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You searched for: Subject "metagenomics" Remove constraint Subject: "metagenomics"
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1. Beyond a reference genome: pangenomes and population genomics of underutilized and orphan crops for future food and nutrition security

Author:
Mark A. Chapman; Yuqi He; Meiliang Zhou
Source:
The new phytologist 2022 v.234 no.5 pp. 1583-1597
ISSN:
0028-646X
Subject:
metagenomics,   etc   ; climate change; nutrition;     Show all 3 Subjects
Abstract:
... Underutilized crops are, by definition, under‐researched compared to staple crops yet come with traits that may be especially important given climate change and the need to feed a globally increasing population. These crops are often stress‐tolerant, and this combined with unique and beneficial nutritional profiles. Whilst progress is being made by generating reference genome sequences, in this Ta ...
DOI:
10.1111/nph.18021

2. HiCBin: binning metagenomic contigs and recovering metagenome-assembled genomes using Hi-C contact maps

Author:
Yuxuan Du; Fengzhu Sun
Source:
Genome biology 2022 v.23 no.1 pp. 63
ISSN:
1474-760X
Subject:
metagenomics,   etc   ; algorithms; chromosomes; genome;     Show all 4 Subjects
Abstract:
... Recovering high-quality metagenome-assembled genomes (MAGs) from complex microbial ecosystems remains challenging. Recently, high-throughput chromosome conformation capture (Hi-C) has been applied to simultaneously study multiple genomes in natural microbial communities. We develop HiCBin, a novel open-source pipeline, to resolve high-quality MAGs utilizing Hi-C contact maps. HiCBin employs the Hi ...
DOI:
10.1186/s13059-022-02626-w

3. Music of metagenomics—a review of its applications, analysis pipeline, and associated tools [Erratum: February 2022, v.22(1); p.137]

Author:
Bilal Wajid; Faria Anwar; Imran Wajid; Haseeb Nisar; Sharoze Meraj; Ali Zafar; Mustafa Kamal Al-Shawaqfeh; Ali Riza Ekti; Asia Khatoon; Jan S. Suchodolski
Source:
Functional & integrative genomics 2022 v.22 no.1 pp. 3-26
ISSN:
1438-793X
Subject:
metagenomics,   etc   ; ecosystems; genome; music; taxonomy;     Show all 5 Subjects
Abstract:
... This humble effort highlights the intricate details of metagenomics in a simple, poetic, and rhythmic way. The paper enforces the significance of the research area, provides details about major analytical methods, examines the taxonomy and assembly of genomes, emphasizes some tools, and concludes by celebrating the richness of the ecosystem populated by the “metagenome.” ...
DOI:
10.1007/s10142-021-00810-y

4. MLR-OOD: A Markov Chain Based Likelihood Ratio Method for Out-Of-Distribution Detection of Genomic Sequences

Author:
Xin Bai; Jie Ren; Fengzhu Sun
Source:
Journal of molecular biology 2022 pp. 167586
ISSN:
0022-2836
Subject:
metagenomics,   etc   ; Markov chain; molecular biology; plasmids;     Show all 4 Subjects
Abstract:
... Machine learning or deep learning models have been widely used for taxonomic classification of metagenomic sequences and many studies reported high classification accuracy. Such models are usually trained based on sequences in several training classes in hope of accurately classifying unknown sequences into these classes. However, when deploying the classification models on real testing data sets, ...
DOI:
10.1016/j.jmb.2022.167586

5. Numerous variants of leucine rich repeats in proteins from nucleo-cytoplasmic large DNA viruses

Author:
Norio Matsushima; Robert H. Kretsinger
Source:
Gene 2022 v.817 pp. 146156
ISSN:
0378-1119
Subject:
metagenomics,   etc   ; DNA; cysteine; genes; hydrophobicity; leucine;     Show all 6 Subjects
Abstract:
... Leucine rich repeats (LRRs) occurring in tandem are 20–29 amino acids long. Eleven LRR types have been recognized. Sequence features of LRRs from viruses were investigated using over 600 LRR proteins from 89 species. Directly before, metagenome data of nucleo-cytoplasmic large dsDNA viruses (NCLDVs) have been published; the 2,074 NCLDVs encode 199,021 proteins. From the NCLDVs 547 LRR proteins wer ...
DOI:
10.1016/j.gene.2021.146156

6. PIMGAVir and Vir-MinION: Two Viral Metagenomic Pipelines for Complete Baseline Analysis of 2nd and 3rd Generation Data

