypic, genomic, and environmental data to define ecologically coherent microbial iron redox cycle guilds. Rather than relying on taxonomy, our framework delineates first-order functional guilds-Fe(III) reducers, Fe(II) oxidizers, and dual-capacity Fe oxidizers/reducers-and resolves second-order guilds based on trait syndromes, such as acidophily, redox flexibility, or metabolic breadth. Trait profiling revealed that iron-cycling capacities frequently transcend phylogenetic boundaries, with multiple guilds converging in chemically stratified hotspots like hot springs, hydrothermal vents, and acid mine drainages. Dual-capacity Fe oxidizers/reducers (e.g., Acidithiobacillus ferrooxidans and Metallosphaera sedula) emerged as overlooked mediators of "cryptic" iron cycling, possessing genomic repertoires capable of toggling between oxidative and reductive modes in response to redox oscillations. Hierarchical clustering and kernel density analyses of ecophysiological traits highlighted niche partitioning along key environmental filters, including pH, iron availability, salinity, and temperature. Collectively, this work introduces the Guild Exploitation Pattern as a conceptual lens for understanding iron microbiome assembly, providing a data-driven foundation for predicting microbial contributions to iron cycling under changing environmental conditions.

IMPORTANCE: Iron redox reactions shape nutrient turnover, contaminant mobility, and primary productivity, yet the microbes driving these processes are often studied in isolation. By integrating decades of data into a trait-based guild framework, we reveal the ecophysiological diversity and niche differentiation of microbial iron redox cycling taxa across environments. Our synthesis exposes major gaps, such as limited trait data for >80% of dual-capacity Fe oxidizing/reducing species and highlights the need for functional trait surveys to complement metagenomics and cultivation efforts. The guild framework presented here advances predictive microbial ecology by linking metabolic traits with environmental gradients, offering a robust foundation for incorporating iron cycling into ecosystem models and biogeochemical forecasts.},
}

@article {pmid41586521,
year = {2026},
author = {Wang, N and Liu, Q and Huo, F and Zhang, S and Lv, S and Mi, T and Liu, H},
title = {Intestinal epithelial Tet2 deficiency reprograms the gut microbiota through bile acid metabolic alterations.},
journal = {mBio},
volume = {},
number = {},
pages = {e0356225},
doi = {10.1128/mbio.03562-25},
pmid = {41586521},
issn = {2150-7511},
abstract = {Epigenetic mechanisms are increasingly recognized as critical regulators of host-microbiota interactions, yet their specific roles in gut homeostasis remain elusive. Here, we demonstrate that intestinal epithelial-specific deletion of the DNA demethylase Tet2 leads to structural abnormalities, impaired barrier function, and remarkable reprogramming of the gut microbiota. Mechanistically, Tet2 deficiency downregulated the apical sodium-dependent bile acid transporter ASBT/Slc10a2, resulting in altered bile acid homeostasis with luminal accumulation of hyocholic acid (HCA). This metabolic shift created a favorable niche for the selective expansion of bile salt hydrolase (BSH)-expressing Lactobacillus species. Furthermore, we identified an age-dependent regulatory role of HCA, which promoted Lactobacillus in young mice but enriched Akkermansia in aged animals. Our findings establish an epigenetic-metabolic-microbial axis centered on Tet2-mediated bile acid regulation, providing new insights into how host epigenetic factors shape the gut microbial ecosystem in an age-sensitive manner.IMPORTANCEWhile the gut microbiota is known to influence host physiology, the molecular mechanisms by which the host epigenetically regulates microbial composition remain largely unexplored. Our work reveals that the epigenetic enzyme Tet2 in intestinal epithelial cells acts as a master regulator of gut microbial ecology by modulating bile acid metabolism. The discovery that Tet2 deletion drives hyocholic acid (HCA) accumulation-which exerts age-dependent effects on Lactobacillus and Akkermansia-provides a novel principle for understanding host-microbe interactions across the lifespan. By linking epithelial DNA demethylation to bile acid transport and microbial phenotype, we establish a previously unrecognized Tet2-ASBT-HCA pathway that expands the conceptual framework for microbiota research. These insights open new avenues for therapeutic interventions aimed at reversing microbial dysbiosis through epigenetic or metabolic modulation.},
}

@article {pmid41586352,
year = {2025},
author = {Pandey, A and Dhakar, K},
title = {Extreme thermal environments: reservoirs of industrially important thermozymes.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1739143},
pmid = {41586352},
issn = {1664-302X},
abstract = {Extreme thermal environments, both natural (e.g., hot springs, fumaroles, geysers, mud pots, deep-sea hydrothermal vents) and man-made (e.g., compost heaps, sawdust, coal refuse piles), are rich sources of thermophilic microorganisms, including Bacteria and Archaea. These organisms possess unique adaptations that allow survival and metabolic activity at elevated temperatures, making them valuable sources of thermostable and thermoactive enzymes. This review synthesizes current knowledge on thermophiles, including their phylogeny, adaptation mechanisms, and cultivation strategies. We discuss the industrial applications of thermozymes, such as DNA polymerases and other thermostable enzymes, and highlight the role of genomics, systems biology, and bioinformatics in accelerating enzyme discovery. The review also addresses the astrobiological relevance of thermophiles as models for life in extreme extraterrestrial environments and emphasizes the importance of conservation and sustainable use of natural thermal habitats. Collectively, this overview provides a comprehensive perspective on the ecological, biotechnological, and fundamental research significance of thermophiles and their enzymes.},
}

@article {pmid41584899,
year = {2026},
author = {Zhou, H and Li, L and Gong, Y and Liu, H and Wu, H and Bravo, A and Soberón, M and Zheng, J and Peng, D and Sun, B and Sun, M},
title = {Geographic and seasonal variation of culturable bacteria associated with the diseased silkworm (Bombyx mori).},
journal = {Current research in microbial sciences},
volume = {10},
number = {},
pages = {100529},
pmid = {41584899},
issn = {2666-5174},
abstract = {The domesticated silkworm, Bombyx mori, is critically impacted by bacterial pathogens, yet the environmental and ecological drivers of their spatiotemporal dynamics remain poorly defined. In this study, 514 bacterial strains were isolated from diseased and healthy silkworm larvae across major sericultural regions in China. Through 16S rRNA gene sequencing and multi-tier pathogenicity assays, 51 isolates were identified as potential novel insect pathogens. Fulfilling Koch's postulates via oral infection tests, the pathogenicity of nine strains belonging to the genera Raoultella, Stenotrophomonas, and Citrobacter were confirmed, while the remaining isolates are considered putative pathogens. All isolates were classified into 33 genera within the phyla Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes, with Enterobacter, Bacillus, and Serratia being the most prevalent. Multivariate analysis indicated that geographic and climatic factors-specifically distance from the coastline and key thermal and radiative variables-collectively explained a significant though modest portion of the variance in bacterial community composition. Bacterial diversity correlated positively with cocoon yield. Guangxi presented the highest potential pathogen diversity and co-infection frequency, aligning with its intensive sericulture practices. Seasonal analyses indicated higher bacterial abundance and virulence in spring-summer compared to summer-autumn. Many isolates are taxonomically affiliated with genera containing insect gut microbiota, plant-associated bacteria, and human (opportunistic) pathogens, suggesting diverse environmental and anthropogenic origin. The detection of bacteria related to mulberry phyllosphere microbes underscore the role of host plant ecology in shaping the silkworm microbiome. These findings illuminate the ecological drivers of silkworm-associated bacterial communities and highlight the complex microbial connections within sericulture ecosystems, suggesting potential pathways relevant to a One Health perspective. Furthermore, the repository of 514 identified bacterial isolates from the model lepidopteran B. mori here provides a valuable resources for exploring novel biocontrol agents against other lepidopteran pests.},
}

@article {pmid41584691,
year = {2026},
author = {Forte, L and Parabita, N and Santoro, M and Longobardi, F and Natrella, G and Quiñones, J and Ponnampalam, EN and Tomasevic, I and De Palo, P and Maggiolino, A},
title = {From rumen to milk: Dietary polyphenols in dairy cows-A critical review.},
journal = {Veterinary and animal science},
volume = {31},
number = {},
pages = {100569},
pmid = {41584691},
issn = {2451-943X},
abstract = {Polyphenols represent a large and structurally diverse family of plant secondary metabolites with bioactive properties. In ruminants, these compounds can influence rumen fermentation, microbial ecology, and nutrient metabolism, offering potential benefits for animal health, productivity, and environmental sustainability. This review synthesizes evidence on the fate of dietary polyphenols in dairy cows from ingestion to their possible secretion into milk. It outlines the main dietary sources and classes of polyphenols, their microbial biotransformations in the rumen, and subsequent host metabolism involving absorption, conjugation, and systemic circulation. Particular attention is given to the mechanisms of mammary uptake and secretion, where most compounds appear as conjugated metabolites such as glucuronides, sulfates, and urolithins rather than parent forms. Although the transfer efficiency from feed to milk is typically low, consistent detection of isoflavone derivatives, phenyl-γ-valerolactones, urolithins, and hippuric acid demonstrates the feasibility of diet-to-milk modulation. Factors affecting bioavailability and transfer include polyphenol structure, dietary matrix, dose, rumen microbiota composition, animal physiology, and feed processing. Advances in high-resolution analytical techniques have improved the characterization of these low-abundance metabolites, yet large variability among studies persists. In vivo studies indicate that polyphenol-derived metabolites in bovine milk occur at low ng/mL to low µg/mL levels, with compounds such as equol, enterolactone, urolithins, phenyl-γ-valerolactones and phenolic acids typically detected in the sub-micromolar range. Overall, dietary polyphenols offer promising opportunities to improve ruminant health and produce milk with enhanced functional quality, but quantitative and mechanistic research is still required to optimize feeding strategies and understand their contribution to milk bioactivity.},
}

@article {pmid41584621,
year = {2026},
author = {Garcia-Rodriguez, AF and Moreno-Racero, FJ and Álvarez, R and Colmenero-Flores, JM and Knicker, H and Rosales, MA},
title = {Biochar enhances nitrogen use efficiency in lettuce by promoting its metabolic assimilation.},
journal = {Plant and soil},
volume = {518},
number = {1},
pages = {299-317},
pmid = {41584621},
issn = {0032-079X},
abstract = {BACKGROUND AND AIMS: Peat replacement with biochar (BC) offers a sustainable strategy in horticultural substrates but its effects on plant nitrogen (N) metabolism and N use efficiency (NUE) remain unclear. This study tested whether vineyard-pruning-derived BC can boost NUE and metabolic activity in lettuce, providing a pathway toward more productive and sustainable horticulture.

METHODS: Plant substrates (BC, peat and vermiculite) were prepared in the following proportions (v:v:v): B0 (0:70:30), B15 (15:55:30) and B30 (30:40:30) for growing lettuce (Lactuca sativa L. var. Batavia) under greenhouse conditions for 31 days. We assessed plant growth and physiological traits, quantified N species and calculated NUE parameters and the activities of key N assimilation enzymes.

RESULTS: B30 plants produced 44.2% more biomass and 23.2% larger leaf area than B0, resulting in lower specific leaf area and greater succulence. BC addition decreased available NO₃⁻ and NH₄⁺ in substrate and roots without causing any plant stress symptoms, as chlorophyll content and PSII efficiency remained stable. B30 increased N uptake flux, N utilization efficiency, partial N balance, and N productivity by 31.8%, 34.8%, 27.8%, and 13.8%, respectively, relative to B0, coinciding with enhanced N-assimilation enzymatic activity. Despite lower total N in roots and shoots, protein accumulation increased, indicating more efficient N conversion into organic compounds.

CONCLUSION: These findings demonstrate the potential of BC-based substrates (especially 30% BC) to enhance lettuce productivity by improving NUE through the stimulation of N assimilation pathway, offering a promising strategy to optimize N-fertilizer needs to support more sustainable agriculture and soil management practices.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11104-025-07997-0.},
}

@article {pmid41582111,
year = {2026},
author = {Afonso, AC and Botting, J and Simões, M and Simões, L and Liu, J and Saavedra, MJ},
title = {Ultrastructure Analysis by Cryo-Electron Tomography Revealed Mesosomes in the Gram-negative Delftia Acidovorans.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02698-2},
pmid = {41582111},
issn = {1432-184X},
abstract = {Delftia acidovorans, a Gram-negative bacterium commonly found in diverse environments, can occasionally cause infections in immunocompromised individuals. Despite its environmental prevalence and clinical relevance, there is a notable lack of studies on the cellular ultrastructure of D. acidovorans. Characterizing this aspect is essential for understanding the bacterium aggregation behavior, which significantly influences biofilm formation, environmental adaptability, and potential pathogenicity in clinical contexts. This study employs cryo-electron tomography to investigate the cellular ultrastructure of Delftia acidovorans. Our observations of D. acidovorans revealed a supercoiling pattern in flagellar filaments and diverse outer membrane projections. Our major finding was the observation of cytoplasmic membrane invaginations resembling mesosomes seen in Gram-positive bacteria, offering new insights into the cellular architecture and potential functions of these structures in Gram-negative bacteria. Together, these ultrastructural insights reveal adaptations potentially linked to environmental persistence and interspecies aggregation.},
}

@article {pmid41579275,
year = {2026},
author = {Sasaki, K and Emoto, S and Yokoyama, Y and Ishihara, S},
title = {Circulating tumor DNA methylation and gut microbiota in colorectal cancer: diagnostic, prognostic, and therapeutic implications.},
journal = {International journal of clinical oncology},
volume = {},
number = {},
pages = {},
pmid = {41579275},
issn = {1437-7772},
abstract = {Colorectal cancer remains one of the leading causes of cancer-related mortality worldwide, and early detection is essential for improving outcomes. Advances in liquid biopsy technologies and microbiota research have shed new light on diagnostic and therapeutic strategies for colorectal cancer. Notably, circulating tumor DNA methylation has emerged as a sensitive and specific biomarker for early detection, recurrence surveillance, and treatment monitoring. Recent progress in methylation-based assays, including stool- and plasma-derived approaches, highlights their potential clinical utility; however, challenges remain in detecting minimal residual disease at the earliest stages. Parallel to these developments, the gut microbiota has been recognized as a critical modulator of colorectal carcinogenesis and treatment response. Specific bacterial species, such as Fusobacterium nucleatum, polyketide synthase-positive Escherichia coli, and enterotoxigenic Bacteroides fragilis, have been implicated in tumor initiation and progression through epigenetic reprogramming, including aberrant DNA methylation. Microbial metabolites, particularly short-chain fatty acids such as butyrate, influence DNA methyltransferase activity and histone modifications, linking microbial ecology to the host epigenome. Microbiota composition also affects responses to chemotherapy, radiotherapy, and immunotherapy, underscoring its potential as a predictive biomarker and therapeutic target. Integrating circulating tumor DNA methylation profiling with microbiota analysis provides a promising strategy for personalized colorectal cancer management, combining early detection with treatment outcome prediction. This review summarizes the current evidence and future directions at the interface of DNA methylation and the gut microbiota, emphasizing their synergistic role as composite biomarkers in precision oncology.},
}

@article {pmid41576057,
year = {2026},
author = {Lagneaux, P and Widjaja, N and Lagneaux, B and Nguyen, TKC and Licandro, H and Winckler, P and Waché, Y},
title = {Optical photothermal infrared (OPTIR) spectroscopy assisted by machine learning for lactic acid bacteria identification at strain level.},
journal = {The Analyst},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5an01093d},
pmid = {41576057},
issn = {1364-5528},
abstract = {Lactic acid bacteria (LAB) are widely used in food, health, and biotechnology sectors, where accurate strain level identification is critical. Conventional methods, such as 16S rRNA sequencing, PCR-based fingerprinting (RAPD, AFLP), and MALDI-TOF mass spectrometry are powerful tools to identify bacteria at species level but often fail to resolve closely related strains due to limited taxonomic resolution, protocol sensitivity, or database dependence. In this study, we evaluated the capacity of Optical photothermal infrared (OPTIR) spectroscopy, a single-cell vibrational imaging technique, combined with supervised neural networks, to classify LAB at both species and strain levels. A total of 13 strains were analysed, including five Lactiplantibacillus plantarum, one Lactiplantibacillus pentosus, one Limosilactobacillus fermentum, three Lacticaseibacillus casei/paracasei, and three Streptococcus thermophilus, covering both intra- and inter-species diversity. Spectral data from LAB were acquired using a mIRage LS OPTIR system, preprocessed, and used to train a fully connected neural network for each level. The models achieved macro F1-scores of 97% for species level and 91% for strain level classification. These results demonstrate the potential of OPTIR, when integrated with machine learning, as a robust tool for high-resolution bacterial classification, with promising applications in microbiological quality control, probiotic selection, and microbial ecology.},
}

@article {pmid41575584,
year = {2026},
author = {Ma, Y and Xu, Q and Sun, F and Wang, X and Zhou, W and Yue, M and Gao, L and Li, W},
title = {Potassium-Solubilizing Bacteria Mediate Light-Potassium Synergy to Enable Native Pueraria lobata to Outcompete Invasive Mikania micrantha.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02695-5},
pmid = {41575584},
issn = {1432-184X},
support = {2022A1515011169//National Natural Science Foundation of China-Guangdong Joint Fund/ ; 2023S017084//Guangdong Province Science and Technology Innovation Strategic Special Project/ ; 2022s037//the Maoming City Science and Technology Plan Project/ ; 32172430//National Natural Science Foundation of China/ ; },
abstract = {The invasive vine Mikania micrantha H. B. K. poses severe threats to biodiversity and ecosystem stability in tropical and subtropical regions, calling for sustainable ecological approaches. This study explores how the native legume Pueraria lobata var. thomsonii Benth displaces M. micrantha in the field, with a focus on the synergistic roles of light capture advantage and rhizosphere potassium (K) dynamics driven by specialized bacteria. In competitive ecotones, P. lobata demonstrated superior growth and photosynthetic performance relative to M. micrantha. Its main stem length was 1.31 times greater, while net photosynthetic rate, stomatal conductance, and chlorophyll content were 80%, 110.7%, and 21.4% higher, respectively. Soils associated with P. lobata contained significantly higher available K, correlated with enhanced enzyme activities, indicating a "microbe-enzyme-K" activation cascade. P. lobata specifically enriched efficient potassium‑solubilizing bacteria (KSB), such as Pseudomonas and Acinetobacter. Isolated KSB strains exhibited K‑solubilizing and plant‑growth‑promoting capacities and increased the competitive balance index of P. lobata in inoculation assays. Partial least‑squares discriminant analysis confirmed that KSB‑mediated K mobilization boosted stem elongation primarily by improving photosynthetic potassium use efficiency (PKUE), forming a reinforcing "light-K-microbe" loop that drives competitive displacement. This work establishes a "microbe‑mediated invasion suppression" framework, demonstrating how a native plant can couple superior light‑use efficiency with a specialized rhizosphere microbiome to outcompete an invasive species. We propose that managing potassium‑solubilizing microbiomes offers a sustainable strategy for ecological restoration in K‑limited ecosystems.},
}

