School Science Lessons
2017-08-18 SP MF
Please send comments to: J.Elfick@uq.edu.au

Bacteria
9.7.0 Microbiology

Table of contents

4.0.0 Bacteria

4.0.1 Bacteria experiments

4.0.0 Bacteria
4.12.8 Acetic acid bacteria
Acetobacter genus
Actinomyces genus
4.17 Actinomycetes, Phylum: Actinobacteria, Order: Actinomycetales
19.3.11 Aflatoxin, Microbial contamination of food
Agrobacterium genus
4.1.8 Anaerobic chemotropic bacteria
4.1.2 Anoxygenic phototropic bacteria
9.5.7 Anti-microbial disinfectants affect growth of Escherichia coli
4.3.22 Antiseptics, Sensitivity of micro-organisms to antiseptics
Azotobacter genus
Bacillus genus, ("bacillus" is term for a genus and a basic shape)
4.03 Bacillus, Rod-shaped bacteria, bacillus
4.21 Bacteria, Archaeobacteria, Archaea
4.01 Bacteria classified by shape
4.06.0 Bacteria classified by diseases
1.2.0 Bacteria classified by phylum
4.3.0 Bacteria classified by physiology
19.3.14 Bacteria in food, the 2 hour and 4 hour rule
4.07 Bacteria in humans, bacterial diseases
2.1.11 Bacteria NOT suitable for use in schools
9.5.0 Bacterial infections, germ theory, Pasteur, Koch
9.1.2.5 Bacterial smear, Make a heat-fixed stained bacterial smear
Bacteroides genus
Bartonella genus
Bifidobacteria genus
4.12.9 Bioluminescent and related bacteria
9.2.0 Bti insecticide
4.23 Bordetella pertusssis
Borrelia genus
4.2.5 Budding bacteria / appendage bacteria., (stalked bacteria)
Campylobacter genus
Chlamydia genus
Clostridium genus
4.12.5 Colourless sulfur-oxidizing bacteria
4.24 Conjugation in bacteria, Escherichia coli
Corynebacterium genus
4.1.1 Cyanobacteria
4.12.4 Denitrifying bacteria, denitrifiers, denitrification
6.6.1 Different bacteria, (Primary)
9.2.32 DRBC, (food spoilage medium)
4.22 Endosymbionts
Enterococcus genus
Escherichia genus
Fusobacterium genus
Gardnerella genus
Gentamicin, C21H43N5O7
16.3.4.1b Geosmin, earth smells, rain smells and cut grass smells
3.11.0 Gram stain, Gram-negative, Gram-positive
4.1.5 Green nonsulfur bacteria
4.1.6 Green sulfur bacteria
4.1.7 Green, multicellular filamentous bacteria
Haemophilus genus
Helicobacter genus
4.12.6 Hydrogen-oxidizing bacteria
Lactobacillus genus
19.1.6.0 Leavening agents
Legionella genus
4.26 Lenski's experiments with Escherichia coli
Leptospira genus
Listeria genus
19.3.4.5 Meat, roasting meat
4.13 Methane-producing bacteria
4.12.7 Methanotrophs, methane to methanol
Micrococcus genus
Mycoplasma genus
4.19 Mycoplasmas
4.2.1 Myxobacteria
4.3.0 Micro-organisms
4.1.0 Microbiology cultures
2.1.0 Microbiology safety
9.1.2.0 Microbiology techniques
Micromonospora
16.1.10 Milk testing, Inhibitor test
16.1.11 Milk testing, Pasteurized milk test
Mycobacterium genus
Neisseria genus
4.12.1 Nitrifying bacteria, nitrification
Nitrobacter genus
6.39 Nitrogen cycle, (Primary)
4.12.3 Nitrogen-fixing bacteria
4.2.3 Nonphotosynthetic, non-fruiting gliding bacteria
4.1.0 Oxygenic phototropic bacteria
9.5.5 Pasteur's spontaneous generation experiment
Photobacterium genus
Pseudomonas genus
4.1.3 Purple sulfur bacteria
4.1.4 Purple nonsulfur bacteria
Ralstonia genus
Rhizobium genus
Rhodospirillum genus
4.18 Rickettsias and chlamydias
Salmonella genus
9.3.1 SCOBY, Symbiotic Colony Of Bacteria and Yeast
9.4.1 Sensitivity to drugs determined by genes
Serratia genus
4.2.4 Sheathed bacteria
Sisomicin, C19H37N5O7
4.1.6 Soil bacteria that decompose urea
6.0.16 Soil nitrogen bacteria, nitrogen-fixing bacteria, Rhizobium
4.2.7 Spiral and curved bacteria
Spirillum genus
4.06.9 Spirochaetae, spirochaete, (spirochete)
Staphylococcus genus
Streptobacillus genus
Streptococcus genus
Streptomyces genus
4.1.7 Streptomycin, Prepare streptomycin using Streptomyces griseus
4.2.2 Sulfate and sulfur-reducing proteobacteria
9.4.0 Sulfonamides, sulfa drugs
4.20 Sulfur-reducing bacteria
9.211.1 Teeth scrapings
Triponema genus
Vibrio, Comma-shaped bacteria
9.214 VRE bacteria, (Vancomycin Resistant Bacteria)
Xanthomonas genus
16.2.7 Yoghurt
9.3.0 Yoghurt and lactic acid bacteria

Escherichia genus
9.5.7 Anti-microbial disinfectants affect growth of Escherichia coli
4.07 Bacteria in humans, bacterial diseases
4.3.6 Breakdown of starch by micro-organisms
16.2.4 Cheese, (See 2.4, Rennet)
4.24 Conjugation in bacteria, Escherichia coli
10.10.3 Cystitis, "honeymoon disease", Escherichia coli

4.01 Bacteria classified by shape
4.02 Spherical cocci, (coccus)
4.03 Rod-shaped bacteria, bacillus
4.04 Spiral bacteria, spirillum, spirochete, vibrio

4.0.1 Bacteria experiments
4.24 Conjugation in bacteria, Escherichia coli
6.6.1 Different bacteria, (Primary)
4.3.5 Estimate bacteria in water
9.35 Succession in a pond community, hay infusion cultures, Protozoa
Microbiology
6.9.16.1 Rhizobium, root nodules in legumes, (Agriculture)
9.211.1 Teeth scrapings

