@article {pmid40373669,
year = {2025},
author = {Rescan, M and Gros, M and Borrego, CM},
title = {Multidimensional tolerance landscapes reveal antibiotic-environment interactions affecting population dynamics of wastewater bacteria.},
journal = {Water research},
volume = {282},
number = {},
pages = {123720},
doi = {10.1016/j.watres.2025.123720},
pmid = {40373669},
issn = {1879-2448},
abstract = {City sewers harbor diverse bacterial communities that are continuously exposed to a myriad of antibiotic residues resulting from human consumption and excretion. Despite their sub-inhibitory concentrations in sewage, these pharmaceutical residues affect the growth rate and the yield of susceptible wastewater-associated bacteria. Moreover, environmental conditions in sewers are complex, including variations in temperature and, in many coastal city sewers, salinity. These variables can modulate antibiotic tolerance and therefore affect the dynamics of microbial populations. To explore such interactions between antibiotics and abiotic environmental factors, we built continuous multivariate tolerance landscapes for three bacterial species commonly detected in sewage: Escherichia coli, the emerging pathogen Streptococcus suis, and a typical sewer dweller, Arcobacter cryaerophilus. We projected their intrinsic growth rate and carrying capacity onto a complex environment including temperature, salinity, and a range of concentrations of two antibiotics frequently measured in urban wastewater (ciprofloxacin and azithromycin). We revealed that antibiotic tolerance was maximal at salinities close to seawater for both E. coli and S. suis, and that the direction of the interaction between antibiotics and temperature is species dependent. In E. coli, we additionally observed a third-order interaction among salinity, temperature and antibiotics, highlighting the limits of predicting field dynamics of bacterial populations using standard laboratory measures. We projected these tolerance curves onto time series data of temperature and conductivity measured in the sewers of Barcelona. Our model highlights that low concentrations of antibiotics could exclude the most sensitive species, while interactions between antibiotics, temperature, and salinity substantially affected the dynamics of the more tolerant ones.},
}

@article {pmid40373649,
year = {2025},
author = {Rosa-Masegosa, A and Vilchez-Vargas, R and Gorrasi, S and Monteoliva-García, A and Gonzalez-Martinez, A and Gonzalez-Lopez, J and Muñoz-Palazon, B},
title = {Unraveling the composition and succession of the microbial community in aerobic granular sludge treating urban wastewater with high load from hospital effluent.},
journal = {Chemosphere},
volume = {381},
number = {},
pages = {144483},
doi = {10.1016/j.chemosphere.2025.144483},
pmid = {40373649},
issn = {1879-1298},
abstract = {The treatment of wastewater containing high concentrations of pharmaceutical compounds is a challenge that has not yet been fully resolved. In this study, the occurrence of pharmaceutical and the bacterial and fungal communities were investigated during the treatment of urban wastewater including the hospital effluents using aerobic granular sludge technology. The physic-chemical results pointed out the capability of this technology to remove high rates of organic matter (97 %), total suspended solids (90 %), and nitrogen (85 %) without compromising the granular integrity and properties. The obtained data of pharmaceuticals remarked that the influent concentration had a strong effect on the removal ratio. The better average pharmaceutical removal performances were for carbamazepine (60-85 %), ketoprofen(50-60 %), cyclophosphamide(∼70 %), and trimethoprim(70 %), while the most recalcitrant compound was diclofenac. The molecular analysis exposed the relevance of endogenous microbial loads in the raw wastewater, especially in the start-up period. The mature granules demonstrated the strong selection of granules-forming bacteria, whereas the fungal populations took a longer period to be stable in granular biomass. Once the reactor was stable, the system was able to compete successfully with the influent microorganisms and avoid the spreading of pathogen microorganisms in the effluent, achieving excellent macro-pollutant and micro-pollutant removal ratios.},
}

@article {pmid40373419,
year = {2025},
author = {Orsi, AS and Lemos Junior, WJF and Alegbeleye, OO and Muniz, DC and Horita, CN and Sant'Ana, AS},
title = {Sodium chloride reduction in meat processing: Microbial shifts, spoilage risks, and metagenomic insights.},
journal = {Meat science},
volume = {226},
number = {},
pages = {109848},
doi = {10.1016/j.meatsci.2025.109848},
pmid = {40373419},
issn = {1873-4138},
abstract = {This review evaluated the impact of sodium chloride (NaCl) reduction or substitution on the microbial ecology of meat products, with a focus on how these changes affect shelf life and safety. Reducing NaCl in fresh meat products promotes the growth of psychrotrophic spoilage bacteria, such as Pseudomonas sp., which thrive at low temperatures, and mesophilic pathogens like Escherichia coli and Staphylococcus aureus, particularly under inadequate storage conditions. In cured and fermented meats, such as salami, lowering NaCl levels disrupts the balance of salt-tolerant microorganisms, notably lactic acid bacteria (LAB) and coagulase-negative staphylococci, potentially leading to increased spoilage and pathogen proliferation. In smoked meats, the combination of reduced NaCl and altered microbial ecology, including a shift toward LAB dominance, may weaken the inhibitory effects on spore-forming bacteria like Clostridium botulinum. Additionally, using metagenomics, we explore the shifts in microbial communities observed in studies involving meat, revealing critical insights into the composition and diversity of bacteria in meat products, as well as the gaps in research on the impact of NaCl reduction and/or substitution on the microbiota. This review provides a comprehensive understanding of these microbial shifts, highlighting the distinct responses of psychrotrophic, mesophilic, and LAB groups to NaCl modification and the need to understand the effects of these alternatives on the meat product microbiome, as well as the neglected microorganisms that can affect the quality and safety of these products.},
}

@article {pmid40372110,
year = {2025},
author = {Rohrhofer, J and Wolflehner, V and Schweighardt, J and Koidl, L and Stingl, M and Zehetmayer, S and Séneca, J and Pjevac, P and Untersmayr, E},
title = {Gastrointestinal Barrier Disruption in Post-COVID Syndrome Fatigue Patients.},
journal = {Allergy},
volume = {},
number = {},
pages = {},
doi = {10.1111/all.16593},
pmid = {40372110},
issn = {1398-9995},
support = {//WE&ME Foundation/ ; //Medizinisch-Wissenschaftlicher Fond des Buergermeisters der Bundeshauptstadt Wien/ ; },
abstract = {BACKGROUND: Post-COVID Syndrome (PCS) is the term for a condition with persistent symptoms in a proportion of COVID-19 patients after asymptomatic, mild, or severe disease courses. Numbers vary, but the current estimate is that after COVID-19 approximately 10% develop PCS. The aim of our study was to evaluate the impact of SARS-CoV-2 infection on the gastrointestinal (GI) tract and associations with the development of PCS with fatigue, post-exertional malaise (PEM), orthostatic dysregulation, autonomous dysregulation, and/or neurocognitive dysregulation.

METHODS: By combining medical record data from a prospective observational study with symptom analysis before, during, and after SARS-CoV-2 infection, we aimed to identify potential risk factors and predictive markers for PCS. Additionally, we analyzed blood, saliva, and stool samples from this well-characterized PCS patient cohort to biologically validate our findings.

RESULTS: We identified significant associations between pre-existing GI complaints and the development of PCS Fatigue. PCS patients showed higher LBP/sCD14 ratios, lower IL-33 levels, and higher IL-6 levels compared to control groups. Our results highlight the critical role of the GI tract in PCS development of post-viral Fatigue.

CONCLUSION: We propose that the viral infection disrupts pathways related to the innate immune response and GI barrier function, evidenced by intestinal low-grade inflammation and GI barrier leakage. Monitoring GI symptoms and markers before, during, and after SARS-CoV-2 infection is crucial for identifying predictive clinical phenotypes in PCS. Understanding the interaction between viral infections, immune responses, and gut integrity could lead to more effective diagnostic and treatment strategies, ultimately reducing the burden on PCS patients.},
}

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

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

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

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

@article {pmid40366070,
year = {2025},
author = {Herz, CT and Kulterer, OC and Prager, M and Marculescu, R and Prager, G and Kautzky-Willer, A and Hacker, M and Trajanoski, S and Köfeler, HC and Gallé, B and Haug, AR and Berry, D and Kiefer, FW},
title = {Bariatric surgery promotes recruitment of brown fat linked to alterations in the gut microbiota.},
journal = {European journal of endocrinology},
volume = {192},
number = {5},
pages = {603-611},
doi = {10.1093/ejendo/lvaf081},
pmid = {40366070},
issn = {1479-683X},
support = {P 27391//Austrian Science Fund/ ; 17094//Medical Scientific Fund of the Mayor of the City of Vienna/ ; //Austrian Diabetes Association Research Fund/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Adipose Tissue, Brown/metabolism/diagnostic imaging ; Female ; *Bariatric Surgery ; Male ; Middle Aged ; Adult ; *Obesity, Morbid/surgery/metabolism/microbiology ; Fatty Acids, Volatile/metabolism/blood ; Positron Emission Tomography Computed Tomography ; Energy Metabolism/physiology ; Weight Loss/physiology ; },
abstract = {OBJECTIVE: The mechanisms of bariatric surgery-induced weight loss and metabolic improvements are still incompletely understood and reach beyond malabsorption or calorie restriction. We sought to investigate the effect of bariatric surgery on brown adipose tissue (BAT) activity and a potential connection with changes in energy metabolism, the gut microbiota, and short-chain fatty acid (SCFA) composition.

METHODS: We included 32 subjects (25 females) with morbid obesity and analyzed their metabolic profile, gut microbiota composition, circulating SCFAs, energy expenditure, and cold-induced BAT activity using [18F]Fluorodeoxyglucose-positron emission tomography-computed tomography before and up to 1 year after bariatric surgery.

RESULTS: Twelve months after surgery, the percentage of individuals with active BAT had increased from 28% to 53%. The BAT-negative (BATneg) individuals who had an adverse metabolic profile at baseline compared with subjects with active BAT (BATpos) showed a greater metabolic benefit after surgery. While no changes in overall gut bacterial diversity were observed between BATpos and BATneg, the abundance of 3 specific bacterial families, including Akkermansiaceae, Pasteurellaceae, and Carnobacteriaceae, was distinctly regulated between BAT groups. The bacterial genera most strongly increased in BATpos vs BATneg subjects were all positively correlated with BAT volume and BAT activity. Finally, circulating concentrations of the SCFAs acetate, butyrate, and propionate rose after bariatric surgery and were related to bacterial genera such as Akkermansia, Dialister, and Lachnospiraceae FCS020 group, all known SCFA producers.

CONCLUSIONS: Bariatric surgery helps recruit active BAT in individuals with obesity and is linked to distinct alterations in the gut microbiome and SCFA composition.

TRIAL REGISTRATION NUMBER: ClinicalTrials.gov (NCT03168009).},
}

Humans
*Gastrointestinal Microbiome/physiology
*Adipose Tissue, Brown/metabolism/diagnostic imaging
Female
*Bariatric Surgery
Male
Middle Aged
Adult
*Obesity, Morbid/surgery/metabolism/microbiology
Fatty Acids, Volatile/metabolism/blood
Positron Emission Tomography Computed Tomography
Energy Metabolism/physiology
Weight Loss/physiology

@article {pmid40361280,
year = {2025},
author = {Wan, SH and Xu, Y and Xu, W and Leung, SKK and Yu, EYN and Yung, CCM},
title = {Environmental Heterogeneity Drives Ecological Differentiation in Vibrio Populations Across Subtropical Marine Habitats.},
journal = {Environmental microbiology},
volume = {27},
number = {5},
pages = {e70107},
doi = {10.1111/1462-2920.70107},
pmid = {40361280},
issn = {1462-2920},
support = {AoE/P-601/23-N//Research Grants Council of Hong Kong/ ; },
mesh = {*Vibrio/genetics/classification/isolation & purification ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Seawater/microbiology ; *Ecosystem ; Hong Kong ; Temperature ; Salinity ; Chaperonin 60/genetics ; Bays/microbiology ; },
abstract = {Elucidating how environmental gradients structure bacterial communities remains fundamental to microbial ecology. We investigated Vibrio population dynamics across contrasting subtropical marine environments in Hong Kong over a year period. Using an integrated approach combining cultivation techniques with molecular analyses of Hsp60 and 16S rRNA genes, we characterised the population structure between a coastal site (Clear Water Bay) and an estuarine site (Deep Bay). The estuarine environment consistently harboured higher Vibrio abundances (10[4]-10[7] copies/mL) compared to coastal waters (10[2]-10[4] copies/mL), with significantly greater phylogenetic diversity. Multivariate analyses revealed salinity as the primary driver of community differentiation between sites, while temperature governed seasonal succession patterns. Phylogenetic analysis of 1521 Vibrio isolates identified three distinct ecological groups corresponding to specific temperature-salinity niches, with evidence of habitat-specific thermal adaptations among closely related strains. Experimental characterisation of thermal performance curves confirmed physiological differentiation between warm- and cool-temperature adapted strains despite high genetic similarity (> 97% Hsp60 gene sequence identity). Several abundant species detected via amplicon sequencing (including V. navarrensis and V. mimicus) displayed site-specific ecotypes but remained uncultivated, highlighting methodological constraints in community characterisation. Our findings demonstrate how environmental heterogeneity drives fine-scale ecological differentiation in Vibrio populations, providing insights into mechanisms of bacterial adaptation in dynamic marine environments.},
}

*Vibrio/genetics/classification/isolation & purification
Phylogeny
RNA, Ribosomal, 16S/genetics
*Seawater/microbiology
*Ecosystem
Hong Kong
Temperature
Salinity
Chaperonin 60/genetics
Bays/microbiology

@article {pmid40359204,
year = {2025},
author = {Ghyselinck, J and Verstrepen, L and Rakebrandt, M and Marynissen, S and Daminet, S and Marzorati, M},
title = {In vitro fermentation of yeast cell walls (mannan-oligosaccharide) and purified β-glucans modulates the colonic microbiota of dogs with inflammatory bowel disease and demonstrates protective effects on barrier integrity and anti-inflammatory properties.},
journal = {PloS one},
volume = {20},
number = {5},
pages = {e0322877},
doi = {10.1371/journal.pone.0322877},
pmid = {40359204},
issn = {1932-6203},
mesh = {Animals ; Dogs ; *Inflammatory Bowel Diseases/microbiology/veterinary ; *Gastrointestinal Microbiome/drug effects ; *Mannans/metabolism/pharmacology ; *beta-Glucans/pharmacology/metabolism ; Prebiotics ; *Saccharomyces cerevisiae/metabolism/chemistry ; *Cell Wall/metabolism/chemistry ; Humans ; Fermentation ; *Colon/microbiology ; Caco-2 Cells ; *Anti-Inflammatory Agents/pharmacology ; *Oligosaccharides/metabolism ; RNA, Ribosomal, 16S/genetics ; Intestinal Mucosa ; },
abstract = {Inflammatory bowel disease (IBD) is characterized by a disruption of intestinal homeostasis, chronic inflammation, and dysbiosis. Prebiotic supplementation may be useful for managing IBD in dogs. The aim of the study is to investigate the effects of two prebiotics, Biolex MB40 or Leiber Beta-S, on the gut microbiota isolated from three dogs with IBD, using the Colon-on-a-plate technology. Biolex MB40 and Leiber Beta-S contain concentrated 1,3-1,6- β-D-glucan isolated from the Saccharomyces cerevisiae cell walls. Biolex MB40 also contains mannan-oligosaccharide (MOS). Wells of the Colon-on-a-plate set up were inoculated with fecal suspensions and supplemented with either Biolex MB40 and Leiber Beta-S, or no test product (blank). Following 48h incubation, bacterial metabolites were measured and 16S rRNA targeted gene sequencing was performed. Colonic supernatants were added to a Caco-2/THP1 co-culture model to evaluate their effects on barrier integrity upon inflammation-induced barrier disruption and interleukin (IL)-10 production. Acetate and propionate concentrations were significantly increased versus blank with Biolex MB40, and biologically relevant numerical increases were observed with Leiber Beta-S supplementation. A donor-dependent, biologically relevant increase in butyrate was observed with both test products versus blank. Alpha diversity and microbiota biomass were increased, as well as the abundance of the five predominant phyla with both test products relative to blank. The greatest increases in abundance were observed for the Bacteroidetes and Firmicutes phyla. Fermentation of both test products had a protective effect on the gut epithelial barrier (measured by transepithelial electrical resistance) that was donor dependent. IL-10 production was significantly increased with Biolex MB40 supplementation for all donors, and with Leiber Beta-S supplementation for one donor. These in vitro findings confirm a prebiotic effect for both products and suggest that supplementation with either Biolex MB40 or Leiber Beta-S may have beneficial effects on the gut microbiota of dogs with IBD.},
}

Animals
Dogs
*Inflammatory Bowel Diseases/microbiology/veterinary
*Gastrointestinal Microbiome/drug effects
*Mannans/metabolism/pharmacology
*beta-Glucans/pharmacology/metabolism
Prebiotics
*Saccharomyces cerevisiae/metabolism/chemistry
*Cell Wall/metabolism/chemistry
Humans
Fermentation
*Colon/microbiology
Caco-2 Cells
*Anti-Inflammatory Agents/pharmacology
*Oligosaccharides/metabolism
RNA, Ribosomal, 16S/genetics
Intestinal Mucosa

@article {pmid40358239,
year = {2025},
author = {Waegenaar, F and Pluym, T and Vermeulen, E and De Gusseme, B and Boon, N},
title = {Impact of flushing procedures on drinking water biostability and invasion susceptibility in distribution systems.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0068625},
doi = {10.1128/aem.00686-25},
pmid = {40358239},
issn = {1098-5336},
abstract = {UNLABELLED: Ensuring high-quality drinking water remains challenging, as complaints about odors, discoloration, or contamination persist. In Belgium and beyond, traditional flushing is a common curative strategy that involves discharging large water volumes through hydrants while the network remains in use. In some cases, free chlorine (0.5 mg/L) is added, and consumers are advised not to drink the water. However, flushing can alter water biostability, potentially increasing susceptibility to microbial invasion. This study used a pilot-scale drinking water distribution system with three identical 100 m polyvinyl chloride(PVC) loops (DN 80 mm) to assess the impact of flushing with and without chlorination as practiced in chlorinated networks. Loop 1 was flushed with tap water and sodium hypochlorite (NaOCl), followed by two non-chlorinated flushes, loop 2 was unflushed, and loop 3 underwent three flushes. Biostability was assessed using online flow cytometry, and susceptibility to bacterial invasion (Aeromonas media, Pseudomonas putida, and Serratia fonticola) was evaluated in the days following flushing. The water had a 7-day residence time. Results showed that chlorinated flushing promoted microbial regrowth (3.8 × 10[5] vs 2.0 × 10[5] and 1.6 × 10[5] cells/mL for loops 1, 2, and 3, respectively), primarily of resident Sphingopyxis spp. Biofilm cell densities (~4 × 10[6] cells/cm[2]) remained stable across conditions. Bacterial indicators declined over time, with P. pudita and S. fonticola surviving longer (>100 hours) than A. media (13 hours). Decay rates were highest in chlorinated loops, likely due to increased microbial competition. For example, the decay constant of S. fonticola at 20°C was -0.082 h[-1], -0.042 h[-1], and -0.027 h[-1] for loops 1, 2, and 3, respectively.

IMPORTANCE: Traditional flushing is used as a curative strategy to solve unwanted quality issues during distribution, yet its impact on microbial biostability remains poorly understood. This study provides critical insights into how traditional flushing, both with and without chlorination, influences microbial regrowth and susceptibility to invasion. Findings reveal that chlorinated flushing promotes the regrowth of resident drinking water bacteria while accelerating the decay of introduced unwanted bacterial indicators, emphasizing the complex trade-off between microbial control and system stability. Understanding these dynamics is essential for optimizing flushing procedures, minimizing unintended consequences, and improving distribution system resilience.},
}

@article {pmid40358205,
year = {2025},
author = {An, Y and Garcia, SL and Hambäck, PA},
title = {Microbial transfer through fecal strings on eggs affects leaf beetle microbiome dynamics.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0172324},
doi = {10.1128/msystems.01723-24},
pmid = {40358205},
issn = {2379-5077},
abstract = {UNLABELLED: Gut microbiomes of holometabolous insects can be strongly affected by metamorphosis. Previous studies suggest that microbiome colonization and community development often rely on specialized transmission routes between host life stages. However, there is a lack of comparative studies of microbial community dynamics from different transmission mechanisms. We compared the gut microbial community dynamics across life stages in five Galerucella species that differ in their potential microbial transfer mechanism by sequencing amplicons of the 16S rRNA gene. Females of three of the studied species place a fecal string on top of the egg, which may enhance the transfer of gut microbes, whereas females of the two other species do not. We found that the α-diversity was more stable between life stages in fecal string-placer species compared with the non-fecal string-placer species. Moreover, there were consistent microbiome differences between species, with multiple taxa in each species consistently appearing in all life stages. Fecal strings placed on eggs seem to play an important role in the diversity and dynamics of gut bacteria in Galerucella species, facilitating the vertical transfer of gut bacteria between host insect generations. Alternative, but less efficient, transmission routes appear to occur in non-fecal string-placer species.

IMPORTANCE: We explore the consequences of having different mechanisms for transferring and establishing the gut microbiome between generations on gut microbial community dynamics. This process is often problematic in holometabolous insects, which have a complete metamorphosis between larval and adult stages. In our previous research, we found that females of some species within the genus Galerucella (Chrysomelidae) place a fecal string on the eggs, which is later consumed by the hatching larvae, whereas other species in the same genus do not have this behavior. In this paper, we therefore quantify the microbial community dynamics across all life stages in five Galerucella beetles (three with and two without fecal strings). Our results also indicate that the dynamics are much more stable in the species with fecal strings, particularly in the early life stages.},
}

@article {pmid40356667,
year = {2025},
author = {Martínez-Mota, R and Vásquez-Aguilar, AA and Hernández-Rodríguez, D and Suárez-Domínguez, EA and Krömer, T},
title = {Close neighbors, not intruders: investigating the role of tank bromeliads in shaping faunal microbiomes.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19376},
doi = {10.7717/peerj.19376},
pmid = {40356667},
issn = {2167-8359},
mesh = {Animals ; *Diptera/microbiology ; Larva/microbiology ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Mexico ; *Bromeliaceae/microbiology ; *Bacteria/genetics/classification ; Ecosystem ; },
abstract = {BACKGROUND: Tropical montane cloud forests contain high levels of epiphyte diversity. Epiphytic tank bromeliads play an important role in the functioning of these ecosystems and provide a microhabitat for many species of invertebrates. Microbial ecology theory suggests that the environment serves as a source of microbes for animals, but the contribution of this factor to the composition of an animal microbiome varies. In this study, we examined the extent to which tank bromeliads (Tillandsia multicaulis) serve as a source of microbes for two species of fly larvae in a cloud forest fragment in central Veracruz, Mexico.

METHODS: We used 16S rRNA sequencing to characterize the bacterial communities in the organic matter within bromeliad tanks and in the whole bodies (surface and gut) of larvae from two fly taxa (Austrophorocera sp., Tachinidae, and Copestylum sp., Syrphidae) that inhabit these bromeliads. To assess the contribution of bromeliads to the microbiome of the fly larvae, we conducted fast expectation-maximization microbial source tracking (FEAST) analysis.

RESULTS: The bacterial communities in bromeliad tanks were primarily composed of Pseudomonadota, Acidobacteriota, Bacteroidota, Verrucomicrobiota, and Spirochaetota. Similarly, communities of the fly larvae contained Pseudomonadota, Bacteroidota, Bacillota, and Actinomycetota. Bromeliad tanks exhibited the highest bacterial richness, followed by Copestylum and Austrophorocera larvae. Beta diversity analyses indicated that bacterial communities clustered by species. We found a modest contribution of bromeliads to the fly microbiome, with nearly 30% of the larvae microbiome traced to the organic matter deposited in the tanks.

