Significant Differences In Abundance Research Articles

A global perspective on the abundance, diversity and mobility of antibiotic resistance genes in Escherichia coli

IntroductionEscherichia coli (E. coli), a ubiquitous opportunistic pathogen, poses a growing threat to human health due to the increasing prevalence of antibiotic resistance. However, a comprehensive understanding of the global distribution, diversity, and transmission of antibiotic resistance genes (ARGs) in E. coli remains lacking, hindering effective strategies to combat resistance.MethodsIn this study, we analyzed 94,762 E. coli genome sequences obtained from the NCBI database using advanced bioinformatics tools. ARGs were identified by comparing sequences against a custom ARG database using BLAST. Mobile genetic element (MGE)-associated ARGs were identified by matching with ISfinder databases. Global distribution of ARGs was analyzed by clustering mobile ARG sequences with 99% genetic similarity.ResultsOur analysis revealed that 50.51% of the E. coli genome sequences contained ARGs, totaling 301,317 identified ARG sequences. These ARGs were categorized into 12 major classes and 229 subtypes. Notably, ARGs associated with multi-drug resistance (MDR), β-lactams, macrolide-lincosamide-streptogramins (MLS), tetracyclines, and aminoglycosides were particularly abundant, with the subtypes mdtK, macB, and ampC being especially prevalent. Additionally, significant differences in ARG abundance and diversity were observed across countries, with higher diversity found in high-income nations. Furthermore, 9.28% of the ARG sequences were linked to MGEs, accounting for 98.25% of all ARG subtypes. Notably, 4.20% of mobile ARGs were identified in over 20 countries, with β-lactam and aminoglycoside ARGs being the most widespread.DiscussionThis study provides a comprehensive overview of the global distribution and transmission of ARGs in E. coli. The high abundance of MDR and β-lactam-related ARGs, along with their widespread transmission across countries, highlights the urgent need for global surveillance and control measures. Furthermore, the strong association between ARGs and MGEs underscores the role of horizontal gene transfer in the spread of resistance. The observed variations in ARG diversity between countries suggest that socioeconomic factors, such as healthcare infrastructure and antibiotic usage patterns, significantly influence ARG prevalence. These findings are crucial for informing global strategies to mitigate the spread of antibiotic resistance and improve public health outcomes.

Community assembly and potential function analysis of the endophyte in Eucommia ulmoides

Endophytes play a pivotal role in protecting host plants from both biotic and abiotic stresses, promoting the production of active components (AC) and plant growth. However, the succession of the endophyte community in Eucommia ulmoides (E. ulmoides), particularly the community assembly and function, has not been extensively investigated. In this study, we employed high-throughput sequencing and bioinformatics tools to analyze endophyte diversity across different tree ages, parts, and periods. We examined the population differences, correlations, community assembly mechanisms, and functional roles of these endophytes. Functional predictions via PICRUSt2 revealed that most endophytic fungal functions were linked to biosynthesis, with significant differences in biosynthetic functional abundance across parts and periods. In contrast, the metabolic activity of endophytic bacteria remained stable across different periods and parts. Correlation analysis further confirmed a strong positive relationship between ACs and certain endophytic fungi. Among them, the fungal phyla Ascomycota and Basidiomycota were identified as key contributors to the metabolism of chlorogenic acid (CA), while Aucubin was significantly positively correlated with several endophytic bacteria. These findings provide valuable insights into the functional roles and community assembly mechanism of E. ulmoides endophytes, as well as their symbiotic relationships.

Associations of Chronic Marijuana Use with Changes in Salivary Microbiome

The legalization of marijuana (MJ) for medicinal and recreational use has raised concerns about its potential impact on health, including oral health. While MJ use has been linked to poor oral health, its effects on the composition of the oral microbiome remain unclear. This cross-sectional study analyzed saliva samples from chronic MJ users (n = 18) and nonusers (n = 20) to investigate MJ-related changes in salivary microbiome composition. We identified significant differences in the relative abundance of 16 taxa, including seven species, such as Megasphaera micronucliformis, Prevotella melaninogenica, and Streptococcus anginosus. Additionally, five species showed positive correlations with cumulative lifetime MJ use, including Streptococcus vestibularis and Streptococcus parasanguinis. By grouping salivary microbial communities into clusters based on their association with periodontal health, we found that the cluster with species associated with poor periodontal health had the highest percentage of MJ users. Moreover, MJ use significantly contributed to variance in microbial communities in individuals with relatively good periodontal health. These findings suggest that chronic MJ use is associated with alterations in the salivary microbiome, highlighting its potential broader impact on oral and systemic health.

