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Tuesday, August 27, 2024

Disease

From Wikipedia, the free encyclopedia

A disease is a particular abnormal condition that adversely affects the structure or function of all or part of an organism and is not immediately due to any external injury. Diseases are often known to be medical conditions that are associated with specific signs and symptoms. A disease may be caused by external factors such as pathogens or by internal dysfunctions. For example, internal dysfunctions of the immune system can produce a variety of different diseases, including various forms of immunodeficiency, hypersensitivity, allergies, and autoimmune disorders.

In humans, disease is often used more broadly to refer to any condition that causes pain, dysfunction, distress, social problems, or death to the person affected, or similar problems for those in contact with the person. In this broader sense, it sometimes includes injuries, disabilities, disorders, syndromes, infections, isolated symptoms, deviant behaviors, and atypical variations of structure and function, while in other contexts and for other purposes these may be considered distinguishable categories. Diseases can affect people not only physically but also mentally, as contracting and living with a disease can alter the affected person's perspective on life.

Death due to disease is called death by natural causes. There are four main types of disease: infectious diseases, deficiency diseases, hereditary diseases (including both genetic and non-genetic hereditary diseases), and physiological diseases. Diseases can also be classified in other ways, such as communicable versus non-communicable diseases. The deadliest diseases in humans are coronary artery disease (blood flow obstruction), followed by cerebrovascular disease and lower respiratory infections. In developed countries, the diseases that cause the most sickness overall are neuropsychiatric conditions, such as depression and anxiety.

The study of disease is called pathology, which includes the study of etiology, or cause.

Terminology

Concepts

In many cases, terms such as disease, disorder, morbidity, sickness and illness are used interchangeably; however, there are situations when specific terms are considered preferable.

Disease

The term disease broadly refers to any condition that impairs the normal functioning of the body. For this reason, diseases are associated with the dysfunction of the body's normal homeostatic processes. Commonly, the term is used to refer specifically to infectious diseases, which are clinically evident diseases that result from the presence of pathogenic microbial agents, including viruses, bacteria, fungi, protozoa, multicellular organisms, and aberrant proteins known as prions. An infection or colonization that does not and will not produce clinically evident impairment of normal functioning, such as the presence of the normal bacteria and yeasts in the gut, or of a passenger virus, is not considered a disease. By contrast, an infection that is asymptomatic during its incubation period, but expected to produce symptoms later, is usually considered a disease. Non-infectious diseases are all other diseases, including most forms of cancer, heart disease, and genetic disease.

Acquired disease

An acquired disease is one that began at some point during one's lifetime, as opposed to disease that was already present at birth, which is congenital disease. Acquired sounds like it could mean "caught via contagion", but it simply means acquired sometime after birth. It also sounds like it could imply secondary disease, but acquired disease can be primary disease.

Acute disease

An acute disease is one of a short-term nature (acute); the term sometimes also connotes a fulminant nature

Chronic condition or chronic disease

A chronic disease is one that persists over time, often for at least six months, but may also include illnesses that are expected to last for the entirety of one's natural life.

Congenital disorder or congenital disease

A congenital disorder is one that is present at birth. It is often a genetic disease or disorder and can be inherited. It can also be the result of a vertically transmitted infection from the mother, such as HIV/AIDS.

Genetic disease

A genetic disorder or disease is caused by one or more genetic mutations. It is often inherited, but some mutations are random and de novo.

Hereditary or inherited disease

A hereditary disease is a type of genetic disease caused by genetic mutations that are hereditary (and can run in families)

Iatrogenic disease

An iatrogenic disease or condition is one that is caused by medical intervention, whether as a side effect of a treatment or as an inadvertent outcome.

Idiopathic disease

An idiopathic disease has an unknown cause or source. As medical science has advanced, many diseases with entirely unknown causes have had some aspects of their sources explained and therefore shed their idiopathic status. For example, when germs were discovered, it became known that they were a cause of infection, but particular germs and diseases had not been linked. In another example, it is known that autoimmunity is the cause of some forms of diabetes mellitus type 1, even though the particular molecular pathways by which it works are not yet understood. It is also common to know certain factors are associated with certain diseases; however, association does not necessarily imply causality. For example, a third factor might be causing both the disease, and the associated phenomenon.

Incurable disease

A disease that cannot be cured. Incurable diseases are not necessarily terminal diseases, and sometimes a disease's symptoms can be treated sufficiently for the disease to have little or no impact on quality of life.

Primary disease

A primary disease is a disease that is due to a root cause of illness, as opposed to secondary disease, which is a sequela, or complication that is caused by the primary disease. For example, a common cold is a primary disease, where rhinitis is a possible secondary disease, or sequela. A doctor must determine what primary disease, a cold or bacterial infection, is causing a patient's secondary rhinitis when deciding whether or not to prescribe antibiotics.

Secondary disease

A secondary disease is a disease that is a sequela or complication of a prior, causal disease, which is referred to as the primary disease or simply the underlying cause (root cause). For example, a bacterial infection can be primary, wherein a healthy person is exposed to bacteria and becomes infected, or it can be secondary to a primary cause, that predisposes the body to infection. For example, a primary viral infection that weakens the immune system could lead to a secondary bacterial infection. Similarly, a primary burn that creates an open wound could provide an entry point for bacteria, and lead to a secondary bacterial infection.

Terminal disease

A terminal disease is one that is expected to have the inevitable result of death. Previously, AIDS was a terminal disease; it is now incurable, but can be managed indefinitely using medications.

Illness

The terms illness and sickness are both generally used as synonyms for disease; however, the term illness is occasionally used to refer specifically to the patient's personal experience of their disease. In this model, it is possible for a person to have a disease without being ill (to have an objectively definable, but asymptomatic, medical condition, such as a subclinical infection, or to have a clinically apparent physical impairment but not feel sick or distressed by it), and to be ill without being diseased (such as when a person perceives a normal experience as a medical condition, or medicalizes a non-disease situation in their life – for example, a person who feels unwell as a result of embarrassment, and who interprets those feelings as sickness rather than normal emotions). Symptoms of illness are often not directly the result of infection, but a collection of evolved responses – sickness behavior by the body – that helps clear infection and promote recovery. Such aspects of illness can include lethargy, depression, loss of appetite, sleepiness, hyperalgesia, and inability to concentrate.

Disorder

A disorder is a functional abnormality or disturbance that may or may not show specific signs and symptoms. Medical disorders can be categorized into mental disorders, physical disorders, genetic disorders, emotional and behavioral disorders, and functional disorders. The term disorder is often considered more value-neutral and less stigmatizing than the terms disease or illness, and therefore is preferred terminology in some circumstances. In mental health, the term mental disorder is used as a way of acknowledging the complex interaction of biological, social, and psychological factors in psychiatric conditions; however, the term disorder is also used in many other areas of medicine, primarily to identify physical disorders that are not caused by infectious organisms, such as metabolic disorders.

Medical condition or health condition

A medical condition or health condition is a broad concept that includes all diseases, lesions, disorders, or nonpathologic condition that normally receives medical treatment, such as pregnancy or childbirth. While the term medical condition generally includes mental illnesses, in some contexts the term is used specifically to denote any illness, injury, or disease except for mental illnesses. The Diagnostic and Statistical Manual of Mental Disorders (DSM), the widely used psychiatric manual that defines all mental disorders, uses the term general medical condition to refer to all diseases, illnesses, and injuries except for mental disorders. This usage is also commonly seen in the psychiatric literature. Some health insurance policies also define a medical condition as any illness, injury, or disease except for psychiatric illnesses.

