Metagenome sequencing
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This study applies an effective deep learning framework for the classification of microbial sequences. The proposed architecture combines a sequence embedding layer with other layers of a bidirectional Long Short-Term Memory, Seft-attention, and Dropout mechanisms for feature learning. Experimental results demonstrate the strength of the proposed method on datasets of real metagenomes.
7p vilarry 01-04-2024 7 1 Download
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Despite the increasing recognition that microbial communities within the human body are linked to health, we have an incomplete understanding of the environmental and molecular interactions that shape the composition of these communities.
13p vibransone 28-03-2024 7 1 Download
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Populations of closely related microbial strains can be simultaneously present in bacterial communities such as the human gut microbiome. We recently developed a de novo genome assembly approach that uses read cloud sequencing to provide more complete microbial genome drafts, enabling precise differentiation and tracking of strain-level dynamics across metagenomic samples.
17p vibransone 28-03-2024 9 1 Download
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Metagenomic next-generation sequencing (mNGS) of body fluids is an emerging approach to identify occult pathogens in undiagnosed patients. We hypothesized that metagenomic testing can be simultaneously used to detect malignant neoplasms in addition to infectious pathogens.
11p vibransone 28-03-2024 2 1 Download
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Metagenome sampling bias for geographical location and lifestyle is partially responsible for the incomplete catalog of reference genomes of gut microbial species. Thus, genome assembly from currently underrepresented populations may effectively expand the reference gut microbiome and improve taxonomic and functional profiling.
20p vibransone 28-03-2024 5 2 Download
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Antimicrobial resistance (AMR) is rising at an alarming rate and complicating the management of infectious diseases including lower respiratory tract infections (LRTI). Metagenomic next-generation sequencing (mNGS) is a recently established method for culture-independent LRTI diagnosis, but its utility for predicting AMR has remained unclear.
12p viellison 28-03-2024 2 2 Download
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Ebook "Prokaryotic systems biology (Advances in experimental medicine and biology, Volume 883)" focuses on innovative experimental and computational approaches for charting interaction networks in bacterial species.
326p duongthandue0501 28-02-2024 3 1 Download
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Ebook "Species diversity and community structure: Novel patterns and processes in plants, insects, and fungi" introduces recent progress in the study of species diversity and community structures in terrestrial organisms conducted by three groups at Kyoto University. First, it explains species diversity and the functioning of fungi in Asian regions as outlined by metagenomic approaches using next-generation sequencing technology. The advances in high-throughput sequencing technologies accelerate the speed of species inventorying, especially for microorganisms.
70p manmanthanhla0201 26-02-2024 2 1 Download
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Part 2 book "Environmental microbiology - Methods and protocols" includes content: Investigation of biological activities in situ; high throughput genomic approaches for environmental microbiology, metagenomics using next generation sequencing.
107p oursky10 04-12-2023 4 2 Download
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Binh Chau hot spring locates in Bung Rieng commune, Xuyen Moc district, Ba Ria - Vung Tau province, and is the second hottest hot spring in Vietnam. Up to date, the microbial diversity of this hot spring has been mainly evaluated using the culture-dependent methods, thus, it could not be able to assess all of microorganisms there.
11p vimulcahy 18-09-2023 5 3 Download
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In a previous study, a gene GL0694641 coding for endoglucanase containing 3 domains GH5- CBM72-CBM72 was exploited from metagenomic DNA data of bacteria in Vietnamese goats’ rumen. The gene (eg5) encoding the mature enzyme (without signal peptide coding sequence) was optimized codons, artificially synthesized, and inserted into the pET22b(+) vector at NcoI and XhoI to generate expression vector pET22-eg5 for expression of the gene in Eschrichia coli.
11p vicaptainmarvel 21-04-2023 5 2 Download
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Metagenomics allows us to acquire the potential resources from both cultivatable and uncultivable microorganisms in the environment. Here, shotgun metagenome sequencing was used to investigate microbial communities from the surface layer of low grade copper tailings that were industrially bioleached at the Dexing Copper Mine, China.
12p vinarcissa 21-03-2023 4 1 Download
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Cellobiohydrolase (EC 3.2.1.91) is one of the important enzymes involved in cellulose hydrolysis. In this study, the gene sequences encoding cellobiohydrolase were extracted from the metagenome DNA data of microorganisms surrounding white-rot fungi in Cuc Phuong National Park based on the KEGG database. 73 ORFs encoding cellobiohydrolase were obtained, of which 15 ORFs contained complete genes, 6 ORFs with functional regions.
8p vineville 08-02-2023 5 1 Download
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With the advances in the next-generation sequencing technologies, researchers can now rapidly examine the composition of samples from humans and their surroundings. To enhance the accuracy of taxonomy assignments in metagenomic samples, we developed a method that allows multiple mismatch probabilities from different genomes.
11p vihagrid 30-01-2023 6 3 Download
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In order to determine the role of the database in taxonomic sequence classification, we examine the influence of the database over time on k-mer-based lowest common ancestor taxonomic classification. We present three major findings: the number of new species added to the NCBI RefSeq database greatly outpaces the number of new genera; as a result, more reads are classified with newer database versions, but fewer are classified at the species level; and Bayesian-based re-estimation mitigates this effect but struggles with novel genomes.
10p vigalileogalilei 27-02-2022 11 1 Download
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Whole metagenome shotgun (WMGS) sequencing is a method that provides insights into the genomic composition and arrangement of complex microbial consortia. Here, we report how WMGS coupled with a cultivation approach allows the isolation of novel bifidobacteria from animal fecal samples.
6p vigalileogalilei 27-02-2022 12 1 Download
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We describe a method that adds long-read sequencing to a mix of technologies used to assemble a highly complex cattle rumen microbial community, and provide a comparison to short read-based methods. Long-read alignments and Hi-C linkage between contigs support the identification of 188 novel virus-host associations and the determination of phage life cycle states in the rumen microbial community.
18p vielonmusk 30-01-2022 15 0 Download
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Reconstructing genomic segments from metagenomics data is a highly complex task. In addition to general challenges, such as repeats and sequencing errors, metagenomic assembly needs to tolerate the uneven depth of coverage among organisms in a community and differences between nearly identical strains.
14p vielonmusk 30-01-2022 13 0 Download
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As metagenomic studies move to increasing numbers of samples, communities like the human gut may benefit more from the assembly of abundant microbes in many samples, rather than the exhaustive assembly of fewer samples. We term this approach leaderboard metagenome sequencing.
14p vielonmusk 30-01-2022 9 0 Download
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The MinHash algorithm has proven effective for rapidly estimating the resemblance of two genomes or metagenomes. However, this method cannot reliably estimate the containment of a genome within a metagenome. Here, we describe an online algorithm capable of measuring the containment of genomes and proteomes within either assembled or unassembled sequencing read sets.
13p vielonmusk 30-01-2022 14 0 Download