Taxonomic Origin Research Articles

Contrasting Effects of Leaf Litter Quality and Diversity on Oviposition of Mosquitoes.

The quality and diversity of leaf litter are important variables in determining the availability of energy in detritus-based food webs. These factors can be represented by the stoichiometric proportion between carbon and multiple nutrients, and the mixture of litter from different taxonomic and/or functional origins. In aquatic ecosystems, factors that accelerate litter decomposition can influence the secondary productivity of planktonic microbiota, which act as a link between litter and higher trophic levels. This study aimed to analyze the influence of litter quality and diversity on the oviposition behavior of medically important mosquitoes. We hypothesized that both factors would have a positive effect on the attraction of female mosquitoes and would stimulate a greater amount of oviposition. To test this hypothesis, microcosms containing isolated leaf litter leachates from four plant species were used to manipulate gradients of litter quality, and microcosms with all leachates combined were used to test the effects of litter diversity. The results showed a positive effect of litter quality (p < 0.05) on mosquito oviposition rate, with lower C:P ratio litter species (high-quality litter) presenting higher oviposition rates than litter species with high C:P ratios (low-quality litter). However, contrary to our expectations, litter diversity had a negative effect (p = 0.002) on the magnitude of egg-laying by mosquitoes. Our results highlight the importance of litter quality and diversity for insect reproductive behavior. Our data shows that litter quality can serve as a crucial indicator of a suitable environment utilized by female mosquitoes for oviposition. This finding can enhance our ability to understand and develop effective methods for mitigating the reproduction of medically significant mosquitoes, whether by allowing us to predict, based on the composition of vegetation species, areas more prone to mosquito infestation, or by using high-quality litter in oviposition traps. Furthermore, maintaining vegetation diversity can help control mosquito reproduction.

Trompe l’oeil fossils from Silurian quartzites of Sierra Morena (South Spain): a taphonomic approach on the study of a coral-like structure

ABSTRACT Some circular fossils showing radial structures concentrated in a small area have been recorded from the Criadero Quartzite, 1 km north from El Centenillo village (Iberian Central Zone, SE Spain). The fossils resembling cnidarians have been studied in detail, both at the field and in the laboratory. The specimens have been preserved in thick-grained quartz sandstones. They were analysed in thin sections and rock samples using optical microscopy, micro-reflectance spectroscopy, Fourier transform infrared–attenuated total reflectance spectroscopy, scanning electron microscopy with energy-dispersive X-ray spectroscopy and epifluorescence microscopy. The radial structure is composed of ridges and grooves, which correspond to clear and dark ochre bands filled with middle-sized, angular-elongated quartz grains without tractive structures. Mineralogical analyses reveal that composition is based on quartz and illite in both areas. The morphological and compositional features of the fossils have been compared with a set of ichnofossils of multiple taxonomic origins and ages without conclusive results. The preservation is probably produced by the existence of microbial mats on the sand floor and the impression of moulds by authigenic cementation by an unidentified organism. To elucidate the nature of the producer, potentially soft-bodied cnidarian, including fossil medusae and sea anemone, further investigations are needed.

Marine Non-Indigenous Species Dynamics in Time and Space within the Coastal Waters of the Republic of Ireland

Documenting temporal and spatial occurrence trends of Non-Indigenous Species (NIS) is essential to understand vectors and pathways of introduction, and for horizon scanning for future introductions. This study provides an overview of marine NIS found in the Republic of Ireland up to 2020. Taxonomic groups, species origin, and location of first reporting (counties) were compiled and analysed focusing on the last three decades. While the unambiguous characterisation of introduction events is challenging, analysis of 110 species corroborated the global weight of evidence that shipping activities to/from ports and marinas are the most likely vectors and pathways in Ireland. A comparable review study for the Netherlands revealed that most NIS were first introduced to mainland Europe and subsequently would take on average &gt;15 years to reach Ireland. In the last two decades there has been an increase in NIS-focused surveys in Ireland. Incorporating data from these surveys in centralized national repositories such as the National Biodiversity Data Centre, will strongly aid the evaluation of potential NIS management responses. Furthermore, the availability of robust baseline data as well as predictions of future invaders and their associated vectors and pathways will facilitate the effective application of emerging monitoring technologies such as DNA-based approaches.

