16  References

17 Academic References

Afshinnekoo, Ebrahim, Cem Meydan, Shanin Chowdhury, Dyala Jaroudi, Collin Boyer, Nick Bernstein, Julia M. Maritz, et al. 2015. “Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics.” Cell Systems 1 (1): 72–87. https://doi.org/10.1016/j.cels.2015.01.001.
Ameringen, Michael, Jasmine Turna, Beth Patterson, Amy Pipe, Randi Q. Mao, Rebecca Anglin, and Michael G. Surette. 2019. “The Gut Microbiome in Psychiatry: A Primer for Clinicians.” Depression and Anxiety, July. https://doi.org/10.1002/da.22936.
Azad, Meghan B, Theodore Konya, Heather Maughan, David S Guttman, Catherine J Field, Malcolm R Sears, Allan B Becker, James A Scott, Anita L Kozyrskyj, and CHILD Study Investigators. 2013. “Infant Gut Microbiota and the Hygiene Hypothesis of Allergic Disease: Impact of Household Pets and Siblings on Microbiota Composition and Diversity.” Allergy, Asthma & Clinical Immunology 9 (1): 15. https://doi.org/10.1186/1710-1492-9-15.
Barr, Jeremy J., Rita Auro, Mike Furlan, Katrine L. Whiteson, Marcella L. Erb, Joe Pogliano, Aleksandr Stotland, et al. 2013. “Bacteriophage Adhering to Mucus Provide a Non-Host-Derived Immunity.” Proceedings of the National Academy of Sciences of the United States of America 110 (26): 10771–76. https://doi.org/10.1073/pnas.1305923110.
Bassis, Christine M., Nicholas M. Moore, Karen Lolans, Anna M. Seekatz, Robert A. Weinstein, Vincent B. Young, and Mary K. Hayden. 2017. “Comparison of Stool Versus Rectal Swab Samples and Storage Conditions on Bacterial Community Profiles.” BMC Microbiology 17 (1). https://doi.org/10.1186/s12866-017-0983-9.
Blaser, Martin J. 2015. Missing Microbes: How the Overuse of Antibiotics Is Fueling Our Modern Plagues. New York: Picador.
Bütof, L., N. Wiesemann, M. Herzberg, M. Altzschner, A. Holleitner, F. Reith, and D. H. Nies. 2018. “Synergistic Gold–Copper Detoxification at the Core of Gold Biomineralisation in Cupriavidus Metallidurans.” Metallomics 10 (2): 278–86. https://doi.org/10.1039/C7MT00312A.
Chivian, D., E. L. Brodie, E. J. Alm, D. E. Culley, P. S. Dehal, T. Z. DeSantis, T. M. Gihring, et al. 2008. “Environmental Genomics Reveals a Single-Species Ecosystem Deep Within Earth.” Science 322 (5899): 275–78. https://doi.org/10.1126/science.1155495.
David, Lawrence A., Arne C. Materna, Jonathan Friedman, Maria I. Campos-Baptista, Matthew C. Blackburn, Allison Perrotta, Susan E. Erdman, and Eric J. Alm. 2014. “Host Lifestyle Affects Human Microbiota on Daily Timescales.” Genome Biology 15 (7): R89. https://doi.org/10.1186/gb-2014-15-7-r89.
David, Lawrence A., Corinne F. Maurice, Rachel N. Carmody, David B. Gootenberg, Julie E. Button, Benjamin E. Wolfe, Alisha V. Ling, et al. 2014. “Diet Rapidly and Reproducibly Alters the Human Gut Microbiome.” Nature 505 (7484): 559–63. https://doi.org/10.1038/nature12820.
De Palma, Giada, Inmaculada Nadal, Maria Carmen Collado, and Yolanda Sanz. 2009. “Effects of a Gluten-Free Diet on Gut Microbiota and Immune Function in Healthy Adult Human Subjects.” British Journal of Nutrition 102 (08): 1154. https://doi.org/10.1017/S0007114509371767.
Dommels, Y. E. M., R. A. Kemperman, Y. E. M. P. Zebregs, R. B. Draaisma, A. Jol, D. A. W. Wolvers, E. E. Vaughan, and R. Albers. 2009. “Survival of Lactobacillus Reuteri DSM 17938 and Lactobacillus Rhamnosus GG in the Human Gastrointestinal Tract with Daily Consumption of a Low-Fat Probiotic Spread.” Applied and Environmental Microbiology 75 (19): 6198–6204. https://doi.org/10.1128/AEM.01054-09.
Dufresne, C., and E. Farnworth. 2000. “Tea, Kombucha, and Health: A Review.” Food Research International 33 (6): 409–21. https://doi.org/10.1016/S0963-9969(00)00067-3.
