High Diversity Research Articles

Research on teachers of colour and minoritised teachers in majoritarian education systems: A scoping review of the literature in the last two decades

AbstractThe world map is changing due to waves of immigration, population and demographic changes in mainland Europe and North America. There is a growing need for a more diverse teacher workforce to close the racial and ethnic gap between students and teachers in populations with high diversity. The scholarship discussing integration challenges facing teachers of colour and minority teachers in majoritarian education systems has yet to be exhaustively analysed and synthesised. Moreover, the literature remains fragmented despite numerous studies emphasising the significance of supporting teachers of colour and minority teachers to ensure equity and inclusiveness in majoritarian education systems to better represent the student body. This study reviews the literature through a bibliometric analysis of 387 peer‐reviewed papers on this topic published between 2000 and 2024, followed by a synthesis of the top‐cited papers. First, we emphasised the importance of researching the integration of minority teachers and teachers of colour to understand their contribution to students' thriving and the transformation of education systems towards diversity and inclusion. The quantitative analysis is followed by a systematic qualitative synthesis of the top 18 cited papers. The results highlighted that most research on minority teachers and teachers of colour is from the United States and the United Kingdom. They also highlighted the necessity of revisiting curriculums and enhancing relationships with children to raise awareness about issues of systemic racism, cultural responsiveness and deeper inclusion. Recommendations emphasise addressing systemic racism and enhancing cultural responsiveness. These findings can guide future research, policies and practices to support minority teachers' integration and better represent student diversity. Context and implicationsRationale for this studyThe world map is changing due to waves of immigration, population shift, and demographic changes, highlighting the growing need for a more diverse teaching workforce to close the racial and ethnic gaps between students and teachers in highly diverse populations. However, the scholarship discussing the integration challenges faced by teachers of colour and minority teachers in majoritarian education systems remains fragmented and has yet to be exhaustively analysed and synthesised. Therefore, this paper presents a mixed‐methods systematic review of recent international evidence on the integration of minority teachers and teachers of colour in majoritarian education systems worldwide.Why the new findings matterThis research contributes to further insights in the scholarship foci, including identifying several research gaps related to the integration of teachers of colour and minority teachers. Our findings can inform future policies by enhancing understanding of the unique needs and challenges faced by minoritised teachers within various political, social and educational contexts. This knowledge can guide the training, recruitment, mentoring and retention of minority teachers. Additionally, further comparative research on this topic is necessary to enrich knowledge and contribute to diverse models for preparing, recruiting and retaining teachers of colour, thereby enhancing diversity in schools and fostering the success of minority students. Therefore, this study not only enriches our understanding of the current state of research but also sets the stage for future inquiries that could inform more nuanced and effective educational policies and practices worldwide.Implications for educational researchers and policy makersOur research findings offer valuable insights for scholars, policy makers, superintendents and school principals who are committed to conducting future empirical research, systematic reviews or implementing policies for the equitable inclusion of minoritised teachers in majoritarian education systems. These insights aim to promote deep diversity and representation. Key takeaways include: This systematic review identifies a research gap concerning the integration of teachers of colour and minority teachers. Addressing this gap involves understanding their unique needs and challenges within various political, social and educational contexts. There is a need for further comparative research on this topic to enhance knowledge and contribute to developing varied models for preparing, recruiting and retaining teachers of colour, thereby improving diversity in schools and supporting the success of minority students. Future policy design and implementation at both the district and school levels should focus on the training, recruitment, mentoring and retention of minority teachers. This includes identifying positive ecological dynamics at both district and school levels that support the integration of minority teachers and teachers of colour. In today‘s era of digital literacy and artificial intelligence (AI), we recommend researching the applicability, usage and impact of AI programs in enhancing equitable hiring processes. This research should explore how AI can be used to detect early warning signs of exclusion or marginalisation that may contribute to turnover among minority teachers, and how it can facilitate supportive interventions.

Intergroup bias in perceived trustworthiness among few or many minimal groups

In diversifying societies, people are inevitably exposed to an increasing number of outgroups. As impressions of outgroups are more negative than those of ingroups, this may overall lead to more negative social attitudes and behaviors. In six preregistered experiments (Ntotal = 1832) using a minimal group paradigm, we investigated whether the mere number of groups influences the perceived trustworthiness of ingroups, outgroups, and the total population. Our results consistently show that higher diversity does not decrease overall population trustworthiness, despite a larger number of outgroups. This is because of a stronger intergroup bias such that ingroups receive an additional boost in trustworthiness judgments when there are more outgroups. Our experiments show that these effects are not due to objective or perceived group sizes or greater attitude differences toward the group-defining attributes. Instead, people seem to perceive members of their ingroup as more similar to themselves if there is a higher number of outgroups and high similarity is related to high perceived trustworthiness.

