Monday, November 16, 2020

438 - Bacteria Bait Bug Babies

Drosophila fruit fly
By André Karwath
CC BY-SA 2.5
This episode: Actinomycete bacteria are often helpful to insects, but some can be deadly yet still attractive!

Download Episode (5.7 MB, 8.3 minutes)

Show notes:
Microbe of the episode: Streptomyces corchorusii


Takeaways
Actinomycete bacteria do a lot of interesting things. They grow like fungi, with mycelia and spores, and produce many interesting compounds, including antibiotics and other useful pharmaceuticals. They often team up with insects, producing such compounds to assist them in competing with other organisms or resisting disease.

But such amazingly helpful powers of chemistry can also be amazingly harmful. In this study, multiple strains of these bacteria were able to kill fruit fly larvae that ingested their spores. The toxin the bacteria produced was a chemical that interferes with cells' DNA-protein interactions. The bacteria also produced an odor that, in certain concentrations, lured the larvae to their doom.

Journal Paper:
Ho LK, Daniel-Ivad M, Jeedigunta SP, Li J, Iliadi KG, Boulianne GL, Hurd TR, Smibert CA, Nodwell JR. 2020. Chemical entrapment and killing of insects by bacteria. Nat Commun 11:4608.

Other interesting stories:
Also news, Feedspot ranked BacterioFiles in the top 5 virology podcasts! Check out the list for other good shows about viruses.

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Monday, November 9, 2020

437 - Balmy Bacteria Build Bone

Porous interior of bone
By Daniel Ullrich Threedots
CC BY-SA 3.0
This episode: Warmth helps mice build stronger bones, mediated by bacteria producing certain compounds!

Download Episode (6.8 MB, 9.9 minutes)

Show notes:
Microbe of the episode: Aquaspirillum serpens


Takeaways
Bones aren't just solid, structural supports for the body's tissues. They're active and alive, housing important components of the immune system, and also capable of being broken down and built up in response to changes in the body's interactions with the environment. Various things can affect bone mass and health, including nutrition, temperature, age, and even the body's microbes.

In this study, two of these effects are found to interact. Warmth leads to increased bone density in mice, and this effect can be attributed to the microbes in the mice, and transmitted from one mouse to another just by transplanting microbes adapted to warmth. Even the particular chemicals the microbes produce that mediate this effect are discovered.

Journal Paper:
Chevalier C, Kieser S, Çolakoğlu M, Hadadi N, Brun J, Rigo D, Suárez-Zamorano N, Spiljar M, Fabbiano S, Busse B, Ivanišević J, Macpherson A, Bonnet N, Trajkovski M. 2020. Warmth Prevents Bone Loss Through the Gut Microbiota. Cell Metab 32:575-590.e7.

Other interesting stories:

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Monday, October 26, 2020

436 - Copper Concentrates Culture Current

Geobacter sulferreducens
By Mantapia11147,
CC BY-SA 4.0
This episode: Copper electrodes, rather than killing bacteria in microbial fuel cells, allow them to generate higher densities of electric current!

Download Episode (5.0 MB, 7.2 minutes)

Show notes:
Microbe of the episode: Xipapillomavirus 2


Takeaways
Copper is widely used as a way to make surfaces and materials antimicrobial, to cut down on the spread of pathogens in hospitals and other environments. Among other mechanisms, it reacts with oxygen to form reactive oxygen species that are very harsh on microbial proteins. But copper is also a good electrical conductor, which would be useful to use in microbial fuel cells, which exploit bacterial metabolism to generate electricity. Microbes form biofilms on an electrode and transfer electrons to it as a way for them to generate energy. Most such fuel cells have used graphite electrodes to avoid toxicity.

In this study, fuel cell bacteria grew well on a copper electrode in an oxygen-free environment. The copper actually allowed them to increase the amount of current they produced per unit of area, as ionic copper diffused through the biofilm and allowed electrons to flow through the biofilm to the electrode from layers farther from the electrode that otherwise would not have access. Even graphite electrodes could be improved by adding these copper ions to the biofilm directly.

Journal Paper:
Beuth L, Pfeiffer CP, Schröder U. 2020. Copper-bottomed: electrochemically active bacteria exploit conductive sulphide networks for enhanced electrogeneity. Energy Environ Sci 13:3102–3109.