The microRNAome of Strongylus vulgaris larvae and their excretory/secretory products with identification of parasite-derived microRNAs in horse arterial tissue

The equine bloodworm, Strongylus vulgaris, is a highly pathogenic parasite causing potentially fatal vascular and intestinal damage. Parasites express and release microRNAs (miRNAs) for internal regulation and to modulate host immunity. The complete set of miRNAs expressed by S. vulgaris (the S. vulgaris miRNAome) remains unannotated and the aim of this study was to annotate the miRNAome of L4 and L5 stages of S. vulgaris, and to examine differences in miRNA abundance between larval stages and sexes. Furthermore, we aimed to determine if miRNAs were detectable in excretory/secretory products (ESPs) from larvae and in arterial tissue from their predilection site, the cranial mesenteric artery (CMA). Larvae were collected from naturally infected foals, and categorized by sex and stage. A subset of larvae was snap-frozen, while those remaining were incubated and the (ESPs) collected. Arterial tissue samples were collected from the CMA. Small RNA sequencing, followed by a custom bioinformatic pipeline, was used for annotation. We identified 142 S. vulgaris miRNAs in larvae and 136 in ESPs. Significant differences in miRNA abundance were observed between larvae and ESPs, and between L5 females (L5Fs) and L5 males (L5Ms), L4s and L5Fs, and L4s and L5Ms. No differences were found between L4s and L5s overall. In ESPs, several miRNAs were differentially abundant across all groups. Validation through quantitative real-time PCR (qPCR) detected selected miRNAs and their differential abundance in larvae and ESPs. One parasite-derived miRNA was detected in some of the horse arterial tissue samples but at very low levels. This study provided the first annotation of the S. vulgaris miRNAome. Most of the annotated larval miRNAs were also detectable in ESPs, and differences in miRNA abundance between sexes were found for larvae, and between sexes and stages for ESPs. Parasite-derived miRNAs were, however, not consistently detectable in the surrounding host arterial tissue.

A Trp-574-Leu mutation in acetolactate synthase confers imazamox resistance in barnyardgrass (Echinochloa crus-galli) from China

Abstract Barnyardgrass [Echinochloa crus-galli (L.) P. Beauv.] is increasingly infesting imidazolinone-tolerant (IMI-T) rice fields in China, imazamox resistance of E. crus-galli has become the major concern for weed management in IMI-T rice fields. In this study, the susceptible population JLGY-3 (S) and the suspected resistant population JHXY-2 (R) collected from IMI-T rice fields were used as research subjects. When treated with imazamox, JHXY-2 (R) population showed a high level of herbicide resistance with a resistance index (RI) of 31.2. JHXY-2 (R) was cross-resistant to all five acetolactate synthase (ALS) inhibitors from different chemical families, but sensitive to herbicides inhibiting acetyl-CoA carboxylase (ACCase). In order to understand the reason why JHXY-2 (R) was resistant to imazamox, we performed experiments to characterize potential TSR and NTSR mechanisms. A trp-574-leu amino acid mutation in ALS and low imazamox ALS sensitivity were the main mechanism underlying imazamox resistance in this JHXY-2 (R) population. There was no significant difference in ALS gene expression and ALS protein abundance between R and S populations. High-performance liquid chromatography-tandem mass spectrometry analysis showed enhanced metabolism of imazamox in JHXY-2 (R), which was in contrast to the results of pretreatment with a metabolic enzyme inhibitor. Treatments with the P450/GST inhibitors did not alter the resistance level of JHXY-2 (R) against imazamox. To further clarify the NTSR mechanism of JHXY-2 (R), transcriptome sequencing showed that there was almost no significant difference in the expression of P450 and GST metabolic enzyme genes between R and S populations, and only GST-U1 showed a significant induction in R population. In conclusion, amino acid mutation and higher enzyme activity of ALS are the main causes of imazamox resistance in JHXY-2 (R). However, given the differences in imazamox residues in the leaves of the E. crus-galli, there may still be undetectable NTSR that are causing imazamox resistance in the R population.

