Microbial Genomics · 2022
Finding the right fit: evaluation of short-read and long-read sequencing approaches to maximize the utility of clinical microbiome data
Gehrig et al.
The evidence base
The research behind every report.
Every GutID report is interpreted against published literature. This is that literature in full, with a short note on what each paper covers and what kind of study it is, so you can judge how much weight it carries.
Nutrients · 2020
The Firmicutes/Bacteroidetes ratio: a relevant marker of gut dysbiosis in obese patients?
Magne et al.
Circulation Research · 2021
The gut microbiome in hypertension
Avery et al.
94 papers cited in the back of every report
30+ peer-reviewed publications using the long-read approach behind Titan-1
Papers cited in every report
2023
Mechanism
Role of the Gut Microbiome in the Development of Atherosclerotic Cardiovascular Disease
Ahmad Al Samarraie et al. · International Journal of Molecular Sciences, 24(6), 5420-5420
Reviews the gut microbiome’s proposed role in atherosclerotic cardiovascular disease. Gut–heart axis.
Read the paper (opens in a new tab) ↗2021
Mechanism
The Gut Microbiome in Hypertension
Avery et al. · Circulation Research, 128(7), 934-950
Review of the gut microbiome in high blood pressure. Gut–heart axis.
Read the paper (opens in a new tab) ↗2023
Mechanism
The Long-Term Effects of a Low–Fermentable Oligosaccharides, Disaccharides, Monosaccharides, and Polyols Diet for Irritable Bowel Syndrome Management
Bardacke et al. · Current Developments in Nutrition, 7(10), 101997
Examines longer-term outcomes of the low-FODMAP diet in IBS management.
Read the paper (opens in a new tab) ↗2022
Mechanism
Type 2 Diabetes and the Microbiome
Barlow & Mathur · Journal of the Endocrine Society, 7(2), bvac184
Review of the microbiome in type 2 diabetes. Gut–metabolism axis.
Read the paper (opens in a new tab) ↗2019
Mechanism
Short-Chain Fatty Acid Propionate Protects From Hypertensive Cardiovascular Damage
Bartolomaeus et al. · Circulation, 139(11), 1407-1421
Experimental study of the short-chain fatty acid propionate in hypertensive cardiovascular damage.
Read the paper (opens in a new tab) ↗2023
Mechanism
Deciphering psychobiotics’ mechanism of action: bacterial extracellular vesicles in the spotlight
Bleibel et al. · Frontiers in Microbiology, 14
Reviews how psychobiotics might act, focusing on bacterial extracellular vesicles. Gut–brain axis.
Read the paper (opens in a new tab) ↗2022
Mechanism
Trimethylamine N-oxide reduction is related to probiotic strain specificity: A systematic review
Cantero et al. · Nutrition Research, 104, 29-35
Systematic review of TMAO and probiotic strain specificity, relevant to how TMAO is reported.
Read the paper (opens in a new tab) ↗2016
Mechanism
Interplay between bile acid metabolism and microbiota in irritable bowel syndrome
Dior et al. · Neurogastroenterology and Motility, 28(9), 1330-1340
Studies bile acid metabolism alongside gut bacteria in IBS.
Read the paper (opens in a new tab) ↗2020
Mechanism
Bifidobacterium adolescentis as a key member of the human gut microbiota in the production of GABA
Duranti et al. · Scientific Reports, 10
Examines a named organism’s part in GABA production. Underpins how neurotransmitter-related organisms are read.
Read the paper (opens in a new tab) ↗2023
Mechanism
The dietary source of trimethylamine N-oxide and clinical outcomes: an unexpected liaison
Evans et al. · Ndt Plus, 16(11), 1804-1812
Looks at where dietary TMAO comes from and how it relates to clinical outcomes.
Read the paper (opens in a new tab) ↗2022
Mechanism
Finding the right fit: evaluation of short-read and long-read sequencing approaches to maximize the utility of clinical microbiome data
Gehrig et al. · Microbial Genomics, 8(3)
Independent comparison of short-read and long-read sequencing for clinical microbiome work. This is the paper the Titan-1 comparison table draws on.
Read the paper (opens in a new tab) ↗2023
Mechanism
Microbiota from Alzheimer’s patients induce deficits in cognition and hippocampal neurogenesis
Grabrucker et al. · Brain, 146(12)
Transfer study testing whether microbiota from Alzheimer’s patients affect cognition in animals. Gut–brain axis.
