Showing posts with label biofilms. Show all posts
Showing posts with label biofilms. Show all posts

Monday, September 4, 2023

482 - Colony Concentric Clock Construction

Bacillus subtilis
By Y tambe,
CC BY-SA 3.0
This episode: Single-celled bacteria can act independently to create patterns and structure in their biofilm communities!
Download Episode (9.6 MB, 14.0 minutes)

Show notes:
Microbe of the episode: Dictyostelium discoideum Skipper virus

News item

Takeaways
Large multicellular organisms like us have interesting mechanisms for using one set of genetic instructions present in all cells to form a large, complex community of many different types of cells with different structures and functions, all working together. Single-celled microbes do not have the same requirements for genetic or structural complexity, but they do often display interesting communal patterns and behaviors.

In this study, bacteria growing in colonies on agar displayed a particular mechanism of pattern formation previously seen only in eukaryotes, called segmentation clock or clock and wavefront process. In this process, the cells in the colony are all acting individually without communication with each other, but nevertheless form a repeating ring structure in the colony as it grows, possibly allowing some measure of differentiation of cells that could help the community survive various challenges.

Journal Paper:
Chou K-T, Lee DD, Chiou J, Galera-Laporta L, Ly S, Garcia-Ojalvo J, Süel GM. 2022. A segmentation clock patterns cellular differentiation in a bacterial biofilm. Cell 185:145-157.e13.

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Monday, July 11, 2022

470 - Super Small Symbionts Soothe Symptoms

Tiny symbiont Saccharibacteria (yellow-green)
on host bacteria (red)
By Utter et al.,
CC BY-SA 4.0


This episode: Tiny bacteria that live on larger bacteria reduce the inflammation and gum disease the bigger microbes cause in the mouths of mice!

Download Episode (6.3 MB, 9.2 minutes)

Show notes:
Microbe of the episode: Actinomadura viridilutea

Takeaways
Even bacteria can be hosts to smaller symbionts living on them. Some kinds of these extremely tiny bacteria live in various parts of our bodies, and are sometimes associated with inflammation and the resulting disease. But being associated with something isn't necessarily the same as causing that thing.

In this study, tiny bacteria living on other bacteria in the mouths of mice were found to reduce the inflammation caused by their bacterial hosts, resulting in less gum disease and bone loss in the jaw. Even when the tiny bacteria were no longer present, their former bacterial hosts were still less disruptive to the mouse mouth.

Journal Paper:
Chipashvili O, Utter DR, Bedree JK, Ma Y, Schulte F, Mascarin G, Alayyoubi Y, Chouhan D, Hardt M, Bidlack F, Hasturk H, He X, McLean JS, Bor B. 2021. Episymbiotic Saccharibacteria suppresses gingival inflammation and bone loss in mice through host bacterial modulation. Cell Host Microbe 29:1649-1662.e7.

Other interesting stories:

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Monday, December 6, 2021

466 - Microbes Mining Mars Minerals

Basalt close up
By Helgi, CC BY-SA 4.0
This episode: Bacteria are able to extract metals from rocks for industrial use, even in microgravity!

Download Episode (6.2 MB, 9.0 minutes)

Show notes:
Microbe of the episode: Decapod ambidensovirus 1

News item

Takeaways
As humanity makes progress toward becoming an interplanetary species, consideration is needed on how travelers can survive and thrive in distant places. These methods may look very different from what works well on Earth, with differences in gravity, atmosphere, and access to resources. For example, mining for materials for construction may not be feasible using methods common on Earth. An alternative may be biomining, using microbes that can selectively extract and purify specific metals from minerals.

In this study, the European Space Agency tested the ability of several microbes to extract vanadium from rocks in different gravity conditions, on the International Space Station. Two out of three microbes were able to extract twice as much vanadium as was extracted in the absence of microbes, both on a planet and up in space.