As it is more value-neutral than terms like disease, the term medical condition is sometimes preferred by people with health issues that they do not consider deleterious. However, by emphasizing the medical nature of the condition, this term is sometimes rejected, such as by proponents of the autism rights movement.

The term medical condition is also a synonym for medical state, in which case it describes an individual patient's current state from a medical standpoint. This usage appears in statements that describe a patient as being in critical condition, for example.

Morbidity

Morbidity (from Latin morbidus 'sick, unhealthy') is a diseased state, disability, or poor health due to any cause. The term may refer to the existence of any form of disease, or to the degree that the health condition affects the patient. Among severely ill patients, the level of morbidity is often measured by ICU scoring systems. Comorbidity, or co-existing disease, is the simultaneous presence of two or more medical conditions, such as schizophrenia and substance abuse.

In epidemiology and actuarial science, the term morbidity (also morbidity rate or morbidity frequency) can refer to either the incidence rate, the prevalence of a disease or medical condition, or the percentage of people who experience a given condition within a given timeframe (e.g., 20% of people will get influenza in a year). This measure of sickness is contrasted with the mortality rate of a condition, which is the proportion of people dying during a given time interval. Morbidity rates are used in actuarial professions, such as health insurance, life insurance, and long-term care insurance, to determine the premiums charged to customers. Morbidity rates help insurers predict the likelihood that an insured will contract or develop any number of specified diseases.

Pathosis or pathology

Pathosis (plural pathoses) is synonymous with disease. The word pathology also has this sense, in which it is commonly used by physicians in the medical literature, although some editors prefer to reserve pathology to its other senses. Sometimes a slight connotative shade causes preference for pathology or pathosis implying "some [as yet poorly analyzed] pathophysiologic process" rather than disease implying "a specific disease entity as defined by diagnostic criteria being already met". This is hard to quantify denotatively, but it explains why cognitive synonymy is not invariable.

Syndrome

A syndrome is the association of several signs and symptoms, or other characteristics that often occur together, regardless of whether the cause is known. Some syndromes such as Down syndrome are known to have only one cause (an extra chromosome at birth). Others such as Parkinsonian syndrome are known to have multiple possible causes. Acute coronary syndrome, for example, is not a single disease itself but is rather the manifestation of any of several diseases including myocardial infarction secondary to coronary artery disease. In yet other syndromes, however, the cause is unknown. A familiar syndrome name often remains in use even after an underlying cause has been found or when there are a number of different possible primary causes. Examples of the first-mentioned type are that Turner syndrome and DiGeorge syndrome are still often called by the "syndrome" name despite that they can also be viewed as disease entities and not solely as sets of signs and symptoms.

Predisease

Predisease is a subclinical or prodromal vanguard of a disease. Prediabetes and prehypertension are common examples. The nosology or epistemology of predisease is contentious, though, because there is seldom a bright line differentiating a legitimate concern for subclinical or premonitory status and the conflict of interest–driven over-medicalization (e.g., by pharmaceutical manufacturers) or de-medicalization (e.g., by medical and disability insurers). Identifying legitimate predisease can result in useful preventive measures, such as motivating the person to get a healthy amount of physical exercise, but labeling a healthy person with an unfounded notion of predisease can result in overtreatment, such as taking drugs that only help people with severe disease or paying for treatments with a poor benefit–cost ratio.

One review proposed three criteria for predisease:

a high risk for progression to disease making one "far more likely to develop" it than others are- for example, a pre-cancer will almost certainly turn into cancer over time
actionability for risk reduction – for example, removal of the precancerous tissue prevents it from turning into a potentially deadly cancer
benefit that outweighs the harm of any interventions taken – removing the precancerous tissue prevents cancer, and thus prevents a potential death from cancer.

Types by body system

Mental: Mental illness is a broad, generic label for a category of illnesses that may include affective or emotional instability, behavioral dysregulation, cognitive dysfunction or impairment. Specific illnesses known as mental illnesses include major depression, generalized anxiety disorders, schizophrenia, and attention deficit hyperactivity disorder, to name a few. Mental illness can be of biological (e.g., anatomical, chemical, or genetic) or psychological (e.g., trauma or conflict) origin. It can impair the affected person's ability to work or study and can harm interpersonal relationships. The term insanity is used technically as a legal term.
Organic: An organic disease is one caused by a physical or physiological change to some tissue or organ of the body. The term sometimes excludes infections. It is commonly used in contrast with mental disorders. It includes emotional and behavioral disorders if they are due to changes to the physical structures or functioning of the body, such as after a stroke or a traumatic brain injury, but not if they are due to psychosocial issues.

Stages

In an infectious disease, the incubation period is the time between infection and the appearance of symptoms. The latency period is the time between infection and the ability of the disease to spread to another person, which may precede, follow, or be simultaneous with the appearance of symptoms. Some viruses also exhibit a dormant phase, called viral latency, in which the virus hides in the body in an inactive state. For example, varicella zoster virus causes chickenpox in the acute phase; after recovery from chickenpox, the virus may remain dormant in nerve cells for many years, and later cause herpes zoster (shingles).

Acute disease: An acute disease is a short-lived disease, like the common cold.
Chronic disease: A chronic disease is one that lasts for a long time, usually at least six months. During that time, it may be constantly present, or it may go into remission and periodically relapse. A chronic disease may be stable (does not get any worse) or it may be progressive (gets worse over time). Some chronic diseases can be permanently cured. Most chronic diseases can be beneficially treated, even if they cannot be permanently cured.
Clinical disease: One that has clinical consequences; in other words, the stage of the disease that produces the characteristic signs and symptoms of that disease. AIDS is the clinical disease stage of HIV infection.
Cure: A cure is the end of a medical condition or a treatment that is very likely to end it, while remission refers to the disappearance, possibly temporarily, of symptoms. Complete remission is the best possible outcome for incurable diseases.
Flare-up

See also: Exacerbation
A flare-up can refer to either the recurrence of symptoms or an onset of more severe symptoms.
Progressive disease: Progressive disease is a disease whose typical natural course is the worsening of the disease until death, serious debility, or organ failure occurs. Slowly progressive diseases are also chronic diseases; many are also degenerative diseases. The opposite of progressive disease is stable disease or static disease: a medical condition that exists, but does not get better or worse.
Refractory disease: A refractory disease is a disease that resists treatment, especially an individual case that resists treatment more than is normal for the specific disease in question.
Subclinical disease: Also called silent disease, silent stage, or asymptomatic disease. This is a stage in some diseases before the symptoms are first noted.
Terminal phase: If a person will die soon from a disease, regardless of whether that disease typically causes death, then the stage between the earlier disease process and active dying is the terminal phase.
Recovery: See also: Convalescence and Recuperation
Recovery can refer to the repairing of physical processes (tissues, organs etc.) and the resumption of healthy functioning after damage causing processes have been cured.

Extent

Localized disease: A localized disease is one that affects only one part of the body, such as athlete's foot or an eye infection.
Disseminated disease: A disseminated disease has spread to other parts; with cancer, this is usually called metastatic disease.
Systemic disease: A systemic disease is a disease that affects the entire body, such as influenza or high blood pressure.