Climate, demography, immunology, and virology combine to drive two decades of dengue virus dynamics in Cambodia

The incidence of dengue virus disease has increased globally across the past half-century, with highest number of cases ever reported in 2019 and again in 2023. We analyzed climatological, epidemiological, and phylogenomic data to investigate drivers of two decades of dengue in Cambodia, an understudied endemic setting. Using epidemiological models fit to a 19-y dataset, we first demonstrate that climate-driven transmission alone is insufficient to explain three epidemics across the time series. We then use wavelet decomposition to highlight enhanced annual and multiannual synchronicity in dengue cycles between provinces in epidemic years, suggesting a role for climate in homogenizing dynamics across space and time. Assuming reported cases correspond to symptomatic secondary infections, we next use an age-structured catalytic model to estimate a declining force of infection for dengue through time, which elevates the mean age of reported cases in Cambodia. Reported cases in >70-y-old individuals in the 2019 epidemic are best explained when also allowing for waning multitypic immunity and repeat symptomatic infections in older patients. We support this work with phylogenetic analysis of 192 dengue virus (DENV) genomes that we sequenced between 2019 and 2022, which document emergence of DENV-2 Cosmopolitan Genotype-II into Cambodia. This lineage demonstrates phylogenetic homogeneity across wide geographic areas, consistent with invasion behavior and in contrast to high phylogenetic diversity exhibited by endemic DENV-1. Finally, we simulate an age-structured, mechanistic model of dengue dynamics to demonstrate how expansion of an antigenically distinct lineage that evades preexisting multitypic immunity effectively reproduces the older-age infections witnessed in our data.

Robustness and reliability of single-cell regulatory multi-omics with deep mitochondrial mutation profiling.

The detection of mitochondrial DNA (mtDNA) mutations in single cells holds considerable potential to define clonal relationships coupled with information on cell state in humans. Previous methods focused on higher heteroplasmy mutations that are limited in number and can be influenced by functional selection, introducing biases for lineage tracing. Although more challenging to detect, intermediate to low heteroplasmy mtDNA mutations are valuable due to their high diversity, abundance, and lower propensity to selection. To enhance mtDNA mutation detection and facilitate fine-scale lineage tracing, we developed the single-cell Regulatory multi-omics with Deep Mitochondrial mutation profiling (ReDeeM) approach, an integrated experimental and computational framework. Recently, some concerns have been raised about the analytical workflow in the ReDeeM framework. Specifically, it was noted that the mutations detected in a single molecule per cell are enriched on edges of mtDNA molecules, suggesting they resemble artifacts reported in other sequencing approaches. It was then proposed that all mutations found in one molecule per cell should be removed. We detail our error correction method, demonstrating that the observed edge mutations are distinct from previously reported sequencing artifacts. We further show that the proposed removal leads to massive elimination of bona fide and informative mutations. Indeed, mutations accumulating on edges impact a minority of all mutation calls (for example, in hematopoietic stem cells, the excess mutations on the edge account for only 4.3%-7.6% of the total). Recognizing the value of addressing edge mutations even after applying consensus correction, we provide an additional filtering option in the ReDeeM-R package. This approach effectively eliminates the position biases, leads to a mutational signature indistinguishable from bona fide mitochondrial mutations, and removes excess low molecule high connectedness mutations. Importantly, this option preserves the large majority of unique mutations identified by ReDeeM, maintaining the ability of ReDeeM to provide a more than 10-fold increase in variant detection compared to previous methods. Additionally, the cells remain well-connected. While there is room for further refinement in mutation calling strategies, the significant advances and biological insights provided by the ReDeeM framework are unique and remain intact. We hope that this detailed discussion and analysis enables the community to employ this approach and contribute to its further development.

Sequence types of enteroaggregative Escherichia coli strains recovered from human, animal, and environmental sources: India

In the current study, we report whole genome sequencing (WGS) data on EAEC strains from India to identify lineages and different sequence types (STs) in our geographical regions across North India. We performed WGS comparative genomics characterization to examine the diversity of 122 EAEC strains collected from a large geographic area from clinical (Human sources) and non-clinical sources (animal and environmental sources). M-PCR for 21 virulence genes was performed. A triplex PCR detected phylogenetic groups A, B1, B2, and D was done. All strains were genome-sequenced, and bioinformatics analysis was performed. EAEC isolates belonged to 29 sequence types, further clustered into 11 clonal complexes, among which CC38 was the largest, containing 38 isolates mainly belonging to two ST types (ST38 and ST315). CC10 was the most diverse group, comprising 8 STs (ST43, ST2706, ST1286, ST 10, ST167, ST34, ST227, and ST4305). The most frequently detected virulence gene among the 96 clinical EAEC isolates was astA (87.5%), followed by ORF3 (62.5%), and aap (54.1 %). ST131, known for multidrug resistance and causing various diseases, was detected in acute diarrhea cases and animal sources, underscoring its clinical significance. These findings indicate the high diversity of EAEC and different sources of unique ST types of EAEC. The study reinforces the One Health approach, highlighting the interconnection between human health, animal reservoirs, and environmental sources in EAEC transmission dynamics. The identification of EAEC strains in animals suggests the zoonotic potential of these pathogens, necessitating comprehensive surveillance and control measures. The study emphasizes the need for continued surveillance and a One Health approach to address the complex transmission dynamics of EAEC.