Author:
Emilio Mastriani; Kathrina Mae Bienes; Gary Wong; Nicolas Berthet
Source:
Viruses 2022 v.14 no.6 pp. -
ISSN:
1999-4915
Subject:
metagenomics,   etc   ; Internet; computer software; nanopores; scientists;     Show all 5 Subjects
Abstract:
... The taxonomic classification of viral sequences is frequently used for the rapid identification of pathogens, which is a key point for when a viral outbreak occurs. Both Oxford Nanopore Technologies (ONT) MinION and the Illumina (NGS) technology provide efficient methods to detect viral pathogens. Despite the availability of many strategies and software, matching them can be a very tedious and tim ...
DOI:
10.3390/v14061260

7. Diverse heliorhodopsins detected via functional metagenomics in freshwater Actinobacteria, Chloroflexi and Archaea

Author:
Ariel Chazan; Andrey Rozenberg; Kentaro Mannen; Takashi Nagata; Ran Tahan; Shir Yaish; Shirley Larom; Keiichi Inoue; Oded Béjà; Alina Pushkarev
Source:
Environmental microbiology 2022 v.24 no.1 pp. 110-121
ISSN:
1462-2912
Subject:
metagenomics,   etc   ; Actinobacteria; Archaea; Chloroflexi; freshwater; microbiology; rhodopsin;     Show all 7 Subjects
Abstract:
... The recently discovered rhodopsin family of heliorhodopsins (HeRs) is abundant in diverse microbial environments. So far, the functional and biological roles of HeRs remain unknown. To tackle this issue, we combined experimental and computational screens to gain some novel insights. Here, 10 readily expressed HeR genes were found using functional metagenomics on samples from two freshwater environ ...
DOI:
10.1111/1462-2920.15890

8. Performance of Five Metagenomic Classifiers for Virus Pathogen Detection Using Respiratory Samples from a Clinical Cohort

Author:
Ellen C. Carbo; Igor A. Sidorov; Anneloes L. van Rijn-Klink; Nikos Pappas; Sander van Boheemen; Hailiang Mei; Pieter S. Hiemstra; Tomas M. Eagan; Eric C. J. Claas; Aloys C. M. Kroes; Jutte J. C. de Vries
Source:
Pathogens 2022 v.11 no.3 pp. -
ISSN:
2076-0817
Subject:
metagenomics,   etc   ; genome; humans; microbial detection; sequence diversity; viruses;     Show all 6 Subjects
Abstract:
... Viral metagenomics is increasingly applied in clinical diagnostic settings for detection of pathogenic viruses. While several benchmarking studies have been published on the use of metagenomic classifiers for abundance and diversity profiling of bacterial populations, studies on the comparative performance of the classifiers for virus pathogen detection are scarce. In this study, metagenomic data ...
DOI:
10.3390/pathogens11030340

9. Data Filtering Algorithm for DNA Metabarcoding Studies of Ecological Communities

Author:
A. Yu. Krasnopeev; Yu. S. Bukin; S. A. Potapov; O. I. Belykh
Source:
Russian journal of genetics 2022 v.58 no.2 pp. 223-234
ISSN:
1022-7954
Subject:
metagenomics,   etc   ; DNA; DNA barcoding; algorithms; confidence interval; species diversity;     Show all 6 Subjects
Abstract:
... Determination of taxonomic diversity of communities is an important stage in many ecological and monitoring studies of ecosystems. As a rule, these studies involve amplicon metagenomics techniques (metabarcoding). In particular, the metagenomic approach is widely used in the analysis of microbial communities. Thus, the number (coverage) of decoded nucleotide sequences determines the representative ...
DOI:
10.1134/S1022795422020089

10. Low-rank matrix denoising for count data using unbiased Kullback-Leibler risk estimation

Author:
Jérémie Bigot; Charles Deledalle
Source:
Computational statistics & data analysis 2022 v.169 pp. 107423
ISSN:
0167-9473
Subject:
metagenomics,   etc   ; data analysis; mathematical theory; risk; risk estimate; surveys;     Show all 6 Subjects
Abstract:
... Many statistical studies are concerned with the analysis of observations organized in a matrix form whose elements are count data. When these observations are assumed to follow a Poisson or a multinomial distribution, it is of interest to focus on the estimation of either the intensity matrix (Poisson case) or the compositional matrix (multinomial case) when it is assumed to have a low rank struct ...
DOI:
10.1016/j.csda.2022.107423

