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Our Scientific Foundation

 

At Biomine Health, everything we do is grounded in science. Our test is built on a decade of microbiome research, bioinformatics, and human health expertise.

 

We carefully select the latest peer-reviewed studies to ensure that the insights you receive are not only personalised, but also scientifically robust.

 

In this section, you'll find two types of resources:

 

  • Key scientific papers that shape how we understand the microbiome and its role in gut and overall wellbeing.

  • Supporting studies that directly inform the specific sections in your Biomine report.​

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Whether you're a science lover or just curious, this page is here to help you go deeper.

Featured Papers

Definition and Scope of Prebiotics

This paper redefines what prebiotics are, expanding beyond just fibers to include a broader range of compounds. It clarifies that prebiotics are substances selectively used by beneficial microbes to improve health.

Full paper

The Interplay Between Diet and the Gut Microbiome

This comprehensive review explains how different diets—from Mediterranean to Western—shape the gut microbiome, and how these dietary-microbe interactions affect metabolic health, immunity, and disease risk.

Full paper

Host and Microbiota Metabolic Signals in Ageing and Longevity

This review details how the metabolic dialogue between host and microbes changes over time. It explores how gut microbes can influence lifespan by modulating inflammation, mitochondrial function, and nutrient-sensing pathways.

Full paper

Shaping the Future of Probiotics and Prebiotics

A broad, visionary review of where the fields of probiotics and prebiotics are heading. It explores new microbial candidates, mechanisms of action, regulatory trends, and how precision nutrition is shaping next-gen products like synbiotics and postbiotics.

Full paper

Roles of the Gut Microbiome in Weight Management

The gut microbiome plays a critical role in how our bodies gain or lose weight. This paper explores how microbes influence energy balance, appetite, and fat storage—and how they may be harnessed for better long-term weight control.

Full paper

The Gut Microbiota–Brain Axis in Behaviour and Disorders

This review unpacks how gut bacteria influence brain development and function. It connects microbial activity to mood, cognition, and disorders like autism and depression, highlighting the gut–brain axis as a promising target for future therapies.

Full paper

Diet–Microbiota Interactions and Personalized Nutrition

This review explores how diet affects each person's microbiome in unique ways. It explains that a "one-size-fits-all" approach to nutrition doesn’t work, but rather, personalised diets based on your microbiome could improve health.

Full paper

Impact on the Pathogenesis of Obesity and Beyond

This article examines how alterations in the gut microbiome contribute to obesity and its complications, including diabetes and metabolic syndrome. It discusses microbial mechanisms that affect fat storage, insulin sensitivity, and inflammation.

Full paper

The Gut Microbiome as a Modulator of Healthy Ageing

Ageing alters the microbiome, but the microbiome also influences how we age. This paper explores how specific microbes and their metabolites can support healthier ageing and help prevent age-related diseases like frailty and cognitive decline.

Full paper

Scientific References Behind Your Report

Microbiome Health
Microbial diversity
Dysbiosis index
Enterotype

  • Malinen E, et al. Association of symptoms with gastrointestinal microbiota in irritable bowel syndrome. World J Gastroenterol. 2010.

  • Arumugam M, et al. Enterotypes of the human gut microbiome. Nature. 2011.

  • Wu GD, et al. Linking long-term dietary patterns with gut microbial enterotypes. Science. 2011.

  • Koren O, et al. A guide to enterotypes across the human body: meta-analysis of microbial community structures in human microbiome datasets. PLoS Comput Biol. 2013.

  • Ley RE, et al. Gut microbiota in 2015: Prevotella in the gut: choose carefully. Nat Rev Gastroenterol Hepatol. 2016.

  • Mobeen F, et al. Enterotype variations of the healthy human gut microbiome in different geographical regions. Bioinformation. 2018.

  • Heeney DD, et al. Intestinal Lactobacillus in health and disease, a driver or just along for the ride? Curr Opin Biotechnol. 2018.

  • Costea PI, et al. Enterotypes in the landscape of gut microbial community composition. Nat Microbiol. 2018.

  • Naumova N, et al. Human gut microbiome response to short-term Bifidobacterium-based probiotic treatment. Indian J Microbiol. 2020.

  • Markowiak-Kopeć P, et al. The effect of probiotics on the production of short-chain fatty acids by human intestinal microbiome. Nutrients. 2020.

  • Bulygin I, et al. Absence of enterotypes in the human gut microbiomes reanalyzed with non-linear dimensionality reduction methods. PeerJ. 2023.

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Gut-Body Interaction
Gut-immune-axis

  • Zheng D, et al. Interaction between microbiota and immunity in health and disease. Cell Research. 2020.

  • Robinson I, et al. Assessing the performance of a novel stool-based microbiome test that predicts response to first line immune checkpoint inhibitors in multiple cancer types. MDPI Cancers. 2023.

