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      <title>Gut Busters: Exploring Diet-driven Immune Modulation and Changes to the Human Microbiome by Ruby Chen</title>
      <link>https://padlet.com/rubyschen04/cf788r5xlk1rlsom</link>
      <description>HMB385 Digital Poster Assignment: Adapted from Wastyk, H. C. et al. Cell. 184(16). https://doi.org/10.1016/j.cell.2021.06.019.</description>
      <language>en-us</language>
      <pubDate>2025-03-20 20:29:18 UTC</pubDate>
      <lastBuildDate>2025-03-24 02:08:44 UTC</lastBuildDate>
      <webMaster>hello@padlet.com</webMaster>
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         <title>Successful Diet Changes/Maintenance!</title>
         <author>rubyschen04</author>
         <link>https://padlet.com/rubyschen04/cf788r5xlk1rlsom/wish/3375634642</link>
         <description><![CDATA[<p><strong>Intake of High-Fiber diet Arm  🍌:</strong></p><ul><li><p>↑ <strong>Carbohydrate</strong>, vegetable protein, and calories, iron, magnesium, potassium, vitamin C, &amp; calcium</p></li><li><p>↓ Animal protein, &amp; sodium</p></li></ul><p><strong>Intake of High-Fermented-foods diet Arm 🧫  : </strong></p><ul><li><p>↑ <strong>Animal protein</strong> (by virtue of eating more fermented foods like yogurt, kefir, etc.)</p></li></ul><p>(Wastyk, H. C. et al., <em>Cell</em>, 2021)</p>]]></description>
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         <pubDate>2025-03-20 22:56:35 UTC</pubDate>
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         <title>🎯Background: Let&#39;s Get Into It!</title>
         <author>ashleyhnwai</author>
         <link>https://padlet.com/rubyschen04/cf788r5xlk1rlsom/wish/3377606203</link>
         <description><![CDATA[<p><strong><mark>Diet</mark></strong><mark> is ONE of the MANY factors that are </mark><em><mark>integral and multifaceted</mark></em><mark> in its influence on the composition &amp; function of the </mark><strong><mark>gastrointestinal microbiome/metabolome</mark></strong><mark> throughout life</mark> (Wastyk, H. C. et al., <em>Cell</em>, 2021)</p><ul><li><p>Of which extends to the underlying interplay between the <strong>intestinal barrier </strong>&amp;<strong> </strong>the<strong> immune system</strong> (Conlon, A and Bird, A. R., <em>Nutrients</em>, 2014; Rinninella, E et al., <em>Best Pract Res Clin Gastroenterol</em>, 2023). </p></li></ul><p><br/></p><p>Lifestyle shifts following ‘<strong>westernization</strong>’ has led to a  <strong>significant rise</strong> in....</p><ul><li><p><strong>Dysbiosis</strong></p></li><li><p><strong>Metabolic</strong> (i.e., diabetes) &amp; <strong>non-communicable chronic diseases (NCCDs)</strong></p></li><li><p><strong>Inflammatory markers</strong></p></li><li><p><strong>Body Mass Index</strong> (BMI) </p></li><li><p><strong>Reduced microbial taxa (diversity)</strong> &amp; <strong>Markers of host health </strong></p></li></ul><p>(Wastyk, H. C. et al., Cell, 2021)</p>]]></description>
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         <pubDate>2025-03-22 16:44:56 UTC</pubDate>
         <guid>https://padlet.com/rubyschen04/cf788r5xlk1rlsom/wish/3377606203</guid>
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         <title>⚠️Experiment Question⚠️</title>
         <author>ashleyhnwai</author>
         <link>https://padlet.com/rubyschen04/cf788r5xlk1rlsom/wish/3377607001</link>
         <description><![CDATA[<p>Building onto the concept of gut microbiota adaptability following short-term changes in diet, the selected experiment focused on <strong><mark>the</mark></strong><mark> </mark><strong><em><mark>effects of two microbiota targeted dietary interventions (fermented foods vs. plant-based fiber) on the immune system, and microbiome in healthy (human) adults</mark> </em></strong>(Wastyk, H. C. et al., <em>Cell</em>, 2021).</p>]]></description>
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         <pubDate>2025-03-22 16:46:44 UTC</pubDate>
         <guid>https://padlet.com/rubyschen04/cf788r5xlk1rlsom/wish/3377607001</guid>
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         <title>What are the major findings and relevant critical analysis? 🧐</title>
         <author>sunjingyiaaa517</author>
         <link>https://padlet.com/rubyschen04/cf788r5xlk1rlsom/wish/3377629888</link>
         <description><![CDATA[<p><strong>🍽️Diet largely influences the host gut microbiota composition (diversity, species composition and density) &amp; immune system (inflammation and health status).</strong></p><p><br/></p><p>🥦After <strong><mark>High-fiber diet</mark> </strong>intervention<strong>:</strong> <strong>No diversity increase</strong>.</p><p><strong>Due to:</strong> </p><ul><li><p>Short 10-week intervention is <strong>too hurried</strong> for microbiota reconstruction*</p></li><li><p>Modern <strong>excessive sanitation</strong> measures (e.g. overuse of food chemical sanitizers) reducing bacterial diversity &amp; exchanging</p></li><li><p>Insufficient gut bacteria <strong>cultivation</strong> requiring simultaneous ingestion of fiber-rich foods &amp; desired bacteria</p></li><li><p>Caucasian <strong>genetic</strong> <strong>deficiency</strong> of certain bacterial species that Caucasian subjects lost some bacteria that can metabolize glycans.</p></li></ul><p>*microbiota reconstruction: change in modeling of microbiota diversity, density &amp; composition (i.e. various species)</p><p><br/></p><p>🧀After <strong><mark>High-fermented-food diet</mark> </strong>intervention<strong>:</strong> there is an <strong>increase</strong> in gut microbiota diversity &amp; <strong>decrease</strong> in inflammatory proteins synthesis &amp; NCCDs incidence (Wastyk, H. C. et al., Cell, 2021)<strong><em>.</em></strong></p><p><br/></p>]]></description>
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         <pubDate>2025-03-22 17:41:14 UTC</pubDate>
         <guid>https://padlet.com/rubyschen04/cf788r5xlk1rlsom/wish/3377629888</guid>
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         <title>👫Participants</title>
         <author>ashleyhnwai</author>
         <link>https://padlet.com/rubyschen04/cf788r5xlk1rlsom/wish/3377636246</link>
         <description><![CDATA[<p><strong>Total 17-week protocol</strong> (10-week dietary intervention) with participants (<em>N </em>= 381 → 39) randomized by number generator to the <strong>high-fiber diet</strong> (<em>n</em> = 21) OR <strong>high-fermented foods diet </strong>(<em>n</em> = 18) (Wastyk, H. C. et al., Cell, 2021).</p><p><br/></p><p><strong>⭐️<em><mark>Final Participant Characteristics: </mark></em></strong></p><p>(<strong>Analysis </strong>used<strong> </strong>(<em>n</em>=18) in each arm)</p><ul><li><p>Average <strong>BMI</strong> 25 ± 4 kg/m²</p></li><li><p>Average <strong>age</strong> 51 ± 12 years</p></li><li><p>73% <strong>Female</strong> </p></li><li><p>81% <strong>Caucasian</strong> </p><p>(Wastyk, H. C. et al., <em>Cell</em>, 2021)</p></li></ul>]]></description>
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         <pubDate>2025-03-22 17:56:31 UTC</pubDate>
         <guid>https://padlet.com/rubyschen04/cf788r5xlk1rlsom/wish/3377636246</guid>
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         <title>What is the significance/major contributions of the study? 👍</title>
         <author>sunjingyiaaa517</author>
         <link>https://padlet.com/rubyschen04/cf788r5xlk1rlsom/wish/3377637465</link>
         <description><![CDATA[<p><strong>👩🏼‍🏫<mark>Enhancing</mark></strong><mark> </mark><strong><mark>understanding</mark></strong> of distinct individual participant's gut bacterial and immune <strong>response</strong> to diet change = promoting <strong><mark>personalized diet recommendation</mark></strong></p><p><br/></p><p>🦠<mark>Construction of </mark><strong><mark>mechanistic models</mark></strong>: to investigate the <strong>causality</strong> between diet and host response = enabling <strong><mark>global health improvement</mark> </strong>and <strong><mark>health burden alleviation</mark> </strong>(Wastyk, H. C. et al., Cell, 2021)<strong><em>.</em></strong></p>]]></description>
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         <pubDate>2025-03-22 17:59:21 UTC</pubDate>
         <guid>https://padlet.com/rubyschen04/cf788r5xlk1rlsom/wish/3377637465</guid>
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         <title>📝Design: Diet &amp; Variables</title>
         <author>ashleyhnwai</author>
         <link>https://padlet.com/rubyschen04/cf788r5xlk1rlsom/wish/3377638295</link>
