Nutr Res Pract.  2015 Jun;9(3):242-248. 10.4162/nrp.2015.9.3.242.

Comparison of the gut microbiota profile in breast-fed and formula-fed Korean infants using pyrosequencing

  • 1The Graduate School of Clinical Health Sciences, Ewha Womans University, Seoul 120-750, Korea.
  • 2Department of Nutritional Science and Food Management, Ewha Womans University, 52, Ewhayeodae-gil, Seodaemun-gu, Seoul 120-750, Korea.
  • 3ChunLab, Inc. Seoul 151-742, Korea.
  • 4Department of Life Science, Hallym University, Gangwon 200-702, Korea.
  • 5Department of Pediatrics, School of Medicine, Ewha Womans University, Seoul 158-710, Korea.
  • 6Arante Women's Hospital, Seoul 150-836, Korea.
  • 7Department of Life Science, Global Top 5 Research Program, Ewha Womans University, Seoul 120-750, Korea.


Feeding in infancy is the most significant determinant of the intestinal microbiota in early life. The aim of this study was to determine the gut microbiota of Korean infants and compare the microbiota obtained between breast-fed and formula-fed Korean infants.
We analyzed the microbial communities in fecal samples collected from twenty 4-week old Korean (ten samples in each breast-fed or formula-fed) infants using pyrosequencing.
The fecal microbiota of the 4-week-old Korean infants consisted of the three phyla Actinobacteria, Firmicutes, and Proteobacteria. In addition, five species, including Bifidocbacterium longum, Streptococcus salivarius, Strepotococcus lactarius, Streptococcus pseudopneumoniae, and Lactobacillus gasseri were common commensal intestinal microbiota in all infants. The predominant intestinal microbiota in the breast-fed infants (BFI) included the phylum Actinobacteria (average 70.55%), family Bifidobacteriacea (70.12%), genus Bifidobacterium (70.03%) and species Bifidobacterium longum (69.96%). In the microbiota from the formula-fed infants (FFI), the proportion of the phylum Actinobacteria (40.68%) was less, whereas the proportions of Firmicutes (45.38%) and Proteobacteria (13.85%) as well as the diversity of each taxonomic level were greater, compared to those of the BFI. The probiotic species found in the 4-week-old Korean infants were Bifidobacterium longum, Streptococcus salivarius, and Lactobacillus gasseri. These probiotic species accounted for 93.81% of the microbiota from the BFI, while only 63.80% of the microbiota from the FFI. In particular, B. longum was more abundant in BFI (69.96%) than in FFI (34.17%).
Breast milk supports the growth of B. longum and inhibits others. To the best of our knowledge, this study was the first attempt to analyze the gut microbiota of healthy Korean infants according to the feeding type using pyrosequencing. Our data can be used as a basis for further studies to investigate the development of intestinal microbiota with aging and disease status.


Gut microbiota; breast-fed; formula-fed; pyrosequencing

MeSH Terms

Milk, Human


  • Fig. 1 Aggregate microbiota composition at pylum/family level from fecal samples of 4 wks old infants. (A) Breast-fed infants, (B) Formula-fed infants.

  • Fig. 2 Heatmap analysis of the species detected from pyrosequencing of fecal samples from 4 wks old BFI and FFI. The data contained in the matrix are represented by black and white colors. The minimum ratio of a taxon is displayed as an individual sample. The cut-off value was set to 1%. BFI, Breast-fed infants; FFI, Formula-fed infants

  • Fig. 3 The compositions of probiotics at the species level in fecal samples from 4-week-old BFI and FFI. etc., bacteria other than probiotics; BFI, Breast-fed infants; FFI, Formula-fed infants

  • Fig. 4 Scatter plots showing the proportions of Bifidobacterium sequences with respect to the total sequences obtained from pyrosequencing 16S rRNA genes associated with feeding type. Mean values (horizontal lines) and significance values (P, Mann-Whitney) are shown. BFI, Breast-fed infants; FFI, Formula-fed infants


