C. difficile and the
Microbiome: Scan Article 05 R.E. Ley, D.A. Peterson, and J.I. Gordon,
"Ecological and Evolutionary Forces Shaping Microbial Diversity in the
Human Intestine," Cell 124, 837–848 (2006).
Focus on Figure 1 and Table
1. Post a PCRC on the blog.
The Systems Biology of COVID-19 and the SARS-CoV-2 virus. The class will build a foundation that includes the emergence of complexity, simple biological subsystems, their reductionist and equivalent toy and organ-chip models, and the measurements required to specify model architecture and parameters. Applications to biology, physiology, medicine, chemical and biological defense, pharmacology, drug discovery, and toxicology. UGrad: PHYS 240 01 and BME 290B; Grad: PHYS 326 and BME 395C.
Cameron Togrye
ReplyDeleteAsgn_4B/Ecological and Evolutionary Forces...Human Intestine
0. Knew: There is a high amount of genetically unique microorganisms that exist in the human gut, however these various genetic sequences span only a few bacterial and archaebacterial divisions.
1. Learned: There are two evolutionary pressures present in the human gut. The top down pressure which would tend towards stability and redundancy in microbial species, and the bottom up pressure which would lead to niche specialization between microbes in the microbiome.
2. Pressing: What is the mechanism by which microbiome residing organisms would able to evolve to suit a specific species (so as to co-evolve with them). Would this require fecal matter to some how be distributed to new members of the species? And isn't this means of 'inheritance' to fragile to be viable due to the chance nature of it?
3. Presentation: The microbiomes of other organisms and how they compare to humans
4. The inner workings of the microbiome can be seen as a systems biology problem as thousands of various species of bacteria and their proteins interact to produce the emergent property that is our effective digestion.
Kate Jones
ReplyDeleteAssignment 4B Article 5
0. Knew: I knew that the bacteria in our gut help us digest and absorb nutrients that we are not equipped to handle without them such as cellulose. I also knew that our intestines contain an enormous amount of bacteria that are for the most part harmless to our bodies.
1. Learned: I did not know that Archaea also exist in the gut. I learned that these organisms are responsible for the last step in extracting energy from organic compounds and are in control of the thermodynamics. I had not considered that while higher levels impose constraints on lower levels, the emergent properties from the bacteria affect host fitness.
2. Pressing ?: Table 1 explains that gut microbiota are first introduced from the external environment primarily from parent to child and that hygiene practices could have altered the transmission process. What then happens to the digestive process in children with SCID who cannot interact with the environment in order to acquire these bacteria necessary for digestion?
3. Presentation: If an important aspect of reproduction among bacteria is the ability to exchange fragments of genes, why then are the bacteria in the gut so different and have the ability to carry out such different functions if they are always in contact with one another? Is there some sort of control mechanism keeping bacteria from becoming too similar and exchanging too much information over time?
4. It could be interesting to analyze the effects having different types of bacteria in different ratios might have on overall health of the host. Perhaps some balance of bacterial types would help combat another ailment in the body.
Arman Chowdhury
ReplyDeleteAssignment 4B
0. Knew: Microbial communities are similar in members of a given family; babies acquire their initial microbiota from their mother.
1. Learned: The gut microbiota in adults is dominated by members of just two divisions of bacteria – Bacteroidetes and Firmicutes- and contains about 9 divisions in total (in soil where plant polysaccharides are also degraded, there are at least 20 bacterial divisions). Bacteria in the gut can “differentiate” genetically by lateral gene transfer via phage, mobile element-mediated insertions (?), conjugal transfer, and uptake of naked extracellular DNA. Babies delivered by caesarian section have an altered colonization pattern relative to their vaginally-delivered counterparts.
2. Pressing ?: Why does the human gut naturally select only two major divisions of bacteria to dominate in the microbiome (one answer could be: the gut offers fewer chemical niches to its microbiota than a habitat such as soil)?
3. Presentation: The organization is clear and the language generally easy to understand. The table labeled “Key Questions and Future Studies” is very helpful to contextualize the material.
4. Thoughts: The policing of the microbiome by the immune system is an interesting phenomena, although much is not known. Since the microbiome “exists” in close presence of an active immune system, can the whole GI tract then be labeled as an external/ intermediate environment separate from the “true” human body?
