Microbes in the News #2


Copycat fungus deceives immune system and deactivates body’s response to infection

Date: March 28, 2019          Source: University of Sheffield


Summary: New research shows fungi can make similar chemical signals as our immune system. These chemicals enter the body and make humans more likely to get an infection.


Connections: Just today in class we talked about the immune system and how it captures microbes.


Critical Analysis: Fungi have always produced chemicals similar to those released in our immune system. Up until know, we haven’t known the function of these chemicals. Now, research shows that when exposed to these chemicals the fungi can grow more easily than when the host is unexposed. I found it especially interesting that the fungus does not suppress the immune system in any ways. These fungi immune chemicals named prostoglandins activate a specific immune system pathway. This pathway prevents over-stimulation of the immune system. Ultimately this makes the body unable to fight off the fungal infection. What is even more dangerous is that opportunistic infections from usually commensal bacteria pose a danger while these postoglandins deceive the body. Once the body is tricked into shutting down the immune system, bacteria that our bodies always host begin to grow out of control.


Question: Would it be possible for microbiologists to isolate these prostoglandins in order to treat diseases in which the immune system attacks itself?

Pumping May Alter the Microbes in Breast Milk

Article: “Pumping may be linked to an altered microbial mix in breast milk” by Laura Sanders


Source:  Science News

Date Published:  April 1, 2019

Summary:  A study compared the microbial makeup of breast milk from mothers who do not pump at all to breast milk from mothers who pump.   Although the microbes in breast milk is fairly unique from person to person, the researchers found two main differences.   The milk from women who pumped had more bacteria that could cause infections under optimal conditions and fewer bifidobacteria, which are thought to be beneficial bacteria.   It is still unknown as to what impact these differences have on the children, if any, and the origin for these bacteria is also under debate.   Some believe the bacteria from the gut travel to the breast and get into the milk, while others think that babies’ oral bacteria affects the bacteria in the breast.   There is some evidence that ‘baby backwash’ might trigger infection-fighting proteins in milk when the baby is fed directly from the breast, so this would not occur in milk that is pumped.

Connections:  This is related to what we were talking about with the human microbiome and how it can be affected by many different factors.   The way a mother feeds her baby not only affects the microbiome of the baby but the microbiome of her breast and breast milk, as well.

Critical Analysis:  I did not know that the way a baby receives breast milk can change the type of bacteria that occur within the breast milk itself.   Since the milk is made within the mother, I thought that only factors within the mother would affect it, so it is really interesting that babies play such a large role in that microbiome.   The information appears to be scientifically accurate since the author included some quotes from one of the scientists who did the research and did not add much of her own opinion when talking about the information from the research.   It was written well to relay the information from the scientists to people who may not have any science background.   It was easy to understand and follow.

Question:  Once the mother is done breast feeding, do any of the microbes remain in the breast?   Do they get flushed out with the milk or die?   If they do remain, are they there for the rest of her life or will they eventually go away?

A2: Microbes in the News (Post 2)

Harnessing Soil Microbes to Enhance Crop Performance


March 28, 2019


This article explains that some organizations (the organization they used as an example was the Agriculture and Food Development Authority (TEAGASC)) have been using bacteria to modify different plants’ genome. This has been done for a while using Agrobacterium tumefaciens, but because of limitations, they were looking into alternative bacteria that could perform the same function. They found a bacterium, Ensifer adherens, which can modify a plant’s genome easier than A. tumefaciens. Plants treat A. tumefaciens as something to guard against, which makes modifying certain plants difficult because some plants have a resistance. On the other hand, many plants recognize E. adherens as a symbiotic bacterium. As such, they do not have the same resistance as they do with the A. tumefaciens. The article then discusses some practical applications that E. adherens has been used for already.

We have been covering in class recently how humans control the growth of bacteria with many different antibacterial methods. I found it interesting that even plants have antibacterial methods that make them resilient to certain strains of bacteria. I believe that this story was scientifically accurate, I just would have liked more information on how E. adherens differed from A. tumefaciens to result in more of a symbiotic relationship. Although, I believe that editing out all of the information would make it so a wider variety of audience would be more likely to read the article. All in all, I found this article interesting and informative.

My question is: Is there any other widely-used bacterium that has been identified that can genetically modify plants?


