@article {pmid40835811,
year = {2025},
author = {Luzics, S and Baka, E and Otto, M and Kosztik, J and Szalontai, H and Bata-Vidács, I and Nagy, I and Tóth, Á and Táncsics, A and Pápai, M and Nagy, I and Orsini, M and Kukolya, J},
title = {High-quality de novo genome assembly and functional genomic insights into Thermobifida alba DSM43795[T], a mesophilic actinobacterium isolated from garden soil.},
journal = {Biologia futura},
volume = {},
number = {},
pages = {},
pmid = {40835811},
issn = {2676-8607},
support = {K142686//National Research, Development and Innovation Office/ ; EKÖP- 24- VI/MATE-3//Ministry for Culture and Innovation from the source of the National Research, Development and Innovation Fund/ ; EKÖP-MATE/2024/25/D//Ministry for Culture and Innovation from the source of the National Research, Development and Innovation Fund/ ; },
abstract = {Thermobifida alba DSM43795[T], a mesophilic actinobacterium isolated from garden soil, plays a vital role in lignocellulose degradation and holds biotechnological and pharmaceutical potential. We present a high-quality, complete de novo genome assembly of T. alba DSM43795[T] using combined PacBio long-read and Illumina short-read sequencing, resulting in a single circular chromosome of 4.9 Mbp with 72.1% GC content. Comparative genomics with the thermophilic relative T. fusca YX revealed 83.39% average nucleotide identity and extensive genome synteny alongside niche-specific differences. Functional annotation identified 4345 genes, including a rich complement of carbohydrate-active enzymes (CAZymes) such as glycoside hydrolases (GHs), esterases, and polysaccharide lyases, supporting versatile plant biomass degradation. GH gene sets were largely conserved between the species in both gene number and distribution, but T. alba uniquely encodes a novel GH10 endo-xylanase near a characterised palindrome regulatory sequence, indicating species-specific regulation. We hypothesise that thermophilic adaptation in T. fusca requires more proteins for ribosome integrity and amino acid metabolism, with reduced emphasis on carbohydrate metabolism and defence compared to T. alba. Moreover, T. alba harbours a broader array of defence-related genes and mobile genetic elements, including integrases and transposases. Although lacking a complete CRISPR-Cas system, two CRISPR arrays were detected, suggesting alternative immune strategies. Virulence factor homologs shared by both species likely reflect environmental survival rather than pathogenicity. This genomic characterisation elucidates T. alba's metabolic versatility and ecological adaptations, laying the groundwork for its potential applications in biomass conversion, environmental biotechnology, and drug discovery.},
}

@article {pmid40835614,
year = {2025},
author = {Ma, H and Cornadó, D and Raaijmakers, JM},
title = {The soil-plant-human gut microbiome axis into perspective.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {7748},
pmid = {40835614},
issn = {2041-1723},
support = {32201402//National Natural Science Foundation of China (National Science Foundation of China)/ ; 202206205006//China Scholarship Council (CSC)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Soil Microbiology ; *Plants/microbiology ; Soil/chemistry ; Ecosystem ; Animals ; },
abstract = {Microbiomes of soil, plants, and the animal gut are pivotal for key life processes such as nutrient cycling, stress resilience, and immunity. While studies have hinted at a shared microbial reservoir connecting these environments, compelling evidence of a soil-plant-gut microbiome axis is scarce. This perspective explores the potential continuum and diversification of microbes along this axis, highlighting specific microorganisms capable of moving from soil to plants to the human gut. A conceptual framework is proposed to better understand the mechanisms driving interactions among these microbiomes. We also examine how soil, plant, and gut microbiomes may co-evolve and influence one another through reciprocal effects. We consider external environmental factors that could strengthen their interconnections, potentially creating beneficial feedback loops that impact ecosystem and human health.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Soil Microbiology
*Plants/microbiology
Soil/chemistry
Ecosystem
Animals

@article {pmid40830705,
year = {2025},
author = {Oulkhir, FE and Allaoui, A and Idbella, A and Danouche, M and Bargaz, A and Biskri, L and Idbella, M},
title = {Bacillus subtilis ED24 Controls Fusarium culmorum in Wheat Through Bioactive Metabolite Secretion and Modulation of Rhizosphere Microbiome.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {89},
pmid = {40830705},
issn = {1432-184X},
mesh = {*Triticum/microbiology/growth & development ; *Fusarium/growth & development/drug effects/physiology ; *Bacillus subtilis/physiology/metabolism ; *Rhizosphere ; *Plant Diseases/microbiology/prevention & control ; *Microbiota ; Soil Microbiology ; Plant Roots/microbiology ; Endophytes/physiology ; Fungicides, Industrial/pharmacology ; },
abstract = {Fusarium culmorum is a soil-borne fungal pathogen causing root and stem rot, seedling blight, and significant yield losses in small grain cereals, including wheat. This study aimed to evaluate the antifungal potential of Bacillus subtilis ED24, an endophytic strain isolated from Ziziphus lotus (L.) roots, and its effects on wheat growth and yield under controlled conditions. In vitro assays demonstrated that B. subtilis ED24 inhibited F. culmorum mycelial growth by up to 87%, associated with the secretion of 37 distinct secondary metabolites, predominantly involved in carbon cycling. In pot experiments, B. subtilis ED24 significantly enhanced wheat germination (85%) and growth compared to infected plants treated with the chemical fungicide tebuconazole. Although nutrient analysis showed significantly higher shoot nitrogen (32.34 mg/pot) and phosphorus (2.41 mg/pot) contents in the B. subtilis ED24 treatment compared to tebuconazole (8.11 and 0.18 mg/pot, respectively), no significant differences were observed when compared to the infected control (C-). Similarly, B. subtilis ED24 led to improved thousand grain weight (40.4 g), protein content (19.98%), and ash content (1.95%) relative to tebuconazole (29.1 g, 18.31%, and 1.74%, respectively), yet these values did not differ significantly from the infected control (C-). Notably, the number of seeds per pot was significantly increased by B. subtilis ED24 compared to the infected control (C-) (113.8 seeds/pot vs. 54.2 seeds/pot). Additionally, B. subtilis ED24 modulated the wheat rhizosphere microbiome, enriching beneficial taxa such as Eurotiomycetes fungal class and the bacterial genus Paramesorhizobium. These findings suggest that the antifungal activity and growth-promoting effects of B. subtilis ED24 are likely mediated through the synthesis of unique bioactive metabolites and microbiome modulation, offering a promising sustainable alternative to chemical fungicides in wheat production.},
}

*Triticum/microbiology/growth & development
*Fusarium/growth & development/drug effects/physiology
*Bacillus subtilis/physiology/metabolism
*Rhizosphere
*Plant Diseases/microbiology/prevention & control
*Microbiota
Soil Microbiology
Plant Roots/microbiology
Endophytes/physiology
Fungicides, Industrial/pharmacology

@article {pmid40828659,
year = {2025},
author = {Wang, X and Chen, Z and Liu, C and Zhang, Z and Deng, Y and Tao, L and Tiedje, JM and Deng, J},
title = {Type I-F CRISPR-associated transposons contribute to genomic plasticity in Shewanella and mediate efficient programmable DNA integration.},
journal = {Microbial genomics},
volume = {11},
number = {8},
pages = {},
doi = {10.1099/mgen.0.001476},
pmid = {40828659},
issn = {2057-5858},
abstract = {The genome plasticity of species and strains in the genus Shewanella is closely associated with the diverse mobile genetic elements embedded in its genomes. One mobile element with potential for accurate and efficient DNA insertion in Shewanella is the type I-F3 CRISPR-associated transposon (I-F3 CAST). However, relatively little is known about the distribution and ecological significance of I-F3 CASTs and whether they could be suitable as a tool for targeted genetic manipulation in situ. To better understand the distribution of I-F3 CASTs in Shewanella, we analysed 602 Shewanella genomes. We found that I-F3 CASTs were present in 12% of all genomes, although differences in both gene arrangement and integration locus were observed. These Shewanella I-F3 CASTs carried up to 89 cargo genes, which were associated with diverse functions, including defence, resistance and electron transfer, demonstrating an important role in genomic diversification and ecological adaptation. We tested whether the I-F3 CAST present in Shewanella sp. ANA-3 enhanced gene insertion, both in situ and in a heterologous host. We observed I-F3 CAST-mediated crRNA-targeted integration of the supplied genes into the pyrF locus in Shewanella sp. ANA-3. Heterologous gene insertion with high integration efficiency in Escherichia coli was also demonstrated using a simplified version of ANA-3 I-F3 CAST. Altogether, this work highlights the important role of I-F3 CASTs in promoting genomic plasticity of the Shewanella genus and demonstrates the gene-editing capability of ANA-3-CAST both endogenously and heterologously.},
}

@article {pmid40824433,
year = {2025},
author = {Schneider, T},
title = {Interactions at sea: on the microbiome life-cycle and biogeochemical processes.},
journal = {History and philosophy of the life sciences},
volume = {47},
number = {3},
pages = {41},
pmid = {40824433},
issn = {1742-6316},
abstract = {The marine phycosphere is a microscale mucosal region of microbiomes surrounding a phytoplankton cell. The phycosphere (analogous to the terrestrial rhizosphere) is where microbial interactions navigate the biochemistry of the sea. The study of this microsphere deals with the causal relation enigma between two spatiotemporal scales: the micro-communal interactions and the macro-level of the biogeochemical cycles (Stocker, Science, 338(6107), 628-633, 2012); Segev et al., eLife, 5, e17473, 2016; Seymour et al., Nature Microbiology 2, Article 17065, 2017). This study of communities and ecosystems looks at metabolic interactions and interdependence relations, not focusing on biodiversity as the object of study. Following marine microbial ecology, an epistemic view of interactions and inter-communal relations seems to take the bulk of consideration. In this paper, I ask what it is about the sea that promotes an interactionist epistemic framework that is different than other fields in microbial ecology. Using Helen Longino's interactionist ontology (2020, 2021), I ask whether the sea presents a unique epistemic framework focusing on understanding interactions and interdependence. I look into the insights marine environmental studies may provide to the methodological and conceptual challenges in understanding microbial ecological stability and life cycles. By paralleling marine and soil microbial ecology, I highlight the distinct features of the water column that offer a unique epistemic and methodological framework focused on interactions and interdependence. Exploring microbial ecology at sea, I detail its epistemic advantages in shaping an interactionist theoretical and conceptual framework.},
}

@article {pmid40824088,
year = {2025},
author = {Baty, JJ and Drozdick, AK and Pfeiffer, JK},
title = {Pseudomonas aeruginosa rhamnolipids stabilize human rhinovirus 14 virions.},
journal = {Journal of virology},
volume = {},
number = {},
pages = {e0093125},
doi = {10.1128/jvi.00931-25},
pmid = {40824088},
issn = {1098-5514},
abstract = {Many mammalian viruses encounter bacteria and bacterial molecules over the course of infection. Previous work has shown that the microbial ecology of the gut plays an integral role in poliovirus and coxsackievirus infection, where bacterial glycans can facilitate virus-receptor interactions, enhance viral replication, and stabilize viral particles. However, how airway bacteria alter respiratory viral infection is less understood. Therefore, we investigated whether a panel of airway bacteria affects rhinovirus stability. We found that Pseudomonas aeruginosa, an opportunistic airway pathogen, protects human rhinovirus 14 (HRV14) from acid or heat inactivation. Further investigation revealed that P. aeruginosa rhamnolipids, glycolipids with surfactant properties, are necessary and sufficient for stabilization of rhinovirus virions. However, airway bacteria did not stabilize HRV16, a distantly related rhinovirus with higher capsid stability. Taken together, this work demonstrates that specific molecules produced by an opportunistic airway pathogen can influence a respiratory virus.IMPORTANCEBacteria can enhance viral stability and infection for enteric members of the Picornaviridae, such as poliovirus and coxsackievirus; however, whether bacteria influence respiratory picornaviruses is unknown. In this study, we examined the impacts of airway bacteria on rhinovirus, a major etiological agent of the common cold. We found that Pseudomonas aeruginosa protects human rhinovirus 14 from both acid and heat inactivation through rhamnolipids. Overall, this work demonstrates bacterial effects on respiratory viruses through specific bacterial molecules.},
}

@article {pmid40821451,
year = {2025},
author = {Pignon, E and Schaerli, Y},
title = {Deciphering microbial spatial organization: insights from synthetic and engineered communities.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf107},
pmid = {40821451},
issn = {2730-6151},
abstract = {Microbial communities are frequently organized into complex spatial structures, shaped by intrinsic cellular traits, interactions between community members, initial growth condition or environmental factors. Understanding the mechanisms that drive these spatial patterns is essential for uncovering fundamental principles of microbial ecology and for developing applications. Using genetic engineering and synthetic microbial communities allows us to decipher how specific parameters influence spatial organization. In this review, we highlight recent studies that leverage synthetic microbial communities to deepen our understanding of microbial spatial ecology. We begin by exploring how initial conditions, such as cell density and relative species abundance, influence spatial organization. We then focus on studies that examine the role of individual microbial traits, such as cell shape and motility. Next, we discuss the impact of contact-dependent and long-range interactions, including metabolite exchange and toxin release. Furthermore, we highlight the influence of environmental factors on spatial dynamics. Finally, we address the current limitations of synthetic approaches and propose future directions to bridge the gap between engineered and natural systems.},
}

@article {pmid40816674,
year = {2025},
author = {Hou, N and Yin, X and Wang, W and Huang, X and Fang, Y and Vancov, T and Sardans, J and Tariq, A and Zeng, F and Wiesmeier, M and Peñuelas, J},
title = {Soil carbon stabilization associated with iron-aluminum complexes and microbial communities in paddy.},
journal = {Environmental research},
volume = {},
number = {},
pages = {122601},
doi = {10.1016/j.envres.2025.122601},
pmid = {40816674},
issn = {1096-0953},
abstract = {Rice paddies play a pivotal role in global carbon cycling, offering significant potential for climate change mitigation and sustainable agriculture. This study investigates the synergistic effects of long-term fertilization, iron-aluminum-soil organic carbon (Fe(Al)-SOC) complexes, and microbial communities on soil organic carbon (SOC) stabilization across major rice-growing regions. Black soils exhibited the highest SOC content (43.9 g kg[-1]), surpassing other soils by 41.6-82.6%, suggesting distinct stabilization mechanisms. Key findings include: (1) Fe(Al)-SOC complexes and aromatic carbon (20.4% in black soils) jointly enhanced long-term SOC preservation; (2) CO2 emissions were controlled by nitrogen (N) and phosphorus (P) stoichiometry and physical protection within 0.25-0.5 mm aggregates; (3) Bacterial abundance negatively correlated with SOC and light fraction organic carbon (LFOC) levels, concomitant with reduced CO2 emissions; and (4) N/P fertilization boosted carbonyl-C (recalcitrant pool) while maintaining Alkyl-C (31.7% in brick-red soils), indicating balanced C stabilization. Critically, we demonstrate that Fe/Al-microbial interactions-where Fe/Al complexes modulate microbial composition and activity-are central to SOC storage. These results provide a mechanistic framework for optimizing rice cultivation practices to maximize soil carbon storage through the synergistic management of mineral-organic complexes, microbial ecology, and fertilization strategies.},
}

@article {pmid40815158,
year = {2025},
author = {Berman, HL and McKenney, EA and Roche, CE and Michalski, S and Kwon, SH and Weichel, E and Matson, A and Nichols, LM and Alvarado, S and Horvath, JE and Dunn, RR},
title = {Cooking-class style fermentation as a context for co-created science and engagement.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0266024},
doi = {10.1128/spectrum.02660-24},
pmid = {40815158},
issn = {2165-0497},
abstract = {Fermented foods have been consumed for thousands of years and have been used as a model system to study community succession and other ecological questions. Additionally, cooking classes offer opportunities to learn about food preparation and history. In the present study, scientists and chefs delivered cooking-class style workshops in which participants learned the recipes of one of three fermented foods and the microbial ecology within these foods. Participants prepared jars of chow chow, kimchi, or kombucha to set up experiments to study microbial community succession and pH changes. The fermented foods were also used to test the following hypotheses: that increasing the number of substrates results in increased alpha diversity, and that phylogenetically diverse substrates will lead to greater beta diversity among microbial communities. Microbial communities contained lactic and acetic acid bacteria described previously in fermented foods, and indicator species were identified for cabbage and radish substrates in kimchi. Finally, we qualitatively comment on the experience of developing workshops with chefs and the use of participatory science in these experiments.IMPORTANCEThe present study demonstrates the utility of using fermented foods as an inexpensive and effective tool to investigate ecological phenomena and engage the public in microbiology and ecology through cooking-class style workshops. We also model a creative, interdisciplinary collaboration between scientists and chefs.},
}

@article {pmid40812185,
year = {2025},
author = {Common, JE and Payne, RP},
title = {Microbial Makeover: Skin microbiome reset after stem cell transplantation.},
journal = {Cell host & microbe},
volume = {33},
number = {8},
pages = {1318-1320},
doi = {10.1016/j.chom.2025.07.014},
pmid = {40812185},
issn = {1934-6069},
abstract = {Inborn errors of immunity disrupt host-microbe interactions. In this issue of Cell Host & Microbe, Che et al.[1] examine DOCK8-deficient individuals undergoing stem cell transplantation and show that immune reconstitution rebalances the skin microbiome, underscoring the central role of immunity in shaping cutaneous microbial ecology.},
}

@article {pmid40809134,
year = {2024},
author = {Casey, J and Bennion, B and D'haeseleer, P and Kimbrel, J and Marschmann, G and Navid, A},
title = {Transporter annotations are holding up progress in metabolic modeling.},
journal = {Frontiers in systems biology},
volume = {4},
number = {},
pages = {1394084},
pmid = {40809134},
issn = {2674-0702},
abstract = {Mechanistic, constraint-based models of microbial isolates or communities are a staple in the metabolic analysis toolbox, but predictions about microbe-microbe and microbe-environment interactions are only as good as the accuracy of transporter annotations. A number of hurdles stand in the way of comprehensive functional assignments for membrane transporters. These include general or non-specific substrate assignments, ambiguity in the localization, directionality and reversibility of a transporter, and the many-to-many mapping of substrates, transporters and genes. In this perspective, we summarize progress in both experimental and computational approaches used to determine the function of transporters and consider paths forward that integrate both. Investment in accurate, high-throughput functional characterization is needed to train the next-generation of predictive tools toward genome-scale metabolic network reconstructions that better predict phenotypes and interactions. More reliable predictions in this domain will benefit fields ranging from personalized medicine to metabolic engineering to microbial ecology.},
}

@article {pmid40804729,
year = {2025},
author = {Rezaei, Z and Amoozegar, MA and Moghimi, H},
title = {Innovative approaches in bioremediation: the role of halophilic microorganisms in mitigating hydrocarbons, toxic metals, and microplastics in hypersaline environments.},
journal = {Microbial cell factories},
volume = {24},
number = {1},
pages = {184},
pmid = {40804729},
issn = {1475-2859},
abstract = {Hypersaline environments are ecologically, industrially, and scientifically important because they host unique extremophiles used in biotechnology, bioremediation, and enzyme production. These habitats are seriously threatened by three common contaminants: hydrocarbon pollutants, toxic metals, and microplastics. In particular, the remediation of hazardous substances under extreme conditions is challenging due to limited accessibility and bioavailability of pollutants, harsh physicochemical conditions, reduced microbial abundance and diversity, and instability of enzymes. Halophiles are extremophilic microorganisms that thrive in high-salt environments, exhibiting notable metabolic diversity and resilience, and play a critical role in overcoming these challenges. Their ability to degrade recalcitrant pollutants makes them valuable for bioremediation in contaminated hypersaline ecosystems. Advancements in engineering tools and synthetic biology have revolutionized halophile-based biotechnologies. Techniques like gene editing and recombinant DNA have facilitated the precise modification of halophiles, enabling them to efficiently target and degrade toxic compounds and significantly improve their bioremediation potential. Furthermore, with the rapid progress of omics approaches, identifying new halophilic microbes, their enzymes, and their metabolic pathways is now becoming possible. Despite these advances, challenges remain in optimizing genetically tractable strains, ensuring biosafety, and understanding microbial ecology for scalable, safe, and cost-effective applications. This review provides an overview of halophilic and halotolerant microorganisms, their habitat, and their unique adaptations to saline and hypersaline environments. Key pollutants threatening extreme environments, as well as the ability of halophiles to degrade them, are also discussed. Additionally, it highlights current challenges, including the introduction of engineered halophiles into natural ecosystems, scaling up bioprocesses, cost management, and regulatory concerns, and explains future perspectives to address these issues. Ultimately, it emphasizes the need for advanced research to fully harness the potential of halophiles in sustainable bioremediation.},
}

@article {pmid40804168,
year = {2025},
author = {Sun, L and Wen, X and Li, L and Li, M and Xing, X and Zhang, Z and Dong, C},
title = {Formation and sustenance mechanism of bacterial diversity in nutrient-deficient environment of indoor stadium.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {29685},
pmid = {40804168},
issn = {2045-2322},
abstract = {Bacterial diversity has been found in indoor stadiums which can be considered as a specific nutrient-deficient environment (NDE), it remains a mystery and opens to new ideas why the bacterial diversity can be formed and maintained in NDE of indoor stadiums, since it is obvious to violate the famous competitive exclusion principle (CEP) in ecology. In the article, five most common genera, Pseudomonas, Acinetobacter, Exiguobacterium, Sphingobacterium, Chryseobacterium in indoor stadiums were selected and periodically sampled to supervise the dynamic characteristics of bacterial community. Based on quorum sensing (QS) and non-monotonic interspecific interaction (NMII) in combination with microbial ecology, clustering analysis and experimental observation, a new hypothesis was put forward to elucidate QS and NMII of substrate location information (SLI) mechanism driving bacterial community succession with high diversity in NDE of indoor stadium. A valid cellular automation (CA) model was derived from assumptions directly, and the CA simulation sufficiently proved that QS and NMII of SLI can effectively weaken interspecific competition to drive the spatiotemporal succession of bacterial community in NDE of indoor stadium towards a climax community with high richness and evenness, namely bacterial diversity. The succession mechanism confirmed by CA simulation can set up a theoretical framework for comprehensive apprehension about ecological effect of QS with NMII of SLI sharing on formation and sustenance of bacterial diversity in NDE of indoor stadium.},
}

@article {pmid40802392,
year = {2025},
author = {Shaikenova, K and Issabekova, S and Sadenova, M and Omarova, K and Uskenov, R},
title = {Synergistic impact of integrated mechanical, physical, and chemical disinfection on microbial ecology and morphophysiological development in dairy calves.},
journal = {Brazilian journal of biology = Revista brasleira de biologia},
volume = {85},
number = {},
pages = {e295880},
doi = {10.1590/1519-6984.295880},
pmid = {40802392},
issn = {1678-4375},
abstract = {The article presents the results of studies of the influence of the complex process of cleaning and disinfection of the dispensary using mechanical, physical and chemical methods on the growth and development of calves of the dairy period. The dispensary for calves is divided into two rooms, where there were animals of the control and experimental groups selected by the method of pairs of analogues in the same feeding and maintenance conditions. Studies before the treatment of rooms for calves showed a massive growth of bacilli and bacteria - 100%, mold fungi - 80%, yeast - 20%, actinomycetes - 80%. After processing the room for calves of the experimental group, the number of microorganisms during mechanical treatment, microbial contamination decreased by 31%, during physical treatment by 62%, and during chemical treatment by 95%. Monitoring of live weight, exterior features of calves showed that the live weight of calves of the experimental group of monthly calves averaged 58.9 kg, and the control group 58.6 kg, respectively. In the second month, the live weight of the experimental was 7.5 kg or 9.1% more than the control. And also for all body measurements, the experimental group exceeded the control group by an average of 10%. The results of the study of hematological parameters showed that in the experimental group they are all within the normal range, whereas in the control group the content of leukocytes is 13.2 * 109 liters, lymphocytes are 7.7 * 109 liters higher than normal, which indicates inflammatory processes in the body of calves.},
}

