Search results for "taxonomic"
showing 10 items of 148 documents
Consequences of organ choice in describing bacterial pathogen assemblages in a rodent population
2017
SUMMARYHigh-throughput sequencing technologies now allow for rapid cost-effective surveys of multiple pathogens in many host species including rodents, but it is currently unclear if the organ chosen for screening influences the number and identity of bacteria detected. We used 16S rRNA amplicon sequencing to identify bacterial pathogens in the heart, liver, lungs, kidneys and spleen of 13 water voles (Arvicola terrestris) collected in Franche-Comté, France. We asked if bacterial pathogen assemblages within organs are similar and if all five organs are necessary to detect all of the bacteria present in an individual animal. We identified 24 bacteria representing 17 genera; average bacterial…
Assessing the effect of mercury pollution on cultured benthic foraminifera community using morphological and eDNA metabarcoding approaches
2018
Mercury (Hg) is a highly toxic element for living organisms and is known to bioaccumulate and biomagnify. Here, we analyze the response of benthic foraminifera communities cultured in mesocosm and exposed to different concentrations of Hg. Standard morphological analyses and environmental DNA metabarcoding show evidence that Hg pollution has detrimental effects on benthic foraminifera. The molecular analysis provides a more complete view of foraminiferal communities including the soft-walled single-chambered monothalamiids and small-sized hard-shelled rotaliids and textulariids than the morphological one. Among these taxa that are typically overlooked in morphological studies we found poten…
Two new resinicolous mycocalicioid fungi from the Acadian Forest: One new to science, the other new to North America
2016
Abstract Chaenothecopsis claydenii is described as new from New Brunswick, Canada, and C. eugenia, also from New Brunswick, is reported for the first time in North America. Both species grow on the resin of Picea spp. in the Acadian Forest and bring to 91 the number of calicioid lichens and fungi known for the ecoregion. Diagnoses and information on the taxonomy and ecology of each species is provided, as is a worldwide key to the mycocalicioid taxa growing on conifer resin.
Accelerating metagenomic read classification on CUDA-enabled GPUs.
2016
Metagenomic sequencing studies are becoming increasingly popular with prominent examples including the sequencing of human microbiomes and diverse environments. A fundamental computational problem in this context is read classification; i.e. the assignment of each read to a taxonomic label. Due to the large number of reads produced by modern high-throughput sequencing technologies and the rapidly increasing number of available reference genomes software tools for fast and accurate metagenomic read classification are urgently needed. We present cuCLARK, a read-level classifier for CUDA-enabled GPUs, based on the fast and accurate classification of metagenomic sequences using reduced k-mers (…
Taxonomic Classification for Living Organisms Using Convolutional Neural Networks
2017
Taxonomic classification has a wide-range of applications such as finding out more about evolutionary history. Compared to the estimated number of organisms that nature harbors, humanity does not have a thorough comprehension of to which specific classes they belong. The classification of living organisms can be done in many machine learning techniques. However, in this study, this is performed using convolutional neural networks. Moreover, a DNA encoding technique is incorporated in the algorithm to increase performance and avoid misclassifications. The algorithm proposed outperformed the state of the art algorithms in terms of accuracy and sensitivity, which illustrates a high potential f…
Active and secreted IgA-coated bacterial fractions from the human gut reveal an under-represented microbiota core
2013
AbstractHost-associated microbiota varies in distribution depending on the body area inhabited. Gut microbes are known to interact with the human immune system, maintaining gut homoeostasis. Thus, we studied whether secreted-IgA (S-IgA) coat specific microbial taxa without inducing strong immune responses. To do so, we fractionated gut microbiota by flow cytometry. We found that active and S-IgA-coated bacterial fractions were characterized by a higher diversity than those observed in raw faecal suspensions. A long-tail effect was observed in family distribution, revealing that rare bacteria represent up to 20% of total diversity. While Firmicutes was the most abundant phylum, the majority …
Advances in the knowledge of South African Riella (Sphaerocarpales) and a new endemic species, Riella trigonospora
2014
Cultures of soil sediments collected in June 2012 from saltpans and vleis from five South African localities have revealed two new, geographically distant, populations of the endemic Riella alatospora, confirmed the presence of Riella purpureospora from Blouvlei in the Cape Town area and uncovered a new endemic species, Riella trigonospora. The new species obtained from cultures from five sampled localities is described and illustrated. It is dioicous and characterised by acuminate to rostrate, papillose involucres and by a unique spore morphology. The spores are dark purple, as in R. purpureospora, and have an irregular discontinuous wing at the equatorial plane, which suggests a morpholog…
Preservation and decay of plant remains in two Palaeolithic sites: Abrigo de la Quebrada and Cova de les Cendres (Eastern Spain). What information ca…
2020
Abstract Plant remains are quickly affected by post-depositional processes once they are deposited in archaeological sites. In normal conditions, decomposing organisms cause their decay and final disappearance unless a preservation agent, as carbonisation or mineralisation, inhibit their activity. Moreover, physical and chemical processes could also lead to the partial or total destruction of the archaeobotanical assemblage. Thus, an analysis of their characteristics is useful for an assessing of the taphonomic processes. Archaeobotanical assemblages from two Palaeolithic sites, Abrigo de la Quebrada and Cova de les Cendres, have been analysed in terms of taxonomic composition of the assemb…
Determinants and Congruence of Species Richness Patterns across Multiple Taxonomic Groups on a Regional Scale
2012
Applying multiple generalized regression models, we studied spatial patterns in species richness for different taxonomic groups (amphibians, reptiles, grasshoppers, plants, mosses) within the German federal state Rhineland-Palatinate (RP). We aimed (1) to detect their centres of richness, (2) to rate the influence of climatic and land-use parameters on spatial patterns, and (3) to test whether patterns are congruent between taxonomic groups in RP. Centres of species richness differed between taxonomic groups and overall richness was the highest in the valleys of large rivers and in different areas of southern RP. Climatic parameters strongly correlated with richness in all taxa whereas land…