Read the paper (opens in a new tab) ↗2022
Mechanism
Role of Microbiota-Gut-Brain Axis in Regulating Dopaminergic Signaling
Hamamah et al. · Biomedicines, 10(2), 436
Reviews the gut–brain axis in dopamine signaling.
Read the paper (opens in a new tab) ↗2014
Mechanism
Expert consensus document. The International Scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic
Hill et al. · Nature Reviews Gastroenterology & Hepatology, 11(8), 506-514
The ISAPP consensus definition of "probiotic". This is the definition the report uses.
Read the paper (opens in a new tab) ↗2022
Mechanism
B Vitamins and Their Roles in Gut Health
Hossain et al. · Microorganisms, 10(6), 1168
Reviews B vitamins in gut health, including bacterial synthesis.
Read the paper (opens in a new tab) ↗2021
Mechanism
Associations of healthy food choices with gut microbiota profiles
Koponen et al. · The American Journal of Clinical Nutrition, 114(2), 605-616
Population study relating healthy food choices to gut community profiles.
Read the paper (opens in a new tab) ↗2019
Mechanism
Optimizing microbiome sequencing for small intestinal aspirates: validation of novel techniques through the REIMAGINE study
Leite et al. · BMC Microbiology, 19(1)
Methods work on sequencing small intestinal aspirates, relevant to what stool can and cannot show about the small intestine.
Read the paper (opens in a new tab) ↗2019
Mechanism
Effects of regulating gut microbiota on the serotonin metabolism in the chronic unpredictable mild stress rat model
Li et al. · Neurogastroenterology and Motility, 31(10), e13677
Rat model study of gut bacteria and serotonin metabolism under chronic stress. Gut–brain axis.
Read the paper (opens in a new tab) ↗2023
Mechanism
Gut Barrier Dysfunction and Bacterial Lipopolysaccharides in Colorectal Cancer
Li et al. · Journal of Gastrointestinal Surgery, 27(7), 1466-1472
Examines barrier dysfunction and bacterial LPS in colorectal cancer. Background to how barrier and LPS-bearing organisms are reported.
Read the paper (opens in a new tab) ↗2021
Mechanism
New Insights Into Gut-Bacteria-Derived Indole and Its Derivatives in Intestinal and Liver Diseases
Li et al. · Frontiers in Pharmacology, 12
Reviews bacterially produced indole compounds in intestinal and liver disease.
Read the paper (opens in a new tab) ↗2022
Mechanism
Gut bacterial profiles in Parkinson’s disease: A systematic review
Li et al. · CNS Neuroscience & Therapeutics, 28(9), 1359-1372
Systematic review of gut bacterial profiles reported in Parkinson’s disease.
Read the paper (opens in a new tab) ↗2020
Mechanism
Potential Bidirectional Relationship Between Periodontitis and Alzheimer’s Disease
Liccardo et al. · Frontiers in Physiology, 11(11)
Reviews a possible two-way link between gum disease and Alzheimer’s, context for oral-origin organisms found in the gut.
Read the paper (opens in a new tab) ↗2020
Mechanism
Trimethylamine N-Oxide Generated by the Gut Microbiota Is Associated with Vascular Inflammation: New Insights into Atherosclerosis
Liu & Dai · Mediators of Inflammation, 2020, 1-15
Reviews bacterially generated TMAO in relation to vascular inflammation.
Read the paper (opens in a new tab) ↗2020
Mechanism
The Firmicutes/Bacteroidetes Ratio: A Relevant Marker of Gut Dysbiosis in Obese Patients?
Magne et al. · Nutrients, 12(5), 1474
Questions how much weight the F/B ratio should carry as a dysbiosis marker. Directly relevant to how the report presents that ratio.
Read the paper (opens in a new tab) ↗2019
Mechanism
Discovery and inhibition of an interspecies gut bacterial pathway for Levodopa metabolism
Maini Rekdal et al. · Science, 364(6445), eaau6323
Identifies a gut bacterial pathway that metabolizes levodopa, a worked example of bacteria altering a drug.