3.11.0 Gram stain, Gram-negative, Gram-positive
3.11.0 Gram stain, microscopy stain
4.11 Gram negative anaerobic cocci
4.07 Gram negative aerobic rods and cocci
4.12.0 Gram negative chemolithotrophic bacteria
4.10 Gram negative cocci and coccobacilli
4.8 Gram negative facultative anaerobic rods
4.14 Gram positive cocci
4.15 Gram positive, endospore-forming rods and cocci
4.16 Gram positive, non-sporing rods, asporogenous

4.3.0 Bacteria classified by physiology
[Items 4.1.0 to 4.199 based on the David Bergey classification]
4.12.8 Acetic acid bacteria, mother of vinegar
4.17 Actinomycetes and related bacteria
4.12.9 Bioluminescent and related bacteria
4.2.5 Budding bacteria / appendage bacteria, (stalked bacteria)
4.12.5 Colourless sulfur-oxidizing bacteria
4.12.4 Denitrifying bacteria, denitrifiers, denitrification
4.2.0 Gliding bacteria, fruiting bacteria, leave visible trail of slime
4.11 Gram negative anaerobic cocci
4.7 Gram negative aerobic rods and cocci
4.12.0 Gram negative chemolithotrophic bacteria
4.10 Gram negative cocci and coccobacilli
4.8 Gram negative facultative anaerobic rods
4.14 Gram positive cocci
4.15 Gram positive, endospore-forming rods and cocci
4.16 Gram positive, non-sporing rods, asporogenous
4.12.6 Hydrogen-oxidizing bacteria
4.13 Methane-producing bacteria
4.12.7 Methanotrophs, (methane to methanol)
4.19 Mycoplasmas
4.12.1 Nitrifying bacteria, nitrification
4.12.3 Nitrogen-fixing bacteria
4.1.0 Oxygenic phototropic bacteria
4.18 Rickettsias and chlamydias
4.2.4 Sheathed bacteria
4.04 Spiral and curved bacteria, aerobic, motile, helical / vibrioid, Gram-negative

4.1.0 Oxygenic phototropic bacteria
4.1.0 Oxygenic phototropic bacteria
4.1.8 Anaerobic chemotropic bacteria
4.1.2 Anoxygenic phototropic bacteria, purple sulfur bacteria, internal sulfur granules
4.1.1 Cyanobacteria
4.1.5 Green nonsulfur bacteria
4.1.6 Green sulfur bacteria
4.1.7 Multicellular filamentous green bacteria
4.1.3 Purple sulfur bacteria, external sulfur granules
4.1.4 Purple nonsulfur bacteria

4.2.0 Gliding bacteria, fruiting bacteria, leave visible trail of slime
4.2.1 Myxobacteria
4.2.3 Nonphotosynthetic, nonfruiting gliding bacteria
4.2.2 Sulfate and sulfur-reducing proteobacteria
4.20 Sulfur-reducing bacteria
4.21 Archaeobacteria, Archaea [may also occur above]
4.23 Bordetella pertussis
4.22 Endosymbionts

Acetobacter, Phylum: Proteobacteria, Class: Alphaproteobacteria, Order: Rhodospirillales, Family: Acetobacteraceae
Acetobacter aceti, spoils beers and wines, oxidizes ethanol, producing acetic acid
4.12.8 Acetic acid bacteria
2.1.1 Fermentation, Safety in school science
4.2.4 Make wine from grape juice and vinegar from wine
16.3 Open a drinking coconut for coconut water, (See: 4.Acetobacter xylinum)
4.2.6 Prepare vinegar with Acetobacter aceti, (Experiment)
19.1.4 Prepare vinegar from wine, (See: 2.Acetobacter cerevisiae, 3. and 7.)
9.3.1 SCOBY, Symbiotic Colony Of Bacteria and Yeast

Actinomyces
Actinomyces, Phylum: Actinobacteria, Class: Actinobacteria, Order: Actinomycetales, Family: Actinomycetaceae
4.17 Actinomycetes, Phylum Actinobacteria, order Actinomycetales, (See: Actinomyces)
9.14.5 Compost inspection, (See: 4.)

Agrobacterium
Agrobacterium, Phylum: Proteobacteria, Class: Alpha Proteobacteria, Order: Rhizobiales, Family: Rhizobiaceae
Agrobacterium rhizogenes, pathogenic crown gall of peaches and roses
Agrobacterium rubi, pathogenic crown gall of grape
Agrobacterium tumefaciens, induces tumours in plants, non-pathogenic crown gall on base of stems or roots
4.7 Gram negative aerobic rods and cocci
4.12.3 Nitrogen-fixing bacteria
9.9.7 Nodules and galls
4.03 Rod-shaped bacteria, bacillus

Azotobacter
Azotobacter, Phylum: Proteobacteria, Class: Gammaproteobacteria, Order: Pseudomonadales, Family: Azotobacteraceae
Azotobacter vinclandii, free-living nitrogen fixer
4.03 Rod-shaped bacteria, bacillus
4.7 Gram negative aerobic rods and cocci
4.12.3 Nitrogen-fixing bacteria

