scholarly journals EukRef: phylogenetic curation of ribosomal RNA to enhance understanding of eukaryotic diversity and distribution

2018 ◽  
Author(s):  
Javier del Campo ◽  
Martin Kolisko ◽  
Vittorio Boscaro ◽  
Luciana F. Santoferrara ◽  
Ramon Massana ◽  
...  
Keyword(s):  
Sequence Data ◽  
Sequencing Data ◽  
Environmental Sequencing ◽  
Eukaryotic Diversity ◽  
Microbial Eukaryotes ◽  
Reference Databases ◽  
Environmental Sequences ◽  
Lineage Diversity

AbstractEnvironmental sequencing has greatly expanded our knowledge of micro-eukaryotic diversity and ecology by revealing previously unknown lineages and their distribution. However, the value of these data is critically dependent on the quality of the reference databases used to assign an identity to environmental sequences. Existing databases contain errors, and struggle to keep pace with rapidly changing eukaryotic taxonomy, the influx of novel diversity, and computational challenges related to assembling the high-quality alignments and trees needed for accurate characterization of lineage diversity. EukRef (eukref.org) is a community driven initiative that addresses these challenges by bringing together taxonomists with expertise spanning the complete eukaryotic tree of life and microbial ecologists that actively use environmental sequencing data for the purpose of developing reliable reference databases across the diversity of microbial eukaryotes. EukRef organizes and facilitates rigorous sequence data mining and annotation by providing protocols, guidelines and tools to do so.

scholarly journals Fig. S1 & Tables S1-S4

2021 ◽  
Author(s):  
E. De Crop
Keyword(s):  
Sequence Data ◽  
Western Palearctic ◽  
Biogeographical Regions ◽  
Biogeographic Regions ◽  
Preliminary Study ◽  
Taxonomical Classification ◽  
Taxonomical Position ◽  
Environmental Sequences ◽  
Australasian Region

Figure S1. Overview map of the biogeographical regions used for Table 1. Biogeographic regions are based on biogeographic realms (https://ecoregions2017.appspot.com/), with three major differences: Western Palearctic (Western part of the Palearctic realm), Asia (Eastern part of the Palearctic realm combined with the Indo-Malay realm), and Australasia (Australasian realm combined with the Oceanian realm). The Palearctic realm was spilt into Western Palearctic and Eastern Palearctic, Eastern Palearctic and the Indo-Malay realm form together the Asia region, and the Australasian realm is combined with the Oceania realm to form the Australasian region.Table S1. List of described Lactifluus species, together with the year of description, taxonomical classification (subgenus, section), the indication of how this taxonomical position was defined, the source(s) of this classification, and notes.Table S2. Extra information on the preliminary study of metabarcoding data of the genus Lactifluus, retrieved from the GlobalFungi website.Table S3. Overview of the results of the preliminary study of metabarcoding data of the genus Lactifluus, retrieved from the GlobalFungi website. Due to the generally shorter length and lower quality of environmental sequence data, the numbers in the table are to be considered an estimate.Table S4. List of the putative new species found in the environmental sequences. References of studies cited are given in S3.

scholarly journals Metagenomic Composition Analysis of an Ancient Sequenced Polar Bear Jawbone from Svalbard

Genes ◽  
2018 ◽  
Vol 9 (9) ◽  
pp. 445 ◽  
Author(s):  
Diogo Pratas ◽  
Morteza Hosseini ◽  
Gonçalo Grilo ◽  
Armando Pinho ◽  
Raquel Silva ◽  
...  
Keyword(s):  
Polar Bear ◽  
Modern Human ◽  
Composition Analysis ◽  
Sequencing Data ◽  
Microbial Genomes ◽  
Extant Species ◽  
Highly Sensitive ◽  
Reference Databases ◽  
Viral Sequences

