Episódios

  • This episode: Many organisms produce the smell of earth, geosmin, and many others can sense it–but why?

    Download Episode (6.0 MB, 8.7 minutes)

    Show notes:
    Microbe of the episode: Acidianus spindle-shaped virus 1

    News item
    Takeaways The smell of soil or earth is one of the most recognizable smells, and comes largely from a chemical called geosmin, produced by many different kinds of bacteria. Many animal species are sensitive to geosmin, some attracted by it and others repelled. But it is still not entirely understood what is the evolutionary benefit to the microbes that produce it, or the reason why different animals are sensitive to it in different ways.

    In this study, different geosmin-producing bacteria were paired with tiny bacteria-eating roundworms, nematodes, to see how the chemical affected their interactions. Production of geosmin affected the worms' movement, apparently inducing them to avoid colonies of the producing microbes in some cases, though the worms still sometimes fed on the bacteria. Adding geosmin to colonies of different bacteria did not affect the worms' behavior though, so other factors seem to be involved.



    Journal Paper:

    Zaroubi L, Ozugergin I, Mastronardi K, Imfeld A, Law C, Gélinas Y, Piekny A, Findlay BL. 2022. The Ubiquitous Soil Terpene Geosmin Acts as a Warning Chemical. Appl Environ Microbiol 88:e00093-22.

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  • This episode: Slime mold amoebas Fonticula alba have interesting and unique foraging and reproductive behaviors!

    Download Episode (7.3 MB, 10.6 minutes)

    Show notes:
    Microbe of the episode: Cajanus cajan Panzee virus

    News item
    Takeaways How did life develop from single-celled organisms acting independently into the complex, multicellular organisms we see and are today? Although it is difficult to look back through time to study how ancient organisms may have developed along this path, it is possible to investigate modern organisms that occupy a zone in between single-celled and multicellular, to see if we can get some hints to our own development, and also learn about some interesting microbes along the way!

    This study into the social amoeba, or slime mold, Fonticula alba, finds that the individual amoebal cells in a population join together into collectives and break apart into individuals at different stages of their complex life cycle, depending on the status of the bacteria around them that they forage as prey. The investigators tease out the various pathways taken by these amoebas.

    Journal Paper:

    Toret C, Picco A, Boiero-Sanders M, Michelot A, Kaksonen M. 2022. The cellular slime mold Fonticula alba forms a dynamic, multicellular collective while feeding on bacteria. Curr Biol 32:1961-1973.e4.

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  • This episode: A probiotic strain of E. coli can target and destroy pathogens that survive a treatment of antibiotics!

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    Show notes:
    Microbe of the episode: Streptomyces griseoruber

    Takeaways Antibiotic resistance is becoming more and more of a problem as bacterial pathogens develop resistance to more and more drugs. For some people who develop an infection that is resistant to everything, it's as if they were living back in the days before antibiotics were discovered, when all they could do was pray for survival. New antibiotics are needed, but even more needed are new ways of approaching treatment of infections, using innovative approaches and combinations of therapeutics.

    In this study, a probiotic strain of Escherichia coli was used to target potentially pathogenic E. coli bacteria that can survive treatment with a particularly effective type of antibiotic, fluoroquinolones. This probiotic strain, called Nissle, delivers toxins directly to the survivors, preventing resistant pathogens from proliferating.

    Journal Paper:
    Hare PJ, Englander HE, Mok WWK. 2022. Probiotic Escherichia coli Nissle 1917 inhibits bacterial persisters that survive fluoroquinolone treatment. J Appl Microbiol 132:4020–4032.

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  • This episode: Incorporating light-absorbing molecules into bacterial membranes can allow bacteria to use solar energy to transform nitrogen gas into fertilizer!

    Download Episode (6.5 MB, 9.9 minutes)

    Show notes:
    Microbe of the episode: Wheat dwarf virus

    Takeaways Turning nitrogen gas into biologically useful compounds, such as protein or ammonia for fertilizer, is an essential part of the global nitrogen cycle and therefore, for agriculture. Today much fertilizer is produced from nitrogen gas by a chemical process that requires large amounts of energy, contributing to global warming. But certain bacteria can perform the same process using special enzymes much more efficiently.

    In this study, a light-absorbing molecule was inserted into the cell membrane of some of these bacteria, allowing them to use light energy directly to power the nitrogen converting enzymes. These "biohybrids" were able to produce convert significantly more nitrogen gas and produce additional bacterial biomass from it, showing promise for using such an approach for more sustainable microbial fertilizer production.

