C.
difficile and the Microbiome: Read Article 04 F. Bäckhed, R.E. Ley,
J.L. Sonnenburg, D.A. Peterson and J.I. Gordon "Host-Bacterial Mutualism
in the Human Intestine," Science, 307 (5717): 1915-1920 (2005).
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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 4A/ Host-Bacterial Mutualism
0. Knew: The human gut plays host to a community of microbes which can have a population up to 100 trillion, and that the number of the microorganisms far exceeds the number of human cells in our body.
1. Learned: One species of bacteria found in the human gut is B. thetaiotaomicron, which has 226 predicted glycoside hydrolases (our genome only codes for 98), is capable of changing its carbohydrate surface via various cell mechanisms in order to evade periodic sweeps by the host immune system.
2. Pressing: How does a human fetus develop its microbiome? There is not direct connection between the gut of the mother and the developing gut of the fetus, and aren't the microbiome bacteria of the mother isolated to the mother's gut? Do newly born babies come out of the womb with a underdeveloped, or non-existent microbiome? Also, can most of these bacteria survive outside the gut, or have they evolved to be as dependent on us as we are on them?
3. Description of the some of the key players in the human microbiome and the roles they serve
4. I thought it was interesting that the CFB division of bacteria predominantly associated with bacteria experienced accelerated differentiation from the other divisions of bacteria (it is the most derived). It is also interesting to note that various sub-groups of CFB seem to be associated with particular groups of mammals which implies ancient CFB co-evolved with specific mammal species.
Kate Jones
ReplyDeleteAssignment 4A Article 4
0. Knew: I knew that humans needed a large amount of very diverse bacteria in the digestive tract in order to properly digest foods but that the diversity within each person is relatively constant.
1. Learned: I did not know that the diversity of bacteria in the gut is a result of host selection and coevolution. It makes sense though that at the microbial level, bacteria compete for space and resources, and at the host level, the type of bacteria in the gut affects host health and functionality which provides another form of natural selection because the bacteria need a healthy host.
2. Pressing ?: If the microbiota largely determine the energy balance and efficiency within the host, are doctors and researchers likely to attempt to alter the gut microbiota of overweight or underweight patients in order to help them return to a healthy size? Would this be a reasonable approach?
3. Presentation: The positive attributes of gut microbe that allow them to thrive such as the ability to respond to changes in diet and even change the carbohydrate surface to evade an immune response
4. I thought that the comparison of mice with and without exposure to microorganisms very interesting because it highlighted the fact that a considerable amount of the work our body does, specifically in the digestive system, relies on other organisms. This is important to keep in mind in any sort of modeling of the digestive system and even determining model organisms for modeling gastrointestinal diseases.
James Pino
ReplyDeleteAssignment 4A
0:Knew: Very little about the bacteria in the gut, except it existed and was large.
1:Learned: The diversity of bacteria in the gut. The importance of understanding the coupling of how human and the bacteria use eachother. That it is probable that diets and microbiota are coupled with weight. This seems to explain why some people have different experiences with different diets.
2: Pressing: When does a human obtain a microbiome? Can we modify it to control weight?
3:Presentation: Information about the role of bacteria in the intestine.
4:Thoughts: I never really thought about how diverse the bacteria is within our bodies. I know it is importance, but I am curious to what extent we need to really understand it to understand humans. More hermeneutics I suppose
Shuaipeng "Jimmy" Zhang
ReplyDeleteAssignment 4A
0. Knew: The presence and proliferation of bacteria in the gut and the impact that they have on digestion. The variety of bacteria present varies from individual to individual.
1. Learned: The finer details of the mechanism of the Bacteroides thetaiotaomicron. Conventially Raised rats had 40% more total body fat than rats raised without exposure to microorganisms. The immense diversity of bacteria present in the gut.
2. Pressing ?: It was stated in the article that bacteria which have symbiotic relationships with the host have a higher chance of success than bacteria which don't. If this is the case, why is there such a high prevalence of parasites in the body? Since hurting the host directly affects the parasite's habitat, and its survival, why are there so many malignant species present?