         <description><![CDATA[<p><strong>BASELINE (W-2) to END OF MAINTENANCE (W10):</strong></p><p><strong>⭐️VARIABLES:</strong></p><p><strong>*</strong><em>Collected </em><strong><em>stool (microbiota metabolic output, function, and composition) </em></strong><em>and</em><strong><em> blood samples (immune system markers) </em></strong>(Wastyk, H. C. et al., <em>Cell</em>, 2021)</p><ul><li><p><strong><mark>Primary Outcome Variable</mark>: </strong><em>Cytokine Response Score (CRS)</em></p></li><li><p><strong><mark>Secondary Outcome Variable</mark>: </strong>Change in gut microbiome composition/diversity</p></li></ul><p><br/></p><p><strong>⭐️DIET: </strong></p><p><em>*High fiber/fermented food consumption </em><strong><em>increased </em></strong><em>every two weeks.</em></p><p><strong><em><mark>High Fiber Diet</mark>:</em></strong><em> </em></p><p><em>Vegetables, nuts, grains, fruits, seeds, etc.,</em></p><ul><li><p><strong><em>Baseline</em></strong><em>:</em> Mean 21.5 ± 8.0g/day</p></li><li><p><strong><em>Maintenance</em></strong><em>: </em>Mean<em> </em>45.1 ± 10.7g/day</p></li></ul><p><strong><em><mark>High Fermented-Foods Diet</mark>: </em></strong></p><p><em>Fermented vegetables, cottage cheese, vegetable brine, kombucha, fermented non-alcoholic beverages, etc.,</em></p><ul><li><p><strong><em>Baseline</em></strong><em>: </em>Mean 0.4 ± 0.6g/day</p></li><li><p><strong><em>Maintenance</em></strong><em>: </em>Mean 6.3 ± 2.9g/day</p></li></ul><p>(Wastyk, H. C. et al., Cell, 2021)</p>]]></description>
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         <pubDate>2025-03-22 18:01:18 UTC</pubDate>
         <guid>https://padlet.com/rubyschen04/cf788r5xlk1rlsom/wish/3377638295</guid>
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         <title>Any weaknesses that require improvement? 🙋🏼‍♀️</title>
         <author>sunjingyiaaa517</author>
         <link>https://padlet.com/rubyschen04/cf788r5xlk1rlsom/wish/3377642496</link>
         <description><![CDATA[<p><strong>📊<mark>Small</mark></strong><mark> </mark><strong><mark>sample size</mark></strong> with only 18 people per arm <strong>decreases statistical strength</strong>.</p><p><strong>⏳<mark>Short study duration</mark></strong> (10 weeks) <strong>cannot</strong> explore <strong>long-term efficacy, safety</strong> &amp; <strong>stability</strong>.</p><p><strong>🔕<mark>No control group</mark></strong> <strong>cannot</strong> exclude impacts of <strong>confounding factors</strong>.</p><p>👩🏼<strong><mark>Limited single subjects</mark></strong> which are mainly healthy Caucasian women around age 51 (Wastyk, H. C. et al., Cell, 2021)<strong><em>.</em></strong></p>]]></description>
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         <pubDate>2025-03-22 18:12:22 UTC</pubDate>
         <guid>https://padlet.com/rubyschen04/cf788r5xlk1rlsom/wish/3377642496</guid>
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         <title>Why PLANT-BASED FIBER?</title>
         <author>ashleyhnwai</author>
         <link>https://padlet.com/rubyschen04/cf788r5xlk1rlsom/wish/3377644427</link>
         <description><![CDATA[<p><strong><mark>Plant-Based Fiber Importance on </mark><em><mark>Microbiota: </mark></em> </strong><em>Increased dietary fiber intake aids in...</em></p><ul><li><p><strong>Producing microbiota-accessible carbohydrates (MACs)</strong>--benefits metabolism of microbiota taxa (Wastyk, H. C. et al., <em>Cell</em>, 2021)</p></li><li><p><strong>Increasing microbiome richness/diversity</strong> (increased beneficial bacterial taxa like that of <em>Akkermansia, Bifidobacterium, Lactobacillus</em>) (Howard, E. J. et al., <em>J Nutr</em>, 2024)</p></li><li><p><strong>Lessening low-density lipoprotein cholesterol concentrations</strong> within the blood<strong> </strong>(Sidju, S. R. K. et al., <em>Nutrients</em>, 2023).</p></li><li><p><strong>Enabling bacterial fermentation → Short-chain fatty acids </strong>(i.e., butryrate, propionate, acetate) = enhancing metabolic homeostasis = colonic gut peptide release (i.e., glucagon-like peptide-1 (GLP-1)) (Howard, E. J. et al., <em>J Nutr,</em> 2024)</p></li><li><p><strong>Microbiota possessing distinct functionalities depending on fiber viscosity, type, &amp; solubility</strong> (Howard, E. J. et al., <em>J Nutr</em>, 2024).</p></li></ul><p>==&gt; I.e., High viscosity, <strong>β-Glucan</strong> (soluble-fiber) from oats = enhanced glucose homeostasis</p><p>==&gt; I.e., Low viscosity, <strong>dextrin </strong>(soluble-fiber) from wheat = enhanced insulin sensitivity</p><ul><li><p><strong>Modifying immune system function via metabolites</strong> = <strong>Reduces local &amp; systemic means of inflammation  </strong>(Wastyk, H. C. et al., <em>Cell</em>, 2021)</p></li></ul><p><br/></p><p>Exemplified by how in-vivo mice models with <strong>high-fiber diets defended against myocardial infarction</strong>—stopped unfavorable remodeling and diminished infarct size (Zhao, J et al., <em>Front Microbiol</em>, 2022).</p>]]></description>
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         <pubDate>2025-03-22 18:17:45 UTC</pubDate>
         <guid>https://padlet.com/rubyschen04/cf788r5xlk1rlsom/wish/3377644427</guid>
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         <title>Why FERMENTED FOOD?</title>
         <author>ashleyhnwai</author>
         <link>https://padlet.com/rubyschen04/cf788r5xlk1rlsom/wish/3377644492</link>
         <description><![CDATA[<p><strong><mark>Fermented Food Importance on </mark><em><mark>Microbiota</mark>: </em></strong>Popularity resurged due to their historic potential (i.e., <strong>Lactobacillus)</strong> that has been LESSENED due to current diet (Wastyk, H. C. et al., <em>Cell</em>, 2021)</p><ul><li><p><strong>Microbial fermentation alters food properties</strong>—converts phenolic compounds + complex carbohydrates → bioactive metabolites (i.e., SCFA))—<strong>boosting immune function &amp; response </strong>(Stiemsma, L et al., <em>J Nutr</em>, 2020)</p></li></ul><p>==&gt; <strong>More microbial metabolites</strong> like <em>tryptophan</em> (for serotonin), <em>polyphenolic compounds</em> (for bioavailability), and <em>bile acids </em>(for metabolism)) (Balasubramanian, R et al., <em>Neurosci Biobehav Rev</em>, 2024)</p><ul><li><p><strong>Pathway aid (gut-to-brain information communication/relay) </strong>(Balasubramanian, R et al., <em>Neurosci Biobehav Rev</em>, 2024)</p></li><li><p><strong>Gut microbiome diversity </strong>(Wastyk, H. C. et al., <em>Cell</em>, 2021)</p></li><li><p><strong>Nutrionally rich &amp; environmentally sustainable alternative</strong> (i.e., protein-rich legume fermentation with lactic acid bacteria (LAB) OVER that of animal meat) <strong>for novel strains of probiotics</strong> (Valentino, V et al., <em>Microb Biotechnol</em>, 2024).</p></li><li><p><strong>Anti-nutrient reduction </strong>(Dimidi, E et al., <em>Nutrients</em>, 2019), <strong>Anti-microbial peptides</strong></p></li><li><p><strong>Gut barrier maintenance &amp; pH modification</strong></p></li><li><p><strong>Biogenic amines </strong>(Dimidi, E et al., <em>Nutrients</em>, 2019) </p></li><li><p><strong>Probiotic effects </strong>(metabolic pathway reprogramming) (Dimidi, E et al., <em>Nutrients</em>, 2019)</p></li></ul><p><br/></p><p>Exemplified by how consuming <strong>kefir</strong> (a type of fermented food) can eradicate Helicobacter pylori, and malabsorption of lactose (Dimidi, E et al., <em>Nutrients</em>, 2019).</p>]]></description>
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         <pubDate>2025-03-22 18:17:58 UTC</pubDate>
         <guid>https://padlet.com/rubyschen04/cf788r5xlk1rlsom/wish/3377644492</guid>
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         <title>📝Design: Phases</title>
         <author>ashleyhnwai</author>
         <link>https://padlet.com/rubyschen04/cf788r5xlk1rlsom/wish/3377648057</link>
         <description><![CDATA[<p><strong>⭐️4 PHASES:</strong></p><ol><li><p><mark>"Baseline"</mark>: <strong>3-Week</strong> Pre-Intervention</p></li><li><p><mark>"Ramp"</mark>: <strong>4-Week</strong> Ramp Phase (<strong>progressive increase</strong> in respective diet (arm) intake)</p></li><li><p><mark>"Maintenance"</mark>: <strong>6-Week</strong> Maintenance Phase (consistent consumption of respective diet (arm) at <strong>high</strong> levels)</p></li><li><p><mark>"Choice"</mark>: <strong>4-Week </strong>Choice Period (respective diet (arm) level to the <strong>wanted extent</strong> of participants)</p></li></ol><p>(Wastyk, H. C. et al., Cell, 2021)</p><p><br/></p><p><strong>⭐️ IMPORTANT NOTE:</strong></p><p><em>*Participants did </em><strong><em>not</em></strong><em> increase consumption of food constituting the opposing arm. And, </em><strong><em>varied (no consistent subcategories) </em></strong><em>in types of fermented/fiber food consumed </em>(Wastyk, H. C. et al., <em>Cell</em>, 2021).</p>]]></description>
