Search Results (82)

Monitoring microplastic pollution relies increasingly on bioindicators that integrate environmental exposure across habitats. This review presents animals explicitly proposed as microplastic bioindicators in recent literature and qualitatively evaluates their appropriateness using established biomonitoring criteria encompassing ecological, physiological, and methodological dimensions. In aquatic systems, bivalves (clams and mussels) demonstrate high suitability due to wide distribution, habitat-specific feeding, effective microplastic retention, and well-established analytical protocols. Fish exhibit intermediate suitability, as ecological representativeness and retention vary among species, and standardized methods often require multi-species approaches. Sessile organisms, including barnacles and sea anemones, align strongly with all three dimensions through spatial fidelity, effective retention, and methodological ease. Crustaceans and sponges also exhibit robust ecological relevance and high retention, with sponges uniquely integrating fine particles over time. Terrestrial and aerial indicators, such as carabid beetles and insectivorous birds, provide complementary coverage with moderate physiological integration and feasible ethical sampling. Sea turtles demonstrate exceptional physiological integration and methodological robustness at regional scales, despite non-sedentary behavior. Overall, taxa combining sedentary or spatially faithful ecology, effective microplastic retention, and standardized laboratory applicability, particularly bivalves, sponges, barnacles, sea anemones, and sediment-associated crustaceans, emerge as the most suitable bioindicators. Future research should prioritize harmonized, multi-taxa frameworks to improve standardization, cross-ecosystem comparability, and long-term microplastic monitoring. Full article

Identifying plant-growth-promoting rhizobacteria tolerant to saline–alkali conditions is critical for developing effective microbial agents and multi-strategy approaches to remediate saline–alkali soil. Two salt–alkali-tolerant bacterial strains—phosphorus-solubilizing Bacillus pumilus JL-C and cellulose-decomposing B. halotolerans XW-3—were isolated from saline–alkali soil, with both exhibiting multiple plant-growth-promoting properties, including nitrogen fixation and the generation of indole-3-acetic acid, siderophores, and 1-aminocyclopropane-1-carboxylate deaminase. Alfalfa pot experiments were conducted under four treatments: a control, the strain JL-C treatment, the strain XW-3 treatment, and a co-inoculation treatment (JL-C/XW-3), all mixed with corn straw and applied to the saline–alkali soil. The results demonstrated that the co-inoculation treatment yielded the most significant growth-promoting effects on alfalfa, showing enhanced antioxidant enzyme activities; increased contents of proline, soluble sugar, and protein; reduced malondialdehyde content; lowered pH and electrical conductivity; elevated activities of key enzymes; and increased levels of available nitrogen, phosphorus, potassium, and organic matter content in the soil. The pot experiments were confirmed by field experiments. The results of 16S rRNA high-throughput sequencing revealed changes in the bacterial community composition in the alfalfa rhizosphere, showing shifts in the relative abundance of several bacterial taxa often reported as plant-associated or potentially beneficial. This study establishes a combined remediation strategy for saline–alkali soil utilizing complex microbial agents and corn straw. Full article

Overwinter Syndrome (OWS) affects grass carp (Ctenopharyngodon idellus) aquaculture in China, causing high mortality and economic losses under low temperatures. Failure of antibiotic therapies shows limits of the ‘low–temperature–pathogen’ model and shifts focus to mucosal barrier dysfunction and host–microbiome interactions in OWS. We compared healthy and diseased grass carp collected from the same pond using histopathology, transcriptomics, proteomics, and metagenomics. This integrated approach was used to characterize intestinal structure, microbial composition, and host molecular responses at both taxonomic and functional levels. Results revealed a three-layer barrier failure in OWS fish: the physical barrier was compromised, with structural damage and reduced mucosal index; microbial dysbiosis featured increased richness without changes in diversity or evenness, and expansion of the virobiota, notably uncultured Caudovirales phage; and mucosal immune dysregulation indicated loss of local immune balance. Multi-omics integration identified downregulation of lysosome-related and glycosphingolipid biosynthesis pathways at transcript and protein levels, with disrupted nucleotide metabolism. Overall gut microbial richness, rather than individual taxa abundance, correlated most strongly with host gene changes linked to immunity, metabolism, and epithelial integrity. Although biological replicates were limited by natural outbreak sampling, matched high-depth multi-omics datasets provide exploratory insights into OWS-associated intestinal dysfunction. In summary, OWS entails a cold-triggered breakdown of intestinal barrier integrity and immune homeostasis. This breakdown is driven by a global restructuring of the gut microbiome, which is marked by increased richness, viral expansion, and functional shifts, ultimately resulting in altered host–microbe crosstalk. This ecological perspective informs future mechanistic and applied studies for disease prevention. Full article

