Taxonomic Levels Research Articles

The effect of anthelmintic treatment and efficacy on the faecal microbiota of healthy adult horses

Changes to the faecal microbiota of horses associated with administration of anthelmintic drugs is poorly defined. This study included horses with cyathostomin infection where susceptibility and resistance to oxfendazole and abamectin was known. This study assessed the changes to the faecal microbiota associated with administration of two different anthelmintics in this population. Twenty-four adult horses were included. Faecal egg counts were performed on all horses prior to random allocation into abamectin (n=8), oxfendazole (n=8) or Control groups (n=8) and at Day 14 post treatment. Faecal samples were collected for microbiota analysis prior to anthelmintic administration and on Day 3 and Day 14. From each faecal sample, DNA was extracted prior to PCR amplification, next generation sequencing and analysis using QIIME2. Anthelmintic treatment was associated with changes in alpha diversity (p <0.05), with increased evenness and diversity at Day 14 and increased richness at Day 3 within the abamectin group. Differences in relative abundance of bacteria at the phyla, family and genus taxonomic levels occurred after treatment; indicating that the microbiota was altered with anthelmintic administration. The results support that anthelmintic administration and removal of cyathostomins from the large intestine of horses is associated with changes in the faecal microbiota. The results suggest that removal of cyathostomins is associated with greater differences in microbiota, compared to anthelmintic drug administration that is ineffective in reducing cyathostomin infection. Cyathostomin removal was supported by adequate reduction of faecal egg counts, determined by faecal egg count reduction testing.

Unveiling the mysteries of Asian herbivores resource partitioning in tropical wet-grassland ecosystem

Ecological niche partitioning is fundamental for the coexistence of sympatric species. However, the relationship between herbivore body size and forage availability on resource segregation and selection remains debatable. This study quantifies the niche differentiation and selectivity of forage species consumed by six Asian large herbivores (SLH), including mega-herbivores like Greater one-horned rhino (Rhinoceros unicornis), Asian elephant (Elephas maximus) and Asiatic wild buffalo (Bubalus arnee), and meso-herbivores like swamp deer (Rucervus duvaucelii), hog deer (Axis porcinus) and sambar (Rusa unicolor) in tropical wet-grasslands of the Brahmaputra floodplains. We hypothesized that body size influences dietary niche breadth and interspecific dietary similarities or dissimilarities, while forage availability influences forage selectivity among Asian herbivores. We used micro-histological technique, harvest method and Jacobs Index to quantify SLH foraging patterns, forage availability and preference, respectively. Results of the study revealed high niche breadth for elephant (0.56>Bs≤0.74) among mega-herbivores and for sambar (0.49>Bs≤0.64) among meso-herbivores. SLH showed a significant positive correlation between body size and niche breadth in wet season. High dietary overlap was recorded between buffalo and hog deer (0.79–0.86) and swamp deer and hog deer (0.75–0.86) among SLH, rhino and buffalo (0.80–0.83) among mega-herbivores, and swamp deer and hog deer (0.75–0.86) among meso-herbivores. High dietary dissimilarity was recorded between elephant and swamp deer (36–37 %), elephant and buffalo (27–33 %), and swamp deer and sambar (27–29 %). Compared to dry season (1354.54 ±641.30 g m˗2), significantly higher biomass was recorded in wet season (3026.93 ±1632.65 g m˗2; p<0.05). From dry to wet season, rhino, buffalo and hog deer shift their preferred forage from dicot to monocot. Dicot was the most preferred forage of elephant among mega-herbivores, and monocot of swamp deer and sambar among meso-herbivores. Mega- and meso-herbivores avoid invasives Merremia umbellata and Mimosa spp., while meso-herbivores avoid Mikania micrantha. Body size explains niche partitioning only for rhino, elephant and swamp deer. Forage availability contributed to niche breadth and forage preference. In conclusion, forage segregation, despite being challenging to interpret at taxonomic level, influences niche partitioning among mega- and meso-herbivores.

