scholarly journals Emerging Parasitic Protists: The Case of Perkinsea

2022 ◽  
Vol 12 ◽  
Author(s):  
Sarah Itoïz ◽  
Sebastian Metz ◽  
Evelyne Derelle ◽  
Albert Reñé ◽  
Esther Garcés ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Infectious Agent ◽  
Disease Emergence ◽  
Ecological Traits ◽  
Host Preferences ◽  
Wide Range ◽  
Permanent Loss ◽  
Negative Impacts ◽  
Environmental Sequences ◽  
Freshwater Environments

The last century has witnessed an increasing rate of new disease emergence across the world leading to permanent loss of biodiversity. Perkinsea is a microeukaryotic parasitic phylum composed of four main lineages of parasitic protists with broad host ranges. Some of them represent major ecological and economical threats because of their geographically invasive ability and pathogenicity (leading to mortality events). In marine environments, three lineages are currently described, the Parviluciferaceae, the Perkinsidae, and the Xcellidae, infecting, respectively, dinoflagellates, mollusks, and fish. In contrast, only one lineage is officially described in freshwater environments: the severe Perkinsea infectious agent infecting frog tadpoles. The advent of high-throughput sequencing methods, mainly based on 18S rRNA assays, showed that Perkinsea is far more diverse than the previously four described lineages especially in freshwater environments. Indeed, some lineages could be parasites of green microalgae, but a formal nature of the interaction needs to be explored. Hence, to date, most of the newly described aquatic clusters are only defined by their environmental sequences and are still not (yet) associated with any host. The unveiling of this microbial black box presents a multitude of research challenges to understand their ecological roles and ultimately to prevent their most negative impacts. This review summarizes the biological and ecological traits of Perkinsea—their diversity, life cycle, host preferences, pathogenicity, and highlights their diversity and ubiquity in association with a wide range of hosts.

scholarly journals Validation and standardization of DNA extraction and library construction methods for metagenomics-based human fecal microbiome measurements

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Dieter M. Tourlousse ◽  
Koji Narita ◽  
Takamasa Miura ◽  
Mitsuo Sakamoto ◽  
Akiko Ohashi ◽  
...  
Keyword(s):  
Dna Extraction ◽  
High Throughput Sequencing ◽  
Performance Metrics ◽  
Collaborative Study ◽  
Human Microbiome ◽  
Second Phase ◽  
Intermediate Precision ◽  
Fecal Microbiome ◽  
Library Construction ◽  
Wide Range

Abstract Background Validation and standardization of methodologies for microbial community measurements by high-throughput sequencing are needed to support human microbiome research and its industrialization. This study set out to establish standards-based solutions to improve the accuracy and reproducibility of metagenomics-based microbiome profiling of human fecal samples. Results In the first phase, we performed a head-to-head comparison of a wide range of protocols for DNA extraction and sequencing library construction using defined mock communities, to identify performant protocols and pinpoint sources of inaccuracy in quantification. In the second phase, we validated performant protocols with respect to their variability of measurement results within a single laboratory (that is, intermediate precision) as well as interlaboratory transferability and reproducibility through an industry-based collaborative study. We further ascertained the performance of our recommended protocols in the context of a community-wide interlaboratory study (that is, the MOSAIC Standards Challenge). Finally, we defined performance metrics to provide best practice guidance for improving measurement consistency across methods and laboratories. Conclusions The validated protocols and methodological guidance for DNA extraction and library construction provided in this study expand current best practices for metagenomic analyses of human fecal microbiota. Uptake of our protocols and guidelines will improve the accuracy and comparability of metagenomics-based studies of the human microbiome, thereby facilitating development and commercialization of human microbiome-based products.

ASSESSING ENVIRONMENTAL IMPACTS DURING NATURAL DISASTER: THE DEVELOPMENT OF A RAPID ENVIRONMENTAL ASSESSMENT METHODOLOGY

2002 ◽  
Vol 04 (04) ◽  
pp. 475-492 ◽  
Author(s):  
CHARLES KELLY
Keyword(s):  
Environmental Impact ◽  
Impact Assessment ◽  
Environmental Impact Assessment ◽  
Environmental Conditions ◽  
Environmental Damage ◽  
Assessment Procedure ◽  
Disaster Victims ◽  
Wide Range ◽  
Negative Impacts ◽  
The Impact

