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Classification and Quantification of Bacteriophage Taxa in Human Gut Metagenomes

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Classification and Quantification of Bacteriophage Taxa in Human Gut Metagenomes The ISME Journal (2014) 8, 1551–1552 & 2014 International Society for Microbial Ecology All rights reserved 1751-7362/14 www.nature.com/ismej CORRIGENDA Links between plant and fungal communities across a deforestation chronosequence in the Amazon rainforest Rebecca C Mueller, Fabiana S Paula, Babur S Mirza, Jorge LM Rodrigues, Klaus Nu¨ sslein and Brendan JM Bohannan The ISME Journal (2014) 8, 1551; doi:10.1038/ismej.2014.62 Correction to: The ISME Journal (2014) 8, In addition, the sequence listed for ITS2 was 1548–1550; doi:10.1038/ismej.2013.253; published incorrectly listed as the sequence for ITS2-Melam- online 23 January 2014 spora. The correct sequence for the ITS2 primer used in this study is 50-GCTGCGTTCTTCATCGA Since the publication of this article, the authors TGC-30. have identified errors in the Supplementary Finally, the concentration of the dNTPs is listed Information, mainly concerning the listed primer at mM, but should be in mM. sequences. The errors have now been rectified, and the There was a deletion in the primer sequence listed correct Supplementary Information now appears for the second stage PCR. The erroneous sequence on the online version of the article. In addition, was 50-AAGCAGAAGACGGCATACGAGATCGGTCT it also accompanies the online version of this GGCATTCCTGC-30, but the correct primer sequence corrigendum. is 50-AAGCAGAAGACGGCATACGAGATCGGTCTC The authors apologise for any inconvenience GGCATTCCTGC-30. caused. Classification and quantification of bacteriophage taxa in human gut metagenomes Alison S Waller, Takuji Yamada, David M Kristensen, Jens Roat Kultima, Shinichi Sunagawa, Eugene V Koonin and Peer Bork The ISME Journal (2014) 8, 1551–1552; doi:10.1038/ismej.2014.66 Correction to: The ISME Journal (2014) 8, The correct figure is shown here. 1391–1402; doi:10.1038/ismej.2014.30; published The error has now been rectified, and the correct online 13 March 2014 article appears in this issue. The html and online pdf versions have also been rectified, and now carry Since the publication of this article, the authors the correct paper. have identified an error in Figure 1a, namely that the The Authors would like to apologize for any columns were not clustered and the column labels inconvenience this may have caused. were incorrect, in that 252.Gut.PFPR and 61.Gut. Virome were reversed. Corrigenda 1552 ab 252 gut metagenomic samples GOS252.Gut.PFPR61.Gut.Virome252.Gut.total Genera marker genes 1 000 Microvirus 0 0 0 0.1 Tectivirus 0 0.3 0 0.5 T1–like viruses 0 0.2 0 0.3 Lambda–like viruses (rcll 17%) 0 0 0.2 0 Lactococcus phage ul36 (rcll 67%) 0 0 0.6 0.7 936 group of lactococcal phages 0 0.4 0.7 0.5 Phi29–like viruses 0.5 0 0.5 0.9 N4–like viruses 0.8 0 0 0 unclass.Autographivirinae.1132574 0000 SP6–like viruses 0 0.7 0.6 0.8 T7–like viruses 0.7 0 0 0.2 I3–like viruses 0000.1 PhiKZ–like viruses 0 0.5 0.2 0.6 Mu–like viruses (rcll 50%) 0.4 0.8 0.2 0.8 Hp1likevirus 0.2 0 0 0.3 P2–like viruses PB1likevirus 0.2 0 0 0.2 PhiCD119likevirus 0 0.6 0.4 0.4 FelixO1likevirus 0.1 0 0.2 0 Subfamily marker genes 0.6 0 0.7 0.9 Gokushovirinae 0.8 0.9 0.9 0.9 Autographivirinae 0 111 Picovirinae 0.5 0 0.4 0.4 Peduovirinae 0.3 0.7 1 0.8 Spounavirinae 0.9 0 0 0 Tevenvirinae 0.2 0.6 1 -3 -1 1 3 relative rank log10 abundance per Gbp Cladogram Branch Colors Microviridae Myoviridae Tectiviridae Picovirinae Siphoviridae Autographvirinae Podoviridae Peduovirinae Figure 1 Taxonomic classification and quantification of phages in the human gut and the Oceans. (a) Relative rank of phage taxa in the human gut and the Ocean. The abundance of each taxon was used to determine its rank, and the relative rank is then the rank divided by the maximum rank in that sample set. Thereby, a relative rank of 1 is the most abundant taxon in that sample. Each column represents one of the four different sample sets: GOS (82 samples from the Global Ocean Sampling Expedition), 252.Gut.PFPR (only the subset of prophage-encoded genes in 252 gut metagenome samples), 61.Gut.Virome (all of the genes with 61 samples from three published studies of virus-enriched gut metagenomes), 252.Gut.total (all of the genes contained within 252 gut metagenome samples). The columns are clustered by similarity, as illustrated by the dendrogram below the columns. (b) Abundance of each phage taxon within the 252 human gut samples (total metagenomic genes). These abundances were derived by dividing the length-normalized base coverages by the total gene abundance in each sample, and multiplied by 109 to yield the abundance per Gbp. For those taxa for which marker genes are not quantitative (see Materials and methods), the recall is indicated in brackets. The ISME Journal.
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