@article {pmid41574941,
year = {2026},
author = {Lhoste, E and David, J and Ponsin, V and Maikel, R and Lazar, CS},
title = {Seasons and vertical dynamics influence community composition in a flooded and abandoned mica mine.},
journal = {FEMS microbiology ecology},
volume = {102},
number = {2},
pages = {},
pmid = {41574941},
issn = {1574-6941},
abstract = {Artificial lakes formed from past mining activities represent unique but underexplored ecosystems that support diverse microbial communities. This study examined how seasonal variation and depth influence bacterial, archaeal, and micro-eukaryotic assemblages in the stratified water column of the Blackburn Mine (Outaouais, Quebec, Canada). Water and biofilm samples were collected by technical divers from the surface to 52 m during spring, summer, and autumn of 2021-2022, and analyzed by 16S/18S rRNA gene sequencing. Seasonal changes had little effect on physicochemical parameters but strongly shaped microbial community composition, together with depth. Archaeal taxa displayed greater stability across depths compared to bacteria and eukaryotes. Oxygen profiles defined three ecological zones: an oxic layer dominated by Actinobacteria and the methanogen Methanosarcina; a transition zone enriched in Chlorobium and methanogens such as Methanospirillum and Methanosaeta; and an anoxic layer containing sulfur-reducing (Desulfomonile, Desulfobacca), sulfur-oxidizing (Sulfuricurvum), and methane-cycling archaea. Eukaryotic communities included algae, particularly Chrysophyceae, and diverse protists. These findings suggest that microbial communities in the mine are integral to sulfur and carbon cycling, emphasizing the ecological significance of such stratified, mining-associated aquatic systems. The Blackburn mine provides valuable insight into how anthropogenic legacies shape microbial diversity and ecosystem functioning in artificial aquatic environments.},
}

@article {pmid41571998,
year = {2026},
author = {Cheng, C and Bennett, BD and Savalia, P and Asrari, H and Biel, C and Evans, KA and Tang, R and Thrash, JC},
title = {Cell cycle dysregulation of globally important SAR11 bacteria resulting from environmental perturbation.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41571998},
issn = {2058-5276},
support = {Investigator in Aquatic Microbial Ecology Award//Simons Foundation/ ; Early Career Investigator in Marine Microbial Ecology and Evolution Award//Simons Foundation/ ; },
abstract = {Genome streamlining is hypothesized to occur in bacteria as an adaptation to resource-limited environments but can result in gene losses affecting fundamental aspects of cellular physiology. The most abundant marine microorganisms, SAR11 (order Pelagibacterales), exhibit canonical genome streamlining, but the consequences of this genotype on core cellular processes such as cell division remain unexplored. Here, analysis of 470 SAR11 genomes revealed widespread absence of key cell cycle control genes. Growth experiments demonstrated that although SAR11 bacteria maintain a normal cell cycle under oligotrophic conditions, they exhibit growth inhibition and aneuploidy when exposed to nutrient enrichment, carbon source shifts or temperature stress. Detailed growth measurements and antibiotic inhibition experiments showed that these phenotypes resulted from cell division disruption with continuing DNA replication, leading to heterogeneous subpopulations of normal and polyploid cells. This vulnerability raises questions about microbial genome evolution and the evolutionary trade-offs between adaptation to stable nutrient-limited conditions and physiological resilience.},
}

@article {pmid41571114,
year = {2026},
author = {Han, H and Wang, S and Zhou, L and Li, S and Huang, J and Peng, X},
title = {Insights into impact of tire additives on activated sludge systems: Treatment performance, extracellular polymeric substances, and microbial community.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134049},
doi = {10.1016/j.biortech.2026.134049},
pmid = {41571114},
issn = {1873-2976},
abstract = {This study systematically investigated the impacts of seven common tire additives (TAs) and their derivatives on the performance and microbial ecology of an activated sludge system exposed to environmental concentrations (0.2-20.0 μg/L) over 160 days. While most individual TAs showed minimal effects, the mixture of TAs (MIX) and 2-((4-Methylpentan-2-yl)amino)-5-(phenylamino)cyclohexa-2,5-diene-1,4-dione (6PPD-Q) significantly inhibited nitrogen removal efficiency. At 20.0 μg/L, the abundances of key nitrification and denitrification genes (amoA, nirK, nirS, nosZ) were markedly suppressed, leading to reductions in NH4[+]-N (12-14%) and total nitrogen (18-23%) removal efficiencies. The impairment was associated with elevated oxidative stress level, as indicated by a sharp increase in reactive oxygen species (0.9-1.1 fold) and lactate dehydrogenase (1.5-2.1 fold) release, alongside suppressed adenosine triphosphate (ATP) synthesis. Concurrently, sludge settleability deteriorated and mixed liquor volatile suspended solids (MLVSS) decreased, which correlated with reduced sludge hydrophobicity and enhanced hydrogen bond intensity (3435 cm[-1]). Microbial community restructuring was observed, with tolerant genera (e.g., Comamonadaceae, Rhodobacteraceae) increasing, while key nitrogen-removing genera (e.g., Nitrosomonas, Thauera) decreased. Three-dimensional fluorescence spectroscopy analysis revealed a decline in tryptophan and tyrosine like proteins in tightly bound extracellular polymeric substances. Molecular docking demonstrated that 6PPD-Q exhibited the strongest binding affinity to tryptophan and tyrosine synthases, suggesting a high potential for enzymatic interference even at low concentrations. This study demonstrated that MIX and 6PPD-Q, at environmental concentrations, significantly affect activated sludge systems and investigated the mechanisms involved, thereby providing important evidence for the ecological risk assessment of such pollutants during wastewater treatment.},
}

@article {pmid41570927,
year = {2026},
author = {Magalhães, AP and Jorge, P and Neiva, J and Sousa, AM and Cerca, N and Pereira, MO},
title = {Contribution of viable but non culturable cells and small colony variants in antibiotic insusceptibility and therapeutic failure against S. aureus and P. aeruginosa biofilm co-infections.},
journal = {Microbial pathogenesis},
volume = {212},
number = {},
pages = {108312},
doi = {10.1016/j.micpath.2026.108312},
pmid = {41570927},
issn = {1096-1208},
abstract = {P. aeruginosa and S. aureus are often co-isolated from biofilm-associated infections, such as those afflicting cystic fibrosis (CF) patients. Biofilms, along with the interspecies interactions, play a significant role in fostering antibiotic insusceptibility, contributing to infection chronicity. Previously, we showed that S. aureus adopts a viable but non-culturable (VBNC) state in biofilms with P. aeruginosa. Here, we aimed to gain insight into the impact of VBNC and phenomena such as phenotypic switching on antimicrobial treatment and vice-versa. Single- and dual-species biofilms of two isolates from each species were characterised in terms of viability, culturability, clonal diversification, and pathogenic potential, upon treatment with ciprofloxacin and vancomycin. Data show that S. aureus became less susceptible to antibiotics in its VBNC state induced by P. aeruginosa and by the treatments. P. aeruginosa's susceptibility to ciprofloxacin diminished in dual-species biofilms, suggesting mutual benefits. Following treatment, S. aureus persisted as VBNC in the dual-species biofilm and its tolerance to ciprofloxacin endured after planktonic regrowth. P. aeruginosa triggered S. aureus's small colony variants (SCV), but P. aeruginosa's rugose SCV probably explains S. aureus's protection due to enhanced biofilm formation. This work sheds light on P. aeruginosa and S. aureus' co-increased tolerance to antibiotics, with cooperative interactions, phenotypic diversification, and VBNC underpinning this and the persistence of S. aureus within P. aeruginosa biofilms. This work is the first relating S. aureus's decreased susceptibility in dual-species biofilms to its VBNC state. Findings highlight the importance of microbial ecology, viability and colony morphotyping studies when designing treatments for multispecies infections.},
}

@article {pmid41568955,
year = {2026},
author = {Baborski, A and Rohland, O and Wuenschmann, T and Bauer, M and Allen, RJ and Busch, A},
title = {Biofilm-derived bile duct microbiota in liver transplantation: high-quality genomes of Klebsiella pneumoniae, Enterococcus faecalis, and Enterococcus faecium.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0088625},
doi = {10.1128/mra.00886-25},
pmid = {41568955},
issn = {2576-098X},
abstract = {We present draft genomes of Klebsiella pneumoniae (K. pneumoniae), Enterococcus faecalis (E. faecalis), and Enterococcus faecium (E. faecium) isolated from a bilioenteric catheter after liver transplantation. Genome sizes were 5.58 Mb, 2.95 Mb, and 2.78 Mb, with G+C contents of 57.25%, 37.6%, and 37.99%, respectively, highlighting biofilm-associated bile duct colonizers.},
}

@article {pmid41568039,
year = {2025},
author = {Dong, W and Chen, S and Hu, Y},
title = {Editorial: Diversity, function, and application of microbes in the fermentation or production of traditional food.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1751159},
doi = {10.3389/fmicb.2025.1751159},
pmid = {41568039},
issn = {1664-302X},
}

@article {pmid41567175,
year = {2026},
author = {Hussain, N and Ramadan, A and Al Haddad, AHI and Alfahl, Z},
title = {A Review of Emerging Biomarkers Connecting Diabetes and Ischemic Stroke: Implications for Early Detection and Risk Stratification.},
journal = {Journal of diabetes research},
volume = {2026},
number = {},
pages = {2719491},
pmid = {41567175},
issn = {2314-6753},
mesh = {Humans ; *Biomarkers/blood ; *Ischemic Stroke/diagnosis/blood/genetics ; Early Diagnosis ; Risk Assessment ; Risk Factors ; *Diabetes Mellitus/blood/diagnosis/genetics ; },
abstract = {Diabetes substantially increases the risk of ischemic stroke through complex metabolic, inflammatory, and vascular mechanisms, yet early identification of high-risk individuals remains challenging. This narrative review synthesizes emerging circulating and genomic biomarkers that illuminate the pathways linking diabetes and ischemic stroke and evaluates their potential for early detection and precise risk stratification. Systematic searches of PubMed, Scopus, and Web of Science identified 141 relevant studies examining biomarkers, genetic and epigenetic factors, or risk prediction models in adults with diabetes. Evidence highlights several biomarker domains. Inflammatory markers such as high-sensitivity C-reactive protein, interleukin-6, and tumor necrosis factor-α indicate immune activation driving atherogenesis and plaque instability. Endothelial markers, including endothelin-1, soluble vascular cell adhesion molecule-1, and asymmetric dimethylarginine, reflect endothelial dysfunction and a prothrombotic state. Metabolic indicators, notably glycated hemoglobin, adipokines, and lipoprotein(a), capture cumulative glycemic burden, adipose signaling, and inherited atherothrombotic risk. Genetic and epigenetic measures, including polygenic risk scores, microRNAs, long noncoding RNAs, and DNA methylation, quantify inherited susceptibility and molecular imprints of the diabetic environment. Renal markers such as albuminuria and reduced eGFR reflect microvascular injury and consistently associate with stroke risk. Multimarker panels and multi-omics integration using machine learning approaches show promise for improving predictive accuracy, though standardization, external validation, and demonstration of clinical utility are needed. Integrating these biomarkers with established clinical risk factors could transform stroke prevention in diabetes from reactive to proactive, enabling personalized, mechanism-informed strategies for early detection and risk stratification.},
}

Humans
*Biomarkers/blood
*Ischemic Stroke/diagnosis/blood/genetics
Early Diagnosis
Risk Assessment
Risk Factors
*Diabetes Mellitus/blood/diagnosis/genetics

@article {pmid41566387,
year = {2026},
author = {Xu, M and Chen, S and Pei, H and Hu, L and Zhang, Y},
title = {Engineering bacteriophages for gut health: precision antimicrobials and beyond.},
journal = {Journal of nanobiotechnology},
volume = {24},
number = {1},
pages = {62},
pmid = {41566387},
issn = {1477-3155},
support = {12275192//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Bacteriophages/genetics ; Phage Therapy/methods ; *Gastrointestinal Microbiome/drug effects ; Animals ; Precision Medicine ; *Anti-Infective Agents/pharmacology ; Inflammatory Bowel Diseases/therapy/microbiology ; Colorectal Neoplasms/therapy/microbiology ; },
abstract = {Engineered bacteriophages are emerging as a promising class of precision antimicrobials at a time when gastrointestinal diseases are increasingly linked to microbial dysbiosis, antibiotic resistance, and disruptions in host-microbe interactions. Conventional antibiotics often provide limited benefit in these settings because they lack selectivity and fail to restore microbial ecology. Advances in synthetic biology and nanotechnology have made it possible to redesign phages with enhanced specificity, expanded functionality, and improved stability, positioning them as versatile tools for microbiota-centered therapies. This review summarizes the major engineering approaches, and examines their applications in inflammatory bowel disease (IBD), colorectal cancer (CRC), and infectious enteritis. Key mechanistic insights into pathogen targeting, immune modulation, and barrier protection are highlighted. Remaining challenges, such as ensuring long-term stability, avoiding resistance development, and enabling scalable manufacturing, are discussed together with emerging interdisciplinary strategies that may advance the clinical translation of personalized phage therapies.},
}

Humans
*Bacteriophages/genetics
Phage Therapy/methods
*Gastrointestinal Microbiome/drug effects
Animals
Precision Medicine
*Anti-Infective Agents/pharmacology
Inflammatory Bowel Diseases/therapy/microbiology
Colorectal Neoplasms/therapy/microbiology

@article {pmid41565754,
year = {2026},
author = {Solís-Marín, FA and Vergara-Ovando, C and Rojas-Oropeza, M and Calderón-Gutiérrez, F and Medina-Tanco, G and Cabirol, N},
title = {Asterinides sp. an endemic stygobitic seastar from an anchialine cave and its interactions among prokaryotic communities.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-36065-5},
pmid = {41565754},
issn = {2045-2322},
support = {PAPIIT-IN207021//Dirección General de Asuntos del Personal Académico, Universidad Nacional Autónoma de México/ ; PAPIIT-IN207021//Dirección General de Asuntos del Personal Académico, Universidad Nacional Autónoma de México/ ; Posgraduate grant//Universidad Nacional Autónoma de México/ ; },
abstract = {Anchialine caves house a vast variety of organisms that support complex ecological relationships among themselves and their environment. The following study was made in the anchialine karst cave El Aerolito, found on Cozumel Island, Quintana Roo, Mexico. It explores the relationship between wall microbial mats and the diet of Asterinides sp., an endemic stygobitic seastar. Wall microbial mats inside the cave were sampled and the stomach microbiome of Asterinides sp. was obtained through regurgitation. Asterinides sp. sampling was made through the Catcher Collection Chamber (CCC), an innovative technology for the exploration of these ecosystems. The obtained results suggest that microbial mats are part of the diet of Asterinides sp. The following results highlight the potential relevance of the microbial communities inside the trophic chain present in El Aerolito. Additionally, the methodology presented here provides a useful framework for future ecological research in El Aerolito cave.},
}

@article {pmid41563471,
year = {2026},
author = {Luo, W and Liu, P and Qiu, Y and Li, M and Huang, Y},
title = {Diversity and Functional Analysis of Epiphytic and Endophytic Bacteria in Three Different Parts of Brasenia Schreberi.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02688-w},
pmid = {41563471},
issn = {1432-184X},
support = {24XJQN04//Nanchang Normal University 2024 Youth Science and Technology Talent Training Project/ ; NSBSJJ2023003//Nanchang Normal University Doctoral Research Start-up Fund/ ; 24FZZX13//Nanchang Normal University Funds for Improvement and Research/ ; },
}

@article {pmid41563055,
year = {2026},
author = {Sadiq, S and Xue, P and Tang, Y and Du, M and Van Brussel, K and McBratney, AB and Holmes, EC and Minasny, B},
title = {Limited effect of short- to mid-term storage conditions on an Australian farmland soil RNA virome.},
journal = {Journal of virology},
volume = {},
number = {},
pages = {e0145925},
doi = {10.1128/jvi.01459-25},
pmid = {41563055},
issn = {1098-5514},
abstract = {Soils represent one of the largest and most diverse reservoirs of microbial life on Earth, yet their associated RNA viruses remain underexplored compared to animal and aquatic systems. Viral discovery in soils has been further limited by technical hurdles, particularly difficulties in obtaining sufficient yields of high-quality RNA for sequencing. To address this, we evaluated a range of storage and preservation strategies, including the use of commercial preservative solutions and ultra-cold snap-freezing, followed by standardized RNA extraction, sequencing, and virus discovery pipelines. This work aimed to establish minimum sample storage requirements that maintain RNA integrity, generate sufficient RNA sequencing data, and subsequently enable reliable soil virome characterization. While no preservative solution proved effective, "neat" soil samples were stable at 2°C-8°C and -30°C for at least 2 weeks, and at -80°C for at least 3 months, with no measurable reduction in RNA quality, sequencing data, or viral abundance and diversity. From 32 resulting libraries, we identified 1,475 putative novel RNA viruses, with the majority belonging to the microbe-associated phylum Lenarviricota. Several novel viruses formed divergent clusters with other environmentally derived sequences distantly related to traditionally animal-associated families, such as the Astroviridae and Picornaviridae. Furthermore, unique clusters within the Picobirnaviridae, Alsuvirucetes, Ghabrivirales, and Amabiliviricetes comprised exclusively Australian viruses, suggesting instances of region-specific evolution. Together, these findings highlight soils as rich reservoirs of RNA viral diversity and provide practical minimum standards for storage, expanding opportunities to investigate the ecological and evolutionary roles of RNA viruses in terrestrial systems.IMPORTANCERNA viruses are the most abundant and diverse biological entities on Earth and are likely present in all other organisms and ecosystems, including soil-dwelling invertebrates, microbes, and plants. Despite this, their diversity and role in soil systems remain largely unknown. Methodological challenges in preserving and extracting sufficient quantities of RNA from soils have hindered the study of these communities. Here, we identified 1,475 previously undescribed RNA viruses in Australian soils while systematically testing different preservation strategies. The significance of our research lies in the demonstration that snap-freezing soil is a viable and robust storage strategy for at least 3 months, while also highlighting the extraordinary scale of viral diversity present in terrestrial environments. This work establishes a foundation for reliable exploration of terrestrial RNA viruses, improving the accessibility of more remote environmental viromes and enabling future efforts to integrate them into broader models of microbial ecology and ecosystem function.},
}