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         <pubDate>2025-03-22 18:25:53 UTC</pubDate>
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         <title>What can be further investigated as the future directions? 🗺️</title>
         <author>sunjingyiaaa517</author>
         <link>https://padlet.com/rubyschen04/cf788r5xlk1rlsom/wish/3377648068</link>
         <description><![CDATA[<ol><li><p>The diet change effects on <mark>different subjects</mark> <strong>with disease, immune impairment </strong>and<strong> inflammation </strong>or on <strong>younger</strong> people with <strong>different races</strong> than white can be examined for efficacy &amp; stability of dietary change.</p></li><li><p>The diet alteration with simultaneous consumption of <strong> high fiber and fermented food</strong> can be explored for its <strong><mark>synergetic effects</mark> </strong>on host microbiota composition &amp; immune status (Wastyk, H. C. et al., Cell, 2021)<strong><em>.</em></strong></p></li><li><p>The <strong><mark>long-term</mark></strong><mark> study</mark> (e.g. with duration of about four months dietary change intervention) may be conducted for <strong>long-term effectiveness, safety </strong>&amp;<strong> clinical feasibility</strong>. </p></li></ol>]]></description>
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         <pubDate>2025-03-22 18:25:57 UTC</pubDate>
         <guid>https://padlet.com/rubyschen04/cf788r5xlk1rlsom/wish/3377648068</guid>
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         <title>🔬Why THIS Experiment?</title>
         <author>ashleyhnwai</author>
         <link>https://padlet.com/rubyschen04/cf788r5xlk1rlsom/wish/3377652567</link>
         <description><![CDATA[<p><strong><mark>Microbial profiles</mark></strong><mark> can </mark><em><mark>change</mark></em><mark> depending on the </mark><strong><mark>composition of diet</mark></strong>--it has been identified that <em>gut microbiota can be bettered following a ‘healthy diet' → </em><strong>allowing for possible disease/metabolic disorder combat</strong> (Conlon, A and Bird, A. R., <em>Nutrients</em>, 2014). </p><p><br/></p><p><strong>Exemplified</strong> in a random control trial involving patients with ulcerative colitis: </p><ul><li><p><em>Anti-inflammatory diets in combination with fecal microbiota transplantations (FMT)</em> exhibited <strong>greater results--better long-term remission maintenance</strong>--compared to that of standard (medical) treatment (Rinninella, E et al., <em>Best Pract Res Clin Gastroenterol</em>, 2023).</p></li></ul><p><br/></p><p>Highlighting the <strong>potential</strong> for human <em>gut microbiota modulation (</em><strong><em>by diet</em></strong><em>) against disease</em>. <mark>And, as each nutrient can possesses a distinct/certain effect on the gut microbiota, </mark><em><mark>there is a </mark></em><strong><em><mark>rising interest</mark></em></strong><em><mark> in investigating the benefits of certain dietary combinations, patterns, and bases</mark> </em>(Rinninella, E et al., <em>Best Pract Res Clin Gastroenterol</em>, 2023).</p><p><em>→</em> <strong>High-fermented food</strong> vs. <strong>high plant-based fiber</strong>.</p><p><br/></p>]]></description>
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         <pubDate>2025-03-22 18:39:07 UTC</pubDate>
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         <title>References</title>
         <author>ashleyhnwai</author>
         <link>https://padlet.com/rubyschen04/cf788r5xlk1rlsom/wish/3377654091</link>
         <description><![CDATA[<p><strong><em>Acknowledgement</em></strong><em>: Reference List was created by all group members for their respective citations.</em></p><p><br/></p><ol><li><p>Allan, S. M., &amp; Rothwell, N. J. (2001). Cytokines and acute neurodegeneration. <em>Nature Reviews Neuroscience, 2</em>(10), 734–744. <a rel="noopener noreferrer nofollow" href="https://doi.org/10.1038/35094583">https://doi.org/10.1038/35094583 </a></p></li><li><p>Balasubramanian, R., Schneider, E., Gunnigle, E., Cotter, P. D., &amp; Cryan, J. F. (2024). Fermented foods: Harnessing their potential to modulate the microbiota-gut-brain axis for mental health. <em>Neuroscience and biobehavioral reviews</em>, <em>158</em>, 105562. <a rel="noopener noreferrer nofollow" href="https://doi.org/10.1016/j.neubiorev.2024.105562">https://doi.org/10.1016/j.neubiorev.2024.105562</a></p></li><li><p>Caffrey, E. B., Sonnenburg, J. L., &amp; Devkota, S. (2024). Our extended microbiome: The human-relevant metabolites and biology of fermented foods. <em>Cell Metabolism</em>, <em>36</em>(4), 684–701. <a rel="noopener noreferrer nofollow" href="https://doi.org/10.1016/j.cmet.2024.03.007">https://doi.org/10.1016/j.cmet.2024.03.007</a></p></li><li><p>Cantarel, B. L., Coutinho, P. M., Rancurel, C., Bernard, T., Lombard, V., &amp; Henrissat, B. (2009). The carbohydrate-active enzymes database (CAZy): An expert resource for glycogenomics. <em>Nucleic Acids Research, 37</em>(Database issue), D233–D238. <a rel="noopener noreferrer nofollow" href="https://doi.org/10.1093/nar/gkn663">https://doi.org/10.1093/nar/gkn663</a> </p></li><li><p>Chen, L., Liu, B., Ren, L., Du, H., Fei, C., Qian, C., Li, B., Zhang, R., Liu, H., Li, Z., &amp; Ma, Z. (2023). High-fiber diet ameliorates gut microbiota, serum metabolism and emotional mood in type 2 diabetes patients. <em>Frontiers in Cellular and Infection Microbiology</em>, <em>13</em>. <a rel="noopener noreferrer nofollow" href="https://doi.org/10.3389/fcimb.2023.1069954">https://doi.org/10.3389/fcimb.2023.1069954</a></p></li><li><p>Chen, Y.-R., Zheng, H.-M., Zhang, G.-X., Chen, F.-L., Chen, L.-D., &amp; Yang, Z.-C. (2020). High <em>Oscillospira</em> abundance indicates constipation and low BMI in the Guangdong Gut Microbiome Project. <em>Scientific Reports, 10</em>(1), 9364. <a rel="noopener noreferrer nofollow" href="https://doi.org/10.1038/s41598-020-66369-z">https://doi.org/10.1038/s41598-020-66369-z </a></p></li><li><p>Conlon, M., &amp; Bird, A. (2014). The Impact of Diet and Lifestyle on Gut Microbiota and Human Health. <em>Nutrients</em>, <em>7</em>(1), 17–44. <a rel="noopener noreferrer nofollow" href="https://doi.org/10.3390/nu7010017">https://doi.org/10.3390/nu7010017</a></p></li><li><p>Cotillard, A., Kennedy, S. P., Kong, L. C., Prifti, E., Pons, N., Le Chatelier, E., Almeida, M., Quinquis, B., Levenez, F., Galleron, N., Gougis, S., Rizkalla, S., Batto, J.-M., Renault, P., ANR MicroObes Consortium, Dore, J., Zucker, J.-D., Clement, K., &amp; Ehrlich, S. D. (2013). Dietary intervention impact on gut microbial gene richness. <em>Nature, 500</em>(7464), 585–588. <a rel="noopener noreferrer nofollow" href="https://doi.org/10.1038/nature12480">https://doi.org/10.1038/nature12480 </a></p></li><li><p>De Filippo, C., Cavalieri, D., Di Paola, M., Ramazzotti, M., Poullet, J. B., Massart, S., Collini, S., Pieraccinim G., &nbsp; Lionetti, P. (2010). Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. <em>Proceedings of the National Academy of Sciences, 107</em>(33), 14691–14696. <a rel="noopener noreferrer nofollow" href="https://doi.org/10.1073/pnas.1005963107">https://doi.org/10.1073/pnas.1005963107</a> </p></li><li><p>Delannoy-Bruno, O., Desai, C., Castillo, J. J., Couture, G., Barve, R. A., Lombard, V., Henrissat, B., Cheng, J., Han, N., Hayashi, D. K., Meynier, A., Vinoy, S., Lebrilla, C. B., Marion, S., Heath, A. C., Barratt, M. J., &amp; Gordon, J. I. (2022). An approach for evaluating the effects of dietary fiber polysaccharides on the human gut microbiome and plasma proteome. <em>Proc Natl Acad Sci USA, 119</em>(20). <a rel="noopener noreferrer nofollow" href="https://doi.org/10.1073/pnas.2123411119">https://doi.org/10.1073/pnas.2123411119 </a></p></li><li><p>Derrien, M., Belzer, C., &amp; de Vos, W. M. (2017). Akkermansia muciniphila and its role in regulating host functions. <em>Microbial Pathogenesis, 106</em>, 171–181. <a rel="noopener noreferrer nofollow" href="https://doi.org/10.1016/j.micpath.2016.02.005">https://doi.org/10.1016/j.micpath.2016.02.005</a></p></li><li><p>Dimidi, E., Cox, S. R., Rossi, M., &amp; Whelan, K. (2019). Fermented Foods: Definitions and Characteristics, Impact on the Gut Microbiota and Effects on Gastrointestinal Health and Disease.