Dysbiosis (also called dysbacteriosis) is characterized by a disruption to the microbiome resulting in an imbalance in the microbiota, changes in their functional composition and metabolic activities, or a shift in their local distribution. For example, a part of the human microbiota such as the skin flora, gut flora, or vaginal flora, can become deranged (unbalanced), when normally dominating species become underrepresented and species that normally are outcompeted or contained increase to fill the void. Due to perceived implications in diverse diseases, there has been a rapid growth in research and innovation interest in different approaches to counteract dysbiosis. Similar to the human gut microbiome, diverse microbes colonize the plant rhizosphere, and dysbiosis in the rhizosphere, can negatively impact plant health. Dysbiosis is most commonly reported as a condition in the gastrointestinal tract or plant rhizosphere.

Typical microbial colonies found on or in the body are benign or beneficial. These appropriately sized microbial colonies carry out a series of helpful and necessary functions, such as aiding in digestion. They also help protect the body from infiltration by pathogenic microbes. These beneficial microbial colonies compete with each other for space and resources. However, when this balance is disturbed, these colonies exhibit a decreased ability to check each other's growth, which can then lead to overgrowth of one or more of the disturbed colonies which may further damage some of the other smaller beneficial ones in a vicious cycle. As more beneficial colonies are damaged, making the imbalance more pronounced, more overgrowth issues occur because the damaged colonies are less able to check the growth of the overgrowing ones. If this goes unchecked long enough, a pervasive and chronic imbalance between colonies will set in, which ultimately minimizes the beneficial nature of these colonies as a whole.

Any disruption of the body's microbiota is able to lead to dysbiosis. Dysbiosis in the gut happens when the bacteria in the gastrointestinal tract become unbalanced. There are many causes for dysbiosis in the gut. Some reasons include, but are not limited to:  

Bacteria in the human gut's intestines are the most diverse in the human body and play a vital role in human health. In the gastrointestinal tract, dysbiosis manifests particularly during small intestinal bacterial overgrowth (SIBO), commonly caused by a decrease in the passage of food and waste through the gastrointestinal tract following surgery or other pre-existing conditions. SIBO is characterized by symptoms of abdominal pain, diarrhea, discomfort after eating, and malnutrition. Similarly, dysbiosis manifests during small intestinal fungal overgrowth (SIFO) caused by excessive population levels of fungi in a bowel. SIFO can be characterized by GI symptoms (vomiting, diarrhea) in those previously immunocompromised. The consumer's dietary habits can be one of the most influential factors on the gut's microbiota. Diets high in carbohydrates and refined sugars are common links to dysbiosis in the gut, whereas those rich in fruits, vegetables, and fish oils are considered more favorable to the gut due to their anti-inflammatory properties. Many diseases, such as IBD, Type 2 Diabetes, Crohn's, and even allergies, are suggested to be due, in part, to an alteration in the microbiome of the gut. Probiotics can sometimes cause mild gas and bloating in people who first start taking them, especially at high doses, as their body gets used to having new gut bacteria introduced into their gut.

The mouth is frequently exposed to novel microbes from the environment, and this can lead to microbial disturbances in the mouth as well as in the stomach and intestines. Hygiene and nutritional variation are imperative in preventing oral diseases such as gingivitis, tooth decay, and cavities, which are linked to altered microbial communities in the oral cavity. Oral pathogens can affect multiple microbiota compartments of the body and alter systemic processes, such as immunological alterations or digestion issues. Smoking, drinking, oral intercourse, and advanced age are all associated with oral dysbiosis.

There are a number of types of microorganisms that reside in and on the human skin, collectively known as the skin flora. Normal healthy microbial communities may have some positive effects. Altered microbial composition and diversity (dysbiosis), may play a role in some non-infectious skin conditions such as acne, atopic dermatitis, psoriasis, and rosacea. In more extreme cases, such as cellulitis, a pathogenic bacteria can infect the skin, the most common being Streptococci species and Staphylococcus aureus.

The vagina contains a microbiome (vaginal flora) that can become disturbed and result in conditions such as bacterial vaginosis. Alterations in vaginal flora can also affect vaginal health in reproduction, as well as one's risk of acquiring and the subsequent severity of sexually transmitted infections.

Dysbiosis can occur during many stages of life and can be triggered by many different sources. Antibiotics, for example, are often a significant contributor to disruptions in microbiomes. This occurs because not all microbes will be affected by the antibiotic in the same way, and so it can change the balance of different types of microbes as well as changing the total number of microbes. Antibiotic usage during young childhood development can lead to adverse gut issues (dysbiosis) in adulthood. The gut microbiome is altered from antibiotics and is linked to future gut disease, i.e., IBD, ulcerative colitis, obesity, etc. The intestinal immune system is directly influenced by the gut microbiome and can be hard to recover if damaged through antibiotics. The use of minocycline in acne vulgaris has been associated with skin and gut dysbiosis.