Microbial Ecology

TWiM #314: Microbes Sculpt Our Planet and Manage Information

Podcast and Annotation Information

1. Paper Abstracts

1.1. Snippet paper; discussion starts at 3:54 minutes

The Most Interesting Things (according to students)

We still don’t know how deep microbes live within the earth. The crust of the earth is between 3 and 43 miles thick, while we have only drilled 7.6 miles into the earth. We cannot be sure whether or not there are more microbes beneath the crust or in areas of the crust that cannot yet be reached. Lovelock’s Gaia hypothesis is mentioned in the podcast, which theorizes that the Earth itself could be thought of as a living creature that absorbs, stores, and transforms energy. This is a very interesting and inviting way to think about the planet we live on!

The article has no abstract. See the full article on the New York Times website.

1.2. Main paper; discussion starts at 24:50 minutes

The Most Interesting Things (according to students)

The podcast had a great discussion around the main paper on the connections between insulin pumps and glucose monitors. The pumps and monitors are fully mechanical devices that measure interstitial glucose concentrations and dispense insulin when needed. This is similar to the functioning of the bioelectronics discussed in the paper, however, bacteria take the role of the chemical dispensers. It was interesting that ABLE reduced the conductance of the ECG. This showed that it was effective in playing an important role in signaling and mitigating symptoms that were caused by psoriasis.

The abstract cannot be copied due to licensing restrictions. Please see licensing information and links to the article at the journal’s web page and/or PubMed in Section 8.1.

2. Vision and Change Core Concepts and 2024 ASM Fundamental Statements

Snippet Main
Vision and Change Topics
  • Metabolic Pathways (V&C_MP)
  • Microbial Ecology (V&C_ME)
  • Impact of Microorganisms (V&C_IM)
  • Structure and Function (V&C_SF)
  • Microbial Ecology (V&C_ME)
ASM Fundamental Statements
  • Fundamental Statement 12 (ASM_12): Bacterial and Archaea exhibit extensive metabolic diversity, including nitrogen fixation, methane production, and anoxygenic photosynthesis, many of which are unique to these two domains.
  • Fundamental Statement 20 (ASM_20): Microbes are ubiquitous, found in diverse and dynamic ecosystems, where they use available resources and often form complex communities.
  • Fundamental Statement 6 (ASM_6): The distinct structures and processes in microbes can be targets for interspecies competition, antimicrobial treatments, and host immunity.
  • Fundamental Statement 22 (ASM_22): Most microbes interact with hosts in beneficial or neutral ways, with a minority having a detrimental impact on their host.
  • Fundamental Statement 26 (ASM_26): Humans leverage microbes and their products to address problems and improve quality of life.

3.  Potential Learning Objectives for the Podcast

The student will be able to: Paper1 Order2
  • Define chemolithotroph.
  • Identify characteristics of extreme bacteria.
 S L
  • Predict a microbe’s metabolism based on a microbe’s natural habitat.
  • Hypothesis conditions for culturing microbes from extreme environments.
 S H
  • Identify outcomes of healthy inflammation.
  • Identify the likely order of ABLE device use.
 M L
  • Predict how skin depth affects electrical signals.
  • Use a descriptions to compare the novel technology to existing systems and identify analogs between each.
 M H

1 Papers: Snippet (S) or Main (M)

2 Learning Objectives: Lower Order or Higher Order (H)

4. Techniques Described (with Time Stamps)

Here is a link to a bio-dictionary that has many, but not all definitions if you need a definition: Explore Biology Bio-Dictionary

4.1. Snippet Paper

  • Microbial Culturing (9:38–10:31): These are methods to grow microbes in laboratory environments rather than their native environment.  Here, the researchers discuss the fact that many environments here on Earth have microbes. These collective microbes together make up what we know as the microbiome. For example, the atmosphere and the ground we stand on are created and transformed by microbes. These microbes can be isolated from the earth’s crust as monocultures.
  • Sterile Technique (11:13–12:32): This is a method to ensure microbial cultures isolated from the environment are not contaminated and that scientists also do not contaminate the environment either. When drilling deep into the surface of planets to look for bacteria, scientists have started sterilizing drilling and mining equipment so as to not introduce surface microbes to buried microbes.

