High Abundance Research Articles

Potential effect of the gut microbiome on tumour response to anti-cancer treatment in patients diagnosed with pancreatic ductal adenocarcinoma.

757 Background: Chemotherapy is the standard of care for pancreatic ductal adenocarcinoma (PDAC), however, recent research has identified bacteria in the human gut microbiome that may influence patient response to chemotherapy. These bacteria are also present in faeces, and are thought to be representative of the bacteria in the pancreatic ductal system. Preliminary studies have suggested that patients with more advanced PDAC demonstrate lower levels of Firmicutes, and higher levels of Proteobacteria. Additionally, research has shown bacteria in the Firmicutes phylum possess several anti-cancer properties, which may improve patient treatment response, meanwhile, Gammaproteobacteria (Proteobacteria phylum), have been shown to attenuate gemcitabine efficacy and worsen treatment response. Methods: This prospective study involved 14 participants with locally advanced PDAC. Participants received combinations of Gemcitabine, Nab-Paclitaxel, and durvalumab (immunotherapy). Participant tumours were assessed every 8 weeks using radiological imaging according to RECIST v1.1, and serum CA19-9 levels were analysed monthly. Gut microbial profiling was completed on stool samples taken pre-treatment using PacBio HiFi full-length 16S rRNA sequencing. Results: 16S rRNA sequencing identified that of the 4 patients that died due to disease progression, 3 patients had a low Firmicutes abundance, and a high Proteobacteria abundance. The rother patient demonstrated low levels of Actinobacteriota and Bacteroidota, and a low bacterial diversity. One participant showed a significant increase in CA19-9 (1066.7%), and exhibited a low abundance of Actinobacteriota and Bacteroidota, a high abundance of Proteobacteria, and a low diversity. 5 participants demonstrated a significant treatment response (according to CA19-9 and RECIST analysis), with 4 patients showing a high Firmicutes abundance, high levels of Actinobacteriota or Bacteroidota, and low levels of Proteobacteria. The remaining patient demonstrated a low abundance of Firmicutes and Proteobacteria, yet, displayed the highest abundance of Actinobacteriota and Bacteroidota. Conclusions: This exploratory study suggests an association between microbial composition and treatment response, with Firmicutes potentially being associated with an improved treatment response, and Proteobacteria with a worsened response. We believe this study to be one of the first to explore correlation of microbiome with clinical treatment response in PDAC.

Enhancing the interactions of ion-tagged oligonucleotides and magnetic ionic liquid supports for the sequence-specific extraction of hepatitis B virus DNA.

Infections from the hepatitis B virus (HBV) are a major risk factor for hepatocellular carcinoma, one of the most common types of liver cancer. Circulating cell-free DNA (ccfDNA) in human plasma can be used as a non-invasive biomarker for diagnosing HBV-related liver diseases. The isolation of target ccfDNA sequences is often challenging due to the co-extraction of highly abundant non-target DNA from samples. Ion-tagged oligonucleotide (ITO) probes coupled with magnetic ionic liquids (MIL) support have emerged as a promising methodology for sequence-specific DNA extractions to address challenges associated with solid supports such as streptavidin-coated magnetic bead. ITOs, disubstituted ion-tagged oligonucleotide (DTO), and ion-tagged disubstituted oligonucleotide (ITDO) probes featuring various substituents including linear alkyl, branched alkyl, and perfluoroalkyl moieties were examined to enhance hydrophobic and fluorophilic interactions between the probes and a trihexyl(tetradecyl)phosphonium manganese(II) hexafluoroacetylacetonate ([P66614+][Mn(hfacac)3-]) MIL support. The ITO-MIL approach was optimized by adjusting the annealing temperature (45°C), molar ratio of target DNA to ITO probe (1:100), and ionic strength (200mM NaCl) to maximize the extraction of target DNA. The 3-allyl-1-(23-bis(pentylthio)propyl)imidazolium bromide ([AI(C5S)2+][Br-])-ITO probe featuring a branched alkyl substituent yielded a higher loading efficiency (48.05±6.72%) due to increased hydrophobic ITO-MIL interactions, compared to that of 24.57±4.40% for the 3-allyl-1-(3-(pentylthio)propyl)imidazolium bromide ([AIC5S+][Br-])-ITO probe with a linear alkyl substituent. The high affinity of ITO-MILinteractions minimized the loss of probe during successive wash steps, yielding an approximate 10-fold greater amount of extracted target DNA using the [AI(C5S)2+][Br-])-ITO probe compared to [AIC5S+][Br-])-ITO probe. This study provides novel synthetic approaches for tailoring probe substituents using thiol-ene and thiol-yne "click" chemistry. Hydrophobic and fluorophilic ITO-MIL interactions were systematically investigated. Optimal conditions for the ITO-MIL method significantly improved the amount of extracted DNA. The ITO-MIL method using the [AI(C5S)2+][Br-]-HBV-ITO probe demonstrated selective extraction of target HBV DNA in both DI water and diluted human plasma containing a high abundance of background DNA.

