Infestation of the skin by arthropods is characterized by itching and excoriations, such as pediculosis caused by lice attached to hairs, or scabies caused by mites burrowing into the stratum corneum. At the site of bites, mouth parts may be found associated with a mixed infiltrate of lymphocytes, macrophages, and eosinophils. Arthropods also can serve as vectors for other pathogens, such as Borrelia burgdorferi, the agent of Lyme disease, which is transmitted by deer ticks.
The microbiome is the diverse microbial population of bacteria, fungi, and viruses found in or on the human body (e.g., in the intestinal tract, skin, upper airway, and vagina). While most of these organisms do not harm the healthy host, a few cause diseases such as skin and soft-tissue infections (Staphylococcus aureus and Streptococcus pyogenes), acne (Propionibacterium acnes), and tooth decay (Streptococcus mitus). The microbiome has important roles in normal health and development. In the intestinal tract, the normal flora are responsible for absorption of digested foods, for maintaining the integrity of the epithelium and the normal functioning of the intestinal immune system, and for competitively inhibiting invasion and colonization by potentially pathogenic microbes. The gut microbiome is also emerging as a regulator of nutritional status.
New techniques of bacterial identification relying on ribosomal RNA sequencing have dramatically improved our understanding of the microbiome:
In healthy individuals, the microbiome is very diverse. For example, there are estimated to be over 1000 species of bacteria in the normal intestinal flora of an individual. In a healthy person, a part of the bacterial population at various body sites is relatively stable over time, but may be altered by diet and environment.
The diversity of bacteria is greatest in the oral cavity and the stool, intermediate on the skin, and least in the vagina.
The bacterial microbiomes at various body sites are partially similar in different individuals.
Dysbiosis refers to changes in composition of the microbiome that are associated with disease. These changes may result from therapies or various pathophysiologic conditions, including the following:
Use of some antibiotics is an important risk factor for intestinal infections caused by toxin-producing Clostridium difficile. These antibiotics kill or inhibit normal commensal bacteria, allowing overgrowth of C. difficile. Restoration of the microbiome by duodenal infusion of stool containing commensal flora from healthy donors successfully treats C. difficile infection in many individuals who have relapsed after antibiotic therapy.
The microbiome in the stool of obese individuals is less diverse than that of lean individuals, and the proportions of bacterial phyla differ as well. The proportions of these phyla in obese individuals who change their diet and lose weight shifts to resemble that of lean individuals. Experimental animals gain more weight when colonized with bacterial populations associated with a high-fat diet than when colonized with bacterial populations associated with a normal diet.
The intestinal bacterial populations in individuals with inflammatory bowel disease are altered, with reduced diversity and changes in the proportions of bacterial phyla, compared to individuals without inflammatory bowel disease. Interestingly, inflammatory bowel disease also is associated with changes in the viral populations in stool. The specific roles of different viruses and bacteria in gastrointestinal dysbiosis is an area of very active investigation.
There are several methods for identifying microorganisms in tissue and body fluids:
Culture. Bacterial and fungal cultures remain essential for diagnostic testing, in conjunction with additional methods, but culture of viruses has been replaced to a great extent by alternative methods.