human gut flora

Overview

The human gut flora, also referred to as the gut microbiota or intestinal microbiome, comprises the vast and diverse community of microorganisms — predominantly bacteria, but also archaea, fungi, viruses, and protists — that colonize the gastrointestinal tract. Estimated to harbor trillions of microbial cells encoding tens of millions of genes, this ecosystem represents one of the most complex and metabolically active environments in the human body. The dominant bacterial phyla in healthy adults include Firmicutes, Bacteroidota (formerly Bacteroidetes), Actinobacteria, and Proteobacteria, with their relative abundances shaped by host genetics, age, diet, geographic origin, and pharmaceutical exposures.

Far from being passive residents, gut microorganisms perform critical physiological functions: fermenting dietary fiber into short-chain fatty acids (SCFAs), synthesizing vitamins, educating and calibrating the host immune system, maintaining intestinal barrier integrity, modulating bile acid metabolism, and producing a broad repertoire of bioactive Metabolites that circulate systemically. Disruption of this community — termed dysbiosis — has been linked to an expanding spectrum of conditions extending well beyond the gastrointestinal tract, including metabolic disorders, neurodegenerative diseases, cancers, autoimmune conditions, and psychiatric illnesses. The gut microbiota's capacity to influence remote organ systems via the gut-liver axis, gut-lung axis, and microbiota-gut-brain axis has positioned it as a central subject in translational medicine and multi-omics research.

Focus of Latest Publications

Recent research demonstrates that human gut flora plays a central role in regulating metabolic health, intestinal barrier integrity, and systemic aging phenotypes. Multiple studies employed multi-omics approaches—including metagenomic profiling, metabolomics, and transcriptomics—to characterize how gut microbiota composition and function mediate age-associated decline. Dietary polyphenol interventions, such as purple sweet potato anthocyanins, were shown to remodel aging-associated microbiota and restore intestinal epithelial barrier function through a "microbiota-autophagy-stem cell" axis, concurrently alleviating motor coordination impairment, hepatic lipid dysregulation, and insulin resistance. Similarly, wholegrain rye diets were investigated for their capacity to modulate gut microbiota composition in the context of weight loss and cardiometabolic risk reduction, contrasting with refined wheat consumption. Fecal microbiota transplantation experiments confirmed the causal contribution of microbiota remodeling to intestinal stem cell rejuvenation and systemic health outcomes.

The microbiota-gut-brain axis emerged as a unifying mechanism across multiple disease contexts. Fecal microbiota from elderly donors with comorbid Alzheimer's disease and type 2 diabetes showed the greatest dysbiosis, characterized by enrichment of pro-inflammatory taxa, depletion of butyrate-producing genera, and loss of neuroprotective metabolic pathways; transfer of this dysbiotic microbiota to recipient mice suppressed hippocampal neurotrophic gene expression and induced cognitive alterations. Pharmacological interventions targeting the microbiota—including sibelium prophylaxis for migraine and hydroxytyrosol from olive oil for posttraumatic stress responses—preserved or restored microbial diversity and stability, with effects attributed to preserved short-chain fatty acid (SCFA) production and reduced neuroinflammation. Conversely, pathological dietary patterns, such as habitual ultra-processed food intake in inflammatory bowel disease patients and type 2 diabetes-induced dysbiosis, were associated with intestinal barrier disruption, pro-inflammatory metabolite profiles, and exacerbation of systemic outcomes including periodontitis and impaired cardiometabolic health.

Emerging evidence implicates human gut flora dysbiosis in immune tolerance and cancer-related complications. Gut microbiota composition was identified as a potential mediator of immune-related adverse events in patients receiving immune checkpoint inhibitor immunotherapy, particularly ICI colitis. Multi-omics Mendelian randomization analysis causally linked specific gut microbial taxa and metabolic pathways—including valine, leucine, and isoleucine biosynthesis—to aortic stenosis risk through systemic inflammation and plasma metabolite alterations. Additionally, altered microbiota and reduced SCFA levels were documented in patients with acute ischemic stroke complicated by active cancer, suggesting that dysbiosis may contribute to stroke pathophysiology through metabolic and immune dysfunction. Collectively, these studies underscore human gut flora as a modifiable therapeutic target whose composition and metabolic output influence intestinal barrier function, systemic inflammation, neurological health, and age-associated disease susceptibility.

Key Publications

• NEWJun Biomedical publication details. (PubMed Database, 2026, PMID 42316995)
• NEWJun Habitual Ultra-processed Food Intake Is Associated with Gut Dysbiosis and Pro-inflammatory Metabolite Profiles in Korean Patients with IBD. (Digestive diseases and sciences, 2026, PMID 42319657): "We investigated whether habitual UPF intake is associated with specific microbiota and metabolite profiles in Korean patients with IBD."
• NEWJun Bridging the airway microbiome and targeted therapy in bronchiectasis: multi-omics insights, endotypes and emerging therapies. (The European respiratory journal, 2026, PMID 42276744): "Despite the breadth of descriptive microbiome data, translation into clinically actionable diagnostics or therapies has been limited."
• May Hydroxytyrosol Mitigates Anxiety-Like Behaviors After a Traumatic Experience in Aged Mice in Parallel With Increased Neurogenesis in the Ventral and Dorsal Dentate Gyrus, and Preservation of Gut Microbiota Composition. (Journal of neurochemistry, 2026, PMID 42059580): "Furthermore, we examined its influence on gut microbiota composition, given the well-established role of the microbiota-gut-brain axis in memory and stress regulation."
• May Comorbid Alzheimer's Disease and Type 2 Diabetes Microbiota Shape Age-Associated Gut-Brain Axis Profiles. (Aging cell, 2026, PMID 42015224): "...potentially mediated by the gut microbiota, yet the neurobiological impact of comorbid AD+T2DM microbiota from elderly donors remains unexplored."
• Apr Microbiota and immune-related adverse events in cancer immunotherapy. (Nature reviews. Cancer, 2026, PMID 41992000): "We focus on ICI colitis, a common irAE that has strong association with the gut microbiome."
• Apr Causal relationship between gut microbiome, plasma metabolites, inflammation, and aortic stenosis: A multi-omics Mendelian randomization analysis. (Medicine, 2026, PMID 41961656): "Mendelian randomization analysis has shown that 7 gut microbiota, 80 metabolites, 29 immune cells phenotypes, and 6 circulating inflammatory proteins are causally associated with AS."
• May Effects of hypocaloric wholegrain rye vs refined wheat diets on weight loss, cardiometabolic risk factors and gut microbiota: A 12-week randomized controlled trial. (Clinical nutrition (Edinburgh, Scotland), 2026, PMID 41861447): "Wholegrain rye foods have shown promising effects on metabolic regulation and weight-loss, which may be mediated via gut microbiota and derived metabolites."
• May Sibelium exerts anti-migraine effects by remodeling the gut microbiota and regulating metabolic and immune pathways of the brain-gut axis. (International immunopharmacology, 2026, PMID 41846063): "The effects of sibelium on gut microbiota and the underlying mechanism for migraine prevention were investigated."
• May T2DM-Induced Gut Dysbiosis Exacerbates Periodontitis Through Intestinal Barrier Disruption and Redox Imbalance. (Journal of clinical periodontology, 2026, PMID 41834217): "To investigate the potential role and underlying mechanisms of gut microbiota in type 2 diabetes mellitus (T2DM)-exacerbated periodontitis."