> For the complete documentation index, see [llms.txt](https://pop-lab.gitbook.io/microbiome-story-dice/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://pop-lab.gitbook.io/microbiome-story-dice/the-symbols.md). # The symbols Here we provide detailed information about the different symbols you may encounter on the microbiome story dice, describing both how the symbol may be used to create a story, and highlighting the microbiome-related relevance of the symbol.\ \ Importantly, these are just guidelines on how the symbols may be interpreted. Feel free to come up with your own interpretation, particularly in the context of the full set of dice that were rolled. The other players will let you know if they accept your interpretation.

Symbol	Meaning
	Baby. Can represent a human baby, or can be used as a modifier with another symbol, e.g., baby + cow = calf. The structure of the microbiome of newborns in mammals and other animals is critical for the development of organs and of the immune system. The mode of birth (e.g., vaginal versus Cesarean section) as well as early feeding (e.g., bottle versus breast-fed) can impact the infant's gut microbiome, however the implications for health are not yet understood.
	Mouse (or rodent). The mouse is a commonly used model organism for the study of the microbiome. While the microbiome of mice (in all body sites) is quite different from that of humans, mouse models enable studies that could not be performed in humans, such as growing mice without any bacteria in or on their bodies (germ-free or gnotobiotic mice) which allows researchers to build their microbiome in a controlled way.
	Person. Can represent a human, or can be used as a modifier with another symbol to represent the adult, e.g., person + cow = adult cow. We simply could not live without the microbiomes that inhabit our body. Microbes are critical for our development and they process our food so that we can digest it. Disruptions in the normal microbiome have been associated with illnesses, and microbiome-based treatments have been shown to be effective for some conditions (e.g., recurrent Clostridium difficile colitis)
	Chicken. Can represent an actual chicken, or some other type of poultry. Like for all animals, microbial communities within the bodies of chickens are important for their health. From an agricultural point of view there's substantial interest in using microbiome changes to improve nutrition and/or promote growth. There is also hope that microbiome interventions can reduce illness and colonization with human pathogens such as Salmonella or Campylobacter which can lead to foodborne illness outbreaks.
	Cow. Like in all animals, microbial communities within the bodies of cows are important for their health. In ruminants, microbes play an outsized role since microbial fermentation in their foregut is critical for extracting nutrients from the plant material they eat. Scientists are interested in manipulating rumen bacteria in order to improve the efficiency of nutrient extraction, or to expand the range of plants that cows can effectively consume (a particularly important consideration in the context of climate change). Also of interest are explorations into the use of microbiome-related interventions to reduce illness and the need for antibiotic treatment (which is believed to contribute to increasing rates of antibiotic resistant infections in humans).
	Pig. Like in all animals, the microbial communities within the bodies of pigs are important for their health. Given the increased rates of antibiotic resistance, microbiome-related interventions that can prevent or treat illnesses in pigs are of particular interest. Furthermore, pigs are generally seen as a good model for humans, both because of the size of their organs, and because they are omnivores. Thus, microbiome interventions intended for humans may first be tried out in pigs to assess both safety and efficacy. Finally, pig meat can be fermented to preserve it, such as in sausages, or as nem chua - a traditional Vietnamese dish.
	Fish. Can represent either fish or other water-dwelling animals. Microbial communities live on and within fish and contribute to their health. Since water is also full of microbes and viruses, there's substantial interest in learning how fish are affected by changes in the microbial communities in the water. There are also interesting fish-microbe interactions, such as anglerfish that recruit bioluminescent bacteria which can generate light within their "lure" organ to attract prey. Also, fish meat may be preserved or transformed through bacterial fermentation.
	Hair and skin. Bacteria, fungi, and viruses colonize the skin of virtually all animals. In humans, certain bacteria, such as Propionibacterium acnes, can feed on sebum (the oily substance produced in hair roots/follicles) and cause infections such as acne. There is substantial interest in learning how microbiome-related interventions can be used to prevent or treat such infections without the use of antibiotics, as well as in the role microbes play in other skin conditions, such as eczema, diabetic ulcers, or Staphylococcus aureus (particularly antibiotic-resistant MRSA) infections.
	Tooth. Either representing a tooth or the oral cavity more generally. Can also be used as a adjective in conjunction with another symbol, e.g., tooth + fish = oral cavity of fish. The oral cavity is the first place where our body encounters foodborne bacteria (including pathogens), and healthy oral microbial communities may represent a first line of defense against illness. Disruptions in oral microbiota are also associated with a range of conditions such as gum disease (periodontitis) and cavities (caries). Also, some studies suggest that oral bacteria entering our blood stream can harm other organs such as the heart.