Anthropogenic stressors increasingly threaten freshwater biodiversity, with fish communities particularly sensitive to habitat modification. This study evaluates how river morphological alterations influence fish assemblage structure in 114 mountain rivers of the Southern Carpathians, assessing whether such changes cause species loss or drive shifts toward disturbance-tolerant communities. Using a multi-scale analytical framework integrating non-metric multidimensional scaling, redundancy analysis, and variance partitioning, we quantified the contributions of spatial, catchment, and local habitat variables to community patterns. Spatial- and catchment-scale factors explained the largest variance in fish assemblages (12% in adults and 17% in small-bodied fish). However, morphological pressures proved significant in shaping community structure with clear ecological consequences. Weirs and embankments reduced abundances of rheophilic species (flow-dependent) by 27–38%, potamodromous by 23–42%, invertivorous by 26–49%, benthic by 40–46% and lithophilic taxa by 27–41%, indicating the loss of habitat specialists. In contrast, limnophilic taxa (preferring slow or still water) increased 25 times, phytophilic spawners by 17–41%, and tolerant species by 10%, reflecting biotic homogenization. By integrating a trait-based approach, this study highlights functional shifts that may be overlooked in species-level assessments. It underscores the need to couple local habitat restoration with catchment-scale management to conserve fish biodiversity and maintain natural ecological gradients in mountain river systems. Full article

Saxitoxin (STX) is one of the most potent marine neurotoxins, produced by several species of freshwater cyanobacteria and marine dinoflagellates. Although omics-based approaches have advanced our understanding of STX biosynthesis in recent decades, the origin, regulation, and ecological drivers of STX in dinoflagellates remain poorly resolved. Specifically, dinoflagellate STX biosynthetic genes (sxt) are extremely fragmented, inconsistently expressed, and unevenly distributed between toxic and non-toxic taxa. Environmental studies further report inconsistent relationships between abiotic factors and STX production, suggesting regulation across multiple genomic, transcriptional, post-transcriptional, and epigenetic levels. These gaps prevent a comprehensive understanding of STX biosynthesis in dinoflagellates and limit the development of accurate predictive models for harmful algal blooms (HABs) and paralytic shellfish poisoning (PSP). Artificial intelligence (AI), including machine learning and deep learning, offers new opportunities in ecological pattern recognition, molecular annotation, and data-driven prediction. This review explores the current state of knowledge and persistent knowledge gaps in dinoflagellate STX research and proposes an AI-integrated multi-omics framework highlighting recommended models for sxt gene identification (e.g., DeepFRI, ProtTrans, ESM-2), evolutionary reconstruction (e.g., PhyloGAN, GNN, PhyloVAE, NeuralNJ), molecular regulation (e.g., MOFA+, LSTM, GRU, DeepMF), and toxin prediction (e.g., XGBoost, LightGBM, LSTM, ConvLSTM). By integrating AI with diverse biological datasets, this novel framework outlines how AI can advance fundamental understanding of STX biosynthesis and inform future applications in HAB monitoring, seafood safety, and PSP risk management in aquaculture and fisheries. Full article