&nbsp;<em>Nutrients</em>,&nbsp;<em>11</em>(8), 1806. <a rel="noopener noreferrer nofollow" href="https://doi.org/10.3390/nu11081806">https://doi.org/10.3390/nu11081806</a></p></li><li><p>Granado-Serrano, A. B., Martin-Gari, M., Ssnchez, V., Riart Solans, M., Berdun, R., Ludwig, I. A., Rubio, L., Vilaprinyo, E., Portero-Otin, M., &amp; Serrano, J. C. E. (2019). Faecal bacterial and short-chain fatty acids signature in hypercholesterolemia. <em>Scientific Reports, 9,</em> 1772. <a rel="noopener noreferrer nofollow" href="https://doi.org/10.1038/s41598-019-38874-3">https://doi.org/10.1038/s41598-019-38874-3 </a></p></li><li><p>Hamad, I., Cardilli, A., Côrte-Real, B. F., Dyczko, A., Vangronsveld, J., &amp; Kleinewietfeld, M. (2022). High-Salt Diet Induces Depletion of Lactic Acid-Producing Bacteria in Murine Gut.&nbsp;<em>Nutrients</em>,&nbsp;<em>14</em>(6), 1171. <a rel="noopener noreferrer nofollow" href="https://doi.org/10.3390/nu14061171">https://doi.org/10.3390/nu14061171</a></p></li><li><p>Hamamah, S., Amin, A., Al-Kassir, A. L., Chuang, J., &amp; Covasa, M. (2023). Dietary Fat Modulation of Gut Microbiota and Impact on Regulatory Pathways Controlling Food Intake.&nbsp;<em>Nutrients</em>,&nbsp;<em>15</em>(15), 3365. <a rel="noopener noreferrer nofollow" href="https://doi.org/10.3390/nu15153365">https://doi.org/10.3390/nu15153365</a></p></li><li><p>Howard, E. J., Meyer, R. K., Weninger, S. N., Martinez, T., Wachsmuth, H. R., Pignitter, M., Auñon-Lopez, A., Kangath, A., Duszka, K., Gu, H., Schiro, G., Laubtiz, D., &amp; Duca, F. A. (2024). Impact of Plant-Based Dietary Fibers on Metabolic Homeostasis in High-Fat Diet Mice via Alterations in the Gut Microbiota and Metabolites.&nbsp;<em>The Journal of nutrition</em>,&nbsp;<em>154</em>(7), 2014–2028. <a rel="noopener noreferrer nofollow" href="https://doi.org/10.1016/j.tjnut.2024.05.003">https://doi.org/10.1016/j.tjnut.2024.05.003</a></p></li><li><p>Ionita-Mindrican, C.-B., Ziani, K., Mittitelu, M., Oprea, E., Neacsu, S. M., Moroson, E., Dumitrescu, D.-E., Rosca, A. C., Draganescu, D., &amp; Negrei, C. (2022). Therapeutic benefits and dietary restrictions of fiber intake: A state of the art review. <em>Nutrients, 14</em>(13), 2641. <a rel="noopener noreferrer nofollow" href="https://doi.org/10.3390/nu14132641">https://doi.org/10.3390/nu14132641 </a></p></li><li><p>Jeyaram, K., Lahti, L., Tims, S., Hans, Gelder, van, Willem, Smidt, H., &amp; Zoetendal, E. G. (2025). Fermented foods affect the seasonal stability of gut bacteria in an Indian rural population. <em>Nature Communications</em>, <em>16</em>(1). <a rel="noopener noreferrer nofollow" href="https://doi.org/10.1038/s41467-025-56014-6">https://doi.org/10.1038/s41467-025-56014-6 </a></p></li><li><p>Klimenko, N. S., Tyakht, A. V., Popenko, A. S., Vasiliev, A. S., Altukhov, I. A., Ischenko, D. S., Shashkova, T. I., Efimova, D. A., Nikogosov, D. A., Osipenko, D. A., Musienko, S. V., Selezneva, K. S., Baranova, A., Kurilshikov, A. M., Toshchakov, S. M., Korzhenkov, A. A., Samarov, N. I., Shevchenko, M. A., Tepliuk, A. V., &amp; Alexeev, D. G. (2018). Microbiome responses to an uncontrolled short-term diet intervention in the frame of the citizen science project. <em>Nutrients, 10</em>(5), 576. <a rel="noopener noreferrer nofollow" href="https://doi.org/10.3390/nu10050576">https://doi.org/10.3390/nu10050576 </a></p></li><li><p>Leeuwendaal, N. K., Stanton, C., O’Toole, P. W., &amp; Beresford, T. P. (2022). Fermented Foods, Health and the Gut Microbiome. <em>Nutrients</em>, <em>14</em>(7), 1527. <a rel="noopener noreferrer nofollow" href="https://pubmed.ncbi.nlm.nih.gov/35406140/">https://pubmed.ncbi.nlm.nih.gov/35406140/</a></p></li><li><p>Le Chatelier, E., Nielsen, T., Qin, J., Prifti, E., Hildebrand, F., Falony, G., Almeida, M., Arumugam, M., Batto, J.-M., Kennedy, S., Leonard, P., Li, J., Burgdorf, K., Grarup, N., Jorgensen, T., Brandslund, I., Nielsen, H. B., Juncker, A. S., Bertalan, M., Levenez, F., ... Pedersen, O. (2013). Richness of human gut microbiome correlates with metabolic markers. <em>Nature, 500</em>(7464), 541–546. <a rel="noopener noreferrer nofollow" href="https://doi.org/10.1038/nature12506">https://doi.org/10.1038/nature12506 </a></p></li><li><p>Li, C.-J. (Ed.). (2014). <em>Butyrate: Food sources, functions and health benefits</em>. Nova Science Publishers.</p></li><li><p>Liu, S., Li, E., Sun, Z., Fu, D., Duan, G., Jiang, M., Yu, Y., Mei, L., Yang, P., Tang, Y., &amp; Zheng, P. (2019). Altered gut microbiota and short chain fatty acids in Chinese children with autism spectrum disorder. <em>Scientific Reports, 9</em>, Article 287. <a rel="noopener noreferrer nofollow" href="https://doi.org/10.1038/s41598-018-38218-9">https://doi.org/10.1038/s41598-018-38218-9 </a></p></li></ol>]]></description>
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         <pubDate>2025-03-22 18:44:38 UTC</pubDate>
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         <title>Did Alpha Diversity Change 🤔</title>
         <author>gabriella505kim</author>
         <link>https://padlet.com/rubyschen04/cf788r5xlk1rlsom/wish/3377658113</link>
         <description><![CDATA[<p><strong>Researchers hypothesized</strong> → alpha diversity would increase as fiber consumption increased </p><p><br/></p><p><strong>Results</strong> → <mark>hypothesis NOT supported</mark> ❌</p><p><br/></p><p>📚 <strong>Previous literature</strong> has often linked high fiber diets to increased microbial diversity, based on both interventional animal studies and long term associations in humans (Sonnenburg, E., et al., <em>Nature</em>, 2016; De Filipo, C., et al., <em>PNAS</em>, 2010; Le Chatelier, E., et al., <em>Nature, </em>2013). However, this was not consistent with the current study. </p><p><br/></p><p><strong>∴ </strong>Over the course of the intervention, there was <strong><mark>no change in alpha diversity</mark></strong></p>]]></description>
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         <pubDate>2025-03-22 18:56:37 UTC</pubDate>
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         <title>Comparative analysis to other publication ⚖️</title>
         <author>sunjingyiaaa517</author>
         <link>https://padlet.com/rubyschen04/cf788r5xlk1rlsom/wish/3377663682</link>
         <description><![CDATA[<p><strong>Similarity:</strong></p><ol><li><p><strong><mark>Similar change</mark></strong> of <strong><mark>gut</mark></strong><mark> </mark><strong><mark>microbiota</mark></strong><mark> &amp; </mark><strong><mark>inflammation</mark></strong><mark> </mark><strong><mark>condition</mark></strong> in response to high-fiber diet: There was a study investigating the high-fiber diet effects on type II diabetes participants that high-fiber foods <strong>increased</strong> the <strong>density</strong>, <strong>diversity</strong> and <strong>composition</strong> of the participants’ gut <strong>microbiota</strong> and <strong>decreased</strong> the <strong>inflammation</strong> condition, which were similar to the results of our selected paper.</p></li><li><p><strong><mark>Small sample size</mark>:</strong> Chen’s research also adoped small sample size with only <strong>n=9</strong> for treatment group and n=8 for control group, <strong>reducing</strong> the <strong>statistical power</strong>.</p></li><li><p><strong><mark>Short study duration</mark></strong> (4 weeks of high-fiber-diet treatment) <strong>cannot</strong> explore <strong>long-term effectiveness, safety</strong> &amp; <strong>stability</strong>.</p></li><li><p><strong><mark>Limited single subjects</mark></strong> with only type II diabetes patients whose glycosylated hemoglobin (HbA1c) measurements are 6.5-12%, <strong>excluding</strong> those who suffered from other chronic diseases (including type I diabetes, severe mental disorders, liver cirrhosis, cancers, cardiovascular diseases, etc.) and ingested prebiotics and antibiotics three months ago. Maybe the subjects’ age, gender and race could be further clarified for reference.</p></li></ol><p><br/></p><p><strong>Contrast:</strong></p><ol><li><p><strong>Presence</strong> of <strong><mark>control group</mark></strong>: providing the <strong>baseline</strong> level for <strong>comparing</strong> the <strong>differences</strong> in effects (e.g. blood sugar &amp; lipid levels) and <strong>eliminating</strong> the confounding factors’ impacts.