@article {pmid41561919,
year = {2026},
author = {Phyu, KK and Zhi, S and Liang, J and Yang, Z and Zhao, R and Liu, J and Cao, Y and Wang, H and Zhang, K},
title = {Dataset on microbial community structure in response to microalgal cultivation in dairy wastewater.},
journal = {Data in brief},
volume = {64},
number = {},
pages = {112407},
pmid = {41561919},
issn = {2352-3409},
abstract = {This data article describes a comprehensive dataset investigating the dynamics between microalgae, bacteria, and pollutant removal in dairy wastewater treatment. Data was collected from a 12-day laboratory-scale experiment employing three distinct cultivation systems: monoculture, co-culture, and sequential culture of four algal/cyanobacterial strains (Chlorella sorokiniana, Euglena gracilis, Synechocystis sp., and Desertifilum tharense). The generated dataset includes high-frequency measurements of water quality parameters (COD, NH4 [+]-N, TN, TP), algal physiological data (biomass production, total chlorophyll, biochemical compositions like proteins, lipids, and polysaccharides), and 16S rRNA gene sequencing data of the associated bacterial communities, which were fractionated into free-living and tightly bound phycosphere populations. The reuse potential of this data is significant. It provides a detailed profile of microbial community assembly driven by different cultivation strategies and environmental factors, offering a benchmark for future ecological studies in engineered systems. Researchers in the fields of wastewater biotechnology, microbial ecology, and synthetic ecology can reuse this data to validate microbial interaction models, optimize consortia design for bioremediation, and inform life-cycle assessments of algal-based treatment processes. The dataset generated in this study is publicly available in the NCBI BioProject repository under the accession number [PRJNA1265442].},
}

@article {pmid41558125,
year = {2026},
author = {Armstrong, R},
title = {Biocatalytic surfaces in architecture.},
journal = {Current opinion in biotechnology},
volume = {97},
number = {},
pages = {103435},
doi = {10.1016/j.copbio.2025.103435},
pmid = {41558125},
issn = {1879-0429},
abstract = {This review explores the reconceptualisation of microbial colonisation on buildings: from a detrimental process (biofouling) to a source of beneficial, programmable biocatalysis. Strategies for embedding microbial and fungal communities into architectural materials to perform functions such as bioremediation, biomineralisation, and energy generation are explored. The analysis includes the multiscalar design of bioreceptive substrates, engineered living paints, mycelium composites, and probiotic surfaces, which transform passive structures into metabolically active interfaces. These approaches are regarded as Engineered Eco-Ornamentation, where surface design intentionally supports microbial ecology and urban metabolism. The integration of these living systems with computational modelling and digital fabrication to create adaptive building systems is considered. Key challenges include scaling biological processes for architectural application, ensuring long-term material durability, and aligning metabolic activity with practical construction constraints. Addressing these challenges positions functionally designed biocatalytic surfaces as a foundational research field for more regenerative and ecologically integrated architecture.},
}

@article {pmid41557960,
year = {2026},
author = {Machushynets, NV and Terlouw, BR and Zhang, L and Du, C and Al Ayed, K and Schill, J and Trebosc, V and Elsayed, SS and Pieren, M and Liles, MR and Medema, MH and Martin, NI and van Wezel, GP},
title = {Diversification of Tridecaptin Chemical Space via a Chimeric Biosynthetic Pathway in Paenibacillus.},
journal = {Journal of natural products},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jnatprod.5c01298},
pmid = {41557960},
issn = {1520-6025},
abstract = {Paenibacillus species produce a wide array of bioactive nonribosomal peptides (NRPs). The structural diversity of NRPs is shaped by various diversification strategies that support bacterial ecological adaptation and create opportunities for new antibiotic discovery. Here, we show that chimeric biosynthesis occurs within the family of tridecaptin antibiotics. Genome mining revealed that 15 Paenibacillus strains harbored both a full tridecaptin BGC and a stand-alone tridecaptin-like NRPS predicted to encode a truncated decamer. The encoded NRPS domain architectures suggested the capability of these strains to produce multiple tridecaptin variants through collaborative action between this tridecaptin-like NRPS and a second NRPS homologous with TriE encoded within the complete tridecaptin BGC. Indeed, Paenibacillus sp. JJ-1683 produced both tridecaptin A5 and tridecaptin B1, while deletion of triE in the canonical BGC prevented the biosynthesis of all tridecaptins. This provides strong evidence for the existence of chimeric biosynthesis of lipopeptide antibiotics. Bioactivity testing revealed that the synthetic analogue of tridecaptin A5, Oct-TriA5, has unusual broad-spectrum activity against Gram-positive and Gram-negative ESKAPE pathogens, while Oct-TriB1 displays moderate activity against Gram-negative strains and is not active against Gram-positive bacteria. We hypothesize that chimeric biosynthesis is a strategy that enables bacteria to produce compounds with distinct chemistry and bioactivity profiles.},
}

@article {pmid41557197,
year = {2026},
author = {Dos Santos, JFM and Mello, IS and da Cruz, ILS and Soares, MA},
title = {Non-Saccharomyces yeasts contribute to longevity, mitigated protein toxicity, and protection against abiotic stress in Caenorhabditis elegans.},
journal = {Archives of microbiology},
volume = {208},
number = {3},
pages = {128},
pmid = {41557197},
issn = {1432-072X},
support = {445388/2024-2//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; },
mesh = {Animals ; *Caenorhabditis elegans/microbiology/physiology/genetics ; *Longevity ; Caenorhabditis elegans Proteins/genetics/metabolism ; Oxidative Stress ; Probiotics ; *Stress, Physiological ; *Cryptococcus/physiology/isolation & purification ; Amyloid beta-Peptides/toxicity ; *Yeasts/physiology/isolation & purification ; Saccharomyces/physiology/isolation & purification ; DNA-Binding Proteins ; Receptor, Insulin ; Transcription Factors ; },
abstract = {The search for probiotic microorganisms that can be applied beyond gut health has advanced into areas that seek to promote longevity and to prevent neurodegenerative diseases. In this study, we have investigated non-Saccharomyces strains isolated from the Amazon, Cerrado, and Pantanal biomes and evaluated how they affect Caenorhabditis elegans. During our initial screening, based on increased body size and population, we selected eight yeast strains and characterized their cells. Then, we selected three of these strains for in vivo testing. Cryptococcus sp._T038 and Cryptococcus sp._T248 prolonged longevity and reduced the effects of thermal and oxidative stress in C. elegans. Hanseniaspora opuntiae_W164 and Saccharomyces boulardii_SB delayed beta-amyloid-induced paralysis in C. elegans CL4176. The antioxidant genes of the DAF-2/SKN-1 pathway were activated by Cryptococcus_T038 and _T248 and H. opuntiae_W164 in C. elegans strain LD1171 (GCS-1p::GFP) and by Cryptococcus_T038, H. opuntiae_W164, and S. boulardii_SB in C. elegans strain CF1553 (SOD-3p::GFP). These data reinforce that wild yeasts are potential functional probiotics.},
}

Animals
*Caenorhabditis elegans/microbiology/physiology/genetics
*Longevity
Caenorhabditis elegans Proteins/genetics/metabolism
Oxidative Stress
Probiotics
*Stress, Physiological
*Cryptococcus/physiology/isolation & purification
Amyloid beta-Peptides/toxicity
*Yeasts/physiology/isolation & purification
Saccharomyces/physiology/isolation & purification
DNA-Binding Proteins
Receptor, Insulin
Transcription Factors

@article {pmid41554215,
year = {2026},
author = {Mekureyaw, MF and Pandey, C and Sorty, AM and Hennessy, RC and Nicolaisen, MH and Liu, F and Nybroe, O and Roitsch, T},
title = {Biofilm formation by Pseudomonas putida KT2440 contributes to improve tomato drought stress resilience and priming for enhanced gene regulation.},
journal = {Journal of plant physiology},
volume = {317},
number = {},
pages = {154704},
doi = {10.1016/j.jplph.2026.154704},
pmid = {41554215},
issn = {1618-1328},
abstract = {Pseudomonas putida KT2440 is a plant growth-promoting rhizobacterium (PGPR), known to enhance tolerance to pathogen infection, but its role in drought stress mitigation remains largely unexplored. This study aimed to assess whether inoculation with KT2440 improves tomato tolerance to drought. Inoculation with the KT2440 wild type (WT) significantly improved ecophysiological drought stress responses by increasing leaf water potential and photosynthetic rate. It also resulted in an impact on the holobiont cell physiology through modulation of the activity signature of key enzymes of carbohydrate (e.g., PGM and vacInv) and antioxidant (e.g., GR, MDHAR, and cwPOX) metabolism under drought conditions. To functionally assess the role of biofilm formation in drought response, biofilm-deficient mutants KT2440 Alg, with only one gene cluster for the exopolysaccharide alginate deleted, and KT2440 Q, with four exopolysaccharide gene clusters (alg, bcs, pea and peb) deleted, were used. Inoculation with these two mutants led to reduced drought resilience, with partial or complete loss of protective effects in the Alg and Q mutants, respectively. This was reflected in lowered leaf water potential, photosynthetic rate, and reduced antioxidant and carbohydrate metabolism enzyme activities compared to inoculation with the corresponding wild type. Global RNA sequencing revealed that under drought conditions 360 % more genes were differentially regulated in the presence of KT2440 WT compared to the mock inoculated control, whereas this value decreased again to only 140 % more differentially regulated genes after recovery from the drought stress. Thus, KT2440 specifically primes the plant for a much more pronounced transcriptional response only during the impact of drought, thus providing resilience protection on demand. This priming for enhanced abiotic stress responsiveness was partially dependent on the ability to form biofilm. Both under well-watered and drought stress the number of differentially regulated genes was strongly reduced in plants inoculated with KT2440 Q compared to WT. Gene ontology and expression analyses showed significant upregulation of pathways involved in photosynthesis, phytohormone signaling, antioxidant metabolism, and drought resilience in KT2440-inoculated plants. Although KT2440 WT showed higher biofilm formation compared to the Alg and Q mutants, the strains did not differ in their ability for root colonization. These findings provide novel insights into the contribution of biofilm formation to PGPR-mediated drought tolerance and protection on demand via priming for enhanced transcriptional regulation under stress, supporting the potential of KT2440 for environmentally friendly mitigating of drought stress responses in crops.},
}

@article {pmid41553662,
year = {2026},
author = {Sarkar, B and Bag, S and Mandal, A and Saha, D and Saha, S and Bhaduri, R and Chatterjee, S},
title = {Cresol Derivatives from Bacillus subtilis as Natural Oviposition Modulator of Culex quinquefasciatus: A Molecular Docking Approach.},
journal = {Applied biochemistry and biotechnology},
volume = {},
number = {},
pages = {},
pmid = {41553662},
issn = {1559-0291},
abstract = {Mosquitoes rely heavily on olfactory cues for locating suitable oviposition sites, with microbial communities in aquatic habitats playing a crucial role in producing volatile organic compounds (VOCs) that influence mosquito behaviour. In this study, we isolated Bacillus subtilis DHB13 from the breeding habitat of Culex quinquefasciatus, a major vector of several human diseases. The partial 16S rRNA gene sequence of the isolate has been submitted to NCBI GenBank with the accession number PV698100. The identity and resistance profile of the strain was confirmed through biochemical and antibiotic susceptibility tests. The bacterial suspension demonstrated a notable oviposition activity index (OAI) of 0.77 ± SE, with moderate variation among treatments (F(3, 8) = 3.631, p = 0.0642). Multiple comparison analysis (Tukey's test) showed that OAI values for DHB13-treated media did not differ significantly from natural habitat water but were significantly higher than the sterile control, indicating a biologically relevant attraction of gravid female mosquitoes. LC-MS analysis of the bacterial culture supernatant revealed the presence of three cresol derivatives: diisopropyl-m-cresol, 3-ethyl-p-cresol, and 6-ethyl-o-cresol. These compounds were evaluated through molecular docking against Cx. quinquefasciatus Odorant Binding Protein 1 (CxOBP1), a protein known to mediate olfactory-driven oviposition behaviour. However, mosquito olfaction involves several OBPs, receptors, and enzymes, so interaction with CxOBP1 represents only part of this complex sensory system. Molecular docking revealed strong binding of CxOBP1 with diisopropyl-m-cresol (-6.7 kcal/mol), 3-ethyl-p-cresol (-6.2 kcal/mol), and 6-ethyl-o-cresol (-5.9 kcal/mol), indicating potential oviposition attractant activity. All three ligands were found to bind within a conserved binding pocket of CxOBP1, behavioural assays confirmed the oviposition-stimulant properties of the bacterial suspension, indicating that the detected compounds mimic natural semio-chemicals such as p-cresol, previously recognized as an oviposition cue. These findings reinforce the role of microbiota in shaping mosquito reproductive behaviour through the production of volatile attractants. Moreover, they highlight the potential of using microbial VOCs as environmentally sustainable tools for mosquito surveillance and vector control. This integrative approach linking microbial ecology, chemical analysis, and mosquito behaviour provides novel insights for the development of attractant-based control strategies.},
}

@article {pmid41553583,
year = {2026},
author = {Zavřel, T and Pohland, AC and Pfennig, T and Matuszyńska, AB and Tóth, SZ and Bernát, G and Červený, J},
title = {Estimating the redox state of the plastoquinone pool in algae and cyanobacteria via OJIP fluorescence: perspectives and limitations.},
journal = {Photosynthesis research},
volume = {164},
number = {1},
pages = {6},
pmid = {41553583},
issn = {1573-5079},
}

@article {pmid41551586,
year = {2026},
author = {Rahlff, J and Amato, P},
title = {A look into the virosphere of clouds: A world yet to be explored.},
journal = {Current research in microbial sciences},
volume = {10},
number = {},
pages = {100545},
pmid = {41551586},
issn = {2666-5174},
abstract = {Clouds are aqueous atmospheric systems hosting diverse and active microorganisms. Viruses may also persist despite harsh conditions, support active viral infections, and contribute to microbial dynamics during aerial transport. However, assessing viruses, and even more, virus-bacteria interactions in the atmospheric environment is highly challenging, and knowledge remains very limited. Here, based on current knowledge in cloud microbiology, we estimate the cloud virome at ∼10[21] virus particles globally. One out of a million of cloud droplets is susceptible to host virus-bacteria interactions, which represents considerable volume at global scale, and we discuss potential implications for microbial ecology. We finally propose future research directions to explore further the cloud virosphere and its ecological roles.},
}

@article {pmid41222968,
year = {2026},
author = {Le, OTH and Chu, LK and Pham, QV and Tran, HT and Nguyen, HN and Nguyen, HT and Dinh, HT},
title = {Enhancing compost maturity and nitrogen content through cocomposting of chicken feather waste with rice husk and vegetable residues.},
journal = {Journal of the Air & Waste Management Association (1995)},
volume = {},
number = {},
pages = {1-13},
doi = {10.1080/10962247.2025.2587011},
pmid = {41222968},
issn = {2162-2906},
abstract = {Chicken feather waste is a potential low-cost nitrogen source for fertilizer production. However, due to its recalcitrant biodegradability, low C/N ratio, and high water content, composting chicken feather waste requires amendments. Optimizing the initial substrate composition plays a key role in improving composting performance. This study investigated the effects of varying chicken feather waste proportions, which altered the initial C/N ratio of the composting substrate, on the physicochemical evolution and final product quality of compost mixtures containing rice husk as a bulking agent and readily degradable vegetable residues. The substrates were composted in static compost bins of 20 L for 126 days under ambient conditions (~28°C). Significant differences were observed in physicochemical evolution and compost quality. A higher proportion of chicken feather waste or a lower initial C/N ratio led to increased total nitrogen (TN), extractable NH4[+], and SO4[2‒] concentrations during composting and in the final products. The addition of rice husk and vegetable residue improved the germination index of compost products from chicken feather waste. It was found that more-nutrient-rich compost could be produced by co-composting chicken feather waste with a low C/N ratio.Implications: This study highlights the interrelation of cosubstrates (rice husk, vegetable residue) in the decomposition of chicken feather waste. Nutrient-rich composts were obtained when chicken feather waste was cocomposted with low C/N ratios. Higher proportion of chicken feather waste or lower initial C/N ratio of composting substrate increased total N, extractable NH4[+], and SO4[2-] concentrations in compost product. Cocomposting of chicken feather waste with rice husk and vegetable residue enhanced compost maturity and germination index. The findings contribute a scientific basis for promoting the utilization of chicken feather waste to produce N-rich fertilizer.},
}

@article {pmid41549150,
year = {2026},
author = {Negi, R and Sharma, B and Jyothi, RS and Gupta, A and Parastesh, F and Kaur, T and Jhamta, S and Thakur, N and Singh, S and Yadav, N and Yadav, AN},
title = {Phyllosphere microbiome: Exploring the unexplored frontiers for precision agricultural and environmental sustainability.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {2},
pages = {50},
pmid = {41549150},
issn = {1573-0972},
mesh = {*Microbiota ; *Agriculture/methods ; Bacteria/classification/metabolism/genetics/isolation & purification ; Fungi/metabolism/classification ; *Plant Leaves/microbiology ; *Plants/microbiology ; },
abstract = {The phyllosphere, encompassing the aerial surfaces of plants, represents one of the largest microbial habitats on Earth and plays a pivotal yet underutilized role in sustainable agriculture and environmental health. Colonized by diverse bacterial, fungal, and yeast communities, the phyllosphere microbiome significantly influences plant growth, disease resistance, nutrient dynamics, and abiotic stress tolerance. These microorganisms engage in complex interactions with host plants, often functioning as biofertilizers, biopesticides, and stress protectants by producing phytohormones, antimicrobial metabolites, and stress-responsive compounds. Importantly, phyllospheric microbes also contribute to atmospheric and ecological balance by participating in carbon and nitrogen cycling, degrading volatile organic compounds (VOCs), and mitigating air pollution. However, despite their immense potential, the practical application of phyllospheric microbes remains limited by challenges such as environmental instability, poor field persistence, and incomplete functional characterization. The highly variable microclimate of the leaf surface poses survival barriers to both native and introduced microbial inoculants. Moreover, the specificity of plant-microbe associations and the complexity of microbial interactions necessitate precision-based approaches for successful deployment. Recent advances in omics technologies, microbial consortia engineering, and nano-enabled delivery systems provide new opportunities to overcome these limitations. A deeper understanding of phyllosphere microbial ecology, combined with innovations in synthetic biology and ecological modeling, can facilitate the development of robust microbial tools tailored to specific crops and climates. Harnessing the potential of phyllospheric microorganisms is not merely an academic pursuit, it is a strategic imperative for transitioning toward climate-resilient, low-input, and ecologically sound agricultural systems.},
}

