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1. CHEER: HierarCHical taxonomic classification for viral mEtagEnomic data via deep leaRning

Author:
Shang, Jiayu; Sun, Yanni
Source:
Methods 2021 v.189 pp. 95-103
ISSN:
1046-2023
Subject:
metagenomics,   etc   ; RNA viruses; models;     Show all 3 Subjects
Abstract:
... The fast accumulation of viral metagenomic data has contributed significantly to new RNA virus discovery. However, the short read size, complex composition, and large data size can all make taxonomic analysis difficult. In particular, commonly used alignment-based methods are not ideal choices for detecting new viral species. In this work, we present a novel hierarchical classification model named ...
DOI:
10.1016/j.ymeth.2020.05.018

2. Metagenomic tools in microbial ecology research

Author:
Taş, Neslihan; de Jong, Anniek EE; Li, Yaoming; Trubl, Gareth; Xue, Yaxin; Dove, Nicholas C
Source:
Current opinion in biotechnology 2021 v.67 pp. 184-191
ISSN:
0958-1669
Subject:
metagenomics,   etc   ; DNA; biotechnology; evolution; taxonomy;     Show all 5 Subjects
Abstract:
... Ability to directly sequence DNA from the environment permanently changed microbial ecology. Here, we review the new insights to microbial life gleaned from the applications of metagenomics, as well as the extensive set of analytical tools that facilitate exploration of diversity and function of complex microbial communities. While metagenomics is shaping our understanding of microbial functions i ...
DOI:
10.1016/j.copbio.2021.01.019

3. Combining species distribution models and population genomics underlines the determinants of range limitation in an emerging parasite

Author:
Mathieu‐Bégné, Eglantine; Loot, Géraldine; Mazé‐Guilmo, Elise; Mullet, Valentin; Genthon, Clémence; Blanchet, Simon
Source:
Ecography 2021 v.44 no.2 pp. 307-319
ISSN:
0906-7590
Subject:
metagenomics,   etc   ; ectoparasites; freshwater fish; genome; geographical distribution;     Show all 5 Subjects
Abstract:
... Understanding the drivers of species distribution is necessary in order to properly predict the future geographical ranges of colonizing species. Yet this task is challenging for species involved in intimate interactions, such as parasites, since their distribution is likely shaped by a complex interplay between environmental‐related and host‐related factors. Here we developed an original approach ...
DOI:
10.1111/ecog.05301

4. Metagenomic Information Recovery from Human Stool Samples Is Influenced by Sequencing Depth and Profiling Method

Author:
Santiago-Rodriguez, Tasha M.; Garoutte, Aaron; Adams, Emmase; Nasser, Waleed; Ross, Matthew C.; La Reau, Alex; Henseler, Zachariah; Ward, Tonya; Knights, Dan; Petrosino, Joseph F.; Hollister, Emily B.
Source:
Genes 2020 v.11 no.11
ISSN:
2073-4425
Subject:
metagenomics,   etc   ; feces; genes; microbiome;     Show all 4 Subjects
Abstract:
... Sequencing of the 16S rRNA gene (16S) has long been a go-to method for microbiome characterization due to its accessibility and lower cost compared to shotgun metagenomic sequencing (SMS). However, 16S sequencing rarely provides species-level resolution and cannot provide direct assessment of other taxa (e.g., viruses and fungi) or functional gene content. Shallow shotgun metagenomic sequencing (S ...
DOI:
10.3390/genes11111380

5. Strategies for Discovering New Antibiotics from Bacteria in the Post-Genomic Era

Author:
Zhu, Jia-Wei; Zhang, Si-Jia; Wang, Wen-Guang; Jiang, Hui
Source:
Current microbiology 2020 v.77 no.11 pp. 3213-3223
ISSN:
0343-8651
Subject:
metagenomics,   etc   ; antibiotic resistance; antibiotics;     Show all 3 Subjects
Abstract:
... New antibiotics are urgently required in clinical treatment and agriculture with the development of antimicrobial resistance. However, products discovered by repeating previous strategies are either not antibiotics or already known antibiotics. There is a growing demand for efficient strategies to discover new antibiotics. With the continuous improvement of gene sequencing technology and genomic d ...
DOI:
10.1007/s00284-020-02197-8

6. ERRATUM TO: Application of shotgun metagenomics to smoked salmon experimentally spiked: Comparison between sequencing and microbiological data using different bioinformatic approaches

