scholarly journals Salvaging high-quality genomes of microbial species from a meromictic lake using a hybrid sequencing approach

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Yu-Hsiang Chen ◽  
Pei-Wen Chiang ◽  
Denis Yu Rogozin ◽  
Andrey G. Degermendzhy ◽  
Hsiu-Hui Chiu ◽  
...  
Keyword(s):  
Novel Species ◽  
Bacterial Genome ◽  
Meromictic Lake ◽  
Robust Method ◽  
High Quality ◽  
Microbial Species ◽  
Metagenomic Assembly

AbstractMost of Earth’s bacteria have yet to be cultivated. The metabolic and functional potentials of these uncultivated microorganisms thus remain mysterious, and the metagenome-assembled genome (MAG) approach is the most robust method for uncovering these potentials. However, MAGs discovered by conventional metagenomic assembly and binning are usually highly fragmented genomes with heterogeneous sequence contamination. In this study, we combined Illumina and Nanopore data to develop a new workflow to reconstruct 233 MAGs—six novel bacterial orders, 20 families, 66 genera, and 154 species—from Lake Shunet, a secluded meromictic lake in Siberia. With our workflow, the average N50 of reconstructed MAGs greatly increased 10–40-fold compared to when the conventional Illumina assembly and binning method were used. More importantly, six complete MAGs were recovered from our datasets. The recovery of 154 novel species MAGs from a rarely explored lake greatly expands the current bacterial genome encyclopedia.

scholarly journals Complete and high-quality genomes of novel microbial species from a meromictic lake using a workflow combining long- and short-read sequencing platforms

2021 ◽  
Author(s):  
Yu-Hsiang Chen ◽  
Pei-Wen Chiang ◽  
Denis Yu Rogozin ◽  
Andrey Georgievich Degermendzhy ◽  
Hsiu-Hui Chiu ◽  
...  
Keyword(s):  
Novel Species ◽  
Bacterial Genome ◽  
Meromictic Lake ◽  
High Quality ◽  
Good Opportunity ◽  
Short Read ◽  
Sequencing Technologies ◽  
Complete Genomes ◽  
Long Read ◽  
Sequencing Platforms

Background: Most of Earth's bacteria have yet to be cultivated. The metabolic and functional potentials of these uncultivated microorganisms thus remain mysterious, and the metagenome-assembled genome (MAG) approach is the most robust method for uncovering these potentials. However, MAGs discovered by conventional metagenomic assembly and binning methods are usually highly fragmented genomes with heterogeneous sequence contamination, and this affects the accuracy and sensitivity of genomic analyses. Though the maturation of long-read sequencing technologies provides a good opportunity to fix the problem of highly fragmented MAGs as mentioned above, the method's error-prone nature causes severe problems of long-read-alone metagenomics. Hence, methods are urgently needed to retrieve MAGs by a combination of both long- and short-read technologies to advance genome-centric metagenomics. Results: In this study, we combined Illumina and Nanopore data to develop a new workflow to reconstruct 233 MAGs-six novel bacterial orders, 20 families, 66 genera, and 154 species-from Lake Shunet, a secluded meromictic lake in Siberia. Those new MAGs were underrepresented or undetectable in other MAGs studies using metagenomes from human or other common organisms or habitats. Using this newly developed workflow and strategy, the average N50 of reconstructed MAGs greatly increased 10-40-fold compared to when the conventional Illumina assembly and binning method were used. More importantly, six complete MAGs were recovered from our datasets, five of which belong to novel species. We used these as examples to demonstrate many novel and intriguing genomic characteristics discovered in these newly complete genomes and proved the importance of high-quality complete MAGs in microbial genomics and metagenomics studies. Conclusions: The results show that it is feasible to apply our workflow with a few additional long reads to recover numerous complete and high-quality MAGs from short-read metagenomes of high microbial diversity environment samples. The unique features we identified from five complete genomes highlight the robustness of this method in genome-centric metagenomic research. The recovery of 154 novel species MAGs from a rarely explored lake greatly expands the current bacterial genome encyclopedia and broadens our knowledge by adding new genomic characteristics of bacteria. It demonstrates a strong need to recover MAGs from diverse unexplored habitats in the search for microbial dark matter.