CONCLUSIONS: Our data suggest that the microbiome of flies, which inhabit tank bromeliads during their larval stage, is nourished to some extent by the bacterial communities present in the organic matter within the tank.},
}

Animals
*Diptera/microbiology
Larva/microbiology
RNA, Ribosomal, 16S/genetics
*Microbiota
Mexico
*Bromeliaceae/microbiology
*Bacteria/genetics/classification
Ecosystem

@article {pmid40356640,
year = {2025},
author = {Sun, Z and Hu, Y and Yang, YX and Lei, MY and Han, ZM and Cheng, L and Wang, W and Han, M and Lyu, ZL and Yang, LM},
title = {Changes in the diversity of ginseng endophyte flora driven by Fusarium solani.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1554706},
doi = {10.3389/fmicb.2025.1554706},
pmid = {40356640},
issn = {1664-302X},
abstract = {Endophytic flora serves a crucial function as a secondary line of defense against pathogen invasion in plants. To investigate the mechanisms underlying the relationship between changes in endophytic flora and ginseng root rot, exhumate beneficial endophytic bacteria, and explore biological management approaches for ginseng root rot. In this study, we used Illumina high-throughput sequencing and bioinformatics analysis to investigate the characteristics and differences in endophytic microbial community structure between healthy ginseng (HG) and diseased ginseng (BLS) after Fusarium solani infection. The findings revealed that as ginseng root rot increased, the diversity and richness of endophytic bacterial communities increased before decreasing, but the diversity and richness of endophytic fungal communities decreased. The dominating bacterial phylum in ginseng roots was Proteobacteria, which declined in quantity as the disease progressed. Ascomycota was the dominating fungal phylum among endophytes, and its prevalence grew as the disease progressed. At the genus level, the relative abundance of Rhodococcus, Stenotrophomonas, Variovorax, and Achromobacter species increased with the occurrence of ginseng root rot, in contrast, Pantoea and Pseudomonas species decreased in relative abundance as the prevalence of ginseng root rot increased. The relative abundance of the pathogenic fungi Gibberella, Nectria, Ilyonectria, and Alternaria in ginseng roots increased as the disease progressed. Endophytic fungal LEfSe research revealed that Neonectria was the particular biomarker discovered in the highly susceptible group. Additionally, commensal nutrient-type fungi appeared to be absent in moderately susceptible ginseng, but pathognomic nutrient-type fungi grew, coupled with potentially pathogenic fungi, exacerbating the condition. These results suggest that there is a pattern of response of ginseng endophytic microbial diversity to disease infestation. In this work, we investigated the impact of varying degrees of root rot on ginseng's endophytic flora structure. The study's findings give a theoretical framework for understanding the microecological processes of ginseng root rot via the lens of microbial ecology and applying biological control tools.},
}

@article {pmid40356172,
year = {2025},
author = {Cardinali, F and Rampanti, G and Harasym, J and Lucci, P and Ferrocino, I and Pacetti, D and Fanesi, B and Milanović, V and Garofalo, C and Petruzzelli, A and Savelli, D and Gabucci, C and Aquilanti, L and Osimani, A},
title = {Comprehensive profiling of smoked cheese from raw goat's milk handcrafted in Lower Silesia (Poland).},
journal = {Food research international (Ottawa, Ont.)},
volume = {211},
number = {},
pages = {116398},
doi = {10.1016/j.foodres.2025.116398},
pmid = {40356172},
issn = {1873-7145},
mesh = {*Cheese/microbiology/analysis ; Animals ; Goats ; Fatty Acids/analysis ; Volatile Organic Compounds/analysis ; Poland ; *Milk/microbiology/chemistry ; *Food Microbiology ; *Food Handling/methods ; Consumer Behavior ; Humans ; *Smoke ; Colony Count, Microbial ; },
abstract = {This study aimed to explore the distinctive characteristics of smoked cheese made from raw goat's milk, labelled "Produkt polski" and crafted in the Lower Silesia region of Poland. A comprehensive range of analyses was performed, including physico-chemical and morpho-textural evaluations, microbial counts, and a metataxonomic investigation to uncover the microbial diversity occurring in the cheese. The volatile organic compounds (VOCs) and the total fatty acid composition were also determined. Additionally, a consumer test based on a hedonic scale was conducted to capture the subjective experience of the product's appeal. The cheese samples revealed water activity (aw) ranging between 0.901 ± 0.003 and 0.926 ± 0.001, with pH levels between 5.08 ± 0.15 and 5.44 ± 0.01. Regarding fatty acid composition, all of the smoked cheeses displayed a similar profile, with saturated fatty acids dominating (SFA, ∼75 %), followed by monounsaturated (MUFA, ∼22 %) and polyunsaturated fatty acids (PUFA, ∼3 %). Microbial analysis revealed thriving populations, including lactococci (up to 8.63 ± 0.07 log colony-forming units g[-1]), thermophilic cocci (up to 6.85 ± 0.08 log cfu g[-1]), lactobacilli (up to 9.50 ± 0.04 log cfu g[-1]), enterococci (up to 5.93 ± 0.00 log cfu g[-1]), and eumycetes (up to 2.68 ± 0.48 log cfu g[-1]). Metataxonomic analysis identified dominant bacterial taxa such as Lactobacillus, Lactococcus, and Leuconostoc, as well as Carnobacterium and Lacticaseibacillus. Among the 24 lactic acid bacteria cultures isolated, the closest relatives to Enterococcus, Lacticaseibacillus, Lactococcus, and Leuconostoc were identified. Some isolates demonstrated promising pro-technological traits, positioning them as potential adjunct cultures for improving fermented dairy products. The volatile profile of the smoked cheese was particularly intriguing, with a total of 87 VOCs detected, categorized as esters (18), ketones (14), hydrocarbons (11), acids (10), phenols (11), alcohols (8), furans (5), lactones (4), aldehydes (3), and other compounds (3). Sensory evaluation revealed a moderate appreciation for the cheese's appearance, whereas the smoked flavor elicited the most varied scores, highlighting its strong impact on consumer preference.},
}

*Cheese/microbiology/analysis
Animals
Goats
Fatty Acids/analysis
Volatile Organic Compounds/analysis
Poland
*Milk/microbiology/chemistry
*Food Microbiology
*Food Handling/methods
Consumer Behavior
Humans
*Smoke
Colony Count, Microbial

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

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

@article {pmid40354775,
year = {2025},
author = {Frazier, CF and Harris, TD and DelSontro, T and Grossart, HP and Sturm, BSM and Murry, JM and Ising, A},
title = {Phytoplankton abundance and methane emissions are minimally impacted by environmentally-relevant glyphosate concentrations in small-scale outdoor mesocosms.},
journal = {Water research},
volume = {283},
number = {},
pages = {123764},
doi = {10.1016/j.watres.2025.123764},
pmid = {40354775},
issn = {1879-2448},
abstract = {Glyphosate is one of the most widely applied agrochemicals in North America and can be directly transported via runoff into non-target aquatic habitats. Yet, our understanding of how this herbicide affects aquatic ecosystems is limited; past studies have often focused on single species effects and/or used herbicide concentrations several orders of magnitude higher than what has been reported in contaminated aquatic systems. Further, glyphosate in aquatic systems has the potential to alter greenhouse gas emissions (methane) if it is broken down for phosphate utilization by bacteria under specific environmental conditions (i.e., oxygen, nutrient concentrations). In this study, we assessed the temporal changes in nutrients, phytoplankton, copy number of genes associated with breakdown of glyphosate or production of methane (phnJ, mcrA), and methane concentrations in 12-day mesocosms with amendments of glyphosate, nitrogen, and/or phosphorus. We found glyphosate at environmentally-relevant concentrations (∼4 ug/L) did not confer changes in overall ratios and total concentrations of nutrients, or abundance of any major phytoplankton group (cyanobacteria, diatoms, green algae), methane concentration or flux, or gene copy numbers of phnJ and mcrA. Our results suggest that the relatively low concentrations of glyphosate we used (relative to levels used in toxicological studies) did not cause major changes over short time periods in mesocosms, and that the potential for glyphosate to increase greenhouse gas emissions in aquatic systems requires specific conditions to occur and may not be universal in contaminated systems.},
}

@article {pmid40354740,
year = {2025},
author = {Rodrigo, MA and Puche, E and Muñoz-Colmenares, M and Sánchez-Carrillo, S},
title = {Vascular macrophytes versus charophytes: how the macrophyte type and warming affect the sediment microbial community and the production of greenhouse gases.},
journal = {Journal of environmental management},
volume = {386},
number = {},
pages = {125654},
doi = {10.1016/j.jenvman.2025.125654},
pmid = {40354740},
issn = {1095-8630},
abstract = {In the global warming context, adaptive management strategies involve the conservation and restoration of inland waters by planning the reintroduction of macrophytes to substantially mitigate greenhouse gas emissions (GHG). The selection of appropriate species is crucial. We studied the influence of two submerged macrophyte species on GHG production, sediment-oxygen microprofiles, and microbial community composition under two thermal regimes by means of a microcosm experiment. We chose the phanerogam Myriophyllum spicatum, more typical of meso-eutrophic habitats, and the charophyte Chara hispida, more frequent in oligotrophic waters and belonging to a much less studied macrophyte group, which, moreover, exhibit contrasting functional traits (i.e., roots versus rhizoids). The presence of both macrophyte types considerably reduced the diurnal diffusive CO2 emissions due to their photosynthetic activity compared to bare-sediment situations. The radial oxygen loss of M. spicatum roots provided aerobic-microaerobic conditions beyond the first sediment centimeter, in contrast to more anoxic sediments created by C. hispida. As a result of this, each type of macrophyte determined a particular sediment microbiome. Despite dissolved CH4 being greater in the presence of plants, no statistical differences in CH4 diffusive flux caused by the presence or absence of plants was found. We demonstrated how the presence, or not, of macrophytes is more important than warming (in our case with a temperature difference of 3 °C) in relation to GHG emissions. Both species, being perennial, provide ecosystem services year-round and are strong candidates for management strategies aimed at transforming new or restored aquatic ecosystems into carbon sinks.},
}

@article {pmid40353721,
year = {2025},
author = {Pellitier, PT and Kling, MM and Qin, C and Van Nuland, ME and Zhu, K and Peay, KG},
title = {Wind Patterns Influence the Dispersal and Assembly of North American Soil Fungal Communities.},
journal = {Ecology letters},
volume = {28},
number = {5},
pages = {e70130},
doi = {10.1111/ele.70130},
pmid = {40353721},
issn = {1461-0248},
support = {1845544//Directorate for Biological Sciences/ ; 1926335//Directorate for Biological Sciences/ ; 2010897//Directorate for Biological Sciences/ ; 2244711//Directorate for Biological Sciences/ ; },
mesh = {*Wind ; *Soil Microbiology ; *Fungi/physiology/genetics ; North America ; *Mycobiome ; Spores, Fungal/physiology ; Climate Change ; Models, Biological ; },
abstract = {Wind is the primary dispersal mechanism of most fungal spores but is rarely considered in studies of fungal communities, limiting inference of assembly mechanisms and forecasting responses to climate change. We compiled wind-connectivity models-'windscapes'-to model potential dispersal of fungal spores at the continental scale and linked them with a molecular dataset of North American soil fungi. Our analyses demonstrate that prevailing windflow patterns exhibit a significantly stronger signal on fungal community structure than do geographic distances amongst sites. Notably, the signature of wind was detectable for mushrooms and fungi producing primarily wind-dispersed spores. Contrastingly, fungi primarily reliant on animal dispersal exhibited a strong signature of geographic distance but not wind-connectivity. Additionally, we show that directionally 'downwind' sites are more diverse than comparatively 'upwind' sites. Altogether, our findings suggest that future wind patterns will shape the adaptation potential of fungal communities dispersing into suitable climatic niches.},
}

*Wind
*Soil Microbiology
*Fungi/physiology/genetics
North America
*Mycobiome
Spores, Fungal/physiology
Climate Change
Models, Biological

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

@article {pmid40352645,
year = {2025},
author = {Quinn, LK and Sharma, K and Faber, KT and Orphan, VJ},
title = {Clear as mud redefined: Tunable transparent mineral scaffolds for visualizing microbial processes below ground.},
journal = {PNAS nexus},
volume = {4},
number = {5},
pages = {pgaf118},
doi = {10.1093/pnasnexus/pgaf118},
pmid = {40352645},
issn = {2752-6542},
abstract = {Microbes inhabiting complex porous microenvironments in sediments and aquifers catalyze reactions that are critical to global biogeochemical cycles and ecosystem health. However, the opacity and complexity of porous sediment and rock matrices have considerably hindered the study of microbial processes occurring within these habitats. Here, we generated microbially compatible, optically transparent mineral scaffolds to visualize and investigate microbial colonization and activities occurring in these environments, in laboratory settings and in situ. Using inexpensive synthetic cryolite mineral, we produced optically transparent scaffolds mimicking the complex 3D structure of sediments and rocks by adapting a suspension-based, freeze-casting technique commonly used in materials science. Fine-tuning of parameters, such as freezing rate and choice of solvent, provided full control of pore size and architecture. The combined effects of scaffold porosity and structure on the movement of microbe-sized particles, tested using velocity tracking of fluorescent beads, showed diverse yet reproducible behaviors. The scaffolds we produced are compatible with epifluorescence microscopy, allowing the fluorescence-based identification of colonizing microbes by DNA-based staining and fluorescence in situ hybridization (FISH) to depths of 100 µm. Additionally, Raman spectroscopy analysis indicates minimal background signal in regions used for measuring deuterium and [13]C enrichment in microorganisms, highlighting the potential to directly couple D2O or [13]C stable isotope probing and Raman-FISH for quantifying microbial activity at the single-cell level. To demonstrate the relevance of cryolite scaffolds for environmental field studies, we visualized their colonization by diverse microorganisms within rhizosphere sediments of a coastal seagrass plant using epifluorescence microscopy. The tool presented here enables highly resolved, spatially explicit, and multimodal investigations into the distribution, activities, and interactions of underground microbes typically obscured within opaque geological materials until now.},
}

@article {pmid40352477,
year = {2025},
author = {Coltman, BL and Motheramgari, K and Tatto, N and Gasser, B},
title = {Identification and functional analysis of growth rate associated long non-coding RNAs in Komagataella phaffii.},
journal = {Computational and structural biotechnology journal},
volume = {27},
number = {},
pages = {1693-1705},
doi = {10.1016/j.csbj.2025.04.028},
pmid = {40352477},
issn = {2001-0370},
abstract = {Long non-coding RNAs (lncRNAs) are a regulatory feature that have been reported to operate on both transcriptional and translational levels. With DNA-based prediction still limited, lncRNAs are most reliably identified through genome-guided mapping of RNA-Seq data. Reports of lncRNAs in yeast have been increasing in recent years and changes in their expression levels have often been associated with stressful conditions. As the transition to near zero-growth conditions likely imposes stress, we used RNA-Seq data from the non-conventional, biotechnologically established yeast Komagataella phaffii, cultivated in glucose-limited retentostats, to identify the expression of lncRNAs. Using an adapted bioinformatics pipeline, we identified 168 mostly novel lncRNAs from the K. phaffii retentostat RNA-Seq data, 36 of which demonstrate likely growth-associated expression changes. lncRNA expression levels were associated to that of possible interaction partners, in both cis and trans, suggesting potential roles in regulatory adaptations. Our analysis indicates that lncRNAs likely contribute to how K. phaffii responds to changing environmental conditions, as exemplified here by the adaptation to extremely slow growth.},
}

@article {pmid40349898,
year = {2025},
author = {Moghaddam, ZS and Dehghan, A and Halimi, S and Najafi, F and Nokhostin, A and Naeini, AE and Akbarzadeh, I and Ren, Q},
title = {Bacterial Extracellular Vesicles: Bridging Pathogen Biology and Therapeutic Innovation.},
journal = {Acta biomaterialia},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.actbio.2025.05.028},
pmid = {40349898},
issn = {1878-7568},
abstract = {The main role of bacterial extracellular vesicles (BEVs) has been associated with various processes such as intercellular communication and host-pathogen interactions. This comprehensive review explores the multifaceted functions of BEVs across different biological domains, emphasizing their multifaceted functions as contributors both to disease and as carriers of therapeutic possibilities. We examine the intricate interactions of BEVs within bacterial communities and between bacteria and hosts, their involvement in disease development through cargo delivery mechanisms, and their beneficial impact to microbial ecology. The review places a strong emphasis on BEVs' applications in biomedical sciences, where they are revolutionizing vaccine development, targeted drug delivery, and cancer therapy. By utilizing the inherent properties of BEVs for controlled drug release, targeted antigen delivery, and immune modulation, they offer a promising frontier in precision medicine. In addition, the diagnostic potential of BEVs is explored through their biomarker capabilities, providing valuable insights into disease states and treatment efficacy. Looking forward, this review underscores the challenges and opportunities in translating BEV research to clinical practice, promoting the use of standardized methods in BEV characterization and scaling up production. The diverse abilities of BEVs, ranging from contributing to pathogen virulence to driving therapeutic innovation, highlight their potential as a cornerstone in the future of biomedical advancements. STATEMENT OF SIGNIFICANCE: Bacterial extracellular vesicles (BEVs) are emerging as pivotal players in both pathogenesis and therapeutic innovation. This review explores their dual nature as agents of disease and as promising biomaterials in biomedical applications, and provides a comprehensive survey on their involvement in disease mechanisms and microbial ecology, and their potential in biomedical applications such as vaccine development, targeted drug delivery, cancer therapy and diagnosis. It highlights the complex interactions of BEVs within bacterial communities and between bacteria and hosts. This review also addresses current advancements, challenges, and opportunities in translating BEV research into clinical practice. The insights presented here position BEVs as a cornerstone in the future of biomedical advancements, advocating for standardized methods in BEV characterization and scalable production techniques.},
}

@article {pmid40348966,
year = {2025},
author = {Van Hee, S and Segurado Luchsinger, AE and Cusumano, A and Masschelein, J and Jacquemyn, H and Lievens, B and Luchsinger, AES},
title = {The plant-beneficial fungus Trichoderma harzianum T22 modulates plant metabolism and negatively affects Nezara viridula.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {615},
pmid = {40348966},
issn = {1471-2229},
support = {C24E/19/052//KU Leuven/ ; },
mesh = {*Hypocreales/physiology ; Animals ; Plant Leaves/metabolism/microbiology ; Herbivory ; Metabolome ; *Capsicum/microbiology/metabolism ; Plant Roots/microbiology/metabolism ; Plant Defense Against Herbivory ; },
abstract = {BACKGROUND: Plant-beneficial fungi play an important role in enhancing plant health and resistance against biotic and abiotic stresses. Although extensive research has focused on their role in eliciting plant defences against pathogens, their contribution to induced resistance against herbivorous insects and the underlying mechanisms remain poorly understood. In this study, we used insect bioassays and untargeted metabolomics to investigate the impact of root inoculation of sweet pepper with the plant-beneficial fungus Trichoderma harzianum T22 on direct defence responses against the insect herbivore Nezara viridula.

RESULTS: We observed reduced relative growth rate of N. viridula on leaves of fungus-inoculated plants, with no change in mortality. Untargeted metabolomic analyses revealed that inoculation with T. harzianum did not affect the leaf metabolome in the absence of herbivory five weeks after inoculation. However, compared to non-inoculated plants, inoculated plants exhibited significant metabolic alterations in herbivore-damaged leaves following N. viridula feeding, while changes in the metabolic profile of distant leaves were less pronounced. Notably, metabolites involved in the shikimate-phenylpropanoid pathway, known to be involved in plant defence responses, displayed higher accumulation in damaged leaves of inoculated plants compared to non-inoculated plants.

CONCLUSION: Our results indicate that root inoculation with T. harzianum T22 affects plant defences against N. viridula, leading to reduced insect performance. Metabolite-level effects were primarily observed in damaged leaves, suggesting that the priming effect mainly results in localized metabolite accumulation at the site of attack. Future research should focus on identifying the detected compounds and determining their role in impairing N. viridula performance.},
}

*Hypocreales/physiology
Animals
Plant Leaves/metabolism/microbiology
Herbivory
Metabolome
*Capsicum/microbiology/metabolism
Plant Roots/microbiology/metabolism
Plant Defense Against Herbivory

@article {pmid40347612,
year = {2025},
author = {Rodríguez-Seijo, A and Pérez-Rodríguez, P and Arias-Estévez, M and Gómez-Armesto, A and Conde-Cid, M and Santás-Miguel, V and Campillo-Cora, C and Ollio, I and Lloret, E and Martínez-Martínez, S and Zornoza, R and Waeyenberge, L and Schrader, S and Brandt, KK and Loit, K and Põldmets, M and Shanskiy, M and Peltoniemi, K and Hagner, M and Calviño, DF},
title = {Occurrence, persistence and risk assessment of pesticide residues in European wheat fields: A continental scale approach.},
journal = {Journal of hazardous materials},
volume = {494},
number = {},
pages = {138291},
doi = {10.1016/j.jhazmat.2025.138291},
pmid = {40347612},
issn = {1873-3336},
abstract = {Pesticide residues in agricultural soils represent an environmental concern that requires special attention due to their potential ecological and public health risks. We analyzed 614 pesticides in 188 wheat fields across Europe subjected to both conventional and organic farming systems. At least one pesticide residue was detected in 141 soils. Seventy-eight pesticides or their metabolites were detected. The presence of pesticides was significantly higher in both number and concentration in conventional fileds (up to 0.98 mg kg[-1]) compared to organically managed sites (up to 0.40 mg kg[-1]). A total of 88 % of conventional fields and 63 % of organic fields contained two or more pesticides. Conversion from conventional to organic farming does not guarantee that soils will be pesticide-free in the short term. Fenbutatin oxide was the most frequently detected pesticide in both farming systems, followed by AMPA. Other substances, such as boscalid, epoxiconazole, diflufenican, tebuconazole, dinoterb, bixafen, and DEET, were found in ≥ 10 % of samples. Some Persistent Organic Pollutants, including dieldrin, endosulfan sulphate, and chlorpyrifos, were also detected. Ecological risks were higher in conventionally managed fields, with 46 % exhibiting high-risk levels, compared to just 1 % in organic fields. Epoxiconazole and boscalid were the substances with the highest risk levels.},
}

@article {pmid40347236,
year = {2025},
author = {Qi, W and Song, W and Qi, R and Li, Y and Yang, H and Li, Y and Chang, Z},
title = {Land Use Types Drive the Distinct Patterns of Bacterial and Fungal Communities in Soils from the Semi-arid Area.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {43},
pmid = {40347236},
issn = {1432-184X},
support = {2021-XBQNXZ-001//The West Light Foundation of Chinese Academy of Science/ ; DD20242544//The Ecological Protection and Restoration Support Survey Project of China Geological Survey/ ; },
mesh = {*Soil Microbiology ; China ; *Bacteria/classification/isolation & purification/genetics ; *Fungi/classification/isolation & purification/genetics ; Soil/chemistry ; Biodiversity ; Grassland ; Ecosystem ; Desert Climate ; Agriculture ; *Microbiota ; Farms ; Mycobiome ; },
abstract = {Land types and ways of utilization significantly influence soil microbial communities in arid and semi-arid regions, which are vital for nutrient cycling and ecosystem functionality. In this study, the soil bacterial and fungal communities of five land types, including natural grasslands, farmlands, artificial grasslands, uncultivated lands, and riverbeds in the semi-arid lower reaches of the Heihe River, China, were investigated. Farmlands exhibited the highest bacterial Chao1 richness and Shannon diversity, while uncultivated soils had the lowest bacterial Chao1 richness. Fungal diversity was highest in uncultivated soils compared to farmlands. Principal coordinate analysis (PCoA) showed distinct microbial community structures across land types, with Actinobacteria, Proteobacteria, Firmicutes, and Chloroflexi dominating bacterial communities, and Ascomycota and Basidiomycota dominating fungal communities. Life history strategies revealed distinct patterns between bacterial and fungal communities within farmland soils and artificial grassland soils. Microbial community assembly in natural grasslands was primarily deterministic, with limited stochastic influence, while farmlands exhibited mixed assembly processes. Co-occurrence network analysis showed more stable and cooperative microbial networks in natural grasslands, while farmland networks were more competitive and reliant on key species. These findings provide important insights into the role of land use in shaping microbial diversity and ecosystem function, offering guidance for sustainable land management in semi-arid oasis regions.},
}

*Soil Microbiology
China
*Bacteria/classification/isolation & purification/genetics
*Fungi/classification/isolation & purification/genetics
Soil/chemistry
Biodiversity
Grassland
Ecosystem
Desert Climate
Agriculture
*Microbiota
Farms
Mycobiome

@article {pmid40347194,
year = {2025},
author = {Su, QY and Zhang, JT and Gao, HJ and Zhang, Y and Luo, J and Cao, TY and Yang, MY and Zhang, SX},
title = {Mechanism and clinical utility of abatacept in the treatment of rheumatoid arthritis.},
journal = {Expert opinion on drug safety},
volume = {},
number = {},
pages = {},
doi = {10.1080/14740338.2025.2505542},
pmid = {40347194},
issn = {1744-764X},
abstract = {INTRODUCTION: Abatacept, a biological disease-modifying antirheumatic drug(bDMARD), has demonstrated unique and effective therapeutic properties for rheumatoid arthritis (RA).