The Complex Taxonomy of ‘Nubian’ in Context

The meaning of the word ‘Nubian’ in Middle Palaeolithic archaeology has changed markedly since its first published use in 1965 in the context of the Nubian rescue campaign in southern Egypt and northern Sudan. Initially referring to two types of prepared point cores, ‘Nubian’ later became attached to a widespread technocomplex in the 1990s and in more recent research describes a specific Levallois reduction strategy. In this review, we situate ‘Nubian’ in its geographic and historical contexts, exploring how its terminology and concepts emerged, developed, and are now viewed in the frame of subsequent research. Whilst the taxonomic origin of the Nubian descriptor—as a technology or technocomplex—is associated with this region of northeastern Africa, its widespread distribution, as shown in the works presented in this collection, suggests that Nubian reduction played as complex a role in past human behaviour and cultural dynamics as it does in current archaeological debates.

Distribution of potato mosaic viruses on plants of the Petota Dumort. section of &lt;i&gt;Solanum&lt;/i&gt; L. in the VIR collection

Background. Potato due to its vegetative propagation is affected by viruses, among which potato viruses Y (PVY), S (PVS) and M (PVM) are spread across all Russia’s territory. The VIR collection presents the diversity of the potato gene pool, including potato cultivars and related tuber-forming species. Diagnostics of viral infections in plants saved for several years by obtaining tuber reproductions is an important part of the work on the conservation and sustainable utilization of the potato gene pool. The purpose of the work was to evaluate the distribution of PVX, PVY, PVS and PVM on plants of potato cultivars and related Solanum spp. in the VIR field collection. Material and methods. Evaluation covered 315 accessions representing all groups of the potato gene pool. Diagnosis by enzyme-linked immunosorbent assay (ELISA) was carried out on plants that did not display symptoms of a virus infection. The Russian test system of RPA “BioTechnologies” and foreign one of Bioreba AG (Switzerland) were used. Statistical data processing was performed by the Statistica StatSoft 13 program. Results. Mosaic viruses are distributed with different frequencies on potato plants in the field collection: PVM dominates, detected in 64% of potato accessions; PVY is found in 41 %, PVX on 24 %, and PVS in 18 % of accessions. The connection between the botanical and taxonomic origin of potato accessions and their infection with viruses has been confirmed. Among wild species, more than half of accessions, while among cultivated species, only 5% are affected by XBK. PVM, on the contrary, was detected in a significant part (77–91%) of cultivated potato accessions. and much less frequently (16%) in accessions of wild species. Cvs, ‘Grand’, ‘Krasa Meshchery’, ‘Yantar’ and ‘Nur-Alem’, hybrids 99-1-3, 952-35 and 914-5-2018, accessions of wild species from North America, and cultivated species Solanum goniocalyx Juz. et Buk. (k-9922) are not affected by viruses.

Pollen from urban flora in the ephemeral nests of solitary Megachile bees in three temperate and subtropical cities of Argentina

Cities are anthropogenic habitats that are home to many taxonomically diverse groups of bees and contribute to their conservation due to the abundance of flowers and nesting substrates. However, the pollen diet composition of nest provisions for most urban bees in South America is poorly studied and therefore the characteristics of the urban flora needed for their survival remains unknown. Pollen analysis was employed to study the diet composition of the wild solitary bees Megachile infima Vachal, M. pusilla Pérez and Megachile spp. that all nest in urban environments in two eco-regions in Argentina. Nests were found in preexisting small holes within human-made structures (walls, hosepipes, water taps), natural substrates (hollow stems) or in semi-exposed spaces within four courtyards of three cities. Pollen from brood provisions from these nests were compared with pollen grains from the available flowering plants surrounding the nests. In the temperate city La Plata from the Pampean eco-region, 23 pollen types from 14 families and five unidentified types were present. The most abundant were Styphnolobium japonicum (Fabaceae, Papilionoideae) and Picris echioides (Asteraceae). In the two subtropical cities from the Chaco eco-region, 15 types from eight families and four unidentified types were present, with Phoenix (Arecaceae) and Punica granatum (Lythraceae) being the most abundant. Although bees were polylectic, the presence of pollen in nests was not evenly distributed, which may be related to resource abundance, pollen attributes, and floral morphology. This study provides evidence of forage versatility of Megachile bees on pollen plants from diverse taxonomic origin and status of naturalization, flowering stratum and city microhabitat.

