{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,13]],"date-time":"2026-10-13T09:14:24Z","timestamp":1791882864170,"version":"4.3.4"},"reference-count":38,"publisher":"Springer Science and Business Media LLC","issue":"1","funder":[{"DOI":"10.13039\/100004440","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["100974\/C\/13\/Z"],"award-info":[{"award-number":["100974\/C\/13\/Z"]}],"id":[{"id":"10.13039\/100004440","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"publisher","award":["BB\/J004529\/1"],"award-info":[{"award-number":["BB\/J004529\/1"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"publisher","award":["BB\/M011216\/1"],"award-info":[{"award-number":["BB\/M011216\/1"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Genomics"],"published-print":{"date-parts":[[2017,12]]},"DOI":"10.1186\/s12864-017-4229-x","type":"journal-article","created":{"date-parts":[[2017,11,2]],"date-time":"2017-11-02T13:19:14Z","timestamp":1509628754000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":55,"title":["Optimisation of 16S rRNA gut microbiota profiling of extremely low birth weight infants"],"prefix":"10.1186","volume":"18","author":[{"given":"Cristina","family":"Alcon-Giner","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shabhonam","family":"Caim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Suparna","family":"Mitra","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jennifer","family":"Ketskemety","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Udo","family":"Wegmann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John","family":"Wain","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gusztav","family":"Belteki","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paul","family":"Clarke","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lindsay J.","family":"Hall","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2017,11,2]]},"reference":[{"key":"4229_CR1","unstructured":"WHO. November 2016. \nhttp:\/\/www.who.int\/mediacentre\/factsheets\/fs363\/en\/\n\n. Accessed 2 Mar 2017."},{"key":"4229_CR2","doi-asserted-by":"publisher","unstructured":"Melville JM, Moss TJ. The immune consequences of preterm birth. Front Neurosci. 2013;7:79. doi:\n10.3389\/fnins.2013.00079\n\n.","DOI":"10.3389\/fnins.2013.00079"},{"key":"4229_CR3","doi-asserted-by":"crossref","first-page":"16024","DOI":"10.1038\/nmicrobiol.2016.24","volume":"1","author":"MK Gibson","year":"2016","unstructured":"Gibson MK, Wang B, Ahmadi S, Burnham C-AD, Tarr PI, Warner BB, et al. Developmental dynamics of the preterm infant gut microbiota and antibiotic resistome. Nature microbiology. 2016;1:16024.","journal-title":"Nature microbiology"},{"issue":"6","key":"4229_CR4","doi-asserted-by":"crossref","first-page":"341","DOI":"10.1038\/nri.2016.42","volume":"16","author":"MG Rooks","year":"2016","unstructured":"Rooks MG, Garrett WS. Gut microbiota, metabolites and host immunity. Nat Rev Immunol. 2016;16(6):341.","journal-title":"Nat Rev Immunol"},{"issue":"1","key":"4229_CR5","first-page":"26050","volume":"26","author":"JM Rodr\u00edguez","year":"2015","unstructured":"Rodr\u00edguez JM, Murphy K, Stanton C, Ross RP, Kober OI, Juge N, et al. The composition of the gut microbiota throughout life, with an emphasis on early life. Microb Ecol Health Dis. 2015;26(1):26050.","journal-title":"Microb Ecol Health Dis"},{"issue":"1-2","key":"4229_CR6","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1038\/pr.2014.161","volume":"77","author":"MP Sherman","year":"2014","unstructured":"Sherman MP, Zaghouani H, Niklas V. Gut microbiota, the immune system, and diet influence the neonatal gut-brain axis. Pediatr Res. 2014;77(1-2):127\u201335.","journal-title":"Pediatr Res"},{"issue":"1","key":"4229_CR7","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1186\/2049-2618-2-38","volume":"2","author":"MW Groer","year":"2014","unstructured":"Groer MW, Luciano AA, Dishaw LJ, Ashmeade TL, Miller E, Gilbert JA. Development of the preterm infant gut microbiome: a research priority. Microbiome. 