487 - Probiotic Pulverizes Pathogen Persisters

E. coli

This episode: A probiotic strain of E. coli can target and destroy pathogens that survive a treatment of antibiotics!
Download Episode (8.2 MB, 12 minutes)

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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486 - Biohybrid Bacteria Build Biomass

Azotobacter vinelandii

This episode: Incorporating light-absorbing molecules into bacterial membranes can allow bacteria to use solar energy to transform nitrogen gas into fertilizer!
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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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485 - Small Cell Sculpts Sticky Snot Sphere

Mucosphere with captured prey
Larsson et al. 2022.
Nat Commun 13:1301
CC BY 4.0

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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484 - Bacteriophages Boost Brains

Lysogenic phage
By Rolf Lood et al.
BMC Microbiology
2008, 8:139
CC BY 2.5

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

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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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483 - Recycling Resources Raises Robustness

E. coli

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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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

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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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481 - Hijacker-Host Sequence Swap

Megavirus
By Chantal Abergel,
CC BY-SA 3.0

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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480 - Bait Bottlenecks Bear Bacteria

Black bear
By Diginatur
CC BY-SA 3.0

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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479 - Uncomplicated Critters Conquer Cancer

T. adhaerens
By Fortunato et al. 2021.
PLOS Biol e3001471
CC BY 4.0

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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478 - Babies Bear Bacterial Birthright

E. coli, a common gut microbe

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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477 - Hijackers Hitchhike on Hyphal Highways

Phage stuck to non-host bacterium
By You et al, 2022,
ISMEJ 16:1275-1283
CC BY 4.0

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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476 - Bamboo Breakdown Benefits Beetle Babies

Bamboo
By I Kenpei,
CC BY-SA 3.0

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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475 - Modifying Mixed Microbiota

Escherichia coli

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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474 - Stalker Cells Stop Seafood Sickness

Halobacteriovorax predator cells
By Ooi et al, 2021,
Microbiology 167:001113
CC BY-NC

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

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

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