P-328 Uterine Fluid microbiome composition in fertile controls and infertile women

Abstract Study question Is the microbiome of the Uterine Fluid (UF) related to outcomes of frozen-thawed blastocyst transfer? Summary answer Microbiome of UF collected by double-sheated catheter shows Lactobacilli as the most abundant species but does not relate to outcomes of frozen-thawed blastocyst transfer. What is known already The microbiome of UF has been described to be largely dominated (&amp;gt;90%) by Lactobacilli and has been shown to be markedly associated with the outcomes of embryo transfer. Nonetheless, previous reports have not collected UF by avoiding vaginal/cervical contamination through a double-sheated catheter. Study design, size, duration Observational study conducted at Fondazione IRCCS Ca’Granda Ospedale Maggiore Policlinico and IRCCS Ospedale San Raffaele, Milan, Italy. n = 13 fertile controls underwent UF sampling in the pre-receptive (LH + 2) and receptive (LH + 7) phase of a monitored natural cycle and n = 48 infertile women underwent UF sampling on day LH + 7 of the monitored natural cycle preceding that of their first frozen-thawed blastocyst transfer. UF was sampled by aspiration with a double-sheated catheter (commonly used for embryo transfer. Participants/materials, setting, methods Microbiome analysis was conducted following the Illumina protocol for V3-V5 regions of the 16S rRNA and using the Illumina MiSeq instrument. Raw sequencing data processing encompassed quality controls, and QIIME 2 scripts were employed to obtain taxonomic abundances (taxonomic levels L2-L7). Alpha (within sample), and beta (among samples) diversity and differential expression at taxonomic level (using limma, Bioconductor library) were calculated. Main results and the role of chance UF microbiome analysis showed lack of separation between samples from the two Centres, confirming the reproducibility of the technique. UF microbiome was also found to be stable throughout the menstrual cycle, with no diversity observed between LH + 2 and LH + 7 samples in the population of fertile controls (p = 0.9, Adonis test on beta diversity; confirmed by differential abundance tests based on linear regression models at taxonomic levels). UF of fertile controls showed Lactobacillus Helveticus as the most abundant species (16.2%), followed by other Lactobacilli (unspecified) (12.1 %), Lactobacillus Iners (11.8%), Streptococcus (unspecified) (6.8%), Bifidobacterium (4.7%) and Gardnerella (1.9 %). In women who achieved successful implantation after FET, the most abundant species was L. Helveticus (58.1%) followed by L. Iners (9.8%), Acinetobacter lwoffii (5.9%) and other Lactobacilli (unspecified) (4.0%). No statistically significant differences were found in linear regression comparisons at taxonomic level with UF of women with failed implantation, in whom most abundant species were L. Helveticus (50.4%, p = 0.11), L. Iners (15.8%, p = 0.95), other Lactobacilli (unspecified) (13.7%, p = 0.17) and Garnderella (6.5%, p = 0.19). The proportion of Lactobacillus- dominated (&amp;gt;90%) samples was 50% (n = 10/20) in infertile women achieving successful implantation and 46% (n = 13/28) in infertile women with failed implantation (p = 0.8). Limitations, reasons for caution These results are preliminary and only include the first n = 48 patients of the total n = 249 patients that will be enrolled. A larger sample is required to further investigate possible relations between UF microbiome composition and implantation outcomes. Wider implications of the findings As UF microbiome was found to be stable between cycle phases and it is non-invasively collected, it could be analysed in the same cycle in which ET is scheduled. This might increase accuracy compared to current tests for endometrial receptivity, that have to be performed in the cycle before ET. Trial registration number RF-2019-12369460

New Technique for Identification of Ichthyoplankton and Its Application in Biomonitoring Studies, Management and Conservation of Neotropical Fish.

Despite significant advancements in ichthyoplankton collection and data processing, challenges persist in the taxonomic identification of these organisms, particularly their eggs. To overcome these challenges, a novel technique has been developed to facilitate the identification of live eggs collected directly in wild. This user-friendly technique includes the collection, processing of the material, and field incubation. Sampling must be conducted using a pelagic net towed at low speed, preferably during early evening. The material processing involves pre-sorting and sorting to remove eggs and larvae. The separated eggs, kept in an aerated bowl, can be identified based on their morphological and meristic characteristics. Unidentified eggs can be placed in plastic bags with oxygen and incubated directly in the aquatic environment for 48-72 h. After this incubation period, the hatched larvae at the yolk-sac or preflexion stage, are identified to the lowest possible taxonomic level. Depending on the study's purpose, hatched larvae and field-collected larvae can be transported to research centers for further development, released back into the natural environment, or fixed to complete the collection. The application of this technique supports management and monitoring programs by identifying spawning areas through egg identification, forming broodstock, and replenishing threatened species, thereby enhancing scientific collections of ichthyoplankton. Additionally, it reduces mortality in ichthyoplankton techniques, including endangered species. Therefore, we believe that this novel taxonomic technique for identifying live ichthyoplankton represents a paradigm shift in the monitoring, management, and conservation of fish, as well as in ecological stewardship and advances in this area of research.