Read the paper (opens in a new tab) ↗2013
Mechanism
Role of commensal and probiotic bacteria in human health: a focus on inflammatory bowel disease
Martín et al. · Microbial Cell Factories, 12(1), 71
Reviews commensal and probiotic organisms in health, focused on IBD.
Read the paper (opens in a new tab) ↗2023
Mechanism
The Intestinal and Skin Microbiome in Patients with Atopic Dermatitis and Their Influence on the Course of the Disease: A Literature Review
Mazur et al. · Healthcare, 11(5), 766
Literature review covering both gut and skin communities in atopic dermatitis. Gut–immune axis and skin.
Read the paper (opens in a new tab) ↗2017
Mechanism
Neurotransmitters: The Critical Modulators Regulating Gut-Brain Axis
Mittal et al. · Journal of Cellular Physiology, 232(9), 2359-2372
Reviews neurotransmitters as the mediators of the gut–brain axis.
Read the paper (opens in a new tab) ↗2022
Mechanism
Gamma aminobutyric acid production by commercially available probiotic strains
Monteagudo-Mera et al. · Journal of Applied Microbiology, 134(2)
Tests GABA production across commercially available probiotic strains, relevant when a specific supplement is being considered.
Read the paper (opens in a new tab) ↗2021
Mechanism
Probiotics for Alzheimer’s Disease: A Systematic Review
Naomi et al. · Nutrients, 14(1), 20
Systematic review of probiotic studies in Alzheimer’s disease.
Read the paper (opens in a new tab) ↗2023
Mechanism
The Low-FODMAP Diet, IBS, and BCFAs: Exploring the Positive, Negative, and Less Desirable Aspects—A Literature Review
Nikolaki et al. · Microorganisms, 11(10), 2387-2387
Reviews the low-FODMAP diet in IBS including its drawbacks, useful when a report suggests it.
Read the paper (opens in a new tab) ↗2023
Mechanism
The gut microbiome and hypertension
O’Donnell et al. · Nature Reviews Nephrology, 19
Review of the gut microbiome in hypertension. Gut–heart axis.
Read the paper (opens in a new tab) ↗2023
Mechanism
Natural Product Co-Metabolism and the Microbiota–Gut–Brain Axis in Age-Related Diseases
Obrenovich et al. · Life, 13(1), 41
Reviews host–bacteria co-metabolism of natural products along the gut–brain axis in aging.
Read the paper (opens in a new tab) ↗2021
Mechanism
Glutamate and depression: Reflecting a deepening knowledge of the gut and brain effects of a ubiquitous molecule
Onaolapo & Onaolapo · World Journal of Psychiatry, 11(7), 297-315
Reviews glutamate across gut and brain in depression.
Read the paper (opens in a new tab) ↗2022
Mechanism
Medicinal Plants and Their Impact on the Gut Microbiome in Mental Health: A Systematic Review
Pferschy-Wenzig et al. · Nutrients, 14(10), 2111
Systematic review of medicinal plants, the gut community and mental health.
Read the paper (opens in a new tab) ↗2020
Mechanism
ACG Clinical Guideline
Pimentel et al. · The American Journal of Gastroenterology, 115(2), 165-178
American College of Gastroenterology clinical guideline on small intestinal bacterial overgrowth. A guideline, not a study.
Read the paper (opens in a new tab) ↗2022
Mechanism
The Gut Microbiota in Inflammatory Bowel Disease
Qiu et al. · Frontiers in Cellular and Infection Microbiology, 12, 733992
Review of the gut community in inflammatory bowel disease.
Read the paper (opens in a new tab) ↗2021
Mechanism
Meta-analysis of the Parkinson’s disease gut microbiome suggests alterations linked to intestinal inflammation
Romano et al. · npj Parkinson’s Disease, 7(1)
Meta-analysis pooling gut microbiome datasets in Parkinson’s disease.
Read the paper (opens in a new tab) ↗2022
Mechanism
The dietary treatment of histamine intolerance reduces the abundance of some histamine-secreting bacteria of the gut microbiota in histamine intolerant women: A pilot study
Sánchez-Pérez et al. · Frontiers in Nutrition, 9
Pilot study of a low-histamine diet and histamine-secreting gut bacteria. Small, and described as a pilot.
Read the paper (opens in a new tab) ↗2022
Mechanism
Gut microbiota and obesity: New insights
Sarmiento-Andrade et al. · Frontiers in Nutrition, 9
Review of the gut community in obesity. Gut–metabolism axis.