	Lungs. Either representing the lungs themselves or the entire respiratory system. Can also be used as an adjective in conjunction with another symbol, e.g., lungs + fish = gills. In humans/mammals it was long thought that the healthy lungs are sterile, primarily because the high concentration of oxygen was believed to be harmful to microorganisms. Recent studies have shown, however, that certain bacteria can colonize the lungs. Studying lung microbial communities is difficult since sampling devices can be contaminated by bacteria from the nasal or oral passages. Nonetheless, a better understanding of the bacteria found in the lung is important for addressing conditions such as cystic fibrosis where pathogens (such as Pseudomonas aeruginosa) can infect the lungs due to mucus build-up.
	Reproductive system. Can either be used standalone to represent the human reproductive system or in conjunction with another symbol (e.g., the chicken reproductive system). In healthy humans, the vaginal microbiota contribute to reproductive system health and can provide some protection against sexually transmitted illnesses. Disruptions in the normal vaginal microbiota have been associated with a range of conditions such as bacterial vaginosis and pre-term labor.
	Gastrointestinal system. Can be used standalone to implicitly assume the human gastrointestinal system or in conjunction with another symbol (e.g., the gastrointestinal tract of cows). The microbiome gastrointestinal tract has, arguably, the biggest impact on human health. Microbes are important in early life by shaping the development of the gut organs themselves as well as the development of the immune system. Gut microbes digest the food we eat releasing nutrients that can be absorbed by our body, and bacteria also produce beneficial compounds such as short-chain fatty acids - a favorite "food" for intestinal cells. Disruptions in the gut microbiota are associated with a range of conditions such as C. difficile colitis or Chron's disease.
	Brain (or nervous system). Can be used standalone to implicitly assume the human brain, or in conjunction with another symbol (e.g., a chicken brain). The human brain is generally believed to be sterile, due to the blood-brain barrier, though some believe the brain may host microbial communities like other body sites that were previously thought to be sterile. Even if the brain itself may not have a microbiome, there is substantial research interest in the gut-brain axis - the hypothesis being that gut microbial communities can affect our brain and mental health through the many nerves found in the gastrointestinal tract. Gut bacteria can also produce neuroactive compounds such as serotonin.
	Beer. Can also be used to symbolize other fermented drinks, such as kombucha or kvass. While yeasts typically perform the bulk of the work of transforming the sugars in grain into the alcohol in beer, bacterial fermentation can help produce certain flavor, such as the tart flavor of sours. Furthermore, bacteria are important for growing the ingredients of beer (typically barley and hops). Bacteria may also appear as contaminants during the brewing process, introducing undesired flavors or halting the fermentation process altogether.
	Wine. Like beer, wine making typically relies on yeasts to convert the sugars in grapes into alcohol and flavor compounds. Bacterial fermentation (also called malolactic fermentation) is frequently also employed to add further flavor compounds to the wine. Soil microbial communities are also important in the cultivation of grapes and it is believed that microbes in the vineyard soil or on the grapes may contribute to the famed "terroir" - distinctive flavor properties of wines grown in certain regions. As for beer, undesired bacteria may introduce off-flavors or disrupt the fermentation process altogether.
	Cheese. Can also be used to symbolize any other fermented milk product. Bacteria, frequently in conjunction with fungi, are key to transforming milk protein and fats into the many types of cheese we enjoy. There is substantial research aimed at understanding how certain desired (and undesired) flavor compounds are produced by bacteria. Also, undesired bacteria may disrupt the fermentation process, lead to spoilage, or foodborne illness (e.g., Listeria is a foodborne pathogen that may be found in soft cheeses). Furthermore, the bacteria themselves may get "sick" - a viral infection of bacteria in a dairy fermenter led to the discovery of CRISPR - a type of immune system that bacteria employ to fight off viral infections. The bacterial CRISPR system was later engineered into a precise gene-editing technology that is now widely used in biotechnology and also applied in humans to correct certain genetic defects.
