174 Bartram AK, Lynch MDJ, Stearns JC, Moreno-Hagelsieb G, Neufeld JD. Generation of multimillionsequence 16S rRNA gene libraries from complex microbial communities by assembling paired-end illumine reads. Appl Environ Microbiol (2011) 77(11):3846-52. doi: 10.1128/AEM.02772-10. Bokulich NA, Joseph CM, Allen G, Benson AK, Mills DA. Next-generation sequencing reveals significant bacterial diversity of botrytized wine. PLoS One (2012) 7(5):e36357. doi: 10.1371/journal.pone.0036357. 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):335-6. doi: 10.1038/ nmeth.f.303. Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics (2010) 26(19):24601. doi: 10.1093/bioinformatics/btq461. Masella AP, Bartram AK, Truszkowski JM, Brown DG, Neufeld JD. PANDAseq: paired-end assembler for illumina sequences. Bioinformatics (2012) 13:31. doi: 10.1186/1471-2105-13-31. Ludwig W, Strunk O, Westram R, Richter L, Meier H, Yadhukumar, Buchner A, et al. ARB: a software environment for sequence data. Nucleic Acids Res (2004) 32(4):1363-71. doi: 10.1093/nar/gkh293. Oksanen JR, Blanchet FG, Friendly M, Kindt R, Legendre P, McGlinn D, et al. Vegan: community ecology package (2016) https://cran.r-project.org/web/packages/vegan/index.html. Ruigrok RAAA, Collij V, Sureda P, Klaassen MAY, Bolte LA, Jansen BH, et al. The Composition and Metabolic Potential of the Human Small Intestinal Microbiota Within the Context of Inflammatory Bowel Disease. J Crohns Colitis (2021) 15(8):1326-1338. doi: 10.1093/ecco-jcc/jjab020. Kastl AJ Jr, Terry NA, Wu GD, Albenberg LG. The Structure and Function of the Human Small Intestinal Microbiota: Current Understanding and Future Directions. Cell Mol Gastroenterol Hepatol (2020) 9(1):3345. doi: 10.1016/j.jcmgh.2019.07.006. Villmones HC, Haug ES, Ulvestad E, Grude N, Stenstad T, Halland A, et al. Species Level Description of the Human Ileal Bacterial Microbiota. Sci Rep (2018) 8(1):4736. doi: 10.1038/s41598-018-23198-5. Fyderek K, Strus M, Kowalska-Duplaga K, Gosiewski T, Wedrychowicz A, Jedynak-Wasowicz U, et al. Mucosal bacterial microflora and mucus layer thickness in adolescents with inflammatory bowel disease. World J Gastroenterol (2009) 15(42):5287-94. doi: 10.3748/wjg.15.5287. Peng L, Li ZR, Green RS, Holzman IR, Lin J. Butyrate enhances the intestinal barrier by facilitating tight junction assembly via activation of AMP-activated protein kinase in Caco-2 cell monolayers. J Nutr (2009) 139(9):1619-25. doi: 10.3945/jn.109.104638. Wang HB, Wang PY, Wang X, Wan YL, Liu YC. Butyrate enhances intestinal epithelial barrier function via up-regulation of tight junction protein Claudin-1 transcription. Dig Dis Sci (2012) 57(12):3126-35. doi: 10.1007/s10620-012-2259-4. Parada Venegas D, De la Fuente MK, Landskron G, González MJ, Quera R, Dijkstra G, et al. Short Chain Fatty Acids (SCFAs)-Mediated Gut Epithelial and Immune Regulation and Its Relevance for Inflammatory Bowel Diseases. Front Immunol (2019) 10:277. doi: 10.3389/fimmu.2019.00277. Louis P, Flint HJ. Diversity, metabolism and microbial ecology of butyrate-producing bacteria from the human large intestine. FEMS Microbiol Lett (2009) 294(1):1-8. doi: 10.1111/j.1574-6968.2009.01514.x. von Martels JZH, Sadaghian Sadabad M, Bourgonje AR, Blokzijl T, Dijkstra G, Faber KN, et al. The role of gut microbiota in health and disease: In vitro modeling of host-microbe interactions at the aerobe-anaerobe interphase of the human gut. Anaerobe (2017) 44:3-12. doi: 10.1016/j.anaerobe.2017.01.001. Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature (2012) 486(7402):207-14. doi: 10.1038/nature11234. Maukonen J, Simões C, Saarela M. The currently used commercial DNA-extraction methods give different results of clostridial and actinobacterial populations derived from human fecal samples. FEMS Microbiol Ecol (2012) 79(3):697-708. doi: 10.1111/j.1574-6941.2011.01257.x. Chapter 5 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35
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