</p></li><li><p><strong><mark>Different subjects</mark></strong>: <strong>type II diabetes patients</strong> whose HbA1c measurements are 6.5-12%, which is different from our selected paper (subjects are mainly <strong>healthy Caucasian women</strong> <strong>around age 51 </strong>(Wastyk, H. C. et al., Cell, 2021)).</p></li><li><p><strong><mark>Metabolic improvement</mark></strong>: However, in addition to the microbiota composition and immune change, the researchers found that participants’ <strong>blood sugar</strong> and <strong>lipid homeostasis</strong> were <strong>ameliorated</strong> with <strong>rised</strong> level of insulin and <strong>dropped</strong> level of triglyceride.</p></li><li><p><strong><mark>Mental improvement</mark></strong>: They also explored the participants’ <strong>mood response</strong> to the dietary change, showing the <strong>improved</strong> <strong>anxiety</strong> and <strong>depression</strong> status.</p></li><li><p><strong><mark>Multiaspect understanding</mark></strong>: The results <strong>enhance</strong> the <strong>understanding</strong> of diet alteration effects on <strong>microbiota composition, inflammation, metabolic </strong>and<strong> meatal health among chronic-diseased people</strong>, demonstrating a <strong>multiaspect</strong> appreciation of diet-indued health improvement.</p></li><li><p><strong><mark>Extensive enhancement</mark></strong><mark> of </mark><strong><mark>global health</mark></strong>: A <strong>wider global health guidance</strong> can be proposed in terms of <strong>high-fiber diet recommendation</strong> for both <strong>type II diabetes</strong> patients and <strong>healthy</strong> people, and <strong>global health </strong>may be largely <strong>improved</strong> subsequently (Chen et al., <em>Front Cell Infect Microbiol</em>, 2023)</p></li></ol>]]></description>
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         <pubDate>2025-03-22 19:15:10 UTC</pubDate>
         <guid>https://padlet.com/rubyschen04/cf788r5xlk1rlsom/wish/3377663682</guid>
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         <title>Unexpected findings 😲</title>
         <author>sunjingyiaaa517</author>
         <link>https://padlet.com/rubyschen04/cf788r5xlk1rlsom/wish/3377760437</link>
         <description><![CDATA[<ol><li><p>The process of bacterial diversity increase is <strong>sluggish</strong> = <strong><mark>stubbornness</mark> </strong>of<strong> fast microbiota reconstruction</strong> caused by diet alteration. </p></li><li><p>The<strong> fermented foods </strong>are <strong>not</strong> the <strong>main providers</strong> of<strong> </strong>new bacteria = eating high fermented food does <strong><mark>not have an direct influence</mark></strong> on microbiota reconstruction.</p></li><li><p>The <strong><mark>origin</mark> of newly acquired taxa</strong> remains <strong><mark>ambiguous</mark></strong>, but maybe these new taxa are from the surroundings, or they have already existed before the study starts just without detection.</p></li></ol><p>(Wastyk, H. C. et al., Cell, 2021)<strong><em>.</em></strong></p>]]></description>
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         <pubDate>2025-03-23 01:31:12 UTC</pubDate>
         <guid>https://padlet.com/rubyschen04/cf788r5xlk1rlsom/wish/3377760437</guid>
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         <title>What About Microbial Proteins Per Gram Stool 🤔</title>
         <author>gabriella505kim</author>
         <link>https://padlet.com/rubyschen04/cf788r5xlk1rlsom/wish/3377833280</link>
         <description><![CDATA[<p><strong>Researchers found </strong>→ increase in microbial proteins per gram stool ✅</p><p><br/></p><p><strong>They inferred </strong>→ it was bacteria already present that grew</p><p><br/></p><p><strong>∴  </strong>Since no new bacterial species were detected, and there was an increase in microbial proteins per gram stool (total bacterial biomass),<strong> <mark>it is likely bacteria already present in the microbiome that is growing</mark></strong><mark>.</mark> </p>]]></description>
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         <pubDate>2025-03-23 05:17:24 UTC</pubDate>
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         <title>Growing Bacteria: Good or Bad at Fiber Degradation? </title>
         <author>gabriella505kim</author>
         <link>https://padlet.com/rubyschen04/cf788r5xlk1rlsom/wish/3377838188</link>
         <description><![CDATA[<p><strong>Researchers found</strong> →<em> </em>an increase in 11 types of carbohydrate active enzymes (CAZymes)  ⬆️</p><p><br/></p><p><strong>Method</strong> → metagenomic sequencing 🧬</p><p><br/></p><p>📚 <strong>Previous studies</strong> have also reported similar findings. For example, one study investigating fiber rich snacks found that increased consumption led to a significant increase in CAZyme gene abundance (Delannoy-Bruno, O., et al., <em>Proc Natl Acad Sci USA<sub>, </sub></em>2022). </p><p><br/></p><p><strong>∴ </strong>This suggests it was <strong><mark>bacteria adept at fiber degradation that increased</mark></strong> in abundance</p>]]></description>
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         <pubDate>2025-03-23 05:28:50 UTC</pubDate>
         <guid>https://padlet.com/rubyschen04/cf788r5xlk1rlsom/wish/3377838188</guid>
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         <title>🍔🍟Implications of a &#39;WESTERNIZED&#39; Diet?</title>
         <author>ashleyhnwai</author>
         <link>https://padlet.com/rubyschen04/cf788r5xlk1rlsom/wish/3377853928</link>
         <description><![CDATA[<p><strong><mark>Characteristics of '</mark><em><mark>Westernized</mark></em><mark>'</mark></strong><mark> </mark><strong><mark>Diets:  </mark><em>HIGH in... </em> </strong></p><p>*(↓) indicates a <em>reduction in beneficial microbial bacterium that were previously dominant in pre-'Westernized' diets.</em></p><p>(Statovci, D et al., <em>Front Immunol</em>, 2017)</p><ul><li><p><strong>Fatty processed/domesticated meat, red-meat</strong> (↓<em>Streptococcus bovis/gallolyticus</em>) (Severino, A et al., <em>Best Pract Res Clin Gastroenterol</em>, 2024)</p></li><li><p><strong>Sugar/artificial sweeteners</strong> (↓<em>Lactobacillus, </em>↓ <em>Bifidobacteria) </em>(Ruiz-Ojeda, F. J. et al., <em>Adv Nutr</em>, 2019)<em>, </em><strong>corn-derived fructose syrup  </strong></p></li><li><p><strong>Salt</strong> (↓ <em>Akkermansia</em>) (Hamad, I et al., <em>Nutrients</em>, 2022)</p></li><li><p><strong>Refined grains</strong> (↓<em>Faecalibacterium</em>) </p></li><li><p><strong>Saturated fat </strong>(↓ <em>Bacteroidetes) </em>(Hamamah, S et al., <em>Nutrients</em>, 2023)</p></li></ul><p><br/></p><p>Overall, this diet is <strong><em>significantly LOW </em></strong><em>in</em><strong><em> </em></strong>fiber, fermented food, nutrient dense/diverse foods, fruits, whole grains, unsaturated fat, vegetables, omega-3 fatty acids, etc.,<em>. </em></p>]]></description>
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         <pubDate>2025-03-23 06:20:25 UTC</pubDate>
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         <title>Primary Outcomes! – What was observed in the Immune System?</title>
         <author>rubyschen04</author>
         <link>https://padlet.com/rubyschen04/cf788r5xlk1rlsom/wish/3378110993</link>
         <description><![CDATA[<p>Primary 1️⃣ Outcome: </p><ul><li><p>Cytokine response from baseline to end-of-intervention was <strong>not statistically different</strong> in both treatment arms.</p><p>⇨<strong> Simultaneously, NO</strong> changes in overall general health, perceived stress, well-being, fatigue, physical activity levels or cognition throughout the study (Wastyk, H. C. et al., <em>Cell</em>, 2021).</p></li></ul><p><br></p><p><mark>🔍</mark><em><mark> Hypothesis:</mark></em> Long-term changes in diet (e.g. chronic nutrient deficiencies) can alter immune responses <em>unfavourably</em>, impairing cytokine production and response (Rossio, J. L. 1999). The short duration of the study may not have been long enough to see <em>beneficial</em> effects on the immune system (e.g. increased cytokine production, etc). </p>]]></description>
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         <pubDate>2025-03-23 14:48:40 UTC</pubDate>
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         <title>Secon-dairy Outcomes! – What happened in the gut?</title>
