scholarly journals On a Non-Discrete Concept of Prokaryotic Species

2020 ◽  
Vol 8 (11) ◽  
pp. 1723
Author(s):  
Juan M. Gonzalez ◽  
Elena Puerta-Fernández ◽  
Margarida M. Santana ◽  
Bhagwan Rekadwad
Keyword(s):  
Species Concept ◽  
Current Knowledge ◽  
Sequencing Technologies ◽  
Prokaryotic Diversity ◽  
Eukaryotic Microorganisms ◽  
Prokaryotic Species ◽  
Genome Features ◽  
Taxonomic Concept ◽  
Discrete Values ◽  
Continuous Concept

The taxonomic concept of species has received continuous attention. A microbial species as a discrete box contains a limited number of highly similar microorganisms assigned to that taxon, following a polyphasic approach. In the 21st Century, with the advancements of sequencing technologies and genomics, the existence of a huge prokaryotic diversity has become well known. At present, the prokaryotic species might no longer have to be understood as discrete values (such as 1 or 2, by homology to Natural numbers); rather, it is expected that some microorganisms could be potentially distributed (according to their genome features and phenotypes) in between others (such as decimal numbers between 1 and 2; real numbers). We propose a continuous species concept for microorganisms, which adapts to the current knowledge on the huge diversity, variability and heterogeneity existing among bacteria and archaea. Likely, this concept could be extended to eukaryotic microorganisms. The continuous species concept considers a species to be delimited by the distance between a range of variable features following a Gaussian-type distribution around a reference organism (i.e., its type strain). Some potential pros and cons of a continuous concept are commented on, offering novel perspectives on our understanding of the highly diversified prokaryotic world, thus promoting discussion and further investigation in the field.

Molecular Genetics of Early- and Late-Onset Alzheimer’s Disease

2020 ◽  
Vol 20 ◽  
Author(s):  
Md. Sahab Uddin ◽  
Sharifa Hasana ◽  
Md. Farhad Hossain ◽  
Md. Siddiqul Islam ◽  
Tapan Behl ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Massively Parallel Sequencing ◽  
Late Onset ◽  
Current Knowledge ◽  
The Elderly ◽  
Apoe Ε4 ◽  
Sequencing Technologies ◽  
Genetic Components ◽  
Ε4 Allele

: Alzheimer’s disease (AD) is the most common form of dementia in the elderly and this complex disorder is associated with environmental as well as genetic components. Early-onset AD (EOAD) and late-onset AD (LOAD, more common) are major identified types of AD. The genetics of EOAD is extensively understood with three genes variants such as APP, PSEN1, and PSEN2 leading to disease. On the other hand, some common alleles including APOE are effectively associated with LOAD identified but the genetics of LOAD is not clear to date. It has been accounted that about 5% to 10% of EOAD patients can be explained through mutations in the three familiar genes of EOAD. The APOE ε4 allele augmented the severity of EOAD risk in carriers, and APOE ε4 allele was considered as a hallmark of EOAD. A great number of EOAD patients, who are not genetically explained, indicate that it is not possible to identify disease- triggering genes yet. Although several genes have been identified through using the technology of next-generation sequencing in EOAD families including SORL1, TYROBP, and NOTCH3. A number of TYROBP variants were identified through exome sequencing in EOAD patients and these TYROBP variants may increase the pathogenesis of EOAD. The existence of ε4 allele is responsible for increasing the severity of EOAD. However, several ε4 allele carriers live into their 90s that propose the presence of other LOAD genetic as well as environmental risk factors that are not identified yet. It is urgent to find out missing genetics of EOAD and LOAD etiology to discover new potential genetics facets which will assist to understand the pathological mechanism of AD. These investigations should contribute to developing a new therapeutic candidate for alleviating, reversing and preventing AD. This article based on current knowledge represents the overview of the susceptible genes of EOAD, and LOAD. Next, we represent the probable molecular mechanism which might elucidate the genetic etiology of AD and highlight the role of massively parallel sequencing technologies for novel gene discoveries.

