Paired lungs appear beside open alveolar sacs and comparable sacs containing pale translucent material in parts of multiple air spaces.
Pulmonary teaching reconstruction Editorially reviewed

Representative pneumonia orientation without a specific pathogen, subtype, distribution, fluid composition, oxygenation, severity, treatment need, prognosis, or diagnosis.

WikiBiome / Microbiome MedicineNLM-MeSH-condition-, NHLBI-pneumonia-, and literal-output-audit-informed reconstruction
Scientific media record1 verified identifier
Subject
Pneumoniacondition
Identifiers
MeSH:D011014
Review
Editorial review completeIdentifiers authority-verified · Accessibility validated · · pneumonia|pneumonia-pathology-v1.webp
Digital source
Trained-algorithmic mediaCreated with a trained generative algorithm and reviewed by WikiBiome for subject identity, scientific framing, identifiers, provenance, and accessibility.
License
CC BY-SA 4.0Created

Pneumonia is infection of the lung parenchyma, most commonly caused by Streptococcus pneumoniae, Klebsiella pneumoniae, Haemophilus influenzae, and viruses (influenza, SARS-CoV-2).

In the WikiBiome framework, pneumonia exemplifies the metal battleground at the host-pathogen interface—the outcome of infection depends on the competition for zinc, manganese, and iron between host nutritional immunity and pathogen metal acquisition systems.

Evidence map4 cited passagesInspect provenance +
01
Metal Ecology

Zinc vs. manganese: Host calprotectin sequesters both Zn and Mn at infection sites. S. pneumoniae responds by upregulating high-affinity Mn transporters (PsaA) to maintain Mn-SOD defense against oxidative killing. Zinc can directly inhibit pneumococcal manganese uptake, providing a mechanistic basis for zinc supplementation in pneumonia.

02
Metal Ecology

Iron: Pneumonia pathogens deploy siderophores and heme acquisition systems; host hepcidin elevation during infection restricts systemic iron.

03
Metal Ecology

Infection metallomics: Siderophore and metallophore detection in patient specimens enables pathogen identification and outcome prediction in critical care.

04
Gut-Lung Axis

COVID-19 pneumonia is compounded by gut barrier failure and endotoxemia.

Integrated microbiome signature

One disease. Five evidence layers.

A generated systems view of the metals, organisms, host sequestration signals, ecological conditions, and microbial functions indexed for Pneumonia.

01

Evidence layer

Metallomic signature

Elements and antioxidants reported as elevated, accumulated, depleted, or systemically altered.

Elevated or accumulated

0

No structured signals indexed yet.

Depleted or redistributed

0

No structured signals indexed yet.

02

Evidence layer

Taxonomic signature

Organisms reported as enriched or depleted, with their indexed functional context kept beside the name.
Enriched taxa0

No structured taxa indexed yet.

Depleted taxa0

No structured taxa indexed yet.

03

Evidence layer

Nutritional immunity

Host metal-withholding, inflammatory, antioxidant, and microbial-metabolite signals indexed in the signature.

Elevated host signals

0

No structured signals indexed yet.

Depleted protective signals

0

No structured signals indexed yet.

04

Evidence layer

Ecological state

The environmental conditions that connect the organism-level observations into a system.
WB.ECO / SYSTEM MODEL0 connected states

No structured ecological features indexed yet.

EnvironmentCommunity structureHost response
05

Evidence layer

Virulence functions

Microbial structures, enzymes, and acquisition systems implicated by the linked evidence.

No structured virulence functions indexed yet.

Encyclopedia article

The disease record, in full.

The original WikiBiome disease narrative remains intact beneath the generated signature atlas.

Metal Ecology#

Zinc vs. manganese: Host Calprotectin (S100A8/A9) sequesters both zinc (Zn) and manganese (Mn) at infection sites. S. pneumoniae responds by upregulating high-affinity manganese transporters (PsaA) to maintain manganese-SOD defense against oxidative killing.

Zinc can directly inhibit pneumococcal manganese uptake, providing a mechanistic basis for zinc supplementation in pneumonia.[1]Eijkelkamp et al. 2014 — Extracellular Zinc Competitively Inhibits Manganese Uptake in Streptococcus pneumoniaeBart A. Eijkelkamp, Jacqueline R. Morey, Stephanie L. Neville et al. · 2014Open reference 1

Iron: Pneumonia pathogens deploy siderophores and heme acquisition systems; host Hepcidin elevation during infection restricts systemic iron.[2]Infection metallomics for critical care in the post-COVID eraPatil RH, Luptakova D, Havlicek V · 2021Open reference 2

Infection metallomics: Siderophore and metallophore detection in patient specimens enables pathogen identification and outcome prediction in critical care.[2]Infection metallomics for critical care in the post-COVID eraPatil RH, Luptakova D, Havlicek V · 2021Open reference 2

Gut-Lung Axis#

Gut Dysbiosis increases pneumonia susceptibility via impaired systemic immune priming. COVID-19 pneumonia is compounded by gut barrier failure and Endotoxemia.[3]Brown et al. 2024 — Pathophysiology, Diagnosis, and Management of Neuroinflammation in COVID-19Rachel L Brown, Laura Benjamin, Michael P Lunn et al. · 2024Open reference 3 Antibiotic treatment of pneumonia disrupts gut Colonization Resistance, enabling secondary infections.

Cross-References#

Generated evidence record

References 5

Numbered by first appearance in the article, then reconciled with its declared source list.

  1. 1

    Bart A. Eijkelkamp, Jacqueline R. Morey, Stephanie L. Neville et al. (2014). Eijkelkamp et al. 2014 — Extracellular Zinc Competitively Inhibits Manganese Uptake in Streptococcus pneumoniae. PLoS ONE.

  2. 2

    Patil RH, Luptakova D, Havlicek V (2021). Infection metallomics for critical care in the post-COVID era. Mass Spectrometry Reviews.

  3. 3

    Rachel L Brown, Laura Benjamin, Michael P Lunn et al. (2024). Brown et al. 2024 — Pathophysiology, Diagnosis, and Management of Neuroinflammation in COVID-19. BMJ (British Medical Journal).

  4. 4

    Srivastava J, Chandra H, Singh N et al. (2016). Understanding the Development of Environmental Resistance Among Microbes: A Review. Clean - Soil, Air, Water.

  5. 5

    Achdout H, Vitner EB, Politi B et al. (2021). Increased lethality in influenza and SARS-CoV-2 coinfection is prevented by influenza immunity but not SARS-CoV-2 immunity. Nature Communications.

Knowledge graph

Article network

Researcher discussion

Connect the evidence

Publicly readable discussion by ORCID-authenticated researchers. Questions, interpretation, methods, corrections, and new evidence stay attached to this record.

0 posts

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Transparent record

Activity and accepted changes

Accepted researcher context, editorial status, public discussion, and upstream Git revisions are shown together. Pending, declined, and withdrawn proposals remain private.

2 events
  1. published revision

    Complete corpus-wide Dysbiosis linking

    Karen Pendergrass · +1 −1

    Inspect exact Git diff ↗
  2. published revision

    massive wiki expansion: 149 stubs fixed, 100+ new pages, Rule 15 scan, keystone papers

    WikiBiome Deploy Bot · +47 −0

    Inspect exact Git diff ↗
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5 references · 1 content records · 822 corpus pages