Other interesting stories:

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Monday, October 19, 2020

435 - Invader Introducing Infrared Invokes Immunity

Mouse with darkened tumor
By Yi et al. 2020,
Sci Adv 6:eaba3546
CC BY-NC 4.0

This episode: Combining Salmonella with something called photoimmunotherapy to attack tumors in multiple ways!

Download Episode (8.2 MB, 11.9 minutes)

Show notes:
Microbe of the episode: Shimwellia blattae

Takeaways
Distinguishing healthy from unhealthy tissue is one of the big challenges when dealing with cancer. Since cancer is derived from healthy tissue, there are many similarities between them that make it hard to target it specifically. This is especially important when cancer is spread in multiple places throughout the body, as opposed to a single tumor that can be removed locally.

In this study, bacteria modified to make them safer were injected into mice with tumors. The bacteria alone were capable of doing some damage to the tumors, and this damage happened to make the tumors darker. Using this color change, the scientists targeted the tumors with lasers to heat them up and kill them in an isolated manner. This had the added benefit of inducing an immune response against the cancer that could target it throughout the body.

Journal Paper:
Yi X, Zhou H, Chao Y, Xiong S, Zhong J, Chai Z, Yang K, Liu Z. 2020. Bacteria-triggered tumor-specific thrombosis to enable potent photothermal immunotherapy of cancer. Science Advances 6:eaba3546.

Other interesting stories:

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Monday, September 28, 2020

434 - Killer Carries Compact Cas

T4 bacteriophage
By Victoramuse
CC BY-SA 4.0
This episode: Large phage discovered that contains a compact version of the CRISPR/Cas defense/gene editing system!

Download Episode (5.9 MB, 8.6 minutes)

Show notes:
Microbe of the episode: Stenotrophomonas virus IME13

News item

Takeaways
CRISPR/Cas systems have made a lot of things in gene editing much easier in certain organisms. It's almost as easy as just getting the cells to produce the Cas protein and putting in an RNA sequence to tell it where to go! But in some cases, these requirements are too much to work well.

In this study, a more compact version of CRISPR/Cas was discovered in large bacteriophages. These systems help the viruses compete with other viruses and defend against host defenses sometimes. The Cas protein is half the size of the standard Cas most used in gene editing, and it has fewer other requirements to function in new cells, so it could be better in versatility and potential in applications with strict space constraints.

Journal Paper:
Pausch P, Al-Shayeb B, Bisom-Rapp E, Tsuchida CA, Li Z, Cress BF, Knott GJ, Jacobsen SE, Banfield JF, Doudna JA. 2020. CRISPR-CasΦ from huge phages is a hypercompact genome editor. Science 369:333–337.

Other interesting stories:

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Monday, September 21, 2020

433 - Probiotic Promotes Pathogen Peacefulness

E. coli in lumen of organoid
From Pradhan and Weiss, 2020
mBio 11(4):e01470-20
CC BY 4.0

This episode: A probiotic can protect intestine-like cell growths from destruction by pathogens, but it can also be infected by a virus that makes it more harmful to intestinal cells!

Download Episode (6.9 MB, 10.1 minutes)

Show notes:
Microbe of the episode: Euphorbia yellow mosaic virus

News item

Takeaways
There are many strains of Escherichia coli. Some are pathogenic, in the gut or the urinary tract, and a subset of those are very dangerous, such as the enterohemorrhagic O157:H7 strain. Many others are commensals, living peacefully as part of our gut community. And some strains can be beneficial to the host, protecting from and reducing the severity of disease. One such strain is called E. coli Nissle.

This study used an advanced model of human intestines called organoids, where stem cells are induced to develop into hollow spheres of intestinal epithelium in which all cell types of a normal intestinal wall are represented. E. coli pathogens typically destroy these organoids and escape from inside, but Nissle was able to prevent this destruction and enable coexistence between the pathogen and the host cells. Nissle suffered for this protection though; O157:H7 carries a toxin-encoding phage that can infect and kill susceptible E. coli strains. Those Nissle cells that survived this infection could resist the phage, but were not as beneficial to the organoids due to the toxin they now produced.