Bacillus
Bacillus, Phylum: Firmicutes, Class: Bacilli, Order: Bacillales, Family: Bacillaceae
Bacillus ammoniagenes, bacteria from the colon reacts with ammonia from the urinary area to cause "nappy rash" in babies
Bacillus amylobacter, NOT suitable for use in schools
Bacillus anthracis, anthrax, in hoofed animals, rarely in humans as cutaneous anthrax black scab, (eschar), may become fatal,
NOT suitable for use in schools
Bacillus cereus, soil bacteria, may cause food poisoning, (enterotoxins), is NOT suitable for use in schools
Bacillus influenzae, (Haemophilus influenzae), first genome described of a free-living organism
Bacillus licheniformis, decomposes protein
Bacillus megaterium, produces lipase, protease and PHB, has specific cell size, suppresses fungus Rhizoctonia solani
Bacillus mycoides, has specific tendency to form colonies
Bacillus stearothermophilus, grows at 65oC
Bacillus subtilis, decomposes starch to produces amylase, lipase and protease, Suitable for school use, Used for biotechnology and
for teaching, suppresses the fungus Alternaria helianthi, seedling blight of sunflowers.
Bacillus subtilis produces the non-specific protease enzyme Subtilisin, serine endopeptidase, used in laundry powders and
dishwashing detergents, e.g. Clorox 2 laundry bleach.
4.03 Rod-shaped bacteria, bacillus
4.3.6 Breakdown of starch by micro-organisms, Bacillus subtilis
9.2.0 Bti insecticide, (mosquito control), Bacillus thuringiensis
4.1.1 Colonies of different micro-organisms, Bacillus subtilis
4.12.4 Denitrifying bacteria, denitrifiers, denitrification, Bacillus denitrificans
4.12.0 Gram negative chemolithotrophic bacteria
4.15 Gram positive, endospore-forming rods and cocci
6.5.0 Infectious diseases, (pigs), Bacillus anthracis
16.13.8.4 Integrated pest management, (IPM), (See 5. Biological control), Bacillus thuringiensis
7.1.3 Lactase, Bacillus subtilis
4.1.7 Prepare streptomycin using Streptomyces griseus
4.1.9 Presence of bactericidal substances using a coin and Bacillus mycoides
6.10 Preservatives or antimicrobials, (See 3.Propionates), Bacillus subtilis
4.3.22 Sensitivity of micro-organisms to antiseptics, Bacillus subtilis
4.1.8 Streptomycin on Bacillus subtilis using the small disc test
9.3.14 Tests for lipase activity, castor oil, milk, Bacillus subtilis

Bacteroides
Bacteroides, Phylum: Bacteroidetes, Class: Bacteroidetes, Order: Bacteroidales, Family: Bacteroidaceae
Many in colon.
Gram-negative, anaerobic, non-sporeforming bacteria.
Colitis and colon cancer.
4.06.2 Phylum: Bacteroidetes
Bacteroides fragilis
Bacteroides forsythus
Bacteroides thetaiotaomicron uses glycan metabolism in the colon to harvest additional energy from otherwise indigestible sugars,
e.g. galactose and mannose.

Bartonella
Bartonella, Phylum: Proteobacteria, Class: Alpha Proteobacteria, Order: Rhizobiales, Family: Bartonellaceae, insect vectors
Bartonella henselae, cat scratch fever.

Bifidobacteria
Bifidobacteria, Phylum: Actinobacteria, Class: Actinobacteria, Order: Bifidobacteriales, Family: Bifidobacteriaceae
Gram positive, non-sporeforming, lactic acid bacteria
Bifidobacterium bifidum, (Lactobacillus bifidus), "friendly" bacteria in intestine of breast-fed infants against pathogens, some
yogurts and probiotics.

Borrelia
Borrelia, Phylum: Spirochaetes, Class: Spirochaetes, Order: Spirochaetales, Family: Spirochaetaceae
Borrelia burgdorferi, carried by lice and ticks on mice and deer, causes relapsing fever and Lyme disease
Borrelia burgdorferi sensu stricto, North America,
B. garinii, and B. afzelii, Europe, all cause Lyme disease
Borrelia burgdorferi, (carried by tick Ixodes holocyclus in Australia)
Borrelia recurrentis, (louse-borne relapsing fever)
Borrelia hermsii / Borrelia duttoni / Borrelia parkeri, (tick-borne relapsing fever).

Campylobacter
Campylobacter, Phylum: Proteobacteria, Class: Epsilonproteobacteria, Order: Campylobacterales, Family: Campylobacteraceae
twisted, cork-screw
Campylobacter jejeuni, in contaminated food, (especially poultry), high fever, diarrhoea, gastroenteritis, distributed world wide.

Chlamydia
Chlamydia, Phylum: Chlamydiae, Class: Chlamydiae, Order: Chlamydiales, Family: Chlamydiaceae, (chlamidial infections)
10.9.1 Chlamydial pelvic inflammatory disease, (PID), Chlamydia trachomatis
4.18 Rickettsias and chlamydias
4.1.3 Chlamydia
Chlamydia trachomatis, causes 1. Chlamydial Pelvic Inflammatory Disease, PID
2. Trachoma, (Granular Conjunctivitis),
3. Lymphogranuloma venereum, (Climatic bubo), STI infection of lymph glands
Chlamydia suis, affects pigs
Chlamydia muridarum, affects mice
Chlamydia pneumoniae, atherosclerosis.

Clostridium
Clostridium, Phylum: Firmicutes, Class: Clostridia, Order: Clostridiales, Family: Clostridiaceae
Many species of Clostridium in bowel.
4.03 Rod-shaped bacteria, bacillus
4.12.0 Gram negative chemolithotrophic bacteria
4.15 Gram positive, endospore-forming rods and cocci
(1) Clostridium botulinum, soil or water bacteria, in improperly preserved food, causes botulism, food poisoning often from canned
food, destroyed by high temperature cooking, the toxin may affect central nervous system so it is a neurological disease.
Botulinum toxins are the most poisonous known substances for humans.
Clostridium botulinum, may cause sudden infant death syndrome.
(2) Clostridium sporogenes, a strain of Clostridium botulism does not produce botulism neurotoxins, and is often found in soil.
Recently, a New Zealand milk company announced the presence of Clostridium botulism in its milk powder to cause concern
and panic in countries that import milk products from New Zealand. However, the bacterium was in fact Clostridium sporogenes!

(3) Clostridium difficile, may colonize bowel, cause "antibiotic-induced diarrhoea" or pseudomembranous colitis, chief cause of
nosocomial, (hospital-acquired), diarrhoea
(4) 4.12.3 Clostridium pasteurianum, Nitrogen-fixing bacteria
(5) Clostridium perfringens, anaerobic soil bacteria, cause food poisoning and gas gangrene, (enterotoxin), is NOT suitable for use
in schools, commonly isolated from faeces
(6) Clostridium tetani, tetanus, (lockjaw), from infected wounds, toxin causes contraction of muscles, is NOT suitable for use in
schools, in normal bowel flora for up to 25% of population.