AREAS COVERED: This review offers an in-depth examination of the mechanism by which abatacept exerts its effects in RA treatment and assesses its efficacy and safety based on a range of studies. We conducted a comprehensive search of PubMed, Embase databases, Web of Science, the Cochrane Library, MEDLINE, Wanfang Data, and CNKI from the time the databases were created until 30 July 2024.

EXPERT OPINION: By modulating the CD28 and CD80/CD86 costimulatory signaling pathways, abatacept is instrumental in regulating immune cells and cytokines implicated in the pathogenesis RA. Longitudinal studies have highlighted its capacity to mitigate disease advancement and maintain joint functionality. The most frequently reported adverse effects associated with abatacept are headache, nausea, and upper respiratory tract infections, which are typically self-resolving. The incidence of serious infections was not high, mainly various types of bacterial pneumonia. Comparative safety analyses of abatacept with other DMARDs yield encouraging results. As our understanding of the mechanism of action of abatacept improves, we may be able to better identify appropriate biologic therapies and advanced combination therapies for RA patients and ultimately improve patient outcomes.},
}

@article {pmid40346393,
year = {2025},
author = {Leiter, N and Wohlschläger, M and Versen, M and Harter, SD and Kießlich, T and Lederer, F and Clauß, S and Schlosser, D and Armanu, EG and Eberlein, C and Heipieper, HJ and Löder, MGJ and Laforsch, C},
title = {Effects of defined organic layers on the fluorescence lifetime of plastic materials.},
journal = {Analytical and bioanalytical chemistry},
volume = {},
number = {},
pages = {},
pmid = {40346393},
issn = {1618-2650},
support = {FKZ 031B0828A//Bundesministerium für Bildung und Forschung/ ; 391977956 - SFB 1357//Deutsche Forschungsgemeinschaft/ ; },
abstract = {Plastics have become an integral part of modern life, and linked to that fact, the demand for and global production of plastics are still increasing. However, the environmental pollution caused by plastics has reached unprecedented levels. The accumulation of small plastic fragments-microplastics and nanoplastics-potentially threatens organisms, ecosystems, and human health. Researchers commonly employ non-destructive analytical methods to assess the presence and characteristics of microplastic particles in environmental samples. However, these techniques require extensive sample preparation, which represents a significant limitation and hinders a direct on-site analysis. In this context, previous investigations showed the potential of fluorescence lifetime imaging microscopy (FLIM) for fast and reliable identification of microplastics in an environmental matrix. However, since microplastics receive an environmental coating after entering nature, a challenge arises from organic contamination on the surface of microplastic particles. How this influences the fluorescence signal and the possibility of microplastic detection are unknown. To address this research gap, we exposed acrylonitrile butadiene styrene (ABS) and polyethylene terephthalate (PET) plastic samples to peptides, proteins, bacteria, and a filamentous fungus to induce organic contamination and mimic environmental conditions. We analyzed the fluorescence spectra and lifetimes of the samples using fluorescence spectroscopy and frequency-domain fluorescence lifetime imaging microscopy (FD-FLIM), respectively. Our results demonstrate that reliably identifying and differentiating ABS and PET was possible via FD-FLIM, even in the presence of these biological contaminations. These findings highlight the potential of this technique as a valuable tool for environmental monitoring and plastic characterization, offering a rapid and efficient alternative to currently used analytical methods.},
}

@article {pmid40345255,
year = {2025},
author = {Feng, J and Zhang, C and Bao, J and Xu, Q and Gan, Y and Hu, Y},
title = {A modified variable flip angle release device for endoscopic titanium clips.},
journal = {Endoscopy},
volume = {57},
number = {S 01},
pages = {E396-E397},
doi = {10.1055/a-2584-1271},
pmid = {40345255},
issn = {1438-8812},
support = {2024GZL-CX58//Xiamen High-quality Development Medical Innovation Fund/ ; },
}

@article {pmid40343785,
year = {2025},
author = {Moukarzel, R and Waller, LP and Jones, EE and Ridgway, HJ},
title = {Arbuscular mycorrhizal fungal symbiosis in New Zealand ecosystems: challenges and opportunities.},
journal = {Letters in applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/lambio/ovaf070},
pmid = {40343785},
issn = {1472-765X},
abstract = {Arbuscular mycorrhizal fungi (AMF) are obligate biotrophs that form a symbiotic and mutualistic relationship with most terrestrial plants, playing an important role in plant growth, nutrient acquisition, and ecosystem stability. This review synthesizes current knowledge on AMF colonization in plants within New Zealand ecosystems, including the challenges and opportunities of molecular identification techniques used in characterizing AMF communities in natural and managed systems. The ecosystem services provided by AMF, such as improved growth parameters, enhanced nutrition, and disease control, are discussed in detail, highlighting their significance in sustainable agriculture and natural ecosystems. Additionally, the role of AMF in invasion ecology was examined, revealing their dual potential to either facilitate or hinder invasive plant species. Despite significant advances in understanding AMF biology, future research is needed to explore the underlying mechanisms of AMF-plant interactions and to address the challenges caused by changing environmental conditions. This review focused on the importance of AMF in promoting ecosystem resilience and suggests avenues for future research to harness their full potential in agricultural and ecological contexts.},
}

@article {pmid40343125,
year = {2025},
author = {Tóth, VR},
title = {The impact of epiphytic algae on the foliar traits of Potamogeton perfoliatus.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1561709},
doi = {10.3389/fpls.2025.1561709},
pmid = {40343125},
issn = {1664-462X},
abstract = {This study investigated the effect of epiphyton on foliar traits of a submerged rooted macrophyte, Potamogeton perfoliatus, in a shallow freshwater lake, highlighting its influence on the ecological dynamics of littoral zones in aquatic ecosystems. It was shown that the limnological characteristics of the sampling sites (water chlorophyll-a, total suspended matter and coloured dissolved organic matter content) had no significant effect on the average values of epiphytic algal content found on pondweed leaves, while influencing the plasticity of these data. The responses of morphological and physiological traits of submerged macrophytes to accumulated epiphyton demonstrate the complexity of their relationship: epiphyton colonisation had no relevant effect on leaf morphology (except leaf length) and leaf pigment content (except Chl-a/Chl-b ratio), however, this study highlights the significant influence of epiphytic algal biomass on photophysiological traits of submerged macrophyte leaves, as 5 out of 6 photophysiological traits were affected. The results highlight the importance of considering epiphyte colonisation when seeking to understand the ecological functioning of littoral aquatic ecosystems. Furthermore, the complex interactions between epiphytes and submerged rooted macrophytes should be considered in integrated lake management and environmental protection policies. These interactions play an important, though ambiguous role in shaping habitat variability and overall ecosystem health in littoral zones.},
}

@article {pmid40341906,
year = {2025},
author = {Shoemaker, WR and Sánchez, Á and Grilli, J},
title = {Macroecological patterns in experimental microbial communities.},
journal = {PLoS computational biology},
volume = {21},
number = {5},
pages = {e1013044},
doi = {10.1371/journal.pcbi.1013044},
pmid = {40341906},
issn = {1553-7358},
abstract = {Ecology has historically benefited from the characterization of statistical patterns of biodiversity within and across communities, an approach known as macroecology. Within microbial ecology, macroecological approaches have identified universal patterns of diversity and abundance that can be captured by effective models. Experimentation has simultaneously played a crucial role, as the advent of high-replication community time-series has allowed researchers to investigate underlying ecological forces. However, there remains a gap between experiments performed in the laboratory and macroecological patterns documented in natural systems, as we do not know whether these patterns can be recapitulated in the lab and whether experimental manipulations produce macroecological effects. This work aims at bridging the gap between experimental ecology and macroecology. Using high-replication time-series, we demonstrate that microbial macroecological patterns observed in nature exist in a laboratory setting, despite controlled conditions, and can be unified under the Stochastic Logistic Model of growth (SLM). We found that demographic manipulations (e.g., migration) impact observed macroecological patterns. By modifying the SLM to incorporate said manipulations alongside experimental details (e.g., sampling), we obtain predictions that are consistent with macroecological outcomes. By combining high-replication experiments with ecological models, microbial macroecology can be viewed as a predictive discipline.},
}

@article {pmid40338317,
year = {2025},
author = {Graziosi, S and Deloche, L and Januario, M and Selosse, MA and Deveau, A and Bach, C and Chen, Z and Murat, C and Iotti, M and Rech, P and Zambonelli, A},
title = {Newly Designed Fluorescence In Situ Hybridization Probes Reveal Previously Unknown Endophytic Abilities of Tuber magnatum in Herbaceous Plants.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {42},
pmid = {40338317},
issn = {1432-184X},
support = {K272X8 - CUP J53D23010090006//European Union - NextGenerationEU under the National Recovery and Resilience Plan (PNRR) - Mission 4 Education and research - Component 2 From research to business - Investment 1.1 Notice Prin 2022 - DD N. 104 del 2/2/2022, from title "Interactions of the white truffle Tuber magnatum with soil microbiome and plants"/ ; K272X8 - CUP J53D23010090006//European Union - NextGenerationEU under the National Recovery and Resilience Plan (PNRR) - Mission 4 Education and research - Component 2 From research to business - Investment 1.1 Notice Prin 2022 - DD N. 104 del 2/2/2022, from title "Interactions of the white truffle Tuber magnatum with soil microbiome and plants"/ ; ANR-11-LABX-0002-01//The French National Research Agency (ANR), 'Investissements d'Avenir' program, Lab of Excellence ARBRE, UMR IaM./ ; ANR-11-LABX-0002-01//The French National Research Agency (ANR), 'Investissements d'Avenir' program, Lab of Excellence ARBRE, UMR IaM./ ; ANR-11-LABX-0002-01//The French National Research Agency (ANR), 'Investissements d'Avenir' program, Lab of Excellence ARBRE, UMR IaM./ ; ANR-11-LABX-0002-01//The French National Research Agency (ANR), 'Investissements d'Avenir' program, Lab of Excellence ARBRE, UMR IaM./ ; },
mesh = {*Endophytes/genetics/isolation & purification/physiology ; *In Situ Hybridization, Fluorescence/methods ; Plant Roots/microbiology ; *Mycorrhizae/genetics/isolation & purification/physiology ; *Ascomycota/genetics/isolation & purification/physiology ; Symbiosis ; Italy ; Polymerase Chain Reaction ; Hyphae/genetics ; },
abstract = {Tuber magnatum Picco (the Italian white truffle) is the most valuable and widely appreciated truffle. It is an ectomycorrhizal fungus known to associate with many broadleaf tree species. However, its mycorrhizae are rarely observed in the field, suggesting possible alternative symbiotic strategies, such as endophytism with non-ectomycorrhizal plants. In order to test potential endophytic interactions of T. magnatum with wild plants, a combination of polymerase chain reaction (PCR) and Fluorescence In Situ Hybridization (FISH) approaches were used. Specific FISH probes for T. magnatum were designed, tested in vitro on hyphae and/or ectomycorrhizae, and selected for their specificity. These probes were then used on a wide variety root samples of wild plants collected from three T. magnatum production areas in Italy and previously tested for the presence of T. magnatum mycelium using PCR-specific primers. Molecular analyses detected the presence of T. magnatum in 21 of 100 plant samples analyzed. FISH analysis confirmed the extracellular presence of active T. magnatum hyphae inside the root system of Carex pendula Huds plant. This study provides the first evidence of T. magnatum acting as an endophyte in an herbaceous plant. The newly designed, highly specific T. magnatum FISH probes can be used for further investigations to confirm the endophytic tendencies of T. magnatum and to understand their influence on the life cycle and biology of this fungus.},
}

*Endophytes/genetics/isolation & purification/physiology
*In Situ Hybridization, Fluorescence/methods
Plant Roots/microbiology
*Mycorrhizae/genetics/isolation & purification/physiology
*Ascomycota/genetics/isolation & purification/physiology
Symbiosis
Italy
Polymerase Chain Reaction
Hyphae/genetics

@article {pmid40336837,
year = {2025},
author = {Couch, CE and Xavier, R and Beechler, BR},
title = {Editorial: Parasite, host, and microbiome interactions in natural host systems.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1589627},
doi = {10.3389/fmicb.2025.1589627},
pmid = {40336837},
issn = {1664-302X},
}

@article {pmid40335733,
year = {2025},
author = {Guo, Y and Tian, L and Zhu, X and Liu, S and Wang, L and Li, W},
title = {Antagonism of Bacillus velezensis ZGE166 Against the Pathogenic Fungi Causing Corm Rot Disease in Saffron (Crocus sativus L.).},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {40},
pmid = {40335733},
issn = {1432-184X},
mesh = {*Bacillus/physiology/genetics/isolation & purification ; *Crocus/microbiology/growth & development ; Rhizosphere ; *Plant Diseases/microbiology/prevention & control ; Soil Microbiology ; *Antibiosis ; *Fungi/physiology ; Genome, Bacterial ; Phylogeny ; },
abstract = {Saffron can be infected with pathogenic fungi that cause corm rot as it grows and multiplies, which can reduce the quality and yield of saffron. Corm rot has become one of the most serious diseases of saffron. In this study, rhizosphere bacteria were isolated from saffron rhizosphere soil, and bacteria exhibiting antagonistic effects against corm rot pathogenic fungi were screened using in vitro plate co-culture assays and dual-compartment agar plate systems. Selected strains were further evaluated for hydrolase activity determination and PGP potential assessment. Among them, Bacillus velezensis showed the best disease resistance activity. The degradative enzyme production and some beneficial characteristics of Bacillus velezensis for plant growth promotion were evaluated. It was found that Bacillus velezensis possesses nitrogen fixing, NH3-producing, IAA production, and ACC-deaminating enzymes. The whole genome sequence of this strain was annotated and analyzed. The genome of Bacillus velezensis consists of a circular chromosome of 3,908,025 bp base pairs, with a guanine and cytosine content of 46.64%. There are 3737 protein-coding genes, including 86 tRNA genes, 27 rRNA genes, and 85 sRNA genes. The genome also contains four genomic islands, two pre-phages, and one transposon. The prediction of the secondary metabolic accumulation gene cluster demonstrated that the genome sequence of ZGE166 encodes 12 gene clusters involved in the synthesis of secondary metabolites, including macrolactin H, bacillaene, fengycin, difficidin, and bacillibactin. In summary, strain ZGE166 Bacillus velezensis has the potential to be developed as a biological agent.},
}

*Bacillus/physiology/genetics/isolation & purification
*Crocus/microbiology/growth & development
Rhizosphere
*Plant Diseases/microbiology/prevention & control
Soil Microbiology
*Antibiosis
*Fungi/physiology
Genome, Bacterial
Phylogeny

@article {pmid40335388,
year = {2025},
author = {Dwivedi, SL and Vetukuri, RR and Kelbessa, BG and Gepts, P and Heslop-Harrison, P and Araujo, ASF and Sharma, S and Ortiz, R},
title = {Exploitation of rhizosphere microbiome biodiversity in plant breeding.},
journal = {Trends in plant science},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tplants.2025.04.004},
pmid = {40335388},
issn = {1878-4372},
abstract = {Climate change-induced stresses are perceived by plants at the root-soil interface, where they are alleviated through interactions between the host plant and the rhizosphere microbiome. The recruitment of specific microbiomes helps mitigate stress, increases resistance to pathogens, and promotes plant growth, development, and reproduction. The structure of the rhizosphere microbiome is shaped by crop domestication and variations in ploidy levels. Here we list key genes that regulate rhizosphere microbiomes and host genetic traits. We also discuss the prospects for rigorous analysis of symbiotic interactions, research needs, and strategies for systematically utilizing microbe-crop interactions to improve crop performance. Finally, we highlight challenges of maintaining live rhizosphere microbiome collections and mining heritable variability to enhance interactions between host plants and their rhizosphere microbiomes.},
}

@article {pmid40334664,
year = {2025},
author = {Sandin, MM and Renaudie, J and Suzuki, N and Not, F},
title = {Extant diversity, biogeography, and evolutionary history of Radiolaria.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2025.04.032},
pmid = {40334664},
issn = {1879-0445},
abstract = {Since Ernst Haeckel and the Challenger expedition (1872-1876), Radiolaria have been known as ubiquitous and abundant star-shaped oceanic plankton. Their exquisite biomineralized skeletons left an extensive fossil record extremely valuable for biostratigraphic and paleo-environmental research. In contemporary oceans, there is growing evidence that Radiolaria are significant contributors to marine food webs and global biogeochemical cycles. Here we provide a comprehensive morpho-molecular framework to assess the extant diversity, biogeography, and evolutionary history of Radiolaria. Our analyses reveal that half of radiolarian diversity is morphologically undescribed, with a large part forming three hyper-diverse environmental clades, named Rad-A, Rad-B, and Rad-C. We suggest that most of this undescribed diversity comprises skeleton-less life forms or endosymbionts, explaining their elusive, yet abundant, nature. Phylogenetic analyses highlight the need for a major revision of high-level Radiolaria taxonomy, including placement of Collodaria within the order Nassellaria. Global metabarcoding surveys show that Radiolaria contributes more than 12% to the total eukaryotic community, displaying distinct biogeographic patterns with the skeleton-less lineages at depth and photosymbiont-bearing lineages in the surface. Fossil calibration of a molecular clock revealed the first appearance of Radiolaria ∼760 million years ago (mya), the development of the skeleton in the early Paleozoic (∼500 mya), and the onset of photosymbiotic relationships during the mid to late Mesozoic (∼140 mya), related to geological periods of oligotrophy and anoxia. The results presented here provide a robust framework for developing new perspectives on early eukaryotic diversification, paleo-environmental impacts on plankton evolution, and marine microbial ecology in rapidly evolving ecosystems.},
}

@article {pmid40333193,
year = {2025},
author = {Hodžić, A and Kunert, M and Berry, D},
title = {Protocol for the visualization of bacteria in the tick gut using whole-mount fluorescence in situ hybridization.},
journal = {STAR protocols},
volume = {6},
number = {2},
pages = {103814},
doi = {10.1016/j.xpro.2025.103814},
pmid = {40333193},
issn = {2666-1667},
abstract = {The tick gut harbors a relatively diverse microbial community that includes commensal, beneficial, and pathogenic bacterial species. Here, we present a protocol for the visualization of bacteria in the tick gut using whole-mount fluorescence in situ hybridization. We describe steps for tick dissection, tissue fixation, hybridization, washing, and mounting. We then detail procedures for microscopy imaging of the whole-mounted samples. Although the procedure is designed for gut tissue samples, it can be readily modified for use with other tissue types. For complete details on the use and execution of this protocol, please refer to Hodžić et al.[1].},
}

@article {pmid40333163,
year = {2025},
author = {Touati, A and Ibrahim, NA and Idres, T},
title = {Disarming Staphylococcus aureus: Review of Strategies Combating This Resilient Pathogen by Targeting Its Virulence.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/pathogens14040386},
pmid = {40333163},
issn = {2076-0817},
support = {IMSIU-DDRSP2501//The Deanship of Scientific Research at Imam Mohammad Ibn Saud Islamic University (IMSIU)/ ; },
mesh = {Humans ; *Staphylococcal Infections/microbiology/drug therapy ; Virulence/drug effects ; *Staphylococcus aureus/drug effects/pathogenicity/physiology ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Biofilms/drug effects/growth & development ; *Virulence Factors/antagonists & inhibitors/metabolism ; Quorum Sensing/drug effects ; Methicillin-Resistant Staphylococcus aureus/drug effects/pathogenicity ; Animals ; },
abstract = {Staphylococcus aureus is a formidable pathogen notorious for its antibiotic resistance and diverse virulence mechanisms, including toxin production, biofilm formation, and immune evasion. This article explores innovative anti-virulence strategies to disarm S. aureus by targeting critical virulence factors without exerting bactericidal pressure. Key approaches include inhibiting adhesion and biofilm formation, neutralizing toxins, disrupting quorum sensing (e.g., Agr system inhibitors), and blocking iron acquisition pathways. Additionally, interventions targeting two-component regulatory systems are highlighted. While promising, challenges such as strain variability, biofilm resilience, pharmacokinetic limitations, and resistance evolution underscore the need for combination therapies and advanced formulations. Integrating anti-virulence strategies with traditional antibiotics and host-directed therapies offers a sustainable solution to combat multidrug-resistant S. aureus, particularly methicillin-resistant strains (MRSA), and mitigate the global public health crisis.},
}

Humans
*Staphylococcal Infections/microbiology/drug therapy
Virulence/drug effects
*Staphylococcus aureus/drug effects/pathogenicity/physiology
*Anti-Bacterial Agents/pharmacology/therapeutic use
Biofilms/drug effects/growth & development
*Virulence Factors/antagonists & inhibitors/metabolism
Quorum Sensing/drug effects
Methicillin-Resistant Staphylococcus aureus/drug effects/pathogenicity
Animals

@article {pmid40333144,
year = {2025},
author = {Plewa-Tutaj, K and Chmielewska, Z and Twarużek, M and Kosicki, R and Soszczyńska, E},
title = {An Analysis of the Mycotoxins, Cytotoxicity, and Biodiversity of Airborne Molds Belonging to Aspergillus Genera Isolated from the Zoological Garden.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/pathogens14040332},
pmid = {40333144},
issn = {2076-0817},
support = {"MINIATURA 6," grant 2022/06/X/NZ8/00430//National Science Centre, Poland/ ; },
mesh = {*Mycotoxins/toxicity/analysis ; *Aspergillus/isolation & purification/classification/genetics/metabolism ; *Air Microbiology ; *Biodiversity ; Animals ; Humans ; },
abstract = {The present study aimed to identify airborne molds of the Aspergillus genus and to determine the secondary metabolite profiles and toxicity of dominant fungal species isolated from various locations in the Wroclaw Zoological Garden. Air samples were collected using a MAS-100 air sampler and analyzed for fungal colony-forming units (CFU). Morphological and molecular methods, including ITS sequencing, were employed for dominant mold identification. The most frequently encountered species were A. fumigatus and A. niger, while A. pseudoglaucus and A. nomius were the least common. The high prevalence of species from sections Nigri, Flavi, and Fumigati suggests their adaptability to the zoo environment. A total of 17 Aspergillus isolates were analyzed for both their capacity to induce cellular toxicity and their production of mycotoxins. The results indicated that all isolates exhibited cellular toxicity, with 70.6% displaying levels of toxicity that were medium to high. Furthermore, the mycotoxicological analysis revealed that only A. fumigatus strains were capable of producing mycotoxins, specifically gliotoxin. The study underscores the discrepancy between the levels of toxicity and the production of mycotoxins, thereby suggesting the presence of additional cytotoxic metabolites. These findings emphasize the need for a comprehensive understanding of the complex interplay between fungal metabolites and their consequences for human health.},
}

*Mycotoxins/toxicity/analysis
*Aspergillus/isolation & purification/classification/genetics/metabolism
*Air Microbiology
*Biodiversity
Animals
Humans

