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Research Paper

The effect of early probiotic exposure on the preterm infant gut microbiome development

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Article: 1951113 | Received 15 Dec 2020, Accepted 24 Jun 2021, Published online: 15 Jul 2021

References

  • Goldenberg RL, Culhane JF, Iams JD, Romero R. Epidemiology and causes of preterm birth. Lancet. 2008;371(9606):75–15. doi:10.1016/S0140-6736(08)60074-4.
  • Dammann O, Leviton A, Gappa M, Dammann CEL. Lung and brain damage in preterm newborns, and their association with gestational age, prematurity subgroup, infection/inflammation and long term outcome. BJOG An Int J Obstet Gynaecol. 2005;112(suppl 1):4–9. doi:10.1111/j.1471-0528.2005.00576.x.
  • The United Nations Inter-agency Group for Child Mortality Estimation. Levels and trends in child mortality. 2019.
  • Neu J, Walker WA. Necrotizing Enterocolitis. N Engl J Med. 2011;364(3):255–264. doi:10.1056/NEJMra1005408.
  • Lin PW, Stoll BJ. Necrotising enterocolitis. Lancet. 2006;368(9543):1271–1283. doi:10.1016/S0140-6736(06)69525-1.
  • Gritz EC, Bhandari V. The human neonatal gut microbiome: a brief review. Front Pediatr. 2015;3:17. doi:10.3389/fped.2015.00017.
  • La Rosa PS, Warner BB, Zhou Y, Weinstock GM, Sodergren E, Hall-Moore CM, Stevens HJ, Bennett WE, Shaikh N, Linneman LA, et al. Patterned progression of bacterial populations in the premature infant gut. Proc Natl Acad Sci. 2014;111(34):12522–12527. doi:10.1073/pnas.1409497111.
  • Coggins SA, Wynn JL, Weitkamp J-H. Infectious causes of necrotizing enterocolitis. Clin Perinatol. 2015;42(1):133–154. doi:10.1016/j.clp.2014.10.012.
  • Haak BW, Wiersinga WJ. The role of the gut microbiota in sepsis. Lancet Gastroenterol Hepatol. 2017;2(2):135–143. doi:10.1016/S2468-1253(16)30119-4.
  • Olm MR, Bhattacharya N, Crits-Christoph A, Firek BA, Baker R, Song YS, Morowitz MJ, Banfield JF. Necrotizing enterocolitis is preceded by increased gut bacterial replication, Klebsiella, and fimbriae-encoding bacteria. Sci Adv. 2019;5(12):eaax5727. doi:10.1126/sciadv.aax5727.
  • Pammi M, Cope J, Tarr PI, Warner BB, Morrow AL, Mai V, Gregory KE, Kroll JS, McMurtry V, Ferris MJ, et al. Intestinal dysbiosis in preterm infants preceding necrotizing enterocolitis: a systematic review and meta-analysis. Microbiome. 2017;5(1):31. doi:10.1186/s40168-017-0248-8.
  • Deshpande G, Rao S, Athalye-Jape G, Conway P, Patole S. Probiotics in very preterm infants: the PiPS trial. Lancet. 2016;388(10045):655. doi:10.1016/S0140-6736(16)31271-5.
  • Jacobs SE, Tobin JM, Opie GF, Donath S, Tabrizi SN, Pirotta M, Morley CJ, Garland SM. Probiotic effects on late-onset sepsis in very preterm infants: a randomized controlled trial. pediatrics. 2013;132(6):1055–1062. doi:10.1542/peds.2013-1339.
  • Mohan R, Koebnick C, Schildt J, Schmidt S, Mueller M, Possner M, Radke M, Blaut M. Effects of bifidobacterium lactis Bb12 supplementation on intestinal microbiota of preterm infants: a double-blind, placebo-controlled, randomized study. J Clin Microbiol. 2006;44(11):4025–4031. doi:10.1128/JCM.00767-06.
  • Plummer EL, Bulach DM, Murray GL, Jacobs SE, Tabrizi SN, Garland SM. Gut microbiota of preterm infants supplemented with probiotics: sub-study of the ProPrems trial. BMC Microbiol. 2018;18(1):184. doi:10.1186/s12866-018-1326-1.