A2: Social bacterium, M. xanthus cooperate when food is scarce

Article Title/Link and Date: A social bacterium with versatile habits – January 22, 2019

Source: ScienceDaily

Myxocoxxus xanthus is a particularly cooperative predatory species that swarm together hunting other microorganisms in the soil.   When food is scarce thousands aggregate in fruiting bodies and form resting spores, allowing them to withstand hunger and drought.   The study referenced in the article found a surprising amount of genetic diversity and social behavior within the species cooperative, which had previously been theorized to be socially ubiquitous.   The researchers isolated communities of common ancestors and noticed differences social behavior arising from mutations within the ancestrally separated communities.   Diversity appears to be frequent in bacterial social groups, and it is speculated diverse cooperatives are evolutionarily favored over homogeneous ones.

This journal article and study touches on a lot of topics we have discussed in class.   A single species conglomerate utilizing the motile mechanisms of pili, and secretory lubrication.   They are predatory heterotrophs, and the article discusses cooperative interactions within the species similar to bio-films or localizing human microbiomes.

We know secretory mobility is metabolically demanding and so the predatory cooperative must be effective hunters to sustain their lifestyle.   Studying the yellow fruiting bodies of the dormant species was an effective measure of social variability, but I found the results more exciting.   Understanding the extent of diversity within a phylogenetically limited community I think speaks volumes about genetic variability, and the fluidity of useful genes.

Bio-films are cooperatives of bacteria that conjoin to increase their chances of survival.   I am curious how this study could better inform bio-film interactions?   It would be interesting if a variety of species that serve the same functional role in the community were similar in diversity to a single species with a unified role.   This could reinforce the importance of gene expression over taxonomic classification.   This is merely wild speculation at this point.

A2: Microbes in the News (Post 3)

Title: Study finds previously unknown mechanism for microbes to save energy in lean times

Source: News-Medical

Date Published: March 20, 2019

Article Link:  https://www.news-medical.net/news/20190320/Study-finds-previously-unknown-mechanism-for-microbes-to-save-energy-in-lean-times.aspx

Summary:  This article is a review done on some recent research in the world of Microbiology, looking at a mechanism utilized by microbes when they are nutrient limited. Using electron microscopy a group of scientists from the Imperial College of London analyzed flagella on two species of Gammaproteobacteria under nutrient limited conditions. They determined that when there is a lack of nutrients these bacteria can enter a lower energy state to conserve energy by ‘ejecting’ or ridding themselves of their flagella that normally use lots of energy.

Connections:  We’ve learned about both structures bacteria have that helps them move around, which include flagella (the focus of the study). Plus how bacteria can conserve or use energy, which is the key reason for this mechanism being used in bacteria.

Critical analysis:  I found it interesting how bacteria can adapt so efficiently to conserve energy when exposed to nutrient limited environments. I was unaware they could eject or get rid of their energy expensive flagella. I believe this paper was scientifically accurate as it was written as a direct review of a scientific paper on the topic. Effectively taking what would be a dense, hard to read for the general public, lab report and turning it into an easy to understand article that highlights the key points of the research.

Question:  What other structures or energy expensive mechanisms could bacteria limit or get rid of in nutrient limited environments?

A2: Microbes in the news — Yeast produce low-cost, high-quality cannabinoids


Yeast produce low-cost, high-quality cannabinoids


Synthetic biologists at UC Berkeley have engineered brewer’s yeast to produce some of the main components in marijuana including THC and CBD among others.


The developing field of synthetic biology is based on taking the tools that we are using in class, such as whole-genome sequencing, and our knowledge of how microbiology works to modify and create solutions to modern problems.

Critical Analysis:

Synthetic biology is an amazing and quickly developing field with the potential to take   a future we have only seen in science fiction and turn it into reality. This is an incredible technical achievement showcasing our developing mastery over the fundamental building blocks of life. I knew something like this was coming, I can see the economic incentives for this, I am sure the people behind this will end up fabulously wealthy, but I still can not stop myself from facepalming. Of all the amazing and wondrous potential synthetic biology holds… this had to be the top of my news feed today.


I cannot begin to imagine the legal ramifications, how the hell do you regulate something like this?

New technique provides a better understanding of bacteria evolution


New technique pinpoints milestones in the evolution of bacteria
Results show bacterial genomes provide “shadow history’ of animal evolution.
Jennifer Chu, MIT News Office February 7, 2019


Danielle S. Gruen, J. M. (2019, January). Paleozoic diversification of terrestrial chitin-degrading bacterial lineages. BMC Evolutionary Biology, 19-34. Retrieved from https://bmcevolbiol.biomedcentral.com/articles/10.1186/s12862-019-1357-8


—  Summary:  Researchers from MIT have established organism relationships between fungi and bacteria by reviewing the gene for chitinase (an enzyme which helps to break down chitin). Their review of the mutations, and similarities across different species has allowed them to create an evolutionary tree which correlates microbial evolution with fungal evolution. They found that approximately 450 to 350 million years ago, diversification of three separate bacterial groups diversified as the result of gene transfer with a chitinase utilizing fungi. Below is the resulting evolutionary tree with the fungi identified by purple lines and bacteria with blue lines.