@article {pmid40333133,
year = {2025},
author = {Niculescu, AG and Mitache, MM and Grumezescu, AM and Chifiriuc, MC and Mihai, MM and Tantu, MM and Tantu, AC and Popa, LG and Grigore, GA and Cristian, RE and Popa, MI and Vrancianu, CO},
title = {From Microbial Ecology to Clinical Challenges: The Respiratory Microbiome's Role in Antibiotic Resistance.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/pathogens14040355},
pmid = {40333133},
issn = {2076-0817},
support = {CNFIS-FDI-2024-F-0484 INOVEX//University of Bucharest/ ; Pillar III, Component C9/Investment no. 8 (I8) - contract CF 68//; Ministry of Research, Innovation and Digitalization through the National Recovery and Resilience Plan (PNRR) of Romania/ ; project no. 23020101, Contract no. 7N from 3 January 2023//The core program within the National Research Development and Innovation Plan, 2022-2027', carried out with the support of the Ministry of Research, Innovation and Digitalization (MCID)/ ; },
mesh = {Humans ; *Microbiota/drug effects ; Anti-Bacterial Agents/pharmacology/therapeutic use ; *Respiratory Tract Infections/microbiology/drug therapy ; *Drug Resistance, Microbial ; Probiotics ; *Drug Resistance, Bacterial ; *Respiratory System/microbiology ; },
abstract = {Antibiotic resistance represents a growing public health threat, with airborne drug-resistant strains being especially alarming due to their ease of transmission and association with severe respiratory infections. The respiratory microbiome plays a pivotal role in maintaining respiratory health, influencing the dynamics of antibiotic resistance among airborne pathogenic microorganisms. In this context, this review proposes the exploration of the complex interplay between the respiratory microbiota and antimicrobial resistance, highlighting the implications of microbiome diversity in health and disease. Moreover, strategies to mitigate antibiotic resistance, including stewardship programs, alternatives to traditional antibiotics, probiotics, microbiota restoration techniques, and nanotechnology-based therapeutic interventions, are critically presented, setting an updated framework of current management options. Therefore, through a better understanding of respiratory microbiome roles in antibiotic resistance, alongside emerging therapeutic strategies, this paper aims to shed light on how the global health challenges posed by multi-drug-resistant pathogens can be addressed.},
}

Humans
*Microbiota/drug effects
Anti-Bacterial Agents/pharmacology/therapeutic use
*Respiratory Tract Infections/microbiology/drug therapy
*Drug Resistance, Microbial
Probiotics
*Drug Resistance, Bacterial
*Respiratory System/microbiology

@article {pmid40332344,
year = {2025},
author = {Figueiredo, JEF and Marins, MS and Silva, FC and Ribeiro, VP and Diniz, GdFD and Rodrigues, VA and Oliveira-Paiva, CA and Lana, UGdP and Ferreira, LVS and Sousa Tinoco, SMd and Cruz-Magalhães, V},
title = {Draft genome of the endophytic Bacillus velezensis CNPMS-22 isolated from maize leaves.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0127924},
doi = {10.1128/mra.01279-24},
pmid = {40332344},
issn = {2576-098X},
abstract = {Bacillus velezensis has been widely used as a biocontrol agent and plant growth promoter in agricultural bio-inputs. The genome of the endophytic bacterial strain CNPMS-22 isolated from maize leaves was sequenced, and the results showed that the strain is a Bacillus velezensis species.},
}

@article {pmid40329925,
year = {2025},
author = {Razzaq Meo, S and Van de Wiele, T and Defoirdt, T},
title = {Indole signaling in Escherichia coli: a target for antivirulence therapy?.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2499573},
doi = {10.1080/19490976.2025.2499573},
pmid = {40329925},
issn = {1949-0984},
mesh = {*Indoles/metabolism/pharmacology ; *Escherichia coli/drug effects/metabolism/pathogenicity/genetics ; Humans ; *Signal Transduction/drug effects ; *Escherichia coli Infections/microbiology/drug therapy ; Virulence/drug effects ; Quorum Sensing/drug effects ; *Anti-Bacterial Agents/pharmacology ; Virulence Factors/metabolism/genetics/antagonists & inhibitors ; Animals ; Escherichia coli Proteins/metabolism/genetics ; Biofilms/drug effects/growth & development ; },
abstract = {Pathogenic Escherichia coli are a major cause of infections in both humans and animals, leading to conditions such as severe diarrheal diseases, urinary tract infections, enteritis, and septicemia. To combat bacterial infections, antibiotics are widely utilized. However, the extensive and inappropriate use of antibiotics has fueled the development and spread of antibiotic resistance, posing a significant challenge to the effective treatment of E. coli. There is consequently an urgent need to explore alternative therapies to control such infections. This review provides an overview of the recent findings concerning indole signaling in E. coli. E. coli uses indole as a quorum sensing molecule, and indole signaling has been reported to decrease various virulence factors in pathogenic E. coli, including motility, biofilm formation, adherence to host cells, expression of the LEE pathogenicity island, and formation of attaching and effacing lesions. This makes indole signaling an interesting target for the development of new therapeutics in the framework of antivirulence therapy. Both natural and synthetic indole analogues have been explored as potential virulence inhibitors. This alternative approach could be advantageous, as it will exert less selective pressure for resistance development than conventional antibiotics.},
}

*Indoles/metabolism/pharmacology
*Escherichia coli/drug effects/metabolism/pathogenicity/genetics
Humans
*Signal Transduction/drug effects
*Escherichia coli Infections/microbiology/drug therapy
Virulence/drug effects
Quorum Sensing/drug effects
*Anti-Bacterial Agents/pharmacology
Virulence Factors/metabolism/genetics/antagonists & inhibitors
Animals
Escherichia coli Proteins/metabolism/genetics
Biofilms/drug effects/growth & development

@article {pmid40329550,
year = {2025},
author = {Jenkins, GB and Boyd, ES and Danchin, A and Hervé, V and Huggett, MJ and Sánchez, Á and Trevorrow, P},
title = {Environmental Microbiology and Environmental Microbiology Reports: Two Journals, One Goal.},
journal = {Environmental microbiology},
volume = {27},
number = {5},
pages = {e70078},
doi = {10.1111/1462-2920.70078},
pmid = {40329550},
issn = {1462-2920},
}

@article {pmid40329526,
year = {2025},
author = {Ory, F and Dainat, B and Würgler, O and Wenger, F and Roetschi, A and Braillard, L and Charrière, JD and Dietemann, V},
title = {Ecology and Pathogenicity for Honey Bee Brood of Recently Described Paenibacillus melissococcoides and Comparison With Paenibacillus dendritiformis, Paenibacillus thiaminolyticus.},
journal = {Environmental microbiology reports},
volume = {17},
number = {3},
pages = {e70089},
doi = {10.1111/1758-2229.70089},
pmid = {40329526},
issn = {1758-2229},
mesh = {Bees/microbiology ; Animals ; *Paenibacillus/pathogenicity/genetics/isolation & purification/classification ; Virulence ; Spores, Bacterial ; Paenibacillus larvae ; Phylogeny ; Larva/microbiology ; },
abstract = {Honey bee colonies contain thousands of individuals living in close proximity in a thermally homeostatic nest, creating ideal conditions for the thriving of numerous pathogens. Among the bacterial pathogens, Paenibacillus larvae infects larvae via the nutritive jelly that adult workers feed them, causing the highly contagious American foulbrood disease. Further Paenibacillus species were anecdotally found in association with honey bees, including when affected by another disease, European foulbrood (EFB). However, their pathogenicity remains largely unknown. Our results indicate that Paenibacillus dendritiformis, Paenibacillus thiaminolyticus and newly described Paenibacillus melissococcoides are pathogenic towards honey bee brood and that their virulence correlates with their sporulation ability, which confers them resistance to the bactericidal properties of the nutritive jelly. Our survey occasionally but increasingly detected P. melissococcoides in confirmed and idiopathic cases of EFB but never in healthy colonies, suggesting that this bacterium is an emerging pathogen of honey bee brood. Overall, our results suggest that virulence traits allowing a pathogenic or opportunistically pathogenic habit towards honey bee brood are frequent in Paenibacillus spp., but that their degree of adaptation to this host varies. Our study clarifies the ecology of this ubiquitous genus, especially when infecting honey bees.},
}

Bees/microbiology
Animals
*Paenibacillus/pathogenicity/genetics/isolation & purification/classification
Virulence
Spores, Bacterial
Paenibacillus larvae
Phylogeny
Larva/microbiology

@article {pmid40327698,
year = {2025},
author = {Clegg, T and Gross, T},
title = {Cross-feeding creates tipping points in microbiome diversity.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {19},
pages = {e2425603122},
doi = {10.1073/pnas.2425603122},
pmid = {40327698},
issn = {1091-6490},
mesh = {*Microbiota/physiology ; *Biodiversity ; *Models, Biological ; },
abstract = {A key unresolved question in microbial ecology is how the extraordinary diversity of microbiomes emerges from the interactions among their many functionally distinct populations. This process is driven in part by the cross-feeding networks that help to structure these systems, in which consumers use resources to fuel their metabolism, creating by-products which can be used by others in the community. Understanding the effects of cross-feeding presents a major challenge, as it creates complex interdependencies between populations which can be hard to untangle. We address this problem using the tools of network science to develop a structural microbial community model. Using methods from percolation theory, we identify feasible community states for cross-feeding network structures in which the needs of consumers are met by metabolite production across the community. We identify tipping points at which small changes in structure can cause the catastrophic collapse of cross-feeding networks and abrupt declines in microbial community diversity. Our results are an example of a well-defined tipping point in a complex ecological system and provide insight into the fundamental processes shaping microbiomes and their robustness. We further demonstrate this by considering how network attacks affect community diversity and apply our results to show how the apparent difficulty in culturing the microbial diversity emerges as an inherent property of their cross-feeding networks.},
}

*Microbiota/physiology
*Biodiversity
*Models, Biological

@article {pmid40327084,
year = {2025},
author = {Zhang, M and Hu, Y and Ma, Y and Hou, T and Wang, J and Che, Q and Chen, B and Wang, Q and Feng, G},
title = {Soil Bacterial Diversity and Community Structure of Cotton Rhizosphere under Mulched Drip-Irrigation in Arid and Semi-arid Regions of Northwest China.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {39},
pmid = {40327084},
issn = {1432-184X},
mesh = {*Gossypium/microbiology/growth & development ; *Rhizosphere ; *Soil Microbiology ; China ; *Bacteria/classification/genetics/isolation & purification ; Soil/chemistry ; *Agricultural Irrigation/methods ; Biodiversity ; Desert Climate ; Microbiota ; Alkaline Phosphatase/genetics ; },
abstract = {Xinjiang is situated in an arid and semi-arid region, where abundant heat and sunlight create highly favorable conditions for cotton cultivation. Xinjiang's cotton output accounts for nearly one-quarter of global production. Moreover, the implementation of advanced planting techniques, such as 'dwarfing, high-density, early-maturing' strategies combined with mulched drip irrigation, ensures stable and high yields in this region. Despite these advancements, limited research has focused on the microbial mechanisms in cotton fields employing these advanced planting methods. In this study, high-throughput sequencing technology was utilized to investigate the diversity and composition of bacterial and phoD (Alkaline phosphatases encoding gene) communities in the rhizosphere of cotton grown under different yield levels in Xinjiang Province, China. The Mantel test, redundancy analysis (RDA) and partial least squares path modeling (PLS-PM) were employed to explore the interactions between soil bacterial and phoD communities, their network structures, and environmental factors. The bacterial and phoD communities in the cotton rhizosphere were predominantly composed of nine bacterial phyla (i.e., Proteobacteria, Actinobacteria, Acidobacteria, Gemmatimonadetes, Chloroflexi, Bacteroidetes, Rokubacteria, Firmicutes, and Nitrospirae) and five phoD phyla (i.e., Proteobacteria, Actinobacteria, Planctomycetes, Acidobacteria, and Firmicutes), respectively. Alpha diversity analysis indicated that the medium yield cotton field (MYF) exhibited higher bacterial richness and diversity indices compared to low yield (LYF) and high yield (HYF) fields. The symbiotic network analysis of LYF revealed greater values of average degree, number of edges, and modularity, suggesting a more complex network structure in both bacterial and phoD communities. The Mantel test, RDA, and PLS-PM model identified soil pH, electrical conductivity (EC), organic phosphorus (OP), available phosphorus (AP), total nitrogen (TN), microbial biomass carbon (MBC), and clay content as the main driving factors influencing changes in the rhizosphere bacterial community diversity and network structure. These findings provide a theoretical basis for future research aimed at improving soil quality and cotton yield.},
}

*Gossypium/microbiology/growth & development
*Rhizosphere
*Soil Microbiology
China
*Bacteria/classification/genetics/isolation & purification
Soil/chemistry
*Agricultural Irrigation/methods
Biodiversity
Desert Climate
Microbiota
Alkaline Phosphatase/genetics

@article {pmid40324073,
year = {2025},
author = {Hoffman, PF},
title = {Ecosystem relocation on Snowball Earth: Polar-alpine ancestry of the extant surface biosphere?.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {20},
pages = {e2414059122},
doi = {10.1073/pnas.2414059122},
pmid = {40324073},
issn = {1091-6490},
support = {EAR-0417422//NSF (NSF)/ ; },
mesh = {*Ecosystem ; Earth, Planet ; Oceans and Seas ; Ice Cover ; Fossils ; Biological Evolution ; },
abstract = {Geological observations informed by climate dynamics imply that the oceans were 99.9% covered by light-blocking ice shelves during two discrete, self-reversing Snowball Earth epochs spanning a combined 60 to 70 Myr of the Cryogenian Period (720 to 635 Ma). The timescale for initial ice advances across the tropical oceans is ~300 y in an ice-atmosphere-ocean general circulation model in Cryogenian paleogeography. Areas of optically thin oceanic ice are usually invoked to account for fossil marine phototrophs, including macroscopic multicellular eukaryotes, before and after each Snowball, but different taxa. Ecosystem relocation is a scenario that does not require thin marine ice. Assume that long before Cryogenian Snowballs, diverse supra- and periglacial biomes were established in polar-alpine regions. When the Snowball onsets occurred, those biomes migrated in step with their ice margins to the equatorial zone of net sublimation. There, they prospered and evolved, their habitat areas expanded, and the cruelty of winter reduced. Nutrients were supplied by dust (loess) derived from cozonal ablative lands where surface winds were strong. When each Snowball finally ended, those biomes were mostly inundated by the meltwater-dominated and rapidly warming lid of a nutrient-rich but depauperate ocean. Some taxa returned to the mountaintops while others restocked the oceans. This ecosystem relocation scenario makes testable predictions. The lineages required for post-Cryogenian biotic radiations should be present in modern polar-alpine biomes. Legacies of polar-alpine ancestry should be found in the genomes of living organisms. Examples of such tests are highlighted herein.},
}

*Ecosystem
Earth, Planet
Oceans and Seas
Ice Cover
Fossils
Biological Evolution

@article {pmid40323108,
year = {2025},
author = {Oz, A and Mairesse, O and Raikin, S and Hanani, H and Mor, H and Dafny Yelin, M and Sharon, I},
title = {Pear flower and leaf microbiome dynamics during the naturally occurring spread of Erwinia amylovora.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0001125},
doi = {10.1128/msphere.00011-25},
pmid = {40323108},
issn = {2379-5042},
abstract = {Erwinia amylovora is the causal pathogen of fire blight, a contagious disease that affects apple and pear trees and other members of the family Rosaceae. In this study, we investigated the community dynamics of the pear flower microbiome in an agricultural setting during the naturally occurring infection of E. amylovora. Five potential factors were considered: collection date, the flower's phenological stage, location on the tree, location within the orchard, and pear cultivar. The phenological stage and the collection date were identified as the most important factors associated with pear flower microbiome composition, while the location of the tree in the orchard and the flower's location on the tree had a marginal effect. The leaf microbiome reflected that of the abundant phenological stage on each date. The flower microbiome shifted toward E. amylovora dominating the community as time and phenological stages progressed, leading to a decreased community diversity. The E. amylovora population was represented almost exclusively by six amplicon sequence variants (ASVs) with similar proportions throughout the entire collection period. Other taxa, including Pseudomonas, Pantoea, Lactobacillus, and Sphingomonas, were represented by dozens of ASVs, and different succession patterns in their populations were observed. Some of the taxa identified include known antagonists to E. amylovora. Overall, our results suggest that flower physiology and the interaction with the environment are strongly associated with the pear flower microbiome and should be considered separately. Taxon-specific succession patterns under E. amylovora spread should be considered when choosing candidates for antagonist-based treatments for fire blight.IMPORTANCEThe spread of pathogens in plants is an important ecological phenomenon and has a significant economic impact on agriculture. Flowers serve as the entry point for E. amylovora, but members of the flower microbiome can inhibit or slow down the proliferation and penetration of the pathogen. Knowledge about leaf and flower microbiome response to the naturally occurring spread of E. amylovora is still lacking. The current study is the first to describe the Rosaceae flower microbiome dynamics during the naturally occurring infection of E. amylovora. Unlike previous studies, the study design enabled us to evaluate the contribution of five important environmental parameters to community composition. We identified different ASV succession patterns across different taxa in the flower consortia throughout the season. These results contribute to our understanding of plant microbial ecology during pathogen spread and can help improve biological treatments for fire blight.},
}

@article {pmid40322584,
year = {2025},
author = {Zschaubitz, E and Schröder, H and Glackin, CC and Vogel, L and Labrenz, M and Sperlea, T},
title = {A benchmark analysis of feature selection and machine learning methods for environmental metabarcoding datasets.},
journal = {Computational and structural biotechnology journal},
volume = {27},
number = {},
pages = {1636-1647},
pmid = {40322584},
issn = {2001-0370},
abstract = {Next-Generation Sequencing methods like DNA metabarcoding enable the generation of large community composition datasets and have grown instrumental in many branches of ecology in recent years. However, the sparsity, compositionality, and high dimensionality of metabarcoding datasets pose challenges in data analysis. In theory, feature selection methods improve the analyzability of eDNA metabarcoding datasets by identifying a subset of informative taxa that are relevant for a certain task and discarding those that are redundant or irrelevant. However, general guidelines on selecting a feature selection method for application to a given setting are lacking. Here, we report a comparison of feature selection methods in a supervised machine learning setup across 13 environmental metabarcoding datasets with differing characteristics. We evaluate workflows that consist of data preprocessing, feature selection and a machine learning model by their ability to capture the ecological relationship between the microbial community composition and environmental parameters. Our results demonstrate that, while the optimal feature selection approach depends on dataset characteristics, feature selection is more likely to impair model performance than to improve it for tree ensemble models like Random Forests. Furthermore, our results show that calculating relative counts impairs model performance, which suggests that novel methods to combat the compositionality of metabarcoding data are required.},
}

@article {pmid40322503,
year = {2025},
author = {Mandal, A and Ghosh, A and Kumar, G and Bhadury, P},
title = {Dataset of benthic foraminiferal community structure from sediment eDNA of Sundarbans mangrove ecosystem.},
journal = {Data in brief},
volume = {60},
number = {},
pages = {111554},
pmid = {40322503},
issn = {2352-3409},
abstract = {Sundarbans, the world's largest contiguous mangrove wetland, a UNESCO World Heritage Site and a RAMSAR site formed on the delta of Ganga-Brahmaputra-Meghna (GBM) and influenced by coastal water entering from the Bay of Bengal contribute immensely to biodiversity and blue economy. To track the changes driven by natural and anthropogenic stressors, sediment based environmental DNA (eDNA) biomonitoring of benthic foraminifera communities, an important biological group sensitive to changes, has been initiated along with estimation of dissolved nutrients from estuarine surface water of Sundarbans. In pre-monsoon of 2022 (June), sediment cores and surface water were collected as well as in situ environmental parameters were measured from two pre-designated sampling points of Sundarbans to elucidate the benthic foraminifera community based on sediment eDNA approach. Based on Oxford Nanopore Technologies (ONT) sequencing in MinION platform, high abundance of Sorites sp., Elphidium excavatum, Textularia gramen, Quinqueloculina sp. and Trochammina hadai were detected. The increasing nutrient concentrations and elucidated benthic foraminiferal signals can contribute towards tracking the state of ecological health of Sundarbans. This study is aimed at generating baseline information on mangrove benthic foraminifera communities using sediment eDNA based high-throughput sequencing.},
}

@article {pmid40319780,
year = {2025},
author = {Attiani, V and Smidt, H and van der Wielen, PWJJ},
title = {Investigating spatial and temporal dynamics in microbial community composition of multiple full-scale slow sand filters in drinking water treatment.},
journal = {Water research},
volume = {282},
number = {},
pages = {123751},
doi = {10.1016/j.watres.2025.123751},
pmid = {40319780},
issn = {1879-2448},
abstract = {Slow sand filters (SSFs) are essential for producing high-quality and sustainable drinking water, relying on chemical, physical, and microbial processes to remove nutrients, organic matter, and pathogens. Despite numerous studies on the physical and chemical mechanisms in SSFs, the microbial processes and dynamics remain poorly understood. This study bridges this knowledge gap by investigating the spatial and temporal dynamics of prokaryotic communities within SSFs, by analysing different depths and the top layer, the Schmutzdecke (SCM), over time in full-scale SSFs from different drinking water treatment plants in The Netherlands. Utilising 16S ribosomal RNA gene-targeted amplicon sequencing and quantitative PCR, we observed a horizontally uniform prokaryotic community at each depth at all analysed SSFs, suggesting effective influent water and nutrient distribution, regardless of filter size or influent inlet design. Vertically, however, the prokaryotic composition varied significantly, with the SCM showing higher biomass and diversity compared to the deeper layers. This study identified a core prokaryotic community, including the families Nitrospiraceae, Pirellulaceae, Nitrosomonadaceae, Gemmataceae, and Vicinamibacteriaceae, consistent across various depths and SSFs, and in the SCMs of different ages. Their presence suggests a central role in supporting key biological processes in SSFs such as organic matter degradation and nitrification. Additionally, the relative abundance of archaea increased with sand depth in all SSFs, suggesting their adaptation to lower-nutrient conditions found in deeper layers. Analysis of the SCM over time showed that after scraping, the prokaryotic community gradually adapted, with minimal biomass increase during the first 3.6 years, eventually evolving into a mature, diverse, and even prokaryotic community. Our findings highlight the presence of spatially distinct microbial communities at various depths of SSFs, suggesting the removal of specific compounds in distinct sand layers. Moreover, the persistence of a core prokaryotic community across different SSFs, SCM maturation stages, and even after disturbances like scraping, demonstrates that the biology in SSFs is resilient and likely ensures reliable SSF performance. It also implies possibilities for earlier SSF operational restart after cleaning than is conventionally done, but with continuous monitoring of water quality parameters to ensure microbial safety. These findings lay the groundwork for future research to focus on these microorganisms and their functional potential.},
}

@article {pmid40319213,
year = {2025},
author = {Liu, Y and Hu, Y and Ma, B and Wang, Z and Wei, B},
title = {Gut Microbiota and Exercise: Probiotics to Modify the Composition and Roles of the Gut Microbiota in the Context of 3P Medicine.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {38},
pmid = {40319213},
issn = {1432-184X},
mesh = {*Probiotics/administration & dosage/pharmacology ; Humans ; *Gastrointestinal Microbiome/drug effects/physiology ; *Exercise/physiology ; Athletic Performance/physiology ; Precision Medicine ; Animals ; },
abstract = {Prolonged and intense physical activity can trigger stress response mechanisms across various physiological systems-including the cardiovascular, respiratory, gastrointestinal, musculoskeletal, and neuroendocrine systems-disrupting energy metabolism, immune function, redox balance, and hormonal regulation. Critically, when not accompanied by adequate recovery, such exertion may impair rather than enhance athletic performance. In parallel, there has been growing interest in probiotics as natural, safe, and accessible dietary supplements with the potential to support performance and recovery. Emerging evidence highlights the pivotal role of the gut microbiome in mediating communication along the gut-brain and gut-muscle axes, thereby influencing not only metabolic and immune functions but also neuromuscular adaptation and fatigue resistance. This review explores the mechanisms through which probiotics may enhance exercise performance, mitigate exercise-induced fatigue, and improve physiological adaptation via modulation of inflammation, oxidative stress, and metabolic signaling pathways. Framed within the context of predictive, preventive, and personalized medicine (3P medicine), this paper emphasizes the diagnostic and therapeutic potential of personalized probiotic strategies in optimizing athletic performance through the qualitative and quantitative assessment of microbiota and host responses.},
}