*Microbiota
*Agriculture/methods
Bacteria/classification/metabolism/genetics/isolation & purification
Fungi/metabolism/classification
*Plant Leaves/microbiology
*Plants/microbiology

@article {pmid41548260,
year = {2026},
author = {Ravikumar, BN and Carvajal-Arroyo, JM and Jia, M and Ganigué, R},
title = {Ecophysiological characterization of thermophilic anammox process: Impact of environmental conditions and wastewater constituents on the activity of a novel granular thermophilic anammox culture.},
journal = {Water research},
volume = {292},
number = {},
pages = {125402},
doi = {10.1016/j.watres.2026.125402},
pmid = {41548260},
issn = {1879-2448},
abstract = {Understanding the ecophysiology of thermophilic anammox bacteria is crucial for expanding anaerobic ammonium oxidation (anammox)-based nitrogen removal to warm (>45[0]C), nitrogen-rich and carbon-deficient wastewaters (bCOD/N < 3 g/g) such as, centrate from thermophilic anaerobic digesters. Despite recent enrichments of thermophilic anammox cultures, their ecophysiological responses to process variables remain largely unknown. This study provides the first systematic characterization of the short-term response of a granular thermophilic anammox culture, enriched in Candidatus Brocadia sp., to key environmental conditions (pH, temperature, salinity) and wastewater constituents (ammonium, nitrite, phosphate, sulfide, volatile fatty acids (VFAs)). The culture displayed an optimal pH range of 7.3-7.8 and a temperature optimum of 50-53 °C, the highest short-term activity temperature recorded for any anammox species, yet. Ammonium caused only slight inhibition (IC50>57 mM), and free ammonia was not the primary inhibitory species, in contrast to mesophilic observations. Thermophilic Ca. Brocadia culture showed higher salinity (IC50=159 mM NaCl) and phosphate tolerance (IC50=44.9 mM) tolerance than most mesophilic counterparts, whereas nitrite (IC50=25.9 mM) and sulfide (IC50=0.03 mM H2S) elicited strong inhibition. Among VFAs, propionate was the most inhibitory (IC50=22 mM), while low concentrations (2.5 mM) of acetate and formate slightly enhanced anammox activity. These results identify the inhibitory thresholds and operational boundaries of thermophilic anammox systems, demonstrating that the culture is sufficiently robust for application in warm nitrogenous wastewaters, paving the way for developing sustainable and cost-efficient wastewater treatment technologies for high temperatures.},
}

@article {pmid41547661,
year = {2026},
author = {Dasgupta, M and Maity, A and Sarker, RK and Paul, P and Chakraborty, P and Sarkar, S and Roy, R and Malik, M and Das, S and Tribedi, P},
title = {Antibiotic-phytochemical combinations against Enterococcus faecalis: a therapeutic strategy optimized using response surface methodology.},
journal = {Antonie van Leeuwenhoek},
volume = {119},
number = {2},
pages = {41},
pmid = {41547661},
issn = {1572-9699},
support = {TNU/R&D/MG/24/02//The Neotia University/ ; TNU/R&D/MP/2021/010//The Neotia University/ ; },
mesh = {*Enterococcus faecalis/drug effects ; *Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests ; *Phytochemicals/pharmacology ; Vancomycin/pharmacology ; Ciprofloxacin/pharmacology ; Drug Synergism ; Benzoquinones/pharmacology ; },
abstract = {Enterococcus faecalis, a Gram-positive bacterium that causes nosocomial infections, has been reported to be resistant to several antibiotics, posing a significant threat to public healthcare. In the present study, we explored a combinatorial therapeutic approach involving conventional antibiotics alongside phytochemicals against E. faecalis. Vancomycin and ciprofloxacin were chosen for the current study due to their different modes of action. The minimum inhibitory concentration (MIC) of cuminaldehyde and thymoquinone was found to be 500 µg/mL and 30 µg/mL, respectively. Co-administering vancomycin with thymoquinone or cuminaldehyde reduced the MIC of vancomycin from 5 to 2 µg/mL, resulting in a 60% drop in MIC dose. Ciprofloxacin's MIC reduced from 1.5 to 1 µg/mL in the presence of the same phytochemicals, resulting in 33% reduction in its MIC dose. Furthermore, fractional inhibitory concentration indices (FICI) suggested additive interactions (FICI range: 0.66-1) between the antibiotics and phytochemicals against E. faecalis. Since precision dosing is important for any combinatorial application, we explored response surface methodology (RSM) to optimize dosing regimens of the selected compounds. It was observed that the predicted optimal concentrations of the test compounds (in different combinations) could closely match the actual observations when tested under the in-vitro laboratory conditions (R[2] range: 0.97-0.99). These findings suggested that combining conventional antibiotics with phytochemicals may offer a promising strategy to enhance the antimicrobial efficacy for effective control of infections caused by E. faecalis.},
}

*Enterococcus faecalis/drug effects
*Anti-Bacterial Agents/pharmacology
Microbial Sensitivity Tests
*Phytochemicals/pharmacology
Vancomycin/pharmacology
Ciprofloxacin/pharmacology
Drug Synergism
Benzoquinones/pharmacology

@article {pmid41547536,
year = {2026},
author = {Banik, M and Bashyal, S and Ahmed, KA and Banik, K and Dua, K and Choi, JP and Paudel, KR and Majumder, R},
title = {The Gut Microbiome of Australian Cats and Dogs: Dietary Influences, Health Impacts, and Emerging Research.},
journal = {Veterinary journal (London, England : 1997)},
volume = {},
number = {},
pages = {106566},
doi = {10.1016/j.tvjl.2026.106566},
pmid = {41547536},
issn = {1532-2971},
abstract = {The gut microbiome plays a pivotal role in the health, metabolism, and behaviour of companion animals, yet comprehensive syntheses of its composition and functional relevance in cats and dogs in Australia are overlooked and remain limited globally. This review synthesises current knowledge on the gut microbial communities inhabiting the gastrointestinal tracts of dog and cats, with a particular focus on taxonomic diversity, dietary modulation, and associations with disease states within Australian context. Core phyla including Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria dominate the canine and feline gut, but marked interspecies and individual variability is shaped by factors such as feeding practices, living environment, obesity, and chronic disease. Recent studies have elucidated functional signatures linked to conditions ranging from the influence of microplastics to pet gut health, as well as gut-microbiome transmission between pets and their owners, highlighting this area as a promising field of investigation. In parallel, this review contextualizes the broader landscape of pet ownership in Australia, where nearly 70% of households own pets, and significant resources are devoted to nutrition, veterinary care, and preventive health. Emerging evidence also suggests bidirectional influences between pets and their human companions' microbiota, highlighting opportunities for integrated approaches. We identify critical knowledge gaps, including the need for region-specific microbial baselines, standardized methodologies, and controlled intervention trials targeting microbiome modulation and transmission. By consolidating advances across microbial ecology, veterinary medicine, and translational research, this review provides a foundation for future studies that aim to harness the diagnostic and therapeutic potential of the pet microbiome, thereby improving health outcomes for animals and humans alike.},
}

@article {pmid41546932,
year = {2026},
author = {Verduzco Garibay, M and Hernández-Guardado, I and Yebra-Montes, C and Díaz-Torres, O and Fernández Del Castillo, A and Díaz-Vázquez, D and Kreft, JU and Cortés-Aguilar, J and Senés-Guerrero, C and Gradilla-Hernández, MS},
title = {Exploring the resilience of playa lake ecosystems to climate change: A microbial perspective.},
journal = {Journal of environmental management},
volume = {399},
number = {},
pages = {128474},
doi = {10.1016/j.jenvman.2025.128474},
pmid = {41546932},
issn = {1095-8630},
abstract = {Playa lakes, ephemeral water bodies found in arid and semi-arid regions, are increasingly impacted by climate change. The Mexican playa Lake Atotonilco has experienced a significant decline in water volume, leading to increased salinity and making it a valuable model for assessing climate impacts. Using 16S rRNA sequencing, this study investigated the responses of microbial communities and their contributions to key biogeochemical cycles, including those related to greenhouse gas dynamics. Spatial differences in physicochemical parameters were observed: channels and wastewater treatment plant (WWTP) effluent showed elevated BOD5, COD, coliforms, and pH above regulatory limits, whereas the lake displayed higher DO but increased TP and TKN. Bacterial communities exhibited marked seasonal and depth-related shifts, reflecting strategies that support ecosystem resilience. To robustly identify differentially abundant taxa, two methods (ANCOM-BC2 and DESeq2) were implemented, which consistently detected significant differences across seasons. Despite strong environmental fluctuations, a core microbial community persisted, suggesting functional continuity in biogeochemical cycling. This study provides a comprehensive assessment of microbial dynamics in a playa lake, integrating community structure with physicochemical variability to reveal bacterial responses to climate-driven environmental change. Because playa and other shallow lakes worldwide are experiencing increasing desiccation, salinization, and nutrient imbalances, defining these microbial processes is essential for anticipating ecological change. This study provides a needed baseline for future research and offers key insights for managing climate-vulnerable aquatic ecosystems in arid regions.},
}

@article {pmid41545601,
year = {2026},
author = {Shin, S and Bang, D and Lee, M and Kang, Y},
title = {Heavy Rain, Less Bloom Under Heat: Succession of Size-Structured Phytoplankton Community Without Biomass Increases in a Monsoonal Korean Coastal Ecosystem.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02680-4},
pmid = {41545601},
issn = {1432-184X},
support = {R2025011//National Institute of Fisheries Science/ ; NRF2022R1C1C1008380//National Research Foundation of Korea/ ; },
}

@article {pmid41545035,
year = {2026},
author = {Eggestein, A and Rauer, D and Herrmann, SM and Kolek, F and Leier-Wirtz, V and Urban, S and Foesel, B and Schloter, M and Bhattacharyya, M and Pyrri, I and Reiger, M and Schwierzeck, V and Hülpüsch, C and Traidl-Hoffmann, C and Damialis, A and Gilles, S},
title = {A Walk in the Park: Influence of Natural Co-Exposure to Grass Pollen and Fungal Spores on Nasal Mycobiome and Cytokine Responses.},
journal = {Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology},
volume = {},
number = {},
pages = {},
doi = {10.1111/cea.70216},
pmid = {41545035},
issn = {1365-2222},
support = {//Christine Kühne-Center for Allergy Research and Education (CK-Care)/ ; },
abstract = {BACKGROUND: During the grass flowering season, fungal spores are abundant in outdoor air. We tested for co-sensitisations to grass pollen and fungal spores, assessed the degree of co-exposure, and studied its impact on the nasal mycobiome and immune responses.

METHODS: Fungi-specific IgE-levels were studied in 277 individuals with and without grass pollen sensitisation. In a small cohort (n = 7), exposure to grass pollen and fungal spores was monitored during 5 consecutive indoor and outdoor stays in a flowering meadow and correlated with changes in the nasal mycobiome. Cytokines of nasal epithelial cells were studied under stimulation with recombinant grass pollen allergens, with and without fungal spores derived from outdoor isolates.

RESULTS: IgE-sensitisation against the studied fungi was significantly more frequent among individuals with grass pollen sensitisation than among those without grass pollen sensitisation. Outdoor exposure resulted in changes in the nasal mycobiome, with a transitory enrichment of environmental fungi, for example, Cladosporium species. Most of the fungi cultivated from outdoor air samples belonged to the genera Fusarium, Cladosporium and Penicillium. Apical co-stimulation of nasal epithelial cells with grass pollen allergens and Fusarium, Cladosporium or Penicillium spores led to an increased loss of transepithelial electrical resistance and induction of pro-inflammatory cytokine release compared to mono-stimulation.

CONCLUSION: Frequent co-exposure to fungal spores and grass pollen may increase the chance of acquiring a co-sensitisation to both allergens. Environmental fungi interact with and transitorily change the local mycobiome. Under co-exposure, fungal spores induce nasal inflammation and foster immune responses to otherwise poorly immunogenic pollen allergens.},
}

@article {pmid41544570,
year = {2026},
author = {Aminullah, N and Langar, H and Mahaq, O and Azizi, MN and Zahir, A},
title = {Microbial ecology, functional implications, and associated factors influencing poultry intestinal health.},
journal = {Veterinary immunology and immunopathology},
volume = {293},
number = {},
pages = {111065},
doi = {10.1016/j.vetimm.2026.111065},
pmid = {41544570},
issn = {1873-2534},
abstract = {Gut health is a dynamic phenomenon regulated by the balanced interaction among gastrointestinal tract morphological structure, resident microbiota, and available nutrients, producing an integrated barrier that ensures efficient physiological functions, enhanced immune competence and optimal productivity. Gut health is recognised as a crucial factor for optimum management, farming economy, and sustainable commercial poultry production. Poultry gut health has become a central focus, particularly following restrictions applied on the use of antimicrobial growth promoters in poultry production due to rising global concerns about microbial resistance. Intestinal integrity and health are being regulated by microbiota metabolites such as short-chain fatty acids (SCFAs), which modulate intestinal morphogenesis vis-à-vis villus size, crypt depth and physiological functions, including feed digestion, nutrients synthesis and absorption, and immune response. Any disturbances arising from nutritional imbalances, microbial infections, environmental stress, or poor management practices compromise epithelial health, barrier integrity, and physiological functions, leading to impaired growth performance and productivity. This review provides an overview of poultry gut health, highlighting the interdependence of gut microbiota, gut morphogenesis, physiology, environmental factors affecting gut health, and management approaches for sustainable poultry production.},
}

@article {pmid41540283,
year = {2026},
author = {Bueno, RS and Catania, V and Auteri, M and Grilli, E and di Iorio, T and di Sarra, A and Castaldi, S and Quatrini, P},
title = {Patterns and Drivers of Plant Arbuscular Mycorrhizal Traits Across a Pedo-Climatic Gradient in Mediterranean Agroecosystems Under Desertification Risk.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02689-9},
pmid = {41540283},
issn = {1432-184X},
abstract = {Desertification is a global concern, reducing vegetation cover and soil fertility. Arbuscular mycorrhizal symbiosis (AM), the most common plant-fungi association, can enhance plant fitness and stress tolerance. Despite its significance, comprehensive data on community-wide patterns and drivers of plant AM traits are limited in the Mediterranean, one of the regions most vulnerable to desertification. We examined four traits: colonization frequency, intensity, arbuscule abundance, and spore density in the rhizosphere of 20 plant species across ten agroecosystems in desertification-prone areas of Italy, Spain, and Portugal. We analysed whether these traits varied across Raunkiær's plant life forms and were affected by vegetation cover, soil properties, precipitation, and temperature, both overall and regionally, to explore potential context-dependency. All plants showed a high frequency of AMF colonization, with an average intensity of 54%, indicating obligate AMF interactions, and arbuscule abundance was significantly correlated with spore density. These traits were significantly higher in microhabitats dominated by trees and shrubs compared to those dominated by herbaceous plants. Phanerophytes (perennials) presented lower trait values than therophytes (annuals), while the highest values were found in hemicryptophytes. Lampedusa, a region with hotter and drier climate conditions in Southern Europe, had significantly lower AMF trait levels, though Spanish site values resembled those in Sicily more than Portugal. Soil organic carbon, nitrogen, and the overall positive interaction between precipitation and temperature significantly influenced all AMF traits. However, the magnitude and direction of soil and climate related effects differed among regions, indicating strong context dependency. Our study contributes to better define indicators for monitoring desertification and evaluating restoration efforts while highlighting the need of site-specific evaluations and careful interpretation of broad generalisations.},
}

@article {pmid41537975,
year = {2026},
author = {Sless, T and Chau, K and Nguyen, P and Rehan, S},
title = {Microbial communities of wild bees and comparative phylogenetics of key bacterial taxa across the bee tree of life.},
journal = {Proceedings. Biological sciences},
volume = {293},
number = {2062},
pages = {},
doi = {10.1098/rspb.2025.1823},
pmid = {41537975},
issn = {1471-2954},
support = {//Natural Sciences and Engineering Research Council of Canada/ ; },
mesh = {Animals ; Bees/microbiology ; Phylogeny ; *Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics/analysis ; *Microbiota ; *Fungi/classification/genetics/isolation & purification ; DNA Barcoding, Taxonomic ; },
abstract = {Recent years have seen a rapidly growing interest in the study of microbiomes to understand the health and well-being of host animals. Within bees, much of this work has focused on managed species of agricultural importance, such as honeybees and bumblebees. However, unmanaged wild bees are also vital to both agricultural and natural systems, and studying their microbial associates is essential to understanding the impacts of microbiomes on bee health. We used metabarcoding based on 16S rRNA and internal transcribed spacer region (ITS1) loci to identify bacterial and fungal associates of adult bees from 16 species, 10 genera and 5 families, representing a diverse sampling of wild bees common to eastern North America. Overall, Apilactobacillus was the largest component of bacterial communities, while fungal communities were dominated by Cladosporium. Alpha diversity of both bacteria and fungi differed significantly across genera and species, while beta diversity varied at all taxonomic levels. Additionally, we conducted a broad phylogenetic comparison of bacterial communities across bees using previously published 16S rRNA datasets and contrasted these findings with functional traits across the bee tree of life. Several bacterial taxa showed evidence of strong phylogenetic signal in prevalence, while the presence of corbiculae was more strongly associated with bacterial community composition than sociality or nesting habit. This study provides expanded insights into the microbial associates of wild bees, as well as the broadest investigation to date into patterns of phylogenetic conservation in bacterial communities across a total of 42 species representing the five most diverse bee families.},
}

Animals
Bees/microbiology
Phylogeny
*Bacteria/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics/analysis
*Microbiota
*Fungi/classification/genetics/isolation & purification
DNA Barcoding, Taxonomic

@article {pmid41536172,
year = {2026},
author = {Carboni, S and Asangba, AE and Melin, AD},
title = {Microbial Contributions to Primate Reproduction.},
journal = {Evolutionary anthropology},
volume = {35},
number = {1},
pages = {e70023},
pmid = {41536172},
issn = {1520-6505},
mesh = {Animals ; *Primates/microbiology/physiology ; Female ; *Reproduction/physiology ; *Microbiota/physiology ; Male ; Humans ; Pregnancy ; Anthropology, Physical ; Sexual Behavior, Animal ; Biological Evolution ; Copulation/physiology ; },
abstract = {Reproduction is a complex process, and microbes play a far greater role than previously imagined. This review explores the ways that microbiomes influence the rich tapestry of reproductive processes and outcomes within the primate lineage, including pre-copulatory and post-copulatory mechanisms. We discuss microbiomes in a sexual selection framework, specifically how they might influence mate choice and sexual competition across multiple sensory modalities. We then consider how copulatory behavior and mating systems may in turn shape reproductive microbiomes. Moving to post-copulatory processes, we discuss the potential impact of microbes on cryptic choice and sperm competition and call for additional research in this area. Finally, we explore the influence of microbes on pregnancy outcomes, emphasizing evolutionary perspectives often overlooked in clinical research. Importantly, we compare human studies to those on nonhuman primates, bridging the two areas of inquiry and outlining future research directions. Our aim is to highlight the vast potential for microbes to contribute to all stages of reproduction, and to inspire creative, synthetic future research that moves forward this fascinating area of inquiry.},
}

Animals
*Primates/microbiology/physiology
Female
*Reproduction/physiology
*Microbiota/physiology
Male
Humans
Pregnancy
Anthropology, Physical
Sexual Behavior, Animal
Biological Evolution
Copulation/physiology

@article {pmid41534871,
year = {2026},
author = {Xie, Y and Artacho, A and Yu, X and Bi, M and Li, H and Li, Y and Roccuzzo, A and Mira, A and Rosier, BT and Tonetti, MS},
title = {Oral-Rinse-Sourced Microbiota in Oral Health and Diseases in a Representative US Adult Population: Implications for Diagnostics.},
journal = {Journal of clinical periodontology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jcpe.70101},
pmid = {41534871},
issn = {1600-051X},
support = {JYLJ202404//Clinical+ programme of the Ninth People's Hospital/ ; },
abstract = {AIMS: To investigate the associations between oral-rinse microbiota and distinct oral conditions, and further evaluate its potential ability to distinguish periodontitis severity.

