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Symbios & Microbiome
| Question | Answer |
|---|---|
| Symbioses: | microbes live with macroorganisms and other microorganisms in long-term relationships called symbioses. |
| Mutualisms: | interactions where both organisms interact to the benefit of both. Most mutualistic organisms evolved together (coevolution) over millions of years. |
| Lichens: | Symbiotic organisms, often leafy or crusty, found on rocks, soil, tree trunks, and roofs. Mainly a fungus partnered with a photosynthetic alga or cyanobacterium, but also host diverse bacteria and archaea. |
| Lichen Mutualism: | The phototroph produces organic carbon (and sometimes fixes nitrogen), while the fungus provides structure, protection, and access to inorganic nutrients. This cooperation enables survival in harsh environments. |
| Lichen Growth Forms: | Lichens grow in three main forms — foliose (leaf-like), fruticose (branched or bushy), and crustose (flat and crusty) — allowing them to colonize a wide range of surfaces and habitats. |
| Lichen Internal Structure: | Stratified layers with the phototrophic algal layer near the top for light capture, embedded in fungal hyphae that form the main body. Hyphae anchor the lichen and extract nutrients from substrates through chemical weathering. |
| Legume–Root Nodule Symbiosis: | A mutualism between legumes (e.g., soybeans, clover, beans) and nitrogen-fixing Rhizobia. Rhizobia convert atmospheric nitrogen to ammonia for the plant, while the plant supplies carbohydrates, enabling growth in nitrogen-poor soils. |
| Rhizobia: | Nitrogen-fixing bacteria (mostly Alpha- or Betaproteobacteria) that live freely in soil or as endosymbionts in legume root nodules, converting atmospheric nitrogen to ammonia to support plant growth. |
| Effects of Legume–Root Nodule Symbiosis: | Leads to significant increases in combined nitrogen in soil. Nodulated legumes grow well in areas where other plants would not. |
| Host Specificity in Legume–Rhizobia Symbiosis: | Different Rhizobia species are compatible with specific legume hosts, determined by molecular signals exchanged during infection. For example, strains that nodulate peas usually cannot infect clover or soybeans. |
| Cross-Inoculation Group: | A classification of legumes that can be nodulated by the same Rhizobia species or strain. Legumes in the same group share compatible signaling pathways, allowing the same bacteria to form nitrogen-fixing symbioses with multiple related plants. |
| Nitrogenases: | Enzymes produced by nitrogen-fixing bacteria that convert atmospheric nitrogen (N₂) into usable forms, but are inactivated by oxygen (O₂). |
| Leghemoglobin: | An oxygen-binding protein found in legume root nodules that acts as an "oxygen buffer" by binding free oxygen to protect nitrogenases from oxygen inactivation while still allowing bacteria to generate energy through aerobic respiration. |
| Legume–Root Nodule Symbiosis Mechanism: | Rhizobia attach to root hairs and release Nod factors, triggering root hair curling and entry. They travel through an infection thread, form nodules, and become bacteroids, fixing nitrogen in exchange for nutrients and protection. |
| Bacteroids: | The differentiated form of rhizobial bacteria within legume root nodule cells that are dependent on the plant for fuel (pyruvate) to power nitrogen fixation; they are enclosed within a symbiosome membrane inside the plant cell cytoplasm. |
| Oxygen Sequestration: | Leghemoglobin binds free oxygen in root nodules, keeping oxygen low for nitrogenase activity while allowing enough for bacteroid aerobic respiration to produce ATP. |
| Mycorrhizae: | Mutualistic fungi–root associations where fungi enhance water and nutrient uptake (especially phosphorus) and receive carbohydrates from the plant, improving growth, stress tolerance, and soil health. |
| Ectomycorrhizae: | Ectomycorrhizae remain outside of the plant roots. Fungal cells form an extensive sheath around the outside of the root with only a little penetration into the root tissue. Found primarily in forest trees, particularly boreal and temperate forests. |
| Arbuscular Mycorrhizae: | fungal mycelium becomes deeply embedded within the root tissue and is called arbuscular mycorrhizae. More common than ectomycorrhizae. Found in > 80 percent of terrestrial plant species but cannot be cultured in pure culture. |
| Strigolactones: | Plant-produced signaling molecules (Myc factors) that attract mycorrhizal fungi to plant roots and initiate the symbiotic relationship. |
| Hyphopodium (HP): | Specialized fungal structures that form on the root epidermis where the fungal hyphae attach and penetrate into the root cortex to establish the endomycorrhizal association. |
| How do Mycorrhizal Fungi Assist Plants? | Improve nutrient absorption and help promote plant growth. This is due to the greater surface area provided by the fungal mycelium. |
| Horizontal Transmission: | The acquisition of microbial symbionts from an environmental reservoir rather than from a parent organism |
| Vertical (Heritable) Transmission: | The acquisition of microbial symbionts directly from a parent, passed down from generation to generation |
| Obligate Symbionts: | Symbionts that lack a free-living replicative stage and are essential for the host's survival or reproduction; heritable symbionts of insects are obligate |
| Primary Symbionts: | Essential bacterial symbionts that are required for the host insect to reproduce; restricted to specialized cells called bacteriocytes and transmitted vertically from parent to offspring. |
| Bacteriocytes: | Specialized insect cells that house primary bacterial symbionts, ensuring their maintenance and vertical transmission across generations. |
| Feminization: | A reproductive manipulation by endosymbiotic bacteria that turns genetic males into functional females. In the false spider mite Brevipalpus phoenicis, this produces haploid female parthenogens, eliminating males from the population. |
| Secondary Symbionts: | Non-essential bacteria that are not present in all host individuals and may inhabit different cell types or live outside cells. They persist by providing benefits like nutrition, stress tolerance, or protection against pathogens. |
| Rickettsia: | Bacterial symbionts that can act as reproductive parasites. In whiteflies, infection doubles offspring production, manipulating host reproduction to enhance bacterial transmission. |
| Wolbachia: | Intracellular bacterial symbionts that manipulate host reproduction. One method is cytoplasmic incompatibility, where sperm from infected males sterilizes uninfected females, giving infected females a reproductive advantage. |
| Examples of Parasitic Symbionts That Manipulate Host’s Reproductive Tissue: | Rickettsia and Wolbachia |
| Genome Reduction in Primary Symbionts: | Primary symbionts undergo extreme genome shrinkage (~2–8 Mbp → 160–800 kbp), keeping genes essential for host fitness and losing catabolic genes. They depend on the host for metabolism and specialize in nutrient provision, unlike pathogens. |
| Herbivores: | animals that consume plants |
| Carnivores: | animals that consume meat |
| Omnivores: | animals that consume both plants and meat |
| Herbivores & History: | phylogenetics suggests that different lineages evolved a herbivorous lifestyle. |
| Foregut Fermentation: | Microbial fermentation of plant material occurs in a specialized chamber before the small intestine (e.g., rumen), allowing breakdown of cellulose and other polysaccharides before nutrient absorption. Examples: ruminants like sheep, colobine monkeys. |
| Hindgut Fermentation: | Microbial fermentation occurs in the cecum or large intestine after the small intestine, aiding in digestion of plant fibers. Examples: horses, rabbits, some primates, rodents, and reptiles. |
| Cellulose: | The main component of plant fibers, an insoluble polysaccharide that herbivores cannot digest without symbiotic microbes. |
| Ruminants: | Herbivorous mammals (e.g., cows, sheep, goats) with a multi-chambered foregut, including the rumen, where microbes break down cellulose and other plant polysaccharides. |
| Rumen: | The main fermentation chamber in ruminants, preceding the true stomach (abomasum), hosting dense microbial communities that digest plant material; often studied via fistulas for direct sampling. |
| Reticulum: | A foregut compartment that works with the rumen to trap smaller food particles and support microbial fermentation before passing food to the omasum and abomasum. |
| Cellulolytic Microbes: | Rumen microorganisms that produce enzymes to break down cellulose (cellulolysis) and starch (amylolysis) into glucose, which is then fermented by the microbial community. |
| Volatile Fatty Acids (VFAs): | Short-chain fatty acids—mainly acetate, propionate, and butyrate — produced during rumen fermentation and absorbed into the bloodstream as the ruminant’s primary energy source. |
| Rumen Fermentation Process: | Feed containing cellulose, starch, and sugars is broken down by microbial enzymes into glucose, then fermented into pyruvate, lactate, succinate, and VFAs, with byproducts like methane (CH₄), CO₂, H₂, and water expelled by eructation. |
| Rumen Microbial Density: | Rumen contents contain extremely high microbial populations, about 10¹⁰–10¹¹ microbes per gram, making it one of the densest microbial ecosystems. |
| Rumen Microbial Nutrition | Rumen microbes synthesize essential amino acids and vitamins for the host and serve as a high-quality protein source when digested as they pass to the lower digestive tract. |
