Matrix Effects on the Delivery Efficacy of Bifidobacterium animalis subsp. lactis BB-12 on Fecal Microbiota, Gut Transit Time, and Short-Chain Fatty Acids in Healthy Young Adults

Zhaoyong Ba, Yujin Lee, Huicui Meng, Penny M Kris-Etherton, Connie J Rogers, Zachery T Lewis, David A Mills, Emily J Furumoto, M Laura Rolon, Jennifer A Fleming, Robert F Roberts, Zhaoyong Ba, Yujin Lee, Huicui Meng, Penny M Kris-Etherton, Connie J Rogers, Zachery T Lewis, David A Mills, Emily J Furumoto, M Laura Rolon, Jennifer A Fleming, Robert F Roberts

Abstract

Probiotics are consumed in fermented dairy products or as capsules for their putative health benefits. However, little research has been done to evaluate the effects of the delivery matrix on the health benefits of probiotics in humans. To examine the effects of delivering Bifidobacterium animalis subsp. lactis BB-12 (BB-12) (log10 10 ± 0.5 CFU/day) via a yogurt smoothie versus a capsule, we monitored the fecal microbiota, gut transit times (GTTs), and fecal excretion of short-chain fatty acids (SCFAs) in healthy adults. In a randomized, four-period, crossover study performed in a partially blind manner, 36 adults were recruited and randomly assigned to four treatments: control yogurt smoothie (YS), yogurt smoothie with BB-12 added prefermentation (PRE), yogurt smoothie with BB-12 added postfermentation (POST), and capsule containing BB-12 (CAP). Participants' fecal microbiota was assessed using 16S rRNA sequencing, GTTs via SmartPill, and fecal SCFAs by gas chromatography (GC) before (baseline) and after each intervention. Participants had significantly higher percentage of Streptococcus after consuming YS versus CAP (P = 0.01). Bifidobacterium-specific terminal restriction fragment length polymorphism analysis revealed a significantly higher percentage of B. animalis after consuming PRE and POST compared to baseline, YS, CAP, and final washout (P < 0.0001). The predominant SCFAs were negatively correlated with GTTs. Consumption of BB-12 delivered in a yogurt smoothie or capsule did not significantly alter the composition of the gut microbiota, GTTs, or fecal SCFA concentration of the study cohort. However, daily consumption of BB-12 in yogurt smoothie may result in higher relative abundance of B. animalis in healthy adults. (This trial has been registered at ClinicalTrials.gov under identifier NCT01399996.) IMPORTANCE Bifidobacterium animalis subsp. lactis BB-12 is a probiotic strain that has been used worldwide since 1985. It has commonly been delivered in fermented dairy products for perceived benefits associated with gut health and enhanced immune function. In addition to fermented dairy products, many new probiotic-containing alternatives such as probiotic-containing juice, probiotic-containing chocolate, and capsules have been developed. While these products provide more options for people to access probiotics, little research has been done on the effect of delivery matrix (dairy versus nondairy) on their efficacy in humans. In addition, it was unclear how yogurt fermentation may influence the survival of BB-12 in the product or on its performance in vivo. The significance of our study is in simultaneously assessing the effect of BB-12, alone and in different delivery vehicles, on the gut transit time, fecal short-chain fatty acids, and the composition of the gut microbiota of the study cohort.

Keywords: BB-12; gut microbiota; gut transit time; probiotics; short-chain fatty acids.