Effects of water temperature on zooplankton abundance and biomass in the southwestern Barents Sea: Implications for Arctic monitoring and management

Zooplankton exhibit rapid responses to environmental changes owing to predominantly short life cycles. However, at higher latitudes, the maximum age of mesozooplankton organisms can reach 2 and even 5 years, with such organisms potentially comprising a substantial proportion of communities. Despite this, there is limited understanding of the prolonged responses of zooplankton to temperature fluctuations in the southern Barents Sea. To address this gap, zooplankton were sampled during analogous seasons over a two-year period (2011 and 2012) characterized by an increasing water temperature trend. Our findings revealed a spatial shift from a community with lower abundance and biomass, situated within the area dominated by Coastal Water and Atlantic Water, to a community with higher abundance and biomass in colder waters influenced by the Arctic Water mass. Within the latter community, we identified 17 species as relevant indicators, with significant differences in both fidelity and specificity observed for Triconia borealis and Aglantha digitale. Redundancy analysis indicated water temperature recorded 10 months prior as the sole significant predictor of population characteristics in both years. Relationships between water temperature and abundance/biomass were computed for the 2011 dataset and the resultant equations used to predict 2012 zooplankton parameters. No significant differences were found between predicted and observed data. These findings suggest the utility of our data for forecasting autumn zooplankton population status, which, given ongoing Arctic warming and the critical trophic role of zooplankton for fish, could aid ecosystem monitoring and inform fisheries management in the Barents Sea from a short-term perspective.

Developmental Toxicity of Alkylated PAHs and Substituted Phenanthrenes: Structural Nuances Drive Diverse Toxicity and AHR activation

Polycyclic aromatic hydrocarbons (PAHs) are a diverse class of chemicals that occur in complex mixtures including parent and substituted PAHs. To understand the hazard posed by complex environmental PAH mixtures, we must first understand the structural drivers of activity and mode of action of individual PAHs. Understanding the toxicity of alkylated PAHs is important as they often occur in higher abundance in environmental matrices and can be more biologically active than their parent compounds. 104 alkylated PAHs were screened from 11 different parent compounds with emphasis on substituted phenanthrenes and their structurally dependent toxicity differences. Using a high-throughput early life stage zebrafish assay, embryos were exposed to concentrations between 0.1 to 100 μM and assessed for morphological and behavioral outcomes. The aryl hydrocarbon receptor (AHR) is often implicated in the toxicity of PAHs and the induction of cytochrome P4501A (cyp1a) is an excellent biomarker of Ahr activation. Embryos were evaluated for cyp1a induction using a fluorescence reporter line. Alkyl and polar phenanthrene derivatives were further assessed for spatial cyp1a expression and Ahr dependence of morphological effects. In the alkyl PAH screen 35 (33.7%) elicited a morphological or behavioral response and of those 23 (65%) also induced cyp1a. 31 (29.8%) of the chemicals only induced cyp1a. Toxicity varied substantially in response to substitution location, the amount of ring substitutions and alkyl chain length. Cyp1a induction varied by parent compound group and was a poor indicator of morphological or behavioral outcomes. Polar phenanthrenes were more biologically active than alkylated phenanthrene derivatives and their toxicity was not dependent upon the Ahr2, Ahr1a or Ahr1b when tested individually, despite cyp1a induction by 50% of polar phenanthrenes. Our results demonstrated that induction of cyp1a did not always correlate with PAH toxicity or Ahr dependence and that the type and location of phenanthrene substitution determined potency.