  • AlFaleh K, Anabrees J. Probiotics for prevention of necrotizing enterocolitis in preterm infants. Evidence-Based Child Heal A Cochrane Rev J. 2014;9(3):584–671. doi:10.1002/ebch.1976.
  • CHP VDA, van Goudoever JB, Shamir R, Domellöf M, Embleton ND, Hojsak I, Lapillonne A, Mihatsch WA, Berni Canani R, Bronsky J, et al. Probiotics and preterm infants: a position paper by the european society for paediatric gastroenterology hepatology and nutrition committee on nutrition and the european society for paediatric gastroenterology hepatology and nutrition working group for Pr. J Pediatr Gastroenterol Nutr. 2020;70(5):664–680. doi:10.1097/MPG.0000000000002655.
  • Sharif S, Meader N, Oddie SJ, Rojas-Reyes MX, McGuire W. Probiotics to prevent necrotising enterocolitis in very preterm or very low birth weight infants. Cochrane Database Syst Rev. 2020;10(10):CD005496. doi:10.1002/14651858.CD005496.pub5.
  • Athalye-Jape G, Patole S. Probiotics for preterm infants - time to end all controversies. Microb Biotechnol. 2019;12(2):249–253. doi:10.1111/1751-7915.13357.
  • Zmora N, Zilberman-Schapira G, Suez J, Mor U, Dori-Bachash M, Bashiardes S, Kotler E, Zur M, Regev-Lehavi D, Brik RBZ, et al. Personalized gut mucosal colonization resistance to empiric probiotics is associated with unique host and microbiome features. Cell. 2018;174(6):1388–1405.e21. doi:10.1016/j.cell.2018.08.041.
  • Costeloe K, Hardy P, Juszczak E, Wilks M, Millar MR. Bifidobacterium breve BBG-001 in very preterm infants: a randomised controlled phase 3 trial. Lancet. 2016;387(10019):649–660. doi:10.1016/S0140-6736(15)01027-2.
  • Manzoni P. Use of lactobacillus casei subspecies rhamnosus gg and gastrointestinal colonization by candida species in preterm neonates. J Pediatr Gastroenterol Nutr. 2007;45(Suppl 3):S190–4. doi:10.1097/01.mpg.0000302971.06115.15.
  • Splichalova A, Jenistova V, Splichalova Z, Splichal I. Colonization of preterm gnotobiotic piglets with probiotic lactobacillus rhamnosus gg and its interference with salmonella typhimurium. Clin Exp Immunol. 2019;195(3):381–394. doi:10.1111/cei.13236.
  • Mirpuri J, Sotnikov I, Myers L, Denning TL, Yarovinsky F, Parkos CA, Denning PW, Louis NA. Lactobacillus rhamnosus (LGG) regulates IL-10 signaling in the developing murine colon through upregulation of the il-10r2 receptor subunit. PLoS One. 2012;7(12):e51955. doi:10.1371/journal.pone.0051955.
  • Grimm V, Radulovic K, Riedel CU, Gerlach RG. Colonization of C57BL/6 mice by a potential probiotic bifidobacterium bifidum strain under germ-free and specific pathogen-free conditions and during experimental colitis. PLoS One. 2015;10(10):e0139935. doi:10.1371/journal.pone.0139935.
  • Lambæk ID, Fonnest G, Gormsen M, Brok J, Greisen G. Probiotics to prevent necrotising enterocolitis in very preterm infants. Dan Med J. 2016;63:3.
  • Smith B, Bodé S, Skov TH, Mirsepasi H, Greisen G, Krogfelt KA. Investigation of the early intestinal microflora in premature infants with/without necrotizing enterocolitis using two different methods. Pediatr Res. 2012;71(1):115–120. doi:10.1038/pr.2011.1.
  • Optimising Bacterial SB. DNA extraction from faecal samples: comparison of three methods. Open Microbiol J. 2011;5(1):14–17. doi:10.2174/1874285801105010014.
  • Nunes I, Jacquiod S, Brejnrod A, Holm PE, Johansen A, Brandt KK, Priemé A, Sørensen SJ. Coping with copper: legacy effect of copper on potential activity of soil bacteria following a century of exposure. FEMS Microbiol Ecol. 2016;92(11):fiw175. doi:10.1093/femsec/fiw175.
  • Takai K, Horikoshi K. Rapid detection and quantification of members of the archaeal community by quantitative PCR using fluorogenic probes. Appl Environ Microbiol. 2000;66(11):5066–5072. doi:10.1128/AEM.66.11.5066-5072.2000.