Comprehensive physiological and genomic characterization of a potential probiotic strain, Lactiplantibacillus plantarum ILSF15, isolated from the gut of tribes of Odisha, India

Characterizing probiotic features of organisms isolated from diverse environments can lead to the discovery of novel strains with promising functional features and health attributes. The present study attempts to characterize a novel probiotic strain isolated from the gut of the tribal population of Odisha, India. Based on 16S rRNA-based phylogeny, the strain was identified as a species of the Lactiplantibacillus genus and was named Lactiplantibacillus plantarum strain ILSF15. The current investigation focuses on elucidating this strain’s genetic and physiological properties associated with probiotic attributes such as biosafety risk, host adaptation/survival traits, and beneficial functional features. The novel strain was observed, in vitro, exhibiting features such as acid/bile tolerance, adhesion to the host enteric epithelial cells, cholesterol assimilation, and pathogen exclusion, indicating its ability to survive the harsh environment of the human GIT and resist the growth of harmful microorganisms. Additionally, the L. plantarum ILSF15 strain was found to harbor genes associated with the metabolism and synthesis of various bioactive molecules, including amino acids, carbohydrates, lipids, and vitamins, highlighting the organism’s ability to efficiently utilize diverse resources and contribute to the host’s nutrition and health. Several genes involved in host adaptation/survival strategies and host-microbe interactions were also identified from the ILSF15 genome. Moreover, L. plantarum strains, in general, were found to have an open pangenome characterized by high genetic diversity and the absence of specific lineages associated with particular habitats, signifying its versatile nature and potential applications in probiotic and functional food industries.

The Diatom Diversity and Ecological Status of a Tufa-Depositing River through eDNA Metabarcoding vs. a Morphological Approach-A Case Study of the Una River (Bosnia and Herzegovina).

Tufa deposits in karst rivers are unique habitats created by mutual interactions between specific environmental and biotope features and inhabited by diatoms as a highly abundant and diverse algal group. This pilot study aimed to investigate the diversity of diatom communities on tufa depositing habitats and assess the Una River's ecological status using a comparative molecular and morphological approach for diatom identification. The 312 base pairs of the rbcL gene were barcoded and analyzed using MiSeq reads and amplicon sequence variants (ASVs) obtained by the DADA2 pipeline. The reference database Diat.barcode v7 was used for taxonomic assignment. The morphological identification of the diatoms was carried out in parallel. In total, the combined dataset revealed 46 taxa identified at genus rank, 125 on the subgenus, and 145 on combined taxonomy rank. The metabarcoding approach mostly leads to a lower number of identified taxa at species rank (58 in molecular vs. 119 in optical inventory), resulting in higher values of beta diversity and heterogeneity in diatom assemblages in samples obtained by morphological approach. Despite the high percentage of taxonomically not assigned diatom ASVs to the species rank, high Shannon diversity index values and a similar number of taxa per locations compared to the morphological approach were obtained. Taxa Achnanthidium minutissimum (Kützing) Czarnecki, Achnanthidium pyrenaicum (Hustedt) H.Kobayasi, Amphora pediculus (Kützing) Grunow, Diatoma vulgaris Bory, Navicula cryptotenella Lange-Bertalot, and Navicula tripunctata (O.F.Müller) Bory were identified at all locations in both inventories. Although limited consistency in the diatom abundances between the two inventory datasets was found, a similar grouping of samples was observed connected to the river's longitudinal gradient. The data obtained using molecular approach in most sites indicated a mostly lower ecological status (good or moderate) compared to the data obtained from the morphological approach (high, good, and moderate). The potential of environmental DNA (eDNA) diatom metabarcoding for water monitoring and diversity studies is undeniable, but to fully realize the benefits of these methods in the future, it is essential to standardize protocols and expand the reference database for species found in specific habitats, such as tufa deposits.

