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The Gut Microbiome's Systemic Impacts

The gut microbiome's impacts on the whole body, including on other body site's microbiomes.


Review, 2020: Intestinal Dysbiosis in, and Enteral Bacterial Therapies for, Systemic Autoimmune Diseases

Bacterial sensing via neuronal Nod2 regulates appetite and body temperature (Apr 2022, mice) "These findings demonstrate that a direct dialog occurs between the gut microbiota and the brain"

"These results indicate that the commensal mycobiome may be a crucial factor in gut and systemic immunological disorders, based on systemic diffusion of either cytokines, fungal products or metabolites, or micromycetous translocation" (2018):

"They suggest that ASD likely develops in children due to a gut microbiome impact on the detoxification process in the gut. And this, in turn, allows environmental toxins to enter the bloodstream where they injure mitochondria in brain cells, leading to symptoms related to ASD." (Oct 2020)

Due to intestinal wall inflammation and degradation of intercellular tight junctions, gut-derived uremic toxins translocate into the bloodstream and exert systemic effects. In this review, we discuss the evidence supporting a role for gut-derived uremic toxins in promoting multiorgan dysfunction via inflammatory, oxidative stress, and apoptosis pathways. End-organ effects include vascular calcification, kidney fibrosis, anemia, impaired immune system, adipocyte dysfunction with insulin resistance, and low turnover bone disease (2018):

Bacterial Dissemination to the Brain in Sepsis. When Sepsis Patients Face Brain Impairment, Is Gut Bacteria to Blame? (2018): -

Gut Microbiome Diversity Predicts Blood Infections in Pediatric Patients With Cancer (2018):

Mastitis, which affects nearly all lactating mammals including human, is generally thought to be caused by local infection of the mammary glands. Here, using bovine mastitis which is the most costly disease in the dairy industry as a model, we showed that intestinal microbiota alone can lead to mastitis Cow-to-mouse fecal transplantations suggest intestinal microbiome as one cause of mastitis (2018).

Antibiotics Increase Mouse Susceptibility to Dengue, West Nile, and Zika. The authors suggest the antibiotics may have compromised the animals’ immunity by altering their microbiomes.

Gut microbiota and host defense in critical illness (2017):

Oral antibiotics for systemic infections/symptoms.


Article: Bone and the Microbiome Have a Brittle Relationship. Animal studies and a few small clinical trials show it’s possible to get commensal microbes to protect against bone loss, rather than contribute to it. (July 2019)

Review, 2023: Gut Microbiome - Should we treat the gut and not the bones?

Commentary, 2019: A Link between the Gut and Bone: Bone Health Impacted by Changes in Gut Microbiota

Review, 2018: Gut Microbiome and Bone:

Review, 2018: Bone and the gut microbiome: a new dimension

Review, 2017: Gut Microbiota, Immune System, and Bone

Review, 2017: From Osteoimmunology to Osteomicrobiology: How the Microbiota and the Immune System Regulate Bone

Bone loss is ameliorated by fecal microbiota transplantation through SCFA/GPR41/ IGF1 pathway in sickle cell disease mice (Nov 2022)

Fecal microbiota transplantation ameliorates bone loss in mice with ovariectomy-induced osteoporosis via modulating gut microbiota and metabolic function (Sep 2022)

Scientists identify gut bacteria linked to bone density, strength (Sep 2023) A two-cohort study on the association between the gut microbiota and bone density, microarchitecture, and strength.

Analysis of the associations between the human fecal microbiome and bone density, structure and strength: the MrOS cohort (Feb 2022, N = 831) "Our findings bolster the view that the gut microbiome is associated with clinically important measures of bone health"

The gut microbiota is a transmissible determinant of skeletal maturation (Jan 2021, mice)

Specific Commensal Bacterium Critically Regulates Gut Microbiota Osteoimmunomodulatory Actions During Normal Post‐Pubertal Skeletal Growth and Maturation (Jan 2020, mice)

Unintended side effects: Antibiotic disruption of the gut microbiome dysregulates skeletal health (Jan 2019, mice) - Antibiotic Perturbation of Gut Microbiota Dysregulates Osteoimmune Cross Talk in Postpubertal Skeletal Development

Components of the Gut Microbiome that Influence Bone Tissue‐Level Strength (May 2021, mice)

Microbiota regulates bone marrow mesenchymal stem cell lineage differentiation and immunomodulation (2017):

Mechanisms of gut microbiota-mediated bone remodeling (2018):

Linking the Gut Microbiota to Bone Health in Anorexia Nervosa (2018):

Gut Microbiota and Bone Health (2017):

Immunology of Gut-Bone Signaling (2017):

Osteomicrobiology: A New Cross-Disciplinary Research Field (2017):

Commensal Microbiota Enhance Both Osteoclast and Osteoblast Activities. (2018)

The gut microbiome and immune systems influence bone growth after mild TBI (Dec 2021) Gut microbiome depletion and repetitive mild traumatic brain injury differentially modify bone development in male and female adolescent rats.