    Journal Paper:
    Chen Z, Quek G, Zhu J, Chan SJW, Cox‐Vázquez SJ, Lopez‐Garcia F, Bazan GC. 2023. A Broad Light‐Harvesting Conjugated Oligoelectrolyte Enables Photocatalytic Nitrogen Fixation in a Bacterial Biohybrid. Angew Chem Int Ed 62:e202307101.

    Other interesting stories:

    Update on using mosquito bacteria to block mosquito-borne viruses

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  • This episode: A marine protist predator traps prey microbes in an attractive bubble of mucus, eats what it wants, and lets the rest sink, possibly sequestering significant amounts of carbon!

    Download Episode (7.8 MB, 11.4 minutes)

    Show notes:
    Microbe of the episode: Bat associated cyclovirus 1

    News item

    Takeaways The oceans have a lot of unique, unexplored life in them. This is true on a macro level but even more on a microscopic level, with many different kinds of microbes of various groups with fascinating life strategies. And despite being microscopic, with enough of them around, they can affect the whole planet's climate in significant ways.

    In this study, one protist species gets most of its nutrients from photosynthesis, but what it can't get from the sun, it takes from prey microbes by force. To catch its prey, it creates an intricate bubble of mucus called a mucosphere, and waits for other microbes to swim into it, thinking it is food, and get stuck. Then the predator chooses the prey cell it wants and abandons the rest, letting them sink to the ocean floor and locking away the carbon they contain in the process.

    Journal Paper:
    Larsson ME, Bramucci AR, Collins S, Hallegraeff G, Kahlke T, Raina J-B, Seymour JR, Doblin MA. 2022. Mucospheres produced by a mixotrophic protist impact ocean carbon cycling. Nat Commun 13:1301.

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  • This episode: Certain phages in the gut are linked with increases in performance on some cognitive tests!

    Download Episode (7.5 MB, 10.9 minutes)

    Show notes:
    Microbe of the episode: Streptomyces bikiniensis

    News item

    Takeaways Our gut microbiota includes a large number of viruses, mostly bacteriophages. These fall into two groups, the lytic kind that infects and reproduces itself immediately in a host, and the lysogenic kind that can integrate its genome into the host bacterial genome and remain dormant for long periods.

    In this study, a higher proportion of lysogenic phages was correlated with increased performance on cognitive tests in multiple species. In humans, men showed a small increase in some tests and women in others. In mice and fruit flies, transplant or ingestion of phages was linked to increased memory performance. Journal Paper:
    Mayneris-Perxachs J, Castells-Nobau A, Arnoriaga-Rodríguez M, Garre-Olmo J, Puig J, Ramos R, Martínez-Hernández F, Burokas A, Coll C, Moreno-Navarrete JM, Zapata-Tona C, Pedraza S, Pérez-Brocal V, Ramió-Torrentà L, Ricart W, Moya A, Martínez-García M, Maldonado R, Fernández-Real J-M. 2022. Caudovirales bacteriophages are associated with improved executive function and memory in flies, mice, and humans. Cell Host Microbe 30:340-356.e8.

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  • This episode: Adding tags to proteins to increase their degradation can help engineered bacteria grow and survive better under various conditions!

    Download Episode (7.3 MB, 10.4 minutes)

    Show notes:
    Microbe of the episode: Lactococcus virus sk1

    News item

    Takeaways Engineering bacteria with new genetic pathways allows us to use them in many new and promising applications. Some of these are industrial fermentations, growing large quantities of bacteria to use as catalysts for production of chemicals of interest, such as biofuels. But in other cases, engineered microbes can be most useful in less controlled environments, such as the soil. In these situations, the engineering can throw off their natural metabolic balance, making them less tolerant of the stresses of such environments.

    In this study, a solution to this issue was tested using protein tags that signal the bacterial enzymes to degrade the engineered proteins. A variety of tags allowed for a variety of rates of degradation, allowing engineers to tune in the ideal rate. Bacteria with these engineered tags grew better in nutrient limited conditions than those without. Journal Paper:
    Szydlo K, Ignatova Z, Gorochowski TE. 2022. Improving the Robustness of Engineered Bacteria to Nutrient Stress Using Programmed Proteolysis. ACS Synth Biol 11:1049–1059.

    Other interesting stories:

    Microbes found in tap water could influence composition of the gut microbiome (paper)

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  • 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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  • This episode: Gene transfers between viruses and eukaryotes have happened many times throughout evolutionary history!

