free-living ameba (microscopic unicellular eukaryotic, organisms) most common in soil and water, that can cause rare, but severe infections of the eye, skin, and central nervous system. It can enter the eyes through contact lens use, cuts, or skin wounds or by being inhaled into the lungs. The three diseases caused by Acanthamoeba are:
Acanthamoeba keratitis – An infection of the eye that typically occurs in healthy persons and can result in permanent visual impairment or blindness.
Granulomatous Amebic Encephalitis (GAE) – A serious infection of the brain and spinal cord that typically occurs in persons with a compromised immune system.
Disseminated infection – An infection where the germ enters the body through a single entry point (a cut, wound, or through the nostrils) and then disperses throughout the body. This widespread infection that can affect the skin, sinuses, lungs, and other organs independently or in combination.  It is also more common in persons with a compromised immune system.

Acetobacter is bacteria converting alcohol to acetic acid and oxidizing lactate and acetate into carbon dioxide and water. 
It is used in the commercial production of vinegar, as fermentation starter cultures, and is found in gut microbiomes of some living organisms. 

Acetobacter aceti bacteria are a widespread group of gram-negative, obligate aerobic rods which oxidize ethanol (alcohol) into ethanoic (acetic) acid. They occur mainly in sugary, acidic and/or alcoholic surroundings and play a positive, neutral, or detrimental roles in food and beverages. It can be found in mangoes, bananas, sugar cane, sweet potato, coffee, cameroon grass, ragi, tea, pineapple, and mealy bugs. 

Several hundred mold species found in various climates worldwide. Belongs to Ascomycota (sac fungi) group. Common contaminants of starchy foods (such as bread and potatoes), and grow in or on many plants and trees. Aspergillus niger can be found growing on damp walls, as a major component of mildew. Aspergillus oryzae can be found in Japanese sake where it is used to break down the starches (rice, manioc) into simpler sugars. Some Aspergillus species are pathogenic. Aspergillus flavus produces aflatoxin which is both a toxin and a carcinogen, and which can contaminate foods such as nuts. The most common causing allergic disease are Aspergillus fumigatus and Aspergillus clavatus.

bacteria causing anthrax - common disease of livestock and, occasionally, of humans - and the only obligate pathogen (can't survive for long outside of the human body) within the genus Bacillus. it belongs to B.cereus family,  present in many types of soil, sediment and plants.
There are 89 known strains of B. anthracis.

Bacillus species are almost ubiquitous in nature, e.g. in soil, but also occur in extreme environments such as high pH (B. alcalophilus), high temperature (B. thermophilus), or high salt (B. halodurans). B. thuringiensis produces a toxin that can kill insects and thus has been used as insecticide.

a lactic acid-forming Firmicute bacteria that can cause milk to coagulate  and may play a role in food spoilage of highly acidic, tomato-based products.  It is often used as probiotic in veterinary applications, especially in pigs, cattle, poultry, and shrimp. There is evidence that B. coagulans may help humans to improve vaginal flora, reduce abdominal pain and bloating and increase immune response to viral challenges. It might be even beneficial in preventing cancer. Spore-forming strains of B. coagulans strains are used in some countries as probiotics for patients on antibiotics. 
Commercial probiotics with this bacteria include Ganeden BC30 (added to a variety of functional foods and beverages),  Nutribiome, Thorne Research, Schiff, Solaray and many other brands of probiotics. 

rod-shaped, Gram-positive  Firmicute bacteria naturally found in soil and vegetation.. Bacillus subtilis is a notable food spoiler, causing ropiness in bread and related food. It is known for its ability to form a small, tough, protective and metabolically dormant endospore.

Bacillus subtilis is currently used for oral bacteriotherapy and bacterioprophylaxis of gastrointestinal disorders (mostly as a direct result of antibiotic treatment), many of which lead to diarrhea, as an oral probiotic. Commercial B. subtilis probiotic preparations include Enterogermina and Biosubtyl. 

Ingestion of significant quantities of B. subtilis is thought to restore the normal microbial flora following extensive antibiotic use or illness (see this 1994 review). Probiotic preparations of B. subtilis are sold commercially in most European countries, although little is understood about how these bacteria exert their therapeutic benefit. B. subtilis is a gram-positive, nonpathogenic, spore-forming organism normally found in the soil, and the robustness of spores is thought to enable passage across the gastric barrier, where a proportion of spores germinate in the small intestine and populate, albeit briefly, the intestinal tract

A 1999 study found that two commercial preparations of probiotic bacteria purported to contain B. subtilis contain instead Bacillus species that are closely (Biosubtyl) and distantly (Enterogermina) related toB. subtilis. This finding is medically important and raises the question of whether any nonpathogenic, gram-positive microorganism can serve as a probiotic agent.

Bacteroidetes bacteria that is part of the normal flora of the human colon but can cause infection if it gets into bloodstream during surgery, disease, or trauma.
Bacteroides fragilis may prevent intestinal inflammatory disease as this 
bacteria produces Polysaccharide A (PSA), which suppresses the inflammatory response of the immune system (by suppressing IL-17 production). The combination of Bacteroides fragilis ATCC 25285, Clostridium difficile ATCC 700057 and Fusobacterium necrophorum ATCC 25286 produce odor associated with flatulence. 

Bacteroidetes is a diverse group of bacteria common in human gut, in marine and freshwater systems. Their levels rise as body weight is decreased. The name of this bacterial phylum changed several times over the past years and is also known as the Cytophaga–Flexibacter–Bacteroides (CFB) group. It includes four classes: Bacteroidia (858 strains), Flavobacteria (3583 strains), Sphingobacteria (787 strains), and Cytophagia (765 strains), and many unclassified strains representing around 7000 different species (NCBI, October 2010). They are non-motile, flagellated, or move by gliding.

Bacteroidetes in the gut are responsible for degradation of high molecular weight organic matter, i.e., proteins and carbohydrates. Their genomes appear to be highly plastic and frequently reorganized through genetic rearrangements, helping them to adaptation to distinct ecological niches.