METHODS: Oral-rinse-sourced microbiota with 16S ribosomal RNA sequencing from 3770 adults in US National Health and Nutrition Examination Survey 2009-2012 were analysed across oral health, caries, periodontitis, co-existing caries and periodontitis and edentulism. Diagnostic potential of the oral-rinse microbiota for periodontitis severity was evaluated using multi-class random forest (RF) model with internal validation and external validation in an independent cohort (n = 392).

RESULTS: Oral condition accounted for substantial variance in oral-rinse microbiota, revealing disease or tooth loss-associated shifts. Increasing acidogenic/aciduric taxa (Veillonella, Lactobacillus, Atopobium) or periodontitis-associated taxa (Filifactor, Treponema, Tannerella) were identified in caries-only or periodontitis-only groups, respectively, while the co-existing disease group showed overlapping shifts. Taxa shifted dose-dependently with increasing periodontitis severity. The RF model achieved moderate performance in identifying severe periodontitis, with the area under the receiver operating characteristic curve (AUROC) of 0.81 (0.75-0.87) internally and 0.83 (0.77-0.88) externally. Key contributing taxa aligned with established periodontitis-associated genera, supporting model interpretability.

CONCLUSION: Based on our results, oral-rinse microbiota captures disease-specific signatures across oral conditions, supporting its potential as a non-invasive tool to monitor oral microbial ecology and assess periodontitis severity at the population level.},
}

@article {pmid41534410,
year = {2026},
author = {Cardinali, F and Rampanti, G and Lucci, P and Ferrocino, I and Pacetti, D and Fanesi, B and Ismaiel, L and Milanović, V and Garofalo, C and Petruzzelli, A and Savelli, D and Gabucci, C and Aquilanti, L and Osimani, A},
title = {Novel insights into hákarl: A deep dive into the microbiological and physico-chemical features of Iceland's traditional fermented shark.},
journal = {International journal of food microbiology},
volume = {450},
number = {},
pages = {111629},
doi = {10.1016/j.ijfoodmicro.2026.111629},
pmid = {41534410},
issn = {1879-3460},
abstract = {Hákarl, the traditional Icelandic product obtained from the fermentation of Greenland shark (Somniosus microcephalus), represents a unique food item from both cultural and microbiological perspectives. This study investigated commercial samples of hákarl using an integrated approach, combining physico-chemical analyses, lipid and volatile profiling, metataxonomic sequencing, and microbial isolation. Results confirmed the alkaline nature of the product (pH ∼8) and a water activity (aw) of 0.96, sufficient to sustain an active and diverse microbial community. Lipid profiling revealed the predominance of monounsaturated fatty acids, with differences in PUFA and DHA levels between the analyzed producers, consistent with nutritionally favorable characteristics. Microbiological analysis highlighted bacterial communities dominated by Firmicutes, particularly Bacilli and Clostridia, with significant abundances of Tissierella creatinini and Atopostipes suicloacalis. Culture-dependent methods led to the isolation of Carnobacterium antarcticum cultures, which were subsequently characterized for their enzymatic activities. These findings suggest potential biotechnological applications of the isolates, especially in fermentation and aroma development. Volatile compound analysis identified thirteen VOCs including alcohols, aldehydes, ketones, phenols, sulfur- and nitrogen-containing compounds. Trimethylamine was the predominant metabolite responsible for the strong ammonia-like odor, followed by phenol and sulfur-containing compounds, which also contributed to the sensory profile. Overall, the results provide novel insights into the microbial ecology, physico-chemical traits, and volatile characteristics of hákarl, confirming its variability linked to artisanal production methods. The study emphasizes hákarl's role as a reservoir of pro-technological microorganisms and advances current understanding of the factors influencing its safety, quality, and identity as traditional fermented food.},
}

@article {pmid41533097,
year = {2026},
author = {Huertas-Díaz, L and Hosek, J and Gram-Hansen, D and Frei, R and Roduit, C and Sasaki, M and Lauener, RP and Schwab, C and , },
title = {pH-Dependent Effects of Short-chain Carboxylic Acids and Buffer Systems On Clostridioides difficile in Vitro and in Vivo.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02694-6},
pmid = {41533097},
issn = {1432-184X},
abstract = {The spore-forming anaerobe Clostridioides difficile colonizes the highly dynamic gut environment early after birth, frequently without causing disease. In this study, we aimed to determine how environmental conditions indicative of the infant gut impacted prevalence and physiology of C. difficile. We examined the effect of pH, fermentation derived short-chain carboxylic acids (SCCA) and buffering systems combining in vitro and in vivo analysis, and experimental and modelling approaches. In vivo, the prevalence of Clostridioides significantly increased between 3 months (30.2%) and 12 months (56.2%) after birth. At 12 months, the occurrence of Clostridioides was the highest in feces with near neutral pH (6.7 (IQR 6.5‒7.3). In vitro, C. difficile showed pH-dependent growth and metabolic activity with an optimum around pH 5.8-6.3. Most SCCA conferred antimicrobial activity at pH 5.2 and 6.1 while at pH 6.5, high concentrations of SCCA promoted growth. The presence of phosphate buffer enhanced antimicrobial activity of SCCA, particularly at lower pH values (5.2-5.8). Two multilinear regression models indicated that ionic strength was inversely related to optical density in vitro, while in vivo, the abundance of Clostridioides was inversely linked to the presence of undissociated SCCA. Together, this study highlights that the that occurrence and performance of the opportunistic pathogen C. difficile was affected by chemical systems such as pH, the presence of buffer systems and concentration and chemical state of SCCA. Our results suggest novel targets that could be modulated to impact C. difficile colonization.},
}

@article {pmid41531331,
year = {2026},
author = {Wu, H and Xu, S and Chen, Y and Yuan, Z and Yao, Y and Hao, J and Han, L},
title = {Phenazine-1-Carboxamide from Streptomyces Suppresses Phytophthora nicotianae via CDC48-Targeted Mitochondrial Disruption.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.70383},
pmid = {41531331},
issn = {1365-3040},
support = {32272594//National Natural Science Foundation of China/ ; 2024QCY-KXJ-097//Technology Innovation Leading Program of Shaanxi/ ; },
abstract = {Phytophthora nicotianae is a plant-pathogenic oomycete, posing a serious threat to global agriculture due to its highly destructive infections and challenges in management. To explore a biologically based disease management strategy, we investigated Streptomyces ardesiacus HL-06, which produces phenazine-1-carboxamide (PCN), a potent anti-oomycete metabolite that effectively suppresses the growth of P. nicotianae in vitro and reduces tobacco black shank severity by over 80% under field conditions, surpassing the efficacy of commercial fungicides. Mechanistically, we identified CDC48, a AAA+ ATPase essential for mitochondrial homeostasis, as the direct molecular target of PCN. Drug affinity responsive target stability (DARTS), molecular docking, and isothermal titration calorimetry revealed that PCN binds to CDC48's ATPase domain, thereby disrupting mitochondrial protein quality control. This interaction leads to mitochondrial cristae loss, ATP synthase inhibition, and reactive oxygen species (ROS) accumulation, ultimately triggering oomycete apoptosis. This is the first report of a phenazine compound targeting a eukaryotic AAA+ ATPase, revealing a novel mode of action against oomycete pathogens. Our findings integrate microbial ecology with chemical biology, positioning PCN as a promising eco-friendly candidate for sustainable plant disease management.},
}

@article {pmid41531312,
year = {2026},
author = {Boldt, J and Porten, C and Haeckl, FPJ and Hug, JJ and Panter, F and Steglich, M and Wink, J and Overmann, J and Göker, M and Krug, D and Müller, R and Nübel, U},
title = {Phylogeny-Aware Metabologenomics Accurately Assigns Natural Products to Biosynthetic Gene Clusters.},
journal = {Microbial biotechnology},
volume = {19},
number = {1},
pages = {e70298},
doi = {10.1111/1751-7915.70298},
pmid = {41531312},
issn = {1751-7915},
support = {09.720//Deutsches Zentrum für Infektionsforschung/ ; },
mesh = {*Multigene Family ; *Biological Products/metabolism ; *Phylogeny ; *Biosynthetic Pathways/genetics ; *Metabolomics/methods ; Genomics/methods ; Mass Spectrometry ; },
abstract = {Tens of thousands of biosynthetic gene clusters (BGCs) have been identified in microbial genomes, but the vast majority of associated natural products (NPs) and their underlying biosyntheses remain unknown. Metabologenomics approaches integrate genomic and metabolomic datasets to statistically associate BGCs to their cognate NPs, yet often suggest many false links. Here, we show that incorporating information on the producer strains' phylogeny greatly improves accuracy. We sequenced 72 Sorangium spp. genomes (myxobacteria), predicting 2030 BGCs in 265 gene cluster families (GCFs). Mass spectrometry (MS[1]) revealed 99 metabolite families (MFs) from the same strains. Using a phylogeny-aware statistical analysis, we identified 43 high-confidence associations between GCFs and MFs, correctly including 89% of previously characterised links and reducing spurious associations by 33-fold, compared to simple correlational analysis. Our approach identified previously unknown BGCs for rowithocin and an undescribed poly-glycosylated NP. It also identified a distinct BGC associated with the production of chlorotonil C variants and refined the BGC for maracen. This study demonstrates the effectiveness of phylogeny-aware metabologenomics as a scalable strategy for NP discovery and biosynthetic pathway elucidation, and provides a roadmap to improved analyses of paired-omics data towards NP discovery.},
}

*Multigene Family
*Biological Products/metabolism
*Phylogeny
*Biosynthetic Pathways/genetics
*Metabolomics/methods
Genomics/methods
Mass Spectrometry

@article {pmid41528150,
year = {2026},
author = {Guo, M and Xia, Z and He, X and Wan, S and Wang, Y and Fan, S and Pérez-Moreno, J and Yang, Z and Yang, C and Liu, D and Yu, F},
title = {High-throughput sequencing reveals endophytic bacterial differentiation of common truffles (Tuber spp.) in China: diversity, biogeographical patterns, and fungal health implications.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0186625},
doi = {10.1128/spectrum.01866-25},
pmid = {41528150},
issn = {2165-0497},
abstract = {UNLABELLED: As valuable hypogeous fungi, truffles depend on fruiting-body-associated microorganisms for lifecycle functions like growth and nutrient cycling. This study sampled fruiting bodies of 10 Tuber species from 16 sites across six major truffle-producing provinces in China, characterizing endophytic bacterial communities via high-throughput sequencing and multivariate analysis. Proteobacteria dominated the endophytic bacteria, with Bradyrhizobium as the prevalent genus. Significant genus-level compositional differences occurred across provenances and species: Bradyrhizobium reached 99.80% relative abundance in Tuber sinense from Mengzi, Yunnan, versus 7.90% in Tuber shii from Dali (12.6-fold difference). Shannon diversity indices (n = 48) revealed striking species- and altitude-related variations (P < 0.001): Tuber lijiangense (5.111) and T. shii (5.091) had the highest diversity, while T. sinense (1.336) had the lowest (3.8-fold gap). Subtropical Dali samples exhibited a sevenfold higher diversity compared to those from the Mengzi region, which is geographically closer to the tropics. Non-metric scaling and principal coordinates analysis identified environmental factors (soil, climate) and host species as primary drivers, with species effects potentially overriding environment. Five core taxa (all Rhizobiales) suggested nitrogen-fixing roles, while Variovorax (via linear discriminant analysis effect size) emerged as an external-disturbance-sensitive opportunist. This study clarifies endophytic bacterial variation patterns and drivers, identifies key taxa, and informs truffle ecological interactions, providing a scientific basis for sustainable resource management and conservation.

IMPORTANCE: This study underscores the critical importance of truffle endophytic bacteria in mediating fungal health and ecological resilience, addressing a major knowledge gap in hypogeous fungal microbiome research. By integrating high-throughput sequencing across 10 Tuber species in China, we reveal how bacterial communities (dominated by Bradyrhizobium) shape biogeographical patterns and functional roles like nitrogen fixation. These findings advance understanding of microbe-fungal symbioses, with direct applications for sustainable truffle cultivation (e.g., microbial inoculants) and climate-resilient management-aligning perfectly with AEM's focus on applied microbial ecology and biotechnological relevance.},
}

@article {pmid41524991,
year = {2026},
author = {Ding, Q and Li, J and Xue, F and Cui, W and Hu, S and Yu, L and Huang, W and Li, L and Cheng, P},
title = {Distinct soil microbial community composition and structure: evidence from soil inside and outside the cattle farm.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {57},
number = {1},
pages = {31},
pmid = {41524991},
issn = {1678-4405},
support = {No. 32402941//National Natural Science Foundation of China/ ; No. 2308085QC108//Natural Science Foundation of Anhui Province/ ; No.rc392109//Talent research fund project of Anhui Agricultural University/ ; },
mesh = {*Soil Microbiology ; Cattle ; Animals ; Soil/chemistry ; *Bacteria/classification/genetics/isolation & purification ; Manure/microbiology ; Farms ; *Fungi/classification/genetics/isolation & purification ; *Microbiota ; Biodiversity ; },
abstract = {The contrast between the soils inside and outside the cattle farm may reflect the prolonged manure exposure within the farm, potentially creating distinct properties and microbial structure. However, comparative studies are scarce on the microbial composition and co-occurrence patterns between soils inside and outside the cattle farm. To address this gap, this study combined Illumina MiSeq sequencing with co-occurrence network analysis and soil physicochemical characterization to compare the microbial community structures between the two sites. The soil inside the cattle farm exhibited higher microbial alpha diversity than that outside the farm. Volcano plots revealed significant differences in the relative abundances of microbial taxa between sites. Notably, the relative abundances of Devosia was significantly higher inside the cattle farm, whereas Paenibacillus and Nitrospira were markedly higher outside the cattle farm (|log2FC| ≥ 1.2). The fungal network inside the cattle farm demonstrated higher complexity and stability than outside, with larger nodes and edges (Nodes: 194 vs. 153; Edges: 13231 vs. 8007) and superior topological characteristics. To elucidate the specific manure-induced environmental factors driving these differences, Mantel tests confirmed that soil organic carbon and alkali-hydrolyzable nitrogen significantly influenced the microbial communities. This study identifies the specific manure-derived drivers of microbial community structure and network stability, providing critical insights for utilizing cattle manure to improve soil microbial ecology and thereby contributing to sustainable agricultural management.},
}

*Soil Microbiology
Cattle
Animals
Soil/chemistry
*Bacteria/classification/genetics/isolation & purification
Manure/microbiology
Farms
*Fungi/classification/genetics/isolation & purification
*Microbiota
Biodiversity

@article {pmid41520335,
year = {2026},
author = {Sang, J and Li, S and Xu, C and Pan, X and Zhu, Y and Li, Y and Ma, C and Zhang, Y and Chen, S and Qiu, Q and Si, H and Huang, Z and Wang, J and Jiao, J and Li, Z},
title = {Rumen microbiome biogeography and ventral epithelial architecture in three ruminant species.},
journal = {Cell reports},
volume = {45},
number = {1},
pages = {116779},
doi = {10.1016/j.celrep.2025.116779},
pmid = {41520335},
issn = {2211-1247},
abstract = {Ruminants thrive in diverse ecosystems by leveraging their rumen microbiome to ferment fibrous plants. However, the spatial biogeography of rumen microbiome and the genetic diversity of the ventral rumen epithelium remain unknown. Here, we present a multi-omics study in roe deer, sika deer, and sheep, integrating region-resolved microbiome and metabolome across 11 ruminal sacs, as well as single-cell RNA sequencing (scRNA-seq), assay for transposase-accessible chromatin using sequencing (ATAC-seq), and bulk RNA sequencing (RNA-seq) of ventral epithelium. We reveal species-specific microbial compositions and metabolic capacities contributing to differences in short-chain fatty acid and vitamin B production. We uncover functional divergence, genomic specialization, and metabolic changes across the microbiome of distinct ruminal sacs. Single-cell profiling reveals changes of immune responses and structural remodeling of the ruminal ventral epithelium. We demonstrate that vitamin B12 promotes epithelial growth and we identify genes enhancing stem cell differentiation. Our results highlight variation in microbial ecology and epithelial architecture among three ruminant species, offering insights to improve livestock productivity.},
}

