Milk- and solid-feeding practices and daycare attendance are associated with differences in bacterial diversity, predominant communities, and metabolic and immune function of the infant gut microbiome

Amanda L. Thompson1, Andrea Monteagudo-Mera2, Maria B. Cadenas2, Michelle Lampl3, M. Andrea Azcarate‐Peril4
1Department of Anthropology, University of North Carolina, Chapel Hill, NC, USA
2Microbiome Core Facility, Center for Gastrointestinal Biology and Disease, University of North Carolina Chapel Hill, NC, USA.
3Department of Anthropology and Center for the Study of Human Health, Emory University Atlanta, GA, USA.
4Microbiome Core Facility, Center for Gastrointestinal Biology and Disease, University of North Carolina Chapel Hill, NC, USA ; Department of Cell Biology and Physiology, School of Medicine, University of North Carolina Chapel Hill, NC, USA.

Tóm tắt

Từ khóa


Tài liệu tham khảo

Abubucker, 2012, Metabolic reconstruction for metagenomic data and its application to the human microbiome, PLoS Comput. Biol, 8, e1002358, 10.1371/journal.pcbi.1002358

Amarri, 2006, Changes of gut microbiota and immune markers during the complementary feeding period in healthy breast-fed infants, J. Pediatr. Gastroenterol. Nutr, 42, 488, 10.1097/01.mpg.0000221907.14523.6d

Augustine, 2013, Early child care and illness among preschoolers, J. Health Soc. Behav, 54, 315, 10.1177/0022146513496106

Aycicek, 2006, Breast milk provides better antioxidant power than does formula, Nutrition, 22, 616, 10.1016/j.nut.2005.12.011

Azcarate-Peril, 2006, Transcriptional and functional analysis of oxalyl-coenzyme A (CoA) decarboxylase and formyl-CoA transferase genes from Lactobacillus acidophilus, Appl. Environ. Microbiol, 72, 1891, 10.1128/AEM.72.3.1891-1899.2006

Beck, 1998, The apbE gene encodes a lipoprotein involved in thiamine synthesis in Salmonella typhimurium, J. Bacteriol, 180, 885, 10.1128/JB.180.4.885-891.1998

Cabrera-Rubio, 2012, The human milk microbiome changes over lactation and is shaped by maternal weight and mode of delivery, Am. J. Clin. Nutr, 96, 544, 10.3945/ajcn.112.037382

Candela, 2012, Intestinal microbiota is a plastic factor responding to environmental changes, Trends Microbiol, 20, 385, 10.1016/j.tim.2012.05.003

Caporaso, 2010, QIIME allows analysis of high-throughput community sequencing data, Nat. Methods, 7, 335, 10.1038/nmeth.f.303

Chabriere, 1999, Crystal structures of the key anaerobic enzyme pyruvate:ferredoxin oxidoreductase, free and in complex with pyruvate, Nat. Struct. Biol, 6, 182, 10.1038/5870

Chapman, 2002, Role of Escherichia coli curli operons in directing amyloid fiber formation, Science, 295, 851, 10.1126/science.1067484

Coppa, 1993, Changes in carbohydrate composition in human milk over 4 months of lactation, Pediatrics, 91, 637, 10.1542/peds.91.3.637

Davis, 2011, Barcoded pyrosequencing reveals that consumption of galactooligosaccharides results in a highly specific bifidogenic response in humans, PLoS ONE, 6, e25200, 10.1371/journal.pone.0025200

De Filippo, 2010, 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, 107, 14691, 10.1073/pnas.1005963107

de Lorenzo, 1986, Aerobactin biosynthesis and transport genes of plasmid ColV-K30 in Escherichia coli K-12, J. Bacteriol, 165, 570, 10.1128/jb.165.2.570-578.1986

Devine, 2013, Impact of ileocecal resection and concomitant antibiotics on the microbiome of the murine jejunum and colon, PLoS ONE, 8, e73140, 10.1371/journal.pone.0073140

Donnet-Hughes, 2010, Potential role of the intestinal microbiota of the mother in neonatal immune education, Proc. Nutr. Soc, 69, 407, 10.1017/S0029665110001898

Edgar, 2010, Search and clustering orders of magnitude faster than BLAST, Bioinformatics, 26, 2460, 10.1093/bioinformatics/btq461