scholarly journals An easy and robust method for the isolation of high quality RNA from coconut tissues

2020 ◽  
Vol 48 ◽  
pp. 78-85
Author(s):  
Amjad Iqbal ◽  
Yaodong Yang ◽  
Yi Wu ◽  
Jing Li ◽  
Muhammad Hamayun ◽  
...  
Keyword(s):  
Robust Method ◽  
High Quality

scholarly journals Closed and High-Quality Bacterial Genome Sequences of the Oligo-Mouse-Microbiota Community

2021 ◽  
Vol 10 (17) ◽  
Author(s):  
Quentin Lamy-Besnier ◽  
Romain Koszul ◽  
Laurent Debarbieux ◽  
Martial Marbouty
Keyword(s):  
Murine Model ◽  
Bacterial Genome ◽  
Chromosome Conformation Capture ◽  
Genome Sequences ◽  
Pacbio Sequencing ◽  
High Quality ◽  
Chromosome Conformation

ABSTRACT The Oligo-Mouse-Microbiota (OMM12) gnotobiotic murine model is an increasingly popular model in microbiota studies. However, following Illumina and PacBio sequencing, the genomes of the 12 strains could not be closed. Here, we used genomic chromosome conformation capture (Hi-C) data to reorganize, close, and improve the quality of these 12 genomes.

scholarly journals PlasClass improves plasmid sequence classification

2019 ◽  
Author(s):  
David Pellow ◽  
Itzik Mizrahi ◽  
Ron Shamir
Keyword(s):  
State Of The Art ◽  
Bacterial Genome ◽  
Unknown Origin ◽  
The State ◽  
Sequence Classification ◽  
Genome Sequences ◽  
Plasmid Sequence ◽  
Link Type ◽  
Classification Tool ◽  
Metagenomic Assembly

AbstractBackgroundMany bacteria contain plasmids, but separating between contigs that originate on the plasmid and those that are part of the bacterial genome can be difficult. This is especially true in metagenomic assembly, which yields many contigs of unknown origin. Existing tools for classifying sequences of plasmid origin give less reliable results for shorter sequences, are trained using a fraction of the known plasmids, and can be difficult to use in practice.ResultsWe present PlasClass, a new plasmid classifier. It uses a set of standard classifiers trained on the most current set of known plasmid sequences for different sequence lengths. PlasClass outperforms the state-of-the-art plasmid classification tool on shorter sequences, which constitute the majority of assembly contigs, while using less time and memory.ConclusionsPlasClass can be used to easily classify plasmid and bacterial genome sequences in metagenomic or isolate assemblies. It is available from: https://github.com/Shamir-Lab/PlasClass

scholarly journals QRREM method for the isolation of high-quality RNA from the complex matrices of coconut

2019 ◽  
Vol 39 (1) ◽  
Author(s):  
Amjad Iqbal ◽  
Yaodong Yang ◽  
Rashad Qadri ◽  
Yi Wu ◽  
Jing Li ◽  
...  
Keyword(s):  
Cost Effectiveness ◽  
Extraction Method ◽  
Rna Extraction ◽  
The Other ◽  
Plant Tissues ◽  
Betel Nut ◽  
Robust Method ◽  
Plant Metabolites ◽  
High Quality ◽  
Spring Onion

Abstract Complex plant tissues vary in hardness, i.e. some are succulent, while others are complex to break. Besides, plant metabolites, such as polysaccharides, proteins, polyphenols and lipids, can greatly interfere with the RNA extraction. So, in order to obtain a high-quality RNA from the complex tissues (like coconut endosperm, coconut apple and coconut leaf bud) rich in secondary metabolites, a robust method is demanded. Several methods (MRIP, CTAB and TRIZOL) have been used previously for the isolation of quality RNA from the coconut tissues, but without any success. The present study will provide with the details of a new method (Quick and Reliable RNA Extraction Method or QRREM), which have efficiently isolated the intact RNA form the complex tissues of coconut compared with CTAB, Trizol and RNA plant. The method has been validated for the isolation of high-quality intact RNA from the other available plant species (Areca/betel nut, mint and spring onion). The method has various advantages over the other methods in terms of time and cost effectiveness. Furthermore, the resulted RNA from various tissues of coconut performed well in the downstream experiments, i.e. reverse transcription and PCR for the production and amplification of cDNA.