         <author>rubyschen04</author>
         <link>https://padlet.com/rubyschen04/cf788r5xlk1rlsom/wish/3378119483</link>
         <description><![CDATA[<p>Secon-<em>dairy</em> 2️⃣ Outcomes:</p><p><br/></p><p><strong>Summary</strong> in the high-fibre arm 🍌 :</p><p>↑ in the genus <strong><em>Lachnospira</em></strong>;</p><p>↑ stool softness (as per GSRS).</p><p><br/></p><p><strong>Summary </strong>in the high-fermented-food arm 🥛 :</p><p>↓&nbsp; in the genus <strong><em>Lachnospira</em></strong>;</p><p>↓ inflammatory markers;</p><p>↑ microbiota diversity;</p><p>↑ initial bloating (as per GSRS; subsided by the end of the maintenance phase).</p><p>(Wastyk, H. C. et al., <em>Cell</em>, 2021)</p>]]></description>
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         <pubDate>2025-03-23 15:01:11 UTC</pubDate>
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         <title>Regardless of diet changes, the Microbiota stayed INDIVIDUALIZED!</title>
         <author>rubyschen04</author>
         <link>https://padlet.com/rubyschen04/cf788r5xlk1rlsom/wish/3378122256</link>
         <description><![CDATA[<p><strong>No major clustering</strong> based on the treatment arm was observed (Wastyk, H. C. et al., <em>Cell</em>, 2021). </p><p><br/></p><p>🔗 This reinforces the idea that the <strong>gut microbiome is altered by factors outside of just dietary habits</strong>. </p><ul><li><p>This is concurrent with studies that show that a complex microbial community can be altered by many factors like lifestyle, genetics and even mode of delivery at birth (Wen, L., &amp; Duffy, A., <em>J. Nutr</em>, 2017; Stiemsma et al., <em>J. Nutr</em>, 2020).</p></li></ul>]]></description>
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         <pubDate>2025-03-23 15:05:44 UTC</pubDate>
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         <title>Let&#39;s Discuss → Fermented-Food Arm Results!</title>
         <author>rubyschen04</author>
         <link>https://padlet.com/rubyschen04/cf788r5xlk1rlsom/wish/3378128336</link>
         <description><![CDATA[]]></description>
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         <pubDate>2025-03-23 15:15:52 UTC</pubDate>
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         <title>🦠 Fermented-food intake increases microbiota diversity 🦠 </title>
         <author>rubyschen04</author>
         <link>https://padlet.com/rubyschen04/cf788r5xlk1rlsom/wish/3378165224</link>
         <description><![CDATA[<ul><li><p><strong>Overall ↑ in ɑ-diversity</strong> (as seen with observed ASVs, phylogenetic diversity and Shannon diversity testing)</p><ul><li><p>This was exemplified in a more recent study; the fermented-food diet resulted in an increased ɑ-diversity (Leeuwendaal, N. K. et al., <em>Nutrients, </em>2022). Interestingly, in Wastyk et al.'s and Leeuwendaal et al.'s study alike, this same increase was not seen in the fibre-diet participants. </p></li></ul></li><li><p><strong>NO</strong> increase in relative abundance of microbial species per gram of stool.&nbsp;</p></li></ul><p>(Wastyk, H. C. et al., <em>Cell</em>, 2021)</p>]]></description>
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         <pubDate>2025-03-23 16:18:33 UTC</pubDate>
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         <title>🧬 Let&#39;s get specific: What Microbes Changed?</title>
         <author>rubyschen04</author>
         <link>https://padlet.com/rubyschen04/cf788r5xlk1rlsom/wish/3378176895</link>
         <description><![CDATA[<ul><li><p><strong>9 ASVs</strong> (amplicon sequence variants) <strong><mark>increased</mark></strong> over the course of the intervention:</p><ul><li><p>All in the <strong><em>Firmicutes</em></strong> phylum: (4) in the <strong><em>Lachnospiraceae</em></strong> family, (2) in the <strong><em>Ruminococcaceae</em></strong> family, and (1) in the <strong><em>Streptococcaceae</em></strong> family.</p></li></ul></li></ul><p><strong><mark>🔗</mark><em><mark> Link</mark></em></strong><em><mark>:</mark></em> Unno et al.'s study in healthy women between ages 20-24 shows that the ingestion of fermented-milk leads to a significant increase in <em>Firmicutes </em>(longitudinally), relative to <em>Bacteroidetes </em>(Unno, T. et al., <em>JDS</em>, 2015). These results mirror Wastyk et al.'s.</p><p>(Wastyk, H. C. et al., Cell, 2021)</p>]]></description>
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         <pubDate>2025-03-23 16:39:06 UTC</pubDate>
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         <title>Eating your Bacteria? Or no...? 🧄 </title>
         <author>rubyschen04</author>
         <link>https://padlet.com/rubyschen04/cf788r5xlk1rlsom/wish/3378179696</link>
         <description><![CDATA[<p>Insignificant/little overlap between <strong>increased microbiome ASVs</strong> and ASVs <em>IN the fermented-foods</em> → <strong>Indirect</strong> effect (Wastyk, H. C. et al., <em>Cell</em>, 2021).</p><p><br/></p><p><strong><mark>🔍</mark><em><mark> Hypothesis</mark></em></strong>: A study explains that even when fermented foods are injested by the host, they themselves become further fermented and interact with the GI tract in a novel way (Caffrey, E. B. et al., <em>Cell Metab</em>, 2024). This may lead to the creation and detection of new bacterial taxa.</p>]]></description>
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         <pubDate>2025-03-23 16:44:28 UTC</pubDate>
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         <title>Fermented-food intake decreases CAZyme abundance 🥯 </title>
         <author>rubyschen04</author>
         <link>https://padlet.com/rubyschen04/cf788r5xlk1rlsom/wish/3378193325</link>
         <description><![CDATA[<p>↓ <em>Relative</em> abundance 8 CAZymes&nbsp;(Wastyk, H. C. et al., <em>Cell</em>, 2021)</p><ul><li><p><em>(3)</em> starch-degrading and <em>(5)</em> plant degrading</p></li></ul><p><br/></p><p><strong><mark>🔗</mark><em><mark> Link &amp; Further Study</mark></em></strong>: A recent study of a rural Indian population in Manipur –a self-declared fermented-foods eating population (consuming mostly fermented soybeans and milk)– have gut microbiomes extremely abundant in <em>Prevotella</em>. <em>Prevotella</em> shows, amongst all Bacteroidota (in the phylum), the lowest potential to produce CAZymes and short-chain fatty acids (SCFAs) in the gut (Jeyaram, K. et al., <em>Nat Commun</em>, 2025). Thus, consuming a high-fermented-food diet may have increased <em>Prevotella</em> in the gut of participants. Further investigation is required to asses the existence of a correlation or causation.<br></p>]]></description>
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         <pubDate>2025-03-23 17:07:26 UTC</pubDate>
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         <title>🩹 Fermented-food intake decreases markers of inflammation </title>
         <author>rubyschen04</author>
         <link>https://padlet.com/rubyschen04/cf788r5xlk1rlsom/wish/3378206896</link>
         <description><![CDATA[<p><strong>↑</strong> Cytokine levels at a steady state → low-grade inflammation (across the body)</p><p><br/></p><p>Cytokine profiling → ↓ in <strong>19/93 cytokines</strong></p><ul><li><p>Longitudinal decreases in pro-inflammatory cytokines, such as IL-6,&nbsp; CXCL10,&nbsp; IL-18, etc.</p></li></ul><p>(Wastyk, H. C. et al., <em>Cell</em>, 2021)</p>]]></description>
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         <pubDate>2025-03-23 17:32:13 UTC</pubDate>
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         <title>What about the Gut-Brain Axis? 🧠 </title>
         <author>rubyschen04</author>
         <link>https://padlet.com/rubyschen04/cf788r5xlk1rlsom/wish/3378211432</link>
         <description><![CDATA[<p>These <strong>inflammatory species</strong> (e.g. IL-6, CXCL10, etc.) are often observed as byproducts of M1 microglia, the “<em>immune cells of the brain</em>”. M1 over-activation can lead to <strong>neurodegeneration</strong>, and <strong>neuroinflammation</strong> (Alan, S. M. &amp; Rothwell, N. J., <em>Nat Rev Neurosci</em>, 2001).  </p><p><br/></p><p><mark>🔍 </mark><strong><em><mark>Link &amp; Hypothesis</mark></em></strong>: Fermented foods may have a neuroprotective effect, by way of immune system modulation. Further supported by a moderately-well established relationship in the literature; a fermented-food diet leads to an increase in brain-derived neurotropic factor (BDNF; enhancing neuronal health and differentiation) and a decrease in cognitive decline symptoms and inflammation (Porras-García, E. et al., <em>Front Nutr</em>, 2023). </p>]]></description>