Author:
De Cesare, Alessandra; Oliveri, Chiara; Lucchi, Alex; Pasquali, Frederique; Pamp, Sünje Johanna; Mordhorst, Hanne; Wylezich, Claudia; Poulsen, Casper; Manfreda, Gerardo
Source:
Italian journal of food safety 2020 v.9 no.1 pp. 8991
ISSN:
2239-7132
Subject:
metagenomics,   etc   ; bioinformatics; smoked salmon;     Show all 3 Subjects
Abstract:
... The authors would like to correct the authorship in this publication, for the below-mentioned reason. ...
DOI:
10.4081/ijfs.2020.8991
PubMed:
32300574
PubMed Central:
PMC7154600

7. Comparative genomics identifies thousands of candidate structured RNAs in human microbiomes

Author:
Fremin, Brayon J.; Bhatt, Ami S.
Source:
Genome biology 2021 v.22 no.1 pp. 100
ISSN:
1474-760X
Subject:
metagenomics,   etc   ; RNA; automation; genome; humans; microbiome; ribosomes; sequence analysis;     Show all 8 Subjects
Abstract:
... BACKGROUND: Structured RNAs play varied bioregulatory roles within microbes. To date, hundreds of candidate structured RNAs have been predicted using informatic approaches that search for motif structures in genomic sequence data. The human microbiome contains thousands of species and strains of microbes. Yet, much of the metagenomic data from the human microbiome remains unmined for structured RN ...
DOI:
10.1186/s13059-021-02319-w

8. Computational methods for chromosome-scale haplotype reconstruction

Author:
Garg, Shilpa
Source:
Genome biology 2021 v.22 no.1 pp. 101
ISSN:
1474-760X
Subject:
metagenomics,   etc   ; biodiversity; diploidy; genetic variation; genome; haplotypes; polyploidy;     Show all 7 Subjects
Abstract:
... High-quality chromosome-scale haplotype sequences of diploid genomes, polyploid genomes, and metagenomes provide important insights into genetic variation associated with disease and biodiversity. However, whole-genome short read sequencing does not yield haplotype information spanning whole chromosomes directly. Computational assembly of shorter haplotype fragments is required for haplotype recon ...
DOI:
10.1186/s13059-021-02328-9

9. Bacteriophage ecology of fermented foods: anything new under the sun?

Author:
Paillet, Thomas; Dugat-Bony, Eric
Source:
Current opinion in food science 2021 v.40 pp. 102-111
ISSN:
2214-7993
Subject:
metagenomics,   etc   ; bacteriophages; biotopes; dynamics; fermentation; food science; knowledge; microscopy; occurrence;     Show all 9 Subjects
Abstract:
... Bacteriophage ecology has raised an increasing attention over the past few years, thanks to the improvement and contributions of microscopy, comparative genomics and viral metagenomics methods. Fermented foods host dense and diverse microbial communities and, therefore, represent an ideal biotope for bacteriophages. If their occurrence in such environments has been demonstrated decades ago, data h ...
DOI:
10.1016/j.cofs.2021.03.007

10. Enzymatic and non-enzymatic functional attributes of plant microbiome

Author:
Das, Joyati; Yadav, Sunil Kumar; Ghosh, Srayan; Tyagi, Kriti; Magotra, Ankita; Krishnan, Aiswarya; Jha, Gopaljee
Source:
Current opinion in biotechnology 2021 v.69 pp. 162-171
ISSN:
0958-1669
Subject:
metagenomics,   etc   ; biotechnology; host plants; microbiome; phytobiome; plant growth; sustainable agriculture;     Show all 7 Subjects
Abstract:
... Microbiome plays an important role in plant growth and adaptation to various environmental conditions. The cross-talk between host plant and microbes (including microbe–microbe interactions) plays a crucial role in shaping the microbiome. Recent studies have highlighted that plant microbiome is enriched in genes encoding enzymes and natural products. Several novel antimicrobial compounds, bioactiv ...
DOI:
10.1016/j.copbio.2020.12.021

11. The wall lizards of the Balkan peninsula: Tackling questions at the interface of phylogenomics and population genomics

