Microbiomes

Question 1

What is a holobiont?

Answer 1

Host and microbiome.

Question 2

Describe alpha diversity.

Answer 2

Alpha diversity describes the community in one place, which can range in scale from the collective human microbiome, an individual human host, a body site, or a small region of a body site. From the host’s perspective, functional diversity (physiological diversity), rather than taxonomic diversity, is a more important property of the microbiome. Another way to define functional diversity is the genetic potential of the microbiome, the accessory genome.

Question 3

Describe functional resilience and functional redundancy.

Answer 3

Alpha diversity is widely believed to confer functional resilience to microbiomes. This is based on functional redundancy, which describes multiple species that share similar, if not identical, roles in ecosystem functionality. The hypothesis is that if a perturbation eliminates one species, another species capable of the same function within the community will likely survive and replace the lost species.

Question 4

Describe beta diversity.

Answer 4

a measure of the similarity of communities, normally based on pair-wise comparisons. Microbiomes of individual humans have high beta diversity, meaning that they are compositionally dissimilar, and species overlap between individual microbiomes tends to be low. Because of functional redundancy, many experts think individuals’ microbiomes may be less functionally than taxonomically distinct. Thus, microbiomes with high beta diversity might still be highly similar in terms of overall ecosystem functionality.

Question 5

Describe community assembly.

Answer 5

Community assembly encompasses processes that shape the species composition of ecological communities. Assembly is both deterministic, due to strong selective pressures, and stochastic, due to the random presence of microbial species. Drivers of microbiome assembly can generally be classified as either selective pressures or sources of populations (inocula), or in some cases, both.

Question 6

Name some drivers of community assembly.

Answer 6

• Gestational age
• Vaginal versus Caesarean delivery
• Breast milk versus formula feeding
• Maternal microbiome
• Geographical location
• Exposure to pets and livestock
• Weaning and diet
• Antibiotics

Question 7

Describe breastmilk.

Answer 7

Human milk oligosaccharides (HMOs) occurring in breast milk are a family of carbohydrates that include five monosaccharide building blocks, comprising over 100 distinct oligosaccharides. There is substantial variability in the combinations of HMOs occurring in the milk of individual mothers. Humans lack the necessary enzymes (CAZymes) to degrade HMOs. Instead HMOs feed and select beneficial gut microbiome members, particularly certain Bifidobacterium spp., that have co-evolved with humans. These Bifidobacterium spp. exclude other potentially harmful bacteria via multiple mechanisms. One mechanism reduces cross-feeding, which could potentially feed harmful bacteria. Breast milk additionally contains antibodies that protect the infant and hormones that influence the infant. And, there is growing evidence that breast milk contains beneficial bacteria that colonize the infant gut. The composition of all the components in breast milk are temporally variable, changing over the course of each day and over the age of the infant.

Question 8

Describe the microbiome of a human being as they age.

Answer 8

For most people, their microbiome is fairly stable over the course of their lives. During infancy, the microbiome is unstable and strongly influenced by perturbations and dietary changes. The introduction of solid food substantially alters the microbiome, as does weaning. By about 3 years of age, the microbiome becomes more stable and has higher alpha diversity than before. The microbiome is usually relatively stable through childhood, adolescence and middle-age. During advanced age, the microbiome composition typically shifts and decreases in alpha diversity. The age when that shift occurs varies among individuals and appears to be correlated with declining health. Importantly, these trends vary greatly among individuals.

Question 9

Describe the perturbation of antibiotics.

Answer 9

While antibiotics can be life-saving, their overuse may have unintended negative health effects via their disruption of the microbiome. Note that systemic antibiotics may influence most body sites. Antibiotics appear to have particularly strong and long-lasting effects on the developing infant microbiome. Once the microbiome stabilizes during childhood, it appears to become more resilient to antibiotic treatment, normally responding with a temporary compositional shift and then returning to a community composition similar to what it was before treatment. Repeated antibiotic treatments appear to increase the chance of a lasting shift in the community.