    Download Episode (7.5 MB, 10.9 minutes)

    Show notes:
    Microbe of the episode: Mycoplasma subdolum

    News item

    Takeaways As we’ve all seen recently, viruses can cause a lot of trouble. Their biology requires them to be parasites inside the cells of their hosts, and they can cause devastating disease, so it’s hard to think of them as having played important roles in the development of life on Earth, including our own evolution.

    However, this study found thousands of apparent historical transfers of genes from virus to host or from host to virus in the cells of all kinds of different eukaryotes. Some of these genes play important roles in the cell, helping to make them what they are. Journal Paper:
    Irwin NAT, Pittis AA, Richards TA, Keeling PJ. 2022. Systematic evaluation of horizontal gene transfer between eukaryotes and viruses. Nat Microbiol 7:327–336.

    Other interesting stories:

    Building a device that translates signals from one microbe to communicate with another Cloaking antitumor bacteria to fight cancer without immune system interference

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  • This episode: Human-based food used as bait by hunters can reduce bears' gut microbe diversity!

    Download Episode (5.9 MB, 8.6 minutes)

    Show notes:
    Microbe of the episode: Actinomadura verrucosospora

    News item

    Takeaways Gut microbes are important for the health of most animals. In humans, many things can affect our gut microbe community, including diet, medications, and lifestyle. Eating a varied diet with diverse kinds of plant-based foods can maintain a healthy, functional community of many different kinds of microbe. However, eating mostly highly processed grain-based foods can reduce the diversity and functionality of the gut community.

    This is also true in bears. In this study, when bears consumed more processed, grain-based human foods via hunters leaving such foods out as bait, the gut communities in these bears had reduced diversity of microbes. The effects of this reduced diversity were not determined, but it is reasonable to assume it was not good for the bears’ overall health. Journal Paper:
    Gillman SJ, McKenney EA, Lafferty DJR. 2022. Human-provisioned foods reduce gut microbiome diversity in American black bears (Ursus americanus). J Mammal 103:339–346.

    Other interesting stories:

    3D-printed electrode structures harvest electricity from bacterial photosynthesis Gut microbes are important for helping tadpoles survive in warmer conditions

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  • This episode: Simple microscopic animals can survive extreme radiation by ejecting damaged cells that might otherwise become cancer!

    Download Episode (7.3 MB, 9.2 minutes)

    Show notes:
    Microbe of the episode: Helleborus net necrosis virus

    News item

    Takeaways Any multicellular organism with different types of cells needs some sort of cell regulation, to keep each cell type doing what it’s supposed to do for the good of the organism as a whole. We know what happens when this regulation fails and one type of cells starts multiplying out of control: cancer.

    However, cancer has never yet been observed in certain organisms, including the simple microscopic animal Trichoplax adhaerens. In this study, these animals are exposed to large amounts of radiation and then observed over years to see if they can develop cancer or have interesting mechanisms of resisting it. Journal Paper:
    Fortunato A, Fleming A, Aktipis A, Maley CC. 2021. Upregulation of DNA repair genes and cell extrusion underpin the remarkable radiation resistance of Trichoplax adhaerens. PLOS Biol 19:e3001471.

    Other interesting stories:

    Genes transferred from bacteria to algae helped land plants evolve

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  • This episode: How family members share gut microbes across multiple generations!

    Download Episode (7.3 MB, 10.7 minutes)

    Show notes:
    Microbe of the episode: Dyozetapapillomavirus 1

    Takeaways Our gut’s microbial communities can greatly influence our health, for good or bad. The makeup of these communities can be influenced by many factors, including genetics, health status, diet, and other aspects of the environment we live in. We’ve learned a lot about this topic recently, but there’s a lot more we still don’t understand.

    In this study, gut microbe samples from individuals spanning multiple generations in the same families were compared, to see how much influence family relationships and cohabitation could have on the gut communities. Both genetic relationship and living together had influences on which gut microbes different people shared. Journal Paper:
    Valles-Colomer M, Bacigalupe R, Vieira-Silva S, Suzuki S, Darzi Y, Tito RY, Yamada T, Segata N, Raes J, Falony G. 2022. Variation and transmission of the human gut microbiota across multiple familial generations. 1. Nat Microbiol 7:87–96.

    Other interesting stories:

    Simple modification to interesting bacteria make them excrete nitrogen fertilizer Making carbon dioxide into useful chemicals with bacteria

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  • This episode: Bacteriophages can hitch a ride on bacteria they don't infect to travel through soil on fungal filaments, potentially helping their carriers by infecting and killing their competitors!