scholarly journals Internet sex-seeking is inconsistently linked with sexual risk in men who have sex with men: systematic review of within-subjects comparisons

Sexual Health ◽  
2015 ◽  
Vol 12 (3) ◽  
pp. 183 ◽  
Author(s):  
G. J. Melendez-Torres ◽  
Elizabeth Nye ◽  
Chris Bonell
Keyword(s):  
Systematic Review ◽  
Health Promotion ◽  
Sexual Risk ◽  
Full Text ◽  
Target Person ◽  
Robust Method ◽  
High Quality ◽  
Within Subjects ◽  
Internet Sex ◽  
Sex With Men

Background Internet sex-seeking has been associated at the person level with sexual risk. However, the most robust method of encounter-level inference to determine associations between internet sex-seeking and sexual risk is to compare encounters against each other. We systematically reviewed within-subjects comparisons of sexual encounters that tested associations between internet sex-seeking and sexual risk in men who have sex with men. Methods: We systematically searched databases on 9 July 2013, then screened records and full-text articles in duplicate and independently. Studies were synthesised narratively. Results: Four studies were included. Although studies were generally of high quality, the findings were inconsistent and did not show clear evidence of a relationship between internet sex-seeking and sexual risk. Conclusions: Further research in internet sex-seeking among men who have sex with men is required, particularly as internet-enabled sexual sociality continues to evolve. Internet-based health promotion may wish to target person-level features instead of encounter-specific characteristics.

Facile polyol synthesis of CuS nanocrystals with a hierarchical nanoplate structure and their application for electrocatalysis and photocatalysis

RSC Advances ◽  
2016 ◽  
Vol 6 (83) ◽  
pp. 80361-80367 ◽  
Author(s):  
Wenlong Fu ◽  
Maochang Liu ◽  
Fei Xue ◽  
Xixi Wang ◽  
Zhidan Diao ◽  
...  
Keyword(s):  
Polyol Synthesis ◽  
Robust Method ◽  
High Quality

The article describes a robust method for the facile polyol synthesis of high-quality CuS nanocrystals with a controlled hierarchical nanoplate structure.

scholarly journals Microbial genomes from non-human primate gut metagenomes expand the primate-associated bacterial tree of life with over 1000 novel species

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Serena Manara ◽  
Francesco Asnicar ◽  
Francesco Beghini ◽  
Davide Bazzani ◽  
Fabio Cumbo ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Novel Species ◽  
Human Microbiome ◽  
Intestinal Microbiome ◽  
Human Populations ◽  
Microbial Species ◽  
In Captivity ◽  
Evolutionary Trajectories ◽  
Specific Species ◽  
Human Primate

Abstract Background Humans have coevolved with microbial communities to establish a mutually advantageous relationship that is still poorly characterized and can provide a better understanding of the human microbiome. Comparative metagenomic analysis of human and non-human primate (NHP) microbiomes offers a promising approach to study this symbiosis. Very few microbial species have been characterized in NHP microbiomes due to their poor representation in the available cataloged microbial diversity, thus limiting the potential of such comparative approaches. Results We reconstruct over 1000 previously uncharacterized microbial species from 6 available NHP metagenomic cohorts, resulting in an increase of the mappable fraction of metagenomic reads by 600%. These novel species highlight that almost 90% of the microbial diversity associated with NHPs has been overlooked. Comparative analysis of this new catalog of taxa with the collection of over 150,000 genomes from human metagenomes points at a limited species-level overlap, with only 20% of microbial candidate species in NHPs also found in the human microbiome. This overlap occurs mainly between NHPs and non-Westernized human populations and NHPs living in captivity, suggesting that host lifestyle plays a role comparable to host speciation in shaping the primate intestinal microbiome. Several NHP-specific species are phylogenetically related to human-associated microbes, such as Elusimicrobia and Treponema, and could be the consequence of host-dependent evolutionary trajectories. Conclusions The newly reconstructed species greatly expand the microbial diversity associated with NHPs, thus enabling better interrogation of the primate microbiome and empowering in-depth human and non-human comparative and co-diversification studies.