Read the paper (opens in a new tab) ↗2022
Mechanism
Probiotics in Irritable Bowel Syndrome: a Review of Their Therapeutic Role
Satish Kumar et al. · Cureus, 14(4)
Reviews the therapeutic role studied for probiotics in IBS.
Read the paper (opens in a new tab) ↗2023
Mechanism
Desulfovibrio in the Gut: The Enemy within?
Singh et al. · Microorganisms, 11(7), 1772
Reviews the genus Desulfovibrio and the case for and against treating it as harmful.
Read the paper (opens in a new tab) ↗2018
Mechanism
Neurotransmitter modulation by the gut microbiota
Strandwitz · Brain Research, 1693(Pt B), 128-133
Reviews how gut bacteria produce and modulate neurotransmitters. Foundational for the gut–brain section.
Read the paper (opens in a new tab) ↗2022
Mechanism
The Potential Role of Gut Microbiota in Alzheimer’s Disease: From Diagnosis to Treatment
Varesi et al. · Nutrients, 14(3), 668
Reviews the gut community in Alzheimer’s disease across diagnosis and treatment.
Read the paper (opens in a new tab) ↗2018
Mechanism
Bile Acid Deficiency in a Subgroup of Patients With Irritable Bowel Syndrome With Constipation Based on Biomarkers in Serum and Fecal Samples
Vijayvargiya et al. · Clinical Gastroenterology and Hepatology, 16(4), 522-527
Identifies a bile-acid-deficient subgroup within constipation-predominant IBS.
Read the paper (opens in a new tab) ↗2022
Mechanism
Metagenomics of Parkinson’s disease implicates the gut microbiome in multiple disease mechanisms
Wallen et al. · Nature Communications, 13(1)
Large metagenomic study of the gut microbiome in Parkinson’s disease.
Read the paper (opens in a new tab) ↗2021
Mechanism
Lactobacillus lactis and Pediococcus pentosaceus‐driven reprogramming of gut microbiome and metabolome ameliorates the progression of non‐alcoholic fatty liver disease
Yu et al. · Clinical and Translational Medicine, 11(12)
Experimental study of two named strains in non-alcoholic fatty liver disease.
Read the paper (opens in a new tab) ↗2022
Mechanism
Probiotics Bring New Hope for Atherosclerosis Prevention and Treatment
Zhai et al. · Oxidative Medicine and Cellular Longevity, 2022, 1-13
Reviews probiotics in atherosclerosis prevention and treatment.
Read the paper (opens in a new tab) ↗2023
Mechanism
Vitamin D alleviates non-alcoholic fatty liver disease via restoring gut microbiota and metabolism
Zhang et al. · Frontiers in Microbiology, 14
Experimental study of vitamin D in non-alcoholic fatty liver disease, via the gut community.
Read the paper (opens in a new tab) ↗2021
Diet
The Role of the Gut Microbiota on the Beneficial Effects of Ketogenic Diets
Attaye et al. · Nutrients, 14(1), 191
Reviews the gut microbiota’s role in how ketogenic diets act.
Read the paper (opens in a new tab) ↗2021
Diet
Effects of dietary fibers, micronutrients, and phytonutrients on gut microbiome: a review
Beane et al. · Applied Biological Chemistry, 64(1), 36
Broad review of fibers, micronutrients and phytonutrients as inputs to the gut community.
Read the paper (opens in a new tab) ↗2018
Diet
Health Effects and Sources of Prebiotic Dietary Fiber
Carlson et al. · Current Developments in Nutrition, 2(3)
Covers what counts as a prebiotic fiber, where it is found, and the health effects studied.
Read the paper (opens in a new tab) ↗2023
Diet
Effect of Non-Nutritive Sweeteners on the Gut Microbiota
Conz et al. · Nutrients, 15(8), 1869
Reviews the evidence on non-nutritive sweeteners and gut bacterial composition.
Read the paper (opens in a new tab) ↗2020
Diet
Nuts and their Effect on Gut Microbiota, Gut Function and Symptoms in Adults: A Systematic Review and Meta-Analysis of Randomised Controlled Trials
Creedon et al. · Nutrients, 12(8), 2347
Systematic review and meta-analysis of randomized trials of nut intake, covering composition, gut function and symptoms.