Author:
Psonis, Nikolaos; Antoniou, Aglaia; Karameta, Emmanouela; Darriba, Diego; Stamatakis, Alexandros; Lymberakis, Petros; Poulakakis, Nikos
Source:
Molecular phylogenetics and evolution 2021 v.159 pp. 107121
ISSN:
1055-7903
Subject:
metagenomics,   etc   ; genome; mitochondrial DNA; monophyly; Southern European region;     Show all 5 Subjects
Abstract:
... Wall lizards of the genus Podarcis (Sauria, Lacertidae) are the predominant reptile group in southern Europe, including 24 recognized species. Mitochondrial DNA data have shown that, with the exception of P. muralis, the Podarcis species distributed in the Balkan peninsula form a species group that is further sub-divided into two subgroups: the one of “P. tauricus” consisting of P. tauricus, P. mi ...
DOI:
10.1016/j.ympev.2021.107121

12. Metagenomic insights into dissemination of antibiotic resistance across bacterial genera in wastewater treatment

Author:
Cheng, Xiaoxiao; Xu, Jiannong; Smith, Geoffrey; Zhang, Yanyan
Source:
Chemosphere 2021 v.271 pp. 129563
ISSN:
0045-6535
Subject:
metagenomics,   etc   ; antibiotic resistance; chlorination; disinfection; host range; wastewater treatment;     Show all 6 Subjects
Abstract:
... The aim of this study was to evaluate the impacts of conventional wastewater treatment processes including secondary treatment and chlorination on the removal of antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB), and to assess the association of ARGs with their potential hosts in each treatment process. The results showed chlorination with subinhibitory concentration (<8 m ...
DOI:
10.1016/j.chemosphere.2021.129563

13. Synergistic interactions of Desulfovibrio and Petrimonas for sulfate-reduction coupling polycyclic aromatic hydrocarbon degradation

Author:
Qian, Youfen; Xu, Meiying; Deng, Tongchu; Hu, Wenzhe; He, Zhili; Yang, Xunan; Wang, Bin; Song, Da; Chen, Letian; Huang, Youda; Sun, Guoping
Source:
Journal of hazardous materials 2021 v.407 pp. 124385
ISSN:
0304-3894
Subject:
metagenomics,   etc   ; Desulfovibrio; carboxylation; metabolites; microbial communities; phenanthrenes; remediation; sediments; sulfates;     Show all 9 Subjects
Abstract:
... Microbial sulfate-reduction coupling polycyclic aromatic hydrocarbon (PAH) degradation is an important process for the remediation of contaminated sediments. However, little is known about core players and their mechanisms in this process due to the complexity of PAH degradation and the large number of microorganisms involved. Here we analyzed potential core players in a black-odorous sediment usi ...
DOI:
10.1016/j.jhazmat.2020.124385

14. Complete genomes derived by directly sequencing freshwater bloom populations emphasize the significance of the genus level ADA clade within the Nostocales

Author:
Dreher, Theo W.; Davis, Edward W.; Mueller, Ryan S.
Source:
Harmful algae 2021 v.103 pp. 102005
ISSN:
1568-9883
Subject:
metagenomics,   etc   ; Anabaena; Aphanizomenon; Dolichospermum; freshwater; genome; monophyly; morphs; poisonous algae;     Show all 9 Subjects
Abstract:
... The genome sequences of 16 Nostocales cyanobacteria have been determined. Most of them are complete or near-complete genome sequences derived by long-read metagenome sequencing of recent harmful algal blooms (HABs) in freshwater lakes without the potential bias of culture isolation. The genomes are all members of the recently recognized ADA clade (Driscoll et al., Harmful Algae, 77:93, 2018), whic ...
DOI:
10.1016/j.hal.2021.102005

15. Microbial diversity and functionality of traditional fermented milk products of India: Current scenario and future perspectives

Author:
Mallappa, Rashmi Hogarehalli; Balasubramaniam, Chandrasekhar; Nataraj, Basavaprabhu Haranahalli; Ramesh, Chette; Kadyan, Saurabh; Pradhan, Diwas; Muniyappa, Santhosh Kumar; Grover, Sunita
Source:
International dairy journal 2021 v.114 pp. 104941
ISSN:
0958-6946
Subject:
metagenomics,   etc   ; diet; fermentation; fermented milk; metabolites; metabolomics; India;     Show all 7 Subjects
Abstract:
... Fermented foods and beverages are consumed globally as an integral part of daily diet. The uniqueness of fermented milk products originated in India are an outcome of dynamic socio-cultural habits developed over the centuries. The vast microbial diversity and metabolic footprints of these products correspond to their regional specific techno-functional and sensory attributes. Though these products ...
DOI:
10.1016/j.idairyj.2020.104941