  • Comeau AM, Douglas GM, Langille MGI, Eisen J. Microbiome helper: a custom and streamlined workflow for microbiome research. MSystems. 2017;2(1):1. doi:10.1128/mSystems.00127-16.
  • Callahan BJ, Wong J, Heiner C, Oh S, Theriot CM, Gulati AS, McGill SK, Dougherty MK. High-throughput amplicon sequencing of the full-length 16S rRNA gene with single-nucleotide resolution. Nucleic Acids Res. 2019;47(18):e103–e103. doi:10.1093/nar/gkz569.
  • Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol. 2019;37(8):852–857. doi:10.1038/s41587-019-0209-9.
  • Bokulich NA, Kaehler BD, Rideout JR, Dillon M, Bolyen E, Knight R, Huttley GA, Gregory Caporaso J. Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin. Microbiome. 2018;6(1):90. doi:10.1186/s40168-018-0470-z.
  • Zheng J, Wittouck S, Salvetti E, Franz CMAP, Harris HMB, Mattarelli P, O’Toole PW, Pot B, Vandamme P, Walter J, et al. A taxonomic note on the genus lactobacillus: description of 23 novel genera, emended description of the genus lactobacillus beijerinck 1901, and union of lactobacillaceae and leuconostocaceae. Int J Syst Evol Microbiol. 2020;70(4):2782–2858. doi:10.1099/ijsem.0.004107.
  • Davis NM, Proctor DM, Holmes SP, Relman DA, Callahan BJ. Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data. Microbiome. 2018;6(1):226. doi:10.1186/s40168-018-0605-2.
  • Janssen S, McDonald D, Gonzalez A, Navas-Molina JA, Jiang L, Xu ZZ, Winker K, Kado DM, Orwoll E, Manary M, et al. Phylogenetic placement of exact amplicon sequences improves associations with clinical information. MSystems. 2018;3(3):3. doi:10.1128/mSystems.00021-18.
  • Douglas GM, Maffei VJ, Zaneveld JR, Yurgel SN, Brown JR, Taylor CM, Huttenhower C, Langille MGI. PICRUSt2 for prediction of metagenome functions. Nat Biotechnol. 2020;38(6):685–688. doi:10.1038/s41587-020-0548-6.
  • McMurdie PJ, Holmes S, Watson M. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One. 2013;8(4):e61217. doi:10.1371/journal.pone.0061217.
  • Kurtz ZD, Müller CL, Miraldi ER, Littman DR, Blaser MJ, Bonneau RA, von Mering C. Sparse and compositionally robust inference of microbial ecological networks. PLOS Comput Biol. 2015;11(5):e1004226. doi:10.1371/journal.pcbi.1004226.
  • R Core Team (2020). R: a language and environment for statistical computing. R A lang environ stat comput r found stat comput vienna, Austria. 2020.
  • Mandal S, Van Treuren W, White RA, Eggesbø M, Knight R, Peddada SD. Analysis of composition of microbiomes: a novel method for studying microbial composition. Microb Ecol Heal Dis. 2015;26(1):27663. doi:10.3402/mehd.v26.27663.
  • Subirana I, Sanz H, Vila J. Building bivariate tables: the comparegroups package for R. J Stat Softw. 2014;57(12):1–16. doi:10.18637/jss.v057.i12.
  • Dixon P. VEGAN, a package of R functions for community ecology. J Veg Sci. 2003;14(6):927–930. doi:10.1111/j.1654-1103.2003.tb02228.x.
  • Wickham H ggplot2: elegant graphics for data analysis using the grammar of graphics. 2016.
  • Gu Z, Gu L, Eils R, Schlesner M, Brors B. circlize implements and enhances circular visualization in R. Bioinformatics. 2014;30(19):2811–2812. doi:10.1093/bioinformatics/btu393.
  • Gu Z, Eils R, Schlesner M. Complex heatmaps reveal patterns and correlations in multidimensional genomic data. Bioinformatics. 2016;32(18):2847–2849. doi:10.1093/bioinformatics/btw313.
  • Yatsunenko T,Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, Magris M, Hidalgo G, Baldassano RN, Anokhin AP, et al. Human gut microbiome viewed across age and geography. Nature. 2012;486(7402):222–227. doi:10.1038/nature11053.