    Download Episode (7.1 MB, 10.3 minutes)

    Show notes:
    Microbe of the episode: Epinotia aporema granulovirus

    News item

    Takeaways For tiny bacteria, partially dry soil can be like a vast system of caverns, with particles of soil separated by air-filled spaces much bigger than individual bacteria. Not all bacteria can swim through liquid, and those that can’t simply try to thrive as best they can wherever they may be. But for those that can swim, fungi and other filamentous organisms can form bridges between soil particles that motile bacteria can swim across, reaching new places.

    In this study, phages were found to hitch a ride on bacteria they don’t normally infect, crossing fungus-like filaments to new places and infecting the bacteria they find there. The bacteria carrying them can also benefit from this interaction, since the phages help the carrier bacteria compete and establish a colony in the new location. Journal Paper:
    You X, Kallies R, Kühn I, Schmidt M, Harms H, Chatzinotas A, Wick LY. 2022. Phage co-transport with hyphal-riding bacteria fuels bacterial invasion in a water-unsaturated microbial model system. 5. ISME J 16:1275–1283.

    Other interesting stories:

    Fungus species discovered in spacecraft assembly facility Oral microbes uniquely influence immune system interaction with mouth bones

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  • This episode: Beetles inoculate bamboo with a fungus that consumes the bamboo sugars to feed the beetle larvae!

    Download Episode (7.7 MB, 11.2 minutes)

    Show notes:
    Microbe of the episode: Saccharomyces cerevisiae virus L-BC (La)

    News item

    Video: Lizard beetle laying its egg

    Takeaways The structural polymers that make up plants, such as cellulose, can be difficult for many organisms to digest. Some kinds of bacteria and fungi can do it, and some animals (cows, pandas, termites) partner with these microbes to be able to eat otherwise indigestible plant material. This includes insects such as leaf-cutter ants that farm external gardens of microbes, providing them plant material and then eating the resulting microbial growth.

    In this study, the lizard beetle lays its eggs in bamboo and inoculates the walls of the bamboo with a fungus that provides food to the larvae. Chemical analyses suggest that the fungus only consumes the simple sugars in the bamboo rather than breaking down the tougher polymers, which raises questions about the evolution of this interaction. Journal Paper:
    Toki W, Aoki D. 2021. Nutritional resources of the yeast symbiont cultivated by the lizard beetle Doubledaya bucculenta in bamboos. Sci Rep 11:19208.

    Other interesting stories:

    Using bacteria to detect and target colon cancer for imaging (paper) Filters made from kombucha cultures could work better than synthetic types

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  • This episode: New techniques allow specific modifications in certain members of a complex community of microbes, without isolating them in pure culture first!

    Download Episode (11.5 MB, 16.7 minutes)

    Show notes:
    Microbe of the episode: Tomato golden mosaic virus

    News item

    Takeaways The technology for understanding and manipulating microbial genetics has come a long way in a short time. It used to take years even to sequence a small genome, and now thousands can be sequenced in just a few days. The technology to change and even create genetic sequences is also much further advanced now than just a few decades ago. But still, many analyses and modifications require a pure culture of a microbe to carry out.

    This study tested a method for modification of single or multiple species in a community of many. The method allows for identification of which species were successfully modified in targeted ways, and can allow the modified species to be extracted and studied individually. Journal Paper:
    Rubin BE, Diamond S, Cress BF, Crits-Christoph A, Lou YC, Borges AL, Shivram H, He C, Xu M, Zhou Z, Smith SJ, Rovinsky R, Smock DCJ, Tang K, Owens TK, Krishnappa N, Sachdeva R, Barrangou R, Deutschbauer AM, Banfield JF, Doudna JA. 2022. Species- and site-specific genome editing in complex bacterial communities. 1. Nat Microbiol 7:34–47.

    Other interesting stories:

    Microbes that degrade plastic may be increasing in response to plastic pollution Algae in ocean communicate with each other using fluorescence

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  • This episode: Predatory bacteria could protect lobster farms from disease-causing bacteria!

    Download Episode (4.8 MB, 7 minutes)

    Show notes:
    Microbe of the episode: Gordonia rubripertincta

    Takeaways Antibiotics have done wonders for controlling bacterial pathogens. Many people have lived that would otherwise have died, and some industries have produced much more than they would have, particularly those involved in animal farming. However, more and more targeted pathogens are developing resistance to the antibiotics we have, and new ones are harder to discover, so alternative approaches are needed.