Evaluation of Rumen Microbes For Milk Fat Yield in Cattle Based on 16S rRNA Amplicon Metagenomic Sequencing

Background: Ruminal microbes support growth, lactation and maintenance of animals by providing energy and protein yielding nutrients. Metagenomics is the study of microbial communities directly in their natural environments such as soil, water, gut samples etc. The 16S rRNA gene sequencing is one of the basic genetic markers for the characterisation of prokaryote microorganism community. Current study exploited complex gut microbial communities present in cattle rumen based on variation in milk fat yield. Methods: The study was conducted in cattle reared at University Livestock Farm, Kerala Veterinary and Animal Sciences University. Twelve healthy cattle in the initial stages of lactation (less than three months) were selected and divided into two groups of six each based on high and low milk fat composition. Rumen samples were collected and DNA was isolated. Amplicons of 16S rRNA has been generated from metagenomic DNA targeting V3 and V4 hyper variable regions. Qiime2 was used for analysis for 16S rRNA amplicon sequencing. Result: Results revealed that a total of 38,28,241 sequences were obtained after demultiplexing. Majority of sequence length ranged around 295 to 301 nucleotides for forward reads and 216 to 300 nucleotides for reverse reads. After denoising, a total of 6,62,498 sequences were obtained. Clustering (de-replication) produced 711 unique sequence features. In kingdom level of taxonomy, for bacterial kingdom, there was no significant difference in abundance of organisms for high milk fat yield and low milk fat yield cows. For archaea, significant difference observed between abundance of high milk fat and low milk fat groups at five per cent level in the current study.

Analysis of Physiology Theory Question Papers for Competency-Based Medical Education Implementation in Gujarat: A Pilot Study.

Introduction Theory question papers form an important part of assessment in medical education. As per the Competency-Based Medical Education (CBME) guidelines 2019, questions should test higher levels of cognition. This pilot study analyzes 60 question papers from different universities in Gujarat for their construct and content validity. The aim was to analyze the quality of physiology question papers from various medical universities in Gujarat to gain insights into assessment quality and its alignment with the CBME guidelines. The objectives were twofold: to evaluate the "construct validity" and "content validity" of these physiology theory question papers over the past three years according to the CBME standards. Methods An observational study using a cross-sectional records-based approach was carried out, evaluating 60 summative exam question papers in physiology from eight different universities of Gujarat for their construct and content validity. Using Bloom's taxonomy, the learning level of the cognitive domain for the questions asked was assessed. The findings compared and displayed a sample of papers. Results A total of 1842 questions were analyzed from the 60 question papers of eight different universities of the Gujarat state. The study found that the questions asked for different levels of cognition in Bloom's taxonomy, i.e., remember, understand, apply, analyze, evaluate, and create, were 560 (30.40%), 434 (23.26%), 222 (12.05%), 118 (6.41%), 94 (5.10%), and 0.00%, respectively. A total of 414 (22.48%) questions did not have any verb, so they did not fit into any level of Bloom's taxonomy. The majority of questions (1773, 96.25%) were asked from the core competencies, while a small percentage (69, 3.75%) of questions were asked from the non-core competencies of physiology. Conclusion The majority of questions in the summative question papers in physiology were of level "remember" and "understand" as per Bloom's taxonomy. Of the questions, 26% did not have any verb. There is a need to incorporate more questions testing higher levels of cognition and to use blueprints by universities. Faculty training is also necessary to bring about course correction.

Genotypic Identification of Trees Using DNA Barcodes and Microbiome Analysis of Rhizosphere Microbial Communities.