Feehley, Taylor, Catherine H. Plunkett, Riyue Bao, Sung Min Choi Hong, Elliot Culleen, Pedro Belda-Ferre, Evelyn Campbell, et al. 2019. “Healthy Infants Harbor Intestinal Bacteria That Protect Against Food Allergy.” Nature Medicine 25 (3): 448–53. https://doi.org/10.1038/s41591-018-0324-z.
Frank, D. N., A. L. St. Amand, R. A. Feldman, E. C. Boedeker, N. Harpaz, and N. R. Pace. 2007. “Molecular-Phylogenetic Characterization of Microbial Community Imbalances in Human Inflammatory Bowel Diseases.” Proceedings of the National Academy of Sciences 104 (34): 13780–85. https://doi.org/10.1073/pnas.0706625104.
Hannigan, Geoffrey D., Melissa B. Duhaime, Mack T. Ruffin, Charlie C. Koumpouras, and Patrick D. Schloss. 2018. “The Diagnostic Potential & Interactive Dynamics of the Colorectal Cancer Virome.” bioRxiv, October. https://doi.org/10.1101/152868.
Herrán, Alexandra R., Jénifer Pérez-Andrés, Alberto Caminero, Esther Nistal, Santiago Vivas, José María Ruiz de Morales, and Javier Casqueiro. 2017. “Gluten-Degrading Bacteria Are Present in the Human Small Intestine of Healthy Volunteers and Celiac Patients.” Research in Microbiology, May. https://doi.org/10.1016/j.resmic.2017.04.008.
Hope, B. K., R. Baker, E. D. Edel, A. T. Hogue, W. D. Schlosser, R. Whiting, R. M. McDowell, and R. A. Morales. 2002. An Overview of the Salmonella Enteritidis Risk Assessment for Shell Eggs and Egg Products.” Risk Analysis: An Official Publication of the Society for Risk Analysis 22 (2): 203–18.
Horneck, G., D. M. Klaus, and R. L. Mancinelli. 2010. “Space Microbiology.” Microbiology and Molecular Biology Reviews 74 (1): 121–56. https://doi.org/10.1128/MMBR.00016-09.
Hotchin, J., P. Lorenz, A. Markusen, and C. Hemenway. 1967. The Survival of Micro-Organisms in Space. Further Rocket and Balloon-Borne Exposure Experiments.” Life Sciences and Space Research 5: 1–6.
Jaspers, E., and J. Overmann. 2004. “Ecological Significance of Microdiversity: Identical 16S rRNA Gene Sequences Can Be Found in Bacteria with Highly Divergent Genomes and Ecophysiologies.” Applied and Environmental Microbiology 70 (8): 4831–39. https://doi.org/10.1128/AEM.70.8.4831-4839.2004.
Jing, Xin, Nathan J. Sanders, Yu Shi, Haiyan Chu, Aimée T. Classen, Ke Zhao, Litong Chen, Yue Shi, Youxu Jiang, and Jin-Sheng He. 2015. “The Links Between Ecosystem Multifunctionality and Above- and Belowground Biodiversity Are Mediated by Climate.” Nature Communications 6 (1). https://doi.org/10.1038/ncomms9159.
Khan, Sehroon, Sadia Nadir, Zia Ullah Shah, Aamer Ali Shah, Samantha C. Karunarathna, Jianchu Xu, Afsar Khan, Shahzad Munir, and Fariha Hasan. 2017. “Biodegradation of Polyester Polyurethane by Aspergillus Tubingensis.” Environmental Pollution 225 (June): 469–80. https://doi.org/10.1016/j.envpol.2017.03.012.
Kobziar, Leda N., Melissa R. A. Pingree, Heather Larson, Tyler J. Dreaden, Shelby Green, and Jason A. Smith. 2018. “Pyroaerobiology: The Aerosolization and Transport of Viable Microbial Life by Wildland Fire.” Ecosphere 9 (11). https://doi.org/10.1002/ecs2.2507.
Kothary, Mahendra H., and Uma S. Babu. 2001. INFECTIVE DOSE OF FOODBORNE PATHOGENS IN VOLUNTEERS: A REVIEW.” Journal of Food Safety 21 (1): 49–68. https://doi.org/10.1111/j.1745-4565.2001.tb00307.x.
Kraal, Laurens, Sahar Abubucker, Karthik Kota, Michael A. Fischbach, and Makedonka Mitreva. 2014. “The Prevalence of Species and Strains in the Human Microbiome: A Resource for Experimental Efforts.” Edited by Niyaz Ahmed. PLoS ONE 9 (5): e97279. https://doi.org/10.1371/journal.pone.0097279.