Classification

Diseases may be classified by cause, pathogenesis (mechanism by which the disease is caused), or by symptoms. Alternatively, diseases may be classified according to the organ system involved, though this is often complicated since many diseases affect more than one organ.

A chief difficulty in nosology is that diseases often cannot be defined and classified clearly, especially when cause or pathogenesis are unknown. Thus diagnostic terms often only reflect a symptom or set of symptoms (syndrome).

Classical classification of human disease derives from the observational correlation between pathological analysis and clinical syndromes. Today it is preferred to classify them by their cause if it is known.

The most known and used classification of diseases is the World Health Organization's ICD. This is periodically updated. Currently, the last publication is the ICD-11.

Causes

Diseases can be caused by any number of factors and may be acquired or congenital. Microorganisms, genetics, the environment or a combination of these can contribute to a diseased state.

Only some diseases such as influenza are contagious and commonly believed infectious. The microorganisms that cause these diseases are known as pathogens and include varieties of bacteria, viruses, protozoa, and fungi. Infectious diseases can be transmitted, e.g. by hand-to-mouth contact with infectious material on surfaces, by bites of insects or other carriers of the disease, and from contaminated water or food (often via fecal contamination), etc. Also, there are sexually transmitted diseases. In some cases, microorganisms that are not readily spread from person to person play a role, while other diseases can be prevented or ameliorated with appropriate nutrition or other lifestyle changes.

Some diseases, such as most (but not all) forms of cancer, heart disease, and mental disorders, are non-infectious diseases. Many non-infectious diseases have a partly or completely genetic basis (see genetic disorder) and may thus be transmitted from one generation to another.

Social determinants of health are the social conditions in which people live that determine their health. Illnesses are generally related to social, economic, political, and environmental circumstances. Social determinants of health have been recognized by several health organizations such as the Public Health Agency of Canada and the World Health Organization to greatly influence collective and personal well-being. The World Health Organization's Social Determinants Council also recognizes Social determinants of health in poverty.

When the cause of a disease is poorly understood, societies tend to mythologize the disease or use it as a metaphor or symbol of whatever that culture considers evil. For example, until the bacterial cause of tuberculosis was discovered in 1882, experts variously ascribed the disease to heredity, a sedentary lifestyle, depressed mood, and overindulgence in sex, rich food, or alcohol, all of which were social ills at the time.

When a disease is caused by a pathogenic organism (e.g., when malaria is caused by Plasmodium), one should not confuse the pathogen (the cause of the disease) with disease itself. For example, West Nile virus (the pathogen) causes West Nile fever (the disease). The misuse of basic definitions in epidemiology is frequent in scientific publications.

Types of causes

Airborne: An airborne disease is any disease that is caused by pathogens and transmitted through the air.
Foodborne: Foodborne illness or food poisoning is any illness resulting from the consumption of food contaminated with pathogenic bacteria, toxins, viruses, prions or parasites.
Infectious: Infectious diseases, also known as transmissible diseases or communicable diseases, comprise clinically evident illness (i.e., characteristic medical signs or symptoms of disease) resulting from the infection, presence and growth of pathogenic biological agents in an individual host organism. Included in this category are contagious diseases – an infection, such as influenza or the common cold, that commonly spreads from one person to another – and communicable diseases – a disease that can spread from one person to another, but does not necessarily spread through everyday contact.
Lifestyle: A lifestyle disease is any disease that appears to increase in frequency as countries become more industrialized and people live longer, especially if the risk factors include behavioral choices like a sedentary lifestyle or a diet high in unhealthful foods such as refined carbohydrates, trans fats, or alcoholic beverages.
Non-communicable: A non-communicable disease is a medical condition or disease that is non-transmissible. Non-communicable diseases cannot be spread directly from one person to another. Heart disease and cancer are examples of non-communicable diseases in humans.

Prevention

Many diseases and disorders can be prevented through a variety of means. These include sanitation, proper nutrition, adequate exercise, vaccinations and other self-care and public health measures, such as obligatory face mask mandates.

Treatments

Medical therapies or treatments are efforts to cure or improve a disease or other health problems. In the medical field, therapy is synonymous with the word treatment. Among psychologists, the term may refer specifically to psychotherapy or "talk therapy". Common treatments include medications, surgery, medical devices, and self-care. Treatments may be provided by an organized health care system, or informally, by the patient or family members.

Preventive healthcare is a way to avoid an injury, sickness, or disease in the first place. A treatment or cure is applied after a medical problem has already started. A treatment attempts to improve or remove a problem, but treatments may not produce permanent cures, especially in chronic diseases. Cures are a subset of treatments that reverse diseases completely or end medical problems permanently. Many diseases that cannot be completely cured are still treatable. Pain management (also called pain medicine) is that branch of medicine employing an interdisciplinary approach to the relief of pain and improvement in the quality of life of those living with pain.

Treatment for medical emergencies must be provided promptly, often through an emergency department or, in less critical situations, through an urgent care facility.

Epidemiology

Epidemiology is the study of the factors that cause or encourage diseases. Some diseases are more common in certain geographic areas, among people with certain genetic or socioeconomic characteristics, or at different times of the year.

Epidemiology is considered a cornerstone methodology of public health research and is highly regarded in evidence-based medicine for identifying risk factors for diseases. In the study of communicable and non-communicable diseases, the work of epidemiologists ranges from outbreak investigation to study design, data collection, and analysis including the development of statistical models to test hypotheses and the documentation of results for submission to peer-reviewed journals. Epidemiologists also study the interaction of diseases in a population, a condition known as a syndemic. Epidemiologists rely on a number of other scientific disciplines such as biology (to better understand disease processes), biostatistics (the current raw information available), Geographic Information Science (to store data and map disease patterns) and social science disciplines (to better understand proximate and distal risk factors). Epidemiology can help identify causes as well as guide prevention efforts.

In studying diseases, epidemiology faces the challenge of defining them. Especially for poorly understood diseases, different groups might use significantly different definitions. Without an agreed-on definition, different researchers may report different numbers of cases and characteristics of the disease.

Some morbidity databases are compiled with data supplied by states and territories health authorities, at national levels or larger scale (such as European Hospital Morbidity Database (HMDB)) which may contain hospital discharge data by detailed diagnosis, age and sex. The European HMDB data was submitted by European countries to the World Health Organization Regional Office for Europe.

Burdens of disease

Disease burden is the impact of a health problem in an area measured by financial cost, mortality, morbidity, or other indicators.

There are several measures used to quantify the burden imposed by diseases on people. The years of potential life lost (YPLL) is a simple estimate of the number of years that a person's life was shortened due to a disease. For example, if a person dies at the age of 65 from a disease, and would probably have lived until age 80 without that disease, then that disease has caused a loss of 15 years of potential life. YPLL measurements do not account for how disabled a person is before dying, so the measurement treats a person who dies suddenly and a person who died at the same age after decades of illness as equivalent. In 2004, the World Health Organization calculated that 932 million years of potential life were lost to premature death.