Edwards, 1989, Isolation and direct complete nucleotide determination of entire genes. Characterization of a gene coding for 16S ribosomal RNA, Nucleic Acids Res, 17, 7843, 10.1093/nar/17.19.7843

Fallani, 2011, Determinants of the human infant intestinal microbiota after the introduction of first complementary foods in infant samples from five European centres, Microbiology, 157(Pt 5), 1385, 10.1099/mic.0.042143-0

Fanaro, 2003, Intestinal microflora in early infancy: composition and development, Acta Paediatr, 91, 48, 10.1111/j.1651-2227.2003.tb00646.x

Favier, 2002, Molecular monitoring of succession of bacterial communities in human neonates, Appl. Environ. Microbiol, 68, 219, 10.1128/AEM.68.1.219-226.2002

Fierer, 2008, The influence of sex, handedness, and washing on the diversity of hand surface bacteria, Proc. Natl. Acad. Sci. U.S.A, 105, 17994, 10.1073/pnas.0807920105

Fierer, 2010, Forensic identification using skin bacterial communities, Proc. Natl. Acad. Sci. U.S.A, 107, 6477, 10.1073/pnas.1000162107

Gill, 2006, Metagenomic analysis of the human distal gut microbiome, Science, 312, 1355, 10.1126/science.1124234

Gomez-Llorente, 2013, Three main factors define changes in fecal microbiota associated with feeding modality in infants, J. Pediatr. Gastroenterol. Nutr, 57, 461, 10.1097/MPG.0b013e31829d519a

Greiner, 2011, Effects of the gut microbiota on obesity and glucose homeostasis, Trends Endocrinol. Metab, 22, 117, 10.1016/j.tem.2011.01.002

Guarner, 2003, Gut flora in health and disease, Lancet, 361, 512, 10.1016/S0140-6736(03)12489-0

Gutierrez-Castrellon, 2014, Diarrhea in preschool children and lactobacillus reuteri: a randomized controlled trial, Pediatrics, 133, e904, 10.1542/peds.2013-0652

Harmsen, 2000, Analysis of intestinal flora development in breast-fed and formula-fed infants by using molecular identification and detection methods, J. Pediatr. Gastroenterol. Nutr, 30, 61, 10.1097/00005176-200001000-00019

Hopkins, 2005, Characterisation of intestinal bacteria in infant stools using real-time PCR and northern hybridisation analyses, FEMS Microbiol. Ecol, 54, 77, 10.1016/j.femsec.2005.03.001

Ip, 2007, Breastfeeding and Maternal and Infant Health Outcomes in Developed Countries

Jeurink, 2013, Human milk: a source of more life than we imagine, Benef. Microbes, 4, 17, 10.3920/BM2012.0040

Knights, 2011, Supervised classification of human microbiota, FEMS Microbiol. Rev, 35, 343, 10.1111/j.1574-6976.2010.00251.x

Koenig, 2011, Succession of microbial consortia in the developing infant gut microbiome, Proc. Natl. Acad. Sci. U.S.A, 108, 4578, 10.1073/pnas.1000081107

Kurokawa, 2007, Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes, DNA Res, 14, 169, 10.1093/dnares/dsm018

Langille, 2013, Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences, Nat. Biotechnol, 31, 814, 10.1038/nbt.2676

Lozupone, 2006, UniFrac—an online tool for comparing microbial community diversity in a phylogenetic context, BMC Bioinformatics, 7, 371, 10.1186/1471-2105-7-371

Lozupone, 2005, UniFrac: a new phylogenetic method for comparing microbial communities, Appl. Environ. Microbiol, 71, 8228, 10.1128/AEM.71.12.8228-8235.2005

Marques, 2010, Programming infant gut microbiota: influence of dietary and environmental factors, Curr. Opin. Biotechnol, 21, 149, 10.1016/j.copbio.2010.03.020

Martinez, 2010, Resistant starches types 2 and 4 have differential effects on the composition of the fecal microbiota in human subjects, PLoS ONE, 5, e15046, 10.1371/journal.pone.0015046

Matamoros, 2013, Development of intestinal microbiota in infants and its impact on health, Trends Microbiol, 21, 167, 10.1016/j.tim.2012.12.001

Mountzouris, 2002, Intestinal microflora of human infants and current trends for its nutritional modulation, Br. J. Nutr, 87, 405, 10.1079/BJN2002563

