Longitudinal changes in the gut microbiome of infants on total parenteral nutrition

Tan, M., Abernethy, L. & Cooke, R. Improving head growth in preterm infants—a randomised controlled trial II: MRI and developmental outcomes in the first year. Arch Dis. Child Fetal Neonatal Ed. 93, F342–F346 (2008).

Ehrenkranz, R. A. et al. Early nutrition mediates the influence of severity of illness on extremely LBW infants. Pedia. Res. 69, 522–529 (2011).

Demehri, F. R., Barrett, M. & Teitelbaum, D. H. Changes to the intestinal microbiome with parenteral nutrition. Nutr. Clin. Pr. 30, 798–806 (2015).

Miyasaka, E. A. et al. Total parenteral nutrition-associated lamina propria inflammation in mice is mediated by a MyD88-dependent mechanism. J. Immunol. 190, 6607–6615 (2013).

Deplancke, B. et al. Selective growth of mucolytic bacteria including Clostridium perfringens in a neonatal piglet model of total parenteral nutrition. Am. J. Clin. Nutr. 76, 1117–1125 (2002).

Fanaroff, A. A. et al. Trends in neonatal morbidity and mortality for very low birthweight infants. Am. J. Obstet. Gynecol. 196, 147.e1–147.e8 (2007).

Fitzgibbons, S. C. et al. Mortality of necrotizing enterocolitis expressed by birth weight categories. J. Pedia. Surg. 44, 1072–1076 (2009).

Hintz, S. R. Neurodevelopmental and growth outcomes of extremely low birth weight infants after necrotizing enterocolitis. Pediatrics 115, 696–703 (2005).

Park, H. W., Lee, N. M., Kim, J. H., Kim, K. S. & Kim, S. N. Parenteral fish oil-containing lipid emulsions may reverse parenteral nutrition-associated cholestasis in neonates: a systematic review and meta-analysis. J. Nutr. 145, 277–283 (2015).

Teitelbaum, D. H. & Tracy, T. Parenteral nutrition-associated cholestasis. Semin Pedia. Surg. 10, 72–80 (2001).

Pammi, M. et al. Intestinal dysbiosis in preterm infants preceding necrotizing enterocolitis: a systematic review and meta-analysis. Microbiome 5, 1–15 (2017).

Korpela, K. et al. Intestinal microbiota signatures associated with histological liver steatosis in pediatric-onset intestinal failure. JPEN 41, 238–248 (2017).

Harris, P. A. et al. Research electronic data capture (REDCap)—a metadata-driven methodology and workflow process for providing translational research informatics support. J. Biomed. Inf. 42, 377–381 (2009).

Edgar, R. C. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nature 10, 996–998 (2013).

Quast, C. et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41, D590–D596 (2012).

Methé, B. A. et al. A framework for human microbiome research. Nature 486, 215–221 (2012).

Aagaard, K. et al. The Human Microbiome Project strategy for comprehensive sampling of the human microbiome and why it matters. FASEB J. 27, 1012–1022 (2013).

Harvey, R. B. et al. Qualitative and quantitative comparison of gut bacterial colonization in enterally and parenterally fed neonatal pigs. Curr. Issues Intest Microbiol 7, 61–64 (2006).

Huang, Y., Guo, F., Li, Y., Wang, J. & Li, J. Fecal microbiota signatures of adult patients with different types of short bowel syndrome. J. Gastroenterol. Hepatol. 32, 1949–1957 (2017).

Lilja, H. E., Wefer, H., Nyström, N., Finkel, Y. & Engstrand, L. Intestinal dysbiosis in children with short bowel syndrome is associated with impaired outcome. Microbiome 3, 1–6 (2015).

Shiga, H. et al. Changes of faecal microbiota in patients with Crohn’s disease treated with an elemental diet and total parenteral nutrition. Dig. Liver Dis. 44, 736–742 (2012).

Parm, Ü., Metsvaht, T., Ilmoja, M.-L. & Lutsar, I. Gut colonization by aerobic microorganisms is associated with route and type of nutrition in premature neonates. Nutr. Res. 35, 496–503 (2015).

Chu, D. M. et al. Maturation of the infant microbiome community structure and function across multiple body sites and in relation to mode of delivery. Nat. Med 23, 314–326 (2017).

Jost, T., Lacroix, C., Braegger, C. P. & Chassard, C. New insights in gut microbiota establishment in healthy breast fed neonates. PLoS ONE 7, e44595 (2012).

Mazmanian, S. K., Round, J. L. & Kasper, D. L. A microbial symbiosis factor prevents intestinal inflammatory disease. Nature 453, 620–625 (2008).

Troy, E. B. & Kasper, D. L. Beneficial effects of Bacteroides fragilis polysaccharides on the immune system. Front Biosci. 15, 25–34 (2010).

Ganguli, K. et al. Probiotics prevent necrotizing enterocolitis by modulating enterocyte genes that regulate innate immune-mediated inflammation. Am. J. Physiol. Gastrointest. Liver Physiol. 304, G132–G141 (2013).

Fukuda, S. et al. Bifidobacteria can protect from enteropathogenic infection through production of acetate. Nature 469, 543–547 (2011).

Belzer, C. & de Vos, W. M. Microbes inside—from diversity to function: the case of Akkermansia. ISME J. 6, 1449–1458 (2012).

Shin, N.-R. et al. An increase in the Akkermansia spp. population induced by metformin treatment improves glucose homeostasis in diet-induced obese mice. Gut 63, 727–735 (2014).

Seregin, S. S. et al. NLRP6 protects Il10−/− mice from colitis by limiting colonization of Akkermansia muciniphila. Cell Rep. 19, 733–745 (2017).

Durand, L. et al. Microbial diversity associated with the hydrothermal shrimp Rimicaris exoculatagut and occurrence of a resident microbial community. FEMS Microbiol Ecol. 71, 291–303 (2010).

Bäckhed, F. et al. Dynamics and stabilization of the human gut microbiome during the first year of life. Cell Host Microbe 17, 690–703 (2015).

Gupta, R. W. et al. Histamine-2 receptor blockers alter the fecal microbiota in premature infants. J. Pedia. Gastroenterol. Nutr. 56, 397–400 (2013).

Wang, Y. et al. 16S rRNA gene-based analysis of fecal microbiota from preterm infants with and without necrotizing enterocolitis. ISME J. 3, 944–954 (2009).

Oddie, S. J., Young, L. & McGuire, W. Slow advancement of enteral feed volumes to prevent necrotising enterocolitis in very low birth weight infants. Cochrane Database Syst. Rev. 114, 1597–37 (2017).

Rozé, J. C. et al. Nutritional strategies and gut microbiota composition as risk factors for necrotizing enterocolitis in very-preterm infants. Am. J. Clin. Nutr. 106, 821–830 (2017).

Wang, P. et al. Alterations in intestinal microbiota relate to intestinal failure-associated liver disease and central line infections. J. Pedia. Surg. 52, 1318–1326 (2017).

Wildhaber, B. E., Yang, H., Spencer, A. U., Drongowski, R. A. & Teitelbaum, D. H. Lack of enteral nutrition—effects on the intestinal immune system. J. Surg. Res. 123, 8–16 (2005).

Ralls, M. W., Demehri, F. R., Feng, Y., Woods Ignatoski, K. M. & Teitelbaum, D. H. Enteral nutrient deprivation in patients leads to a loss of intestinal epithelial barrier function. Surgery 157, 732–742 (2015).