Possible effects of shipping routes on coral reef degradation and diversity in Karimunjawa Marine National Park, Java Sea

The Karimunjawa Marine National Park, situated in the Java Sea, Indonesia, is renowned for its rich biodiversity and lively coral reefs. However, amidst the backdrop of this natural beauty, concerns have been raised regarding the potential impacts of shipping activities on the health and diversity of these fragile ecosystems. The increase in maritime traffic, including commercial vessels, tourist boats, and fishing vessels, traversing through the Karimunjawa Marine National Park, raises significant environmental concerns. The movement of these vessels, especially along specific shipping routes, has the potential to disturb and damage coral reefs through various mechanisms. Hence, this study aimed to investigate the possible impacts of shipping routes on the coral abundance and diversity and the coral health in the Karimunjawa Islands, Java Sea, Indonesia. This study categorized ship routes into West Route, East Route, and Non-Route and assessed coral health and diversity across 15 islands. Key metrics analyzed included coral disease prevalence, coral cover, diversity index, species richness, relative abundance, and evenness, using 15 × 2 m belt transects at 3 and 8 m depths with three repetitions each. Statistical analysis revealed significant differences in coral abundance and species richness among ship-route groups, but no significant depth-related differences. These results suggest that while shipping routes affect certain aspects of coral health and diversity, other factors may be more influential in shaping coral disease prevalence and overall diversity in Karimunjawa reefs.

Assessing antimicrobial resistance in pasture-based dairy farms: a 15-month surveillance study in New Zealand.

Antimicrobial resistance is a global public and animal health concern. Antimicrobial resistance genes (ARGs) have been detected in dairy farm environments globally; however, few longitudinal studies have utilized shotgun metagenomics for ARG surveillance in pasture-based systems. This 15-month study aimed to undertake a baseline survey using shotgun metagenomics to assess the relative abundance and diversity of ARGs in two pasture-based dairy farm environments in New Zealand with different management practices. There was no statistically significant difference in overall ARG relative abundance between the two dairy farms (P = 0.321) during the study period. Compared with overseas data, the relative abundance of ARG copies per 16S rRNA gene in feces (0.08-0.17), effluent (0.03-0.37), soil (0.20-0.63), and bulk tank milk (0.0-0.12) samples was low. Models comparing the presence or absence of resistance classes found in >10% of all feces, effluent, and soil samples demonstrated no statistically significant associations (P > 0.05) with "season," and only multi-metal (P = 0.020) and tetracycline (P = 0.0003) resistance were significant at the "farm" level. Effluent samples harbored the most diverse ARGs, some with a recognized public health risk, whereas soil samples had the highest ARG relative abundance but without recognized health risks. This highlights the importance of considering the genomic context and risk of ARGs in metagenomic data sets. This study suggests that antimicrobial resistance on pasture-based dairy farms is low and provides essential baseline ARG surveillance data for such farming systems.IMPORTANCEAntimicrobial resistance is a global threat to human and animal health. Despite the detection of antimicrobial resistance genes (ARGs) in dairy farm environments globally, longitudinal surveillance in pasture-based systems remains limited. This study assessed the relative abundance and diversity of ARGs in two New Zealand dairy farms with different management practices and provided important baseline ARG surveillance data on pasture-based dairy farms. The overall ARG relative abundance on these two farms was low, which provides further evidence for consumers of the safety of New Zealand's export products. Effluent samples harbored the most diverse range of ARGs, some of which were classified with a recognized risk to public health, whereas soil samples had the highest ARG relative abundance; however, the soil ARGs were not classified with a recognized public health risk. This emphasizes the need to consider genomic context and risk as well as ARG relative abundance in resistome studies.