Dual-layer elemental sulfur-packed denitrification reactor to control sulfate generation and sulfide discharge by two-point inlet and internal recirculation.

In this study, an elemental sulfur (S0) autotrophic denitrification reactor (SADR) and a wood chunk and S0 mixotrophic denitrification reactor (WSMDR) were constructed with dual-layers to effectively remove nitrate from water using two-inlets and internal recirculation. The denitrification rates were 66-114 and 70-104 g-N/(m3·d) for the SADR and WSMDR, respectively. Sulfate production was 5.5-5.9 and 3.2-4.5 mg SO42-/mg reduced N in the SADR and WSMDR, respectively, being lower than theoretical value. In addition, there was no sulfide emission from either reactor. Chlorobium, Chlorobaculum, Ignavibacterium, Sulfuritalea, and Thiobacillus were involved in nitrate reduction in both reactors. Chlorobiaceae had the highest abundance and played an essential role in maintaining the integrity of the co-occurrence pattern. The abundance of functional genes positively correlated with the denitrification performance. This study demonstrates that the operation of two-inlets and internal recirculation can effectively reduce byproduct generation, thereby promoting the practical application of the SADR and WSMDR.

The impact of the structural transformation mechanism of fulvic acid on redox capacity during composting with different biowastes.

Fulvic acid (FA) derived from composting functions can act as electron shuttle, facilitating and expediting the redox reaction during the composting process. However, limited research has been conducted on the redox capacity and structural transformation of FA during composting with different biowastes. The Fe (II) production quantity of the single S. oneidensis MR-1 (MR-1), MR-1 with FA derived from lignocellulose-rich and lignin-rich composting after 300h inoculation were up to 2.28, 3.67 and 2.52mmol/L, indicating the redox capacity of FA in lignocellulose-rich composts was stronger than that in lignin-rich composting. Furthermore, two-dimensional correlation spectroscopy revealed that FA derived from lignocellulose-rich composting exhibited a layer-by-layer structure, characterized by aromatic functional groups and other groups. In contrast, FA obtained from lignin-rich composting displayed an arrangement where the inner aromatic functional groups were obstructed by the methyl group. The structural equation model revealed that the high relative abundance and aromatic functional groups of FA derived from lignocellulose-rich composting process exert a direct influence on the reduction of Fe (III)-citrate, and the methyl groups of FA obtained from lignin-rich composting process also directly linked to the reduction of Fe (III)-citrate. The present study thus posited that the quantity of aromatic functional groups within outer of FA structure during composting constituted a crucial factor influencing its redox capacity. The findings offer novel insights into the transformation mechanism of FA derives from diverse biowastes and its redox characteristics, thereby providing significant guidance for the application of FA in mitigating environment pollutants.

Elemental-organic geochemical evidence for the lacustrine metalimnetic oxygen minimum dynamics in the Mid-Late Triassic Chang 7 shales

The Middle-Late Triassic Ordos Basin has gained increasing attention due to its significance in recording the earliest known recovery-radiation of terrestrial aquatic ecosystems following the Permian-Triassic mass extinction (PTME) and its abundant non-renewable resources. Despite numerous attempts to elucidate mechanisms for high organic carbon burial, the pattern of carbon cycle and its associated environmental variations remain largely unknown, probably ascribed to multi-periodic deposition of volcanic ashes and complex lacustrine depositional architectures. Herein, we reconstructed environmental variations within basinal and global contexts and identified the formation of metalimnetic oxygen minimum area in paleo-lacustrine environments. Our results demonstrate a shift of oxygen-deficient and organic matter hyper-enriched areas from the central basin in the lower part of Chang 7-3 (interval I) towards the periphery in the upper part (interval II). This transition is ascribed to enhanced weathering intensity but weakened volcanic activity, which is contemporaneous with terrestrial bio-evolution across the Mid-Late Triassic boundary. In addition, the contemporary variations in carbon isotopes and relatively sea and lacustrine levels around the Paleo-Tethys Ocean, along with the rare occurrence of high redox metal abundances in lacustrine environments, indicate a (intermittent) water connection between the Ordos Basin and Paleo-Tethys Ocean during the latest Middle Triassic to early Late Triassic. We hypothesize that mild to moderate volcanic activity induced genetic disturbance and stimulated bio-irradiation in the late Ladinian. In contrast, intensified weathering resulted in biological proliferation but also transiently elevated morality in the early Carnian, which appears to be the prelude of spectacular Triassic terrestrial radiation that dominates modern ecosystems.