DNA barcodes can provide accurate identification of plants. We used previously reported DNA primers targeting the internal transcribed spacer (ITS1) region of the nuclear ribosomal cistron, internal transcribed spacer (ITS2), and chloroplast trnL (UAA) intron to identify four trees at Bergen Community College. Two of the four trees were identified as Acer rubrum and Fagus sylvatica. However, Quercus was only identified at the genus level, and the fourth tree did not show similar identification between barcodes. Next-generation sequencing of 16S rRNA genes showed that the predominant bacterial communities in the rhizosphere mainly consisted of the Pseudomonadota, Actinomycetota, Bacteroidota, and Acidobacteriota. A. rubrum showed the most diverse bacterial community while F. sylvatica was less diverse. The genus Rhodoplanes showed the highest relative bacterial abundance in all trees. Fungal ITS sequence analysis demonstrated that the communities predominantly consisted of the Ascomycota and Basidiomycota. Quercus showed the highest fungi diversity while F. sylvatica showed the lowest. Russula showed the highest abundance of fungi genera. Average similarity values in the rhizosphere for fungi communities at the phylum level were higher than for bacteria. However, at the genus level, bacterial communities showed higher similarities than fungi. Similarity values decreased at lower taxonomical levels for both bacteria and fungi, indicating each tree has selected for specific bacterial and fungal communities. This study confirmed the distinctiveness of the microbial communities in the rhizosphere of each tree and their importance in sustaining and supporting viability and growth but also demonstrating the limitations of DNA barcoding with the primers used in this study to identify genus and species for some of the trees. The optimization of DNA barcoding will require additional DNA sequences to enhance the resolution and identification of trees at the study site.

Spatial disaggregation of a legacy soil map to support digital soil and land evaluation assessments in Scotland

In recent years, the importance of soils and soil functions has been recognised for supporting the delivery of ecosystem services and for the realisation of international initiatives, such as the UN Sustainable Development Goals. At the same time, Digital Soil Mapping (DSM) has emerged as a modelling technique that can satisfy increased end-user needs for new soil datasets by producing fine resolution soils and soil property maps to support complex digital soil and land evaluation assessments. Spatial disaggregation is a popular DSM technique that is used to transform legacy soil maps to more spatially-explicit soils datasets, which can also be used in conjunction with soil databases to generate digital soil property maps. In this study, we performed spatial disaggregation of the National Soil Map of Scotland (originally published at 1:250,000 scale) at the taxonomic level of Soil Series, with the specific objective to facilitate the production of harmonised digital soil property maps to support soil and land evaluation assessments in Scotland through linking to the Scottish Soil Database. We divided Scotland into Landscape Units of similar soil and landform characteristics and trained probability random forest models within each Landscape Unit using area-proportion random sampling of both single- and multiple- (complex) Soil Series map units and selected environmental covariates to produce Soil Series probability layers at 50 m grid resolution. The performance of the disaggregated Soil Series maps was evaluated using prediction uncertainties of individual soil types and independent soil profile classifications. Evaluation results indicated that the random forest algorithm was successful in promoting effective spatial disaggregation of both single soil and complex soil polygons and provided good prediction accuracies for most soil types with the exception of some of the least extensive soil types typically found within complex map units. This was attributed mainly to algorithm's tendency to favour dominant, more extensive classes, along with its difficulty to distinguish between similar soils within spatially diverse areas. However, training Soil Series models at a Landscape Unit level instead of nationally helped to limit both the underestimation of these minority soil types and the overestimation of the dominant ones. In addition, map evaluation results showed the usefulness of using the generated conditional Soil Series probabilities for exploring soil spatial variability, especially within complex areas such as river floodplains covered by multiple alluvial and non-alluvial soils. Overall, this study demonstrates the potential of using spatial disaggregation to extract pedological knowledge embedded in legacy soil maps and use it to generate new dynamic and harmonised soil and soil property maps by effectively using readily-available and easily-updated soils information from existing databases.

Bloom’s Taxonomy and Prospective Teachers’ Preparation in Pakistan

The analysis of application of Bloom's Taxonomy in the future teachers’ preparation of Pakistan is the aim of this study where gender differences, program differences and semester effects are considered. The researchers developed questionnaire and examined the data using IBM SPSS statistics software. The results point to the fact that female participants are more likely than men to display mastery of lower-level skills as defined by Bloom's taxonomy, such as "remembering" and "understanding, and males tend to excel at thinking critically and analytically, i.e. "analyzing" and "evaluating" according to Bloom's taxonomy. On the other hand, the students of the first, second and third years of the Bachelor of Education (B.Ed.) program were found to be scoring higher than M.Phil. participants. Additionally, freshman students were shown to have stronger achievements at the earlier levels of Bloom's Taxonomy compared to later-year students. These inferences, therefore, indicate the necessity of personalized educational strategies as well as staff development programs to raise the standards of education in Pakistani schools

