Pseudomonadota is a major phylum of Gram-negative bacteria. Currently, they are considered the predominant phylum within the realm of bacteria. They are naturally found as pathogenic and free-living (non-parasitic) genera. The phylum comprises six classes Acidithiobacilia, Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Hydrogenophilia, and Zetaproteobacteria. The Pseudomonadota are widely diverse, with differences in morphology, metabolic processes, relevance to humans, and ecological influence.
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.
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.
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.
Porphyromonas gingivalis belongs to the phylum Bacteroidota and is a nonmotile, Gram-negative, rod-shaped, anaerobic, pathogenic bacterium. It forms black colonies on blood agar.
Oral microbiology is the study of the microorganisms (microbiota) of the oral cavity and their interactions between oral microorganisms or with the host. The environment present in the human mouth is suited to the growth of characteristic microorganisms found there. It provides a source of water and nutrients, as well as a moderate temperature. Resident microbes of the mouth adhere to the teeth and gums to resist mechanical flushing from the mouth to stomach where acid-sensitive microbes are destroyed by hydrochloric acid.
Peptidoglycan recognition protein 1, PGLYRP1, also known as TAG7, is an antibacterial and pro-inflammatory innate immunity protein that in humans is encoded by the PGLYRP1 gene.
The Human Microbiome Project (HMP) was a United States National Institutes of Health (NIH) research initiative to improve understanding of the microbiota involved in human health and disease. Launched in 2007, the first phase (HMP1) focused on identifying and characterizing human microbiota. The second phase, known as the Integrative Human Microbiome Project (iHMP) launched in 2014 with the aim of generating resources to characterize the microbiome and elucidating the roles of microbes in health and disease states. The program received $170 million in funding by the NIH Common Fund from 2007 to 2016.
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.
Oral ecology is the microbial ecology of the microorganisms found in mouths. Oral ecology, like all forms of ecology, involves the study of the living things found in oral cavities as well as their interactions with each other and with their environment. Oral ecology is frequently investigated from the perspective of oral disease prevention, often focusing on conditions such as dental caries, candidiasis ("thrush"), gingivitis, periodontal disease, and others. However, many of the interactions between the microbiota and oral environment protect from disease and support a healthy oral cavity. Interactions between microbes and their environment can result in the stabilization or destabilization of the oral microbiome, with destabilization believed to result in disease states. Destabilization of the microbiome can be influenced by several factors, including diet changes, drugs or immune system disorders.
Prevotella is a genus of Gram-negative bacteria.
Porphyromonas is a Gram-negative, non-spore-forming, obligately anaerobic and non-motile genus from the family Porphyromonadaceae. There were 16 different Porphyromonas species documented as of 2015, which reside in both animal and human reservoirs. It was discovered more recently that Porphyromonas also exist in the environment, albeit to a lesser extent. This genus is notably implicated in the modulation of oral cavity, respiratory tract, and gastrointestinal tract disease states. It is suggested that Porphyromonas either operate as benign bacteria pertinent to host immunity or are potential pathobionts that opportunistically provoke diseased states when homeostasis is disrupted. Despite its characterization not being fully elucidated due to sparse research, various studies report the prevalence of this genus at 58.7% in healthy states compared with 41.3% in diseased states.
Tannerella forsythia is an anaerobic, Gram-negative bacterial species of the Bacteroidota phylum. It has been implicated in periodontal diseases and is a member of the red complex of periodontal pathogens. T. forsythia was previously named Bacteroides forsythus and Tannerella forsythensis.
The Lachnospiraceae are a family of obligately anaerobic, variably spore-forming bacteria in the order Eubacteriales that ferment diverse plant polysaccharides to short-chain fatty acids and alcohols (ethanol). These bacteria are among the most abundant taxa in the rumen and the human gut microbiota. Members of this family may protect against colon cancer in humans by producing butyric acid. Lachnospiraceae have been found to contribute to diabetes in genetically susceptible (ob/ob) germ-free mice.
Muribaculum is a genus from the family of Muribaculaceae, with one known species.
Parabacteroides is a Gram-negative, anaerobic, non-spore-forming genus from the family Tannerellaceae.
The salivary microbiome consists of the nonpathogenic, commensal bacteria present in the healthy human salivary glands. It differs from the oral microbiome which is located in the oral cavity. Oral microorganisms tend to adhere to teeth. The oral microbiome possesses its own characteristic microorganisms found there. Resident microbes of the mouth adhere to the teeth and gums. "[T]here may be important interactions between the saliva microbiome and other microbiomes in the human body, in particular, that of the intestinal tract."
Porphyromonas cangingivalis is a bacterium from the genus Porphyromonas which occur in the periodontal pockets of dogs. Porphyromonas cangingivalis can cause periodontitis in animals.
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.
The evolution of the human oral microbiome is the study of microorganisms in the oral cavity and how they have adapted over time. There are recent advancements in ancient dental research that have given insight to the evolution of the human oral microbiome. Using these techniques it is now known what metabolite classes have been preserved and the difference in genetic diversity that exists from ancient to modern microbiota. The relationship between oral microbiota and its human host has changed and this transition can directly be linked to common diseases in human evolutionary past. Evolutionary medicine provides a framework for reevaluating oral health and disease and biological anthropology provides the context to identify the ancestral human microbiome. These disciplines together give insights into the oral microbiome and can potentially help contribute to restoring and maintaining oral health in the future.