The quality-adjusted life year (QALY) and disability-adjusted life year (DALY) metrics are similar but take into account whether the person was healthy after diagnosis. In addition to the number of years lost due to premature death, these measurements add part of the years lost to being sick. Unlike YPLL, these measurements show the burden imposed on people who are very sick, but who live a normal lifespan. A disease that has high morbidity, but low mortality, has a high DALY and a low YPLL. In 2004, the World Health Organization calculated that 1.5 billion disability-adjusted life years were lost to disease and injury. In the developed world, heart disease and stroke cause the most loss of life, but neuropsychiatric conditions like major depressive disorder cause the most years lost to being sick.

Disease category	Percent of all YPLLs lost, worldwide	Percent of all DALYs lost, worldwide	Percent of all YPLLs lost, Europe	Percent of all DALYs lost, Europe	Percent of all YPLLs lost, US and Canada	Percent of all DALYs lost, US and Canada
Infectious and parasitic diseases, especially lower respiratory tract infections, diarrhea, AIDS, tuberculosis, and malaria	37%	26%	9%	6%	5%	3%
Neuropsychiatric conditions, e.g. depression	2%	13%	3%	19%	5%	28%
Injuries, especially motor vehicle accidents	14%	12%	18%	13%	18%	10%
Cardiovascular diseases, principally heart attacks and stroke	14%	10%	35%	23%	26%	14%
Premature birth and other perinatal deaths	11%	8%	4%	2%	3%	2%
Cancer	8%	5%	19%	11%	25%	13%

Society and culture

How a society responds to diseases is the subject of medical sociology.

A condition may be considered a disease in some cultures or eras but not in others. For example, obesity can represent wealth and abundance, and is a status symbol in famine-prone areas and some places hard-hit by HIV/AIDS. Epilepsy is considered a sign of spiritual gifts among the Hmong people.

Sickness confers the social legitimization of certain benefits, such as illness benefits, work avoidance, and being looked after by others. The person who is sick takes on a social role called the sick role. A person who responds to a dreaded disease, such as cancer, in a culturally acceptable fashion may be publicly and privately honored with higher social status. In return for these benefits, the sick person is obligated to seek treatment and work to become well once more. As a comparison, consider pregnancy, which is not interpreted as a disease or sickness, even if the mother and baby may both benefit from medical care.

Most religions grant exceptions from religious duties to people who are sick. For example, one whose life would be endangered by fasting on Yom Kippur or during the month of Ramadan is exempted from the requirement, or even forbidden from participating. People who are sick are also exempted from social duties. For example, ill health is the only socially acceptable reason for an American to refuse an invitation to the White House.

The identification of a condition as a disease, rather than as simply a variation of human structure or function, can have significant social or economic implications. The controversial recognition of diseases such as repetitive stress injury (RSI) and post-traumatic stress disorder (PTSD) has had a number of positive and negative effects on the financial and other responsibilities of governments, corporations, and institutions towards individuals, as well as on the individuals themselves. The social implication of viewing aging as a disease could be profound, though this classification is not yet widespread.

Lepers were people who were historically shunned because they had an infectious disease, and the term "leper" still evokes social stigma. Fear of disease can still be a widespread social phenomenon, though not all diseases evoke extreme social stigma.

Social standing and economic status affect health. Diseases of poverty are diseases that are associated with poverty and low social status; diseases of affluence are diseases that are associated with high social and economic status. Which diseases are associated with which states vary according to time, place, and technology. Some diseases, such as diabetes mellitus, may be associated with both poverty (poor food choices) and affluence (long lifespans and sedentary lifestyles), through different mechanisms. The term lifestyle diseases describes diseases associated with longevity and that are more common among older people. For example, cancer is far more common in societies in which most members live until they reach the age of 80 than in societies in which most members die before they reach the age of 50.

Language of disease

An illness narrative is a way of organizing a medical experience into a coherent story that illustrates the sick individual's personal experience.

People use metaphors to make sense of their experiences with disease. The metaphors move disease from an objective thing that exists to an affective experience. The most popular metaphors draw on military concepts: Disease is an enemy that must be feared, fought, battled, and routed. The patient or the healthcare provider is a warrior, rather than a passive victim or bystander. The agents of communicable diseases are invaders; non-communicable diseases constitute internal insurrection or civil war. Because the threat is urgent, perhaps a matter of life and death, unthinkably radical, even oppressive, measures are society's and the patient's moral duty as they courageously mobilize to struggle against destruction. The War on Cancer is an example of this metaphorical use of language. This language is empowering to some patients, but leaves others feeling like they are failures.

Another class of metaphors describes the experience of illness as a journey: The person travels to or from a place of disease, and changes himself, discovers new information, or increases his experience along the way. He may travel "on the road to recovery" or make changes to "get on the right track" or choose "pathways". Some are explicitly immigration-themed: the patient has been exiled from the home territory of health to the land of the ill, changing identity and relationships in the process. This language is more common among British healthcare professionals than the language of physical aggression.

Some metaphors are disease-specific. Slavery is a common metaphor for addictions: The alcoholic is enslaved by drink, and the smoker is captive to nicotine. Some cancer patients treat the loss of their hair from chemotherapy as a metonymy or metaphor for all the losses caused by the disease.

Some diseases are used as metaphors for social ills: "Cancer" is a common description for anything that is endemic and destructive in society, such as poverty, injustice, or racism. AIDS was seen as a divine judgment for moral decadence, and only by purging itself from the "pollution" of the "invader" could society become healthy again. More recently, when AIDS seemed less threatening, this type of emotive language was applied to avian flu and type 2 diabetes mellitus. Authors in the 19th century commonly used tuberculosis as a symbol and a metaphor for transcendence. People with the disease were portrayed in literature as having risen above daily life to become ephemeral objects of spiritual or artistic achievement. In the 20th century, after its cause was better understood, the same disease became the emblem of poverty, squalor, and other social problems.

Antioxidative stress

From Wikipedia, the free encyclopedia
https://en.wikipedia.org/wiki/Antioxidative_stress

Antioxidative stress is an overabundance of bioavailable antioxidant compounds that interfere with the immune system's ability to neutralize pathogenic threats. The fundamental opposite is oxidative stress, which can lead to such disease states as coronary heart disease or cancer.

Antioxidant compounds reduce reactive oxygen species (ROS), which reduces emitted free-radicals. When ROS function is impaired, there is more susceptibility to atopic disorders or diseases due to impairment of the attack-kill-present-respond behavior of the Th-1 immune response chain. Over-consumption of antioxidants could thus lead to antioxidative stress, where antioxidants might weaken or block the adaptive stress responses and cause dangerous health conditions and cause harm.

Health effects

The concept of antioxidative stress may best be described by excessive or detrimental nutritional consumption of a diet rich in antioxidants, unbalancing the immune systems' pathogenic response processes. Serious health conditions can result if these processes are chronically unbalanced, ranging from acute to chronic. Immunological stress by over-supplementation of antioxidants facilitates adverse health effects specifically including allergies, asthma, and physiological alterations (especially of the skin).

Many foods contain antioxidant content, while numerous dietary supplements are exceptionally rich in antioxidants. Products marketed with health benefits routinely tout antioxidant content as a beneficial product aspect without consideration of overall dietary oxidative balances. This is generally due to the biological effects of antioxidants being misunderstood in popular culture, focusing only on their beneficial qualities to reduce ROS to prevent excessive free-radicals which may otherwise lead to well-known disease conditions.