THE PROJECT-BASED LEARNING (STEM MODEL) IN FUNDAMENTAL PHYSICS LEARNING

The education involves STEM combines four fields: S for Science, T for Technology, E for Engineering, and M for Mathematics. STEM education is under the Malaysian Education Development Plan (PPPM) 2013-2025, to enhance the high interest and motivation to study these four fields. Subsequently, the academic achievement of the STEM subjects can be improved. Therefore, this study aims to study the usage of the STEM model in the learning process of fundamental physics subject, characterized by higher-order thinking skills. The sample in this study was students from the Centre of Foundation Studies in Science of Universiti Putra Malaysia. Two groups are formed: the group that will produce the model (developer groups) and the group that will use the model in the learning process (user groups). The user groups are given a Pre-Achievement Test (Pre-AT) to determine their initial skills on the related topic. At the same time, the developer groups develop the STEM model, which acts as a learning tool for the usage groups. Then, after being exposed to the STEM model for 2 months, the user groups are requested to answer a Post-Achievement Test (Post-AT). The performance of Pre-AT and Post-AT are compared since these tests use a similar level of Bloom's taxonomy. Moreover, both groups need to answer the same surveys regarding the model's formation and evaluate the model's satisfaction in the learning process. Based on the analysis results, it was found that using the STEM model enhances the understanding of physics concepts, and subsequently increase the critical thinking and problem-solving skills among students. In addition, the STEM model development enhances the skills of project-based learning (PBL) among students.

Comparative study of traditional and DNA-based methods for environmental impact assessment: A case study of marine aggregate extraction in the North Sea

Environmental impact assessments of marine aggregate extraction are traditionally conducted based on morphological characteristics of macrobenthos, which is time-consuming, labour-intensive and requires specific taxonomic expert knowledge. Bulk DNA metabarcoding is suggested as a promising alternative. This study compares the traditional morphological and the bulk DNA metabarcoding method to assess the impact of sand extraction activities on three sandbanks in the Belgian North Sea. Substantial differences in the detected species were observed between methods: Abundant and/or large macrobenthos species were detected by both methods, while small species or species with an exoskeleton were usually only detected by the morphological method. Taxa uniquely detected by bulk DNA metabarcoding could be explained by specimens identified at a higher taxonomic level by morphology, or by specimens with very low read numbers, probably representing species missed in the morphological sorting process, DNA traces on the specimens or false positives during PCR amplification efficiency. Despite the difference in detected species, comparable alpha and beta diversity patterns were observed by both methods, indicating that bulk DNA metabarcoding can effectively detect the overall ecological changes associated with sand extraction. We further demonstrate that bulk DNA metabarcoding reduces sample processing both in time (44 % faster) and cost (26 % cheaper) compared to the morphology-based identification. However, biomass quantification remains challenging for bulk DNA metabarcoding since of the ten most abundant genera, only two genera (Echinocardium and Ophelia) showed a significant positive correlation between biomass and read numbers. Additionally, bulk DNA metabarcoding does not provide information on life stages or size of the identified specimens. As such, our results underpin the complementary nature of both methods, wherein DNA-based analyses allow for rapid detection of community changes (as similar patterns in alpha and beta diversity and biotic index were observed), while morphology-based analyses provide additional information on e.g. secondary production (biomass) and size composition. We show how the strengths of both methods can be combined to assess the impact of sand extraction.

Pomegranate Juice Supplemented with Inulin Modulates Gut Microbiota and Promotes the Production of Microbiota-Associated Metabolites in Overweight/Obese Individuals: A Randomized, Double-Blind, Placebo-Controlled Trial.

Pomegranate juice (PJ) and inulin have been reported to ameliorate diet-induced metabolic disorders by regulating gut microbiota dysbiosis. However, there was a lack of clinical evidence for the combined effects of PJ and inulin on regulating gut microbiota in individuals with metabolic disorders. A double-blind, parallel, randomized, placebo-controlled trial was conducted, and 68 overweight/obese individuals (25 ≤ BMI ≤ 35 kg/m2) were randomly assigned to receive 200 mL/d PJ, PJ supplemented with inulin, or placebo for 3 weeks. Our results showed that PJ and PJ+inulin did not significantly alter the levels of anthropometric and blood biochemical indicators after 3 weeks of treatment. However, there was an increasingly significant impact from placebo to PJ to PJ+inulin on the composition of gut microbiota. Detailed bacterial abundance analysis further showed that PJ+inulin treatment more profoundly resulted in significant changes in the abundance of gut microbiota at each taxonomic level than PJ. Moreover, PJ+inulin treatment also promoted the production of microbiota-associated short-chain fatty acids and pomegranate polyphenol metabolites, which correlated with the abundance of the bacterial genus. Our results suggested that PJ supplemented with inulin modulates gut microbiota composition and thus promotes the production of microbiota-associated metabolites that exert potential beneficial effects in overweight/obese subjects.

