Reconstructing Draft Genomes Using Genome Resolved Metagenomics Reveal Arsenic Metabolizing Genes and Secondary Metabolites in Fresh Water Lake in Eastern India

1. Bhateria, R, Jain, D. Water quality assessment of lake water: a review. Sustain Water Resour. Manag. 2016;2:161-173.
Google Scholar | Crossref2. Zhang, K, Yang, X, Kattel, G, Lin, Q, Shen, J. Freshwater lake ecosystem shift caused by social-economic transitions in Yangtze River Basin over the past century. Sci Rep. 2018;8:17146.
Google Scholar | Crossref | Medline3. Newton, RJ, Jones, SE, Eiler, A, McMahon, KD, Bertilsson, S. A guide to the natural history of freshwater lake bacteria. Microbiol Mol Biol Rev. 2011;75:14-49.
Google Scholar | Crossref | Medline4. Ma, Y, Li, J, Wu, J, et al. Bacterial and fungal community composition and functional activity associated with lake wetland water level gradients. Sci Rep. 2018;8:760.
Google Scholar | Crossref | Medline5. Williamson, CESJ, Vincent, WF, Smol, JP. Lakes and reservoirs as sentinels, integrators, and regulators of climate change. Limnol Oceanography. 2009;54:2273-2282.
Google Scholar | Crossref6. Basu, SKZP . Rabindra Sarovar: the last oasis in the city of Kolkata, India. https://www.researchgate.net/publication/277559105_Rabindra_Sarovar_The_last_oasis_in_the_city_of_Kolkata_India. Updated 2015.
Google Scholar7. Blahova, L, Babica, P, Adamovsky, O, Kohoutek, J, Marsalek, B, Blaha, L. Analyses of cyanobacterial toxins (microcystins, cylindrospermopsin) in the reservoirs of the Czech Republic and evaluation of health risks. Environ Chem Lett. 2008;6:223-227.
Google Scholar | Crossref8. Blahova, L, Babica, P, Marsalkova, E, Marsalek, B, Blaha, L. Concentrations and seasonal trends of extracellular microcystins in freshwaters of the Czech Republic results of the national monitoring program. Clean-Soil Air Water. 2007;35:348-354.
Google Scholar | Crossref9. Yannarell, A, Kent, A. Bacteria, distribution and community structure. https://experts.illinois.edu/en/publications/bacteria-distribution-and-community-structure. Updated 2009.
Google Scholar10. Kurilkina, MI, Zakharova, YR, Galachyants, YP, et al. Bacterial community composition in the water column of the deepest freshwater Lake Baikal as determined by next-generation sequencing. FEMS Microbiol Ecol. 2016;92:fiw094.
Google Scholar | Crossref | Medline11. Thomas, F, Hehemann, JH, Rebuffet, E, Czjzek, M, Michel, G. Environmental and gut bacteroidetes: the food connection. Front Microbiol. 2011;2:93.
Google Scholar | Crossref | Medline12. Azam, F, Worden, AZ. Oceanography. Microbes, molecules, and marine ecosystems. Science. 2004;303:1622-1624.
Google Scholar | Crossref | Medline13. Boon, E, Meehan, CJ, Whidden, C, Wong, DH, Langille, MG, Beiko, RG. Interactions in the microbiome: communities of organisms and communities of genes. FEMS Microbiol Rev. 2014;38:90-118.
Google Scholar | Crossref | Medline14. Dunivin, TK, Yeh, SY, Shade, A. A global survey of arsenic-related genes in soil microbiomes. BMC Biology. 2019;17:45.
Google Scholar | Crossref | Medline15. Andres, J, Bertin, PN. The microbial genomics of arsenic. FEMS Microbiol Rev. 2016;40:299-322.
Google Scholar | Crossref | Medline16. Dunivin, TK, Miller, J, Shade, A. Taxonomically-linked growth phenotypes during arsenic stress among arsenic resistant bacteria isolated from soils overlying the Centralia coal seam fire. PLoS ONE. 2018;13:e0191893.
Google Scholar | Crossref | Medline17. Newman, DJ, Cragg, GM. Natural products as sources of new drugs from 1981 to 2014. J Natural Prod. 2016;79:629-661.
Google Scholar | Crossref | Medline | ISI18. Gokhale, RS, Sankaranarayanan, R, Mohanty, D. Versatility of polyketide synthases in generating metabolic diversity. Curr Opin Struct Biol. 2007;17:736-743.
Google Scholar | Crossref | Medline19. Koglin, A, Walsh, CT. Structural insights into nonribosomal peptide enzymatic assembly lines. Nat Prod Rep. 2009;26:987-1000.
Google Scholar | Crossref | Medline20. Wang, H, Fewer, DP, Sivonen, K. Genome mining demonstrates the widespread occurrence of gene clusters encoding bacteriocins in cyanobacteria. PLoS ONE. 2011;6:e22384.
Google Scholar21. Riley, MA, Wertz, JE. Bacteriocins: evolution, ecology, and application. Annu Rev Microbiol. 2002;56:117-137.
Google Scholar | Crossref | Medline | ISI22. Yang, SC, Lin, CH, Sung, CT, Fang, JY. Antibacterial activities of bacteriocins: application in foods and pharmaceuticals. Front Microbiol. 2014;5:241.
Google Scholar | Medline23. Cotter, PD, Ross, RP, Hill, C. Bacteriocins—a viable alternative to antibiotics? Nat Rev Microbiol. 2013;11:95-105.
Google Scholar | Crossref | Medline24. Russell, JB, Mantovani, HC. The bacteriocins of ruminal bacteria and their potential as an alternative to antibiotics. J Mol Microbiol Biotechnol. 2002;4:347-355.
