Unexpected absence of ribosomal protein genes from metagenome-assembled genomes

  • Hug LA, Baker BJ, Anantharaman K, Brown CT, Probst AJ, Castelle CJ, et al. A new view of the tree of life. Nat Microbiol. 2016;1:16048.

    Article 
    PubMed 

    Google Scholar
     

  • Castelle CJ, Wrighton KC, Thomas BC, Hug LA, Brown CT, Wilkins MJ, et al. Genomic expansion of domain archaea highlights roles for organisms from new phyla in anaerobic carbon cycling. Curr Biol. 2015;25:690–701.

    Article 
    PubMed 

    Google Scholar
     

  • Brown CT, Hug LA, Thomas BC, Sharon I, Castelle CJ, Singh A, et al. Unusual biology across a group comprising more than 15% of domain Bacteria. Nature. 2015;523:208–11.

    Article 
    PubMed 

    Google Scholar
     

  • Dutilh BE, Cassman N, McNair K, Sanchez SE, Silva GGZ, Boling L, et al. A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes. Nat Commun. 2014;5:4498.

    Article 
    PubMed 

    Google Scholar
     

  • van Kessel MAHJ, Speth DR, Albertsen M, Nielsen PH, Op den Camp HJM, Kartal B, et al. Complete nitrification by a single microorganism. Nature. 2015;528:555–9.

    Article 
    PubMed 

    Google Scholar
     

  • Daims H, Lebedeva EV, Pjevac P, Han P, Herbold C, Albertsen M, et al. Complete nitrification by Nitrospira bacteria. Nature. 2015;528:504–9.

    Article 
    PubMed 

    Google Scholar
     

  • Nishimura Y, Yoshizawa S. The OceanDNA MAG catalog contains over 50,000 prokaryotic genomes originated from various marine environments. Sci Data. 2022;9:305.

    Article 
    PubMed 

    Google Scholar
     

  • Almeida A, Mitchell AL, Boland M, Forster SC, Gloor GB, Tarkowska A, et al. A new genomic blueprint of the human gut microbiota. Nature. 2019;568:499–504.

    Article 
    PubMed 

    Google Scholar
     

  • Li D, Luo R, Liu C-M, Leung C-M, Ting H-F, Sadakane K, et al. MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices. Methods. 2016;102:3–11.

    Article 
    PubMed 

    Google Scholar
     

  • Wu Y-W, Tang Y-H, Tringe SG, Simmons BA, Singer SW. MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm. Microbiome. 2014;2:26.

    Article 
    PubMed 

    Google Scholar
     

  • 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.

    Article 
    PubMed 

    Google Scholar
     

  • Yang C, Chowdhury D, Zhang Z, Cheung WK, Lu A, Bian Z, et al. A review of computational tools for generating metagenome-assembled genomes from metagenomic sequencing data. Comput Struct Biotechnol J. 2021;19:6301–14.

    Article 
    PubMed 

    Google Scholar
     

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

    Article 
    PubMed 

    Google Scholar
     

  • Chen L-X, Anantharaman K, Shaiber A, Eren AM, Banfield JF. Accurate and complete genomes from metagenomes. Genome Res. 2020;30:315–33.

    Article 
    PubMed 

    Google Scholar
     

  • Zhang Y, Ji P, Wang J, Zhao F. RiboFR-Seq: a novel approach to linking 16S rRNA amplicon profiles to metagenomes. Nucleic Acids Res. 2016;44:e99.

    Article 
    PubMed 

    Google Scholar
     

  • Maguire F, Jia B, Gray KL, Lau WYV, Beiko RG, Brinkman FSL. Metagenome-assembled genome binning methods with short reads disproportionately fail for plasmids and genomic Islands. Microb Genomics. 2020;6:436.

    Article 

    Google Scholar
     

  • 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;11:1144–6.

    Article 
    PubMed 

    Google Scholar
     

  • Pride DT, Meinersmann RJ, Wassenaar TM, Blaser MJ. Evolutionary Implications of Microbial Genome Tetranucleotide Frequency Biases. Genome Res. 2003;13:145–58.

    Article 
    PubMed 

    Google Scholar
     

  • Feng Y, Wang Y, Zhu B, Gao GF, Guo Y, Hu Y. Metagenome-assembled genomes and gene catalog from the chicken gut microbiome aid in deciphering antibiotic resistomes. Commun Biol. 2021;4:1305.

    Article 
    PubMed 

    Google Scholar
     

  • Su P, Wicaksono WA, Li C, Michl K, Berg G, Wang D, et al. Recovery of metagenome-assembled genomes from the phyllosphere of 110 rice genotypes. Sci Data. 2022;9:254.

    Article 
    PubMed 

    Google Scholar
     

  • Nayfach S, Roux S, Seshadri R, Udwary D, Varghese N, Schulz F, et al. A genomic catalog of Earth’s microbiomes. Nat Biotechnol. 2021;39:499–509.