Species delimitation in Charipinae hyperparasitoids (Hymenoptera: Figitidae) is notoriously difficult due to their minute size and limited morphological variability. Traditional diagnostic characters sometimes show intraspecific variation, raising concerns about their reliability. Here, we applied an integrative taxonomic framework to evaluate species boundaries among six species of Alloxysta Förster and four species of Phaenoglyphis Förster. We combined a morphological dataset of 53 characters with data from three molecular markers (COI, ITS2, and 16S rRNA) and reconstructed phylogenies under maximum-likelihood criteria. Phylogenies consistently recovered morphologically defined taxa as well-supported clades, confirming the overall reliability of traditional characters (pronotal and propodeal carinae, radial cell shape, and flagellomere proportions). On the other hand, molecular evidence refined certain species limits and highlighted cases of potential cryptic variation. Our results demonstrate that morphology still provides a strong baseline for Charipinae taxonomy, but integration with molecular data yields more robust and stable classifications. This study underscores the value of multi-locus approaches for resolving taxonomic ambiguities and provides a framework for future ecological and evolutionary research on these hyperparasitoid wasps. Full article

Gliomas, particularly glioblastoma multiforme, remain among the most lethal brain tumours despite multimodal therapy. Increasing evidence indicates that systemic factors, including the gut microbiota, may influence glioma progression through immune, metabolic, and neurochemical pathways. We conducted a comprehensive systematic review in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) 2020 guidelines to synthesize recent evidence on the role of gut and intratumoral microbiota in glioma biology. Peer-reviewed studies published within the last five years were identified through structured searches of major biomedical databases, and original studies using human cohorts, animal models, or Mendelian randomization approaches were included. The 17 studies met the eligibility criteria. Glioma was consistently associated with gut dysbiosis characterized by a reduced Firmicutes:Bacteroidetes ratio and enrichment of Verrucomicrobia, particularly Akkermansia, alongside decreased short-chain fatty acids and altered neurotransmitter profiles, contributing to neuroinflammation, immune suppression, and blood–brain barrier dysfunction. Antigenic mimicry by Bacteroidetes-derived peptides may impair antitumour T-cell responses, while intratumoral Fusobacteriota and Proteobacteria appear to promote angiogenesis and pro-inflammatory chemokine expression. In contrast, SCFA-producing taxa such as Ruminococcaceae and probiotic genera including Lactobacillus and Bifidobacterium show protective associations. Evidence is limited by small cohorts and methodological heterogeneity. Standardized humanized models and integrated multi-omics approaches are required to clarify causal mechanisms and support microbiome-targeted therapies in glioma. Full article

×Trititrigia cziczinii Tzvelev is a promising crop developed through distant hybridization between Elytrigia intermedia (Host) Nevski (=Thinopyrum intermedium (Host) Barkworth & D.R. Dewey) and Triticum aestivum L., followed by backcrossing with wheat. This study elucidates the genomic composition of this hybrid and its parental taxa using molecular phylogenetic analysis of nuclear (ITS, ETS) and chloroplast (trnK–rps16, ndhF) DNA markers, complemented by Next-Generation Sequencing (NGS) of the 18S–ITS1–5.8S rDNA region. Results from Sanger sequencing revealed that the primary nuclear ribosomal DNA (rDNA) of the hybrid originates from Triticum aestivum; a finding strongly supported by both Bayesian inference and Maximum Likelihood analyses. Chloroplast DNA data unequivocally indicate maternal inheritance from T. aestivum. In contrast, ETS sequence analysis showed phylogenetic affinity to Elytrigia intermedia, suggesting complex genomic reorganization or chimeric sequence formation in the hybrid. NGS data corroborate the dominance of T. aestivum-like ribotypes in the hybrid’s rDNA pool, with only a minor fraction identical to the main ribotype of E. intermedia. Genetic structure analysis further revealed geographic heterogeneity in the genomic composition of E. intermedia populations. The predominance of the wheat genome in ×T. cziczinii is likely a consequence of stabilizing backcrosses and illustrates a case of rDNA elimination from one parental genome during hybridization. This research underscores the complex genomic dynamics in artificial hybrids and the utility of multi-marker phylogenetic approaches for clarifying their origins. Full article