Metagenomic insight into the diffusion signal factor mediated social traits of anammox consortia after starvation.

Biomass starvation is common in biological wastewater treatment. As a social trait of microbial community, how quorum sensing (QS) regulated bacterial trade-off through interactions after starvation remains unclear. This study deciphered the mechanism of anaerobic ammonium oxidation (anammox) consortia in response to starvation, including reducing extracellular electron transfer (EET), adenosine 5'-triphosphate (ATP) content and amino acid metabolism. Metagenomic analysis has shown that the addition of the diffusion signal factor (DSF) resulted in a high abundance of antioxidant genes, which contributed to achieving redox balance in anammox bacteria. There was an enrichment of Geobacter and Methanosarcina, which were QS-responsive direct interspecific electron transfer participants. Furthermore, DSF stimulated the nitrogen and carbon metabolism of Ca. Kuenenia_stuttgartiensis, promoting syntrophy of metabolic intermediates within microbial community. This study highlighted the effect of DSF on the microbial interaction patterns and deciphered the QS-based social traits of anammox consortia after starvation, facilitating the stable operation of the anammox process.

A distinct immunophenotype in children carrying the Blautia enterotype: The Generation R study.

Studies in mouse models and human adults have shown that the intestinal microbiota composition can affect peripheral immune cells. We here examined whether the gut microbiota compositions affect B and T-cell subsets in children. The intestinal microbiota was characterized from stool samples of 344 10-year-old children from the Generation R Study by performing 16S rRNA sequencing. Bray-Curtis dissimilarity was used to cluster distinct microbiome compositions (enterotypes). B-cell and T-cell phenotypes were defined by 11-color-flow cytometry. Linear regression models with adjustment for lifestyle and child characteristics were performed to determine associations between enterotypes and immune cell numbers. Three enterotypes with distinct microbiota composition were found, characterized by high abundance of Prevotella, Bacteroides and Blautia. Children with the Blautia enterotype had decreased numbers of plasmablasts, CD4+ central memory (Tcm) T cells and follicular T-helper cells (Tfh), while Th22 cells and CD4+ effector memory (Tem) T cells, CD27-IgA+ memory B cells and CD27-IgE+ memory B cells, were increased in these children. In addition, in children with the Blautia enterotype CD4+ Tcm cell numbers expressing the β7 integrin, which can pair with α4 to mediate intestinal homing were also lower, while CD4+β7+ Tem cell numbers were higher than in the other enterotypes. The Blautia enterotype showed features beneficial for human health. Enterotypes were associated with differences in memory B- and T-cell compartments. This study is unique in the detailed analysis of the B and T-cell compartment and the intestinal microbiome in a large generic pediatric cohort, enabling correction for child and maternal covariates. These outcomes could guide further studies about the impact of intestinal microbiome intervention, for instance through diet and microbiota metabolites such as short chain fatty acid production.

Distribution and identification of Aedes mosquitoes, vectors of Dengue virus in Abéché, Chad

Aedes mosquitoes, vectors of dengue, chikungunya, Zika, and yellow fever, represent a significant threat to public health due to their role in transmitting these diseases. Their emergence in Chad, driven by increasing urbanization and demographic expansion, raises considerable concerns. The aim of this study is to better understand the diversity and the role of Aedes mosquitoes in dengue transmission in the city of Abéché, Chad. This is a cross-sectional study conducted over four months, from July to October 2024. Mosquitoes were collected using human bait techniques in nine neighborhoods of Abéché. The samples were then subjected to morphological identification, followed by viral RNA extraction and RT-PCR analysis to detect dengue virus. The results show that out of 370 mosquitoes captured, 85.9% (n = 318) belonged to Aedes genus, of which 95% (n = 305) were Aedes albopictus and 4.6% (n = 13) were Aedes aegypti. There is no evidence of dengue virus in all analyzed mosquitos’ samples. This study highlights the significant presence of Aedes mosquitoes, particularly Aedes albopictus, in the city of Abéché, Chad, where they constitute the dominant species. Despite their high abundance and known role as vectors of dengue, none of the analyzed mosquitoes tested positive for the dengue virus. These findings underscore the importance of continued entomological surveillance and further research to better understand the distribution, dynamics, and potential role of Aedes mosquitoes in disease transmission in Chad. Such efforts are crucial for developing effective vector control strategies and mitigating the risk of dengue outbreaks in the region.