4.2. Main Paper

  • Inflammatory Mouse Model (24:56–31:27):  Mouse models are often used to study processes related to human disease.  Here, the authors introduce bacteria to invade the skin of a mouse, this action triggers an inflammatory response, where even the peripheral nerves, similarly detecting the bacterial components, are simultaneously signaling to turn off the response. They made it unique in the sense that they used electronics and bacteria commonly found on the skin to mimic the innate homeostatic regulation that is necessary to down regulate our immune system.
  • Cell Staining (41:55–42:43):  This is a microscopy technique used to visualize changes in tissues and cells by applying compounds that stain different features.  Here, the researchers used Hematoxylin and Eosin stain (commonly called H&E stain) and immunohistochemistry to identify different cell types and tissues. These staining techniques allowed the researchers to view psoriatic skin lesion damage, quantify macrophage activity, and identify blood vessel dilation.

5. Connections to General Microbiology Processes/Concepts (with Time Stamps)

5.1. Snippet Paper

  • Electron Transport Chain (7:54–8:25): Chemolithotrophs utilize inorganic molecules within their electron transport chain as oxidizing agents to generate ATP instead of using organic molecules such as NADH.
  • Chemotrophy vs Phototrophy (7:54–8:47): The microbes in the paper make their own energy by obtaining minerals from their surrounding environment. This makes sense because they are so far beneath the surface of the earth that they probably don’t receive any sunlight to make their own energy through photosynthesis.
  • Carbon Fixation (14:08–14:15): Desulforudis audaxviator created organic carbon compounds from inorganic compounds such as CO2.

5.2. Main Paper

  • Inflammatory Response (24:56–31:27): Pattern Recognition Receptors on our cells detect Pathogen Molecular Patterns on microbes which triggers the inflammatory pathway as a way to activate the immune system and defend our body. In the podcast, they talk about the interaction between the human immune system and microbes. They then explain how prolonged activation of the inflammatory response can lead to several autoimmune diseases.
  • Regulation of Gene Expression (35:00–43:49): The ABLE device was efficient in reducing the conductance of the ECG. By using various chemical messengers to send and receive information to other cells, the ABLE system utilizes the messengers to control inflammation and ultimately reduce the symptoms caused by psoriasis.

6. Podcast Questions

  1. Chemolithotrophs reduce _______ for electron transport and ATP generation.
    1. organics
    2. sunlight
    3. minerals
    4. oxygen
  2. Desulforudis audaxviator is a bacterium that was identified 2.8 km or1.7 miles below the earth’s surface.  Which of the following is are noted as characteristics of this bacterium?
    1. fixes inorganic carbon compounds
    2. has a single polar flagellum
    3. is baguette-shaped and dark red
    4. tolerates temperatures up to 80C
    5. uses energy from decaying uranium
  3. The deepest and most productive gold mine in North America, the Homestead Mine, is up to 370 miles in length and 1.5 miles below the surface. In this mine, a group of bacteria called Thiothrix was found. Based on its habitat/location, what does Thiothrix most likely used in its metabolism?
    1. Iron
    2. Nitrogen
    3. Sulfur
    4. oxygen
  4. If you were to want to grow these extreme bacteria in the lab, what conditions would you likely need to provide?
    1. inorganic medium compounds
    2. high atmospheric pressure
    3. anaerobic growth conditions
    4. extreme low temperature
  5. Which of the following is/are associated with healthy inflammation?
    1. antigen presentation
    2. anti-microbial defense
    3. wound healing
    4. lysosomal degradation
  6. Identify the organism that is an opportunistic pathogen given its description.
    1. Coccidioides immitis is a highly virulent fungus that is native to desert-type soils and causes fever and coughing in otherwise healthy individuals.
    2. Streptococcus agalactiae colonizes the gastrointestinal tract of healthy adults without symptoms, but can cause sepsis, meningitis, and pneumonia.
    3. Saccharomyces cerevisiae is used to make bread rise and  can colonize the human gut and may have anti-inflammatory and antibacterial properties.
    4. Cucumber Mosaic Virus infects many species of plants, causing yellowing, shriveled leaves, and necrosis, but may allow beetroot to be drought tolerant.
  7. In conditions like psoriasis, the skin thickens when cells grow on top of each other.  Skin depth can be measured by its ability to conduct an electrical signal.  The loss of electrical signaling is quantified as impedance.  What are the relative levels of impedance you would expect for normal and psoriatic skin?
    1. Normal skin would have low impedance and psoriatic skin would have high impedance.
    2. Normal skin would have high impedance and psoriatic skin would have low impedance.
    3. Normal skin would have no impedance and psoriatic skin would have impedance.
    4. Normal skin would have high impedance and psoriatic skin would have no impedance.
  8. Bio-integrated living electronics can be used to regulate inflammation and promote skin regeneration. All of the following have a role in managing inflammation. What is the most likely order for their use.

