Viruses in the context of Microbiology

Hand washing (or handwashing), also called hand hygiene, is the process of cleaning the hands with soap or handwash and water to eliminate bacteria, viruses, dirt, microorganisms, and other potentially harmful substances. Drying of the washed hands is part of the process as wet and moist hands are more easily recontaminated. If soap and water are unavailable, hand sanitizer that is at least 60% (v/v) alcohol in water can be used as long as hands are not visibly excessively dirty or greasy. Hand hygiene is central to preventing the spread of infectious diseases in home and everyday life settings. Meta-analyses have shown that regular hand washing in community settings can significantly reduce respiratory and gastrointestinal infection

The World Health Organization (WHO) recommends washing hands for at least 20 seconds before and after certain activities. These include the five critical times during the day where washing hands with soap is important to reduce fecal-oral transmission of disease: after using the toilet (for urination, defecation, menstrual hygiene), after cleaning a child's bottom (changing diapers), before feeding a child, before eating and before/after preparing food or handling raw meat, fish, or poultry.

Regulation of gene expression, or gene regulation, includes a wide range of mechanisms that are used by cells to increase or decrease the production of specific gene products (protein or RNA). Sophisticated programs of gene expression are widely observed in biology, for example to trigger developmental pathways, respond to environmental stimuli, or adapt to new food sources. Virtually any step of gene expression can be modulated, from transcriptional initiation, to RNA processing, and to the post-translational modification of a protein. Often, one gene regulator controls another, and so on, in a gene regulatory network.

Gene regulation is essential for viruses, prokaryotes and eukaryotes as it increases the versatility and adaptability of an organism by allowing the cell to express protein when needed. Although as early as 1951, Barbara McClintock showed interaction between two genetic loci, Activator (Ac) and Dissociator (Ds), in the color formation of maize seeds, the first discovery of a gene regulation system is widely considered to be the identification in 1961 of the lac operon, discovered by François Jacob and Jacques Monod, in which some enzymes involved in lactose metabolism are expressed by E. coli only in the presence of lactose and absence of glucose.

Rosalind Elsie Franklin (25 July 1920 – 16 April 1958) was an English chemist and X-ray crystallographer. Her work was central to the understanding of the molecular structures of DNA (deoxyribonucleic acid), RNA (ribonucleic acid), viruses, coal, and graphite. Although her works on coal and viruses were appreciated in her lifetime, Franklin's contributions to the discovery of the structure of DNA were largely unrecognised during her life, for which Franklin has been variously referred to as the "wronged heroine", the "dark lady of DNA", the "forgotten heroine", a "feminist icon", and the "Sylvia Plath of molecular biology".

Franklin graduated in 1941 with a degree in natural sciences from Newnham College, Cambridge, and then enrolled for a PhD in physical chemistry under Ronald George Wreyford Norrish, the 1920 Chair of Physical Chemistry at the University of Cambridge. Disappointed by Norrish's lack of enthusiasm, she took up a research position under the British Coal Utilisation Research Association (BCURA) in 1942. The research on coal helped Franklin earn a PhD from Cambridge in 1945. Moving to Paris in 1947 as a chercheur (postdoctoral researcher) under Jacques Mering at the Laboratoire Central des Services Chimiques de l'État, she became an accomplished X-ray crystallographer. After joining King's College London in 1951 as a research associate, Franklin discovered some key properties of DNA, which eventually facilitated the correct description of the double helix structure of DNA. Owing to disagreement with her director, John Randall, and her colleague Maurice Wilkins, Franklin was compelled to move to Birkbeck College in 1953.

Gut microbiota, gut microbiome, or gut flora are the microorganisms, including bacteria, archaea, fungi, and viruses, that live in the digestive tracts of animals. The gastrointestinal metagenome is the aggregate of all the genomes of the gut microbiota. The gut is the main location of the human microbiome. The gut microbiota has broad impacts, including effects on colonization, resistance to pathogens, maintaining the intestinal epithelium, metabolizing dietary and pharmaceutical compounds, controlling immune function, and even behavior through the gut–brain axis.

The microbial composition of the gut microbiota varies across regions of the digestive tract. The colon contains the highest microbial density of any human-associated microbial community studied so far, representing between 300 and 1000 different species. Bacteria are the largest and to date, best studied component and 99% of gut bacteria come from about 30 or 40 species. About 55% of the dry mass of feces is bacteria. Over 99% of the bacteria in the gut are anaerobes, but in the cecum, aerobic bacteria reach high densities. It is estimated that the human gut microbiota has around a hundred times as many genes as there are in the human genome.

