1.
Goodrich, JK, Davenport, ER, Beaumont, M, et al. (2016) Genetic determinants of the gut microbiome in UK twins. Cell Host Microbe
19, 731–743.
2.
Yatsunenko, T, Rey, FE, Manary, MJ, et al. (2012) Human gut microbiome viewed across age and geography. Nature
486, 222–227.
3.
Mueller, S, Saunier, K, Hanisch, C, et al. (2005) Differences in fecal microbiota in different European study populations in relation to age, gender, and country: a cross-sectional study. Appl Environ Microbiol
72, 1027–1033.
4.
Dethlefsen, L, Huse, SM, Relman, DA, et al. (2008) The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol
6, e1000255.
5.
Wu, GD, Chen, J, Hoffmann, C, et al. (2011) Linking long-term dietary patterns with gut microbial enterotypes. Science
334, 105–108.
6.
David, LA, Maurice, CF, Carmody, RN, et al. (2013) Diet rapidly and reproducibly alters the human gut microbiome. Nature
505, 559–563.
7.
Foerster, J, Maskarinec, G, Reichardt, N, et al. (2014) The influence of whole grain products and red meat on intestinal microbiota composition in normal weight adults: a randomized crossover intervention trial. PLOS ONE
9, e109606.
8.
King, DE, Mainous, AG & Lambourne, CA (2012) Trends in dietary fiber intake in the United States, 1999–2008. J Acad Nutr Diet
112, 642–648.
9.
Ministry of Health (2015) Eating and Activity Guidelines for New Zealand Adults. Wellington, New Zealand: Ministry of Health.
10.
Gibson, GR, Hutkins, R, Sanders, ME, et al. (2017) The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of prebiotics. Nat Rev Gastroenterol Hepatol
14, 491–502.
11.
Tap, J, Furet, JP, Bensaada, M, et al. (2015) Gut microbiota richness promotes its stability upon increased dietary fibre intake in healthy adults. Environ Microbiol
17, 4954–4964.
12.
Tuohy, KM, Finlay, RK, Wynne, AG, et al. (2001) A human volunteer study on the prebiotic effects of HP-inulin – faecal bacteria enumerated using fluorescent in situ hybridisation (FISH). Anaerobe
7, 113–118.
13.
Tuohy, KM, Kolida, S, Lustenberger, AM, et al. (2001) The prebiotic effects of biscuits containing partially hydrolysed guar gum and fructo-oligosaccharides – a human volunteer study. Br J Nutr
86, 341–348.
14.
de Preter, V, Vanhoutte, T, Huys, G, et al. (2008) Baseline microbiota activity and initial bifidobacteria counts influence responses to prebiotic dosing in healthy subjects. Aliment Pharmacol Ther
27, 504–513.
15.
Kolida, S, Meyer, D & Gibson, GR (2007) A double-blind placebo-controlled study to establish the bifidogenic dose of inulin in healthy humans. Eur J Clin Nutr
61, 1189–1195.
16.
Bouhnik, Y, Raskine, L, Champion, K, et al. (2007) Prolonged administration of low-dose inulin stimulates the growth of bifidobacteria in humans. Nutr Res
27, 187–193.
17.
Eid, N, Osmanova, H, Natchez, C, et al. (2015) Impact of palm date consumption on microbiota growth and large intestinal health: a randomised, controlled, cross-over, human intervention study. Br J Nutr
114, 1226–1236.
18.
Griffin, NW, Ahern, PP, Cheng, J, et al. (2017) Prior dietary practices and connections to a human gut microbial metacommunity alter responses to diet interventions. Cell Host Microbe
21, 84–96.
19.
Healey, G, Brough, L, Butts, C, et al. (2016) Influence of habitual dietary fibre intake on the responsiveness of the gut microbiota to a prebiotic: protocol for a randomised, double-blind, placebo-controlled, cross-over, single-centre study. BMJ Open
6, e012504.
20.
Healey, G, Brough, L, Murphy, R, et al. (2016) Validity and reproducibility of a habitual dietary fibre intake short food frequency questionnaire. Nutrients
8, 3–9.
21.
Ministry of Health & Department of Health and Ageing (2006) Nutrient Reference Values for Australia and New Zealand- Executive Summary. Canberra, Australia: Ministry of Health & Department of Health and Ageing.
22.
University of Otago & Ministry of Health (2011) A Focus on Nutrition: Key Findings of the 2008/09 New Zealand Adult Nutrition Survey. Wellington, New Zealand: University of Otago & Ministry of Health.
23.
Dunn, S, Datta, A, Kallis, S, et al. (2011) Validation of a food frequency questionnaire to measure intakes of inulin and oligofructose. Eur J Clin Nutr
65, 402–408.
24.
van Loo, J, Coussement, P, de Leenheer, L, et al. (1995) On the presence of inulin and oligofructose as natural ingredients in the western diet. Crit Rev Food Sci Nutr
35, 525–552.