Correlation with medical conditions

Many antioxidative compounds are also antinutrients, such as phenolic compounds, found in plant foods belonging to the families of phenolic acids, flavonoids, isoflavonoids, and tocopherols, among others. Phenolic compounds found in foods generally contribute to their astringency and may also reduce the availability of certain minerals such as zinc. Zinc deficiency is characterized by growth retardation, loss of appetite, and impaired immune function. In more severe cases, zinc deficiency causes hair loss, diarrhea, delayed sexual maturation, impotence, hypogonadism in males, and eye and skin lesions.

High-dose supplements of antioxidants may be linked to health risks in some cases, including higher mortality rates. For example, high doses of beta-carotene and vitamin E was found to increase the risk of lung cancer and overall mortality in smokers. High doses of vitamin E may increase risks of prostate cancer and one type of stroke. Antioxidant supplements may also interact with some medicines.

Role of free-radicals

The primary factor in antioxidants causing or promoting the aforementioned health issues, is the attenuation or inactivation of reactive oxygen species (ROS), which immune system responders use to kill or destroy pathogens, mainly bacteria and fungi. ROS produce free-radicals as a by-product of the oxygen burst used to kill pathogens. Excess free-radicals that are not effectively scavenged and collected result in oxidative stress that can also be harmful.

Free-radicals are not the enemy that popular culture has made them out to be, as they aid in proper biochemical signaling that make them necessary in a healthy immune system. Several complex biological free-radical collection systems already exist for the purpose of scavenging, which normally, do not require augmentation by supplementation of antioxidants to function nominally.

Role in disease

Antioxidants attenuate the Th-1 immune response, responsible for eliminating bacterial and fungal threats, while the Th-2 immune response compensates for a weak Th-1 response by increasing its own responders, which may be not only ineffective, but overall destructive to healthy surrounding tissues, thus harmful. The net result: over-supplementation of antioxidants are a direct, underlying cause of allergenic diseases and skin alterations, spurring signs (objective indications) and symptoms (subjective states) of localized and disseminated medical conditions.

Because of the low-level biochemical nature of these immunological systems and their processes, the consequences of antioxidative stress can result in overlying symptoms, leading or contributing to chronic, co-morbid, localized, and/or disseminated disease states, that are clinically challenging to successfully treat.

A diet rich in anti-oxidants could allow for skin alterations such as acute acne or chronic non-infectious lesions, especially when the Th-1 immune process is persistently compromised by an overload of dietary antioxidant sources, like daily ingesting of vitamin C supplements, for example. Allergenic reactions by invading atopic pathogens, well beyond the scope of microbiota, can become initial factors triggering chronic atopic disease.

When relating to atopic skin conditions caused by chronic antioxidative stress, symptoms similar to Chronic granulomatous disease (CGD) may appear, a disease where phagocytes have an impaired ability to destroy pathogens due to a genetic inability to effectively kill pathogens by ROS, versus supplementation induced inability caused by antioxidative stress.

Dietary balance

Nearly all living creatures consume antioxidants in some quantity. Inadequate consumption of dietary antioxidants can be detrimental. For example, a deficiency of vitamin C is a primary cause of scurvy. Vitamin C can be ingested by eating certain fruits. A dietary balance of oxidants and antioxidants are critical in maintaining optimal health.

There have been studies on antioxidant capacities of various supplements and compounds. However, there has not been a dietary system devised to quantify what levels of oxidants or antioxidants are "healthy". Unfortunately, in laboratory testing, there is no single gold standard assay to determine clinically-accepted antioxidant capacity due to numerous available assay methods, though there are several accepted popular assays that can be merged into a final result to produce a representative antioxidative value. Resulting values are subjective because assay methods comprising a final value can vary drastically between individual assay results.

Additionally, such a value does not highlight prevalence in types of antioxidants compounds over others (like lycopene versus ascorbic acid), meaning that while a resulting content value between two substances may be similar, though the potential overlying resulting effect can differ, making clinical assessments of resulting symptoms highly unreliable as to the underlying condition. However, a Norwegian scientific study created a table of 3139 products over a period of eight years, with normalized values based on a modified assay, giving a more comprehensive picture when comparing a variety of food antioxidant capacities.

While it is not known what constitutes healthy oxidative levels, it is known that regular exercise essentially tightens this balance, by both emitting more ROS, while reducing the capacity of leukocytes for oxidant release. Available antioxidant research has noted the significant challenge in determining what qualifies as oxidative and antioxidative stress, citing a wide range of variables to consider, such as a person's physiology, status, environment, and other factors.

Precipitating nutritional factors

Numerous nutritional substances, compounds, and foods have some degree of antioxidant capacity. High-capacity antioxidants include, but not limited to, vitamins C and E, resveratrol and flavonoids (e.g. wine), Sangre de grado (Croton lechleri) aka Dragons Blood, green and black teas, cloves, cinnamon, most commonly used spices and herbs, mints, several berry and nut species, coffee and chocolates.

Normal intake of antioxidants, traditionally considered staples of healthy food, may exert beneficial properties towards some disease states such as neurological disorders, inflammatory conditions, and depression. However, chronic unbalanced ingestion or high quantity supplementation could result in serious ailments due to the suppression of ROS. Allergies, asthma, bacterial and fungal infections of the skin (alterations) are known conditions that stem from antioxidant stress.

Components of antioxidants

There are many types of antioxidant compounds. Examples are, but not limited to, Carotenoids (Beta-carotene, Lycopene), Lutein, Manganese, Magnesium, Selenium, Vitamin A (retinol), Vitamin C (ascorbic acid, ascorbates), and Vitamin E (α-Tocopherol, tocotrienols), and many more. These compounds can be found as ingredients in various products, or as components of ingredients, or as broader categorical classifications of components. Determining the compound makeup of a product or ingredient allows for general identification of antioxidant compounds, and thus, the potential antioxidant content a product exhibits.

Research

Because overall research and reporting on antioxidative stress is sparse, a fundamental knowledge gap exists in this medically-significant field. Long-term effects of chronic antioxidant stress are not well-researched. Safe levels of antioxidant consumption have yet to be established in human diets. The lack of overall awareness of the subject has invoked comparatively few clinical or field studies, sparse data and statistics, and may suggest a valuable field of nutritional research has been categorically dismissed or overlooked.

Assays for oxidative stress and antioxidant reserves are offered by at least one diagnostic company. Diagnosing antioxidative stress is currently extremely rare due to factors such as widespread unfamiliarity, lacking proper understanding in the clinical environment, and trivial modern medical training on the subject. Speculatively, when considering the general abundance of oxidative stress-related conditions (e.g. cancer), a comparable statistical population of antioxidative stress-related conditions (e.g. allergies) is hypothetically viable, based upon available documented research regarding the known resulting pathology of antioxidative stress.

Endosymbiont

From Wikipedia, the free encyclopedia

https://en.wikipedia.org/wiki/Endosymbiont

A representation of the endosymbiotic theory

An endosymbiont or endobiont is an organism that lives within the body or cells of another organism. Typically the two organisms are in a mutualistic relationship. Examples are nitrogen-fixing bacteria (called rhizobia), which live in the root nodules of legumes, single-cell algae inside reef-building corals, and bacterial endosymbionts that provide essential nutrients to insects.