Genomic SNPs resolve the phylogeny of an ancient amphibian island radiation from the Seychelles

Unusually for oceanic islands, the granitic Seychelles host multiple lineages of endemic amphibians. This includes an ancient (likely ca. 60 million years) radiation of eight caecilian species, most of which occur on multiple islands.These caecilians have a complicated taxonomic history and their phylogenetic inter-species relationships have been difficult to resolve. Double-digest RAD sequencing (ddRADseq) has been applied extensively to phylogeography and increasingly to phylogenetics but its utility for resolving ancient divergences is less well established. To address this, we applied ddRADseq to generate a genome-wide SNP panel for phylogenomic analyses of the Seychelles caecilians, whose phylogeny has so far not been satisfactorily resolved with traditional DNA markers. Based on 129,154 SNPs, we resolved deep and shallow splits, with strong support. Our findings demonstrate the capability of genome-wide SNPs for evolutionary inference at multiple taxonomic levels and support the recently proposed synonymy of Grandisonia Taylor, 1968 with Hypogeophis Peters, 1879. We revealed three clades of Hypogeophis (large-, medium- and short-bodied) and identify a single origin of the diminutive, stocky-bodied and pointy-snouted phenotype.

Moth Biodiversity in Central Kerala: A Comprehensive Examination of Urban and High-Altitude Habitats With New Distribution Record of Palaeosetidae

The order Lepidoptera, encompassing both butterflies and moths, many species within lepidoptera plays a pivotal role in ecosystem dynamics as key pollinators. Moths, constituting the vast majority within this order, serve as essential contributors to biodiversity in the Indian subcontinent, with over 12,000 known species. Despite their ecological significance, our understanding of moth diversity in India remains incomplete. This study addresses this knowledge gap by conducting a focused survey of moths in central Kerala between May 2019 and December 2021. Utilizing a standardized methodology involving moth trapping with white cloth and mercury vapor bulbs, we recorded and analyzed 483 moth species spanning 44 families. Notably, this investigation documented the presence of the family Palaeosetidae in Kerala for the first time including two species previously reported only from the Khasi Hills. Additionally, the first-ever sighting of Corgatha semipardata in India and the presence of Cirrhochrista fuscusa in South India were reported. Temporal activity patterns of moths revealed intriguing variations, and a meticulous identification process resulted in classifications at various taxonomic levels. Erebidae emerged as the most speciose family, predominantly in urban areas, while Crambidae, Geometridae, and Noctuidae thrived in high-altitude regions, indicating habitat diversity. Furthermore, this study sheds light on the challenge of identifying moths without specimen collection, particularly for microlepidoptera, which needs further research in this area. The observation of Macroglossum genus caterpillars suggests the possibility of migration, opening avenues for future investigations into moth movement patterns. In conclusion, our research highlights the rich diversity of moths in central Kerala and emphasizes the importance of conserving ecosystems and host plants in urban areas. While providing valuable insights, this study acknowledges its limitations due to a limited duration and calls for extensive research to comprehensively assess moth species richness in the region, offering a crucial foundation for future studies focused on moth diversity.

Prevalence and underlying mechanisms of phylosymbiosis in land plants

Abstract Phylosymbiosis, the congruence of microbiome composition with host phylogeny, is a valuable framework for investigating plant–microbe associations and their evolutionary ecology. This review assesses the prevalence of phylosymbiosis across the plant kingdom, elucidates the fundamental ecological and evolutionary processes contributing to its occurrence based on previous research and explores commonly used methods for identifying phylosymbiosis. We find that the presence of phylosymbiosis may be influenced by both phylogenetic distance and the taxonomic level at which host plants are examined, with the strength of associations potentially decreasing as the taxonomic scale becomes finer. Notably, the endophytic microbiome exhibits a stronger phylosymbiosis signal compared with the epiphytic or rhizosphere-associated microbiomes. Microorganisms such as fungi and bacteria can yield highly variable evidence for phylosymbiosis due to differences in colonization, transmission or functional characteristics. We also outline how the four community assembly processes (dispersal, selection, diversification and drift) contribute to the establishment and maintenance of host–microbe phylosymbiosis. Furthermore, we highlight the diversity of methods employed to detect phylosymbiosis, which involves three key processes: constructing host phylogenies, assessing microbial data and statistically evaluating the correlation between host phylogeny and microbial composition. Remarkably different methodologies across studies make comparisons between findings challenging. To advance our understanding, future research is expected to explore phylosymbiosis at lower taxonomic levels and investigate different microbial communities coexisting synergistically within the same host. Understanding the relative importance of community assembly processes in driving phylosymbiosis will be critical for gaining deeper insights into the ecology and evolution of host–microbe interactions.