scholarly journals A Deep Dive into Genome Assemblies of Non-vertebrate Animals

2021 ◽  
Author(s):  
Nadège Guiglielmoni ◽  
Ramón Rivera-Vicéns ◽  
Romain Koszul ◽  
Jean-François Flot
Keyword(s):  
Genome Assembly ◽  
Current Knowledge ◽  
Genome Structure ◽  
Deep Dive ◽  
Sequencing Technologies ◽  
Current State ◽  
Animal Diversity ◽  
And Function ◽  
Genome Assemblies ◽  
Genome Projects

Non-vertebrate species represent about ~95% of known metazoan (animal) diversity. They remain to this day relatively unexplored genetically, but understanding their genome structure and function is pivotal for expanding our current knowledge of evolution, ecology and biodiversity. Following the continuous improvements and decreasing costs of sequencing technologies, many genome assembly tools have been released, leading to a significant amount of genome projects being completed in recent years. In this review, we examine the current state of genome projects of non-vertebrate animal species. We present an overview of available sequencing technologies, assembly approaches, as well as pre and post-processing steps, genome assembly evaluation methods, and their application to non-vertebrate animal genomes.

scholarly journals Exploring Eimeria Genomes to Understand Population Biology: Recent Progress and Future Opportunities

Genes ◽  
2020 ◽  
Vol 11 (9) ◽  
pp. 1103
Author(s):  
Damer P. Blake ◽  
Kate Worthing ◽  
Mark C. Jenkins
Keyword(s):  
Population Biology ◽  
Production Control ◽  
Current Knowledge ◽  
Eimeria Species ◽  
Vast Number ◽  
Profit Margins ◽  
Operational Taxonomic Units ◽  
Sequencing Technologies ◽  
Live Parasite ◽  
Review Current

Eimeria, protozoan parasites from the phylum Apicomplexa, can cause the enteric disease coccidiosis in all farmed animals. Coccidiosis is commonly considered to be most significant in poultry; due in part to the vast number of chickens produced in the World each year, their short generation time, and the narrow profit margins associated with their production. Control of Eimeria has long been dominated by routine chemoprophylaxis, but has been supplemented or replaced by live parasite vaccination in a minority of production sectors. However, public and legislative demands for reduced drug use in food production is now driving dramatic change, replacing reliance on relatively indiscriminate anticoccidial drugs with vaccines that are Eimeria species-, and in some examples, strain-specific. Unfortunately, the consequences of deleterious selection on Eimeria population structure and genome evolution incurred by exposure to anticoccidial drugs or vaccines are unclear. Genome sequence assemblies were published in 2014 for all seven Eimeria species that infect chickens, stimulating the first population genetics studies for these economically important parasites. Here, we review current knowledge of eimerian genomes and highlight challenges posed by the discovery of new, genetically cryptic Eimeria operational taxonomic units (OTUs) circulating in chicken populations. As sequencing technologies evolve understanding of eimerian genomes will improve, with notable utility for studies of Eimeria biology, diversity and opportunities for control.

scholarly journals Composition and Function of Chicken Gut Microbiota

Animals ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 103 ◽  
Author(s):  
Ivan Rychlik
Keyword(s):  
Gut Microbiota ◽  
Current Knowledge ◽  
Rapid Development ◽  
Specific Model ◽  
Sequencing Technologies ◽  
Chicken Gut Microbiota ◽  
And Function ◽  
Experimental Group ◽  
Intended Use

Studies analyzing the composition of gut microbiota are quite common at present, mainly due to the rapid development of DNA sequencing technologies within the last decade. This is valid also for chickens and their gut microbiota. However, chickens represent a specific model for host–microbiota interactions since contact between parents and offspring has been completely interrupted in domesticated chickens. Nearly all studies describe microbiota of chicks from hatcheries and these chickens are considered as references and controls. In reality, such chickens represent an extreme experimental group since control chicks should be, by nature, hatched in nests in contact with the parent hen. Not properly realising this fact and utilising only 16S rRNA sequencing results means that many conclusions are of questionable biological relevance. The specifics of chicken-related gut microbiota are therefore stressed in this review together with current knowledge of the biological role of selected microbiota members. These microbiota members are then evaluated for their intended use as a form of next-generation probiotics.

scholarly journals Deep Hypersaline Anoxic Basins as Untapped Reservoir of Polyextremophilic Prokaryotes of Biotechnological Interest