Characterization of bovine vaginal microbiota using 16S rRNA sequencing: associations with host fertility, longevity, health, and production

Due to their potential impact on the host’s phenotype, organ-specific microbiotas are receiving increasing attention in several animal species, including cattle. Specifically, the vaginal microbiota of ruminants is attracting growing interest, due to its predicted critical role on cows’ reproductive functions in livestock contexts. Notably, fertility disorders represent a leading cause for culling, and additional research would help to fill relevant knowledge gaps. In the present study, we aimed to characterize the vaginal microbiota of a large cohort of 1171 female dairy cattle from 19 commercial herds in Northern France. Vaginal samples were collected using a swab and the composition of the microbiota was determined through 16S rRNA sequencing targeting the V3–V4 hypervariable regions. Initial analyses allowed us to define the core bacterial vaginal microbiota, comprising all the taxa observed in more than 90% of the animals. Consequently, four phyla, 16 families, 14 genera and a single amplicon sequence variant (ASV) met the criteria, suggesting a high diversity of bacterial vaginal microbiota within the studied population. This variability was partially attributed to various environmental factors such as the herd, sampling season, parity, and lactation stage. Next, we identified numerous significant associations between the diversity and composition of the vaginal microbiota and several traits related to host’s production and reproduction performance, as well as reproductive tract health. Specifically, 169 genera were associated with at least one trait, with 69% of them significantly associated with multiple traits. Among these, the abundances of Negativibacillus and Ruminobacter were positively correlated with the cows’ performances (i.e., longevity, production performances). Other genera showed mixed relationships with the phenotypes, such as Leptotrichia being overabundant in cows with improved fertility records and reproductive tract health, but also in cows with lower production levels. Overall, the numerous associations underscored the complex interactions between the vaginal microbiota and its host. Given the large number of samples collected from commercial farms and the diversity of the phenotypes considered, this study marks an initial step towards a better understanding of the intimate relationship between the vaginal microbiota and the dairy cow’s phenotypes.

Sustainability of the community model of avocado production in the Monarch Butterfly Biosphere Reserve, Michoacán, México

The avocado is a commodity crop that has generated severe environmental and social impacts in Michoacán, the world’s leading producer. Current studies overlook the diversity of avocado production by focusing on Michocán’s central region, while the regions of a more recent expansion remain poorly studied. We analyzed the model of avocado production in five indigenous communities in the municipality of Zitácuaro that have part of their territory within the Monarch Butterfly Biosphere Reserve. We use the Framework for the Evaluation of Management Systems using Sustainability Indicators to characterize and evaluate the sustainability of the Community Model of Avocado Production (CMAP). Based on 42 interviews with producers, we identified eleven critical points related to environmental (small-scale production; forest conservation; high prophylactic use of agrochemicals; high dependence on irrigation), economic (high crop diversity; low profitability; high yield loss to pests; low economic diversification), and social (high dependence on technical advisors; low dependence on labor force external to the community; few changes in land ownership) aspects of sustainability. The CMAP has productive and socio-political characteristics that represent strengths and weaknesses for its sustainability. The main environmental results suggest that the avocado expansion (2007–2022) in the communities did not involve a change in forest land use. Socially, the CMAP favors the local workforce and facilitates the maintenance of land ownership. The sustainability of CMAP is mostly limited by its economic aspects. With adequate economic support for socially and environmentally sustainable productive practices, the CMAP can improve the local livelihoods while promoting forest conservation.

Phenolics and enzyme inhibitors from the Patagonian Empetrum rubrum berries

The small fruits from Empetrum rubrum were consumed by Native Americans in southern Patagonia. Two samples collected close to the Magellan Street and the Beagle channel in Tierra del Fuego were investigated. Three different extracts from the berries were analyzed, namely: methanol, phenolic-enriched (PEE) and ethyl acetate (EtOAc). The total phenolic, flavonoid, procyanidin and anthocyanin content of the extracts was determined. The effect of the extracts towards the metabolic syndrome-associated enzymes α-glucosidase, α-amylase and pancreatic lipase was assessed. In addition, the antioxidant capacity was measured using DPPH, FRAP, TEAC and ORAC assays. The composition of the extracts was determined by HPLC-MS/MS. Seventy-one compounds were identified for the first time in the berries, including 10 anthocyanins, 35 flavonoids, 11 phenylpropanoids and 13 procyanidins. The main compounds were quantified by HPLC-DAD. The extracts displayed strong activity as α-glucosidase inhibitors, with IC50 values ranging from 0.10 to 0.19 μg/mL for the PEE and 0.82–1.95 μg/mL for the EtOAc extracts, respectively. The results show high chemical diversity and differences with the boreal species E. nigrum.