Influence of Growth Support on the Diversity, Composition, and Functionality of Microbial Communities Associated with Tillandsia recurvata

Tillandsia recurvata is an epiphytic plant commonly found in tropical regions and colonizes tree trunks, fences, and power wires. This plant plays an important role in interacting with trees, sharing microorganisms, and performing specific functions in the process of tree colonization. The objective of this study was to evaluate and compare the microbiomes of T. recurvata collected from two different locations (trees and fences) and two plant tissues (leaves and roots). The hypothesis of this study was that the microbiome of T. recurvata is composed of microorganisms that would provide nutritional support to compensate for the lack of nutrients in a particular growth support. The results showed significant differences in microbial diversity between trees and fences, with trees exhibiting higher richness and more complex microbial networks. Proteobacteria was the most prevalent bacterial phylum, with Actinobacteria and Sphingomonas also playing key roles in nitrogen fixation and plant growth. Fungal communities were similar across locations, with Ascomycota and Basidiomycota being predominant, but Paraconiothyrium and Nigrospora showed significant differences in abundance between trees and fences. Functional analysis indicated similar metabolic profiles across leaf and root samples, with key functions for T. recurvata including carbohydrate and amino acid metabolism, stress control, and biofertilization.

Mosquito Species Composition in Nasarawa Local Government Area, Nasarawa State, Nigeria

Study’s Excerpt The resting densities, biting rates, and indoor mosquito populations in Nasarawa LGA were assessed. Prokopack aspirator is applied for morning mosquito collection and the dissecting microscope for identification of species-specific attributes. The results highlight critical areas for targeted vector control to mitigate malaria transmission in the region. Full Abstract Numerous mosquito species are capable of carrying various tropical diseases. This study ascertained the composition of mosquitoes in Nasarawa Local Government Area, Nasarawa State, Central Nigeria. Adult mosquitoes were collected between 0600 and 0900 hours in the morning using a battery-operated Prokopack aspirator. The mosquitoes were then placed in a petri dish with proper labelling and taken to a laboratory for identification and dissection. Using a dissecting microscope and identification key, mosquitoes were sorted and morphologically classified according to their morphological features. The mosquito midgut was dissected to check for sporozoites infectivity. The man-biting rate (MBR) and indoor resting density (IRD) were computed. A total of 314 adult mosquitoes, spanning four species and belonging to the Anopheline and Culicine mosquito groups, were found to be resting indoors with An. gambiae representing 39.2% of the total composition. A significant difference in mosquito abundance (χ2= 58.866, df = 3, P=0.001) was observed between the four species that were reported. There is no discernible variation in the mosquito composition in the research region (χ2= 4.861, df = 2, P = 0.088). A statistically significant variance in sex was noted (χ2=285.235, df = 2, P = 0.000). The biting rate was recorded at 2.6 bites per person per night, and an indoor resting density of 5.23 mosquitoes per room per night was recorded. There was a noteworthy distinction in the abdomen condition of the mosquitoes (χ2 = 45.564, df = 3, p < 0.001). Mosquito species abundance in October was 200 (63.7%), compared to 114 (36.3) in September. Nonetheless, a noteworthy distinction was observed in the abundance of mosquito species throughout the research months (χ2= 7.5076, df = 1, P-value = 0.006). Based on the study's findings that provided insight into the species composition of the mosquito population in the study area, it is recommended to remove possible breeding grounds, promote the use of insecticide-treated nets, and prioritize interrupting vector-human contact as a means of halting the spread of malaria parasites.

Inferring post-transcriptional regulation within and across cell types in human testis.