Corynebacterium
Corynebacterium, Phylum: Actinobacteria, Order: Actinomycetales, Family: Corynebacteriaceae
Consistent skin flora, may cause acne
Corynebacterium amycolatum, hospital-acquired endocarditis
Corynebacterium diphtheriae, diphtheria, formerly in normal flora before diphtheria toxoid, immunization

Enterococcus,
Enterococcus, Phylum: Firmicutes, Class: Bacilli, Order: Lactobacillales, Family: Enterococcaceae, (Aerococcus)
Enterococcus faecalis, (Streptococcus faecalis), intestinal flora, indicates faecal pollution, antibiotic resistant, hospital infection
9.214 VRE bacteria, (Vancomycin Resistant Bacteria), nosocomial, (hospital-acquired) infection
16.3.5.1 Aesculin, (Escalin), (identifies Enterococcus)

Escherichia
Escherichia, Phylum Proteobacteria, Class: Gammaproteobacteria, Order: Enterobacteriales, Family: Enterobacteriaceae
See diagram 9.3.70: T4 bacteriophage attacks Escherichia coli,
Escherichia coli, (Theodor Escherich, 1857-1911, Austria), pathogenic strains cause inflammation of urethra, (urethritis), and bladder,
(cystitis), "honeymoon disease", "traveller's diarrhoea", intestinal bacteria, food poisoning, certain strains cause gastroenteritis,
haemorrhage colitis, haemolytic uremic syndrome, neonatal meningitis.
Escherichia coli may release vitamin K and is an indicator for contamination by faeces.
Human faeces are 30% dry weight of dead bacteria.
Escherichia coli is used for genetic experiments on bacteria, Suitable for school use.

Fusobacterium
Fusobacterium, Phylum: Fusobacteria, Order: Fusobacteriales, Family: Fusobacteriaceae
Rod-shaped bacillus with pointed ends
Fusobacterium necrophorum
, Lemierre's syndrome, throat abscess
Fusobacterium nucleatum
Fusobacterium polymorphum

Gardnerella
Gardnerella, Phylum: Actinobacteria, Class: Actinobacteria, Order: Bifidobacteriales, Family: Bifidobacteriaceae
Gardnerella vaginalis, (Haemophilus vaginalis)
10.10.1 Bacterial vaginosis, Gardnerella vaginalis, non-specific vaginitis, (not associated with STDs), watery discharge

Helicobacter.
Phylum: Proteobacteria, Class: Epsilonproteobacteria, Order: Campylobacterales, Family: Helicobacteraceae
Helix shape, sheathed flagella, Gram-negative, enclosed within two membranes infects the mucus lining of the stomach and
duodenum causing peptic ulcers, gastritis, and duodenitis.
Helicobacter pylori, (Campylobacter pylori), causes ulcers in the gastric lining, stomach ulcers, peptic ulcers, enteritis, chronic
gastritis.

Haemophilus
Haemophilus, Phylum: Proteobacteria, Class: Gammaproteobacteria, Order: Pasteurellales, Family: Pasteurellaceae
Gram negative, coccobacillus
Haemophilus influenzae, (Pfeiffer's bacillus, Bacillus influenzae), secondary invader to viral influenza, meningitis in infants before
Hflu-type B vaccine.

Klebsiella
Klebsiella, Phylum: Proteobacteria, Class: Gammaproteobacteria, Order: Enterobacteriales, Family: Enterobacteriaceae, rod shape.
Klebsiella pneumoniae can produce Klebsiella Pneumoniae Carbapenemases, (KPC), that inactivate many types of antibiotics.
Carbapenems are a type of beta-lactam antibiotics.
An enzyme annuls the effectiveness of modern antibiotics and tends to infect patients who have experienced surgery or other invasive
procedures in hospitals.
Klebsiella pneumoniae causes inflammation of lungs, klebsiella pneumonia, urinary tract infections, and bacteremia.
Infections are difficult to treat and are often fatal.
Many strains of Klebsiella can fix nitrogen, i.e. they can reduce atmospheric nitrogen to ammonia and amino acids.

Lactobacillus
Lactobacillus, Phylum Firmicutes, Class: Bacilli, Order: Lactobacillales, Family: Lactobacillaceae
Lactobacillus, (over 120 species), converts lactose to lactic acid, in decaying plant substances, is benign in vagina and intestines,
extensively used as a leavening agent to make fermentation products.
Lactobacillus bulgaricus, is used to produce yoghurt, curds, ferments glucose and lactose to produce lactic acid.
Lactobacilli acid formation causing dental caries
Lactobacillus acidophilus, (Doderlein's bacillus), ferments glycogen in vaginal epithelium to low pH lactic acid against pathogens.
16.1.5 Acidity test
16.2.3 Butter and butter oil
16.2.4 Cheese
16.2.9 Cream
9.212 Ginger beer "plant"
4.16 Gram positive, non-sporing rods
16.1.10 Inhibitor test
16.1.5.1 Lactic acid, 2-hydroxypropanoic acid, C3H6O3
Lactic acid in milk digestion
19.1.6.0 Leavening agents
4.2.3 Prepare lactic acid with sourdough
4.2.1 Prepare yoghurt
4.3.17 Prepare yoghurt, test milk quality
16.1.6 Resazurin microscopy stain, test for milk
9.3.1 SCOBY, Symbiotic Colony Of Bacteria and Yeast
9.3.0 Yoghurt and lactic acid bacteria "Yakult"
16.2.7 Yoghurt

Legionella
Legionella, Phylum: Proteobacteria, Class: Gammaproteobacteria, Order: Legionellales, Family: Legionellaceae
Legionella pneumophila, (Legionnaires' pneumonia).

Leptospira
Leptospira, Phylum: Spirochaetes, Class: Spirochaetes, Order: Spirochaetales, Family: Leptospiraceae
Leptospira species causes leptospirosis
Leptospira interrogans.

Listeria
Listeria, Phylum: Firmicutes, Class: Bacilli, Order: Bacillales, Family: Listeriaceae
Listeria monocytogenes, an intracellular pathogen, causes listeriosis, affecting people with weakened immune systems, especially
dangerous for the elderly, pregnant women and diabetics, causes fever, headache, tiredness, cramps, diarrhoea, nausea and
premature birth.
However, healthy people may not be affected.
Listeria infection may be caused by contamination of raw milk and processed milk products
4.16 Gram positive, non-sporing rods
4.07 Bacteria in humans, bacterial diseases.

Mycobacterium
Mycobacterium, Phylum: Actinobacteria, Order: Actinomycetales, Suborder: Corynebacterineae, Family: Mycobacteriaceae
Mycobacterium leprae, Hansen's disease, (leprosy), affects skin, mucous membranes, nerves to cause skin numbness and lumps,
deformed limbs.
Mycobacterium tuberculosis, contagious lung infection that can spread to other tissues, (TB)
4.17 Actinomycetes and related bacteria
3.12 ZiehlNeelsen stain, (acid-fast stain).