Read the paper (opens in a new tab) ↗2021
Diet
Dietary Fiber Modulates the Gut Microbiota
Cronin et al. · Nutrients, 13(5), 1655
Review of how dietary fiber acts on gut community composition.
Read the paper (opens in a new tab) ↗2019
Diet
Fermented Foods: Definitions and Characteristics, Impact on the Gut Microbiota and Effects on Gastrointestinal Health and Disease
Dimidi et al. · Nutrients, 11(8), 1806
Defines what fermented foods are and reviews their studied effects on the gut and GI health.
Read the paper (opens in a new tab) ↗2021
Diet
Resistant starch, microbiome, and precision modulation
Dobranowski & Stintzi · Gut Microbes, 13(1), 1926842
Reviews resistant starch as a targeted way to shift the gut community.
Read the paper (opens in a new tab) ↗2021
Diet
Nutritional Components in Western Diet Versus Mediterranean Diet at the Gut Microbiota–Immune System Interplay. Implications for Health and Disease
García-Montero et al. · Nutrients, 13(2), 699
Compares Western and Mediterranean dietary patterns at the point where the gut community meets the immune system.
Read the paper (opens in a new tab) ↗2022
Diet
The gastrointestinal and microbiome impact of a resistant starch blend from potato, banana, and apple fibers: A randomized clinical trial using smart caps
Hanes et al. · Frontiers in Nutrition, 9
Randomized clinical trial of a resistant starch blend, measuring both GI and microbiome outcomes.
Read the paper (opens in a new tab) ↗2022
Diet
Predicting Personalized Responses to Dietary Fiber Interventions: Opportunities for Modulation of the Gut Microbiome to Improve Health
Kok et al. · Annual Review of Food Science and Technology, 14, 157-182
Reviews why fiber interventions work differently in different people, and what predicts the response.
Read the paper (opens in a new tab) ↗2019
Diet
Beneficial Effects of Dietary Polyphenols on Gut Microbiota and Strategies to Improve Delivery Efficiency
Kumar Singh et al. · Nutrients, 11(9), 2216
Reviews dietary polyphenols and the gut community, including the practical problem of delivery.
Read the paper (opens in a new tab) ↗2022
Diet
Fermented Foods, Health and the Gut Microbiome
Leeuwendaal et al. · Nutrients, 14(7), 1527
Review of fermented foods in relation to the gut microbiome and health.
Read the paper (opens in a new tab) ↗2020
Diet
Fatty Acid Diets: Regulation of Gut Microbiota Composition and Obesity and Its Related Metabolic Dysbiosis
Machate et al. · International Journal of Molecular Sciences, 21(11), 4093
Reviews dietary fat composition in relation to the gut community and metabolic dysbiosis.
Read the paper (opens in a new tab) ↗2021
Diet
Effect on gut microbiota of a 1-y lifestyle intervention with Mediterranean diet compared with energy-reduced Mediterranean diet and physical activity promotion: PREDIMED-Plus Study
Muralidharan et al. · The American Journal of Clinical Nutrition, 114(3), 1148-1158
A one-year randomized lifestyle intervention comparing two Mediterranean-diet arms, with gut composition as an outcome.
Read the paper (opens in a new tab) ↗2023
Diet
Western diet influences on microbiome and carcinogenesis
Newsome et al. · Seminars in Immunology, 67, 101756
Reviews the Western dietary pattern in relation to the microbiome and cancer development.
Read the paper (opens in a new tab) ↗2021
Diet
Vitamins, the gut microbiome and gastrointestinal health in humans
Pham et al. · Nutrition Research, 95, 35-53
Reviews the two-way relationship between vitamins and the gut community in humans.
Read the paper (opens in a new tab) ↗2023
Diet
β-glucans: a potential source for maintaining gut microbiota and the immune system
Ravindra Pal Singh & Bhardwaj · Frontiers in Nutrition, 10, 1143682
Reviews β-glucans as a dietary input to the gut community and immune function.
Read the paper (opens in a new tab) ↗2022
Diet
Non-nutritive sweeteners and their impacts on the gut microbiome and host physiology
Richardson & Frese · Frontiers in Nutrition, 9, 988144
Reviews non-nutritive sweeteners across both microbiome and host physiology.