Enhancing surveillance for dengue fever in Oyo State, Nigeria – a one health approach

BackgroundDengue fever (DF) poses a growing global threat, necessitating a comprehensive one-health approach to address its complex interplay between human, animal, and environmental factors. In Oyo State, Nigeria, the true burden of DF remains unknown due to underdiagnosis and misdiagnosis as malaria, exacerbated by poor health-seeking behavior, weak surveillance systems, and inadequate health infrastructure. Adopting a one-health approach is crucial to understanding the dynamics of DF transmission.MethodsA cross-sectional study was conducted from January 2022 to April 2023 in 10 high-risk LGAs of Oyo State. It involved screening DENV in 289 febrile human blood samples and 1,015 Aedes species mosquitoes. Viral RNA from human and mosquito specimens was extracted and analyzed using RT-qPCR. A one-step lateral flow immunoassay cassette test kit detected DENV-specific IgM and IgG in humans. DENV IgM-positive participants were screened for Lassa Virus (LASV) to rule out coinfection due to an outbreak of Lassa fever. Mosquitoes recovered were morphologically identified and classified using appropriate taxonomical keys. Meteorological data was obtained from the Nigeria Meteorological Agency. Data was abridged as proportions and correlation analysis was performed.ResultThe overall seroprevalence of DENV was 128/289 (44.2%) with 19/289 (6.6%) and 109/289 (37.7%) being IgM and IgG positive respectively. DENV was detected all year round with more cases in the rainy season. LASV and DENV coinfection were detected in a participant. DENV RT-qPCR analysis in febrile patients and mosquitoes was negative. There was a high abundance of Aedes aegypti (79.5%) in all the locations surveyed with Aedes albopictus (12.3%) detected in Ido LGA and Ibadan South-East LGA and Aedes simpsoni (9.1%) in Iwajowa LGA. DF shows moderate to strong positive correlations with Aedes mosquito population, humidity, and rainfall (r = 0.419–0.61, p < 0.05), and a negative correlation with temperature (r =—0.465, p < 0.05).ConclusionThe study reveals a significant burden of DENV in Oyo State. The presence of both IgM and IgG antibodies suggests past exposure and possible recent circulation of the virus. The co-detection of LASV and DENV in one participant highlights the likely potential for co-infection. Although DENV was not detected in febrile patients and mosquitoes through RT-qPCR, the high abundance of Aedes species underscores the risk of transmission. These findings emphasize the need for enhanced surveillance systems, strengthened laboratory services, targeted vector control, and increased awareness.

Intermetallic Layers with Tuned Na Nucleation and Transport for Anode-Free Sodium Metal Batteries.

Sodium metal batteries without pre-deposited Na (anode-free) and with a limited amount of Na metal (anode-less) have attracted increasing attention due to their competitive energy density and the high abundance of sodium. However, severe interfacial issues result in poor cycling stability and low Coulombic efficiency. Here, the lightweight interphase layers composed of intermetallic nanoparticles (Sn-Cu and Sn-Ni) are applied to improve Na plating/stripping behaviors. These layers provide uniform seeding sites with high sodiophilicity and support fast ion transport. A reversible Na plating/stripping behavior, featuring a high Coulombic efficiency of ∼99.95% with a minor standard deviation of 0.0013, for 500 cycles at 1 mA cm-2 and 1 mAh cm-2 is achieved on SnCu-coated Al. Consequently, the anode-free Na3V2(PO4)3 full cell with a high loading of 7.6 mg cm-2 exhibits a capacity retention of 90% after 200 cycles. This strategy provides an effective pathway toward anode-free sodium metal batteries.

Transcriptome of Anaplastic Thyroid Cancer Reveals Two Molecular Subtypes with Distinct Tumor Microenvironment and Prognosis.