Micrococcus
Micrococcus, Phylum: Actinobacteria, Order: Micrococcales, Family: Micrococcaceae
Micrococcus luteus, (Sarcina lutea), has yellow colonies, specific colony colour, Suitable for school use
4.12.4 Denitrifying bacteria, denitrifiers, denitrification, Micrococcus denitrificans.

Micromonospora
Micromonospora, Phylum: Actinobacteria, Order: Actinomycetales, Family: Micromonosporaceae
Micromonospora echinospora, produces the antibiotic extremely toxic calicheamicins, which may be used as an anti-cancer
drug because it target DNA, causing strand scission
Micromonospora inositola, produces the antibiotic sisomicin
Sisomicin, C19H37N5O7, antibiotic
Micromonospora inyonensis, produces the antibiotics mutamicin, netilmicin, sisomicin
Micromonospora purpureochromogenes, produces the antibiotic gentamicin.

Gentamicin, C21H43N5O7, amminoglycoside from fermentation of Micromonospora purpurea or M. echinospora, inhibits protein
synthesis, antimicrobial against strains of Pseudomonas, Proteus, Staphylococcus, Streptococcus, however may be nephrotoxic
Gentamicin C, aminoglycoside from Gram-negative bacteria, prevents protein synthesis, growth of mycoplasma
Gentamicin sulfate, broad spectrum antibiotic

Neisseria
Neisseria, Phylum: Proteobacteria, Class: Betaproteobacteria, Order: Neisseriales, Family: Neisseriaceae
Gram negative cocci, often in pharynx.
Neisseria meningitidis, meningococcal meningitis
10.9.5 Gonorrhoea, urethral / vaginal discharge, "the clap", Neisseria gonorrhoeae.

Nitrobacter
Nitrobacter, Phylum: Proteobacteria, Class: Alpha Proteobacteria, Order: Rhizobiales, Family: Bradyrhizobiaceae
Nitrobacter winogradskyi, Nitrococcus mobilis, Nitrospira, oxidize the nitrite to nitrate and so are called "true nitrifying
bacteria" or "nitrate producing bacteria".
Nitrobacter oxidizes nitrite to nitrate.
Nitrobacter, oxidation of the nitrites into nitrates, NO3-, nitrification.
2HNO2 + O2 + Nitrobacter --> 2HNO3 + energy
NO2- + O2 --> NO3-.

Nitrosomonas
Nitrosomonas, Phylum: Proteobacteria, Class: Beta Proteobacteria, Order: Nitrosomonadales, Family: Nitrosomonadaceae
Nitrosomonas europaea, Nitrosococcus oceani, Nitrosolobus multiformis, Nitrosospira, Nitrosovibrio
Nitrosomonas converts ammonia to nitrites, NO2-, nitrification.
Aerobic Gram-negative bacteria reduce inorganic nitrogen compounds.
Nitrosomonas, Nitrosolobus, Nitrosococcus oxidize ammonia and ammonia compounds to nitrous acid and are called nitrosifyers.
2NH3 + 3O2 + Nitrosomonas europaea --> 2HNO2 + 2H2O + energy
nitrous acid + bases --> nitrates.

Nostoc
Nostoc, Phylum: Cyanobacteria, Class: -, Order: Nostocales, Family: Nostocaceae, "star jelly"
Blue-green algae Phylum Cyanidophyta, Nostoc azollae
Anabaena azollae lives in symbiosis with the free-floating water-fern, Azolla filiculoides, (Division: Pteridophyta).
The Azolla symbiosis has been used to sustain agricultural productivity in south-east Asia for over a thousand years.

Proteus vulgaris NOT suitable for use in schools.

Pseudomonas
Pseudomonas, Phylum: Proteobacteria, Class: Gammaproteobacteria, Order: Pseudomonadales, Family: Pseudomonadaceae
Pseudomonas acruginosa, is NOT suitable for use in schools
9.5.8 Pseudomonas aeruginosa, is NOT suitable for use in schools, soil bacteria, food poisoning, infections, e.g. burns, urinary
and respiratory tract, hospital-acquired infection
4.12.6 Pseudomonas carboxydororans, hydrogen oxidizing bacteria
Pseudomonas fluorescens, fluorescent, decomposes gelatine, floating mats of bacteria
4.1.7 Prepare streptomycin using Streptomyces griseus, (See: Pseudomonas fluorescens)
Pseudomonas solanacearum, is NOT suitable for use in schools,
Pseudomonas syringae, bacterial gall on oleanders and lilac, angular leaf spot on cucurbits, e.g. cucumbers, halo blight of beans
Pseudomonas tabacci, NOT suitable for use in schools
Pseudomonas tumefaciens, crown gall organism.

Ralstonia
Ralstonia, Phylum: Proteobacteria, Class: Beta Proteobacteria, Order: Burkholderiales, Family: Ralstoniaceae
14.4 Comparing bacterial wilt and fusarium wilt, (in bananas).

Rhizobium
Rhizobium, Phylum: Proteobacteria, Class: Alphaproteobacteria, Order: Rhizobiales, Family: Rhizobiaceae
Rhizobium leguminosarum, used to study symbiotic nitrogen fixation in nodules on legume roots,
9.70 Rhizobium in legumes
4.13 Rhizobium, nitrogen-fixing bacteria, (root nodules)
Nitrogen-fixing bacteria fix aerobic nitrogen into combined nitrogen in the soil that is available to plants by combining gaseous
nitrogen with carbon and hydrogen to make organic molecules.
Many organic molecules come from bacterially fixed nitrogen.
Rhizobium radicicola enters the root hairs of some legumes and
pass to the root cortex where nodules form.
The fixed nitrogen compounds in the root nodules are available to other plants when the first plant dies.
The strain of rhizobium found in peas, beans and clover has cilia over the whole cell.
The strain of Rhizobium found in cowpea, peanut and Cassia has a single cilium at one end.
Seeds of legume crops, e.g., alfalfa, beans, clovers, peas, soybeans may be inoculated with cultures of Rhizobium to increase yield.

Rhodospirillum
Rhodospirillum, Phylum: Proteobacteria, Class: Alphaproteobacteria, Order: Rhodospirillales, Family: Rhodospirillaceae
Gram-negative, pink-coloured nitrogen-fixing bacteria rods
Rhodospirillum rubrum, Suitable for school use.

