DA BOM: The Best In Microbiology News February 2021

Microbiology Roundup: Extremophiles for antibiotics, fecal transplants, the microbes of panda's lovemaking, transposon sequencing in agriculture, and new insights into V. cholera's biofilm-forming proteins.

It's the end of the month so what new microbiology news is there? We'll tell you everything you need to know in The Best Of Microbiology (Da Bom). This is our monthly segment to bring you our favorite microbe-related news we found in the last month. We give you a quick synopsis of news from extremophiles, biotechnology, medical, marine, food, agriculture, and environmental microbiology! What's your favorite? Tell us in a comment below!

Extremophiles & Space ‘Crobes

Microbes called extremophiles might combat superbugs, biowarfare agents - by Max Blau

• A $50K trip on the same boat James Cameron used to help film Titanic allowed Joe Ng to obtain samples from a hydrothermal vent field thousands of feet below the Atlantic Oceans Surface!

• Lack of funding led to the samples sitting in the freezer in a Huntsville Alabama lab for almost 15 years. Finally, Joe Ng was able to process these samples when funding for the research came not from academia or pharmaceuticals, but from the military. They were looking for ways to protect and treat troops from biological weapons such as anthrax.

• Military Defense officials are turning to biologists to address the real concern of superbugs (drug-resistant bacteria) as Big Pharma doesn’t seem to be doing enough new antibiotic research.

• Superbugs are on track to kill more people than cancer by 2050!

• Ng’s lab extracted the DNA of some of the samples and inserted it into Bacteria (a clone) and tested them for antibiotic activity.

• The lab has created over 200,000 clones each with a different fragment of DNA and has tested only a fraction of them. There are 6 so far that have made antibiotics.

• Eventually, they will test the clones that make antibiotics against surrogates or microbes that are stand-ins for another (they are genetically related but less deadly) and if results are good they will be sent to a facility that can test on the real dangerous microbes.

Food & Agriculture Microbiology

Elucidating essential genes in plant-associated pseudomonas protegens Pf-5 using transposon insertion sequencing - Belinda K Fabian, Christie foster, Amy J Asher, Liam D. H. Elbourne, Amy K. Cain, Karl Hassan, Sasha G. Tetu, Ian T. Paulsen

• Transposon Insertion Sequencing is a technique whereby researchers create a dense mutant library of a single organism. In the case of this paper, they estimate they had one insertion every 27bp of the genome! After sequencing, the researchers can count how many mutants are found in each gene. Genes that have very few insertions are thought to be essential because mutants with insertions in these genes did not survive.

• What they found in their over 500,000 transposon mutants library were 446 genes which are essential to the 6109 gene genome. 446 gene is only 7.3% of the whole Pseudomonas protegens pf-5 genome!

• Pseudomonas is a highly diverse genus. Pseudomonas protegens Pf-5, which is a common plant-microbe, has also been known to be able to fight off pathogens from a wide range of crops including cotton, wheat, cucumber, and tomatoes, by producing antibiotics.

• They compared this particular pseudomonas strain with 3 other Pseudomonas strains, P. simiae, P. syringae (which can create snowflakes and is a common plant pathogen, see our blog post for more details), and P. aeruginosa which is an opportunistic human pathogen. They found that all four species share a large number of essential genes but, of course, also had their own set of unique genes. They actually found that 80% of the essential genes in Pf-5 overlapped with essential genes in P. aeruginosa the human pathogen strains

• Of course, the essential genes all depend on the stressors in the environment. In this study, they just looked at the microbes in a cushy setting, agar plates. They note that additional studies including a range of conditions that more closely represent the rhizosphere environment Pf-5 inhabits may assist with determining niche-specific essential genes.

Pathogen Profiles & Medical Microbiology

BipA exerts temperature-dependent translational control of biofilm-associated colony morphology in Vibrio cholerae - Santos, T. P et al.

• A protein has been discovered in Vibrio cholerae, allowing them to adapt to the changing temperatures. This protein is called BipA.