The linkages between disaster and environmental damage are recognized as important to predicting, preventing and mitigating the impact of disasters. Environmental Impact Assessment (EIA) procedures are well developed for non-ndisaster situations. However, they are conceptually and operationally inappropriate for use in disaster conditions, particularly in the first 120 days after the disaster has begun. The paper provides a conceptual overview of the requirements for an environmental impact assessment procedure appropriate for disaster conditions. These requirements are captured in guidelines for a Rapid Environmental Impact Assessment (REA) for use in disasters. The REA guides the collection and assessment of a wide range of factors which can indicate: (1) the negative impacts of a disaster on the environment, (2) the impacts of environmental conditions on the magnitude of a disaster and, (3) the positive or negative impacts of relief efforts on environmental conditions. The REA also provides a foundation for recovery program EIAs, thus improving the overall post disaster recovery process. The REA is designed primarily for relief cadres, but is also expected to be usable as an assessment tool with disaster victims. The paper discusses the field testing of the REA under actual disaster conditions.

scholarly journals Growth of Thermophilic and Hyperthermophilic Fe(III)-Reducing Microorganisms on a Ferruginous Smectite as the Sole Electron Acceptor

2007 ◽  
Vol 74 (1) ◽  
pp. 251-258 ◽  
Author(s):  
Kazem Kashefi ◽  
Evgenya S. Shelobolina ◽  
W. Crawford Elliott ◽  
Derek R. Lovley
Keyword(s):  
Electron Acceptor ◽  
Major Element ◽  
Solid Phase ◽  
Active Role ◽  
Sedimentary Environments ◽  
Major Element Chemistry ◽  
Wide Range ◽  
Structural Iron ◽  
Ferruginous Smectite ◽  
Freshwater Environments

ABSTRACT Recent studies have suggested that the structural Fe(III) within phyllosilicate minerals, including smectite and illite, is an important electron acceptor for Fe(III)-reducing microorganisms in sedimentary environments at moderate temperatures. The reduction of structural Fe(III) by thermophiles, however, has not previously been described. A wide range of thermophilic and hyperthermophilic Archaea and Bacteria from marine and freshwater environments that are known to reduce poorly crystalline Fe(III) oxides were tested for their ability to reduce structural (octahedrally coordinated) Fe(III) in smectite (SWa-1) as the sole electron acceptor. Two out of the 10 organisms tested, Geoglobus ahangari and Geothermobacterium ferrireducens, were not able to conserve energy to support growth by reduction of Fe(III) in SWa-1 despite the fact that both organisms were originally isolated with solid-phase Fe(III) as the electron acceptor. The other organisms tested were able to grow on SWa-1 and reduced 6.3 to 15.1% of the Fe(III). This is 20 to 50% less than the reported amounts of Fe(III) reduced in the same smectite (SWa-1) by mesophilic Fe(III) reducers. Two organisms, Geothermobacter ehrlichii and archaeal strain 140, produced copious amounts of an exopolysaccharide material, which may have played an active role in the dissolution of the structural iron in SWa-1 smectite. The reduction of structural Fe(III) in SWa-1 by archaeal strain 140 was studied in detail. Microbial Fe(III) reduction was accompanied by an increase in interlayer and octahedral charges and some incorporation of potassium and magnesium into the smectite structure. However, these changes in the major element chemistry of SWa-1 smectite did not result in the formation of an illite-like structure, as reported for a mesophilic Fe(III) reducer. These results suggest that thermophilic Fe(III)-reducing organisms differ in their ability to reduce and solubilize structural Fe(III) in SWa-1 smectite and that SWa-1 is not easily transformed to illite by these organisms.

scholarly journals Reviewing Effective Factors of Alimentary Deficiency in Animals Reproductive Functions

2021 ◽  
Vol 11 (2) ◽  
pp. 157-169
Author(s):  
Pavlo Skliarov ◽  
Serhiy Fedorenko ◽  
Svitlana Naumenko ◽  
Oleksandr Onyshchenko ◽  
Alina Pasternak ◽  
...  
Keyword(s):  
Reproductive Function ◽  
Optimal Level ◽  
The Body ◽  
Reproductive Capacity ◽  
Toxic Substances ◽  
Prevention Measures ◽  
Animal Reproduction ◽  
Number Of Factors ◽  
Wide Range ◽  
Negative Impacts