*Probiotics/administration & dosage/pharmacology
Humans
*Gastrointestinal Microbiome/drug effects/physiology
*Exercise/physiology
Athletic Performance/physiology
Precision Medicine
Animals

@article {pmid40316823,
year = {2025},
author = {Ben Ammar, FE and Hkiri, AE and Zaafouri, K and Saidane Bchir, F and Hamdi, M},
title = {Enhanced growth of Chlorella sorokiniana on ash-enriched treated wastewater for large-scale lipid and chlorophyll a production using a hybrid raceway photobioreactor.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {40316823},
issn = {1614-7499},
abstract = {Nutrient concentration in microalgal cultivation media greatly influences microalgal growth and macromolecules production. In the present study, treated urban wastewater was used as a medium for Chlorella sorokiniana, incorporating mineral components and ashes in batch culture. The aim was to assess the combined effect of nutrients on microalgal growth, Chlorophyll a content, and lipid production using customized experimental design and response surface methodology. Another objective was to evaluate response improvement after using hybrid raceway photobioreactor HRPBR. The results showed that the highest microalgal biomass growth as well as the highest Chlorophyll a and lipid concentrations was obtained using 2015 mg. L[-1]of NaNO3 and 2086.76 mg. L[-1] of NaHCO3 with a mineral solution concentration of 120 mg. L[-1]. After the HRPBR cultivation, Chlorophyll a content increased from 40.26 to 65.04 mg. L[-1] and the lipid content rose from 37 to 40% and then to 68% under starvation conditions. In these circumstances, the FA profile of Chlorella sorokiniana became in line with the requirements of the European biodiesel standard. Thus, the low-cost nutrient sources for culture medium formulation can be used to culture C. sorokiniana as an efficient strain for sustainable and cost-effective biofuel production.},
}

@article {pmid40312782,
year = {2025},
author = {Kynast, D and Reverey, F and Ganzert, L and Grossart, HP and Lischeid, G and Kolb, S},
title = {Detectable land use impact on methanotrophs and methanogens in kettle hole sediments but not on net methane production potentials.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf050},
pmid = {40312782},
issn = {1574-6941},
abstract = {Kettle holes (KH) are dynamic freshwater systems and potential sources of the greenhouse gas methane. Due to their small size (<1 hectare), KHs are subject to inorganic and organic matter input from their terrestrial surroundings governed by land use. Matter inputs include inorganic solutes that are alternative electron acceptors and impact on methanotrophs and methanogens. Thus, they might affect methane net production. We sampled 10 kettle hole sediments embedded in landscapes with either agricultural or forest land use and determined their (i) potential net methane production rates, (ii) the composition of their microbial communities and (iii) physicochemical soil parameters. Potential net methane production did not significantly differ by land use type but between single KHs. However, land use type had a strong impact on methanotroph and methanogen and on total bacterial and archaeal microbiota structure. Relative abundances of methanotrophs and methanogens were significantly higher in agricultural KHs and their relative abundances were among the most influential variables projecting net methane production potentials along with nutrient status and water content. Land use type was thus identified a major factor that impacts on the structure and biodiversity of general and methane-cycling microbiota, but it did not affect net methane production potentials.},
}

@article {pmid40312547,
year = {2025},
author = {Hu, L and Zhang, K and Xu, Y and Zheng, X and Waterman, JM and Ouyang, X and Wu, Z and Shen, Z and He, Y and Ma, B and Robert, CAM and Raaijmakers, JM and Ye, M and Erb, M and Xu, J},
title = {Herbivory-induced green leaf volatiles increase plant performance through jasmonate-dependent plant-soil feedbacks.},
journal = {Nature plants},
volume = {},
number = {},
pages = {},
pmid = {40312547},
issn = {2055-0278},
support = {32372775//National Natural Science Foundation of China (National Science Foundation of China)/ ; 200355//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; },
abstract = {Plants influence each other chemically by releasing leaf volatiles and root exudates, but whether and how these two phenomena interact remains unknown. Here we demonstrate that volatiles that are released by herbivore-attacked leaves trigger plant-soil feedbacks, resulting in increased performance of different plant species. We show that this phenomenon is due to green leaf volatiles that induce jasmonate-dependent systemic defence signalling in receiver plants, which results in the accumulation of beneficial soil bacteria in the rhizosphere. These soil bacteria then increase plant growth and enhance plant defences. In maize, a cysteine-rich receptor-like protein kinase, ZmCRK25, is required for this effect. In four successive year-field experiments, we demonstrate that this phenomenon can suppress leaf herbivore abundance and enhance maize growth and yield. Thus, volatile-mediated plant-plant interactions trigger plant-soil feedbacks that shape plant performance across different plant species through broadly conserved defence signalling mechanisms and changes in soil microbiota. This phenomenon expands the repertoire of biologically relevant plant-plant interactions in space and time and holds promise for the sustainable intensification of agriculture.},
}

@article {pmid40310547,
year = {2025},
author = {Calcagnile, M and Quarta, E and Sicuro, A and Pecoraro, L and Schiavone, R and Tredici, SM and Talà, A and Corallo, A and Verri, T and Stabili, L and Alifano, P},
title = {Effect of Bacillus velezensis MT9 on Nile Tilapia (Oreochromis Niloticus) Intestinal Microbiota.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {37},
pmid = {40310547},
issn = {1432-184X},
support = {ARS01_01053//Ministero dell'Istruzione e del Merito/ ; ARS01_01053//Ministero dell'Istruzione e del Merito/ ; CUP B83C22002930006//European Union Next Generation EU (PNRR)/ ; },
mesh = {Animals ; *Bacillus/physiology/genetics ; *Cichlids/microbiology ; *Gastrointestinal Microbiome/drug effects ; *Probiotics/administration & dosage/pharmacology ; RNA, Ribosomal, 16S/genetics ; Aquaculture ; Bacteria/classification/genetics/isolation & purification ; Animal Feed/analysis ; },
abstract = {In recent years, there has been a growing interest in the use of probiotics in aquaculture, due to their effectiveness on production, safety, and environmental friendliness. Probiotics, used as feed additives and as an alternative to antibiotics for disease prevention, have been shown to be active as growth promoters, improving survival and health of farmed fish. In this study, we have investigated the ability of the strain Bacillus velezensis MT9, as potential probiotic, to modulate the intestinal microbiota of the Nile tilapia (Oreochromis niloticus) fed with the Bacillus velezensis-supplemented feed in an experimental aquaculture plant. The analysis of the microbial community of the Nile tilapia by culture-based and 16S rRNA gene metabarcoding approaches demonstrated that B. velezensis MT9 reshapes the fish intestinal microbiota by reducing the amounts of opportunistic Gram-negative bacterial pathogens belonging to the phylum of Proteobacterium (Pseudomonadota) and increasing the amounts of beneficial bacteria belonging to the phyla Firmicutes (Bacillota) and Actinobacteria (Actinomycetota). Specifically, dietary supplementation of Nile tilapia with B. velezensis MT9 resulted in an increase in the relative abundance of bacteria of the genus Romboutsia, which has a well-documented probiotic activity, and a decrease in the relative abundance of Gammaproteobacteria of the genera Aeromonas and Vibrio, which include opportunistic pathogens for fish, and Escherichia/Shigella, which may pose a risk to consumers. The whole genome sequence of B. velezensis MT9 was then determined. Genome analysis revealed several peculiarities of B. velezensis MT9 compared to other B. velezensis reference strains including specific metabolic traits, differences in two-component and quorum sensing systems as well as the potential ability to produce a distinct array of secondary metabolites, which could explain the strong ability of this strain to modulate the intestinal microbiota of the Nile tilapia.},
}

Animals
*Bacillus/physiology/genetics
*Cichlids/microbiology
*Gastrointestinal Microbiome/drug effects
*Probiotics/administration & dosage/pharmacology
RNA, Ribosomal, 16S/genetics
Aquaculture
Bacteria/classification/genetics/isolation & purification
Animal Feed/analysis

@article {pmid40309103,
year = {2025},
author = {Cong, X and Liu, X and Zhou, D and Xu, Y and Liu, J and Tong, F},
title = {Characterization and comparison of the fecal bacterial microbiota in Red Back Pine Root Snake (Oligodon formosanus) and Chinese Slug-Eating Snake (Pareas chinensis).},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1575405},
pmid = {40309103},
issn = {1664-302X},
abstract = {INTRODUCTION: The gastrointestinal tracts and oral cavities of animals harbor complex microbial communities that assist hosts in nutrient absorption and immune responses, thereby influencing behavior, development, reproduction, and overall health.

METHODS: We utilized metagenomic sequencing technology to conduct a detailed analysis of the fecal bacterial communities of six Red Back Pine Root Snakes (Oligodon formosanus, XT) and three Chinese Slug-Eating Snakes (Pareas chinensis, Z) individuals. The microbial composition was assessed through taxonomic profiling, alpha diversity analysis, and functional annotation using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database.

RESULTS: The results indicated that Proteobacteria, Bacteroidetes, Firmicutes, Verrucomicrobia, Actinobacteria, and Fusobacteria were the dominant phyla in XT samples, while Z samples additionally contained Patescibacteria. Alpha diversity analysis revealed significant differences in species abundance at the family level, with Z samples exhibiting higher microbial richness than XT. Furthermore, KEGG analysis showed that XT had higher functional gene abundance in pathways related to transcription, translation, environmental adaptation, membrane transport, cellular communities (prokaryotes), motility, and replication/repair compared to Z.

DISCUSSION: This study provides a comparative analysis of their gut microbiomes, offering valuable insights for future research on zoonotic diseases, host-microbe interactions, and ecological, evolutionary, behavioral, and seasonal influences on snake microbiota. These findings contribute to a broader understanding of microbial ecology in reptiles and its implications for conservation and disease dynamics.},
}

@article {pmid40307095,
year = {2025},
author = {Zhang, D and Gao, JT and Zhou, SG},
title = {Microbial electrotaxis: rewiring environmental microbiomes.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2025.04.005},
pmid = {40307095},
issn = {1878-4380},
abstract = {Electric fields in sediments and soils are critical yet overlooked drivers of microbial ecology. This review examines the importance of electrotaxis in shaping microbial community dynamics and ecology models, surpassing traditional frameworks centered on chemotaxis. We analyze evidence that electric field gradients influence microbial community structure, function, and biogeochemical cycles in natural environments. Current mechanistic models, primarily based on eukaryotic systems, insufficiently explain bacterial electrotactic responses, necessitating new conceptual frameworks that integrate electrochemical and biological perspectives. We also evaluate its applications in environmental and microbiome engineering, with future research recommendations and methodologies in electrotaxis research. This synthesis aims to establish electrotaxis as an essential consideration in microbial ecology, presenting both challenges and opportunities for advancing our understanding of microbial ecosystems.},
}

@article {pmid40305681,
year = {2025},
author = {Bennett, BD and Meier, DAO and Lanclos, VC and Asrari, H and Coates, JD and Thrash, JC},
title = {Polyhydroxybutyrate production by freshwater SAR11 (LD12).},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf087},
pmid = {40305681},
issn = {1751-7370},
abstract = {SAR11 bacteria (order Pelagibacterales) are oligotrophs and often the most abundant bacterioplankton in aquatic environments. A subset of sequenced SAR11 genomes, predominantly in the brackish and freshwater SAR11 subclades, contain homologs of pha genes, which in other organisms confer the ability to store carbon and energy via polyhydroxyalkanoate polymers. Here, we investigated the relevance of polyhydroxyalkanoate production to SAR11 biology. Phylogenetics showed that Pha proteins occurred on a long branch and provided evidence for origin at the common ancestor of the brackish IIIa and freshwater LD12 subclades, followed by horizontal transfer within SAR11. Using the LD12 representative "Candidatus Fonsibacter ubiquis" strain LSUCC0530, we found that many LSUCC0530 cells contained a single Nile red-staining granule, confirmed that the cells produced polyhydroxybutyrate, a common form of polyhydroxyalkanoate, and estimated the total polyhydroxybutyrate content in the cells. We heterologously expressed the LSUCC0530 phaCAB locus in Escherichia coli, finding it to be functional and the likely origin of the polyhydroxybutyrate. We also determined that, irrespective of changes to carbon, nitrogen, and phosphorus concentrations, a similar fraction of LSUCC0530 cells generated polyhydroxybutyrate granules and expression of the phaCAB locus remained constant. We suggest that polyhydroxybutyrate synthesis in LSUCC0530 may be constitutively active due to the slow growth dynamics and minimal regulation that characterize SAR11 bacteria. This work characterizes polymer storage in SAR11, providing new insights into the likely fitness advantage for cells harboring this metabolism.},
}

@article {pmid40304437,
year = {2025},
author = {Kardish, MR and Stachowicz, JJ},
title = {More Than a Stick in the Mud: Eelgrass Leaf and Root Bacterial Communities Are Distinct From Those on Physical Mimics.},
journal = {Environmental microbiology reports},
volume = {17},
number = {3},
pages = {e70086},
doi = {10.1111/1758-2229.70086},
pmid = {40304437},
issn = {1758-2229},
support = {//UC Davis Center for Population Biology/ ; OCE 1829992//National Science Foundation/ ; //National Science Foundation GRFP/ ; TG-DEB160008//Extreme Science and Engineering Discovery Environment (XSEDE)/ ; //Gordon and Betty Moore Foundation/ ; },
mesh = {*Zosteraceae/microbiology ; *Plant Roots/microbiology ; *Plant Leaves/microbiology ; *Microbiota ; *Bacteria/classification/genetics/isolation & purification/metabolism ; RNA, Ribosomal, 16S/genetics ; },
abstract = {We examine the role of physical structure versus biotic interactions in structuring host-associated microbial communities on a marine angiosperm, Zostera marina, eelgrass. Across several months and sites, we compared microbiomes on physical mimics of eelgrass roots and leaves to those on intact plants. We find large, consistent differences in the microbiome of mimics and plants, especially on roots, but also on leaves. Key taxa that are more abundant on leaves have been associated with microalgal and macroalgal disease and merit further investigation to determine their role in mediating plant-microalgal-pathogen interactions. Root associated taxa were associated with sulphur and nitrogen cycling, potentially ameliorating environmental stresses for the plant. Our work identifies targets for future work on the functional role of the seagrass microbiome in promoting the success of these angiosperms in the sea through identifying components of microbial communities that are specific to seagrasses.},
}

*Zosteraceae/microbiology
*Plant Roots/microbiology
*Plant Leaves/microbiology
*Microbiota
*Bacteria/classification/genetics/isolation & purification/metabolism
RNA, Ribosomal, 16S/genetics

@article {pmid40303429,
year = {2025},
author = {Zhao, C and Zhang, J and Chen, Y and Yang, L and Chen, H and Liang, Y and Wang, W and He, S and Luo, Y and Zhang, J and Zhang, H and Yang, S and Guo, G and Dai, W and Yang, Z and Chen, J and Zhou, Y and Khan, WU and Liu, G and Jiang, Y and Zhu, T and Xu, Y and García-Caparros, P and Van de Peer, Y and Xue, JY and Chen, C and Zhang, L and Chen, F},
title = {Water lily pond: a multiomics database for water lilies.},
journal = {Horticulture research},
volume = {12},
number = {6},
pages = {uhaf076},
pmid = {40303429},
issn = {2662-6810},
}

@article {pmid40302853,
year = {2025},
author = {Gharbi, D and Neumann, FH and Podile, K and McDonald, M and Linde, JH and Frampton, M and Liebenberg, JL and Cilliers, S and Mmatladi, T and Nkosi, P and Paledi, K and Piketh, S and Staats, J and Burger, RP and Havenga, H and Garland, RM and Bester, P and Lebre, PH and Ricci, C},
title = {Exposure to outdoor aerospora and associated respiratory health risks among adults in Potchefstroom, North-West province, South Africa.},
journal = {Frontiers in allergy},
volume = {6},
number = {},
pages = {1568669},
pmid = {40302853},
issn = {2673-6101},
abstract = {BACKGROUND: Data on allergic rhinitis and respiratory health metrics are limited for South Africa, with grass pollen as a key outdoor aeroallergen. Exotic trees such as plane trees and ragweed produce highly allergenic pollen, dominating indigenous trees and weeds. Pollen allergy prevalence data is lacking in cities of North-West province such as Potchefstroom.

OBJECTIVES: This study aimed to (i) assess the prevalence of allergies to major aeroallergens, including Poaceae (grasses), Cupressus/Hesperocyparis (cypresses), Platanus (plane tree), Ulmus (elm), Quercus (oak), Betula (birch), Olea (olive), Artemisia (sagebrush), Amaranthus (amaranth), Plantago (plantain), Morus (mulberry), and Ambrosia (ragweed), along with fungal spores such as Alternaria, Cladosporium, and Penicillium/Aspergillus, and (ii) investigate the monthly incidence of major aeroallergens and reactivity levels in sensitized adults in Potchefstroom.

METHODS: Skin prick tests (SPTs) were performed on 202 adults aged 18-64 years with confirmed allergic symptoms during a field campaign at North-West University (NWU)'s Potchefstroom campus. A test panel of grass, weed, tree, and fungal spore extracts previously identified via aerobiological monitoring was used. Symptom scores were recorded using ISAAC questionnaires; Spearman's statistical correlation between symptom frequency and monthly aeroallergen concentrations were analyzed.

RESULTS: Among the participants, 184 (91%) exhibited positive SPT reactions: 104 (57%) are monosensitized to pollen, 45 (24%) to fungal spores, and 35 (19%) are polysensitized. Aeroallergen prevalence was higher in females (73%) than in males (27%). The most common pollen allergens were Cynodon dactylon (Bermuda grass) (85%), Zea mays (maize) (46%), Platanus spp. (plane tree) (35%), and Ulmus campestris (field elm) (33%). Among fungal spores, Alternaria was the most common (93%), followed by Cladosporium (27%). A significant and positive statistical correlation was found between allergic rhinitis symptoms and monthly pollen concentrations of Betula, Morus, Platanus, and Quercus.

DISCUSSION & CONCLUSION: This pilot study linked aeroallergens detected in Potchefstroom with allergy profiles of local residents. The findings highlight the need for more comprehensive regional studies that integrate allergen testing with aerobiological data. Raising awareness and implementing health strategies are essential for managing allergic rhinitis in South Africa. More affordable and available SPTs kits, adapted to allergy prevalence in South Africa, are strongly suggested.},
}

@article {pmid40301344,
year = {2025},
author = {Zhu, C and Wu, L and Ning, D and Tian, R and Gao, S and Zhang, B and Zhao, J and Zhang, Y and Xiao, N and Wang, Y and Brown, MR and Tu, Q and , and Ju, F and Wells, GF and Guo, J and He, Z and Nielsen, PH and Wang, A and Zhang, Y and Chen, T and He, Q and Criddle, CS and Wagner, M and Tiedje, JM and Curtis, TP and Wen, X and Yang, Y and Alvarez-Cohen, L and Stahl, DA and Alvarez, PJJ and Rittmann, BE and Zhou, J},
title = {Global diversity and distribution of antibiotic resistance genes in human wastewater treatment systems.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {4006},
pmid = {40301344},
issn = {2041-1723},
support = {EF-2025558//National Science Foundation (NSF)/ ; 32371724//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82202299//National Natural Science Foundation of China (National Science Foundation of China)/ ; 61872218//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Wastewater/microbiology ; Humans ; Sewage/microbiology ; *Drug Resistance, Microbial/genetics ; *Bacteria/genetics/drug effects/classification/isolation & purification ; *Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; Water Purification ; *Drug Resistance, Bacterial/genetics ; Interspersed Repetitive Sequences/genetics ; },
abstract = {Antibiotic resistance poses a significant threat to human health, and wastewater treatment plants (WWTPs) are important reservoirs of antibiotic resistance genes (ARGs). Here, we analyze the antibiotic resistomes of 226 activated sludge samples from 142 WWTPs across six continents, using a consistent pipeline for sample collection, DNA sequencing and analysis. We find that ARGs are diverse and similarly abundant, with a core set of 20 ARGs present in all WWTPs. ARG composition differs across continents and is distinct from that of the human gut and the oceans. ARG composition strongly correlates with bacterial taxonomic composition, with Chloroflexi, Acidobacteria and Deltaproteobacteria being the major carriers. ARG abundance positively correlates with the presence of mobile genetic elements, and 57% of the 1112 recovered high-quality genomes possess putatively mobile ARGs. Resistome variations appear to be driven by a complex combination of stochastic processes and deterministic abiotic factors.},
}

*Wastewater/microbiology
Humans
Sewage/microbiology
*Drug Resistance, Microbial/genetics
*Bacteria/genetics/drug effects/classification/isolation & purification
*Genes, Bacterial
Anti-Bacterial Agents/pharmacology
Water Purification
*Drug Resistance, Bacterial/genetics
Interspersed Repetitive Sequences/genetics

@article {pmid40301151,
year = {2025},
author = {Kaufmann, H and Salvador, C and Salazar, VW and Cruz, N and Dias, GM and Tschoeke, D and Campos, L and Sawabe, T and Miyazaki, M and Maruyama, F and Thompson, F and Thompson, C},
title = {Genomic Repertoire of Twenty-Two Novel Vibrionaceae Species Isolated from Marine Sediments.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {36},
pmid = {40301151},
issn = {1432-184X},
mesh = {*Geologic Sediments/microbiology ; *Vibrionaceae/genetics/classification/isolation & purification ; *Genome, Bacterial ; Phylogeny ; Japan ; *Seawater/microbiology ; Genetic Variation ; },
abstract = {The genomic repertoire of vibrios has been extensively studied, particularly regarding their metabolic plasticity, symbiotic interactions, and resistance mechanisms to environmental stressors. However, little is known about the genomic diversity and adaptations of vibrios inhabiting deep-sea marine sediments. In this study, we investigated the genomic diversity of vibrios isolated from deep-sea core sediments collected using a manned submersible off Japan. A total of 50 vibrio isolates were obtained and characterized phenotypically, and by genome sequencing. From this total, we disclosed 22 novel species examining genome-to-genome distance, average amino acid identity, and phenotypes (Alivibrio: 1; Enterovibrio: 1; Photobacterium: 8; Vibrio: 12). The novel species have fallen within known clades (e.g., Fisheri, Enterovibrio, Profundum, and Splendidus) and novel clades (JAMM0721, JAMM0388, JAMM0395). The 28 remainder isolates were identified as known species: Aliivibrio sifiae (2), A. salmonicida (1), Enterovibrio baiacu (1), E. norvegicus (1), Photobacterium profundum (3), P. angustum (1), P. chitiniliticum (1), P. frigidiphilum (1), Photobacterium indicum (1), P. sanguinicancri (1). P. swingsii (2), Vibrio alginolyticus (3), V. anguillarum (1), V. campbellii (1), V. fluvialis (1), V. gigantis (1), V. lentus (1), V. splendidus (4), and V. tasmaniensis (1). Genomic analyses revealed that all 50 vibrios harbored genes associated with high-pressure adaptation, including sensor kinases, chaperones, autoinducer-2 (AI-2) signaling, oxidative damage repair, polyunsaturated fatty acid biosynthesis, and stress response mechanisms related to periplasmic and outer membrane protein misfolding under heat shock and osmotic stress. Additionally, alternative sigma factors, trimethylamine oxide (TMAO) respiration, and osmoprotectant acquisition pathways were identified, further supporting their ability to thrive in deep-sea environments. Notably, the genomes exhibited a high prevalence of antibiotic resistance genes, with antibiotic efflux pumps being the most abundant group. The ugd gene expanded in number in some novel species (Photobacterium satsumensis sp. nov. JAMM1754: 4 copies; Vibrio makurazakiensis sp. nov. JAMM1826: 3 copies). This gene may confer antibiotic (polymyxin) resistance to these vibrios.},
}

