Chapter 1

Moeller, Andrew H., et al. “Cospeciation of Gut Microbiota with Hominids.” Science, vol. 353, no. 6297, 22 July 2016, pp. 380–382. https://doi.org/10.1126/science.aaf3951.

Moeller, Andrew H. “The Shrinking Human Gut Microbiome.” Current Opinion in Microbiology, vol. 38, Aug. 2017, pp. 30–35. https://doi.org/10.1016/j.mib.2017.04.002.

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Amato, Katherine R., et al. “Convergence of Human and Old World Monkey Gut Microbiomes Demonstrates the Importance of Human Ecology over Phylogeny.” Genome Biology, vol. 20, no. 201, 8 Oct. 2019. https://doi.org/10.1186/s13059-019-1807-z.

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Martínez, Inés, et al. “The Gut Microbiota of Rural Papua New Guineans: Composition, Diversity Patterns, and Ecological Processes.” Cell Reports, vol. 11, no. 4, 28 Apr. 2015, pp. 527–538. https://doi.org/10.1016/j.celrep.2015.03.049.

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Chapter 2

Faith, Jeremiah J., et al. “The Long-Term Stability of the Human Gut Microbiota.” Science, vol. 341, no. 6141, 5 July 2013, article 1237439. https://doi.org/10.1126/science.1237439.

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Chapter 3

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Mueller, Noel T., et al. “Does Vaginal Delivery Mitigate or Strengthen the Intergenerational Association of Overweight and Obesity? Findings from the Boston Birth Cohort.” International Journal of Obesity, vol. 41, no. 4, Apr. 2017, pp. 497–501. https://doi.org/10.1038/ijo.2016.219.

Dominguez-Bello, Maria G., et al. “Partial Restoration of the Microbiota of Cesarean-Born Infants via Vaginal Microbial Transfer.” Nature Medicine, vol. 22, no. 3, Mar. 2016, pp. 250–253. https://doi.org/10.1038/nm.4039.

Callaway, Ewen. “Scientists Swab C-Section Babies with Mothers’ Microbes.” Nature, 1 Feb. 2016, https://www.nature.com/articles/nature.2016.19275. Accessed 23 Apr. 2025.

Yan, Jing, et al. “The Association between Breastfeeding and Childhood Obesity: A Meta-Analysis.” BMC Public Health, vol. 14, no. 1267, 13 Dec. 2014. https://doi.org/10.1186/1471-2458-14-1267.

Tham, Rachel, et al. “Breastfeeding and the Risk of Dental Caries: A Systematic Review and Meta-Analysis.” Acta Paediatrica, vol. 104, no. 467, Dec. 2015, pp. 62–84. https://doi.org/10.1111/apa.13118.

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Horta, Bernardo L., Cesar Loret de Mola, and Cesar G. Victora. “Long-Term Consequences of Breastfeeding on Cholesterol, Obesity, Systolic Blood Pressure and Type 2 Diabetes: A Systematic Review and Meta-Analysis.” Acta Paediatrica, vol. 104, no. 467, Dec. 2015, pp. 30–37. https://doi.org/10.1111/apa.13133.

Victora, Cesar G., et al. “Breastfeeding in the 21st Century: Epidemiology, Mechanisms, and Lifelong Effect.” The Lancet, vol. 387, no. 10017, 30 Jan. 2016, pp. 475–490. https://doi.org/10.1016/S0140-6736(15)01024-7.

Differding, Moira K., et al. “Timing of Complementary Feeding Is Associated with Gut Microbiota Diversity and Composition and Short Chain Fatty Acid Concentrations over the First Year of Life.” BMC Microbiology, vol. 20, no. 56, 11 Mar. 2020. https://doi.org/10.1186/s12866-020-01723-9.

Checa-Ros, Ana, et al. “Current Evidence on the Role of the Gut Microbiome in ADHD Pathophysiology and Therapeutic Implications.” Nutrients, vol. 13, no. 1, 16 Jan. 2021, p. 249. https://doi.org/10.3390/nu13010249.

Liu, Conglin, et al. “Microbial Dysbiosis and Childhood Asthma Development: Integrated Role of the Airway and Gut Microbiome, Environmental Exposures, and Host Metabolic and Immune Response.” Frontiers in Immunology, vol. 13, 30 Sept. 2022. https://doi.org/10.3389/fimmu.2022.1028209.

Calcaterra, Valeria, et al. “Precocious Puberty and Microbiota: The Role of the Sex Hormone–Gut Microbiome Axis.” Frontiers in Endocrinology, vol. 13, 21 Oct. 2022. https://doi.org/10.3389/fendo.2022.1000919.

