Major faecal microbiota shifts in composition and diversity with age in a geographically restricted cohort of mothers and their children

FEMS Microbiology Ecology

Volumn 87, Issue 1, 2014, Pages 280-290

  Avershina, Ekaterina ^a   Storrø, Ola ^b   Øien, Torbjørn ^b   Johnsen, Roar ^b   Pope, Phil ^a   Rudi, Knut ^a  

^a NORWEGIAN UNIVERSITY OF LIFE SCIENCES   (Norway)

^b NORWEGIAN UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Norway)

Author keywords

16S rRNA gene; Gut microbiota; Infant

Indexed keywords

COHORT ANALYSIS; COMMUNITY COMPOSITION; DATA SET; FECAL COLIFORM; INDIVIDUAL VARIATION; NEONATE; PREGNANCY; SPECIES DIVERSITY;

NORWAY; SOR TRONDELAG; TRONDHEIM;

RNA 16S;

16S RRNA GENE; ADULT; AGE; ARTICLE; BACTERIUM; BIODIVERSITY; CLASSIFICATION; COHORT ANALYSIS; FECES; FEMALE; GASTROINTESTINAL TRACT; GENETICS; HUMAN; INFANT; INTESTINE FLORA; ISOLATION AND PURIFICATION; MALE; MICROBIOLOGY; MICROFLORA; MOTHER; NEWBORN; NORWAY; PREGNANCY; PRESCHOOL CHILD;

16S RRNA GENE; GUT MICROBIOTA; INFANT;

ADULT; AGE FACTORS; BACTERIA; BIODIVERSITY; CHILD, PRESCHOOL; COHORT STUDIES; FECES; FEMALE; GASTROINTESTINAL TRACT; HUMANS; INFANT; INFANT, NEWBORN; MALE; MICROBIOTA; MOTHERS; NORWAY; PREGNANCY; RNA, RIBOSOMAL, 16S;

EID: 84891490550     PISSN: 01686496     EISSN: 15746941     Source Type: Journal    
DOI: 10.1111/1574-6941.12223     Document Type: Article

References (41)