The gut microbiota plays an essential role in human health through its contributions to immune regulation, metabolism, pathogen defence and disease susceptibility. Despite this significance, most gut microbiome research remains disproportionately focused on high-income countries, resulting in a limited and underrepresented view of global microbial diversity. This bias is evident in Africa, where populations, including those in South Africa, show unique combinations of genetic variation, dietary patterns and environmental exposures that are insufficiently captured in current datasets but offer opportunities to uncover novel insights into microbial evolution and its influences on health across diverse settings. In response to this gap, this review synthesises global patterns in gut microbiota composition and diversity while situating South African findings within this broader context. We examine evidence across microbial domains, including bacteria, fungi, viruses, archaea, protozoa and helminths, and highlight the impact of dietary transitions and environmental exposures on microbial community structure. Although still emerging, research on the gut microbiome of South African populations consistently reports contrasts between rural and urban populations, with rural groups enriched in fibre-fermenting and anti-inflammatory taxa, whereas urban communities often exhibit reduced diversity and features of dysbiosis linked to Westernisation. However, limited sample sizes, heterogeneous methodologies and absence of multi-omic approaches constrain robust interpretation. These lacunae in current knowledge emphasise the urgent need for large-scale, longitudinal studies that reflect South Africa’s demographic and geographic diversity. Strengthening this evidence will not only help identify microbial signatures linked to modifiable lifestyle factors but will also guide nutrition, prevention and screening programmes to improve health in African populations. Full article

Urban densification threatens biodiversity, yet conventional greenspace expansion is constrained by limited land availability. Living wall systems (LWS) offer potential biodiversity enhancement through vertical green infrastructure, though their ecological value remains underexplored. This study evaluated the biodiversity performance of three LWS in Plymouth, UK, using multi-taxa surveys to assess invertebrate communities, bird assemblages, and bat activity. A scoping review of 2638 publications revealed limited research on LWS biodiversity, with only 27% of biodiversity-focused papers referencing specific species. Field surveys employed standardised protocols including flower-visiting pollinator observations, spider assessments, soil invertebrate extraction using Tullgren funnels, acoustic bird monitoring, and bat emergence surveys across soil-based and hydroponic systems. Results demonstrated that soil-based LWS supported significantly higher invertebrate diversity than hydroponic systems, with 481 soil invertebrates recorded across 19 families. Plant species composition strongly influenced biodiversity outcomes, with Hedera helix, Erigeron karvinskianus, and Lonicera japonica attracting the most pollinator species (5 each). Bird abundance was significantly higher at LWS sites compared to control areas, with confirmed breeding by three species. However, current UK Biodiversity Net Gain frameworks undervalue LWS contributions due to their classification as artificial habitats. These findings indicate that appropriately designed soil-based LWS can deliver meaningful urban biodiversity benefits when integrated with strategic plant selection and species-based valuation approaches. Full article

Abdominal fat deposition is an important economic trait in poultry, as excessive accumulation reduces feed efficiency and carcass yield. The gut microbiota is known to influence host energy metabolism and fat storage, suggesting its potential involvement in fat deposition. This study examined the relationship between intestinal microbiota and abdominal fat deposition in an F₂ population derived from Cherry Valley Ducks (♂) × Runzhou Crested White Ducks (♀) at 42 days of age. Based on abdominal fat rate, ducks with values of 0–0.75% and 1.5–2.25% were defined as the low (LF) and high (HF) abdominal fat groups, respectively. A combined multi-omics approach was used, including 16S rRNA gene sequencing, metagenomics, and whole transcriptomics, to compare high and low abdominal fat rate groups. 16S rRNA gene sequencing results showed that the cecum had the highest microbial diversity among all intestinal segments (duodenum, jejunum, ileum, and rectum) and was significantly enriched in carbohydrate metabolism pathways, highlighting its key role in nutrient utilization and growth. Therefore, the cecum was selected for further analysis. Metagenomic analysis of the cecum contents revealed significantly different intestinal microbial β diversity between the high and low abdominal fat rate groups (p < 0.05). The low abdominal fat rate group was enriched in beneficial microorganisms such as Paenibacillus, Butyrivibrio, Coprococcus, Ruminococcaceae, Veillonellaceae (Clostridiales), and Firmicutes. Conversely, the high abdominal fat rate group was characterized by an increased abundance of Bacteroidetes, including both beneficial and potentially pathogenic taxa such as Alistipes and Eggerthellales. The integrated analysis of metagenomic and whole transcriptome sequencing showed that Firmicutes and Bacteroidetes were not only related to energy metabolism, lipid metabolism, and amino acid metabolism, but also to the expression of FGF2, FKBP5, PNPLA2, PLIN3, FGFR2, DGAT2, and ACER2. In addition, Firmicutes and Bacteroidetes were also associated with 7 lncRNAs: XR_003493494.1, XR_003492471.1, XR_001190174.3, TCONS_00005095, XR_001190238.3, TCONS_00005095, and XR_003492841.1. In conclusion, this study highlights that the cecal microbiota is closely associated with abdominal fat deposition in ducks, elucidating its potential influence on host metabolism and gene expression. These findings enhance our understanding of the gut microbiota’s relationship with obesity and offer new strategies to modulate gut–microbe interactions to reduce abdominal fat accumulation in poultry. Full article