Background: Although patients with anaplastic thyroid cancer (ATC) generally have a poor prognosis and there are currently no effective treatment options, survival and response to therapy vary between patients. Genomic and transcriptomic profiles of ATC have been reported; however, a comprehensive study of the tumor microenvironment (TME) of ATC is still lacking. This study aimed to elucidate the TME characteristics associated with ATC and their prognostic implications. Methods: We analyzed bulk RNA transcriptomic data from 1,634 samples-including 476 normal thyroid tissues, 25 benign thyroid adenomas, 340 RAS-like and 719 BRAFV600E-like differentiated thyroid cancers (DTC-R and DTC-B, respectively), and 74 ATCs. We assessed the TME and molecular characteristics of these thyroid cancer subtypes using deconvolution analysis. Results: The TME of ATC was characterized by a high abundance of immune cells and fibroblasts and a low abundance of epithelial cells compared to other thyroid histologies. During its malignant evolution, ATC exhibited an ecotype more closely related to DTC-B than RAS-like DTC (DTC-R). Furthermore, we identified two distinct molecular subtypes within ATC with significant differences in their TMEs. We termed the subtype with increased immune cells and fibroblasts as ATC-immune-fibroblast (ATC-IF) and the subtype with elevated epithelial and endothelial cells as ATC-epithelial-endothelial (ATC-E). The ATC-IF group had worse disease-specific survival (log-rank p = 0.035), higher ERK scores, and lower thyroid differentiation scores than the ATC-E group. While both ATC subtypes had elevated immune cells and fibroblasts compared to DTC-R and DTC-B, this increase was more pronounced in ATC-IF, with a marked rise in myeloid lineage cells and promigratory fibroblasts. Immune checkpoint gene expression and epithelial-mesenchymal transition scores were significantly higher in the ATC-IF group than in the ATC-E group. Conclusion: ATC shows a TME distinct from that of DTC and can be further divided into two molecular subtypes-each with its own unique TME. The ATC-IF group, with a poorer prognosis and higher ERK score, is enriched in immune cells and fibroblasts, which may represent potential therapeutic targets.

The Effects of the Addition of Secondary Phyllosilicate Minerals on the Decomposition Process and Products of Maize Straw in Black Soil

The interaction between secondary phyllosilicate minerals and straw is crucial for preserving soil organic carbon (SOC) and fertility. However, the specific mechanism through which these minerals affect straw decomposition and its products in northeast China’s black soil remains unclear. In this study, montmorillonite, illite, and vermiculite were mixed with quartz sand and maize straw, inoculated with microbes, and incubated to analyze the effects of different secondary phyllosilicate minerals on the degradation of organic components in maize straw and the formation of soil humus. The results showed that montmorillonite significantly facilitated the decomposition of maize straw hemicellulose and lignin, which decreased by 95.85% and 76.38%, respectively. Conversely, vermiculite decelerated hemicellulose and lignin degradation. Regarding soil organic acids, lactic acid and malic acid were predominant, with the highest content being found after the montmorillonite treatment. Montmorillonite was the most effective in enhancing extractable humic-like substances, which increased by 71.68%. Montmorillonite increased the content of G0 (water dispersion group), G1 (sodium ion dispersion group), and G2 (sodium grinding dispersion group) complexes. The addition of secondary phyllosilicate minerals increased the organic carbon (OC) content in the G0, G1, and G2 samples, with montmorillonite demonstrating the most pronounced effect. Secondary phyllosilicate minerals increased the abundance of fungi, particularly Ascomycota, with the highest abundance being found after the montmorillonite treatment. In conclusion, our results indicated that montmorillonite facilitated the decomposition of lignocellulose in maize straw, enhanced the accumulation of humus, and promoted the formation of organic–mineral complexes. These findings provide valuable insights into the interaction between secondary phyllosilicate minerals and maize straw and have important implications for improving the quality of black soil in northeast China.