1 = Delivery of living cells to inflamed tissues with sensor-based monitoring of physiology to mimic the homeostatic regulation.

2 = Coordinate electrical signaling and collect information from the skin in order to manage the biosafety of the bacteria.

3 = Apply a current to uncouple the membrane potential of microbes to cause bacterial death.

    1. 1, 2, 3
    2. 3, 2, 1
    3. 1, 3, 2
    4. 2, 1, 3
  1. The novel biomedical technology discussed in this podcast uses monitoring disease in real time and adjusting treatment as needed. Of the options below, which is most different to the novel biomedical technology system?
    1. A pacemaker monitors heart rate and rhythm.  It intercedes by delivering electrical signal when the rate or rhythm is abnormal.
    2. A washing machine has a sensor to adjust the water level to the amount of material inside, even if more material is added.
    3. A live, attenuated vaccine is injected intramuscularly and produces an immune response to protect against specific  viruses.
    4. An embedded glucose monitor detects blood sugar levels communicates with the insulin pump to deliver insulin to the patient.

7. Figure Reading Exercises

The following are two figure reading exercises, one from the main paper (Figure 3ACDGH) and another from the commentary piece, which has only one figure (Figure 1).

7.1. First Figure Reading Exercise

7.1.1. Learning Objectives

Students will be able to:

  • Predict the purpose of an ABLE component based on diagrams.
  • Identify the uses of the ABLE based on the experimental results that are shown.
  • Use data presented to justify ABLE as an effective system for monitoring/screening of psoriasis.
  • Use data presented to justify ABLE as an effective system for treatment of psoriasis.
Experimental Background (Shi et al., Figure 3ACDGH)

An interface between biomedical equipment and biological tissue would lead to improvements in diagnosis and treatments for many skin conditions including psoriasis.  With this goal in mind, Shi et al. (2024) created active biointegrated living electronics (ABLE), which they tested for  signal recording in the diagnosis and treatment of psoriasis.  They compared electrical signal recording by comparing the device recording to an electrocardiogram for heart (panel C) and  skin of psoriasis-affected and control people (panel D).  They next tested the diagnostic and treatment ability of the device by determining whether the device could detect differences in psoriatic and healthy skin as treatment was administered (panel G, H).  Finally, the examined whether the device could be internally disinfected, which is visualized by bacterial staining and normalized viability (panel I).

  • Figure 3 cannot be copied due to licensing restrictions. Please see licensing information and links to the article at the journal’s web page and/or PubMed in Section 8.1.

