scholarly journals Diversity and Colonization Strategies of Endolithic Cyanobacteria in the Cold Mountain Desert of Pamir

2020 ◽  
Vol 9 (1) ◽  
pp. 6
Author(s):  
Nataliia Khomutovska ◽  
Asunción de los Ríos ◽  
Iwona Jasser
Keyword(s):  
Extreme Environments ◽  
Rrna Gene ◽  
Climate Conditions ◽  
Microbial Adaptation ◽  
Composition And Structure ◽  
Electron Mode ◽  
Backscattered Electron ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Endolithic Communities

Microorganisms can survive in extreme environments and oligotrophic habitats thanks to their specific adaptive capacity. Due to its severe and contrasting climate conditions, the cold mountain desert in Eastern Pamir provides a unique environment for analyzing microbial adaptation mechanisms occurring within colonization of endolithic habitats. This study aims to investigate the composition and structure of endolithic microbial communities and analyze the interactions between microorganisms and colonized lithic substrates. Endolithic biofilms were examined using scanning electron microscopy in backscattered electron mode (SEM-BSE) and next-generation sequencing (NGS) applying amplicon sequence variants (ASVs) approach. The investigation of the V3–V4 region of 16S rRNA gene revealed that endolithic communities are dominated by Actinobacteria (26%), Proteobacteria (23%), and Cyanobacteria (11.4%). Cyanobacteria were represented by Oxyphotobacteria with a predominance of subclasses of Oscillatoriophycidae, Synechococcophycideae, and Nostocophycidae as well as the rarely occurring Sericytochromatia. The positive correlation between the contribution of the orders Synechococcales and Rhizobiales to community structure suggests that some functionally closed taxa of Cyanobacteria and Proteobacteria can complement each other, for example, in nitrogen fixation in endolithic communities. The endolithic communities occurring in Eastern Pamir were identified as complex systems whose composition and structure seem to be influenced by the architecture of microhabitats and related microenvironmental conditions.

scholarly journals Structure of Microbial Communities When Complementary Effluents Are Anaerobically Digested

2021 ◽  
Vol 11 (3) ◽  
pp. 1293
Author(s):  
Ana Eusébio ◽  
André Neves ◽  
Isabel Paula Marques
Keyword(s):  
Anaerobic Digestion ◽  
Microbial Communities ◽  
Volatile Fatty Acids ◽  
Olive Mill Wastewater ◽  
Organic Load ◽  
Rrna Gene ◽  
Bacterial Populations ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Olive Mill

Olive oil and pig productions are important industries in Portugal that generate large volumes of wastewater with high organic load and toxicity, raising environmental concerns. The principal objective of this study is to energetically valorize these organic effluents—piggery effluent and olive mill wastewater—through the anaerobic digestion to the biogas/methane production, by means of the effluent complementarity concept. Several mixtures of piggery effluent were tested, with an increasing percentage of olive mill wastewater. The best performance was obtained for samples of piggery effluent alone and in admixture with 30% of OMW, which provided the same volume of biogas (0.8 L, 70% CH4), 63/75% COD removal, and 434/489 L CH4/kg SVin, respectively. The validation of the process was assessed by molecular evaluation through Next Generation Sequencing (NGS) of the 16S rRNA gene. The structure of the microbial communities for both samples, throughout the anaerobic process, was characterized by the predominance of bacterial populations belonging to the phylum Firmicutes, mainly Clostridiales, with Bacteroidetes being the subdominant populations. Archaea populations belonging to the genus Methanosarcina became predominant throughout anaerobic digestion, confirming the formation of methane mainly from acetate, in line with the greatest removal of volatile fatty acids (VFAs) in these samples.

scholarly journals Advances and Limitations of Next Generation Sequencing in Animal Diet Analysis

Genes ◽  
2021 ◽  
Vol 12 (12) ◽  
pp. 1854
Author(s):  
Gang Liu ◽  
Shumiao Zhang ◽  
Xinsheng Zhao ◽  
Chao Li ◽  
Minghao Gong
Keyword(s):  
Next Generation Sequencing ◽  
Environmental Changes ◽  
Diet Analysis ◽  
Next Generation ◽  
Application Range ◽  
Promising Tool ◽  
Composition And Structure ◽  
Next Generation Sequencing Ngs ◽  
Animal Diet ◽  
Generation Sequencing

Diet analysis is a critical content of animal ecology and the diet analysis methods have been constantly improving and updating. Contrary to traditional methods of high labor intensity and low resolution, the next generation sequencing (NGS) approach has been suggested as a promising tool for dietary studies, which greatly improves the efficiency and broadens the application range. Here we present a framework of adopting NGS and DNA metabarcoding into diet analysis, and discuss the application in aspects of prey taxa composition and structure, intra-specific and inter-specific trophic links, and the effects of animal feeding on environmental changes. Yet, the generation of NGS-based diet data and subsequent analyses and interpretations are still challenging with several factors, making it possible still not as widely used as might be expected. We suggest that NGS-based diet methods must be furthered, analytical pipelines should be developed. More application perspectives, including nutrient geometry, metagenomics and nutrigenomics, need to be incorporated to encourage more ecologists to infer novel insights on they work.

scholarly journals Molecular phylogenetic study of rare weed-field species of the genus Avena L.