    Article 
    PubMed 

    Google Scholar
     

  • Singleton CM, Petriglieri F, Kristensen JM, Kirkegaard RH, Michaelsen TY, Andersen MH, et al. Connecting structure to function with the recovery of over 1000 high-quality metagenome-assembled genomes from activated sludge using long-read sequencing. Nat Commun. 2021;12:2009.

    Article 
    PubMed 

    Google Scholar
     

  • Mukherjee S, Stamatis D, Bertsch J, Ovchinnikova G, Sundaramurthi JC, Lee J, et al. Genomes OnLine Database (GOLD) v.8: overview and updates. Nucleic Acids Res. 2021;49:D723–D733.

    Article 
    PubMed 

    Google Scholar
     

  • Katz K, Shutov O, Lapoint R, Kimelman M, Brister JR, O’Sullivan C. The Sequence Read Archive: a decade more of explosive growth. Nucleic Acids Res. 2022;50:D387–D390.

    Article 
    PubMed 

    Google Scholar
     

  • 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;25:1043–55.

    Article 
    PubMed 

    Google Scholar
     

  • Parks DH, Chuvochina M, Rinke C, Mussig AJ, Chaumeil P-A, Hugenholtz P. GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy. Nucleic Acids Res. 2022;50:D785–D794.

    Article 
    PubMed 

    Google Scholar
     

  • Chaumeil P-A, Mussig AJ, Hugenholtz P, Parks DH. GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics. 2019;36:1925–7.

    PubMed 

    Google Scholar
     

  • Eddy SR. Accelerated Profile HMM Searches. PLoS Comput Biol. 2011;7:e1002195.

    Article 
    PubMed 

    Google Scholar
     

  • Matsen FA, Kodner RB, Armbrust EV. pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree. BMC Bioinformatics. 2010;11:538.

    Article 
    PubMed 

    Google Scholar
     

  • Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun. 2018;9:5114.

    Article 
    PubMed 

    Google Scholar
     

  • Price MN, Dehal PS, Arkin AP. FastTree 2 – approximately maximum-likelihood trees for large alignments. PLoS One. 2010;5:e9490.

    Article 
    PubMed 

    Google Scholar
     

  • Ondov BD, Treangen TJ, Melsted P, Mallonee AB, Bergman NH, Koren S, et al. Mash: fast genome and metagenome distance estimation using MinHash. Genome Biol. 2016;17:132.

    Article 
    PubMed 

    Google Scholar
     

  • Pachiadaki MG, Brown JM, Brown J, Bezuidt O, Berube PM, Biller SJ, et al. Charting the complexity of the marine microbiome through single-cell genomics. Cell. 2019;179:1623–.e11.

    Article 
    PubMed 

    Google Scholar
     

  • Chijiiwa R, Hosokawa M, Kogawa M, Nishikawa Y, Ide K, Sakanashi C, et al. Single-cell genomics of uncultured bacteria reveals dietary fiber responders in the mouse gut microbiota. Microbiome. 2020;8:5.

    Article 
    PubMed 

    Google Scholar
     

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

    Article 
    PubMed 

    Google Scholar
     

  • Aramaki T, Blanc-Mathieu R, Endo H, Ohkubo K, Kanehisa M, Goto S, et al. KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold. Bioinformatics. 2020;36:2251–2.

    Article 
    PubMed 

    Google Scholar
     

  • 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.

    Article 
    PubMed 

    Google Scholar
     

  • Li W, O’Neill KR, Haft DH, Dicuccio M, Chetvernin V, Badretdin A, et al. RefSeq: Expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation. Nucleic Acids Res. 2021;49:D1020–D1028.

    Article 
    PubMed 

    Google Scholar
     

  • Li H-Y, Wang H, Wang H-T, Xin P-Y, Xu X-H, Ma Y, et al. The chemodiversity of paddy soil dissolved organic matter correlates with microbial community at continental scales. Microbiome. 2018;6:187.

    Article 
    PubMed 

    Google Scholar
     

  • Hildebrand F, Gossmann TI, Frioux C, Özkurt E, Myers PN, Ferretti P, et al. Dispersal strategies shape persistence and evolution of human gut bacteria. Cell Host Microbe. 2021;29:1167–76e9.

    Article 
    PubMed 

    Google Scholar
     

  • Sunagawa S, Coelho LP, Chaffron S, Kultima JR, Labadie K, Salazar G, et al. Structure and function of the global ocean microbiome. Science. 2015;348:1261359.

    Article 
    PubMed 

    Google Scholar
     

  • Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010;26:2460–1.

    Article 
    PubMed 

    Google Scholar
     

  • Buchfink B, Reuter K, Drost H-G. Sensitive protein alignments at tree-of-life scale using DIAMOND. Nat Methods. 2021;18:366–8.

    Article 
    PubMed 

    Google Scholar
     

  • Kanehisa M, Furumichi M, Sato Y, Ishiguro-Watanabe M, Tanabe M. KEGG: Integrating viruses and cellular organisms. Nucleic Acids Res. 2021;49:D545–D551.

    Article 
    PubMed 

    Google Scholar
     

  • Yu K, Zhang T. Construction of customized sub-databases from NCBI-nr database for rapid annotation of huge metagenomic datasets using a combined BLAST and MEGAN approach. PLoS One. 2013;8:e59831.