Plastomes of Nothofagus reflect a shared biogeographic history in Patagonia.

Plastomes are used in phylogenetic reconstructions because of their relatively conserved nature. Nonetheless, some limitations arise, particularly at lower taxonomic levels due to reduced interspecific polymorphisms and frequent hybridization events that result in unsolved phylogenies including polytomies and reticulate evolutionary patterns. Next-generation sequencing technologies allow access to genomic data and strongly supported phylogenies, yet biased topologies may be obtained due to insufficient taxon sampling. We analyze the hypothesis that intraspecific plastome diversity reflects biogeographic history and hybridization cycles among taxa. We generated 12 new plastome sequences covering distinct latitudinal locations of all species of subgenus Nothofagus from North Patagonia. Chloroplast genomes were assembled, annotated, and searched for simple sequence repeats (SSRs). Phylogenetic reconstructions included species and sampled locations. The six Nothofagus species analyzed were of similar size and structure; only Nothofagus obliqua of subgenus Lophozonia, used as an outgroup, presented slight differences in size. We detected a variable number of SSRs in distinct species and locations. Phylogenetic analyses of plastomes confirmed that subgenus Nothofagus organizes into two monophyletic clades each consisting of individuals of different species. We detected a geographic structure within subgenus Nothofagus and found evidence of local chloroplast sharing due to past hybridization, followed by adaptive introgression and ecological divergence. These contributions enrich the comprehension of transversal evolutionary mechanisms such as chloroplast capture and its implications for phylogenetic and phylogenomic analyses.

Testing ultraconserved elements (UCEs) for phylogenetic inference across bivalves (Mollusca: Bivalvia)

Bivalves constitute an important resource for fisheries and as cultural objects. Bivalve phylogenetics has had a long tradition using both morphological and molecular characters, and genomic resources are available for a good number of commercially important species. However, relationships among bivalve families have been unstable and major conflicting results exist between mitogenomics and results based on Sanger-based amplicon sequencing or phylotranscriptomics. Here we design and test an ultraconserved elements probe set for the class Bivalvia with the aim to use hundreds of loci without the need to sequence full genomes or transcriptomes, which are expensive and complex to analyze, and to open bivalve phylogenetics to museum specimens. Our probe set successfully captured 1,513 UCEs for a total of 263,800 bp with an average length of 174.59 ± 3.44 per UCE (ranging from 28 to 842 bp). Phylogenetic testing of this UCE probe set across Bivalvia and within the family Donacidae using different data matrices and methods for phylogenetic inference shows promising results at multiple taxonomic levels. In addition, our probe set was able to capture large numbers of UCEs for museum specimens collected before 1900 and from DNAs properly stored, of which many museums and laboratories are well stocked. Overall, this constitutes a novel and useful resource for bivalve phylogenetics.

Diversity and compositional differences in the oral microbiome of oral squamous cell carcinoma patients and healthy controls: a scoping review.

The human oral microbiome may play a role in the development of oral squamous cell carcinoma. The aim of this scoping review was to examine microbial diversity and differences in the composition of the oral microbiome between OSCC patients and healthy controls. A literature search (in PubMed and Embase.com) was performed on January 9, 2023. The outcome variables used from the included studies of this review were alpha- and beta diversity and oral microbiome composition profiles for each taxonomic level (phylum-, class-, order-, genus- and species level). Thirteen out of 423 studies were included in this review compromising 1,677 subjects, of which 905 (54.0%) were OSCC patients and 772 (46.0%) were healthy controls. Most studies found a higher alpha diversity in the OSCC patient group and significantly different beta diversities between OSCC patient samples and healthy control samples. Studies reported more abundant Fusobacteria (on phylum level), Fusobacterium (on genus level), Fusobacterium nucleatum, Porphyromonas endodontalis and Prevotella intermedia (on species level) in OSCC patients. The healthy control group had more abundant Actinobacteria (on phylum level), Streptococcus and Veilonella (on genus level) and Veilonella parvula (on species level) according to most studies. Our findings show differences in oral microbiome diversity and composition in OSCC patients. Clinical implications demand continuing study. Development of internationally accepted standard procedures for oral sample collection and oral microbiota analysis is needed for more conclusive and clinically relevant comparisons in future research.