7.1.2. Questions

  1. The researchers perform a number of experiments using their ABLE technology.  Which of the following were not tested in these experiments?
    1. Electrophysiological signal recording
    2. Electromagnetic signal recording
    3. Diagnosis of psoriasis
    4. Treatment of psoriasis
  2. What is the purpose of the hydrogel, which is shown in Figure 3B, E, and I?
    1. To disinfect the rat epidermis
    2. To protect the skin during treatment
    3. To provide a habitat for bacterial growth
    4. To prevent the flow of electricity
  3. What are some of the visible psoriasiform features that ABLE has been shown to treat successfully (panel G)?
    1. Erythema: a skin condition that causes redness, inflammation, or discoloration of the skin or mucous membranes.
    2. Induration: thickening and hardening of soft tissue, especially the skin.
    3. Desquamation: the medical term for peeling skin, which is the process by which the body sheds dead skin cells from the epidermis, or outermost layer of skin.
    4. All of the above
  4. Which panel(s) shows data testing the ability of ABLE to monitor psoriasis?  Was ABLE successful? What is your evidence?
    1. H; yes; H compares impedance of signal (ABLE) to PSI scores (visual) and both score are reduced by ABLE treatment compared to control.
    2. D; yes; D compares the ECG signal for psoriasis patients and healthy patients with psoriasis being statistically different than controls.
    3. I; yes; I shows that bacteria involved in the psoriatic infection can be killed with the application of electricity delivered via electrodes.
    4. C; yes; C shows that electrocardiogram signaling and ABLE signal recovery are nearly equivalent with ABLE improved at stage III.

7.2. Second Figure Reading Exercise (Commentary Paper)

7.2.1. Learning Objectives

Students will be able to:

  • Identify key features of homeostatic regulation using the model diagram.
  • Identify key features of the device mimicking homeostatic regulation using the model diagrams.
  • Perform comparative analysis of innate and device homeostatic signaling.
Experimental Background (Olofsson et al., Figure 1)

Health is maintained when physiological systems are balanced, for example, when inflammation is started during an immune response and resolves when a pathogen is cleared.  However, this homeostatic balance can be disrupted and cause disease.  Olofsson (2024) provides a model and overview of inflammatory homeostasis as it relates to the primary literature paper Shi et al (2024) in the same issue of Science.  In addition to the model of skin homeostasis that depicts  the controlling and monitoring signals that the nervous system uses (left panel), the author also provides an overview of Shi’s medical/biological device proposed for both monitoring and treating disease (right panel).

  • Figure 1 cannot be copied due to licensing restrictions. Please see licensing information and links to the article at the journal’s web page and/or PubMed in Section 8.3.

7.2.2. Questions

  1. Which system is responsible for both monitoring and resolving physiologic signals in the innate skin environment?
    1. Inflammed skin
    2. Immune system
    3. Nervous system
    4. Electronic sensors
  2. In the innate model. monitoring and resolving molecules are released or produced and are identified as _______ and _____ , respectively.
    1. immune cell; control signal
    2. inflammation-associated factor; control signal
    3. control signal; neuron
    4. inflammed skin; inflammation-associated factor
  3. What part of the adaptive medical device mimics the control signal in the innate system?
    1. sensor/electronics
    2. hydrogel
    3. therapeutic bacteria
    4. disease-resolving factor
  4. What part of the adaptive medical device mimics the monitoring system  in the innate system?
    1. sensor/electronics
    2. hydrogel
    3. therapeutic bacteria
    4. disease-resolving factor

8. Paper Information and Licensing

8.1. Snippet paper

8.2. Main paper

  • Shi J, Kim S, Li P, Dong F, Yang C, Nam B, Han C, Eig E, Shi LL, Niu S, Yue J, Tian B. 2024. Active biointegrated living electronics for managing inflammation. Science. 384(6699): 1023-1030. doi: 10.1126/science.adl1102.
  • This article is not licensed for Creative Commons use; thus, the abstract and figures cannot be copied here. Please see the article at the journal’s web page: https://www.science.org/doi/10.1126/science.adl1102

8.3. Commentary paper

  • Olofsson PS. 2024. Living bioelectronics resolve inflammation. Science. 384(6699):962-963. doi: 10.1126/science.adp5201.
  • This article is not licensed for Creative Commons use; thus, the abstract and figures cannot be copied here. Please see the article at the journal’s web page.

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Podcast Annotation and Resources in Microbiology Copyright © 2025 by Rebecca Seipelt-Thiemann; Nancy Boury; Gwendowlyn S. Knapp; Amaya Garcia Costas; and Patrick Armstrong is licensed under a Creative Commons Attribution 4.0 International License, except where otherwise noted.

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