Antimicrobial resistance (AMR or AR) occurs when microbes evolve mechanisms that protect them from antimicrobials, which are drugs used to treat infections. This resistance affects all classes of microbes, including bacteria (antibiotic resistance), viruses (antiviral resistance), parasites (antiparasitic resistance), and fungi (antifungal resistance). Together, these adaptations fall under the AMR umbrella, posing significant challenges to healthcare worldwide. Misuse and improper management of antimicrobials are primary drivers of this resistance, though it can also occur naturally through genetic mutations and the spread of resistant genes.

Antibiotic resistance, a significant AMR subset, enables bacteria to survive antibiotic treatment, complicating infection management and treatment options. Resistance arises through spontaneous mutation, horizontal gene transfer, and increased selective pressure from antibiotic overuse, both in medicine and agriculture, which accelerates resistance development.

A fomite (/ˈfoʊmaɪt/) or fomes (/ˈfoʊmiːz/) is any inanimate object that, when contaminated with or exposed to infectious agents (such as pathogenic bacteria, viruses or fungi), can transfer disease to a new host.

Gastroenteritis, also known as infectious diarrhea, is an inflammation of the gastrointestinal tract including the stomach and intestine. Symptoms may include diarrhea, vomiting, and abdominal pain. Fever, lack of energy, and dehydration may also occur. This typically lasts less than two weeks. Although it is not related to influenza, in Canada and the United States it is often referred to as "stomach flu".

Gastroenteritis is usually caused by viruses; however, gut bacteria, parasites, and fungi can also cause gastroenteritis. In children, rotavirus is the most common cause of severe disease. In adults, norovirus and Campylobacter are common causes. Eating improperly prepared food, drinking contaminated water or close contact with a person who is infected can spread the disease. Treatment is generally the same with or without a definitive diagnosis, so testing to confirm is usually not needed.

Septic shock is a potentially fatal medical condition that occurs when sepsis, which is organ injury or damage in response to infection, leads to dangerously low blood pressure and abnormalities in cellular metabolism. The Third International Consensus Definitions for Sepsis and Septic Shock (Sepsis-3) defines septic shock as a subset of sepsis in which particularly profound circulatory, cellular, and metabolic abnormalities are associated with a greater risk of mortality than with sepsis alone. Patients with septic shock can be clinically identified by requiring a vasopressor to maintain a mean arterial pressure of 65 mm Hg or greater and having serum lactate level greater than 2 mmol/L (>18 mg/dL) in the absence of hypovolemia. This combination is associated with hospital mortality rates greater than 40%.

The primary infection is most commonly caused by bacteria, but also may be caused by fungi, viruses, or parasites. It may be located in any part of the body, but most commonly in the lungs, brain, urinary tract, skin, or abdominal organs. It can cause multiple organ dysfunction syndrome (formerly known as multiple organ failure) and death if not treated immediately.

Martinus Willem Beijerinck (Dutch pronunciation: [mɑrˈtinʏs ˈʋɪləm ˈbɛiərɪŋk], 16 March 1851 – 1 January 1931) was a Dutch microbiologist and botanist who was one of the founders of virology and environmental microbiology. He is credited with the co-discovery of viruses (1898), which he called "contagium vivum fluidum".

Acute septic arthritis, infectious arthritis, suppurative arthritis, pyogenic arthritis, osteomyelitis, or joint infection is the invasion of a joint by an infectious agent resulting in joint inflammation. Generally speaking, symptoms typically include redness, heat and pain in a single joint associated with a decreased ability to move the joint. Onset is usually rapid. Other symptoms may include fever, weakness and headache. Occasionally, more than one joint may be involved, especially in neonates, younger children and immunocompromised individuals. In neonates, infants during the first year of life, and toddlers, the signs and symptoms of septic arthritis can be deceptive and mimic other infectious and non-infectious disorders.

In children, septic arthritis is usually caused by non-specific bacterial infection and commonly hematogenous, i.e., spread through the bloodstream. Septic arthritis and/or acute hematogenous osteomyelitis usually occurs in children with no co-occurring health problems. Other routes of infection include direct trauma and spread from a nearby abscess. Other less common cause include specific bacteria as mycobacterium tuberculosis, viruses, fungi and parasites. In children, however, there are certain groups that are specifically vulnerable to such infections, namely preterm infants, neonates in general, children and adolescents with hematologic disorders, renal osteodystrophy, and immune-compromised status. In adults, vulnerable groups include those with an artificial joint, prior arthritis, diabetes and poor immune function. Diagnosis is generally based on accurate correlation between history-taking and clinical examination findings, and basic laboratory and imaging findings like joint ultrasound.