Animal reproduction is one of the main factors limiting the efficiency of livestock production. Its optimal level is possibly achieved when certain conditions are created for animals. As reproduction is a complex reflex process depending on neuroendocrine regulatory mechanisms, the character and strength of stimuli, which, in turn, is due to a number of factors. Under normal conditions, the body of animals is affected by many different factors, which are appropriately transformed and specified by positive or negative reactions. Inhibitory factors include air pool, saturated with harmful substances and gases, ionizing radiation, poor water quality along with altered redox properties, hypokinesia combined with poor unbalanced feeding, systematic chronic stress, presence of toxic substances in feed, and the deficiency of vitamins and other bioantioxidants in feed or their excessive spending. Of the wide range of genetic and paratypic factors of negative impacts on reproductive capacity, the most common one is alimentary, which causes impaired reproductive function due to deficiencies in the rules, regulations, and feeding regime of animals. In particular, the alimentary can be associated with both general malnutrition (starvation) and overfeeding (obesity). However, the alimentary form of infertility mostly occurs due to low-quality diets when the diet lacks vital components (mainly vitamins, macro-, and micronutrients) or the quantitative ratios of the ingredients are violated. This is possible even if the total nutritional value of the diet meets the established requirements for the physiological needs of the body. Vitamins, micro-, and macronutrients are ecologically deficient factors of disturbance of animal reproductive function, the influence of which is observed on all processes of reproduction, from fertilization to the postpartum period and the preservation of young animals. The pathogenesis of their insufficiency is associated with the violation of steroido-, gameto-, and embryogenesis and the emergence of ante-, intra-, neo- and postnatal pathologies, respectively. Therefore, treatments and prevention measures should be aimed at providing animals with biologically complete balanced feeding and replenishment of the body with vitamins and minerals. However, all these issues remain incompletely studied and need further research.

ViDiT–CACTUS: an inexpensive and versatile library preparation and sequence analysis method for virus discovery and other microbiology applications

2018 ◽  
Vol 64 (10) ◽  
pp. 761-773 ◽  
Author(s):  
Joost T.P. Verhoeven ◽  
Marta Canuti ◽  
Hannah J. Munro ◽  
Suzanne C. Dufour ◽  
Andrew S. Lang
Keyword(s):  
Influenza A ◽  
High Throughput Sequencing ◽  
Low Cost ◽  
Quality Data ◽  
Library Preparation ◽  
Virus Discovery ◽  
Influenza A Viruses ◽  
Wide Range ◽  
Functional Profiling ◽  
Biology Laboratory

High-throughput sequencing (HTS) technologies are becoming increasingly important within microbiology research, but aspects of library preparation, such as high cost per sample or strict input requirements, make HTS difficult to implement in some niche applications and for research groups on a budget. To answer these necessities, we developed ViDiT, a customizable, PCR-based, extremely low-cost (less than US$5 per sample), and versatile library preparation method, and CACTUS, an analysis pipeline designed to rely on cloud computing power to generate high-quality data from ViDiT-based experiments without the need of expensive servers. We demonstrate here the versatility and utility of these methods within three fields of microbiology: virus discovery, amplicon-based viral genome sequencing, and microbiome profiling. ViDiT–CACTUS allowed the identification of viral fragments from 25 different viral families from 36 oropharyngeal–cloacal swabs collected from wild birds, the sequencing of three almost complete genomes of avian influenza A viruses (>90% coverage), and the characterization and functional profiling of the complete microbial diversity (bacteria, archaea, viruses) within a deep-sea carnivorous sponge. ViDiT–CACTUS demonstrated its validity in a wide range of microbiology applications, and its simplicity and modularity make it easily implementable in any molecular biology laboratory, towards various research goals.

scholarly journals Climate structuring of Batrachochytrium dendrobatidis infection in the threatened amphibians of the northern Western Ghats, India

2018 ◽  
Vol 5 (6) ◽  
pp. 180211 ◽  
Author(s):  
Christopher J. Thorpe ◽  
Todd R. Lewis ◽  
Matthew C. Fisher ◽  
Claudia J. Wierzbicki ◽  
Siddharth Kulkarni ◽  
...  
Keyword(s):  
Western Ghats ◽  
Batrachochytrium Dendrobatidis ◽  
Coastal Region ◽  
First Record ◽  
Climatic Conditions ◽  
Ecological Traits ◽  
Temperature Changes ◽  
Reverse Pattern ◽  
Wide Range ◽  
The Western Ghats

