Flushed contents from the intestinal tract, including the rectal portion and excluding the stomach, were used for DNA isolation (Additional file 1) and PCR amplification after which individually barcoded amplicons were pooled and sequenced using 454 technology [36]. Sequence data was binned into the individual samples using the barcoded tags and subsequently cleaned from artifacts. Diversity estimates were calculated using Mothur [37]. Representative OTU sequences were compared to the SILVA SSU ref NR V108 database
[38] (http://www.arb-silva.de) using BlastN [39] and classified using the LCA algorithm in Megan [40]. Acknowledgements We thank Jonathan E. Colman for the collection of specimens and the Norwegian Sequencing Centre (http://www.sequencing.uio.no) for 454 amplicon sequencing. We are also grateful for the https://www.selleckchem.com/products/eft-508.html efforts of two anonymous reviewers, whose insightful comments and suggestions helped improve this manuscript. This work was initiated during the Research Council of Norway (RCN) project “Genome sequencing of cod by exclusive use of ultra-high-throughput sequencing technology (#187940)” and supported by RCN project “Functional and comparative immunology of a teleost’s world without MHC II (#222378)”. The raw BI 10773 amplicon sequences are deposited at the SRA archive with run number SRR579544. Electronic supplementary material Additional file 1: Supplementary section containing detailed methods, analyses
and supplementary tables. (PDF 215
KB) References 1. Ivanov II, Littman DR: Modulation of immune homeostasis by commensal bacteria. Curr Opin Microbiol 2011,14(1):106–114.PubMedCrossRef 2. Maynard CL, Elson CO, Hatton RD, Weaver CT: Reciprocal interactions of the intestinal microbiota and immune system. Nature 2012,489(7415):231–241.PubMedCrossRef Buspirone HCl 3. Tap J, Mondot S, Levenez F, Pelletier E, Caron C, Furet J-P, Ugarte E, Muñoz-Tamayo R, Paslier DLE, Nalin R, et al.: Towards the human intestinal microbiota phylogenetic core. Environ Microbiol 2009,11(10):2574–2584.PubMedCrossRef 4. Rawls JF, Samuel BS, Gordon JI: LY3039478 chemical structure Gnotobiotic zebrafish reveal evolutionarily conserved responses to the gut microbiota. Proc Natl Acad Sci USA 2004,101(13):4596–4601.PubMedCrossRef 5. Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, et al.: A human gut microbial gene catalogue established by metagenomic sequencing. Nature 2010,464(7285):59–65.PubMedCrossRef 6. Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto J-M, et al.: Enterotypes of the human gut microbiome. Nature 2011,473(7346):174–180.PubMedCrossRef 7. The Human Microbiome Consortium: Structure, function and diversity of the healthy human microbiome. Nature 2012,486(7402):207–214.CrossRef 8. Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, Ley RE, Sogin ML, Jones WJ, Roe BA, Affourtit JP, et al.: A core gut microbiome in obese and lean twins.