Microbiota diversity and stability of the preterm neonatal ileum and colon of two infants

Eoin Barrett, Caitriona M Guinane, C Anthony Ryan, Eugene M Dempsey, Brendan P Murphy, Paul W O'Toole, Gerald F Fitzgerald, Paul D Cotter, R Paul Ross, Catherine Stanton, Eoin Barrett, Caitriona M Guinane, C Anthony Ryan, Eugene M Dempsey, Brendan P Murphy, Paul W O'Toole, Gerald F Fitzgerald, Paul D Cotter, R Paul Ross, Catherine Stanton

Abstract

The composition of the microbiota associated with the human ileum and colon in the early weeks of life of two preterm infants was examined, with particular emphasis on the Lactobacillus and Bifidobacterium members. Culturing work showed that bifidobacteria and lactobacilli in the ileostomy changed over time, compared with the colostomy effluent where there was far less variation. The colostomy infant was dominated by two phyla, Actinobacteria and Firmicutes, while in the ileostomy samples, Proteobacteria emerged at the expense of Actinobacteria. Bacteroidetes were only detected following the reversal of the ileostomy in the final fecal sample and were not detected in any colonic fluid samples. Clostridia levels were unstable in the colostomy fluid, suggesting that the ileostomy/colostomy itself influenced the gut microbiota, in particular the strict anaerobes. Pyrosequencing analysis of microbiota composition indicated that bifidobacteria and lactobacilli are among the dominant genera in both the ileal and colonic fluids. Bifidobacteria and lactobacilli levels were unstable in the ileostomy fluid, with large reductions in numbers and relative proportions of both observed. These decreases were characterized by an increase in proportions of Streptococcus and Enterobacteriaceae. Clostridium was detected only in the colonic effluent, with large changes in the relative proportions over time.

© 2013 The Authors. Published by Blackwell Publishing Ltd.

Figures

Figure 1
Figure 1
Enumeration of Lactobacillus and Bifidobacterium in ileal fluid over time. • Log Bifidobacterium cfu/mL; ◊ Log Lactobacillus cfu/mL. A – administration of antibiotics, B – sepsis, suspected necrotizing enterocolitis and administration of antibiotics, C – laparotomy, D – donor milk, E – intestinal perforation, and F – necrotizing enterocolitis.
Figure 2
Figure 2
Enumeration of Lactobacillus and Bifidobacterium in colon fluid over time. • Log Bifidobacterium cfu/mL; ◊ Log Lactobacillus cfu/mL. A – laporotomy, B – administration of antibiotics, C – breast milk fortifier, D – six-in-one and PVC vaccination, E – vaccination milk, F – six-in-one vaccination, G – infant formula, and H – solid food.
Figure 3
Figure 3
The relative proportion of bacteria isolated from ileal fluid over time as determined by 16s rRNA gene amplicon sequencing. (a) Relative proportion of phyla over time, Actinobacteria ; Proteobacteria ; Firmicutes ; Bacteroidetes. (b) Relative proportion of families over time, Enterobacteriaceae ; Veillonellaceae ; Clostridiaceae ; Streptococcaceae ; Bifidobacteriaceae ; Lactobacillaceae ; other families ; Enterococcaceae ; Bacteroidaceae ; Staphyloccaceae . (c) Relative proportion of genera over time, Bifidobacterium; Enterobacteriaceae-associated genera ; Haemophilus; Bacteroides; Streptococcus; Veillonella; Lactobacillus; other genera ; Enterococcus; Leuconostoc; Staphylococcus.
Figure 4
Figure 4
The relative proportion of bacteria isolated from colon fluid over time as determined by 16s rRNA gene amplicon sequencing. (a) The relative proportion of phyla over time, Actinobacteria ; Proteobacteria ; Firmicutes . (b) Relative proportion of families over time, Enterobacteriaceae ; Veillonellaceae ; Clostridiaceae ; Clostridiales Family XI incertae sedis ; Streptococcaceae ; Bifidobacteriaceae ; Lactobacillaceae ; other families . (c) Proportion of genera over time, Bifidobacterium; Enterobacteriaceae-associated genera ; Haemophilus; Streptococcus ; VeillonellaLactobacillus; other genera ; Enterococcus; Anaerococcus; Clostridium.

