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1. Assessing taxonomic metagenome profilers with OPAL

Author:
Meyer, Fernando; Bremges, Andreas; Belmann, Peter; Janssen, Stefan; McHardy, Alice C.; Koslicki, David
Source:
Genome biology 2019 v.20 no.1 pp. 51
ISSN:
1474-760X
Subject:
metagenomics,   etc   ; data collection; humans; microbiome;     Show all 4 Subjects
Abstract:
... The explosive growth in taxonomic metagenome profiling methods over the past years has created a need for systematic comparisons using relevant performance criteria. The Open-community Profiling Assessment tooL (OPAL) implements commonly used performance metrics, including those of the first challenge of the initiative for the Critical Assessment of Metagenome Interpretation (CAMI), together with ...
DOI:
10.1186/s13059-019-1646-y

2. A metagenomic analysis of the pre-enrichment step for the isolation of Salmonella spp. from pig feces

Author:
Langlais, Mélodie; Thibodeau, Alexandre; Fravalo, Philippe
Source:
Journal of microbiological methods 2019 v.157 pp. 43-46
ISSN:
0167-7012
Subject:
metagenomics,   etc   ; Salmonella; bacteria; feces; swine;     Show all 5 Subjects
Abstract:
... The bacterial short pre-enrichment culture step is important for the proper detection and isolation of Salmonella spp. from pig feces. Using metagenomics, we showed that pre-enrichment of Salmonella was favored not only by inhibiting the growth of competing bacteria but also by increasing its fitness. ...
DOI:
10.1016/j.mimet.2018.12.014

3. bin3C: exploiting Hi-C sequencing data to accurately resolve metagenome-assembled genomes

Author:
DeMaere, Matthew Z.; Darling, Aaron E.
Source:
Genome biology 2019 v.20 no.1 pp. 46
ISSN:
1474-760X
Subject:
metagenomics,   etc   ; algorithms; genome; microorganisms; time series analysis;     Show all 5 Subjects
Abstract:
... Most microbes cannot be easily cultured, and metagenomics provides a means to study them. Current techniques aim to resolve individual genomes from metagenomes, so-called metagenome-assembled genomes (MAGs). Leading approaches depend upon time series or transect studies, the efficacy of which is a function of community complexity, target abundance, and sequencing depth. We describe an unsupervised ...
DOI:
10.1186/s13059-019-1643-1

4. Correction to: Comprehensive benchmarking and ensemble approaches for metagenomic classifiers

Author:
McIntyre, Alexa B. R.; Ounit, Rachid; Afshinnekoo, Ebrahim; Prill, Robert J.; Hénaff, Elizabeth; Alexander, Noah; Minot, Samuel S.; Danko, David; Foox, Jonathan; Ahsanuddin, Sofia; Tighe, Scott; Hasan, Nur A.; Subramanian, Poorani; Moffat, Kelly; Levy, Shawn; Lonardi, Stefano; Greenfield, Nick; Colwell, Rita R.; Rosen, Gail L.; Mason, Christopher E.
Source:
Genome biology 2019 v.20 no.1 pp. 72
ISSN:
1474-760X
Subject:
metagenomics,   etc   ; genetic techniques and protocols; genome;     Show all 3 Subjects
Abstract:
... Following publication of the original article [1], the authors would like to highlight the following two corrections. ...
DOI:
10.1186/s13059-019-1687-2

5. Correction to: A metagenomic study of the rumen virome in domestic caprids

Author:
Namonyo, Samuel; Wagacha, Maina; Maina, Solomon; Wambua, Lillian; Agaba, Morris
Source:
Archives of virology 2018 v.163 no.12 pp. 3421
ISSN:
0304-8608
Subject:
metagenomics,   etc   ; goats; rumen;     Show all 3 Subjects
Abstract:
... Unfortunately, the original article was online published with error in the results section. The error is correction by this erratum. ...
DOI:
10.1007/s00705-018-4046-9

6. Correction to: Genome-resolved metagenomics of sugarcane vinasse bacteria

Author:
Cassman, Noriko A.; Lourenço, Késia S.; do Carmo, Janaína B.; Cantarella, Heitor; Kuramae, Eiko E.
Source:
Biotechnology for biofuels 2018 v.11 no.1 pp. 270
ISSN:
1754-6834
Subject:
metagenomics,   etc   ; bacteria; sugarcane; vinasse;     Show all 4 Subjects
Abstract:
... The original version of the article contained a mistake. The accession number has been incorrectly published in the Availability of data and materials section. ...
DOI:
10.1186/s13068-018-1254-1