(Gruen, et al. 2019)

—  Connections:  This connects with: Microbial evolution, metabolism, and diversification.
Chitinase allows these bacteria to metabolize chitin as an energy source. This allowed diversification of microbes into new niches ones chitin became more prolific in the environment. Gene transfer was said to make it difficult to genomically identify or differentiate bacterial strains, but here the gene transfer has allowed a better understanding.

—  Critical analysis: I found this article very interesting because, most evolutionary trees are based on rRNA sequencing (highly conserved due to form/function). The use of chitinase to correlate evolutionary relationships between fungus and bacteria is interesting. Especially since the origin of chitinase was in a Fungi (a microorganism that doesn’t look like a microorganism) and the gene has been horizontally transferred to bacteria.

The story was very well written and after reading the original journal publication, it was factually and accurately written. The author did as great job in conveying the information to the general population without losing the integrity of the research. I appreciate the writing style and how it helps those (like myself) who aren’t as well versed in the scientific nomenclature, to understand the information and findings from the research.


—  Question:  How many other highly conserved coding regions can we isolate and use in this manner? Are enzymes such as chitinase always highly conserved, or is there slight variations in the conformation, allowing it to mutate without ruining the function of the enzyme?

-Samantha Smith

Assignment 2 Microbes in The News

How a Fungus can Cripple your Immune System

February 8, 2019

Source: Science Daily:  Friedrich-Schiller-Universitaet Jena



In this article the scientists conduct a study about how the fungus  Aspergillus fumigatus  is able to turn off an enzyme that is used by immune cells to communicate between each other. Healthy individuals are not very affected by the fungus, but it is dangerous to individuals who are immune difficient, such as individuals who suffer from AIDs.


This does connect to when we were explaining what makes a microorganism. We discussed that fungi are covered under microorganisms, but we haven’t touched on fungus too much. This is a special adaptation specific to this type of microorganisms.

Critical Analysis:

I found this article very interesting in the fact that we often tell people that breathing in a certain fungus can “take years off your life’ and this fungus actually can. I learned to the extent that fungus can actually do this, I think people often assume that the air they breathe is healthy as long as it looks and smells pure, but this fungus has spores that can float through the air and be completely undetectable. I did not realize how potentially dangerous fungi can be, and it kind of opens your eyes to how vigilant people who have immune difficiencies have to be about their health.


How can we protect people who have immune defficiencies from these type of problems?




A2: Microbes in the News

Germs in Your Gut Are Talking to Your Brain. Scientists Want to Know What They’re Saying.

Jan. 29th, 2019 By Carl Zimmer

LINK: https://www.nytimes.com/2019/01/28/health/microbiome-brain-behavior-dementia.html?rref=collection%2Ftimestopic%2FBacteria&action=click&contentCollection=science&region=stream&module=stream_unit&version=latest&contentPlacement=2&pgtype=collection

Summary: Over the last few years several studies have linked particular microbes in mice intestine to traits in brain health and behavior. Some of these correlations have also been observed in humans. Alzheimer’s in mice have been found to be linked to the amount of bacteria living in the mouse gut. By putting mice on antibiotics an observable decrease of protein formation in the brain that causes Alzheimer’s was seen and transplanting the bacteria back into the mice caused the protein build up to resume. The article also talks bout other neuro problems that could be caused by certain bacteria or a lack there of. Introducing microorganisms from a depressed human into a normal mouse caused it to give up sooner in a particular experiment.

Connection: Microorganisms can release particular compounds as a result of metabolism dependent on their species and the boime they are in. Some of the compounds produced by microorganisms can be toxic, so it could be possible for some of the microorganism’s byproducts to have other impacts on mammals. There are many examples of mammalian microbes being dependent on particular microorganisms.

Critical Analysis: The articles comes off as very credible and offers sources throughout. it does not seem unreasonable for the mammalian microbiome to have an impact on the brain. By extension the particular microbes living within a mammal could also have an impact on brain chemistry through the gut’s microbiome and its interplay with other systems.k

Question: What would be some creative ways to pinpoint which specific microbe is responsible for producing an affect on a mammalian brain?