High ectomycorrhizal relative abundance during winter at the treeline

Abstract The rhizosphere is the soil region around plant roots hosting a diverse microbial community, influencing nutrient availability and how plants react to extreme conditions. However, our understanding of the fungi biodiversity and the impact of environmental variations on this biodiversity is still in its infancy. Our study investigates fungal communities’ diversity and functional traits in the rhizosphere of Nothofagus pumilio, one of the few winters deciduous treeline species in the world, forming the treeline in southern South America. At four distinct locations covering 10° latitude, we collected soil samples at treeline and 200 meters below over four seasons during a single year. We employed ITS metabarcoding to elucidate fungal community structures. Our results reveal that fungal diversity was mainly determined by latitudinal variation, with higher levels during warmer seasons and lower altitudes. Interestingly, we found a marked dominance of ectomycorrhizal (EcM) fungi at the treeline, particularly during the winter. In contrast, saprotrophic fungi were more abundant at lower altitudes, particularly during the warmer spring and summer seasons. These findings highlight the temporal and spatial dynamics of rhizospheric fungal communities and their potential roles in ecological processes, emphasizing the value of these communities as indicators of environmental change in high-elevation forests.

Genomic and Proteomic Analyses of Bacterial Communities of Ixodes scapularis Ticks from Broome County, New York

The microbial communities of Ixodes scapularis, the primary vector of Lyme disease in North America, exhibit regional variations that may affect pathogen transmission and vector competence. We analyzed bacterial communities in I. scapularis ticks collected from Broome County, New York, using 16S rRNA gene sequencing (18 ticks) as well as mass spectrometry-based proteomics (36 ticks). According to the 16S rRNA analysis, the endosymbiont Rickettsia buchneri was the most abundant species, with significantly higher (p = 0.0011) abundance in females (54.76%) compared to males (31.15%). We detected Borreliella burgdorferi in 44.44% of ticks and Anaplasma phagocytophilum in two nymphs but in high relative abundances (12.73% and 46.46%). Male ticks exhibited higher bacterial diversity, although the community composition showed no significant clustering by sex or life stage. Co-occurrence analysis revealed negative associations between R. buchneri and Pseudomonas (p = 0.0245), but no associations with B. burgdorferi. Proteomic analysis identified 12 R. buchneri-specific proteins, additionally detecting the protozoan pathogen Babesia microti in 18.18% of females. These findings provide the first comprehensive characterization of I. scapularis microbiomes in the Southern Tier region of New York and suggest broader distribution of R. buchneri across tick life stages than previously recognized, with potential implications for pathogen transmission dynamics.

Volatile Constituents of Four Hypericum Species Native to Greece

The genus Hypericum (Hypericaceae), comprising approximately 500 taxa classified into 22 sections, has remained largely unexplored in terms of its chemical composition, with existing studies on a limited number of species revealing significant chemical polymorphism. This study investigates the volatile profiles of four Hypericum species (H. rumeliacum subsp. apollinis, H. vesiculosum, H. delphicum, and H. olympicum) through GC-MS analysis. Hypericum rumeliacum subsp. apollinis, collected from Mt. Parnassos, exhibited a high abundance of sesquiterpenes hydrocarbons (32.5%) and oxygenated sesquiterpenes (29.7%). Hypericum vesiculosum collected from Mt. Chelmos was rich in oxygenated monoterpenes (33.5%), followed by benzyl derivatives (25.9%). Hypericum delphicum and H. olympicum, collected from the island of Evvia, showed a predominance of alkanes (35.8%) and oxygenated sesquiterpenes (31.9%) in H. delphicum and sesquiterpenes hydrocarbons (41.2%) and oxygenated sesquiterpenes (29.9%) in H. olympicum. Our findings provide new data on the volatile profile of H. vesiculosum and enhance existing information on other species, highlighting notable chemical diversity within the genus Hypericum.

Metagenomic profiling of plaque microbiota in Indian subjects: identified hidden ecological tapestry.