Background/Objectives: The incidence of early-onset colorectal cancer (EOCRC) is rising worldwide, although its biological and clinical features remain incompletely understood. Emerging evidence implicates gut microbial dysbiosis as a key driver of EOCRC pathogenesis, acting through complex interactions with host genetics, mucosal immunity, and early-life exposures. This review synthesizes current evidence on EOCRC-specific microbial signatures, delineates host–microbiome interactions, and evaluates how these insights may inform precision prevention, early detection, and therapeutic strategies. Methods: A systematic literature search was conducted in PubMed, Scopus, and Web of Science up to August 2025, using combinations of “early-onset colorectal cancer,” “gut microbiome,” “dysbiosis,” and “host–microbiome interactions.” Both clinical and preclinical studies were included. Extracted data encompassed microbial composition, mechanistic insights, host-related factors, and microbiome-targeted interventions. Evidence was synthesized narratively to highlight consistent patterns, methodological limitations, and translational implications. Results: EOCRC is consistently associated with enrichment of pro-inflammatory and genotoxic taxa (e.g., Fusobacterium nucleatum, colibactin-producing Escherichia coli, enterotoxigenic Bacteroides fragilis) and depletion of short-chain fatty acid–producing commensals. Multi-omics analyses reveal distinct host–microbiome signatures influenced by germline predisposition, mucosal immunity, sex, and early-life exposures. However, substantial methodological heterogeneity persists. Collectively, these data point to candidate microbial biomarkers for early detection and support the rationale for microbiome-targeted preventive and adjunctive therapeutic approaches. Conclusions: EOCRC harbors unique microbial and host–environmental features that distinguish it from late-onset disease. Integrating host determinants with microbiome signatures provides a framework for precision prevention and tailored therapeutic strategies. Future priorities include harmonizing methodologies, validating microbial biomarkers in asymptomatic young adults, and rigorously testing microbiome-targeted interventions in clinical trials. Full article

This study investigates the biodeterioration of mosaic surfaces in a semi-confined archaeological environment along the Phlegraean coast (Baiae, Italy), focusing on the interaction between salt efflorescence and phototrophic biofilms. A multi-analytical approach was employed, integrating in situ observations with ex situ analyses, including SEM/EDS, FTIR spectroscopy, and metabarcoding (16S and 18S rRNA), to characterize both abiotic and biotic alteration patterns. Results highlight subtle traces of spatial differentiation: samples from the more exposed sector showed a more consistent colonization by halotolerant and halophilic taxa, particularly among Halobacteria and Rubrobacter, along with abundant sodium, chloride, and sulfate signals suggestive of active salt crystallization. Protected areas exhibit a comparable presence of salts with less diverse halophilic communities that vary along a vertical gradient of light exposure. The integration of chemical and biological data supports a model in which salt stress and biofilm development are co-dependent and synergistic in driving surface degradation. These findings emphasize the need for context-specific conservation strategies that account for the combined action of environmental salinity and microbial communities on historical materials. Full article