7. Marine Synechococcus isolates representing globally abundant genomic lineages demonstrate a unique evolutionary path of genome reduction without a decrease in GC content

Author:
Lee, Michael D.; Ahlgren, Nathan A.; Kling, Joshua D.; Walworth, Nathan G.; Rocap, Gabrielle; Saito, Mak A.; Hutchins, David A.; Webb, Eric A.
Source:
Environmental microbiology 2019 v.21 no.5 pp. 1677-1686
ISSN:
1462-2912
Subject:
metagenomics,   etc   ; Prochlorococcus; Synechococcus; carbon cycle; genome; geographical distribution; oceanography; oceans;     Show all 8 Subjects
Abstract:
... Synechococcus, a genus of unicellular cyanobacteria found throughout the global surface ocean, is a large driver of Earth's carbon cycle. Developing a better understanding of its diversity and distributions is an ongoing effort in biological oceanography. Here, we introduce 12 new draft genomes of marine Synechococcus isolates spanning five clades and utilize ~100 environmental metagenomes largely ...
DOI:
10.1111/1462-2920.14552

8. Metagenomic analysis of the inhibitory effect of chromium on microbial communities and removal efficiency in A2O sludge

Author:
Sun, Fu-Lin; Fan, Lei-Lei; Wang, You-Shao; Huang, Li-Yan
Source:
Journal of hazardous materials 2019 v.368 pp. 523-529
ISSN:
0304-3894
Subject:
metagenomics,   etc   ; biochemical pathways; chromium; denitrification; genes; microbial communities; microorganisms; sludge;     Show all 8 Subjects
Abstract:
... This is the first study exploring the effects of persistent Cr(VI) treatment on microbial communities and function as well as the process efficiency of an A2O system. The inhibitory effect was clearly higher at a high Cr(VI) concentration than a low Cr(VI) concentration, and different Cr(VI) concentrations had distinct effects on the microbial communities as well as on the performance efficiency o ...
DOI:
10.1016/j.jhazmat.2019.01.076

9. Genome-scale phylogenetics reveals a monophyletic Zoopagales (Zoopagomycota, Fungi)

Author:
Davis, William J.; Amses, Kevin R.; Benny, Gerald L.; Carter-House, Derreck; Chang, Ying; Grigoriev, Igor; Smith, Matthew E.; Spatafora, Joseph W.; Stajich, Jason E.; James, Timothy Y.
Source:
Molecular phylogenetics and evolution 2019 v.133 pp. 152-163
ISSN:
1055-7903
Subject:
metagenomics,   etc   ; Nematoda; Rotifera; Zoopagales; fungi; genome; monophyly; mycoparasites; predators; proteins;     Show all 10 Subjects
Abstract:
... Previous genome-scale phylogenetic analyses of Fungi have under sampled taxa from Zoopagales; this order contains many predacious or parasitic genera, and most have never been grown in pure culture. We sequenced the genomes of 4 zoopagalean taxa that are predators of amoebae, nematodes, or rotifers and the genome of one taxon that is a parasite of amoebae using single cell sequencing methods with ...
DOI:
10.1016/j.ympev.2019.01.006

10. Cyanobacterial diversity in the algal–bacterial consortia from Subarctic regions: new insights from the rock baths at White Sea Coast

Author:
Kublanovskaya, A.; Chekanov, K.; Solovchenko, A.; Lobakova, E.
Source:
Hydrobiologia 2019 v.830 no.1 pp. 17-31
ISSN:
0018-8158
Subject:
metagenomics,   etc   ; Cyanobacteria; coasts; databases; environmental factors; habitats; microbial communities; taxonomy;     Show all 8 Subjects
Abstract:
... Cyanobacteria characterized by exceptional tolerance to environmental stresses often become pioneer settlers in habitats with harsh conditions. There, they can constitute the core of microbial communities. The taxonomic composition of the cyanobacterial component of algal–bacterial consortia dwelling in a habitat with particularly harsh conditions (rock baths at the coast of Kandalaksha Bay of the ...
DOI:
10.1007/s10750-018-3844-0

11. Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle

Author:
Pasolli, Edoardo; Asnicar, Francesco; Manara, Serena; Zolfo, Moreno; Karcher, Nicolai; Armanini, Federica; Beghini, Francesco; Manghi, Paolo; Tett, Adrian; Ghensi, Paolo; Collado, Maria Carmen; Rice, Benjamin L.; DuLong, Casey; Morgan, Xochitl C.; Golden, Christopher D.; Quince, Christopher; Huttenhower, Curtis; Segata, Nicola
Source:
Cell 2019 v.176 no.3 pp. 649-662.e20
ISSN:
0092-8674
Subject:
metagenomics,   etc   ; genes; geography; humans; infant development; lifestyle; microbiome; microorganisms; mouth;     Show all 9 Subjects
Abstract:
... The body-wide human microbiome plays a role in health, but its full diversity remains uncharacterized, particularly outside of the gut and in international populations. We leveraged 9,428 metagenomes to reconstruct 154,723 microbial genomes (45% of high quality) spanning body sites, ages, countries, and lifestyles. We recapitulated 4,930 species-level genome bins (SGBs), 77% without genomes in pub ...
DOI:
10.1016/j.cell.2019.01.001

12. Molecular and Evolutionary Determinants of Bacteriophage Host Range

Author:
de Jonge, Patrick A.; Nobrega, Franklin L.; Brouns, Stan J.J.; Dutilh, Bas E.
Source:
Trends in microbiology 2019 v.27 no.1 pp. 51-63
ISSN:
0966-842X
Subject:
metagenomics,   etc   ; bacteriophages; evolution; host range; hosts; models; species diversity;     Show all 7 Subjects
Abstract:
... The host range of a bacteriophage is the taxonomic diversity of hosts it can successfully infect. Host range, one of the central traits to understand in phages, is determined by a range of molecular interactions between phage and host throughout the infection cycle. While many well studied model phages seem to exhibit a narrow host range, recent ecological and metagenomics studies indicate that ph ...
DOI:
10.1016/j.tim.2018.08.006

13. ASAR: visual analysis of metagenomes in R

Author:
Orakov, Askarbek N; Sakenova, Nazgul K; Sorokin, Anatoly; Goryanin, Igor I
Source:
Bioinformatics 2018 v.34 no.8 pp. 1404-1405
ISSN:
1460-2059
Subject:
metagenomics,   etc   ; bioinformatics; microbial communities; taxonomy;     Show all 4 Subjects
Abstract:
... Functional and taxonomic analyses are critical steps in understanding interspecific interactions within microbial communities. Currently, such analyses are run separately, which complicates interpretation of results. Here we present the ASAR interactive tool for simultaneous analysis of metagenomic data in three dimensions: taxonomy, function, metagenome. An interactive data analysis tool for sele ...
DOI:
10.1093/bioinformatics/btx775

14. Using Metagenomics to Characterize an Expanding Virosphere

Author:
Zhang, Yong-Zhen; Shi, Mang; Holmes, Edward C.
Source:
Cell 2018 v.172 no.6 pp. 1168-1172
ISSN:
0092-8674
Subject:
metagenomics,   etc   ; RNA viruses; genome; viruses;     Show all 4 Subjects
Abstract:
... We know less about viruses than any other lifeform. Fortunately, metagenomics has led to a massive expansion in the known diversity of the virosphere. Here, we discuss how metagenomics has changed our understanding of RNA viruses and present some of the remaining challenges, including characterization of the “dark matter” of divergent viral genomes. ...
DOI:
10.1016/j.cell.2018.02.043

15. Characterisation of three novel α-L-arabinofuranosidases from a compost metagenome

Author:
Fortune, Brent; Mhlongo, Sizwe; van Zyl, Leonardo Joaquim; Huddy, Robert; Smart, Mariette; Trindade, Marla
Source:
BMC biotechnology 2019 v.19 no.1 pp. 22
ISSN:
1472-6750
Subject:
metagenomics,   etc   ; Escherichia coli; alpha-N-arabinofuranosidase; cellobiose; composts; genes; hydrolysis; pH; synergism; temperature; thermal stability;     Show all 11 Subjects
Abstract:
... BACKGROUND: The importance of the accessory enzymes such as α-L-arabinofuranosidases (AFases) in synergistic interactions within cellulolytic mixtures has introduced a paradigm shift in the search for hydrolytic enzymes. The aim of this study was to characterize novel AFase genes encoding enzymes with differing temperature optima and thermostabilities for use in hydrolytic cocktails. RESULTS: Thre ...
DOI:
10.1186/s12896-019-0510-1