Figures

FIG 1
FIG 1
Taxonomic cladogram of LDA effect size comparing the relative abundance of taxa in males and females. Significantly discriminant taxon nodes are colored and branch areas are shaded according to the highest-ranked variety for that taxon. For each taxon detected, the corresponding node in the taxonomic cladogram is colored according to the highest-ranked group for that taxon. If the taxon is not significantly different between groups, the corresponding node is colored yellow (66).
FIG 2
FIG 2
UPGMA tree based on weighted UniFrac distance (beta diversity) demonstrating the hierarchical relationships between the fecal samples. The code is participant’s study identifier (ID) followed by treatment period (i.e., TP1 is the first treatment period, BL is baseline, FL5 is final washout). The inside color bar indicates participant ID, and the outside color bar indicates the gender (female [F] or male [M]) of each participant. The data indicate that samples from each individual tend to cluster together regardless of treatment.
FIG 3
FIG 3
Weighted UniFrac distance PCoA of bacterial communities with jackknife support grouped by treatment and gender. There were no patterns of clustering when samples were colored by treatments, while samples tend to cluster based on gender, suggesting a gender difference.
FIG 4
FIG 4
Relative proportion of Bifidobacterium species in the stool DNA samples before treatment (baseline), after each treatment, and after final washout as determined by Bif-TRFLP (AluI).
FIG 5
FIG 5
Schematic diagram for randomization design. The treatments are shown in boxes as follows: A, yogurt smoothie without BB-12 (YS); B, yogurt smoothie with BB-12 added postfermentation (POST); C, yogurt smoothie with BB-12 added prefermentation (PRE); D, BB-12-containing capsule (CAP).