@article {pmid40795028,
year = {2025},
author = {Park, HS and Chavarria, X and Shatta, A and Kang, D and Oh, S and Choi, DY and Choi, JH and Kim, M and Cho, YH and Yi, MH and Kim, JY},
title = {Distinct microbial communities of drain flies (Clogmia albipunctata) across sites with differing human influence.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnaf078},
pmid = {40795028},
issn = {1574-6968},
abstract = {Drain flies (Clogmia albipunctata) are insects that thrive in humid urban environments such as bathrooms drains and sewage systems. While their role in pathogen transmission has been suggested, little is known about their microbiome or ecology in non-clinical contexts. Using 16S rRNA gene metabarcoding, we characterized the bacterial communities of drain flies from three locations in South Korea, public bathrooms from a college in Seoul, a rural port in Ulleungdo island, and a highly frequented public park in Yeouido. In total, we obtained 221 families and 1 474 features. We found significant differences in microbiome composition and diversity as well as a small core microbiome shared among locations, with environmental bacteria such as Pseudomonas and Ralstonia being the dominant taxa across samples. The majority of the detected amplicon sequence variants (ASV) were not shared among locations. These findings suggest drain fly transport a location-specific environmental bacteria. Notably, we also identified ASVs of potential clinical relevance, including Mycobacterium, Acinetobacter baumanii, Providencia, and Nocardia. This is the first metagenomic insight into the microbiome of this species and adds to a renewed interest in the role that non-hematophagous insects play in urban microbial ecology and the spread of microbes.},
}

@article {pmid40793771,
year = {2025},
author = {Bhandari, R and Wong, AC-N and Lee, JC and Boyd, A and Shelby, K and Ringbauer, J and Kang, DS},
title = {Microbiome composition and co-occurrence dynamics in wild Drosophila suzukii are influenced by host crop, fly sex, and sampling location.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0260824},
doi = {10.1128/spectrum.02608-24},
pmid = {40793771},
issn = {2165-0497},
abstract = {Microbial control of insect pests offers promising alternatives to traditional pesticides. However, the microbial communities and factors influencing these communities within insect hosts remain poorly understood. This study examined the whole-body bacterial communities in wild Drosophila suzukii, commonly known as spotted wing Drosophila (SWD). Fly samples were collected from two farms growing wild Himalayan blackberries near blueberry crops, one blackberry farm, and one elderberry farm across four locations in the United States. Our analyses showed significant differences in microbial communities in flies across various host crops and sampling locations. We identified co-occurring bacterial genera, dominated by Gluconobacter and Morganella, and the overall microbiome was distinct from those found in laboratory-grown flies. Our findings suggest that the host crop, sex of the fly, sampling location, and their interactions play a crucial role in shaping microbial communities in SWD, indicating the influence of various ecological interactions. While no significant differences in microbiome composition were observed between male and female flies, network analysis revealed distinct sex-specific microbial co-occurrence patterns. Female flies displayed a more stable and interconnected microbial network than male flies, suggesting that sex-specific factors might influence bacterial interactions. Interestingly, the most abundant microbial taxa were not necessarily the most connected in the networks, showing that less abundant taxa may also play a significant role in shaping the fly microbiome. This study underscores the complexity of microbial ecology in SWD and highlights the necessity of considering these dynamics when developing pest management strategies in agriculture.IMPORTANCEStudies on the microbiome of spotted wing Drosophila (SWD) have primarily focused on laboratory-reared flies in controlled environments and fed artificial diets. In contrast, we examined microbial communities in wild flies from various host crops across four locations in the United States. Our findings show that these communities are distinct from those of laboratory-grown flies and are influenced by the fly's sex, host crop, geographical location, and their interactions. Our study identifies several dominant bacterial genera across samples, suggesting that these may represent the core microbial communities in wild SWD. Given that microbial communities influence physiological activities in SWD, manipulating the microbiome may have either a positive or negative impact on insect fitness. This study enhances our understanding of microbial dynamics in understudied wild SWD populations, emphasizing the importance of these dynamics in effective integrated pest management strategies.},
}

@article {pmid40791242,
year = {2025},
author = {Song, HC and Elsheikha, H and Yang, T and Cong, W},
title = {Global spillover of land-derived microbes to Ocean hosts: Sources, transmission pathways, and one health threats.},
journal = {Environmental science and ecotechnology},
volume = {27},
number = {},
pages = {100603},
pmid = {40791242},
issn = {2666-4984},
abstract = {Terrestrial pathogens are increasingly being detected in marine organisms, raising concerns about ecosystem sustainability, biodiversity loss, and threats to human health. Over the past two decades, reports of microbial contaminants crossing from land to sea have increased, suggesting shifts in pathogen ecology driven by environmental changes and human activities. Pathogens originating on land can spread, adapt, and persist in marine environments, infecting a wide range of hosts and potentially re-entering terrestrial environments. Despite growing recognition of this issue, a comprehensive understanding of the distribution, diversity, and transmission pathways of these pathogens in marine ecosystems remains limited. In this Review, we provide a global analysis of terrestrial pathogen contamination in marine animal populations. Drawing from pathogen detection data across 66 countries, we used phylogenetic methods to infer land-to-sea transmission routes. We identified 179 terrestrial pathogen species, including 38 bacterial, 39 viral, 80 parasitic, and 22 fungal species, in 20 marine host species. Terrestrial pathogens are not only widespread but also highly diverse in marine ecosystems, highlighting the frequency and ecological significance of cross-system microbial exchange. By revealing the scale and complexity of land-to-sea pathogen flow, we show that climate change, pollution, and other anthropogenic pressures may intensify pathogen spillover events, with potential feedback effects on terrestrial systems. This highlights the urgent need for integrated surveillance and policy frameworks acknowledging the interconnectedness of terrestrial and marine health. Our work advocates a One Health approach to microbial ecology, stressing the need to safeguard marine and human populations from emerging cross-system threats.},
}

@article {pmid40787310,
year = {2025},
author = {S, S and Nayak, P and Pal, K},
title = {Exploring the Microbial Peptides Derived from the Human Gut Microbiota to Regulate Class B GPCRS Using an In Silico Approach.},
journal = {ACS omega},
volume = {10},
number = {30},
pages = {33270-33287},
pmid = {40787310},
issn = {2470-1343},
abstract = {Class B G-protein coupled receptors (GPCRs) are significant therapeutic recipients in cardiovascular, neurological, and metabolic diseases. The human gut microbiome is a complex microbial ecology recently identified as a possible source of bioactive peptides that control host physiological functions. Candidate peptides were found using advanced bioinformatics tools including sequence homology analysis, structure modeling, and molecular docking. These peptides were then evaluated for their binding affinity and potential functional regulation of the GPCR activity. Molecular dynamics simulations offered additional insights regarding the stability and interaction diversity of peptide-receptor complexes, highlighting receptor conformational state of G-protein interaction. The findings identify unique microbial peptides capable of influencing class B GPCR function, providing important insights into microbiome-host interactions and therapeutic potential. This study emphasizes the gut microbiome's previously untapped potential as a source of GPCR modulators, opening up new avenues for microbiome-driven therapy approaches for metabolic and endocrine disorders.},
}

@article {pmid40783766,
year = {2025},
author = {Son, SJ and Wu, X and Roh, HW and Cho, YH and Hong, S and Nam, YJ and Hong, CH and Park, S},
title = {Distinct gut microbiota profiles and network properties in older Korean individuals with subjective cognitive decline, mild cognitive impairment, and Alzheimer's disease.},
journal = {Alzheimer's research & therapy},
volume = {17},
number = {1},
pages = {187},
pmid = {40783766},
issn = {1758-9193},
support = {HR21C1003//the Ministry of Health and Welfare, Republic of Korea/ ; HR21C1003//the Ministry of Health and Welfare, Republic of Korea/ ; RS-2019-NR040055//National Research Foundation of Korea (NRF), funded by the Ministry of Science and ICT/ ; RS-2019-NR040055//National Research Foundation of Korea (NRF), funded by the Ministry of Science and ICT/ ; RS-2023-00208567//National Research Foundation of Korea (NRF), funded by the Ministry of Science and ICT/ ; },
abstract = {BACKGROUND: The gut microbiota may influence cognitive function via the gut-brain axis. This study aimed to investigate the gut microbiota profiles of 346 older Korean individuals with subjective cognitive decline but no symptoms (SCD), mild cognitive impairment (MCI), or Alzheimer’s disease (AD).

METHODS: Participants aged an average of 72.3 years underwent the profiling of cognitive function, amyloid-β (Aβ) deposition, apolipoprotein E (APOE) genetic variants, depression status, nutrition, and lifestyles. Human fecal bacterial FASTA/Q data (SCD, n = 24; MCI, n = 246; AD, n = 76) were processed using Quantitative Insights Into Microbial Ecology 2 (QIIME2) tools. Operational taxonomic units (OTUs) and their counts were assigned with the National Center for Biotechnology Information Basic Local Alignment Search Tool (BLAST). Machine learning models (random forest and XGBoost) identified key bacterial taxa differentiating groups.

RESULTS: Redundancy analysis revealed associations between gut microbiota composition and cognitive function, age, gender, nutritional status, and body mass index. All three groups shared 71 common bacterial genera with distinct taxonomic profiles across cognitive states. The AD group uniquely harbored Hominisplanchenecus and Lentihominibacter, while the SCD group exclusively contained Anaerosacchariphilus and Anaerobutyricum. Phascolarctobacterium was shared between the AD and MCI groups, and Anaerostipes between the MCI and SCD groups. The SCD group showed significantly elevated Bifidobacterium catenulatum, Anaerobutyricum hallii, and Anaerostipes hadrus. Network analysis demonstrated greater microbial community complexity in the SCD group compared to the MCI and AD groups. Gut bacteria correlated with depression, Aβ deposition, APOE status, and cognitive scores.

CONCLUSIONS: This study identified distinct gut microbiota profiles associated with different stages of cognitive impairment in older Korean adults. The observed associations between gut bacterial composition and cognitive function, neurodegeneration biomarkers, and related clinical factors suggest potential relationships that warrant further investigation. These findings contribute to the growing understanding of gut-brain interactions in cognitive aging.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13195-025-01820-9.},
}

@article {pmid40781808,
year = {2025},
author = {Jalili, M and Mazloomirad, F and Jalilian, FA},
title = {The effect of bacteriophage in oral health: developing microbial ecology and emerging potential therapeutic target.},
journal = {Future microbiology},
volume = {20},
number = {12},
pages = {807-816},
pmid = {40781808},
issn = {1746-0921},
mesh = {Humans ; *Bacteriophages/physiology ; *Phage Therapy/methods ; *Mouth/microbiology/virology ; *Oral Health ; Biofilms/growth & development ; Microbiota ; *Bacteria/virology ; *Periodontal Diseases/therapy/microbiology ; },
abstract = {The human oral cavity provides a convenient entry point for viruses and bacteria from the environment. The role of these viral communities remains unclear; however, many of them are bacteriophages that may actively influence the ecology of bacterial communities within the oral cavity. Bacteriophages are abundant and influential components of the oral microbiome and play a crucial role in shaping microbial ecology in oral health. They dynamically interact with oral bacteria, influencing biofilm formation, bacterial population structure, antibiotic resistance, and metabolic functions, thereby affecting disease progression and microbial community dynamics. Recent advances in studies have increased our understanding of oral phages and their impact on the amelioration of oral diseases such as periodontal disease. Nowadays, phage therapy has been identified as a potential therapeutic approach for major oral pathogens. The advantages of phage therapy include low toxicity, high specificity, the ability to penetrate biofilm structures, and the ability to replicate continuously in pathogenic bacteria. Hence, the aim of this review is to provide a comprehensive study about the role of bacteriophages as potential therapeutic target in oral health. Additionally, further studies are necessary to evaluate the role of phages in oral health and to develop safe and effective clinical applications in dentistry.},
}

Humans
*Bacteriophages/physiology
*Phage Therapy/methods
*Mouth/microbiology/virology
*Oral Health
Biofilms/growth & development
Microbiota
*Bacteria/virology
*Periodontal Diseases/therapy/microbiology

@article {pmid40780001,
year = {2025},
author = {Grimard-Conea, M and Reyes, EV and Marchand-Senécal, X and Faucher, SP and Prévost, M},
title = {In situ dosing of monochloramine in a hospital hot water system results in drastic microbial communities changes.},
journal = {The Science of the total environment},
volume = {997},
number = {},
pages = {180204},
doi = {10.1016/j.scitotenv.2025.180204},
pmid = {40780001},
issn = {1879-1026},
abstract = {Understanding changes in microbial composition under selective pressures is crucial to assess the emergence of resistant taxa and the survival of drinking water-associated pathogens. This study evaluated the impact of in situ monochloramine disinfection in a hospital hot water system on bacterial (16S rRNA gene amplicon sequencing, 112 samples) and eukaryotic communities (18S rRNA gene amplicon sequencing, 103 samples), and on general microbial measurements (180 samples), including adenosine triphosphate (ATP) and flow cytometry counts. After the onset of treatment, ATP decreased by 1.2- and 3.5-fold, and total cell counts (TCC) dropped by 1- and 2-log at distal and system sites, respectively. During the dosage interruption (27-day), TCC rebounded to pre-treatment levels, but viability percentage decreased, indicating that cells were predominantly damaged. Low-use sites (e.g., showerheads) showed elevated ATP (>15 pg/mL) and TCC (10[5]-10[6] cells/L). Monochloramine drastically altered bacterial and eukaryotic communities. Alpha-diversity showed increased amplicon sequence variant richness during treatment, driven by new, low-abundant taxa, while Beta-diversity revealed distinct shifts in community composition over time, with tight or looser clusters corresponding to each treatment phase. Post-treatment, temporal and spatial heterogeneity was evident across distal sites, while elevated temperatures, consistent flow, and higher monochloramine concentrations in the hot water system resulted in more uniform communities at system sites. Additionally, the persistence of potential pathogenic strains belonging to Legionella and Mycobacterium genera highlights the value of comprehensive risk assessments. These findings emphasize the need to understand microbial shifts under disinfection stress and their public health implications, offering new insights into how treatment interventions shape microbial ecology and pathogen dynamics.},
}

@article {pmid40777436,
year = {2025},
author = {Shrestha Gurung, BD and Rayamajhi, M and Maharjan, N and Do, T and Bhandari, D and Yadav, R and Aryal, S and Gnimpieba, EZ},
title = {Forecasting Urban Wastewater Microbiome Dynamics Using a Digital Twin Framework.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {40777436},
issn = {2692-8205},
support = {P20 GM103443/GM/NIGMS NIH HHS/United States ; },
abstract = {Urban wastewater microbiomes are complex and temporally dynamic, offering valuable insight into community-scale microbial ecology and potential public health trends. However, existing wastewater-based studies often remain descriptive, lacking tools for predictive modeling. In this study, we introduce a digital twin framework that forecasts microbial abundance trajectories in urban wastewater using an interpretable generative model, Q-net. Trained on a 30-week longitudinal metagenomic dataset from seven wastewater treatment plants, the model captures temporal microbial dynamics with high fidelity (R 2 > 0.97 for key taxa; R 2 = 0.998 at the final timepoint). Beyond accurate forecasting, Q-net provides transparent model structure through conditional inference trees and enables simulation of realistic microbial trends under hypothetical scenarios. This work demonstrates the potential of digital twins to move wastewater microbiome studies from static snapshots to dynamic, predictive systems, with broad implications for environmental monitoring and microbial ecosystem modeling.},
}

@article {pmid40777262,
year = {2025},
author = {Weiss, AS and Santos-Santiago, JA and Keenan, O and Smith, AB and Knight, M and Zackular, JP and Tamayo, R},
title = {Enterococcus faecalis modulates phase variation in Clostridioides difficile.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {40777262},
issn = {2692-8205},
support = {R01 AI143638/AI/NIAID NIH HHS/United States ; R01 AI188648/AI/NIAID NIH HHS/United States ; },
abstract = {To adapt and persist in the gastrointestinal tract, many enteric pathogens, including Clostridioides difficile, employ strategies such as phase variation to generate phenotypically heterogeneous populations. Notably, the role of the gut microbiota and polymicrobial interactions in shaping population heterogeneity of invading pathogens has not been explored. Here, we show that Enterococcus faecalis, an opportunistic pathogen that thrives in the inflamed gut during C. difficile infection, can impact the phase variable CmrRST signal transduction system in C. difficile. The CmrRST system controls multiple phenotypes including colony morphology, cell elongation, and cell chaining in C. difficile. Here we describe how interactions between E. faecalis and C. difficile on solid media lead to a marked shift in C. difficile phenotypes associated with phase variation of CmrRST. Specifically, E. faecalis drives a switch of the C. difficile population to the cmr-ON state leading to chaining and a rough colony morphology. This phenomenon preferentially occurs with E. faecalis among the enterococci, as other enterococcal species do not show a similar effect, suggesting that the composition of the polymicrobial environment in the gut is likely critical to shaping C. difficile population heterogeneity. Our findings shed light on the complex role that microbial ecology and polymicrobial interactions can have in the phenotypic heterogeneity of invading pathogens.},
}

@article {pmid40771314,
year = {2025},
author = {Wang, L and Wang, H and Wu, J and Ji, C and Wang, Y and Gu, M and Li, M and Yang, H},
title = {Gut microbiota and metabolomics in metabolic dysfunction-associated fatty liver disease: interaction, mechanism, and therapeutic value.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1635638},
pmid = {40771314},
issn = {2235-2988},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Metabolomics ; Dysbiosis ; Liver/metabolism/pathology ; Animals ; *Fatty Liver/metabolism/therapy/microbiology ; *Non-alcoholic Fatty Liver Disease/metabolism/therapy/microbiology ; Biomarkers ; Precision Medicine ; },
abstract = {The global epidemic of Metabolic dysfunction-associated fatty liver disease (MAFLD) urgently demands breakthroughs in precision medicine strategies. Its pathogenesis centers on the cascade dysregulation of the gut microbiota-metabolite-liver axis: microbial dysbiosis drives hepatic lipid accumulation and fibrosis by suppressing short-chain fatty acid synthesis, activating the TLR4/NF-κB inflammatory pathway, and disrupting bile acid signaling. Metabolomics further reveals characteristic disturbances including free fatty acid accumulation, aberrantly elevated branched-chain amino acids (independently predictive of hepatic steatosis), and mitochondrial dysfunction, providing a molecular basis for disease stratification. The field of precision diagnosis is undergoing transformative innovation-multi-omics integration combined with AI-driven analysis of liver enzymes and metabolic biomarkers enables non-invasive, ultra-high-accuracy staging of fibrosis. Therapeutic strategies are shifting towards personalization: microbial interventions require matching to patient-specific microbial ecology, drug selection necessitates efficacy and safety prediction, and synthetically engineered "artificial microbial ecosystems" represent a cutting-edge direction. Future efforts must establish a "multi-omics profiling-AI-powered dynamic modeling-clinical validation" closed-loop framework to precisely halt MAFLD progression to cirrhosis and hepatocellular carcinoma by deciphering patient-specific mechanisms.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Metabolomics
Dysbiosis
Liver/metabolism/pathology
Animals
*Fatty Liver/metabolism/therapy/microbiology
*Non-alcoholic Fatty Liver Disease/metabolism/therapy/microbiology
Biomarkers
Precision Medicine

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

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

@article {pmid40704792,
year = {2025},
author = {Zhang, M and Zhang, C and Ramos, A and Whitaker, RJ and Whiteley, M},
title = {Conserved cross-domain protein-to-mRNA ratios enable proteome prediction in microbes.},
journal = {mBio},
volume = {16},
number = {8},
pages = {e0141125},
pmid = {40704792},
issn = {2150-7511},
support = {GBMF9195//Gordon and Betty Moore Foundation/ ; R01 DE023193/DE/NIDCR NIH HHS/United States ; R01DE020100/DE/NIDCR NIH HHS/United States ; R01 DE020100/DE/NIDCR NIH HHS/United States ; R01DE023193/DE/NIDCR NIH HHS/United States ; },
abstract = {UNLABELLED: Microbial communities are often studied by measuring gene expression (mRNA levels), but translating these data into functional insights is challenging because mRNA abundance does not always predict protein levels. Here, we present a strategy to bridge this gap by deriving gene-specific RNA-to-protein conversion factors that improve the prediction of protein abundance from transcriptomic data. Using paired mRNA-protein data sets from seven bacteria and one archaeon, we identified orthologous genes where mRNA levels poorly predicted protein abundance, yet each gene's protein-to-RNA ratio was consistent across these diverse organisms. Applying the resulting conversion factors to mRNA levels dramatically improved protein abundance predictions, even when the conversion factors were obtained from distantly related species. Remarkably, conversion factors derived from bacteria also enhanced protein prediction in an archaeon, demonstrating the robustness of this approach. This cross-domain framework enables more accurate functional inference in microbiomes without requiring organism-specific proteomic data, offering a powerful new tool for microbial ecology, systems biology, and functional genomics.

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

@article {pmid40701356,
year = {2025},
author = {Hu, L and Ye, Y and Li, Y and Tan, X and Liu, X and Zhang, T and Wang, J and Du, Z and Ye, M},
title = {Bacteria-algae synergy in carbon sequestration: Molecular mechanisms, ecological dynamics, and biotechnological innovations.},
journal = {Biotechnology advances},
volume = {83},
number = {},
pages = {108655},
doi = {10.1016/j.biotechadv.2025.108655},
pmid = {40701356},
issn = {1873-1899},
mesh = {*Biotechnology/methods ; *Microalgae/metabolism ; *Carbon Sequestration ; *Bacteria/metabolism ; Carbon Dioxide/metabolism ; Photosynthesis ; Carbon/metabolism ; },
abstract = {Rising atmospheric CO2 levels require innovative strategies to increase carbon sequestration. Bacteria-algae interactions, as pivotal yet underexplored drivers of marine and freshwater carbon sinks, involve multiple mechanisms that amplify CO2 fixation and long-term storage. This review systematically describes the synergistic effects of bacteria-algae consortia spanning both microalgae (e.g., Chlorella vulgaris and Phaeodactylum tricornutum) and macroalgae (e.g., Macrocystis and Laminaria) on carbon sequestration. These effects include (1) molecular-level regulation (e.g., signal transduction via N-acyl-homoserine lactones (AHLs), and horizontal gene transfer), (2) ecological facilitation of recalcitrant dissolved organic carbon (RDOC) formation, and (3) biotechnological applications in wastewater treatment and bioenergy production. We highlight that microbial crosstalk increases algal photosynthesis by 20-40 % and contributes to 18.9 % of kelp-derived RDOC storage. Furthermore, engineered systems integrating algal-bacterial symbiosis achieve greater than 80 % nutrient removal and a 22-35 % increase in CO2 fixation efficiency (compared with axenic algal systems), demonstrating their dual role in climate mitigation and a circular economy. This review is the first to integrate molecular mechanisms (e.g., quorum sensing), ecological carbon transformation processes (e.g., the formation of RDOC), and applications in synthetic biology (e.g., CRISPR-engineered consortia) into a unified framework. Moreover, the novel strategy "microbial interaction network optimization" for enhancing carbon sinks is proposed. However, scalability challenges persist, including light limitations in photobioreactors and the ecological risks of synthetic consortia. By bridging microbial ecology with synthetic biology, this work provides a roadmap for harnessing bacteria-algae synergy to achieve carbon neutrality.},
}

*Biotechnology/methods
*Microalgae/metabolism
*Carbon Sequestration
*Bacteria/metabolism
Carbon Dioxide/metabolism
Photosynthesis
Carbon/metabolism