16. Increasing diversity of swine parvoviruses and their epidemiology in African pigs

Author:
Afolabi, Kayode Olayinka; Iweriebor, Benson Chuks; Okoh, Anthony Ifeanyi; Obi, Larry Chikwelu
Source:
Infection, genetics, and evolution 2019 v.73 pp. 175-183
ISSN:
1567-1348
Subject:
metagenomics,   etc   ; Parvovirinae; epidemiological studies; herds; monitoring; pathogens; pork industry; swine; viruses; Africa;     Show all 10 Subjects
Abstract:
... Detection of infectious viral agents has been on the increase globally with the advent and usage of more sensitive and selective novel molecular techniques in the epidemiological study of viral diseases of economic importance to the swine industry. The observation is not different for the pig-infecting member of the subfamily Parvovirinae in the family Parvoviridae as the application of novel mole ...
DOI:
10.1016/j.meegid.2019.04.029

17. ARGA, a pipeline for primer evaluation on antibiotic resistance genes

Author:
Wei, Ziyan; Wu, Yueni; Feng, Kai; Yang, Min; Zhang, Yu; Tu, Qichao; Wang, Jun; Deng, Ye
Source:
Environment international 2019 v.128 pp. 137-145
ISSN:
0160-4120
Subject:
metagenomics,   etc   ; amino acid sequences; antibiotic resistance genes; antibiotics; databases; molecular biology; nucleotide sequences; oligodeoxyribonucleotides; surveys;     Show all 9 Subjects
Abstract:
... Molecular biology techniques have assisted in the investigation of antibiotic resistance genes (ARGs) from various environments. However, their accuracy relies on primer quality and data interpretation, both of which require a full-coverage sequence database for ARGs. Here, based upon the abandoned Antibiotic Resistance Genes Database (ARDB), we created an updated sequence database of antibiotic r ...
DOI:
10.1016/j.envint.2019.04.030

18. Influence of swabbing solution and swab type on DNA recovery from rigid environmental surfaces

Author:
You, Hee Sang; Lee, Song Hee; Ok, Yeon Jeong; Kang, Hee-Gyu; Sung, Ho Jung; Lee, Ji Yeong; Kang, Sang Sun; Hyun, Sung Hee
Source:
Journal of microbiological methods 2019 v.161 pp. 12-17
ISSN:
0167-7012
Subject:
metagenomics,   etc   ; DNA; Escherichia coli; Staphylococcus aureus; cotton; forensic sciences; glycerol; polysorbates; sampling;     Show all 9 Subjects
Abstract:
... Determination of the metagenome has become an important component of forensic identification, which requires efficient environmental sampling techniques. Therefore, in this study, we compared the efficiency of sample collection using swabbing with cotton swabs and three types of medical swabs (S7, S22, S24) along with three different solutions: phosphate-buffered saline (PBS), 1% Tween 20 + 1% gly ...
DOI:
10.1016/j.mimet.2019.04.011

19. Mining of camel rumen metagenome to identify novel alkali-thermostable xylanase capable of enhancing the recalcitrant lignocellulosic biomass conversion

Author:
Ariaeenejad, Shohreh; Maleki, Morteza; Hosseini, Elnaz; Kavousi, Kaveh; Moosavi-Movahedi, Ali A.; Salekdeh, Ghasem Hosseini
Source:
Bioresource technology 2019 v.281 pp. 343-350
ISSN:
0960-8524
Subject:
metagenomics,   etc   ; DNA; biomass; biotransformation; camels; genes; lignocellulose; mining; pH; rumen; screening; temperature; thermal stability; xylanases;     Show all 14 Subjects
Abstract:
... The aim of this study was to isolate and characterize novel alkali-thermostable xylanase genes from the mixed genome DNA of camel rumen metagenome. In this study, a five-stage computational screening procedure was utilized to find the primary candidate enzyme with superior properties from the camel rumen metagenome. This enzyme was subjected to cloning, purification, and structural and functional ...
DOI:
10.1016/j.biortech.2019.02.059

20. Microbial synergistic interactions for reductive dechlorination of polychlorinated biphenyls

Author:
Wang, Shanquan; Chen, Chen; Zhao, Siyan; He, Jianzhong
Source:
The Science of the total environment 2019 v.666 pp. 368-376
ISSN:
0048-9697
Subject:
metagenomics,   etc   ; Dehalococcoides mccartyi; Desulfovibrio; Methanosarcina; beneficial microorganisms; dechlorination; enzymes; microbial communities; polychlorinated biphenyls; synergism;     Show all 10 Subjects
Abstract:
... Dehalococcoides usually work closely with other beneficial microorganisms for removal of halogenated organic compounds at contaminated sites. Traditional microbial cultivation is necessary but not enough to gain insights into key microbial populations and their interactions in complex communities. In this study, we cultivated and characterized two D. mccartyi strains (CG3 and SG1), and further rev ...
DOI:
10.1016/j.scitotenv.2019.02.283