16. Molecular biology interventions for activity improvement and production of industrial enzymes

Author:
Kant Bhatia, Shashi; Vivek, Narisetty; Kumar, Vinod; Chandel, Neha; Thakur, Meenu; Kumar, Dinesh; Yang, Yung-Hun; Pugazendhi, Arivalagan; Kumar, Gopalakrishnan
Source:
Bioresource technology 2021 v.324 pp. 124596
ISSN:
0960-8524
Subject:
metagenomics,   etc   ; catalytic activity; directed evolution; molecular biology; substrate specificity; technology;     Show all 6 Subjects
Abstract:
... Metagenomics and directed evolution technology have brought a revolution in search of novel enzymes from extreme environment and improvement of existing enzymes and tuning them towards certain desired properties. Using advanced tools of molecular biology i.e. next generation sequencing, site directed mutagenesis, fusion protein, surface display, etc. now researchers can engineer enzymes for improv ...
DOI:
10.1016/j.biortech.2020.124596

17. Experimental infrastructure requirements for quantitative research on microbial communities

Author:
Kleerebezem, Robbert; Stouten, Gerben; Koehorst, Jasper; Langenhoff, Alette; Schaap, Peter; Smidt, Hauke
Source:
Current opinion in biotechnology 2021 v.67 pp. 158-165
ISSN:
0958-1669
Subject:
metagenomics,   etc   ; DNA; biotechnology; circular economy; ecosystems; infrastructure; quantitative analysis;     Show all 7 Subjects
Abstract:
... Natural microbial communities are composed of a large diversity of interacting microorganisms, each with a specific role in the functional properties of the ecosystem. The objectives in microbial ecology research are related to identifying, understanding and exploring the role of these different microorganisms. Because of the rapidly increasing power of DNA sequencing and the rapid increase of gen ...
DOI:
10.1016/j.copbio.2021.01.017

18. Metagenomic deep sequencing obtains taxonomic and functional profiles of Haemaphysalis longicornis that vary in response to different developmental stages and sexes

Author:
Zhang, Ruiling; Zhang, Qian; Yu, Guangfu; Zhang, Zhong
Source:
Experimental & applied acarology 2021 v.83 no.2 pp. 285-300
ISSN:
0168-8162
Subject:
metagenomics,   etc   ; Haemaphysalis longicornis; Proteobacteria; acarology; females; metabolism; microbial communities; ticks;     Show all 8 Subjects
Abstract:
... Ticks can transmit numerous pathogens and harbor diverse microbial communities. Considerable progress has been made in the characterization of the bacterial profiles of ticks, whereas other members of tick microbiota (such as fungi and viruses) and the functional characteristics of ticks warrant further exploration. To investigate the taxonomic and functional profiles and explore potential pathoge ...
DOI:
10.1007/s10493-020-00582-3

19. ViralRecall—A Flexible Command-Line Tool for the Detection of Giant Virus Signatures in ‘Omic Data

Author:
Aylward, Frank O.; Moniruzzaman, Mohammad
Source:
Viruses 2021 v.13 no.2
ISSN:
1999-4915
Subject:
metagenomics,   etc   ; DNA; bioinformatics; biosphere; data collection; evolution; viral genome; viruses;     Show all 8 Subjects
Abstract:
... Giant viruses are widespread in the biosphere and play important roles in biogeochemical cycling and host genome evolution. Also known as nucleo-cytoplasmic large DNA viruses (NCLDVs), these eukaryotic viruses harbor the largest and most complex viral genomes known. Studies have shown that NCLDVs are frequently abundant in metagenomic datasets, and that sequences derived from these viruses can als ...
DOI:
10.3390/v13020150

20. Library Preparation Based on Transposase Assisted RNA/DNA Hybrid Co-Tagmentation for Next-Generation Sequencing of Human Noroviruses

Author:
Zhang, Zilei; Liu, Danlei; Wang, Dapeng; Wu, Qingping
Source:
Viruses 2021 v.13 no.1
ISSN:
1999-4915
Subject:
metagenomics,   etc   ; DNA; Norovirus; RNA; humans; transposases; viral genome; virus transmission;     Show all 8 Subjects
Abstract:
... Human noroviruses (HuNoVs) are one of the leading causes of foodborne illnesses globally. The viral genome is the most essential information for viral source tracing and viral transmission pattern monitoring. However, whole genome sequencing of HuNoVs is still challenging due to the sequence heterogeneity among different genotypes and low titer in samples. To address this need, in this study, the ...
DOI:
10.3390/v13010065