	Bread. OK, to make bread you don't really need bacteria and many breads are made without any raising agent or with the help of yeast. However bacteria are important for some types of bread, such as sourdough. Bacterial fermentation of the flour generates acidity (which can help prevent harmful microbes from persisting in the bread - raw flour is pretty dirty, just think about the animals that you may find in grain piles). Bacterial fermentation can also produce flavor compounds that enhance the taste of the bread. There is also evidence that even after all bacteria have been killed during baking, the compounds they produced can keep harmful fungi and bacteria at bay, thereby increasing the shelf-life of sourdough bread.
	Sausage. Can also be used to represent other type of fermented meat. Bacteria are important for transforming minced meat into sausage or salami, as well as for preserving other types of meat. Bacterial fermentation, together with dehydration and salting, prevents spoilage, and also introduces desired flavor compounds. Bacterial fermentation can also detoxify meats that otherwise would be harmful to humans (a good example is fermented Greenland shark - an Icelandic delicacy).
	Cabbage. Can also be used to represent other types of fermented vegetables. Bacterial fermentation has long been used to extend the shelf life of fresh vegetables throughout the world, giving us delicacies such as sauerkraut and kimchi. Since fermentation is frequently natural (relying on environmental microbes and yeasts rather than defined starter cultures), particularly within the many households that pickle their own vegetables, there is strong interest in better understanding the interplay between the microbes present at the start of fermentation and the flavor profile and safety of the final product.
	Legumes. Legumes have special nodules in their roots that contain bacterial communities able to "fix" nitrogen, that is to take atmospheric nitrogen and convert it into molecules that can be absorbed by plants. As an aside, nitrogen is a key building block of nucleic acids, such as DNA, thus all living things need nitrogen in order to build new cells. For this reason, legumes are frequently planted on agricultural fields as part of crop rotations, helping to increase the nitrogen in soil, making it available for future crops to use. Legumes are also preserved through fermentation - soy sauce, miso paste, and tempeh, are all different forms of fermented soy beans.
	Wheat. Can also represent other grains, such as barley, oats, rice, or rye. Wheat is a major source of food for the world, but its success required substantial adaptation to allow it to effectively grow in most climates. As for other plants, the microbial communities in soil can affect the growth of wheat and may also determine its ability to overcome stresses such as drought. Bacteria and yeasts also play an important role into transforming wheat into food - bread (particularly sourdough bread that relies on lactic acid bacteria for its distinctive taste and longer shelf life), beer, kvass, boza, and others.
	Maize/corn. Like other plants, the health of maize depends on soil microbes that help provide the plant with food. Native Americans used to cultivate corn together with beans and squash (the so called "three sisters"), which helped to bring to the soil nitrogen-fixing bacteria (bacteria that can transform atmospheric nitrogen into a form that can be absorbed by plant roots - legumes are particularly effective of promoting the growth of such bacteria). Like other grains, maize is also fermented to create various foods. Notably, bourbon production starts by fermenting a mixture of grains that contains at least 50% maize. Also, a traditional South and Central American drink, chicha, is usually made by fermenting corn, and in Africa a traditional dish is ogi - a fermented corn porridge.
	Crab. Can also be used to represent other crustaceans. Like for other sea creatures, their health is affected by both the microbiome of the water and their own microbiome. Climate change, pollution, and habitat disruptions are impacting crab fisheries, something that is quite evident in Maryland where the beloved blue crab is frequently imported from the Gulf of Mexico due to reduced populations in the Chesapeake Bay. There is hope that a better understanding of crab-associated microbiomes could contribute to interventions that mitigate some of the stresses that affect crabs.
	Lobster or crayfish. Like other water-dwelling creatures, their health is affected by their own microbiome and that of their environment. Climate change, habitat disruptions, and pollution all affect lobster/crayfish health which is a particular concern for the corresponding fishing industries. Crayfish may also be a convenient model organism for studying the gut-brain axis, specifically the role that molecules produced by bacteria in the crayfish gut play in modulating behaviors.
	Oyster. Can be used to represent shellfish more generally. Oysters feed by filtering water, thus they are severely impacted by toxins or harmful organisms in their surroundings. The oyster microbiome may hold the key to improving their resilience in the face of climate or human-caused disruptions. At the same time, due to their ability to filter large volumes of water, oysters, together with microbes, may be harnessed to remediate contaminated waterways.
	Dolphin. Can also be used to represent other marine mammals. As is the case for all animals, the microbes associated with the bodies of dolphins are important for their health. Since they spend their lives in water (which may contain higher concentrations of bacteria than air), there is interest in understanding how the microbiome of water as well as of the fish that dolphins eat impact the dolphin microbiome.