2014;2(1):38.","journal-title":"Microbiome"},{"issue":"12","key":"4229_CR8","doi-asserted-by":"crossref","first-page":"e83304","DOI":"10.1371\/journal.pone.0083304","volume":"8","author":"RM Torrazza","year":"2013","unstructured":"Torrazza RM, Ukhanova M, Wang X, Sharma R, Hudak ML, Neu J, et al. Intestinal microbial ecology and environmental factors affecting necrotizing enterocolitis. PLoS One. 2013;8(12):e83304.","journal-title":"PLoS One"},{"issue":"6","key":"4229_CR9","doi-asserted-by":"crossref","first-page":"629","DOI":"10.3390\/ph5060629","volume":"5","author":"K Mikami","year":"2012","unstructured":"Mikami K, Kimura M, Takahashi H. Influence of maternal bifidobacteria on the development of gut bifidobacteria in infants. Pharmaceuticals. 2012;5(6):629\u201342.","journal-title":"Pharmaceuticals"},{"issue":"7","key":"4229_CR10","doi-asserted-by":"crossref","first-page":"429","DOI":"10.1016\/j.syapm.2016.07.004","volume":"39","author":"M-J Kwak","year":"2016","unstructured":"Kwak M-J, Kwon S-K, Yoon J-K, Song JY, Seo J-G, Chung MJ, et al. Evolutionary architecture of the infant-adapted group of Bifidobacterium species associated with the probiotic function. Syst Appl Microbiol. 2016;39(7):429\u201339.","journal-title":"Syst Appl Microbiol"},{"key":"4229_CR11","doi-asserted-by":"crossref","unstructured":"O'Callaghan A, van Sinderen D. Bifidobacteria and their role as members of the human gut microbiota. Front Microbiol 2016;7.","DOI":"10.3389\/fmicb.2016.00925"},{"issue":"5","key":"4229_CR12","doi-asserted-by":"crossref","first-page":"959","DOI":"10.1016\/j.jpeds.2013.12.050","volume":"164","author":"W Tarnow-Mordi","year":"2014","unstructured":"Tarnow-Mordi W, Soll RF. Probiotic supplementation in preterm infants: it is time to change practice. J Pediatr. 2014;164(5):959\u201360.","journal-title":"J Pediatr"},{"issue":"1","key":"4229_CR13","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1186\/s40168-015-0087-4","volume":"3","author":"AW Walker","year":"2015","unstructured":"Walker AW, Martin JC, Scott P, Parkhill J, Flint HJ, Scott KP. 16S rRNA gene-based profiling of the human infant gut microbiota is strongly influenced by sample processing and PCR primer choice. Microbiome. 2015;3(1):26.","journal-title":"Microbiome"},{"issue":"9","key":"4229_CR14","doi-asserted-by":"crossref","first-page":"635","DOI":"10.1038\/nrmicro3330","volume":"12","author":"P Yarza","year":"2014","unstructured":"Yarza P, Yilmaz P, Pruesse E, Gl\u00f6ckner FO, Ludwig W, Schleifer K-H, et al. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat Rev Microbiol. 2014;12(9):635.","journal-title":"Nat Rev Microbiol"},{"issue":"5","key":"4229_CR15","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1038\/nmeth.f.303","volume":"7","author":"JG Caporaso","year":"2010","unstructured":"Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010;7(5):335\u20136.","journal-title":"Nat Methods"},{"issue":"5","key":"4229_CR16","doi-asserted-by":"crossref","first-page":"614","DOI":"10.1093\/bioinformatics\/btt593","volume":"30","author":"J Zhang","year":"2013","unstructured":"Zhang J, Kobert K, Flouri T, Stamatakis A. PEAR: a fast and accurate Illumina paired-end reAd mergeR. Bioinformatics. 2013;30(5):614\u201320.","journal-title":"Bioinformatics"},{"key":"4229_CR17","unstructured":"Gordon A, Hannon G. Fastx-toolkit. FASTQ\/A short-reads preprocessing tools. (unpublished) \nhttp:\/\/hannonlab.cshl.edu\/fastx_toolkit\/\n\n. 2010;5."