Endosymbiosis played key roles in the development of eukaryotes and plants. Roughly 2.2 billion years ago an archaeon absorbed a bacterium through phagocytosis, that eventually became the mitochondria that provide energy to almost all living eukaryotic cells. Approximately 1 billion years ago, some of those cells absorbed cyanobacteria that eventually became chloroplasts, organelles that produce energy from sunlight. Some 100 million years ago, UCYN-A, a nitrogen-fixing bacterium, became an endosymbiont of the marine alga Braarudosphaera bigelowii, eventually evolving into a nitroplast. Similarly, Diatoms in the family Rhopalodiaceae have evolved a diazoplast, a nitrogen-fixing organelle.

Symbionts are either obligate (require their host to survive) or facultative (can survive independently). The most common examples of obligate endosymbiosis are mitochondria and chloroplasts, which reproduce via mitosis in tandem with their host cells. Some human parasites, e.g. Wuchereria bancrofti and Mansonella perstans, thrive in their intermediate insect hosts because of an obligate endosymbiosis with Wolbachia spp. They can both be eliminated by treatments that target their bacterial host.

Etymology

Endosymbiosis comes from the Greek: ἔνδον endon "within", σύν syn "together" and βίωσις biosis "living".

Symbiogenesis

Symbiogenesis theory holds that eukaryotes evolved via absorbing prokaryotes. Typically, one organism envelopes a bacterium and the two evolve a mutualistic relationship. The absorbed bacteria (the endosymbiont) eventually lives exclusively within the host cells. This fits the concept of observed organelle development.

Typically the endosymbiont's genome shrinks, discarding genes whose roles are displaced by the host. For example the Hodgkinia genome of Magicicada cicadas is much different from the prior freestanding bacteria. The cicada life cycle involves years of stasis underground. The symbiont produces many generations during this phase, experiencing little selection pressure, allowing their genomes to diversify. Selection is episodic (when the cicadas reproduce). The original Hodgkinia genome split into three much simpler endosymbionts, each encoding only a few genes—an instance of punctuated equilibrium producing distinct lineages. The host requires all three symbionts.

Transmission

Symbiont transmission is the process where the host acquires its symbiont. Since symbionts are not produced by host cells, they must find their own way to reproduce and populate daughter cells as host cells divide. Horizontal, vertical, and mixed-mode (hybrid of horizonal and vertical) transmission are the three paths for symbiont transfer.

Horizontal

Horizontal symbiont transfer (horizontal transmission) is a process where a host acquires a facultative symbiont from the environment or another host. The Rhizobia-Legume symbiosis (bacteria-plant endosymbiosis) is a prime example of this modality. The Rhizobia-legume symbiotic relationship is important for processes such as the formation of root nodules. It starts with flavonoids released by the legume host, which causes the rhizobia species (endosymbiont) to activate its Nod genes. These Nod genes generate lipooligosaccharide signals that the legume detects, leading to root nodule formation. This process bleeds into other processes such as nitrogen fixation in plants. The evolutionary advantage of such an interaction allows genetic exchange between both organisms involved to increase the propensity for novel functions as seen in the plant-bacterium interaction (holobiont formation).

Vertical

Vertical transmission takes place when the symbiont moves directly from parent to offspring. In horizontal transmission each generation acquires symbionts from the environment. An example is nitrogen-fixing bacteria in certain plant roots, such as pea aphid symbionts. A third type is mixed-mode transmission, where symbionts move horizontally for some generations, after which they are acquired vertically.

Wigglesworthia, a tsetse fly symbiont, is vertically transmitted (via mother's milk). When a symbiont reaches this stage, it resembles a cellular organelle, similar to mitochondria or chloroplasts. In vertical transmission, the symbionts do not need to survive independently, often leading them to have a reduced genome. For instance, pea aphid symbionts have lost genes for essential molecules and rely on the host to supply them. In return, the symbionts synthesize essential amino acids for the aphid host. When a symbiont reaches this stage, it begins to resemble a cellular organelle, similar to mitochondria or chloroplasts. Such dependent hosts and symbionts form a holobiont. In the event of a bottleneck, a decrease in symbiont diversity could compromise host-symbiont interactions, as deleterious mutations accumulate.

Hosts

Invertebrates

The best-studied examples of endosymbiosis are in invertebrates. These symbioses affect organisms with global impact, including Symbiodinium (corals), or Wolbachia (insects). Many insect agricultural pests and human disease vectors have intimate relationships with primary endosymbionts.

Insects

Scientists classify insect endosymbionts as Primary or Secondary. Primary endosymbionts (P-endosymbionts) have been associated with their insect hosts for millions of years (from ten to several hundred million years). They form obligate associations and display cospeciation with their insect hosts. Secondary endosymbionts more recently associated with their hosts, may be horizontally transferred, live in the hemolymph of the insects (not specialized bacteriocytes, see below), and are not obligate.

Primary

Among primary endosymbionts of insects, the best-studied are the pea aphid (Acyrthosiphon pisum) and its endosymbiont Buchnera sp. APS, the tsetse fly Glossina morsitans morsitans and its endosymbiont Wigglesworthia glossinidia brevipalpis and the endosymbiotic protists in lower termites. As with endosymbiosis in other insects, the symbiosis is obligate. Nutritionally-enhanced diets allow symbiont-free specimens to survive, but they are unhealthy, and at best survive only a few generations.

In some insect groups, these endosymbionts live in specialized insect cells called bacteriocytes (also called mycetocytes), and are maternally-transmitted, i.e. the mother transmits her endosymbionts to her offspring. In some cases, the bacteria are transmitted in the egg, as in Buchnera; in others like Wigglesworthia, they are transmitted via milk to the embryo. In termites, the endosymbionts reside within the hindguts and are transmitted through trophallaxis among colony members.

Primary endosymbionts are thought to help the host either by providing essential nutrients or by metabolizing insect waste products into safer forms. For example, the putative primary role of Buchnera is to synthesize essential amino acids that the aphid cannot acquire from its diet of plant sap. The primary role of Wigglesworthia is to synthesize vitamins that the tsetse fly does not get from the blood that it eats. In lower termites, the endosymbiotic protists play a major role in the digestion of lignocellulosic materials that constitute a bulk of the termites' diet.

Bacteria benefit from the reduced exposure to predators and competition from other bacterial species, the ample supply of nutrients and relative environmental stability inside the host.

Primary endosymbionts of insects have among the smallest of known bacterial genomes and have lost many genes commonly found in closely related bacteria. One theory claimed that some of these genes are not needed in the environment of the host insect cell. A complementary theory suggests that the relatively small numbers of bacteria inside each insect decrease the efficiency of natural selection in 'purging' deleterious mutations and small mutations from the population, resulting in a loss of genes over many millions of years. Research in which a parallel phylogeny of bacteria and insects was inferred supports the belief that primary endosymbionts are transferred only vertically.

Attacking obligate bacterial endosymbionts may present a way to control their hosts, many of which are pests or human disease carriers. For example, aphids are crop pests and the tsetse fly carries the organism Trypanosoma brucei that causes African sleeping sickness. Studying insect endosymbionts can aid understanding the origins of symbioses in general, as a proxy for understanding endosymbiosis in other species.

The best-studied ant endosymbionts are Blochmannia bacteria, which are the primary endosymbiont of Camponotus ants. In 2018 a new ant-associated symbiont, Candidatus Westeberhardia Cardiocondylae, was discovered in Cardiocondyla. It is reported to be a primary symbiont.