Marine Drugs ◽  
2020 ◽  
Vol 18 (2) ◽  
pp. 91 ◽  
Author(s):  
Stefano Varrella ◽  
Michael Tangherlini ◽  
Cinzia Corinaldesi
Keyword(s):  
New Species ◽  
Secondary Metabolites ◽  
Deep Sea ◽  
Current Knowledge ◽  
Strong Impact ◽  
Biotechnological Applications ◽  
Prokaryotic Diversity ◽  
Anoxic Basins ◽  
Isolated Species

Deep-sea hypersaline anoxic basins (DHABs) are considered to be among the most extreme ecosystems on our planet, allowing only the life of polyextremophilic organisms. DHABs’ prokaryotes exhibit extraordinary metabolic capabilities, representing a hot topic for microbiologists and biotechnologists. These are a source of enzymes and new secondary metabolites with valuable applications in different biotechnological fields. Here, we review the current knowledge on prokaryotic diversity in DHABs, highlighting the biotechnological applications of identified taxa and isolated species. The discovery of new species and molecules from these ecosystems is expanding our understanding of life limits and is expected to have a strong impact on biotechnological applications.

The Triatoma phyllosoma species group (Hemiptera: Reduviidae: Triatominae), vectors of Chagas disease: Diagnoses and a key to the species

Zootaxa ◽  
2021 ◽  
Vol 5023 (3) ◽  
pp. 335-365
Author(s):  
LAURA RENGIFO-CORREA ◽  
JUAN LUIS x JUAN LUIS TÉLLEZ-RENDÓN ◽  
LYDA ESTEBAN ◽  
HERÓN HUERTA ◽  
JUAN J. MORRONE
Keyword(s):  
Cryptic Species ◽  
Chagas Disease ◽  
Reproductive Behavior ◽  
Species Concept ◽  
Current Knowledge ◽  
Species Group ◽  
Species Status ◽  
Taxonomic Key ◽  
Species Complexes

The Triatoma phyllosoma species group includes 17 species of kissing bugs, most of them implicated in the transmission of Chagas disease in the Americas. The species of this group are T. bassolsae Alejandre-Aguilar, Nogueda-Torres, Cortéz-Jímenez, Jurberg, Galvão & Carcavallo, 1999, T. brailovskyi Martínez, Carcavallo & Pelaez, 1984, T. dimidiata (Latreille, 1811), T. gerstaeckeri (Stål, 1859), T. gomeznunezi Martínez, Carcavallo & Juberg, 1994, T. hegneri Mazzotti, 1940, T. huehuetenanguensis Lima-Cordón, Monroy, Stevens, Rodas, Rodas, Dorn & Justi, 2019, T. indictiva Neiva, 1912, T. longipennis Usinger, 1939, T. mazzottii Usinger, 1941, T. mexicana (Herrich-Schaeffer, 1848), T. mopan Dorn, Justi, Dale, Stevens, Galvão, Lima-Cordón & Monroy, 2018, T. pallidipennis (Stål, 1872), T. phyllosoma (Burmeister, 1835), T. picturata Usinger, 1939, T. recurva (Stål, 1868), and T. sanguisuga (LeConte, 1855). The validity of some species of the group was uncertain, because of both cryptic species and hybrid occurrence. Species exhibiting these particularities were formerly classified in the T. dimidiata and T. phyllosoma complexes. Although we recognize the historical value of these species complexes, we do not recommend their further use. Instead, we recognize the T. phyllosoma species group here reviewed, considering the current knowledge of the systematics and reproductive behavior of the group. We implement the cohesion species concept, validating the species status of T. bassolsae, T. longipennis, T. mazzottii, T. pallidipennis, T. phyllosoma, and T. picturata. We also provide diagnoses, photographs and a taxonomic key including the recently described species.  

scholarly journals On the Diversity of Phyllodocida (Annelida: Errantia), with a Focus on Glyceridae, Goniadidae, Nephtyidae, Polynoidae, Sphaerodoridae, Syllidae, and the Holoplanktonic Families