References

    1. Adlerberth I, Wold AE. Establishment of the gut microbiota in Western infants. Acta Paediatr. 2009;98:229–238.
    1. Ahrne S, Lonnermark E, Wold AE, Aberg N, Hesselmar B, Saalman R, et al. Lactobacilli in the intestinal microbiota of Swedish infants. Microbes Infect. 2005;7:1256–1262.
    1. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25:3389–3402.
    1. Arboleya S, Binetti A, Salazar N, Fernandez N, Solis G, Hernandez-Barranco A, et al. Establishment and development of intestinal microbiota in preterm neonates. FEMS Microbiol. Ecol. 2012;79:763–772.
    1. Biasucci G, Benenati B, Morelli L, Bessi E, Boehm G. Cesarean delivery may affect the early biodiversity of intestinal bacteria. J. Nutr. 2008;138:1796S–1800S.
    1. Bjorkstrom MV, Hall L, Soderlund S, Hakansson EG, Hakansson S, Domellof M. Intestinal flora in very low-birth weight infants. Acta Paediatr. 2009;98:1762–1767.
    1. Booijink CCGM, El-Aidy S, Rajilic-Stojanovic M, Heilig H, Troost FJ, Smidt H, et al. High temporal and inter-individual variation detected in the human ileal microbiota. Environ. Microbiol. 2010;12:3213–3227.
    1. Butel M-J, Suau A, Campeotto F, Magne F, Aires J, Ferraris L, et al. Conditions of bifidobacterial colonization in preterm infants: a prospective analysis. J. Pediatr. Gastroenterol. Nutr. 2007;44:577–582.
    1. Caplan MS. Probiotic and prebiotic supplementation for the prevention of neonatal necrotizing enterocolitis. J. Perinatol. 2009;29:S2–S6.
    1. Cerning J. Production of exopolysaccharides by lactic acid bacteria and dairy propionibacteria. Lait. 1995;75:463–472.
    1. Chang JY, Shin SM, Chun J, Lee J-H, Seo J-K. Pyrosequencing-based molecular monitoring of the intestinal bacterial colonization in preterm infants. J. Pediatr. Gastroenterol. Nutr. 2011;53:512–519.
    1. Chierici R, Fanaro S, Saccomandi D, Vigi V. Advances in the modulation of the microbial ecology of the gut in early infancy. Acta Paediatr. 2003;92:56–63.
    1. Coakley M, Johnson MC, McGrath E, Rahman S, Ross RP, Fitzgerald GF, et al. Intestinal bifidobacteria that produce trans-9, trans-11 CLA: a fatty acid with anti-proliferative activity against SW480 and HT-29 colon cancer cells. Nutr. Cancer. 2006;56:95–102.
    1. Crittenden RG, Martinez NR, Playne MJ. Synthesis and utilisation of folate by yoghurt starter cultures and probiotic bacteria. Int. J. Food Microbiol. 2003;80:217–222.
    1. Deguchi Y, Morishita T, Mutai M. Comparative studies on synthesis of water-soluble vitamins among human species of bifidobacteria. Agric. Biol. Chem. 1985;49:13–19.
    1. Dennison B. Definition of preterm delivery. Br. Med. J. 1976;2:1449.
    1. Deshpande G, Rao S, Patole S. Probiotics for prevention of necrotising enterocolitis in preterm neonates with very low birthweight: a systematic review of randomised controlled trials. Lancet. 2007;369:1614–1620.
    1. Dial MS. Proton pump inhibitor use and enteric infections. Am. J. Gastroenterol. 2009;104:S10–S16.
    1. DiGiulio DB, Romero R, Amogan HP, Kusanovic JP, Bik EM, Gotsch F, et al. Microbial prevalence, diversity and abundance in amniotic fluid during preterm labor: a molecular and culture-based investigation. PLoS ONE. 2008;3:10.