Diversity analysis of cyanobacterial flora from the Tatapani Hot Spring of Chhattisgarh and exploration of their industrially as well as environmentally valuable properties

The present study investigates the cyanobacterial diversity of Tatapani hot spring, Chhattisgarh, India, using a polyphasic approach, their pigment system, biofuel properties and ability to bioremediate emerging pollutant triclosan. While the microscopic analyses of the natural samples reflected high cyanobacterial diversity with all morpho-forms, physicochemical studies revealed temperature being the major factor affecting the cyanobacterial distribution in the hot spring. Among the 22 collected cyanobacterial samples, 14 were grown successfully under laboratory conditions and 10 of them showed optimum growth at 45 °C. However, four strains displayed preference for lower temperature (27 °C) for optimum growth. The polyphasic characterization of 14 strains revealed that all the thermophiles belonged to the genus Mastigocladus whereas the strains Sytonema sp. TPJ-3, Calothrix sp. TPB-2, Westiellopsis sp. TPR-29 and Desikacharya sp. TPB-4 constituted the group of mesophiles. Calothrix sp. TPB-2 was identified as a novel genus (Neocalothrix thermalis) based on distinct morphology and phylogenetic position with unique ITS folding pattern. Additionally, our study disclosed the production of comparatively higher amounts of pigments and medium chain length fatty acids (C16 to C18) by the thermophilic strains, which indicated their potential to be used as feedstocks for pigments and biofuel production respectively. Although the triclosan bioremediation study reflected considerable triclosan removal efficiencies of all the strains, most impressive results were observed in case of Westiellopsis sp. TPR-29 (93.08 %) and Mastigocladus sp. TA-8 (91.92 %). Moreover, the in-silico study-based revelation of high triclosan binding ability of cyanobacterial laccase (−5.8 and − 5.4 kcal/mol) and catechol 2,3-dioxygenase (−5.9 and − 6.0 kcal/mol) suggested the probable triclosan degrading potential of Westiellopsis and Mastigocladus. Conclusively, the Tatapani hot spring represents a unique environment with the dominance of true-branched heterocytous thermophilic cyanobacteria that have enormous potential to remove triclosan and produce high amounts of pigments and medium chain length fatty acids.

Tick-Borne Diseases in Sub-Saharan Africa: A Systematic Review of Pathogens, Research Focus, and Implications for Public Health.

Sub-Saharan Africa, with its hot and humid climate, is a conducive zone for tick proliferation. These vectors pose a major challenge to both animal and human health in the region. However, despite the relevance of emerging diseases and evidence of tick-borne disease emergence, very few studies have been dedicated to investigating zoonotic pathogens transmitted by ticks in this area. To raise awareness of the risks of tick-borne zoonotic diseases in sub-Saharan Africa, and to define a direction for future research, this systematic review considers the trends of research on tick-borne bacteria, parasites, and viruses from 2012 to 2023, aiming to highlight the circulation of these pathogens in ticks, cattle, sheep, goats, and humans. For this purpose, three international databases were screened to select 159 papers fitting designed inclusion criteria and used for qualitative analyses. Analysis of these studies revealed a high diversity of tick-borne pathogens in sub-Saharan Africa, with a total of 37 bacterial species, 27 parasite species, and 14 viruses identified. Among these, 27% were zoonotic pathogens, yet only 11 studies investigated their presence in humans. Furthermore, there is growing interest in the investigation of bacteria and parasites in both ticks and ruminants. However, research into viruses is limited and has only received notable interest from 2021 onwards. While studies on the detection of bacteria, including those of medical interest, have focused on ticks, little consideration has been given to these vectors in studies of parasites circulation. Regarding the limited focus on zoonotic pathogens transmitted by ticks, particularly in humans, despite documented cases of emerging zoonoses and the notable 27% proportion reported, further efforts should be made to fill these gaps. Future studies should prioritize the investigation of zoonotic pathogens, especially viruses, which represent the primary emerging threats, by adopting a One Health approach. This will enhance the understanding of their circulation and impact on both human and animal health. In addition, more attention should be given to the risk factors/drivers associated to their emergence as well as the perception of the population at risk of infection from these zoonotic pathogens.

What evidence exists on the effect of the main European lowland crop and grassland management practices on biodiversity indicator species groups? a systematic map