Single-cell tissue atlases commonly use RNA abundances as surrogates for protein abundances. Yet, protein abundance also depends on the regulation of protein synthesis and degradation rates. To estimate the contributions of such post transcriptional regulation, we quantified the proteomes of 5,883 single cells from human testis using 3 distinct mass spectrometry methods (SCoPE2, pSCoPE, and plexDIA). To distinguish between biological and technical factors contributing to differences between protein and RNA levels, we developed BayesPG , a Bayesian model of transcript and protein abundance that systematically accounts for technical variation and infers biological differences. We use BayesPG to jointly model RNA and protein data collected from 29,709 single cells across different methods and datasets. BayesPG estimated consensus mRNA and protein levels for 3,861 gene products and quantified the relative protein-to-mRNA ratio (rPTR) for each gene across six distinct cell types in samples from human testis. About 28% of the gene products exhibited significant differences at protein and RNA levels and contributed to about 1, 500 significant GO groups. We observe that specialized and context specific functions, such as those related to spermatogenesis are regulated after transcription. Among hundreds of detected post translationally modified peptides, many show significant abundance differences across cell types. Furthermore, some phosphorylated peptides covary with kinases in a cell-type dependent manner, suggesting cell-type specific regulation. Our results demonstrate the potential of inferring protein regulation in from single-cell proteogenomic data and provide a generalizable model, BayesPG , for performing such analyses.

Deciphering the Cape Gooseberry Fruits Mycobiome for Further Safety Improvement Postharvest.

Cape gooseberries are exquisitely flavored fruits; their rapid deterioration reduces their shelf life. Understanding the unique mycobiome of fruit peels is an essential step in identifying the taxa causing postharvest loss. The current study proposes to analyze the fungal communities of cape gooseberry peels collected from an organic orchard at unripe and ripe stages and purchased from open-air market sites, using the ITS2 region metabarcoding. According to the Kruskal-Wallis test, there were no statistically significant differences found in either the phylogenetic or non-phylogenetic alpha diversity indices. Significant differences in fungal communities were observed between the market and orchard groups based on beta diversity results. Ascomycota (85.72-96.76%), Basidiomycota (3.21-13.91%), and Chytridiomycota (0.07-9.35%) were the most common fungal phyla, their abundance varying with the ripening stage and origin. Dothideomycetes in the orchard group and Saccharomycetes in the market group were the two most prevalent classes. Furthermore, we investigate which taxa showed a significant difference in abundance between the two conditions (market vs. orchard) using the analysis of compositions of microbiomes with bias correction (ANCOM-BC) test. Regardless of the phase, the orchard samples exhibited a notable increase in the mean absolute abundance of various beneficial fungal taxa, including Tilletiopsis washingtonensis and Articulospora proliferata, whereas the market samples demonstrated a high abundance of harmful yeasts and molds such as Meyerozyma guilliermondii, Candida railenensis, and Botrytis caroliniana. Although it is unclear how these microorganisms augment at the market sites and might impact the fruit quality after harvest, from a fruit safety perspective, it is essential to comprehend the diversity and variation of the mycobiome composition at different ripening stages to further develop strategies to improve food safety postharvest.

Distinct bacterial and eukaryotic communities reflect the specificity of different coral reefs in the South China Sea

The microbial composition of surrounding waters is crucial for the health of coral reefs and holds significant value for understanding the complexity and environmental adaptability of coral reef ecosystems. This study reveals the spatial heterogeneity and diversity characteristics of bacterial and eukaryotic communities in different coral reef regions of the South China Sea. Chao and Shannon indices showed significant differences (p < 0.05) in diversity of bacterial and eukaryotic communities across different coral reefs. PCoA (principal coordinate analysis) indicates significant differences in community composition among regions, highlighting the crucial role of coral reef environmental heterogeneity on microbial community. NST (normalized stochasticity ratio) analysis indicates that community assembly in coral reef areas is more influenced by ecological stochastic processes. Major bacterial groups include Proteobacteria, Cyanobacteria, and Bacteroidota, while dominant eukaryotic groups include Dinophyceae, Apicomplexa, Bacillariophyta, Florideophyceae, Mamiellophyceae, Syndiniales, Prasino-Clade-VII, and Ascomycota, each showing significant abundance differences across coral reef regions (p < 0.05). High abundance of Rhodobacterales and Flavobacteriales are detected in all coral reef waters. Correlation analysis indicates that temperature, pH, and salinity are important factors affecting the bacterial and eukaryotic communities. This study reveals the spatial heterogeneity of microbial communities in coral reef regions of South China Sea and underscores the significant impact of marine environmental heterogeneity on community structure.

Immune Dysregulation in the Oral Cavity during Early SARS-CoV-2 Infection.

