scholarly journals Assembly of hundreds of novel bacterial genomes from the chicken caecum

2019 ◽  
Author(s):  
Laura Glendinning ◽  
Robert D. Stewart ◽  
Mark J. Pallen ◽  
Kellie A. Watson ◽  
Mick Watson
Keyword(s):  
Fish Meal ◽  
Short Chain Fatty Acids ◽  
Nitrogen Recycling ◽  
Bacterial Genomes ◽  
Carbohydrate Active Enzymes ◽  
Core Microbiome ◽  
Future Studies ◽  
Illumina Data ◽  
And Function ◽  
Caecal Microbiota

AbstractChickens are a highly important source of protein for a large proportion of the human population. The caecal microbiota plays a crucial role in chicken nutrition through the production of short chain fatty acids, nitrogen recycling and amino acid production. In this study we sequenced DNA from caecal contents samples taken from 24 chickens belonging to either a fast or slower growing breed consuming either a vegetable-only diet or a diet containing fish meal. We utilised 1.6T of Illumina data to construct 469 draft metagenome-assembled bacterial genomes, including 460 novel strains, 283 novel species and 42 novel genera. We compared our genomes to data from eight EU countries and show that these genomes are abundant within European chicken flocks. We also compared the abundance of our genomes, and the carbohydrate active enzymes they produce, between our chicken groups and demonstrate that there are both breed- and diet-specific microbiomes, as well as an overlapping core microbiome. This data will form the basis for future studies examining the composition and function of the chicken caecal microbiota.

scholarly journals Plasma Neurofilament Light and Future Declines in Cognition and Function in Alzheimer’s Disease in the FIT-AD Trial

2021 ◽  
pp. 1-11
Author(s):  
Danni Li ◽  
Lin Zhang ◽  
Nathaniel W. Nelson ◽  
Michelle M. Mielke ◽  
Fang Yu
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Daily Living ◽  
Short Term ◽  
Neurofilament Light Chain ◽  
Neurofilament Light ◽  
Linear Mixed Effects ◽  
Future Studies ◽  
Rate Of Decline ◽  
And Function

Background: Utilities of blood-based biomarkers in Alzheimer’s disease (AD) clinical trials remain unknown. Objective: To evaluate the ability of plasma neurofilament light chain (NfL) to predict future declines in cognition and activities of daily living (ADL) outcomes in 26 older adults with mild-to-moderate AD dementia from the FIT-AD Trial. Methods: Plasma NfL was measured at baseline and 3 and 6 months. Cognition and ADL were assessed using the AD Assessment Scale-Cognition (ADAS-Cog) and AD Uniform Dataset Instruments and Disability Assessment for Dementia (DAD), respectively, at baseline, 3, 6, 9, and 12 months. Linear mixed effects models were used to examine the associations between baseline or change in plasma NfL and changes in outcomes. Results: Higher baseline plasma NfL was associated with greater rate of decline in ADAS-Cog from baseline to 6 months (standardized estimate of 0.00462, p = 0.02853) and in ADL from baseline to 12 months (standardized estimate of –0.00284, p = 0.03338). Greater increase in plasma NfL in short term from baseline to 3 months was associated with greater rate of decline in memory and ADL from 3 to 6 months (standardized estimate of –0.04638 [0.003], p = 0.01635; standardized estimate of –0.03818, p = 0.0435) and greater rate of decline in ADL from 3 to 12 month (standardized estimate of –0.01492, p = 0.01082). Conclusion: This study demonstrated that plasma NfL might have the potential to predict cognitive and function decline up to 12 months. However, future studies with bigger sample sizes need to confirm the findings.

scholarly journals Breeder Diet Strategies for Generating Ttpa-Null and Wild-Type Mice with Low Vitamin E Status to Assess Neurological Outcomes

2020 ◽  
Vol 4 (11) ◽  
Author(s):  
Katherine M Ranard ◽  
Matthew J Kuchan ◽  
John W Erdman
Keyword(s):  
Animal Model ◽  
Vitamin E ◽  
Mouse Model ◽  
Wild Type ◽  
Future Studies ◽  
Neurological Outcomes ◽  
Transfer Protein ◽  
And Function ◽  
The Brain ◽  
Vitamin E Status

ABSTRACT Studying vitamin E [α-tocopherol (α-T)] metabolism and function in the brain and other tissues requires an animal model with low α-T status, such as the transgenic α-T transfer protein (Ttpa)–null (Ttpa−/−) mouse model. Ttpa+/− dams can be used to produce Ttpa−/− and Ttpa+/+mice for these studies. However, the α-T content in Ttpa+/− dams’ diet requires optimization; diets must provide sufficient α-T for reproduction, while minimizing the transfer of α-T to the offspring destined for future studies that require low baseline α-T status. The goal of this work was to assess the effectiveness and feasibility of 2 breeding diet strategies on reproduction outcomes and offspring brain α-T concentrations. These findings will help standardize the breeding methodology used to generate the Ttpa−/− mice for neurological studies.