Journal Paper:
Pradhan S, Weiss AA. 2020. Probiotic Properties of Escherichia coli Nissle in Human Intestinal Organoids. mBio 11(4):e01470-20.

Other interesting stories:

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Monday, September 7, 2020

432 - Moses Microbes Maintain Moisture

Gypsum
This episode: Bacteria living in the driest place on earth have ways to extract water from the mineral structures of rocks!

Download Episode (3.7 MB, 5.4 minutes)

Show notes:
Microbe of the episode: Irkut lyssavirus

News item

Takeaways
Microbes living in extremely dry conditions have it tough. Water is important both for the chemistry and structure of all cells. Desert microbes are very good at acquiring and holding on to the water they can find, but in places such as the Atacama Desert in Chile, there's almost none available.

However, microbes can be very resourceful. In this study, phototrophs were discovered that can actually extract water molecules bound up in the crystalline structure of the mineral gypsum, and this allows them to survive in hyperarid regions. They do this by secreting organic acid molecules to etch the rock and release the water, converting gypsum to anhydrite, which is a mineral with the same chemical structure except without the water.

Journal Paper:
Huang W, Ertekin E, Wang T, Cruz L, Dailey M, DiRuggiero J, Kisailus D. 2020. Mechanism of water extraction from gypsum rock by desert colonizing microorganisms. Proc Natl Acad Sci 117:10681–10687.

Other interesting stories:

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Monday, August 31, 2020

431 - Conductive Cables Control Carbon

Cable bacteria around
plant roots
From Scholz et al. 2020
Nat Commun 11:1878

This episode: Cable bacteria around rice roots transport electrons and help prevent formation of methane!

Thanks to Vincent Scholz for his contribution!  
Download Episode (5.7 MB, 8.3 minutes)

Show notes:
Microbe of the episode: Vibrio alginolyticus

News item

Takeaways
Transforming other things into methane is a great way to make a living for some kinds of microbes. These tend to live under still water, like in rice fields or wetlands, or in the guts of cattle. And while this methane could be useful as natural gas if collected, it's a much more potent greenhouse gas than carbon dioxide when released into the atmosphere.

In this study, cable bacteria were inoculated into rice pots in the lab. Cable bacteria transfer electrons from deeper down in the ground up to the surface to generate energy, and in the process generate sulfate. This sulfate allows other microbes to outcompete the methane producers, reducing the amount of methane produced from rice cultivation in the lab. This may be helpful to reduce greenhouse gas emissions from rice agriculture.

Journal Paper:
Scholz VV, Meckenstock RU, Nielsen LP, Risgaard-Petersen N. 2020. Cable bacteria reduce methane emissions from rice-vegetated soils. 1. Nat Commun 11:1878.

Other interesting stories:

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Monday, August 24, 2020

430 - Dextrose Deposits Delay Dormancy

E. coli
This episode: Bacteria that can store sugar as glycogen have multiple advantages when food is only available sporadically!
Download Episode (7.2 MB, 10.4 minutes)

Show notes:
Microbe of the episode: Carnivore bocaparvovirus 3

Takeaways
Almost all habitats experience some sort of change and fluctuation; very few are totally stable, depending on the timeframe. So strategies to change and adapt with changing conditions can greatly help an organism thrive. For example, methods of storing energy are helpful when food is only available sporadically.

Some bacteria, like humans, can store sugar in a polymer called glycogen, which can be quickly produced when food is abundant and quickly broken down to ease a transition to fasting. In this study, bacteria that could produce and use glycogen were able to stay active longer and grow better in the face of intermittent starvation. They were even better able to acquire new food when more became available.

Journal Paper:
Sekar K, Linker SM, Nguyen J, Grünhagen A, Stocker R, Sauer U. 2020. Bacterial Glycogen Provides Short-Term Benefits in Changing Environments. Appl Environ Microbiol 86.

Other interesting stories:

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Monday, August 17, 2020

429 - Springtails Smell, Spread Streptomyces

Springtail Folsomia candida
By Andy Murray
CC BY-SA 2.0

This episode: Bacteria in soil produce smells to attract arthropods that eat them but also spread their spores!