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

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

@article {pmid40600721,
year = {2025},
author = {Peters, DI and Shin, IJ and Deever, AN and Kaspar, JR},
title = {Design, development, and validation of new fluorescent strains for studying oral streptococci.},
journal = {Microbiology spectrum},
volume = {13},
number = {8},
pages = {e0016825},
pmid = {40600721},
issn = {2165-0497},
support = {P30 CA016058/CA/NCI NIH HHS/United States ; R03 DE031766/DE/NIDCR NIH HHS/United States ; R03DE031766/DE/NIDCR NIH HHS/United States ; },
mesh = {Biofilms/growth & development ; *Luminescent Proteins/genetics/metabolism ; Humans ; Streptococcus gordonii/genetics ; *Streptococcus/genetics/metabolism/physiology ; *Mouth/microbiology ; Streptococcus mutans/genetics/metabolism ; Green Fluorescent Proteins/genetics/metabolism ; Red Fluorescent Protein ; Streptococcus sanguis/genetics ; Microscopy, Confocal ; },
abstract = {Bacterial strains that are genetically engineered to constitutively produce fluorescent proteins have aided our study of bacterial physiology, biofilm formation, and interspecies interactions. Here, we report on the construction and utilization of new strains that produce the blue fluorescent protein mTagBFP2, the green fluorescent protein sfGFP, and the red fluorescent protein mScarlet-I3 in species Streptococcus gordonii, Streptococcus mutans, and Streptococcus sanguinis. Gene fragments, developed to contain the constitutive promoter Pveg, the fluorescent gene of interest, as well as aad9, providing resistance to the antibiotic spectinomycin, were inserted into selected open reading frames on the chromosome that were both transcriptionally silent and whose loss caused no measurable changes in fitness. All strains, except for sfGFP in S. sanguinis, were validated to produce a detectable and specific fluorescent signal. Individual stains, along with extracellular polymeric substances (EPS) within biofilms, were visualized and quantified through either widefield or super-resolution confocal microscopy approaches. Finally, to validate the ability to perform single-cell-level analysis using the strains, we imaged and analyzed a triculture mixed-species biofilm of S. gordonii, S. mutans, and S. sanguinis grown with and without the addition of human saliva. Quantification of the loss in membrane integrity using a SYTOX dye revealed that all strains had increased loss of membrane integrity with water or human saliva added to the growth media, but the proportion of the population stained by the SYTOX dye varied by species. In all, these fluorescent strains will be a valuable resource for the continued study of oral microbial ecology.IMPORTANCEStreptococci are among the earliest colonizers of the soft and hard tissues of the oral cavity and are contributors to the oral health status of the host, with involvement in dental caries, endodontic infections, periodontal disease, and the development of oral cancer. Strains genetically modified to produce fluorescent proteins that can be either visualized through microscopy imaging or quantified by their specific fluorescent intensity signal are critical tools toward the study of individual or mixed-species cultures. Our report here details the development and testing of several new strains of fluorescent oral streptococci that can be utilized in the study of microbial ecology, increasing both the availability of tools and documenting experimental approaches toward in vitro assay applications such as the study of intermicrobial interactions.},
}

Biofilms/growth & development
*Luminescent Proteins/genetics/metabolism
Humans
Streptococcus gordonii/genetics
*Streptococcus/genetics/metabolism/physiology
*Mouth/microbiology
Streptococcus mutans/genetics/metabolism
Green Fluorescent Proteins/genetics/metabolism
Red Fluorescent Protein
Streptococcus sanguis/genetics
Microscopy, Confocal

@article {pmid40568985,
year = {2025},
author = {Zhao, J and Brandt, G and Gronniger, JL and Wang, Z and Li, J and Hunt, DE and Rodriguez-R, LM and Hatt, JK and Konstantinidis, KT},
title = {Quantifying the contribution of the rare biosphere to natural disturbances.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
pmid = {40568985},
issn = {1751-7370},
support = {OCE 1416673 and DEB 1831582//US National Science Foundation/ ; ICER 2033934, DEB 2224819//US National Science Foundation/ ; },
mesh = {Metagenome ; *Ecosystem ; *Microbiota ; },
abstract = {Understanding how populations respond to disturbances represents a major goal for microbial ecology. While several hypotheses have been advanced to explain microbial community compositional changes in response to disturbance, appropriate data to test these hypotheses is scarce, due to the challenges in delineating rare vs. abundant taxa and generalists vs. specialists, a prerequisite for testing the theories. Here, we operationally define these two key concepts by employing the patterns of coverage of a (target) genome by a metagenome to identify rare populations, and by borrowing the proportional similarity index from macroecology to identify generalists. We applied these concepts to time-series (field) metagenomes from the Piver's Island Coastal Observatory to establish that coastal microbial communities are resilient to major perturbations such as tropical cyclones and (uncommon) cold or warm temperature events, in part due to the response of rare populations. Therefore, these results provide support for the insurance hypothesis [i.e. the rare biosphere has the buffering capacity to mitigate the effects of disturbance]. Additionally, generalists appear to contribute proportionally more than specialists to community adaptation to perturbations like warming, supporting the disturbance-specialization hypothesis [i.e. disturbance favors generalists]. Several of these findings were also observed in replicated laboratory mesocosms that aimed to simulate disturbances such as a rain-driven washout of microbial cells and a labile organic matter release from a phytoplankton bloom. Taken together, our results advance understanding of the mechanisms governing microbial population dynamics under changing environmental conditions and have implications for ecosystem modeling.},
}

Metagenome
*Ecosystem
*Microbiota

@article {pmid40556886,
year = {2025},
author = {Klein, ML and Erikson, CB and McCabe, CJ and Huang, L and Rodrigues, JLM and Mitloehner, FM},
title = {Limited effects of tannin supplementation on the dairy cattle fecal microbiome with modulation of metabolites.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1570127},
pmid = {40556886},
issn = {1664-302X},
abstract = {Tannins are plant secondary metabolites that bind organic carbon (C) and nitrogen (N), potentially altering substrate bioavailability for enteric fermentation in ruminants. This interaction may reduce greenhouse gas (GHG) emissions and influence nitrogen partitioning. Given tannins' resistance to ruminal degradation and persistence through the gastrointestinal tract, this study investigated the effects of a tannin-based feed additive on fecal microbial diversity, fecal chemical composition, and GHG emissions. Twenty-four early- to mid-lactation dairy cows were randomized to receive either a tannin-based feed additive (TRT; containing condensed and hydrolyzable tannins from Schinopsis quebracho-colorado [Schltdl.]) or a control diet (CON) for 64 days. Cows were blocked by parity, dry matter intake, milk yield, body weight, and days in milk. Fecal samples were collected on days 0, 16, 32, and 64 and analyzed using 16S rRNA gene amplicon sequencing. Fecal C, N, and indole-3-lactate were measured, and GHG emissions (N2O, CH4, CO2) were assessed via 14-day laboratory incubation. A total of 1,538 amplicon sequence variants were identified, with Firmicutes as the dominant phylum. Fecal phylogenetic diversity showed a significant treatment × day interaction (p < 0.01), with TRT cows exhibiting reduced microbial diversity from day 16 to 64. Fecal C and N concentrations were significantly lower (p < 0.01) in TRT cows on day 16, while indole-3-lactate levels were higher on day 64 (p = 0.02). GHG emissions did not differ significantly between treatments. The tannin-based feed additive influenced fecal microbial community structure and select chemical parameters but did not significantly affect GHG emissions from feces. These findings suggest that dietary tannins may modulate gut microbial ecology with minimal impact on downstream manure-related emissions.},
}

@article {pmid40184706,
year = {2025},
author = {He, L and Li, J and Tang, L and Wang, Y and Zhao, X and Ding, K and Xu, L and Gu, L and Cheng, S and Wei, YY},
title = {Applying side-stream gas recirculation to promote anaerobic digestion of food waste under ammonia stress: Overlooked impact of gaseous atmospheres on microorganisms.},
journal = {Water research},
volume = {281},
number = {},
pages = {123571},
doi = {10.1016/j.watres.2025.123571},
pmid = {40184706},
issn = {1879-2448},
mesh = {*Ammonia ; Anaerobiosis ; Bioreactors/microbiology ; Hydrogen ; Gases ; Food Loss and Waste ; },
abstract = {High ammonia concentrations can be toxic to microorganisms, leading to the accumulation of hydrogen (H2) and acids in anaerobic digestion (AD) system. In this study, a side gas recycling strategy (SGR), coupled with a primary reactor and a small side-stream reactor, which recirculates biogas between primary reactor and side reactor was employed to mitigate ammonia inhibition. This approach enabled the mesophilic side-stream gas recirculation system (SMGR) and the thermophilic side-stream gas recirculation system (STGR) to ultimately withstand ammonia stress levels of 2.5 g/L and 3.5 g/L, respectively, while maintaining lower hydrogen partial pressures. In contrast, the control group experienced system failure at an ammonia concentration of 2 g/L. Enzyme activity, microbial community, and metaproteomic analysis indicated that the side reactor enriched microorganisms with strong hydrogen-utilizing capacity, while the primary reactor was enriched with Methanosaeta. Furthermore, key pathways related to propionate metabolism, ABC transporters, and methane production were enhanced in the primary reactor, along with increased ATPase activity. The activity of key enzymes involved in AD was also significantly enhanced. This study enhances the understanding of the impact of gas atmosphere control on the microbial ecology and metabolic characteristics of AD system, providing valuable insights and practical guidance for the development of Engineering applications in this field.},
}

*Ammonia
Anaerobiosis
Bioreactors/microbiology
Hydrogen
Gases
Food Loss and Waste

@article {pmid40179787,
year = {2025},
author = {Wang, Z and Tu, S and Shehzad, K and Hou, J and Xiong, S and Cao, M},
title = {Comparative study of organosilicon and inorganic silicon in reducing cadmium accumulation in wheat: Insights into rhizosphere microbial communities and molecular regulation mechanisms.},
journal = {Journal of hazardous materials},
volume = {492},
number = {},
pages = {138061},
doi = {10.1016/j.jhazmat.2025.138061},
pmid = {40179787},
issn = {1873-3336},
mesh = {*Triticum/metabolism/growth & development/drug effects ; *Cadmium/metabolism ; *Silicon/pharmacology/chemistry ; Rhizosphere ; *Soil Pollutants/metabolism ; Microbiota/drug effects ; Soil Microbiology ; },
abstract = {Silicon is widely used as a "quality element" and "stress resistance element" in crop production and the remediation of heavy metal-contamination soils. Compared to inorganic silicon, organosilicon has unique properties such as amphiphilicity, low surface energy and high biocompatibility. Our previous research has confirmed the effectiveness of organosilicon-modified fertilizers in inhibiting Cadmium (Cd) absorption in wheat. Therefore, it is of great importance to further explore the potential mechanisms and comprehensive benefits of organosilicon. In this study, the microbiological and molecular mechanisms by which organosilicon reduces Cd concentration in wheat compared to inorganic silicon were investigated in depth. The findings indicated that, in comparison with inorganic silicon, organosilicon exhibited a more remarkable efficacy. Specifically, it was more effective in reducing the Cd concentration in wheat grains, achieving a reduction range of 35-39 % as opposed to the 23-28 % reduction achieved by inorganic silicon. Moreover, it manifested a greater ability to mitigate health risks, with a reduction range of 33-42 % compared to the 25-30 % reduction of inorganic silicon. Furthermore, organosilicon contributed to a significant increase in wheat yield, with a growth range of 11-14 % in contrast to the 8-11 % increase from inorganic silicon. Additionally, it enhanced the quality of the grains, substantially improving the protein content and amino acid content. The comparative advantages of organosilicon over inorganic silicon would be firstly due to the reduction of the bioavailability of soil Cd by increasing the available silicon content in the soil and improving the soil microbial ecology (increasing the abundance of Bacillus, Pseudomonas, Massilia and Talaromyces and reducing the enrichment of Fusarium). Secondly, organosilicon achieved vacuolar compartmentalization of Cd by upregulating the expression of the ABC transporter gene (TaABCB7), thereby alleviating Cd toxicity and restricting Cd transport from leaves to grains. Meanwhile, organosilicon increased the wheat yield by optimizing the availability of soil nutrients and enhancing photosynthesis. These results demonstrate the immense potential of organosilicon in mitigating heavy metal contamination in crops.},
}

*Triticum/metabolism/growth & development/drug effects
*Cadmium/metabolism
*Silicon/pharmacology/chemistry
Rhizosphere
*Soil Pollutants/metabolism
Microbiota/drug effects
Soil Microbiology

@article {pmid40041702,
year = {2025},
author = {Xu, Z and Chen, J and Liang, W and Chen, ZL and Wu, W and Xia, X and Chen, B and He, D and Liu, H},
title = {Contrasting diversity patterns between microeukaryotic and prokaryotic communities in cold-seep sediments.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf002},
pmid = {40041702},
issn = {2730-6151},
abstract = {Cold seeps are hotspots of biodiversity. However, the quantification of the microbial diversity, particularly that of microeukaryotes, remains scarce and little is known about the active groups. In this study we investigated the diversity and activity of prokaryotes and microeukaryotes in the Haima cold seep sediments in the northern South China Sea using both DNA (whole community) and RNA (active community) signatures. We found that, in general, prokaryotes had lower diversity in the seep sediment than in non-seep regions while microeukaryotes showed the opposite pattern. This finding could be explained by the dominance of homogeneous selection in the prokaryotic community while microeukaryotic communities were less affected by environmental selection, harboring high richness of abundant groups in the seep regions. The compositional difference between DNA and RNA communities was much larger in microeukaryotes than prokaryotes, which could be reflected by the large number of inactive microeukaryotic taxa. Compared to the whole community, the seep-active groups, e.g. among microeukaryotes, Breviatea, Labyrinthulomycetes, and Apicomplexa were more sensitive to and directly influenced by environmental factors, suggesting their pivotal roles in ecosystem biodiversity and functions. This study provides insight into the distinct diversity patterns and regulating mechanisms that occur between prokaryotic and microeukaryotic communities in cold-seep sediments, deepening our understanding of microbial ecology in deep-sea extreme habitats.},
}

@article {pmid39752189,
year = {2025},
author = {Bloomfield, SJ and Hildebrand, F and Zomer, AL and Palau, R and Mather, AE},
title = {Ecological insights into the microbiology of food using metagenomics and its potential surveillance applications.},
journal = {Microbial genomics},
volume = {11},
number = {1},
pages = {},
pmid = {39752189},
issn = {2057-5858},
mesh = {*Metagenomics/methods ; *Food Microbiology ; Metagenome ; Bacteria/genetics/classification/isolation & purification ; Salmonella/genetics/isolation & purification/classification ; Drug Resistance, Bacterial/genetics ; Escherichia coli/genetics/isolation & purification/classification ; },
abstract = {A diverse array of micro-organisms can be found on food, including those that are pathogenic or resistant to antimicrobial drugs. Metagenomics involves extracting and sequencing the DNA of all micro-organisms on a sample, and here, we used a combination of culture and culture-independent approaches to investigate the microbial ecology of food to assess the potential application of metagenomics for the microbial surveillance of food. We cultured common foodborne pathogens and other organisms including Escherichia coli, Klebsiella/Raoultella spp., Salmonella spp. and Vibrio spp. from five different food commodities and compared their genomes to the microbial communities obtained by metagenomic sequencing following host (food) DNA depletion. The microbial populations of retail food were found to be predominated by psychrotrophic bacteria, driven by the cool temperatures in which the food products are stored. Pathogens accounted for a small percentage of the food metagenome compared to the psychrotrophic bacteria, and cultured pathogens were inconsistently identified in the metagenome data. The microbial composition of food varied amongst different commodities, and metagenomics was able to classify the taxonomic origin of 59% of antimicrobial resistance genes (ARGs) found on food to the genus level, but it was unclear what percentage of ARGs were associated with mobile genetic elements and thus transferable to other bacteria. Metagenomics may be used to survey the ARG burden, composition and carriage on foods to which consumers are exposed. However, food metagenomics, even after depleting host DNA, inconsistently identifies pathogens without enrichment or further bait capture.},
}

*Metagenomics/methods
*Food Microbiology
Metagenome
Bacteria/genetics/classification/isolation & purification
Salmonella/genetics/isolation & purification/classification
Drug Resistance, Bacterial/genetics
Escherichia coli/genetics/isolation & purification/classification

@article {pmid39651889,
year = {2025},
author = {Wang, J and Schamp, CN and Hudson, LK and Chaggar, HK and Bryan, DW and Garman, KN and Radosevich, M and Denes, TG},
title = {Whole-genome sequencing and metagenomics reveal diversity and prevalence of Listeria spp. from soil in the Nantahala National Forest.},
journal = {Microbiology spectrum},
volume = {13},
number = {1},
pages = {e0171224},
pmid = {39651889},
issn = {2165-0497},
mesh = {*Soil Microbiology ; *Listeria/genetics/classification/isolation & purification ; *Metagenomics ; *Whole Genome Sequencing ; North Carolina ; *Forests ; *Genome, Bacterial ; *Phylogeny ; Humans ; Listeriosis/microbiology/epidemiology/transmission ; Listeria monocytogenes/genetics/classification/isolation & purification ; Metagenome ; Prevalence ; Soil/chemistry ; },
abstract = {UNLABELLED: Listeria spp. are widely distributed environmental bacteria associated with human foodborne illness. The ability to detect and characterize Listeria strains in the natural environment will contribute to improved understanding of transmission routes of contamination. The current standard for surveillance and outbreak source attribution is whole-genome sequencing (WGS) of Listeria monocytogenes clinical isolates. Recently, metagenomic sequencing has also been explored as a tool for the detection of Listeria spp. in environmental samples. This study evaluated soil samples from four locations across altitudes ranging from 1,500 to 4,500 ft in the Nantahala National Forest in North Carolina, USA. Forty-two Listeria isolates were cultured and sequenced, and 12 metagenomes of soil bacterial communities were generated. These isolates comprised 14 distinct strains from five species, including Listeria cossartiae subsp. cayugensis (n = 8; n represents the number of distinct strains), L. monocytogenes (n = 3), "Listeria swaminathanii" (Lsw) (n = 1), Listeria marthii (n = 1), and Listeria booriae (n = 1). Most strains (n = 13) were isolated from lower altitudes (1,500 or 2,500 ft), while the L. swaminathanii strain was isolated from both higher (4,500 ft) and lower (1,500 ft) altitudes. Metagenomic analysis of soil described a reduction in both bacterial community diversity and relative abundance of Listeria spp. as the altitude increased. Soil pH and cation exchange capacity were positively correlated (P < 0.05) with the abundance of Listeria spp. as detected by metagenomics. By integrating culture-independent metagenomics with culture-based WGS, this study advances current knowledge regarding distribution of Listeria spp. in the natural environment and suggests the potential for future use of culture-independent methods in tracking the transmission of foodborne pathogens.

IMPORTANCE: As a foodborne pathogen, Listeria continues to cause numerous illnesses in humans and animals. Studying the diversity and distribution of Listeria in soil is crucial for understanding potential sources of contamination and developing effective strategies to prevent foodborne outbreaks of listeriosis. Additionally, examining the ecological niches and survival mechanisms of Listeria in natural habitats provides insights into its persistence and adaptability, informing risk assessments and public health interventions. This research contributes to a broader understanding of microbial ecology and the factors influencing foodborne pathogen emergence, ultimately enhancing food safety and protecting public health. Moreover, using a metagenomic approach provides a detailed understanding of the soil microbial ecosystems, leading to more effective monitoring and control of foodborne pathogens. This study also highlights the potential for integrating metagenomics into routine surveillance systems for food safety in the near future.},
}

*Soil Microbiology
*Listeria/genetics/classification/isolation & purification
*Metagenomics
*Whole Genome Sequencing
North Carolina
*Forests
*Genome, Bacterial
*Phylogeny
Humans
Listeriosis/microbiology/epidemiology/transmission
Listeria monocytogenes/genetics/classification/isolation & purification
Metagenome
Prevalence
Soil/chemistry

@article {pmid39545729,
year = {2024},
author = {Beaudry, MS and Bhuiyan, MIU and Glenn, TC},
title = {Enriching the future of public health microbiology with hybridization bait capture.},
journal = {Clinical microbiology reviews},
volume = {37},
number = {4},
pages = {e0006822},
pmid = {39545729},
issn = {1098-6618},
support = {R01 AI148667/AI/NIAID NIH HHS/United States ; 75D30118C02889, 75D30120R67837//HHS | Centers for Disease Control and Prevention (CDC)/ ; 1R01AI148667-01A1//HHS | National Institutes of Health (NIH)/ ; },
mesh = {Humans ; Bacteria/genetics/classification/isolation & purification ; Fungi/classification/genetics/isolation & purification ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; *Microbiological Techniques/methods/trends ; Nucleic Acid Hybridization/methods ; *Public Health ; },
abstract = {SUMMARYPublic health microbiology focuses on microorganisms and infectious agents that impact human health. For years, this field has relied on culture or molecular methods to investigate complex samples of public health importance. However, with the increase in accuracy and decrease in sequencing cost over the last decade, there has been a transition to the use of next-generation sequencing in public health microbiology. Nevertheless, many available sequencing methods (e.g., shotgun metagenomics and amplicon sequencing) do not work well in complex sample types, require deep sequencing, or have inherent biases associated with them. Hybridization bait capture, also known as target enrichment, brings in solutions for such limitations. It is an increasingly popular technique to simultaneously characterize many thousands of genetic elements while reducing the amount of sequencing needed (thereby reducing the sequencing costs). Here, we summarize the concept of hybridization bait capture for public health, reviewing a total of 35 bait sets designed in six key topic areas for public health microbiology [i.e., antimicrobial resistance (AMR), bacteria, fungi, parasites, vectors, and viruses], and compare hybridization bait capture to previously relied upon methods. Furthermore, we provide an in-depth comparison of the three most popular bait sets designed for AMR by evaluating each of them against three major AMR databases: Comprehensive Antibiotic Resistance Database, Microbial Ecology Group Antimicrobial Resistance Database, and Pathogenicity Island Database. Thus, this article provides a review of hybridization bait capture for public health microbiologists.},
}

Humans
Bacteria/genetics/classification/isolation & purification
Fungi/classification/genetics/isolation & purification
High-Throughput Nucleotide Sequencing/methods
Metagenomics/methods
*Microbiological Techniques/methods/trends
Nucleic Acid Hybridization/methods
*Public Health

@article {pmid39298326,
year = {2024},
author = {Gordon, JI and Barratt, MJ and Hibberd, MC and Rahman, M and Ahmed, T},
title = {Establishing human microbial observatory programs in low- and middle-income countries.},
journal = {Annals of the New York Academy of Sciences},
volume = {1540},
number = {1},
pages = {13-20},
doi = {10.1111/nyas.15224},
pmid = {39298326},
issn = {1749-6632},
support = {//Fondazione Internazionale Premio Balzan/ ; //Bill and Melinda Gates Foundation/ ; /NH/NIH HHS/United States ; /NH/NIH HHS/United States ; },
mesh = {Humans ; *Developing Countries ; Global Health ; *Microbiota ; },
abstract = {Studies of the human microbiome are progressing rapidly but have largely focused on populations living in high-income countries. With increasing evidence that the microbiome contributes to the pathogenesis of diseases that affect infants, children, and adults in low- and middle-income countries (LMICs), and with profound and rapid ongoing changes occurring in our lifestyles and biosphere, understanding the origins of and developing microbiome-directed therapeutics for treating a number of global health challenges requires the development of programs for studying human microbial ecology in LMICs. Here, we discuss how the establishment of long-term human microbial observatory programs in selected LMICs could provide one timely approach.},
}

Humans
*Developing Countries
Global Health
*Microbiota

@article {pmid38965531,
year = {2024},
author = {Babajanyan, SG and Garushyants, SK and Wolf, YI and Koonin, EV},
title = {Microbial diversity and ecological complexity emerging from environmental variation and horizontal gene transfer in a simple mathematical model.},
journal = {BMC biology},
volume = {22},
number = {1},
pages = {148},
pmid = {38965531},
issn = {1741-7007},
support = {Intramural Research Program//U.S. National Library of Medicine/ ; },
mesh = {*Gene Transfer, Horizontal ; *Microbiota/genetics ; Biodiversity ; Symbiosis/genetics ; Models, Theoretical ; Models, Biological ; },
abstract = {BACKGROUND: Microbiomes are generally characterized by high diversity of coexisting microbial species and strains, and microbiome composition typically remains stable across a broad range of conditions. However, under fixed conditions, microbial ecology conforms with the exclusion principle under which two populations competing for the same resource within the same niche cannot coexist because the less fit population inevitably goes extinct. Therefore, the long-term persistence of microbiome diversity calls for an explanation.

RESULTS: To explore the conditions for stabilization of microbial diversity, we developed a simple mathematical model consisting of two competing populations that could exchange a single gene allele via horizontal gene transfer (HGT). We found that, although in a fixed environment, with unbiased HGT, the system obeyed the exclusion principle, in an oscillating environment, within large regions of the phase space bounded by the rates of reproduction and HGT, the two populations coexist. Moreover, depending on the parameter combination, all three major types of symbiosis were obtained, namely, pure competition, host-parasite relationship, and mutualism. In each of these regimes, certain parameter combinations provided for synergy, that is, a greater total abundance of both populations compared to the abundance of the winning population in the fixed environment.