Linear plasmids in Klebsiella and other Enterobacteriaceae

2021 ◽  
Author(s):  
Jane Hawkey ◽  
Hugh Cottingham ◽  
Alex Tokolyi ◽  
Ryan R Wick ◽  
Louise M Judd ◽  
...  
Keyword(s):  
Plasmid Stability ◽  
Bacterial Species ◽  
Salmonella Typhi ◽  
Multidrug Resistant ◽  
Linear Plasmid ◽  
Extrachromosomal Dna ◽  
Linear Plasmids ◽  
Future Studies ◽  
And Function

Linear plasmids are extrachromosomal DNA that have been found in a small number of bacterial species. To date, the only linear plasmids described in the Enterobacteriaceae family belong to Salmonella, first found in Salmonella Typhi. Here, we describe a collection of 12 isolates of the Klebsiella pneumoniae species complex in which we identified linear plasmids. We used this collection to search public sequence databases and discovered an additional 74 linear plasmid sequences in a variety of Enterobacteriaceae species. Gene content analysis divided these plasmids into five distinct phylogroups, with very few genes shared across more than two phylogroups. The majority of linear plasmid-encoded genes are of unknown function, however each phylogroup carried its own unique toxin-antitoxin system and genes with homology to those encoding the ParAB plasmid stability system. Passage in vitro of the 12 linear plasmid-carrying Klebsiella isolates in our collection (which include representatives of all five phylogroups) indicated that these linear plasmids can be stably maintained, and our data suggest they can transmit between K. pneumoniae strains (including members of globally disseminated multidrug resistant clones) and also between diverse Enterobacteriaceae species. The linear plasmid sequences, and representative isolates harbouring them, are made available as a resource to facilitate future studies on the evolution and function of these novel plasmids.

scholarly journals Metagenomic Comparisons between Soft and Hard Feces of Plateau Pikas (Ochotona curzoniae)

Animals ◽  
2022 ◽  
Vol 12 (2) ◽  
pp. 149
Author(s):  
Haibo Fu ◽  
Wenjing Li
Keyword(s):  
Amino Acids ◽  
Fatty Acids ◽  
16S Rdna ◽  
Microbial Metabolism ◽  
Short Chain Fatty Acids ◽  
Short Chain ◽  
Future Studies ◽  
Ochotona Curzoniae ◽  
The Future ◽  
First Time

The division of hard and soft feces is an effective digestion strategy in the order Lagomorpha. Although previous studies have reported that hard and soft feces differ in morphology and component, the discrepancy in the microbiome remains unclear. This study explored the microbiomes of hard and soft feces in plateau pikas by sequencing the V3 and V4 regions of 16S rDNA. We found that hard feces harbored higher Firmicutes, while soft feces harbored higher Akkermansia. Increased rare bacterial taxa were observed in hard feces compared with soft feces. Moreover, hard and soft feces displayed a greater difference in terms of core operational taxonomy units (OTUs) compared to the total OTUs. The soft feces showed enhancements in all predicted Kyoto Encyclopedia of Genes and Genomes (KEGG) functions, indicating an advancing microbial metabolism compared to hard feces. The significantly upregulated pathways in soft feces were mainly enriched in metabolism of energy and carbohydrate, glycan biosynthesis, cofactors and vitamins, and amino acids—all of which are associated with increased contents of microbial proteins, vitamins, and short-chain fatty acids. Our study reports, for the first time, the differential microbiomes between hard and soft feces of pikas and provides direction for the future studies on cecotrophy.

scholarly journals Unexpected cryptic species among streptophyte algae most distant to land plants

2021 ◽  
Vol 288 (1963) ◽  
Author(s):  
Iker Irisarri ◽  
Tatyana Darienko ◽  
Thomas Pröschold ◽  
Janine M. R. Fürst-Jansen ◽  
Mahwash Jamy ◽  
...  
Keyword(s):  
Land Plants ◽  
Comparative Genomic ◽  
Future Studies ◽  
Form And Function ◽  
Genomic Studies ◽  
Plant Form ◽  
Phylogenomic Analyses ◽  
And Function ◽  
Shed Light ◽  
Green Lineage