Download Episode (6.2 MB, 9.0 minutes)

Show notes:
Microbe of the episode: Blotched snakehead virus

News item

Takeaways
Soil, especially after a rain, often has a characteristic "earthy" smell. This soil smell is actually the result of certain bacteria producing a volatile chemical called geosmin. Many geosmin producers are in the Streptomyces genus, which produces a large variety of interesting chemicals, but geosmin is one of the few that is nearly universal in the genus.

This study found that insect-like arthropods called springtails are attracted to geosmin. These animals usually feed on fungi, but they will also eat bacteria when available. Despite this result, the bacteria continue to produce the chemical, which is linked to their sporulation cycle. The study found that springtails carry intact bacterial spores to new places stuck to the insides and outsides of the animal, and this enhances the dispersal ability of the bacteria.

Journal Paper:
Becher PG, Verschut V, Bibb MJ, Bush MJ, Molnár BP, Barane E, Al-Bassam MM, Chandra G, Song L, Challis GL, Buttner MJ, Flärdh K. 2020. Developmentally regulated volatiles geosmin and 2-methylisoborneol attract a soil arthropod to Streptomyces bacteria promoting spore dispersal. 6. Nat Microbiol 5:821–829.

Other interesting stories:

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Monday, August 10, 2020

428 - Microbes May Manage Mysteries


This episode: The skin microbes that people leave behind may be used to identify them, even after other people have touched the same surface!


Download Episode (5.4 MB, 7.9 minutes)

Show notes:
Microbe of the episode: Actinobacillus lignieresii

Takeaways
The microbial communities in and on our bodies are highly complex and highly varied between people; this complexity has raised the question of whether the microbes that people transfer onto things they touch could be used in forensics, to track their movement and activity, like fingerprints or DNA evidence. One difficulty with this approach is that microbe communities are constantly changing as conditions change or other microbes are introduced.

This study simulated such microbial tracking in a couple of scenarios, such as touching door handles in an office building and touching various surfaces in a home in a mock burglary. Tracking a person on door handles worked fairly well for up to an hour after the contact, even if other people had also touched the same door handles. However, the accuracy of identifying the "burglar" in a home was not very high, but modifying the analysis from looking at the community as a whole to only rare microbes relatively unique to an individual improved the results.

Journal Paper:
Hampton-Marcell JT, Larsen P, Anton T, Cralle L, Sangwan N, Lax S, Gottel N, Salas-Garcia M, Young C, Duncan G, Lopez JV, Gilbert JA. 2020. Detecting personal microbiota signatures at artificial crime scenes. Forensic Sci Int 313:110351.

Other interesting stories:

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Monday, August 3, 2020

427 - Simple Cells Stay Strong

Fluorescent SimCells
By Fan et al. 2020,
PNAS 117(12):6752
CC BY 4.0
This episode: Bacterial cells with their genomes removed can still be active and useful!


Download Episode (10.2 MB, 14.9 minutes)

Show notes:
Microbe of the episode: Rosavirus A

Takeaways
Microbes have amazing biochemical transformation abilities, creating and breaking down many compounds and proteins. This makes them great candidates for many purposes, in medicine, industry, and environmental remediation. In some of these purposes, though, there are risks associated with adding foreign microbes, especially engineered ones, that can replicate themselves and possibly persist, into new places.

To avoid this risk, this study turns intact bacteria into SimCells, simplified entities with most of their genetic material removed, leaving only the proteins and other components and just enough DNA to accomplish desired tasks. These SimCells were able to continue performing tasks for around 10 days before running out of the cellular resources needed to keep going. One of these tasks was producing a compound that damaged cancer cells in a dish but left non-cancerous cells unharmed.

Journal Paper:
Fan C, Davison PA, Habgood R, Zeng H, Decker CM, Salazar MG, Lueangwattanapong K, Townley HE, Yang A, Thompson IP, Ye H, Cui Z, Schmidt F, Hunter CN, Huang WE. 2020. Chromosome-free bacterial cells are safe and programmable platforms for synthetic biology. Proc Natl Acad Sci 117:6752–6761.

Other interesting stories:

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Monday, July 27, 2020

426 - Sensory Cilia Supply Susceptibility

C. elegans roundworm
By Bob Goldstein, UNC Chapel Hill
CC BY-SA 3.0
This episode: A fungus paralyzes its tiny worm prey by acting on the worm's own sensory hairs!