Non-Indigenous Species Dynamics in Time and Space within the Coastal Waters of The Netherlands

Information on temporal and spatial trends with regard to the introduction of non-indigenous species (NIS) is often sparsely available. These trends may potentially help improve the design and focus of monitoring programs, give insights into new pathways and hotspots, and facilitate horizon scanning. We provide an overview of 215 marine and brackish water NIS recorded in The Netherlands. Temporal trends over the most recent three decades for taxonomic groups, species origin, introduction vectors, and water systems were analysed. We attempt to explain the observed patterns and discuss factors that hamper their explanation. A shift in the region of origin from Pacific to W Atlantic can potentially be linked to legislation prohibiting Pacific oyster imports, whereas a subsequent shift backwards cannot. Case studies illustrate that NIS may not be first detected in the water systems where they were originally introduced. Additionally, it is shown that changes in allegedly native species’ distribution or seasonal pattern should be linked to an introduced cryptic NIS instead. We also discuss the shortcomings of monitoring programs that were originally not focused on NIS, the importance of naturalists’ observations, and the added value of a more recent network that is focused on NIS detection in the coastal waters of The Netherlands.

PepGM: A probabilistic graphical model for taxonomic inference of viral proteome samples with associated confidence scores.

Inferring taxonomy in mass spectrometry-based shotgun proteomics is a complex task. In multi-species or viral samples of unknown taxonomic origin, the presence of proteins and corresponding taxa must be inferred from a list of identified peptides which is often complicated by protein homology: many proteins do not only share peptides within a taxon but also between taxa. However, correct taxonomic inference is crucial when identifying different viral strains with high sequence homology-considering, e.g., the different epidemiological characteristics of the various strains of SARS-CoV-2. Additionally, many viruses mutate frequently, further complicating the correct identification of viral proteomic samples. We present PepGM, a probabilistic graphical model for the taxonomic assignment of virus proteomic samples with strain-level resolution and associated confidence scores. PepGM combines the results of a standard proteomic database search algorithm with belief propagation to calculate the marginal distributions, and thus confidence scores, for potential taxonomic assignments. We demonstrate the performance of PepGM using several publicly available virus proteomic datasets, showing its strain-level resolution performance. In two out of eight cases, the taxonomic assignments were only correct on the species level, which PepGM clearly indicates by lower confidence scores. PepGM is written in Python and embedded into a Snakemake workflow. It is available on https://github.com/BAMeScience/PepGM.

UltraSEQ, a Universal Bioinformatic Platform for Information-Based Clinical Metagenomics and Beyond.

Applied metagenomics is a powerful emerging capability enabling the untargeted detection of pathogens, and its application in clinical diagnostics promises to alleviate the limitations of current targeted assays. While metagenomics offers a hypothesis-free approach to identify any pathogen, including unculturable and potentially novel pathogens, its application in clinical diagnostics has so far been limited by workflow-specific requirements, computational constraints, and lengthy expert review requirements. To address these challenges, we developed UltraSEQ, a first-of-its-kind accurate and scalable metagenomic bioinformatic tool for potential clinical diagnostics and biosurveillance utility. Here, we present the results of the evaluation of our novel UltraSEQ pipeline using an in silico-synthesized metagenome, mock microbial community data sets, and publicly available clinical data sets from samples of different infection types, including both short-read and long-read sequencing data. Our results show that UltraSEQ successfully detected all expected species across the tree of life in the in silico sample and detected all 10 bacterial and fungal species in the mock microbial community data set. For clinical data sets, even without requiring data set-specific configuration setting changes, background sample subtraction, or prior sample information, UltraSEQ achieved an overall accuracy of 91%. Furthermore, as an initial demonstration with a limited patient sample set, we show UltraSEQ's ability to provide antibiotic resistance and virulence factor genotypes that are consistent with phenotypic results. Taken together, the above-described results demonstrate that the UltraSEQ platform offers a transformative approach for microbial and metagenomic sample characterization, employing a biologically informed detection logic, deep metadata, and a flexible system architecture for the classification and characterization of taxonomic origin, gene function, and user-defined functions, including disease-causing infections. IMPORTANCE Traditional clinical microbiology-based diagnostic tests rely on targeted methods that can detect only one to a few preselected organisms or slow, culture-based methods. Although widely used today, these methods have several limitations, resulting in rates of cases of an unknown etiology of infection of >50% for several disease types. Massive developments in sequencing technologies have made it possible to apply metagenomic methods to clinical diagnostics, but current offerings are limited to a specific disease type or sequencer workflow and/or require laboratory-specific controls. The limitations associated with current clinical metagenomic offerings result from the fact that the backend bioinformatic pipelines are optimized for the specific parameters described above, resulting in an excess of unmaintained, redundant, and niche tools that lack standardization and explainable outputs. In this paper, we demonstrate that UltraSEQ uses a novel, information-based approach that enables accurate, evidence-based predictions for diagnosis as well as the functional characterization of a sample.