	Poop? This symbol is intended to be the "poop" emoji with a spoon stuck in it, but some people interpret it as ice cream. Either works - if you prefer to think of it as ice cream, see the "cheese" symbol for a description of the use of microbes in dairy. The original intent for this symbol was to represent "fecal matter transplant" - a medical intervention that involves taking fecal matter from a healthy donor and introducing it into a patient in order to restore the diversity of their gut microbiome. This intervention is particularly effective (more so than antibiotics) in treating C. difficile colitis - a debilitating gastrointestinal infection that primarily affects elderly patients and is often triggered by antibiotic treatment.
	Toilet. The development of sanitation has been one of the most consequential inventions of humankind, helping to reduce illness and making it possible for us to live in densely-populated cities. Microbial communities play a critical role in transforming the waste, in both wastewater treatment plants and septic tanks, so that it can be safely disposed of in the environment. While water treatment originally was concerned with the microbiological safety of the waste (in order to prevent the spread of human pathogens), increasingly there is interest in developing approaches for removing residual medication and other chemical pollutants, such as microplastics.
	Toxic spill. Human activity is generating large amounts of toxic compounds that make their way into the environment (both intentionally and unintentionally). Such toxic materials can impact the environmental microbiome, as was prominently evident in studies performed after the Deepwater Horizon oil spill in the Gulf of Mexico. At the same time, environmental microbes may be the key to undoing the negative effects of pollutants, either by degrading/detoxifying compounds, or by transforming them into forms that do not dissolve in water, thus preventing their further spread.
	Medication. Microbes can be used to manufacture medication, either directly (e.g., many antibiotics are naturally produced by bacteria), or through genetic engineering (e.g., insulin produced by genetically-modified E. coli). At the same time, medication can impact the microbial communities in our bodies. We certainly expect an effect when taking antibiotics since they are medicines developed to kill bacteria, but many other medications also impact our microbiome. A good example is metformin, medicine often used in the treatment of type-II diabetes. Early attempts to find associations between the gut microbiome and diabetes discovered false associations caused simply by the effect metformin had on the human gut microbiome. Finally, gut bacteria are sometimes needed to activate medicines - a class of medication called azo drugs require gut bacteria to modify them in order to have an effect. Some people may lack the bacteria able to perform this function, leading to treatment failure.
	Factory. Industrial activity has a big impact on our entire world including the microbial communities present in the environment and in our bodies. Pollution has been associated with changes in our bodies' microbial communities, and the microbiome is viewed as a potential contributor to conditions, such as asthma, that are triggered or made worse by pollution. From a different point of view, however, microbial communities can be harnessed to perform various industrial processes, e.g., to produce useful compounds, or to detoxify industrial waste.
	Mountain. Mountains provide a range of interesting opportunities for microbiome research. By analyzing the microbial communities found on mountains, we can learn a lot about adaptation to stresses such as drought (e.g., the high-altitude Atacama desert in Chile), ultraviolet light exposure, or lower concentrations of oxygen. Runoff from mountain glaciers can provide a largely unpolluted source of water enabling comparative studies with microbes exposed to urban runoff. Melted glaciers may also release into the environment microbes that had been encased in ice for hundreds of years or more, providing insights into how the microbes populating the earth have changed. Finally, mountains allow us to explore how our microbiome adapts as our bodies are exposed to the stresses of higher altitudes.
	Ocean. Oceans cover the majority of the surface of the world and they harbor a tremendous bacterial diversity much of which remains unexplored. Studying ocean microbiomes provides interesting insights into the evolution and adaptation of microbes, as well as into the ways in which microbes disperse throughout the world (e.g., how do microbes jump from one unique environment, such as a hydrothermal vent, to another similar environment thousands of miles away?) Around deep-sea hydrothermal vents, microbial communities have learned how to exploit the mineral-rich water and convert minerals into food that sustains complex ecosystems despite high pressure and absence of light. Ocean microbes are also believed to harbor genes that can generate useful chemical compounds, such as anti-cancer agents.
	River. Could also be used to represent pastureland or some other open fields. Like all parts of our world, rivers contain microbial communities, however it is difficult to define what a "river microbiome" is given that water is constantly washing any free living microorganisms downstream. Rivers may be a good environment to study the spread of microbes as well as the effects of flooding or agricultural runoff after storms. Also, stable microbial communities may form as biofilms on rocks and other structures.