Download Episode (6.0 MB, 8.7 minutes)

Show notes:
Microbe of the episode: Bat associated cyclovirus 9

Takeaways
Not all predators are fast or agile; some are sneaky, or good trap builders, or just good chemists. The predator club includes animals but also plants and even fungi. For example, the oyster mushroom fungus can paralyze roundworms in the soil that touch its filaments, then degrade their bodies and consume their nutrients.

The mechanism of this paralysis has been a mystery, but it's one step closer to being solved. This study found that intact sensory cilia, little hairs on the worm's head that help it sense its surroundings, are required for the paralysis to work. Worms with mutations in the structure of their cilia were protected from paralysis. How exactly the fungus acts on these cilia and the neurons they connect to, though, is still unknown.

Journal Paper:
Lee C-H, Chang H-W, Yang C-T, Wali N, Shie J-J, Hsueh Y-P. 2020. Sensory cilia as the Achilles heel of nematodes when attacked by carnivorous mushrooms. Proc Natl Acad Sci 117:6014–6022.

Other interesting stories:

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Monday, June 22, 2020

425 - Paired Predators Prevent Pathogen Persistence

Haloed plaques, Bdellovibrio,
and bacteriophage
By Hobley et al. 2020,
J Bacteriol 202(6), CC BY 4.0
This episode: A bacteriophage and bacterial predator can wipe out a population of bacteria that could develop resistance to each individually!

Thanks to Laura Hobley, J. Kimberley Summers, and Jan-Ulrich Kreft for their contributions!

Also a note: I will be taking a short break from podcasts while I rebuild my collection of awesome microbiology stories to talk about.


Download Episode (6.8 MB, 9.9 minutes)

Show notes:
Microbe of the episode: Blackbird associated gemycircularvirus 1

Takeaways
Bacteriophages and bacterial predators that prey on other bacteria are both very good at killing large numbers of bacteria. But bacteria as a whole are also very good at surviving being killed in large numbers; there are almost always a few that have the right genes to overcome whatever is doing the killing. This is what makes the threat of antibiotic resistance so scary, and why phage therapy is both very promising and very limited.

In this study, however, a combination of phages and the bacterial predator Bdellovibrio bacteriovorans is able to completely eradicate a population of bacteria, or at least reduce their numbers below a detectable level. A mathematical model based on these data predicts that despite the two killers working independently, they can effectively eliminate all the individual prey organisms that would otherwise be able to resist killing by either one alone.

Journal Paper:
Hobley L, Summers JK, Till R, Milner DS, Atterbury RJ, Stroud A, Capeness MJ, Gray S, Leidenroth A, Lambert C, Connerton I, Twycross J, Baker M, Tyson J, Kreft J-U, Sockett RE. 2020. Dual Predation by Bacteriophage and Bdellovibrio bacteriovorus Can Eradicate Escherichia coli Prey in Situations where Single Predation Cannot. J Bacteriol 202.

Other interesting stories:

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Monday, June 15, 2020

424 - Stranger Cells Switch Stable States

Lactobacillus bacteria

Pelzer et al. 2012, PLOS One e49965

This episode: Certain bacteria can greatly affect the makeup of a microbial community, even if they quickly disappear!

Thanks to Dr. Daniel Amor for his contribution!


Download Episode (6.3 MB, 9.2 minutes)

Show notes:
Microbe of the episode: Gadgets Gully virus

News item

Takeaways
Microbial communities show more than just competition between species. Stable assemblies of many species can exist for long periods in places like the human gut, despite constant minor shifts in conditions. More major shifts, or invaders like pathogens coming in and taking over, can cause big disruptions in the community and lead to long-term gut dysbiosis, which can be, interestingly, also a stable community. 

This study shows that invaders into a community, even if they don't persist for very long, can cause a shift from one stable state to another, by favoring the dominance of a species or group that was not dominant before, for example by changing the pH of the environment. So competition is always present. This could be helpful to know for efforts to intentionally shift community structures.

Journal Paper:
Amor DR, Ratzke C, Gore J. 2020. Transient invaders can induce shifts between alternative stable states of microbial communities. Sci Adv 6:eaay8676.