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         <pubDate>2025-03-23 17:39:11 UTC</pubDate>
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         <title>🛡️ Changes in Immune Cell Abundance and Signalling </title>
         <author>rubyschen04</author>
         <link>https://padlet.com/rubyschen04/cf788r5xlk1rlsom/wish/3378212357</link>
         <description><![CDATA[<ul><li><p>↓ Decrease in overall endogenous signalling</p></li><li><p>↑ Effector memory CD4+ cell abundance</p></li><li><p>NO change in signalling capacity of immune cells (CD4+, CD8+, and B cells) in both arms.</p></li></ul><p>(Wastyk, H. C. et al., <em>Cell</em>, 2021)</p>]]></description>
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         <pubDate>2025-03-23 17:41:06 UTC</pubDate>
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         <title>Let&#39;s Discuss → Fiber Arm Results!</title>
         <author>gabriella505kim</author>
         <link>https://padlet.com/rubyschen04/cf788r5xlk1rlsom/wish/3378247813</link>
         <description><![CDATA[]]></description>
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         <pubDate>2025-03-23 18:48:41 UTC</pubDate>
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         <title>References Continued:</title>
         <author>ashleyhnwai</author>
         <link>https://padlet.com/rubyschen04/cf788r5xlk1rlsom/wish/3378265390</link>
         <description><![CDATA[<ol start="24"><li><p>Porras-García, E., de, I., Juan Gavala González, &amp; José Carlos Fernández‐García. (2023). Potential neuroprotective effects of fermented foods and beverages in old age: a systematic review. <em>Frontiers in Nutrition</em>, <em>10</em>. <a rel="noopener noreferrer nofollow" href="https://doi.org/10.3389/fnut.2023.1170841">https://doi.org/10.3389/fnut.2023.1170841</a></p></li><li><p>Rinninella, E., Tohumcu, E., Raoul, P., Fiorani, M., Cintoni, M., Mele, M. C., Cammarota, G., Gasbarrini, A., &amp; Ianiro, G. (2023). The role of diet in shaping human gut microbiota. <em>Best practice &amp; research. Clinical gastroenterology</em>, <em>62-63</em>, 101828.<a rel="noopener noreferrer nofollow" href="https://doi.org/10.1016/j.bpg.2023.101828"> https://doi.org/10.1016/j.bpg.2023.101828</a></p></li><li><p>Ruiz-Ojeda, F. J., Plaza-Díaz, J., Sáez-Lara, M. J., &amp; Gil, A. (2019). Effects of Sweeteners on the Gut Microbiota: A Review of Experimental Studies and Clinical Trials. <em>Advances in nutrition (Bethesda, Md.)</em>, <em>10</em>(suppl_1), S31–S48.<a rel="noopener noreferrer nofollow" href="https://doi.org/10.1093/advances/nmy037"> https://doi.org/10.1093/advances/nmy037</a></p></li><li><p>Rossio, J. L. (1999). Cytokines and Nutritional Status: Possible Correlations and Investigations. In<a rel="noopener noreferrer nofollow" href="http://www.ncbi.nlm.nih.gov"> </a><a rel="noopener noreferrer nofollow" href="https://www.ncbi.nlm.nih.gov/books/NBK230989/">https://www.ncbi.nlm.nih.gov/books/NBK230989/</a>. National Academies Press (US).</p></li><li><p>Severino, A., Tohumcu, E., Tamai, L., Dargenio, P., Porcari, S., Rondinella, D., Venturini, I., Maida, M., Gasbarrini, A., Cammarota, G., &amp; Ianiro, G. (2024). The microbiome-driven impact of western diet in the development of noncommunicable chronic disorders. <em>Best practice &amp; research. Clinical gastroenterology</em>, <em>72</em>, 101923.<a rel="noopener noreferrer nofollow" href="https://doi.org/10.1016/j.bpg.2024.101923"> https://doi.org/10.1016/j.bpg.2024.101923</a></p></li><li><p>Sidhu, S. R. K., Kok, C. W., Kunasegaran, T., &amp; Ramadas, A. (2023). Effect of Plant-Based Diets on Gut Microbiota: A Systematic Review of Interventional Studies. <em>Nutrients</em>, <em>15</em>(6), 1510.</p></li><li><p>Sonnenburg, E. D., Smits, S. A., Tikhonov, M., Higginbottom, S. K., Wingreen, N. S., &amp; Sonnenburg, J. L. (2016). Diet-induced extinctions in the gut microbiota compound over generations. <em>Nature, 529</em>(7585), 212–215.<a rel="noopener noreferrer nofollow" href="https://doi.org/10.1038/nature16504"> https://doi.org/10.1038/nature16504</a></p></li><li><p>So, D., Whelan, K., Rossi, M., Morrison, M., Holtmann, G., Kelly, J. T., Shanahan, E. R., Staudacher, H. M., &amp; Campbell, K. L. (2018). Dietary fiber intervention on gut microbiota composition in healthy adults: A systematic review and meta-analysis. <em>The American Journal of Clinical Nutrition, 107</em>(6), 965–983.<a rel="noopener noreferrer nofollow" href="https://doi.org/10.1093/ajcn/nqy041"> https://doi.org/10.1093/ajcn/nqy041</a></p></li><li><p>Statovci, D., Aguilera, M., MacSharry, J., &amp; Melgar, S. (2017). The Impact of Western Diet and Nutrients on the Microbiota and Immune Response at Mucosal Interfaces. <em>Frontiers in immunology</em>, <em>8</em>, 838.<a rel="noopener noreferrer nofollow" href="https://doi.org/10.3389/fimmu.2017.00838"> https://doi.org/10.3389/fimmu.2017.00838</a></p></li><li><p>Stiemsma, L. T., Nakamura, R. E., Nguyen, J. G., &amp; Michels, K. B. (2020). Does Consumption of Fermented Foods Modify the Human Gut Microbiota? <em>The Journal of Nutrition</em>, <em>150</em>(7).<a rel="noopener noreferrer nofollow" href="https://doi.org/10.1093/jn/nxaa077"> https://doi.org/10.1093/jn/nxaa077</a></p></li><li><p>Taormina, V. M., Unger, A. L., Schiksnis, M. R., Torres-Gonzalez, M., &amp; Kraft, J. (2020). Branched-chain fatty acids: An underexplored class of dairy-derived fatty acids. <em>Nutrients, 12</em>(9), 2875.<a rel="noopener noreferrer nofollow" href="https://doi.org/10.3390/nu12092875"> https://doi.org/10.3390/nu12092875</a></p></li><li><p>Unno, T., Choi, J.-H., Hur, H.-G., Sadowsky, M. J., Ahn, Y.-T., Huh, C.-S., Kim, G.-B., &amp; Cha, C.-J. (2015). Changes in human gut microbiota influenced by probiotic fermented milk ingestion. <em>Journal of Dairy Science</em>, <em>98</em>(6), 3568–3576.<a rel="noopener noreferrer nofollow" href="https://doi.org/10.3168/jds.2014-8943"> https://doi.org/10.3168/jds.2014-8943</a></p></li><li><p>Valentino, V., Magliulo, R., Farsi, D., Cotter, P. D., O'Sullivan, O., Ercolini, D., &amp; De Filippis, F. (2024). Fermented foods, their microbiome and its potential in boosting human health. <em>Microbial biotechnology</em>, <em>17</em>(2), e14428.<a rel="noopener noreferrer nofollow" href="https://doi.org/10.1111/1751-7915.14428"> https://doi.org/10.1111/1751-7915.14428</a></p></li><li><p>Wastyk H. C., Fragiadakis G. K., Perelman D., et al. Gut-microbiota-targeted diets modulate human immune status. (2021). <em>Cell.</em> 2021;184(16):4137–4153. doi:10.1016/j.cell.2021.06.019</p></li><li><p>Wen, L., &amp; Duffy, A. (2017). Factors Influencing the Gut Microbiota, Inflammation, and Type 2 Diabetes. <em>The Journal of Nutrition</em>, <em>147</em>(7), 1468S1475S.<a rel="noopener noreferrer nofollow" href="https://doi.org/10.3945/jn.116.240754"> https://doi.org/10.3945/jn.116.240754</a></p></li><li><p>Valles-Colomer, M., Falony, G., Darzi, Y., Tigchelaar, E. F., Wang, J., Tito, R. Y., Schiweck, C., Kurilshikov, A., Joossens, M., Wijmenga, C., Claes, S., Van Oudenhove, L., Zhernakova, A., Vieira-Silva, S., &amp; Raes, J. (2019). The neuroactive potential of the human gut microbiota in quality of life and depression. <em>Nature Microbiology, 4</em>(4), 623–632. <a rel="noopener noreferrer nofollow" href="https://doi.org/10.1038/s41564-018-0337-x">https://doi.org/10.1038/s41564-018-0337-x </a></p></li><li><p>Zhao, J., Cheng, W., Lu, H., Shan, A., Zhang, Q., Sun, X., Kang, L., Xie, J., &amp; Xu, B. (2022). High fiber diet attenuate the inflammation and adverse remodeling of myocardial infarction <em>via</em> modulation of gut microbiota and metabolites. <em>Frontiers in microbiology</em>, <em>13</em>, 1046912.<a rel="noopener noreferrer nofollow" href="https://doi.org/10.3389/fmicb.2022.1046912"> https://doi.org/10.3389/fmicb.2022.1046912</a></p><p><br/></p></li></ol>]]></description>
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         <pubDate>2025-03-23 19:23:57 UTC</pubDate>
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      <item>
         <title>A Shift in Metabolic Output</title>
         <author>gabriella505kim</author>
         <link>https://padlet.com/rubyschen04/cf788r5xlk1rlsom/wish/3378268963</link>