Dental plaque biofilms are the primary etiologic factor for various chronic oral infectious diseases. In recent years, dental plaque shows enormous potential to know about an individual microbiota. Various microbiome studies of oral cavity from different geographical locations reveals abundance of microbial species. Although, the representation of Indian population in this respect is limited, which make us curious to undergo this study. This study investigates the dental plaque microbiota of North Indian individuals based on their age, gender, and dietary patterns; specifically, food preference and availability of water source using 16S rRNA metagenomics analysis. The findings from this study revealed that Streptococcus levels are high across genders, age groups, and water source, highlighting its role as a predominant dental caries associated species like Streptococcus mutans, Streptococcus pyogenes, Streptococcus sobrinus and Streptococcus oralis in the studied population groups. Additionally, the abundance of Actinomyces is observed higher in young individuals and females whereas Fusobacterium and Leptotrichia were high in elderly individuals. Moreover, non-vegetarians have higher abundance of Streptococcus and Fusobacterium, whereas vegetarians show higher abundance of Prevotella and Leptotrichia. The study also highlights the influence of water type on bacterial composition of dental plaque in the studied population i.e., individuals consuming underground water has high abundance of Streptococcus, whereas individuals consuming RO water exhibit elevated Prevotella and Leptotrichia. Insights emerged from the analysis illuminates the complex dynamics of microbiota in dental plaque among North Indians. This study also highlight that this variation of microbiome is influenced by age, gender, and dietary habits (vegetarian or non-vegetarian lifestyle). These results will fill a significant knowledge gap regarding the Indian dental plaque microbiome but also offer a foundation to conduct metagenome studies and potential therapeutic implications for future personalized oral health interventions.

Contribution of poultry farm practice to the structure and composition of bacterial communities in the soil of poultry farms in Lagos, Nigeria

BackgroundPoultry farming practices can impact soil health by altering its microbial and organic composition. On one hand, this could improve soil fertility, but on the other, it may pose health risks to humans and the environment. In this study, we assessed the microbial community structure and composition of poultry litter impacted soil in poultry farms in Lagos Nigeria.MethodsComposite soil samples were collected from two farms (PF01A and PF02B) in a poultry estate and from a pristine environment (CTR) without farming activity. Metagenomic analysis was performed using 16S rRNA gene amplicon sequencing and bioinformatics analysis.ResultsThe most abundant phyla in poultry-impacted soils were Firmicutes (54–69%), Bacteroidetes (18–19%), and Actinobacteria (3–17%), with a low relative abundance of Proteobacteria (7%). In contrast, CTR soil was dominated by the phylum Proteobacteria (30%) and had a low relative abundance of Bacteroidetes (2%). Bacteria strains, including Jeotgalibaca arthritidis, Lysinibacillus jejuensis, and the novel species Enterococcus lemanii and Enterococcus eurekensis, were among dominant taxa in PF01A and PF02B.Some dominant bacterial species such as Corynbacterium xerosis and Ignatzschineria indica have been implicated in human infections and are known to be multidrug resistant.ConclusionIn this study, a high abundance of bacterial operational taxonomic units (OTUs) were found in soil from poultry farms. The presence of poultry litter significantly changed the composition of the bacterial community in the soil. This alteration did not only affect the microbial structure and health of the soil, it also increased the presence of clinically important bacteria, which could pose potential risks to public health.

Biodegradation of polyethylene with polyethylene-group-degrading enzyme delivered by the engineered Bacillus velezensis.

Microplastics (MPs) pose an emerging threat to vegetable growing soils in Harbin, which have a relatively high abundance (11,065 n/kg) with 17.26 of potential ecological risk of single polymer hazard (EI) and 33.92 of potential ecological risk index (PERI). Polyethylene (PE) is the main type of microplastic pollution in vegetable growing soils in Harbin. In this study, the engineered Bacillus velezensis with polyethylene-group-degrading enzyme pathway (BCAv-PEase) was constructed to enhance the degradation of MPs of PE (PE-MPs). BCAv-PEase increased the biodegradation of PE-MPs, promoted weight loss of PE films, elevated surface tension, and decreased the surface hydrophobicity of PE through upregulating activities of depolymerases, dehydrogenase, and catalase. Mechanism analysis showed that BCAv-PEase degraded PE-MPs by promoting the secretion of PEase, thereby leading to the generation of new oxygenated functional groups within the PE-MPs substrate, which further accelerated the metabolic pathway of PE-MPs. The analysis of the microbial community during the PE-MPs degradation processes revealed that BCAv-PEase emerged as the principal bacterial player and stimulated the abundance of microbes and functional genes associated with the biodegradation of PE. In conclusion, this study provides a potential mechanism for biodegradation of PE-MPs mediated by BCAv-PEase via modulating substrate selectivity and optimizing biocatalytic pathways.