CONCLUSIONS: The results of this modeling study show that basic phenomena that are universal in microbial communities, namely, environmental variation and HGT, provide for stabilization and persistence of microbial diversity, and emergence of ecological complexity.},
}

*Gene Transfer, Horizontal
*Microbiota/genetics
Biodiversity
Symbiosis/genetics
Models, Theoretical
Models, Biological

@article {pmid38691424,
year = {2024},
author = {Xiong, X and Othmer, HG and Harcombe, WR},
title = {Emergent antibiotic persistence in a spatially structured synthetic microbial mutualism.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {38691424},
issn = {1751-7370},
support = {R01 GM121498/GM/NIGMS NIH HHS/United States ; R01-GM121498/NH/NIH HHS/United States ; },
mesh = {*Escherichia coli/drug effects/genetics/growth & development ; *Anti-Bacterial Agents/pharmacology ; *Symbiosis ; *Salmonella enterica/drug effects/genetics ; Coculture Techniques ; Microbial Interactions ; Ampicillin/pharmacology ; Drug Resistance, Bacterial ; },
abstract = {Antibiotic persistence (heterotolerance) allows a subpopulation of bacteria to survive antibiotic-induced killing and contributes to the evolution of antibiotic resistance. Although bacteria typically live in microbial communities with complex ecological interactions, little is known about how microbial ecology affects antibiotic persistence. Here, we demonstrated within a synthetic two-species microbial mutualism of Escherichia coli and Salmonella enterica that the combination of cross-feeding and community spatial structure can emergently cause high antibiotic persistence in bacteria by increasing the cell-to-cell heterogeneity. Tracking ampicillin-induced death for bacteria on agar surfaces, we found that E. coli forms up to 55 times more antibiotic persisters in the cross-feeding coculture than in monoculture. This high persistence could not be explained solely by the presence of S. enterica, the presence of cross-feeding, average nutrient starvation, or spontaneous resistant mutations. Time-series fluorescent microscopy revealed increased cell-to-cell variation in E. coli lag time in the mutualistic co-culture. Furthermore, we discovered that an E. coli cell can survive antibiotic killing if the nearby S. enterica cells on which it relies die first. In conclusion, we showed that the high antibiotic persistence phenotype can be an emergent phenomenon caused by a combination of cross-feeding and spatial structure. Our work highlights the importance of considering spatially structured interactions during antibiotic treatment and understanding microbial community resilience more broadly.},
}

*Escherichia coli/drug effects/genetics/growth & development
*Anti-Bacterial Agents/pharmacology
*Symbiosis
*Salmonella enterica/drug effects/genetics
Coculture Techniques
Microbial Interactions
Ampicillin/pharmacology
Drug Resistance, Bacterial

@article {pmid37970497,
year = {2023},
author = {Lee, JH and Kim, S and Kim, ES and Keum, GB and Doo, H and Kwak, J and Pandey, S and Cho, JH and Ryu, S and Song, M and Cho, JH and Kim, S and Kim, HB},
title = {Comparative analysis of the pig gut microbiome associated with the pig growth performance.},
journal = {Journal of animal science and technology},
volume = {65},
number = {4},
pages = {856-864},
pmid = {37970497},
issn = {2055-0391},
abstract = {There are a variety of microorganisms in the animal intestine, and it has been known that they play important roles in the host such as suppression of potentially pathogenic microorganisms, modulation of the gut immunity. In addition, the gut microbiota and the livestock growth performance have long been known to be related. Therefore, we evaluated the interrelation between the growth performance and the gut microbiome of the pigs from 3 different farms, with pigs of varied ages ready to be supplied to the market. When pigs reached average market weight of 118 kg, the average age of pigs in three different farms were < 180 days, about 190 days, and > 200 days, respectively. Fecal samples were collected from pigs of age of 70 days, 100 days, 130 days, and 160 days. The output data of the 16S rRNA gene sequencing by the Illumina Miseq platform was filtered and analyzed using Quantitative Insights into Microbial Ecology (QIIME)2, and the statistical analysis was performed using Statistical Analysis of Metagenomic Profiles (STAMP). The results of this study showed that the gut microbial communities shifted as pigs aged along with significant difference in the relative abundance of different phyla and genera in different age groups of pigs from each farm. Even though, there was no statistical differences among groups in terms of Chao1, the number of observed operational taxonomic units (OTUs), and the Shannon index, our results showed higher abundances of Bifidobacterium, Clostridium and Lactobacillus in the feces of pigs with rapid growth rate. These results will help us to elucidate important gut microbiota that can affect the growth performance of pigs.},
}

@article {pmid37354976,
year = {2023},
author = {Kable, ME and Chin, EL and Huang, L and Stephensen, CB and Lemay, DG},
title = {Association of Estimated Daily Lactose Consumption, Lactase Persistence Genotype (rs4988235), and Gut Microbiota in Healthy Adults in the United States.},
journal = {The Journal of nutrition},
volume = {153},
number = {8},
pages = {2163-2173},
doi = {10.1016/j.tjnut.2023.06.025},
pmid = {37354976},
issn = {1541-6100},
mesh = {Male ; Female ; Humans ; Adult ; United States ; Lactose ; *Lactose Intolerance/genetics ; *Gastrointestinal Microbiome/genetics ; Cross-Sectional Studies ; RNA, Ribosomal, 16S/genetics ; Dairy Products ; Lactase/genetics ; Genotype ; },
abstract = {BACKGROUND: Lactase persistence (LP) is a heritable trait in which lactose can be digested throughout adulthood. Lactase nonpersistent (LNP) individuals who consume lactose may experience microbial adaptations in response to undigested lactose.

OBJECTIVES: The objective of the study was to estimate lactose from foods reported in the Automated Self-Administered 24-Hour Dietary Assessment Tool (ASA24) and determine the interaction between lactose consumption, LP genotype, and gut microbiome in an observational cross-sectional study of healthy adults in the United States (US).

METHODS: Average daily lactose consumption was estimated for 279 healthy US adults, genotyped for the lactase gene -13910G>A polymorphism (rs4988235) by matching ASA24-reported foods to foods in the Nutrition Coordinating Center Food and Nutrient Database. Analysis of covariance was used to identify whether the A genotype (LP) influenced lactose and total dairy consumption, with total energy intake and weight as covariates. The 16S rRNA V4/V5 region, amplified from bacterial DNA extracted from each frozen stool sample, was sequenced using Illumina MiSeq (300 bp paired-end) and analyzed using Quantitative Insights Into Microbial Ecology (QIIME)2 (version 2019.10). Differential abundances of bacterial taxa were analyzed using DESeq2 likelihood ratio tests.

RESULTS: Across a diverse set of ethnicities, LP subjects consumed more lactose than LNP subjects. Lactobacillaceae abundance was highest in LNP subjects who consumed more than 12.46 g/d (upper tercile). Within Caucasians and Hispanics, family Lachnospiraceae was significantly enriched in the gut microbiota of LNP individuals consuming the upper tercile of lactose across both sexes.

CONCLUSIONS: Elevated lactose consumption in individuals with the LNP genotype is associated with increased abundance of family Lactobacillaceae and Lachnospriaceae, taxa that contain multiple genera capable of utilizing lactose. This trial was registered on clinicaltrials.gov as NCT02367287.},
}

Male
Female
Humans
Adult
United States
Lactose
*Lactose Intolerance/genetics
*Gastrointestinal Microbiome/genetics
Cross-Sectional Studies
RNA, Ribosomal, 16S/genetics
Dairy Products
Lactase/genetics
Genotype

@article {pmid37338363,
year = {2023},
author = {Ye, L and Yang, X and Zhang, B and Zhou, J and Tian, H and Zhang, X and Li, X},
title = {Seasonal Succession of Fungal Communities in Native Truffle (Tuber indicum) Ecosystems.},
journal = {Applied and environmental microbiology},
volume = {89},
number = {7},
pages = {e0019523},
pmid = {37338363},
issn = {1098-5336},
mesh = {Ecosystem ; Seasons ; *Mycobiome ; *Ascomycota ; *Mycorrhizae ; Soil ; Soil Microbiology ; },
abstract = {Truffles are a rare underground fungus and one of the most expensive, and sought-after kitchen ingredients in the world. Microbial ecology plays an important role in the annual growth cycle of truffles, but fungal communities in native truffle ecosystems are still largely unknown, especially for Tuber indicum from China. In this study, the spatial and temporal dynamics of soil physicochemical properties and fungal communities were described associated with four T. indicum-producing plots (TPPs) and one non-truffle-producing plot in four successive growing seasons. A total of 160 biological samples were collected, 80 of which were used for the determination of 10 soil physicochemical indices and 80 for Illumina-based analysis of the fungal microbiome. Soil physicochemical properties and fungal communities exhibited considerable seasonal variation. Ascomycetes, Basidiomycetes, and Mucormycoides dominated. The core microbiome work on the microecological changes in TPPs, and the identified core members contribute to the seasonal succession of communities. The genus Tuber occupies a central position in healthy TPPs. There was a strong correlation between soil physicochemical properties and fungal communities. The genus Tuber showed a positive correlation with Ca, Mg, and total nitrogen, but a negative correlation with total phosphorus and available potassium. This study describes the complex ecological dynamics of soil physicochemical indices and fungal communities occurring during the annual cycle of Tuber indicum, and highlights the succession of core communities in truffle plots, which contribute to better protection of native truffle ecosystems and control of mycorrhizal fungal contamination in artificial truffle plantations in China. IMPORTANCE The spatial and temporal dynamics of soil physicochemical properties and fungal communities associated with four Tuber indicum-producing plots and one non truffle producing plot in four different growing seasons are described. Soil physicochemical properties and fungal communities exhibited considerable seasonal variation. This study examines the complex ecological dynamics of soil physicochemical indices and fungal communities occurring during the annual cycle of Tuber indicum and highlights the succession of core communities in truffle plots, which contributes to better protection of native truffle ecosystems and control of mycorrhizal fungal contamination in artificial truffle plantations in China.},
}

Ecosystem
Seasons
*Mycobiome
*Ascomycota
*Mycorrhizae
Soil
Soil Microbiology

@article {pmid36061686,
year = {2022},
author = {Liu, B and Chen, J and Li, Y},
title = {Keystone Microorganisms Regulate the Methanogenic Potential in Coals with Different Coal Ranks.},
journal = {ACS omega},
volume = {7},
number = {34},
pages = {29901-29908},
pmid = {36061686},
issn = {2470-1343},
abstract = {Microorganisms are the core drivers of coal biogeochemistry and are closely related to the formation of coalbed methane. However, it remains poorly understood about the network relationship and stability of microbial communities in coals with different ranks. In this study, a high-throughput sequencing data set was analyzed to understand the microbial co-occurrence network in coals with different ranks including anthracite, medium-volatile bituminous, and high-volatile bituminous. The results showed similar topological properties for the microbial networks among coals with different ranks, but a great difference was found in the microbial composition in different large modules among coals with different ranks, and these three networks had three, four, and four large modules with seven, nine, and nine phyla, respectively. Among these networks, a total of 46 keystone taxa were identified in large modules, and these keystone taxa were different in coals with different ranks. Bacteria dominated the keystone taxa in the microbial network, and these bacterial keystone taxa mainly belonged to phyla Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria. Besides, the removal of the key microbial data could reduce the community stability of microbial communities in bituminous coals. A partial least-squares path model further showed that these bacterial keystone taxa indirectly affected methanogenic potential by maintaining the microbial community stability and bacterial diversity. In summary, these results showed that keystone taxa played an important role in determining the community diversity, maintaining the microbial community stability, and controlling the methanogenic potential, which is of great significance for understanding the microbial ecology and the geochemical cycle of coal seams.},
}

@article {pmid35938717,
year = {2022},
author = {Okazaki, Y and Nakano, SI and Toyoda, A and Tamaki, H},
title = {Long-Read-Resolved, Ecosystem-Wide Exploration of Nucleotide and Structural Microdiversity of Lake Bacterioplankton Genomes.},
journal = {mSystems},
volume = {7},
number = {4},
pages = {e0043322},
pmid = {35938717},
issn = {2379-5077},
mesh = {*Lakes/microbiology ; Ecosystem ; Nucleotides ; Metagenome ; Bacteria/genetics ; *Bacteriophages/genetics ; },
abstract = {Reconstruction of metagenome-assembled genomes (MAGs) has become a fundamental approach in microbial ecology. However, a MAG is hardly complete and overlooks genomic microdiversity because metagenomic assembly fails to resolve microvariants among closely related genotypes. Aiming at understanding the universal factors that drive or constrain prokaryotic genome diversification, we performed an ecosystem-wide high-resolution metagenomic exploration of microdiversity by combining spatiotemporal (2 depths × 12 months) sampling from a pelagic freshwater system, high-quality MAG reconstruction using long- and short-read metagenomic sequences, and profiling of single nucleotide variants (SNVs) and structural variants (SVs) through mapping of short and long reads to the MAGs, respectively. We reconstructed 575 MAGs, including 29 circular assemblies, providing high-quality reference genomes of freshwater bacterioplankton. Read mapping against these MAGs identified 100 to 101,781 SNVs/Mb and 0 to 305 insertions, 0 to 467 deletions, 0 to 41 duplications, and 0 to 6 inversions for each MAG. Nonsynonymous SNVs were accumulated in genes potentially involved in cell surface structural modification to evade phage recognition. Most (80.2%) deletions overlapped with a gene coding region, and genes of prokaryotic defense systems were most frequently (>8% of the genes) overlapped with a deletion. Some such deletions exhibited a monthly shift in their allele frequency, suggesting a rapid turnover of genotypes in response to phage predation. MAGs with extremely low microdiversity were either rare or opportunistic bloomers, suggesting that population persistency is key to their genomic diversification. The results concluded that prokaryotic genomic diversification is driven primarily by viral load and constrained by a population bottleneck. IMPORTANCE Identifying intraspecies genomic diversity (microdiversity) is crucial to understanding microbial ecology and evolution. However, microdiversity among environmental assemblages is not well investigated, because most microbes are difficult to culture. In this study, we performed cultivation-independent exploration of bacterial genomic microdiversity in a lake ecosystem using a combination of short- and long-read metagenomic analyses. The results revealed the broad spectrum of genomic microdiversity among the diverse bacterial species in the ecosystem, which has been overlooked by conventional approaches. Our ecosystem-wide exploration further allowed comparative analysis among the genomes and genes and revealed factors behind microbial genomic diversification, namely, that diversification is driven primarily by resistance against viral infection and constrained by the population size.},
}

*Lakes/microbiology
Ecosystem
Nucleotides
Metagenome
Bacteria/genetics
*Bacteriophages/genetics

@article {pmid35134909,
year = {2022},
author = {Foster-Nyarko, E and Pallen, MJ},
title = {The microbial ecology of Escherichia coli in the vertebrate gut.},
journal = {FEMS microbiology reviews},
volume = {46},
number = {3},
pages = {},
pmid = {35134909},
issn = {1574-6976},
mesh = {Animals ; Bacteria ; *Escherichia coli ; *Escherichia coli Infections/microbiology ; Symbiosis ; Vertebrates ; },
abstract = {Escherichia coli has a rich history as biology's 'rock star', driving advances across many fields. In the wild, E. coli resides innocuously in the gut of humans and animals but is also a versatile pathogen commonly associated with intestinal and extraintestinal infections and antimicrobial resistance-including large foodborne outbreaks such as the one that swept across Europe in 2011, killing 54 individuals and causing approximately 4000 infections and 900 cases of haemolytic uraemic syndrome. Given that most E. coli are harmless gut colonizers, an important ecological question plaguing microbiologists is what makes E. coli an occasionally devastating pathogen? To address this question requires an enhanced understanding of the ecology of the organism as a commensal. Here, we review how our knowledge of the ecology and within-host diversity of this organism in the vertebrate gut has progressed in the 137 years since E. coli was first described. We also review current approaches to the study of within-host bacterial diversity. In closing, we discuss some of the outstanding questions yet to be addressed and prospects for future research.},
}

Animals
Bacteria
*Escherichia coli
*Escherichia coli Infections/microbiology
Symbiosis
Vertebrates

@article {pmid34989745,
year = {2022},
author = {Hua, Q and Han, Y and Zhao, H and Zhang, H and Yan, B and Pei, S and He, X and Li, Y and Meng, X and Chen, L and Zhong, F and Li, D},
title = {Punicalagin alleviates renal injury via the gut-kidney axis in high-fat diet-induced diabetic mice.},
journal = {Food & function},
volume = {13},
number = {2},
pages = {867-879},
doi = {10.1039/d1fo03343c},
pmid = {34989745},
issn = {2042-650X},
mesh = {Animals ; Diabetes Mellitus, Experimental/*complications ; Diabetic Nephropathies/*drug therapy ; *Diet, High-Fat ; Fatty Acids, Volatile/metabolism ; Gastrointestinal Microbiome/*drug effects ; Gene Expression Regulation/drug effects ; Hydrolyzable Tannins/*pharmacology ; Inflammation/metabolism ; Kidney/*metabolism ; Mice ; Mice, Inbred C57BL ; Pomegranate/chemistry ; },
abstract = {Diabetic renal injury was associated with dysbiosis of the gut microbiota and intestinal barrier. Punicalagin (PU) from pomegranates potentially impacts the microbial ecosystem, intestinal barrier, and renal function. Therefore, we hypothesized that PU may improve diabetic renal injury by modulating the gut-kidney axis. The present study evaluated the effect of PU on the gut-kidney axis and kidney function in a diabetic renal injury mouse model induced by a high-fat diet (HFD). Mice were fed a HFD without PU or with at doses of 50 and 100 mg kg[-1] d[-1] for 8 weeks. Targeted metabolomics by GC-MS and 16S rRNA sequencing were implemented to determine short-chain fatty acids (SCFAs) and microbes. Further RNA sequencing analyses were performed to determine which differentially expressed genes were changed by PU. Compared with the DM model group, PU supplementation improved diabetic renal injury, ameliorated kidney architecture and function, and reshaped gut microbial ecology. Additionally, PU reversed HFD-induced gut barrier dysfunction, promoted cecal SCFA concentrations and inhibited serum lipopolysaccharide (LPS) and diamine oxidase (DAO) levels. Moreover, correlation analysis found that cecal SCFAs were significantly negatively correlated with inflammation-related genes in the kidney. The present results indicated that PU, a promising bioactive polyphenol, successfully improved diabetic renal injury, most likely through the gut-kidney axis.},
}

Animals
Diabetes Mellitus, Experimental/*complications
Diabetic Nephropathies/*drug therapy
*Diet, High-Fat
Fatty Acids, Volatile/metabolism
Gastrointestinal Microbiome/*drug effects
Gene Expression Regulation/drug effects
Hydrolyzable Tannins/*pharmacology
Inflammation/metabolism
Kidney/*metabolism
Mice
Mice, Inbred C57BL
Pomegranate/chemistry

@article {pmid34958387,
year = {2022},
author = {Kable, ME and Chin, EL and Storms, D and Lemay, DG and Stephensen, CB},
title = {Tree-Based Analysis of Dietary Diversity Captures Associations Between Fiber Intake and Gut Microbiota Composition in a Healthy US Adult Cohort.},
journal = {The Journal of nutrition},
volume = {152},
number = {3},
pages = {779-788},
doi = {10.1093/jn/nxab430},
pmid = {34958387},
issn = {1541-6100},
mesh = {Adolescent ; Adult ; Aged ; Cross-Sectional Studies ; Diet ; Dietary Fiber/analysis ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Humans ; Middle Aged ; RNA, Ribosomal, 16S/analysis/genetics ; Young Adult ; },
abstract = {BACKGROUND: Diet patterns are a significant and modifiable contributing factor to the composition of the human gut microbiota.

OBJECTIVES: We set out to identify reproducible relationships between diet and gut microbial community composition in a diverse, healthy US adult cohort.

METHODS: We collected 2 to 3 automated self-administered 24-hour dietary recalls over 10-14 days, together with a single stool sample, from 343 healthy adults in a cross-sectional phenotyping study. This study examined a multi-ethnic cohort balanced for age (18-65 years), sex, and BMI (18.5-45 kg/m2). Dietary data were edited to a tree format according to published methods. The tree structure was annotated with the average total grams of dry weight, fat, protein, carbohydrate, or fiber from each food item reported. The alpha and beta diversity measurements, calculated using the tree structure, were analyzed relative to the microbial community diversity, determined by a Quantitative Insights Into Microbial Ecology (QIIME) 2 analysis of the bacterial 16S ribosomal RNA V4 region, sequenced from stool samples. K-means clustering was used to form groups of individuals consuming similar diets, and gut microbial communities were compared among groups using differential expression analysis for sequence count data.

RESULTS: The alpha diversity of diet dry weight was significantly correlated with the gut microbial community alpha diversity (r = 0.171). The correlation improved when diet was characterized using grams of carbohydrates (r = 0.186) or fiber (r = 0.213). Bifidobacterium was enriched with diets containing higher levels of total carbohydrate from cooked grains. Lachnospira, was enriched with diet patterns containing high consumption of fiber from fruits excluding berries.

CONCLUSIONS: The tree structure, annotated with grams of carbohydrate, is a robust analysis method for comparing self-reported diet to the gut microbial community composition. This method identified consumption of fiber from fruit robustly associated with an abundance of pectinolytic bacterial genus, Lachnospira, in the guts of healthy adults. This trial was registered at clinicaltrials.gov as NCT02367287.},
}

Adolescent
Adult
Aged
Cross-Sectional Studies
Diet
Dietary Fiber/analysis
Feces/microbiology
*Gastrointestinal Microbiome/genetics
Humans
Middle Aged
RNA, Ribosomal, 16S/analysis/genetics
Young Adult

@article {pmid37938641,
year = {2021},
author = {Röttjers, L and Vandeputte, D and Raes, J and Faust, K},
title = {Null-model-based network comparison reveals core associations.},
journal = {ISME communications},
volume = {1},
number = {1},
pages = {36},
pmid = {37938641},
issn = {2730-6151},
support = {STG/16/006//KU Leuven (Katholieke Universiteit Leuven)/ ; STG/16/006//KU Leuven (Katholieke Universiteit Leuven)/ ; 801747//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 801747//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 30770923//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; 30770923//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; },
abstract = {Microbial network construction and analysis is an important tool in microbial ecology. Such networks are often constructed from statistically inferred associations and may not represent ecological interactions. Hence, microbial association networks are error prone and do not necessarily reflect true community structure. We have developed anuran, a toolbox for investigation of noisy networks with null models. Such models allow researchers to generate data under the null hypothesis that all associations are random, supporting identification of nonrandom patterns in groups of association networks. This toolbox compares multiple networks to identify conserved subsets (core association networks, CANs) and other network properties that are shared across all networks. We apply anuran to a time series of fecal samples from 20 women to demonstrate the existence of CANs in a subset of the sampled individuals. Moreover, we use data from the Global Sponge Project to demonstrate that orders of sponges have a larger CAN than expected at random. In conclusion, this toolbox is a resource for investigators wanting to compare microbial networks across conditions, time series, gradients, or hosts.},
}

@article {pmid33952552,
year = {2021},
author = {Tang, H and Bohannon, L and Lew, M and Jensen, D and Jung, SH and Zhao, A and Sung, AD and Wischmeyer, PE},
title = {Randomised, double-blind, placebo-controlled trial of Probiotics To Eliminate COVID-19 Transmission in Exposed Household Contacts (PROTECT-EHC): a clinical trial protocol.},
journal = {BMJ open},
volume = {11},
number = {5},
pages = {e047069},
pmid = {33952552},
issn = {2044-6055},
support = {R03 AG064260/AG/NIA NIH HHS/United States ; },
mesh = {*COVID-19 ; Double-Blind Method ; Humans ; Pandemics ; *Probiotics ; RNA, Ribosomal, 16S/genetics ; Randomized Controlled Trials as Topic ; SARS-CoV-2 ; Treatment Outcome ; },
abstract = {INTRODUCTION: The COVID-19 pandemic has proven to be an unprecedented challenge to worldwide health, and strategies to mitigate the spread and severity of COVID-19 infection are urgently needed. Emerging evidence suggests that the composition of the gut microbiome and modification of microbial ecology via probiotics can affect susceptibility to a wide range of infections, including respiratory tract infections. In this study, we aim to evaluate the effects of the probiotic Lactobacillus rhamnosus GG (LGG) versus placebo on COVID-19 infection status and the gut microbiome in subjects with a household contact who has tested positive for COVID-19.