Notes on taxonomic position and origin of two phasmids from Trinidad and Tobago (Phasmatodea, Occidophasmata, Diapheromeridae)

The geographical origin of Caribbiopheromera jamaicana Zompro, 2001, is discussed and called into question, while Clonistria caputaurata Bellanger et al., 2012, is synonymised with Bostra trinitatis Werner, 1929, which is transferred to the genus Clonistria Stål, 1875.

Comparison of long- and short-read metagenomic assembly for low-abundance species and resistance genes.

Recent technological and computational advances have made metagenomic assembly a viable approach to achieving high-resolution views of complex microbial communities. In previous benchmarking, short-read (SR) metagenomic assemblers had the highest accuracy, long-read (LR) assemblers generated the most contiguous sequences and hybrid (HY) assemblers balanced length and accuracy. However, no assessments have specifically compared the performance of these assemblers on low-abundance species, which include clinically relevant organisms in the gut. We generated semi-synthetic LR and SR datasets by spiking small and increasing amounts of Escherichia coli isolate reads into fecal metagenomes and, using different assemblers, examined E. coli contigs and the presence of antibiotic resistance genes (ARGs). For ARG assembly, although SR assemblers recovered more ARGs with high accuracy, even at low coverages, LR assemblies allowed for the placement of ARGs within longer, E. coli-specific contigs, thus pinpointing their taxonomic origin. HY assemblies identified resistance genes with high accuracy and had lower contiguity than LR assemblies. Each assembler type's strengths were maintained even when our isolate was spiked in with a competing strain, which fragmented and reduced the accuracy of all assemblies. For strain characterization and determining gene context, LR assembly is optimal, while for base-accurate gene identification, SR assemblers outperform other options. HY assembly offers contiguity and base accuracy, but requires generating data on multiple platforms, and may suffer high misassembly rates when strain diversity exists. Our results highlight the trade-offs associated with each approach for recovering low-abundance taxa, and that the optimal approach is goal-dependent.

QNABpredict: Quick, accurate, and taxonomy-aware sequence-based prediction of content of nucleic acid binding amino acids.

Protein sequence-based predictors of nucleic acid (NA)-binding include methods that predict NA-binding proteins and NA-binding residues. The residue-level tools produce more details but suffer high computational cost since they must predict every amino acid in the input sequence and rely on multiple sequence alignments. We propose an alternative approach that predicts content (fraction) of the NA-binding residues, offering more information than the protein-level prediction and much shorter runtime than the residue-level tools. Our first-of-its-kind content predictor, qNABpredict, relies on a small, rationally designed and fast-to-compute feature set that represents relevant characteristics extracted from the input sequence and a well-parametrized support vector regression model. We provide two versions of qNABpredict, a taxonomy-agnostic model that can be used for proteins of unknown taxonomic origin and more accurate taxonomy-aware models that are tailored to specific taxonomic kingdoms: archaea, bacteria, eukaryota, and viruses. Empirical tests on a low-similarity test dataset show that qNABpredict is 100 times faster and generates statistically more accurate content predictions when compared to the content extracted from results produced by the residue-level predictors. We also show that qNABpredict's content predictions can be used to improve results generated by the residue-level predictors. We release qNABpredict as a convenient webserver and source code at http://biomine.cs.vcu.edu/servers/qNABpredict/. This new tool should be particularly useful to predict details of protein-NA interactions for large protein families and proteomes.

Diversity of Bacterial Secondary Metabolite Biosynthetic Gene Clusters in Three Vietnamese Sponges.