scholarly journals MicroPIPE: An end-to-end solution for high-quality complete bacterial genome construction

2021 ◽  
Author(s):  
Valentine Murigneux ◽  
Leah W. Roberts ◽  
Brian M. Forde ◽  
Minh-Duy Phan ◽  
Nguyen Thi Khanh Nhu ◽  
...  
Keyword(s):  
Bacterial Genome ◽  
Sequence Type ◽  
Bacterial Isolates ◽  
Bacterial Genomes ◽  
High Quality ◽  
Oxford Nanopore ◽  
Long Read ◽  
Complete Bacterial Genome ◽  
Assembly Pipeline ◽  
End To End

AbstractOxford Nanopore Technology (ONT) long-read sequencing has become a popular platform for microbial researchers; however, easy and automated construction of high-quality bacterial genomes remains challenging. Here we present MicroPIPE: a reproducible end-to-end bacterial genome assembly pipeline for ONT and Illumina sequencing. To construct MicroPIPE, we evaluated the performance of several tools for genome reconstruction and assessed overall genome accuracy using ONT both natively and with Illumina. Further validation of MicroPIPE was carried out using 11 sequence type (ST)131 Escherichia coli and eight publicly available Gram-negative and Gram-positive bacterial isolates. MicroPIPE uses Singularity containers and the workflow manager Nextflow and is available at https://github.com/BeatsonLab-MicrobialGenomics/micropipe.

scholarly journals Iterative Subtractive Binning of Freshwater Chronoseries Metagenomes Identifies of over Four Hundred Novel Species and their Ecologic Preferences

2019 ◽  
Author(s):  
LM Rodriguez-R ◽  
D Tsementzi ◽  
C Luo ◽  
KT Konstantinidis
Keyword(s):  
Novel Species ◽  
Preference Score ◽  
Freshwater Ecosystems ◽  
Habitat Specialization ◽  
Sequencing Technology ◽  
High Quality ◽  
Sample Representation ◽  
High Degree ◽  
Lacustrine Ecosystem

AbstractRecent advances in sequencing technology and accompanying bioinformatic pipelines have allowed unprecedented access to the genomes of yet-uncultivated microorganisms from a wide array of natural and engineered environments. However, the catalogue of available genomes from uncultivated freshwater microbial populations remains limited, and most genome recovery attempts in freshwater ecosystems have only targeted few specific taxa. Here, we present a novel genome recovery pipeline, which incorporates iterative subtractive binning and apply it to a time series of metagenomic datasets from seven connected locations along the Chattahoochee River (Southeastern USA). Our set of Metagenome-Assembled Genomes (MAGs) represents over four hundred genomospecies yet to be named, which substantially increase the number of high-quality MAGs from freshwater lakes and represent about half of the total microbial community sampled. We propose names for two novel species that were represented by high-quality MAGs: “Candidatus Elulimicrobium humile” (“Ca. Elulimicrobiota” in the “Patescibacteria” group) and “Candidatus Aquidulcis frankliniae” (“Chloroflexi”). To evaluate the prevalence of these species in the chronoseries, we introduce novel approaches to estimate relative abundance and a habitat-preference score that control for uneven quality of the genomes and sample representation. Using these metrics, we demonstrate a high degree of habitat-specialization and endemicity for most genomospecies observed in the Chattahoochee lacustrine ecosystem, as well as wider species ecological ranges associated with smaller genomes and higher coding densities, indicating an overall advantage of smaller, more compact genomes for cosmopolitan distributions.

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