Enterococcus is a large genus of lactic acid bacteria of the phylum Bacillota. Enterococci are gram-positive cocci that often occur in pairs (diplococci) or short chains, and are difficult to distinguish from streptococci on physical characteristics alone. Two species are common commensal organisms in the intestines of humans: E. faecalis (90–95%) and E. faecium (5–10%). Rare clusters of infections occur with other species, including E. casseliflavus, E. gallinarum, and E. raffinosus.
The human microbiome is the aggregate of all microbiota that reside on or within human tissues and biofluids along with the corresponding anatomical sites in which they reside, including the gastrointestinal tract, skin, mammary glands, seminal fluid, uterus, ovarian follicles, lung, saliva, oral mucosa, conjunctiva, and the biliary tract. Types of human microbiota include bacteria, archaea, fungi, protists, and viruses. Though micro-animals can also live on the human body, they are typically excluded from this definition. In the context of genomics, the term human microbiome is sometimes used to refer to the collective genomes of resident microorganisms; however, the term human metagenome has the same meaning.
Bacillota is a phylum of bacteria, most of which have gram-positive cell wall structure. The renaming of phyla such as Firmicutes in 2021 remains controversial among microbiologists, many of whom continue to use the earlier names of long standing in the literature.
Gardnerella vaginalis is a species of Gram-variable-staining facultative anaerobic bacteria. The organisms are small non-spore-forming, nonmotile coccobacilli.
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.
Lacticaseibacillus rhamnosus is a bacterium that originally was considered to be a subspecies of L. casei, but genetic research found it to be a separate species in the L. casei clade, which also includes L. paracasei and L. zeae. It is a short Gram-positive homofermentative facultative anaerobic non-spore-forming rod that often appears in chains. Some strains of L. rhamnosus bacteria are being used as probiotics, and are particularly useful in treating infections of the female urogenital tract, most particularly very difficult to treat cases of bacterial vaginosis. The species Lacticaseibacillus rhamnosus and Limosilactobacillus reuteri are commonly found in the healthy female genito-urinary tract and are helpful to regain control of dysbiotic bacterial overgrowth during an active infection. L. rhamnosus sometimes is used in dairy products such as fermented milk and as non-starter-lactic acid bacterium (NSLAB) in long-ripened cheese. While frequently considered a beneficial organism, L. rhamnosus may not be as beneficial to certain subsets of the population; in rare circumstances, especially those primarily involving weakened immune system or infants, it may cause endocarditis. Despite the rare infections caused by L. rhamnosus, the species is included in the list of bacterial species with qualified presumed safety (QPS) status of the European Food Safety Agency.
Bacteroides is a genus of Gram-negative, obligate anaerobic bacteria. Bacteroides species are non endospore-forming bacilli, and may be either motile or nonmotile, depending on the species. The DNA base composition is 40–48% GC. Unusual in bacterial organisms, Bacteroides membranes contain sphingolipids. They also contain meso-diaminopimelic acid in their peptidoglycan layer.
Bacteroides fragilis is an anaerobic, Gram-negative, pleomorphic to rod-shaped bacterium. It is part of the normal microbiota of the human colon and is generally commensal, but can cause infection if displaced into the bloodstream or surrounding tissue following surgery, disease, or trauma.
Dysbiosis 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, with normally dominating species underrepresented and normally outcompeted or contained species increasing to fill the void. 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.
Veillonella are Gram-negative bacteria anaerobic cocci, unlike most Bacillota, which are Gram-positive bacteria. This bacterium is well known for its lactate fermenting abilities. It is a normal bacterium in the intestines and oral mucosa of mammals. In humans they have been implicated in cases of osteomyelitis and endocarditis, for example with the species Veillonella parvula.
Prevotella is a genus of Gram-negative bacteria.
Clostridium innocuum is an anaerobic, non-motile, gram-positive bacterium that reproduces by sporulation. While there are over 130 species of Clostridium, C. innocuum is the third most commonly isolated. Although it is not normally considered an aggressive human pathogen, it has been isolated in some disease processes. C. innocuum and other Clostridium line the oropharynx and gastrointestinal tract, and are considered normal gut flora.