Secondary

The pea aphid (Acyrthosiphon pisum) contains at least three secondary endosymbionts, Hamiltonella defensa, Regiella insecticola, and Serratia symbiotica. Hamiltonella defensa defends its aphid host from parasitoid wasps. This symbiosis replaces lost elements of the insect's immune response.

One of the best-understood defensive symbionts is the spiral bacteria Spiroplasma poulsonii. Spiroplasma sp. can be reproductive manipulators, but also defensive symbionts of Drosophila flies. In Drosophila neotestacea, S. poulsonii has spread across North America owing to its ability to defend its fly host against nematode parasites. This defence is mediated by toxins called "ribosome-inactivating proteins" that attack the molecular machinery of invading parasites. These toxins represent one of the first understood examples of a defensive symbiosis with a mechanistic understanding for defensive symbiosis between an insect endosymbiont and its host.

Sodalis glossinidius is a secondary endosymbiont of tsetse flies that lives inter- and intracellularly in various host tissues, including the midgut and hemolymph. Phylogenetic studies do not report a correlation between evolution of Sodalis and tsetse. Unlike Wigglesworthia, Sodalis has been cultured in vitro.

Cardinium and many other insects have secondary endosymbionts.

Marine

Extracellular endosymbionts are represented in all four extant classes of Echinodermata (Crinoidea, Ophiuroidea, Echinoidea, and Holothuroidea). Little is known of the nature of the association (mode of infection, transmission, metabolic requirements, etc.) but phylogenetic analysis indicates that these symbionts belong to the class Alphaproteobacteria, relating them to Rhizobium and Thiobacillus. Other studies indicate that these subcuticular bacteria may be both abundant within their hosts and widely distributed among the Echinoderms.

Some marine oligochaeta (e.g., Olavius algarvensis and Inanidrillus spp.) have obligate extracellular endosymbionts that fill the entire body of their host. These marine worms are nutritionally dependent on their symbiotic chemoautotrophic bacteria lacking any digestive or excretory system (no gut, mouth, or nephridia).

The sea slug Elysia chlorotica's endosymbiont is the algae Vaucheria litorea. The jellyfish Mastigias have a similar relationship with an algae. Elysia chlorotica forms this relationship intracellularly with the algae's chloroplasts. These chloroplasts retain their photosynthetic capabilities and structures for several months after entering the slug's cells.

Trichoplax have two bacterial endosymbionts. Ruthmannia lives inside the animal's digestive cells. Grellia lives permanently inside the endoplasmic reticulum (ER), the first known symbiont to do so.

Paracatenula is a flatworm which have lived in symbiosis with an endosymbiotic bacteria for 500 million years. The bacteria produce numerous small, droplet-like vesicles that provide the host with needed nutrients.

Dinoflagellates

Dinoflagellate endosymbionts of the genus Symbiodinium, commonly known as zooxanthellae, are found in corals, mollusks (esp. giant clams, the Tridacna), sponges, and the unicellular foraminifera. These endosymbionts capture sunlight and provide their hosts with energy via carbonate deposition.

Previously thought to be a single species, molecular phylogenetic evidence reported diversity in Symbiodinium. In some cases, the host requires a specific Symbiodinium clade. More often, however, the distribution is ecological, with symbionts switching among hosts with ease. When reefs become environmentally stressed, this distribution is related to the observed pattern of coral bleaching and recovery. Thus, the distribution of Symbiodinium on coral reefs and its role in coral bleaching is an important in coral reef ecology.

Phytoplankton

In marine environments,endosymbiont relationships are especially prevalent in oligotrophic or nutrient-poor regions of the ocean like that of the North Atlantic. In such waters, cell growth of larger phytoplankton such as diatoms is limited by (insufficient) nitrate concentrations. Endosymbiotic bacteria fix nitrogen for their hosts and in turn receive organic carbon from photosynthesis. These symbioses play an important role in global carbon cycling.

One known symbiosis between the diatom Hemialus spp. and the cyanobacterium Richelia intracellularis has been reported in North Atlantic, Mediterranean, and Pacific waters. Richelia is found within the diatom frustule of Hemiaulus spp., and has a reduced genome. A 2011 study measured nitrogen fixation by the cyanobacterial host Richelia intracellularis well above intracellular requirements, and found the cyanobacterium was likely fixing nitrogen for its host. Additionally, both host and symbiont cell growth were much greater than free-living Richelia intracellularis or symbiont-free Hemiaulus spp. The Hemaiulus-Richelia symbiosis is not obligatory, especially in nitrogen-replete areas.

Richelia intracellularis is also found in Rhizosolenia spp., a diatom found in oligotrophic oceans. Compared to the Hemaiulus host, the endosymbiosis with Rhizosolenia is much more consistent, and Richelia intracellularis is generally found in Rhizosolenia. There are some asymbiotic (occurs without an endosymbiont) Rhizosolenia, however there appears to be mechanisms limiting growth of these organisms in low nutrient conditions. Cell division for both the diatom host and cyanobacterial symbiont can be uncoupled and mechanisms for passing bacterial symbionts to daughter cells during cell division are still relatively unknown.

Other endosymbiosis with nitrogen fixers in open oceans include Calothrix in Chaetoceros spp. and UNCY-A in prymnesiophyte microalga. The Chaetoceros-Calothrix endosymbiosis is hypothesized to be more recent, as the Calothrix genome is generally intact. While other species like that of the UNCY-A symbiont and Richelia have reduced genomes. This reduction in genome size occurs within nitrogen metabolism pathways indicating endosymbiont species are generating nitrogen for their hosts and losing the ability to use this nitrogen independently. This endosymbiont reduction in genome size, might be a step that occurred in the evolution of organelles (above).

Protists

Mixotricha paradoxa is a protozoan that lacks mitochondria. However, spherical bacteria live inside the cell and serve the function of the mitochondria. Mixotricha has three other species of symbionts that live on the surface of the cell.

Paramecium bursaria, a species of ciliate, has a mutualistic symbiotic relationship with green alga called Zoochlorella. The algae live in its cytoplasm.

Platyophrya chlorelligera is a freshwater ciliate that harbors Chlorella that perform photosynthesis.

Strombidium purpureum is a marine ciliate that uses endosymbiotic, purple, non-sulphur bacteria for anoxygenic photosynthesis.

Paulinella chromatophora is a freshwater amoeboid that has a cyanobacterium endosymbiont.

Many foraminifera are hosts to several types of algae, such as red algae, diatoms, dinoflagellates and chlorophyta. These endosymbionts can be transmitted vertically to the next generation via asexual reproduction of the host, but because the endosymbionts are larger than the foraminiferal gametes, they need to acquire algae horizontally following sexual reproduction.

Several species of radiolaria have photosynthetic symbionts. In some species the host digests algae to keep the population at a constant level.

Hatena arenicola is a flagellate protist with a complicated feeding apparatus that feeds on other microbes. When it engulfs a green Nephroselmis alga, the feeding apparatus disappears and it becomes photosynthetic. During mitosis the algae is transferred to only one of the daughter cells, while the other cell restarts the cycle.

In 1966, biologist Kwang W. Jeon found that a lab strain of Amoeba proteus had been infected by bacteria that lived inside the cytoplasmic vacuoles. This infection killed almost all of the infected protists. After the equivalent of 40 host generations, the two organisms become mutually interdependent. A genetic exchange between the prokaryotes and protists occurred.

