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Functional metagenomics
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Recent evidence suggests that immunotherapy efficacy in melanoma is modulated by gut microbiota. Few studies have examined this phenomenon in humans, and none have incorporated metatranscriptomics, important for determining expression of metagenomic functions in the microbial community.
14p
vibransone
28-03-2024
7
2
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Antimicrobial-resistant bacteria and their antimicrobial resistance (AMR) genes can spread by hitchhiking in human guts. International travel can exacerbate this public health threat when travelers acquire AMR genes endemic to their destinations and bring them back to their home countries.
21p
vibransone
28-03-2024
2
2
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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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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
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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
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Gut microbiome community composition differs between cervical cancer (CC) patients and healthy controls, and increased gut diversity is associated with improved outcomes after treatment. We proposed that functions of specific microbial species adjoining the mucus layer may directly impact the biology of CC.
16p
vialfrednobel
23-12-2023
5
3
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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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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
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In ruminants, early rumen development is vital for efficient fermentation that converts plant materials to human edible food such as milk and meat. Here, we investigate the extent and functional basis of host-microbial interactions regulating rumen development during the first 6 weeks of life.
16p
vielonmusk
30-01-2022
16
0
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The ocean microbiome represents one of the largest microbiomes and produces nearly half of the primary energy on the planet through photosynthesis or chemosynthesis. Using recent advances in marine genomics, we explore new applications of oceanic metagenomes for protein structure and function prediction.
14p
vielonmusk
30-01-2022
10
0
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Microbial populations exhibit functional changes in response to different ambient environments. Although whole metagenome sequencing promises enough raw data to study those changes, existing tools are limited in their ability to directly compare microbial metabolic function across samples and studies.
18p
viarchimedes
26-01-2022
7
0
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Eubacterium rectale is one of the most prevalent human gut bacteria, but its diversity and population genetics are not well understood because large-scale whole-genome investigations of this microbe have not been carried out.
27p
viarchimedes
26-01-2022
15
1
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Genomes computationally inferred from large metagenomic data sets are often incomplete and may be missing functionally important content and strain variation. We introduce an information retrieval system for large metagenomic data sets that exploits the sparsity of DNA assembly graphs to efficiently extract subgraphs surrounding an inferred genome.
16p
viarchimedes
26-01-2022
6
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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Expression screening of environmental DNA (eDNA) libraries is a popular approach for the identification and characterization of novel microbial enzymes with promising biotechnological properties. In such “functional metagenomics” experiments, inserts, selected on the basis of activity assays, are sequenced with high throughput sequencing technologies. Assembly is followed by gene prediction, annotation and identification of candidate genes that are subsequently evaluated for biotechnological applications.
10p
vilarryellison
29-10-2021
9
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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Composting is an important technique for environment-friendly degradation of organic material, and is a microbe-driven process. Previous metagenomic studies of composting have presented a general description of the taxonomic and functional diversity of its microbial populations, but they have lacked more specific information on the key organisms that are active during the process.
19p
vitzuyu2711
29-09-2021
4
2
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Diversity-generating retroelements (DGRs) are a unique family of retroelements that generate sequence diversity of DNA to benefit their hosts by introducing variations and accelerating the evolution of target proteins.
11p
visilicon2711
20-08-2021
9
1
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Human gut microbial communities have been known to produce vitamins, which are subsequently absorbed by the host in the large intestine. However, the relationship between species with vitamin pathway associated functional features or their gene abundance in different states of health and disease is lacking.
11p
visilicon2711
20-08-2021
9
2
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Metagenomes can be analysed using different approaches and tools. One of the most important distinctions is the way to perform taxonomic and functional assignment, choosing between the use of assembly algorithms or the direct analysis of raw sequence reads instead by homology searching, k-mer analysys, or detection of marker genes.
16p
viansan2711
30-07-2021
15
2
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