Journal Paper:
Cockell CS, Santomartino R, Finster K, Waajen AC, Nicholson N, Loudon C-M, Eades LJ, Moeller R, Rettberg P, Fuchs FM, Van Houdt R, Leys N, Coninx I, Hatton J, Parmitano L, Krause J, Koehler A, Caplin N, Zuijderduijn L, Mariani A, Pellari S, Carubia F, Luciani G, Balsamo M, Zolesi V, Ochoa J, Sen P, Watt JAJ, Doswald-Winkler J, Herová M, Rattenbacher B, Wadsworth J, Everroad RC, Demets R. 2021. Microbially-Enhanced Vanadium Mining and Bioremediation Under Micro- and Mars Gravity on the International Space Station. Front Microbiol 12:663.

Other interesting stories:

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Monday, July 19, 2021

458 - Slimy Cells Stop Sinking

Colonies of strains with
different floating strengths
By Kessler et al. 2021,
J Bacteriol 203(11):e00023-21
CC BY 4.0
This episode: Bacteria can resist the force of gravity in liquid culture by covering themselves with goopy sugar polymers like parachutes!

Download Episode (10.4 MB, 15.2 minutes)

Show notes:
Microbe of the episode: Brevicoryne brassicae virus

Takeaways
Put bacteria in a centrifuge, and most of the time you end up with a compact pellet of cells at the bottom of the tube, and mostly cell-free liquid above it. Bacteria do have ways to remain suspended in liquid, even without constant stirring or shaking of the container, but swimming, for example, consumes energy.

In this study, artificial selection allowed the discovery of bacteria that could resist centrifuging speeds up to 15000 times the force of gravity, remaining suspended in liquid instead of forming a pellet. Production of polysaccharide was important, but not sufficient; for the most resistance to sinking, bacteria had to attach the polysaccharide to their cell surface, to act as a sort of parachute.

Journal Paper:
Kessler NG, Caraballo Delgado DM, Shah NK, Dickinson JA, Moore SD. 2021. Exopolysaccharide Anchoring Creates an Extreme Resistance to Sedimentation. J Bacteriol 203(11):e00023-21.

Other interesting stories:

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Monday, April 5, 2021

450 - Subterranean Spotlights Support Cyanobacteria

Carlsbad Caverns
By Eric Guinther, Marshman
CC BY-SA 3.0
This episode: Lighting in caves open to tourists supports the growth of unwanted photosynthetic bacteria!

Thanks to Zoë Havlena for her contribution!

Download Episode (6.6 MB, 9.5 minutes)

Show notes:
Microbe of the episode: Dill cryptic virus 2

Takeaways
Caves can contain amazing beauty, intricate geological formations formed by minerals, water, and time. Some, such as Carlsbad Caverns in New Mexico, have been fitted with instruments to allow tourists to pass through and see the wonders within; definitely a worthwhile experience.

Caves also have their own natural microbiota that can live within them, in the dark, somewhat cold, and nutrient-poor conditions. But with the lighting installed to allow tourism, photosynthetic microbes have been able to take hold in the communities of these show caves. These microbes can outcompete the natural microbes, and can cause discoloration and unwanted growths on cave formations. They are difficult to remove without much effort and the risk of damaging the cave formations themselves. 

This study looked at the effects of the color of lighting in the caves, as well as other factors, on the growth of these so-called "lampenflora." It supports new efforts and methods to control the issue.

Journal Paper:
Havlena Z, Kieft TL, Veni G, Horrocks RD, Jones DS. 2021. Lighting Effects on the Development and Diversity of Photosynthetic Biofilm Communities in Carlsbad Cavern, New Mexico. Appl Environ Microbiol 87.

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Monday, February 1, 2021

446 - Biofilm Benefits Bone Braces

Biofilm-coated implant
By Tan et al. 2020,
Sci Adv 6:eaba5723
CC BY-NC 4.0
This episode: The biofilm that probiotic bacteria can leave behind on a titanium implant seems to help it integrate better with the existing skeleton, with less inflammation and risk of infection!

