Endometriosis at the metal–microbe–immune interface
How low-nickel dietary responses, red meat and heme iron, microbial signals, and nutritional immunity define a research program in endometriosis.
Microbial Metallomics
Explore the evidence
Search the site’s research summaries, paper reviews, and essays. Filter by topic, format, or source study design, and take a reading catalog with you.
This is a catalog of this site’s coverage, not a systematic review or a ranking of evidence quality. Dates refer to pages; study-design labels describe the source discussed, where explicitly identified.
Explore two connected deep-dive series: Host metal defenses and Unexpected metal biology.
66 articles
Vancomycin and zinc: starvation, assembly and resistance
Vancomycin can bind zinc, yet added zinc can also strengthen its activity in resistant bacteria. The experiments distinguish starvation from drug assembly.
Transferrin, ferritin and the race to recycle heme
How transferrin, ferritin, haptoglobin and hemopexin route iron, protect tissue and face microbial piracy—and which experiments distinguish those effects.
Silymarin, metal binding and the liver
Milk-thistle chemistry can bind or reduce metals, but nickel protection, lead measurements and human liver trials answer different mechanistic questions.
Parkinson’s dementia: shared copper depletion, distinct metal patterns
Brain copper loss in Parkinson’s dementia overlaps Alzheimer’s but differs by region. What this signature enables for microbial metallomics research.
Lactoferrin: iron withholding and microbial countermeasures
How lactoferrin withholds iron, disrupts microbial behavior, and faces bacterial countermeasures—and what oral human studies actually establish.
Hepcidin and ferroportin: iron redistribution in host defense
How hepcidin controls ferroportin, redistributes iron during inflammation, and creates different tradeoffs for microbes and red-cell production.
Glutathione, metals and the mitochondrial reserve
How glutathione supports enzymes, binds metals and enters mitochondria—and what drug metabolism does and does not establish about shared cellular reserve.
Dementia’s regional metal signatures
Dementia brain-metal signatures reveal regional copper loss and iron gain. A critical review connects these patterns to testable microbial-metallomics research.
Can probiotic yeast carry metals out of the gut?
How Saccharomyces boulardii and other yeasts bind lead, arsenic and mercury—and which experiments can distinguish adsorption from lasting removal.
Bile, metal export and the route back
Bile carries metal-containing cargo, but bile acids, glutathione complexes, copper pumps and microbial transformations govern different steps toward elimination.
Alzheimer’s disease: copper depletion and regional metal contrasts
Alzheimer’s brain copper loss and regional iron and zinc changes reveal a spatial disease signature—and define experiments for microbial metallomics.
Tampon Metals and the Vaginal Microbiome: The Blind Spot in the Risk Assessment
A 2026 FDA risk assessment by Jin et al. calls the metals in tampons safe, but only for one endpoint: the fraction absorbed systemically into the blood. That verdict rests on a single word, bioavailable. The vaginal microbes live on the surface, not in the bloodstream, and were never assessed.
Iron Fortification and the Kenyan Infant Gut Microbiome
A full review of Jaeggi et al. (Gut 2015): iron-fortified porridge increased pathogenic E. coli and enterobacteria, cut bifidobacteria, and inflamed the gut in Kenyan infants.
The Metal–Microbiome–Disease Axis: Who Gets the Metal?
Metals change microbial ecology; microbes change metal chemistry; inflammation changes local metal access. Follow the mechanisms connecting exposure, nutritional immunity, and disease.
Metals, the Microbiome, and Parkinson's: A Gut-First Pathway to Neurodegeneration
How heavy-metal exposure may reshape the gut microbiome and feed gut-first alpha-synuclein pathology in Parkinson's disease - a metallomic-microbiome view.
Mercury, Methylmercury, and the Microbiome: How Gut Microbes Shape Neurotoxic Risk
How gut microbes methylate and demethylate mercury via hgcAB and merB, how mercury reshapes the microbiome, and why this shapes methylmercury neurotoxic risk.