Bacteria in Children’s Throats Found Strongly Associated with Bone and Joint Infections: - Association between oropharyngeal carriage of Kingella kingae and osteoarticular infection in young children: a case–control study (2017):

Probiotics and prebiotics:

Prebiotics, Bone and Mineral Metabolism (2017):

Prebiotics and Bone (2017):

Prebiotics, Probiotics, and Synbiotics Affect Mineral Absorption, Bone Mineral Content, and Bone Structure (2007):

Probiotics (Lactobacillus reuteri 6475) can protect the skeletons of older women. The women who received the powder with active bacteria had lost only half as much bone in the skeleton compared with those who received inactive powders (2018):

Probiotics (Lactobacillus rhamnosus GG) increase bone volume in healthy mice (2018):

The Microbial Metabolite Butyrate Stimulates Bone Formation via T Regulatory Cell-Mediated Regulation of WNT10B Expression (2018):


Review, Sep 2023: Elucidating the Role of the Microbiome in Ocular Diseases

Review, Nov 2021: The gut microbiota in retinal diseases

Fecal Microbial Transplant in Individuals with Immune-mediated Dry Eye (Jun 2021, n=10, Sjögren's) "Five individuals subjectively reported improved dry eye symptoms 3 months after FMT"

Eye diseases long thought to be purely genetic might be caused in part by bacteria that escape the gut and travel to the retina (Feb 2024, mice) CRB1-associated retinal degeneration is dependent on bacterial translocation from the gut.

Alterations in the gut bacterial microbiome in fungal Keratitis (inflammatory disease of the eye) patients (2018): - "Our study demonstrates dysbiosis in the gut bacterial microbiomes of FK patients compared to HC. Further, based on inferred functions, it appears that dysbiosis in the gut of FK subjects is strongly associated with the disease phenotype with decrease in abundance of beneficial bacteria and increase in abundance of pro-inflammatory and pathogenic bacteria"

Alterations in gut bacterial and fungal microbiomes are associated with bacterial Keratitis, an inflammatory disease of the human eye (2018):

Gut microbiome has been implicated in the pathogenesis of uveitis. This short review will summarize the few studies linking gut or oral microbiota to diabetic retinopathy (DR), glaucoma, and age-related macular degeneration (AMD). Finally, we will propose the gut-retina axis, related but distinct from the gut-brain axis. (2018): | And Gut Fungal Microbiome in Uveitis (2019):


Review, Jul 2020: Gut microbiome a promising target for management of respiratory diseases

Fungus from the intestinal mucosa can affect lung health. Our microbiome can impair our immune system through the harmless fungus Candida albicans. Human Anti-fungal Th17 Immunity and Pathology Rely on Cross-Reactivity against Candida albicans (Feb 2019).

Can We Restore the Lung Microbiome with Fecal Microbiota Transplant (FMT)? (2018) "This murine model results suggest a potential role and effectiveness of gut FMT as a therapeutic measure for MDR bacterial infection in the lungs"

The [gut] Microbiome Regulates Pulmonary Responses to Ozone in Mice (2018): "[gut] microbiome impacts allergic airway responses, including airway hyperresponsiveness, a characteristic feature of asthma. Here we examined the role of the microbiome in pulmonary responses to a non-allergic asthma trigger, ozone. Our data indicate that the [gut] microbiome contributes to ozone-induced airway hyperresponsiveness, likely via its ability to produce short chain fatty acids."

Impact of gut colonization with butyrate producing microbiota on respiratory viral infection following allo-HCT (2018): - "Patients with higher abundances of butyrate producing bacteria were a five-fold less likely to develop viral LRTI, independent of other factors (adjusted HR=0.22, 95% CI 0.04 - 0.69). Higher representation of butyrate-producing bacteria in the fecal microbiota is associated with increased resistance against respiratory viral infection with LRTI in allo-HCT patients."