Streptophytes are one of the major groups of the green lineage (Chloroplastida or Viridiplantae). During one billion years of evolution, streptophytes have radiated into an astounding diversity of uni- and multicellular green algae as well as land plants. Most divergent from land plants is a clade formed by Mesostigmatophyceae, Spirotaenia spp. and Chlorokybophyceae. All three lineages are species-poor and the Chlorokybophyceae consist of a single described species, Chlorokybus atmophyticus. In this study, we used phylogenomic analyses to shed light into the diversity within Chlorokybus using a sampling of isolates across its known distribution. We uncovered a consistent deep genetic structure within the Chlorokybus isolates, which prompted us to formally extend the Chlorokybophyceae by describing four new species. Gene expression differences among Chlorokybus species suggest certain constitutive variability that might influence their response to environmental factors. Failure to account for this diversity can hamper comparative genomic studies aiming to understand the evolution of stress response across streptophytes. Our data highlight that future studies on the evolution of plant form and function can tap into an unknown diversity at key deep branches of the streptophytes.

scholarly journals The iron-responsive genome of the chiton Acanthopleura granulata

2020 ◽  
Author(s):  
Rebecca M. Varney ◽  
Daniel I. Speiser ◽  
Carmel McDougall ◽  
Bernard M. Degnan ◽  
Kevin M. Kocot
Keyword(s):  
Iron Transport ◽  
West Indian ◽  
The Other ◽  
The West ◽  
Major Clade ◽  
Future Studies ◽  
Form And Function ◽  
Genetic Mechanisms ◽  
Molluscan Evolution ◽  
And Function

ABSTRACTMolluscs biomineralize structures that vary in composition, form, and function, prompting questions about the genetic mechanisms responsible for their production and the evolution of these mechanisms. Chitons (Mollusca, Polyplacophora) are a promising system for studies of biomineralization because they build a range of calcified structures including shell plates and spine- or scale-like sclerites. Chitons also harden the calcified teeth of their rasp-like radula with a coat of iron (as magnetite). Here we present the genome of the West Indian fuzzy chiton Acanthopleura granulata, the first from any aculiferan mollusc. The A. granulata genome contains homologs of many biomineralization genes identified previously in conchiferan molluscs. We expected chitons to lack genes previously identified from pathways conchiferans use to make biominerals like calcite and nacre because chitons do not use these materials in their shells. Surprisingly, the A. granulata genome has homologs of many of these genes, suggesting that the ancestral mollusc had a more diverse biomineralization toolkit than expected. The A. granulata genome has features that may be specialized for iron biomineralization, including a higher proportion of genes regulated directly by iron than other molluscs. A. granulata also produces two isoforms of soma-like ferritin: one is regulated by iron and similar in sequence to the soma-like ferritins of other molluscs, and the other is constitutively translated and is not found in other molluscs. The A. granulata genome is a resource for future studies of molluscan evolution and biomineralization.SIGNIFICANCE STATEMENTChitons are molluscs that make shell plates, spine- or scale-like sclerites, and iron-coated teeth. Currently, all molluscs with sequenced genomes lie within one major clade (Conchifera). Sequencing the genome of a representative from the other major clade (Aculifera) helps us learn about the origins and evolution of molluscan traits. The genome of the West Indian Fuzzy Chiton, Acanthopleura granulata, reveals chitons have homologs of many genes other molluscs use to make shells, suggesting all molluscs share some shell-making pathways. The genome of A. granulata has more genes that may be regulated directly by iron than other molluscs, and chitons produce a unique isoform of a major iron-transport protein (ferritin), suggesting that chitons have genomic specializations that contribute to their production of iron-coated teeth.

scholarly journals Structure and Function of Multimeric G-Quadruplexes

Molecules ◽  
2019 ◽  
Vol 24 (17) ◽  
pp. 3074 ◽  
Author(s):  
Sofia Kolesnikova ◽  
Edward A. Curtis
Keyword(s):  
Nucleic Acid ◽  
Building Blocks ◽  
Structure And Function ◽  
Limited Information ◽  
Functional Elements ◽  
Future Studies ◽  
And Function ◽  
Nucleic Acid Structures ◽  
Sequence Requirements ◽  
Order Structures

G-quadruplexes are noncanonical nucleic acid structures formed from stacked guanine tetrads. They are frequently used as building blocks and functional elements in fields such as synthetic biology and also thought to play widespread biological roles. G-quadruplexes are often studied as monomers, but can also form a variety of higher-order structures. This increases the structural and functional diversity of G-quadruplexes, and recent evidence suggests that it could also be biologically important. In this review, we describe the types of multimeric topologies adopted by G-quadruplexes and highlight what is known about their sequence requirements. We also summarize the limited information available about potential biological roles of multimeric G-quadruplexes and suggest new approaches that could facilitate future studies of these structures.