References

    1. Tuohy K, Rouzaud G, Bruck W, Gibson G. 2005. Modulation of the human gut microflora towards improved health using prebiotics - assessment of efficacy. Curr Pharm Des 11:75–90. doi:10.2174/1381612053382331.
    1. Sender R, Fuchs S, Milo R. 2016. Revised estimates for the number of human and bacteria cells in the body. PLoS Biol 14:e1002533. doi:10.1371/journal.pbio.1002533.
    1. Clausen MR, Bonnen H, Tvede M, Mortensen PB. 1991. Colonic fermentation to short-chain fatty acids is decreased in antibiotic-associated diarrhea. Gastroenterology 101:1497–1504. doi:10.1016/0016-5085(91)90384-w.
    1. Tamboli CP, Neut C, Desreumaux P, Colombel JF. 2004. Dysbiosis in inflammatory bowel disease. Gut 53:1–4. doi:10.1136/gut.53.1.1.
    1. Ley RE, Backhed F, Turnbaugh P, Lozupone CA, Knight RD, Gordon JI. 2005. Obesity alters gut microbial ecology. Proc Natl Acad Sci U S A 102:11070–11075. doi:10.1073/pnas.0504978102.
    1. Ley RE, Turnbaugh PJ, Klein S, Gordon JI. 2006. Human gut microbes associated with obesity. Nature 444:1022–1028. doi:10.1038/4441022a.
    1. 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. doi:10.1038/nature05414.
    1. Million M, Maraninchi M, Henry M, Armougom F, Richet H, Carrieri P, Valero R, Raccah D, Vialettes B, Raoult D. 2012. Obesity-associated gut microbiota is enriched in Lactobacillus reuteri and depleted in Bifidobacterium animalis and Methanobrevibacter smithii. Int J Obes (Lond) 36:817–825. doi:10.1038/ijo.2011.153.
    1. Cadwell K, Patel KK, Maloney NS, Liu TC, Ng ACY, Storer CE, Head RD, Xavier R, Stappenbeck TS, Virgin HW. 2010. Virus-plus-susceptibility gene interaction determines Crohn’s disease gene Atg16L1 phenotypes in intestine. Cell 141:1135–1145. doi:10.1016/j.cell.2010.05.009.
    1. Alonso VR, Guarner F. 2013. Linking the gut microbiota to human health. Br J Nutr 109:S21–S27. doi:10.1017/S0007114512005235.
    1. Engelbrektson AL, Korzenik JR, Sanders ME, Clement BG, Leyer G, Klaenhammer TR, Kitts CL. 2006. Analysis of treatment effects on the microbial ecology of the human intestine. FEMS Microbiol Ecol 57:239–250. doi:10.1111/j.1574-6941.2006.00112.x.
    1. Corrêa NBO, Péret Filho LA, Penna FJ, Lima FMLS, Nicoli JR. 2005. A randomized formula controlled trial of Bifidobacterium lactis and Streptococcus thermophilus for prevention of antibiotic-associated diarrhea in infants. J Clin Gastroenterol 39:385–389. doi:10.1097/01.mcg.0000159217.47419.5b.
    1. Raahave D. 2015. Faecal retention: a common cause in functional bowel disorders, appendicitis and haemorrhoids–with medical and surgical therapy. Dan Med J 62:B5031.
    1. Wichmann A, Allahyar A, Greiner TU, Plovier H, Lundén GÖ, Larsson T, Drucker DJ, Delzenne NM, Cani PD, Bäckhed F. 2013. Microbial modulation of energy availability in the colon regulates intestinal transit. Cell Host Microbe 14:582–590. doi:10.1016/j.chom.2013.09.012.
    1. Joint FAO/WHO Working Group on Drafting Guidelines for the Evaluation of Probiotics in Food. 2002. Guidelines for the Evaluation of Probiotics in Food. Report of a joint FAO/WHO working group on drafting guidelines for evaluation of probiotics in food. Joint FAO/WHO Working Group on Drafting Guidelines for the Evaluation of Probiotics in Food, London, Ontario, Canada.
    1. Hill C, Guarner F, Reid G, Gibson GR, Merenstein DJ, Pot B, Morelli L, Canani RB, Flint HJ, Salminen S, Calder PC, Sanders ME. 2014. Expert consensus document: the International Scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic. Nat Rev Gastroenterol Hepatol 11:506–514. doi:10.1038/nrgastro.2014.66.
    1. Kalliomäki M, Salminen S, Arvilommi H, Kero P, Koskinen P, Isolauri E. 2001. Probiotics in primary prevention of atopic disease: a randomised placebo-controlled trial. Lancet 357:1076–1079. doi:10.1016/S0140-6736(00)04259-8.