Google Scholar | Medline25. Oh, S, Caro-Quintero, A, Tsementzi, D, et al. Metagenomic insights into the evolution, function, and complexity of the planktonic microbial community of Lake Lanier, a temperate freshwater ecosystem. Appl Environ Microbiol. 2011;77:6000-6011.
Google Scholar | Crossref | Medline | ISI26. Babraham, B . FastQC a quality control tool for high throughput sequence data. https://www.bioinformatics.babraham.ac.uk/projects/fastqc/.
Google Scholar27. Chen, S, Zhou, Y, Chen, Y, Gu, J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018;34:i884-i890.
Google Scholar | Crossref | Medline28. Glass, EM, Wilkening, J, Wilke, A, Antonopoulos, D, Meyer, F. Using the metagenomics RAST server (MG-RAST) for analyzing shotgun metagenomes. Cold Spring Harbor Protocols 2010;2010:pdbprot5368.
Google Scholar | Crossref | Medline29. Parks, DH, Tyson, GW, Hugenholtz, P, Beiko, RG. STAMP: statistical analysis of taxonomic and functional profiles. Bioinformatics. 2014;30:3123-3124.
Google Scholar | Crossref | Medline30. Bankevich, A, Nurk, S, Antipov, D, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012;19:455-477.
Google Scholar | Crossref | Medline | ISI31. Nurk, S, Meleshko, D, Korobeynikov, A, Pevzner, PA. metaSPAdes: a new versatile metagenomic assembler. Genome Res. 2017;27:824-834.
Google Scholar | Crossref | Medline32. Kang, DD, Froula, J, Egan, R, Wang, Z. MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities. PeerJ. 2015;3:e1165.
Google Scholar | Crossref33. Parks, DH, Imelfort, M, Skennerton, CT, Hugenholtz, P, Tyson, GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015;25:1043-1055.
Google Scholar | Crossref | Medline34. Parks, DH, Rinke, C, Chuvochina, M, et al. Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life. Nat Microbiol. 2017;2:1533-1542.
Google Scholar | Crossref | Medline35. Olm, MR, Brown, CT, Brooks, B, Banfield, JF. dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. ISME J. 2017;11:2864-2868.
Google Scholar | Crossref | Medline36. Bowers, RM, Kyrpides, NC, Stepanauskas, R, et al. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nat Biotechnol. 2017;35:725-731.
Google Scholar | Crossref | Medline37. Rodriguez, RL, Gunturu, S, Harvey, WT, et al. The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level. Nucleic Acids Res. 2018;46:W282-W288.
Google Scholar | Crossref38. Chaumeil, PA, Mussig, AJ, Hugenholtz, P, Parks, DH. GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics. 2019;36:1925-1927.
Google Scholar39. Seemann, T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30:2068-2069.
Google Scholar | Crossref | Medline | ISI40. Overbeek, R, Olson, R, Pusch, GD, et al. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res. 2014;42:D206-D214.
Google Scholar | Crossref41. Szklarczyk, D, Franceschini, A, Wyder, S, et al. STRING v10: protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Res. 2015;43:D447-D452.
Google Scholar | Crossref | Medline42. Kanehisa, M, Sato, Y, Morishima, K. BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences. J Mol Biol. 2016;428:726-731.
Google Scholar | Crossref | Medline43. Pritchard, LGR, Humphris, S, Elphinstone, JG, Toth, IK. Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens. Anal Methods. 2016;8:12-24.
Google Scholar | Crossref44. Parks, DH. CompareM: a software toolkit which supports performing large-scale comparative genomic analyses. https://github.com/dparks1134/CompareM. Updated 2014.
Google Scholar45. Team, R. Core. R: A language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing; 2013.
Google Scholar46. Na, SI, Kim, YO, Yoon, SH, Ha, SM, Baek, I, Chun, J. UBCG: up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol. 2018;56:280-285.
Google Scholar | Crossref | Medline47. Letunic, I, Bork, P. Interactive Tree Of Life (iTOL) v4: recent updates and new developments. Nucleic Acids Res. 2019;47:W256-W259.
Google Scholar | Crossref48. Yin, Y, Mao, X, Yang, J, Chen, X, Mao, F, Xu, Y. dbCAN: a web resource for automated carbohydrate-active enzyme annotation. Nucleic Acids Res. 2012;40:W445-W451.
Google Scholar | Crossref49. van Heel, AJ, de Jong, A, Song, C, Viel, JH, Kok, J, Kuipers, OP. BAGEL4: a user-friendly web server to thoroughly mine RiPPs and bacteriocins. Nucleic Acids Res. 2018;46:W278-W281.
Google Scholar | Medline50. Grissa, I, Vergnaud, G, Pourcel, C. The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats. BMC Bioinformatics. 2007;8:172.
Google Scholar | Crossref | Medline51. Arndt, D, Grant, JR, Marcu, A, et al. PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Res. 2016;44:W16-W21.
Google Scholar | Crossref52. Varani, AM, Siguier, P, Gourbeyre, E, Charneau, V, Chandler, M. ISsaga is an ensemble of web-based methods for high throughput identification and semi-automatic annotation of insertion sequences in prokaryotic genomes. Genome Biol. 2011;12:R30.
Google Scholar | Crossref | Medline53. Altschul, SF, Gish, W, Miller, W, Myers, EW, Lipman, DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403-410.
Google Scholar | Crossref | Medline | ISI54. Saier, MH, Tran, CV, Barabote, RD. TCDB: the Transporter Classification Database for membrane transport protein analyses and information. Nucleic Acids Res. 2006;34:D181-186.
Google Scholar | Crossref | Medline55. Medema, MH, Blin, K, Cimermancic, P, et al. antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. Nucleic Acids Res. 2011;39:W339-W346.
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