Other interesting stories:

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Monday, June 8, 2020

423 - Roundworm Riders Route Rootworm Resistance

Western corn rootworm adult

By Siga, CC BY-SA 4.0

This episode: Helping insect-killing bacterial symbionts of nematodes evolve resistance to chemicals that major corn pests use to defend themselves!


Download Episode (10.0 MB, 14.0 minutes)

Show notes:
Microbe of the episode: Listeria virus PSA

Takeaways
Interactions between species and even kingdoms in nature can be complex and multilayered. This means that when we want to intervene to cause a particular outcome, there may be multiple points at which we can act, but the consequences may be hard to predict.

In this study, action was taken to counteract the damage the Western corn rootworm causes to corn crops, using a tiny roundworm that attacks the insect pest with deadly bacteria. The rootworm defends itself by accumulating plant-produced toxins that inhibit the bacteria. Directed evolution was used to make the bacteria more resistant, and this led to more effective killing of the pest.

Journal Paper:
Machado RAR, Thönen L, Arce CCM, Theepan V, Prada F, Wüthrich D, Robert CAM, Vogiatzaki E, Shi Y-M, Schaeren OP, Notter M, Bruggmann R, Hapfelmeier S, Bode HB, Erb M. 2020. Engineering bacterial symbionts of nematodes improves their biocontrol potential to counter the western corn rootworm. 5. Nat Biotechnol 38:600–608.

Other interesting stories:

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Monday, June 1, 2020

422 - Frigid Phototrophs Fuel Fords

Algae growing in 20-liter bioreactor

Kim et. al, 2020. CC BY 4.0

This episode: Producing both biodiesel and bioethanol fuels from cold-loving Arctic algae!


Download Episode (8.7 MB, 12.6 minutes)

Show notes:
Microbe of the episode: Royal Farm virus

Takeaways
Renewable fuels such as biofuels can allow existing infrastructure and vehicles to continue to operate in a more sustainable manner, which could reduce the cost and impact of switching to new/different systems of transportation like electricity. Economically competitive methods of producing biofuels are still being explored and developed.

In this study, Arctic algae are grown in cold temperatures using only light, carbon dioxide, and a few minerals, and then broken down to produce biodiesel and bioethanol, which can be used as fuel in many different internal combustion engines. The amounts produced are comparable to other algae-based systems being researched, and use of the cold-loving organisms could reduce the cost of production in colder latitudes and seasons.

Journal Paper:
Kim EJ, Kim S, Choi H-G, Han SJ. 2020. Co-production of biodiesel and bioethanol using psychrophilic microalga Chlamydomonas sp. KNM0029C isolated from Arctic sea ice. Biotechnol Biofuel 13:20.

Other interesting stories:

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Monday, May 25, 2020

421 - Nucleocapsids Navigate Nano Nuggets

Gold nanorods bound to phage
Used with permission
This episode: Using phages to target gold nanoparticles to infecting bacteria, then using light to heat the nanoparticles just enough to kill the bacteria!

Thanks to Huan Peng and Raymond Borg for contributing!


Download Episode (10.6 MB, 15.4 minutes)

Show notes:
Microbe of the episode: Pantoea agglomerans

News item

Takeaways
Viruses that infect bacteria, bacteriophages, are often very good at overcoming bacterial defenses and killing them. This raises the possibility, and many times actuality, of using phages to treat bacterial infections that are no longer treatable with antibiotics. But bacteria can evolve resistances to viruses as well as drugs, and using multiplying, evolving entities as treatments in people raises questions about the safety and consistency of the treatment.

This study circumvents these questions by using phages for delivery and targeting of bacteria rather than the therapeutic agent itself. The actual treatment is done with tiny rods of gold, gold nanorods, bound to the phage surface. When a certain wavelength of light hits these nanorods, they vibrate enough to generate enough heat in their immediate surroundings to render nearby bacteria nonviable. Thus the infection is treated in a very localized, targeted way that doesn't leave any active bacteria or phages behind. The authors have plans to study this approach as a topical treatment of wounds.

Journal Paper:
Peng H, Borg RE, Dow LP, Pruitt BL, Chen IA. 2020. Controlled phage therapy by photothermal ablation of specific bacterial species using gold nanorods targeted by chimeric phages. Proc Natl Acad Sci 117:1951–1961.