Recent reviews have reinforced sponge-associated bacteria as a valuable source of structurally diverse secondary metabolites with potent biological properties, which makes these microbial communities promising sources of new drug candidates. However, the overall diversity of secondary metabolite biosynthetic potential present in bacteria is difficult to access due to the fact that the majority of bacteria are not readily cultured in the laboratory. Thus, use of cultivation-independent approaches may allow accessing "silent" and "cryptic" secondary metabolite biosynthetic gene clusters present in bacteria that cannot yet be cultured. In the present study, we investigated the diversity of secondary metabolite biosynthetic gene clusters (BGCs) in metagenomes of bacterial communities associated with three sponge species: Clathria reinwardti, Rhabdastrella globostellata, and Spheciospongia sp. The results reveal that the three metagenomes contain a high number of predicted BGCs, ranging from 282 to 463 BGCs per metagenome. The types of BGCs were diverse and represented 12 different cluster types. Clusters predicted to encode fatty acid synthases and polyketide synthases (PKS) were the most dominant BGC types, followed by clusters encoding synthesis of terpenes and bacteriocins. Based on BGC sequence similarity analysis, 363 gene cluster families (GCFs) were identified. Interestingly, no GCFs were assigned to pathways responsible for the production of known compounds, implying that the clusters detected might be responsible for production of several novel compounds. The KS gene sequences from PKS clusters were used to predict the taxonomic origin of the clusters involved. The KS sequences were related to 12 bacterial phyla with Actinobacteria, Proteobacteria, and Firmicutes as the most predominant. At the genus level, the KSs were most related to those found in the genera Mycolicibacterium, Mycobacterium, Burkholderia, and Streptomyces. Phylogenetic analysis of KS sequences resulted in detection of two known 'sponge-specific' BGCs, i.e., SupA and SwfA, as well as a new 'sponge-specific' cluster related to fatty acid synthesis in the phylum Candidatus Poribacteria and composed only by KS sequences of the three sponge-associated bacterial communities assessed here.

Free tocopherols and tocotrienols in 82 plant species’ oil: Chemotaxonomic relation as demonstrated by PCA and HCA

The tocopherol (T) and tocotrienol (T3) profile were investigated in the present study for four hundred and eighteen plant oil samples, including thirty-one families, eighty-two species, and five cross-species. Fifteen species were dominated by tocotrienols, while sixty-seven – by tocopherols. The mean proportion of γ-T was almost half of the total tocochromanol content (49.3%) in the investigated samples, while α-T constituted to one quarter (25.0%), and the remaining other tocochromanols were present as minor constituents. A strong relationship between the taxonomic plant origin and the presence of the characteristic tocochromanol profile in oils obtained from those plants was noted. This is the first study to demonstrate that not only monocotyledonous, but also dicotyledons families can be rich in tocotrienols. The usefulness of statistical tools – principal component analysis (PCA) and hierarchical cluster analysis (HCA) for plant sample discrimination based on their tocochromanol profile was also shown.

Dendroflora of the BNAU botanical garden and the prospects for its enrichment in connection with the development of the territory as an object of the nature reserve fund

It is shown that the existing dendroflora of the botanical garden of the BSNA is the basis for providing practical training for students of specialties 206 – Horticulture and 205 – Forestry, as well as for conducting scientific research on issues of dendrology, the introduction of ornamental plants, and the development of practical recommendations for the creation of horticulture objects in the conditions of the forest-steppe of Ukraine. The history of the creation of botanical gardens of Ukraine at educational institutions, their role in the development of botanical science, and cognitive value for the training of specialists in natural sciences, as well as their modern aesthetic, educational and environmental role are analyzed. The history of the formation of the biostationary (Botanical Garden) of the BNAU and the formation of its collections is high-lighted. The taxonomic composition, life forms, origin and decorative qualities of woody plants growing in the BNAU Botanical Garden are analyzed. It has been established that currently the dendrocollection of the BNAU Botanical Garden contains 1471 trees, shrubs and vines, which belong to 211 taxa belonging to two divisions of the Pinophyta and Magnoliophyta, 8 subclasses, 27 orders, 35 families, 68 genera. The gymnosperms are represented by one class, 3 orders, 3 families, 10 genera, 23 species and 16 cultivars. From the Pinophyta, the largest number of species (13) and cultivars (19) is united by the family Cupresaceae F. Neger, followed by the family Pianaceae with 13 species and 6 cultivars. From the Magnoliophyta division, the largest number of taxa is represented by the Rosaceae family – 15 genera, 31 species, 2 ornamental forms and 16 cultivars. The second place in terms of representation of genera is occupied by the family Fabaceae Lindl., which is represented in the botanical garden by species from 5 genera. The prospects for enriching the collections of woody plants are revealed, taking into account the reorganization of the biostationary into the BNAU Botanical Garden and the development of its territory as a nature reserve, including further expansion of the collections of woody plants of the Pinophyta and Magnoliophyta departments by representatives of families that are currently absent in the collection, as well as highly decorative species and cultivars that are promising in modern landscaping. The basic principle of organization of the existing and new territory of the Botanical Garden is the formation of collections on a systematic basis, which will allow to use the existing plantings as a basis and supplement them with new taxa. Key words: botanical garden, species, tree, life form, viability, collection, shrub, cultivar, taxon.

