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Shotgun metagenomics
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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
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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
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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
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One of the main challenges in metagenomics is the identification of microorganisms in clinical and environmental samples. While an extensive and heterogeneous set of computational tools is available to classify microorganisms using whole-genome shotgun sequencing data, comprehensive comparisons of these methods are limited.
19p
vialfrednobel
29-01-2022
13
0
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The increasing availability of microbial genomes and environmental shotgun metagenomes provides unprecedented access to the genomic differences within related bacteria. The human oral microbiome with its diverse habitats and abundant, relatively well-characterized microbial inhabitants presents an opportunity to investigate bacterial population structures at an ecosystem scale.
25p
viarchimedes
26-01-2022
11
0
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Staphylococcus aureus is a leading cause of healthcare- and community-associated infections and can be difficult to treat due to antimicrobial resistance. About 30% of individuals carry S. aureus asymptomatically in their nares, a risk factor for later infection, and interactions with other species in the nasal microbiome likely modulate its carriage.
24p
viarchimedes
26-01-2022
8
0
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African populations provide a unique opportunity to interrogate hostmicrobe co-evolution and its impact on adaptive phenotypes due to their genomic, phenotypic, and cultural diversity. We integrate gut microbiome 16S rRNA amplicon and shotgun metagenomic sequence data with quantification of pathogen burden and measures of immune parameters for 575 ethnically diverse Africans from Cameroon.
32p
viarchimedes
26-01-2022
8
0
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Microbiome/host interactions describe characteristics that affect the host's health. Shotgun metagenomics includes sequencing a random subset of the microbiome to analyze its taxonomic and metabolic potential. Reconstruction of DNA fragments into genomes from metagenomes (called metagenome-assembled genomes) assigns unknown fragments to taxa/function and facilitates discovery of novel organisms. Genome reconstruction incorporates sequence assembly and sorting of assembled sequences into bins, characteristic of a genome.
13p
vilarryellison
29-10-2021
10
1
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Exploration of large data sets, such as shotgun metagenomic sequence or expression data, by biomedical experts and medical professionals remains as a major bottleneck in the scientific discovery process. Although tools for this purpose exist for 16S ribosomal RNA sequencing analysis, there is a growing but still insufficient number of user-friendly interactive visualization workflows for easy data exploration and figure generation. The development of such platforms for this purpose is necessary to accelerate and streamline microbiome laboratory research.
11p
vibeauty
23-10-2021
10
1
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In shotgun metagenomics, microbial communities are studied through direct sequencing of DNA without any prior cultivation. By comparing gene abundances estimated from the generated sequencing reads, functional differences between the communities can be identified. However, gene abundance data is affected by high levels of systematic variability, which can greatly reduce the statistical power and introduce false positives. Normalization, which is the process where systematic variability is identified and removed, is therefore a vital part of the data analysis.
17p
vibeauty
23-10-2021
10
2
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Metagenomics is the genomic study of uncultured environmental samples, which has been greatly facilitated by the advent of shotgun-sequencing technologies. One of the main focuses of metagenomics is the discovery of previously uncultured microorganisms, which makes the assignment of sequences to a particular taxon a challenge and a crucial step.
10p
vikentucky2711
26-11-2020
10
1
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Deep shotgun sequencing on next generation sequencing (NGS) platforms has contributed significant amounts of data to enrich our understanding of genomes, transcriptomes, amplified single-cell genomes, and metagenomes.
12p
vikentucky2711
26-11-2020
14
1
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Binning environmental shotgun reads is one of the most fundamental tasks in metagenomic studies, in which mixed reads from different species or operational taxonomical units (OTUs) are separated into different groups. While dozens of binning methods are available, there is still room for improvement.
11p
vikentucky2711
26-11-2020
14
3
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A rapidly increasing flow of genomic data requires the development of efficient methods for obtaining its compact representation. Feature extraction facilitates classification, clustering and model analysis for testing and refining biological hypotheses. “Shotgun” metagenome is an analytically challenging type of genomic data - containing sequences of all genes from the totality of a complex microbial community.
11p
vioklahoma2711
19-11-2020
15
2
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The field of metagenomics (study of genetic material recovered directly from an environment) has grown rapidly, with many bioinformatics analysis methods being developed. To ensure appropriate use of such methods, robust comparative evaluation of their accuracy and features is needed.
19p
vioklahoma2711
19-11-2020
8
1
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Shotgun metagenomics based on untargeted sequencing can explore the taxonomic profile and the function of unknown microorganisms in samples, and complement the shortage of amplicon sequencing. Binning assembled sequences into individual groups, which represent microbial genomes, is the key step and a major challenge in metagenomic research.
15p
vicolorado2711
22-10-2020
16
0
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High-throughput sequencing can establish the functional capacity of a microbial community by cataloging the protein-coding sequences (CDS) present in the metagenome of the community. The relative performance of diferent computational methods for identifying CDS from whole-genome shotgun sequencing is not fully established.
13p
vicolorado2711
22-10-2020
7
0
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Microbial communities have become an important subject of research across multiple disciplines in recent years. These communities are often examined via shotgun metagenomic sequencing, a technology which can offer unique insights into the genomic content of a microbial community.
9p
vicolorado2711
22-10-2020
10
0
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Shotgun metagenomes are often assembled prior to annotation of genes which biases the functional capacity of a community towards its most abundant members. For an unbiased assessment of community function, short reads need to be mapped directly to a gene or protein database.
15p
vicolorado2711
22-10-2020
13
0
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A plant’s microbiota has various implications for the plant’s health and performance; however, the roles of many microbial lineages, particularly Archaea, have not been explored in detail. In the present study, analysis of archaea-specific 16S rRNA gene fragments and shotgun-sequenced metagenomes was combined with visualization techniques to obtain the first insights into the archaeome of a common salad plant, arugula (Eruca sativa Mill.).
10p
caygaocaolon1
13-11-2019
10
0
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