Clostridium tertium is an anaerobic, motile, gram-positive bacterium. Although it can be considered an uncommon pathogen in humans, there has been substantial evidence of septic episodes in human beings. C. tertium is easily decolorized in Gram-stained smears and can be mistaken for a Gram-negative organism. However, C.tertium does not grow on selective media for Gram-negative organisms.
The microbiota are the sum of all symbiotic microorganisms living on or in an organism. The fruit fly Drosophila melanogaster is a model organism and known as one of the most investigated organisms worldwide. The microbiota in flies is less complex than that found in humans. It still has an influence on the fitness of the fly, and it affects different life-history characteristics such as lifespan, resistance against pathogens (immunity) and metabolic processes (digestion). Considering the comprehensive toolkit available for research in Drosophila, analysis of its microbiome could enhance our understanding of similar processes in other types of host-microbiota interactions, including those involving humans. Microbiota plays key roles in the intestinal immune and metabolic responses via their fermentation product, acetate.
Pharmacomicrobiomics, proposed by Prof. Marco Candela for the ERC-2009-StG project call, and publicly coined for the first time in 2010 by Rizkallah et al., is defined as the effect of microbiome variations on drug disposition, action, and toxicity. Pharmacomicrobiomics is concerned with the interaction between xenobiotics, or foreign compounds, and the gut microbiome. It is estimated that over 100 trillion prokaryotes representing more than 1000 species reside in the gut. Within the gut, microbes help modulate developmental, immunological and nutrition host functions. The aggregate genome of microbes extends the metabolic capabilities of humans, allowing them to capture nutrients from diverse sources. Namely, through the secretion of enzymes that assist in the metabolism of chemicals foreign to the body, modification of liver and intestinal enzymes, and modulation of the expression of human metabolic genes, microbes can significantly impact the ingestion of xenobiotics.
The human milk microbiota, also known as human milk probiotics (HMP), encompasses the microbiota–the community of microorganisms–present within the human mammary glands and breast milk. Contrary to the traditional belief that human breast milk is sterile, advancements in both microbial culture and culture-independent methods have confirmed that human milk harbors diverse communities of bacteria. These communities are distinct in composition from other microbial populations found within the human body which constitute the human microbiome.
Cetobacterium somerae is a microaerotolerant, Gram-negative, and rod-shaped anaerobic bacteria found in the gastrointestinal tract of fish living in freshwater ecosystems. The bacteria is also immobile and non-spore forming. C. somerae was first isolated from the feces of children with Autism spectrum disorder. Members of bacteria within the Cetobacterium genus tend to dominate the microbiota of fish in freshwater ecosystems. Cetobacterium somerae also produces vitamin B-12 within the gastrointestinal tract of fish in order to provide nutritional support for growth.
Bilophila wadsworthia is a Gram-negative, obligately anaerobic, catalase-positive, bile-resistant, and asaccharolytic bacillus. Approximately 75% of B. wadsworthia strains are urease positive. B. wadsworthia is linked to various diseases and is not well known due to frequent misidentification of the bacteria, and the National Center for Biotechnology Information is including it the phylum of Proteobacteria. The two unique characteristics of B. wadsworthia are the utilisation of the sulfated amino acid taurine in the production of hydrogen sulfide and the rapid catalase reaction. This bacterium is susceptible to the β-lactam antibiotics imipenem, cefoxitin, and ticarcillin.
Christensenella hongkongensis is a species of clinically relevant gram-positive coccobacilli, first isolated from patients in Hong Kong and Canada in 2006. Although the species remains relatively rare, it has a high mortality rate of up to 50%. Christensenella is thought to be broadly distributed globally, as it has been isolated from patient blood cultures around the world including Hong Kong, South Korea, New Zealand, Canada, Sweden, France and Italy. Fewer than 15 cases of C. hongkongensis have been observed worldwide.
