Now that we know a little bit about how to look at microbial sequence data, we'll discuss some of the factors that determine what someone's gut microbiota looks like. The main factors that influence the gut microbiota are age, diet, antibiotic use, genetics and physiology. Yeast factors change the gut microbiota by changing the selective environment in the gut. What does that mean? Although we can gain new gut microbes during our life, most of the changes that occur are changes in the relative abundances of the microbes that are already in our guts. Basically, we end up having more or less different kinds of bacteria. Imagine you have lots of microbes in your gut that like warm places, and only one or two microbes that prefer cold places. Suddenly your gut becomes colder. After a while, you should only have a few of the microbes that like warmth, but many that like the cold. Although your gut doesn't change temperature much, this is exactly how age, diet, antibiotics, genetics, and physiology affect your gut microbes. They change the environment that the microbes are living in. So that's how they do it, but what exactly do they do? Let's talk about each of these factors individually. We'll start with age. Based on Jessica's lecture during week one, we know that we start with a mostly sterile gut, and start accumulating microbes during and after birth. Therefore, infants and babies have low gut microbial diversity. The gut microbiota can also change dramatically from one day to another as babies come into contact with new people and foods and gain more microbes. Remember the animation that we watched. At about one year of age, our gut microbial communities are much more diverse then when we were born, but they continue to develop as we eat more solid foods and explore the world around us. Our gut microbial community become more diverse and more stable as we become adults. Once we reach adulthood our microbial communities are highly complex and they stay that way for the rest of our lives. However, studies have shown that as we move into old age we begin to lose some of the stability that we had as younger adults. The composition of our gut microbial communities becomes more variable again from day to day and week to week. The changes we see in our gut microbiota with age are much like the changes we see in other aspects of our bodies, like our skin, eye sight, memory, and immune system. Although we don't fully understand all the microbiome changes that occur in old age, they are natural processes that are likely difficult to alter. We can influence other impacts on the gut microbiota, though. Diet is a great example. Both your long term diet habits, as well as short term changes in your diet, can lead to shifts in the kinds of microbes that you have. And as anyone that has ever been on a diet will tell you, while it may be difficult, you do have control over what we eat. Let's address the long term impact of diet on the gut microbiota first. A study by Gary Wu and collaborators show that the general diet a person consumes over a year is strongly correlated with the composition of the gut microbiota. In this study, people who ate a lot of carbohydrates, things like pasta, potatoes, and sugars, tended to have a lot of prevotella bacteria, which you can see in the figure on the right. While people who ate a lot of protein, especially meat, tended to have a lot of bacteroides, which you can see on the left. An examination of microbiota across nations and cultures, by Yatsunenko and collaborators, resulted in similar patterns. Africans from Malawi, who eat mostly corn, and Amerindians from Venezuela, who eat mostly cassava, also had a lot of privatella compared to people in the US and Europe who eat more meat and processed foods. You can see how their gut microbes separate on this plot. Based on these two studies, it seems that if your diet falls into a specific category, your microbes will fall into a category as well. However, short term changes in diet also have an effect on the gut microbiota. In Wu's study, people that were fed a controlled diet that differed from their normal diet for ten days experienced rapid changes in the abundances of different microbes in the gut. On the right, you can see how the dissimilarity between the samples of one person is high between day one and the other days as diet changes. These are the blue columns. Even so, you can see on the left that every person, represented by a different color, had a gut microbiota that still looked more like their original microbiota than like that of someone else. This means the observed changes were relatively minor. But a recent study by Turnbow and colleagues has demonstrated that a more extreme diet change can lead to more extreme microbiota changes over a short time. In this study, volunteers changed their diet dramatically for three days. Some volunteers went vegan, this is the left column of the graphs, and some ate a meat and cheese only diet, these are the right columns of the graph. The first three rows here show you fiber, fat, and protein intake for people on each diet over time. In the last row, you can see the changes in beta diversity or gut microbial community composition. The vegan diet caused a little change, but the meat and cheese diet caused big changes, almost over night. Specifically, there was an increase in bacteria linked to cardiovascular disease like hemophela. Although we still don't know enough about how specific parts of our diet interact with specific microbes to be able to prescribe diets that alter the microbiome and ultimately improve our health, these baseline studies suggest that this type of intervention could become a reality someday. Although diet has one of the largest known impacts on the gut microbiota, antibiotics can also change the gut microbiota dramatically. Antibiotics stop bacteria from doing things, like making proteins, dividing, making cell walls, and transporting nutrients. They can also put holes in cell walls or membranes. Needless to say, none of these things are good for the bacteria, so most bacteria die when they are exposed to antibiotics. As a quick side note, bacteria can evolve to be immune to the effects of antibiotics, something we call antibiotic resistance. This is a serious problem in medicine currently, since it makes us vulnerable to pathogenic bacteria that can't be stopped. I won't talk about that here, but Rob