Inflammatory potential

  • Di Lorenzo F, et al. Lipopolysaccharide structure of Gram-negative populations in the gut microbiota and effects on host interactions. FEMS Microbiol Rev. 2019.

  • Kaczmarczyk M, et al. The gut microbiota is associated with the small intestinal paracellular permeability and the development of the immune system in healthy children during the first two years of life. J Transl Med. 2021.

  • Si J, et al. Gut microbiome signatures distinguish type 2 diabetes mellitus from non-alcoholic fatty liver disease. Comput Struct Biotechnol J. 2021.

  • Qin Q, et al. The relationship between osteoporosis and intestinal microbes in the Henan Province of China. Front Cell Dev Biol. 2021.

  • Ghosh SS, et al. Intestinal barrier dysfunction, LPS translocation, and disease development. J Endocr Soc. 2022.

  • Khorsand B, et al. Overrepresentation of Enterobacteriaceae and Escherichia coli is the major gut microbiome signature in Crohn’s disease and ulcerative colitis; a comprehensive metagenomic analysis of IBDMDB datasets. Front Cell Infect Microbiol. 2022.

  • Nzabarushimana E, et al. Functional profile of host microbiome indicates Clostridioides difficile infection. Gut Microbes. 2022.

  • Peng YC, et al. Gut microbiome dysbiosis in patients with hepatitis B virus-related hepatocellular carcinoma after extended hepatectomy liver failure. Ann Transl Med. 2022.

  • Wallen ZD, et al. Metagenomics of Parkinson’s disease implicates the gut microbiome in multiple disease mechanisms. Nat Commun. 2022.

  • Yan H, et al. Gut microbiome alterations in patients with visceral obesity based on quantitative computed tomography. Front Cell Infect Microbiol. 2022.

  • Zhang W-H, et al. Fecal microbiota transplantation ameliorates active ulcerative colitis by downregulating pro-inflammatory cytokines in mucosa and serum. Front Microbiol. 2022.

  • Di Vincenzo F, et al. Gut microbiota, intestinal permeability, and systemic inflammation: a narrative review. Intern Emerg Med. 2023.

  • Mena-Vázquez N, et al. Adiposity is associated with expansion of the genus Dialister in rheumatoid arthritis patients. Biomed Pharmacother. 2023.

  • Patumcharoenpol P, et al. Exploring longitudinal gut microbiome towards metabolic functional changes associated in atopic dermatitis in early childhood. Biology (Basel). 2023.

  • Squillario M, et al. Gut-microbiota in children and adolescents with obesity: inferred functional analysis and machine-learning algorithms to classify microorganisms. Sci Rep. 2023.

  • Tap J, et al. Global branches and local states of the human gut microbiome define associations with environmental and intrinsic factors. Nat Commun. 2023.

Gut-skin-axis

  • Penders J, et al. Molecular fingerprinting of the intestinal microbiota of infants in whom atopic eczema was or was not developing. Clin Exp Allergy. 2006.

  • Candela M, et al. Unbalance of intestinal microbiota in atopic children. BMC Microbiol. 2012.

  • Eppinga H, et al. Similar depletion of protective Faecalibacterium prausnitzii in psoriasis and inflammatory bowel disease, but not in hidradenitis suppurativa. J Crohn's Colitis. 2016.

  • Tang MF, et al. Eczema susceptibility and composition of fecal microbiota at 4 weeks of age: a pilot study in Chinese infants. Br J Dermatol. 2016.

  • Zheng H, et al. Altered gut microbiota composition associated with eczema in infants. PLoS One. 2016.

  • Vaughn AR, et al. Skin-gut axis: the relationship between intestinal bacteria and skin health. World J Dermatol. 2017.

  • Tan L, et al. The Akkermansia muciniphila is a gut microbiota signature in psoriasis. Exp Dermatol. 2018.

  • Yan HM, et al. Gut microbiota alterations in moderate to severe acne vulgaris patients. J Dermatol. 2018.

  • Hidalgo-Cantabrana C, et al. Gut microbiota dysbiosis in a cohort of patients with psoriasis. Br J Dermatol. 2019.

  • Myers B, et al. The gut microbiome in psoriasis and psoriatic arthritis. Best Pract Res Clin Rheumatol. 2019.

  • Salem I, et al. The gut microbiome as a major regulator of the gut-skin axis. Front Microbiol. 2019.

  • Visser M, et al. Bacterial dysbiosis and translocation in psoriasis vulgaris. Front Cell Infect Microbiol. 2019.

  • Chen L, et al. Skin and gut microbiome in psoriasis: gaining insight into the pathophysiology and finding novel therapeutic strategies. Front Microbiol. 2020.

  • Chen YJ, et al. An altered fecal microbial profiling in rosacea patients compared to matched controls. J Formos Med Assoc. 2020.