    1. Lin H, Su B, Chen A, Lin T, Tsai C, Yeh T, Oh H. 2005. Oral probiotics reduce the incidence and severity of necrotizing enterocolitis in very low birth weight infants. Pedriatrics 115:1–4. doi:10.1542/peds.2004-1463.
    1. Mastrandrea F, Coradduzza G, Sergio G, Minardi A, Manelli M, Ardito S, Murature L. 2004. Probiotics reduce the CD34+ hemopoietic precursor cell increased traffic in allergic subjects. Eur Ann Allergy Clin Immunol 36:118–122.
    1. Rosenfeldt V, Michaelsen KF, Jakobsen M, Larsen CN, Møller PL, Pedersen P, Tvede M, Weyrehter H, Valerius NH, Pærregaard A. 2002. Effect of probiotic Lactobacillus strains in young children hospitalized with acute diarrhea. Pediatr Infect Dis J 21:411–416. doi:10.1097/00006454-200205000-00012.
    1. Vanderhoof JA, Whitney DB, Antonson DL, Hanner TL, Lupo JV, Young RJ. 1999. Lactobacillus GG in the prevention of antibiotic-associated diarrhea in children. J Pediatr 135:564–568. doi:10.1016/S0022-3476(99)70053-3.
    1. Hasler CM, Brown AC, American Dietetic Association . 2009. Position of the American Dietetic Association: functional foods. J Am Diet Assoc 109:735–746. doi:10.1016/j.jada.2009.02.023.
    1. Monroe Mendelsohn Research. 2001. Live active culture (LAC) yogurt survey. Monroe Mendelsohn Research, New York, NY.
    1. Klijn A, Mercenier A, Arigoni F. 2005. Lessons from the genomes of bifidobacteria. FEMS Microbiol Rev 29:491–509. doi:10.1016/j.femsre.2005.04.010.
    1. Jungersen M, Wind A, Johansen E, Christensen J, Stuer-Lauridsen B, Eskesen D. 2014. The science behind the probiotic strain Bifidobacterium animalis subsp. lactis BB-12. Microorganisms 2:92–110. doi:10.3390/microorganisms2020092.
    1. Sanders ME, Marco ML. 2010. Food formats for effective delivery of probiotics. Annu Rev Food Sci Technol 1:65–85. doi:10.1146/annurev.food.080708.100743.
    1. González-Rodríguez I, Ruiz L, Gueimonde M, Margolles A, Sánchez B. 2013. Factors involved in the colonization and survival of bifidobacteria in the gastrointestinal tract. FEMS Microbiol Lett 340:1–10. doi:10.1111/1574-6968.12056.
    1. Degen L, Phillips S. 1996. Variability of gastrointestinal transit in healthy women and men. Gut 39:299–305. doi:10.1136/gut.39.2.299.
    1. Larsen CN, Nielsen S, Kæstel P, Brockmann E, Bennedsen M, Christensen HR, Eskesen DC, Jacobsen BL, Michaelsen KF. 2006. Dose-response study of probiotic bacteria Bifidobacterium animalis subsp lactis BB-12 and Lactobacillus paracasei subsp paracasei CRL-341 in healthy young adults. Eur J Clin Nutr 60:1284–1293. doi:10.1038/sj.ejcn.1602450.
    1. Ringel-Kulka T, Kotch JB, Jensen ET, Savage E, Weber DJ. 2015. Randomized, double-blind, placebo-controlled study of synbiotic yogurt effect on the health of children. J Pediatr 166:1475–1481.e3. doi:10.1016/j.jpeds.2015.02.038.
    1. Pitkala K, Strandberg T, Finne-Soveri U, Ouwehand A, Poussa T, Salminen S. 2007. Fermented cereal with specific bifidobacteria normalizes bowel movements in elderly nursing home residents. A randomized, controlled trial. J Nutr Heal Aging 11:305–311.
    1. Eskesen D, Jespersen L, Michelsen B, Whorwell PJ, Müller-Lissner S, Morberg CM. 2015. Effect of the probiotic strain Bifidobacterium animalis subsp. lactis, BB-12, on defecation frequency in healthy subjects with low defecation frequency and abdominal discomfort: a randomised, double-blind, placebo-controlled, parallel-group trial. Br J Nutr 114:1638–1646. doi:10.1017/S0007114515003347.
    1. Human Microbiome Consortium. 2012. Structure, function and diversity of the healthy human microbiome. Nature 486:207–214. doi:10.1038/nature11234.