    Here, predatory bacteria take the place of antibiotics in a study on farmed spiny lobsters. These predators swim after and attach to prey bacteria, hollowing out their contents to use as nutrients to make more predators. They do not hurt the lobsters, but the study finds they do reduce the number of pathogenic prey organisms injected into the lobsters at the same time. Journal Paper:
    Ooi MC, Goulden EF, Smith GG, Bridle ARY 2021. 2021. Predatory bacteria in the haemolymph of the cultured spiny lobster Panulirus ornatus. Microbiology 167:001113.

    Other interesting stories:

    3D-printing bacterial biofilms Review of latest in oncolytic (cancer-killing) viruses

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  • This episode: A bacteriophage that overcomes the bacterial CRISPR/Cas immune system by interrupting the CRISPR DNA with its own genome!

    Download Episode (6.8 MB, 10 minutes)

    Show notes:
    Microbe of the episode: Wenzhou mammarenavirus

    Takeaways Bacteria have many ways to resist being exploited by bacteriophage viruses, including the adaptable CRISPR/Cas system that uses a piece of viral nucleic acid sequence to target and destroy incoming phages. But phages also have many ways to evade and disrupt bacterial defenses.

    In this study, a phage is discovered that inserts its own genome into the CRISPR/Cas sequence in the bacterial genome, disrupting the bacterial defenses. To escape the defenses while it is doing this insertion, it carries genes for previously-unknown anti-CRISPR proteins. But inserting and removing a viral sequence from the bacterial genome is not always a clean procedure. Journal Paper:
    Varble A, Campisi E, Euler CW, Maguin P, Kozlova A, Fyodorova J, Rostøl JT, Fischetti VA, Marraffini LA. 2021. Prophage integration into CRISPR loci enables evasion of antiviral immunity in Streptococcus pyogenes. 12. Nat Microbiol 6:1516–1525.

    Other interesting stories:

    Great article on the history of phage therapy

    Email questions or comments to bacteriofiles at gmail dot com. Thanks for listening!

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  • This episode: Bacteria can use blobs of disordered proteins to quickly adapt to new conditions!

    Thanks to Dr. Saumya Saurabh for his contribution!

    Download Episode (10.9 MB, 15.9 minutes)

    Show notes:
    Microbe of the episode: Drosophila melanogaster Micropia virus

    Takeaways Bacteria can adapt to environmental fluctuations via mechanisms operating at the various levels of the central dogma, or metabolism (stringent response). Recently, researchers at Stanford University discovered a mechanism that allows bacteria to sense and rapidly adapt to nutrient fluctuations by simply tuning protein self-assembly as a function of nutrient availability. Termed membraneless organelles or condensates, these proteinaceous assemblies can dynamically sequester key signaling enzymes within them in response to environmental cues. Biophysical adaptation mediated by organelles is fast, reversible, and facile; thereby representing a crucial step in the mechanistic understanding of microbial adaptation. Journal Paper:
    Saurabh S, Chong TN, Bayas C, Dahlberg PD, Cartwright HN, Moerner WE, Shapiro L. 2022. ATP-responsive biomolecular condensates tune bacterial kinase signaling. Sci Adv 8:eabm6570.

    Other interesting stories:

    Bacteria produce biofuel from carbon dioxide, light, and solar power-generated electricity Vine that can mimic leaves of different trees may get info from bacteria (paper)

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  • This episode: A phage both kills bacterial pathogens and selects for reduced virulence!

    Download Episode (6.3 MB, 9.9 minutes)

    Show notes:
    Microbe of the episode: Helminthosporium victoriae 145S virus

    News item
    Takeaways Using bacteria-killing viruses to treat bacterial infections, or phage therapy, can be a good alternative to antibiotics in some situations when there are no effective antibiotics for a particular infection. But bacteria can evolve resistance to phages as well as antibiotics, often with little cost to their fitness.

    In this study, a phage not only could treat an infection by attacking the bacteria, but the bacterial hosts that do evolve resistance to the phage do so by getting rid of certain structures that help them to cause more serious infection. Thus, therapy with this phage may both reduce the bacterial load and also make those remaining less virulent. Journal Paper:
    Kortright KE, Done RE, Chan BK, Souza V, Turner PE. 2022. Selection for Phage Resistance Reduces Virulence of Shigella flexneri. Appl Environ Microbiol 88:e01514-21.

    Other interesting stories:

    Plastic-eating bacteria could produce biodegradable plastic Harmless variant of acne bacteria could help prevent more serious skin infection

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  • 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:

    Anti-tumor bacteria: engineered E. coli colonizes tumors and attracts immune response Cats have skin bacteria that could inhibit drug resistant pathogens

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