The sequencing of ancient DNA samples provides a novel way to find, characterize, and distinguish exogenous genomes of endogenous targets. After sequencing, computational composition analysis enables filtering of undesired sources in the focal organism, with the purpose of improving the quality of assemblies and subsequent data analysis. More importantly, such analysis allows extinct and extant species to be identified without requiring a specific or new sequencing run. However, the identification of exogenous organisms is a complex task, given the nature and degradation of the samples, and the evident necessity of using efficient computational tools, which rely on algorithms that are both fast and highly sensitive. In this work, we relied on a fast and highly sensitive tool, FALCON-meta, which measures similarity against whole-genome reference databases, to analyse the metagenomic composition of an ancient polar bear (Ursus maritimus) jawbone fossil. The fossil was collected in Svalbard, Norway, and has an estimated age of 110,000 to 130,000 years. The FASTQ samples contained 349 GB of nonamplified shotgun sequencing data. We identified and localized, relative to the FASTQ samples, the genomes with significant similarities to reference microbial genomes, including those of viruses, bacteria, and archaea, and to fungal, mitochondrial, and plastidial sequences. Among other striking features, we found significant similarities between modern-human, some bacterial and viral sequences (contamination) and the organelle sequences of wild carrot and tomato relative to the whole samples. For each exogenous candidate, we ran a damage pattern analysis, which in addition to revealing shallow levels of damage in the plant candidates, identified the source as contamination.

Physicochemical and bacteriological characterization of hospital effluents and their impact on the environment

2019 ◽  
Author(s):  
Chem Int
Keyword(s):  
Human Health ◽  
Fecal Coliforms ◽  
Chemical Pollution ◽  
Hospital Effluents ◽  
Biological Contaminants ◽  
Almost All ◽  
Direct Discharge ◽  
Significant Chemical

Liquid effluents discharged by hospitals may contain chemical and biological contaminants whose main source is the different substances used for the treatment of patients. This type of rejection can present a sanitary potentially dangerous risk for human health and can provoke a strong degradation of diverse environmental compartments mainly water and soils. The present study focuses on the quality of the liquid effluents of Hassani Abdelkader’s hospital of Sidi Bel-Abbes (West of Algeria). The results reveal a significant chemical pollution (COD: 879 mgO2/L, BOD5: 850 mgO2/L, NH4+ : 47.9 mg/l, NO2- : 4.2 mg/l, NO3- : 56.8 mg/l with respect to WHO standard of 90 mgO2/L, 30 mgO2/L, 0.5 mg/l, 1 mg/l and 1 mg/l respectively). However, these effluents are biodegradable since the ratio COD/BOD5 do not exceeded the value of 2 in almost all samples. The presence of pathogen germs is put into evidence such as pseudomonas, the clostridium, the staphylococcus, the fecal coliforms and fecal streptococcus. These results show that the direct discharge of these effluents constitutes a major threat to human health and the environment.

scholarly journals Comparative genomics reveals new functional insights in uncultured MAST species

2021 ◽  
Author(s):  
Aurelie Labarre ◽  
David López-Escardó ◽  
Francisco Latorre ◽  
Guy Leonard ◽  
François Bucchini ◽  
...  
Keyword(s):  
Energy Metabolism ◽  
Genomic Data ◽  
Proton Pumps ◽  
Functional Annotations ◽  
The Core ◽  
Unicellular Eukaryotes ◽  
Microbial Eukaryotes ◽  
Core Energy ◽  
Marine Surface ◽  
Environmental Sequences

