Fast and accurate metagenotyping of the human gut microbiome with GT-Pro (original) (raw)

• Garud, N. R. & Pollard, K. S. Population genetics in the human microbiome. Trends Genet. 36, 53–67 (2020).
  Article CAS PubMed Google Scholar
• Maini Rekdal, V., Bess, E. N., Bisanz, J. E., Turnbaugh, P. J. & Balskus, E. P. Discovery and inhibition of an interspecies gut bacterial pathway for Levodopa metabolism. Science 364, eaau6323 (2019).
  Article PubMed Google Scholar
• Zeng, Q., Liao, C., Terhune, J. & Wang, L. Impacts of florfenicol on the microbiota landscape and resistome as revealed by metagenomic analysis. Microbiome 7, 155 (2019).
  Article PubMed PubMed Central Google Scholar
• Chattopadhyay, S. et al. High frequency of hotspot mutations in core genes of Escherichia coli due to short-term positive selection. Proc. Natl Acad. Sci. USA 106, 12412–12417 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Treangen, T. J., Ondov, B. D., Koren, S. & Phillippy, A. M. The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes. Genome Biol. 15, 524 (2014).
  Article CAS PubMed PubMed Central Google Scholar
• Schloissnig, S. et al. Genomic variation landscape of the human gut microbiome. Nature 493, 45–50 (2013).
  Article CAS PubMed Google Scholar
• Luo, C. et al. ConStrains identifies microbial strains in metagenomic datasets. Nat. Biotechnol. 33, 1045–1052 (2015).
  Article CAS PubMed PubMed Central Google Scholar
• Nayfach, S., Rodriguez-Mueller, B., Garud, N. & Pollard, K. S. An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography. Genome Res. 26, 1612–1625 (2016).
  Article CAS PubMed PubMed Central Google Scholar
• Costea, P. I. et al. metaSNV: a tool for metagenomic strain level analysis. PLoS ONE 12, e0182392 (2017).
  Article CAS PubMed PubMed Central Google Scholar
• Quince, C. et al. DESMAN: a new tool for de novo extraction of strains from metagenomes. Genome Biol. 18, 181 (2017).
  Article CAS PubMed PubMed Central Google Scholar
• Truong, D. T., Tett, A., Pasolli, E., Huttenhower, C. & Segata, N. Microbial strain-level population structure and genetic diversity from metagenomes. Genome Res. 27, 626–638 (2017).
  Article CAS PubMed PubMed Central Google Scholar
• Wood, D. E. & Salzberg, S. L. Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol. 15, R46 (2014).
  Article PubMed PubMed Central Google Scholar
• Ounit, R., Wanamaker, S., Close, T. J. & Lonardi, S. CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative _k_-mers. BMC Genomics 16, 236 (2015).
  Article CAS PubMed PubMed Central Google Scholar
• Liu, Y., Zhang, L. Y. & Li, J. Fast detection of maximal exact matches via fixed sampling of query _K_-mers and Bloom filtering of index _k_-mers. Bioinformatics 35, 4560–4567 (2019).
  Article CAS PubMed Google Scholar
• Breitwieser, F. P., Baker, D. N. & Salzberg, S. L. KrakenUniq: confident and fast metagenomics classification using unique _k_-mer counts. Genome Biol. 19, 198 (2018).
  Article CAS PubMed PubMed Central Google Scholar
• Phillippy, A. M. et al. Comprehensive DNA signature discovery and validation. PLoS Comput. Biol. 3, e98 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Shajii, A., Yorukoglu, D., William Yu, Y. & Berger, B. Fast genotyping of known SNPs through approximate _k_-mer matching. Bioinforma. 32, i538–i544 (2016).
  Article CAS Google Scholar
• Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P. & Tyson, G. W. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 25, 1043–1055 (2015).
  Article CAS PubMed PubMed Central Google Scholar
• Pasolli, E. et al. Extensive unexplored human microbiome diversity revealed by over 150,000 genomes from metagenomes spanning age, geography, and lifestyle. Cell 176, 649–662.e20 (2019).
  Article CAS PubMed PubMed Central Google Scholar
• Nayfach, S., Shi, Z. J., Seshadri, R., Pollard, K. S. & Kyrpides, N. C. New insights from uncultivated genomes of the global human gut microbiome. Nature 568, 505–510 (2019).
  Article CAS PubMed PubMed Central Google Scholar
• Almeida, A. et al. A new genomic blueprint of the human gut microbiota. Nature 568, 499–504 (2019).
  Article CAS PubMed PubMed Central Google Scholar
• Marçais, G. et al. MUMmer4: a fast and versatile genome alignment system. PLoS Comput. Biol. 14, e1005944 (2018).
  Article CAS PubMed PubMed Central Google Scholar
• Auton, A. et al. A global reference for human genetic variation. Nature 526, 68–74 (2015).
  Article CAS PubMed Google Scholar
• Smith, J. M., Smith, N. H., O’Rourke, M. & Spratt, B. G. How clonal are bacteria? Proc. Natl Acad. Sci. USA 90, 4384 (1993).
  Article CAS PubMed PubMed Central Google Scholar
• Redfield, R. J. Do bacteria have sex? Nat. Rev. Genet. 2, 634–639 (2001).
