Impact of diet in shaping gut microbiota revealed by a comparative study in infants during the first six months of life

Journal of Microbiology and Biotechnology

Volumn 24, Issue 2, 2014, Pages 133-143

  Fan, Wenguang ^a,b   Huo, Guicheng ^a   Li, Xiaomin ^a   Yang, Lijie ^a   Duan, Cuicui ^a  

^a NORTHEAST AGRICULTURAL UNIVERSITY   (China)

^b Hei LongJiang Vocational College   (China)

Author keywords

Breast fed; Formula fed; High throughput sequencing; Infant intestinal microbiota; Mixed fed

Indexed keywords

DNA 16S; RNA 16S; BACTERIAL DNA; RIBOSOME DNA;

ARTICLE; ARTIFICIAL MILK; BACTERIUM DETECTION; BACTERIUM IDENTIFICATION; BIFIDOBACTERIACEAE; BREAST FEEDING; CHINA; COMPARATIVE STUDY; CONTROLLED STUDY; ENTEROBACTERIACEAE; FECES MICROFLORA; FIRMICUTES; HIGH THROUGHPUT SEQUENCING; HUMAN; INFANT; INFANT NUTRITION; INTESTINE FLORA; MICROBIAL DIVERSITY; NONHUMAN; NORMAL HUMAN; PROTEOBACTERIA; SEQUENCE ANALYSIS; SPECIES RICHNESS; BACTERIA; BIOLOGY; CHEMISTRY; CLASSIFICATION; CLUSTER ANALYSIS; DIET; FECES; GASTROINTESTINAL TRACT; GENETICS; MICROBIOLOGY; MICROFLORA; PHYLOGENY; PROCEDURES;

BACTERIA; CHINA; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; DIET; DNA, BACTERIAL; DNA, RIBOSOMAL; FECES; GASTROINTESTINAL TRACT; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; INFANT; MICROBIOTA; PHYLOGENY; RNA, RIBOSOMAL, 16S;

EID: 84896822568     PISSN: 10177825     EISSN: 17388872     Source Type: Journal    
DOI: 10.4014/jmb.1309.09029     Document Type: Article

References (42)