    Article 
    PubMed 

    Google Scholar
     

  • Kislyuk A, Bhatnagar S, Dushoff J, Weitz JS. Unsupervised statistical clustering of environmental shotgun sequences. BMC Bioinformatics. 2009;10:316.

    Article 
    PubMed 

    Google Scholar
     

  • Couvin D, Bernheim A, Toffano-Nioche C, Touchon M, Michalik J, Néron B, et al. CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins. Nucleic Acids Res. 2018;46:W246–W251.

    Article 
    PubMed 

    Google Scholar
     

  • Madin JS, Nielsen DA, Brbic M, Corkrey R, Danko D, Edwards K, et al. A synthesis of bacterial and archaeal phenotypic trait data. Sci Data. 2020;7:170.

    Article 
    PubMed 

    Google Scholar
     

  • Federhen S. The NCBI Taxonomy database. Nucleic Acids Res. 2012;40:D136–D143.

    Article 
    PubMed 

    Google Scholar
     

  • Shen W, Ren H. TaxonKit: a practical and efficient NCBI taxonomy toolkit. J Genet Genomics. 2021;48:844–50.

    Article 
    PubMed 

    Google Scholar
     

  • Tsurumaki M, Saito M, Tomita M, Kanai A. Features of smaller ribosomes in candidate phyla radiation (CPR) bacteria revealed with a molecular evolutionary analysis. RNA. 2022;28:1041–57.

    Article 
    PubMed 

    Google Scholar
     

  • Ravenhall M, Škunca N, Lassalle F, Dessimoz C. Inferring horizontal gene transfer. PLOS Comput Biol. 2015;11:e1004095.

    Article 
    PubMed 

    Google Scholar
     

  • Hacker J, Blum-Oehler G, Muhldorfer I, Tschape H. Pathogenicity islands of virulent bacteria: structure, function and impact on microbial evolution. Mol Microbiol. 1997;23:1089–97.

    Article 
    PubMed 

    Google Scholar
     

  • Domingues S, Harms K, Fricke WF, Johnsen PJ, da Silva GJ, Nielsen KM. Natural transformation facilitates transfer of transposons, integrons and gene cassettes between bacterial species. PLoS Pathog. 2012;8:e1002837.

    Article 
    PubMed 

    Google Scholar
     

  • De La Cruz F, Frost LS, Meyer RJ, Zechner EL. Conjugative DNA metabolism in Gram-negative bacteria. FEMS Microbiol Rev. 2010;34:18–40.

    Article 
    PubMed 

    Google Scholar
     

  • Fu Y, Deiorio-Haggar K, Anthony J, Meyer MM. Most RNAs regulating ribosomal protein biosynthesis in Escherichia coli are narrowly distributed to Gammaproteobacteria. Nucleic Acids Res. 2013;41:3491–503.

    Article 
    PubMed 

    Google Scholar
     

  • Pál C, Papp B, Hurst LD. Highly expressed genes in yeast evolve slowly. Genetics. 2001;158:927–31.

    Article 
    PubMed 

    Google Scholar
     

  • Fraser HB, Hirsh AE, Steinmetz LM, Scharfe C, Feldman MW. Evolutionary rate in the protein interaction network. Science. 2002;296:750–2.

    Article 
    PubMed 

    Google Scholar
     

  • Bratlie MS, Johansen J, Drabløs F. Relationship between operon preference and functional properties of persistent genes in bacterial genomes. BMC Genomics. 2010;11:71.

    Article 
    PubMed 

    Google Scholar
     

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

    Article 
    PubMed 

    Google Scholar
     

  • Bergmann GT, Bates ST, Eilers KG, Lauber CL, Caporaso JG, Walters WA, et al. The under-recognized dominance of Verrucomicrobia in soil bacterial communities. Soil Biol Biochem. 2011;43:1450–5.

    Article 
    PubMed 

    Google Scholar
     

  • Fierer N, Bradford MA, Jackson RB. Toward an ecological classification of soil bacteria. Ecology. 2007;88:1354–64.

    Article 
    PubMed 

    Google Scholar
     

  • Jeske O, Surup F, Ketteniß M, Rast P, Förster B, Jogler M, et al. Developing techniques for the utilization of planctomycetes as producers of bioactive molecules. Front Microbiol. 2016;7:1242.

    Article 
    PubMed 

    Google Scholar
     

  • Sánchez O, Ferrera I, Mabrito I, Gazulla CR, Sebastián M, Auladell A, et al. Seasonal impact of grazing, viral mortality, resource availability and light on the group-specific growth rates of coastal Mediterranean bacterioplankton. Sci Rep. 2020;10:19773.

    Article 
    PubMed 

    Google Scholar
     

  • Kurm V, van der Putten WH, de Boer W, Naus-Wiezer S, Hol WHG. Low abundant soil bacteria can be metabolically versatile and fast growing. Ecology. 2017;98:555–64.

    Article 
    PubMed 

    Google Scholar
     

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