Rickettsia
Rickettsia prowazeki, the body louse, Pediculus humanus corporis, may carry typhus, (Rickettsia prowazeki), trench fever,
(Rochalimaea quintana), and relapsing fever, (Borrellia recurrentis).

Salmonella
Salmonella, Phylum: Proteobacteria, Class: Gammaproteobacteria, Order: Enterobacteriales, Family: Enterobacteriaceae
Salmonella typhi / Salmonella paratyphi, cause typhoid fever / paratyphoid fever, intestinal gastroenteritis and gall bladder
infections, enlarged spleen, infection caused by contaminated food, and infected raw eggs
Salmonella enterica, Serotype Typhimurium DT 104.

Serratia
Serratia, Phylum: Proteobacteria, Class: Gamma Proteobacteria, Order: Enterobacteriales, Family: Enterobacteriaceae
Rod-shaped Gram-negative bacteria, grows as pink slime in bathrooms
Serratia marcescens is NOT suitable for use in schools
4.1.9 Presence of bactericidal substances using a coin and Bacillus mycoides.

Spirillum
Spirillum, Phylum: Proteobacteria, Class: Betaproteobacteria, Order: Nitrosomonadales, Family: Spirillaceae
The 3 basic bacterial cell shapes are coccus, bacillus and spirillum.
Spirillum minus caused rat-bite fever.

Staphylococcus
Staphylococcus, Phylum: Firmicutes, Class: Bacilli, Order: Bacillales, Family: Staphylococcaceae
Staphylococcus albus, (S. epidermis), forms white colonies and is suitable for school use.
Staphylococcus aureus, ("golden staph"), transmitted from the nasal membranes, Gram-positive, golden yellow clusters,
non motile, nonsporeforming facultative anaerobe, common parasite of human and animals, produces several enterotoxins, food
poisoning, (vomiting and diarrhoea), pyrogenic and respiratory infections, toxic shock syndrome, is NOT suitable for use in schools
Indigenous Australians continue to live in conditions of socio-economic disadvantage reflected by a life expectancy 17 years less
than non indigenous Australians, (Australian Institute of Health and Welfare, Australian Bureau of Statistics, 2009).
This disparity is caused by infectious disease.
At Alice Springs Hospital Staphylococcus aureus is the most common pathogen isolated from blood cultures.
This bacterium is associated with serious metastatic complications including infective endocarditis and has a mortality rate approaching
90% if left untreated.

Streptobacillus
Streptobacillus, Phylum Fusobacteria
Rods in chains
Streptobacillus moniliformis
, Rat-bite fever, Haverhill fever.

Streptococcus
Streptococcus, Phylum: Firmicutes, Class: Bacilli, Order: Lactobacillales, Family: Streptococcaceae
Methicillin-resistant Staphylococcus aureus, (MRSA), strain, hospital-acquired resistance to certain antibiotics
Streptococcus mutans, primary bacterium for plaque formation to cause tooth decay.
It needs both glucose and fructose from
the breakdown of sucrose in food and soft drinks to produce plaque and lactic acid
Streptococcus faecalis and Streptococcus faecium, (enterococci), are intestinal bacteria, but live also on plants.
They are indicators of insufficient hygiene, and, together with Escherichia coli, indicate the presence of faecal material
Streptococcus faecalis, (Enterococcus faecalis), Streptococcus lactis, (Lactococcus), sours milk
Streptococcus mutans, and other oral bacteria in dental plaque on teeth, produce acids that dissolve tooth enamel leading to
cavities, (caries), infection of the tooth pulp, (pulpitis), infection of the gum, (gingivitis), infection of the gums and bone,
(peridontitis) Vincent's disease, (ulcerative gingivitis, trench mouth)
Streptococcus mutans, Streptococcus pneumoniae, Streptococcus pyrogenes, Streptococcus thermophilus, ferments
glucose and lactose at 50oC.
Streptococcus pneumoniae, common in upper respiratory tract, invades the lower respiratory tract to cause bacterial
pneumonia, sinusitis, laryngitis, bronchitis, inflammation of the lungs, also, streptococcal meningitis, otitis media.
Streptococcus pyrogenes, inflammation of the throat, sore throat, tonsillitis, ("strep throat"), scarlet fever, necrotizing fasciitis,
(GAS), streptococcal toxic shock syndrome.
Some streptococcal diseases can cause rheumatic fever or nephritis to damage the heart and kidney.
Streptococcus salivarius subsp. thermophilus is used for yoghurt production, with Lactobacillus bulgaricus
Lactobacillus acidophilus occurs naturally in the human gastrointestinal tract, mouth and vagina, and may be used with
Streptococcus salivarius, (subsp. thermophilus), and with Lactobacillus delbrueckii, (subsp. bulgaricus), to produce
acidophilus-type yoghurt.
Leuconostoc citrovorum with Streptococcus lactis convert lactic acid to aldehydes and ketones to produce buttermilk with its
characteristic flavour and aroma.

Streptomyces
Streptomyces, Phylum: Actinobacteria, Class: Actinobacteria, Order: Actinomycetales, Family: Streptomycetaceae
4.1.7 Prepare streptomycin using Streptomyces griseus
Streptomyces bacteria grow in damp soil and form a dust of spores when the soil becomes dry.
When rain hits the dry ground, an aerosol of water and soil can be breathed in to cause the "rain smell", "earth smell", from the terpene
geosmin, C12H22O, produced by Streptomyces antibioticus and Streptomyces coelicolor.
Streptomyces antibioticus, Streptomyces griseus, earth odour of soil, produces streptomycin antibiotic.
Streptomyces scabies, common scab of potatoes, turnips, beetroot, "potato scab".
Steptomyces kanamycetius, amikacin hydrate, C22H43N5O13.xH2O, aminoglycoside broad spectrum antibiotic

Treponema
Treponema, Phylum: Spirochaetes, Class: Spirochaetes, Order: Spirochaetales, Family: Spirochaetaceae
Treponema carateum, (Pinta)
Treponema denticola
Treponema pallidum subspecies, which cause treponematoses, e.g. syphilis, yaws
10.5.12 Syphilis, Treponema pallidum.