Download Episode (5.5 MB, 7.9 minutes)

Show notes:
Microbe of the episode: Methylobacterium organophilum

Takeaways
Skeletal implants make it a lot easier for many people to stay mobile as they age, but the surgical procedure of implanting is risky. Its invasive nature puts stress on the immune system, which puts stress on other systems, and the spread of antibiotic resistance is increasing the risk of a hard-to-treat infection.

In this study, probiotic bacteria grow in a biofilm on titanium implants before being inactivated, leaving only the biofilm behind on the implant. This biofilm-coated implant showed improved bone integration, antimicrobial resistance that was not toxic to the body's own tissues, and reduced inflammation when implanted into rats.

Journal Paper:
Tan L, Fu J, Feng F, Liu X, Cui Z, Li B, Han Y, Zheng Y, Yeung KWK, Li Z, Zhu S, Liang Y, Feng X, Wang X, Wu S. 2020. Engineered probiotics biofilm enhances osseointegration via immunoregulation and anti-infection. Sci Adv 6:eaba5723.

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, 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, 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, December 9, 2019

BacterioFiles 405 - Coated Colonizers Counteract Corrosion

Coated bacteria on a coated surface
Rijavec et al. 2019, Adv Sci 1901408
This episode: Coating metal surfaces with artificial biofilms could help keep the surfaces corrosion-free even in the ocean!

Download Episode (6.3 MB, 9.1 minutes)

Show notes:
Microbe of the episode: Hymenopteran ambidensovirus 1

Takeaways
The ocean can be a harsh place for metal surfaces. Between the water, the salt, and oxygen (near the surface), corrosion is a common reality. Microbes in the ocean can contribute to this too, degrading metal structures to obtain energy for their metabolism. They colonize surfaces in biofilms that can be difficult to remove, a process called biofouling.

In this study, instead of trying to remove or prevent biofilms on surfaces, artificial biofilms were created by coating the surfaces and specially selected bacterial cells with polymers. This approach did not prevent colonization by other organisms in the sea, but preliminary results suggested that the community that did take up residence was not as corrosive as the communities found on uncoated steel.

Journal Paper:
Rijavec T, Zrimec J, Spanning R van, Lapanje A. 2019. Natural Microbial Communities Can Be Manipulated by Artificially Constructed Biofilms. Adv Sci 6:1901408.

Other interesting stories:

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Monday, September 30, 2019

BacterioFiles 397 - Plant Promotes Pathogen-Prohibiting Partner

Bacillus subtilis
By Y tambe, CCBY-SA 3.0
This episode: Plants stimulate their root bacteria to compete better, and these bacteria help the plants resist disease!

Download Episode (7.3 MB, 10.6 minutes)

Show notes:
Microbe of the episode: Bacillus circulans

Takeaways
In some ways, plants' roots are like our gut. They both absorb nutrients, and they both have complex communities of microbes living alongside the host cells. These microbes can assist their hosts in various ways, and get fed in return.

In this study, one species of root bacterium is able to compete against others by producing an antimicrobial compound. The plant stimulates this production with chemical signals, and benefits from its symbionts' increased competitiveness because the bacterium helps the plant resist infection.

Journal Paper:
Ogran A, Yardeni EH, Keren-Paz A, Bucher T, Jain R, Gilhar O, Kolodkin-Gal I. 2019. The Plant Host Induces Antibiotic Production To Select the Most-Beneficial Colonizers. Appl Environ Microbiol 85:e00512-19.

Other interesting stories:

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Monday, October 29, 2018

BacterioFiles 359 - Prokaryotes Provoke Perpendicular Punishment

Strain resistant to toxin
quickly takes over colony
By Despoina Mavridou
This episode: Some bacteria produce DNA-targeting toxins, which provokes a similar retaliation from other strains. Sometimes this hurts the provoker, but sometimes it is very helpful to them!