How Low-Dose Heavy Metals May Reshape the Gut Microbiome to Drive Obesity
Low-dose arsenic, cadmium, and lead may reshape the gut microbiome, depleting SCFA producers and promoting obesity and metabolic syndrome. Evidence examined.
How Dietary Nickel Arms Gut Bacteria — and May Fuel Gut Disease
Dietary nickel activates nickel-dependent virulence enzymes in gut Enterobacteriaceae — a mechanistic pathway that may link nickel exposure to NEC and IBD.
Feeding the Enemy: How Dietary Iron Reshapes the Gut Microbiome and Raises Enteric Infection Risk
Unabsorbed iron can alter the gut microbiome and intestinal inflammation. Human trials show that effects on diarrhea vary by setting and formulation.
Does Lead Harm the Developing Brain Through the Gut Microbiome?
Animal and human cohort studies link lead exposure to gut microbiome dysbiosis, a candidate mediator of lead's neurodevelopmental harm via the gut-brain axis.
Cadmium and the Gut Microbiome: A Hidden Route to Metabolic Disease
Cadmium reshapes the gut microbiome, depletes Lachnospiraceae, weakens the gut barrier, and is linked to hepatic and metabolic dysfunction. An evidence review.
Arsenic and the Gut Microbiome: A Two-Way Street
Arsenic reshapes the gut microbiome, and gut bacteria shape arsenic's toxicity in return. See the bidirectional evidence linking metals, microbes, and disease.
Six Decades of Fertilizer Use Built a Legacy of Cadmium, Nickel, and Lead in Soils and Diets
A food metallomics review (1960–2025) showing how phosphate and urea fertilizers loaded soils, crops, and diets with cadmium, nickel, lead, and chromium.
Heavy Metals and Microbial Metallomics: A New Framework for the US Obesity Epidemic
How dietary cadmium, arsenic, lead, and nickel may disrupt gut microbial metallomics—driving dysbiosis, inflammation, and insulin resistance behind obesity.
Developmental Readiness Is Not Toxicokinetic Safety: Heavy Metals in Vegetable-Based Baby Foods
Developmental readiness for solids does not ensure toxicokinetic safety: leafy greens, brassicas and root crops concentrate lead, cadmium and arsenic in baby foods.
Concentration-Based Heavy Metal Standards to Reduce Real Exposure in Infant and Child Foods
HMTc 2026 sets concentration-based, as-sold action levels for lead, arsenic, cadmium, mercury, nickel and other heavy metals in infant and child foods.
Nickel as a Catalytic Driver of Necrotizing Enterocolitis
Dietary nickel in infant formula may activate nickel-dependent microbial enzymes (urease, glyoxalase I) that drive necrotizing enterocolitis in preterm infants.
A Unified Model for FIP-Associated Gingivitis in Cats: Disrupting Microbial Shielding and Restoring Nutritional Immunity
How itraconazole and lactoferrin may treat FIP-linked gingivitis in cats by disrupting polymicrobial biofilms and restoring metal-based nutritional immunity.
Microbiome Medicine Journal: Restoring Causal Structure to Disease Through Microbial Metallomics
Microbiome Medicine Journal Vol. I sets out a mechanism-first framework linking microbial ecology, host metallome regulation, and metal dyshomeostasis to disease.
From Dysbiosis to Dyshomeostasis: Reframing Parkinson's Through a Metallomic–Microbiome Lens
A metallomics framework reframes Parkinson's as metal dyshomeostasis: iron, manganese, copper, zinc and nickel dysregulation drives dysbiosis and neuron loss.
The MC1R–Parkinson's Link May Be a Metallomic Story, Not a Cosmetic One
A hypothesis linking MC1R red-hair variants to Parkinson's risk via melanin-metal chemistry: how copper, zinc, and iron shape neuromelanin's redox buffering.
Parkinson's Disease as a Disorder of Metal Dyshomeostasis Amplified by Microbial Ecology
A synthesis framework proposing Parkinson's disease begins with heavy-metal dyshomeostasis that drives ferroptosis, gut dysbiosis, and α-synuclein pathology.