Other interesting stories:

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Monday, May 18, 2020

BacterioFiles 420 - Cell Societies Stay Stable

Bacteroides species
This episode: Simplified gut communities growing in bioreactors grow and metabolize reproducibly, with only moderate variations, even when individual members of the community are absent!


Download Episode (8.2 MB, 11.9 minutes)

Show notes:
Microbe of the episode: Citrobacter virus Merlin

Takeaways
The community of microbes in our guts is highly complex, with thousands of species all interacting with each other, with our own cells, and with the contents of our diet. Each region of the gut has a different collection of microbes as well. Many questions remain to be answered about the functions and fluctuations of these communities. How can we study such a complex system? Which species, if any, are most important for its continued function?

In this study, a simplified community of only 14 species is grown repeatedly in bioreactors, and one species at a time is left out of the community to see what will change in its absence. This reveals effects different species have on the overall growth, carbon source consumption, and production of various metabolites relevant to gut health. Some microbes have large effects, but none of them appears to be crucial for the overall function and stability of the community.

Journal Paper:
Gutiérrez N, Garrido D. 2019. Species Deletions from Microbiome Consortia Reveal Key Metabolic Interactions between Gut Microbes. mSystems 4:e00185-19.

Other interesting stories:

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Monday, May 11, 2020

BacterioFiles 419 - Marine Methane Microbe Multiplication

Anaerobic methanotrophs
BacterioFiles is back! This episode: Measuring how quickly marine methane-consuming microbes become active when new methane enters an area!


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Show notes:
Microbe of the episode: Torque teno midi virus 6

Takeaways
Oceans and the organisms living in them have a large effect on the planet, in terms of climate and gases they absorb from or release into the atmosphere. They are a source of much of a potent greenhouse gas, methane, but microbes living in ocean sediments also consume large amounts of methane. These anaerobic methanotrophic archaea generate energy for themselves by transforming methane and sulfate into carbonate and sulfide.

In this study, however, methane-consuming microbes were only found active at sites of methane seepage. Even in sites where methane had previously been present, only few of these microbes were present and active. After enriching samples of these sediments for up to 8 months, still the only activity that was seen was from actively methane-consuming communities. So once dispersed, such communities seem slow to regenerate as the locations of methane seepage shift.

Journal Paper:
Klasek S, Torres ME, Bartlett DH, Tyler M, Hong W-L, Colwell F. 2020. Microbial communities from Arctic marine sediments respond slowly to methane addition during ex situ enrichments. Environ Microbiol 22:1829–1846.

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Monday, March 16, 2020

BacterioFiles 418 - Special Sea Species Swallows Cells

New microbe engulfing prey
By Shiratori et al. 2019
Nat Commun 10(1):1-11, CC BY 4.0
This episode: A newly discovered species of bacteria consumes other bacteria as prey by engulfing them!

Also a note to listeners: Because things are hectic at work right now (unless that changes due to current events), I'm planning to put the show on hold for a few weeks. So if you don't see new episodes, that's why.


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Show notes:
Microbe of the episode: SARS-CoV-2! This is the coronavirus responsible for COVID-19, the current pandemic. For more up-to-date information, please refer to the American Society for Microbiology, This Week in Virology, and other reputable sources. Stay healthy!

Takeaways
There are bacteria living almost every different lifestyle you can think of, including predatory, preying on other bacteria. Since bacterial cells are usually quite rigid, bacterial predators usually consume others either by burrowing inside them or digesting them from outside, rather than engulfing prey like eukaryotes often do.

The study here discovers a new kind of bacteria, in the group called Planctomycetes, known for having unusually flexible cells and internal compartments like eukaryotes. This new species does engulf its prey, including bacteria and even tiny algae, and digests them inside itself. It possesses multiple adaptations that suit it for this lifestyle.

Journal Paper:
Shiratori T, Suzuki S, Kakizawa Y, Ishida K. 2019. Phagocytosis-like cell engulfment by a planctomycete bacterium. Nat Commun 10:1–11.

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Monday, March 9, 2020

BacterioFiles 417 - Bacteriophage Blocks Bacterial Bouncers

Pseudomonas aeruginosa
By Y_tambe, CC BY-SA 3.0
This episode: A phage defends its genome against bacterial host defenses by building a wall to keep them out!