Edwards, Sara M., et al. “The Maternal Gut Microbiome during Pregnancy.” MCN: The American Journal of Maternal/Child Nursing, vol. 42, no. 6, Nov.–Dec. 2017, pp. 310–317. https://doi.org/10.1097/NMC.0000000000000372.

Peters, Brandilyn A., et al. “Spotlight on the Gut Microbiome in Menopause: Current Insights.” International Journal of Women's Health, vol. 14, 10 Aug. 2022, pp. 1059–1072. https://doi.org/10.2147/IJWH.S340491.

Hu, Shiwan, et al. “Gut Microbial Beta-Glucuronidase: A Vital Regulator in Female Estrogen Metabolism.” Gut Microbes, vol. 15, no. 1, 9 Aug. 2023, article 2236749. https://doi.org/10.1080/19490976.2023.2236749.

Jackson, Matthew A., et al. “Signatures of Early Frailty in the Gut Microbiota.” Genome Medicine, vol. 8, no. 1, 29 Jan. 2016, article 8. https://doi.org/10.1186/s13073-016-0262-7.

O'Toole, Paul W., and Marcus J. Claesson. “Gut Microbiota: Changes Throughout the Lifespan from Infancy to Elderly.” International Dairy Journal, vol. 20, no. 4, Apr. 2010, pp. 281–291. https://doi.org/10.1016/j.idairyj.2009.11.010.

Leung, Katherine, and Sandrine Thuret. “Gut Microbiota: A Modulator of Brain Plasticity and Cognitive Function in Ageing.” Healthcare, vol. 3, no. 4, 29 Sept. 2015, pp. 898–916. https://doi.org/10.3390/healthcare3040898.

Marcobal, Angela, et al. “Bacteroides in the Infant Gut Consume Milk Oligosaccharides via Mucus-Utilization Pathways.” Cell Host & Microbe, vol. 10, no. 5, 17 Nov. 2011, pp. 507–514. https://doi.org/10.1016/j.chom.2011.10.007.

Thursby, Eleanor, and Nathalie Juge. “Introduction to the Human Gut Microbiota.” Biochemical Journal, vol. 474, no. 11, 16 May 2017, pp. 1823–1836. https://doi.org/10.1042/BCJ20160510.

Imhann, Floris, et al. “Proton Pump Inhibitors Affect the Gut Microbiome.” Gut, vol. 65, no. 5, May 2016, pp. 740–748. https://doi.org/10.1136/gutjnl-2015-310376.

Wang, Huiying, et al. “Bifidobacterium longum 1714™ Strain Modulates Brain Activity of Healthy Volunteers During Social Stress.” The American Journal of Gastroenterology, vol. 114, no. 7, July 2019, pp. 1152–1162. https://doi.org/10.14309/ajg.0000000000000203.

Maldonado-Contreras, A., et al. “Structure of the Human Gastric Bacterial Community in Relation to Helicobacter pylori Status.” The ISME Journal, vol. 5, 2011, pp. 574–579. https://doi.org/10.1038/ismej.2010.149.

Liu, L., et al. “Transient Gastric Irritation in Neonatal Rats Leads to Changes in Hypothalamic CRF Expression, Depression- and Anxiety-Like Behavior as Adults.” PLOS ONE, vol. 6, no. 5, 12 May 2011, e19498. https://doi.org/10.1371/journal.pone.0019498.

Camilleri, Michael, et al. “Role for Diet in Normal Gut Barrier Function: Developing Guidance within the Framework of Food-Labeling Regulations.” American Journal of Physiology-Gastrointestinal and Liver Physiology, vol. 317, no. 1, 1 July 2019, pp. G17–G39. https://doi.org/10.1152/ajpgi.00063.2019.

Visser, J., et al. “Tight Junctions, Intestinal Permeability, and Autoimmunity: Celiac Disease and Type 1 Diabetes Paradigms.” Annals of the New York Academy of Sciences, vol. 1165, May 2009, pp. 195–205. https://doi.org/10.1111/j.1749-6632.2009.04037.x.

Zhao, J., et al. “The Impact of Gut Microbiota on Post-Stroke Management.” Frontiers in Cellular and Infection Microbiology, vol. 11, 12 Oct. 2021, article 724376. https://doi.org/10.3389/fcimb.2021.724376.