Question 10

List some perturbations of the microbiome.

Answer 10

Antibiotics, changes in exercise, sleep, occupation, personal hygiene, and personal care products.

Question 11

List some functions of the microbiome.

Answer 11

Nutrition, energy harvest, direct pathogen exclusion, immunity.

Question 12

Describe the nutrition function of the microbiome.

Answer 12

Large accessory genome encodes many biochemical functions that the host is incapable of performing. Key among these functions is carbohydrate degradation, microbiome provides CAZy enzymes. As in the rumen, the human colon food web hydrolyses recalcitrant carbohydrates that the host cannot digest (fibre) and ferments the intermediates to volatile fatty acids, usually referred to as short-chain fatty acids (SCFAs). Some of the resulting SCFAs are taken up by the human host, while others are used by microbiome members.
More functions include biosynthesis of vitamins (K and B), amino acids and isoprenoids. The microbiome deconjugates and dehydroxylates bile acids, which modulates lipid uptake by the host, steroid metabolism in the host, and intestinal motility. Members of the gut microbiome can transform components of certain foods to trimethylamine-N-oxide, which is taken up by the host and can negatively affect cardiovascular fitness. Microbial transformation of certain drugs can increase or decrease their efficacy.

Question 13

Describe the energy harvest function of the microbiome.

Answer 13

An obvious effect of the microbiome on energy harvest is the degradation of dietary fibre to SCFAs. However, other less obvious effects appear to be more important. SCFAs from the gut circulate throughout the body, where they affect the serum concentration of leptin (a hormone regulating hunger-satiation). Through bile acid metabolism and possibly other mechanisms, the gut microbiome appears to modulate serum glucose and lipid levels, which influence fat synthesis and many other processes. Non-caloric sweeteners: These sweeteners are compounds that taste sweet but cannot be digested by humans, presumably providing no calories to humans. However, in mice, these sweeteners select for microbiome members who can degrade them, yielding metabolites from which the host can obtain calories. The human gut microbiome composition is associated with obesity. A direct effect of the gut microbiome on obesity has been demonstrated in mice, and human studies are consistent with those findings, but there is much yet to be learned about this relationship.

Question 14

Describe the direct pathogen exclusion function of the microbiome.

Answer 14

The microbiome can exclude pathogens from all body sites via direct mechanisms independent of the host immune system. These direct mechanisms are also referred to as colonization resistance or ecological protection. Competition with pathogens for nutrients (carbohydrates, iron, etc.) and for space (surface). Production of antibiotics that exclude pathogens. Direct
mechanisms of pathogen also include modification of the environment. An example of the latter is when LAB dominate the vaginal microbiome and exclude pathogens by maintaining a very low pH.

Question 15

Describe the immune system development function of the microbiome.

Answer 15

Early-life exposure to microorganisms at mucosal
surfaces is critical to immune development. Exposure serves both to induce immunity and to train for immunotolerance. Early-life perturbations of the microbiome, in some cases, appear to have life-long effects on immune system function. Germ-free animals do not develop functional immune systems.

Question 16

Describe the immune system regulation function of the microbiome.

Answer 16

Throughout the life of the host, the microbiome and
immune system communicate, each modulating the other. Many mechanisms for this communication are known.
- Both innate and adaptive immune mechanisms are involved
- Immune tolerance of microbiome in intestinal lumen
- Immune defense focused on mucosal surfaces
- Microbial metabolites and cell components are signals
- Regulation extends to systemic immunity (beyond the gut)
- Mutualistic and commensal organisms prime immunity against pathogens
- Perturbation of the microbiome can affect immune function

Question 17

Describe the autoimmune disease function of the microbiome.

Answer 17

The gut microbiome has been associated with a number of diseases, including allergy, asthma, autism, colon cancer, Crohn’s disease, diabetes, multiple sclerosis, obesity, rheumatoid arthritis and ulcerative colitis. For most of these diseases, we do not yet know if the
microbiome plays a direct role or merely changes in response to the diseases. However, the role of the microbiome in immune system development and regulation strongly suggests that it may be involved in some or all of these diseases. Inflammation is a key element of most autoimmune diseases. Butyrate inhibits inflammation in the gut.

