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Article References for September 2014 San Francisco Medicine

September 15, 2014 San Francisco Medicine Elisabeth Bik, Erica Goode, Jo Ann T. Hattner, Linda C. Giudice, Payal Bhandarhi, San Francisco Medicine, Susan Anderes 0

References cited in Our Bodies’ Best Buddies by Elisabeth M. Bik

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  2. Costello EK, Lauber CL, Hamady M, Fierer N, Gordon JI, Knight R. Bacterial community variation in human body habitats across space and time. Science. 2009; 326(5960):1694-7 DOI: 10.1126/science.1177486.
  3. Dominguez-Bello MG, Blaser MJ, Ley RE, Knight R. Development of the human gastrointestinal microbiota and insights from high-throughput sequencing. Gastroenterology. 2011; 140:1713–19. DOI: 10.1053/j.gastro.2011.02.011.
  4. Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, Mende DR, Li J, Xu J, Li S, Li D, Cao J, Wang B, Liang H, Zheng H, Xie Y, Tap J, Lepage P, Bertalan M, Batto JM, Hansen T, Le Paslier D, Linneberg A, Nielsen HB, Pelletier E, Renault P, Sicheritz-Ponten T, Turner K, Zhu H, Yu C, Li S, Jian M, Zhou Y, Li Y, Zhang X, Li S, Qin N, Yang H, Wang J, Brunak S, Doré J, Guarner F, Kristiansen K, Pedersen O, Parkhill J, Weissenbach J; MetaHIT Consortium, Bork P, Ehrlich SD, Wang J. A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 2010; 464(7285):59-65. DOI: 10.1038/nature08821.
  5. Ridaura VK1, Faith JJ, Rey FE, Cheng J, Duncan AE, Kau AL, Griffin NW, Lombard V, Henrissat B, Bain JR, Muehlbauer MJ, Ilkayeva O, Semenkovich CF, Funai K, Hayashi DK, Lyle BJ, Martini MC, Ursell LK, Clemente JC, Van Treuren W, Walters WA, Knight R, Newgard CB, Heath AC, Gordon JI. Gut microbiota from twins discordant for obesity modulate metabolism in mice. Science. 2013; 341(6150):1241214. DOI: 10.1126/science.1241214.
  6. David L, Materna AC, Friedman J, Campos-Baptista MI, Blackburn MC, Perrotta A, Erdman SE, and Alm EJ. Host lifestyle affects human microbiota on daily timescales. Genome Biology. 2014; 15:R89. DOI: 10.1186/gb-2014-15-7-r89.
  7. Dethlefsen L, Relman DA. Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proc Natl Acad Sci USA. 2011; 108 Suppl 1: 4554-61. DOI: 10.1073/pnas.1000087107. 
  8. Seekatz AM, Young VB. Clostridium difficile and the microbiota. J Clin Invest. 2014. DOI:10.1172/JCI72336.
  9. Blaser ML. Missing Microbes: How the Overuse of Antibiotics Is Fueling Our Modern Plagues. Henry Holt and Co., Publ. 2014. ISBN-10: 0805098100. 
  10. Vaz LE, Kleinman KP, Raebel MA, Nordin JD, Lakoma MD, Dutta-Linn MM, Finkelstein JA. Recent trends in outpatient antibiotic use in children. Pediatrics. 2014; 133(3):375-85. DOI: 10.1542/peds.2013-2903. 

References cited in The "Second Genome" and Women's Health by Linda C. Giudice, MD, PhD