3. Presentation: The importance of bacteria in the gut, and their effects, complexity, and diversity.
4. Thoughts: The article really emphasized the diversity of bacteria in the gut. It discussed the possibility of altering our energy balance through the use of these bacteria. While that technology is still in the future, its impact on the healthcare industry would be large, since most of the current diseases have roots in obesity.
Arman Chowdhury
ReplyDeleteAssignment 4A
0. Knew: Microbiota, in distal human intestine, and its microbiome provide us with genetic and metabolic attributes we have not been required to evolve on our own, including the ability to harvest otherwise inaccessible nutrients (e.g. plant derived pectin, cellulose, hemicellulose, resistant starches).
1. Learned: The structure and composition of the gut microbiota reflect natural selection at two levels: the microbial level and the host level. The estimated 1200 viral genotypes in human feces suggest that phage attack is a powerful shaper of the gut’s microbial genetic landscape. B. thetaiotaomicron has evolved an elaborate and sizable genome that can mobilize functionally diverse adaptive responses (B. thetaiontaomicron is also a key anaerobic gram-negative bacterial pathogen w/ extreme disease causing potential as well as antibiotic resistance). Caloric value varies between individual consumers according to the composition and operation of their intestinal bioreactors and the microbiota influences their energy balance.
2. Pressing ?: Is greater diversity of the microbiome at the genomic level favorable to humans in terms of efficiently processing food? Can we then introduce more evolved, or genetically engineered, “energy absorbing” bacteria in our gut so that we can gain the same levels of nutrients while eating less amounts, and ultimately reduce food production per population size, and also reduce wastage?
3. Presentation:
4. Thoughts: The paper proposes using the microbiota as a biomarker of diseases within or outside of the GI tract and for monitoring responses to therapeutic interventions in the future, and I’m curious to know how these bacterial populations can be used as biomarkers (observe changes in microbiome “behavior”?)
0. Knew: The human gut is home to a massive amount of microbial life, various species exist in a mutualistic relationship of bacteria aiding in digestion and humans playing host.
ReplyDelete1. There are actually many times more bacterial cells in our bodies than human cells. The concept of evolutionary selection applies in both directions in this system. How heavily the microbiota can influence major factors in the host organisms life (40% more body fat in mice)
2. Question: Besides fecal transplant, are there other therapies that make use primarily of the microbiota?
3. Presentation: The coevolution of gut microbiota and humans and the evolutionary pressures and responses of each.
4. Thoughts: Either I need to read way more scientific literature, or this topic is understudied. I feel like I really haven't heard much about it before, but it seems like it could be a major player in a lot of human patholgies.
Chuck Herring
ReplyDeleteAssignment 4A
0. Knew: Generally, that the microbiota played an important roles in human health.
1. Learned: How the make up of the microbiota affects obesity and how co-evolution with their hosts occurred.
2. Pressing: Does the make up of the microbiota affect celiacs disease and similar diseases.
3. Presentation: How the microbiota has evolved with humans and how it manipulates the complements human biology.
4. Thoughts: How would the macrobiotic be represented in a ooc model?
0. Knew: The microbiome plays a crucial role in our digestion. In the absence of proper gut flora, ability to metabolize otherwise indigestible polysaccharides, such as cellulose, is diminished and risk of infection by unwanted bacteria is increased. One solution to this problem is a fecal transplant to restore gut bacteria.
ReplyDelete1. Learned: The human gut is tightly packed with an extraordinary amount of bacteria. These bacteria co-evolved with us symbiotically. The microbiome can vary significantly between individuals, and these variations can result in increased or decreased metabolic efficiency. Individuals with highly efficient microbiomes may be more susceptible to unhealthy weight gain.
2. If future studies reveal a strong correlation between particular, more efficient variations of the microbiome and obesity, and there were a practical means of diagnosing this difference, would fecal transplant make an effective weight loss treatment? Would a transplant alone be enough, or would an individual's native microbiome have to first be eliminated through antibiotics?
3. Overview of the origin, scope, and importance of the microbiome, as well as a discussion of what benefits the future of research into this area may bring.
4. Thoughts: I especially liked the description of the gut microbiota as a "microbial organ" in the introduction. I thought this was a very eloquent way to summarize all the information presented on an incredibly complex system, and made me quickly realize how much I had yet to understand about gut microbiota.