BackgroundThe intensification of the agricultural practices in Europe over the last decades has drastically transformed the agroecosystems. The simplification of the landscape, the loss of semi-natural habitats and the application of chemicals on crops led to biodiversity decline in agricultural landscapes, raising substantial concerns about the loss of essential ecosystem services, such as pollination or pest control. Depending on the location, the scale and the regional context, different indicator species groups (ISGs) are regularly surveyed to assess the state and trend of biodiversity changes in agroecosystems. Although the high diversity of these ISGs allows assessing different biodiversity aspects (e.g., trophic levels, bio-physical compartments, scale of indication), it complicates the interpretation of the results and thus their practical application. In addition, species diversity metrics are various, from simple species counts to more complex measurements of diversity indices, sometimes with antagonistic responses. Here, to meet the pressing need for synthesis in this complex topic, we follow a standardized systematic map protocol to collect and summarize the literature reporting field evidence of the effects of the main agricultural management practices (AMPs) in arable crops, grasslands and ecological infrastructures on a set of ISGs in European lowland farming areas.MethodsSearches of literature were made using online publication databases, search engine and specialist websites in English. Gathered publications were screened for relevance following inclusion/exclusion criteria published in a prior protocol. We extracted and mapped information about experimental design, monitoring methods, ISGs and AMPs studied and the diversity measures presented in each included publication. These parameters are structured in available data coding sheets.ResultsThe search gathered 20,162 references from which 1208 remained after full text eligibility screening. Main areas studied are in Western Europe, and the number of studies increased exponentially from 1984 to 2022. Most publications are experimental and on-farm studies which assess AMPs effects at the field scale. Main studied AMPs are fertilization, grazing, organic farming, tillage, mowing and herbicide application. Most ISGs used to study their impacts are flora, carabids, spiders, birds, bees and annelids, often combined with other ISGs. The combinations between AMPs and ISGs studied are detailed as well as monitoring methods. The most used diversity measures are abundance, species richness, Shannon index, evenness, and community composition.ConclusionsWe identified several knowledge clusters: (1) organic farming, fertilization, tillage, grazing and mowing impact on a wide range of ISGs, (2) flora response to agricultural practices, (3) annelids response to agronomic interventions that impact soil structure (e.g., tillage, fertilization, crop rotation, crop residue management), (4) butterflies and orthopterans response to mowing and grazing effects in grasslands, (5) the use of bird monitoring for the impact for assessing the efficiency of AES implementation at the landscape scale. We highlight that further research should be conducted on ISGs that are until now poorly studied regarding agricultural practices, such as amphibians, reptiles, gastropods, millipedes and centipedes. More field evidence of the effects of diversification practices such as intercropping, undersowing, intermediate cropping, and agroforestry are needed to draw conclusions on their benefits on biodiversity.

Genetic Characterization, Antibiotic Resistance, and Virulence Genes Profiling of Bacillus cereus Strains from Various Foods in Japan.

Bacillus cereus sensu stricto is a foodborne pathogen that causes food poisoning. Their spore and biofilm-forming abilities persist in various environments and foods. This study investigated the prevalence, virulence, antibiotic resistance, and genetic diversity of B. cereus s. s. strains isolated from various food samples. Of 179 samples, 22.34% were positive for B. cereus s. s., with significantly high detection rates in milk products and raw chicken meat. Forty strains were isolated from positive samples. Matrix-assisted laser desorption ionization/time of flight mass spectrometry analysis revealed nine distinct clusters and multi-locus sequence typing revealed 34 sequence types including 23 novel sequences, demonstrating high genetic diversity among the isolates. PCR analysis revealed that all the strains contained at least one toxin gene, but none contained the cytK gene. Antibiotic resistance tests revealed that all isolates were classified as multidrug-resistant, with high resistance levels, particularly to β-lactam antibiotics and vancomycin, but were susceptible to gentamicin. All isolates showed variations in biofilm formation. This study highlights the significant public health risk due to B. cereus s. s. and underscores the need for stringent monitoring and control measures in food production to manage antimicrobial resistance and ensure food safety.

New species and species diversity of Desmodesmus (Chlorophyceae, Chlorophyta) in Saga City, Japan

Desmodesmus spp. are one of the most dominant components of phytoplankton, which are present in most water bodies. However, identification of the species based only on morphological data is challenging. The aim of the present study was to provide a comprehensive understanding of the actual distribution of the Desmodesmus species in Saga City, Saga Prefecture, Japan. In the present study, 38 water bodies were surveyed between June 2017 and March 2023. A total of 86 culture strains were established from the samples collected from the 21 sites, and identified by molecular phylogenetic analysis, comparison of ITS2 rRNA secondary structures, and observation of surface microstructure. In total, four new species, including D. notatus Demura sp. nov., D. lamellatus Demura sp. nov., D. fragilis Demura sp. nov., and D. reticulatus Demura sp. nov. were proposed and 17 Desmodesmus species were identified as described species. The present study revealed > 20 Desmodesmus species, exhibiting high genetic diversity in a small area.