Nauta, 2013, Relevance of pre- and postnatal nutrition to development and interplay between the microbiota and metabolic and immune systems, Am. J. Clin. Nutr, 98, 586S, 10.3945/ajcn.112.039644

Nielsen, 2007, Impact of diet on the intestinal microbiota in 10-month-old infants, J. Pediatr. Gastroenterol. Nutr, 44, 613, 10.1097/MPG.0b013e3180406a11

Olivares, 2013, Host genotype, intestinal microbiota and inflammatory disorders, Br. J. Nutr, 109, S76, 10.1017/S0007114512005521

Orrhage, 1999, Factors controlling the bacterial colonization of the intestine in breastfed infants, Acta Paediatr, 88, 47, 10.1111/j.1651-2227.1999.tb01300.x

Palmer, 2007, Development of the human infant intestinal microbiota, PLoS Biol, 5, e177, 10.1371/journal.pbio.0050177

Parrett, 1997, In vitro fermentation of carbohydrate by breast fed and formula fed infants, Arch. Dis. Child, 76, 249, 10.1136/adc.76.3.249

Price, 2010, FastTree 2—approximately maximum-likelihood trees for large alignments, PLoS ONE, 5, e9490, 10.1371/journal.pone.0009490

Schwartz, 2012, A metagenomic study of diet-dependent interaction between gut microbiota and host in infants reveals differences in immune response, Genome Biol, 13, r32, 10.1186/gb-2012-13-4-r32

Stevenson, 1996, Organization of the Escherichia coli K-12 gene cluster responsible for production of the extracellular polysaccharide colanic acid, J. Bacteriol, 178, 4885, 10.1128/jb.178.16.4885-4893.1996

Tannock, 2013, Comparison of the compositions of the stool microbiotas of infants fed goat milk formula, cow milk-based formula, or breast milk, Appl. Environ. Microbiol, 79, 3040, 10.1128/AEM.03910-12

Thompson, 2013, Prenatal and postnatal energetic conditions and sex steroids levels across the first year of life, Am. J. Hum. Biol, 25, 643, 10.1002/ajhb.22424

Tlaskal, 1990, The effect of natural and artificial nutrition on vitamin C and E levels in the normal infant, Cesk. Pediatr, 45, 402

Touw, 2013, Data mining in the Life Sciences with Random Forest: a walk in the park or lost in the jungle?, Brief. Bioinformatics, 14, 315, 10.1093/bib/bbs034

Turnbaugh, 2007, The human microbiome project, Nature, 449, 804, 10.1038/nature06244

Vael, 2009, The importance of the development of the intestinal microbiota in infancy, Curr. Opin. Pediatr, 21, 794, 10.1097/MOP.0b013e328332351b

Vaishampayan, 2011, Comparative metagenomics and population dynamics of the gut microbiota in mother and infant, Genome Biol. Evol, 2, 53, 10.1093/gbe/evp057

Vidal, 1998, Isolation of an Escherichia coli K-12 mutant strain able to form biofilms on inert surfaces: involvement of a new ompR allele that increases curli expression, J. Bacteriol, 180, 2442, 10.1128/JB.180.9.2442-2449.1998

Williams, 1999, Functional similarities among two-component sensors and methyl-accepting chemotaxis proteins suggest a role for linker region amphipathic helices in transmembrane signal transduction, Mol. Microbiol, 33, 1093, 10.1046/j.1365-2958.1999.01562.x

Wilson, 1992, Escherichia coli biotin holoenzyme synthetase/bio repressor crystal structure delineates the biotin- and DNA-binding domains, Proc. Natl. Acad. Sci. U.S.A, 89, 9257, 10.1073/pnas.89.19.9257

Wu, 2011, Linking long-term dietary patterns with gut microbial enterotypes, Science, 334, 105, 10.1126/science.1208344

Yatsunenko, 2012, Human gut microbiome viewed across age and geography, Natre, 486, 222, 10.1038/nature11053

Yoshioka, 1983, Development and differences of intestinal flora in the neonatal period in breast-fed and bottle-fed infants, Pediatrics, 72, 317, 10.1542/peds.72.3.317

Zivkovic, 2011, Human milk glycobiome and its impact on the infant gastrointestinal microbiota, Proc. Natl. Acad. Sci. U.S.A, 108, 4653, 10.1073/pnas.1000083107