James Pino
ReplyDeleteAssignment 4B
0:Knew: A little about bacteria involved in the human body.
1:Learned: Concept of evolutionary radiation. Theories of how humans gain their microbiota. Top-down and bottoms-up explanations of redundancies.
2:Pressing: Why are there only 3 human samples for sequences? Has anyone looked at monitoring the diversity after changing diets?
3:Presentation: Sources and constraints of diversity of the microbiota.
4:Thoughts: This is a very complex topic. Many variables to control just when attempting to monitor the microbiota. I wonder what the differences between my microbiota and someones with a normal/healthy diet.
Mark Vander Roest
ReplyDeleteAssignment 4C
0. Knew: Mostly stuff from the previous article - general idea of the microbiome, many different bacterial strains, but low intermediate and deep lineage variation.
1. Learned: Transfer/inoculation theories, more in depth ecological/evolutionary theories applied to this area, top down and bottom up evolutionary pressure, the use of functionally redundant species.
2. Question: How badly do antibiotics wreck our microbiome? Are there methods for probing the microbiomes of ancient animals to study their coevolution with their hosts? Is the microbiome a factor in OOCs or other systems bio considerations?
3. Presentation: Microbiomes and the mechanisms that they use to first inoculate humans. Diversity (or lack thereof) in the gut microbiome. Selection pressure on the microbiota.
4. Thoughts: This paper only seems to ramp up the complexity of systems biology. How are these issues being addressed in the context of host health?
Tim Lee
ReplyDeleteAssignment 4B
0. Knew: General concepts about community growth of bacteria and how they thrive together.
1. Learned: The immense bacterial diversity present in our gut and how different divisions of bacteria affect the bacterial community and the host in a different way.
2. Pressing: How does the immune system adapt to accept the entire diversity of the bacterial population that clearly isn't made from our own bodies? Have these bacteria found a way to present antigens of the host or does the immune system have a special way to overlook them?
3. Presentation: A look into the top-down and bottom-up pressure selections within the diversity of gut bacteria.
4. Thoughts: Figure 3 which showed the branching diversity of all of the bacteria made me realize just how many different parts there are to just maintaining the function of the gut. It's interesting how a similar construct of bacterial communities isn't present in all of the other systems of the body to help with our other functions.
Shuaipeng "Jimmy" Zhang
ReplyDeleteAssignment 4B
0. Knew: The microbiome in the gut, and their relationship with us (their hosts).
1. Learned: Microbiomes in siblings are more similar than those in unrelated individuals. Same with parents and offspring. Top down and bottom up evolutionary pressures in the gut. Lack of variation in intermediate and deep lineages.
2. Pressing ?: This article only addresses the microbiome present in the gut. Are the microbiomes present in other parts of the body, such as the lungs, of equal complexity? And are they also passed on to offspring by parents?
3. Presentation: The evolutionary pressures that bacteria in the gut face. Further emphasis upon the importance of the microbiome.
4. Thoughts: The microbiome is undoubtedly a major aspect of our lives, and that without it, the human race would cease to exist. Understanding this microbiome will dramatically advance medical and scientific research. How has this microbiome evolved over the course of human evolution? Has it remained relatively the same?
Chuck Herring
ReplyDeleteAssignment 4A
0. Knew: What I gained from the first paper, co-evolution of microbiota with their hosts and the important part they play in its host's health.
1. Learned: That firmicutes and Bacteroidetes most likely can not survive outside the body like pathogens, giving some credibility to the idea of microbiota inheritance from mothers of offspring.
2. Pressing: How does the tissue structure of the intestine (shedding of cells and chemical gradients controlling cell proliferation) affect the microbiota?
3. Presentation: How ecological and evolutionary forces shape microbial diversity in the human intestine.
4. Thoughts: What would a microbiota ooc look like and how close are we to making that possible?
Kendra Oliver/4B/Ecological and Evolutionary Forces Shaping Microbial Diversity in the Human Intestine
ReplyDelete0. Knew: Transmission of the GI microbial communities is similar in member of a family because of transmission from mother to child.
1. Learned: Interestingly the gut microbiota in adults is primarily made up of one two type of bacteria while something like soil would have 9 divisions in total. The diversity within the GI occurs genetically through a number of mechanisms that are specific for bacteria including mechanisms like lateral gene transfer via phage, and uptake of naked extracellular DNA.