Sharma, V., et al. “At the Intersection of Gut Microbiome and Stroke: A Systematic Review of the Literature.” Frontiers in Neurology, vol. 12, 24 Sept. 2021, article 729399. https://doi.org/10.3389/fneur.2021.729399.

Nielsen, S. D., N. M. Pearson, and K. Seidler. “The Link between the Gut Microbiota and Parkinson's Disease: A Systematic Mechanism Review with Focus on α-Synuclein Transport.” Brain Research, vol. 1769, 15 Oct. 2021, article 147609. https://doi.org/10.1016/j.brainres.2021.147609.

Romano, S., et al. “Meta-Analysis of the Parkinson's Disease Gut Microbiome Suggests Alterations Linked to Intestinal Inflammation.” NPJ Parkinson's Disease, vol. 7, no. 1, 10 Mar. 2021, article 27. https://doi.org/10.1038/s41531-021-00156-z.

Wallen, Z. D., et al. “Metagenomics of Parkinson’s Disease Implicates the Gut Microbiome in Multiple Disease Mechanisms.” Nature Communications, vol. 13, 2022, article 6958. https://doi.org/10.1038/s41467-022-34667-x.

Yao, L., et al. “Constipation in Parkinson's Disease: A Systematic Review and Meta-Analysis.” European Neurology, vol. 86, no. 1, 2023, pp. 34–44. https://doi.org/10.1159/000527513.

Seo, Do., and David M. Holtzman. “Current Understanding of the Alzheimer’s Disease-Associated Microbiome and Therapeutic Strategies.” Experimental & Molecular Medicine, vol. 56, 2024, pp. 86–94. https://doi.org/10.1038/s12276-023-01146-2.

Chandra, S., S. S. Sisodia, and R. J. Vassar. “The Gut Microbiome in Alzheimer’s Disease: What We Know and What Remains to Be Explored.” Molecular Neurodegeneration, vol. 18, 2023, article 9. https://doi.org/10.1186/s13024-023-00595-7.

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Zhang, T., et al. “Efficacy of Probiotics for Irritable Bowel Syndrome: A Systematic Review and Network Meta-Analysis.” Frontiers in Cellular and Infection Microbiology, vol. 12, 2022, article 859967. https://doi.org/10.3389/fcimb.2022.859967.

Crompton, Simon. “Psychobiotics: Your Microbiome Has the Potential to Improve Your Mental Health, Not Just Your Gut Health.” BBC Science Focus Magazine, 2017, https://www.sciencefocus.com/the-human-body/psychobiotics-your-microbiome-has-the-potential-to-improve-your-mental-health-not-just-your-gut-heath. Accessed 23 Apr. 2025.

Holz, C., et al. “Significant Reduction in Helicobacter pylori Load in Humans with Non-Viable Lactobacillus reuteri DSM17648: A Pilot Study.” Probiotics and Antimicrobial Proteins, vol. 7, 2015, pp. 91–100. https://doi.org/10.1007/s12602-014-9181-3.

Graham, David Y., and Muhammad Miftahussurur. “Helicobacter pylori Urease for Diagnosis of Helicobacter pylori Infection: A Mini Review.” Journal of Advanced Research, vol. 13, 31 Jan. 2018, pp. 51–57. https://doi.org/10.1016/j.jare.2018.01.006.

Camilleri, Michael. “Leaky Gut: Mechanisms, Measurement and Clinical Implications in Humans.” Gut, vol. 68, no. 8, Aug. 2019, pp. 1516–1526. https://doi.org/10.1136/gutjnl-2019-318427.

Twardowska, A., et al. “Identification of Leaky Gut-Related Markers as Indicators of Metabolic Health.” PLOS ONE, 2022.

Hoshiko, Hiroyuki, et al. “Identification of Leaky Gut-Related Markers as Indicators of Metabolic Health in Dutch Adults: The Nutrition Questionnaires Plus (NQplus) Study.” PLOS ONE, vol. 16, no. 6, 2021, article e0252936. https://doi.org/10.1371/journal.pone.0252936.

Makaro, A., et al. “Preventing Bacterial Translocation in Patients with Leaky Gut Syndrome: Nutrition and Pharmacological Treatment Options.” International Journal of Molecular Sciences, 2022.

Cheng, Z., et al. “The Critical Role of Gut Microbiota in Obesity.” Frontiers in Endocrinology (Lausanne), vol. 13, 20 Oct. 2022, article 1025706. https://doi.org/10.3389/fendo.2022.1025706.

Blaak, Ellen E., et al. “Short Chain Fatty Acids in Human Gut and Metabolic Health.” Beneficial Microbes, vol. 11, no. 5, 1 Sept. 2020, pp. 411–455. https://doi.org/10.3920/BM2020.0057.