1. Allen J, Hector D. 2005. Benefits of breastfeeding. NSW Public Health Bull. 16: 42-46.
2. Bäckhed F, Ley RE, Sonnenburg JL, Peterson DA, Gordon JI. 2005. Host-bacterial mutualism in the human intestine. Science 307: 1915-1920.
3. Berseth CL, Thureen PJ, Hay WW. 2006. Development of the gastrointestinal tract. Neonatal Nutr. Metab. 2: 67-73.
4. Bezirtzoglou E, Tsiotsias A, Welling GW. 2011. Microbiota profile in feces of breast-and formula-fed newborns by using fluorescence in situ hybridization (FISH). Anaerobe 17: 478-482.
5. Biasucci G, Benenati B, Morelli L, Bessi E, Boehm G. 2008. Cesarean delivery may affect the early biodiversity of intestinal bacteria. J. Nutr. 138: 1796S-1800S.
6. Biasucci G, Rubini M, Riboni S, Morelli L, Bessi E, Retetangos C. 2010. Mode of delivery affects the bacterial community in the newborn gut. Early Hum. Dev. 86: S13-S15.
7. Chao A, Shen TJ. 2003. Nonparametric estimation of Shannon's index of diversity when there are unseen species in sample. Environ. Ecol. Stat. 10: 429-443.
8. Claesson MJ, Cusack S, O'Sullivan O, Greene-Diniz R, de Weerd H, Flannery E, et al. 2011. Composition, variability, and temporal stability of the intestinal microbiota of the elderly. Proc. Natl. Acad. Sci. USA 108: 4586-4591.
9. De Filippo C, Cavalieri D, Di Paola M, Ramazzotti M, Poullet JB, Massart S, et al. 2011. Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc. Natl. Acad. Sci. USA 107: 14691-14696.
10. de la Cochetiere MF, Piloquet H, des Robert C, Darmaun D, Galmiche JP, Roze JC. 2004. Early intestinal bacterial colonization and necrotizing enterocolitis in infants: the putative role of Clostridium. Pediatr. Res. 56: 366-370.
11. Delzenne NM, Neyrinck AM, Bäckhed F, Cani PD. 2011. Targeting gut microbiota in obesity: effects of prebiotics and probiotics. Nat. Rev. Endocrinol. 7: 639-646.
12. Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M, et al. 2005. Diversity of the human intestinal microbial flora. Science 308: 1635-1638.
13. Fabrice A, Didier R. 2009. Exploring microbial diversity using 16S rRNA high-throughput methods. J. Comput. Sci. Syst. Biol. 2: 074-092.
14. Fallani M, Young D, Scott J, Norin E, Amarri S, Adam R, et al. 2010. Intestinal microbiota of 6-week-old infants across Europe: geographic influence beyond delivery mode, breastfeeding, and antibiotics. J. Pediatr. Gastroenterol. Nutr. 51: 77-84.
15. Fernández L, Langa S, Martín V, Maldonado A, Jiménez E, Martín R, Rodríguez JM. 2013. The human milk microbiota: origin and potential roles in health and disease. Pharmacol. Res. 69: 1-10.
16. Fox PF, Kelly AL. 2006. Indigenous enzymes in milk: overview and historical aspects-Part-2. Int. Dairy J. 16: 517-532.
17. González R, Klaassens ES, Malinen E, de Vos WM, Vaughan EE. 2008. Differential transcriptional response of Bifidobacterium longum to human milk, formula milk, and galactooligosaccharide. Appl. Environ. Microbiol. 74: 4686-4694.
18. Haraszthy VI, Zambon JJ, Sreenivasan PK, Zambon MM, Gerber D, Rego R, Parker C. 2007. Identification of oral bacterial species associated with halitosis. J. Am. Dent. Assoc. 138: 1113-1120.
19. Kassinen A, Krogius-Kurikka L, Mäkivuokko H, Rinttilä T, Paulin L, Corander J, et al. 2007. The fecal microbiota of irritable bowel sydrome patients differs significantly from that of healthy subjects. Gastroenterology 133: 24-33.
20. Klaassens ES, de Vos WM, Vaughan EE. 2007. Metaproteomics approach to study the functionality of the microbiota in the human infant gastrointestinal tract. Appl. Environ. Microbiol. 73: 1388-1392.
21. Koenig JE, Spor A, Scalfone N, Fricker AD, Stombaugh J, Knight R, et al. 2011. Microbes and health sackler colloquium: succession of microbial consortia in the developing infant gut microbiome. Proc. Natl. Acad. Sci. USA 108: 4578-4585.
22. Lecuit M, Suarez F, Lortholary O. 2004. Immunoproliferative small intestinal disease associated with Campylobacter jejuni. Med. Sci. 20: 638-640.
23. Martín R, Langa S, Reviriego C, Jiminez E, Marín ML, Xaus J, et al. 2003. Human milk is a source of lactic acid bacteria for the infant gut. J. Pediatr. 143: 754-758.
24. Martín R, Heilig GHJ, Zoetendal EG, Smidt H, Rodriguez JM. 2007. Diversity of the Lactobacillus group in breast milk and vagina of healthy women and potential role in the colonization of the infant gut. J. Appl. Microbiol. 103: 2638-2644.
25. Moore TA, Hanson CK, Anderson-Berry A. 2011. Colonization of the gastrointestinal tract in neonates: a review. ICAN 3: 291-295.
26. Morelli L. 2008. Postnatal development of intestinal microflora as influenced by infant nutrition. J. Nutr. 138: 1791S-1795S.
27. Neu J, Rushing J. 2011. Cesarean versus vaginal delivery: long-term infant outcomes and the hygiene hypothesis. Clin. Perinatol. 38: 321-331.
28. Palmer C, Bik EM, DiGiulio DB, Relman DA, Brown PO. 2007. Development of the human infant intestinal microbiota. PLoS Biol. 5: e177.
29. Parsonnet J, Friedman GD, Vandersteen DP, Chang Y, Vogelman JH, Orentreich N, Sibley RK. 1991. Helicobacter pylori infection and the risk of gastric carcinoma. N Engl. J. Med. 325: 1127-1131.
30. Penders J, Vink C, Driessen C, London N, Thijs C, Stobberingh EE. 2005. Quantification of Bifidobacterium spp., Escherichia and Clostridium difficile in faecal samples of breast-fed and formula-fed infants by real-time PCR. FEMS Microbiol. Lett. 243: 141-147.
31. Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, et al. 2010. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464: 59-65.
32. Reetta MS, Elaine EV, Christine FF, Joël Doré CE, de VOS VM. 2002. Diversity of Bidobacterium and Lactobacillus spp. In breast-fed and formula-fed infants as assessed by 16S rDNA sequence differences. Microb. Ecol. Health Dis. 14: 97-105.
33. Rinne M, Kalliomaki M, Arvilommi H, Salminen S, Isolauri E. 2005. Effect of probiotics and breastfeeding on the Bifidobacterium and Lactobacillus/Enterococcus microbiota and humoral immune responses. J. Pediatr. 147: 186-191.
34. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, et al. 2009. Introducing Mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75: 7537-7541.
35. Sinkiewicz G, Ljunggren L. 2008. Occurrence of Lactobacillus reuteri in human breast milk. Microb. Ecol. Health Dis. 20: 122-126.
36. Sokol H, Pigneur B, Watterlot L, Lakhdari O, Bermúdez-Humarán LG, Gratadoux JJ, et al. 2008. Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients. Proc. Natl. Acad. Sci. USA 105: 16731-16736.
37. Tamboli CP, Neut C, Desreumaux P, Colombel JF. 2004. Dysbiosis in inflammatory bowel disease. Gut 53: 1-4.
38. Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, Gordon JI. 2006. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444: 1027-1031.
39. Turroni F, Foroni E, Pizzetti P, Giubellini V, Ribbera A, Merusi P, et al. 2009. Exploring the diversity of the bifidobacterial population in the human intestinal tract. Appl. Environ. Microbiol. 75: 1534-1545.
40. Waar K, Degener JE, van Luyn MJ, Harmsen HJ. 2005. Fluorescence in situ hybridization with specific DNA probes offers adequate detection of Enterococcus faecalis and Enterococcus faecium in clinical samples. J. Med. Microbiol. 54: 937-944.
41. Wang Q, Garrity GM, Tiedje JM, Cole JR. 2007. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 73: 5261-5267.
42. Young VB. 2012. The intestinal microbiota in health and disease. Curr. Opin. Gastroenterol. 28: 63-69.