@article {pmid41520281,
year = {2026},
author = {Tang, TWH and Ullah, K and Lee, JJ and Chen, HC and Hsieh, PCH},
title = {Comparative insights into the gut-heart axis: cross-species and cross-population perspectives.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2611617},
pmid = {41520281},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Animals ; *Cardiovascular Diseases/microbiology ; *Heart/physiology ; Swine ; Bacteria/classification/metabolism/genetics/isolation & purification ; Host Microbial Interactions ; Species Specificity ; *Gastrointestinal Tract/microbiology ; Disease Models, Animal ; },
abstract = {Gut microbiota research has rapidly expanded our understanding of host-microbe interactions in cardiovascular diseases, yet translation of these insights remains challenged by species-specific differences and substantial population heterogeneity. In this review, we synthesize current evidence across rodents, swine, non-human primates, and multi-ethnic human cohorts to delineate conserved versus context-dependent features of the gut-heart axis. Rodent models remain indispensable for mechanistic discovery, enabling causal testing through germ-free, antibiotic-treated, and humanized microbiota platforms, whereas large-animal models better replicate human cardiac anatomy, physiology, and microbial ecology. Human studies provide essential clinical relevance, demonstrating that patients with myocardial infarction, coronary artery disease, atrial fibrillation, and heart failure harbor distinct microbial and metabolite signatures. However, these findings vary across populations due to differences in diet, lifestyle, host genetics, medication exposure, and environmental transitions. Despite taxonomic variability, several functional pathways, most notably short-chain fatty acid production, bile acid biotransformation, and aromatic amino acid metabolism generating molecules such as trimethylamine-N-oxide and phenylacetylglutamine, consistently associate with cardiovascular risk. At the same time, population-specific features, including glycan-microbe interactions shaped by ABO and FUT2 genotypes, diet-responsive metabolite profiles, and variable drug-microbiome interactions, highlight the importance of genetic and environmental context. By integrating cross-species and cross-population evidence, this review outlines a framework for identifying robust microbial pathways, clarifying their translational boundaries, and guiding the development of microbiota-informed diagnostics and interventions that account for biological, cultural, and environmental diversity.},
}

Humans
*Gastrointestinal Microbiome/physiology
Animals
*Cardiovascular Diseases/microbiology
*Heart/physiology
Swine
Bacteria/classification/metabolism/genetics/isolation & purification
Host Microbial Interactions
Species Specificity
*Gastrointestinal Tract/microbiology
Disease Models, Animal

@article {pmid41519975,
year = {2026},
author = {Christoffersen, SN and Østergaard, SK and de Jonge, N and Pertoldi, C and Sørensen, JG and Noer, NK and Kristensen, TN and Nielsen, JL and Bahrndorff, S},
title = {Arctic Insects Show a Highly Dynamic Microbiome Shaped by Abiotic and Biotic Variables.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02685-z},
pmid = {41519975},
issn = {1432-184X},
abstract = {Arctic regions are inhabited by terrestrial ectotherms that have adapted to an extreme environment where food resources are limited. The host associated microbiome may partly explain their ability to live under these conditions, but very little is known about the microbiome of Arctic ectotherms. We investigate how the bacterial community of the Greenlandic seed bug (Nysius groenlandicus) and damsel bug (Nabis flavomarginatus) is affected by different abiotic and biotic factors (time, acclimation temperature, humidity, and diet) under both field and laboratory conditions. We found large differences in the bacterial composition and diversity between the two species including species-specific presence of potentially symbiotic bacteria. The bacterial community of both species changed across the season, which may be explained by the changing climatic conditions, such as temperature and humidity. This was further supported by results from the laboratory experiments. We also found that diet changed the bacterial composition in both species and that bacteria could be transferred from prey to predator. Together, these results show that the bacterial community of some Arctic insects are highly dynamic and modulated by different abiotic and biotic factors, suggesting that the microbiome plays an important role for these organisms to persist in an extreme and resource-limited Arctic environment.},
}

@article {pmid41509481,
year = {2026},
author = {Hallberg, ZF and Alvarez-Aponte, ZI and Gaudinier, AC and Taga, ME},
title = {Quenching corrinoid-based interactions in a model bacterial coculture.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {41509481},
issn = {2692-8205},
abstract = {Microbial community structure is driven, in part, by the metabolic interdependencies of resident microbes. Thus, manipulating specific metabolic interactions represents one attractive way to both understand how microbial communities perform complex functions and alter them for therapeutic or environmental effects. However, it is not yet possible to control the availability of those metabolites produced by some members of the community that are required by others. Here, we report the development of a metabolite 'quenching' strategy that disrupts a specific metabolic interaction involving corrinoids, the vitamin B12 family of cofactors, by applying a high-affinity corrinoid-binding protein, BtuG, to bacteria engaged corrinoid cross-feeding. Using a model coculture composed of Sinorhizobium meliloti, a bacterium that produces a corrinoid (cobalamin), and an Escherichia coli strain engineered to be corrinoid-dependent, we demonstrate corrinoid quenching by sequestration of extracellular corrinoid and show that BtuG specifically blocks corrinoid-dependent growth. We use this tool to calculate the amount of cobalamin released by S. meliloti cells and find that the cobalamin release rate is dependent on the growth phase of the producer, increasing to a maximum of approximately 40 cobalamin molecules per minute per cell in late exponential phase. This work establishes a strategy to selectively block microbial interactions that may be more broadly applied to dissecting community structure and function. We expect that applying high-affinity 'molecular sponges' to quench nutrient sharing will allow for the identification of key nutrients that structure microbial communities and empower precision microbiome manipulation strategies.},
}

@article {pmid41292826,
year = {2025},
author = {Backman, T and Cui, J and Caullireau, E and Bleak, E and Bezrukov, I and Girardi, P and Hawks, A and Lasky, JR and Latorre, SM and Erberich, JM and Lopez, L and Neumann, M and Perkins, AM and Symeonidi, E and Azadi, P and Horvath, MP and Muszyński, A and Lang, PLM and Karasov, TL and Burbano, HA},
title = {Persistent trade-offs balance competition and colonization across centuries.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {41292826},
issn = {2692-8205},
support = {T32 GM007276/GM/NIGMS NIH HHS/United States ; T32 AI055434/AI/NIAID NIH HHS/United States ; R24 GM137782/GM/NIGMS NIH HHS/United States ; R35 GM138300/GM/NIGMS NIH HHS/United States ; R35 GM150722/GM/NIGMS NIH HHS/United States ; },
abstract = {Microbial competition drives rapid adaptation, often forcing organisms to specialize in new ecological niches. Adaptations that improve competitive ability can reduce performance in other environments creating trade-offs. Whether such trade-offs persist in nature-or are eroded as lineages adapt through compensatory changes-remains largely unknown. Here we show that a trade-off between competitive ability and host colonization has been stably maintained in natural Pseudomonas populations for centuries. Wild plant-pathogenic Pseudomonas compete using tailocins-phage-derived molecular weapons that bind to specific cell-surface receptors. Genomic surveys and functional assays reveal that the most broadly lethal tailocins remain rare-while the tailocin's production increases competitive killing, it also compromises plant colonization. We determine that the polymorphisms behind this trade-off are not transient - historical genomes spanning two centuries show that the trade-off has been maintained for at least 10[5]-10[6] generations. Our results demonstrate that, in natural populations, a trade-off between competition and pathogenicity is fundamental and not easily overcome.},
}

@article {pmid41518539,
year = {2026},
author = {Kou, C and Li, D and Liu, Z and Gao, W and Zhang, W and Xiong, L and He, L and Li, M and Shu, A and Ma, J and Gao, Z},
title = {Rare Microbial Taxa Dominate the Microecological Landscape of Cadmium Exposure in Rice Rhizosphere.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02690-2},
pmid = {41518539},
issn = {1432-184X},
support = {2023YFD2301301, 2017YFD0301601//This study was supported by National Key R&D Program of China/ ; 2023YFD2301301, 2017YFD0301601//This study was supported by National Key R&D Program of China/ ; 2023YFD2301301, 2017YFD0301601//This study was supported by National Key R&D Program of China/ ; 2023YFD2301301, 2017YFD0301601//This study was supported by National Key R&D Program of China/ ; 2023YFD2301301, 2017YFD0301601//This study was supported by National Key R&D Program of China/ ; 2023YFD2301301, 2017YFD0301601//This study was supported by National Key R&D Program of China/ ; 2023YFD2301301, 2017YFD0301601//This study was supported by National Key R&D Program of China/ ; 2023YFD2301301, 2017YFD0301601//This study was supported by National Key R&D Program of China/ ; 2023YFD2301301, 2017YFD0301601//This study was supported by National Key R&D Program of China/ ; 2023YFD2301301, 2017YFD0301601//This study was supported by National Key R&D Program of China/ ; 2023YFD2301301, 2017YFD0301601//This study was supported by National Key R&D Program of China/ ; 20232BAB215012//The Jiangxi Provincial Natural Science Foundation/ ; 20232BAB215012//The Jiangxi Provincial Natural Science Foundation/ ; 20232BAB215012//The Jiangxi Provincial Natural Science Foundation/ ; 20232BAB215012//The Jiangxi Provincial Natural Science Foundation/ ; 20232BAB215012//The Jiangxi Provincial Natural Science Foundation/ ; 20232BAB215012//The Jiangxi Provincial Natural Science Foundation/ ; 20232BAB215012//The Jiangxi Provincial Natural Science Foundation/ ; 20232BAB215012//The Jiangxi Provincial Natural Science Foundation/ ; 20232BAB215012//The Jiangxi Provincial Natural Science Foundation/ ; 20232BAB215012//The Jiangxi Provincial Natural Science Foundation/ ; 20232BAB215012//The Jiangxi Provincial Natural Science Foundation/ ; 42377309, 42407427//The National Natural Science Foundation of China/ ; 42377309, 42407427//The National Natural Science Foundation of China/ ; 42377309, 42407427//The National Natural Science Foundation of China/ ; 42377309, 42407427//The National Natural Science Foundation of China/ ; 42377309, 42407427//The National Natural Science Foundation of China/ ; 42377309, 42407427//The National Natural Science Foundation of China/ ; 42377309, 42407427//The National Natural Science Foundation of China/ ; 42377309, 42407427//The National Natural Science Foundation of China/ ; 42377309, 42407427//The National Natural Science Foundation of China/ ; 42377309, 42407427//The National Natural Science Foundation of China/ ; 42377309, 42407427//The National Natural Science Foundation of China/ ; SDAST2024QTA012//The Young Talent of Lifting engineering for Science and Technology in Shandong/ ; SDAST2024QTA012//The Young Talent of Lifting engineering for Science and Technology in Shandong/ ; SDAST2024QTA012//The Young Talent of Lifting engineering for Science and Technology in Shandong/ ; SDAST2024QTA012//The Young Talent of Lifting engineering for Science and Technology in Shandong/ ; SDAST2024QTA012//The Young Talent of Lifting engineering for Science and Technology in Shandong/ ; SDAST2024QTA012//The Young Talent of Lifting engineering for Science and Technology in Shandong/ ; SDAST2024QTA012//The Young Talent of Lifting engineering for Science and Technology in Shandong/ ; SDAST2024QTA012//The Young Talent of Lifting engineering for Science and Technology in Shandong/ ; SDAST2024QTA012//The Young Talent of Lifting engineering for Science and Technology in Shandong/ ; SDAST2024QTA012//The Young Talent of Lifting engineering for Science and Technology in Shandong/ ; SDAST2024QTA012//The Young Talent of Lifting engineering for Science and Technology in Shandong/ ; SKL81103//The Funding for the 'First Class Discipline' Construction Project of Shandong Agricultural University/ ; SKL81103//The Funding for the 'First Class Discipline' Construction Project of Shandong Agricultural University/ ; SKL81103//The Funding for the 'First Class Discipline' Construction Project of Shandong Agricultural University/ ; SKL81103//The Funding for the 'First Class Discipline' Construction Project of Shandong Agricultural University/ ; SKL81103//The Funding for the 'First Class Discipline' Construction Project of Shandong Agricultural University/ ; SKL81103//The Funding for the 'First Class Discipline' Construction Project of Shandong Agricultural University/ ; SKL81103//The Funding for the 'First Class Discipline' Construction Project of Shandong Agricultural University/ ; SKL81103//The Funding for the 'First Class Discipline' Construction Project of Shandong Agricultural University/ ; SKL81103//The Funding for the 'First Class Discipline' Construction Project of Shandong Agricultural University/ ; SKL81103//The Funding for the 'First Class Discipline' Construction Project of Shandong Agricultural University/ ; SKL81103//The Funding for the 'First Class Discipline' Construction Project of Shandong Agricultural University/ ; },
abstract = {Cadmium (Cd) contamination in soil is a growing problem, posing a significant threat to soil microorganisms and plant growth. Understanding how Cd exposure disrupts the evolution of soil microbial communities and the mechanisms underlying community remodeling requires further investigation. In this study, the rice rhizosphere treated with 0 (CK), 2.5 (LC), 5 (MC), and 15 (HC) mg kg[-1] Cd was used as a model and combined with 16S rRNA gene sequencing to systematically evaluate the response patterns of rice rhizosphere microbial communities under Cd gradient treatments. The study found that rice rhizosphere microbial communities responded to Cd exposure with a unimodal pattern of "low-promotion and high-suppression". LC treatment significantly increased the alpha diversity of rare fungal taxa and significantly enriched rare genera such as Candidatus Solibacter and Penicillium. Network analysis further confirmed that LC treatment significantly enhanced symbiotic relationships within and across rare taxa. The assembly of abundant bacterial and fungal taxa was consistently dominated by stochastic diffusional constraints, while rare taxa were primarily driven by deterministic homogeneous selection. In summary, rice rhizosphere microbial communities showed specific response patterns under Cd gradient treatment. Rare fungal taxa, as core members, actively responded to Cd exposure, made prominent contributions to shaping the community composition, and played a crucial role in maintaining the complexity and stability of the microbial network.},
}

@article {pmid41518434,
year = {2026},
author = {Klammsteiner, T and Heussler, CD and Stonig, KT and Insam, H and Schlick-Steiner, BC and Steiner, FM},
title = {Stage-Specific Microbiota Transitions Throughout Black Soldier Fly Ontogeny.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02691-1},
pmid = {41518434},
issn = {1432-184X},
abstract = {The growing global population increases the demand for protein, while organic waste management has become more challenging. Alternative protein sources are essential to mitigate the environmental impact of food production. The black soldier fly (BSF; Hermetia illucens) has emerged as an alternative to traditional protein sources (e.g., soybean meal, fishmeal) due to its ability to convert diverse organic waste, addressing both issues simultaneously. This makes the BSF a promising candidate for industrial rearing, with its successful development closely tied to microbial influences on growth and behaviour, particularly bacterial influences on oviposition. In this study, we focus on the microbiota throughout insect development with a special focus on egg surface microbiota and their origin. We analysed the microbiota in the haemolymph and gut of larvae raised on sterilized and non-sterilized feed, pupal cell pulp, the wash of the ovipositor, eggs directly collected after oviposition, ovarian eggs, the empty female abdomen, eggs exposed to adult BSF, and surface-sterilized eggs. Our analysis revealed distinct bacterial community profiles across life stages, indicating a transition from larval dominance of Enterobacteriaceae to Burkholderiaceae on all analysed eggs. At the genus level, larval stages were characterized by Morganella, Escherichia, and Proteus, transitioning to less diverse communities in egg samples predominated by Burkholderia-Caballeronia-Paraburkholderia. Our study reveals that while predominant microbiota persist throughout all life stages, microbial community composition transforms progressively during maturation, particularly before oviposition. Understanding egg surface microbiota and the cues guiding oviposition has the potential to boost egg production and simplify mass harvesting of BSF larvae.},
}

@article {pmid41515900,
year = {2025},
author = {Wu, J and Zhou, L and Qiu, D and Wei, T and Xie, C and Chen, E and Lin, M and Fan, Y},
title = {Integrating Bioinformatics and Experimental Validation Identifies SCD as a Ferroptosis-Related Immune Regulator and Therapeutic Target in Crohn's Disease.},
journal = {International journal of molecular sciences},
volume = {27},
number = {1},
pages = {},
doi = {10.3390/ijms27010019},
pmid = {41515900},
issn = {1422-0067},
support = {2025J011410//the Natural Science Foundation of Fujian Province/ ; 2025J08298//the Natural Science Foundation of Fujian Province/ ; },
mesh = {*Ferroptosis/genetics/immunology ; *Crohn Disease/genetics/immunology/metabolism/pathology/drug therapy ; *Computational Biology/methods ; Humans ; Animals ; Mice ; Disease Models, Animal ; Gene Expression Profiling ; Colitis/genetics/chemically induced/immunology ; },
abstract = {This study investigates the role of ferroptosis-related genes (FRGs) in the intestinal inflammation of Crohn's disease (CD). Through integrated bioinformatics and experimental validation, we identified differentially expressed genes from RNA-seq data and intersected them with known FRGs to obtain ferroptosis-related differentially expressed genes (FEDGs). Functional enrichment and immune infiltration analyses were performed, and seven hub FEDGs were selected using machine learning. A diagnostic model based on these genes showed strong predictive ability. Immune analysis revealed significant associations with macrophages, neutrophils, dendritic cells, and CD4+ T cells. Protein expression of key hub genes was validated in clinical CD samples and a DSS-induced colitis model. Importantly, localized inhibition of SCD alleviated disease severity in experimental colitis. These findings highlight the involvement of ferroptosis in CD immune dysregulation and propose SCD as a potential therapeutic target.},
}

*Ferroptosis/genetics/immunology
*Crohn Disease/genetics/immunology/metabolism/pathology/drug therapy
*Computational Biology/methods
Humans
Animals
Mice
Disease Models, Animal
Gene Expression Profiling
Colitis/genetics/chemically induced/immunology