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ReplyDeleteKendra Oliver/4A/Host-Bacterial Mutualism in the Human Intestine
ReplyDelete0.Knew: Microbiota within the human intestine is diverse and the quality of the symbiotic relationship between humans and microbiota depend on the population within the human intestines. This relation is very important for humans because it allows the microbiome to digest food in ways that benefit us but have not yet developed on our own.
1. Learned: The role of the gut microbiota plays a major role in energy balance. With out the help of microbiota, germ free mice have ~40% reduction in body fat because they are not exposed to the digested polysaccardiades produced from the microbiota.
2. Pressing ?: How has the diversity changed with diet? How many times does the microbiota change in a person life? Is there a shift with age?
3. Presentation: Correlation between microbiota and diet. Does diet matter or is it your microbiota?
4. Thoughts: Can we characterize GI disease based on microbiota composition? Can we culture the exact microbiota required for “proper digestion” and implant it in people suffering for digestive issues?
Cami Johnson
ReplyDeleteAssignment 4A: Article 4
0. Knew: The human gut is home to a large number of bacteria which allow us to digest certain compounds that we would be unable to otherwise.
1. Learned: The gut bacterial population is incredibly vast (10 times more microbes than somatic and germ cells combined). Microbe populations are also far less diverse than you would assume, given that diversity is usually helpful to an ecosystem, especially in such an environment when trying to survive a possible immune response. Certain bacteria are also capable of altering their genome in order to avoid selective sweeps. Additionally, the more efficient that the gut microbiome is at capturing and storing energy, the higher the fat content of the body.
2. Pressing ?: If the high efficiency of a patient's gut microbia is resulting in excessive energy storage leading to obesity, is a possible treatment removing some of the bacteria? Could sequencing an individual's microbiome genome be a useful diagnostic tool in the future?
3. Presentation: The article discussed the microbiome present in the gut, why the bacteria is important, and how those bacteria avoid being removed from the body.
4. Thoughts: First of all, I had no idea how extensive the bacterial population in our gut was. I also found it very interesting how the bacteria evolve with us, adapting to what allows us to survive better so that they can continue to inhabit other hosts.
Priyanka Ravichandran
ReplyDeleteAssignment 4A - Article 4
0. Knew - mutualism vs. commensalism, microbiota is passed on through genes
1. Learned - the human GI contains all three domains of life
2. Pressing - how can we identify more bacteria (since only 8 of the known 55 species have been recognized); with the relatively low diversity, how can the microbiota survive a sudden new attack?
3. Presentation - explained the diversity of microbiota in the gut and how research in this area can be used in the future
4. Thoughts - I didn’t think about potentially using this information to help with the obesity problem, but it could be really useful in that aspect.
Selene van der Walt
ReplyDeleteAssignment 4A
0. Knew: The human digestive system makes use of a host of bacteria to complete its digestive tasks.
1. Learned: More about the interesting process of how these bacteria have co-evolved with humans to get to the stage they are at today, as well as about the particular role these anaerobic bacteria play in breaking down polysaccharides.
2. Pressing ?: To what extent does the make up of gut bacteria vary across populations and with varying disease states? Can this information be used in diagnostic or therapeutic applications?
3. Presentation: The multitude of life that exists within the human GI tract and how it has come to be.
4. Thoughts: I am interested to learn more about how the particular characteristics of the microbiome and it's associated metabolites affect host physiology.
Blog Harvested
ReplyDeleteJPW
Tim Lee
ReplyDeleteAsgn 4A/ Host-Bacterial Mutualism
0. Knew: Immense diversity of bacteria that composes a major part of the digestive process in the human intestine.
1. Learned: More in depth detail of how bacteria work in conjunction to thrive in both the microbial and host level.
2. Pressing: Is there a measurement of bacterial diversity that can indicate the risk of a person for intestinal disease?
3. Presentation: The magnitude of bacterial quantity and diversity and how they relate to each other to strive in both the microbial and host level.
4. Thoughts: I am curious to see if there is a quantitative correlation between the risk of intestinal disease and the diversity of bacteria in a host.