Lim, Mi Young, Hyun Ju You, Hyo Shin Yoon, Bomi Kwon, Jae Yoon Lee, Sunghee Lee, Yun-Mi Song, Kayoung Lee, Joohon Sung, and GwangPyo Ko. 2017. “The Effect of Heritability and Host Genetics on the Gut Microbiota and Metabolic Syndrome.” Gut 66 (6): 1031–38. https://doi.org/10.1136/gutjnl-2015-311326.
Locey, Kenneth J., and Jay T. Lennon. 2016. “Scaling Laws Predict Global Microbial Diversity.” Proceedings of the National Academy of Sciences 113 (21): 5970–75. https://doi.org/10.1073/pnas.1521291113.
Mandal, Siddhartha, Will Van Treuren, Richard A. White, Merete Eggesbø, Rob Knight, and Shyamal D. Peddada. 2015. “Analysis of Composition of Microbiomes: A Novel Method for Studying Microbial Composition.” Microbial Ecology in Health & Disease 26 (0). https://doi.org/10.3402/mehd.v26.27663.
Manrique, Pilar, Benjamin Bolduc, Seth T. Walk, John van der Oost, Willem M. de Vos, and Mark J. Young. 2016. “Healthy Human Gut Phageome.” Proceedings of the National Academy of Sciences 113 (37): 10400–10405. https://doi.org/10.1073/pnas.1601060113.
McDonald, Daniel, Embriette Hyde, Justine W. Debelius, James T. Morton, Antonio Gonzalez, Gail Ackermann, Alexander A. Aksenov, et al. 2018. “American Gut: An Open Platform for Citizen Science Microbiome Research.” Edited by Casey S. Greene. mSystems 3 (3). https://doi.org/10.1128/mSystems.00031-18.
Muñoz-González, Carolina, Carolina Cueva, M. Ángeles Pozo-Bayón, and M. Victoria Moreno-Arribas. 2015. “Ability of Human Oral Microbiota to Produce Wine Odorant Aglycones from Odourless Grape Glycosidic Aroma Precursors.” Food Chemistry 187 (November): 112–19. https://doi.org/10.1016/j.foodchem.2015.04.068.
Myhrvold, Nathan, Chris Young, Maxime Bilet, and Ryan Matthew Smith. 2011. Modernist Cuisine: The Art and Science of Cooking. 1st ed. Bellevue, Wash: Cooking Lab.
Otles, Semih, and Ozlem Cagindi Otles Semih. 2003. “Kefir : A Probiotic Dairy-Composition, Nutritional and Therapeutic Aspects.” Pakistan Journal of Nutrition 2 (2): 54–59. https://doi.org/10.3923/pjn.2003.54.59.
Pollock, Jolinda, Laura Glendinning, Trong Wisedchanwet, and Mick Watson. 2018. “The Madness of Microbiome: Attempting to Find Consensus ‘Best Practice’ for 16S Microbiome Studies.” Applied and Environmental Microbiology, February, AEM.02627–17. https://doi.org/10.1128/AEM.02627-17.
Portune, Kevin J., Alfonso Benítez-Páez, Eva Maria Gomez Del Pulgar, Victor Cerrudo, and Yolanda Sanz. 2017. “Gut Microbiota, Diet, and Obesity-Related Disorders-The Good, the Bad, and the Future Challenges.” Molecular Nutrition & Food Research 61 (1): 1600252. https://doi.org/10.1002/mnfr.201600252.
Rizzello, Carlo G., Maria De Angelis, Raffaella Di Cagno, Alessandra Camarca, Marco Silano, Ilario Losito, Massimo De Vincenzi, et al. 2007. “Highly Efficient Gluten Degradation by Lactobacilli and Fungal Proteases During Food Processing: New Perspectives for Celiac Disease.” Applied and Environmental Microbiology 73 (14): 4499–4507. https://doi.org/10.1128/AEM.00260-07.
Roberts, Seth. 2004. “Self-Experimentation as a Source of New Ideas: Ten Examples about Sleep, Mood, Health, and Weight.” http://www.escholarship.org/uc/item/2xc2h866.
Roberts, Seth Douglass. 2007. The Shangri-La Diet: The No Hunger, Eat Anything, Weight-Loss Plan. Perigee trade pbk. ed. New York: Penguin.
Scott, Karen P., Silvia W. Gratz, Paul O. Sheridan, Harry J. Flint, and Sylvia H. Duncan. 2013. “The Influence of Diet on the Gut Microbiota.” Pharmacological Research 69 (1): 52–60. https://doi.org/10.1016/j.phrs.2012.10.020.
Shade, Ashley. 2017. “Diversity Is the Question, Not the Answer.” The ISME Journal 11 (1): 1–6. https://doi.org/10.1038/ismej.2016.118.