  • Smith B,Mirsepasi-Lauridsen H, Schjørring S, Skov TH, Jensen IDL, Greisen G, Krogfelt KA, et al. Oral intake of probiotics increases the bacterial diversity of the gut microbiome in premature neonates. Microbiol Open, under Revis.
  • Cassir N, Benamar S, La Scola B. Clostridium butyricum : from beneficial to a new emerging pathogen. Clin Microbiol Infect. 2016;22(1):37–45. doi:10.1016/j.cmi.2015.10.014.
  • Miller SI, Ernst RK, Bader MWLPS. TLR4 and infectious disease diversity. Nat Rev Microbiol. 2005;3(1):36–46. doi:10.1038/nrmicro1068.
  • Wilson BR, Bogdan AR, Miyazawa M, Hashimoto K, Tsuji Y. Siderophores in iron metabolism: from mechanism to therapy potential. Trends Mol Med. 2016;22(12):1077–1090. doi:10.1016/j.molmed.2016.10.005.
  • Neal MD, Sodhi CP, Dyer M, Craig BT, Good M, Jia H, Yazji I, Afrazi A, Richardson WM, Beer-Stolz D, et al. A critical role for TLR4 induction of autophagy in the regulation of enterocyte migration and the pathogenesis of necrotizing enterocolitis. J Immunol. 2013;190(7):3541–3551. doi:10.4049/jimmunol.1202264.
  • Van Best N, Trepels-Kottek S, Savelkoul P, Orlikowsky T, Hornef MW, Penders J. Influence of probiotic supplementation on the developing microbiota in human preterm neonates. Gut Microbes. 2020;12(1):1–16. doi:10.1080/19490976.2020.1826747.
  • Henderickx JGE, Zwittink RD, van Lingen RA, Knol J, Belzer C. The preterm gut microbiota: an inconspicuous challenge in nutritional neonatal care. Front Cell Infect Microbiol. 2019;9:85. APR. doi:10.3389/fcimb.2019.00085.
  • Brooks B, Firek BA, Miller CS, Sharon I, Thomas BC, Baker R, Morowitz MJ, Banfield JF. Microbes in the neonatal intensive care unit resemble those found in the gut of premature infants. Microbiome. 2014;2(1):1. doi:10.1186/2049-2618-2-1.
  • Brooks B, Olm MR, Firek BA, Baker R, Thomas BC, Morowitz MJ, Banfield JF. Strain-resolved analysis of hospital rooms and infants reveals overlap between the human and room microbiome. Nat Commun. 2017;8(1):1–7. doi:10.1038/s41467-017-02018-w.
  • Rogier EW, Frantz AL, Bruno MEC, Wedlund L, Cohen DA, Stromberg AJ, Kaetzel CS. Secretory antibodies in breast milk promote long-term intestinal homeostasis by regulating the gut microbiota and host gene expression. Proc Natl Acad Sci. 2014;111(8):3074–3079. doi:10.1073/pnas.1315792111.
  • Lawson MAE, O’Neill IJ, Kujawska M, Gowrinadh Javvadi S, Wijeyesekera A, Flegg Z, Chalklen L, Hall LJ. Breast milk-derived human milk oligosaccharides promote bifidobacterium interactions within a single ecosystem. ISME J. 2020;14(2):635–648. doi:10.1038/s41396-019-0553-2.
  • Toscano M, De Grandi R, Grossi E, Drago L. Role of the human breast milk-associated microbiota on the newborns’ immune system: a mini review. Front Microbiol. 2017; 8 OCT, 10.3389/fmicb.2017.02100
  • Meinzen-Derr J, Poindexter B, Wrage L, Morrow AL, Stoll B, Donovan EF. Role of human milk in extremely low birth weight infants’ risk of necrotizing enterocolitis or death. J Perinatol. 2009;29(1):57–62. doi:10.1038/jp.2008.117.
  • Sullivan S, Schanler RJ, Kim JH, Patel AL, Trawöger R, Kiechl-Kohlendorfer U, Chan GM, Blanco CL, Abrams S, Cotten CM, et al. An exclusively human milk-based diet is associated with a lower rate of necrotizing enterocolitis than a diet of human milk and bovine milk-based products. J Pediatr. 2010;156(4):562–567.e1. doi:10.1016/j.jpeds.2009.10.040.