PARTICIPATORY MODEL OF SOCIAL ENTREPRENEURSHIP DEVELOPMENT AS A DETERMINANT OF VETERANS' AND THEIR FAMILY MEMBERS' REINTEGRATION: THEORETICAL FRAMEWORK

The purpose of the paper is to state the theoretical framework for the formation of a participatory model of social entrepreneurship development as a tool for the reintegration of military personnel, veterans and their family members, based on the identified views of veterans and their family members regarding the role of certain institutions of society in the development processes of social entrepreneurship. Methodology. The research is based on the results of a survey with blocks of questions aimed at studying certain aspects of the participatory approach to the development of social entrepreneurship: the state, hromada, business, education, as well as the specifics of involving veterans and their families in these processes. The study sample included people with the status of combatants, war veterans, and their family members who were participants in the Ukraine-Norway project "Retraining and social adaptation of military personnel and their family members in Ukraine", which was implemented at the Chernihiv Polytechnic National University in 2016-2022. The results of the survey showed that the expectations of veterans and their family members from the state regarding the development of social entrepreneurship are: the establishment of "clear rules of the game" – not only the development and implementation of relevant legislation, but also the formation of transparent and detailed procedures for starting a social enterprise and its development; the development and implementation of programmes for the social reintegration of veterans into civilian life through support for the creation of social enterprises (financial support, preferential taxation). In terms of the role of business in supporting the return of veterans to civilian life through the opening of social enterprises, respondents see it mainly as providing financial support to those social enterprises set up by veterans and their family members. The hromada, as the embodiment of the public sector, appears in the perceptions of veterans and their family members as a centre for social support, for finding ways to protect their rights, and for finding resources to meet their needs (including employment or starting their own business). The opinion of the interviewed veterans and their family members regarding the involvement of education in supporting the development of social entrepreneurship can be summarised as follows: the involvement of experts in the development of effective strategies for the development of both social entrepreneurship in the interest of veterans and education from it; the development of short-term social entrepreneurship training programmes (non-formal education courses) involving business, hromada and government representatives. Practical implications. The revealed results could be used for further scientific and practical research: development of directions of the programme of social and psychological support for reintegration of military personnel, veterans of ATO/UFO and their family members with their active involvement in social entrepreneurship. Value / Originality. The developed theoretical framework for the formation of a participatory model for the development of social entrepreneurship as a tool for the reintegration of military personnel, veterans and their family members, based on the identified views of veterans and their family members regarding the role of certain institutions of society in the development processes of social entrepreneurship, points to further methodological and applied research: the development of a set of recommendations for the practical implementation of the proposed model at different taxonomic levels.

The impact of microplastics polystyrene on the microscopic structure of mouse intestine, tight junction genes and gut microbiota.

Microplastics, which are tiny plastic particles less than 5 mm in diameter, are widely present in the environment, have become a serious threat to aquatic life and human health, potentially causing ecosystem disorders and health problems. The present study aimed to investigate the effects of microplastics, specifically microplastics-polystyrene (MPs-PS), on the structural integrity, gene expression related to tight junctions, and gut microbiota in mice. A total of 24 Kunming mice aged 30 days were randomly assigned into four groups: control male (CM), control female (CF), PS-exposed male (PSM), and PS-exposed female (PSF)(n = 6). There were significant differences in villus height, width, intestinal surface area, and villus height to crypt depth ratio (V/C) between the PS group and the control group(C) (p <0.05). Gene expression analysis demonstrated the downregulation of Claudin-1, Claudin-2, Claudin-15, and Occludin, in both duodenum and jejunum of the PS group (p < 0.05). Analysis of microbial species using 16S rRNA sequencing indicated decreased diversity in the PSF group, as well as reduced diversity in the PSM group at various taxonomic levels. Beta diversity analysis showed a significant difference in gut microbiota distribution between the PS-exposed and C groups (R2 = 0.113, p<0.01), with this difference being more pronounced among females exposed to MPs-PS. KEGG analysis revealed enrichment of differential microbiota mainly involved in seven signaling pathways, such as nucleotide metabolism(p<0.05). The relative abundance ratio of transcriptional pathways was significantly increased for the PSF group (p<0.01), while excretory system pathways were for PSM group(p<0.05). Overall findings suggest that MPs-PS exhibit a notable sex-dependent impact on mouse gut microbiota, with a stronger effect observed among females; reduced expression of tight junction genes may be associated with dysbiosis, particularly elevated levels of Prevotellaceae.