11. Neutral and outlier single nucleotide polymorphisms disentangle the evolutionary history of a coastal Solanaceae species

Author:
Sebastián Guzmán; Giovanna C. Giudicelli; Caroline Turchetto; Aureliano Bombarely; Loreta B. Freitas
Source:
Molecular ecology 2022 v.31 no.10 pp. 2847-2864
ISSN:
0962-1083
Subject:
metagenomics,   etc   ; Petunia; coastal plains; ecology; genome; phylogeography; Brazil; Uruguay;     Show all 8 Subjects
Abstract:
... Speciation begins with the isolation of some individuals or subpopulations due to drivers promoting a diverging genetic distribution. Such isolation may occur, followed by different processes and pressures. Isolation‐by‐distance (IBD), isolation‐by‐adaptation (IBA), and isolation‐by‐colonization (IBC) have been recognized as the main divergence patterns. Still, it is not easy to distinguish which ...
DOI:
10.1111/mec.16441

12. Diversity in the soil virosphere: to infinity and beyond?

Author:
Simon Roux; Joanne B. Emerson
Source:
Trends in microbiology 2022 pp. -
ISSN:
0966-842X
Subject:
metagenomics,   etc   ; community structure; metabolism; microbial communities; microbiome; soil; soil microorganisms;     Show all 7 Subjects
Abstract:
... Viruses are key members of Earth’s microbiomes, shaping microbial community composition and metabolism. Here, we describe recent advances in 'soil viromics', that is, virus-focused metagenome and metatranscriptome analyses that offer unprecedented windows into the soil virosphere. Given the emerging picture of high soil viral activity, diversity, and dynamics over short spatiotemporal scales, we t ...
DOI:
10.1016/j.tim.2022.05.003

13. Fast and accurate distance‐based phylogenetic placement using divide and conquer

Author:
Metin Balaban; Yueyu Jiang; Daniel Roush; Qiyun Zhu; Siavash Mirarab
Source:
Molecular ecology resources 2022 v.22 no.3 pp. 1213-1227
ISSN:
1755-098X
Subject:
metagenomics,   etc   ; data collection; ecology; genome; microbiome; phylogeny; statistical analysis; trees;     Show all 8 Subjects
Abstract:
... Phylogenetic placement of query samples on an existing phylogeny is increasingly used in molecular ecology, including sample identification and microbiome environmental sampling. As the size of available reference trees used in these analyses continues to grow, there is a growing need for methods that place sequences on ultra‐large trees with high accuracy. Distance‐based placement methods have re ...
DOI:
10.1111/1755-0998.13527

14. Investigation of the Phageome and Prophages in French Cider, a Fermented Beverage

Author:
Pierre Ledormand; Nathalie Desmasures; Cédric Midoux; Olivier Rué; Marion Dalmasso
Source:
Microorganisms 2022 v.10 no.6 pp. -
ISSN:
2076-2607
Subject:
metagenomics,   etc   ; DNA; apples; bacteriophages; ciders; fermentation; fermented beverages; filtration; flocculation;     Show all 9 Subjects
Abstract:
... Phageomes are known to play a key role in the functioning of their associated microbial communities. The phageomes of fermented foods have not been studied thoroughly in fermented foods yet, and even less in fermented beverages. Two approaches were employed to investigate the presence of phages in cider, a fermented beverage made from apple, during a fermentation process of two cider tanks, one fr ...
DOI:
10.3390/microorganisms10061203

15. Metagenomic monitoring of soil bacterial community after the construction of a crude oil flowline

Author:
Maria Grazia Bonomo; Luana Calabrone; Laura Scrano; Sabino Aurelio Bufo; Katia Di Tomaso; Euro Buongarzone; Giovanni Salzano
Source:
Environmental monitoring and assessment 2022 v.194 no.2 pp. 48
ISSN:
0167-6369
Subject:
metagenomics,   etc   ; bioremediation; cultivation area; forests; petroleum; soil; soil bacteria; Italy;     Show all 8 Subjects
Abstract:
... This study aimed to assess the metagenomic changes of soil bacterial community after constructing a crude oil flowline in Basilicata region, Italy. Soils identified a total of 56 taxa at the phylum level and 485 at the family level, with a different taxa distribution, especially in samples collected on 2014. Since microbiological diversity occurred in the soils collected after 2013 (the reference ...
DOI:
10.1007/s10661-021-09637-3