talks about it more in his book if you're interested. Antibiotics target bacteria, but they don't target pathogenic bacteria. They generally kill all bacteria in their path. Therefore, you can imagine what happens to your gut microbiota if you take an antibiotic to stop an infection you have from pathogenic bacteria. Your good bacteria will suffer too. That being said, difference types of antibiotics have different effects on your gut microbiota, and different people react differently to antibiotic use. For example, Dethlefsen and colleagues did a study where they gave three people the same round of the same antibiotic. They took samples from each person before giving the antibiotics and afterwards for one year to see what happened to the gut microbiota. You can see the data here. The gray lines indicate an antibiotic series. The gut microbiota changed in every person, but each person took a different amount of time to recover back to the original gut microbiota. One person bounced back almost immediately, another took a few weeks, and the third took a whole year, and even then didn't look quite the same again. If that wasn't interesting enough, Dethlefsen and colleagues continued the study by giving a second dose of antibiotics. Everyone showed a shift in their gut microbiota again, but this time the changes were mostly permanent. So although the effect can vary, antibiotics have a big effect on the gut microbiota. The moral of the story is to take antibiotics when you're sick, but make sure you're sick and that an antibiotic will help before you take them. To counteract the effects of antibiotics, and to alleviate gastrointestinal disorders, like diarrhea and intestinal bowel disease, many people have started to take probiotics. Probiotics are live microorganisms that benefit health when they're administered in sufficient quantities. Probiotics are found in dietary supplements, yogurts and even suppositories. Some have a single strain of bacteria while others have multiple strains. And still, others contain fungal microbes. Although many people take probiotics, we still don't know a lot about them and how they work. Basic research, as well as clinical trials, are currently happening for a number of different probiotics. In the meantime, we know that probiotics appear to be helpful for alleviating the symptoms of diarrhea, intestinal bowel disease, and other gastrointestinal disorders. There's also preliminary evidence that probiotics could be effective against obesity or mood disorders, but we still have a lot to learn before we can say any of this definitively. In addition to environmental factors like diet and antibiotic use, our genetics may also impact the gut microbiota. However, studies examining the effects of our genes on our microbiota have had mixed results, and many of the observed patterns are subtle. Twin studies are often used to understand the importance of genetics versus the environment in determining patterns we see in factors like disease. Take heart disease for example. Remember, monozygotic twins come from the same egg and therefore, have the same DNA, while dizygotic twins do not. The idea is that if monozygotic twins both have heart disease more often than dizygotic twins both have heart disease, genetics is likely playing a role. In contrast, if both monozygotic and dizygotic twins have heart disease equally often, lifestyle factors, like diet and exercise, are more likely to be the main influencing factors. A similar approach has been used for studying the microbiome as well. The idea is that if monozygotic twins have microbiomes that are more similar to each other than dizygotic twins, genetics must be playing a role. Sounds simple, right? Unfortunately, the data from these studies has not been simple at all. Some studies have shown that monozygotic twins are more similar to each other, while others have not. The data are conflicting. Another approach to determining how genetics might be influencing the gut microbiome is to put individuals with different genetics into similar environments and see if their microbes become similar to each other. If they do, environment is more important. If they don't, genetics are more important. These types of experiments would be difficult, and potentially unethical with humans. But there have been a few experiments of this type with mice. In one, mice were placed with a different mother after birth. This mother had different genes than the mouse pup, but even so, the pup ended up looking more like the surrogate mother than its biological mother, in terms of the gut microbial community composition. This suggests that environment is more important than genetics in determining the gut microbiome. Nevertheless, studies that look at the particular genes present in individual mice and people, have shown that the presence or absence of a single gene can change the relative abundance of specific kinds of bacteria in the gut. This is particularly true for genera and species of bacteria. Gene presence or absence doesn't appear to have as much influence on the relative abundances of bacteria at higher taxonomic levels such as the phylum. For example, lactobacillus relative abundances have been shown to vary with host genotype in studies of mice. Also, many of the gene microbe interactions that have been detected involve immune function. For instance, humans with mutations in the MEFV gene get mediterranean fever and auto immune disease. And these individuals also show changes in the gut microbiome. Similarly, mice without TLR5 gene function, which impacts immune function, have distinct gut microbiota. Many of the bacteria that have been found to be influenced by host genetics, are also known to effect immune system function. So it seems that while the impact of host genetics on the gut microbiota may be more limited than the impact of other factors, it does exist. The last major factor influencing the gut microbiota is our physiology. This refers to factors like hormone levels, immune system function, metabolism, et cetera. All of these things can both affect, and be affected, by our gut microbiota, and likely interact with the other factors we've discussed. Instead of talking about that now though, we'll talk about that in separate lectures this week and next week. Because the interactions between our gut microbes and our body are numerous and complex, it will take some extra time to explore them.