scholarly journals Astrocytes: News about Brain Health and Diseases

Biomedicines ◽  
2020 ◽  
Vol 8 (10) ◽  
pp. 394
Author(s):  
Jacopo Meldolesi
Keyword(s):  
Glial Cells ◽  
Present State ◽  
Cell Types ◽  
Present Review ◽  
Brain Health ◽  
Traumatic Injuries ◽  
Future Studies ◽  
Brain Physiology ◽  
And Function

Astrocytes, the most numerous glial cells in the brains of humans and other mammalian animals, have been studied since their discovery over 100 years ago. For many decades, however, astrocytes were believed to operate as a glue, providing only mechanical and metabolic support to adjacent neurons. Starting from a “revolution” initiated about 25 years ago, numerous astrocyte functions have been reconsidered, some previously unknown, others attributed to neurons or other cell types. The knowledge of astrocytes has been continuously growing during the last few years. Based on these considerations, in the present review, different from single or general overviews, focused on six astrocyte functions, chosen due in their relevance in both brain physiology and pathology. Astrocytes, previously believed to be homogeneous, are now recognized to be heterogeneous, composed by types distinct in structure, distribution, and function; their cooperation with microglia is known to govern local neuroinflammation and brain restoration upon traumatic injuries; and astrocyte senescence is relevant for the development of both health and diseases. Knowledge regarding the role of astrocytes in tauopathies and Alzheimer’s disease has grow considerably. The multiple properties emphasized here, relevant for the present state of astrocytes, will be further developed by ongoing and future studies.

scholarly journals Carbohydrate Hydrolytic Potential and Redundancy of an Anaerobic Digestion Microbiome Exposed to Acidosis, as Uncovered by Metagenomics

2019 ◽  
Vol 85 (15) ◽  
Author(s):  
Marie Bertucci ◽  
Magdalena Calusinska ◽  
Xavier Goux ◽  
Corinne Rouland-Lefèvre ◽  
Boris Untereiner ◽  
...  
Keyword(s):  
Anaerobic Digestion ◽  
Hydrolytic Enzymes ◽  
Functional Redundancy ◽  
Special Focus ◽  
Genetic Redundancy ◽  
Bacterial Genomes ◽  
Carbohydrate Active Enzymes ◽  
Anaerobic Reactors ◽  
Hydrolysis Of ◽  
Hydrolytic Potential

ABSTRACTIncreased hydrolysis of easily digestible biomass may lead to acidosis of anaerobic reactors and decreased methane production. Previously, it was shown that the structure of microbial communities changed during acidosis; however, once the conditions are back to optimal, biogas (initially CO2) production quickly restarts. This suggests the retention of the community functional redundancy during the process failure. In this study, with the use of metagenomics and downstream bioinformatics analyses, we characterize the carbohydrate hydrolytic potential of the microbial community, with a special focus on acidosis. To that purpose, carbohydrate-active enzymes were identified, and to further link the community hydrolytic potential with key microbes, bacterial genomes were reconstructed. In addition, we characterized biochemically the specificity and activity of selected enzymes, thus verifying the accuracy of thein silicopredictions. The results confirm the retention of the community hydrolytic potential during acidosis and indicateBacteroidetesto be largely involved in biomass degradation.Bacteroidetesshowed higher diversity and genomic content of carbohydrate hydrolytic enzymes that might favor the dominance of this phylum over other bacteria in some anaerobic reactors. The combination of bioinformatic analyses and activity tests enabled us to propose a model of acetylated glucomannan degradation byBacteroidetes.IMPORTANCEThe enzymatic hydrolysis of lignocellulosic biomass is mainly driven by the action of carbohydrate-active enzymes. By characterizing the gene profiles at the different stages of the anaerobic digestion experiment, we showed that the microbiome retains its hydrolytic functional redundancy even during severe acidosis, despite significant changes in taxonomic composition. By analyzing reconstructed bacterial genomes, we demonstrate thatBacteroideteshydrolytic gene diversity likely favors the abundance of this phylum in some anaerobic digestion systems. Further, we observe genetic redundancy within theBacteroidetesgroup, which accounts for the preserved hydrolytic potential during acidosis. This work also uncovers new polysaccharide utilization loci involved in the deconstruction of various biomasses and proposes the model of acetylated glucomannan degradation byBacteroidetes. Acetylated glucomannan-enriched biomass is a common substrate for many industries, including pulp and paper production. Using naturally evolved cocktails of enzymes for biomass pretreatment could be an interesting alternative to the commonly used chemical pretreatments.

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