The Microbiome and Tuberculosis: Early Evidence for Cross Talk (review, 2018):

Alcohol-associated intestinal dysbiosis impairs pulmonary host defense against Klebsiella pneumoniae (2017):

Gastrointestinal carriage is a major reservoir of K. pneumoniae infection in intensive care patients (2017):


Mechanisms Involved in Gut Microbiota Regulation of Skeletal Muscle (May 2022)

Human gut microbiome impacts skeletal muscle mass via gut microbial synthesis of the short-chain fatty acid butyrate among healthy menopausal women (Sep 2021)

The intestinal microbiota contributes to the growth and physiological state of muscle tissue in piglets (May 2021)

Wound healing:

The beneficial effects of probiotic administration on wound healing and metabolic status in patients with diabetic foot ulcer: A randomized, double-blind, placebo-controlled trial (2017):

Microbial Symbionts Accelerate Wound Healing via the Neuropeptide Hormone Oxytocin (2013):

The Probiotic Mixture VSL#3 Accelerates Gastric Ulcer Healing by Stimulating Vascular Endothelial Growth Factor (2013):

"wounds tend to heal faster on a germ-free animal than they do in a mouse full of bacteria. But even more intriguingly, mice with a skin wound that are fed a live probiotic appear to heal faster than those fed dead bacteria. This suggests that our old friend the immune system may be responding to the gut bacterial infusion and somehow stimulating wound healing." - Jack Gilbert & Rob Knight, but no citation provided.

Role of gut microbiota in intestinal wound healing and barrier function (2018):

The microbiome and its relevance in complex wounds (2019):

Microbiome Imbalances: An Overlooked Potential Mechanism in Chronic Nonhealing Wounds (2019):

Ear wound healing in MRL/MpJ mice is associated with gut microbiome composition and is transferable to non-healer mice via microbiome transplantation (Jul 2021)


See also:

Exploring the role of gut microbiome in male reproduction (review, Dec 2021) "Testicular microbiome and gut microbiome can interact to influence male reproductive function. This study discusses therapeutic options such as probiotics, prebiotics, and fecal microbiota transplantation"

Gut Microbiota Exceeds Cervical Microbiota for Early Diagnosis of Endometriosis (Dec 2021, n=41)

Some other items also listed in other wiki pages:

"the gastrointestinal microbiome influences every organ system in the body" (Mar 2019):

Researchers Uncover Gut Bacteria's Potential Role In Multiple Sclerosis. "We essentially discovered a remote control by which the gut flora can control what is going on at a distant site in the body, in this case the central nervous system" (2018):

The gut microbiota and the brain–gut–kidney axis in hypertension and chronic kidney disease (review, 2018):

Gut microbiota: Neonatal gut microbiota induces lung immunity against pneumonia (2017): - IL-22 mediates mucosal host defense against Gram-negative bacterial pneumonia

Bacterial secretion of histamine within the gut influences immune responses within the lung. (2018):

Regulation of inflammation by microbiota interactions with the host (2017): "Intestinal microbiota influence host response to infection"

Review, 2017: Human Virome "the findings so far indicate that the regulation of the immune response by viruses and other members of the microbiome can affect the outcome of infections"

A specific human-associated gut microbe, Clostridium orbiscindens, produced metabolite that protects mice from influenza through type I interferon (2017): "Specific components of the enteric microbiota have distal effects on responses to lethal infections through modulation of type I IFN"

The intestinal microbiota regulates extra-intestinal immunity via the common mucosal immune system (2018): Upper Respiratory Symptoms, Gut Health and Mucosal Immunity in Athletes.

Review, 2018: The role of the microbiota in infectious diseases

Interplay between viruses and bacterial microbiota in cancer development (2017): "healthy gut microbiota stimulates host immune system resulting in HBV infection clearance; sterilization of gut microbiota with antibiotics reduced the ability of adult mice to clear HBV infection"

"Our current theory is that your gut bacteria determine whether your oral bacteria cause cancer" (2017):

"the gastrointestinal microbiota plays a definitive role in atopy development" (2017):

Associations between infant fungal and bacterial dysbiosis and childhood atopic wheeze in a nonindustrialized setting (2017): "Our findings provide additional support for considering modulation of the gut microbiome as a primary asthma prevention strategy"

Intestinal Microbiota Disruption Reduces Regulatory T Cells and Increases Respiratory Viral Infection Mortality Through Increased IFNγ Production (2018):

Diet plays important role in determining vaginal microbiome (2016): - exact mechanisms unknown.