Vertebrates

The spotted salamander (Ambystoma maculatum) lives in a relationship with the algae Oophila amblystomatis, which grows in its egg cases.

Plants

All vascular plants harbor endosymbionts or endophytes in this context. They include bacteria, fungi, viruses, protozoa and even microalgae. Endophytes aid in processes such as growth and development, nutrient uptake, and defense against biotic and abiotic stresses like drought, salinity, heat, and herbivores.

Plant symbionts can be categorized into epiphytic, endophytic, and mycorrhizal. These relations can also be categorized as beneficial, mutualistic, neutral, and pathogenic. Microorganisms living as endosymbionts in plants can enhance their host's primary productivity either by producing or capturing important resources. These endosymbionts can also enhance plant productivity by producing toxic metabolites that aid plant defenses against herbivores.

Plants are dependent on plastid or chloroplast organelles. The chloroplast is derived from a cyanobacterial primary endosymbiosis that began over one billion years ago. An oxygenic, photosynthetic free-living cyanobacterium was engulfed and kept by a heterotrophic protist and eventually evolved into the present intracellular organelle.

Mycorrhizal endosymbionts appear only in fungi.

Typically, plant endosymbiosis studies focus on a single category or species to better understand their individual biological processes and functions.

Fungal endophytes

Fungal endophytes can be found in all plant tissues. Fungi living below the ground amidst plant roots are known as mycorrhiza, but are further categorized based on their location inside the root, with prefixes such as ecto, endo, arbuscular, ericoid, etc. Fungal endosymbionts that live in the roots and extend their extraradical hyphae into the outer rhizosphere are known as ectendosymbionts.

Arbuscular Mycorrhizal Fungi (AMF)

Arbuscular mycorrhizal fungi or AMF are the most diverse plant microbial endosymbionts. With exceptions such as the Ericaceae family, almost all vascular plants harbor AMF endosymbionts as endo and ecto as well. AMF plant endosymbionts systematically colonize plant roots and help the plant host acquire soil nutrients such as nitrogen. In return it absorbs plant organic carbon products. Plant root exudates contain diverse secondary metabolites, especially flavonoids and strigolactones that act as chemical signals and attracts the AMF. AMF Gigaspora margarita lives as a plant endosymbiont and also harbors further endosymbiont intracytoplasmic bacterium-like organisms. AMF generally promote plant health and growth and alleviate abiotic stresses such as salinity, drought, heat, poor nutrition, and metal toxicity.^[88] Individual AMF species have different effects in different hosts – introducing the AMF of one plant to another plant can reduce the latter's growth.

Endophytic fungi

Endophytic fungi in mutualistic relations directly benefit and benefit from their host plants. They also can help their hosts succeed in polluted environments such as those contaminated with toxic metals. Fungal endophytes are taxonomically diverse and are divided into categories based on mode of transmission, biodiversity, in planta colonization and host plant type. Clavicipitaceous fungi systematically colonize temperate season grasses. Non-clavicipitaceous fungi colonize higher plants and even roots and divide into subcategories. Aureobasidium and preussia species of endophytic fungi isolated from Boswellia sacra produce indole acetic acid hormone to promote plant health and development.

Aphids can be found in most plants. Carnivorous ladybirds are aphid predators and are used in pest control. Plant endophytic fungus Neotyphodium lolii produces alkaloid mycotoxins in response to aphid invasions. In response, ladybird predators exhibited reduced fertility and abnormal reproduction, suggesting that the mycotoxins are transmitted along the food chain and affect the predators.

Endophytic bacteria

Endophytic bacteria belong to a diverse group of plant endosymbionts characterized by systematic colonization of plant tissues. The most common genera include Pseudomonas, Bacillus, Acinetobacter, Actinobacteria, Sphingomonas. Some endophytic bacteria, such as Bacillus amyloliquefaciens, a seed-born endophytic bacteria, produce plant growth by producing gibberellins, which are potent plant growth hormones. Bacillus amyloliquefaciens promotes the taller height of transgenic dwarf rice plants. Some endophytic bacteria genera additionally belong to the Enterobacteriaceae family. Endophytic bacteria typically colonize the leaf tissues from plant roots, but can also enter the plant through the leaves through leaf stomata. Generally, the endophytic bacteria are isolated from the plant tissues by surface sterilization of the plant tissue in a sterile environment. Passenger endophytic bacteria eventually colonize inner tissue of plant by stochastic events while True endophytes possess adaptive traits because of which they live strictly in association with plants. The in vitro-cultivated endophytic bacteria association with plants is considered a more intimate relationship that helps plants acclimatize to conditions and promotes health and growth. Endophytic bacteria are considered to be plant's essential endosymbionts because virtually all plants harbor them, and these endosymbionts play essential roles in host survival. This endosymbiotic relation is important in terms of ecology, evolution and diversity. Endophytic bacteria such as Sphingomonas sp. and Serratia sp. that are isolated from arid land plants regulate endogenous hormone content and promote growth.

Archaea endosymbionts

Archaea are members of most microbiomes. While archaea are abundant in extreme environments, they are less abundant and diverse in association with eukaryotic hosts. Nevertheless, archaea are a substantial constituent of plant-associated ecosystems in the above ground and below ground phytobiome, and play a role in host plant’s health, growth and survival amid biotic and abiotic stresses. However, few studies have investigated the role of archaea in plant health and its symbiotic relationships. Most plant endosymbiosis studies focus on fungal or bacteria using metagenomic approaches.

The characterization of archaea includes crop plants such as rice and maize, but also aquatic plants. The abundance of archaea varies by tissue type; for example archaea are more abundant in the rhizosphere than the phyllosphere and endosphere. This archaeal abundance is associated with plant species type, environment and the plant’s developmental stage. In a study on plant genotype-specific archaeal and bacterial endophytes, 35% of archaeal sequences were detected in overall sequences (achieved using amplicon sequencing and verified by real time-PCR). The archaeal sequences belong to the phyla Thaumarchaeota, Crenarchaeota, and Euryarchaeota.

Bacteria

Some Betaproteobacteria have Gammaproteobacteria endosymbionts.

Fungi

Fungi host endohyphal bacteria; the effects of the bacteria are not well studied. Many such fungi in turn live within plants. These fungi are otherwise known as fungal endophytes. It is hypothesized that the fungi offers a safe haven for the bacteria, and the diverse bacteria that they attract create a micro-ecosystem.

These interactions may impact the way that fungi interact with the environment by modulating their phenotypes. The bacteria do this by altering the fungi's gene expression. For example, Luteibacter sp. has been shown to naturally infect the ascomycetous endophyte Pestalotiopsis sp. isolated from Platycladus orientalis. The Luteibacter sp. influences the auxin and enzyme production within its host, which, in turn, may influence the effect the fungus has on its plant host. Another interesting example of a bacterium living in symbiosis with a fungus is the fungus Mortierella. This soil-dwelling fungus lives in close association with a toxin-producing bacteria, Mycoavidus, which helps the fungus defend against nematodes.

Virus endosymbionts

The human genome project found several thousand endogenous retroviruses, endogenous viral elements in the genome that closely resemble and can be derived from retroviruses, organized into 24 families.

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