Tissue-specific immune responses are critical determinants of health-maintaining homeostasis and disease-related dysbiosis. In the context of COVID-19, oral immune responses reflect local host-pathogen dynamics near the site of infection and serve as important "windows to the body," reflecting systemic responses to the invading SARS-CoV-2 virus. This study leveraged multiplex technology to characterize the salivary SARS-CoV-2-specific immunological landscape (37 cytokines/chemokines and 11 antibodies) during early infection. Cytokine/immune profiling was performed on unstimulated cleared whole saliva collected from 227 adult SARS-CoV-2+ participants and 37 controls. Statistical analysis and modeling revealed significant differential abundance of 25 cytokines (16 downregulated, 9 upregulated). Pathway analysis demonstrated early SARS-CoV-2 infection is associated with local suppression of oral type I/III interferon and blunted natural killer-/T-cell responses, reflecting a potential novel immune-evasion strategy enabling infection. This virus-associated immune suppression occurred concomitantly with significant upregulation of proinflammatory pathways including marked increases in the acute phase proteins pentraxin-3 and chitinase-3-like-1. Irrespective of SARS-CoV-2 infection, prior vaccination was associated with increased total α-SARS-CoV-2-spike (trimer), -S1 protein, -RBD, and -nucleocapsid salivary antibodies, highlighting the importance of COVID-19 vaccination in eliciting mucosal responses. Altogether, our findings highlight saliva as a stable and accessible biofluid for monitoring host responses to SARS-CoV-2 over time and suggest that oral-mucosal immune dysregulation is a hallmark of early SARS-CoV-2 infection, with possible implications for viral evasion mechanisms.

Intestinal microbiota in children with bronchial asthma

Background. Intestinal microbiota is one of the most important factors determining the state of human health, including its influence on the immunological mechanisms regulating the development of allergic diseases in childhood. The role of intestinal microbiota and the gut – lung axis in the development of bronchial asthma (BA) is an important area of research.Aim. To analyze the taxonomic composition of intestinal microbiota in children with BA using 16S rRNA gene sequencing.Materials and methods. The study included patients with BA (n = 50, mean age 10.34 ± 2.99 years) and a group of apparently healthy individuals (n = 49, mean age 10.3 ± 2.8 years). For all patients, medical history was taken, and physical examination and stool test were performed. Patients with BA were assessed for the level of total and specific immunoglobulin (Ig) E and underwent spirometry. The microbiota composition was analyzed by 16S rRNA gene sequencing with subsequent bioinformatic and statistical analysis.Results. Significant differences in the composition of the intestinal microbiota (beta diversity) and a decrease in taxonomic diversity (alpha diversity) were found in patients with BA compared to healthy controls. The intestinal microbiota of patients with BA was characterized by an increase in the abundance of Bacteroides, Parabacteroides, Lachnospira, Roseburia, Akkermansia, Anaerostipes, Sutterella, Odoribacter, Phascolarctobacterium, Butyricimonas, as well as unclassified bacteria from the Rikenellaceae families. The intestinal microbiota of children without BA was characterized by greater abundance of bacteria from Blautia, Bifidobacterium, Dorea, Ruminococcus, Streptococcus, Eubacterium, Acinetobacter, Collinsella, Lactococcus, Catenibacterium genera and unclassified bacteria from the Clostridiaceae and Coriobacteriaceae families. Significant differences in the quantitative abundance of bacteria were revealed depending on the type of sensitization, the level of total IgE, and the value of FEV1.Conclusion. The results obtained indicate the differences in the intestinal microbiota composition in children with BA and healthy children.

Effects of exogenous signaling molecules on anaerobic sludge digestion: Quorum sensing and antibiotic resistance genes

Regulating quorum sensing (QS) signaling molecules could improve wastewater treatment but might increase antibiotic resistance. This study investigated the effects of exogenous C6-HSL on anaerobic sludge under oxytetracycline stress, with a focus on antibiotic resistance genes (ARGs) and the QS response. The results revealed that exogenous oxytetracycline increased the copy number of ARGs by more than 68.8 %. It also facilitated a 3.04-fold increase in the concentration of signaling molecules and increased the abundance of QS genes. Further addition of the C6-HSL accelerated oxytetracycline degradation, and reduced its residual concentration by 70.9 %, alleviating oxytetracycline stress on microbial communities, and correspondingly reducing stress release from AHL by 75.4 %. Importantly, this did not exacerbate antibiotic resistance, with no significant difference (p > 0.05) in the ARG abundance. These findings may provide valuable insights into the relationship between QS process and antibiotic resistance.