},{"issue":"2","key":"4229_CR18","doi-asserted-by":"crossref","first-page":"266","DOI":"10.1093\/bioinformatics\/btp636","volume":"26","author":"JG Caporaso","year":"2009","unstructured":"Caporaso JG, Bittinger K, Bushman FD, DeSantis TZ, Andersen GL, Knight R. PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics. 2009;26(2):266\u20137.","journal-title":"Bioinformatics"},{"issue":"19","key":"4229_CR19","doi-asserted-by":"crossref","first-page":"2460","DOI":"10.1093\/bioinformatics\/btq461","volume":"26","author":"RC Edgar","year":"2010","unstructured":"Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010;26(19):2460\u20131.","journal-title":"Bioinformatics"},{"issue":"D1","key":"4229_CR20","doi-asserted-by":"crossref","first-page":"D590","DOI":"10.1093\/nar\/gks1219","volume":"41","author":"C Quast","year":"2012","unstructured":"Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2012;41(D1):D590\u2013D6.","journal-title":"Nucleic Acids Res"},{"issue":"3","key":"4229_CR21","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","volume":"215","author":"SF Altschul","year":"1990","unstructured":"Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215(3):403\u201310.","journal-title":"J Mol Biol"},{"key":"4229_CR22","volume-title":"Preparation","author":"D Huson","year":"2015","unstructured":"Huson D, Beier S, Buchfink B, Flade I, G\u00f3rska A, El-Hadidi M, et al. MEGAN6-microbiome analysis involving hundreds of samples and billions of reads. In: Preparation; 2015."},{"key":"4229_CR23","unstructured":"Gordon A, Hannon G. Fastx-toolkit. FASTQ\/A short-reads pre-processing tools. Unpublished Available online at: \nhttp:\/\/hannonlab.cshl.edu\/fastx_toolkit\/\n\n. 2010."},{"issue":"suppl_1","key":"4229_CR24","first-page":"D501","volume":"33","author":"KD Pruitt","year":"2005","unstructured":"Pruitt KD, Tatusova T, Maglott DR. NCBI reference sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 2005;33(suppl_1):D501\u2013D4.","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"4229_CR25","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1038\/nmeth.3176","volume":"12","author":"B Buchfink","year":"2015","unstructured":"Buchfink B, Xie C, Huson DH. Fast and sensitive protein alignment using DIAMOND. Nat Methods. 2015;12(1):59\u201360.","journal-title":"Nat Methods"},{"issue":"suppl_2","key":"4229_CR26","doi-asserted-by":"crossref","first-page":"W6","DOI":"10.1093\/nar\/gkl164","volume":"34","author":"J Ye","year":"2006","unstructured":"Ye J, McGinnis S, Madden TL. BLAST: improvements for better sequence analysis. Nucleic Acids Res. 2006;34(suppl_2):W6\u20139.","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"4229_CR27","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1186\/s13104-016-2171-7","volume":"9","author":"K Gerasimidis","year":"2016","unstructured":"Gerasimidis K, Bertz M, Quince C, Brunner K, Bruce A, Combet E, et al. The effect of DNA extraction methodology on gut microbiota research applications. BMC research notes. 2016;9(1):365.","journal-title":"BMC research notes"},{"key":"4229_CR28","doi-asserted-by":"publisher","unstructured":"Choo JM, Leong LE, Rogers GB. Sample storage conditions significantly influence faecal microbiome profiles. Sci Rep. 2015;17;5:16350. doi:\n10.1038\/srep16350\n\n.","DOI":"10.1038\/srep16350"},{"issue":"2","key":"4229_CR29","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1111\/j.1574-6968.2012.02523.x","volume":"329","author":"MI Bahl","year":"2012","unstructured":"Bahl MI, Bergstr\u00f6m A, Licht TR. Freezing fecal samples prior to DNA extraction affects the Firmicutes to Bacteroidetes ratio determined by downstream quantitative PCR analysis. FEMS Microbiol Lett. 2012;329(2):193\u20137.","journal-title":"FEMS Microbiol Lett"},{"key":"4229_CR30","doi-asserted-by":"crossref","first-page":"14","DOI":"10.2174\/1874285801105010014","volume":"5","author":"B Smith","year":"2011","unstructured":"Smith B, Li N, Andersen AS, Slotved HC, Krogfelt KA. Optimising bacterial DNA extraction from faecal samples: comparison of three methods. The Open microbiology journal. 