Coliform bacteria are defined as either motile or non-motile Gram-negative non-spore forming bacilli that possess β-galactosidase to produce acids and gases under their optimal growth temperature of 35–37 °C. They can be aerobes or facultative aerobes, and are a commonly used indicator of low sanitary quality of foods, milk, and water. Coliforms can be found in the aquatic environment, in soil and on vegetation; they are universally present in large numbers in the feces of warm-blooded animals as they are known to inhabit the gastrointestinal system. While coliform bacteria are not normally the cause of serious illness, they are easy to culture, and their presence is used to infer that other pathogenic organisms of fecal origin may be present in a sample, or that said sample is not safe to consume. Such pathogens include disease-causing bacteria, viruses, or protozoa and many multicellular parasites.Every drinking water source must be tested for the presence of these total coliform bacteria.

Food safety (or food hygiene) is used as a scientific method/discipline describing handling, preparation, and storage of food in ways that prevent foodborne illness. The occurrence of two or more cases of a similar illness resulting from the ingestion of a common food is known as a food-borne disease outbreak. Food safety includes a number of routines that should be followed to avoid potential health hazards. In this way, food safety often overlaps with food defense to prevent harm to consumers. The tracks within this line of thought are safety between industry and the market and then between the market and the consumer. In considering industry-to-market practices, food safety considerations include the origins of food including the practices relating to food labeling, food hygiene, food additives and pesticide residues, as well as policies on biotechnology and food and guidelines for the management of governmental import and export inspection and certification systems for foods. In considering market-to-consumer practices, the usual thought is that food ought to be safe in the market and the concern is safe delivery and preparation of the food for the consumer. Food safety, nutrition and food security are closely related. Unhealthy food creates a cycle of disease and malnutrition that affects infants and adults as well.

Food can transmit pathogens, which can result in the illness or death of the person or other animals. The main types of pathogens are bacteria, viruses, parasites, and fungus. The WHO Foodborne Disease Epidemiology Reference Group conducted the only study that solely and comprehensively focused on the global health burden of foodborne diseases. This study, which involved the work of over 60 experts for a decade, is the most comprehensive guide to the health burden of foodborne diseases. The first part of the study revealed that 31 foodborne hazards considered priority accounted for roughly 420,000 deaths in LMIC and posed a burden of about 33 million disability adjusted life years in 2010. Food can also serve as a growth and reproductive medium for pathogens. In developed countries there are intricate standards for food preparation, whereas in lesser developed countries there are fewer standards and less enforcement of those standards. In the US, 5,000 deaths per year were related to foodborne pathogens in 1999. Another main issue is simply the availability of adequate safe water, which is usually a critical item in the spreading of diseases. Food poisoning cannot be completely avoided due to the number of persons involved in the supply chain, as well as the fact that pathogens can be introduced into foods no matter how many precautions are taken.

Mobile genetic elements (MGEs), sometimes called selfish genetic elements, are a type of genetic material that can move around within a genome, or that can be transferred from one species or replicon to another. MGEs are found in all organisms. In humans, approximately 50% of the genome are thought to be MGEs. MGEs play a distinct role in evolution. Gene duplication events can also happen through the mechanism of MGEs. MGEs can also cause mutations in protein coding regions, which alters the protein functions. These mechanisms can also rearrange genes in the host genome generating variation. These mechanisms can increase fitness by gaining new or additional functions. An example of MGEs in evolutionary context are that virulence factors and antibiotic resistance genes of MGEs can be transported to share genetic code with neighboring bacteria. However, MGEs can also decrease fitness by introducing disease-causing alleles or mutations. The set of MGEs in an organism is called a mobilome, which is composed of a large number of plasmids, transposons and viruses.

Defensins are small cysteine-rich cationic proteins across cellular life, including vertebrate and invertebrate animals, plants, and fungi. They are host defense peptides, with members displaying either direct antimicrobial activity, immune signaling activities, or both. They are variously active against bacteria, fungi and many enveloped and nonenveloped viruses. They are typically 18-45 amino acids in length, with three or four highly conserved disulphide bonds.

In animals, they are produced by cells of the innate immune system and epithelial cells, whereas in plants and fungi they are produced by a wide variety of tissues. An organism usually produces many different defensins, some of which are stored inside the cells (e.g. in neutrophil granulocytes to kill phagocytosed bacteria), and others are secreted into the extracellular medium. For those that directly kill microbes, their mechanism of action varies from disruption of the microbial cell membrane to metabolic disruption.

Non-coding DNA (ncDNA) sequences are components of an organism's DNA that do not encode protein sequences. Some non-coding DNA is transcribed into functional non-coding RNA molecules (e.g. transfer RNA, microRNA, piRNA, ribosomal RNA, and regulatory RNAs). Other functional regions of the non-coding DNA fraction include regulatory sequences that control gene expression; scaffold attachment regions; origins of DNA replication; centromeres; and telomeres. Some non-coding regions appear to be mostly nonfunctional, such as introns, pseudogenes, intergenic DNA, and fragments of transposons and viruses. Regions that are completely nonfunctional are called junk DNA.