in

Benchmarking microbial growth rate predictions from metagenomes

  • 1.

    Kirchman DL. Growth rates of microbes in the oceans. Annu Rev Mar Sci. 2016;8:285–309.

    Google Scholar 

  • 2.

    Koch BJ, McHough TA, Hayer M, Schwartz E, Blazewicz SJ, Dijkstra P, et al. Estimating taxon-specific population dynamics in diverse microbial communities. Ecosphere. 2018;9:e02090.

    Google Scholar 

  • 3.

    Vieira-Silva S, Rocha EPC. The systemic imprint of growth and its uses in ecological (meta)genomics. PLoS Genet. 2010;6:e1000808.

    PubMed  PubMed Central  Google Scholar 

  • 4.

    Korem T, Zeevi D, Suez J, Weinberger A, Avnit-Sagi T, Pompan-Lotan M, et al. Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samples. Science. 2015;349:1101–6.

    CAS  PubMed  PubMed Central  Google Scholar 

  • 5.

    Brown CT, Olm MR, Thomas BC, Banfield JF. Measurement of bacterial replication rates in microbial communities. Nat Biotechnol. 2016;34:1256–63.

    CAS  PubMed  PubMed Central  Google Scholar 

  • 6.

    Emiola A, Oh J. High throughput in situ metagenomic measurement of bacterial replication at ultra-low sequencing coverage. Nat Commun. 2018;9:4956.

    PubMed  PubMed Central  Google Scholar 

  • 7.

    Gao Y, Li H. Quantifying and comparing bacterial growth dynamics in multiple metagenomic samples. Nat Methods. 2018;15:1041–4.

    CAS  PubMed  PubMed Central  Google Scholar 

  • 8.

    Noble RT, Fuhrman JA. Use of SYBR Green I for rapid epifluorescence counts of marine viruses and bacteria. Aquat Microb Ecol. 1998;14:113–8.

    Google Scholar 

  • 9.

    Hobbie JE, Daley RJ, Jasper S. Use of nuclepore filters for counting bacteria by fluorescence microscopy. Appl Environ Microbiol. 1977;33:1225–8.

    CAS  PubMed  PubMed Central  Google Scholar 

  • 10.

    Didion JP, Martin M, Collins FS. Atropos: specific, sensitive, and speedy trimming of sequencing reads. PeerJ. 2017;5:e3720.

    PubMed  PubMed Central  Google Scholar 

  • 11.

    Joshi NA, Fass JN. Sickle: asliding-window, adaptive, quality-based trimming tool for FastQ files (Version 1.33) [Software]. 2011. https://github.com/najoshi/sickle.

  • 12.

    Andrews S. FastQC: a quality control tool for high throughput sequence data. 2010. http://www.bioinformatics.babraham.ac.uk/projects/fastqc.

  • 13.

    Nurk S, Meleshko D, Korobeynikov A, Pevzner PA. metaSPAdes: a new versatile metagenomic assembler. Genome Res. 2017;27:824–34.

    CAS  PubMed  PubMed Central  Google Scholar 

  • 14.

    Shen W, Le S, Li Y, Hu F. SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation. PLoS ONE. 2016;11:e0163962.

    PubMed  PubMed Central  Google Scholar 

  • 15.

    Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature. 2005;437:376–80.

    CAS  PubMed  PubMed Central  Google Scholar 

  • 16.

    Treangen TJ, Sommer DD, Angly FE, Koren S, Pop M. Next generation sequence assembly with AMOS. Curr Protoc Bioinformatics. 2011;11:11.8.

  • 17.

    Li W, Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics. 2006;22:1658–9.

    CAS  PubMed  Google Scholar 

  • 18.

    Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM.  arXiv. 2013;1303.3997v2.

  • 19.

    Uritskiy GV, DiRuggiero J, Taylor J. MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis. Microbiome. 2018;6:158.

    PubMed  PubMed Central  Google Scholar 

  • 20.

    Kang DD, Li F, Kirton E, Thomas A, Egan R, An H, et al. MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies. PeerJ. 2019;7:e7359. https://doi.org/10.7717/peerj.7359.

    PubMed  PubMed Central  Google Scholar 

  • 21.

    Alneberg J, Bjarnason BS, de Bruijn I, Schirmer M, Quick J, Ijaz UZ, et al. Binning metagenomic contigs by coverage and composition. Nat Methods. 2014;11:1144.

    CAS  PubMed  Google Scholar 

  • 22.

    Wu Y-W, Simmons BA, Singer SW. MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets. Bioinformatics. 2016;32:605–7.