    1. 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. 2009. A core gut microbiome in obese and lean twins. Nature 457:480–484. doi:10.1038/nature07540.
    1. Lin A, Bik EM, Costello EK, Dethlefsen L, Haque R, Relman DA, Singh U. 2013. Distinct distal gut microbiome diversity and composition in healthy children from Bangladesh and the United States. PLoS One 8:e53838. doi:10.1371/journal.pone.0053838.
    1. Mariat D, Firmesse O, Levenez F, Guimarăes V, Sokol H, Doré J, Corthier G, Furet J-P. 2009. The Firmicutes/Bacteroidetes ratio of the human microbiota changes with age. BMC Microbiol 9:123–126. doi:10.1186/1471-2180-9-123.
    1. Yurkovetskiy L, Burrows M, Khan AA, Graham L, Volchkov P, Becker L, Antonopoulos D, Umesaki Y, Chervonsky AV. 2013. Gender bias in autoimmunity is influenced by microbiota. Immunity 39:400–412. doi:10.1016/j.immuni.2013.08.013.
    1. Mueller S, Saunier K, Hanisch C, Norin E, Alm L, Midtvedt T, Cresci A, Silvi S, Orpianesi C, Verdenelli M, Clavel T, Koebnick C, Zunft H, Dore J, Blaut M. 2006. 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. doi:10.1128/AEM.72.2.1027-1033.2006.
    1. Solano-Aguilar G, Fernandez KP, Ets H, Molokin A, Vinyard B, Urban JF, Gutierrez MF. 2013. Characterization of fecal microbiota of children with diarrhea in 2 locations in Colombia. J Pediatr Gastroenterol Nutr 56:503–511. doi:10.1097/MPG.0b013e318282aa12.
    1. Haro C, Rangel-Zúñiga OA, Alcalá-Díaz JF, Gómez-Delgado F, Pérez-Martínez P, Delgado-Lista J, Quintana-Navarro GM, Landa BB, Navas-Cortés JA, Tena-Sempere M, Clemente JC, López-Miranda J, Pérez-Jiménez F, Camargo A. 2016. Intestinal microbiota is influenced by gender and body mass index. PLoS One 11:e0154090. doi:10.1371/journal.pone.0154090.
    1. Fransen F, van Beek AA, Borghuis T, Meijer B, Hugenholtz F, van der Gaast-de Jongh C, Savelkoul HF, de Jonge MI, Faas MM, Boekschoten MV, Smidt H, El Aidy S, de Vos P. 2017. The impact of gut microbiota on gender-specific differences in immunity. Front Immunol 8:754. doi:10.3389/fimmu.2017.00754.
    1. Santos-Marcos JA, Haro C, Vega-Rojas A, Alcala-Diaz JF, Molina-Abril H, Leon-Acuña A, Lopez-Moreno J, Landa BB, Tena-Sempere M, Perez-Martinez P, Lopez-Miranda J, Perez-Jimenez F, Camargo A. 2019. Sex differences in the gut microbiota as potential determinants of gender predisposition to disease. Mol Nutr Food Res 63:e1800870. doi:10.1002/mnfr.201800870.
    1. Meng H, Ba Z, Lee Y, Peng J, Lin J, Fleming JA, Furumoto EJ, Roberts RF, Kris-Etherton PM, Rogers CJ. 2017. Consumption of Bifidobacterium animalis subsp. lactis BB-12 in yogurt reduced expression of TLR-2 on peripheral blood-derived monocytes and pro-inflammatory cytokine secretion in young adults. Eur J Nutr 56:649–661. doi:10.1007/s00394-015-1109-5.
    1. Benson AK, Kelly SA, Legge R, Ma F, Low SJ, Kim J, Zhang M, Oh PL, Nehrenberg D, Hua K, Kachman SD, Moriyama EN, Walter J, Peterson DA, Pomp D. 2010. Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors. Proc Natl Acad Sci U S A 107:18933–18938. doi:10.1073/pnas.1007028107.
    1. Goodrich JK, Waters JL, Poole AC, Sutter JL, Koren O, Blekhman R, Beaumont M, Van Treuren W, Knight R, Bell JT, Spector TD, Clark AG, Ley RE. 2014. Human genetics shape the gut microbiome. Cell 159:789–799. doi:10.1016/j.cell.2014.09.053.
    1. Meng H, Lee Y, Ba Z, Fleming JA, Furumoto EJ, Roberts RF, Kris-Etherton PM, Rogers CJ. 2015. In vitro production of IL-6 and IFN-γ is influenced by dietary variables and predicts upper respiratory tract infection incidence and severity respectively in young adults. Front Immunol 66:94. doi:10.3389/fimmu.2015.00094.
    1. Lee Y, Ba Z, Roberts RF, Rogers CJ, Fleming JA, Meng H, Furumoto EJ, Kris-Etherton PM. 2017. Effects of Bifidobacterium animalis subsp. lactis BB-12 on the lipid/lipoprotein profile and short chain fatty acids in healthy young adults: a randomized controlled trial. Nutr J 16:39. doi:10.1186/s12937-017-0261-6.