Chapter 5

Rinninella, Emanuele, et al. “What Is the Healthy Gut Microbiota Composition? A Changing Ecosystem across Age, Environment, Diet, and Diseases.” Microorganisms, vol. 7, no. 1, 2019, article 14. https://doi.org/10.3390/microorganisms7010014.

Johnson, Emily L., et al. “Microbiome and Metabolic Disease: Revisiting the Bacterial Phylum Bacteroidetes.” Journal of Molecular Medicine (Berlin), vol. 95, no. 1, Jan. 2017, pp. 1–8. https://doi.org/10.1007/s00109-016-1492-2.

Binda, Claudia, et al. “Actinobacteria: A Relevant Minority for the Maintenance of Gut Homeostasis.” Digestive and Liver Disease, vol. 50, no. 5, May 2018, pp. 421–428. https://doi.org/10.1016/j.dld.2018.02.012.

Portincasa, Piero, et al. “Gut Microbiota and Short Chain Fatty Acids: Implications in Glucose Homeostasis.” International Journal of Molecular Sciences, vol. 23, no. 3, 20 Jan. 2022, article 1105. https://doi.org/10.3390/ijms23031105.

Pham, Van T., et al. “Vitamins, the Gut Microbiome and Gastrointestinal Health in Humans.” Nutrition Research, vol. 95, 2021, pp. 35–53. https://doi.org/10.1016/j.nutres.2021.09.001.

Cani, Patrice D., et al. “Gut Microbiota and Health: Connecting Actors across the Metabolic System.” Nature Reviews Microbiology, vol. 20, no. 5, 2022, pp. 307–322. https://doi.org/10.1038/s41579-021-00641-1.

Strandwitz, Philipp. “Neurotransmitter Modulation by the Gut Microbiota.” Brain Research, vol. 1693, pt. B, 15 Aug. 2018, pp. 128–133. https://doi.org/10.1016/j.brainres.2018.03.015.

Adak, Abhrajit, and Md. R. Khan. “An Insight into Gut Microbiota and Its Functionalities.” Cellular and Molecular Life Sciences, vol. 76, no. 3, Feb. 2019, pp. 473–493. https://doi.org/10.1007/s00018-018-2943-4.

Mondot, Stanislas, et al. “Structural Robustness of the Gut Mucosal Microbiota Is Associated with Crohn's Disease Remission after Surgery.” Gut, vol. 65, no. 6, June 2016, pp. 954–962. https://doi.org/10.1136/gutjnl-2015-309184.

Raymond, François, et al. “The Initial State of the Human Gut Microbiome Determines Its Reshaping by Antibiotics.” The ISME Journal, vol. 10, 2016, pp. 707–720. https://doi.org/10.1038/ismej.2015.148.

Hen, Jing, and Luis Vitetta. “The Role of Butyrate in Attenuating Pathobiont-Induced Hyperinflammation.” Immune Network, vol. 20, no. 2, 4 Feb. 2020, article e15. https://doi.org/10.4110/in.2020.20.e15.

Rizzatti, Gianluca, et al. “Proteobacteria: A Common Factor in Human Diseases.” BioMed Research International, vol. 2017, 2 Nov. 2017, article 9351507. https://doi.org/10.1155/2017/9351507.

Diether, Nicole E., and Benjamin P. Willing. “Microbial Fermentation of Dietary Protein: An Important Factor in Diet–Microbe–Host Interaction.” Microorganisms, vol. 7, no. 1, 13 Jan. 2019, article 19. https://doi.org/10.3390/microorganisms7010019.

Akimbekov, Nurken S., et al. “Vitamin D and the Host-Gut Microbiome: A Brief Overview.” Acta Histochemica et Cytochemica, vol. 53, no. 3, 26 June 2020, pp. 33–42. https://doi.org/10.1267/ahc.20011.

Duranti, Silvia, et al. “Bifidobacterium Adolescentis as a Key Member of the Human Gut Microbiota in the Production of GABA.” Scientific Reports, vol. 10, 2020, article 14112. https://doi.org/10.1038/s41598-020-70986-z.

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Maifeld, Andre, et al. “Fasting Alters the Gut Microbiome Reducing Blood Pressure and Body Weight in Metabolic Syndrome Patients.” Nature Communications, vol. 12, 2021, article 1970. https://doi.org/10.1038/s41467-021-22097-0.

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Chapter 8

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Chapter 9

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