Spatiotemporal changes in the community and demography of mesozooplankton in the eastern Indian sector of the Southern Ocean during austral summer 2018/2019

The Southern Ocean is facing rapid environmental changes. However, few studies have been conducted on the spatiotemporal variability of mesozooplankton communities under recent climatic conditions, particularly in the eastern Indian sector. This study describes the spatiotemporal variability of the mesozooplankton community and the demographics of large copepods and krill in this sector, sampled through a Rectangular Mid-Water Trawl with 1 m2 mouth area (RMT1) during the austral summer of 2018/2019 as part of the KY1804 survey. Cluster analysis indicated that the mesozooplankton community was divided into five groups that showed only small longitudinal differences, as they were affected by oceanic fronts. Part of the variability was explained by physical (local upwelling) and biological features (e.g., the occurrence of species showing a specific spatial distribution, such as Euphausia crystallorophias). Horizontal changes in the zooplankton community structure were not attributed to temporal changes during the 2-month sampling period. The demographics of the dominant species, Calanoides acutus, Calanus propinquus, Metridia gerlacheri, and Thysanoessa macrura, exhibited significant temporal differences in abundance or mean stage index (MSI) between the early and late seasons. These differences matched the growth rates estimated in previous studies, suggesting that their growth during the study period was constant without regional differences. There were no evident changes in the abundance or demographics of Rhinalanus gigas, suggesting that they were in their reproductive season. These species-specific demographics could be explained by the species life cycles: growth in C. acutus and C. propinquus and reproduction in R. gigas during the austral summer. Abundances and MSIs confirmed the growth of dominant copepods and krill during the sampling period; however, no evident seasonal changes were observed in the zooplankton community structure. The findings of this study contribute to the understanding of lower trophic levels in marine ecosystems and the present carbon cycle in the eastern Indian sector of the Southern Ocean.

Fungal communities in three root herbs: Insights and implications

The roots of Astragali Radix (AM), Dioscoreae Rhizome (DR), and Codonopsis Radix (CR) are frequently used in classical tonic formulations and dietary supplements. Given the extended exposure of rhizomes to complex biological environments, it is necessary to investigate the fungal composition of their surface. In this study, the fungal communities in the three root herbs were analyzed by DNA metabarcoding, and an extensive comparison of the fungal diversity at each taxonomic level was carried out. Furthermore, we examined the effects of species, collection site, and processing method on the fungal community. In Astragali Radix and Codonopsis Radix samples, Cladosporium was the predominant genus, with relative abundances of 1.98 %-76.81 % and 1.69 %-85.59 %, respectively. Aspergillus (0.08 %–99.92 %) was the prevailing genus in Dioscoreae Rhizome samples. Meanwhile, a total of 12 potential toxigenic fungi were identified, including Aspergillus restrictus, Fusarium oxysporum, and Penicillium citrinum. Moreover, the variations in fungal diversity and community composition from different collection sites and processing approaches were observed. Linear discriminant analysis effect size indicated significant differences in the relative abundance of genera among the three root herbs. Gibberella and Mucor genera were significantly enriched in Astragali Radix samples, while Yarrowia and Cladosporium genera exhibited significant enrichment in Dioscoreae Rhizome and Codonopsis Radix samples, respectively (p≤0.001). This study presents novel insights into the fungal profiles of three root herbs, thereby providing references for their safe utilization and quality improvement.