Question 18

Describe modern microbiomes and its role in autoimmune diseases.

Answer 18

Autoimmune diseases listed happen more in developed countries. An important hypothesis, which requires further investigation, is that practices that drastically reduced incidences of infectious diseases in developed countries have inadvertently increased incidences of autoimmune diseases. A potential explanation, consistent with the above association between microbiome and autoimmune diseases, is that people in developed countries have microbiomes that have been altered by changes in diet, environmental exposures, and antibiotic use, resulting in a loss of important microbiome functions. Note that most drivers of microbiome assembly differ between developed and developing countries. Similarly, lifestyle factors affecting the microbiome, such as diet, activity, medicine, and environmental exposures, differ between developed and developing countries.

Question 19

Describe the hygiene hypothesis.

Answer 19

A few prominent scientists have proposed that, with socioeconomic development, the modern human microbiome is experiencing a loss of biodiversity that
may have serious health consequences. This theory, linking modern lifestyle, microbiome and autoimmune diseases is sometimes referred to as the hygiene hypothesis. This is a compelling term that makes a complex theory more accessible to non-scientists. However, this term also risks oversimplifying the theory and even misleading people. Clearly, hygiene is a cornerstone of human health and longevity. Further, there is no evidence that exposure to sewage or infectious diseases will benefit the microbiome. Regardless of terminology, the effect of modern life on the microbiome is a very active area of research. Many recent findings support the importance of this theory, but we remain far from a comprehensive mechanistic understanding of the complex associations.

Question 20

Describe dysbiosis.

Answer 20

a microbiome deficient in functions important to its host. This is a vague term generally believed to describe some imbalance in the microbial community that contributes to disease. Dysbiosis is often thought to involve low alpha diversity.

Question 21

Describe a fecal microbiome transplant.

Answer 21

has been shown effective for chronic Clostridium difficile infections of the gut. C. difficile most commonly infects older people following antibiotic treatment. A contributing factor appears to be loss of the pathogen exclusion function of the microbiome due to its perturbation by the antibiotic. For most individuals, treatment with an antibiotic targeting C. difficile will clear the infection. Sometimes not. FMT is thought to re-establish a functional microbiome where antibiotics permanently incapacitated the original one. Risk: particularly potential transfer of viral pathogens. For this reason, there is great interest in developing synthetic microbial communities derived from pure cultures for FMT.

Question 22

Describe probiotics.

Answer 22

commonly used to promote and maintain a “healthy” microbiome for a wide range of health benefits. Probiotics are living microorganisms in either fermented foods (yogurt, kimchee, sauerkraut, pickles, kombucha, etc.) or dietary supplements. There is very limited scientific evidence that probiotics are beneficial.

Question 23

Describe postbiotics.

Answer 23

metabolic products of the microbiome, usually fermentation products. There is strong evidence that fermented foods have health benefits. Note that such
benefits might be due to their probiotic and/or postbiotic components. There are also postbiotic dietary supplements, such as butyrate. Again, we lack rigorous scientific studies examining how postbiotics might be beneficial.

Question 24

Describe prebiotics.

Answer 24

components of the diet that support growth of the microbiome. Mainly, this refers to dietary fibre that is not digested directly by the host but is hydrolyzed and fermented via the gut food web. HMOs are also prebiotics. Prebiotics are generally believed to select for a “healthy” microbiome that produces beneficial metabolites. There is strong evidence that a high fibre diet has health benefits, and it appears likely that the microbiome is involved in some of these benefits.

Question 25

Describe synthetic breast milk.

Answer 25

Very challenging to make because of the compositional complexity and temporal dynamics of breast milk. Relatively simple improvements to formula, such as adding HMOs, are now possible. But, much more understanding is required to develop formula approaching all of the benefits of breast milk. Notably, a complete synthetic breast milk would be prebiotic, probiotic and postbiotic.