Vibrio
Vibrio, Phylum: Proteobacteria, Class: Gammaproteobacteria, Order: Vibrionales, Family: Vibrionaceae
Vibrio cholerae, Vibrio fischeri is NOT suitable for use in schools.
Vibrio cholerae, causes cholera, intestinal infection, diarrhoea, severe dehydration, infected from water contaminated with
human faeces, cholera enterotoxin causes life-threatening diarrhoea.
Vibrio natriegens, (Beneckea natriegens), needs sodium chloride, used to study growth of micro-organisms.
Vibrio parahaemolyticus is a marine bacteria, in guts of fishes, causes food-borne disease, gasteroentritis, from raw sea food
Vibrio vulnificus, wound infection, septicemia, gastrointestinal disease.

Xanthomonas
Xanthomonas, Phylum: Proteobacteria, Class: Gamma Proteobacteria, Order: Xanthomonadales, Family: Xanthomonadaceae
Xanthomonas campestris
Xanthomonas phaseoli is NOT suitable for use in schools

Yersinia
Yersinia, Phylum: Proteobacteria, Class: Gammaproteobacteria, Order: Enterobacteriales, Family: Enterobacteriaceae
Yersinia pestis causes plague, bubonic plague, fever, swelling of lymph nodes, (buboes), that burst releasing pus or bleed under
the skin.
The black death was caused by strains of the bacterium Yersinia pestis identified by analysis of ancient DNA obtained from bodies of
plague victims in England, France, Germany, Italy and the Netherlands.
Yersinia enterocolitica, water and food borne pathogen, found especially in pork.

4.01 Bacteria classified by shape
The 3 basic bacterial cell shapes are coccus, bacillus and spirillum, spiral bacteria.

4.02 Spherical cocci, (coccus)
Diplococci, (Pneumococcus), streptococci, stapylococci, sarsina, tetrad, round, ovoid
| Chlamydia, Chlamydophila psittaci, (Psittacosis) | Diplococcus |
| Enterococcus 9.214 VRE bacteria, (Vancomycin Resistant Bacteria) |
| Gonococcus 10.9.5 Gonorrhoea, Neisseria gonorrhoeae |
|
Nitrococcus | Staphylococcus | Streptococcus |.

4.03 Bacillus
Rod-shaped bacillus
"Bacillus" is a genus of bacteria, but "bacillus", or plural "bacilli", is any rod-shaped bacterium.
For some people, "bacillus" means any pathogenic bacterium.
"Coccobacillus" and "coccobacilli" are short rods.
| Agrobacterium | Azotobacter |
| Bacillus | Bacterium termo | Bacterium vermiforme | Brevibacterium vermiforme |
| Bordetella, (coccobacilli), | Brucella, (coccobacilli), | Clostridium | Corynebacterium |
|Escherichia | Francisella, (coccobacillus), | Haemophilus, (coccobacillus) |
| Legionella | Listeria | Mycobacterium | Mycoplasma, (changes shape) |
| Neisseria, (bean-shape), | Nitrobacter | Nitrosomonas | Nostoc |
| Pseudomonas | Rickettsia | Rhizobium | Salmonella | Shigella | Yersinia |.

4.04 Spirillum, spirochete, vibrio
Spiral bacteria, spirillum, spirochete, vibrio
1. Spirillum, (helical-shape), Campylobacter jejuni, pathogen in food , | Helicobacter pylori, stomach ulcer, (peptic ulcer)
2. Spirochete, Family Spirochaetes | Leptospira, Weil's disease | Treponema, syphilis,yaws | Borrelia, Lyme disease |
3. Vibrio, (comma shape, slight twist) | Vibrio cholera | Nitrobacter | Nitrosomonas | Pseudomonas |
4.06.0 Bacteria classified by diseases

4.06.1 Actinomycetes
Phylum Actinobacteria, Actinomycetes, are pathogens found in soils
Corynebacterium michiganense bacterial canker of tomato, Solanum tuberosum
Actinobacteria, Actinomycetales, Micromonosporaceae
Micromonospora.

4.06.2 Bacteroidetes
 Phylum: Bacteroidetes
Pathogens in the human mouth
Bacteroides
Capnocytophaga, Class: Flavobacteria, Order: Flavobacteriaceae, Family: Flavobacteriaceae
Capnocytophaga canimorsus, commensal, from dog bites
Porphyromonas, Class: Bacteroidetes, Order: Bacteroidales, Family: Porphyromonadaceae
Porphyromonas gingivalis, peridontal disease
Prevotella, Order: Bacteroidales, Family: Prevotellaceae, in gut and vagina, peridontal disease
Prevotella intermedia

4.06.3 Chlamydiaceae
Phylum: Chlamydiae, Order: Chlamydiales, Family: Chlamydiaceae
Chlamydia
Chlamydophila psittaci, (Psittacosis), Chlamydophila pneumoniae

4.06.4 Chlorobacteria
 Phylum Chloroflexi, Chlorobacteria, Green non-sulfur bacteria, photosynthetic bacteria.

4.06.5 Cyanobacteria
Phylum Cyanobacteria are the "blue-green algae".
Unicellular, filamentous, colonial, photosynthetic, nitrogen-fixing bacteria, pigments, (cyanophycin, allo-phycocyanine and
erythro-phycocyanine), algal blooms
Nostoc pruniforme, forms colonies, green-grey, gelatinous spheres
Cylindrospermum, filamentous
The pigment chlorophyll a, (C55H72O5N4Mg), occurs in in plants, algae, and cyanobacteria.

4.06.6 Fusobacteria
Fusobacterium, Phylum: Fusobacteria, Order: Fusobacteriales, Family: Fusobacteriaceae, Genus: Fusobacterium
Fusobacteria, Gram-negative pathogens, cause skin ulcers.

4.06.7 Planctomycetes
Phylum Planctomycetes
Ovoid, budding with holdfast, aquatic bacteria.

4.06.8 Proteobacteria
Phylum Proteobacteria are pathogens
Burkholderia pseudomallei, causes melioidosis disease often occurs after floods in tropical areas
Pseudomonas syringae, causes bacterial blight of mulberry and pea, bacterial brown spot of bean, bacterial canker of stone fruit
Ralstonia solanacearum, causes bacterial wilt disease in bananas
Xanthomonas campestris, bacterial black spot of mango, cucurbits, e.g. cucumbers

4.06.9 Spirochaetae
 Phylum: Spirochaetae, Class: Spirochaetes, Order: Spirochaetales, spirochaete, (spirochete), corkscrew shape
Family Brevinemataceae, Brevinema
Family Brachyspiraceae, Brachyspira pilosicoli, Brachyspira aalborgi, intestinal spirochaetosis
Family Leptospiraceae, Leptospira
Family Spirochaetaceae, Borrelia, Spirochaeta, Treponema.