    1. Lozupone CA, Stombaugh JI, Gordon JI, Jansson JK, Knight R. 2012. Diversity, stability and resilience of the human gut microbiota. Nature 489:220–230. doi:10.1038/nature11550.
    1. Coyte KZ, Schluter J, Foster KR. 2015. The ecology of the microbiome: networks, competition, and stability. Science 350:663–666. doi:10.1126/science.aad2602.
    1. 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. 2011. Linking long-term dietary patterns with gut microbial enterotypes. Science 334:105–108. doi:10.1126/science.1208344.
    1. McNulty NP, Yatsunenko T, Hsiao A, Faith JJ, Muegge BD, Goodman AL, Henrissat B, Oozeer R, Cools-Portier S, Gobert G, Chervaux C, Knights D, Lozupone CA, Knight R, Duncan AE, Bain JR, Muehlbauer MJ, Newgard CB, Heath AC, Gordon JI. 2011. The impact of a consortium of fermented milk strains on the gut microbiome of gnotobiotic mice and monozygotic twins. Sci Transl Med 3:106ra106. doi:10.1126/scitranslmed.3002701.
    1. Lewis ZT, Bokulich NA, Kalanetra KM, Ruiz-Moyano S, Underwood MA, Mills DA. 2013. Use of bifidobacterial specific terminal restriction fragment length polymorphisms to complement next generation sequence profiling of infant gut communities. Anaerobe 19:62–69. doi:10.1016/j.anaerobe.2012.12.005.
    1. Ziarno M, Zaręba D. 2015. Effects of milk components and food additives on survival of three bifidobacteria strains in fermented milk under simulated gastrointestinal tract conditions. Microb Ecol Heal Dis 26:27812. doi:10.3402/mehd.v26.27812.
    1. Lee B, Yin X, Griffey SM, Marco ML. 2015. Attenuation of colitis by Lactobacillus casei BL23 is dependent on the dairy delivery matrix. Appl Environ Microbiol 81:6425–6435. doi:10.1128/AEM.01360-15.
    1. Roy CC, Kien CL, Bouthillier L, Levy E. 2006. Short-chain fatty acids: ready for prime time? Nutr Clin Pract 21:351–366. doi:10.1177/0115426506021004351.
    1. Schwiertz A, Taras D, Schäfer K, Beijer S, Bos NA, Donus C, Hardt PD. 2010. Microbiota and SCFA in lean and overweight healthy subjects. Obesity (Silver Spring) 18:190–195. doi:10.1038/oby.2009.167.
    1. Primec M, Mičetić-Turk D, Langerholc T. 2017. Analysis of short-chain fatty acids in human feces: a scoping review. Anal Biochem 526:9–21. doi:10.1016/j.ab.2017.03.007.
    1. McOrist AL, Miller RB, Bird AR, Keogh JB, Noakes M, Topping DL, Conlon MA. 2011. Fecal butyrate levels vary widely among individuals but are usually increased by a diet high in resistant starch. J Nutr 141:883–889. doi:10.3945/jn.110.128504.
    1. Laake KO, Bjørneklett A, Bakka A, Midtvedt T, Norin KE, Eide TJ, Jacobsen MB, Lingaas E, Axelsen AK, Løtveit T, Vatn MH. 1999. Influence of fermented milk on clinical state, fecal bacterial counts and biochemical characteristics in patients with ileal- pouch- anal-anastomosis. Microb Ecol Health Dis 11:211–217.
    1. Matsumoto M, Aranami A, Ishige A, Watanabe K, Benno Y. 2007. LKM512 yogurt consumption improves the intestinal environment and induces the T-helper type 1 cytokine in adult patients with intractable atopic dermatitis. Clin Exp Allergy 37:358–370. doi:10.1111/j.1365-2222.2007.02642.x.
    1. Lewis S, Heaton K. 1997. Increasing butyrate concentration in the distal colon by accelerating intestinal transit. Gut 41:245–251. doi:10.1136/gut.41.2.245.
    1. Laroia S, Martin J. 1991. Methods for enumerating and propagating bifidobacteria. Cult Dairy Prod J 26:32–34.
    1. Ventura M, Reniero R, Zink R. 2001. Specific identification and targeted characterization of Bifidobacterium lactis from different environmental isolates by a combined multiplex-PCR approach. Appl Environ Microbiol 67:2760–2765. doi:10.1128/AEM.67.6.2760-2765.2001.