Read the paper (opens in a new tab) ↗2020
Diet
Iron Supplementation Influence on the Gut Microbiota and Probiotic Intake Effect in Iron Deficiency—A Literature-Based Review
Rusu et al. · Nutrients, 12(7), 1993
Literature review of iron supplementation, the gut community, and probiotic intake in iron deficiency.
Read the paper (opens in a new tab) ↗2020
Diet
The potential role of vitamin D supplementation as a gut microbiota modifier in healthy individuals
Singh et al. · Scientific Reports, 10, 21641
Studies vitamin D supplementation as a way of altering the gut community in healthy adults.
Read the paper (opens in a new tab) ↗2019
Diet
Sodium, hypertension, and the gut: does the gut microbiota go salty?
Smiljanec & Lennon · American Journal of Physiology. Heart and Circulatory Physiology, 317(6), H1173–H1182
Reviews dietary sodium, blood pressure and the gut community as a possible link between them.
Read the paper (opens in a new tab) ↗2018
Diet
Potential Prebiotic Properties of Nuts and Edible Seeds and Their Relationship to Obesity
Sugizaki & Naves · Nutrients, 10(11), 1645
Reviews nuts and edible seeds as potential prebiotics, and their relationship to obesity.
Read the paper (opens in a new tab) ↗2019
Diet
The Effects of Vegetarian and Vegan Diets on Gut Microbiota
Tomova et al. · Frontiers in Nutrition, 6(47)
Reviews how vegetarian and vegan dietary patterns relate to gut community composition.
Read the paper (opens in a new tab) ↗2022
Diet
Dietary Polyphenol, Gut Microbiota, and Health Benefits
Wang et al. · Antioxidants, 11(6), 1212
Reviews dietary polyphenols, their interaction with gut bacteria, and the health effects studied.
Read the paper (opens in a new tab) ↗2021
Diet
Gut-microbiota-targeted diets modulate human immune status
Wastyk et al. · Cell, 184(16), 4137–4153
A human trial comparing two gut-targeted diets, high fiber and high fermented food, with immune measures as an outcome.
Read the paper (opens in a new tab) ↗2023
Diet
Beer and Microbiota: Pathways for a Positive and Healthy Interaction
Zugravu et al. · Nutrients, 15(4), 844
Reviews beer and its non-alcoholic components in relation to the gut community.
Read the paper (opens in a new tab) ↗2019
Drugs
Proton pump inhibitors and dysbiosis: Current knowledge and aspects to be clarified
Bruno et al. · World Journal of Gastroenterology, 25(22), 2706-2719
Reviews what is established, and what is still unresolved, about proton pump inhibitors and gut bacterial composition.
Read the paper (opens in a new tab) ↗2017
Drugs
Statin therapy causes gut dysbiosis in mice through a PXR-dependent mechanism
Caparrós-Martín et al. · Microbiome, 5(1), 1-15
A mouse study investigating a PXR-dependent route by which statin therapy shifts the gut community.
Read the paper (opens in a new tab) ↗2022
Drugs
Interactions between gut microbiota and berberine, a necessary procedure to understand the mechanisms of berberine
Cheng et al. · Journal of Pharmaceutical Analysis, 12(4), 541-555
Examines how berberine and gut bacteria act on each other, as groundwork for understanding how the compound works.
Read the paper (opens in a new tab) ↗2020
Drugs
Gut bacterial microbiome composition and statin intake—A systematic review
Dias et al. · Pharmacology Research & Perspectives, 8(3), e00601
Systematic review of studies comparing gut bacterial composition in people taking statins.
Read the paper (opens in a new tab) ↗2022
Drugs
Effect of Fructooligosaccharides Supplementation on the Gut Microbiota in Humans: A Systematic Review and Meta-Analysis
Dou et al. · Nutrients, 14(16), 3298
Systematic review and meta-analysis of human trials of fructooligosaccharide (FOS) supplementation.
Read the paper (opens in a new tab) ↗2022
Drugs
Metformin Influence on the Intestinal Microbiota and Organism of Rats with Metabolic Syndrome
Ermolenko et al. · International Journal of Molecular Sciences, 23(12), 6837
Rat study of metformin’s effect on the intestinal microbiota in metabolic syndrome.