AbstractHeterotrophic lineages of stramenopiles exhibit enormous diversity in morphology, lifestyle, and habitat. Among them, the marine stramenopiles (MASTs) represent numerous independent lineages that are only known from environmental sequences retrieved from marine samples. The core energy metabolism characterizing these unicellular eukaryotes is poorly understood. Here, we used single-cell genomics to retrieve, annotate, and compare the genomes of 15 MAST species, obtained by coassembling sequences from 140 individual cells sampled from the marine surface plankton. Functional annotations from their gene repertoires are compatible with all of them being phagocytotic. The unique presence of rhodopsin genes in MAST species, together with their widespread expression in oceanic waters, supports the idea that MASTs may be capable of using sunlight to thrive in the photic ocean. Additional subsets of genes used in phagocytosis, such as proton pumps for vacuole acidification and peptidases for prey digestion, did not reveal particular trends in MAST genomes as compared with nonphagocytotic stramenopiles, except a larger presence and diversity of V-PPase genes. Our analysis reflects the complexity of phagocytosis machinery in microbial eukaryotes, which contrasts with the well-defined set of genes for photosynthesis. These new genomic data provide the essential framework to study ecophysiology of uncultured species and to gain better understanding of the function of rhodopsins and related carotenoids in stramenopiles.

scholarly journals Proteomic Advances in Milk and Dairy Products

Molecules ◽  
2021 ◽  
Vol 26 (13) ◽  
pp. 3832
Author(s):  
Rubén Agregán ◽  
Noemí Echegaray ◽  
María López-Pedrouso ◽  
Radwan Kharabsheh ◽  
Daniel Franco ◽  
...  
Keyword(s):  
Dairy Products ◽  
Two Dimensional Gel Electrophoresis ◽  
Vast Number ◽  
Post Translational Modifications ◽  
Fundamental Parameters ◽  
Complex Fluid ◽  
Proteins And Peptides ◽  
Milk And Dairy Products

Proteomics is a new area of study that in recent decades has provided great advances in the field of medicine. However, its enormous potential for the study of proteomes makes it also applicable to other areas of science. Milk is a highly heterogeneous and complex fluid, where there are numerous genetic variants and isoforms with post-translational modifications (PTMs). Due to the vast number of proteins and peptides existing in its matrix, proteomics is presented as a powerful tool for the characterization of milk samples and their products. The technology developed to date for the separation and characterization of the milk proteome, such as two-dimensional gel electrophoresis (2DE) technology and especially mass spectrometry (MS) have allowed an exhaustive characterization of the proteins and peptides present in milk and dairy products with enormous applications in the industry for the control of fundamental parameters, such as microbiological safety, the guarantee of authenticity, or the control of the transformations carried out, aimed to increase the quality of the final product.

scholarly journals Physicochemical Characterization Cascade of Nanoadjuvant–Antigen Systems for Improving Vaccines

Vaccines ◽  
2021 ◽  
Vol 9 (6) ◽  
pp. 544
Author(s):  
Giuditta Guerrini ◽  
Antonio Vivi ◽  
Sabrina Gioria ◽  
Jessica Ponti ◽  
Davide Magrì ◽  
...  
Keyword(s):  
Immune Response ◽  
Protein Structure ◽  
Physicochemical Properties ◽  
Physicochemical Characterization ◽  
Protein Antigen ◽  
Efficacy And Safety

Adjuvants have been used for decades to enhance the immune response to vaccines, in particular for the subunit-based adjuvants. Physicochemical properties of the adjuvant-protein antigen complexes, such as size, morphology, protein structure and binding, influence the overall efficacy and safety of the vaccine. Here we show how to perform an accurate physicochemical characterization of the nanoaluminum–ovalbumin complex. Using a combination of existing techniques, we developed a multi-staged characterization strategy based on measurements of increased complexity. This characterization cascade has the advantage of being very flexible and easily adaptable to any adjuvant-protein antigen combinations. It will contribute to control the quality of antigen–adjuvant complexes and immunological outcomes, ultimately leading to improved vaccines.

scholarly journals Gut microbiota profiles and characterization of cultivable fungal isolates in IBS patients