    CAS  PubMed  Google Scholar 

  • 23.

    Eren AM, Murat Eren A, Esen ÖC, Quince C, Vineis JH, Morrison HG, et al. Anvi’o: an advanced analysis and visualization platform for ‘omics data. PeerJ. 2015;3:e1319.

    PubMed  PubMed Central  Google Scholar 

  • 24.

    Nissen JN, Sonderby CK, Armenteros JJA, Groenbech CH, Nielsen HB, Petersen TN, et al. Binning microbial genomes using deep learning. bioRxiv. 2018:490078. bioRxiv preprint https://doi.org/10.1101/490078.

  • 25.

    Graham ED, Heidelberg JF, Tully BJ. BinSanity: unsupervised clustering of environmental microbial assemblies using coverage and affinity propagation. PeerJ. 2017;5:e3035.

    PubMed  PubMed Central  Google Scholar 

  • 26.

    Sieber CMK, Probst AJ, Sharrar A, Thomas BC, Hess M, Tringe SG, et al. Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy. Nat Microbiol. 2018;3:836.

    CAS  PubMed  PubMed Central  Google Scholar 

  • 27.

    Parks DH, Chuvochina M, Waite DW, Rinke C, Skarshewski A, Chaumeil P-A, et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol. 2018;36:996–1004.

    CAS  PubMed  Google Scholar 

  • 28.

    Lee MD. GToTree: a user-friendly workflow for phylogenomics. Bioinformatics. 2019;35:4162–4.

    CAS  PubMed  PubMed Central  Google Scholar 

  • 29.

    Kozlov AM, Darriba D, Flouri T, Morel B, Stamatakis A. RAxML-NG: a fast, scalable, and user-friendly tool for maximum likelihood phylogenetic inference. Bioinformatics. 2019;35:4453–5.

    CAS  PubMed  PubMed Central  Google Scholar 

  • 30.

    Hyatt D, Chen G-L, Locascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinforma. 2010;11:119.

    Google Scholar 

  • 31.

    Eddy SR. Accelerated profile HMM searches. PLoS Comput Biol. 2011;7:e1002195.

    CAS  PubMed  PubMed Central  Google Scholar 

  • 32.

    Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32:1792–7.

    CAS  PubMed  PubMed Central  Google Scholar 

  • 33.

    Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics. 2009;25:1972–3.

    PubMed  PubMed Central  Google Scholar 

  • 34.

    Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9:357–9.

    CAS  PubMed  PubMed Central  Google Scholar 

  • 35.

    Harrel FE, Dupont C. Hmisc: Harrell Miscellaneous. R package version 4.2-0. 2019. https://CRAN.R-project.org/package=Hmisc.

  • 36.

    Mouriño-Pérez RR, Worden AZ, Azam F. Growth of Vibrio cholerae O1 in red tide waters off California. Appl Environ Microbiol. 2003;69:6923–31.

    PubMed  PubMed Central  Google Scholar 

  • 37.

    Liu H, Campbell L, Landry MR. Growth and mortality rates of Prochlorococcus and Synechococcus measured with a selective inhibitor technique. Mar Ecol Prog Ser. 1995;116:277–87.

    Google Scholar 

  • 38.

    Liu H, Nolla HA, Campbell L. Prochlorococcus growth rate and contribution to primary production in the equatorial and subtropical North Pacific Ocean. Aquat Microb Ecol. 1997;12:39–47.

    Google Scholar 

  • 39.

    Johnson ZI, Zinser ER, Coe A, McNulty NP, Woodward EMS, Chisholm SW. Niche partitioning among Prochlorococcus ecotypes along ocean-scale environmental gradients. Science. 2006;311:1737–40.

    CAS  PubMed  Google Scholar 

  • 40.

    Rusch DB, Halpern AL, Sutton G, Heidelberg KB, Williamson A, Yooseph S, et al. The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. PLoS Biol. 2007;5:e77.

    PubMed  PubMed Central  Google Scholar 

  • 41.

    Kashtan N, Roggensack SE, Rodrigue S, Thompson JW, Biller SJ, Coe A, et al. Single-cell genomics reveals hundreds of coexisting subpopulations in wild Prochlorococcus. Science. 2014;344:416–20.

    CAS  PubMed  Google Scholar 

  • 42.

    Aylward FO, Eppley JM, Smith JM, Chavez FP, Scholin CA, DeLong EF. Microbial community transcriptional networks are conserved in three domains at ocean basin scales. PNAS. 2015;112:5443–8.

    CAS  PubMed  Google Scholar 

  • 43.