16. Shifts of the new functional marker gene (pahE) of polycyclic aromatic hydrocarbons (PAHs) degrading bacterial population and its relationship with PAHs biodegradation

Author:
Chengyue Liang; Quanhui Ye; Yong Huang; Yun Wang; Zuotao Zhang; Hui Wang
Source:
Journal of hazardous materials 2022 v.437 pp. 129305
ISSN:
0304-3894
Subject:
metagenomics,   etc   ; bacterial communities; biodegradation; bioremediation; genes; genetic markers; mangrove sediments;     Show all 7 Subjects
Abstract:
... Identification of polycyclic aromatic hydrocarbons (PAHs) degrading bacterial populations and understanding their responses to PAHs are crucial for the designing of appropriate bioremediation strategies. In this study, the responses of PAHs-degrading bacterial populations to different PAHs were studied in terms of the compositions and abundance variations of their new functional marker gene (pahE) ...
DOI:
10.1016/j.jhazmat.2022.129305

17. Arabis alpina: A perennial model plant for ecological genomics and life‐history evolution

Author:
Stefan Wötzel; Marco Andrello; Maria C. Albani; Marcus A. Koch; George Coupland; Felix Gugerli
Source:
Molecular ecology resources 2022 v.22 no.2 pp. 468-486
ISSN:
1755-098X
Subject:
metagenomics,   etc   ; Arabidopsis thaliana; Arabis alpina; dissection; ecology; evolution; life history; models;     Show all 8 Subjects
Abstract:
... Many model organisms were chosen and achieved prominence because of an advantageous combination of their life‐history characteristics, genetic properties and also practical considerations. Discoveries made in Arabidopsis thaliana, the most renowned noncrop plant model species, have markedly stimulated studies in other species with different biology. Within the family Brassicaceae, the arctic–alpin ...
DOI:
10.1111/1755-0998.13490

18. Distribution patterns of four Termitomyces species cultivated by a fungus-growing termite, Odontotermes formosanus, in Taiwan

Author:
Masaru Hojo
Source:
Fungal ecology 2022 v.56 pp. 101136
ISSN:
1754-5048
Subject:
metagenomics,   etc   ; DNA; Odontotermes; Termitomyces; climate; databases; ecology; fruits; fungi; phylogeny; Taiwan;     Show all 11 Subjects
Abstract:
... Fungus-growing termites inoculate the obligate symbiotic fungus Termitomyces into the fungus comb in their colonies. In this study, Taiwanese Termitomyces species were determined by diagnostic PCR using the metagenome of the body of Odontotermes formosanus (the only host termite living in Taiwan) as a template. Phylogenetic analyses revealed that four different Termitomyces species are cultivated ...
DOI:
10.1016/j.funeco.2021.101136

19. Harnessing the power of multi‐omics data for predicting climate change response

Author:
Kara K. S. Layton; Ian R. Bradbury
Source:
journal of animal ecology 2022 v.91 no.6 pp. 1064-1072
ISSN:
0021-8790
Subject:
metagenomics,   etc   ; DNA methylation; animal ecology; biodiversity; climate change; epigenetics; multiomics; prediction;     Show all 8 Subjects
Abstract:
... Predicting how species will respond to future climate change is of central importance in the midst of the global biodiversity crisis, and recent work has demonstrated the utility of population genomics for improving these predictions. Here, we suggest a broadening of the approach to include other types of genomic variants that play an important role in adaptation, like structural (e.g. copy number ...
DOI:
10.1111/1365-2656.13619

20. Single-cell metagenomics and metagenomics approaches reveal extracellular electron transfer of psychrophilic electroactive biofilms

Author:
Yang Yang; Anran Fang; Kun Feng; Dawei Zhang; Huihui Zhou; Defeng Xing
Source:
Science of the total environment 2022 v.836 pp. 155606
ISSN:
0048-9697
Subject:
metagenomics,   etc   ; Geobacter; bioelectrochemistry; biofilm; cytochromes; electron transfer; environment; fimbriae; microbiome; riboflavin;     Show all 10 Subjects
Abstract:
... Revealing the metabolic functions and the extracellular electron transfer (EET) process of psychrophilic electroactive biofilms (PEB) is important for understanding the functional adaptability of electroactive bacteria (EAB) to low temperatures. In this study, single cell sorting (SCS)-based metagenomics sequencing was used to characterize the composition and function of the PEB. Biofilm microbiom ...
DOI:
10.1016/j.scitotenv.2022.155606