Read the paper (opens in a new tab) ↗2020
Drugs
RapidAIM: A culture-and metaproteomics-based Rapid Assay of Individual Microbiome responses to drugs
Li et al. · Microbiome, 8(1), 1-16
Describes an assay for testing how one individual’s microbiome responds to particular drugs.
Read the paper (opens in a new tab) ↗2023
Drugs
Fructooligosaccharides (FOS) differentially modify the in vitro gut microbiota in an age-dependent manner
Mahalak et al. · Frontiers in Nutrition, 9, 3212
In vitro work examining whether FOS affects the gut community differently across age groups.
Read the paper (opens in a new tab) ↗2021
Drugs
Review of Rifaximin: A Summary of the Current Evidence and Benefits Beyond Licensed Use
Nathwani et al. · EMJ, 6(3), 94-99
Summary of the evidence for rifaximin, including uses beyond its licensed indications.
Read the paper (opens in a new tab) ↗2019
Drugs
A systematic review of the use of rifaximin for Clostridium difficile infections
Ng et al. · Anaerobe, 55, 35-39
Systematic review of rifaximin used against Clostridium difficile infection.
Read the paper (opens in a new tab) ↗2010
Drugs
Metronidazole effects on microbiota and mucus layer thickness in the rat gut
Pélissier et al. · FEMS Microbiology Ecology, 73(3), 601-610
Rat study of how metronidazole affects gut bacteria and the thickness of the protective mucus layer.
Read the paper (opens in a new tab) ↗2017
Drugs
Eubiotic properties of rifaximin: Disruption of the traditional concepts in gut microbiota modulation
Ponziani et al. · World Journal of Gastroenterology, 23(25), 4491–4499
Argues rifaximin should be understood as modulating the gut community rather than suppressing it.
Read the paper (opens in a new tab) ↗2021
Drugs
Metformin strongly affects gut microbiome composition in high-fat diet-induced type 2 diabetes mouse model of both sexes
Silamiķele et al. · Frontiers in Endocrinology, 12, 626359
Mouse study of metformin and gut composition in type 2 diabetes, analyzed separately by sex.
Read the paper (opens in a new tab) ↗2021
Drugs
Serotonin Reuptake Inhibitors and the Gut Microbiome: Significance of the Gut Microbiome in Relation to Mechanism of Action, Treatment Response, Side Effects, and Tachyphylaxis
Sjöstedt et al. · Frontiers in Psychiatry, 12, 682868
Reviews how SSRIs and the gut microbiome interact, and what that may mean for treatment response and side effects.
Read the paper (opens in a new tab) ↗2020
Drugs
Impact of commonly used drugs on the composition and metabolic function of the gut microbiota
Vich Vila et al. · Nature Communications, 11(1), 362
Population-scale study relating widely used medications to gut composition and metabolic function.
Read the paper (opens in a new tab) ↗2022
Drugs
Resveratrol in Intestinal Health and Disease: Focusing on Intestinal Barrier
Wang et al. · Frontiers in Nutrition, 9, 848400
Reviews resveratrol in intestinal health, with a focus on the gut barrier.
Read the paper (opens in a new tab) ↗2021
Drugs
Effects of Berberine on the Gastrointestinal Microbiota
Zhang et al. · Frontiers in Cellular and Infection Microbiology, 10, 588517
Reviews the reported effects of berberine on gastrointestinal bacteria.
Read the paper (opens in a new tab) ↗2020
Drugs
Effects of Metformin on the Gut Microbiota in Obesity and Type 2 Diabetes Mellitus
Zhang & Hu · Diabetes, Metabolic Syndrome and Obesity: Targets and Therapy, 13, 5003–5014
Reviews metformin and the gut microbiome in obesity and type 2 diabetes.
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94 papers.
These are independent, third-party publications cited in the back of the GutID report. They are not GutID research: work using the long-read approach behind Titan-1 is listed on the publications page. Each note describes what a paper covers and what kind of study it is; it is not a summary of its findings.
The platform
30+ peer-reviewed publications.
Separate from the report’s reference list: the published work using the long-read approach behind Titan-1, including how it compares with 16S-only and shotgun methods.
- Microbial Genomics
- mBio
- Scientific Reports
- PLOS ONE
- Frontiers in Microbiology
- ISME Communications
- Communications Biology
- International Journal of Molecular Sciences