1. Simon GL, Gorbach SL. Intestinal flora in health and disease. Gastroenterology. 1984; 86:174–193.
2. Young VB. The intestinal microbiota in health and disease. Curr Opin Gastroenterol. 2012; 28:63–69.
3. De Filippo C, Cavalieri D, Di Paola M, Ramazzotti M, Poullet JB, Massart S, Collini S, Pieraccini G, Lionetti P. Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc Natl Acad Sci U S A. 2010; 107:14691–14696.
4. Cardona F, Andrés-Lacueva C, Tulipani S, Tinahones FJ, Queipo-Ortuño MI. Benefits of polyphenols on gut microbiota and implications in human health. J Nutr Biochem. 2013; 24:1415–1422.
5. Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto JM, Bertalan M, Borruel N, Casellas F, Fernandez L, Gautier L, Hansen T, Hattori M, Hayashi T, Kleerebezem M, Kurokawa K, Leclerc M, Levenez F, Manichanh C, Nielsen HB, Nielsen T, Pons N, Poulain J, Qin J, Sicheritz-Ponten T, Tims S, Torrents D, Ugarte E, Zoetendal EG, Wang J, Guarner F, Pedersen O, de Vos WM, Brunak S, Doré J, Antolín M, Artiguenave F, Blottiere HM, Almeida M, Brechot C, Cara C, Chervaux C, Cultrone A, Delorme C, Denariaz G, Dervyn R, Foerstner KU, Friss C, van de Guchte M, Guedon E, Haimet F, Huber W, van Hylckama-Vlieg J, Jamet A, Juste C, Kaci G, Knol J, Lakhdari O, Layec S, Le Roux K, Maguin E, Mérieux A, Melo Minardi R, M'rini C, Muller J, Oozeer R, Parkhill J, Renault P, Rescigno M, Sanchez N, Sunagawa S, Torrejon A, Turner K, Vandemeulebrouck G, Varela E, Winogradsky Y, Zeller G, Weissenbach J, Ehrlich SD, Bork P. MetaHIT Consortium. Enterotypes of the human gut microbiome. Nature. 2011; 473:174–180.
6. Wu GD, Chen J, Hoffmann C, Bittinger K, Chen YY, Keilbaugh SA, Bewtra M, Knights D, Walters WA, Knight R, Sinha R, Gilroy E, Gupta K, Baldassano R, Nessel L, Li H, Bushman FD, Lewis JD. Linking long-term dietary patterns with gut microbial enterotypes. Science. 2011; 334:105–108.
7. Fallani M, Young D, Scott J, Norin E, Amarri S, Adam R, Aguilera M, Khanna S, Gil A, Edwards CA, Doré J. Other Members of the INFABIO Team. Intestinal microbiota of 6-week-old infants across Europe: geographic influence beyond delivery mode, breastfeeding, and antibiotics. J Pediatr Gastroenterol Nutr. 2010; 51:77–84.
8. Morelli L. Postnatal development of intestinal microflora as influenced by infant nutrition. J Nutr. 2008; 138:1791S–1795S.
9. Hooper LV. Bacterial contributions to mammalian gut development. Trends Microbiol. 2004; 12:129–134.
10. Penders J, Thijs C, Vink C, Stelma FF, Snijders B, Kummeling I, van den Brandt PA, Stobberingh EE. Factors influencing the composition of the intestinal microbiota in early infancy. Pediatrics. 2006; 118:511–521.
11. Hanson LA, Korotkova M. The role of breastfeeding in prevention of neonatal infection. Semin Neonatol. 2002; 7:275–281.
12. López-Alarcón M, Villalpando S, Fajardo A. Breast-feeding lowers the frequency and duration of acute respiratory infection and diarrhea in infants under six months of age. J Nutr. 1997; 127:436–443.
13. Morrow AL, Rangel JM. Human milk protection against infectious diarrhea: implications for prevention and clinical care. Semin Pediatr Infect Dis. 2004; 15:221–228.
14. Wright AL, Bauer M, Naylor A, Sutcliffe E, Clark L. Increasing breastfeeding rates to reduce infant illness at the community level. Pediatrics. 1998; 101:837–844.
15. Isaacs CE. Human milk inactivates pathogens individually, additively, and synergistically. J Nutr. 2005; 135:1286–1288.
16. Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, Ley RE, Sogin ML, Jones WJ, Roe BA, Affourtit JP, Egholm M, Henrissat B, Heath AC, Knight R, Gordon JI. A core gut microbiome in obese and lean twins. Nature. 2009; 457:480–484.