  1. Bajzer M, Seeley RJ. The intestinal bacteria in obese humans and mice differ from those in lean individuals. Are these bacteria involved in how we regulate body weight, and are they a factor in the obesity epidemic? Nature. 2006; 444:1009-1010.
  2. Round JL, Sarkis K. The gut microbiota shapes intestinal immune responses during health and disease. Nature Reviews Immunology. 2009; 9:313-323. 
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  4. Markle JGM et al. Sex differences in the gut microbiome drive hormone-dependent regulation of autoimmunity. Science. 2013: 339;1084-1088.
  5. Witkin SS, Linhares IM, Giraldo P. Bacterial flora of the female genital tract: Function and immune regulation. Best Pract Res Clin Obstet Gynaecol. 2007; 21(3):347-54. 
  6. Zhou X, Bent SJ, Schneider MG, Davis CC, Islam MR, Forney LJ. Characterization of vaginal microbial communities in adult healthy women using cultivation-independent methods. Microbiology. 2004; 150(Pt 8):2565-73. 
  7. Verhelst R, Verstraelen H, Claeys G, Verschraegen G, Delanghe J, Van Simaey L, De Ganck C, Temmerman M, Vaneechoutte M. Cloning of 16S rRNA genes amplified from normal and disturbed vaginal microflora suggests a strong association between Atopobium vaginae, Gardnerella vaginalis and bacterial vaginosis. BMC Microbiol. 2004; 4:16.
  8. Hyman RW, Fukushima M, Diamond L, Kumm J, Giudice LC, Davis RW. Microbes on the human vaginal epithelium. Proc Natl Acad Sci USA. 2005; 102(22):7952-7. 
  9. Human Microbiome Project Consortium Collaborators (248). Structure, function and diversity of the healthy human microbiome. Nature. 2012; 13:486(7402):207-14. 
  10. Fredricks DN, Fiedler TL, Marrazzo JM. Molecular identification of bacteria associated with bacterial vaginosis. N Engl J Med. 2005; 353(18):1899-911. 
  11. Ravel J, Gajer P, Abdo Z, Schneider GM, Koenig SS, McCulle SL, Karlebach S, Gorle R, Russell J, Tacket CO, Brotman RM, Davis CC, Ault K, Peralta L, Forney LJ. Vaginal microbiome of reproductive-age women. Proc Natl Acad Sci USA. 2011; 15:108 Suppl 1:4680-7. 
  12. Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, Magda Magris M, Glida Hidalgo G, Robert N. Baldassano RN, Andrey P. Anokhin AP, Heath AC, Warner B, Reeder J, Kuczynski J, Caporaso JG, Lozupone CA, Lauber C, Clemente JC, Knights D, Knight R, Gordon JI. Human gut microbiome viewed across age and geography. Nature. 2012; 486:222-228.
  13. Verstraelen H, Verhelst R, Claeys G, De Backer E, Temmerman M, Vaneechoutte M. Longitudinal analysis of the vaginal microflora in pregnancy suggests that L. crispatus promotes the stability of the normal vaginal microflora and that L. gasseri and/or L. iners are more conducive to the occurrence of abnormal vaginal microflora. BMC Microbiol. 2009; 9:116. DOI: 10.1186/1471-2180-9-116. 
  14. Gajer P, Brotman RM, Bai G, Sakamoto J, Schütte UME, Zhong X, Koenig SSK, Fu L, Ma Z, Zhou X, Abdo Z, Forney LJ, Ravel J. Temporal dynamics of the human vaginal microbiota. Sci. Transl. Med. 2012; 4:132ra52.