The effect of the Tethyan seaway closure on the Oligo−Miocene marine benthic diversity and distribution around Eurasia

The Cenozoic evolution of the Tethyan seaway significantly shaped marine and terrestrial biota around Eurasia. The Tethys Ocean connected the Atlantic and the Pacific during the early Cenozoic, allowing marine faunal exchange. However, during the early Miocene, the ‘ Gomphotherium Landbridge’ developed, restricting the marine connection between the proto-Mediterranean in the west and the provinces of the eastern Tethys Ocean. In contrast to the well-documented phenomena of terrestrial mammalian exchange through the land connection brought about by the closure, little is known about its impact on the marine fauna. To assess the overall effect of this separation on the distribution and diversity of marine organisms, we studied the Oligo−Miocene fossil record of marine benthos including Cnidaria, Echinodermata, Foraminifera and Mollusca. We compiled 15 894 reported occurrences from the early Oligocene to late Miocene comprising 1477 genera, 404 families and 85 orders from four faunal provinces and evaluated their palaeobiogeographic patterns. Our study demonstrates that the proportion of genera shared between the eastern and western provinces decreased after the early Miocene. The majority of the non-shared families developed during or after the early Miocene. High faunal diversity during the early Miocene and increasing endemicity among the eastern provinces are consistent with the development of a shallow seaway that supported speciation and reduced biotic exchange. The considerable variation in the magnitude and timing of the response across taxonomic groups reflects the combined effects of preservation bias and the differential responses of fauna. Our study supports an early Miocene initiation of the Tethyan seaway closure, followed by intermittent connectivity before the complete closure. This closure and its climatic consequences influenced the evolution of the Eurasian biota. Future studies should use a multidisciplinary approach combining the fossil record, genetic divergence and climate proxies to fully understand the effects of environmental changes and the seaway closure on marine benthos diversity dynamics.

Development of SSR Markers and Evaluation of Genetic Diversity of Endangered Plant Saussurea involucrata.

The conservation biology field underscores the importance of understanding genetic diversity and gene flow within plant populations and the factors that influence them. This study employs Simple Sequence Repeat (SSR) molecular markers to investigate the genetic diversity of the endangered plant species Saussurea involucrata, offering a theoretical foundation for its conservation efforts. Utilizing sequencing results to screen SSR loci, we designed and scrutinized 18 polymorphic microsatellite primers across 112 samples from 11 populations in the Bayinbuluke region. Our findings reveal high genetic diversity (I = 0.837, He = 0.470) and substantial gene flow (Nm = 1.390) among S. involucrata populations (China, Xinjiang), potentially attributed to efficient pollen and seed dispersal mechanisms. Principal Coordinate Analysis (PCoA) indicates a lack of distinct genetic structuring within the Bayinbuluke populations. The cluster analysis using STRUCTURE reflected the genetic structure of S. involucrata to a certain extent compared with PCoA. The results showed that all samples were divided into four groups. To safeguard this species, we advocate for the in situ conservation of all S. involucrata populations in the area. The SSR markers developed in this study provide a valuable resource for future genetic research on S. involucrata.

Linking watershed formation with the phylogenetic distribution of a soil microscopic fungus in Yunnan Province, China

BackgroundPhylogeographic studies have gained prominence in linking past geological events to the distribution patterns of biodiversity, primarily in mountainous regions. However, such studies often focus on plant taxa, neglecting the intricate biogeographical patterns of microbes, particularly soil microbial communities. This article explores the spatial distribution of the nematode-trapping fungus Arthrobotrys oligospora, a widespread microorganism, in a tectonically active region at the southeastern edge of the Qinghai-Tibetan Plateau. By analysing the genetic variation of this fungus alongside the historical structure of major river watersheds, we sought to uncover potential connections between the two. Our study involved sampling 149 strains from 116 sites across six major watersheds in the region.ResultsThe resulting haplotype network revealed five distinct clusters, each corresponding closely to a specific watershed. These clusters exhibited high haplotype diversity and low nucleotide diversity, supporting the notion of watershed-based segregation. Further analysis of haplotypes shared across watersheds provided evidence for three proposed past river connections. In particular, we found numerous shared haplotypes between the Yangtze and Mekong basins, as well as between the Yangtze and the Red basins. Evidence for a Irrawaddy-Salween-Red and a Yangtze-Pearl-Red river connections were also portrayed in our mapping exercise.ConclusionsThese findings emphasize the crucial role of historical geomorphological events in shaping the biogeography of microbial biodiversity, alongside contemporary biotic and abiotic factors. Watershed perimeters emerged as effective predictors of such patterns, suggesting their suitability as analytical units for regional-scale studies. Our study also demonstrates the potential of microorganisms and phylogeographic approaches to complement traditional geological analyses, providing a more comprehensive understanding of past landscape structure and its evolution.