Thanks to Dr. Despoina Mavridou for her contribution!
Download Episode (7.9 MB, 8.4 minutes)

Show notes:
Microbe of the episode: Mycobacterium virus Athena

News item

Journal Paper:
Gonzalez D, Sabnis A, Foster KR, Mavridou DAI. 2018. Costs and benefits of provocation in bacterial warfare. Proc Natl Acad Sci 115:7593–7598.

Other interesting stories:

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Episode outline:

Monday, August 27, 2018

BacterioFiles 353 - Pathogen Prevents Pathogen Pervasion

Streptococcus (green) and
Staphylococcus (red)
together in biofilm.
By: Reddinger et al, 2018, mBio
This episode: Some bacteria that can cause pneumonia can prevent other bacteria from doing the same!

Download Episode (9.6 MB, 10.5 minutes)

Show notes:
Microbe of the episode: Bell pepper mottle virus

Journal Paper:
Reddinger RM, Luke-Marshall NR, Sauberan SL, Hakansson AP, Campagnari AA. 2018. Streptococcus pneumoniae Modulates Staphylococcus aureus Biofilm Dispersion and the Transition from Colonization to Invasive Disease. mBio 9:e02089-17.

Other interesting stories:

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Episode outline:

Monday, April 30, 2018

BacterioFiles 337 - Gathering Gut Groupings Graphics

Bacteria labeled using FISH
By Velocity2222X
CC BY-SA 3.0
This episode: A simplified bacterial community in mouse guts doesn't have much community structure, relative to other body areas!

Download Episode (8.8 MB, 9.6 minutes)

Show notes:
Microbe of the episode: Rhodomicrobium vannielii

News item

Journal Paper:
Welch JLM, Hasegawa Y, McNulty NP, Gordon JI, Borisy GG. 2017. Spatial organization of a model 15-member human gut microbiota established in gnotobiotic mice. Proc Natl Acad Sci 114:E9105–E9114.

Other interesting stories:
  • Studying the microbes found in Chinese hazy air (paper)
  • Sometimes bacteria modify their environment so hard, it kills them (paper)
  • Some ants' bacteria produce the pheromones they use for guidance
  • Modifying plants' microbiota might be difficult due to microbe diversity

  • Post questions or comments here or email to bacteriofiles@gmail.com. Thanks for listening!

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    Episode outline:

    Monday, February 12, 2018

    BacterioFiles 328 - Focused Phages Fight Films

    Bacteriophages
    By Sherwood Casjens,Elaine Lenk
    CC BY-SA 3.0
    This episode: Phages bound to magnetic nanoparticles can be guided and pulled toward their target, penetrating biofilms to kill harmful microbes!

    Download Episode (9.6 MB, 10.4 minutes)

    Show notes:
    Microbe of the episode: Veillonella alcalescens

    News item

    Journal Paper:
    Li L-L, Yu P, Wang X, Yu S-S, Mathieu J, Yu H-Q, Alvarez PJJ. 2017. Enhanced biofilm penetration for microbial control by polyvalent phages conjugated with magnetic colloidal nanoparticle clusters (CNCs). Environ Sci Nano 4:1817–1826.

    Other interesting stories:
  • Social group membership affects lemur gut microbes
  • Viruses can transfer genes between kingdoms
  • Trace gases in atmosphere enough to support microbes in Antarctica
  • Magnetic bacteria can swim even against the current
  • Engineered bacteria produce internal scaffolds for better biotech productions

  • Post questions or comments here or email to bacteriofiles@gmail.com. Thanks for listening!

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    Episode outline:

    Monday, October 2, 2017

    BacterioFiles 312 - Antibiotic Acts As Agreement

    Quorum sensing scheme
    By Gluckma2, CC BY-SA 4.0
    This episode: Bacteria that produce antibiotic molecule can also use it for communication between cells!

    Download Episode (10 MB, 11 minutes)

    Show notes:
    Microbe of the episode: Rosellinia necatrix victorivirus 1

    Journal Paper:
    Beyersmann PG, Tomasch J, Son K, Stocker R, Göker M, Wagner-Döbler I, Simon M, Brinkhoff T. 2017. Dual function of tropodithietic acid as antibiotic and signaling molecule in global gene regulation of the probiotic bacterium Phaeobacter inhibens. Sci Rep 7:730.