• This protein could hold insight into how other bacteria survive in suboptimal temperatures because this protein is conserved across many bacteria.

• V. cholerae causes a diarrheal disease and also forms biofilm made up of proteins and sugars that protect the bacteria. It is believed V. cholerae need this to infect our intestines.

• This bacteria can be found in water naturally and grown at those temperatures have smooth colonies, but grown at human temperatures the colonies form a biofilm. This is because the human body is a suboptimal temperature for the microbe.

• They found BipA by randomly mutating the bacteria using transposons finding those that created biofilm at lower temperatures had the mutations in the bipA gene. In fact, it was found that this protein reduced the expression of biofilm genes at lower temperatures.

• At higher temperatures, this protein also shows a conformational change, or how the protein is arranged, making it more easily degradable.

• Future research from the lab will, “address the effect of temperature- and BipA-dependent regulation of bacterial physiology during host-environment transitions and the associated potential consequences in cholera transmission and outbreaks.”

• This may support the theory that biofilm enhances V. cholerae’s infectivity. If the bacteria are forming biofilm then they are more prepared for the incoming environment of the human body.

Biotech & Microbial Products

Fecal transplants could help patients on cancer immunotherapy drugs - by Jocelyn Kaiser

• As oncologists deploy many strategies to stop cancer, a new study's preliminary results suggest that Fecal Transplants may show benefits to patients for whom immunotherapy drugs had previously not been effective.

• During a fecal transplant, a stool sample from a healthy donor is moved into the gut of a sick person.

• Amazingly, the gut microbes from the healthy person will populate in the sick person’s gut microbiome and improve their health.

• This method is already in use for colon infections that have not responded to other treatments such as antibiotics, but this study is a start to using fecal transplants for cancer patients.

• Researchers found that some patients that had more success with certain cancer drugs had a gut microbiome that differed from patients that saw less improvement, and those that took antibiotics shortly before or right after treatment started had lower success. This led to the idea that if the gut microbiomes could be transferred somehow from the healthy patient to the sick, could this make the drugs more effective - enter Poop Transplant!

• “Examining biopsies of gut and tumor tissue, the researchers found that post-transplant, the patients’ guts had more of a type of immune cell that senses invaders and activates the immune system; these cells had also infiltrated their tumors along with T cells, indicating that their previously “cold” tumors had become “hot,” or visible to the immune system.”

Environmental & Marine Microbiology

Symbiotic bacteria mediate volatile chemical signal synthesis in a large solitary mammal species - Wenliang Zhou, Dunwu Qi, Ronald R. Swaisgood, Le Wang, Yipeng Jin, Qi Wu, Fuwen Wei & Yonggang Nie.

• Pandas deploy secretions from a specialized gland known as AGS or anogenital gland secretions. This helps the pandas identify each other and tell other pandas about their reproductive status. But what role do the microbes in these glands play in creating these odors? That was the question that Wenliang Zhou, Younggang Nie, and colleagues investigated.

• They used a technique called gas chromatography-mass spectrometry to help them identify all the chemical compounds secreted by this gland. They found 30-50 different compounds!

• They also compared the microbiome of 17 giant panda AGS samples to 18 fecal samples to see if the microbial composition of these two closely associated niches were different. They did find distinct differences in these microbiomes. For instance, AGS was dominated by the phyla (which is one of the largest taxonomic classifications there is) Bacteroidetes and Actinobacteria but these were not found as frequently in feces. They also found the AGS was different in captive pandas compared with wild pandas. With wild pandas having Pseudomonas contributing to lipid metabolism while captive pandas had Psychrobacter.

• So taking together what does this mean? It means the microbes in the AGS may be contributing to the odors that help pandas reproduce. On the flip side, an AGS with an unhealthy microbiome or dysbiosis may interfere with panda reproduction.

• Future research may include experimenting with the AGS microbiome or nutrition of captive pandas to try and promote certain microbes to see if it helps with panda breeding efforts!

Those were our picks! What do you think is the greatest microbiology discovery so far for 2021? Tell us in a comment below!