Batrachochytrium dendrobatidis ( Bd ) is a pathogen killing amphibians worldwide. Its impact across much of Asia is poorly characterized. This study systematically surveyed amphibians for Bd across rocky plateaus in the northern section of the Western Ghats biodiversity hotspot, India, including the first surveys of the plateaus in the coastal region. These ecosystems offer an epidemiological model system since they are characterized by differing levels of connectivity, edaphic and climatic conditions, and anthropogenic stressors. One hundred and eighteen individuals of 21 species of Anura and Apoda on 13 plateaus ranging from 67 to 1179 m above sea level and 15.89 to 17.92° North latitude were sampled. Using qPCR protocols, 79% of species and 27% of individuals tested were positive for Bd . This is the first record of Bd in caecilians in India, the Critically Endangered Xanthophryne tigerina and Endangered Fejervarya cf. sahyadris . Mean site prevalence was 28.15%. Prevalence below the escarpment was 31.2% and 25.4% above. The intensity of infection (GE) showed the reverse pattern. Infection may be related to elevational temperature changes, thermal exclusion, inter-site connectivity and anthropogenic disturbance. Coastal plateaus may be thermal refuges from Bd . Infected amphibians represented a wide range of ecological traits posing interesting questions about transmission routes.

scholarly journals Diat.barcode, an open-access curated barcode library for diatoms

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Frédéric Rimet ◽  
Evgenuy Gusev ◽  
Maria Kahlert ◽  
Martyn G. Kelly ◽  
Maxim Kulikovskiy ◽  
...  
Keyword(s):  
Open Access ◽  
Aquatic Ecosystems ◽  
High Throughput Sequencing ◽  
Lower Cost ◽  
Sequencing Data ◽  
Reference Library ◽  
Culture Collections ◽  
Nucleotide Database ◽  
Environmental Sequences ◽  
Level Identification

Abstract Diatoms (Bacillariophyta) are ubiquitous microalgae which produce a siliceous exoskeleton and which make a major contribution to the productivity of oceans and freshwaters. They display a huge diversity, which makes them excellent ecological indicators of aquatic ecosystems. Usually, diatoms are identified using characteristics of their exoskeleton morphology. DNA-barcoding is an alternative to this and the use of High-Throughput-Sequencing enables the rapid analysis of many environmental samples at a lower cost than analyses under microscope. However, to identify environmental sequences correctly, an expertly curated reference library is needed. Several curated libraries for protists exists; none, however are dedicated to diatoms. Diat.barcode is an open-access library dedicated to diatoms which has been maintained since 2012. Data come from two sources (1) the NCBI nucleotide database and (2) unpublished sequencing data of culture collections. Since 2017, several experts have collaborated to curate this library for rbcL, a chloroplast marker suitable for species-level identification of diatoms. For the latest version of the database (version 7), 605 of the 3482 taxonomical names originally assigned by the authors of the rbcL sequences were modified after curation. The database is accessible at https://www6.inra.fr/carrtel-collection_eng/Barcoding-database.

scholarly journals The Views of the UK Public Towards Routine Neutering of Dogs and Cats

Animals ◽  
2019 ◽  
Vol 9 (4) ◽  
pp. 138 ◽  
Author(s):  
Chanakarn Wongsaengchan ◽  
Dorothy McKeegan
Keyword(s):  
Animal Welfare ◽  
Linear Model ◽  
Policy Making ◽  
General Linear Model ◽  
Male And Female ◽  
Wide Range ◽  
Negative Impacts ◽  
Future Policy ◽  
The Uk ◽  
Level Of Agreement

Despite being routinely recommended by veterinarians, neutering of dogs and cats has both positive and negative impacts on animal welfare and is ethically problematic. We examined attitudes of a sample of the UK public towards routine neutering of dogs and cats using a questionnaire. Respondents indicated their level of agreement with statements describing welfare and ethical reasons ‘for’ and ‘against’ the neutering of male and female dogs and cats. We conducted a general linear model (GLM) analysis to investigate the effects of demographic factors on agreement scores. Respondents (n = 451) expressed views both supporting and opposing neutering. The predominant view (>80%) supported neutering, justified primarily by prevention of unwanted offspring and reproductive diseases. Around 10% of the respondents disagreed and felt that neutering should only be done for medical reasons. Men were less likely than women to support neutering (p < 0.001). Those with meat reduction diets were more likely to be against neutering (p < 0.05) and cat owners supported neutering more than non-cat owners (p < 0.05). Although the data reflected a wide range of ethical views, our findings show that the UK public generally supports the routine neutering of dogs and cats. This insight has implications for future policy-making and compliance with veterinary advice.