@article {pmid41514812,
year = {2026},
author = {Huang, Q and Chang, M and Sun, P},
title = {Early-Life Galacto-Oligosaccharide Supplementation Induces Persistent Immunoglobulin and Metabolic Alterations in Holstein Dairy Calves by Shaping Gut Microbiota.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {1},
pages = {},
doi = {10.3390/ani16010126},
pmid = {41514812},
issn = {2076-2615},
support = {2022YFD1301101//National Key Research and Development Program of China/ ; 2022YFD1300505//National Key Research and Development Program of China/ ; CARS-37//The earmarked fund for China Agriculture Research System/ ; Y2025YC52//Central Public-interest Scientific Institution Basal Research Fund/ ; ASTIP-IAS07//Agricultural Science and Technology Innovation Program/ ; },
abstract = {Early-life development of immune functions is crucial for calf health, growth, and future productivity. Galacto-oligosaccharides (GOSs) have been reported to facilitate ruminal microbial establishment and improve growth in Holstein dairy calves, but their prolonged influence on immunoglobulin levels, hindgut microbiota, and metabolic regulation remains insufficiently understood. This study evaluated the effects of early-life GOS supplementation on immune-related indicators, intestinal microbial ecology, and metabolic profiles in Holstein calves. Twenty-four newborn Holstein female dairy calves were randomly assigned to a control group (CON, n = 12) or a GOS group (GOS, n = 12; 10 g/day from birth to day 28). After supplementation ceased on day 28, calves previously receiving GOS were referred to as the GOSS group (n = 6). Immunoglobulin levels, gut microbiota, and fecal and serum metabolomes were evaluated during supplementation and six weeks after withdrawal. GOS supplementation significantly increased serum IgA and IgG levels during the treatment, with IgG levels remaining elevated for six weeks after discontinued supplementation. Although overall microbial diversity was not markedly altered, GOS selectively enriched bacterial taxa and function pathways linked to amino acid synthesis, unsaturated fatty acid production, and coenzyme-related metabolism. On day 70, GOSS group displayed distinct fecal and serum metabolomic profiles, with altered metabolites primarily associated with vitamin B6, folate, cobalamin metabolism, branched-chain amino acid biosynthesis, and purine and arginine pathways. These results demonstrate that early-life GOS supplementation promotes sustained immune and metabolic alterations following supplementation cessation, potentially mediated by modulation of gut microbial functions. These findings suggest that early dietary GOS supplementation may support physiological maturation in calves and could be useful as a nutritional strategy in calf-rearing systems.},
}

@article {pmid41514032,
year = {2026},
author = {Roncero-Ramos, B and Romano-Rodríguez, E and Mateos-Naranjo, E and Valle-Romero, P and Redondo-Gómez, S},
title = {Hydro- and Xerohalophyte Species Drive Compositional and Functional Divergence in Bacterial Leaf Endosphere.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02679-x},
pmid = {41514032},
issn = {1432-184X},
support = {PAIDI-DOCTOR 21_00571//Junta de Andalucía/ ; FPU21/04133//Ministerio de Universidades/ ; FPU22/02078//Ministerio de Universidades/ ; PID2021-124750NB-I00//Ministerio de Ciencia e Innovación/ ; },
abstract = {Hydro- and xerohalophytes withstand stress thanks to the resistance traits they have, complemented with the functions of their associated microbiota. Besides, given a higher exposition of the phyllosphere to environmental conditions compared to roots, their endospheric bacteria should be more resistant to stress. In this study, we analysed the composition and functional traits of the bacterial leaf endosphere of six xero- and hydrohalophytes species in two seasons. We sequenced their endospheric metagenomes by shotgun and annotated genes related with Plant-Growth-Promoting (PGP) properties. We showed that the composition, structure and functions of the bacterial endosphere are mainly influenced by host plant species, followed by functional type. Moreover, plant species and functional type promoted a different relative abundance of, respectively, 62 and 6 PGP properties. This study shows that not only the composition but also the functionality of the bacterial leaf endosphere of halophytes is more influenced by host species than functional type. Moreover, the leaf endosphere of the different plant species and functional type could be an important source of bacteria with diverse PGP properties.},
}

@article {pmid41513996,
year = {2026},
author = {Zhang, R and Mayer, L and Hikida, H and Shichino, Y and Mito, M and Willemsen, A and Iwasaki, S and Ogata, H},
title = {A giant virus forms a specialized subcellular environment within its amoeba host for efficient translation.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41513996},
issn = {2058-5276},
support = {JP18H02279//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP22H00384//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP23KJ1258//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP24H02307//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JPMJFS2123//MEXT | Japan Science and Technology Agency (JST)/ ; },
abstract = {Many eukaryotic viruses, including amoeba-infecting mimiviruses, have codon usage that deviates from their hosts. However, codon usage patterns that align with the cellular tRNA pool enable efficient translation. How these viruses cope with the mismatch between tRNA supply and demand is unclear. Here we show that Acanthamoeba polyphaga mimivirus (APMV) generates a subcellular area to translate viral mRNAs. tRNA sequencing showed that the tRNA pool was not substantially altered during the infection, even though the virus encodes tRNA genes. Using in situ labelling, we found that viral mRNAs and newly synthesized proteins were localized in the periphery of the viral factory, suggesting that APMV creates a discrete subcellular environment to facilitate translation. Frequently used codons in viral mRNAs had higher tRNA accessibility than the same type of codons in amoeba mRNAs. Our data show how local translation assists the virus in overcoming the mismatch between tRNA supply and demand.},
}

@article {pmid41513647,
year = {2026},
author = {Lu, Y and Eisenhauer, N and Patoine, G and Chen, Y and Heintz-Buschart, A and Küsel, K and Wegner, CE and Buscot, F and Liu, X and Araujo, ASF and Frey, B and Maestre, FT and Vadeboncoeur, M and van den Brink, L and Ponette, Q and Didion, M and Wohlfahrt, G and Gaxiola, A and Branquinho, C and Meesenburg, H and Fukuzawa, K and Adair, EC and Andrić, A and Barna, M and Bei, Q and Bruelheide, H and Caliman, A and Canessa, R and Carbognani, M and Cazzolla Gatti, R and Chen, C and Christiansen, CT and Danger, M and Davydov, EA and de Graaff, MA and Delire, C and Cecco, VD and Martino, LD and Djukic, I and Drollinger, S and Enoki, T and Fekete, I and Fransson, P and Freitag, M and Frenzel, M and Gavilán, RG and Glatzel, S and Glushkova, M and González, G and Gripp, ADR and Haase, P and Hamer, U and Hishi, T and Hiura, T and Hornung, E and Hoshizaki, K and Jäger, H and Jiménez, JJ and Kelly-Slatten, MJ and Kepfer-Rojas, S and Kotroczó, Z and Kriiska, K and Kurokawa, H and Lajtha, K and Loehr, J and Löfgren, S and Maire, V and Martins, RL and Maunoury-Danger, F and Melece, I and Ochoa, V and Ostonen, I and Paquette, A and Parker, WC and Peri, PL and Mast, R and Petraglia, A and Petřík, P and Pușcaș, M and Rebmann, C and Reich, PB and Rillig, MC and Schädler, M and Schaub, M and Schmidt, A and Seeber, J and Serrano, HC and Sousa, AI and Scheu, S and Stefanski, A and Tomaselli, M and Tóth, Z and Trevathan-Tackett, SM and Trogisch, S and Turtureanu, PD and Ursu, TM and Venn, SE and Verstraeten, A and Vijayanathan, J and Vujanović, D and Wagner, M and Weih, M and Zehetner, F and Guerra, CA},
title = {Landscape effects on global soil pathogenic fungal diversity across spatial scales.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-67929-5},
pmid = {41513647},
issn = {2041-1723},
support = {EI 862/29-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
abstract = {Growing evidence has shown that, apart from local environmental factors, changes in landscape-level factors by accelerated land-use change can also shape soil pathogenic fungal diversity. However, the global representativeness of such patterns remains unclear. Here, we assess how pathogenic fungal diversity in 511 soil samples worldwide responds to landscape factors, including landscape complexity index based on eight landscape metrics and quantity of different land cover types across six spatial scales (i.e., surrounding landscape, 250 m to 10,000 m radii from the sampling coordinate). We find that while soil variables explain over half of the variance, pathogenic fungal alpha diversity increases with landscape complexity and crop cover proportion, but decreases with grass and tree cover proportion, together explaining 23.4% of the total variance. Landscape factors have weaker impacts on beta diversity, explaining 13.0% of the variance. Across spatial scales, grassland ecosystems exhibit increasingly stronger responses to landscape variables compared to forest ecosystems. Landscape factors have a higher relative contribution to root-associated fungi than leaf/fruit/seed-associated fungi. Our results emphasize the importance of local factors and the complementary role of landscape patterns in shaping global soil pathogenic fungal distributions, highlighting scale-dependent effects across ecosystems and fungal functional groups.},
}

@article {pmid41511110,
year = {2026},
author = {Gallardo Molina, P and Choi, BI and Vanek, M and Khan, MH and Tomasek, K and Kwant, AN and Dijkstra, P and de Vos, MGJ and Wolfe, AJ},
title = {SimUrine: a novel, fully defined artificial urinary medium for enhanced microbiological research of urinary bacteria.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0155925},
doi = {10.1128/aem.01559-25},
pmid = {41511110},
issn = {1098-5336},
abstract = {UNLABELLED: Urinary tract infections represent one of the most prevalent bacterial diseases, yet current diagnostic and research methodologies are hampered by inadequate culture media that fail to replicate the bladder biochemical environment. Conventional artificial urine formulations contain undefined components, lack essential nutrients, or inadequately support urinary microbiome (urobiome) growth. To address these limitations, we developed SimUrine, a fully defined synthetic urine medium that aims to replicate human bladder chemistry while supporting diverse microbial growth requirements. SimUrine was systematically developed through iterative optimization of multi-purpose artificial urine, incorporating defined concentrations of carbon sources, vitamins, trace elements, and amino acids within physiologically relevant ranges. The modular design enables component substitution without complete reformulation, facilitating customization for culturomics, antimicrobial susceptibility testing, and microbial ecology studies, while reducing batch-to-batch variability associated with authentic urine. Performance evaluation demonstrated SimUrine's capability to support the growth of fastidious urobiome members, including Lactobacillus species, Aerococcus urinae, and Corynebacterium riegelii, which fail to proliferate in conventional minimal media. Physicochemical characterization confirmed that SimUrine formulation exhibits properties within normal human urine ranges for density, conductivity, osmolarity, and viscosity, ensuring physiological relevance. Clinical applications revealed reduced antibiotic susceptibility compared to standard media, suggesting a more accurate representation of in vivo conditions. Co-culture experiments using Escherichia coli and Enterococcus faecalis demonstrated previously unobserved microbial interactions, highlighting SimUrine's utility for investigating urobiome dynamics. SimUrine represents a significant advancement in urobiome research methodology, providing a standardized, reproducible platform for investigating the urobiome under physiologically relevant conditions, potentially improving fundamental understanding and clinical diagnostic approaches.

IMPORTANCE: Urinary tract infections (UTIs) affect millions globally, yet current research and diagnostic methods rely on inadequate culture media that fail to replicate the bladder's unique biochemical environment. This fundamental limitation has hindered accurate UTI research and potentially compromised clinical treatment decisions. SimUrine addresses this critical gap as the first fully defined synthetic urine medium that mimics human bladder chemistry while supporting the growth of diverse urinary microbes. The breakthrough enables the cultivation of urobiome organisms in a minimal medium that resembles natural conditions, revealing novel microbial interactions that influence urinary health. Crucially, SimUrine demonstrates different antimicrobial susceptibility patterns compared to standard clinical media, suggesting current testing protocols may inaccurately predict treatment outcomes. This standardized, reproducible platform eliminates the variability of authentic urine samples while maintaining physiological relevance, potentially transforming urobiome research methodology and providing a new tool for the study of UTIs worldwide.},
}

@article {pmid41508507,
year = {2026},
author = {Lee, G and Heo, S and Jeong, DW},
title = {Origin and prevalence of food-derived coagulase-negative staphylococci in fermentation: impact of protein, lipid, salt, and pH conditions.},
journal = {Food research international (Ottawa, Ont.)},
volume = {225},
number = {},
pages = {118096},
doi = {10.1016/j.foodres.2025.118096},
pmid = {41508507},
issn = {1873-7145},
mesh = {*Staphylococcus/isolation & purification/classification/enzymology/metabolism ; Hydrogen-Ion Concentration ; *Fermentation ; *Food Microbiology ; *Fermented Foods/microbiology ; Coagulase/metabolism ; Sodium Chloride/analysis ; },
abstract = {Coagulase-negative staphylococci (CNS) are primarily detected in protein-rich and high-salt fermented foods, such as fermented meat and soybean products. This review investigates the relationship between CNS species and the nutritional and physicochemical properties of fermented foods, focusing on protein, fat, carbohydrate composition, salt concentration, and pH. Published studies over the past 20 years were systematically analyzed to identify CNS species and their distribution across food types and regions. Among the species, Staphylococcus saprophyticus, S. xylosus, S. equorum, and S. gallinarum were most frequently reported. S. saprophyticus was detected across a broad range of conditions, whereas S. xylosus was more common in acidic environments (pH 4-6). S. equorum dominated in higher pH (5-8) and high-salt (>20%) conditions, whereas S. gallinarum persisted even in salt concentrations exceeding 15%. These findings indicate that nutrient composition, pH, and salt concentration shape the dominant CNS species in fermented foods. Such correlations not only improve our understanding of microbial ecology in fermentation but also provide a basis for the selection and application of tailored starter cultures in the food industry.},
}

*Staphylococcus/isolation & purification/classification/enzymology/metabolism
Hydrogen-Ion Concentration
*Fermentation
*Food Microbiology
*Fermented Foods/microbiology
Coagulase/metabolism
Sodium Chloride/analysis

@article {pmid41506929,
year = {2026},
author = {Rodríguez-Gijón, A and Laso-Pérez, R},
title = {Deep-learning dive into the antimicrobial potential of Archaea.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2025.12.004},
pmid = {41506929},
issn = {1878-4380},
abstract = {The global burden of antimicrobial resistance demands the urgent development of new antibiotics. To face this threat, Torres et al. leveraged deep-learning models to identify archaeal encrypted peptides (termed 'archaeasins') with potential antimicrobial activity. This work highlights Archaea as an underexplored but potentially rich source of antibiotics.},
}

@article {pmid41506577,
year = {2026},
author = {Sagar, K and Priti, K and Chandra, H},
title = {Artificial intelligence in metagenome-assembled genome reconstruction: Tools, pipelines, and future directions.},
journal = {Journal of microbiological methods},
volume = {},
number = {},
pages = {107390},
doi = {10.1016/j.mimet.2026.107390},
pmid = {41506577},
issn = {1872-8359},
abstract = {Metagenomic sequencing has revolutionised the field of microbial ecology, as it has led to cultivation-independent exploration of complicated microbial communities. The assembly of metagenome-assembled genomes has provided genome-scale information about uncultivated microorganisms, but issues such as sequencing errors, fragmented assemblies, residual redundancy, uneven coverage, recovery of low-abundance taxa, and highly diversified taxa continue to impair the quality of these genomes. The latest achievements in artificial intelligence, particularly in machine learning and deep learning, have played a significant role in overcoming these limitations by enhancing quality control, error correction, assembly, binning, refinement, and annotation procedures. It is demonstrated that representation learning and graph-based binning methods have high strain-level resolution and can reduce contamination in complex microbial communities, whereas artificial intelligence-based assemblers and polishing tools improve base-level precision and assembly contiguity. This review synthesises traditional and artificial intelligence-based workflows involved in the reconstruction of metagenome-assembled genomes, encompassing quality control, assembly, binning, refinement, and annotation, as well as quantitative benchmarking of significant artificial intelligence-based pipelines. As future directions, the focus on emerging trends, such as explainable artificial intelligence, federated learning, cloud-native scalable pipelines, multimodal and multi-omics integration, and large language model-based annotation, is covered. In general, the incorporation of artificial intelligence represents a paradigm shift in the reconstruction of metagenome-assembled genomes, allowing for a more relevant, scalable, and biologically informative search of the microbial dark matter in various ecosystems.},
}

@article {pmid41504899,
year = {2026},
author = {Cottorello-Fonsêca, M and Rezende, EGF and Freitas, FRS and Carneiro, RB and Sakamoto, IK and Ribeiro, R and Zaiat, M},
title = {Understanding the kinetics of antibiotic mixture biotransformation and microbial interactions in an anaerobic fixed-bed reactor for wastewater treatment.},
journal = {Bioprocess and biosystems engineering},
volume = {},
number = {},
pages = {},
pmid = {41504899},
issn = {1615-7605},
support = {2020/15087-8//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 22/04367-5//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2019/22532-0//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2020/15087-8//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; Financial Code 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; PCI2022-121990//EU and the State Research Agency (AEI)/ ; PCI2022-121990//EU and the State Research Agency (AEI)/ ; 869178//ERA-NET AquaticPollutants Joint Transnational Call/ ; 869178//ERA-NET AquaticPollutants Joint Transnational Call/ ; },
abstract = {The increase of antibiotics in aquatic environments, along with the emergence of antibiotic-resistant bacteria, highlights the improvement of wastewater treatment technologies. This study investigates a plug-flow structured anaerobic fixed-bed reactor (PF-AnFBR) for removal nine antibiotics representing different classes-an approach rarely explored in anaerobic systems. By integrating spatially resolved sampling along the reactor bed with advanced kinetic modeling, the study provides the first mechanistic evaluation of antibiotic mixture removal in a PF-AnFBR. COD removal remained high (COD > 97%) despite the presence of antibiotics, and significant removal was observed for trimethoprim (100%), sulfamethoxazole (83.3%), and enrofloxacin (81.3%). The first-order model accurately described COD removal, while the reversible biotransformation model (RevBio) successfully captured antibiotic fate (NRMSE < 3.5%), revealing class-specific mechanisms: fluoroquinolones dominated by adsorption (high KD and ksor), sulfonamides exhibiting reversible biotransformation, and trimethoprim characterized by highly irreversible biotransformation. Microbial community and KEGG-based functional analyses identified key taxa (e.g., Pseudomonas, Lactivibrio, Syntrophorhabdus, Methanothrix) and metabolic pathways (ABC transporters, cytochrome P450 enzymes) responsible for antibiotic transformation. By coupling reactor hydrodynamics, kinetic modeling, and microbial ecology, this study provides novel mechanistic insight into the removal of complex antibiotic mixtures in anaerobic fixed-bed reactors and supports PF-AnFBR as a robust technology for decentralized wastewater treatment.},
}

@article {pmid41504158,
year = {2025},
author = {Chen, T and Guo, Y and Liang, D and Li, D and Xing, S and Li, D and Zhang, C and Wang, F},
title = {Discriminative Gut Microbial Signatures in Hyperuricemia and Overweight Populations Revealed by Metagenomic Sequencing.},
journal = {International journal for vitamin and nutrition research. Internationale Zeitschrift fur Vitamin- und Ernahrungsforschung. Journal international de vitaminologie et de nutrition},
volume = {95},
number = {6},
pages = {42590},
doi = {10.31083/IJVNR42590},
pmid = {41504158},
issn = {0300-9831},
support = {S2023KFKT-12//Ministry of Agriculture and Rural Affairs/ ; 2024YFF1107000//National Key Research and Development Program of China/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Hyperuricemia/microbiology ; Male ; Female ; *Overweight/microbiology ; Middle Aged ; Cross-Sectional Studies ; Feces/microbiology ; Adult ; Metagenomics ; Metagenome ; },
abstract = {BACKGROUND: This cross-sectional study aimed to investigate the relationships between gut microbiota compositional alterations and chronic metabolic disorders by analyzing taxonomic diversity, community structure, and species-level differences in individuals with hyperuricemia (HUA) and a history of being overweight. Our findings offer novel insights into microbiota-targeted therapeutic strategies for managing metabolic diseases. A total of 144 participants were recruited and divided into three diagnostic categories: healthy controls (HL, n = 29), hyperuricemia group (HU, n = 24), and overweight (OW, n = 91).