25.
Moshfegh, AJ, Friday, JE, Goldman, JP, et al. (1999) Presence of inulin and oligofructose in the diets of Americans. J Nutr
129, 1407S–1411S.
26.
Mills, A, Patel, A & Crawley, H (2002) Food Portion Sizes, 3rd ed. London: HMSO.
27.
Flint, A, Raben, A, Blundell, JE, et al. (2000) Reproducibility, power and validity of visual analogue scales in assessment of appetite sensations in single test meal studies. Int J Obes
24, 38–48.
28.
Caporaso, JG, Kuczynski, J, Stombaugh, J, et al. (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods
7, 335–336.
29.
Masella, AP, Bartram, AK, Truszkowski, JM, et al. (2012) PANDAseq: paired-end assembler for illumina sequences. BMC Bioinformatics
13, 31.
30.
Edgar, RC (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics
26, 2460–2461.
31.
DeSantis, TZ, Hugenholtz, P, Larsen, N, et al. (2006) Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol
72, 5069–5072.
32.
Wang, Q, Garrity, GM, Tiedje, JM, et al. (2007) Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol
73, 5261–5267.
33.
Kok, RG, Waal, ADE, Schut, F, et al. (1996) Specific detection and analysis of a probiotic Bifidobacterium strain in infant feces. Appl Environ Microbiol
62, 68–3672.
34.
Richardson, AJ, Calder, AG, Stewart, CS, et al. (1989) Simultaneous determination of volatile and non-volatile acidic fermentation products of anaerobes by capillary gas chromatography. Lett Appl Microbiol
9, 5–8.
35.
Holscher, HD, Bauer, LL, Gourineni, V, et al. (2015) Agave inulin supplementation affects the fecal microbiota of healthy adults participating in a randomized, double-blind, placebo-controlled, crossover trial. J Nutr
145, 2025–2032.
36.
Dewulf, EM, Cani, PD, Claus, SP, et al. (2013) Insight into the prebiotic concept: lessons from an exploratory, double blind intervention study with inulin-type fructans in obese women. Gut
62, 1112–1121.
37.
Ramirez-Farias, C, Slezak, K, Fuller, Z, et al. (2009) Effect of inulin on the human gut microbiota: stimulation of Bifidobacterium adolescentis and Faecalibacterium prausnitzii
. Br J Nutr
101, 541–550.
38.
Costabile, A, Kolida, S, Klinder, A, et al. (2010) A double-blind, placebo-controlled, cross-over study to establish the bifidogenic effect of a very-long-chain inulin extracted from globe artichoke (Cynara scolymus) in healthy human subjects. Br J Nutr
104, 1007–1017.
39.
Ramnani, P, Gaudier, E, Bingham, M, et al. (2010) Prebiotic effect of fruit and vegetable shots containing Jerusalem artichoke inulin: a human intervention study. Br J Nutr
104, 233–240.
40.
Scott, KP, Martin, JC, Duncan, SH, et al. (2014) Prebiotic stimulation of human colonic butyrate-producing bacteria and bifidobacteria, in vitro
. Microbiol Ecol
87, 30–40.
41.
Jung, T-H, Jeon, W-M & Han, K-S (2015)
In vitro effects of dietary inulin on human fecal microbiota and butyrate production. J Microbiol Biotechnol
25, 1555–1558.
42.
Scheppach, W (1994) Effects of short chain fatty acids on gut morphology and function. Gut
35, 1 Suppl., S35–S38.
43.
Belenguer, A, Duncan, SH, Calder, AG, et al. (2006) Two routes of metabolic cross-feeding between Bifidobacterium adolescentis and butyrate-producing anaerobes from the human gut. Appl Environ Microbiol
72, 3593–3599.
44.
Brahma, S, Martínez, I, Walter, J, et al. (2017) Impact of dietary pattern of the fecal donor on in vitro fermentation properties of whole grains and brans. J Funct Foods
29, 281–289.
45.
Henson, MA & Phalak, P (2017) Byproduct cross feeding and community stability in an in silico biofilm model of the gut microbiome. Processes
5, 13.
46.
Levitt, M (1971) Volume and composition of human intestinal gas determined by means of an intestinal washout technic. N Engl J Med
284, 1394–1398.
47.
Lin, HV, Frassetto, A, Kowalik, EJ, et al. (2012) Butyrate and propionate protect against diet-induced obesity and regulate gut hormones via free fatty acid receptor 3-independent mechanisms. PLOS ONE
7, e35240.
48.
Sonnenburg, ED, Zheng, H, Joglekar, P, et al. (2010) Specificity of polysaccharide use in intestinal bacteroides species determines diet-induced microbiota alterations. Cell
141, 1241–1252.
49.
Wilson, B & Whelan, K (2017) Prebiotic inulin-type fructans and galacto-oligosaccharides: definition, specificity, function, and application in gastrointestinal disorders. J Gastroenterol Hepatol
32, 64–68.