    1. Embleton ND, Yates R. Probiotics and other preventative strategies for necrotising enterocolitis. Semin. Fetal Neonatal Med. 2008;13:35–43.
    1. Erasmus HD, Ludwig-Auser HM, Paterson PG, Sun DM, Sankaran K. Enhanced weight gain in preterm infants receiving lactase-treated feeds: a randomized, double-blind, controlled trial. J. Pediatr. 2002;141:532–537.
    1. Fanaro S, Chierici R, Guerrini P, Vigi V. Intestinal microflora in early infancy: composition and development. Acta Paediatr. 2003;92:48–55.
    1. Fitzgibbons SC, Ching YM, Yu D, Carpenter J, Kenny M, Weldon C, et al. Mortality of necrotizing enterocolitis expressed by birth weight categories. J. Pediatr. Surg. 2009;44:1072–1076.
    1. Fuller R. Probiotics in man and animals. J. Appl. Bacteriol. 1989;66:365–378.
    1. Gewolb IH, Schwalbe RS, Taciak VL, Harrison TS, Panigrahi P. Stool microflora in extremely low birthweight infants. Arch. Dis. Child. 1999;80:F167–F173.
    1. Haarman M, Knol J. Quantitative real-time PCR assays to identify and quantify fecal Bifidobacterium species in infants receiving a prebiotic infant formula. Appl. Environ. Microbiol. 2005;71:2318–2324.
    1. Harmsen HJM, Wildeboer-Veloo ACM, Raangs GC, Wagendorp AA, Klijn N, Bindels JG, et al. Analysis of intestinal flora development in breast-fed and formula-fed infants by using molecular identification and detection methods. J. Pediatr. Gastroenterol. Nutr. 2000;30:61–67.
    1. Hartman AL, Lough DM, Barupal DK, Fiehn O, Fishbein T, Zasloff M, et al. Human gut microbiome adopts an alternative state following small bowel transplantation. Proc. Natl. Acad. Sci. USA. 2009;106:17187–17192.
    1. Holman RC, Stoll BJ, Curns AT, Yorita KL, Steiner CA, Schonberger LB. Necrotising enterocolitis hospitalisations among neonates in the United States. Paediatr. Perinat. Epidemiol. 2006;20:498–506.
    1. Horbar JD, Badger GJ, Carpenter JH, Fanaroff AA, Kilpatrick S, LaCorte M, et al. Trends in mortality and morbidity for very low birth weight infants, 1991–1999. Pediatrics. 2002;110:143–151.
    1. Hou JW, Yu RC, Chou CC. Changes in some components of soymilk during fermentation with bifidobacteria. Food Res. Int. 2000;33:393–397.
    1. Hoy CM, Wood CM, Hawkey PM, Puntis JWL. Duodenal microflora in very-low-birth-weight neonates and relation to necrotizing enterocolitis. J. Clin. Microbiol. 2000;38:4539–4547.
    1. Huson DH, Auch AF, Qi J, Schuster SC. MEGAN analysis of metagenomic data. Genome Res. 2007;17:377–386.
    1. Jimenez E, Marin ML, Martin R, Odriozola JM, Olivares M, Xaus J, et al. Is meconium from healthy newborns actually sterile? Res. Microbiol. 2008;159:187–193.
    1. Koenig JE, Spor A, Scalfone AL, et al. Succession of microbial consortia in the developing infant gut microbiome. Proc. Natl. Acad. Sci. USA. 2011;108:4578–4585.
    1. La Tuga SM, Ellis JC, Cotton CM, et al. Beyond bacteria: a study of the enteric microbial consortium in extremely low birth weight infants. PLoS ONE. 2011;6:e27858.
    1. Ley RE, Turnbaugh PJ, Klein S, Gordon JI. Microbial ecology – human gut microbes associated with obesity. Nature. 2006;444:1022–1023.
    1. Mackie RI, Sghir A, Gaskins HR. Developmental microbial ecology of the neonatal gastrointestinal tract. Am. J. Clin. Nutr. 1999;69:1035S–1045S.