    Other interesting stories:
  • Bacteria may be key to certain grasses' success (paper)
  • Small-genome bacteria have old school space-saving multi-function enzymes (paper)
  • Using electricity to help microbes clean up pollution (paper) (see here also)
  • Photosynthetic and non-photosynthetic organisms cooperate in ocean
  • Phage therapy with CRISPR-modified viruses

  • Post questions or comments here or email to bacteriofiles@gmail.com. Thanks for listening!

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    Episode outline:

    Monday, September 25, 2017

    BacterioFiles 311 - Synchronized Slimes Spread Slowly

    Bacillus subtilis colonies
    By Debivort, CC BY-SA 3.0
    This episode: Separate groups of bacteria can each thrive better when they take turns growing instead of competing!

    Thanks to Jintao Liu and Rosa Martinez-Corral for their contributions to this episode!

    Download Episode (14.2 MB, 15.5 minutes)

    Show notes:
    Microbe of the episode: Palyam virus

    News item

    Journal Paper:
    Liu J, Martinez-Corral R, Prindle A, Lee DD, Larkin J, Gabalda-Sagarra M, Garcia-Ojalvo J, Süel GM. 2017. Coupling between distant biofilms and emergence of nutrient time-sharing. Science 356:638–642.

    Other interesting stories:
  • Microbe prefers making its own siderophores rather than relying on others' (paper)
  • Deep-sea animals live off microbes that eat oil
  • Correlating gut microbiome differences with anorexia (paper)
  • Having microbes affects mice's perception of internal pain
  • Bacteria that digest gluten could be helpful as probiotics (paper)

  • Post questions or comments here or email to bacteriofiles@gmail.com. Thanks for listening!

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    Episode outline:

    Monday, May 22, 2017

    BacterioFiles 294 - Bacteria Benefit Bad Burns

    Lactobacillus plantarum colonies
    Donald Breakwell et al. 2007. 
    This episode: Probiotic bacteria prevent deadly infections in mice with serious burns!

    Download Episode (6.3 MB, 6.92 minutes)

    Show notes:
    Journal Paper:
    Argenta A, Satish L, Gallo P, Liu F, Kathju S. 2016. Local Application of Probiotic Bacteria Prophylaxes against Sepsis and Death Resulting from Burn Wound Infection. PLOS ONE 11:e0165294.

    Other interesting stories:
  • Bacteria can help cotton plants tolerate salt (paper)
  • Fiber stops microbes from eating protective gut mucus
  • Potential new antibiotics predicted and discovered in human microbes
  • Bacteria communicate to work together against viruses
  • Root bacteria help protect plants against arsenic and infections

  • Post questions or comments here or email to bacteriofiles@gmail.com. Thanks for listening!

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    Monday, May 15, 2017

    BacterioFiles 293 - Millet Microbe Makes Meshes

    Finger millet
    This episode: Bacteria in finger millet roots create special killing traps for damaging fungi!

    Download Episode (7.5 MB, 8.25 minutes)

    Show notes:
    News item

    Journal Paper:
    Mousa WK, Shearer C, Limay-Rios V, Ettinger CL, Eisen JA, Raizada MN. 2016. Root-hair endophyte stacking in finger millet creates a physicochemical barrier to trap the fungal pathogen Fusarium graminearum. Nat Microbiol 1:16167.

    Other interesting stories:
  • Animal study of phage cocktail to treat cholera
  • Soil microbes could help clean up arsenic contamination (paper)
  • Bacteria with nucleus-like structure even have nuclear pore-like structures
  • Using bacteria to find best enzymes for degrading lignin (paper)
  • Making microbial fuel cells with paper

  • Post questions or comments here or email to bacteriofiles@gmail.com. Thanks for listening!

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