17. Zaura E, Keijser BJ, Huse SM, Crielaard W. Defining the healthy "core microbiome" of oral microbial communities. BMC Microbiol. 2009; 9:259.
18. Kim BS, Kim JN, Yoon SH, Chun J, Cerniglia CE. Impact of enrofloxacin on the human intestinal microbiota revealed by comparative molecular analysis. Anaerobe. 2012; 18:310–320.
19. Jeon YS, Chun J, Kim BS. Identification of household bacterial community and analysis of species shared with human microbiome. Curr Microbiol. 2013; 67:557–563.
20. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M, Na H, Park SC, Jeon YS, Lee JH, Yi H, Won S, Chun J. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol. 2012; 62:716–721.
21. Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics. 2011; 27:2194–2200.
22. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol. 2009; 75:7537–7541.
23. Rijkers GT, de Vos WM, Brummer RJ, Morelli L, Corthier G, Marteau P. Health benefits and health claims of probiotics: bridging science and marketing. Br J Nutr. 2011; 106:1291–1296.
24. Chang JY, Shin SM, Chun J, Lee JH, Seo JK. Pyrosequencing-based molecular monitoring of the intestinal bacterial colonization in preterm infants. J Pediatr Gastroenterol Nutr. 2011; 53:512–519.
25. Heikkilä MP, Saris PE. Inhibition of Staphylococcus aureus by the commensal bacteria of human milk. J Appl Microbiol. 2003; 95:471–478.
26. Fan W, Huo G, Li X, Yang L, Duan C. Impact of diet in shaping gut microbiota revealed by a comparative study in infants during the six months of life. J Microbiol Biotechnol. 2014; 24:133–143.
27. Bezirtzoglou E, Tsiotsias A, Welling GW. Microbiota profile in feces of breast- and formula-fed newborns by using fluorescence in situ hybridization (FISH). Anaerobe. 2011; 17:478–482.
28. Tannock GW, Lawley B, Munro K, Gowri Pathmanathan S, Zhou SJ, Makrides M, Gibson RA, Sullivan T, Prosser CG, Lowry D, Hodgkinson AJ. Comparison of the compositions of the stool microbiotas of infants fed goat milk formula, cow milk-based formula, or breast milk. Appl Environ Microbiol. 2013; 79:3040–3048.
29. Yoshioka H, Iseki K, Fujita K. Development and differences of intestinal flora in the neonatal period in breast-fed and bottle-fed infants. Pediatrics. 1983; 72:317–321.
30. Lilly DM, Stillwell RH. Probiotics: growth-promoting factors produced by microorganisms. Science. 1965; 147:747–748.
31. Coppa GV, Gabrielli O, Zampini L, Galeazzi T, Ficcadenti A, Padella L, Santoro L, Soldi S, Carlucci A, Bertino E, Morelli L. Oligosaccharides in 4 different milk groups, Bifidobacteria, and Ruminococcus obeum. J Pediatr Gastroenterol Nutr. 2011; 53:80–87.
32. Marcobal A, Sonnenburg JL. Human milk oligosaccharide consumption by intestinal microbiota. Clin Microbiol Infect. 2012; 18:Suppl 4. 12–15.
33. Conway PL. Selection criteria for probiotic microorganisms. Asia Pac J Clin Nutr. 1996; 5:10–14.
34. Bezirtzoglou E, Romond MB, Romond C. Regulation of the bacterial intestinal implantation in infant born by caesarean section. Comp Immunol Microbiol Infect Dis. 1992; 15:71–74.
35. Thum C, Cookson AL, Otter DE, McNabb WC, Hodgkinson AJ, Dyer J, Roy NC. Can nutritional modulation of maternal intestinal microbiota influence the development of the infant gastrointestinal tract? J Nutr. 2012; 142:1921–1928.
36. Hascoët JM, Hubert C, Rochat F, Legagneur H, Gaga S, Emady-Azar S, Steenhout PG. Effect of formula composition on the development of infant gut microbiota. J Pediatr Gastroenterol Nutr. 2011; 52:756–762.
Full Text Links
  • NRP
export Copy
  • Twitter
  • Facebook
Similar articles
Copyright © 2023 by Korean Association of Medical Journal Editors. All rights reserved.     E-mail: