Microbiome in the context of "Quorum sensing"

All animals on Earth form associations with microorganisms, including protists, bacteria, archaea, fungi, and viruses. In the ocean, animal–microbial relationships were historically explored in single host–symbiont systems. However, new explorations into the diversity of marine microorganisms associating with diverse marine animal hosts is moving the field into studies that address interactions between the animal host and a more multi-member microbiome. The potential for microbiomes to influence the health, physiology, behavior, and ecology of marine animals could alter current understandings of how marine animals adapt to change, and especially the growing climate-related and anthropogenic-induced changes already impacting the ocean environment.

In the oceans, it is challenging to find eukaryotic organisms that do not live in close relationship with a microbial partner. Host-associated microbiomes also influence biogeochemical cycling within ecosystems with cascading effects on biodiversity and ecosystem processes. The microbiomes of diverse marine animals are currently under study, from simplistic organisms including sponges and ctenophores to more complex organisms such as sea squirts and sharks.

A biofilm is a syntrophic community of microorganisms in which cells stick to each other and often also to a surface. These adherent cells become embedded within a slimy extracellular matrix that is composed of extracellular polymeric substances (EPSs). The cells within the biofilm produce the EPS components, which are typically a polymeric combination of extracellular polysaccharides, proteins, lipids and DNA. Because they have a three-dimensional structure and represent a community lifestyle for microorganisms, they have been metaphorically described as "cities for microbes".

Biofilms may form on living (biotic) or non-living (abiotic) surfaces and can be common in natural, industrial, and hospital settings. They may constitute a microbiome or be a portion of it. The microbial cells growing in a biofilm are physiologically distinct from planktonic cells of the same organism, which, by contrast, are single cells that may float or swim in a liquid medium. Biofilms can form on the teeth of most animals as dental plaque, where they may cause tooth decay and gum disease.

Microbiota are the range of microorganisms that may be commensal, mutualistic, or pathogenic found in and on all multicellular organisms, including plants. Microbiota include bacteria, archaea, protists, fungi, and viruses, and have been found to be crucial for immunologic, hormonal, and metabolic homeostasis of their host.

The term microbiome describes either the collective genomes of the microbes that reside in an ecological niche or else the microbes themselves.

Animal feed is food given to domestic animals, especially livestock, in the course of animal husbandry. There are two basic types: fodder and forage. Used alone, the word feed more often refers to fodder. Animal feed is an important input to animal agriculture, and is frequently the main cost of the raising or keeping of animals. Farms typically try to reduce cost for this food, by growing their own, grazing animals, or supplementing expensive feeds with substitutes, such as food waste like spent grain from beer brewing.

Animal wellbeing is highly dependent on feed that reflects a well balanced nutrition. Some modern agricultural practices, such as fattening cows on grains or in feed lots, have detrimental effects on the environment and animals. For example, increased corn or other grain in feed for cows, makes their microbiomes more acidic weakening their immune systems and making cows a more likely vector for E. coli, while other feeding practices can improve animal impacts. For example, feeding cows certain kinds of seaweed, reduces their production of methane, reducing the greenhouse gases from meat production.

Carbon farming is a set of agricultural methods that aim to store carbon in the soil and biomass. The technical term for this is carbon sequestration. The overall goal of carbon farming is to create a net loss of carbon from the atmosphere. This is done by increasing the rate at which carbon is sequestered into soil and plant material. The increase of biomass from roots and the soil's microbiome leads to an increase in the organic matter content of the soil. Increasing organic matter content in soils aids plant growth, improves soil water retention capacity and reduces fertilizer use. Sustainable forest management is another tool that is used in carbon farming. Carbon farming is one component of climate-smart agriculture. It is also one way to remove carbon dioxide from the atmosphere.

Agricultural methods for carbon farming include adjusting how tillage and livestock grazing is done, using organic mulch or compost, working with biochar and terra preta, and changing the crop types. Methods used in forestry include reforestation and bamboo farming. As of 2016, variants of carbon farming reached hundreds of millions of hectares globally, of the nearly 5 billion hectares (1.2×10 acres) of world farmland.

The plant microbiome, also known as the phytomicrobiome, plays roles in plant health and productivity and has received significant attention in recent years. The microbiome has been defined as "a characteristic microbial community occupying a reasonably well-defined habitat which has distinct physio-chemical properties. The term thus not only refers to the microorganisms involved but also encompasses their theatre of activity".

Plants live in association with diverse microbial consortia. These microbes, referred to as the plant's microbiota, live both inside (the endosphere) and outside (the episphere) of plant tissues, and play important roles in the ecology and physiology of plants. "The core plant microbiome is thought to comprise keystone microbial taxa that are important for plant fitness and established through evolutionary mechanisms of selection and enrichment of microbial taxa containing essential functions genes for the fitness of the plant holobiont."

An opportunistic infection is an infection that occurs most commonly in individuals with an immunodeficiency disorder and acts more severely on those with a weakened immune system. These types of infections are considered serious and can be caused by a variety of pathogens including viruses, bacteria, fungi, and parasites. Under normal conditions, such as in humans with uncompromised immune systems, an opportunistic infection would be less likely to cause significant harm and would typically result in a mild infection or no effect at all. These opportunistic infections can stem from a variety of sources, such as a weakened immune system (caused by human immunodeficiency virus and acquired immunodeficiency syndrome), when being treated with immunosuppressive drugs (as in cancer treatment), when a microbiome is altered (such as a disruption in gut microbiota), or when integumentary barriers are breached (as in penetrating trauma). Opportunistic infections can contribute to antimicrobial resistance in an individual making these infections more severe. Some pathogens that cause these infections possess intrinsic resistance (natural resistance) to many antibiotics while others acquire resistance over time through mutations or horizontal gene transfer. Many of these pathogens, such as the bacterium Clostridioides difficile (C. diff), can be present in hosts with uncompromised immune systems without generating any symptoms, and can, in some cases, act as commensals until the balance of the immune system is disrupted. With C. diff and many other pathogens, the overuse or misuse of antibiotics can cause the disruption of normal microbiota and lead to an opportunistic infection caused by antibiotic resistant pathogens. In some cases, opportunistic infections can be labeled as a hospital-acquired infection due to individuals contracting them within a healthcare/hospital setting. In terms of history, there is not one individual that can be attributed for discovering opportunistic infections. Over time and through medical advancement, there have been many scientists that have contributed to the study and treatment options for patients affected by these infections.

A holobiont is an assemblage of a host and the many other species living in or around it, which together form a discrete ecological unit through symbiosis, though there is controversy over this discreteness. The components of a holobiont are individual species or bionts, while the combined genome of all bionts is the hologenome. The holobiont concept was initially introduced by the German theoretical biologist Adolf Meyer-Abich in 1943, and then apparently independently by Dr. Lynn Margulis in her 1991 book Symbiosis as a Source of Evolutionary Innovation. The concept has evolved since the original formulations. Holobionts include the host, virome, microbiome, and any other organisms which contribute in some way to the functioning of the whole. Well-studied holobionts include reef-building corals and humans.