2011;5:14.","journal-title":"The Open microbiology journal"},{"issue":"6","key":"4229_CR31","doi-asserted-by":"crossref","first-page":"2108","DOI":"10.1073\/pnas.1115621109","volume":"109","author":"S Fanning","year":"2012","unstructured":"Fanning S, Hall LJ, Cronin M, Zomer A, MacSharry J, Goulding D, et al. Bifidobacterial surface-exopolysaccharide facilitates commensal-host interaction through immune modulation and pathogen protection. Proc Natl Acad Sci. 2012;109(6):2108\u201313.","journal-title":"Proc Natl Acad Sci"},{"key":"4229_CR32","doi-asserted-by":"publisher","unstructured":"Lindgreen S, Adair KL, Gardner PP. An evaluation of the accuracy and speed of metagenome analysis tools. Sci Rep. 2016;18;6:19233. doi:\n10.1038\/srep19233\n\n.","DOI":"10.1038\/srep19233"},{"issue":"7","key":"4229_CR33","doi-asserted-by":"crossref","first-page":"e0132923","DOI":"10.1371\/journal.pone.0132923","volume":"10","author":"AG Shaw","year":"2015","unstructured":"Shaw AG, Sim K, Randell P, Cox MJ, McClure ZE, Li M-S, et al. Late-onset bloodstream infection and perturbed maturation of the gastrointestinal microbiota in premature infants. PLoS One. 2015;10(7):e0132923.","journal-title":"PLoS One"},{"issue":"2","key":"4229_CR34","first-page":"493","volume":"90","author":"C Milani","year":"2014","unstructured":"Milani C, Lugli GA, Turroni F, Mancabelli L, Duranti S, Viappiani A, et al. Evaluation of bifidobacterial community composition in the human gut by means of a targeted amplicon sequencing (ITS) protocol. FEMS Microbiol Ecol. 2014;90(2):493\u2013503.","journal-title":"FEMS Microbiol Ecol"},{"issue":"3","key":"4229_CR35","doi-asserted-by":"crossref","first-page":"e32543","DOI":"10.1371\/journal.pone.0032543","volume":"7","author":"K Sim","year":"2012","unstructured":"Sim K, Cox MJ, Wopereis H, Martin R, Knol J, Li M-S, et al. Improved detection of bifidobacteria with optimised 16S rRNA-gene based pyrosequencing. PLoS One. 2012;7(3):e32543.","journal-title":"PLoS One"},{"issue":"6","key":"4229_CR36","doi-asserted-by":"crossref","first-page":"452","DOI":"10.1016\/j.compbiolchem.2008.07.021","volume":"32","author":"T Mamedov","year":"2008","unstructured":"Mamedov T, Pienaar E, Whitney SE, TerMaat JR, Carvill G, Goliath R, et al. A fundamental study of the PCR amplification of GC-rich DNA templates. Comput Biol Chem. 2008;32(6):452\u20137.","journal-title":"Comput Biol Chem"},{"issue":"8","key":"4229_CR37","doi-asserted-by":"crossref","first-page":"1312","DOI":"10.1038\/nprot.2008.112","volume":"3","author":"UH Frey","year":"2008","unstructured":"Frey UH, Bachmann HS, Peters J, Siffert W. PCR-amplification of GC-rich regions:'slowdown PCR'. Nat Protoc. 2008;3(8):1312.","journal-title":"Nat Protoc"},{"issue":"1","key":"4229_CR38","doi-asserted-by":"crossref","first-page":"58","DOI":"10.1016\/j.ijfoodmicro.2011.01.025","volume":"149","author":"DA Sela","year":"2011","unstructured":"Sela DA. Bifidobacterial utilization of human milk oligosaccharides. Int J Food Microbiol. 2011;149(1):58\u201364.","journal-title":"Int J Food Microbiol"}],"container-title":["BMC Genomics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12864-017-4229-x.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2017,11,2]],"date-time":"2017-11-02T13:19:40Z","timestamp":1509628780000},"score":1,"resource":{"primary":{"URL":"http:\/\/bmcgenomics.biomedcentral.com\/articles\/10.1186\/s12864-017-4229-x"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,11,2]]},"references-count":38,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2017,12]]}},"alternative-id":["4229"],"URL":"https:\/\/doi.org\/10.1186\/s12864-017-4229-x","relation":{},"ISSN":["1471-2164"],"issn-type":[{"value":"1471-2164","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,11,2]]},"article-number":"841"}}