Question 26

Describe precision medicine.

Answer 26

an approach that seeks to optimize disease prevention, diagnostics and therapeutics based on the unique characteristics of individual patients. Often,
“multiomic” analyses (or systems biology methods) are used to characterize a patient, including analysis of the genome, epigenome and metabolome. The microbiome is not usually included in these analyses, but there is reason to think that might be useful to analyze the holobiont, rather than only the host. The microbiome is involved in diseases. They may metabolize drugs, and it may be useful if predicting how individuals will respond to specific drugs. Because the microbiome strongly influences digestion and nutrition, it may be useful in selecting dietary interventions for individuals. And, personalized manipulation of the microbiome might be effective in treating infectious and autoimmune diseases. These applications of the microbiome in precision medicine are mainly hypothetical and have not been demonstrated. One exception, where research and commercialization have advanced, involves using the fecal microbiome to predict an optimal individual diet, with a specific focus on controlling blood sugar.

Question 27

What are the conclusions about the microbiome in health and medicine?

Answer 27

• Avoid unnecessary use of antibiotics
• A diverse diet low in processed foods and rich in fibre has many benefits, some of which involve the microbiome
• Fermented foods are beneficial, but it is unclear how much benefit is from live organisms and/or microbial products
• FMT is effective as a last-resort treatment for C. difficile and may prove effective for treating other diseases
• Be skeptical of over-generalized or simplistic explanations for how the microbiome affects health; it is a complex topic
• Be skeptical of microbiome-based or microbiome-friendly products; few have proven efficacy
• Be skeptical of microbiome-based diagnostics; few have proven capacity to provide information that is useful for personal health
• Avoid extremes in personal and environmental hygiene; be neither a germophobe nor a microbiomaniac

Question 28

What probably has a more important role in plant microbiomes than animal ones?

Answer 28

fungi

Question 29

Describe the rhizosphere.

Answer 29

the region of soil in the vicinity of plant roots that is influenced by plant exudates. This region consists of a
gradient in chemical, biological and physical properties that change both radially and longitudinally along the root. The rhizosphere has similar bacterial and fungal composition as the bulk soil. Thus, beta diversity is greater among plant compartments than between the bulk soil and rhizosphere. The rhizosphere has less bacterial alpha diversity than the bulk soil, consistent with selective effects of plant exudates. The rhizosphere has the most diverse and functionally complex microbiome of all plant compartments.

Question 30

What do exudates include?

Answer 30

sugars, amino acids, organic acids, enzymes and other substances, that are secreted by living plants, along with microbially modified products of these substances. The component of plant exudates synthesized by plants can also be referred to as photosynthate.

Question 31

Describe the phyllosphere.

Answer 31

The phyllosphere is the total above-ground exterior surface of a plant. Microorganisms inhabiting this compartment are epiphytes. The phyllosphere is lower in nutrient availability than the rhizosphere and endosphere. Exudation is lower in the phyllosphere than the rhizosphere. The phyllosphere microbiome has a substantial component of phototrophic microbes, including lichen which are common in the phyllosphere of many trees. Due to its exposure to the atmosphere, the phyllosphere has much more dynamic and extreme environmental conditions than the other plant compartments. This drives relatively high temporal variability in the phyllosphere microbiome composition.

Question 32

Describe the endosphere.

Answer 32

The endosphere encompasses the area within plant tissues, both within and between plant cells. Microorganisms inhabiting this compartment are endophytes. The endosphere microbiome differs among plant tissues such as roots and leaves as well as among stems, flowers, fruits, etc. The endosphere microbiome has relatively low alpha diversity compared to those of other compartments. Strong selective pressures limit the variability of the endosphere microbiome composition within a particular tissue of a particular plant.

Question 33

Describe plant microbiome assembly and maintenance.

Answer 33

Complex, interrelated factors and interactions. This is particularly true for the rhizosphere where these drivers are most influential. Soil is the primary source for plant microbiome populations. Plant exudates selectively enrich specific microbial populations. Intermicrobial interactions select or exclude particular populations. Exudates also function as chemoattractants for motile microorganisms. Further interactions drive biofilm formation on the plant surface by a subset of microbiome populations. Other interactions drive entry of a smaller subset of populations to the endosphere. Two-
component, three-component or multicomponent sensing and regulatory microbial pathways are involved in microbial responses to the host and other microbes, regulating biofilm formation and facilitating entry of endophytes. Finally, plants can respond
to environmental stresses by changing their pattern of exudation in a manner that selects for a distinct microbiome composition that confers stress-resistance to the plant.

Question 34

How do endophytes enter plant tissues?

Answer 34

Endophytes commonly use lytic enzymes to enter plant tissues. Endophytes minimize the immune response of the host to them by various mechanisms, including diversification of microbial-associated molecular
patterns (MAMPs) recognized by the plant immune system. Endophytes also commonly produce protein domains resembling those of plants, which are thought to mimic the host cell signalling and act as decoys to circumvent plant defences.

Question 35

What are some benefits provided by the plant microbiome?

Answer 35

nutrient acquisition, defence against pathogens and pests, and stress tolerance.

Question 36

Describe microbiome-mediated benefits.

Answer 36

Microbiome-mediated benefits are mostly initiated belowground but can be initiated in any plant compartment. These benefits can be transmitted to other compartments via plant-mediated transport or signals. Complex microorganism–microorganism and plant–microorganism interactions maintain the balance between different members of the microbial community, normally in favor of beneficial microorganisms that contribute to plant health (prevent dysbiosis).

Question 37

Describe nitrogen fixation in plants.

Answer 37

Many plants benefit from nitrogen fixation by members of their microbiome. Legumes have a very complex mutualism with members of Rhizobium that form root nodules where nitrogen is fixed. Similarly, trees in the alder family are mutualistic with members of Frankia that form root nodules and fix nitrogen. Other plants benefit from free-living nitrogen fixing bacteria in their rhizosphere. Transformations by members of the rhizosphere microbiome of compounds with fixed nitrogen (eg, liberating ammonia from organic compounds) also make nitrogen available to plants.

Question 38

Describe mycorrhizal fungi/

Answer 38

They associate with the roots of plants. A large majority of plant species normally have mycorrhizae, and the association is usually mutualistic. Associated mycorrhizae attach to the roots, and their mycelia (filaments) extend outwards from the root, normally beyond the rhizosphere. Typically, plants provide mycorrhizae with photosynthate, and mycorrhizae provide plants with water plus inorganic nutrients, particularly phosphorus. The most common type of mycorrhizae are arbuscular, meaning that they penetrate the root cells forming structures that facilitate nutrient exchange. Other types of mycorrhizae do not penetrate root cells. The mycorrhizal association is so important that plants contribute up to 20% of their photosynthate to mycorrhizae. A common mycorrhizal network often interconnects plants, sometimes over large areas. This network can transport nutrients, allowing plants to subsidize other plants with photosynthate.

Question 39

Describe the nutrient availability of plants.

Answer 39

Rhizosphere microbes can increase the availability of nutrients to plants via several mechanisms. For example, they can transform phosphorous to more bioavailable orthophosphate. They can lower the pH of the rhizosphere solubilizing a variety of nutrients. And, they can secrete siderophores that chelate and mobilize iron.

Question 40

Describe direct pathogen exclusion of plants.

Answer 40

The plant microbiome can protect the host from pathogens by many of the same general mechanisms that animal microbiomes protect their hosts. Thus, the plant microbiome can exclude pathogens via competition for nutrients or space. Members of the plant microbiome can produce antibiotics that inhibit growth of pathogens.

Question 41

Describe induced systemic resistance (ISR) in plants.