  15. Aagaard K, Riehle K, Ma J, Segata N, Mistretta TA, Coarfa C, Raza S, Rosenbaum S, Van den Veyver I, Milosavljevic A, Gevers D, Huttenhower C, Petrosino J, Versalovic J. A metagenomic approach to characterization of the vaginal microbiome signature in pregnancy. PLOS ONE. 2012; 7(6):e36466. 
  16. Hyman RW, Fukushima M, Jiang H, Fung E, Rand L, Johnson B, Vo KC, Caughey AB, Hilton J F, Davis R W, Giudice LC. Diversity of the vaginal microbiome correlates with preterm birth. Reproductive Sciences. 2014; 21: 32-40.
  17. Koren O, Goodrich JK, Cullender TC, Spor A, Laitinen K, Backhed HK, Gonzalez A, Werner JJ, Angenent LT, Knight R, Backhed F, Isolauri E, Salminen S, Ley RE. Host remodeling of the gut microbiome and metabolic changes during pregnancy. Cell. 2012; 150:470-480.
  18. Aagaard K, Ma J, Antony KM, Ganu R, Petrosino J, Versalovic J. The placenta harbors a unique microbiome. Sci. Transl. Med. 2014; 6:237ra65.
  19. Muglia LJ, Katz M. The enigma of spontaneous preterm birth. N Engl J Med. 2010; 362(6):529-35. 
  20. Dominguez-Bello MG, Costello EK, Contreras M, Magris M, Hidalgo G, Fierer N, Knight R. Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proc Natl Acad Sci USA. 2010; 107:11971-11975.
  21. Bergstrom A, Skov TH, Bahl MI, Roager HM, Christensen LB, Eilerskov KT, Molgaard C, Michaelsen KF, Licht TR. Establishment of intestinal microbiota during early life: A longitudinal, explorative study of a large cohort of Danish infants. Appl Environ Microbiol. 2014; 80:2889-2900.
  22. Siddiqui H, Nederbragt AJ, Lagesen K, JeanssonSL Jakobsen KS. Assessing diversity of the female urine microbiota by high throughput sequencing of 16S rDNA amplicons. BMC Microbiology. 2011; 11:244-251.
  23. Alan J, Wolfe AJ, Toh E, Shibata N, Bong B, Kenton K, FitzGerald MP, Mueller ER, Schreckenberger P, Dong Q, Nelson DE, Brubaker L. Evidence of uncultivated bacteria in the adult female bladder. J Clin Microbiol. 2012; 50:1376-1383.
  24. Lewis DA, Brown R, Williams J, White P, Jacobson SK, Marchesi JR, Drake MJ. The human urinary microbiome: Bacterial DNA in voided urine of asymptomatic adults. Front Cell Infect Microbiol. 2013; 3:41.
  25. Brubaker L. Annual Meeting of the Ammerican UroGynecologic Society 2013.
  26. Pearce MM, Hilt EE, Rosenfeld AB, Zilliox MJ, Thomas-White K, Fok C, Kliethermes S, Schreckenberger PC, Brubaker L, Gai X, Wolfe AJ. The female urinary microbiome: A comparison of women with and without urgency urinary incontinence. mBio. 2014; 5(4):e01283-14.
  27. Siddiqui H, Lagesen K, Nederbragt AJ, Jeansson SL, Jakobsen KS. Alterations of microbiota in urine from women with interstitial cystitis. BMC Microbiology. 2012; 12:205-211-215.
  28. Fouts DE, Pieper R, Szpakowski S, Pohl H, Knoclach S, Suh M-H, Huang S-T, Ljungberg I, Sprague BM, Lucas SK, Torralba M, Nelson KE, Groah. Integrated next-generation sequencing of 16S rDNA and metaproteomics differentiate the healthy urine microbiome from asymptomatic bacteriuria in neuropathic bladder associated with spinal cord injury. J Transl Med. 2012; 10:174.
  29. Imirzalioglu C, Hain T, Chakraborty T, Domann E. Hidden pathogens uncovered: Metagenomic analysis of urinary tract infections. Andrologia. 2008; 4066-71.