METHODS: Comprehensive phenotypic profiles and metagenomes were analyzed for fecal samples from the three groups.

RESULTS: Significant differences were observed in psychological states and microbial ecology between the metabolic disorder groups (HU and OW) and the control group (HL) (p < 0.05). Both the overweight individuals and those with HUA presented significant changes in gut microbial composition, with reduced α-diversity indices (Shannon index: HU vs HL Mann-Whitney U = 306; p = 0.462; OW vs HL Mann-Whitney U = 1008; p = 0.040; richness index: HU vs HL Mann-Whitney U = 307; p = 0.469; OW vs HL Mann-Whitney U = 1072; p = 0.092) compared to healthy individuals. Moreover, analysis of the linear discriminant analysis effect size (LEfSe) identified four discriminatory species in the HU group (Alistipes putredinis, Mediterraneibacter faecis, Streptococcus oralis, and Gemella sanguinis), and five in the OW group (Pantoea endophytica, Pantoea vagans, Phocaeicola coprophilus, Ruminococcus SGB4421, and Klebsiella oxytoca), representing potential biomarkers for the progression of chronic metabolic diseases.

CONCLUSION: This study elucidates the characteristics of overweight individuals and those with HUA in terms of phenotypic features and gut microbiota, providing a theoretical reference for gut microbiota-targeted therapies and lifestyle interventions in chronic metabolic diseases.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Hyperuricemia/microbiology
Male
Female
*Overweight/microbiology
Middle Aged
Cross-Sectional Studies
Feces/microbiology
Adult
Metagenomics
Metagenome

@article {pmid41502987,
year = {2026},
author = {Mohan, R and Johnson, SD and Dean, PN and Acharya, A and Byrareddy, SN},
title = {Methods to characterize the vaginal microbiome in a rhesus macaque model of simian human immunodeficiency virus (SHIV) transmission uncover epithelium-associated enrichment of Prevotella.},
journal = {Current research in microbial sciences},
volume = {10},
number = {},
pages = {100526},
pmid = {41502987},
issn = {2666-5174},
abstract = {The vaginal microbiome plays a crucial role in maintaining mucosal integrity and mitigating pathogen transmission, yet its comprehensive characterization remains challenging due to limited sampling and analysis methods. In this study, we aimed to characterize bacterial and fungal taxa diversities in the vaginal microbiomes of Simian Human Immunodeficiency (SHIV)-infected rhesus macaques, as well as their metabolic activities, using three sampling methods. The cervicovaginal lavage (CVL), vaginal swab, and vaginal mucosal tissue methods offer novel insights into microbial diversity and their potential impacts on HIV transmission. Using 16S rRNA and Internal Transcribed Spacer (ITS) sequencing, we assessed bacterial and fungal community composition and abundances, respectively, across all sampling methods. PICRUSt2 was used for functional predictions, and a modified glycosidase assay to further characterize glycan-degrading enzymatic activity in CVL samples. Our findings reveal that tissue samples were uniquely enriched for microbial taxa such as Prevotella spp. and Helicobacter spp., showing notable abundance differences compared to CVL and swab samples. Tissue samples exhibited higher alpha diversity and distinct metabolic prediction profiles, particularly elevated sialidase activity. While fewer differences were found in fungal microbiome composition and diversity, marked correlations were observed between bacterial and fungal taxa, emphasizing complex interkingdom interactions. These results highlight the significance of sampling methods in microbial ecology studies, which should be carefully considered due to their potential influence on pathogen transmission risk.},
}

@article {pmid41502854,
year = {2025},
author = {Su, JW and Qin, SY and Liu, J and Lei, CC and Zhang, XT and Shi, WH and Xie, LH and Liu, Y and Ni, HB and Yu, MY and Liang, HR and Qin, Y and Jiang, J and Sun, HT and Ma, H and Li, ZY and Zhang, XX},
title = {Blastocystis presence alters gut archaeal communities and metabolic functions in Tibetan antelopes (Pantholops hodgsonii).},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1744013},
pmid = {41502854},
issn = {2297-1769},
abstract = {BACKGROUND: Archaea are vital members of the gut microbiota, yet their diversity and functions in high-altitude wildlife remain poorly understood. Understanding their ecological roles can provide insights into host health and microbial community dynamics.

METHODS: We applied metagenome-assembled genome (MAG)-based approaches to investigate gut archaea in Tibetan antelopes (Pantholops hodgsonii) and assess their shifts in the presence of Blastocystis. A total of 463 non-redundant archaeal MAGs were reconstructed and analyzed for taxonomic diversity and functional potential.

RESULTS: The MAGs encompassed 16,189 protein clusters, with over 70% representing potentially novel species, highlighting substantial unexplored archaeal diversity. Alpha diversity showed no significant differences between healthy and Blastocystis-present groups, but beta diversity analysis revealed marked community restructuring, including decreased Methanobacteriota and increased Halobacteriota and Thermoplasmatota in the Blastocystis-present group. Functional annotation indicated changes in energy and nucleotide metabolism and alterations in carbohydrate-active enzyme composition. Additionally, putative viral sequences were detected within archaeal MAGs, suggesting potential virus-microbe interactions.

CONCLUSION: Our findings provide novel insights into the diversity and ecological functions of gut archaea in Tibetan antelopes, offering a foundation for future research on their contributions to host health and microbial ecology.},
}

@article {pmid41501262,
year = {2026},
author = {Carofano, I and Martinez-Sañudo, I and Riegler, M and Hancock, DL and Morrow, JL and Mazzon, L},
title = {Detection of a Conserved Bacterial Symbiosis in non-frugivorous Australian Fruit Flies (Diptera, Tephritidae, Tephritinae) Supports its Widespread Association.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02686-y},
pmid = {41501262},
issn = {1432-184X},
support = {DOR2271053/22//Università degli Studi di Padova/ ; },
abstract = {Several insect lineages, including some fruit flies, have evolved mutualistic associations with primary symbiotic bacteria. Some species of Tephritinae, the most specialized subfamily of fruit flies (Diptera, Tephritidae) harbour co-evolved, vertically transmitted and non-culturable bacterial symbionts in their midgut, known as Candidatus Stammerula spp. (Enterobacteriaceae). While such associations have previously been reported in the Palearctic and Hawaiian Archipelago, their occurrence in Australasia had not been investigated. In this study we assessed the genetic diversity of eight Australian fruit fly's species from six genera belonging to the Tephritini tribe using mitochondrial markers (16 S rRNA and COI-tRNALeu-COII genes) and compared their bacterial diversity using the 16 S rRNA gene. We detected the presence of specific symbiotic bacteria in all sampled species. Analysis of bacterial 16 S rRNA showed that, with one exception, all Australian symbionts clustered in a well-supported monophyletic clade with Ca. Stammerula detected in Palearctic and Hawaiian Tephritini. Distinct Stammerula lineages were identified in several taxa, while two species, Trupanea prolata and Spathulina acroleuca shared identical symbiont sequences and the same host plant. Notably, Australian and Palearctic Sphenella spp. harboured closely related symbionts. The cophylogenetic analysis revealed a substantial congruence between host and symbiont tree, supporting a history of cospeciation and suggesting biogeographic links between Australasian and Palearctic taxa. Overall, the results expand the geographic knowledge of Tephritini-Ca. Stammerula association and highlight a global pattern of co-diversification.},
}

@article {pmid41499160,
year = {2026},
author = {Hai, Q and Li, D and Huang, T and Dang, X and Xu, J and Ma, Z and Zhou, Z},
title = {The Honeybee Gut Microbiome: A Novel Multidimensional Model of Antimicrobial Resistance Transmission and Immune Homeostasis from Environmental Interactions to Health Regulation.},
journal = {FEMS microbiology reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsre/fuag001},
pmid = {41499160},
issn = {1574-6976},
abstract = {The honeybee gut microbiome has emerged as a model system in microbial ecology, valued for its structural stability and host specificity, and has garnered significant attention for elucidating universal principles of host-microbe interactions. This review advocates for the honeybee as a multidisciplinary model organism, highlighting the unique role of its gut microbiota in maintaining colony immune homeostasis, driving host co-evolution, unraveling the transmission mechanisms of antibiotic resistance genes (ARGs), and enhancing host adaptability to environmental stressors. By integrating multidimensional factors, including environmental gradients and apicultural practices, we construct an "Environment-Microbiota-Host Health" interaction framework to transcend the limitations of single-factor analyses. This framework provides a novel paradigm for the ecological containment of antimicrobial resistance, the conservation of pollinator resources, and microbiome-based engineering interventions. The review underscores the unique value of the honeybee model in unraveling social insect-microbe coevolution and resistance transmission dynamics, while also prospecting its application potential in developing novel antimicrobial peptides, designing probiotic formulations, and monitoring environmental resistance.},
}

@article {pmid41499039,
year = {2026},
author = {Madjirebaye, P and Penga, Z and Mueeda, A and Huang, T and Peng, F and Muyan, X and Liua, Z and Mahamat, B and Allasra, Y and Xu, Y and Xiong, T and Xie, M},
title = {Unraveling Streptococcus Thermophilus NCU074001-Based Anti-Diarrheal Actions Via Integrated Immune-Gut Microbiota and Tryptophan Metabolic Pathway Identification.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {41499039},
issn = {1867-1314},
support = {Project No. 20243BCC31004; Project No. S20251709//Key Research and Development Projects of Jiangxi Province/ ; Project No. 20232BCD44005//National Key Laboratory Project/ ; Project No. 2022-PYXM-04//), Jiangxi Medicine Academy of Nutrition and Health Management 2022 Cultivation project/ ; Project No. JXNK202303-05//Agricultural key core technology research project of Jiangxi Province/ ; Project No. JXARS-06//Vegetable Industry Technology System Post Expert Project of Jiangxi Province/ ; Project No. ZDYF2024XDNY277//the Hainan Provincial Key Research and Development Project/ ; },
abstract = {Diarrhea, a common gastrointestinal disorder, is often exacerbated by conventional antibiotic treatments that disrupt gut microbiota, necessitating the exploration of Lactic acid bacteria (LAB) alternatives. This study investigates the therapeutic potential and mechanisms of Streptococcus thermophilus NCU074001 (ST) in a rat model of PEG3350-induced osmotic diarrhea. ST treatment mitigated diarrheal symptoms and improved key markers of intestinal health by acting as a key modulator of the gut ecosystem. Its efficacy was driven by balancing immune responses via elevated IL-10 and suppressed pro-inflammatory cytokines (IL-6, IL-1β, TNF-α, IFN-γ). Furthermore, ST reinforced the intestinal barrier by upregulating MUC2 expression and reshaping gut microbial ecology by suppressing certain genera (Bacteroides and Anaerofilum) while enriching others (Lactobacillus, Akkermansia, Phascolarctobacterium, and Parabacteroides). This taxonomic restoration was accompanied by a functional metabolic shift, characterized by increased production of short-chain fatty acids (acetate and butyrate) and a targeted modulation of tryptophan metabolism that enhanced the production of anti-inflammatory indole derivatives. Correlation analyses suggested potential links between ST-mediated microbiota remodeling and barrier strengthening and immunomodulation. Collectively, these results indicate that ST functions as a promising probiotic integrating immunomodulation, microbiota restoration, and metabolic reprogramming to alleviate diarrhea, and thus presents a promising therapeutic alternative to conventional antibiotics.},
}

@article {pmid41495312,
year = {2026},
author = {Kiran, R and Sharma, M and Subramanian, S and Patil, SA},
title = {Halophilic Anaerobic Cultures Enriched with CO2:H2 from Different Saline Environments Reveal Unknown Autotrophic Bacterial Diversity and Modular Carbon Fixation Pathways.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02654-6},
pmid = {41495312},
issn = {1432-184X},
abstract = {The subsurface sediments of saline-aquatic systems host diverse microbes, with unclear ecological roles and challenging lab cultivability. Chemolithotrophic anaerobes involved in CO2-fixation are one of the poorly studied groups. This study focused on understanding these bacteria from subsurface sediments of four representative saline environments, two marine (i.e., Coastal Arabian and Bay of Bengal seas) and two lake (Sambhar and Lonar) systems through enrichment and metagenomics. Enrichment cultures with bicarbonate/CO2 and hydrogen as the carbon and energy sources, respectively, showed CO2 fixation, producing acetic and formic acids as the major organic products. Enriched culture with Sambhar Lake sediment produced more formic acid (391 ± 8 mg/L) than acetic acid (92 ± 20 mg/L); however, other enriched cultures produced considerably higher acetic acid (up to 966 ± 24 mg/L) than formic acid (up to 367 ± 30 mg/L). The organics production was accompanied by unique thread-like (up to 500 μm long) aggregates, harbouring chains of rod and oval-shaped microbes in all cultures. Metagenome sequencing revealed dominance of Vibrio spp. (relative sequence abundance of 91% to 97%) across all cultures, while canonical CO2-fixing taxa were nearly absent (< 0.01%). KEGG analysis revealed partial genes for various CO2 fixation pathways, including Wood-Ljungdahl, reverse-TCA, dicarboxylate-hydroxybutyrate, hydroxypropionate bicycle, hydroxypropionate-hydroxybutyrate, and the reductive-glycine pathway. The presence of a near-complete serine variant of the reductive glycine pathway, which has been demonstrated in engineered systems, suggests that this pathway may play an operational role in natural systems. The consistent production of organic acids and incomplete pathway representation suggests modular CO2 fixation within the Vibrio-dominated enriched mixed cultures.},
}

@article {pmid41493483,
year = {2026},
author = {Sharma, N and Pal, J and Mahajan, R and Chandel, S and Sud, D and Sanspal, A},
title = {Pathogens without borders: a review on cross-kingdom transmission strategies and pathogenicity of plant and human pathogens.},
journal = {Archives of microbiology},
volume = {208},
number = {2},
pages = {98},
pmid = {41493483},
issn = {1432-072X},
}

@article {pmid41493101,
year = {2026},
author = {Hoffert, M and Gorman, E and Lladser, ME and Fierer, N},
title = {Constructing a "periodic table" of bacteria to map diversity in trait space.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf289},
pmid = {41493101},
issn = {1751-7370},
abstract = {Despite an ever-expanding number of bacterial taxa being discovered, many of these taxa remain uncharacterized with unknown traits and environmental preferences. This diversity makes it challenging to interpret ecological patterns in microbiomes and understand why individual taxa, or assemblages, may vary across space and time. Although we can use information from the rapidly growing databases of bacterial genomes to infer traits, we still need an approach to organize what we know, or think we know, about bacterial taxa to match taxonomic and phylogenetic information to trait inferences. Inspired by the periodic table of the elements, we have constructed a "periodic table" of bacterial taxa to organize and visualize monophyletic groups of bacteria based on the distributions of key traits predicted from genomic data. By analyzing 50 745 genomes across 31 bacterial phyla, we used the Haar-like wavelet transformation, a model-free transformation of trait data, to identify clades of bacteria which are nearly uniform with respect to six selected traits - oxygen tolerance, autotrophy, chlorophototrophy, maximum potential growth rate, GC content, and genome size. The identified functionally uniform clades of bacteria are presented in a concise periodic table-like format to facilitate identification and exploration of bacterial lineages in trait space. While our approach could be improved and expanded in the future, we demonstrate its utility for integrating phylogenetic information with genome-derived trait values to improve our understanding of the bacterial diversity found in environmental and host-associated microbiomes.},
}

@article {pmid41492298,
year = {2025},
author = {Jones, MK and Morris, D and Zhu, H and Marty, AM},
title = {One Health turns 10: A decade at the intersection of human, animal, and environmental health.},
journal = {One health (Amsterdam, Netherlands)},
volume = {21},
number = {},
pages = {101218},
pmid = {41492298},
issn = {2352-7714},
}

@article {pmid41492005,
year = {2026},
author = {Miyamoto, K and Sujino, T},
title = {Microbiota-derived D-amino acids in intestinal homeostasis and inflammatory bowel disease.},
journal = {Inflammation and regeneration},
volume = {},
number = {},
pages = {},
doi = {10.1186/s41232-025-00403-3},
pmid = {41492005},
issn = {1880-9693},
abstract = {Inflammatory bowel disease (IBD) encompasses chronic, relapsing inflammatory disorders of the gastrointestinal tract, which are driven by intricate interactions between the host immune system and intestinal microbiota. Recent studies have revealed that microbiota-derived D-amino acids (D-AAs), once considered biologically inert, play critical roles in maintaining mucosal homeostasis and modulating immune responses. These metabolites, which are increasingly classified as postbiotics, directly influence epithelial barrier integrity, immune cell activity, and microbial ecology. In this review, we summarize the current insights into the biosynthesis, bacterial functions, and immunological implications of D-AAs in the gut, with a particular focus on their involvement in IBD pathogenesis. Specific D-AAs, such as D-alanine, contribute to bacterial cell wall integrity and quorum sensing and interact with host immune cells, alter microbial communities, and regulate mucosal barrier function. Evidence from both human studies and murine models highlights how disrupted D-AAs' metabolism through dysbiosis or impaired host sensing via enzymes such as D-amino acid oxidase (DAO) exacerbates inflammation. Finally, we discuss the translational potential of D-AAs as non-invasive biomarkers and therapeutic targets in IBD, emphasizing the need for integrative multi-omics approaches that connect microbial metabolism with host immune regulation and disease outcomes.},
}