2. Pressing ?: How does the gene expression of the gut change with diversity of the microbiome? Does the immune system ever move into the GI tract? Does the immune system respond to GI cellular changes that occur from the micobiome?
3. Presentation: Temporal resolution to diversity of microbiome?
4. Thoughts: Interesting to consider how the rest of the body (blood) interacts with the microbiome if at all.
0. Knew: The microbiome is a vast and dense microbe environment located within the human gut. A healthy microbiome is crucial for proper digestion. The microbiome can vary significantly between individuals, and this difference can greatly impact the efficiency of an individual's metabolism.
ReplyDelete1. Learned: Techniques for surveying the contents of the microbiome through 16S rRNA sequencing. That infants are born without any gut flora: the microbiome must be transmitted, through contact with parents and other means. More about the co-evolutionary relationship between humans and gut microbes, and what this tells us about our own evolution.
2. Pressing ?: If Bacteroidetes and Firmicutes, which make up a majority of the microbiome, are transmitted from close contact with their family, do individuals raised without a family or prolonged exposure to other individuals with mature microbiomes possess a less diverse microbiome or less efficient metabolosm?
3. How selective pressures drove our co-evolution with the microbiome.
4. Thoughts: The symbiotic relationship between us and our gut microbes is fascinating. It seems that as we begin to understand the microbiome more fully, many more doors to new treatment options for a variety of digestive issues.
Cami Johnson
ReplyDeleteAssignment 4B: Article 5
0. Knew: The microbiome in the gut contains a diverse population of bacteria which allows humans to digest certain compounds that they normally cannot.
1. Learned: The diversity of the bacterial population is influenced by both "top-down" and "bottom-up" evolution. Top-down evolution describes selection on the host. An example of this would be that a bacterial population with functional redundancy would be most beneficial for the survival of the host. Bottom-up evolution describes selection on the bacteria. Competition for resources and the homogenizing factor of lateral gene transfer further complicate this process. The balance between these two evolutionary forces results in the complicated system of the gut microbiome.
2. Pressing ?: If mothers often transfer their gut microbia to their children, does this happen with unrelated caretakers as well? How does consuming certain foods containing inoculated bacteria (yogurt) affect this ecosystem? Can a similar microbiome in two related individuals cause a disease in only one due to the "pathogenic community" resulting from diet or behavior?
3. Presentation: The article discussed the complicated ecosystem of the microbiome in the human gut, focusing on how the evolutionary pressures on the host and on the bacteria affect the makeup of the population.
4. Thoughts: I thought it was very interesting how very efficient microbiomes (arguably too efficient) can cause obesity, but this never gets selected against because obesity doesn't necessarily reduce reproductive fitness. I wonder if either a removal of part of the bacterial population or the addition of new bacteria could reduce obesity.
Priyanka Ravichandran
ReplyDeleteAssignment 4B - Article 5
0. Knew - the gut has a large amount of diverse bacteria; how and why genetic diversification can occur
1. Learned - sequencing 16S rRNA genes can be used to determine the microbial diversity of bacteria in the gut; mothers pass on their microbiota to their children
2. Pressing - It has been shown that humans can pass on their “microbial communities” to their offspring so how can this information be used? Do environmental factors cause changes in an offspring’s microbiota so that they eventually significantly differ from their mothers?
3. Presentation - background information and explanation of the evolution of bacteria in the gut
4. Thoughts - I thought this was a really interesting read because I like biology and genetics. I didn’t know that genes dictated the specific kinds of bacteria that form in the gut. I think looking into this research provides a way for personalized medicine and maybe even a treatment method for celiac patients, or others with similar diseases?
Selene van der Walt
ReplyDeleteAssignment 4B
0. Knew: about the host of bacteria occupying the human intestine and a basic understanding of their evolution and function.
1. Learned: There are 10^23-10^24 microbial cells. Learned about the microbial heirarchy and the way that different selection pressures are put at different places in this hierarchy to produce various changes. Also learned that there are low levels of deep diversity within the microbiome.
2. Pressing ?: Why does the human intestine have much less bacterial and archaeal diversity in lineage than other microbial systems? How is our health affected by the specific composition of our microbiota?
3. Presentation: How various forces shape the evolution of the microbiome in the intestine and the impact thereof on human physiology.
4. Thoughts: I enjoy the concept of the microbial population in the intestines having emergent properties.