         <description><![CDATA[<p><strong>Researchers measured </strong>→ fecal short-chain fatty acids (SCFAs)</p><p><br/></p><p><strong>Found mixed results </strong>→ </p><ul><li><p><mark>Butyrate levels did not increase</mark> ❌</p></li><li><p><mark>Three BCFAs decreased</mark> ✅</p><ul><li><p><em>Isobuytric and isovaleric acid</em> </p><ul><li><p>Previously associated with hypercholesterolemia (Granado-Serrano, A., et al., <em>Scientific Reports, </em>2019) </p></li></ul></li><li><p><em>Valeric acid</em></p><ul><li><p>Previously associated with autism spectrum disorder (Liu, S., et al., <em>Scientific Reports, </em>2019)</p></li></ul></li></ul></li></ul><p><br/></p><p>📚<strong> Previous studies</strong> on dietary fiber interventions have often reported increases in butyrate. For instance, one study observed elevated fecal butyrate levels following fiber consumption (So, D., et al., <em>American Journal of Clinical Nutrition, 2018)</em>. This was not consistent with the current study. </p><p><br/></p><p>📚<strong> Previous studies</strong> also have also linked dairy as sources of BCFAs (Taormina, V., et al., <em>Nutrients, </em>2020). </p><p><br/></p><p>🔍<strong> Note</strong> → As participants reported a decrease in animal protein consumption, its possible the observed decrease in BCFAs can be due to this dietary change. </p><p><br/></p><p><strong>∴ <mark>Metabolic output shifted</mark></strong>, but results were mixed. </p>]]></description>
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         <pubDate>2025-03-23 19:31:47 UTC</pubDate>
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         <title>Did Participants Bite More Than They Could Chew?</title>
         <author>gabriella505kim</author>
         <link>https://padlet.com/rubyschen04/cf788r5xlk1rlsom/wish/3378277426</link>
         <description><![CDATA[<p><strong>Researchers questioned</strong> → why there wasn't a larger microbiota response to the fiber 🤔</p><p><br/></p><p><strong>Hypothesized</strong> → fiber intake exceeded the microbiome's fermentation capabilities </p><p><br/></p><p><strong>Method</strong> → analyzed stool carbohydrates using HP - LC</p><p><br/></p><p><strong>Results </strong>→ <mark>positive correlation found between fiber intake and stool carbohydrate levels</mark> ✅</p><p><br/></p><p><strong>📚 Previous literature </strong>also suggests when fiber intake is increased rapidly or in large amounts, the microbiome may not have the enzymatic capabilities to ferment all of it, possibly leading to digestive symptoms, such as bloating and diarrhea (Ionita-Mindrican, C., et al., <em>Nutrients, </em>2022). As stool carbohydrates increased as fiber intake increased, this was consistent with the study's findings. </p><p><br/></p><p><strong>∴ </strong>Participants' microbiomes were <strong><mark>unable to fully break down the increased fiber</mark></strong>. </p>]]></description>
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         <pubDate>2025-03-23 19:49:00 UTC</pubDate>
         <guid>https://padlet.com/rubyschen04/cf788r5xlk1rlsom/wish/3378277426</guid>
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         <title>Three Distinct Immune Response Groups</title>
         <author>gabriella505kim</author>
         <link>https://padlet.com/rubyschen04/cf788r5xlk1rlsom/wish/3378298721</link>
         <description><![CDATA[<p><strong>Researchers used</strong> → </p><ul><li><p>O-link (multiplex proteomic platform) to measure circulating cytokines</p></li><li><p>CyTOF (single-cell mass cytometry) to measure cell frequency &amp; endogenous signalling</p></li><li><p>Flow cytometry to evaluate signalling capacity</p></li></ul><p><br/></p><p><strong>Participants grouped based on changes in steady-state immune system activation </strong>→ </p><ol><li><p><mark>High inflammation group</mark></p></li><li><p><mark>Low inflammation group I</mark></p></li><li><p><mark>Low inflammation group II</mark></p></li></ol><p><br/></p><p>🔍 <strong>Note</strong> → Variation in fiber subtypes consumed may have contributed to differences in immune responses. </p><p><br/></p><p>∴ Researchers identified <strong><mark>three distinct immune response groups</mark></strong>, suggesting participants differed in how their immune system reacted to the high fiber intervention. </p>]]></description>
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         <pubDate>2025-03-23 20:33:01 UTC</pubDate>
         <guid>https://padlet.com/rubyschen04/cf788r5xlk1rlsom/wish/3378298721</guid>
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         <title>Did Alpha Diversity Differ Between The Groups 🤔</title>
         <author>gabriella505kim</author>
         <link>https://padlet.com/rubyschen04/cf788r5xlk1rlsom/wish/3378298827</link>
         <description><![CDATA[<p><strong>Researchers measured </strong>→ ASVs across the three inflammation groups at baseline ⚖️</p><p><br/></p><p><strong>Found</strong> → </p><ul><li><p><mark>No significant difference between high inflammation and low inflammation I groups</mark> ❌</p></li><li><p><mark>Low inflammation II showed significantly higher alpha diversity</mark> ✅</p></li></ul><p><br/></p><p><strong>∴ </strong>The <strong><mark>low inflammation group II had significantly higher alpha diversity</mark></strong> as baseline, suggesting it may be associated with a more regulated or less inflammatory immune response profile. </p>]]></description>
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         <pubDate>2025-03-23 20:33:16 UTC</pubDate>
         <guid>https://padlet.com/rubyschen04/cf788r5xlk1rlsom/wish/3378298827</guid>
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         <title>🎯Background Continued: Hm, What Is It that We WANT?</title>
         <author>ashleyhnwai</author>
         <link>https://padlet.com/rubyschen04/cf788r5xlk1rlsom/wish/3378335872</link>
         <description><![CDATA[<p>Knowing this, the hope is for the <strong>identification of dietary strategies</strong> that can <em>restore or enhance interactions</em> between the <em>microbiota &amp; host</em> for improved outcomes in health.</p><p>→ Like, <strong>therapeutic strategies combatting pathogenesis </strong>(Wastyk, H. C. et al., <em>Cell</em>, 2021)!</p>]]></description>
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         <pubDate>2025-03-23 21:49:01 UTC</pubDate>
         <guid>https://padlet.com/rubyschen04/cf788r5xlk1rlsom/wish/3378335872</guid>
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         <title>What About Microbiota Composition 🤔</title>
         <author>gabriella505kim</author>
         <link>https://padlet.com/rubyschen04/cf788r5xlk1rlsom/wish/3378338791</link>
         <description><![CDATA[<p><strong>Researchers found </strong>→ </p><ul><li><p><em><mark>Coprococcus</mark></em><mark>, </mark><em><mark>Ruminococcus</mark></em><mark>, </mark><em><mark>Oscillospira</mark></em><mark>, and </mark><em><mark>Anaerostipes</mark></em><mark> were more prevalent in low inflammation groups</mark></p><ul><li><p>These taxa have previously been linked to higher quality of life, better metabolic health, and increased butyrate production (Valles-Colomer, M., et al., <em>Nature Microbiology, </em>2019; Klimenko, N., et al., <em>Nutrients, </em>2018; Chen, Y., et al., <em>Scientific Reports, </em>2020; Li, <em>Butyrate: Food Sources, Functions and Health Benefits, </em>2014).</p></li></ul></li><li><p><em><mark>Akkermansia</mark></em><mark> was more abundant in the high inflammation group</mark></p><ul><li><p>Previously been positively associated with metabolic health (Derrien, M., et al., <em>Microbial Pathogenesis, </em>2017)</p></li></ul></li></ul><p><br/></p><p><strong>📚 Previous literature </strong>investigating fiber rich diets have also reported similar taxa. For example, a recent study examining fiber rich snacks made from peas and oranges observed a significant increase of Lachnospiraceae and Ruminococcus (Delannoy-Bruno, O., et al., <em>Proc Natl Acad Sci USA, </em>2022). </p><p><br/></p><p><strong>∴ <mark>Low inflammation groups were enriched in beneficial taxa</mark></strong> linked to gut health and butyrate production, while <strong><mark>high inflammation participants a different microbial profile</mark></strong>. This suggests that people can respond differently to fiber depending on their individual microbiota.</p>]]></description>
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         <pubDate>2025-03-23 21:55:13 UTC</pubDate>
         <guid>https://padlet.com/rubyschen04/cf788r5xlk1rlsom/wish/3378338791</guid>
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