METHODS AND ANALYSIS: In this double-blinded, randomised, placebo-controlled trial, we will randomise 1132 subjects having a household contact who has recently (≤7 days) tested positive for COVID-19 to daily oral LGG or placebo for 28 days. We hypothesise that taking LGG as a probiotic will protect against COVID-19 infection and reduce the severity of disease in those who become infected (primary endpoint: decreased symptoms), and will be associated with beneficial changes in the composition of the gut microbiome. Stool samples and nasal swabs will be collected to evaluate the microbiome by 16S rRNA sequencing and the presence of SARS-CoV-2 by PCR, respectively. We will also conduct multivariate analysis of demographic, behavioural, temporal, and other variables that may predict development of symptoms and other outcomes.

ETHICS AND DISSEMINATION: This trial is conducted under a Food and Drug Administration Investigational New Drug for LGG, has received ethics approval by the institutional review board of Duke University and enrolment has begun. We plan to disseminate the results in peer-reviewed journals and at national and international conferences.

TRIAL REGISTRATION NUMBER: NCT04399252.},
}

*COVID-19
Double-Blind Method
Humans
Pandemics
*Probiotics
RNA, Ribosomal, 16S/genetics
Randomized Controlled Trials as Topic
SARS-CoV-2
Treatment Outcome

@article {pmid33653941,
year = {2021},
author = {Belk, AD and Duarte, T and Quinn, C and Coil, DA and Belk, KE and Eisen, JA and Quinn, JC and Martin, JN and Yang, X and Metcalf, JL},
title = {Air versus Water Chilling of Chicken: a Pilot Study of Quality, Shelf-Life, Microbial Ecology, and Economics.},
journal = {mSystems},
volume = {6},
number = {2},
pages = {},
pmid = {33653941},
issn = {2379-5077},
abstract = {The United States' large-scale poultry meat industry is energy and water intensive, and opportunities may exist to improve sustainability during the broiler chilling process. By USDA regulation, after harvest the internal temperature of the chicken must be reduced to 40°F or less within 16 h to inhibit bacterial growth that would otherwise compromise the safety of the product. This step is accomplished most commonly by water immersion chilling in the United States, while air chilling methods dominate other global markets. A comprehensive understanding of the differences between these chilling methods is lacking. Therefore, we assessed the meat quality, shelf-life, microbial ecology, and techno-economic impacts of chilling methods on chicken broilers in a university meat laboratory setting. We discovered that air chilling methods resulted in superior chicken odor and shelf-life, especially prior to 14 days of dark storage. Moreover, we demonstrated that air chilling resulted in a more diverse microbiome that we hypothesize may delay the dominance of the spoilage organism Pseudomonas Finally, a techno-economic analysis highlighted potential economic advantages to air chilling compared to water chilling in facility locations where water costs are a more significant factor than energy costs.IMPORTANCE As the poultry industry works to become more sustainable and to reduce the volume of food waste, it is critical to consider points in the processing system that can be altered to make the process more efficient. In this study, we demonstrate that the method used during chilling (air versus water chilling) influences the final product microbial community, quality, and physiochemistry. Notably, the use of air chilling appears to delay the bloom of Pseudomonas spp. that are the primary spoilers in packaged meat products. By using air chilling to reduce carcass temperatures instead of water chilling, producers may extend the time until spoilage of the products and, depending on the cost of water in the area, may have economic and sustainability advantages. As a next step, a similar experiment should be done in an industrial setting to confirm these results generated in a small-scale university lab facility.},
}

@article {pmid32546676,
year = {2020},
author = {Gulino, K and Rahman, J and Badri, M and Morton, J and Bonneau, R and Ghedin, E},
title = {Initial Mapping of the New York City Wastewater Virome.},
journal = {mSystems},
volume = {5},
number = {3},
pages = {},
pmid = {32546676},
issn = {2379-5077},
abstract = {Bacteriophages are abundant members of all microbiomes studied to date, influencing microbial communities through interactions with their bacterial hosts. Despite their functional importance and ubiquity, phages have been underexplored in urban environments compared to their bacterial counterparts. We profiled the viral communities in New York City (NYC) wastewater using metagenomic data collected in November 2014 from 14 wastewater treatment plants. We show that phages accounted for the largest viral component of the sewage samples and that specific virus communities were associated with local environmental conditions within boroughs. The vast majority of the virus sequences had no homology matches in public databases, forming an average of 1,700 unique virus clusters (putative genera). These new clusters contribute to elucidating the overwhelming proportion of data that frequently goes unidentified in viral metagenomic studies. We assigned potential hosts to these phages, which appear to infect a wide range of bacterial genera, often outside their presumed host. We determined that infection networks form a modular-nested pattern, indicating that phages include a range of host specificities, from generalists to specialists, with most interactions organized into distinct groups. We identified genes in viral contigs involved in carbon and sulfur cycling, suggesting functional importance of viruses in circulating pathways and gene functions in the wastewater environment. In addition, we identified virophage genes as well as a nearly complete novel virophage genome. These findings provide an understanding of phage abundance and diversity in NYC wastewater, previously uncharacterized, and further examine geographic patterns of phage-host association in urban environments.IMPORTANCE Wastewater is a rich source of microbial life and contains bacteria, viruses, and other microbes found in human waste as well as environmental runoff sources. As part of an effort to characterize the New York City wastewater metagenome, we profiled the viral community of sewage samples across all five boroughs of NYC and found that local sampling sites have unique sets of viruses. We focused on bacteriophages, or viruses of bacteria, to understand how they may influence the microbial ecology of this system. We identified several new clusters of phages and successfully associated them with bacterial hosts, providing insight into virus-host interactions in urban wastewater. This study provides a first look into the viral communities present across the wastewater system in NYC and points to their functional importance in this environment.},
}

@article {pmid32031212,
year = {2020},
author = {Fenske, GJ and Ghimire, S and Antony, L and Christopher-Hennings, J and Scaria, J},
title = {Integration of culture-dependent and independent methods provides a more coherent picture of the pig gut microbiome.},
journal = {FEMS microbiology ecology},
volume = {96},
number = {3},
pages = {},
doi = {10.1093/femsec/fiaa022},
pmid = {32031212},
issn = {1574-6941},
mesh = {Animals ; Bacteroidetes/genetics ; *Gastrointestinal Microbiome ; Metagenomics ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Swine ; },
abstract = {Bacterial communities resident in the hindgut of pigs, have profound impacts on health and disease. Investigations into the pig microbiome have utilized either culture-dependent, or far more commonly, culture-independent techniques using next generation sequencing. We contend that a combination of both approaches generates a more coherent view of microbiome composition. In this study, we surveyed the microbiome of Tamworth breed and feral pigs through the integration high throughput culturing and shotgun metagenomics. A single culture medium was used for culturing. Selective screens were added to the media to increase culture diversity. In total, 46 distinct bacterial species were isolated from the Tamworth and feral samples. Selective screens successfully shifted the diversity of bacteria on agar plates. Tamworth pigs are highly dominated by Bacteroidetes primarily composed of the genus Prevotella whereas feral samples were more diverse with almost equal proportions of Firmicutes and Bacteroidetes. The combination of metagenomics and culture techniques facilitated a greater retrieval of annotated genes than either method alone. The single medium based pig microbiota library we report is a resource to better understand pig gut microbial ecology and function. It allows for assemblage of defined bacterial communities for studies in bioreactors or germfree animal models.},
}

Animals
Bacteroidetes/genetics
*Gastrointestinal Microbiome
Metagenomics
*Microbiota
RNA, Ribosomal, 16S/genetics
Swine

@article {pmid31506516,
year = {2019},
author = {Bridier, A and Le Grandois, P and Moreau, MH and Prénom, C and Le Roux, A and Feurer, C and Soumet, C},
title = {Impact of cleaning and disinfection procedures on microbial ecology and Salmonella antimicrobial resistance in a pig slaughterhouse.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {12947},
pmid = {31506516},
issn = {2045-2322},
mesh = {Abattoirs ; Animals ; Anti-Bacterial Agents/*pharmacology ; Disinfection/*methods ; *Drug Resistance, Bacterial ; Microbial Sensitivity Tests ; Salmonella/*drug effects ; Salmonella Infections, Animal/*drug therapy/epidemiology/microbiology ; Swine ; Swine Diseases/epidemiology/microbiology/*prevention & control ; },
abstract = {To guarantee food safety, a better deciphering of ecology and adaptation strategies of bacterial pathogens such as Salmonella in food environments is crucial. The role of food processing conditions such as cleaning and disinfection procedures on antimicrobial resistance emergence should especially be investigated. In this work, the prevalence and antimicrobial resistance of Salmonella and the microbial ecology of associated surfaces communities were investigated in a pig slaughterhouse before and after cleaning and disinfection procedures. Salmonella were detected in 67% of samples and isolates characterization revealed the presence of 15 PFGE-patterns belonging to five serotypes: S.4,5,12:i:-, Rissen, Typhimurium, Infantis and Derby. Resistance to ampicillin, sulfamethoxazole, tetracycline and/or chloramphenicol was detected depending on serotypes. 16S rRNA-based bacterial diversity analyses showed that Salmonella surface associated communities were highly dominated by the Moraxellaceae family with a clear site-specific composition suggesting a persistent colonization of the pig slaughterhouse. Cleaning and disinfection procedures did not lead to a modification of Salmonella susceptibility to antimicrobials in this short-term study but they tended to significantly reduce bacterial diversity and favored some genera such as Rothia and Psychrobacter. Such data participate to the construction of a comprehensive view of Salmonella ecology and antimicrobial resistance emergence in food environments in relation with cleaning and disinfection procedures.},
}

Abattoirs
Animals
Anti-Bacterial Agents/*pharmacology
Disinfection/*methods
*Drug Resistance, Bacterial
Microbial Sensitivity Tests
Salmonella/*drug effects
Salmonella Infections, Animal/*drug therapy/epidemiology/microbiology
Swine
Swine Diseases/epidemiology/microbiology/*prevention & control

@article {pmid29134738,
year = {2018},
author = {Xiao, X and Liang, Y and Zhou, S and Zhuang, S and Sun, B},
title = {Fungal community reveals less dispersal limitation and potentially more connected network than that of bacteria in bamboo forest soils.},
journal = {Molecular ecology},
volume = {27},
number = {2},
pages = {550-563},
doi = {10.1111/mec.14428},
pmid = {29134738},
issn = {1365-294X},
mesh = {Biodiversity ; Carbon/metabolism ; China ; Forests ; Fungi/*growth & development ; Microbiota/*genetics ; Plants/genetics/microbiology ; Sasa/genetics/*microbiology ; *Soil Microbiology ; },
abstract = {A central aim of this microbial ecology research was to investigate the mechanisms shaping the assembly of soil microbial communities. Despite the importance of bacterial and fungal mediation of carbon cycling in forest ecosystems, knowledge concerning their distribution patterns and underlying mechanisms remains insufficient. Here, soils were sampled from six bamboo forests across the main planting area of Moso bamboo in southern China. The bacterial and fungal diversities were assessed by sequencing 16S rRNA and ITS gene amplicons, respectively, with an Illumina MiSeq. Based on structural equation modelling, dispersal limitation had strongest impact on bacterial beta diversity, while the mean annual precipitation had a smaller impact by directly or indirectly mediating the soil organic carbon density. However, only the mean annual temperature and precipitation played direct roles in fungal beta diversity. Moreover, the co-occurrence network analyses revealed a possibly much higher network connectivity in the fungal network than in the bacteria. With less dispersal limitation, stronger environmental selection and a potentially more connected network, the fungal community had more important roles in the soil carbon metabolisms in bamboo forests. Fungal beta diversity and the clustering coefficient explained approximately 14.4% and 6.1% of the variation in the carbon metabolic profiles among sites, respectively, but that of bacteria only explained approximately 1.7% and 1.8%, respectively. This study explored soil microbial spatial patterns along with the underlying mechanisms of dispersal limitation, selection and connectivity of ecological networks, thus providing novel insights into the study of the distinct functional traits of different microbial taxa.},
}

Biodiversity
Carbon/metabolism
China
Forests
Fungi/*growth & development
Microbiota/*genetics
Plants/genetics/microbiology
Sasa/genetics/*microbiology
*Soil Microbiology

@article {pmid28680053,
year = {2017},
author = {Cheng, G and Sun, M and Lu, J and Ge, X and Zhang, H and Xu, X and Lou, L and Lin, Q},
title = {Role of biochar in biodegradation of nonylphenol in sediment: Increasing microbial activity versus decreasing bioavailability.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {4726},
pmid = {28680053},
issn = {2045-2322},
mesh = {Bacteria/drug effects ; Biodegradation, Environmental ; Biological Availability ; Charcoal/*chemistry ; Geologic Sediments/chemistry/*microbiology ; Oryza/chemistry ; Phenols/*chemistry/toxicity ; Soil Pollutants/chemistry ; },
abstract = {The observed strong sorption of hydrophobic organic contaminants (HOCs) to biochar presents potential implications for HOCs bioavailability and bioaccessibility in sediments, while biochar could impact sediment microbial ecology. However, the comprehensive study on the effects of biochar on HOC biodegradation coupled with bioavailability and microbial ecology are rarely documented. In this paper, the effects of biochar on the biodegradation of nonylphenol (NP) were investigated using 3 different NP concentrations (20, 50 and 500 mg/Kg) in sediments amended with different percentage of rice straw biochar (RC). Results showed that the influence of RC on NP biodegradation varied with different NP concentrations. At low NP concentrations, RC suppressed NP biodegradation by reducing NP bioavailability, while at high NP concentrations, moderate RC addition promoted biodegradation by reducing toxicity of NP to microbes. The effects of NP on microbial community structures were significant (P < 0.01), but those of RC were not significant (P > 0.05). The RC affected microorganisms through altering NP toxicity, microbial quantity and activity, but not microbial community structures. This study indicated that there could be an optimal biochar percentage in biochar-sediment systems at different HOC concentrations, which strengthened HOC biodegradation process and accelerated biodegradation rate, forming adsorption-biodegradation coupled bioremediation.},
}

Bacteria/drug effects
Biodegradation, Environmental
Biological Availability
Charcoal/*chemistry
Geologic Sediments/chemistry/*microbiology
Oryza/chemistry
Phenols/*chemistry/toxicity
Soil Pollutants/chemistry

@article {pmid27144092,
year = {2016},
author = {Marques, C and Meireles, M and Norberto, S and Leite, J and Freitas, J and Pestana, D and Faria, A and Calhau, C},
title = {High-fat diet-induced obesity Rat model: a comparison between Wistar and Sprague-Dawley Rat.},
journal = {Adipocyte},
volume = {5},
number = {1},
pages = {11-21},
pmid = {27144092},
issn = {2162-3945},
abstract = {In the past decades, obesity and associated metabolic complications have reached epidemic proportions. For the study of these pathologies, a number of animal models have been developed. However, a direct comparison between Wistar and Sprague-Dawley (SD) Rat as models of high-fat (HF) diet-induced obesity has not been adequately evaluated so far. Wistar and SD rats were assigned for 2 experimental groups for 17 weeks: standard (St) and high-fat (HF) diet groups. To assess some of the features of the metabolic syndrome, oral glucose tolerance tests, systolic blood pressure measurements and blood biochemical analysis were performed throughout the study. The gut microbiota composition of the animals of each group was evaluated at the end of the study by real-time PCR. HF diet increased weight gain, body fat mass, mesenteric adipocyte's size, adiponectin and leptin plasma levels and decreased oral glucose tolerance in both Wistar and SD rats. However, the majority of these effects were more pronounced or earlier detected in Wistar rats. The gut microbiota of SD rats was less abundant in Bacteroides and Prevotella but richer in Bifidobacterium and Lactobacillus comparatively to the gut microbiota of Wistar rats. Nevertheless, the modulation of the gut microbiota by HF diet was similar in both strains, except for Clostridium leptum that was only reduced in Wistar rats fed with HF diet. In conclusion, both Wistar and SD Rat can be used as models of HF diet-induced obesity although the metabolic effects caused by HF diet seemed to be more pronounced in Wistar Rat. Differences in the gut microbial ecology may account for the worsened metabolic scenario observed in Wistar Rat.},
}

@article {pmid25567040,
year = {2015},
author = {Huang, YJ and Boushey, HA},
title = {The microbiome in asthma.},
journal = {The Journal of allergy and clinical immunology},
volume = {135},
number = {1},
pages = {25-30},
pmid = {25567040},
issn = {1097-6825},
support = {K23 HL105572/HL/NHLBI NIH HHS/United States ; },
mesh = {Allergens ; Animals ; Asthma/*microbiology ; Environmental Exposure ; Gastrointestinal Tract/*microbiology ; Humans ; *Microbiota ; Respiratory System/microbiology ; Respiratory Tract Infections/microbiology ; Virus Diseases/microbiology ; },
abstract = {The application of recently developed sensitive, specific, culture-independent tools for identification of microbes is transforming concepts of microbial ecology, including concepts of the relationships between the vast complex populations of microbes associated with ourselves and with states of health and disease. Although most work initially focused on the community of microbes (microbiome) in the gastrointestinal tract and its relationship to gastrointestinal disease, interest has expanded to include study of the relationships of the airway microbiome to asthma and its phenotypes and to the relationships between the gastrointestinal microbiome, development of immune function, and predisposition to allergic sensitization and asthma. Here we provide our perspective on the findings of studies of differences in the airway microbiome between asthmatic patients and healthy subjects and of studies of relationships between environmental microbiota, gut microbiota, immune function, and asthma development. In addition, we provide our perspective on how these findings suggest the broad outline of a rationale for approaches involving directed manipulation of the gut and airway microbiome for the treatment and prevention of allergic asthma.},
}

Allergens
Animals
Asthma/*microbiology
Environmental Exposure
Gastrointestinal Tract/*microbiology
Humans
*Microbiota
Respiratory System/microbiology
Respiratory Tract Infections/microbiology
Virus Diseases/microbiology

@article {pmid25033448,
year = {2014},
author = {Baron, JL and Vikram, A and Duda, S and Stout, JE and Bibby, K},
title = {Shift in the microbial ecology of a hospital hot water system following the introduction of an on-site monochloramine disinfection system.},
journal = {PloS one},
volume = {9},
number = {7},
pages = {e102679},
pmid = {25033448},
issn = {1932-6203},
mesh = {Actinobacteria/genetics/growth & development ; Base Sequence ; Biofilms/drug effects/growth & development ; Chloramines/*pharmacology ; Cyanobacteria/genetics/growth & development ; DNA, Bacterial/genetics ; Disinfectants/pharmacology ; Disinfection/*methods ; Drinking Water/*microbiology ; *Hospital Distribution Systems ; Proteobacteria/genetics/growth & development ; RNA, Ribosomal, 16S/genetics ; Sanitary Engineering ; Sequence Analysis, DNA ; Tertiary Care Centers ; Water Microbiology ; Water Purification/*methods ; Water Quality ; },
abstract = {Drinking water distribution systems, including premise plumbing, contain a diverse microbiological community that may include opportunistic pathogens. On-site supplemental disinfection systems have been proposed as a control method for opportunistic pathogens in premise plumbing. The majority of on-site disinfection systems to date have been installed in hospitals due to the high concentration of opportunistic pathogen susceptible occupants. The installation of on-site supplemental disinfection systems in hospitals allows for evaluation of the impact of on-site disinfection systems on drinking water system microbial ecology prior to widespread application. This study evaluated the impact of supplemental monochloramine on the microbial ecology of a hospital's hot water system. Samples were taken three months and immediately prior to monochloramine treatment and monthly for the first six months of treatment, and all samples were subjected to high throughput Illumina 16S rRNA region sequencing. The microbial community composition of monochloramine treated samples was dramatically different than the baseline months. There was an immediate shift towards decreased relative abundance of Betaproteobacteria, and increased relative abundance of Firmicutes, Alphaproteobacteria, Gammaproteobacteria, Cyanobacteria and Actinobacteria. Following treatment, microbial populations grouped by sampling location rather than sampling time. Over the course of treatment the relative abundance of certain genera containing opportunistic pathogens and genera containing denitrifying bacteria increased. The results demonstrate the driving influence of supplemental disinfection on premise plumbing microbial ecology and suggest the value of further investigation into the overall effects of premise plumbing disinfection strategies on microbial ecology and not solely specific target microorganisms.},
}

Actinobacteria/genetics/growth & development
Base Sequence
Biofilms/drug effects/growth & development
Chloramines/*pharmacology
Cyanobacteria/genetics/growth & development
DNA, Bacterial/genetics
Disinfectants/pharmacology
Disinfection/*methods
Drinking Water/*microbiology
*Hospital Distribution Systems
Proteobacteria/genetics/growth & development
RNA, Ribosomal, 16S/genetics
Sanitary Engineering
Sequence Analysis, DNA
Tertiary Care Centers
Water Microbiology
Water Purification/*methods
Water Quality

@article {pmid24704907,
year = {2014},
author = {Brooks, JP and Adeli, A and McLaughlin, MR},
title = {Microbial ecology, bacterial pathogens, and antibiotic resistant genes in swine manure wastewater as influenced by three swine management systems.},
journal = {Water research},
volume = {57},
number = {},
pages = {96-103},
doi = {10.1016/j.watres.2014.03.017},
pmid = {24704907},
issn = {1879-2448},
mesh = {Animal Husbandry/*methods ; Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects/*genetics/*isolation & purification ; Bacterial Proteins/genetics/metabolism ; Drug Resistance, Bacterial/*genetics ; Manure/*microbiology ; Methicillin-Resistant Staphylococcus aureus/drug effects/genetics/isolation & purification ; *Microbiota ; RNA, Ribosomal, 16S/genetics/metabolism ; Real-Time Polymerase Chain Reaction ; Southeastern United States ; Sus scrofa ; Wastewater/*microbiology ; },
abstract = {The environmental influence of farm management in concentrated animal feeding operations (CAFO) can yield vast changes to the microbial biota and ecological structure of both the pig and waste manure lagoon wastewater. While some of these changes may not be negative, it is possible that CAFOs can enrich antibiotic resistant bacteria or pathogens based on farm type, thereby influencing the impact imparted by the land application of its respective wastewater. The purpose of this study was to measure the microbial constituents of swine-sow, -nursery, and -finisher farm manure lagoon wastewater and determine the changes induced by farm management. A total of 37 farms were visited in the Mid-South USA and analyzed for the genes 16S rRNA, spaQ (Salmonella spp.), Camp-16S (Campylobacter spp.), tetA, tetB, ermF, ermA, mecA, and intI using quantitative PCR. Additionally, 16S rRNA sequence libraries were created. Overall, it appeared that finisher farms were significantly different from nursery and sow farms in nearly all genes measured and in 16S rRNA clone libraries. Nearly all antibiotic resistance genes were detected in all farms. Interestingly, the mecA resistance gene (e.g. methicillin resistant Staphylococcus aureus) was below detection limits on most farms, and decreased as the pigs aged. Finisher farms generally had fewer antibiotic resistance genes, which corroborated previous phenotypic data; additionally, finisher farms produced a less diverse 16S rRNA sequence library. Comparisons of Camp-16S and spaQ GU (genomic unit) values to previous culture data demonstrated ratios from 10 to 10,000:1 depending on farm type, indicating viable but not cultivatable bacteria were dominant. The current study indicated that swine farm management schemes positively and negatively affect microbial and antibiotic resistant populations in CAFO wastewater which has future "downstream" implications from both an environmental and public health perspective.},
}

Animal Husbandry/*methods
Animals
Anti-Bacterial Agents/pharmacology
Bacteria/drug effects/*genetics/*isolation & purification
Bacterial Proteins/genetics/metabolism
Drug Resistance, Bacterial/*genetics
Manure/*microbiology
Methicillin-Resistant Staphylococcus aureus/drug effects/genetics/isolation & purification
*Microbiota
RNA, Ribosomal, 16S/genetics/metabolism
Real-Time Polymerase Chain Reaction
Southeastern United States
Sus scrofa
Wastewater/*microbiology