    1. Madan JC, Cowper Salari R, Saxena D, et al. Gut microbial colonisation in premature neonates predicts neonatal sepsis. Arch. Dis. Child. Fetal Neonatal Ed. 2012;97:F456–F462.
    1. Mai V, Young CM, Ukhanova M, Wang X, Sun Y, Casella G, et al. Fecal microbiota in premature infants prior to necrotizing enterocolitis. PLoS ONE. 2011;6:e20647. doi: .
    1. Marques TM, Wall R, Ross RP, Fitzgerald GF, Ryan CA, Stanton C. Programming infant gut microbiota: influence of dietary and environmental factors. Curr. Opin. Biotechnol. 2010;21:149–156.
    1. Martinsen TC, Bergh K, Waldum HL. Gastric juice: a barrier against infectious diseases. Basic Clin. Pharmacol. Toxicol. 2005;96:94–102.
    1. Mattila-Sandholm T, Blaut M, Daly C, Dore L, De Vuyst J, Gibson G, et al. Food, GI-tract functionality and human health cluster: PROEUHEALTH. Microb. Ecol. Health Dis. 2002;14:65–74.
    1. Mikami K, Takahashi H, Kimura M, Isozaki M, Izuchi K, Shibata R, et al. Influence of maternal bifidobacteria on the establishment of bifidobacteria colonizing the gut in infants. Pediatr. Res. 2009;65:669–674.
    1. Mitchell DJ, McClure BG, Tubman TRJ. Simultaneous monitoring of gastric and oesophageal pH reveals limitations of conventional oesophageal pH monitoring in milk fed infants. Arch. Dis. Child. 2001;84:273–276.
    1. Morelli L. Postnatal development of intestinal microflora as influenced by infant nutrition. J. Nutr. 2008;138:1791S–1795S.
    1. Morowitz MJ, Poroyko V, Caplan M, Alverdy J, Liu DC. Redefining the role of intestinal microbes in the pathogenesis of necrotizing enterocolitis. Pediatrics. 2010;125:777–785.
    1. Mshvildadze M, Neu J. Probiotics and prevention of necrotizing enterocolitis. Early Human Dev. 2009;85:S71–S74.
    1. Murphy EF, Cotter PD, Healy S, Marques TM, O'Sullivan O, Fouhy F, et al. Composition and energy harvesting capacity of the gut microbiota: realtionship to diet, obesity and time in mouse models. Gut. 2010;59:1635–1642.
    1. Mshvildadze M, Neu J, Shuster J, Theriaque D, Li N, Mai V. Intestinal microbial ecology in premature infants assessed with non-culture-based techniques. J. Pediatr. 2010;156:20–25.
    1. Neu J, Walker WA. Medical progress: necrotizing enterocolitis. N. Engl. J. Med. 2011;364:255–264.
    1. Newell SJ, Sarkar PK, Durbin GM, Booth IW, McNeish AS. Maturation of the lower esohaggeal sphincter in the preterm baby. Gut. 1988;29:167–172.
    1. O'Flaherty S, Klaenhammer TR. The role and potential of probiotic bacteria in the gut, and the communication between gut microflora and gut/host. Int. Dairy J. 2010;20:262–268.
    1. Ogawa J, Matsumura K, Kishino S, Omura Y, Shimizu S. Conjugated linoleic acid accumulation via 10-hydroxy-12-octadecaenoic acid during microaerobic transformation of linoleic acid by Lactobacillus acidophilus. Appl. Environ. Microbiol. 2001;67:1246–1252.
    1. O'Sullivan O, Coakley M, Lakshminarayanan B, Claesson MJ, Stanton C, O'Toole PW, et al. Correlation of rRNA gene amplicon pyrosequencing and bacterial culture for microbial compositional analysis of faecal samples from elderly Irish subjects. J. Appl. Microbiol. 2011;111:467–473.
    1. O'Toole PW, Claesson MJ. Gut microbiota: changes throughout the lifespan from infancy to elderly. Int. Dairy J. 2010;20:281–291.