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Show notes:
Microbe of the episode: Myroides odoratus and M. odoratimimus

News item

Takeaways
Parasites and their hosts are constantly in arms races with each other, each thriving best when it acquires new and more effective methods of attack, defenses, defenses against defenses, and so on. Bacterial defenses against viruses that infect them mostly involve cutting up viral genomes, either by the indiscriminate specific-cutting restriction enzymes, or by adaptive, sequence-sensing CRISPR/Cas systems.

Bacteriophages have proteins that can defend against the CRISPR/Cas system, but they mostly require the sacrifice of multiple failed infections before the proteins build up enough to defeat the defense. In this study, a phage is discovered that can immediately defend against all DNA-cutting systems, by constructing a nucleus-like protective compartment inside the host.

Journal Paper:
Mendoza SD, Nieweglowska ES, Govindarajan S, Leon LM, Berry JD, Tiwari A, Chaikeeratisak V, Pogliano J, Agard DA, Bondy-Denomy J. 2020. A bacteriophage nucleus-like compartment shields DNA from CRISPR nucleases. Nature 577:244–248.

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Monday, March 2, 2020

BacterioFiles 416 - Oxygen Or Other Oxidizes Iron?

Chlorobium phaeoferrooxidans
By Thompson et al, 2019.
Sci Adv 5:eaav2869.
CC BY-NC 4.0
This episode: Earth's iron deposits could have been created by anaerobic light-harvesting microbes instead of those that make oxygen!


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Show notes:
Microbe of the episode: Streptomyces avidinii

News item

Takeaways
In the ancient earth, the sun was dimmer, the world was colder, and oxygen was rare because photosynthesis had not yet evolved. Without oxygen to oxidize it, iron remained in its soluble, more accessible form, and many organisms took advantage of it for anaerobic metabolism.

But was it photosynthesis and the oxygen it created that transformed most of the planet's iron into its insoluble form, creating large iron deposits in the ground? This study explores the possibility that it was another form of light-harvesting metabolism, called photoferrotrophy, that uses light and the transformation of iron to generate energy. This hypothesis is found to be consistent with the evidence we have about what the early earth was like.

Journal Paper:
Thompson KJ, Kenward PA, Bauer KW, Warchola T, Gauger T, Martinez R, Simister RL, Michiels CC, Llirós M, Reinhard CT, Kappler A, Konhauser KO, Crowe SA. 2019. Photoferrotrophy, deposition of banded iron formations, and methane production in Archean oceans. Sci Adv 5:eaav2869.

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Monday, February 24, 2020

BacterioFiles 415 - Global Glomus Growth Guesses

How mycorrhizal fungi work
By Nefronus, CC BY-SA 4.0
This episode: A global estimate of plants and their root fungi shows how agriculture may have greatly affected soil carbon storage over time!


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Show notes:
Microbe of the episode: Rhizobium virus RHEph4

News item

Takeaways
Even small organisms can have a big effect on the climate of the planet if there are enough of them. This includes trees, which are small relative to the planet, and also includes the fungi that attach to the roots of trees and other plants. These mycorrhizal fungi thread subtly through the soil, some occasionally popping up mushrooms, and transfer valuable nutrients they gather to the trees in exchange for carbon fixed from the air.

Knowing how big an effect a given kind of organism has requires knowing how much of it is around. This study collates data from various surveys of global plant populations and the fungi that interact with their roots, to estimate a global picture of the fungi below our feet. It estimates that a kind of fungus that stores more carbon in the soil may have been replaced in many areas with fungi that store less, or no fungi at all, due to the transformation of land from wild areas to farmland.

Journal Paper:
Soudzilovskaia NA, van Bodegom PM, Terrer C, Zelfde M van’t, McCallum I, Luke McCormack M, Fisher JB, Brundrett MC, de Sá NC, Tedersoo L. 2019. Global mycorrhizal plant distribution linked to terrestrial carbon stocks. Nat Commun 10:1–10.

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Subscribe: Apple Podcasts, Google Podcasts, Android, or RSS. Support the show at Patreon, or check out the show at Twitter or Facebook.