Song, Se Jin, Christian Lauber, Elizabeth K Costello, Catherine A Lozupone, Gregory Humphrey, Donna Berg-Lyons, J Gregory Caporaso, et al. 2013. “Cohabiting Family Members Share Microbiota with One Another and with Their Dogs.” eLife 2 (April). https://doi.org/10.7554/eLife.00458.
Spector, T. D. 2016. Diet Myth: Why the Secret to Health and Weight Loss Is Already in Your Gut.
Thaiss, Christoph A. 2018. “Microbiome Dynamics in Obesity.” Science 362 (6417): 903–4. https://doi.org/10.1126/science.aav6870.
the WISSARD Science Team, Brent C. Christner, John C. Priscu, Amanda M. Achberger, Carlo Barbante, Sasha P. Carter, Knut Christianson, et al. 2014. “A Microbial Ecosystem Beneath the West Antarctic Ice Sheet.” Nature 512 (7514): 310–13. https://doi.org/10.1038/nature13667.
Torre, Rosa de la, Leopoldo G. Sancho, Gerda Horneck, Asunción de los Ríos, Jacek Wierzchos, Karen Olsson-Francis, Charles S. Cockell, Petra Rettberg, Thomas Berger, and Jean-Pierre P. de Vera. 2010. “Survival of Lichens and Bacteria Exposed to Outer Space Conditions – Results of the Lithopanspermia Experiments.” Icarus 208 (2): 735–48. https://doi.org/10.1016/j.icarus.2010.03.010.
Tyler, Andrea D, Michelle I Smith, and Mark S Silverberg. 2014. “Analyzing the Human Microbiome: A How To Guide for Physicians.” The American Journal of Gastroenterology 109 (7): 983–93. https://doi.org/10.1038/ajg.2014.73.
Virgin, Herbert W. 2014. “The Virome in Mammalian Physiology and Disease.” Cell 157 (1): 142–50. https://doi.org/10.1016/j.cell.2014.02.032.
Vriezinga, Sabine L., Renata Auricchio, Enzo Bravi, Gemma Castillejo, Anna Chmielewska, Paula Crespo Escobar, Sanja Kolaček, et al. 2014. “Randomized Feeding Intervention in Infants at High Risk for Celiac Disease.” New England Journal of Medicine 371 (14): 1304–15. https://doi.org/10.1056/NEJMoa1404172.
Wacklin, Pirjo, Harri Mäkivuokko, Noora Alakulppi, Janne Nikkilä, Heli Tenkanen, Jarkko Räbinä, Jukka Partanen, Kari Aranko, and Jaana Mättö. 2011. “Secretor Genotype (FUT2 Gene) Is Strongly Associated with the Composition of Bifidobacteria in the Human Intestine.” Edited by Michael Otto. PLoS ONE 6 (5): e20113. https://doi.org/10.1371/journal.pone.0020113.
Wacklin, Pirjo, Jarno Tuimala, Janne Nikkilä, Sebastian Tims, Harri Mäkivuokko, Noora Alakulppi, Pia Laine, et al. 2014. “Faecal Microbiota Composition in Adults Is Associated with the FUT2 Gene Determining the Secretor Status.” Edited by Christopher Quince. PLoS ONE 9 (4): e94863. https://doi.org/10.1371/journal.pone.0094863.
Walsh, Aaron M., Fiona Crispie, Kieran Kilcawley, Orla O’Sullivan, Maurice G. O’Sullivan, Marcus J. Claesson, and Paul D. Cotter. 2016. “Microbial Succession and Flavor Production in the Fermented Dairy Beverage Kefir.” Edited by Rachel J. Dutton. mSystems 1 (5): e00052–16. https://doi.org/10.1128/mSystems.00052-16.
Walters, William A., Zech Xu, and Rob Knight. 2014. “Meta-Analyses of Human Gut Microbes Associated with Obesity and IBD.” FEBS Letters 588 (22): 4223–33. https://doi.org/10.1016/j.febslet.2014.09.039.
Zhernakova, Alexandra, Alexander Kurilshikov, Marc Jan Bonder, Ettje F. Tigchelaar, Melanie Schirmer, Tommi Vatanen, Zlatan Mujagic, et al. 2016. “Population-Based Metagenomics Analysis Reveals Markers for Gut Microbiome Composition and Diversity.” Science 352 (6285): 565–69. https://doi.org/10.1126/science.aad3369.
Zupancic, Margaret L., Brandi L. Cantarel, Zhenqiu Liu, Elliott F. Drabek, Kathleen A. Ryan, Shana Cirimotich, Cheron Jones, et al. 2012. “Analysis of the Gut Microbiota in the Old Order Amish and Its Relation to the Metabolic Syndrome.” Edited by Farook Thameem. PLoS ONE 7 (8): e43052. https://doi.org/10.1371/journal.pone.0043052.