References cited in Pre- and Probiotic Foods for a Healthy Gut by Jo Ann T. Hattner, MPH RDN and Susan Anderes, MLIS 

  1. Pollan M. Some of my best friends are germs. New York Times Magazine. May 15, 2013.
  2. Food and Agriculture Organization of the United Nations, World Health Organization. Probiotics in food: Health and nutritional properties and guidelines for evaluation. Rome: Food and Agriculture Organization of the United Nations: World Health Organization. 2006; viii:50.
  3. Hattner JAT, Anderes S. Gut Insight: Probiotics and Prebiotics for Digestive Health and Well-Being. San Francisco: Hattner Nutrition. 2009. www.gutinsight.com.
  4. German JB. The future of yogurt: Scientific and regulatory needs. Am J Clin Nutr. 2014; 99(5 Suppl):1271S-8S. DOI: 10.3945/ajcn.113.076844. PubMed PMID: 24695899; PubMed Central PMCID: PMC3985222.
  5. Hertzler SR, Clancy SM. Kefir improves lactose digestion and tolerance in adults with lactose maldigestion. J Am Diet Assoc. 2003; 103(5):582-7. DOI: 10.1053/jada.2003.50111. PubMed PMID: 12728216.
  6. Farnworth ER, Mainville I, Desjardins MP, Gardner N, Fliss I, Champagne C. Growth of probiotic bacteria and bifidobacteria in a soy yogurt formulation. Int J Food Microbiol. 2007; 116(1):174-81. DOI: 10.1016/j.ijfoodmicro.2006.12.015. PubMed PMID: 17292991.
  7. Moshfegh AJ, Friday JE, Goldman JP, Ahuja JK. Presence of inulin and oligofructose in the diets of Americans. J Nutr. 1999; 129(7 Suppl):1407S-11S. Epub 1999/07/08. PubMed PMID: 10395608.
  8. Saavedra JM, Dattilo A. Microbiota of the intestine. Encyclopedia of Human Nutrition: Elsevier. 2013.
  9. van Loo J, Coussement P, de Leenheer L, Hoebregs H, Smits G. On the presence of inulin and oligofructose as natural ingredients in the western diet. Crit Rev Food Sci Nutr. 1995; 35(6):525-52. DOI: 10.1080/10408399509527714. PubMed PMID: 8777017.

References cited in The NIH Human Microbiome Project by Erica Goode, MD

  1. www.commonfund.nih.gov/hmp/initiatives#elucidation
  2. www.microbemaggazias.org/index.php?option=com
  3. Huttenhower C. Functional analysis of the human microbiome, metagenomes, metatranscriptions, and multi-omics. Broad Institute, Raes Lab, VUV-KU Leuwens lecture. July 24, 2013.
  4. Morgan. TiG 2012. Huttenhower, ibid.
  5. Tan P. The neonatal microbiome and NEC. Washington University, St. Louis, collaborative study, NIH HMP. 2014.
  6. Turnbaugh P, Gordon J et al. Washington University, St. Louis. microbemagazine.org. 2013.
  7. Huenemann R. U.C. Berkeley, School of Public Health. Communication, 1968.
  8. Clement K. Bariatric surgery, adipose tissue, and gut microbiota. Int’l. J. of Obesity. 2011;  35:S7-15.
  9. Kong LC et al. Gut microbiota after gastric bypass in human obesity: Increased richness and associations of bacterial genera with adipose tissue genes. Am. J. Clinical Nutrition. 2013; 98:(1), 16-24.
  10. Turnbaugh, ibid.
  11. Aroth T, Sharma R et al. Fermentation potential of the gut micro biome: Implications for energy homeostasis and weight management. Nutr. Rev. 2012; 69:(2), 99-106.

References cited in Why the Microbiome Matters: One Primary Care Physician's Journey toward Understanding Its Significance by Payal Bhandari, MD

  1. Hattner JA. www.gutinsight.com. 2013.
  2. Dong TL, MD. Healthy at Home: Get Well and Stay Well Without Prescriptions.  2014. Published by National Geographic Society.
  3. Robinson, J. Eating on the Wild Side. 2013. Published by Little & Brown.
  4. Metchnikoff E. Essais optimistes; The Prolongation of Life: Optimistic studies. Translated and edited by P. Chalmers Mitchell. 1907. London: Heinemann.
  5. Pesticide Action Network. http://www.panna.org.
  6. Flight I, Clifton P. Cereal grains and legumes in the prevention of coronary heart disease and stroke: A review of the Lliterature. European Journal of Clinical Nutrition. 2006; 60:1145-59. 
  7. USDA Economic Research Service. Loss-adjusted food availability: Spreadsheets. Fresh vegetable consumption. 2008.8 Lad V, MA. The Complete Book of Ayurvedic Home Remedies. 1998. Published by Three Rivers Press. 


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