SARS-CoV-2 virus classification based on stacked sparse autoencoder

Since December 2019, the world has been intensely affected by the COVID-19 pandemic, caused by the SARS-CoV-2. In the case of a novel virus identification, the early elucidation of taxonomic classification and origin of the virus genomic sequence is essential for strategic planning, containment, and treatments. Deep learning techniques have been successfully used in many viral classification problems associated with viral infection diagnosis, metagenomics, phylogenetics, and analysis. Considering that motivation, the authors proposed an efficient viral genome classifier for the SARS-CoV-2 using the deep neural network based on the stacked sparse autoencoder (SSAE). For the best performance of the model, we explored the utilization of image representations of the complete genome sequences as the SSAE input to provide a classification of the SARS-CoV-2. For that, a dataset based on k-mers image representation was applied. We performed four experiments to provide different levels of taxonomic classification of the SARS-CoV-2. The SSAE technique provided great performance results in all experiments, achieving classification accuracy between 92% and 100% for the validation set and between 98.9% and 100% when the SARS-CoV-2 samples were applied for the test set. In this work, samples of the SARS-CoV-2 were not used during the training process, only during subsequent tests, in which the model was able to infer the correct classification of the samples in the vast majority of cases. This indicates that our model can be adapted to classify other emerging viruses. Finally, the results indicated the applicability of this deep learning technique in genome classification problems.

The red ruffed lemur, Varecia rubra (É. Geoffroy Saint-Hilaire, 1812): a comparative morphology investigation of lingual papillae and connective tissue cores.

The morphology of the lingual papillae (filiform, foliate, fungiform, and vallate papillae) and the underlying connective tissue core of the red ruffed lemur (Varecia rubra) of a strepsirrhines species were studied using light and scanning electron microscopy. The filiform papillae distributed at the root of the tongue were larger than the structures distributed at the body and apex. Six to eight vallate papillae were arranged in a Y-shape at the border between the lingual body and the lingual root. Foliate papillae were observed at the posterior lateral border of the tongue. Scanning electron microscopy revealed a primary process and numerous auxiliary processes in the epithelial layer of filiform papillae. After epithelial removal, the connective tissue core of the filiform papilla showed several protrusions surrounding an oval-shaped depression that extended slightly posteriorly, and a large, maple-shaped filiform papilla was seen in the posterior portion of the tongue. The connective tissue cores of the fungiform papillae exhibited a longitudinally ridged cylindrical structure. The connective tissue core of the foliate papillae had numerous tubular projections arranged along a groove with a salivary gland conduit at the base. As a Lemuridae species, the appearance of the fungiform and filiform papillae of the red ruffed lemur is similar to that reported in previous studies of the ring-tailed lemur, with some differences, especially in the filiform papillary connective tissue core at the base and tongue body border. These findings suggest the taxonomic and phylogenetic origins of the lemurs as well as the influence of dietary diversity.

A novel catfish cultured in South China is proved to be Silurus asotus based on morphological and molecular genomic identification

One novel catfish (Chinese called it ‘Gou nian’) widely cultured in China shares the same name with Ictalurus punctatus introduced from America, but is morphologically closed to genus Silurus. For years, the novel catfish was speculated to be an artificial hybrid of S. asotus and S. meridionalis. Therefore, we investigated the correct taxonomic status and origin of the novel catfish by means of morphological and molecular approaches. First, the novel ‘Gou nian’ could not be distinguished from S. asotus and S. meridionalis through anatomical observation, however, it was morphologically similar to S. asotus. Then, the novel ‘Gou nian’ was found not a hybrid of S. asotus and S. meridionalis based on the identification of ITS-2 and RAG-2, moreover, the analysis of COI barcoding found it more likely to be S. asotus. The phylogenic and population genetic analysis of Cyt b showed that the novel ‘Gou nian’ belonged to a taxonomic branch of S. asotus from the Liao River. The results convincingly indicated that the novel catfish is S. asotus and may originate from Northern China. The findings also provided useful implications for aquaculture management of the species.