@article {pmid24296350,
year = {2013},
author = {Hannigan, GD and Grice, EA},
title = {Microbial ecology of the skin in the era of metagenomics and molecular microbiology.},
journal = {Cold Spring Harbor perspectives in medicine},
volume = {3},
number = {12},
pages = {a015362},
pmid = {24296350},
issn = {2157-1422},
support = {P30 AR057217/AR/NIAMS NIH HHS/United States ; R00 AR060873/AR/NIAMS NIH HHS/United States ; AR060873/AR/NIAMS NIH HHS/United States ; AR057217/AR/NIAMS NIH HHS/United States ; },
mesh = {Alphapapillomavirus/physiology ; Biodiversity ; Fungi/physiology ; Humans ; Malassezia/physiology ; Metagenomics/trends ; Microbiology/trends ; Microbiota/physiology ; Skin/*microbiology ; Skin Diseases, Infectious/diagnosis/*microbiology ; },
abstract = {The skin is the primary physical barrier between the body and the external environment and is also a substrate for the colonization of numerous microbes. Previously, dermatological microbiology research was dominated by culture-based techniques, but significant advances in genomic technologies have enabled the development of less-biased, culture-independent approaches to characterize skin microbial communities. These molecular microbiology approaches illustrate the great diversity of microbiota colonizing the skin and highlight unique features such as site specificity, temporal dynamics, and interpersonal variation. Disruptions in skin commensal microbiota are associated with the progression of many dermatological diseases. A greater understanding of how skin microbes interact with each other and with their host, and how we can therapeutically manipulate those interactions, will provide powerful tools for treating and preventing dermatological disease.},
}

Alphapapillomavirus/physiology
Biodiversity
Fungi/physiology
Humans
Malassezia/physiology
Metagenomics/trends
Microbiology/trends
Microbiota/physiology
Skin/*microbiology
Skin Diseases, Infectious/diagnosis/*microbiology

@article {pmid23736549,
year = {2013},
author = {Zhang, N and Liu, W and Yang, H and Yu, X and Gutknecht, JL and Zhang, Z and Wan, S and Ma, K},
title = {Soil microbial responses to warming and increased precipitation and their implications for ecosystem C cycling.},
journal = {Oecologia},
volume = {173},
number = {3},
pages = {1125-1142},
pmid = {23736549},
issn = {1432-1939},
mesh = {Acclimatization/*physiology ; Analysis of Variance ; Bacteria/metabolism ; Carbon Cycle/*physiology ; China ; *Ecosystem ; *Global Warming ; *Rain ; *Soil Microbiology ; },
abstract = {A better understanding of soil microbial ecology is critical to gaining an understanding of terrestrial carbon (C) cycle-climate change feedbacks. However, current knowledge limits our ability to predict microbial community dynamics in the face of multiple global change drivers and their implications for respiratory loss of soil carbon. Whether microorganisms will acclimate to climate warming and ameliorate predicted respiratory C losses is still debated. It also remains unclear how precipitation, another important climate change driver, will interact with warming to affect microorganisms and their regulation of respiratory C loss. We explore the dynamics of microorganisms and their contributions to respiratory C loss using a 4-year (2006-2009) field experiment in a semi-arid grassland with increased temperature and precipitation in a full factorial design. We found no response of mass-specific (per unit microbial biomass C) heterotrophic respiration to warming, suggesting that respiratory C loss is directly from microbial growth rather than total physiological respiratory responses to warming. Increased precipitation did stimulate both microbial biomass and mass-specific respiration, both of which make large contributions to respiratory loss of soil carbon. Taken together, these results suggest that, in semi-arid grasslands, soil moisture and related substrate availability may inhibit physiological respiratory responses to warming (where soil moisture was significantly lower), while they are not inhibited under elevated precipitation. Although we found no total physiological response to warming, warming increased bacterial C utilization (measured by BIOLOG EcoPlates) and increased bacterial oxidation of carbohydrates and phenols. Non-metric multidimensional scaling analysis as well as ANOVA testing showed that warming or increased precipitation did not change microbial community structure, which could suggest that microbial communities in semi-arid grasslands are already adapted to fluctuating climatic conditions. In summary, our results support the idea that microbial responses to climate change are multifaceted and, even with no large shifts in community structure, microbial mediation of soil carbon loss could still occur under future climate scenarios.},
}

Acclimatization/*physiology
Analysis of Variance
Bacteria/metabolism
Carbon Cycle/*physiology
China
*Ecosystem
*Global Warming
*Rain
*Soil Microbiology

@article {pmid1345176,
year = {1992},
author = {Molin, S},
title = {Designing microbes for release into the environment.},
journal = {Science progress},
volume = {76},
number = {300 Pt 2},
pages = {139-148},
pmid = {1345176},
issn = {0036-8504},
mesh = {Bacteria/*genetics ; Containment of Biohazards ; Ecology ; *Genetic Engineering ; },
abstract = {After 20 years in which gene technology has become an important part of modern biotechnology we have seen very beneficial applications of the new techniques in the pharmaceutical industry. We are now entering a second phase involving the deliberate release of genetically engineered organisms into the environment. This next step causes concern because of a low level of predictability of their possible effects. While the risk assessment of microbial release is far from easy, the strain designers also face problems concerning optimization of performance of the organisms. The two groups of actors in this new development--the risk assessors and the strain designers--need the same platform of understanding from the field of microbial ecology, and a number of specific areas which may now be approached by modern technology deserve particular attention. An increased understanding of the activities of microbes in the environment will also allow construction of more predictable, and therefore safer, strains. Biological containment and molecular microbial ecology are two sides of the same coin in the context of release of genetically engineered microorganisms.},
}

Bacteria/*genetics
Containment of Biohazards
Ecology
*Genetic Engineering

@article {pmid40822855,
year = {2025},
author = {Roman, FA and Byrne, T and Martin, RL and Mena-Aguilar, D and Smeltz, RE and Finkelstein, R and Pruden, A and Edwards, MA},
title = {Retrospective Analysis of Drinking Water Microcosm Microbiomes Reveals an Apparent Antagonistic Relationship between and.},
journal = {Environmental science & technology letters},
volume = {12},
number = {8},
pages = {990-996},
doi = {10.1021/acs.estlett.5c00590},
pmid = {40822855},
issn = {2328-8930},
abstract = {(Lp) can sometimes establish in drinking water microbial communities and infect individuals inhaling contaminated aerosols. The premise plumbing portion of the drinking water distribution system is often especially vulnerable to Lp growth. Innovative approaches to intentionally manipulate the microbial ecology to control Lp have been proposed but remain elusive. Here, we retrospectively analyzed 16S rRNA gene amplicon sequences and droplet digital PCR data in samples derived from prior drinking water studies, wherein some inexplicable stochastic variations in the Lp occurrence were observed in replicate microcosms. We discovered an apparent antagonistic relationship between and . This relationship was noted across three water sources (Flint, Detroit, and Blacksburg) and was at least partially mediated by the presence of copper, through either copper pipes or a dosed range of 0-2000 μg/L total copper. The observations of this study, which was conducted under realistic drinking water conditions harboring mixed microbial communities, are consistent with recent pure culture studies reporting that amoebic uptake may be inhibited when are established as amoebal endosymbionts. The findings may help explain the apparent stochastic behavior of Lp in field and research settings and may open a door to new engineered ecological control strategies for Lp.},
}

@article {pmid40818553,
year = {2025},
author = {Galinytė, D and Aroffu, M and Manconi, M and Žilius, M and Rysevaitė-Kyguolienė, K and Karosienė, J and Koreivienė, J and Briedis, V and Pauža, DH and Savickas, A and Ferrer, EE and Manca, ML and Savickienė, N},
title = {Cyano-phycocyanin loaded enriched transfersomes for enhanced topical skin delivery and antioxidant protection.},
journal = {International journal of pharmaceutics},
volume = {},
number = {},
pages = {126079},
doi = {10.1016/j.ijpharm.2025.126079},
pmid = {40818553},
issn = {1873-3476},
abstract = {This study aimed to develop and evaluate cyano-phycocyanin (C-PC)-loaded enriched transfersomes for topical application, improved skin delivery, and antioxidant protection. The main objective was to overcome the limitations associated with C-PC's instability and poor skin permeability due to its high molecular weight and hydrophilicity. Six formulations were prepared using an organic solvent-free two-step method: glycerol-enriched transfersomes (Gly-transfersomes),glycerol and cholesterol-enriched transfersomes (Gly-chol-transfersomes),hyaluronate-enriched transfersomes (Hyal-transfersomes),hyaluronate and cholesterol-enriched transfersomes (Hyal-chol-transfersomes),glycerol and hyaluronate-enriched transfersomes (Hyal-gly-transfersomes), anda combination of all three (Hyal-gly-chol-transfersomes). Empty vesicles were prepared via direct sonication, then C-PC was gently loaded using mild sonication in a temperature-controlled ultrasonic bath. All formulations demonstrated properties suitable for skin delivery, with mean diameters <115 nm, polydispersity indexes <0.2, and zeta potential below -30 mV. Cryo- transmission electron microscopy confirmed spherical, unilamellar or oligolamellar morphology. Gly- and Gly-chol-transfersomes exhibited the highest encapsulation efficiency (∼52 %) and remained stable for up to 8 months at 4 °C. Antioxidant activity of C-PC (∼23-27 μmol TE/g of dry C-PC) was confirmed via DPPH assay. Biological tests on HaCaT cells exposed to H2O2-induced oxidative stress showed ∼80 % cell viability after treatment with C-PC formulations, compared to ∼60 % in untreated cells, indicating cytoprotective activity. Ex vivo skin penetration studies revealed significantly higher C-PC accumulation in the epidermis especially for Gly- and Gly-chol-transfersomes versus aqueous C-PC. These findings confirm the potential of enriched transfersomes as effective carriers to improve the skin delivery and bioactivity of C-PC in antioxidant skin care formulations.},
}

@article {pmid40815942,
year = {2025},
author = {McDonagh, F and Ryan, K and Kovářová, A and Tumeo, A and Clarke, C and Cormican, M and Miliotis, G},
title = {Identification of blaESBL- and blaCARBA- Positive Multi-Drug Resistant Mixta calida Isolates from Distinct Human Hosts.},
journal = {International journal of medical microbiology : IJMM},
volume = {320},
number = {},
pages = {151669},
doi = {10.1016/j.ijmm.2025.151669},
pmid = {40815942},
issn = {1618-0607},
abstract = {OBJECTIVE: This study aimed to investigate the identification of blaCARBA-positive multidrug-resistant Mixta calida isolates from human hosts and to elucidate their genomic determinants in a species-wide context.

METHODS: Two carbapenemase-producing M. calida isolates were received by the Galway Reference Laboratory Service in Ireland between June and July 2024. One isolate originated from a sputum sample, while the other was recovered from a routine screening rectal swab. Initial identification was performed using MALDI-ToF mass spectrometry, with genomic confirmation via 16S rRNA sequencing, digital DNA-DNA hybridization, and Average Nucleotide Identity analysis. Antimicrobial susceptibility testing was conducted using a MicroScan panel, following EUCAST and CLSI guidelines. Whole-genome sequencing, plasmid replicon typing, and antibiotic-resistance-gene and virulence-factor profiling were employed. Comparative analysis included all additional canonical M. calida genomes from NCBI database.

RESULTS: Both Irish isolates were taxonomically placed as M. calida and exhibited multidrug resistance against penicillins, cephalosporins, monobactams and ertapenem. The acquired genes blaKPC-3, blaOXA-9, and blaTEM-122 were detected on plasmid-borne contigs, indicating horizontal acquisition. Seven plasmid replicon types were shared between the two isolates. Both plasmid replicons and acquired antimicrobial-resistance-genes (ARGs) were seldomly identified across the species. Phylogenetic inference based on core genome analysis identified a monophyletic cluster, suggesting a single introductory event.

CONCLUSION: This study documents a dual occurrence of blaCARBA-positive M. calida in human colonisation and infection. The findings highlight the potential for horizontal-gene-transfer to drive the emergence of multidrug-resistant profiles in the species, underscoring the need for enhanced surveillance, diagnostic precision, and targeted infection control strategies to mitigate public health risks.

IMPACT STATEMENT: This study reports blaESBL and blaCARBA-positive multi-drug resistant Mixta calida isolates from distinct human hosts. Genomic analysis revealed the co-occurrence of plasmid-borne resistance genes blaKPC-3, blaOXA-9, and blaTEM-122. Species-wide phylogenetic analysis grouped the two isolates into a monophyletic cluster, suggesting a single introductory event.},
}

@article {pmid40815475,
year = {2025},
author = {Kondrotaite, Z and Petersen, J and Singleton, C and Peces, M and Petriglieri, F and Jensen, TBN and Sereika, M and Daugberg, AOH and Wagner, M and Dueholm, MKD and Nielsen, PH},
title = {Ecophysiology and niche differentiation of three genera of polyphosphate-accumulating bacteria in a full-scale wastewater treatment plant.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0032225},
doi = {10.1128/msystems.00322-25},
pmid = {40815475},
issn = {2379-5077},
abstract = {Polyphosphate-accumulating organisms (PAOs) are the main bacteria responsible for phosphorus removal and recovery in full-scale wastewater treatment plants (WWTPs). They encompass members of the genera Candidatus Accumulibacter, Azonexus (formerly Dechloromonas), and Candidatus Phosphoribacter (formerly Tetrasphaera), with most studies focusing on Ca. Accumulibacter, primarily using lab-scale enrichment cultures. Although members from the three genera often co-exist in full-scale WWTPs, the metabolic capabilities and traits that determine the niche differentiation of the specific species are still unknown. We retrieved 214 high-quality metagenome-assembled genomes from a full-scale plant with phosphorus removal and examined the polyphosphate-related metabolic pathways using genome-resolved metatranscriptomics in the different process tanks in situ and by using short-term incubations ex situ. We observed the co-existence of nine uncultured PAO species from the three genera with clear niche differentiation in the utilization of different carbon sources and involvement in the denitrification process. Additionally, we observed several physiological differences among species of the same genus, indicating variations in niche specialization. This suggests that biological P removal and other processes in full-scale WWTPs are carried out by a complex and diverse PAO community that together ensures stable plant performance.IMPORTANCEThe current understanding of the ecology and physiology of polyphosphate-accumulating organisms (PAOs) is mostly based on Candidatus Accumulibacter, primarily studied in enriched lab-scale studies. Recent taxonomic reclassification revealed that the most studied Ca. Accumulibacter species are either not present or present in low abundance in full-scale wastewater treatment plants (WWTPs). This raises concerns that knowledge from lab-scale studies may not apply to species in full-scale plants. Additionally, the indication of a distinct PAO physiology in Candidatus Phosphoribacter compared to Ca. Accumulibacter and the other abundant PAO Ca. Azonexus poses further questions about the accuracy of the current PAO model. Here, we show that in full-scale plant species from Ca. Accumulibacter, Ca. Azonexus, and Ca. Phosphoribacter always co-exist, and they have distinct niche separations in terms of carbon source utilization and the use of electron acceptors. This co-existence and metabolic diversity indicate that a complex microbial community is crucial for efficient phosphorus removal in full-scale WWTPs.},
}

@article {pmid40812274,
year = {2025},
author = {Bermúdez, JR and Metian, M and Swarzenski, PW and Bank, MS and Bjorøy, Ø and Cajas, J and Bucheli, R and González-Muñoz, R and Lynch, J and Piguave, E and Vargas, N and Vilela, K and Calle, L and Borbor-Cordova, MJ and Gaibor, N},
title = {Marine microplastics on the rise in the Eastern Tropical Pacific: Abundance doubles in 11 years and a ten-fold increase is projected by 2100.},
journal = {Marine pollution bulletin},
volume = {221},
number = {},
pages = {118437},
doi = {10.1016/j.marpolbul.2025.118437},
pmid = {40812274},
issn = {1879-3363},
abstract = {Plastic abundance in the ocean has increased systematically since the mid-20th century. Here we present a time-series dataset of microplastic abundance collected at several stations located in the Eastern Tropical Pacific Ocean off Ecuador from 2008 to 2018. The data reveals a significant and sustained increase in the abundance of microplastics over time across all sampling sites; this implies a homogeneous and sustained input, which likely also occurs at other coastal and marine ecosystems. Fiber strands were the most common microplastic observed, while polyethylene and polypropylene were the principal polymers identified by μFTIR analysis. A forecast model of the time-series data predicted that microplastics will be 3.2, 5.1 and 9.7 times more abundant in 2030, 2050 and 2100, respectively, relative to 2008 observations. These results provide insights into the decade-plus trend in microplastic abundance observed in coastal waters, which have important implications for future marine plastic pollution projections and associated ecosystem impacts.},
}

@article {pmid40812176,
year = {2025},
author = {Ramirez-Villacis, DX and Leon-Reyes, A and Pieterse, CMJ and Raaijmakers, JM},
title = {Born to rewild: Reconnecting beneficial plant-microbiome alliances for resilient future crops.},
journal = {Cell host & microbe},
volume = {33},
number = {8},
pages = {1241-1255},
doi = {10.1016/j.chom.2025.06.017},
pmid = {40812176},
issn = {1934-6069},
abstract = {Plant domestication is a coevolutionary process shaped by human selection, favoring traits supporting modern-day agriculture. This process has reduced genetic diversity and fixed alleles for desirable traits, coinciding with changes in agricultural practices, particularly soil tilling, crop monocultures, and the (over)use of fertilizers and pesticides. The combined effects-collectively termed "domestication syndrome"-have contributed to the homogenization of soil and plant-associated microbial communities, reducing diversity and disrupting beneficial plant-microbiome alliances. Microbiome rewilding has uncovered ecological, genetic, and molecular principles underlying these depleted plant-microbiome partnerships. Studies have revealed ancestral microbial taxa enriched in wild crop relatives, plant genes, and metabolites critical for microbial recruitment, as well as the potential of reintroducing microbes to enhance nutrient uptake, pathogen resistance, and stress tolerance. These findings offer models for restoring such interactions in modern crops. We review the current state of crop microbiome rewilding and highlight how these discoveries are instrumental for designing resilient crop systems.},
}

@article {pmid40812095,
year = {2025},
author = {Rodríguez-González, L and Santás-Miguel, V and Alexandropoulou, S and Rousk, J},
title = {Effects of salinisation on Cu-contaminated vineyard soils: Assessment of changes in microbial communities and resistance to salt, Cu, and antibiotics.},
journal = {Ecotoxicology and environmental safety},
volume = {303},
number = {},
pages = {118838},
doi = {10.1016/j.ecoenv.2025.118838},
pmid = {40812095},
issn = {1090-2414},
abstract = {Climate change increases the risk of soil salinisation in Southern European vineyards. In this study, six of those soils were experimentally salinised, half of which were contaminated with Cu, a widely used fungicide. Changes in soil microbiota were assessed, including bacterial and fungal growth, respiration, carbon use efficiency calculation, and microbial community phospholipid fatty acids composition. The study also investigated whether salinisation induced a shift in the bacterial community toward increased tolerance to salt, Cu, and the antibiotics tetracycline and vancomycin. Results showed that experimental salinisation decreased bacterial growth and respiration, increased fungal growth, and limited fungal, bacterial, and microbial biomass. These effects were strongest in soils with high initial Cu content. In such soils, tolerance to salt stress was more pronounced, and salt-induced tolerance to vancomycin was observed. In contrast, tolerances to Cu and tetracycline antibiotic were not significantly increased by either Cu or salt. Subsequently, the soils underwent leaching, and analyses were repeated. Most changes in microbial parameters and tolerances were reversed, with soil texture being a particularly influential factor. However, leaching caused Cu tolerance in soils that had been salinised and had high Cu content to be greater than in soils that had not been salinised, regardless of whether they had high or low Cu content. After leaching, vancomycin tolerance also became positively correlated with soil Cu content in soils with low Cu levels. This preliminary study explored salinisation effects on soils, revealing possible bacterial resistance linked to past conditions and microbial shifts. Further research is needed to broaden the dataset and explore the underlying mechanisms and microbial species involved.},
}

@article {pmid40811531,
year = {2025},
author = {Guo, D and Liu, Z and Raaijmakers, JM and Xu, Y and Yang, J and Erb, M and Zhang, J and Zhu, YG and Xu, J and Hu, L},
title = {Linalool-triggered plant-soil feedback drives defense adaptation in dense maize plantings.},
journal = {Science (New York, N.Y.)},
volume = {389},
number = {6761},
pages = {eadv6675},
doi = {10.1126/science.adv6675},
pmid = {40811531},
issn = {1095-9203},
abstract = {High planting density boosts crop yields but also heightens pest and pathogen risks. How plants adapt their defenses under these conditions remains unclear. In this study, we reveal that maize enhances its defense in high-density conditions through a plant-soil feedback mechanism triggered by the leaf volatile linalool. Linalool activates jasmonate signaling in neighboring plants and promotes root exudation of benzoxazinoids, especially 2-(2-hydroxy-4,7-dimethoxy-1,4-benzoxazin-3-one)-β-d-glucopyranose (HDMBOA-Glc). These exudates in turn reshape the rhizosphere microbiome composition to favor growth of specific bacterial taxa that trigger broad-spectrum resistance, albeit at the cost of maize growth. This microbiome-driven feedback loop is governed by salicylic acid signaling. Our findings uncover intricate chemical signaling in high-density cropping, which is instrumental for improving soil health and designing sustainable strategies that balance the trade-off between plant growth and defense.},
}

@article {pmid40810014,
year = {2025},
author = {Fischer, MH and Rzepczynska, A and Kjøller, R},
title = {Taxonomic diversity in the global wheat phyllosphere mycobiome - a meta analysis.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1597807},
pmid = {40810014},
issn = {1664-462X},
abstract = {Wheat (Triticum aestivum L.) is a major crop grown on all continents. Due to environmental concerns, it is desirable to reduce the inputs of both chemical pesticides and inorganic fertilizers. However, yield reduction must be expected when switching to low-input systems. To mitigate such losses, the use of natural or introduced microbiomes may provide the key to maintaining sustainable yield. Phyllosphere fungi, both endophytic and phylloplane-associated, colonize aboveground plant structures, some of which have the potential to mitigate biotic and abiotic stressors. A first step toward realizing the potential of the wheat microbiome is to map the current knowledge on wheat phyllosphere fungi. This meta-analysis aims to map the diversity and abundance of fungal taxa associated with the wheat phyllosphere across global wheat-producing areas. To this end, we searched previous published literature and retrieved fungal community data from relevant studies. Retrieved studies included both culturing-based and metabarcoding amplicon sequence-based studies. We retrieved and analyzed 33 studies from five regions across the world, which differed greatly in their taxonomic composition. Across all regions, we found that while the majority of identified genera were unique to individual studies, some genera occurred across all five wheat growing regions, specifically Alternaria, Aspergillus, Bipolaris, Candida, Chaetomium, Cladosporium, Epicoccum, Fusarium, Nigrospora, Penicillium, Pyrenophora, Stemphylium and Trichoderma. Furthermore, we identified that while community composition differed between wheat growing regions, the identification method used was the most significant factor determining the depiction of community composition. We also highlight a lack of research in important wheat growing regions that are important for global wheat production. These considerations and other knowledge gaps are used to pinpoint future research.},
}

@article {pmid40809124,
year = {2024},
author = {Trego, A and Palmeiro-Sánchez, T and Graham, A and Ijaz, UZ and O'Flaherty, V},
title = {First evidence for temperature's influence on the enrichment, assembly, and activity of polyhydroxyalkanoate-synthesizing mixed microbial communities.},
journal = {Frontiers in systems biology},
volume = {4},
number = {},
pages = {1375472},
pmid = {40809124},
issn = {2674-0702},
abstract = {Polyhydroxyalkanoates (PHA) are popular biopolymers due to their potential use as biodegradable thermoplastics. In this study, three aerobic sequencing batch reactors were operated identically except for their temperatures, which were set at 15 °C, 35 °C, and 48 °C. The reactors were subjected to a feast-famine feeding regime, where carbon sources are supplied intermittently, to enrich PHA-accumulating microbial consortia. The biomass was sampled for 16S rRNA gene amplicon sequencing of both DNA (during the enrichment phase) and cDNA (during the enrichment and accumulation phases). All temperatures yielded highly enriched PHA-accumulating consortia. Thermophilic communities were significantly less diverse than those at low or mesophilic temperatures. In particular, Thauera was highly adaptable, abundant, and active at all temperatures. Low temperatures resulted in reduced PHA production rates and yields. Analysis of the microbial community revealed a collapse of community diversity during low-temperature PHA accumulation, suggesting that the substrate dosing strategy was unsuccessful at low temperatures. This points to future possibilities for optimizing low-temperature PHA accumulation.},
}