Prenatal Tobacco Exposure and the Child Gut Microbiome
Prenatal smoking and childhood gut taxa were associated in an observational cohort; the responsible exposure components remain unresolved.
Prenatal Metal Exposure, the Gut Microbiome, and Childhood Intestinal Inflammation
A 2024 PROGRESS cohort study links prenatal copper and cesium exposure, interacting with specific gut microbes, to elevated fecal calprotectin in children.
Prenatal Acetaminophen, the Infant Gut Microbiome, and Childhood Cognition
GESTE cohort links prenatal acetaminophen and caffeine to childhood gut microbiome shifts and cognition; Proteobacteria abundance modified WISC-IV scores.
Pediatric Gut Microbiome Composition in Health: What a Systematic Review Reveals
A systematic review of 42 studies finds geography, diet, and 16S sequencing method, not age, shape healthy children's Firmicutes/Bacteroidetes gut profiles.
Lactoferrin vs. Ferrous Sulfate Through a Metallomics Lens
Meta-analyses show oral lactoferrin can match or outperform ferrous sulfate for iron repletion, lowering IL-6 and hepcidin with fewer gut side effects.
Lactobacillus plantarum 299v and Oral Iron Therapy Tolerance
A randomized trial shows the probiotic Lactobacillus plantarum 299v reduces oral iron side effects and improves iron status in iron-deficiency anemia patients.
Iron- and Zinc-Biofortified Foods and the Gut Microbiota
Systematic review of iron/zinc-biofortified bean and wheat diets in the Gallus gallus model: staples raised SCFA-producing Lactobacillus and cut enteric pathogens.
Iron Supplements and the Gut Microbiome in Reproductive-Age Women: A Randomized Controlled Trial
A 21-day randomized placebo-controlled trial found ferrous fumarate did not significantly alter fecal microbiome composition in Australian reproductive-age women.
Iron Fortification, the Infant Gut Microbiome, and Diarrhea Risk
Iron fortification shifts the infant gut microbiome toward enterobacteria and pathogenic E. coli, cutting protective bifidobacteria and raising diarrhea risk.
Intestinal Biomarkers and the Non-Motor Phenotype of Parkinson's Disease
Parkinson's patients with constipation show higher fecal calprotectin, reduced SCFAs, lower gut diversity, and greater IBD genetic risk, linking gut inflammation to non-motor severity.
HERFD-XAS: High-Resolution X-ray Speciation of Biological Metals
HERFD-XAS sharpens X-ray absorption spectra by rejecting core-hole broadening, resolving mercury, selenium, and arsenic speciation in dilute biological samples for metallomics.
Gut Microbiome and Childhood Stunting in Low- and Middle-Income Countries
Systematic review of 14 studies links childhood stunting in LMICs to inflammatory gut pathobionts and depleted butyrate producers, driving impaired linear growth.
Childhood Blood Metals and the Gut Microbiome: Evidence from the GESTE Cohort
GESTE cohort links childhood blood metals (Mn, Se, Cd, Hg, Pb) to gut microbiome composition in 6-7 year olds; manganese and selenium tied to bacterial phyla.
A Multi-Omics + MR Enterography Model for Predicting Bowel Damage in Crohn's Disease
Two-center study fusing gut microbiome, fecal and serum metabolomics, and MR enterography into a model predicting cumulative Crohn's bowel damage (AUC 0.857).
The Human Microbiome Across Body Sites: Gut, Skin, Oral, Vaginal and Lung
How the human microbiome differs across the gut, skin, oral, vaginal and lung niches, how it is acquired and disrupted, and why heavy-metal exposure matters.
Prenatal Metal Exposure, the Gut Microbiome, and Childhood Depression
A Mexico City birth-cohort study links a prenatal zinc-cobalt profile plus specific gut bacteria to 15.4% higher childhood depression scores at ages 9-11.
Prenatal Lead Exposure and the Childhood Gut Microbiome
Prenatal lead exposure is negatively linked to the childhood gut microbiome: metagenomics from a Mexico City cohort ties maternal Pb to fewer beneficial bacteria.