Background/Objectives: While morphological similarity and incomplete specimens pose a challenge to the precise identification of Coelogyne orchids, accurate species and genus assignment is essential for conservation and CITES enforcement. This study evaluated the efficacy of five DNA barcode regions—rbcL, matK, trnH-psbA, atpF-atpH, and ITS2—and their combinations for species- and genus-level discrimination within the genus Coelogyne, aiming to develop a rapid and simple diagnostic tool for use by customs officers and trade inspectors. This is the first comprehensive comparative analysis of these five barcode regions specifically within Coelogyne, a genus underrepresented in molecular identification studies, and the first to propose multi-locus combinations for potential practical use. This study identified DNA barcode regions with high resolution and reliability, providing a solid basis for practical identification kits. Such tools will enhance CITES enforcement by enabling rapid detection of Coelogyne species in trade, directly supporting their conservation and contributing to the reduction in illegal orchid trade. Methods: Using a CTAB protocol, genomic DNA was extracted from leaf samples belonging to 19 Coelogyne species. Sanger sequencing was performed after PCR amplification using published primer sets for every barcode region. Sequences were modified in BioEdit, and BLASTn (accessed 15 June 2025) was used to compare them to GenBank (NCBI Nucleotide). Amplification efficiency was calculated per locus. Species and genus identification success rates were determined by the congruence of top BLAST hits with morphologically pre-identified taxa. Multi-barcode combinations (matK + rbcL, ITS2 + matK, matK + trnH-psbA, rbcL + trnH-psbA, and matK + rbcL + trnH-psbA) were also assessed. Results: With rbcL, atpF-atpH, and ITS2 yielding ≤11%, the highest single-locus species identification rates were for trnH-psbA (21%) and matK (16%). Among single-locus barcodes, matK showed the highest performance, with 84% genus assignment. ITS2 reached 27%, but genus-level resolution remained limited for the rbcL, trnH-psbA and atpF-atpH barcodes. Multi-barcode approaches maintained species resolution: matK + rbcL + trnH-psbA, matK + rbcL, and matK + trnH-psbA correctly identified 16% of species and achieved 74–79% genus assignment. Conclusions: No single locus achieves robust species discrimination in Coelogyne, but trnH-psbA, matK and atpF-atpH provide the best single-marker performance. Using the matK locus alone, in combination with either trnH-psbA or rbcL, or all three together ensures consistent genus-level identification and significantly improves taxonomic resolution. This study introduces a novel multi-locus barcode strategy tailored to Coelogyne, offering a practical solution for identification and enforcement. While promising, this approach represents a potential application that requires further validation before routine implementation. Full article

The human endometrium, previously considered a sterile environment, is now recognized as a low-biomass but biologically active microbial niche critical to reproductive health. Advances in sequencing technologies, particularly shotgun metagenomics, have provided unprecedented insights into the taxonomic and functional complexity of the endometrial microbiome. While 16S rRNA sequencing has delineated the distinction between Lactobacillus-dominant and non-dominant microbial communities, shotgun metagenomics has revealed additional diversity at the species and strain level, uncovering microbial signatures that remain undetected by amplicon-based approaches. Current evidence supports the association of Lactobacillus dominance with endometrial homeostasis and favorable reproductive outcomes. Dysbiosis, characterized by increased microbial diversity and enrichment of anaerobic taxa such as Gardnerella, Atopobium, Prevotella, and Streptococcus, is linked to chronic endometritis, implantation failure, and adverse IVF results. Beyond compositional differences, the endometrial microbiome interacts with the host through immunological, metabolic, and epigenetic mechanisms. These interactions modulate cytokine signaling, epithelial barrier integrity, and receptivity-associated gene expression, ultimately influencing embryo implantation. However, discrepancies between published studies reflect the lack of standardized protocols for sampling, DNA extraction, and bioinformatic analysis, as well as the inherent challenges of studying low-biomass environments. Factors such as geography, ethnicity, hormonal status, and antibiotic exposure further contribute to interindividual variability. Culturomics approaches complement sequencing by enabling the isolation of viable bacterial strains, offering perspectives for microbiome-based biotherapeutics. Emerging 3D endometrial models provide additional tools to dissect microbiome–host interactions under controlled conditions. Taken together, the growing body of data highlights the potential of endometrial microbiome profiling as a biomarker for reproductive success and as a target for personalized interventions. Future research should focus on integrating multi-omics approaches and functional analyses to establish causal relationships and translate findings into clinical practice. This review gives a new insight into current knowledge on the uterine microbiome and its impact on implantation success, analyzed through the lenses of microbiology, immunology, and oxidative stress. Full article