Response of phyllostomid bat diversity to tree cover types in North-western Ecuador

Agricultural activities affect tropical forest biodiversity; however, some bat species can survive under these anthropogenic changes. We described the characteristics of phyllostomid bat assemblages in tree covers located in 48 plots among four agricultural landscapes of North-western Ecuador. Bats were captured with mist nets installed at a ground level reaching three meters’ height. For each of the plots, we installed a mist net in four types of tree cover (polyspecific live fences, monospecific live fences, cacao plantations, and isolated trees in pastures). We captured 250 phyllostomid bats belonging to 16 species with a trapping effort of 19,200 m2 of net coverage. Polyspecific live fences showed significant differences in relative abundance, richness, and diversity of phyllostomid bats compared to the other three. Frugivorous and nectarivorous guilds were the most abundant, and also exhibited the highest richness among other guilds present in agricultural landscapes. In addition, frugivorous, and nectarivorous guilds increase their abundance and richness in agricultural landscapes, while the animalivorous guild is negatively affected. We recommend installing polyspecific live fences in tropical production systems to support the conservation of phyllostomid bats. We conclude that living fences composed of various plant species favour the abundance, richness, and diversity of phyllostomid bats.

Exploring the Gut Microbiota Landscape in Cow Milk Protein Allergy: Clinical Insights and Diagnostic Implications in Pediatric Patients

Cow milk protein allergy (CMPA) is a significant health concern characterized by adverse immune reactions to cow milk proteins. Biomarkers for the accurate diagnosis and prognosis of CMPA are lacking. This study analyzed the clinical features of CMPA, and 16S RNA sequencing was used to investigate potential biomarkers through fecal microbiota profiling. Children with CMPA exhibit a range of clinical symptoms, including gastrointestinal (83% of patients), skin (53% of patients), and respiratory manifestations (26% of patients), highlighting the complexity of this condition. Laboratory analysis revealed significant differences in red cell distribution width (RDW) and inflammatory markers between the CMPA and control groups, suggesting immune activation and inflammatory responses in CMPA. Microbial diversity analysis revealed higher specific diversity indices in the CMPA group compared with those in control group, with significant differences at the genus and species levels. Bacteroides were more abundant in the CMPA group, whereas Bifidobacterium, Ruminococcus, Faecalibacterium, and Parabacteroides were less abundant. The control group exhibited a balanced microbial profile, with a predominant presence of Bifidobacterium bifidum and Akkermansia muciniphila. The significant abundance of Bifidobacterium in the control group (23.19% vs 9.89% in CMPA) was associated with improved growth metrics such as height and weight, suggesting its potential as a probiotic to prevent CMPA and enhance gut health. Correlation analysis linked specific microbial taxa such as Coprococcus and Bifidobacterium to clinical parameters such as family allergy history, weight and height, providing insights into CMPA pathogenesis. Significant differences in bacterial abundance suggested diagnostic potential, with a panel of 6 bacteria achieving high predictive accuracy (area under curve (AUC) = 0.8708). This study emphasizes the complex relationship between the gut microbiota and CMPA, offering valuable insights into disease mechanisms and diagnostic strategies.

Cervical cancer microbiome analysis: comparing HPV 16 and 18 with other HPV types

Differences in the cervicovaginal microbiome may influence the persistence of HPV and therefore, the progression to cervical cancer. We aimed to analyze and compare the metatranscriptome of cervical cancers positive for HPV 16 and 18 with those positive for other HPV types to understand the microbiome’s influence on oncogenicity. RNA sequencing data from a total of 222 invasive cervical cancer cases (HPV16/18 positive (n=42) and HPV “Other types” (n=180)) were subjected to taxonomy classification (Kraken 2) including bacteria, virus and fungi to the level of species. With a median depth of 288,080.5 reads per sample, up to 107 species (38 bacterial, 16 viral and 53 fungal) were identified. Diversity analyses revealed no significant differences in viral or fungal species between HPV16/18 and other HPV types. Bacterial alpha diversity was significantly higher in the "Other HPV types" group for the Observed index (p=0.0074) (but not for Shannon). Cumulative species curves revealed greater species diversity in the “Other HPV types” group compared to “HPV16/18 but no significant differences in species abundance were found between HPV groups. The study did not detect strong significant microbiome differences between HPV 16/18 and other HPV types in cervical cancers. Further research is necessary to explore potential factors influencing the oncogenicity of different HPV types and their interaction with the cervical microbiome.