1. Avershina E & Rudi K (2013) Is it who you are or what you do that is important in the human gut? Benef Microbes 4: 219-222.
2. Avershina E, Storro O, Oien T, Johnsen R, Wilson R, Egeland T & Rudi K (2013) Succession and correlation-networks of bifidobacteria in a large unselected cohort of mothers and their children. Appl Environ Microbiol 79: 497-507.
3. Bjerke GA, Wilson R, Storro O, Oyen T, Johnsen R & Rudi K (2011) Mother-to-child transmission of and multiple-strain colonization by Bacteroides fragilis in a cohort of mothers and their children. Appl Environ Microbiol 77: 8318-8324.
4. Bro R (1997) PARAFAC. Tutorial and applications. Chemometr Intell Lab Syst 38: 149-171.
5. Caporaso JG, Kuczynski J, Stombaugh J et al. (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7: 335-336.
6. Cardillo G (2007) Cohen's kappa: compute the Cohen's kappa ratio on a 2 × 2 matrix. MATLAB Central File Exchange, MathWorks. Available at: http://www.mathworks.com/matlabcentral/fileexchange/15365.
7. Claesson MJ, Cusack S, O'Sullivan O et al. (2011) Composition, variability, and temporal stability of the intestinal microbiota of the elderly. P Natl Acad Sci USA 108(suppl 1): 4586-4591.
8. De Filippo C, Cavalieri D, Di Paola M et al. (2010) Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. P Natl Acad Sci USA 107: 14691-14696.
9. de Muinck EJ, Øien T, Storrø O, Johnsen R, Stenseth NC, Rønningen KS & Rudi K (2011) Diversity, transmission and persistence of Escherichia coli in a cohort of mothers and their infants. Environ Microbiol Rep 3: 352-359.
10. Edgar RC, Haas BJ, Clemente JC, Quince C & Knight R (2011) UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27: 2194-2200.
11. Favier CF, de Vos WM & Akkermans AD (2003) Development of bacterial and bifidobacterial communities in feces of newborn babies. Anaerobe 9: 219-229.
12. Ginzinger DG (2002) Gene quantification using real-time quantitative PCR: an emerging technology hits the mainstream. Exp Hematol 30: 503-512.
13. Jabot F & Chave J (2011) Analyzing tropical forest tree species abundance distributions using a nonneutral model and through approximate Bayesian inference. Am Nat 178: E37-E47.
14. Jeraldo P, Sipos M, Chia N, et al. (2012) Quantification of the relative roles of niche and neutral processes in structuring gastrointestinal microbiomes. P Natl Acad Sci USA 109: 9692-9698.
15. Jimenez E, Marin ML, Martin R et al. (2008) Is meconium from healthy newborns actually sterile? Res Microbiol 159: 187-193.
16. Koenig JE, Spor A, Scalfone N et al. (2011) Succession of microbial consortia in the developing infant gut microbiome. P Natl Acad Sci USA 108(suppl 1): 4578-4585.
17. Koren O, Goodrich JK, Cullender TC et al. (2012) Host remodeling of the gut microbiome and metabolic changes during pregnancy. Cell 150: 470-480.
18. Ley RE, Peterson DA & Gordon JI (2006) Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell 124: 837-848.
19. Lozupone C & Knight R (2005) UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71: 8228-8235.
20. Magurran AE (2004) Measuring Biological Diversity. Blackwell Science Ltd, Oxford, UK.
21. Makino H, Kushiro A, Ishikawa E et al. (2011) Transmission of intestinal Bifidobacterium longum subsp. longum strains from mother to infant, determined by multilocus sequencing typing and amplified fragment length polymorphism. Appl Environ Microbiol 77: 6788-6793.
22. Marchesi JR (2011) Human distal gut microbiome. Environ Microbiol 13: 3088-3102.
23. Marques TM, Wall R, Ross RP, Fitzgerald GF, Ryan CA & Stanton C (2010) Programming infant gut microbiota: influence of dietary and environmental factors. Curr Opin Biotechnol 21: 149-156.
24. Martin R, Langa S, Reviriego C et al. (2003) Human milk is a source of lactic acid bacteria for the infant gut. J Pediatr 143: 754-758.
25. Martin R, Heilig HG, Zoetendal EG, Jimenez E, Fernandez L, Smidt H & Rodriguez JM (2007) Cultivation-independent assessment of the bacterial diversity of breast milk among healthy women. Res Microbiol 158: 31-37.
26. Nadkarni MA, Martin FE, Jacques NA & Hunter N (2002) Determination of bacterial load by real-time PCR using a broad-range (universal) probe and primers set. Microbiology 148: 257-266.
27. Oien T, Storro O & Johnsen R (2006) Intestinal microbiota and its effect on the immune system-a nested case-cohort study on prevention of atopy among small children in Trondheim: the IMPACT study. Contemp Clin Trials 27: 389-395.
28. Palmer C, Bik EM, DiGiulio DB, Relman DA & Brown PO (2007) Development of the human infant intestinal microbiota. PLoS Biol 5: e177.
29. Ronaghi M (2001) Pyrosequencing sheds light on DNA sequencing. Genome Res 11: 3-11.
30. Rudi K, Moen B, Sekelja M, Frisli T & Lee MR (2012) An eight-year investigation of bovine livestock fecal microbiota. Vet Microbiol 160: 369-377.
31. Satokari R, Gronroos T, Laitinen K, Salminen S & Isolauri E (2009) Bifidobacterium and Lactobacillus DNA in the human placenta. Lett Appl Microbiol 48: 8-12.
32. Sekelja M, Rud I, Knutsen SH, Denstadli V, Westereng B, Naes T & Rudi K (2012) Abrupt temporal fluctuations in the chicken fecal microbiota are explained by its gastrointestinal origin. Appl Environ Microbiol 78: 2941-2948.
33. Sim J & Wright CC (2005) The kappa statistic in reliability studies: use, interpretation, and sample size requirements. Phys Ther 85: 257-268.
34. Skanseng B, Kaldhusdal M & Rudi K (2006) Comparison of chicken gut colonisation by the pathogens Campylobacter jejuni and Clostridium perfringens by real-time quantitative PCR. Mol Cell Probes 20: 269-279.
35. Storro O, Oien T, Dotterud CK, Jenssen JA & Johnsen R (2010) A primary health-care intervention on pre- and postnatal risk factor behavior to prevent childhood allergy. The Prevention of Allergy among Children in Trondheim (PACT) study. BMC Public Health 10: 443.
36. Storro O, Oien T, Langsrud O, Rudi K, Dotterud C & Johnsen R (2011) Temporal variations in early gut microbial colonization are associated with allergen-specific immunoglobulin E but not atopic eczema at 2 years of age. Clin Exp Allergy 41: 1545-1554.
37. Tauler R, Smilde A & Kowalski B (1995) Selectivity, local rank, 3-way data-analysis and ambiguity in multivariate curve resolution. J Chemom 9: 31-58.
38. 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.
39. Whitman WB, Coleman DC & Wiebe WJ (1998) Prokaryotes: the unseen majority. P Natl Acad Sci USA 95: 6578-6583.
40. Yatsunenko T, Rey FE, Manary MJ et al. (2012) Human gut microbiome viewed across age and geography. Nature 486: 222-227.
41. Zimonja M, Rudi K, Trosvik P & Næs T (2008) Multivariate curve resolution of mixed bacterial DNA sequence spectra: identification and quantification of bacteria in undefined mixture samples. J Chemom 22: 309-322.