  • Dei-Cas I, et al. Metagenomic analysis of gut microbiota in non-treated plaque psoriasis patients stratified by disease severity: development of a new Psoriasis-Microbiome Index. Sci Rep. 2020.

  • Hsu D, et al. Role of skin and gut microbiota in the pathogenesis of psoriasis, an inflammatory skin disease. Microecol Med. 2020.

  • Yegorov S, et al. Psoriasis is associated with elevated gut IL-1α and intestinal microbiome alterations. Front Immunol. 2020.

  • De Pessemier B, et al. Gut-skin axis: current knowledge of the interrelationship between microbial dysbiosis and skin conditions. Microorganisms. 2021.

  • Olejniczak-Staruch I, et al. Alterations of the skin and gut microbiome in psoriasis and psoriatic arthritis. Int J Mol Sci. 2021.

  • Park DH, et al. Comparative analysis of the microbiome across the gut-skin axis in atopic dermatitis. Int J Mol Sci. 2021.

  • Mahmud MR, et al. Impact of gut microbiome on skin health: gut-skin axis observed through the lenses of therapeutics and skin diseases. Gut Microbes. 2022.

  • Lee MJ, et al. Disordered development of gut microbiome interferes with the establishment of the gut ecosystem during early childhood with atopic dermatitis. Gut Microbes. 2022.

  • Liu C, et al. Correlation analysis between gut microbiota characteristics and melasma. Front Microbiol. 2022.

  • Thye AY-K, et al. Gut–skin axis: unravelling the connection between the gut microbiome and psoriasis. Biomedicines. 2022.

Weight management

  • Ley RE, et al. Microbial ecology: human gut microbes associated with obesity. Nature. 2006.

  • Turnbaugh PJ, et al. A core gut microbiome in obese and lean twins. Nature. 2009.

  • Schwiertz A, et al. Microbiota and SCFA in lean and overweight healthy subjects. Obesity. 2010.

  • Clarke SF, et al. The gut microbiota and its relationship to diet and obesity. Gut Microbes. 2012.

  • Ahmad R, et al. Gut permeability and mucosal inflammation: bad, good or context dependent. Mucosal Immunol. 2017.

  • Menni C, et al. Gut microbiome diversity and high-fiber intake are related to lower long-term weight gain. Int. Journal of Obesity. 2017.

  • Del Chierico F, et al. Gut microbiota markers in obese adolescent and adult patients: age-dependent differential patterns. Front Microbiol. 2018.

  • Gao X, et al. Body mass index differences in the gut microbiota are gender-specific. Frontiers in Microbiology. 2018.

  • Hjorth MF, et al. Prevotella to Bacteroides ratio predicts body weight and fat loss success on 24-week diets varying in macronutrient composition and dietary fiber: results from a post-hoc analysis. Int. Journal of Obesity. 2018.

  • Heianza Y, et al. Changes in gut microbiota-related metabolites and long-term successful weight loss in response to weight-loss diets: The POUNDS Lost Trial. Diabetes Care. 2018.

  • Frost F, et al. A structured weight loss program increases gut microbiota phylogenetic diversity and reduces levels of Collinsella in obese type 2 diabetics: a pilot study. PLoS ONE. 2019.

  • de Clercq NC, et al. Weight gain after fecal microbiota transplantation in a patient with recurrent underweight following clinical recovery from anorexia nervosa. Psychother Psychosom. 2019.

  • Carmody RN, et al. Roles of the gut microbiome in weight management. Nature Review Microbiology. 2023.

  • van Hul M, et al. The gut microbiota in obesity and weight management: microbes as friends or foe? Nat Rev Endocrinol. 2023.

  • Martel J, et al. Gut barrier disruption and chronic disease. Cell Trends Endocrinol Metab. 2024.

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Digestive Health Conditions
Leaky gut

  • Quévrain E, et al. Identification of an anti-inflammatory protein from Faecalibacterium prausnitzii, a commensal bacterium deficient in Crohn’s disease. Gut. 2016.

  • Hiippala K, et al. The potential of gut commensals in reinforcing intestinal barrier function and alleviating inflammation. Nutrients. 2018.

  • Ghosh S, et al. Regulation of intestinal barrier function by microbial metabolites. Cell Mol Gastroenterol Hepatol. 2021.

  • Kinashi T, et al. Partners in leaky gut syndrome: intestinal dysbiosis and autoimmunity. Front Immunol. 2021.

Irritable bowel syndrome

  • Swidsinski A, et al. Spatial organization and composition of the mucosal flora in patients with inflammatory bowel disease. J Clin Microbiol. 2005.

  • Malinen E, et al. Analysis of the fecal microbiota of irritable bowel syndrome patients and healthy controls with real-time PCR. Am J Gastroenterol. 2005.