    1. Penders J, Thijs C, Vink C, Stelma FF, Snijders B, Kummeling I, et al. Factors influencing the composition of the intestinal microbiota in early infancy. Pediatrics. 2006;118:511–521.
    1. Peterson DA, Frank DN, Pace NR, Gordon JI. Metagenomic approaches for defining the pathogenesis of inflammatory bowel diseases. Cell Host Microbe. 2008;3:417–427.
    1. Rastall RA. Bacteria in the gut: friends and foes and how to alter the balance. J. Nutr. 2004;134:2022S–2026S.
    1. Rotimi VO, Duerden BI. The development of the bacterial-flora in normal neonates. J. Med. Microbiol. 1981;14:51–62.
    1. Satokari RM, Vaughan EE, Favier CF, Dore J, Edwards C, de Vos WM. Diversity of Bifidobacterium and Lactobacillus spp. in breast-fed and formula-fed infants as assessed by 16S rDNA sequence differences. Microb. Ecol. Health Dis. 2002;14:97–105.
    1. Schloss PD, Handelsman J. A statistical toolbox for metagenomics: assessing functional diversity in microbial communities. BMC Bioinformatics. 2008;9:34. doi: .
    1. Simpson PJ, Stanton C, Fitzgerald GF, Ross RP. Genomic diversity and relatedness of bifidobacteria isolated from a porcine cecum. J. Bacteriol. 2003;185:2571–2581.
    1. Sondheimer JM, Clark DA. Gastric pH in healthy preterm infants – effect of age and feeding type. Gastroenterology. 1985;88:1593–1593.
    1. Sondheimer JM, Clark DA, Gervaise EP. Continuous gastric pH measurement in young and older healthy preterm infants receiving formula and clear liquid feedings. J. Pediatr. Gastroenterol. Nutr. 1985;4:352–355.
    1. Sreekumar O, Hosono A. The antimutagenic properties of a polysaccharide produced by Bifidobacterium longum and its cultured milk against some heterocyclic amines. Can. J. Microbiol. 1998;44:1029–1036.
    1. Stark PL, Lee A. The microbial ecology of the large bowel of breast-fed and formula-fed infants during the first year of life. J. Med. Microbiol. 1982;15:189–203.
    1. Sutphen JL, Dillard VL. Effects of maturation and gastric acidity on gastroesophageal reflux in infants. Am. J. Dis. Child. 1986;140:1062–1064.
    1. Urich T, Lanzen A, Qi J, Huson DH, Schleper C, Schuster SC. Simultaneous assessment of soil microbial community structure and function through analysis of the meta-transcriptome. PLoS ONE. 2008;3:13.
    1. Wang YW, Hoenig JD, Malin KJ, Qamar S, Petrof EO, Sun J, et al. 16S rRNA gene-based analysis of fecal microbiota from preterm infants with and without necrotizing enterocolitis. ISME J. 2009;3:944–954.
    1. Washington N, Spensley PJ, Smith CA, Parker M, Bush D, Jackson SJ, et al. Dual pH probe monitoring versus single pH probe monitoring in infants on milk feeds: the impact on diagnosis. Arch. Dis. Child. 1999;81:309–312.
    1. Westerbeek EAM, Lafeber A, van den Berg HN, Knol J, Fetter WPF, van Elburg RM. The intestinal bacterial colonisation in preterm infants: a review of the literature. Clin. Nutr. 2006;25:361–368.
    1. Wexler HM. Bacteroides: the good, the bad, and the nitty-gritty. Clin. Microbiol. Rev. 2007;20:593–621.
    1. Zoetendal EG, Heilig HGHJ, Klaassens EM, Booijink CCGM, Kleerebezem M, Smidt H, et al. Isolation of DNA from bacterial samples of the human gastrointestinal tract. Nat. Protoc. 2006;1:870–873.

Source: PubMed

Sponsorer og samarbeidspartnere

Medisinsk tilstand

Legemiddelintervensjoner

3
Abonnere