Prevalence of Parasitic Infections with Zoonotic Potential in Tilapia: A Systematic Review and Meta-Analysis.

Simple SummaryThe consumption of fish represents a healthy and affordable alternative for a large sector of the population; among the species with the highest consumption worldwide are tilapia. However, its consumption may be associated with health risks of a parasitic type. Through the analysis of the available scientific literature on parasitic prevalence in tilapia, it was observed that fish obtained from the wild and aquaculture represent a risk of parasitosis in human populations. Additionally, a high prevalence of cestodes and a greater diversity of trematodes were found. Finally, the presence of the genus Gnathostoma must stand out. This synthesis of information can be useful as a platform for the develCopment of intervention programs for parasite control, and it also suggests continuing with the study of zoonotic parasites related to the consumption of tilapia in geographical areas of high consumption.Tilapia has a high socioeconomic value in many countries worldwide. However, it has been identified as a zoonotic parasite reservoir. A systematic literature search and meta-analysis were carried out in order to estimate the global prevalence of zoonotic parasites that affect tilapia. The search was performed by three field experts to avoid reviewer bias. Polled prevalence was estimated using a logistic-normal random-effect regression model in the R software. We dealt with the heterogeneity among studies through subgroup analysis, taking into account the continent, country, genus of the host, parasite taxonomic group, sample origin, and type of diagnostic test as moderator variables. Fifty-two eligible articles were identified covering five tilapia genera with a pooled prevalence of 0.14 (95% CI: 0.10–0.20) showed significant heterogeneity (I2 = 98.4; p < 0.001). The subgroup analysis revealed that the most affected host was Sarotherodon, with a prevalence of 0.42 (95% CI: 0.22–0.65). Cestode was the taxonomic group with the largest prevalence (0.40; 95% CI:0.32–0.48), followed by amoeba (0.24; 95% CI: 0.16–0.35) and nematode (0.22; 95% CI: 0.11–0.38), among which, Schyzocotyle spp., Opistorchis spp., Gnathostoma spp. and Vermamoeba spp. have an impact on public health. Significant differences (p < 0.004) were found among continents and countries, with the highest value of prevalence detected in the African continent (0.28; 95% CI: 0.20–0.37), specifically in Tanzania (0.56; 95% CI: 0.22–0.87) and Egypt (0.43; 95% CI: 0.20–0.55). The origin of samples had a significant effect (p < 0.0001) on the detected prevalence, especially from those that showed the highest prevalence (0.24; 95% CI: 0.17–0.33). Finally, there were no differences in prevalence according to the diagnostic test (p = 0.97). Our results provide useful information on the development of epidemiological programs for the control of zoonoses associated with parasites in tilapia and in the design, planning, and implementation of future research.

Inhibition and structure-activity relationship of dietary flavones against three Loop 1-type human gut microbial β-glucuronidases

Gut microbial β-glucuronidases (GUSs) inhibition is a new approach for managing some diseases and medication therapy. However, the structural and functional complexity of GUSs have posed tremendous challenges to discover specific or broad-spectrum GUSs inhibitors using Escherichia coli GUS (EcoGUS) alone. This study first assessed the effects of twenty-one dietary flavones employing three Loop 1-type GUSs of different taxonomic origins, which were considered to be the main GUSs involved in deglucuronidation of small molecules, on p-nitrophenyl-β-D-glucuronide hydrolysis and a structure-activity relationship is preliminarily proposed based on both in vitro assays and a docking study with representative compounds. EcoGUS and Staphylococcus pasteuri GUS showed largely similar inhibition propensities with potencies positively correlating with the total hydroxyl groups and those at ring B of flavones, while docking results revealed strong interactions developed via ring A and/or C. Streptococcus agalactiae GUS (SagaGUS) exhibited distinct inhibition propensities, displaying late-onset inhibition and steep dose-response profiles with most tested compounds. The α-helix in loop 1 region of SagaGUS which causes spatial hindrance but offers a hydrophobic surface for contacting with the carbonyl group on ring C of flavones is believed to be essential for the allosteric inhibition of SagaGUS. Taken together, the study with a series of flavones revealed varied preferences for GUSs belonging to the same Loop 1-type, highlighting the necessity of adopting multi-GUSs instead of EcoGUS alone for screening broad-spectrum GUSs inhibitors or tailoring the inhibition based on specific GUS structure.