scholarly journals Characterization of Stool Virome in Children Newly Diagnosed With Moderate to Severe Ulcerative Colitis

2019 ◽  
Vol 25 (10) ◽  
pp. 1656-1662 ◽  
Author(s):  
Rafal Tokarz ◽  
Jeffrey S Hyams ◽  
David R Mack ◽  
Brendan Boyle ◽  
Anne M Griffiths ◽  
...  
Keyword(s):  
Ulcerative Colitis ◽  
High Throughput Sequencing ◽  
Viral Infections ◽  
Control Group ◽  
Newly Diagnosed ◽  
Control Cohort ◽  
Fecal Samples ◽  
Wide Range ◽  
Irritable Bowel

Abstract Background Viral infections have been suggested as possible triggers for the onset of ulcerative colitis (UC). Methods We employed VirCapSeq-Vert, a high-throughput sequencing virus capture platform, to examine the stool virome of children with newly diagnosed moderate to severe UC. We surveyed fecal samples collected at presentation, after symptom remission, and from a control group diagnosed with irritable bowel syndrome. Results Seventy subjects with UC (mean age 13 years, 45 had moderate symptoms, 25 had severe, 69 of 70 had a Mayo endoscopy subscore 2/3) were studied. We detected a wide range of animal viruses that were taxonomically classified into 12 viral families. A virus was present in 50% of fecal samples collected at presentation, 41% of samples collected after remission, and 40% of samples in our control group. The most frequently identified viruses were diet-based gyroviruses. The UC cohort had a significantly higher prevalence of anelloviruses compared with the control cohort. However, we did not identify a single virus that can be implicated in the onset of UC and did not find an association between UC disease severity and viral presence. Conclusion Presence of virus in stool was not associated with the onset of pediatric UC.

scholarly journals Wild specimens of sand fly phlebotomine Lutzomyia evansi, vector of leishmaniasis, show high abundance of Methylobacterium and natural carriage of Wolbachia and Cardinium types in the midgut microbiome

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Rafael J. Vivero ◽  
Marcela Villegas-Plazas ◽  
Gloria E. Cadavid-Restrepo ◽  
Claudia Ximena Moreno Herrera ◽  
Sandra I. Uribe ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
High Throughput Sequencing ◽  
Sand Fly ◽  
Human Populations ◽  
Rrna Gene ◽  
Remarkable Feature ◽  
Core Microbiome ◽  
Bacterial Phyla ◽  
Wide Range

AbstractPhlebotomine sand flies are remarkable vectors of several etiologic agents (virus, bacterial, trypanosomatid Leishmania), posing a heavy health burden for human populations mainly located at developing countries. Their intestinal microbiota is involved in a wide range of biological and physiological processes, and could exclude or facilitate such transmission of pathogens. In this study, we investigated the Eubacterial microbiome from digestive tracts of Lu. evansi adults structure using 16S rRNA gene sequence amplicon high throughput sequencing (Illumina MiSeq) obtained from digestive tracts of Lu. evansi adults. The samples were collected at two locations with high incidence of the disease in humans: peri-urban and forest ecosystems from the department of Sucre, Colombia. 289,068 quality-filtered reads of V4 region of 16S rRNA gene were obtained and clustered into 1,762 operational taxonomic units (OTUs) with 97% similarity. Regarding eubacterial diversity, 14 bacterial phyla and 2 new candidate phyla were found to be consistently associated with the gut microbiome content. Proteobacteria, Firmicutes, and Bacteroidetes were the most abundant phyla in all the samples and the core microbiome was particularly dominated by Methylobacterium genus. Methylobacterium species, are known to have mutualistic relationships with some plants and are involved in shaping the microbial community in the phyllosphere. As a remarkable feature, OTUs classified as Wolbachia spp. were found abundant on peri-urban ecosystem samples, in adult male (OTUs n = 776) and unfed female (OTUs n = 324). Furthermore, our results provide evidence of OTUs classified as Cardinium endosymbiont in relative abundance, notably higher with respect to Wolbachia. The variation in insect gut microbiota may be determined by the environment as also for the type of feeding. Our findings increase the richness of the microbiota associated with Lu. evansi. In this study, OTUs of Methylobacterium found in Lu. evansi was higher in engorged females, suggesting that there are interactions between microbes from plant sources, blood nutrients and the parasites they transmit during the blood intake.

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