*Geologic Sediments/microbiology
*Vibrionaceae/genetics/classification/isolation & purification
*Genome, Bacterial
Phylogeny
Japan
*Seawater/microbiology
Genetic Variation

@article {pmid40301143,
year = {2025},
author = {Weitzman, CL and Day, K and Brown, GP and Gibb, K and Christian, K},
title = {Differential Temporal Shifts in Skin Bacteria on Wild and Captive Toads.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {35},
pmid = {40301143},
issn = {1432-184X},
support = {DP210102176//Australian Research Council/ ; DP210102176//Australian Research Council/ ; DP210102176//Australian Research Council/ ; DP210102176//Australian Research Council/ ; DP210102176//Australian Research Council/ ; },
abstract = {Skin bacteria on amphibian hosts play an important role in host health, but those communities are also constantly shifting based on environmental and host-related feedback. On some hosts, stability of skin communities depends on relatively abundant taxa, with less abundant taxa more readily entering and exiting the system. Cane toads (Rhinella marina) have invaded widespread, diverse tropical ecosystems, with varying ecology, physiology, and behaviour in different environments. In this study, we described temporal patterns of skin bacterial communities on cane toads at a site in northern Australia through the wet and dry seasons over two years. Toads in the wild population were paired with a captive-held population, housed in a semi-natural environment, to detect effects of time and season on wild toads, explore bacterial transience and volatility in skin taxa, and determine the extent to which skin communities on captive toads represent those on the wild population. We found community differences by captivity status, sampling timepoint, and season, with increased richness in the wet season on wild toads. Bacterial communities also became more similar among individuals (lower dispersion) in the wet season. Captive toads harboured more stable communities over time, likely owing to the reduced bacterial reservoirs experienced while in captivity. We propose that cane toads, with varied movement patterns among their diverse invaded habitats, provide an interesting direction for future work understanding the influences of habitat and movement on skin microbes, and the flexibility of microbial symbiotic interactions in invasive hosts.},
}

@article {pmid40300605,
year = {2025},
author = {Lopez, JA and McKeithen-Mead, S and Shi, H and Nguyen, TH and Huang, KC and Good, BH},
title = {Abundance measurements reveal the balance between lysis and lysogeny in the human gut microbiome.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2025.03.073},
pmid = {40300605},
issn = {1879-0445},
abstract = {The human gut contains diverse communities of bacteriophage, whose interactions with the broader microbiome and potential roles in human health are only beginning to be uncovered. Here, we combine multiple types of data to quantitatively estimate gut phage population dynamics and lifestyle characteristics in human subjects. Unifying results from previous studies, we show that an average human gut contains a low ratio of phage particles to bacterial cells (∼1:100) but a much larger ratio of phage genomes to bacterial genomes (∼4:1), implying that most gut phage are effectively temperate (e.g., integrated prophage and phage-plasmids). By integrating imaging and sequencing data with a generalized model of temperate phage dynamics, we estimate that phage induction and lysis occur at a low average rate (∼0.001-0.01 per bacterium per day), imposing only a modest fitness burden on their bacterial hosts. Consistent with these estimates, we find that the phage composition of a diverse synthetic community in gnotobiotic mice can be quantitatively predicted from bacterial abundances alone while still exhibiting phage diversity comparable to native human microbiomes. These results provide a foundation for interpreting existing and future studies on links between the gut virome and human health.},
}

@article {pmid40299544,
year = {2025},
author = {Veenhof, RJ and McGrath, AH and Champion, C and Dworjanyn, SA and Marzinelli, EM and Coleman, MA},
title = {The role of microbiota in kelp gametophyte development and resilience to thermal stress.},
journal = {Journal of phycology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jpy.70018},
pmid = {40299544},
issn = {1529-8817},
support = {//The University of Sydney/ ; DP200100201//Australian Research Council/ ; //NSW Climate Change Fund/ ; //Holsworth Wildlife Research Endowment/ ; },
abstract = {Ocean warming is driving profound changes in the ecology of marine habitat formers such as kelps, with negative implications for the biodiversity and ecosystem services they support. Thermal stress can disturb associated microbiota that are essential to the healthy functioning of kelp, but little is known about how this process influences early-life stages. Because kelps have a biphasic life cycle, thermal stress dynamics of adult sporophyte microbiota may not reflect those of the free-living haploid gametophyte. We investigated the role of microbial disruption under thermal stress on gametophytes of the kelp Ecklonia radiata and compared sporophyte and gametophyte microbiota. The microbiota of gametophytes changed significantly when the microbiome was disrupted and under increased temperature (26°C), in which putative generalist bacterial taxa proliferated and bacterial families associated with nitrogen fixation decreased. Concurrently, the survival of gametophytes decreased to <10%, and surviving gametophytes did not become fertile when the microbiome was disrupted. The length of gametophytes decreased under both microbial disruption and thermal stress. Taken together, this suggests that the associated microbiota of Ecklonia gametophytes is important for their survival, fertility, and response to warming. Gametophyte and parental sporophyte microbiota were also distinct from the water column but not each other, suggesting vertical transmission of microbiota from one life stage to the next. This study furthers our understanding of the role of microbiota in gametophyte stress tolerance as well as the acquisition of microbiota, which may prove vital in protecting and increasing the stress resilience of these foundation species.},
}

@article {pmid40298441,
year = {2025},
author = {Peng, S-X and Gao, S-M and Lin, Z-L and Luo, Z-H and Zhang, S-Y and Shu, W-S and Meng, F and Huang, L-N},
title = {Biogeography and ecological functions of underestimated CPR and DPANN in acid mine drainage sediments.},
journal = {mBio},
volume = {},
number = {},
pages = {e0070525},
doi = {10.1128/mbio.00705-25},
pmid = {40298441},
issn = {2150-7511},
abstract = {Recent genomic surveys have uncovered candidate phyla radiation (CPR) bacteria and DPANN archaea as major microbial dark matter lineages in various anoxic habitats. Despite their extraordinary diversity, the biogeographic patterns and ecological implications of these ultra-small and putatively symbiotic microorganisms have remained elusive. Here, we performed metagenomic sequencing on 90 geochemically diverse acid mine drainage sediments sampled across southeast China and recovered 282 CPR and 189 DPANN nonredundant metagenome-assembled genomes, which collectively account for up to 28.6% and 31.2% of the indigenous prokaryotic communities, respectively. We found that, remarkably, geographic distance represents the primary factor driving the large-scale ecological distribution of both CPR and DPANN organisms, followed by pH and Fe. Although both groups might be capable of iron reduction through a flavin-based extracellular electron transfer mechanism, significant differences are found in their metabolic capabilities (with complex carbon degradation and chitin degradation being more prevalent in CPR whereas fermentation and acetate production being enriched in DPANN), indicating potential niche differentiation. Predicted hosts are mainly Acidobacteriota, Bacteroidota, and Proteobacteria for CPR and Thermoplasmatota for DPANN, and extensive, unbalanced metabolic exchanges between these symbionts and putative hosts are displayed. Together, our results provide initial insights into the complex interplays between the two lineages and their physicochemical environments and host populations at a large geographic scale.IMPORTANCECandidate phyla radiation (CPR) bacteria and DPANN archaea constitute a significant fraction of Earth's prokaryotic diversity. Despite their ubiquity and abundance, especially in anoxic habitats, we know little about the community patterns and ecological drivers of these ultra-small, putatively episymbiotic microorganisms across geographic ranges. This study is facilitated by a large collection of CPR and DPANN metagenome-assembled genomes recovered from the metagenomes of 90 sediments sampled from geochemically diverse acid mine drainage (AMD) environments across southeast China. Our comprehensive analyses have allowed first insights into the biogeographic patterns and functional differentiation of these major enigmatic prokaryotic groups in the AMD model system.},
}

@article {pmid40297467,
year = {2025},
author = {Deep, A and Sieber, G and Boden, L and David, GM and Baikova, D and Buchner, D and Starke, J and Stach, TL and Reinders, T and Hadžiomerović, U and Beszteri, S and Probst, AJ and Boenigk, J and Beisser, D},
title = {A metatranscriptomic exploration of fungal and bacterial contributions to allochthonous leaf litter decomposition in the streambed.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19120},
pmid = {40297467},
issn = {2167-8359},
mesh = {*Plant Leaves/metabolism/microbiology ; *Bacteria/genetics/metabolism ; *Fungi/genetics/metabolism ; *Rivers/microbiology ; Ecosystem ; Alnus ; Transcriptome ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The decomposition of organic matter is essential for sustaining the health of freshwater ecosystems by enabling nutrient recycling, sustaining food webs, and shaping habitat conditions, which collectively enhance ecosystem resilience and productivity. Bacteria and fungi play a crucial role in this process by breaking down coarse particulate organic matter (CPOM), such as leaf litter, into nutrients available for other organisms. However, the specific contribution of bacteria and their functional interactions with fungi in freshwater sediments have yet to be thoroughly explored. In the following study, we enriched organic matter through the addition of alder (Alnus glutinosa) leaves into artificial stream channels (AquaFlow mesocosms). We then investigated enzyme expression, metabolic pathways, and community composition of fungi and bacteria involved in the degradation of CPOM through metatranscriptomics and amplicon sequencing. Enzymes involved in the degradation of lignin, cellulose, and hemicellulose were selectively upregulated with increased organic matter. Analysis of ITS and 16S rRNA gene sequences revealed that during decomposition, fungal communities were predominantly composed of Basidiomycota and Ascomycota, while bacterial communities were largely dominated by Pseudomonadota and Bacteroidota. The similar gene expression patterns of CPOM degradation related enzymes observed between bacteria and fungi indicate potential functional interaction between these microbial groups. This correlation in enzyme expression may indicate that bacteria and fungi are jointly involved in the breakdown of coarse particulate organic matter, potentially through mutualistic interaction. This study uncovers the specific enzymatic activities of bacteria and fungi and the importance of microbial interactions in organic matter decomposition, revealing their central role in facilitating nutrient cycling and maintaining the ecological health and stability of freshwater ecosystems.},
}

*Plant Leaves/metabolism/microbiology
*Bacteria/genetics/metabolism
*Fungi/genetics/metabolism
*Rivers/microbiology
Ecosystem
Alnus
Transcriptome
RNA, Ribosomal, 16S/genetics

@article {pmid40294427,
year = {2025},
author = {Ran, X and Wang, T and Zhou, M and Li, Z and Wang, H and Tsybekmitova, GT and Guo, J and Wang, Y},
title = {A Novel Perspective on the Instability of Mainstream Partial Nitrification: The Niche Differentiation of Nitrifying Guilds.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c01214},
pmid = {40294427},
issn = {1520-5851},
abstract = {Short-cut biological nitrogen removal (sBNR) favors the paradigm shift toward energy-positive and carbon-neutral wastewater treatment processes. Partial nitrification (PN) is a key approach to provide nitrite for anammox or denitritation during sBNR, and its stability is the precondition for achieving robust nitrogen removal performance. However, maintaining a stable mainstream PN process has been a long-standing challenge. This review analyzes the mainstream PN process from a microbial ecology perspective, focusing on the niche differentiation among nitrifiers. First, we propose that mainstream PN systems are ecologically unstable, and the failure of the mainstream PN process due to the reactivation of nitrite-oxidizing bacteria (NOB) can be regarded as a behavior to restore system stabilization. Thus, maintaining mainstream PN systems primarily relies on enhancing the niche differentiation between ammonia-oxidizing bacteria (AOB) and NOB. We then summarize the realized niches of indigenous nitrifiers within nitrification systems and discuss their ecophysiological characteristics (e.g., cell structure and substrate affinity) that define their specific ecological niches. By comparing the niche breadths of AOB and NOB on various niche axes, we further discuss their niche differentiation and identify the different responses of AOB (resistance) and NOB (resilience) to exogenous perturbations. Finally, we propose outlook for achieving a stable mainstream PN process through an ecological lens. This review provides ecological insights into the instability of the mainstream PN process, which is intended to guide the derivation of optimized strategies from a single-factor approach to integrated solutions.},
}

@article {pmid40294268,
year = {2025},
author = {Sun, W and Wang, J and Wang, G and Jiang, L and Feng, W and Dang, S and Li, M and Jiao, S and Wei, G and Gu, J and Tiedje, JM and Qian, X},
title = {Exposure and health risks of livestock air resistomes.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {18},
pages = {e2403866122},
doi = {10.1073/pnas.2403866122},
pmid = {40294268},
issn = {1091-6490},
support = {42277412 and 42207463//NSF of China/ ; 2024RS-CXTD-68//Shaanxi Innovation Support Program/ ; },
mesh = {Animals ; *Livestock/microbiology ; Humans ; *Air Microbiology ; Anti-Bacterial Agents/pharmacology ; Farms ; Swine ; China ; Chickens ; *Drug Resistance, Microbial/genetics ; *Occupational Exposure ; *Drug Resistance, Bacterial/genetics ; Europe ; },
abstract = {Most of the global antibiotic consumption is by the livestock industry, making livestock farms a hotspot of antibiotic resistance genes (ARGs). Farm air poses direct ARG exposure to workers, but the health risks of air resistomes remain unclear. We evaluated the human exposure and health risks of air resistomes in pig and chicken farms and compared air resistomes in Chinese farms to those in European farms given their long-term restrictions on use of antibiotics in livestock. We found that livestock air was highly enriched in ARGs, with each cell harboring seven times more ARGs than urban air. The daily ARG inhalation of farm workers was equivalent to several years of ARG inhalation by urban residents. ARGs encoding resistance to last-resort antibiotics such as mcr-1 and tetX were detected in farm air, and tetX variants were prevalent in both Chinese and European farms. ARGs in livestock air were highly associated with mobile genetic elements, and conjugation experiments confirmed their cross-phyla transferability. The projected resistome risk of farm air was significantly higher than well-recognized ARG hotspots like air from hospitals, sewage treatment plants, and from animal manures. The diversity, abundance, and risk score of air resistomes in Chinese farms were significantly higher than those in European farms, suggesting that long-term restriction of antibiotic use mitigates antibiotic resistance in the livestock environment. Our results underscore the high exposure of farm workers to ARGs via farm air and highlight its role in ARG dissemination, supporting the importance of antibiotic stewardship practices in combating antibiotic resistance.},
}

Animals
*Livestock/microbiology
Humans
*Air Microbiology
Anti-Bacterial Agents/pharmacology
Farms
Swine
China
Chickens
*Drug Resistance, Microbial/genetics
*Occupational Exposure
*Drug Resistance, Bacterial/genetics
Europe

@article {pmid40293502,
year = {2025},
author = {Cao, X and Liu, H and Zhang, R and Wen, Y and Ma, L and Xu, Z and Wen, L and Zhuo, Y and Liu, D and Wang, L},
title = {Composition, Predicted Functions, and Co-occurrence Networks of Bacteria and Fungi in Hummock Wetlands of Northeastern Inner Mongolia, China.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {34},
pmid = {40293502},
issn = {1432-184X},
support = {YSS2021007//the Funds of Yinshanbeilu Grassland Eco-hydrology National Observation and Research Station/ ; 32160279, 32161143025, 31960249//the National Natural Science Funds, P.R. China/ ; 2022YFHH0017//Science and Technology Major Project of Inner Mongolia/ ; 2022EEDSKJZDZX010, 2022EEDSKJXM005//Ordos Science and Technology Plan/ ; },
mesh = {*Wetlands ; China ; *Fungi/classification/genetics/isolation & purification ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation & purification ; Soil/chemistry ; Ecosystem ; Microbiota ; Biodiversity ; Hydrogen-Ion Concentration ; },
abstract = {Wetland microhabitats, varying in water table position, pH, and biochemical properties, have been understudied in terms of their influence on soil microbial community structure. This study employed amplicon-based gene sequencing to investigate the responses of both fungal and bacterial communities to habitat changes in northeastern Inner Mongolia, China. The results showed that while α-diversity indices (Shannon and Chao1) did not significantly differ between hummocks and hollows, β-diversity analyses revealed distinct microbial community structures in these habitats. Bacterial communities were primarily influenced by soil pH, EC, and AP, whereas fungal communities were affected by pH, AKP, MBC, MBN, and AP. Bacterial interactions were predominant in hollows, whereas fungal interactions were predominant in hummocks. Hummocks significantly enhanced amino acid metabolism function, whereas hollows significantly increased the abundance of endophyte-litter saprotroph-soil saprotroph-undefined saprotroph. This study underscores the importance of habitats in regulating microbial networks and functions, thereby enhancing our understanding of the influence of microhabitats, such as hummocks, on wetland ecosystem structure and function.},
}

*Wetlands
China
*Fungi/classification/genetics/isolation & purification
*Soil Microbiology
*Bacteria/classification/genetics/isolation & purification
Soil/chemistry
Ecosystem
Microbiota
Biodiversity
Hydrogen-Ion Concentration

@article {pmid40287826,
year = {2025},
author = {Gerhardt, K and Ruiz-Perez, CA and Rodriguez-R, LM and Jain, C and Tiedje, JM and Cole, JR and Konstantinidis, KT},
title = {FastAAI: efficient estimation of genome average amino acid identity and phylum-level relationships using tetramers of universal proteins.},
journal = {Nucleic acids research},
volume = {53},
number = {8},
pages = {},
pmid = {40287826},
issn = {1362-4962},
support = {DBI1356288NSF//NSF/ ; },
mesh = {Phylogeny ; *Genome, Bacterial ; *Software ; *Bacteria/genetics/classification ; *Amino Acids/genetics ; *Computational Biology/methods ; },
abstract = {Estimation of whole-genome relatedness and taxonomic identification are two important bioinformatics tasks in describing environmental or clinical microbiomes. The genome-aggregate Average Nucleotide Identity is routinely used to derive the relatedness of closely related (species level) microbial and viral genomes, but it is not appropriate for more divergent genomes. Average Amino-acid Identity (AAI) can be used in the latter cases, but no current AAI implementation can efficiently compare thousands of genomes. Here we present FastAAI, a tool that estimates whole-genome pairwise relatedness using shared tetramers of universal proteins in a matter of microseconds, providing a speedup of up to 5 orders of magnitude when compared with current methods for calculating AAI or alternative whole-genome metrics. Further, FastAAI resolves distantly related genomes related at the phylum level with comparable accuracy to the phylogeny of ribosomal RNA genes, substantially improving on a known limitation of current AAI implementations. Our analysis of the resulting AAI matrices also indicated that bacterial lineages predominantly evolve gradually, rather than showing bursts of diversification, and that AAI thresholds to define classes, orders, and families are generally elusive. Therefore, FastAAI uniquely expands the toolbox for microbiome analysis and allows it to scale to millions of genomes.},
}

Phylogeny
*Genome, Bacterial
*Software
*Bacteria/genetics/classification
*Amino Acids/genetics
*Computational Biology/methods

@article {pmid40287775,
year = {2025},
author = {Ren, H and Hong, H and Zha, B and Lamlom, SF and Qiu, H and Cao, Y and Sun, R and Wang, H and Ma, J and Zhang, H and Sun, L and Yang, Q and Zhou, C and Liu, X and Wang, X and Zhang, C and Zhang, F and Zhao, K and Yuan, R and Abdelghany, AM and Zhang, B and Zheng, Y and Wang, J and Lu, W},
title = {Soybean productivity can be enhanced by understanding rhizosphere microbiota: evidence from metagenomics analysis from diverse agroecosystems.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {105},
pmid = {40287775},
issn = {2049-2618},
mesh = {*Rhizosphere ; *Metagenomics/methods ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Glycine max/microbiology/growth & development ; *Microbiota/genetics ; China ; Fungi/classification/genetics/isolation & purification ; Plant Roots/microbiology ; Archaea/classification/genetics/isolation & purification ; High-Throughput Nucleotide Sequencing ; },
abstract = {BACKGROUND: Microbial communities associated with roots play a crucial role in the growth and health of plants and are constantly influenced by plant development and alterations in the soil environment. Despite extensive rhizosphere microbiome research, studies examining multi-kingdom microbial variation across large-scale agricultural gradients remain limited.

RESULTS: This study investigates the rhizosphere microbial communities associated with soybean across 13 diverse geographical locations in China. Using high-throughput shotgun metagenomic sequencing on the BGISEQ T7 platform with 10 GB per sample, we identified a total of 43,337 microbial species encompassing bacteria, archaea, fungi, and viruses. Our analysis revealed significant site-specific variations in microbial diversity and community composition, underscoring the influence of local environmental factors on microbial ecology. Principal coordinate analysis (PCoA) indicated distinct clustering patterns of microbial communities, reflecting the unique environmental conditions and agricultural practices of each location. Network analysis identified 556 hub microbial taxa significantly correlated with soybean yield traits, with bacteria showing the strongest associations. These key microorganisms were found to be involved in critical nutrient cycling pathways, particularly in carbon oxidation, nitrogen fixation, phosphorus solubilization, and sulfur metabolism. Our findings demonstrate the pivotal roles of specific microbial taxa in enhancing nutrient cycling, promoting plant health, and improving soybean yield, with significant positive correlations (r = 0.5, p = 0.039) between microbial diversity and seed yield.

CONCLUSION: This study provides a comprehensive understanding of the diversity and functional potential of rhizosphere microbiota in enhancing soybean productivity. The findings underscore the importance of integrating microbial community dynamics into crop management strategies to optimize nutrient cycling, plant health, and yield. While this study identifies key microbial taxa with potential functional roles, future research should focus on isolating and validating these microorganisms for their bioremediation and biofertilization activities under field conditions. This will provide actionable insights for developing microbial-based agricultural interventions to improve crop resilience and sustainability. Video Abstract.},
}

*Rhizosphere
*Metagenomics/methods
*Soil Microbiology
*Bacteria/classification/genetics/isolation & purification
*Glycine max/microbiology/growth & development
*Microbiota/genetics
China
Fungi/classification/genetics/isolation & purification
Plant Roots/microbiology
Archaea/classification/genetics/isolation & purification
High-Throughput Nucleotide Sequencing

@article {pmid40287657,
year = {2025},
author = {De Maayer, P and Green, T and Jordan, S and Smits, THM and Coutinho, TA},
title = {Pan-genome analysis of the Enterobacter hormaechei complex highlights its genomic flexibility and pertinence as a multidrug resistant pathogen.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {408},
pmid = {40287657},
issn = {1471-2164},
support = {310030L_204333//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; 310030L_204333//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; 310030L_204333//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; 310030L_204333//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; 310030L_204333//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; },
mesh = {*Enterobacter/genetics/classification/drug effects/pathogenicity ; *Genome, Bacterial ; Phylogeny ; *Drug Resistance, Multiple, Bacterial/genetics ; *Genomics/methods ; Anti-Bacterial Agents/pharmacology ; DNA Transposable Elements ; Plasmids/genetics ; },
abstract = {BACKGROUND: Enterobacter hormaechei is of increasing concern as both an opportunistic and nosocomial pathogen, exacerbated by its evolving multidrug resistance. However, its taxonomy remains contentious, and little is known about its pathogenesis and the broader context of its resistome. In this study, a comprehensive comparative genomic analysis was undertaken to address these issues.

RESULTS: Phylogenomic analysis revealed that E. hormaechei represents a complex, comprising three predicted species, E. hormaechei, E. hoffmannii and E. xiangfangensis, with the latter putatively comprising three distinct subspecies, namely oharae, steigerwaltii and xiangfangensis. The species and subspecies all display open and distinct pan-genomes, with diversification driven by an array of mobile genetic elements including numerous plasmid replicons and prophages, integrative conjugative elements (ICE) and transposable elements. These elements have given rise to a broad, relatively conserved set of pathogenicity determinants, but also a variable set of secretion systems. The E. hormaechei complex displays a highly mutable resistome, with most taxa being multidrug resistant.

