In biology, a pathogen in the oldest and broadest sense, is any organism that can produce disease. A pathogen may also be referred to as an infectious agent, or simply a germ.

The term pathogen came into use in the 1880s. Typically, the term is used to describe an infectious microorganism or agent, such as a virus, bacterium, protozoan, prion, viroid, or fungus. Small animals, such as certain worms or insects, can also cause or transmit disease. However, these animals are usually, in common parlance, referred to as parasites rather than pathogens. The scientific study of microscopic organisms, including microscopic pathogenic organisms, is called microbiology, while parasitology refers to the scientific study of parasites and the organisms that host them.

There are several pathways through which pathogens can invade a host. The principal pathways have different episodic time frames, but soil has the longest or most persistent potential for harboring a pathogen.

Diseases in humans that are caused by infectious agents are known as pathogenic diseases. Not all diseases are caused by pathogens, other causes are, for example, toxins, genetic disorders and the host's own immune system.

Pathogenicity is the potential disease-causing capacity of pathogens. Pathogenicity is related to virulence in meaning, but some authorities have come to distinguish it as a qualitative term, whereas the latter is quantitative. By this standard, an organism may be said to be pathogenic or non-pathogenic in a particular context, but not "more pathogenic" than another. Such comparisons are described instead in terms of relative virulence. Pathogenicity is also distinct from the transmissibility of a virus, which quantifies the risk of infection.

A pathogen may be described in terms of its ability to produce toxins, enter tissue, colonize, hijack nutrients, and its ability to immunosuppress the host.

Virulence evolves when a pathogen can spread from a diseased host, despite the host becoming debilitated. Horizontal transmission occurs between hosts of the same species, in contrast to vertical transmission, which tends to evolve toward symbiosis by linking the pathogen's evolutionary success to the evolutionary success of the host organism. Evolutionary biology proposes that many pathogens evolve an optimal virulence at which the fitness gained by increased replication rates is balanced by trade-offs in reduced transmission, but the exact mechanisms underlying these relationships remain controversial.

Many pathogens are capable of sexual interaction. Among pathogenic bacteria, sexual interaction occurs between cells of the same species by the process of natural genetic transformation.

Applied Microbiology is a peer-reviewed Open Access Journal, encourages on-going international research and articles related to but not limited to Medical microbiology, pathogenic microbes, Pharmaceutical microbiology (antibiotics, enzymes, vitamins, vaccines) Industrial microbiology, Microbial biotechnology, Plant pathology, Veterinary, Food, Agricultural, Soil, Environmental Microbiology, etc.

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