  • Kassinen A, et al. The fecal microbiota of irritable bowel syndrome patients differs significantly from that of healthy subjects. Gastroenterology. 2007.

  • Lyra A, et al. Diarrhea-predominant irritable bowel syndrome distinguishable by 16S rRNA gene phylotype quantification. World J Gastroenterol. 2009.

  • Rajilić-Stojanović M, et al. Global and deep molecular analysis of microbiota signatures in fecal samples from patients with irritable bowel syndrome. Gastroenterology. 2011.

  • Jeffery IB, et al. An irritable bowel syndrome subtype defined by species-specific alterations in fecal microbiota. Gut. 2012.

  • Jalanka-Tuovinen J, et al. Faecal microbiota composition and host–microbe cross-talk following gastroenteritis and in post-infectious irritable bowel syndrome. BMJ Gut. 2014.

  • Rajilić-Stojanović M, et al. Intestinal microbiota and diet in IBS: causes, consequences, or epiphenomena? Am J Gastroenterol. 2015.

  • Lopetuso LR, et al. Gut microbiota in health, diverticular disease, irritable bowel syndrome, and inflammatory bowel diseases: time for microbial markers of gastrointestinal disorders. Dig Dis. 2017.

  • Vich Vila A, et al. Gut microbiota composition and functional changes in inflammatory bowel disease and irritable bowel syndrome. Sci Transl Med. 2018.

  • Enck P, et al. Dysbiosis in functional bowel disorders. Ann Nutr Metab. 2018.

  • Rizzello F. Dietary geraniol ameliorates intestinal dysbiosis and relieves symptoms in irritable bowel syndrome patients: a pilot study. BMC Complement Altern Med. 2018.

  • Hod K, et al. The effect of a multispecies probiotic on microbiota composition in a clinical trial of patients with diarrhea-predominant irritable bowel syndrome. Neurogastroenterol Motil. 2018.

  • Fodor A, et al. Rifaximin is associated with modest, transient decreases in multiple taxa in the gut microbiota of patients with diarrhea-predominant irritable bowel syndrome. Gut Microbes. 2019.

  • Pittayanon R, et al. Gut microbiota in patients with irritable bowel syndrome—A systematic review. Gastroenterology. 2019.

  • Agnello M, et al. Gut microbiome composition and risk factors in a large cross-sectional IBS cohort. BMJ Open Gastroenterol. 2020.

  • Masoodi I, et al. Microbial dysbiosis in irritable bowel syndrome: a single-center metagenomic study in Saudi Arabia. JGH Open. 2020.

  • Yang M, et al. Mucosal-associated microbiota other than luminal microbiota has a close relationship with diarrhea-predominant irritable bowel syndrome. 2020.

  • Barandouzi Z, et al. Altered gut microbiota in irritable bowel syndrome and its association with food components. J Pers Med. 2021.

  • Baldelli V, et al. The role of Enterobacteriaceae in gut microbiota dysbiosis in inflammatory bowel diseases. Microorganisms. 2021.

  • Ghosh S, et al. Regulation of intestinal barrier function by microbial metabolites. Cell Mol Gastroenterol Hepatol. 2021.

  • Kinashi, et al. Partners in leaky gut syndrome: intestinal dysbiosis and autoimmunity. Front Immunol. 2021.

  • Sciavilla P, et al. Gut microbiota profiles and characterization of cultivable fungal isolates in IBS patients. Applied Microbiology and Biotechnology. 2021.

SIBO

  • Pimentel M, et al. ACG clinical guideline: Small intestinal bacterial overgrowth. The American Journal of Gastroenterology. 2020.

  • Ghosal U, et al. Small intestinal bacterial overgrowth in patients with inflammatory bowel disease: A case-control study. Indian Journal of Gastroenterology. 2021.

  • Banaszak M, et al. Association between gut dysbiosis and the occurrence of SIBO, LIBO, SIFO and IMO. Microorganisms. 2023.

  • Knez E, et al. The importance of food quality, gut motility and microbiome in SIBO development and treatment. Nutrition. 2024.

  • Lu S, et al. Differences in clinical manifestations and the fecal microbiome between irritable bowel syndrome and small intestinal bacterial overgrowth. Digestive and Liver Disease. 2024.

Gluten sensitivity

  • Hansen LBS, et al. A low-gluten diet induces changes in the intestinal microbiome of healthy Danish adults. Nature. 2018.

  • Cardoso-Silva D, et al. Intestinal barrier function in gluten-related disorders. Nutrients. 2019.

  • Volta U, et al. Nonceliac wheat sensitivity: An immune-mediated condition with systemic manifestations. Gastroenterology Clinics of North America. 2019.

  • Nobel YR, et al. Lack of effect of gluten challenge on fecal microbiome in patients with celiac disease and non-celiac gluten sensitivity. Clinical and Translational Gastroenterology. 2021.

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