@article {pmid40804956,
year = {2025},
author = {Idres, T and Ibrahim, NA and Lamara, A and Boudjellaba, S and Derguini, A and Basher, NS and Temim, S and Aleissa, MS and Chebloune, Y},
title = {Epidemiological Insights into Maedi-Visna Virus in Algeria: First National Seroprevalence Survey and Risk Factor Profiling in Sheep Herds.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {15},
pages = {},
pmid = {40804956},
issn = {2076-2615},
support = {IMSIU- DDRSP2502//Deanship of Scientific Research at Imam Mohammad Ibn Saud Islamic University (IMSIU)/ ; },
abstract = {Maedi-visna virus (MVV), a small ruminant lentivirus causing chronic multisystemic disease in sheep, poses significant economic burdens due to reduced productivity and a lack of effective treatments. Despite its worldwide prevalence, epidemiological data from Algeria remain absent. This first national seroprevalence study aimed to elucidate MVV distribution, risk factors, and transmission dynamics in Algerian sheep herds. A cross-sectional survey of 1400 sheep across four regions (East, Center, West, South) was conducted, with sera analyzed via indirect ELISA (IDvet). Risk factors (geography, age, sex, breed, farming system) were evaluated using chi-square tests and Cramer's V. Overall seroprevalence was 9.07% (95% CI: 7.57-10.57), with significant variation by sex (females: 20.44% vs. males: 3.68%; p < 0.05), age (1-5 years: 6.86% vs. <1 year: 0.29%; p = 0.01), and region (Central: 3.36% vs. Eastern: 0.86%; p < 0.05). Notably, no association was found with breed or farming system (p ≥ 0.08), contrasting prior studies and suggesting region-specific transmission dynamics. Females exhibited heightened seropositivity, implicating prolonged herd retention and vertical transmission risks. Geographic disparities highlighted industrialized farming in central Algeria as a potential transmission amplifier. Strikingly, seronegative animals in high-prevalence herds hinted at genetic resistance, warranting further investigation. This study provides foundational insights into MVV epidemiology in North Africa, underscoring the need for targeted surveillance, ewe-focused control measures, and genetic research to mitigate transmission. The absence of prior national data elevates its significance, offering actionable frameworks for resource-limited settings and enriching the global understanding of SRLV heterogeneity.},
}

@article {pmid40803134,
year = {2025},
author = {Wu, F and Campbell, BC and Greenfield, P and Hose, GC and Midgley, DJ and George, SC},
title = {There and back again: Genomic insights into microbial life in a recirculating petroleum refinery wastewater biotreatment system.},
journal = {Microbiological research},
volume = {301},
number = {},
pages = {128299},
doi = {10.1016/j.micres.2025.128299},
pmid = {40803134},
issn = {1618-0623},
abstract = {Petroleum refinery wastewater biotreatment relies on microbes to remediate carbon, nitrogen, and sulfur compounds, yet their life strategies and ecological roles remain unclear. This study characterises the ecological functions of 20 metagenome-assembled genomes (MAGs) from a full-scale petroleum refinery wastewater treatment plant in southern China. The taxonomic identity, nutrient metabolism genes (including C/N/S cycling), carbohydrate-active enzymes, and CRISPR-Cas systems of these MAGs were analysed. The recovered MAGs represented bacteria primarily from the Pseudomonadota and Bacteroidota phyla. The major carbon sources for the represented organisms are likely aromatic and aliphatic compounds, as well as carbohydrates including peptidoglycan, chitin, and starch. Almost all MAGs contained genes for nitrate or nitrite reduction, while metabolic pathways for sulfur metabolism were generally less prevalent. Meiothermus sp. bin.89 was the most metabolically versatile MAG. This organism possessed genes that allowed it to recycle biomass, break down aliphatic and monoaromatic compounds, and perform anaerobic respiration using nitrate. However, it was likely the most susceptible to viral predation, as indicated by the high abundance of CRISPR spacers. Overall, the results revealed that stress-tolerant ecological traits were common among organisms in this microbiome, showcasing the ability of the microbes to obtain carbon from aromatic and aliphatic compounds. This study provides a substantial contribution towards future efforts in optimising microbiome stability for pollutant removal in petroleum refinery wastewater biotreatment systems.},
}

@article {pmid40800619,
year = {2025},
author = {van Eijnatten, AL and van Zon, L and Manousou, E and Bikineeva, M and Wubs, ERJ and van der Putten, WH and Morriën, E and Dutilh, BE and Snoek, LB},
title = {SpeSpeNet: an interactive and user-friendly tool to create and explore microbial correlation networks.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf036},
pmid = {40800619},
issn = {2730-6151},
abstract = {Correlation networks are commonly used to explore microbiome data. In these networks, nodes are microbial taxa and edges represent correlations between their abundances. As clusters of correlating taxa (co-abundance clusters) often indicate a shared response to environmental drivers, network visualization contributes to the system understanding. Currently, most tools for creating and visualizing co-abundance networks from microbiome data either require the researcher to have coding skills or are not user-friendly, with high time expenditure and limited customizability. Furthermore, existing tools lack a focus on the association between environmental drivers and the structure of the microbiome, even though many edges in correlation networks can be understood through a shared association of two taxa with the environment. For these reasons, we developed SpeSpeNet (Species-Species Network, https://tbb.bio.uu.nl/SpeSpeNet), a practical and user-friendly R-shiny tool to construct and visualize correlation networks from taxonomic abundance tables. The details of data preprocessing, network construction, and visualization are automated, require no programming ability for the web version, and are highly customizable, including associations with user-provided environmental data. Here, we present the details of SpeSpeNet and demonstrate its utility using three case studies.},
}

@article {pmid40800617,
year = {2025},
author = {Fuschi, A and Merlotti, A and Remondini, D},
title = {Microbiome data: tell me which metrics and I will tell you which communities.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf125},
pmid = {40800617},
issn = {2730-6151},
abstract = {In microbial community studies, analyzing diversity is crucial for uncovering ecological complexity. However, the intrinsic characteristics of Next-gen sequencing data challenge the use of Euclidean metrics for estimating proximity and correlation. Consequently, a variety of distance measures have been developed within ecological frameworks. In this study, we compare several of these metrics-including Bray-Curtis, Canberra, Jensen-Shannon, Hellinger, Euclidean, and Aitchison distances-demonstrating how the choice of metric can significantly influence the interpretation of microbial community structures. Among these, Aitchison distance specifically defined for compositional data shows markedly different behavior from the others, highlighting different features related to the data. We consider two real-world examples: the human gut microbiome sampled using 16S rRNA sequencing with multiple measurements for different patients (G-HMP2) and urban sewage environmental metagenomes collected over time at different sites through shotgun sequencing (E-WADES). We show that, for the same dataset-independently on the sequencing technique or on the sampling context-the community structure depends strongly on the choice of specific metrics. This can be explained by the mathematical properties of the chosen metrics and the specific characteristics of microbiome data, namely their high heterogeneity in species abundance. This provides clear insights into how distance metrics influence interpretation and assists in choosing the most appropriate one for the study objectives.},
}

@article {pmid40799503,
year = {2025},
author = {Parret, L and Simoens, K and De Vrieze, J and Smets, I},
title = {BIO-SPEC: An open-source bench-top parallel bioreactor system.},
journal = {HardwareX},
volume = {23},
number = {},
pages = {e00670},
pmid = {40799503},
issn = {2468-0672},
abstract = {The BIO-SPEC is an open-source, cost-effective, and modular bench-top bioreactor system designed for batch, sequencing batch, and chemostat cultivation. Featuring thermoelectric condensers to eliminate the need for a chiller, it ensures stable long-term operation. Controlled by a Raspberry Pi, the BIO-SPEC offers flexibility in headplate design, gas supply, and feeding strategies, making it a versatile alternative to high-cost commercial systems. This paper details the design, construction, and validation of the BIO-SPEC system, demonstrating its potential to advance microbiology and bioprocessing research through accessible and reliable hardware at a fraction of the cost of commercial systems.},
}

@article {pmid40797302,
year = {2025},
author = {Baborski, A and Barth, SA and Jung, EM and Bloos, F and Rödel, J and Löffler, B and Bauer, M and Busch, A},
title = {Surviving antibiotic treatment as a gut bacterium: genomic characterization of an Enterobacter cloacae.},
journal = {BMC genomic data},
volume = {26},
number = {1},
pages = {56},
pmid = {40797302},
issn = {2730-6844},
abstract = {Enterobacter cloacae complex is a group of common opportunistic pathogens on intensive care units. On intensive care units sepsis is treated with high doses of antibiotics. This treatment does not only eliminate pathogenic bacteria but parts of the microbiome community as well. This leads to an imbalance of the gut microbiome. However, some bacteria can survive such treatment due to certain survival and resistance mechanisms. Not only antibiotic resistance mechanisms but also forming strong communities via biofilm formation promotes cell survival. Here, we investigated the properties of the isolate AT70PIP076 from a sepsis patient treated with piperacillin and tazobactam. After biochemical analysis and MALDI-TOF analysis, the strain was found to be Enterobacter cloacae. In addition to in vitro, antimicrobial susceptibility testing the genome was further investigated in situ regarding antibiotic resistance. Further live/dead staining was performed, and the biofilm formation was investigated using confocal laser microscopy (cLSM). The genome shows the presence of biofilm-associated genes EU554560, bcsABZC_AP010953, ehaB, KF662843, and crl. The understanding of the underlying mechanism of survival of potential pathogens might contribute to elucidate potential treatment options.ObjectivesGenomic analysis of a bacterium that can survive antibiotic treatment within the gut of an antibiotictreated patient to elucidate survival and resistance mechanisms.Data descriptionThe isolate AT70PIP076 was isolated in 2021 from feces collected from a patient treated with Piperacillin and tazobactam. Whole genome DNA was isolated using the Nextera DNA Flex microbial colony extraction protocol and the Nextera Flex DNA preparation kit according to the manufacturer's instructions. Following paired-end sequencing was performed on the MiSeq platform (Illumina, Inc., San Diego, CA, USA) using a 300-cycle MiSeq reagent kit and a read length of 151 bp. Contamination check and identification of 16 S RNA sequences was done by using ContESt16S. The genomic sequence contained 4,988,237 bp and the G + C content is represented at 54.80%. This genome and its associated data set will serve as a useful resource for further analyses.},
}

@article {pmid40797046,
year = {2025},
author = {Wei, L and Chen, S and Qin, Z and Pan, N and Lan, M and Zhang, T and He, R and Liang, H and Deng, W and Mo, C and Yu, K},
title = {Responses of the Coral Symbiont Cladocopium goreaui to Extreme Temperature Stress in Relatively High-Latitude Reefs, South China Sea.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {88},
pmid = {40797046},
issn = {1432-184X},
abstract = {Global climate change has led to frequent extreme temperature events in oceans. Corals are susceptible to extreme high-temperature stress in summer and extreme low-temperature stress in winter in the relatively high-latitude reef areas of the South China Sea (SCS). The most abundant symbiotic coral Symbiodiniaceae in the higher-latitude reefs of the SCS is Cladocopium goreaui, predominantly associating with dominant coral hosts such as Acropora and Porites. However, to date, relatively few studies have focused on the response and mechanism of C. goreaui to the extreme high- and low-temperature stress. In this study, the responses and regulatory mechanisms of the dominant C. goreaui to extreme high- and low-temperature stress were investigated based on physiological indexes, transmission electron microscopy (TEM), and transcriptome analysis. The results showed that (1) under 34 °C heat stress, the disintegration of thylakoids triggered photosynthetic collapse in C. goreaui; survival is enabled through metabolic reprogramming that upregulates five protective pathways and redirects energy via pentose/glucuronate shunting to sustain ATP homeostasis, revealing a trade-off between damage containment and precision energy governance under thermal extremes. (2) Low temperature exposure induced suppression of maximum quantum yield (Fv/Fm), compounded by glutathione pathway inhibition, crippling ROS scavenging. The transcriptome results revealed that C. goreaui prioritizes gene fidelity maintenance under low temperature stress. These findings reveal that energy allocation trade-offs constitute the core strategy of C. goreaui temperature response: prioritizing energy maintenance under high-temperature stress, while safeguarding genetic fidelity at the expense of antioxidant defense under low-temperature stress.},
}

@article {pmid40796291,
year = {2025},
author = {Mohr, AE and Mach, N and Pugh, J and Grosicki, GJ and Allen, JM and Karl, JP and Whisner, CM},
title = {Mechanisms underlying alterations of the gut microbiota by exercise and their role in shaping ecological resilience.},
journal = {FEMS microbiology reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsre/fuaf037},
pmid = {40796291},
issn = {1574-6976},
abstract = {The gut microbiota (GM) is a dynamic ecosystem intricately linked to human health, including metabolic, immune, endocrine, and gastrointestinal functions. Exercise is recognized as a significant modifier of this microbial ecosystem, yet the complexities of this relationship are underexplored. Here, we delve into the multifaceted interactions between structured physical activity and the GM, emphasizing the role of exercise-induced stressors in shaping microbial composition and function. Unique to our review, we discuss the acute effects of different forms of exercise-induced stress on the GM and explore how these responses may influence long-term adaptability, stability, and resilience. Furthermore, we address critical junctures in microbial dynamics leading to shifts between different stable states. Finally, we explore the implications of host-controlled factors such as diet, exercise training, and nutritional supplementation in modulating the microbial community in the gut to optimize athletic performance. We conclude that while the potential to harness the synergistic effects of exercise-induced stressors, dietary interventions, and microbial adaptations appears promising, current evidence remains preliminary, highlighting the need for additional targeted research to guide future strategies that manipulate the GM for optimal health and athletic performance.},
}

@article {pmid40795952,
year = {2025},
author = {Pluer, BD and Travis, J},
title = {The Digestive Microbiome Diversity of the Least Killifish, Heterandria formosa, and Its Implications for Host Adaptability to Varying Trophic Levels.},
journal = {Environmental microbiology reports},
volume = {17},
number = {4},
pages = {e70164},
pmid = {40795952},
issn = {1758-2229},
support = {G2020031598770049//Sigma Xia/ ; //Florida State University/ ; },
abstract = {Symbiotic microbes, in associations with aquatic hosts, aid in the acquisition of nutrients, breakdown xenobiotics, and contribute to immune system function. If associations with microbial communities facilitate host adaptation to different ecosystems, understanding the important ecological factors that act as drivers of differences among conspecific populations' microbiomes can help conservation efforts to promote beneficial interactions between fish and their microbiome for freshwater fish species facing rapid environmental changes. Here we describe the microbial communities in the gut of a freshwater fish, Heterandria formosa, in spring habitats using 16S rRNA sequencing. We quantified microbiota composition and diversity among springs ranging from oligotrophic to near eutrophic to determine the extent to which the microbiota are associated with different environmental conditions. We found higher microbial richness at sites with lower nutrient load stress. At more eutrophic sites, we detected the potential for increased metabolic capacity for pollutant degradation in the associated microbiota. We noted greater phylogenetic similarity between more environmentally similar sites, supporting previous evidence that the microbiota of freshwater fish is influenced by site water chemistry. Our findings bring to light microbial taxa and pathways that might play critical roles in the bioremediation of stressful environmental conditions.},
}

@article {pmid40795673,
year = {2025},
author = {Cano, NO and Borrego, CM and Radjenovic, J},
title = {Irreversible inactivation of multidrug-resistant Gram-positive bacteria using S-functionalized graphene sponge anode.},
journal = {Water research},
volume = {287},
number = {Pt A},
pages = {124300},
doi = {10.1016/j.watres.2025.124300},
pmid = {40795673},
issn = {1879-2448},
abstract = {Graphene sponges functionalized with sulfur were employed as anodes and coupled with N-doped graphene sponge cathodes for electrochemical inactivation of a Gram-positive multidrug-resistant bacterium Enterococcus gallinarum in drinking water. The application of 43.5 A m[-2] resulted in 2.3 log removal of E. gallinarum in one-pass, flow-through mode, at 2.7 kWh m[-3] of energy demand. In the case of non-functionalized graphene sponge electrode, 1.8 log removal of E. gallinarum required 3.8 kWh m[-3]. Moreover, no bacterial regrowth was measured in any of the experiments conducted during storage of the treated samples for 16 h. Indeed, the storage of samples led to an additional 1 log removal for the S-functionalized graphene sponge anode, somewhat higher compared with the 0.7 log removal observed for the non-functionalized electrode. To further decrease the energy consumption and exploit the capacitance of graphene, the flow-through system was operated with intermittent current. Application of 43.5 A m[-2] in an intermittent mode, led to a similar, 2.4 log removal of E. gallinarum but with a significantly reduced energy consumption, from 2.7 with continuous current to 1.8 kWh m[-3]. Scanning electron microscopy analyses of the inactivated bacteria confirmed the irreversible damage to the cell walls due to low-voltage electroporation that co-occurred with the presence of abundant cellular debris resulting from the leakage of intracellular material. Using two sequential reactors equipped with the S-doped graphene sponge anode and N-doped graphene sponge cathode operated at 43.5 A m[-2] of anodic current density resulted in an overall 5.8 log removal of E. gallinarum (including storage) from drinking water, and at the energy consumption of 5.4 kWh m[-3] (i.e., electric energy per order of 0.94 kWh m[-3]). Overall, this study demonstrated the feasibility of using an S-functionalized graphene sponge anode for chlorine-free electrochemical inactivation of a multidrug resistant Gram-positive bacterium from low conductivity drinking water.},
}

@article {pmid40795332,
year = {2025},
author = {Aguilera-Campos, KI and Boisard, J and Törnblom, V and Jerlström-Hultqvist, J and Behncké-Serra, A and Cotillas, EA and Stairs, CW},
title = {Anaerobic breviate protist survival in microcosms depends on microbiome metabolic function.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf171},
pmid = {40795332},
issn = {1751-7370},
abstract = {Anoxic and hypoxic environments serve as habitats for diverse microorganisms, including unicellular eukaryotes (protists) and prokaryotes. To thrive in low-oxygen environments, protists and prokaryotes often establish specialized metabolic cross-feeding associations, such as syntrophy, with other microorganisms. Previous studies show that the breviate protist Lenisia limosa engages in a mutualistic association with a denitrifying Arcobacter bacterium based on hydrogen exchange. Here, we investigate if the ability to form metabolic interactions is conserved in other breviates by studying five diverse breviate microcosms and their associated bacteria. We show that five laboratory microcosms of marine breviates live with multiple hydrogen-consuming prokaryotes that are predicted to have different preferences for terminal electron acceptors using genome-resolved metagenomics. Protist growth rates vary in response to electron acceptors depending on the make-up of the prokaryotic community. We find that the metabolic capabilities of the bacteria and not their taxonomic affiliations determine protist growth and survival and present new potential protist-interacting bacteria from the Arcobacteraceae, Desulfovibrionaceae, and Terasakiella lineages. This investigation uncovers potential nitrogen and sulfur cycling pathways within these bacterial populations, hinting at their roles in syntrophic interactions with the protists via hydrogen exchange.},
}

@article {pmid40790855,
year = {2025},
author = {Xie, R and Yu, H and Wang, Y and Leung, KY and Habimana, O},
title = {Synergistic effects of sodium acetate and calcium on structure and function in multispecies biofilms.},
journal = {Biofouling},
volume = {},
number = {},
pages = {1-16},
doi = {10.1080/08927014.2025.2545940},
pmid = {40790855},
issn = {1029-2454},
abstract = {This investigation scrutinizes the manner in which sodium acetate (SA) and calcium cations (Ca[2+]) independently and collaboratively affect biofilm development. Confocal microscopy revealed that SA (1 mM) increased biofilm biovolume (5.5-fold) and thickness by enhancing microbial growth, while Ca[2+] (1.5 mM) stabilized the matrix via EPS crosslinking. Combined, SA and Ca[2+] synergistically boosted biovolume (1.5-fold) and thickness (21.3 µm) compared to SA alone. 16S rRNA sequencing showed SA-enriched Actinobacteriota (11%) and exopolysaccharide-producing Brevifollis, whereas Ca[2+] improved surface coverage (22.3%). Functional predictions linked SA to purine degradation and Ca[2+] to fatty acid oxidation, aligning with EPS modifications. These findings highlight how carbon sources and divalent cations collaboratively shape biofilm resilience, offering insights for biofilm management in environmental, industrial, and medical settings where SA and Ca[2+] gradients exist.},
}

@article {pmid40789383,
year = {2025},
author = {Rout, AK and Rout, SS and Panda, A and Tripathy, PS and Kumar, N and Parida, SN and Dey, S and Dash, SS and Behera, BK and Pandey, PK},
title = {Potential applications and future prospects of metagenomics in aquatic ecosystems.},
journal = {Gene},
volume = {},
number = {},
pages = {149720},
doi = {10.1016/j.gene.2025.149720},
pmid = {40789383},
issn = {1879-0038},
abstract = {Metagenomics plays a vital role in advancing our understanding of microbial communities and their functional contributions in various ecosystems. By directly sequencing DNA from environmental samples-such as soil, water, air, and the human body-metagenomics enables the identification of previously uncultivable or unknown microorganisms, offering key insights into their ecological functions. Beyond taxonomic classification, metagenomic analyses reveal functional genes and metabolic pathways, facilitating the discovery of enzymes, bioactive compounds, and other molecules with applications in agriculture, biotechnology, and medicine. This review discusses the wide-ranging applications of metagenomics in environmental monitoring, including sample collection, high-throughput sequencing, and data analysis and interpretation. We review different sequencing platforms, library preparation methods, and advanced bioinformatics tools used for quality control, sequence assembly, and both taxonomic and functional annotation. Special focus is given to the role of metagenomics in evaluating microbial responses to environmental stress, contaminant degradation, disease emergence, and climate change. The use of microbial bioindicators for aquatic ecosystem monitoring and toxicological assessments is also examined. A comprehensive evaluation of current bioinformatics pipelines is provided for their effectiveness in processing large-scale metagenomic datasets. As global environmental pressures intensify, integrative meta-omics approaches, including whole-genome metagenomics, will be crucial for understanding the complexity, functions, and dynamics of microbiomes in both natural and affected ecosystems.},
}

@article {pmid40788461,
year = {2025},
author = {Torres, MC and Breyer, GM and da Silva, MERJ and de Itapema Cardoso, MR and Siqueira, FM},
title = {Metagenomic approaches for the quantification of antibiotic resistance genes in swine wastewater treatment system: a systematic review.},
journal = {Molecular biology reports},
volume = {52},
number = {1},
pages = {816},
pmid = {40788461},
issn = {1573-4978},
support = {408693/2022-3//Conselho Nacional de Desenvolvimento Científico e Tecnológico,Brazil/ ; },
mesh = {Swine ; *Wastewater/microbiology ; Animals ; *Metagenomics/methods ; *Drug Resistance, Microbial/genetics ; Metagenome/genetics ; Bacteria/genetics/drug effects ; *Drug Resistance, Bacterial/genetics ; Water Purification/methods ; Computational Biology/methods ; Anti-Bacterial Agents/pharmacology ; },
abstract = {This systematic review aims to identify the metagenomic methodological approaches employed for the detection of antimicrobial resistance genes (ARGs) in swine wastewater treatment systems. The search terms used were metagenome AND bacteria AND ("antimicrobial resistance gene" OR resistome OR ARG) AND wastewater AND (swine OR pig), and the search was conducted across the following electronic databases: PubMed, Scopus, ScienceDirect, Web of Science, Embase, and Cochrane Library. The search was limited to studies published between 2020 and 2024. Of the 220 studies retrieved, eight met the eligibility criteria for full-text analysis. The number of publications in this research area has increased in recent years, with China contributing the highest number of studies. ARGs are typically identified using bioinformatics pipelines that include steps such as quality trimming, assembly, metagenome-assembled genome (MAG) reconstruction, open reading frame (ORF) prediction, and ARG annotation. However, comparing ARGs quantification across studies remains challenging due to methodological differences and variability in quantification approaches. Therefore, this systematic review highlights the need for methodological standardization to facilitate comparison and enhance our understanding of antimicrobial resistance in swine wastewater treatment systems through metagenomic approaches.},
}