Answer 41

Non-pathogenic members of the microbiome can elevate resistance to pathogens and pests by host defense mechanisms. This process involves the phytohormones, jasmonic acid and ethylene. Some microbiome members can produce phytohormones or modulate signaling by phytohormones. ISR increases host defenses, including innate immunity, systemically without exposure of the host to the pathogens or pests. This process is distinct from mechanisms of induction of defenses in response to attack by pathogens or pests.

Question 42

Describe interplant signaling in plants.

Answer 42

When a plant is attacked by a pathogen or pest, it can transmit signaling molecules, including phytohormones, to neighboring plants, conferring ISR in the neighboring plants. This can occur via volatile signaling molecules. Another mechanism involves microbiome members, the transmission of the signal via a common mycorrhizal network.

Question 43

What are some abiotic stresses for plants?

Answer 43

heat, drought, salinity, ROS, frost, freezing, toxic compounds (pollutants).

Question 44

Describe direct protection from abiotic stress tolerance of plants.

Answer 44

Ex: Microbial exopolymers can increase water holding capacity of rhizosphere soil and prevent water loss from roots. Microbial enzymes can inactivate excessive and harmful ROS produced by a plant host. Microbes can detoxify or mineralize many toxic compounds in the plant
host environment.

Question 45

Describe phytohormones from abiotic stress tolerance of plants.

Answer 45

As noted above, members of the microbiome can affect regulation and signaling via phytohormones. Microbiome members can (i) produce certain phytohormones, (ii) modulate signaling via metabolism of phytohormones, and (iii) respond to plant hormones. Recent research has shown that plants and their microbiomes have co-evolved highly complex, phytohormone-based interactions with a wide range of important functions. An emerging paradigm is that the microbiome is an intrinsic component of a plant’s phytohormone signaling system. This system regulates diverse functions, including abiotic stress tolerance. Via phytohormones, the rhizosphere
microbiome can modulate root growth, affecting surface area and the efficiency of water and nutrient uptake by the root system. The microbiome can also prolong root growth during drought by limiting phytohormone production. Similarly, the microbiome can accelerate flower production during drought. Via phytohormones, the microbiome can also modulate plant synthesis of osmoprotectants, ROS, and detoxication enzymes.

Question 46

Describe plant growth-promoting rhizobacteria from plant microbiome applications.

Answer 46

This is a general term for rhizosphere bacteria that stimulate growth and productivity of host plants via diverse mechanisms. One of the first uses of PGPR was inoculation of legumes with nitrogen-fixing Rhizobium spp. Since then, many PGPR have been discovered in plant growth promotion assays. Individual PGPR that
have been investigated, were found to benefit plants via most of the plant microbiome functions and mechanisms discussed above. However, for most PGPR, the mechanisms of growth promotion remain unknown. Some PGPR can persist in the soil community and benefit successive generations of plants. Major challenges for commercialization of PGPR include (i) poorly controlled product composition, (ii) limited shelf-life, and (iii) variable efficacy under differing field conditions.

Question 47

Describe mycorrhizal inocula from plant microbiome applications.

Answer 47

Suitable mycorrhizae for a plant are not always present in a particular soil. Given the importance of mycorrhizal symbionts, they have been incorporated in commercial soil conditioners and seed coatings designed to stimulate crops.

Question 48

Describe ice-minus bacteria from plant microbiome applications.

Answer 48

Frost damage to plants typically involves nucleation of ice crystals by phyllosphere bacteria. Pseudomonas syringae is a common epiphyte that nucleates ice crystals. In the 1980s, an “ice-minus” strain of P. syringae was engineered by deleting the gene encoding a surface protein responsible for nucleation. Field testing showed that applying the ice-minus strain to the phyllosphere of strawberries and potatoes excluded ice-nucleating bacteria and lowered the temperature where frost damage occurs by a few degrees, which is very significant for frost protection. The ice-minus strain was the first genetically modified organism (GMO) approved by US Environmental Protection Agency for field testing. The strain also prompted the first widespread protests against GMOs. 40 years later, the technology has not yet been commercialized because of the financial risk of investing in a technology that remains controversial.