2021 ◽  
Author(s):  
Piero Sciavilla ◽  
Francesco Strati ◽  
Monica Di Paola ◽  
Monica Modesto ◽  
Francesco Vitali ◽  
...  
Keyword(s):  
Candida Albicans ◽  
Gut Microbiota ◽  
Healthy Subjects ◽  
Fungal Isolates ◽  
Key Points ◽  
Health Promoting ◽  
Irritable Bowel

Abstract Studies so far conducted on irritable bowel syndrome (IBS) have been focused mainly on the role of gut bacterial dysbiosis in modulating the intestinal permeability, inflammation, and motility, with consequences on the quality of life. Limited evidences showed a potential involvement of gut fungal communities. Here, the gut bacterial and fungal microbiota of a cohort of IBS patients have been characterized and compared with that of healthy subjects (HS). The IBS microbial community structure differed significantly compared to HS. In particular, we observed an enrichment of bacterial taxa involved in gut inflammation, such as Enterobacteriaceae, Streptococcus, Fusobacteria, Gemella, and Rothia, as well as depletion of health-promoting bacterial genera, such as Roseburia and Faecalibacterium. Gut microbial profiles in IBS patients differed also in accordance with constipation. Sequence analysis of the gut mycobiota showed enrichment of Saccharomycetes in IBS. Culturomics analysis of fungal isolates from feces showed enrichment of Candida spp. displaying from IBS a clonal expansion and a distinct genotypic profiles and different phenotypical features when compared to HS of Candida albicans isolates. Alongside the well-characterized gut bacterial dysbiosis in IBS, this study shed light on a yet poorly explored fungal component of the intestinal ecosystem, the gut mycobiota. Our results showed a differential fungal community in IBS compared to HS, suggesting potential for new insights on the involvement of the gut mycobiota in IBS. Key points • Comparison of gut microbiota and mycobiota between IBS and healthy subjects • Investigation of cultivable fungi in IBS and healthy subjects • Candida albicans isolates result more virulent in IBS subjects compared to healthy subjects

scholarly journals A Methodology Based on FT-IR Data Combined with Random Forest Model to Generate Spectralprints for the Characterization of High-Quality Vinegars

Foods ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 1411
Author(s):  
José Luis P. Calle ◽  
Marta Ferreiro-González ◽  
Ana Ruiz-Rodríguez ◽  
Gerardo F. Barbero ◽  
José Á. Álvarez ◽  
...  
Keyword(s):  
Random Forest ◽  
Raw Materials ◽  
Principal Component ◽  
Hierarchical Cluster ◽  
Raw Material ◽  
Support Vector ◽  
Protected Designation Of Origin ◽  
Ft Ir

Sherry wine vinegar is a Spanish gourmet product under Protected Designation of Origin (PDO). Before a vinegar can be labeled as Sherry vinegar, the product must meet certain requirements as established by its PDO, which, in this case, means that it has been produced following the traditional solera and criadera ageing system. The quality of the vinegar is determined by many factors such as the raw material, the acetification process or the aging system. For this reason, mainly producers, but also consumers, would benefit from the employment of effective analytical tools that allow precisely determining the origin and quality of vinegar. In the present study, a total of 48 Sherry vinegar samples manufactured from three different starting wines (Palomino Fino, Moscatel, and Pedro Ximénez wine) were analyzed by Fourier-transform infrared (FT-IR) spectroscopy. The spectroscopic data were combined with unsupervised exploratory techniques such as hierarchical cluster analysis (HCA) and principal component analysis (PCA), as well as other nonparametric supervised techniques, namely, support vector machine (SVM) and random forest (RF), for the characterization of the samples. The HCA and PCA results present a clear grouping trend of the vinegar samples according to their raw materials. SVM in combination with leave-one-out cross-validation (LOOCV) successfully classified 100% of the samples, according to the type of wine used for their production. The RF method allowed selecting the most important variables to develop the characteristic fingerprint (“spectralprint”) of the vinegar samples according to their starting wine. Furthermore, the RF model reached 100% accuracy for both LOOCV and out-of-bag (OOB) sets.

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