DA BOM: The Best of Microbiology April 2021
This month's Microbiology Roundup includes extremophile microbes that help grow space plants, the diversity of sourdough microbiomes, phages for pandemics, Microbes discovered in evolutionary stasis, what mimiviruses are and so much more...
Extremophiles & Space ‘Crobes
Newly discovered bacteria on space station could help astronauts grow plants on Mars - Chelsea Gohd March 2021
Three new bacteria strains have been discovered on the International Space Station, which could help them grow plants in Space!
As we venture further into space, it will become necessary for astronauts to grow their own food, and besides, who wants to live only on processed packaged food?
Bacteria are necessary for plant development as they are involved with important processes like nitrogen fixation, phosphate solubilization, abiotic stress tolerance, promote growth and protect against disease.
The ISS (International Space Station) is kept as clean as possible for the health and safety of the astronauts on board, but it is not sterile or void of microbes since humans are microbe havens (an average person carrying over 100 trillion microscopic organisms in and on their body!).
The team found a total of four strains that belong to the Methylobacteriaceae family, which are often involved in plant processes - 3 of the strains were previously undiscovered.
Genetic analysis done on the strains showed they are closely related to Methylobacterium indicum, which was isolated from rice seeds.
The team is proposing to name the crop of novel species Methylobacterium ajmalii - after renowned Indian biodiversity scientist Ajma Khan.
Food & Agriculture Microbiology
The diversity and function of sourdough starter microbiomes - Elizabeth A Landis et al. Adapted from our friends at Microbites: Author credit: Anais Biclot.
500 sourdough samples from all over the world were analyzed for their microbial composition. Most samples came from the US, but others came from Europe, Canada, Australia, New Zealand, and Thailand.
Sourdough is made with only two ingredients! Flour and water; easy right? Just lay it out and let some yeast and lactobacilli get in there and start fermenting and farting resulting in the dough rising.
Overall the authors found 7 different bacteria and 35 different yeasts.
Previous studies were conducted on starters from Europe. They focused primarily on the most abundant species.
Here, the authors tried to look at the full diversity and understand where the variability between samples comes from. They looked at their geographic differences, age, storage location (fridge vs room temperature), home characteristics, etc. But out of the 33 parameters they looked at, only 10% explained the variation between community compositions.
They did find some associations between species and parameters, for example, older starters often contained F. sanfranciscensis (named after being discovered in sourdough in San Francisco).
Finally, they found that microbial composition influences dough rise and aroma profiles and that low abundant species were giving different chemical signatures to the sourdough. These species were often overlooked in previous studies.
But there is always more to learn about sourdough! We don’t know how it evolves or the mechanisms for the community assembly.
Pathogen Profiles & Medical Microbiology
Learning From Mistakes: The Role of Phages in Pandemics - By Ahlam Alsaadi and colleagues
Multidrug Resistance Bacteria (MDR) are on the rise due to overuse and misuse of antibiotics. It is becoming increasingly necessary to find new ways to combat disease and one of those ways might be in bacteriophages or viruses to bacteria. This is the enemy of my enemy is my friend in the world of medical microbiology
Antibiotics are a natural weapon of the microbial world and thus microbes are equipped to adapt and create new weapons against these antibiotics. The more they see the antibiotics the better they can equip themselves against them. It’s estimated that antimicrobial-resistant bacterial strains kill 7 million people each year and by 2050 the WHO estimates that deaths from multi-drug resistant (MDR) bacteria will exceed that of cancer, being responsible for 10 million deaths a year!
Phages have a highly specific interaction against certain bacteria meaning they are targeted therapies, safe for humans, and don’t cause the huge dysbiosis we see with antibiotics. It’s also a living arms race; when bacteria find a way to combat phage, phage finds new ways to combat bacteria. It’s not one-sided like antibiotics.
As technologies improve so will phage therapy. A phage’s genome is quite small and not as complex as others. It is getting easier to sequence and characterize a phage’s genome and to engineer them to have more desirable traits like improving storage conditions, efficacy, and host range.
So where is phage therapy today? In December 2020 there were 46 clinical trials that included the term “phage” with only one in Phase II trials which has to do with using a phage cocktail against UTI.
During the last two decades, more than 25 reports of the compassionate use of phage therapy after antibiotic failure have been published. Compassionate use refers to using newer therapeutic methods on individuals who have no more approved therapeutic options available. The FDA has approved phage therapy as a compassionate treatment for COVID-19 patients due to the high incidence of MDR secondary infections which is a huge contributor to the number of lives we’ve lost during this pandemic.
Regulations and funding are some of the biggest barriers the phage researchers face, but it is a promising solution for the MDR problem.
Biotech & Microbial Products
Microbe Discovered In Evolutionary Stasis for Millions of Years - Bigelow Laboratory For Ocean Sciences
In 2008 a bacteria called Candidatus Desulforudis audaxviator was discovered in a gold mine in South Africa that feeds off chemical reactions triggered by radiation.
Because of the microbe's isolation, scientists wanted to study their evolution by comparing samples of this microbe from different areas of the world deep underground and were different chemically from each other and how these differences drove the bacteria's evolution.
They found that these strains were almost identical to each other down to the molecular level. This means that they did not change much in the past 175 million years when the supercontinent Pangaea was still around.
The scientists believe that the lack of evolutionary change is due to its ability to protect against mutations, in essence, stopping evolution.
They think this is due to its enzymes that make copies of DNA called DNA polymerase. This enzyme is usually good at making an exact copy, but it will make a mistake every once in a while.
This bacteria’s version of DNA polymerase seems to be very good at preventing errors from occurring. This is a very desired trait in the biotech field which can use the enzyme from gene therapy to DNA sequencing.
Environmental & Marine Microbiology
Coevolutionary and Phylogenetic Analysis of Mimiviral Replication Machinery Suggest the Cellular Origin of Mimiviruses - Supriya Patil and Kiran Kondabagil Adapted from our friends at Microbites: Author credit: Anais Biclot.
Mimiviruses, when discovered, were thought to be bacteria and therefore were called Mimivirus from “Mimicking Microbes”.
They are so big, in fact, that they were found to be infected by smaller viruses called Sputnik virophages.
The origin of giant viruses is still not well known. However several hypotheses have been proposed.
To test which hypothesis was the most likely Patil and Kondabagil looked at the complexity and the evolution of the Mimivirus DNA replication machinery. To do this, they compared the machinery between different organisms: another virus - bacteriophages (T4), bacteria (E. coli), archaea, eukaryotes, and Mimivirus.
As each of these organisms has different levels of complexity, the authors could compare the machinery between the different organisms and showed that out of the nine replication machinery proteins investigated, five are of eukaryotic origin, two are of bacterial, one of phage origin, and one protein with unknown origin. Based on these results, they propose that Mimiviruses might have evolved from a complex cellular ancestor that over time lost genes by reductive evolution.
However, from which ancestor these giant viruses originate is still not understood and more studies on giant viruses will be needed to fill in this gap of knowledge.
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