Diversity ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 131
Author(s):  
Daniel Martin ◽  
Maria Teresa Aguado ◽  
María-Ana Fernández Álamo ◽  
Temir Alanovich Britayev ◽  
Markus Böggemann ◽  
...  
Keyword(s):  
Species Concept ◽  
Current Knowledge ◽  
Sampling Bias ◽  
Molecular Data ◽  
Nominal Species ◽  
Deep Waters ◽  
European North ◽  
Continental Shelves ◽  
Molecular Barcode ◽  
Group 2

Phyllodocida is a clade of errantiate annelids characterized by having ventral sensory palps, anterior enlarged cirri, axial muscular proboscis, compound chaetae (if present) with a single ligament, and of lacking dorsolateral folds. Members of most families date back to the Carboniferous, although the earliest fossil was dated from the Devonian. Phyllodocida holds 27 well-established and morphologically homogenous clades ranked as families, gathering more than 4600 currently accepted nominal species. Among them, Syllidae and Polynoidae are the most specious polychaete groups. Species of Phyllodocida are mainly found in the marine benthos, although a few inhabit freshwater, terrestrial and planktonic environments, and occur from intertidal to deep waters in all oceans. In this review, we (1) explore the current knowledge on species diversity trends (based on traditional species concept and molecular data), phylogeny, ecology, and geographic distribution for the whole group, (2) try to identify the main knowledge gaps, and (3) focus on selected families: Alciopidae, Goniadidae, Glyceridae, Iospilidae, Lopadorrhynchidae, Polynoidae, Pontodoridae, Nephtyidae, Sphaerodoridae, Syllidae, Tomopteridae, Typhloscolecidae, and Yndolaciidae. The highest species richness is concentrated in European, North American, and Australian continental shelves (reflecting a strong sampling bias). While most data come from shallow coastal and surface environments most world oceans are clearly under-studied. The overall trends indicate that new descriptions are constantly added through time and that less than 10% of the known species have molecular barcode information available.

scholarly journals Evolution of the Bacterial Species Lactobacillus delbrueckii: A Partial Genomic Study with Reflections on Prokaryotic Species Concept

2003 ◽  
Vol 20 (1) ◽  
pp. 93-104 ◽  
Author(s):  
Jacques-Edouard Germond ◽  
Luciane Lapierre ◽  
Michèle Delley ◽  
Beat Mollet ◽  
Giovanna E. Felis ◽  
...  
Keyword(s):  
Species Concept ◽  
Bacterial Species ◽  
Lactobacillus Delbrueckii ◽  
Genomic Study ◽  
Prokaryotic Species

scholarly journals The multifactorial interplay of diet, the microbiome and appetite control: current knowledge and future challenges

2015 ◽  
Vol 74 (3) ◽  
pp. 235-244 ◽  
Author(s):  
Bernard M. Corfe ◽  
Charlotte J. Harden ◽  
Matthew Bull ◽  
Iveta Garaiova
Keyword(s):  
Current Knowledge ◽  
Population Level ◽  
Energy Yield ◽  
Gut Health ◽  
Appetite Control ◽  
Obesity Epidemic ◽  
Sequencing Technologies ◽  
Future Challenges ◽  
Modelling Strategies

The recent availability of high-throughput nucleic acid sequencing technologies has rapidly advanced approaches to analysing the role of the gut microbiome in governance of human health, including gut health, and also metabolic, cardiovascular and mental health,inter alia. Recent scientific studies suggest that energy intake (EI) perturbations at the population level cannot account for the current obesity epidemic, and significant work is investigating the potential role of the microbiome, and in particular its metabolic products, notably SCFA, predominantly acetate, propionate and butyrate, the last of which is an energy source for the epithelium of the large intestine. The energy yield from dietary residues may be a significant factor influencing energy balance. This review posits that the contribution towards EI is governed by EI diet composition (not just fibre), the composition of the microbiome and by the levels of physical activity. Furthermore, we hypothesise that these factors do not exist in a steady state, but rather are dynamic, with both short- and medium-term effects on appetite regulation. We suggest that the existing modelling strategies for bacterial dynamics, specifically for growth in chemostat culture, are of utility in understanding the dynamic interplay of diet, activity and microbiomic organisation. Such approaches may be informative in optimising the application of dietary and microbial therapy to promote health.

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