| Rumen Microbial Diversity | The rumen hosts a complex microbial ecosystem of 300–400 bacterial species, dominated by anaerobes from Firmicutes, Bacteroidetes, Fibrobacteres, and Proteobacteria, identified via 16S rRNA metagenomics. |
| Methanogenic Archaea | Rumen archaea produce methane (CH₄) as a fermentation byproduct, which is expelled by belching. |
| Giant Panda Gut Microbiota: | Pandas have a carnivore-like gut lacking cellulose-digesting enzymes. Microbiota is low in diversity, dominated by Escherichia/Shigella and Streptococcus, with few cellulose degraders, and shows more seasonal than individual variation. |
| What does describing the gut microbiome as an “ancient new organ” imply? | The gut microbiome evolved alongside humans for millions of years and functions as an integrated biological system that regulates immunity, metabolism, and energy balance at the organismal level. |
| Why are conflicts of interest disclosed in microbiome-related research? | Transparency is necessary because microbiome findings increasingly lead to therapeutic products, which could otherwise bias experimental interpretation or clinical translation. |
| What defines the core microbiome? | The core microbiome consists of microbial populations that are consistently required to support essential physiological functions across healthy individuals. |
| Why is the core microbiome considered an essential organ of the human body? | It performs critical biochemical and regulatory functions—such as immune education and metabolic signaling—that cannot be fully encoded by the human genome alone. |
| How long have humans and gut microbes co-evolved, and why does this matter? | Co-evolution over roughly six million years produced mutual dependence, with host physiology adapting to microbial metabolic and immune functions. |
| What does the Black Death example reveal about host–microbe interactions? | Extreme infectious events drove natural selection of immune-related genes, illustrating how microbial exposure shapes long-term human biology. |
| What are coprolites and what do they reveal about ancient gut microbiota? | Coprolites are fossilized feces that preserve dietary residues and microbial activity, offering direct evidence of ancestral gut environments. |
| What do ancient coprolites indicate about ancestral dietary fiber intake? | They show fiber-dominated diets that supplied abundant fermentable substrates, shaping microbiomes adapted for polysaccharide breakdown. |
| How did feast–famine cycles influence metabolic and immune systems? | Recurrent nutritional stress selected for flexible metabolic regulation and immune resilience, with the gut microbiome acting as a key intermediary. |
| Why are the immune and metabolic systems closely linked to the gut microbiome? | Microbial metabolites and signaling molecules directly regulate inflammation, glucose homeostasis, and energy storage. |
| What was the long-term objective of core microbiome research? | To identify stable microbial components whose functional relationships persist despite changes in diet, geography, and disease. |
| Why are taxon-based microbiome analyses insufficient? | They obscure strain-level function, ignore ecological interactions, and collapse functionally opposing microbes into broad categories. |
| Why are microbial guilds a better functional unit than species or genera? | Guilds group metabolically cooperative microbes that collectively influence host physiology, regardless of taxonomic similarity. |
| What maintains gut microbiome stability in healthy individuals? | Stability arises from conserved ecological interactions that preserve functional output even when microbial abundances fluctuate. |
| What characterizes different forms of gut dysbiosis? | Dysbiosis involves loss of beneficial guilds, reduced microbial diversity, or overgrowth of pathobionts that disrupt ecosystem balance. |
| What is the central principle behind CoreGuild™ Therapy? | Restoring beneficial ecological structure is more effective than targeting individual microbes in isolation. |
| How does Foundation Guild nutrition restore gut health? | It selectively feeds beneficial microbes using fermentable carbohydrates, enabling them to outcompete harmful populations. |
| Why do many chronic diseases share a common microbiome-related basis? | Disruption of an evolutionarily conserved gut ecosystem leads to systemic inflammation and metabolic dysfunction across diseases. |
| What defines a healthy gut microbiome state? | A healthy state is marked by ecological dominance of the Foundation Guild that sustains immune tolerance and metabolic homeostasis. |
Created by:
smurtab