Prebiotics Blunt the Gut Cost of Iron-Fortified Cereal in Kenyan Infants
In a Kenyan infant RCT, adding prebiotic GOS/FOS to iron-fortified cereal raised iron absorption 60% and reduced gut inflammation, pathogens, and dysbiosis.
Nutritional Immunity and Trace Metals in Infection
How the host uses iron, zinc, manganese and copper handling as nutritional immunity to starve or poison pathogens, plus metal-based therapeutic strategies.
Metal Availability and Immune Function During Infection
How zinc, iron, manganese, and copper availability shapes neutrophil and macrophage function during infection through nutritional immunity, calprotectin, and phagosomal metal handling.
Iron Chelation Therapy in Transfusion-Dependent Thalassemia
Clinical review of deferoxamine, deferiprone, and deferasirox for transfusion iron overload in thalassemia, covering cardiac and hepatic iron outcomes measured by MRI T2*.
Heavy Metals and the Gut Microbiota: A Systematic Review
Systematic review of 12 human studies links arsenic, lead, mercury, and cadmium exposure to gut microbiota dysbiosis, leaky gut, and disease, with dietary mitigation.
Gallium as an Iron Mimic: Disrupting Pseudomonas Iron Metabolism in Cystic Fibrosis
Gallium substitutes for iron to sabotage Pseudomonas aeruginosa iron metabolism. A Phase 1 CF trial (Goss et al., Sci Transl Med 2018) found IV gallium improved lung function.
Copper in Infectious Disease: Both Sides of the Penny
How the immune system weaponizes copper against pathogens: macrophage copper bursts, phagosomal intoxication, fungal copper detox, and copper nutritional immunity.
Arsenic Exposure Reshapes the Gut Microbiome of Bangladeshi Children, Enriching Resistance-Carrying E. coli
Arsenic-exposed Bangladeshi children carry more gut Proteobacteria and E. coli bearing arsenic-resistance (ars) and antibiotic-resistance-like genes, a metal-microbiome case study.
Proteome-Scale Mapping of Iron-Binding Proteins in Bread Wheat
A proteome-wide scan of bread wheat mapped ~600 iron-binding proteins with Fe(II)/Fe(III) sites coordinated by His, Glu, Asp and Cys, aiding metallomics.
Colorectal cancer: mapping metals, cells, and microbial questions
Colorectal cancer metal maps reveal distinct copper and iron neighborhoods. What they measured, and how to test microbial access, host response and disease.
[NiFe]-Hydrogenase Cofactor Biosynthesis and the Hyp Maturation Proteins (HypA-F) in E. coli
How E. coli builds the NiFe(CN)2CO cofactor of [NiFe]-hydrogenases: the HypA-F maturation proteins, cyanide and CO ligand synthesis, and nickel insertion.
The Zinc Clasp: How Zn2+ Shapes T-Cell Signaling
The zinc clasp is a Zn2+-bridged interface that tethers the kinase Lck to CD4 and CD8 coreceptors, a labile-zinc switch central to T-cell activation and immunity.
The Iron Metalloproteome of Pseudomonas aeruginosa Under Oxic and Anoxic Conditions
Native metalloproteomics maps how Pseudomonas aeruginosa partitions iron across four protein complexes, with denitrification raising iron demand in anoxia.
Nitric Oxide Sensing by the [4Fe-4S] Regulator ArnR
ArnR uses a [4Fe-4S] cluster to sense nitric oxide: NO nitrosylates the cluster, abolishing DNA binding and derepressing nitrate-respiration and hmp genes.
Maternal metallomics: what UPBEAT opens for microbial research
UPBEAT links maternal manganese and phosphorus to later outcomes. What the evidence means, and how to test host and microbial metal handling.
Iron-Sulfur Clusters and Oxygen in Human Disease
How iron-sulfur (Fe-S) cluster biogenesis and oxygen shape human disease: NFS1 in lung cancer, hyperoxia injury, and hypoxia therapy for Friedreich ataxia.