    1. Bouvier M, Meance S, Bouley C, Berta J-L, Grimaud J. 2001. Effects of consumption of a milk fermented by the probiotic strain Bifidobacterium animalis DN-173010 on colonic transit times in healthy humans. Biosci Microflora 20:43–48. doi:10.12938/bifidus1996.20.43.
    1. Lu WZ, Song GH, Gwee KA, Ho KY. 2009. The effects of melatonin on colonic transit time in normal controls and IBS patients. Dig Dis Sci 54:1087–1093. doi:10.1007/s10620-008-0463-z.
    1. Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, Turnbaugh PJ, Fierer N, Knight R. 2011. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc Natl Acad Sci U S A 108:4516–4522. doi:10.1073/pnas.1000080107.
    1. Bokulich NA, Thorngate JH, Richardson PM, Mills DA. 2014. Microbial biogeography of wine grapes is conditioned by cultivar, vintage, and climate. Proc Natl Acad Sci U S A 111:E139–E148. doi:10.1073/pnas.1317377110.
    1. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R. 2010. QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7:335–336. doi:10.1038/nmeth.f.303.
    1. Edgar RC. 2010. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26:2460–2461. doi:10.1093/bioinformatics/btq461.
    1. DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL. 2006. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72:5069–5072. doi:10.1128/AEM.03006-05.
    1. Wang Q, Garrity GM, Tiedje JM, Cole JR. 2007. Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73:5261–5267. doi:10.1128/AEM.00062-07.
    1. Caporaso JG, Bittinger K, Bushman FD, DeSantis TZ, Andersen GL, Knight R. 2010. PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics 26:266–267. doi:10.1093/bioinformatics/btp636.
    1. Haas BJ, Gevers D, Earl AM, Feldgarden M, Ward DV, Giannoukos G, Ciulla D, Tabbaa D, Highlander SK, Sodergren E, Methé B, DeSantis TZ, The Human Microbiome Consortium, Petrosino JF, Knight R, Birren BW. 2011. Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res 21:494–504. doi:10.1101/gr.112730.110.
    1. Price MN, Dehal PS, Arkin AP. 2010. FastTree 2 – approximately maximum-likelihood trees for large alignments. PLoS One 5:e9490. doi:10.1371/journal.pone.0009490.
    1. Bokulich NA, Subramanian S, Faith JJ, Gevers D, Gordon JI, Knight R, Mills DA, Caporaso JG. 2013. Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nat Methods 10:57–59. doi:10.1038/nmeth.2276.
    1. Lozupone C, Hamady M, Knight R. 2006. UniFrac – an online tool for comparing microbial community diversity in a phylogenetic context. BMC Bioinformatics 7:371–314. doi:10.1186/1471-2105-7-371.
    1. Clarke KR. 1993. Non‐parametric multivariate analyses of changes in community structure. Aust J Ecol 18:117–143. doi:10.1111/j.1442-9993.1993.tb00438.x.
    1. Anderson MJ. 2001. A new method for non-parametric multivariate analysis of variance. Austral Ecol 26:32–46. doi:10.1046/j.1442-9993.2001.01070.x.
    1. Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett WS, Huttenhower C. 2011. Metagenomic biomarker discovery and explanation. Genome Biol 12:R60. doi:10.1186/gb-2011-12-6-r60.
    1. García-Villalba R, Giménez-Bastida JA, García-Conesa MT, Tomás-Barberán FA, Carlos Espín J, Larrosa M. 2012. Alternative method for gas chromatography-mass spectrometry analysis of short-chain fatty acids in faecal samples. J Sep Sci 35:1906–1913. doi:10.1002/jssc.201101121.
    1. Fisher LD, Dixon DO, Herson J, Frankowski RF, Hearon MS, Peace KE. 1990. Intention to treat in clinical trials, p 331–350. In Peace KE (ed), Statistical issues in drug research and development. Marcel Dekker, New York, NY.

Source: PubMed

Sponsorer og samarbeidspartnere

Medisinsk tilstand

Legemiddelintervensjoner

3
Abonnere