  Article CAS PubMed Google Scholar
• Lin, M. & Kussell, E. Inferring bacterial recombination rates from large-scale sequencing datasets. Nat. Methods 16, 199–204 (2019).
  Article CAS PubMed Google Scholar
• Ansari, M. A. & Didelot, X. Inference of the properties of the recombination process from whole bacterial genomes. Genetics 196, 253 (2014).
  Article PubMed Google Scholar
• González-Torres, P., Rodríguez-Mateos, F., Antón, J. & Gabaldón, T. Impact of homologous recombination on the evolution of prokaryotic core genomes. mBio. 10, e02494–18 (2019).
  Article PubMed PubMed Central Google Scholar
• Garud, N. R., Good, B. H., Hallatschek, O. & Pollard, K. S. Evolutionary dynamics of bacteria in the gut microbiome within and across hosts. PLoS Biol. 17, e3000102 (2019).
  Article PubMed PubMed Central Google Scholar
• Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Leinonen, R., Sugawara, H. & Shumway, M., International Nucleotide Sequence Database Collaboration. The sequence read archive. Nucleic Acids Res. 39, D19–D21 (2011).
  Article CAS PubMed Google Scholar
• Smits, S. A. et al. Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania. Science 357, 802 (2017).
  Article CAS PubMed PubMed Central Google Scholar
• Zou, Y. et al. 1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses. Nat. Biotechnol. 37, 179–185 (2019).
  Article CAS PubMed PubMed Central Google Scholar
• Turnbaugh, P. J. et al. The Human Microbiome Project. Nature 449, 804–810 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Franzosa, E. A. et al. Gut microbiome structure and metabolic activity in inflammatory bowel disease. Nat. Microbiol. 4, 293–305 (2019).
  Article CAS PubMed Google Scholar
• Issa, M., Ananthakrishnan, A. N. & Binion, D. G. Clostridium difficile and inflammatory bowel disease. Inflamm. Bowel Dis. 14, 1432–1442 (2008).
  Article PubMed Google Scholar
• Rousseau, C. et al. Clostridium difficile colonization in early infancy is accompanied by changes in intestinal microbiota composition. J. Clin. Microbiol. 49, 858–865 (2011).
  Article CAS PubMed PubMed Central Google Scholar
• Vincent, C. et al. Bloom and bust: intestinal microbiota dynamics in response to hospital exposures and Clostridium difficile colonization or infection. Microbiome 4, 12 (2016).
  Article PubMed PubMed Central Google Scholar
• Tierney, B. T. et al. The landscape of genetic content in the gut and oral human microbiome. Cell Host Microbe 26, 283–295.e8 (2019).
  Article CAS PubMed PubMed Central Google Scholar
• Almeida, A. et al. A unified sequence catalogue of over 280,000 genomes obtained from the human gut microbiome. Preprint at bioRxiv https://doi.org/10.1101/762682 (2019).
• Nei, M. & Gojobori, T. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3, 418–426 (1986).
  CAS PubMed Google Scholar
• Chang, C. C. et al. Second-generation PLINK: rising to the challenge of larger and richer datasets. GigaScience 4, 7 (2015).
  Article CAS PubMed PubMed Central Google Scholar
• Edgar, R. C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26, 2460–2461 (2010).
  Article CAS PubMed Google Scholar
• Liu, X. et al. A novel data structure to support ultra-fast taxonomic classification of metagenomic sequences with _k_-mer signatures. Bioinformatics 34, 171–178 (2017).
  Article CAS PubMed Central Google Scholar
• Kokot, M., Długosz, M. & Deorowicz, S. KMC 3: counting and manipulating _k_-mer statistics. Bioinformatics 33, 2759–2761 (2017).
  Article CAS PubMed Google Scholar
• Mende, D. R., Sunagawa, S., Zeller, G. & Bork, P. Accurate and universal delineation of prokaryotic species. Nat. Methods 10, 881–884 (2013).
  Article CAS PubMed Google Scholar
• Hyatt, D. et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinf. 11, 119–119 (2010).
  Article CAS Google Scholar
• Kultima, J. R. et al. MOCAT: a metagenomics assembly and gene prediction toolkit. PLoS ONE 7, e47656 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Sievers, F. et al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol. Syst. Biol. 7, 539 (2011).
  Article PubMed PubMed Central Google Scholar
• Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Segata, N. et al. Metagenomic microbial community profiling using unique clade-specific marker genes. Nat. Methods 9, 811–814 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Gourlé, H., Karlsson-Lindsjö, O., Hayer, J. & Bongcam-Rudloff, E. Simulating Illumina metagenomic data with InSilicoSeq. Bioinformatics 35, 521–522 (2018).
  Article CAS PubMed Central Google Scholar
• Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinforma. 30, 1312–1313 (2014).
  Article CAS Google Scholar
• Olm, M. R., Brown, C. T., Brooks, B. & Banfield, J. F. dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. ISME J. 11, 2864–2868 (2017).
  Article CAS PubMed PubMed Central Google Scholar
• Camacho, C. et al. BLAST+: architecture and applications. BMC Bioinf. 10, 421 (2009).
  Article CAS Google Scholar