	Lake/pond. Lakes and ponds tend to have limited water exchange, thus relatively stable microbial communities can form, offering a great opportunity to study microbial systems at a relative equilibrium. Scientists have explored how microbial communities vary along night/day cycles, seasons, or depth within the lake. The impact of climate on the microbial communities found in lakes is also of substantial interest especially as algal and cyanobacterial blooms have increased in frequency, harming fish and wildlife and even posing a health risk to humans and pets (toxin produced by cyanobacteria may harm us even through just skin contact).
	Agricultural field. Plants rely on microbes in their root systems to obtain nutrients, thus the microbial health of agricultural soils is important for the health of crops. Legumes harbor bacteria in their root systems that can help convert nitrogen from the air into formats that are accessible to plants, thus farmers include legumes during crop rotations intended to maintain the health of the soil. A further practice intended to support the bacteria in the soil and the retention of organic matter is cover cropping - sowing crops that are not intended to be harvested on agricultural fields in between primary crops. The cover crops help promote bacterial growth and are usually plowed back into the soil where they are fermented by soil bacteria to fertilize the soil.
	Coral reefs. Coral reefs are delicate environments and complex microbial communities are critical for maintaining their health. Researchers have associated disruptions in the coral microbiota with ocean warming as well as coral bleaching - a dramatic phenomenon in which corals expel their symbiotic algae which both give them food and help protect them from disease. Without colorful algae, corals appear white.
	Petri dish. Can also represent some other type of culture. Petri dishes are used to select, from complex microbial communities, the organisms that have certain properties. For example, by mimicking the environment that microbes may encounter in the human body, scientists can select certain human pathogens from food samples in order to make sure food is safe to eat (if no pathogens can be grown). Culturing bacteria can take a long time, thus researchers have proposed combining culture with DNA sequencing in order to more quickly determine whether harmful bacteria may be present in a sample.
	Microscope. The first time microbes were ever seen and analyzed was with a microscope. In the 1600s in the Netherlands, Antonie de Leewuenhoek developed one of the world's first microscopes and with it was able to observe microbes in the environment and in our bodies. Ever since microscopy has been a commonly-used tool for exploring microbial communities. Through microscopy, scientists were able to document the "plate count anomaly" - the fact that a lot fewer microbes could be grown in culture than one could see through a microscope. This observation motivated the eventual development of molecular techniques based on DNA sequencing able to analyze microbes that cannot be cultured. Even today, when DNA sequencing is the primary way of analyzing microbial communities, microscopy can provide valuable information, such as details about the spatial organization of microbial communities.
	The R language. Microbiome studies generate vast amounts of data and their analysis requires advanced statistical methods and computational tools. The R language is a computer language specifically designed for performing statistical analyses of large data sets. R is widely used to analyze microbiome data. R was developed as a free alternative to the statistical package S, and is available as an open-source package. Its continued development is supported by the R foundation.
	The Python language. Microbiome studies generate vast amounts of data and their analysis requires the use computational tools. A widely used programming language in microbiome analytics and data science, more generally, is the Python language. While python is a general purpose programming language, several packages are available that offer specialized functionality, such Pandas - a library of data analysis tools - and NetworkX - a library for manipulating graphs and networks. Python is released freely and it's continued development is supported by the Python software foundation.
	Sequencing machine. Most microbiome studies rely on DNA sequencing. Scientists have long recognized the many microbes could not be grown in the laboratory yet could be seen under microscopes (the "plate count anomaly") and the rapid advances in DNA sequencing starting in the late 1990s, and continuing today, have made it possible to start characterizing such unculturable organisms. Sequencing is performed in either a targeted fashion - isolating a single gene or gene segment for analysis - or in an untargeted fashion, wherein the entirety of the DNA in a sample is sequence and analyzed.
	Cloud computing. Can also be used to represent high-performance computing, or just computing more generally. As microbiome data sets increase in size, the computational power of a laptop or even a desktop computer may not be sufficient for analysis. Microbiome scientists increasingly rely on high-performance computational tools for analysis including "cloud computing" - a term defined as network access to a scalable pool of virtual computational resources. Cloud computing can also allow sharing and analysis of massive data sets that cannot be easily downloaded to a local computational infrastructure, with scientists being able to upload analysis software and running it on the data "in the cloud". This is a particularly attractive paradigm for sensitive data (such as data that contain human DNA or other personally-identifiable information) since limiting data movement reduces privacy risks.