Prevalence of plasmid-mediated quinolone resistance genes and biofilm formation in different species of quinolone-resistant clinical Shigella isolates: a cross-sectional study

BackgroundThe purpose of this study was to look into the presence of plasmid-mediated quinolone resistance (PMQR) genes and biofilm formation in several species of clinical Shigella isolates that were resistant to quinolones.MethodsThe stool samples of 150 patients (younger than 10 years) with diarrhea were collected in this cross-sectional study (November 2020 to December 2021). After cultivation of samples on Hektoen Enteric agar and xylose lysine deoxycholate agar, standard microbiology tests, VITEK 2 system, and polymerase chain reaction (PCR) were utilized to identify Shigella isolates. The broth microdilution method was used to determine antibiotic susceptibility. PMQR genes including qnrA, qnrB, qnrC, qnrD, qnrE, qnrS, qnrVC, qepA, oqxAB, aac(6′)-Ib-cr, and crpP and biofilm formation were investigated in quinolone-resistant isolates by PCR and microtiter plate method, respectively. An enterobacterial repetitive intergenic consensus polymerase chain reaction (ERIC-PCR) technique was used to determine the clonal relatedness of quinolone-resistant isolates.ResultsA total of 95 Shigella isolates including S. sonnei (53, 55.8%), S. flexneri (39, 41.1%), and S. boydii (3, 3.2%) were identified. The highest resistance rates of the isolates were against ampicillin (92.6%, n = 88/95). Overall, 42 of 95 (44.2%) isolates were simultaneously resistant against two or more quinolones including 26 (61.9%) S. sonnei and 16 (38.1%) S. flexneri. All isolates were multidrug-resistant (resistance to more than 3 antibiotics). The occurrence of PMQR genes was as follows: qnrS (52.4%), qnrA and aac(6′)-Ib-cr (33.3%), and qnrB (19.0%). The prevalence in species was as follows: 61.5% and 37.5% (qnrS), 19.2% and 56.3% (qnrA), 38.5% and 25.0 (aac(6′)-Ib-cr), and 19.2% and 18.8% (qnrB) for S. sonnei and S. flexneri, respectively. The other PMQR genes were not detected. In total, 52.8% (28/53) of quinolone-susceptible and 64.3% (27/42) of quinolone-resistant isolates were biofilm producers. Biofilm formation was not significantly different between quinolone-resistant and quinolone-susceptible isolates (P-value = 0.299). Quinolone-resistant isolates showed a high genetic diversity according to the ERIC-PCR.ConclusionIt seems that qnrS, qnrA, and aac(6′)-Ib-cr play a significant role in the quinolone resistance among Shigella isolates in our region. Also the quinolone-resistant S. flexneri and S. sonnei isolates had a high genetic diversity. Hence, antibiotic therapy needs to be routinely revised based on the surveillance findings.

Genomic characterization of methicillin-resistant Staphylococcus aureus isolated from patients attending regional referral hospitals in Tanzania

BackgroundMethicillin-resistant Staphylococcus aureus (MRSA) colonization increases the risk of subsequent infection by MRSA strain complex interlinking between hospital and community-acquired MRSA which increases the chance of drug resistance and severity of the disease.ObjectiveGenomic characterization of Staphylococcus aures strains isolated from patients attending regional referral hospitals in Tanzania.MethodologyA laboratory-based cross-sectional study using short read-based sequencing technology, (Nextseq550,Illumina, Inc. San diego, California, USA). The samples used were collected from patients attending selected regional referral hospitals in Tanzania under the SeqAfrica project. Sequences were analyzed using tools available in the center for genomic and epidemiology server, and visualization of the phylogenetic tree was performed in ITOL 6.0. SPSS 28.0 was used for statistical analysis.ResultsAmong 103 sequences of S. aureus, 48.5% (50/103) carry the mecA gene for MRSA. High proportions of MRSA were observed among participants aged between 18 and 34 years (52.4%), in females (54.3%), and among outpatients (60.5%). The majority of observed MRSA carried plasmids rep5a (92.0%), rep16 (90.0%), rep7c (90.0%), rep15 (82.0%), rep19 (80.0%) and rep10 (72.0%). Among all plasmids observed rep5a, rep16, rep20, and repUS70 carried the blaZ gene, rep10 carried the erm(C) gene and rep7a carried the tet(K) gene. MLST and phylogeny analysis reveal high diversity among MRSA. Six different clones were observed circulating at selected regional hospitals and MRSA with ST8 was dominant.ConclusionThe study reveals a significant presence of MRSA in Staphylococcus aureus strains from Tanzanian regional hospitals, with nearly half carrying the mecA gene. MRSA is notably prevalent among young adults, females, and outpatients, showing high genetic diversity and dominance of ST8. Various plasmids carrying resistance genes indicate a complex resistance profile, highlighting the need for targeted interventions to manage MRSA infections in Tanzania.