    Roux S, Trubl G, Goudeau D, Nath N, Couradeau E, Ahlgren NA, et al. Optimizing de novo genome assembly from PCR-amplified metagenomes. PeerJ. 2019;7:e6902.

    PubMed  PubMed Central  Google Scholar 

  • 44.

    Ross A, Somssich IE. A DNA-based real-time PCR assay for robust growth quantification of the bacterial pathogen Pseudomonas syringae on Arabidopsis thaliana. Plant Methods. 2016;12:48.

    PubMed  PubMed Central  Google Scholar 

  • 45.

    Thrash JC, Seitz KW, Baker BJ, Temperton B, Gillies LE, Rabalais NN, et al. Metabolic roles of uncultivated bacterioplankton lineages in the Northern Gulf of Mexico ‘Dead Zone’. MBio. 2017;8:e01017–17.

    CAS  PubMed  PubMed Central  Google Scholar 

  • 46.

    Campbell BJ, Yu L, Straza TRA, Kirchman DL. Temporal changes in bacterial rRNA and rRNA genes in Delaware (USA) coastal waters. Aquat Microb Ecol. 2009;57:123–35.

    Google Scholar 

  • 47.

    Nikrad MP, Cottrell MT, Kirchman DL. Growth activity of gammaproteobacterial subgroups in waters off the west Antarctic Peninsula in summer and fall. Environ Microbiol. 2014;16:1513–23.

    CAS  PubMed  Google Scholar 

  • 48.

    Teira E, Martinez-Garcia S, Lonborg C, Ãlvarez-Salgado XA. Growth rates of different phylogenetic bacterioplankton groups in a coastal upwelling system. Environ Microbiol Rep. 2009;1:545–54.

    PubMed  Google Scholar 

  • 49.

    Alderkamp AC, Sintes E, Herndl GJ. Abundance and activity of major groups of prokaryotic plankton in the coastal North Sea during spring and summer. Aquat Microb Ecol. 2006;45:237–46.

    Google Scholar 

  • 50.

    Suzuki MT, Béjà O, Taylor LT, Delong EF. Phylogenetic analysis of ribosomal RNA operons from uncultivated coastal marine bacterioplankton. Environ Microbiol. 2001;3:323–31.

    CAS  PubMed  Google Scholar 

  • 51.

    Dupont CL, Rusch DB, Yooseph S, Lombardo M-J, Richter RA, Valas R, et al. Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage. ISME J. 2012;6:1186–99.

    CAS  PubMed  Google Scholar 

  • 52.

    Frigaard N-U, Martinez A, Mincer TJ, DeLong EF. Proteorhodopsin lateral gene transfer between marine planktonic Bacteria and Archaea. Nature. 2006;439:847–50.

    CAS  PubMed  Google Scholar 

  • 53.

    Hugoni M, Taib N, Debroas D, Domaizon I, Jouan Dufournel I, Bronner G, et al. Structure of the rare archaeal biosphere and seasonal dynamics of active ecotypes in surface coastal waters. Proc Natl Acad Sci USA. 2013;110:6004–9.

    CAS  PubMed  Google Scholar 

  • 54.

    Galand PE, Gutiérrez-Provecho C, Massana R, Gasol JM, Casamayor EO. Inter-annual recurrence of archaeal assemblages in the coastal NW Mediterranean Sea (Blanes Bay Microbial Observatory). Limnol Oceanogr. 2010;55:2117–25.

    Google Scholar 

  • 55.

    Martin-Cuadrado A-B, Garcia-Heredia I, Moltó AG, López-Úbeda R, Kimes N, López-García P, et al. A new class of marine Euryarchaeota group II from the Mediterranean deep chlorophyll maximum. ISME J. 2015;9:1619–34.

    CAS  PubMed  Google Scholar 

  • 56.

    Needham DM, Fichot EB, Wang E, Berdjeb L, Cram JA, Fichot CG, et al. Dynamics and interactions of highly resolved marine plankton via automated high-frequency sampling. ISME J. 2018;12:2417–32.

    CAS  PubMed  PubMed Central  Google Scholar 

  • 57.

    Mincer TJ, Church MJ, Taylor LT, Preston C, Karl DM, DeLong EF. Quantitative distribution of presumptive archaeal and bacterial nitrifiers in Monterey Bay and the North Pacific Subtropical Gyre. Environ Microbiol. 2007;9:1162–75.

    CAS  PubMed  Google Scholar 


  • Source: Ecology - nature.com

    Did our early ancestors boil their food in hot springs?

    MIT Integrative Microbiology Initiative will stimulate environmental microbiology research