2021 ◽  
Vol 20 (1) ◽  
pp. 108-111
Author(s):  
A. A. Gnutikov ◽  
N. N. Nosov ◽  
I. G. Loskutov ◽  
E. V. Blinova ◽  
A. V. Rodionov
Keyword(s):  
Phylogenetic Study ◽  
Rrna Gene ◽  
Its1 Sequence ◽  
5.8S Rrna Gene ◽  
Molecular Phylogenetic Study ◽  
5.8S Rrna ◽  
C Genome ◽  
Molecular Phylogenetic ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

A molecular phylogenetic study of weed-field species of the genus Avena L. using marker sequences ITS1–5.8S rRNA gene–ITS2 was undertaken. In addition, next-generation sequencing (NGS) was performed on the Illuminaplatform for the ITS1 sequence and the beginning of the gene 5.8S rRNA. Sanger sequencing results revealed the separateclade of microspecies with a good level of support and small level of difference between themselves. According to NGSsequencing data, the two most abundant subgenomes in terms of the number of sequences were identified. Among thecommon sequences of hexaploids, those associated with the C-genome were not found. The presence of unique ribotypeswas shown for A. persica and A. georgica.

scholarly journals Quantitative PCR provides a simple and accessible method for quantitative microbiome profiling

2018 ◽  
Author(s):  
Ching Jian ◽  
Panu Luukkonen ◽  
Hannele Yki-Järvinen ◽  
Anne Salonen ◽  
Katri Korpela
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Quantitative Pcr ◽  
Rrna Gene ◽  
Microbial Community Structures ◽  
Next Generation Sequencing Ngs ◽  
Ngs Data ◽  
Bacterial Groups ◽  
Microbiome Profiling ◽  
Generation Sequencing

AbstractThe use of relative next generation sequencing (NGS) abundance data can lead to misinterpretations of microbial community structures as the increase of one taxon leads to concurrent decrease of the other(s). To overcome compositionality, we provide a quantitative NGS solution, which is achieved by adjusting the relative 16S rRNA gene amplicon NGS data with quantitative PCR (qPCR-based) total bacterial counts. By comparing the enumeration of dominant bacterial groups on different taxonomic levels in human fecal samples using taxon-specific 16S rRNA gene-targeted qPCR we show that quantitative NGS is able to estimate absolute bacterial abundances accurately. We also observed a higher degree of correspondence in the estimated microbe-metabolite relationship when quantitative NGS was applied. Being conceptually and methodologically analogous to amplicon-based NGS, our qPCR-based method can be readily incorporated into the standard, high-throughput NGS sample processing pipeline for more accurate description of interactions within and between the microbes and host.

scholarly journals Genomic constitution of diploid species of the genus Avena L. with A-genome according to the data of the next-generation sequencing (NGS)

2021 ◽  
Vol 20 (1) ◽  
pp. 333-335
Author(s):  
N. N. Nosov ◽  
A. A. Gnutikov ◽  
I. G. Loskutov ◽  
E. V. Blinova ◽  
A. V. Rodionov
Keyword(s):  
Next Generation Sequencing ◽  
Diploid Species ◽  
Rrna Gene ◽  
Next Generation ◽  
Illumina Platform ◽  
5.8S Rrna Gene ◽  
A Genome ◽  
5.8S Rrna ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

For diploid (2x) species with the A-genome, as well as for hexaploid (6x) from the genus Avena, a locus-specific next-generation sequencing (NGS) of the sequence of the region of the internal transcribed spacer ITS1 and the beginning of the 5.8S rRNA gene was carried out on the Illumina platform. The high diversity and heterogeneity of the genomes of diploid species are shown. It was revealed that the genomes of modern diploid oat species are relatively far removed from the hexaploid species. It was found that A. canariensis occupies an isolated position among other diploid species, and also takes only an insignificant role in the formation of hexaploid genomes.

Progress Report: Next-Generation Sequencing (NGS), Multiplex Polymerase Chain Reaction (PCR), and Broad-Range Molecular Assays as Diagnostic Tools for Fever of Unknown Origin (FUO) Investigations in Adults

2021 ◽  
Author(s):  
William F Wright ◽  
Patricia J Simner ◽  
Karen C Carroll ◽  
Paul G Auwaerter
Keyword(s):  
Next Generation Sequencing ◽  
Fever Of Unknown Origin ◽  
Unknown Origin ◽  
Diagnostic Tools ◽  
Rrna Gene ◽  
Next Generation ◽  
Potential Cost ◽  
Microbial Identification ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Abstract Even well into the 21st century, infectious diseases still account for most causes of fever of unknown origin (FUO). Advances in molecular technologies, including broad-range PCR of the 16S rRNA gene followed by Sanger sequencing, multiplex PCR assays, and more recently, next-generation sequencing (NGS) applications, have transitioned from research methods to more commonplace in some clinical microbiology laboratories. They have the potential to supplant traditional microbial identification methods and antimicrobial susceptibility testing. Despite the remaining challenges with these technologies, publications in the past decade justify excitement about the potential to transform FUO investigations. We discuss available evidence using these molecular methods for FUO evaluations, including potential cost-benefits and future directions.