CONCLUSIONS: This study addressed key issues pertaining to the taxonomy of the E. hormaechei complex, which may contribute towards more accurate identification of strains belonging to this species complex in the clinical setting. The pathogenicity determinants identified in this study could serve as a basis for a deeper understanding of E. hormaechei complex pathogenesis and virulence. The extensive nature of multidrug resistance among E. hormaechei complex strains highlights the need for responsible antibiotic stewardship to ensure effective treatment of these emerging pathogens.},
}

*Enterobacter/genetics/classification/drug effects/pathogenicity
*Genome, Bacterial
Phylogeny
*Drug Resistance, Multiple, Bacterial/genetics
*Genomics/methods
Anti-Bacterial Agents/pharmacology
DNA Transposable Elements
Plasmids/genetics

@article {pmid40287646,
year = {2025},
author = {He, L and Zou, Q and Wang, Y},
title = {metaTP: a meta-transcriptome data analysis pipeline with integrated automated workflows.},
journal = {BMC bioinformatics},
volume = {26},
number = {1},
pages = {111},
pmid = {40287646},
issn = {1471-2105},
support = {62102269//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: The accessibility of sequencing technologies has enabled meta-transcriptomic studies to provide a deeper understanding of microbial ecology at the transcriptional level. Analyzing omics data involves multiple steps that require the use of various bioinformatics tools. With the increasing availability of public microbiome datasets, conducting meta-analyses can reveal new insights into microbiome activity. However, the reproducibility of data is often compromised due to variations in processing methods for sample omics data. Therefore, it is essential to develop efficient analytical workflows that ensure repeatability, reproducibility, and the traceability of results in microbiome research.

RESULTS: We developed metaTP, a pipeline that integrates bioinformatics tools for analyzing meta-transcriptomic data comprehensively. The pipeline includes quality control, non-coding RNA removal, transcript expression quantification, differential gene expression analysis, functional annotation, and co-expression network analysis. To quantify mRNA expression, we rely on reference indexes built using protein-coding sequences, which help overcome the limitations of database analysis. Additionally, metaTP provides a function for calculating the topological properties of gene co-expression networks, offering an intuitive explanation for correlated gene sets in high-dimensional datasets. The use of metaTP is anticipated to support researchers in addressing microbiota-related biological inquiries and improving the accessibility and interpretation of microbiota RNA-Seq data.

CONCLUSIONS: We have created a conda package to integrate the tools into our pipeline, making it a flexible and versatile tool for handling meta-transcriptomic sequencing data. The metaTP pipeline is freely available at: https://github.com/nanbei45/metaTP .},
}

@article {pmid40287414,
year = {2025},
author = {Bull, F and Tavaddod, S and Bommer, N and Perry, M and Brackley, CA and Allen, RJ},
title = {Different factors control long-term versus short-term outcomes for bacterial colonisation of a urinary catheter.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {3940},
pmid = {40287414},
issn = {2041-1723},
support = {682237 EVOSTRUC//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council(H2020 Excellent Science - European Research Council)/ ; EXC 2051 - Project-ID 390713860//Deutsche Forschungsgemeinschaft(German Research Foundation)/ ; EP/L015110/1//RCUK | Engineering and Physical Sciences Research Council(EPSRC)/ ; },
abstract = {Urinary catheters are used extensively in hospitals and long-term care and they are highly prone to infection. Understanding the pathways by which bacteria colonise a urinary catheter could guide strategies to mitigate infection, but quantitative models for this colonisation process are lacking. Here we present a mathematical model for bacterial colonisation of a urinary catheter that integrates population dynamics and fluid dynamics. The model describes bacteria migrating up the outside surface of the catheter, spreading into the bladder and being swept through the catheter lumen. Computer simulations of the model reveal that clinical outcomes for long-term versus short-term catheterisation are controlled by different factors: the rate of urine production by the kidneys as opposed to urethral length, catheter surface properties and bacterial motility. Our work may help explain variable susceptibility to catheter-associated urinary tract infection (CAUTI) among individuals and the mixed success of antimicrobial surface coatings. Our model suggests that for long-term catheterised patients, increasing fluid intake or reducing residual urine volume in the bladder may help prevent infection, while antimicrobial surface coatings are predicted to be effective only for short-term catheterised patients. Therefore, different catheter management strategies could be rationally targeted to long-term vs short-term catheterised patients.},
}

@article {pmid40286617,
year = {2025},
author = {Kang, S and Lee, JY and Natsagdorj, A and Matsuki, A and Cho, KS},
title = {Functional adaptation of PM2.5 microbiomes to varying environmental conditions in Northeast Asia: Ulaanbaatar, Seoul, and Noto.},
journal = {The Science of the total environment},
volume = {979},
number = {},
pages = {179495},
doi = {10.1016/j.scitotenv.2025.179495},
pmid = {40286617},
issn = {1879-1026},
abstract = {This study examined the bacterial and fungal communities associated with PM2.5 collected from three geographically distinct locations in Northeast Asia-Ulaanbaatar (high pollution), Seoul (moderate pollution), and Noto (low pollution)-which collectively represent a gradient of urbanization and environmental conditions during the spring sampling period from March 15 to April 7, 2022. Ulaanbaatar exhibited the highest abundance of both bacteria and fungi, yet exhibited the lowest fungal diversity. In contrast, Noto exhibited the lowest microbial abundance but the highest fungal diversity, while Seoul displayed intermediate values. Dominant bacterial genera, including Caldalkalibacillus, Halomonas, and Nesterenkonia, demonstrated notable resilience across all three locations, highlighting their adaptability to diverse environmental conditions. The dominant fungal genera were Cladosporium and Candida. Analyses revealed significant correlations between microbial community structures and environmental factors. In Ulaanbaatar, microbial communities were strongly associated with meteorological parameters such as temperature, humidity, and wind speed. In Seoul, stronger correlations were observed with polycyclic aromatic hydrocarbons (PAHs). Noto exhibited weaker correlations with both meteorological factors and organic compounds. Across all sites, bacteria consistently showed broader niche breadths compared to fungi, reflecting their greater metabolic versatility and resource utilization capacity. Both bacterial and fungal niche breadths generally increased at intermediate concentrations of alkanes and DCAs but declined at extreme concentrations, suggesting optimal survival ranges. These findings highlight the complex interplay of environmental factors and pollutants in shaping microbial community structures and functional diversity across diverse geographical settings during the spring season.},
}

@article {pmid40285533,
year = {2025},
author = {Liao, X and Wang, H and Wu, D and Grossart, HP and Yang, X and Li, L and Wang, Y and Li, S and Li, J and Cao, M and Chen, N and Hu, A},
title = {Geographical and Environmental Factors Differentially Shape Planktonic Microbial Community Assembly and Resistomes Composition in Urban Rivers.},
journal = {Global change biology},
volume = {31},
number = {4},
pages = {e70211},
doi = {10.1111/gcb.70211},
pmid = {40285533},
issn = {1365-2486},
support = {//the Ocean Negative Carbon Emissions (ONCE) Program/ ; 2021QZKK0103//the Second Tibetan Plateau Scientific Expedition and Research Program/ ; 2019QZKK0503//the Second Tibetan Plateau Scientific Expedition and Research Program/ ; 2023YFC3804904//National Key Research and Development Program/ ; },
mesh = {*Microbiota ; *Plankton ; China ; *Rivers/microbiology ; Bacteria/genetics/drug effects ; Urbanization ; },
abstract = {Global urbanization accelerates pollution challenges in urban rivers, including increased transmission of bacterial antibiotic resistance genes (ARGs), severely threatening the health of aquatic ecosystems and human health. Yet, systematic knowledge of differences in distribution and community assembly patterns of bacterial resistance across urban rivers at a continental scale is still insufficient. In this study, we conducted extensive sampling in nine representative urban rivers across China. We used amplicon and shotgun metagenomic sequencing, state-of-the-art bioinformatics, and multivariate statistics to investigate distribution patterns and community assembly mechanisms of planktonic microbiomes (i.e., bacterioplankton and planktonic microeukaryotes), including their resistomes, i.e., ARGs and metal resistance genes (MRGs). Geographical and environmental factors played a pivotal role in shaping distribution patterns of planktonic microbiomes vs. resistomes in the studied urban rivers. Phylogenetic-bin-based null model analysis (iCAMP) indicated that planktonic microbiomes, dominated by dispersal limitation and drift, tend toward spatial heterogeneity. In contrast, planktonic resistomes, driven by deterministic processes, display more similar distribution patterns. Cross-validated Mantel tests revealed that geographical factors (i.e., geographic distance) were the primary regulators of planktonic microbial community assembly, while environmental factors (i.e., temperature) control assembly processes of planktonic resistomes. Our findings provide crucial insights into the mechanisms driving the biogeographical distribution and community assembly of planktonic microbial entities in urban rivers at a continental scale, offering valuable implications for mitigating and managing the spread of ARGs from the environment to humans.},
}

*Microbiota
*Plankton
China
*Rivers/microbiology
Bacteria/genetics/drug effects
Urbanization

@article {pmid40284744,
year = {2025},
author = {Yahya, R and Albaqami, A and Alzahrani, A and Althubaiti, SM and Alhariri, M and Alrashidi, ET and Alhazmi, N and Al-Matary, MA and Alharbi, N},
title = {Comprehensive Genomic Analysis of Klebsiella pneumoniae and Its Temperate N-15-like Phage: From Isolation to Functional Annotation.},
journal = {Microorganisms},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/microorganisms13040908},
pmid = {40284744},
issn = {2076-2607},
support = {NRC21R/053/02//King Abdullah International Medical Research Center/ ; },
abstract = {Antibiotic resistance to Klebsiella pneumoniae poses a major public health threat, particularly in intensive care unit (ICU) settings. The emergence of extensively drug-resistant (XDR) strains complicates treatment options, requiring a deeper understanding of their genetic makeup and potential therapeutic targets. This research delineated an extensively drug-resistant (XDR) Klebsiella pneumoniae strain obtained from an ICU patient and telomeric temperate phage derived from hospital effluent. The bacteria showed strong resistance to multiple antibiotics, including penicillin (≥16 μg/mL), ceftriaxone (≥32 μg/mL), and meropenem (≥8 μg/mL), which was caused by SHV-11 beta-lactamase, NDM-1 carbapenemase, and porin mutations (OmpK37, MdtQ). The strain was categorized as K46 and O2a types and carried virulence genes involved in iron acquisition, adhesion, and immune evasion, as well as plasmids (IncHI1B_1_pNDM-MAR, IncFIB) and eleven prophage regions, reflecting its genetic adaptability and resistance dissemination. The 172,025 bp linear genome and 46.3% GC content of the N-15-like phage showed strong genomic similarities to phages of the Sugarlandvirus genus, especially those that infect K. pneumoniae. There were structural proteins (11.8%), DNA replication and repair enzymes (9.3%), and a toxin-antitoxin system (0.4%) encoded by the phage genome. A protelomerase and ParA/B partitioning proteins indicate that the phage is replicating and maintaining itself in a manner similar to the N15 phage, which is renowned for maintaining a linear plasmid prophage throughout lysogeny. Understanding the dynamics of antibiotic resistance and pathogen development requires knowledge of phages like this one, which are known for their temperate nature and their function in altering bacterial virulence and resistance profiles. The regulatory and structural proteins of the phage also provide a model for research into the biology of temperate phages and their effects on microbial communities. The importance of temperate phages in bacterial genomes and their function in the larger framework of microbial ecology and evolution is emphasized in this research.},
}

@article {pmid40284675,
year = {2025},
author = {Li, M and Liu, X and Chen, W and Xu, H and Huang, F and Yao, Q and Jia, X and Huang, Y},
title = {Alleviating Effect of Lactiplantibacillus plantarum HYY-S10 on Colitis in Mice Based on an Analysis of the Immune Axis in the Intestine.},
journal = {Microorganisms},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/microorganisms13040840},
pmid = {40284675},
issn = {2076-2607},
support = {32302242//the National Natural Science Foundation of China/ ; 2022A1515110426//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 2023B0202040002//Guangdong Provincial Key Research and Development Program/ ; 2022B1212010015//Key Laboratory Project of Guangdong Province/ ; },
abstract = {The pathogenesis of ulcerative colitis (UC) has been fundamentally associated with intestinal microbiota dysbiosis and disruption of immune homeostasis. This study systematically investigates the therapeutic potential of Lactiplantibacillus plantarum HYY-S10 (HYY-S10), a novel strain isolated from De'ang sour tea in Yun an, China, with a focus on its mechanisms for alleviating colitis through the modulation of gut microbiota. Using a dextran sulfate sodium (DSS)-induced colitis model in C57BL/6J mice, our findings demonstrated that seven days of oral supplementation with HYY-S10 (1 × 10[8] CFU/mL, 0.2 mL/10 g body weight) significantly improved Disease Activity Index (DAI) scores and attenuated characteristic colitis symptoms, including progressive weight loss, rectal bleeding, and abnormal stool consistency. Administration of HYY-S10 exhibited significant immunomodulatory effects characterized by the downregulation of pro-inflammatory mediators (such as IL-1β, IL-6, IFN-γ, and LPS) while concomitantly upregulating anti-inflammatory IL-10 expression. Additionally, the strain enhanced intestinal antioxidant capacity by increasing GSH-Px activity, which collectively contributed to the reduction in intestinal inflammation. Furthermore, HYY-S10 demonstrated multifaceted protective effects by ameliorating oxidative stress through the restoration of redox homeostasis and modulation of gut microbial ecology. Probiotic intervention significantly increased short-chain fatty acids (SCFAs) production and notably enhanced the relative abundance of beneficial taxa, including Akkermansia and Ruminococcus_B, while restoring microbial diversity and ecological stability. Collectively, our results demonstrate that HYY-S10 alleviates experimental colitis by modulating the intestinal immune axis and microbiota composition, providing mechanistic insights to support its potential as a probiotic-based therapeutic strategy for UC.},
}

@article {pmid40284595,
year = {2025},
author = {Frazier, AN and Willis, W and Robbe, H and Ortiz, A and Koziel, JA},
title = {Characterization and Assembly Dynamics of the Microbiome Associated with Swine Anaerobic Lagoon Manure Treated with Biochar.},
journal = {Microorganisms},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/microorganisms13040758},
pmid = {40284595},
issn = {2076-2607},
support = {3090-31630-006//USDA-ARS CRIS/ ; },
abstract = {Biochar has significant potential for livestock microbiomes and crop agriculture regarding greenhouse gas emissions reduction. Therefore, a pilot study was designed to investigate the effect of biochar application on the surface of swine manure from an open lagoon and the associated microbial communities. Samples were collected from four different treatment groups: control (n = 4), coarse biochar (n = 4), fine biochar (n = 4), and ultra-fine biochar (n = 4). Additionally, aged manure in bulk was collected (n = 4) to assess alterations from the control group. The method of 16S rRNA amplicon sequencing along with microbial analyses was performed. Diversity was significantly different between aged manure in bulk samples and all treatment groups (Kruskal-Wallis; p < 0.05). Additionally, distinct community compositions were seen using both weighted and unweighted UniFrac distance matrices (PERMANOVA; p < 0.01). Differential abundance analysis revealed four distinct features within all treatment groups that were enriched (q < 0.001): Idiomarina spp., Geovibrio thiophilus, Parapusillimonas granuli, and an uncultured Gammaproteobacteria species. Similarly, Comamonas spp. and Brumimicrobium aurantiacum (q-value < 0.001) were significantly depleted by all the treatments. Stochastic and functional analyses revealed that biochar treatments were not deterministically altering assembly patterns, and functional redundancy was evident regardless of compositional shifts.},
}

@article {pmid40280843,
year = {2025},
author = {Araujo, ASF and Pereira, APA and de Medeiros, EV and Mendes, LW},
title = {Plant-microbe interactions: plants modulating their defenses.},
journal = {Trends in plant science},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tplants.2025.04.001},
pmid = {40280843},
issn = {1878-4372},
abstract = {Plant immunity is mediated by multiple factors, including microbial interactions and gene expression. Keppler et al. identified a set of microbe-responsive genes (general non-self response genes) whose expression or products affect bacterial strain abundance and enhance immunity. We explore how these genes shape alternative plant defense strategies for sustainable agriculture.},
}

@article {pmid40280003,
year = {2025},
author = {Cholet, F and Vignola, M and Quinn, D and Ijaz, UZ and Sloan, WT and Smith, CJ},
title = {Microbial ecology of drinking water biofiltration based on 16S rRNA sequencing: A meta-analysis.},
journal = {Water research},
volume = {281},
number = {},
pages = {123684},
doi = {10.1016/j.watres.2025.123684},
pmid = {40280003},
issn = {1879-2448},
abstract = {Biofiltration, a sustainable water treatment technology relying on microbial processes to remove contaminants, offers a promising approach to achieving the United Nations Sustainable Goal 6 of universal access to clean water and sanitation by 2030. However, a key barrier to optimising biofiltration is the incomplete understanding of the biological mechanisms governing its performance. Despite numerous studies examining how engineering decisions impact biofilter performance and the associated microbiome, the significant influence of geographical location on microbial communities raises the question of whether these findings are universally applicable or location-specific. To address this, we conducted a meta-analysis of 15 biofilter microbiomes using 16S rRNA high-throughput sequencing (HTS) data, mainly originating from rapid gravity and/or granular activated carbon (GAC) filters. Despite different types and scales, results highlight geographical location as the major contributor to microbiome dissimilarity in biofilter samples (Top and Bottom) (R[2]∼ 0.5; p-value<0.001). The same was observed for influent waters (PERMANOVA R[2]= 0.76; p-value<0.001), indicating location-specific microbiomes as opposed to differences driven by different biofilter operating parameters. Irrespective of location, the higher percentage of the microbiome was assembled through deterministic processes (∼55 %) compared to stochastic processes (∼45 %). Finally, our findings suggest that the depth stratification of biofilter microbiomes may be associated with the enrichment of taxa capable of metabolising more complex organic carbon in deeper filter layers (10 enriched pathways in biofilter Bottom layers compared to 3 at the Top). These insights provide a broader understanding of biofiltration microbiomes and offer possible research avenues for targeted and effective biofilter design strategies.},
}

@article {pmid40279085,
year = {2025},
author = {Zheng, F and Zhao, J and Yuan, Z and Gao, Y and Li, Y and Li, Y and Geng, Y and Qiang, Y},
title = {Interpretable drug-target affinity prediction based on pre-trained models' output as embeddings and based on structure-aware cross-attention for feature fusion.},
journal = {Molecular diversity},
volume = {},
number = {},
pages = {},
pmid = {40279085},
issn = {1573-501X},
support = {U21A20469//National Natural Science Foundation of China/ ; 82170716//National Natural Science Foundation of China/ ; 62376183//National Natural Science Foundation of China/ ; 202304051001009//the special fund for Science and Technology Innovation Teams of Shanxi Province/ ; 2020-PT320-005//National Health Commission Key Laboratory of Pneumoconiosis/ ; },
abstract = {The characteristics of protein pockets can better capture the interaction information between proteins and small molecules, thereby improving the performance of drug-target interaction (DTI) prediction tasks. However, pocket data typically need to be predicted using software such as AlphaFold, which would entail a massive workload for datasets ranging from tens of thousands to hundreds of thousands of samples. Moreover, feature representation networks for 3D pocket data are computationally intensive. To address this, we propose simulating 3D pocket data using sequence data through feature fusion of two different objects based on structure cross-attention (CASD). Additionally, precise feature representation is a prerequisite for accurately identifying pocket information. We introduce a method that leverages the output of the last layer of a pre-trained model as an embedding layer for training a new model from scratch. This approach not only incorporates prior knowledge from the pre-trained model but also expands model capacity, enabling more accurate feature representation. Furthermore, we enhance the multimodal representation of small molecule compounds using feature fusion based on structure cross-attention for the same object (CASS), further improving feature representation capabilities. Our cross-attention mechanisms operate at the token-level or node-level, allowing fine-grained capture of interactions between amino acids and atoms. This enables the identification of the contribution score of each atom or amino acid to the task, making our model interpretable for drug-target prediction. Experimental validation demonstrates that our model achieves state-of-the-art predictive performance.},
}

@article {pmid40277367,
year = {2025},
author = {Thapa, BS and Flynn, TM and Jensvold, ZD and Kemner, KM and Sladek, MF and O'Loughlin, EJ and Marshall, CW},
title = {Effects of soluble electron shuttles on microbial iron reduction and methanogenesis.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0222224},
doi = {10.1128/aem.02222-24},
pmid = {40277367},
issn = {1098-5336},
abstract = {In many aquatic and terrestrial ecosystems, iron (Fe) reduction by microorganisms is a key part of biogeochemical cycling and energy flux. The presence of redox-active electron shuttles in the environment potentially enables a phylogenetically diverse group of microbes to use insoluble iron as a terminal electron acceptor. We investigated the impact that different electron shuttles had on respiration, microbial physiology, and microbial ecology. We tested eight different electron shuttles, seven quinones and riboflavin, with redox potentials between 0.217 and -0.340 V. Fe(III) reduction coupled with acetate oxidation was observed with all shuttles. Once Fe(III) reduction began to plateau, a rapid increase in acetate consumption was observed and coincided with the onset of methane production, except in the incubations with the shuttle 9,10-anthraquinone-2-carboxylic acid (AQC). The rates of iron reduction, acetate consumption, methanogenesis, and the microbial communities varied significantly across the different shuttles independent of redox potential. In general, shuttles appeared to reduce the overall diversity of the community compared to no shuttle controls, but certain shuttles were exceptions to this trend. Geobacteraceae were the predominant taxonomic family in all enrichments except in the presence of AQC or 1,2-dihydroxyanthraquinone (AQZ), but each shuttle enriched a unique community significantly different from the no shuttle control conditions. This suggests that the presence of different redox-active electron shuttles can have a large influence on the microbial ecology and total carbon flux in the environment.IMPORTANCEIron is the fourth most abundant element in the Earth's crust, and the reduction of iron by microbes is an important component of global biogeochemical cycles. A phylogenetically diverse group of microbes is capable of conserving energy with oxidized iron as a terminal electron acceptor, but the environmental conditions favoring certain taxonomic clades in iron-reducing environments are unclear. One complicating factor often overlooked in small-scale enrichments is the influence of soluble, redox-active electron shuttles on the rate and microbial ecology of iron reduction. We tested the effects of eight different electron shuttles on microbial physiology and ecology in iron-reducing enrichments derived from a local wetland. Each electron shuttle varied the microbial activity and enriched for a microbial community distinct from the no shuttle control condition. Therefore, in complex subsurface environments with many redox-active compounds present, we propose electron shuttles as a reason for the coexistence of multiple clades of iron-reducing bacteria.},
}

@article {pmid40277363,
year = {2025},
author = {Wang, Y and Yang, L and Wu, W and Feng, Z and He, J and Guo, C and He, J},
title = {Bacillus haimaensis sp. nov.: a novel cold seep-adapted bacterium with unique biosynthetic potential.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0245624},
doi = {10.1128/aem.02456-24},
pmid = {40277363},
issn = {1098-5336},
abstract = {Deep-sea cold seeps harbor unique microbial communities that play crucial roles in biogeochemical cycles and possess potential biotechnological applications. Herein, we report the isolation, characterization, and genomic analysis of a novel Bacillus species, Bacillus haimaensis sp. nov. (type strain CSS-39[T], CCTCC M20241382), obtained from sediments collected at a depth of 1,350 m in the Haima cold seep, South China Sea. Phylogenomic analysis, revealing an average nucleotide identity of 87.78% and a digital DNA-DNA hybridization value of 34.0% with its closest relative B. tianshenii DSM 25879[T], confirms the taxonomic novelty of the genus Bacillus. The complete 4.54 Mb genome of B. haimaensis reveals adaptations to the cold seep environment, including enhanced nutrient acquisition capabilities and stress response mechanisms. Comparative genomic analysis identifies 27 unique gene clusters related to spore germination and sulfate assimilation, suggesting specialized metabolic strategies for this extreme habitat. Furthermore, six biosynthetic gene clusters, including a novel lassopeptide cluster, indicate a potential for secondary metabolite production. Phenotypic characterization demonstrates the strain's ability to utilize diverse carbon sources and tolerate a wide range of environmental conditions. Our findings provide insights into microbial adaptations to deep-sea cold seeps and highlight the potential of B. haimaensis for biotechnological applications in bioremediation and natural product discovery. This study expands our understanding of microbial diversity in extreme marine environments and offers a new model bacterium for investigating bacterial adaptations to deep-sea ecosystems.IMPORTANCEThe discovery of Bacillus haimaensis sp. nov. in the Haima cold seep of the South China Sea represents a significant advancement in our understanding of microbial adaptations to extreme marine environments. This novel species exhibits remarkable metabolic versatility and unique genomic features, providing insights into bacterial survival strategies in nutrient-variable, high-pressure deep-sea ecosystems. Comprehensive genomic analysis reveals distinctive biosynthetic gene clusters, suggesting untapped potential for discovering novel natural product. Furthermore, B. haimaensis exhibits promising capabilities for aromatic compound degradation, indicating potential applications in marine bioremediation. This work not only expands our knowledge of microbial diversity in understudied deep-sea habitats but also highlights the biotechnological promise of extremophiles. The adaptive mechanisms elucidated in B. haimaensis, particularly those related to sporulation and sulfate assimilation, contribute to our broader understanding of microbial ecology in cold seeps and may inform future research on climate change impacts on deep-sea ecosystems.},
}