Swine
*Wastewater/microbiology
Animals
*Metagenomics/methods
*Drug Resistance, Microbial/genetics
Metagenome/genetics
Bacteria/genetics/drug effects
*Drug Resistance, Bacterial/genetics
Water Purification/methods
Computational Biology/methods
Anti-Bacterial Agents/pharmacology

@article {pmid40788124,
year = {2025},
author = {Ferreira, J and Rediers, H},
title = {Draft genome sequences of 25 candidate biocontrol bacteria against Phytophthora cactorum.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0050225},
doi = {10.1128/mra.00502-25},
pmid = {40788124},
issn = {2576-098X},
abstract = {To provide a biocontrol solution for managing the phytopathogen Phytophthora cactorum, bacteria were tested for antagonistic activity in vitro and in planta. This paper presents the draft genomes of 25 candidate biocontrol organisms, providing a solid foundation to decipher the underlying mechanisms of their antagonistic activity.},
}

@article {pmid40781093,
year = {2025},
author = {Kojima, CY and Henson, MW and Coelho, JT and Lanclos, VC and Bañuelas, D and Thrash, JC},
title = {Metagenomes and 1,313 metagenome-assembled genomes from a northern Gulf of Mexico coastal time series.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1388},
pmid = {40781093},
issn = {2052-4463},
support = {OCE-1931113//National Science Foundation (NSF)/ ; Simons Investigator in Aquatic Microbial Ecology Award//Simons Foundation/ ; Faculty Innovation Research Award//USC | Wrigley Institute for Environmental Studies, University of Southern California (USC Wrigley Institute for Environmental Studies)/ ; },
mesh = {Gulf of Mexico ; *Metagenome ; *Water Microbiology ; },
abstract = {Coastal and estuarine systems are hotspots of microbial diversity, activity, and biogeochemical cycling. Despite their importance, we have few comprehensive datasets of microbial populations across space and time from these ecosystems. To improve our understanding of these systems, we generated metagenomes averaging 46 M reads per sample (nearly 389 Gbp total) from four coastal/estuarine locations in the northern Gulf of Mexico across seven timepoints spanning nine months. Using standard methodology combined with a unique assembly and binning approach called subtractive iterative assembly (SIA), we generated 1,313 non-redundant metagenome-assembled genomes (MAGs) with 5% contamination or less and at least 75% completeness. We produced approximately a third of the MAGs through SIA. Actinobacteria and Proteobacteria were represented most. We recovered MAGs of great ecological significance including SAR11, Marine Group I (Thaumarcheaota), Marine Group II Euryarchaeota, SAR324, and Asgardarchaeota. We describe both our methodology using the SIA approach as well as the 28 metagenomes and 1,313 MAGs that provide a rich spatiotemporal dataset with which to study coastal and estuarine microbiology.},
}

Gulf of Mexico
*Metagenome
*Water Microbiology

@article {pmid40779244,
year = {2025},
author = {Sung, J and Choi, DH and Lee, Y and Kim, JH and Shin, HH and Kim, YE and Choi, JH and Noh, JH and Gobler, CJ and Park, BS},
title = {Temperature-Driven Intraspecific Diversity in Paralytic Shellfish Toxin Profiles of the Dinoflagellate Alexandrium pacificum and Intragenic Variation in the Saxitoxin Biosynthetic Gene, sxtA4.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {87},
pmid = {40779244},
issn = {1432-184X},
support = {20163MFDS641//Ministry of Food and Drug Safety/ ; 20163MFDS641//Ministry of Food and Drug Safety/ ; 20163MFDS641//Ministry of Food and Drug Safety/ ; 20163MFDS641//Ministry of Food and Drug Safety/ ; 20163MFDS641//Ministry of Food and Drug Safety/ ; 20163MFDS641//Ministry of Food and Drug Safety/ ; 20163MFDS641//Ministry of Food and Drug Safety/ ; 20210469//Ministry of Oceans and Fisheries/ ; 20210469//Ministry of Oceans and Fisheries/ ; RS-2021-KS211530//Ministry of Oceans and Fisheries/ ; RS-2023-00209356//Ministry of Science and ICT, South Korea/ ; },
mesh = {*Dinoflagellida/genetics/metabolism/growth & development ; *Saxitoxin/biosynthesis/genetics ; *Genetic Variation ; Temperature ; Harmful Algal Bloom ; Phylogeny ; },
abstract = {Alexandrium pacificum, a globally distributed dinoflagellate, is well-known for causing harmful algal blooms and producing Paralytic Shellfish Toxins (PSTs), a threat to marine life and human health. The frequency and intensity of Alexandrium blooms have increased in recent decades, driven, in some cases, by increasing temperatures. Here, we investigated the temperature-dependent (15 °C, 20 °C, 25 °C, and 30 °C) growth rates and paralytic shellfish toxin profiles of eight A. pacificum strains while concurrently examining differences in sequences of the saxitoxin biosynthetic gene, sxtA4. While maximum cell densities were lowest at 30 °C, toxin production per cell was highest at higher temperatures that inhibited growth, with greater diversity of toxin analogs peaking at 30 °C, as confirmed by the higher Shannon's diversity index obtained for the toxin profiles with the increasing temperatures. Furthermore, genetic analysis of the sxtA4 gene showed that greater genetic diversity-quantified by nucleotide diversity (π) ranging from 9.91 to 30.21 across strains-was positively correlated with this wider array of toxin analogs (Shannon's diversity index; p < 0.0001). Conserved regions within the gene were identified, suggesting that these regions may play important structural or functional roles in the saxitoxin biosynthetic pathway. These findings highlight the role of temperature, genetic diversity, and sxtA4 conserved regions in influencing toxin production and profiles in Alexandrium. Further research into the genetic mechanisms underlying saxitoxin biosynthesis will improve our understanding of Alexandrium's adaptability to changing temperatures. Such insights are essential for effective ecosystem management and safeguarding public health.},
}

*Dinoflagellida/genetics/metabolism/growth & development
*Saxitoxin/biosynthesis/genetics
*Genetic Variation
Temperature
Harmful Algal Bloom
Phylogeny

@article {pmid40778431,
year = {2025},
author = {Maillard, F and Beatty, BH and Geisen, S and Lara, E and Kennedy, PG},
title = {Secondary Decomposers Meet Their Predators: Decomposition Stage and Substrate Quality Jointly Structure Microbial Brown Food Webs During Fungal Necromass Decay.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e70060},
doi = {10.1111/mec.70060},
pmid = {40778431},
issn = {1365-294X},
support = {DEB #2038293//National Science Foundation/ ; },
abstract = {Mycelial residues, also known as fungal necromass, represent a substantial fraction of soil organic matter (SOM) pools in terrestrial ecosystems worldwide. Although microbial decomposers are increasingly recognised as key drivers of fungal necromass carbon stock formation, the diversity and composition of their microbial predators-and the roles these predators play in mediating fungal necromass decomposition-have not been explored to date. To address this gap, we produced fungal necromass of varying biochemical quality from Hyaloscypha bicolor and decomposed it in forest topsoil in Minnesota, USA, to investigate how microbial decomposer (bacteria and fungi) and predator (protists and nematodes) communities differ between soil and necromass. We also examined whether microbial predators influence the abundance of fungal necromass decomposers and affect necromass decomposition rates. Over two sampling times (4 and 12 weeks), necromass exhibited rapid early mass loss followed by reduced decay, with a higher stabilised mass in high melanin necromass. Microbial abundances were higher in necromass than in surrounding soil, especially in low melanin necromass. Community composition of both decomposers and their predators differed between soil and necromass and shifted markedly with necromass quality and decomposition stage. Predator community composition was linked to bacterial and fungal abundances at both early and late stages of decay and was marginally associated with decomposition rates. We conclude that fungal necromass acts as a microbial 'hotspot' not only for decomposers but also for their predators. These findings highlight the importance of microbial predator-decomposer interactions to better understand the formation of fungal-derived SOM.},
}

@article {pmid40775374,
year = {2025},
author = {Krasenbrink, J and Hanson, BT and Weiss, AS and Borusak, S and Tanabe, TS and Lang, M and Aichinger, G and Hausmann, B and Berry, D and Richter, A and Marko, D and Mussmann, M and Schleheck, D and Stecher, B and Loy, A},
title = {Sulfoquinovose is exclusively metabolized by the gut microbiota and degraded differently in mice and humans.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {184},
pmid = {40775374},
issn = {2049-2618},
support = {10.55776/DOC69//Austrian Science Fund/ ; 10.55776/COE7//Austrian Science Fund/ ; 10.55776/DOC69//Austrian Science Fund/ ; 10.55776/COE7//Austrian Science Fund/ ; 10.55776/DOC69//Austrian Science Fund/ ; 10.3030/101205556//HORIZON EUROPE Marie Sklodowska-Curie Actions/ ; 395357507 "SFB1371"//Deutsche Forschungsgemeinschaft/ ; EvoGutHealth, 865615/ERC_/European Research Council/International ; 503-5-7-06.712_00 and 503-5-7-06.709_00//Germany Centre for Infection Research/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Humans ; Mice ; Mice, Inbred C57BL ; Feces/microbiology ; *Bacteria/metabolism/classification/genetics/isolation & purification ; Male ; Hydrogen Sulfide/metabolism ; Female ; },
abstract = {BACKGROUND: Sulfoquinovose (SQ) is a green-diet-derived sulfonated glucose and a selective substrate for a limited number of human gut bacteria. Complete anaerobic SQ degradation via interspecies metabolite transfer to sulfonate-respiring bacteria produces hydrogen sulfide, which has dose- and context-dependent health effects. Here, we studied potential SQ degradation by the mammalian host and the impact of SQ supplementation on human and murine gut microbiota diversity and metabolism.

RESULTS: [13]CO2 breath tests with germ-free C57BL/6 mice gavaged with [13]C-SQ were negative. Also, SQ was not degraded by human intestinal cells in vitro, indicating that SQ is not directly metabolized by mice and humans. Addition of increasing SQ concentrations to human fecal microcosms revealed dose-dependent responses of the microbiota and corroborated the relevance of Agathobacter rectalis and Bilophila wadsworthia in cooperative degradation of SQ to hydrogen sulfide via interspecies transfer of 2,3-dihydroxy-1-propanesulfonate (DHPS). Similar to the human gut microbiome, the genetic capacity for SQ or DHPS degradation is sparsely distributed among bacterial species in the gut of conventional laboratory mice. Escherichia coli and Enterocloster clostridioformis were identified as primary SQ degraders in the mouse gut. SQ and DHPS supplementation experiments with conventional laboratory mice and their intestinal contents showed that SQ was incompletely catabolized to DHPS. Although some E. clostridioformis genomes encode an extended sulfoglycolytic pathway for both SQ and DHPS fermentation, SQ was only degraded to DHPS by a mouse-derived E. clostridioformis strain.

CONCLUSIONS: Our findings suggest that SQ is solely a nutrient for the gut microbiota and not for mice and humans, emphasizing its potential as a prebiotic. SQ degradation by the microbiota of conventional laboratory mice differs from the human gut microbiota by absence of DHPS degradation activity. Hence, the microbiota of conventional laboratory mice does not fully represent the SQ metabolism in humans, indicating the need for alternative model systems to assess the impact of SQ on human health. This study advances our understanding of how individual dietary compounds shape the microbial community structure and metabolism in the gut and thereby potentially influence host health. Video Abstract.},
}

Animals
*Gastrointestinal Microbiome/physiology
Humans
Mice
Mice, Inbred C57BL
Feces/microbiology
*Bacteria/metabolism/classification/genetics/isolation & purification
Male
Hydrogen Sulfide/metabolism
Female

@article {pmid40774531,
year = {2025},
author = {Morales, MLP and Capurro, L and Bordert, F and Chenia, H and Alonso, C and Bentos, FR and Boccardi, L and Brugnoli, E and They, NH and Agostini, VO and Leães Pinho, GL},
title = {Evaluating macrophyte extracts as eco-friendly antifouling additives for freshwater made-man structures: a field assessment.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {126952},
doi = {10.1016/j.envpol.2025.126952},
pmid = {40774531},
issn = {1873-6424},
abstract = {Biofouling on artificial aquatic surfaces yields substantial economic losses and operational challenges. Traditional antifouling strategies often rely on synthetic chemical coatings, which have harmful environmental impacts, thus environmentally sustainable solutions, such as natural antifouling compounds are increasingly being sought. Extracts derived from the aquatic macrophytes Pontederia crassipes and Typha domingensis have demonstrated potential antifouling properties in preliminary studies; however, their efficacy under natural field conditions remains unverified. This study is the first to evaluate the antifouling potential of these macrophyte extracts when incorporated with epoxy coatings in a natural freshwater environment (Salto Grande Reservoir, Uruguay River). Stainless steel substrates were treated with 2.5, 5, and 10 g L[-1] of lyophilized macrophyte extracts combined with epoxy and compared to uncoated and epoxy-coated controls. Over a 165-hour period, biofouling was assessed via chlorophyll levels, bacterial counts, macro-organism presence and attachment and taxonomic diversity. Analytical techniques, including gas and liquid chromatography, along with Fourier transform infrared spectroscopy, were employed to identify active compounds in extracts. The P. crassipes extract at 5 and 10 g L[-1] exhibited superior antifouling efficacy compared to T. domingensis. Coatings with P. crassipes significantly reduced bacterial colonization (37%), algae growth (for different photosynthetic pigments), fungal presence, and macro-organism attachment (not found), while promoting the occurrence of opportunistic taxa less conducive to fouling. The observed antifouling activity may be attributed to specific chemical compounds, including long-chain hydrocarbons and phenolic derivatives, identified in the extracts. The study findings demonstrate the field antifouling efficacy of macrophyte extracts incorporated with epoxy coatings, highlighting P. crassipes as a particularly promising, sustainable antifouling candidate. Its high biomass availability and ease of cultivation enhance its potential for industrial-scale development as natural antifouling agents. This work provides critical insights into developing eco-friendly antifouling coatings that minimize environmental impact while maintaining efficacy in biofouling control being the first study to prove in a natural environment the antifouling potential of these macrophytes.},
}

@article {pmid40770074,
year = {2025},
author = {Myers, T and Song, SJ and Chen, Y and De Pessemier, B and Khatib, L and McDonald, D and Huang, S and Gallo, R and Callewaert, C and Havulinna, AS and Lahti, L and Roeselers, G and Laiola, M and Shetty, SA and Kelley, ST and Knight, R and Bartko, A},
title = {Chronological age estimation from human microbiomes with transformer-based Robust Principal Component Analysis.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {1159},
pmid = {40770074},
issn = {2399-3642},
mesh = {Humans ; *Aging ; *Biometry/methods ; *Deep Learning ; *Gastrointestinal Microbiome ; *Principal Component Analysis/methods ; *Skin Microbiome ; Software Validation ; },
abstract = {Deep learning for microbiome analysis has shown potential for understanding microbial communities and human phenotypes. Here, we propose an approach, Transformer-based Robust Principal Component Analysis(TRPCA), which leverages the strengths of transformer architectures and interpretability of Robust Principal Component Analysis. To investigate benefits of TRPCA over conventional machine learning models, we benchmarked performance on age prediction from three body sites(skin, oral, gut), with 16S rRNA gene amplicon(16S) and whole-genome sequencing(WGS) data. We demonstrated prediction of age from longitudinal samples and combined classification and regression tasks via multi-task learning(MTL). TRPCA improves age prediction accuracy from human microbiome samples, achieving the largest reduction in Mean Absolute Error for WGS skin (MAE: 8.03, 28% reduction) and 16S skin (MAE: 5.09, 14% reduction) samples, compared to conventional approaches. Additionally, TRPCA's MTL approach achieves an accuracy of 89% for birth country prediction across 5 countries, while improving age prediction from WGS stool samples. Notably, TRPCA uncovers a link between subject and error prediction through residual analysis for paired samples across sequencing method (16S/WGS) and body site(oral/gut). These findings highlight TRPCA's utility in improving age prediction while maintaining feature-level interpretability, and elucidating connections between individuals and microbiomes.},
}

Humans
*Aging
*Biometry/methods
*Deep Learning
*Gastrointestinal Microbiome
*Principal Component Analysis/methods
*Skin Microbiome
Software Validation

@article {pmid40768991,
year = {2025},
author = {Li, J and Sun, Q and Wang, S and Lei, K},
title = {Environmental gradients drive the ecological dynamics of bacterioplankton in the East China Sea based on eDNA metabarcoding.},
journal = {Marine pollution bulletin},
volume = {221},
number = {},
pages = {118539},
doi = {10.1016/j.marpolbul.2025.118539},
pmid = {40768991},
issn = {1879-3363},
abstract = {Understanding the interactions between environmental factors and ecological processes that shape bacterioplankton is a fundamental goal of microbial ecology. With increasing urbanization and environmental stress, marine coastal ecosystems necessitate careful evaluation of microbial dynamics. Environmental DNA was utilized to investigate bacterioplankton in the coastal waters of the East China Sea, revealing distinct environmental gradients that significantly shape bacterioplankton community composition. Distinct spatial differentiation of microbial assemblages was observed along these gradients, primarily driven by nitrogen-related nutrient dynamics. Furthermore, shifts in coastal habitats have driven a transition in community assembly processes from predominantly stochastic to deterministic mechanisms. Changes in environmental conditions also increase the vulnerability of offshore bacterioplankton networks, compromising their stability. These findings emphasize the critical role of environmental gradients in forming coastal microbial community composition, offering valuable insights for advancing marine ecosystem management, biodiversity conservation, and sustainable environmental policies.},
}

@article {pmid40767881,
year = {2025},
author = {Fowler, AE and McFrederick, QS and Adler, LS},
title = {Correction to: Pollen Diet Diversity does not Affect Gut Bacterial Communities or Melanization in a Social and Solitary Bee Species.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {86},
doi = {10.1007/s00248-025-02573-6},
pmid = {40767881},
issn = {1432-184X},
}

@article {pmid40767488,
year = {2025},
author = {Harris, JE and Bledsoe, RB and Guha, S and Omari, H and Crandall, SG and Burghardt, LT and Couradeau, E},
title = {The activity of soil microbial taxa in the rhizosphere predicts the success of root colonization.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0045825},
doi = {10.1128/msystems.00458-25},
pmid = {40767488},
issn = {2379-5077},
abstract = {UNLABELLED: Plant-beneficial microbes have great potential to improve sustainability in agriculture. Still, managing beneficial microbes is challenging because the impact of microbial dormancy on community assembly across the soil, rhizosphere, and endosphere is poorly understood. We address this gap with the first documented use of Biorthogonal Non-Canonical Amino Acid Tagging (BONCAT) to probe active microbes in the soil-to-root gradient. Using nodule-forming legume Trifolium incarnatum, we confirmed that BONCAT is suitable for labeling endospheric microbes with microscopy. Next, we coupled BONCAT to Flow Cytometer Activated Cell Sorting (FACS) and 16S rRNA amplicon sequencing to probe patterns of microbial activity and the structure of the active microbial community across the soil, rhizosphere, root, and nodule with a native soil microbial community. As expected, we found 10 times higher microbial activity in the endosphere than in the rhizosphere or bulk soil, likely due to increased plant resources. Finally, we revealed that microbial activity in the rhizosphere was significantly associated with successful endosphere colonization, more so than microbial abundance alone. This last finding has implications for the development of microbial inoculants, suggesting colonizing plant roots is linked to a microbe's ability to overcome dormancy once deployed in the soil.

IMPORTANCE: Most soil microbes are dormant, so they must exit dormancy to have the potential to carry out plant-beneficial functions. It is unclear if dormant microbes revive in proximity to plant-produced resources and if overcoming dormancy in the soil is important for successful plant colonization. We use a novel microbial activity probing technique for the first time on and in plant roots, and with it, we observe microbes increased in activity 10× inside plant tissues compared to the soil, likely in response to plant-produced resources. In complex, native microbial communities, we observe that microbes that are active and abundant are more likely to colonize plant roots successfully than just abundant microbes. Our research shows that plants could be leveraged to promote a distinct active microbial community from the native soil, a discovery that has the potential to improve sustainability in agriculture.},
}

@article {pmid40766845,
year = {2025},
author = {Zheng, N and Yu, HL and Zhang, BJ and Wang, D and Ji, YL and Dai, LL and Li, W and Li, SH and Hu, ZL and Zheng, YS},
title = {Metagenomic next-generation sequencing-based characterization of the viral spectrum in clinical pulmonary and peripheral blood samples of patients.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1562965},
pmid = {40766845},
issn = {2235-2988},
mesh = {Humans ; *High-Throughput Nucleotide Sequencing ; *Metagenomics/methods ; *Bronchoalveolar Lavage Fluid/virology ; *Virome/genetics ; *Viruses/genetics/classification/isolation & purification ; Female ; Male ; Middle Aged ; Adult ; Aged ; *Lung/virology ; *Blood/virology ; Bacteria/classification/genetics/isolation & purification ; *Virus Diseases/virology ; },
abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) enables comprehensive profiling of viral communities in clinical samples. However, comparative analyses of the virome across anatomical compartments and disease states remain limited. This study aims to characterize the virome in bronchoalveolar lavage fluid (BALF) and peripheral blood samples from patients with various clinical conditions using mNGS.

METHODS: A total of 338 clinical samples-including 240 BALF and 69 blood samples for DNA sequencing, and 18 BALF and 11 blood samples for RNA sequencing-underwent shotgun metagenomic sequencing. Following removal of host-derived reads, high-quality non-human sequences were aligned to a viral reference database. Virome composition was assessed through alpha and beta diversity metrics. Principal coordinates analysis was used to evaluate disease-related variation, and virus-bacteria associations in BALF were investigated via Spearman correlation.

RESULTS: Sequencing yielded an average of 51 million raw reads per sample, resulting in approximately 8 million non-human reads after host filtering. Distinct virome profiles were observed between BALF and blood samples. Bacteriophages dominated all groups, with Siphoviridae and Myoviridae as the most abundant families, although only 13.6% of viral abundance could be assigned to known families. Diversity analyses revealed significant differences between BALF and peripheral blood, and DNA-sequenced BALF samples showed disease-specific viral signatures in pulmonary infections. In contrast, tumor presence had no significant effect on virome composition in either BALF or blood. Network analysis identified complex virus-bacteria correlations in BALF, with genera such as Haemophilus, Megasphaera, and Treponema as key bacterial hosts.

CONCLUSIONS: This study reveals pronounced differences in virome composition between the respiratory and circulatory systems and highlights the specific influence of pulmonary disease-but not tumors-on the pulmonary virome. The observed virus-bacteria networks provide novel insights into pulmonary microbial ecology and underscore the importance of integrating host and disease context in virome studies.},
}

Humans
*High-Throughput Nucleotide Sequencing
*Metagenomics/methods
*Bronchoalveolar Lavage Fluid/virology
*Virome/genetics
*Viruses/genetics/classification/isolation & purification
Female
Male
Middle Aged
Adult
Aged
*Lung/virology
*Blood/virology
Bacteria/classification/genetics/isolation & purification
*Virus Diseases/virology

@article {pmid40766442,
year = {2025},
author = {Rathod, D and Silverman, JD},
title = {PCR Bias Impacts Microbiome Ecological Analyses.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {40766442},
issn = {2692-8205},
support = {R01 GM148972/GM/NIGMS NIH HHS/United States ; },
abstract = {Polymerase Chain Reaction (PCR) is a critical step in amplicon-based microbial community profiling, allowing the selective amplification of marker genes such as 16S rRNA from environmental or host-associated samples. Despite its widespread use, PCR is known to introduce amplification bias, where some DNA sequences are preferentially amplified over others due to factors such as primer-template mismatches, sequence GC content, and secondary structures. Although these biases are known to affect transcript abundance, their implications for ecological metrics remain poorly understood. In this study, we conduct a comprehensive evaluation of how PCR-bias influences both within-samples (α -diversity) and between-sample (β -diversity) analyses. We show that perturbation-invariant diversity measures remain unaffected by PCR bias, but widely used metrics such as Shannon diversity and Weighted-Unifrac are sensitive, with their values varying according to the true community composition. To address this, we provide theoretical and empirical insight into how PCR-induced bias varies across ecological analyses and community structures, and we offer practical guidance on when bias-correction methods should be applied. Our findings highlight the importance of selecting appropriate diversity metrics for PCR-based microbial ecology workflows and offer guidance for improving the reliability of diversity analyses.},
}