scholarly journals Microbial biodiversity of thermal water and mud in an Italian spa by metagenomics: a pilot study

2017 ◽  
Vol 18 (4) ◽  
pp. 1456-1465 ◽  
Author(s):  
Stefania Paduano ◽  
Federica Valeriani ◽  
Vincenzo Romano-Spica ◽  
Annalisa Bargellini ◽  
Paola Borella ◽  
...  
Keyword(s):  
Microbial Community ◽  
Water Distribution ◽  
Thermal Water ◽  
Hot Spring ◽  
Water Distribution Network ◽  
Rrna Gene ◽  
Sequences Analysis ◽  
Next Generation Sequencing Ngs ◽  
First Time ◽  
Generation Sequencing

Abstract In literature, the microbial diversity of hot spring waters has been the focus of extensive research, while there is a paucity of studies on thermal water distribution network of spa centres and, as yet, no studies have been carried out on the bacterial population of thermal muds. In this context, the aim of our study is to characterize the microbial community of sulphurous-bromine-iodine thermal water and mud within an Italian spa complex using Next Generation Sequencing (NGS) technologies. This is the first report of microbiome characterization along a water supply network from the spring to points of use within a spa. According to the 16S rRNA gene sequences analysis, our data highlight the presence of a typical microbial community, mainly composed of sulphur-cycling bacteria belonging to Desulfomonile, Thermodesulfovibrio, Geothermobacterium, Thermus, Thiofaba and Syntrophomonas genera. In addition, the characterization and evolution of the bacterial community in thermal muds during the maturation process is investigated for the first time. Interestingly, the microbiome of mature mud resulted dominated by bacteria capable of lipid biosynthesis, suggesting that these bacteria may play a role in the anti-rheumatic properties of thermal mud.

The origin of Alopecurus × brachystylus Peterm. according to the results of next-generation sequencing (NGS)

2020 ◽  
Vol 19 (1) ◽  
pp. 5-7
Author(s):  
A. A. Gnutikov ◽  
N. N. Nosov ◽  
E. O. Punina ◽  
A. V. Rodionov
Keyword(s):  
Next Generation Sequencing ◽  
Phylogenetic Study ◽  
Rrna Gene ◽  
Next Generation ◽  
Illumina Platform ◽  
Its1 Sequence ◽  
Molecular Phylogenetic Study ◽  
Molecular Phylogenetic ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

A molecular phylogenetic study of the hybrid species Alopecurus × brachystylus Peterm. and somesupposed ancestral taxa was carried out. Next-generation sequencing (NGS) of the ITS1 sequence and the start of the5.8S rRNA gene was used on the Illumina platform. According to NGS sequencing, genome of the A. × brachystylusforms common subgenomes with representatives of the section Alopecurium: A. geniculatus and A. aequalis, as well asrepresentatives of the type section: A. pratensis, A. arundinaceus, and alpine A. vlassowii. In addition, it was found thatA. vlassowii (section Alopecurus) contains sequences identical to the species of another section, Alopecurium.

scholarly journals Tendentious effects of automated and manual metagenomic DNA purification protocols on broiler gut microbiome taxonomic profiling

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Gabor Fidler ◽  
Emese Tolnai ◽  
Aniko Stagel ◽  
Judit Remenyik ◽  
Laszlo Stundl ◽  
...  
Keyword(s):  
Large Scale ◽  
Magnetic Bead ◽  
Positive Influence ◽  
Optimal Choice ◽  
Rrna Gene ◽  
Taxonomic Profiling ◽  
High Consistency ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Significant Positive Influence

AbstractHere, we developed protocols to improve sensitivity, rigor and comparability of 16S rRNA gene amplification-based next-generation sequencing (NGS) results. A thorough study was performed by evaluating extraction efficiency with respect to the yield, purity, fragmentation of the purified DNA, and sequencing metrics considering the number of quality reads, amplicon sequence variants (ASVs), community structure and biodiversity. We identified batch-effects that significantly bias broiler gastrointestinal tract (GIT) community compositions and made recommendations to improve sensitivity, consistency, and cross-study comparability. We found that the purity of the extracted nucleic acid had a strong effect on the success rate of downstream library preparations. The preparation of stool bacterial suspensions from feces showed a significant positive influence on community biodiversity by enriching Gram-negative bacteria and cataloguing low abundant taxa with greater success than direct processing of fecal material. Applications relying on the automated Roche MagNa Pure 24 magnetic-bead based method provided results with high consistency therefore it seems to be the optimal choice in large-scale studies for investigating broiler GIT microbiota.

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