@article {pmid40276016,
year = {2025},
author = {Papazlatani, C and Wagner, A and Chen, Z and Zweers, H and de Boer, W and Garbeva, P},
title = {Enhancement of production of pathogen-suppressing volatiles using amino acids.},
journal = {Current research in microbial sciences},
volume = {8},
number = {},
pages = {100385},
pmid = {40276016},
issn = {2666-5174},
abstract = {Bacterial volatile organic compounds can play a significant role in antagonistic interactions. Enhancing the production of bacterial volatiles that suppress the growth of soil-borne phytopathogenic fungi, has perspective as a sustainable disease control strategy. In the present study, we explored the potential of stimulating Burkholderia AD24 and Paenibacillus AD87 to produce volatiles that suppress the growth of the plant pathogenic fungi Fusarium culmorum PV and Rhizoctonia solani AG2.2IIIb. We provided the bacterial strains with a mixture of amino acids that can serve as precursor molecules in metabolic routes leading to emission of suppressive bacterial volatiles. Only Burkholderia AD24 was stimulated to produce a volatile blend that led to higher suppression of both pathogens. Subsequent analysis of the volatile composition emitted by Burkholderia AD24 in the presence of amino acids, showed higher abundance of antifungal compounds, including sulfur compounds (DMDS), pyrazines (2,5-dimethyl pyrazine) and carbohydrates (3-methyl-1-butanol). Follow-up trials with single amino acids revealed a pathogen specific response effect. When Burkholderia AD24 was cultivated in the presence of glutamine and asparagine, the emitted volatile blend suppressed the growth of F. culmorum, whereas when cultivated in the presence of glycine, glutamine, arginine and lysine the volatile blend suppressed the growth of R. solani. Analysis of the volatile blend composition showed differences between the amino acid treatments. Our findings show that amino acid precursor molecules can stimulate the production of fungistatic volatiles but the sensitivity of the fungal pathogens to these bacterial volatiles varies. This should be considered in future application strategies.},
}

@article {pmid40275504,
year = {2025},
author = {Ekemezie, SC and Davis, CC and Russo, MV and Carpenter, LP and Russell, AL},
title = {Pollen-microbe interactions in nectar weakly influence bee foraging behavior.},
journal = {Integrative and comparative biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/icb/icaf017},
pmid = {40275504},
issn = {1557-7023},
abstract = {Plant-pollinator interactions are frequently affected by microbes that grow on flowers. Bacteria and yeast commonly grow within floral nectar, which is a sugar-rich floral reward often sought out by pollinators. Nectar is also commonly contaminated with protein-rich pollen. Microbes can induce this pollen to germinate or burst within the nectar, which potentially results in pollen nutrients being made available to nectar foraging pollinators. Yet whether pollen-microbe interactions in nectar impact pollinator behavior remains unknown. We therefore investigated how a common nectar yeast (Metschnikowia reukaufii) and bacteria (Acinetobacter nectaris) affected pollen germination and bursting within artificial nectar and effects on bumble bee (Bombus impatiens) foraging behavior. We found that both bacteria and yeast reduced the proportion of intact pollen in nectar, with bacteria inducing the most germination and bursting. Although microbes may thus potentially increase the quality of the nectar reward via increased access to pollen nutrients, we did not observe effects on bee flower preference. Similarly, bees did not show increased constancy (i.e., fidelity to one flower type across flower visits) to nectar contaminated with pollen and microbes. In contrast, bees were much more likely to reject flowers with nectar contaminated with pollen and yeast alone or together, relative to flowers that offered uncontaminated nectar. Altogether, our work suggests pollen-microbe interactions within nectar may have relatively minor influences on pollinator foraging behavior. We discuss possible explanations and implications of these results for plant and pollinator ecology.},
}

@article {pmid40273553,
year = {2025},
author = {Ballan, D and Picot, A and Rolland, N and Bovo, C and Prévost, C and Coton, E and Mounier, J},
title = {Diversity of spoilage microorganisms associated with fresh fruits and vegetables in French households.},
journal = {International journal of food microbiology},
volume = {437},
number = {},
pages = {111204},
doi = {10.1016/j.ijfoodmicro.2025.111204},
pmid = {40273553},
issn = {1879-3460},
abstract = {Food loss and waste generated throughout the food chain are major concerns in today's society. A high level of food waste occurs at the household's level and fresh fruit and vegetable (FFV) spoilage caused by microbial growth accounts for a large part of these losses. While numerous studies focused on spoilage microorganism diversity from primary production to distribution, little is known about those involved at the household level. In this context, this study aimed at investigating which FFV are usually wasted depending on the season and storage conditions at households, and identifying the microorganisms associated with spoiled FFV. During two periods (summer and autumn), 346 spoiled FFV samples were collected using a citizen science approach in 49 households in the Brest area (Finistère, Brittany, France). About three quarters of spoiled FFV collected originated from room temperature storage and 75 % were collected during summer. Among the studied samples, 75 % showed microbial growth after plating onto agar-based medium, and therefore, were likely spoiled because of microbial spoilage. Overall, 183 molds, 31 yeasts and 96 bacteria were isolated and identified using MALDI-TOF MS and sequencing. Among the 42 different mold species identified, Penicillium spp. were the most common representing more than 50 % of mold isolates followed by Botrytis (12.4 %), Mucor (8.6 %) and Cladosporium (7.6 %) spp. Hanseniaspora uvarum and Aureobasidium pullulans were the most prevalent yeast species while bacterial isolates showed the highest diversity of all identified organisms (49 species) with Pseudomonas spp., enterobacteria and lactic acid bacteria representing the most frequently isolated taxa. This study shows for the first time the microbial diversity associated with spoiled FFV of which a large proportion were stored at room temperature, suggesting that a better usage of FFV refrigeration could help reduce FFV waste in households.},
}

@article {pmid40270585,
year = {2025},
author = {Zheng, Z and Gong, Z and Zhang, R and Lin, X and Hong, W and Song, L},
title = {Potential pathogens drive ARGs enrichment during biofilms formation on environmental surfaces.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf057},
pmid = {40270585},
issn = {2730-6151},
abstract = {The enrichment of antibiotic resistance genes (ARGs) on environmental surfaces is a fundamental question in microbial ecology. Understanding the processes driving ARG variations can provide clues into their transfer mechanisms between phases and offer insights for public health management. In this study, we examined microbiota, potential pathogen, and ARG dynamics on two common environment surfaces-polyvinyl chloride (PVC) and carbon steel (CS)-under environmental stress (induced by landfill leachate flow) in a Center for Disease Control and Prevention Biofilm Reactor using metagenomics and quantitative polymerase chain reaction-Chip techniques. Contrary to the expected changes in biofilms morphology and physiochemical properties, microbiota, potential pathogens, and ARGs exhibited a divergence-convergence pattern, primarily shaped by attachment surface properties and, subsequently, biofilm maturity during biofilms formation. During this process, ARG levels in biofilms gradually increased to and exceeded the levels in the surrounding environment, but with a distinct structure (P < .05). Furthermore, 1.93- and 3.05-fold increases in the concentrations of mobile genetic elements intI-1 in PVC and CS biofilms, respectively, suggested their important role in the transfer and spread of ARGs within the biofilm matrix. Although potential pathogens were less abundant (3.48%-5.63%) in the biofilms microbiota, they accounted for 18.28%-45.16% of the ARG hosts and harbored multiple ARGs. Pathogens significantly impacted ARG enrichment (Procrustes analysis: P = .0136, M[2] = 0.34) although microbiota development also influenced this process (P = .0385, M[2] = 0.67). These results suggest that pathogens are key in shaping ARG enrichment in biofilms. Our findings provide dynamic insights into resistome enrichment on environmental surfaces.},
}

@article {pmid40270532,
year = {2025},
author = {Ma, J and Wang, M and Sun, Y and Zheng, Y and Lai, S and Zhang, Y and Wu, Y and Jiang, C and Shen, F},
title = {Cockroach Microbiome Disrupts Indoor Environmental Microbial Ecology with Potential Public Health Implications.},
journal = {Environment & health (Washington, D.C.)},
volume = {3},
number = {4},
pages = {380-391},
doi = {10.1021/envhealth.4c00216},
pmid = {40270532},
issn = {2833-8278},
abstract = {Cockroaches pose a significant global public health concern. However, besides the well-recognized cockroach-induced allergy, the potential impact of the cockroach microbiome on human health through various means is not yet fully elucidated. This study aimed to clarify the health impacts of cockroaches by investigating the microbial interactions among cockroaches, the indoor environment, and humans. We simultaneously collected cockroach, indoor environment (indoor air and floor dust), and human (exhaled breath condensate and skin) samples from residential areas in five cities representing distinct climate zones in China. The 16S rDNA sequencing results revealed that cockroaches harbor diverse bacterial populations that vary across different cities. The prevalence of potential pathogenic bacteria (PPB) in cockroaches ranged from 1.1% to 58.9%, with dominant resistance genes conferring resistance to tetracycline, macrolide, and beta-lactam. The relationships between the cockroach microbiome and the associated environmental and human microbiomes were explored by using fast expectation-maximization microbial source tracking (FEAST). The potential contribution of cockroach bacteria to the floor dust-borne microbiome and indoor airborne microbiome was estimated to be 5.6% and 1.3%, respectively. Similarly, the potential contribution of cockroach PPB to the floor dust-borne microbiome and indoor airborne microbiome was calculated to be 4.0% and 1.2%, respectively. In residences with cockroach infestations, the contribution of other sources to the indoor environment was slightly increased. Collectively, the role of cockroaches in the transmission of microorganisms, particularly pathogenic bacteria and antibiotic resistance genes, cannot be overlooked.},
}

@article {pmid40268300,
year = {2025},
author = {Goyal, A and Chure, G},
title = {Paradox of the Sub-Plankton: Plausible Mechanisms and Open Problems Underlying Strain-Level Diversity in Microbial Communities.},
journal = {Environmental microbiology},
volume = {27},
number = {4},
pages = {e70094},
doi = {10.1111/1462-2920.70094},
pmid = {40268300},
issn = {1462-2920},
mesh = {*Biodiversity ; *Microbiota ; *Bacteria/genetics/classification ; Gene Transfer, Horizontal ; Genetic Variation ; Ecosystem ; Biological Evolution ; },
abstract = {Microbial communities are often complex and highly diverse, typically with dozens of species sharing spatially-restricted environments. Within these species, genetic and ecological variation often exists at a much finer scale, with closely related strains coexisting and competing. While the coexistence of strains in communities has been heavily explored over the past two decades, we have no self-consistent theory of how this diversity is maintained. This question challenges our conventional understanding of ecological coexistence, typically framed around species with clear phenotypic and ecological differences. In this review, we synthesise plausible mechanisms underlying strain-level diversity (termed microdiversity), focusing on niche-based mechanisms such as nutrient competition, neutral mechanisms such as migration, and evolutionary mechanisms such as horizontal gene transfer. We critically assess the strengths and caveats of these mechanisms, acknowledging key gaps that persist in linking genetic similarity to ecological divergence. Finally, we highlight how the origin and maintenance of microdiversity could pose a major challenge to conventional ecological thinking. We articulate a call-to-arms for a dialogue between well-designed experiments and new theoretical frameworks to address this grand conceptual challenge in understanding microbial biodiversity.},
}

*Biodiversity
*Microbiota
*Bacteria/genetics/classification
Gene Transfer, Horizontal
Genetic Variation
Ecosystem
Biological Evolution

@article {pmid40267173,
year = {2025},
author = {Bull, CT and Salgado-Salazar, C and Romberg, MK and Allen, C and Kantor, M and Handoo, Z and Aboughanem-Sabanadzovic, N and Sabanadzovic, S and Coutinho, T},
title = {Plant Pathogen Name Game: Cross Kingdom Review for the Naming of Biotic Agents Associated with Plants.},
journal = {Annual review of phytopathology},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-phyto-111424-090412},
pmid = {40267173},
issn = {1545-2107},
abstract = {To communicate across scientific disciplines, regulatory bodies, and the agricultural community, the naming of plant pathogens assigned to specific taxa is critical. Here, we provide an overview of the nomenclatural systems governing the naming of plant-pathogenic nematodes, fungi, oomycetes, prokaryotes, and viruses. Although we focus on the nature of the nomenclatural codes, we briefly discuss fundamental principles of taxonomy, including classification and identification. Key elements of the codes of nomenclature that ensure stability and clarity when naming species of pathogens are defined. When comparing the practice of nomenclature across different kingdoms, the classification and nomenclatural systems differ, and thus unique challenges are faced. We provide guidance from the codes and current practice for naming novel species. When there are nomenclatural conflicts, international committees play a critical role in their resolution. They also play a role in updating the codes to reflect new advancements in science. With this review, we aim to assist plant pathologists, journal editors, and those in related fields by providing an entrée to the legalistic requirements of the codes. Authors must consult and follow the rules of the appropriate code for any proposal of new or new combinations of names. To those interested in naming new species (or renaming the current ones), we recommend collaborations with experts in the field of taxonomy to ensure that rules for accurate and consistent naming practices and procedures are followed and to increase the likelihood that the proposed nomenclature is correct and acceptable.},
}

@article {pmid40196585,
year = {2025},
author = {Dellicour, S and Gámbaro, F and Jacquot, M and Lequime, S and Baele, G and Gilbert, M and Pybus, OG and Suchard, MA and Lemey, P},
title = {Comparative performance of novel viral landscape phylogeography approaches.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {40196585},
issn = {2692-8205},
support = {/WT_/Wellcome Trust/United Kingdom ; R01 AI153044/AI/NIAID NIH HHS/United States ; R01 AI162611/AI/NIAID NIH HHS/United States ; U19 AI135995/AI/NIAID NIH HHS/United States ; },
abstract = {The fast rate of evolution in RNA viruses implies that their evolutionary and ecological processes occur on the same time scale. Genome sequences of these pathogens can therefore contain information about the processes that govern their transmission and dispersal. In particular, landscape phylogeographic approaches use phylogeographic reconstructions to investigate the impact of environmental factors and variables on the spatial spread of viruses. Here, we extend and improve existing approaches and develop three novel landscape phylogeographic methods that can test the impact of continuous environmental factors on the diffusion velocity of viral lineages. In order to evaluate the different methods, we also implemented two simulation frameworks to test and compare their statistical performance. The results enable us to formulate clear guidelines for the use of three complementary landscape phylogeographic approaches that have sufficient statistical power and low rates of false positives. Our open-source methods are available to the scientific community and can be used to investigate the drivers of viral spread, with potential benefits for understanding virus epidemiology and designing tailored intervention strategies.},
}

@article {pmid40266732,
year = {2025},
author = {Duque-Granda, D and Vivero-Gómez, RJ and González Ceballos, LA and Junca, H and Duque, SR and Aroca Aguilera, MC and Castañeda-Espinosa, A and Cadavid-Restrepo, G and Gómez, GF and Moreno-Herrera, CX},
title = {Exploring the Diversity of Microbial Communities Associated with Two Anopheles Species During Dry Season in an Indigenous Community from the Colombian Amazon.},
journal = {Insects},
volume = {16},
number = {3},
pages = {},
doi = {10.3390/insects16030269},
pmid = {40266732},
issn = {2075-4450},
support = {Hermes 57545//Universidad Nacional de Colombia/ ; },
abstract = {Malaria disease affects millions of people annually, making the Amazon Basin a major hotspot in the Americas. While traditional control strategies rely on physical and chemical methods, the Anopheles microbiome offers a promising avenue for biological control, as certain bacteria can inhibit parasite development and alter vector immune and reproductive systems, disrupting the transmission cycle. For this reason, this study aimed to explore the bacterial communities in An. darlingi and An. triannulatus s.l., including breeding sites, immature stages, and adults from San Pedro de los Lagos (Leticia, Amazonas) through next-generation sequencing of the 16S rRNA gene. The results revealed a higher bacterial genus richness in the L1-L2 larvae of An. triannulatus s.l. Aeromonas and Enterobacter were prevalent in most samples, with abundances of 52.51% in L3-L4 larvae and 48.88% in pupae of An. triannulatus s.l., respectively. In breeding site water, Verrucomicrobiota bacteria were the most dominant (52.39%). We also identified Delftia (15.46%) in An. triannulatus s.l. pupae and Asaia (98.22%) in An. triannulatus, linked to Plasmodium inhibition, and Elizabethkingia, in low abundances, along with Klebsiella and Serratia, known for paratransgenesis potential. Considering the high bacterial diversity observed across the different mosquito life stages, identifying bacterial composition is the first step towards developing new strategies for malaria control. However, the specific roles of these bacteria in anophelines and the malaria transmission cycle remain to be elucidated.},
}

@article {pmid40266381,
year = {2025},
author = {Cuny, MAC and Gloder, G and Bourne, ME and Kalisvaart, SN and Verreth, C and Crauwels, S and Cusumano, A and Lievens, B and Poelman, EH},
title = {Parasitoid Calyx Fluid and Venom Affect Bacterial Communities in Their Lepidopteran Host Labial Salivary Glands.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {33},
pmid = {40266381},
issn = {1432-184X},
support = {ALWOP.368//Netherlands Organization for Scientific Research/ ; ALWOP.368//Netherlands Organization for Scientific Research/ ; ALWOP.368//Netherlands Organization for Scientific Research/ ; ALWOP.368//Netherlands Organization for Scientific Research/ ; ALWOP.368//Netherlands Organization for Scientific Research/ ; G.0961.19 N//Flemish Fund for Scientific Research/ ; G.0961.19 N//Flemish Fund for Scientific Research/ ; G.0961.19 N//Flemish Fund for Scientific Research/ ; G.0961.19 N//Flemish Fund for Scientific Research/ ; },
mesh = {Animals ; *Salivary Glands/microbiology ; *Wasps/physiology ; *Bacteria/classification/genetics/isolation & purification/drug effects ; *Microbiota ; Larva/parasitology/microbiology ; Host-Parasite Interactions ; *Butterflies/microbiology/parasitology ; Hemolymph/microbiology ; Polydnaviridae/physiology ; *Wasp Venoms/pharmacology ; *Moths/microbiology/parasitology ; },
abstract = {The influence of gut and gonad bacterial communities on insect physiology, behaviour, and ecology is increasingly recognised. Parasitism by parasitoid wasps alters many physiological processes in their hosts, including gut bacterial communities. However, it remains unclear whether these changes are restricted to the gut or also occur in other tissues and fluids, and the mechanisms underlying such changes are unknown. We hypothesise that host microbiome changes result from the injection of calyx fluid (that contain symbiotic viruses known as polydnaviruses) and venom during parasitoid oviposition and that these effects vary by host tissue. To test this, we microinjected Pieris brassicae caterpillars with calyx fluid and venom from Cotesia glomerata, using saline solution and natural parasitism by C. glomerata as controls. We analysed changes in the bacterial community composition in the gut, regurgitate, haemolymph, and labial salivary glands of the host insects. Multivariate analysis revealed distinct bacterial communities across tissues and fluids, with high diversity in the salivary glands and haemolymph. Parasitism and injection of calyx fluid and venom significantly altered bacterial communities in the salivary glands. Differential abundance analysis showed that parasitism affected bacterial relative abundance in the haemolymph, and that Wolbachia was only found in the haemolymph of parasitized caterpillars. Altogether, our findings reveal that parasitism influences the host haemolymph microbiome, and both parasitism and injection of calyx fluid and venom drive changes in the bacterial community composition within the host salivary glands. Given that the composition of salivary glands can influence plant response to herbivory, we discuss these results in the broader context of plant-parasitoid interactions.},
}

Animals
*Salivary Glands/microbiology
*Wasps/physiology
*Bacteria/classification/genetics/isolation & purification/drug effects
*Microbiota
Larva/parasitology/microbiology
Host-Parasite Interactions
*Butterflies/microbiology/parasitology
Hemolymph/microbiology
Polydnaviridae/physiology
*Wasp Venoms/pharmacology
*Moths/microbiology/parasitology

@article {pmid40262702,
year = {2025},
author = {Zhang, S and Sun, C},
title = {Ecological divergence of marine bacteria Alteromonas mediterranea.},
journal = {Molecular phylogenetics and evolution},
volume = {},
number = {},
pages = {108359},
doi = {10.1016/j.ympev.2025.108359},
pmid = {40262702},
issn = {1095-9513},
abstract = {Alteromonas mediterranea, originally designated as A. macleodii, is a deep-sea ecotype that plays an important ecological role in the ocean. However, a comprehensive understanding of their biogeographic distribution and evolutionary histories remains limited. In this study, our analysis indicated that A. mediterranea members could adapt contrasting marine ecosystems and flourish in nutrient-rich habitats such as feces and coral reefs. No significant correlations between the relative abundance of A. mediterranea members and the environmental variables were identified. Phylogenetic analysis and geographic patterns of A. mediterranea strains suggested that they could be clustered into two clades (clade Ⅰ and clade Ⅱ). In contrast, many distinct genomic traits exist between these clades, such as the complete genes encoding cytochrome o ubiquinol oxidase only involved in clade Ⅱ. Genes were more likely to be lost in the evolutionary history of A. mediterranea relatives. Gene loss might be a major force in all phylogenetic groups driving the distinct clades. Adaptation to different biotopes resulted in the functional differentiation of A. mediterranea members, with the loss of genes encoding carbohydrate-active enzymes. Genes acquired horizontally from unclassified bacteria, and Proteobacteria represented by Gammaproteobacteria played key roles in the functional diversification of A. mediterranea in marine habitats. Given these data, these results are useful for information supplementation of A. mediterranea strains, particularly for making significant advances in understanding marine microbial ecology within different clonal frames using genome-wide recruitments.},
}

@article {pmid40262432,
year = {2025},
author = {Wu, G and Zhang, H and Huang, T and Song, Y and Liu, X and Liu, X and Wang, X and Pei, T and Xu, G and Wang, Z},
title = {Hydraulic and thermal performance trigger the deterministic assembly of water microbiomes: From biogeographical homogenization to machine learning model.},
journal = {Water research},
volume = {282},
number = {},
pages = {123626},
doi = {10.1016/j.watres.2025.123626},
pmid = {40262432},
issn = {1879-2448},
abstract = {Water quality at the point of consumption has long been a health issue because of the potential for microbial ecology. However, research on water hydraulic performance remains in its infancy, and in particular, little is known about the effects of thermal performance during winter. This study explored the effects of stagnation and municipal heating on microbial communities in tap water, focusing on spatial and temporal variations in microbial community composition. The results revealed that stagnation significantly alters the microbial community, especially in heating areas, where the temperature exacerbates microbial growth. Furthermore, hydraulic and thermal performance drive deterministic assembly processes in microbial communities, as evidenced by the reductions in β-diversity, normalized stochasticity ratio (NST), and neutral community model (NCM) fit. Machine learning models revealed that stagnation time greater than 8 h results in increased community abundance because of longer exposure to organic matter and nutrients. The study finding illustrate the importance of environmental influences on microbial community dynamics, and provide valuable insights into the water microbial community, particularly in areas with prolonged stagnation.},
}