4.07 Bacteria in humans, bacterial diseases
See diagram 9.205: A bacterium | See diagram 9.205.1: Different bacteria
In the healthy person both the human genome and the microbiome, (of bacteria), contribute to metabolic pathways
Bacteria contribute to the health of a person in the following ways:
1. Toxin degeneration
2. Micronutrient synthesis
3. Glycan and amino acid metabolism
Microorganisms are used to make foods, e.g. yoghurt and cheese.
Other microorganisms "spoil" food, given the appropriate conditions such as temperature, pH and moisture.
Microbial contamination accounted for 34% of all food recalls by Food Standards Australia New Zealand, (FSANZ), between
1 January 1990 and 31 December 2004.
Of these recalls, 41% were due to Listeria monocytogenes contamination; 19% were due to Salmonella contamination and 13%
were from Escherichia coli contamination.
Those most affected by food poisoning are the elderly, the young and immune suppressed individuals
Bacterial diseases
Actinomycosis, Anthrax, Bartonellosis, Brucellosis, Buruli ulcer, Campylobacter enteritis, Cat-scratch disease,
Chancroid, Conjunctivitis / Keratitis, Diarrhoea disease, Diphtheria, Ehrlichioses, Gonococcus infections, Granuloma inguinale,
Leprosy, Leptospiros, Listeriosis, Melioidosis, Meningitis, Mycetomix, Nocardiosis, Parapertussis, Plague, Pneumonia,
Rat bite fever, Rickettsioses, Salmonellosis, Shigellosis, Trench fever, Tuberculosis, Tularemia, Typhoid fever, Vibrio cholera,
Yersiniosis.

4.1.0 Oxygenic phototropic bacteria
Purple phototropic bacteria get their energy from light but do not give off oxygen.
They have their own type of chlorophyll and carotenoid pigments.
Purple sulfur bacteria normally respire anaerobically and oxygen hinders their growth. They use hydrogen sulfide in an aquatic habitat
that has light but no oxygen.

4.1.1 Cyanobacteria
Anabaena, Calothrix, Chamaespiphon, Cyanothece, Gloeobacter, Gloeocapsa, Gloethece, Microcystis, Myxobaktron,
Nodularia, Nostoc, Oscillatoria, Pleurocapsa, Prochlorothrix, Scytonema, Spirulina, Stigonema, Synechococcus,
Synechocystis, Trichodesmium


4.1.2 Anoxygenic phototropic bacteria
These purple sulfur bacteria, have internal sulfur granules
Chromatium okenii, photosynthetic sulfur bacteria that deposit sulfur outside the cells
Amoebobacter, Lamprobacter, Lamprocystis, Thiocapsa, Thiocystis, Thiodictyon, Thiopedia, Thiospirillum.

4.1.3 Proteobacteria, Gammaproteobacteria
Purple sulfur bacteria, Phylum: Proteobacteria, Class: Gammaproteobacteria, Order: Chromatiales
Convert H2S --> S
Family Chromatiaceae
Family Ectothiorhodospiraceae
Ectothiorhodospira mobilis are photosynthetic sulfur bacteria that deposit sulfur outside the cells
Family Granulosicoccaceae
Family Halothiobacillaceae.

4.1.4 Proteobacteria, Alphaproteobacteria
Purple nonsulfur bacteria, Phylum: Proteobacteria, Class: Alphaproteobacteria, Order: Rhodospirillales,
Family: Rhodospirillaceae
They are mostly anaerobic and do not use hydrogen sulfide.
They are rods, curved rods, ovoid, flagellated, ring shape or spiral shape and are used to treat odorous swine wastewater.
Rhodobacter adriaticus, Rhodomicrobium, Rhodopila, Rhodospirillum rubrum, Rhodopseudomonas capsulata, Rhodyclus.

4.1.5 Chlorobacteria
Green nonsulfur bacteria
Phylum Chloroflexi, Chlorobacteria, Green non-sulfur bacteria, photosynthetic bacteria
Heliobacillus, Heliobacterium.

4.1.6 Green sulfur bacteria
Anacalochloris, Chlorobium, Chloroherpeton, Pelodictyon, Prosthecochloris.

4.1.7 Multicellular filamentous green bacteria
Chloroflexus, Chloronema, Heliothrix, Oscillochloris.

4.1.8 Anaerobic chemotropic bacteria
Erythrobacter.

4.2.1 Myxobacteria
Myxobacteria form rod-shape aggregates to form fruiting bodies when nutrients are low.
Chondromyces crocatus, Mellitangium erectum, Myxococcus stipitatus.

4.2.2 Sulfate and sulfur-reducing proteobacteria
They are sulfur or sulfate reducers, anaerobic, and live in an oxygen free aquatic habitat.
Desulfomaculum is soil dwelling and causes tinned meat spoilage called "sulfide stinker".

4.2.3 Nonphotosynthetic, nonfruiting gliding bacteria
Archangium, Cytophaga, Leucothrix, Lysobacter, Pelonema, Simonsiella, Sorangium, Thermonema
Beggiatoa is a filamentous gliding bacterium that oxidizes sulfur compounds in sulfur springs, sewage works and hydrothermal
vents, rotting seaweed, and the surface of plant roots in swamps.

4.2.4 Sheathed bacteria
They live within a sheath that becomes a tube, and are found in sewage works, and the blooms in autumn leaves
Clonothrix, Crenothrix, Leptothrix, Sphaerotilus.

4.2.5 Budding bacteria / appendage bacteria, (stalked bacteria)
They have extensions, (prosthecae), involved in reproduction
Blastobacter, Caulobacter, Gallionella, Gemmata, Kuznezovia, Metallogenium.

4.2.7 Spiral and curved bacteria
They are aerobic, motile, helical / vibrioid, Gram-negative.
Alteromonas, Aquaspirillum, Azospirillum, Campylobacter, Cellvibrio, Halovibrio, Helicobacter, Herbaspirillum,
Marinomonas, Micavibrio, Oceanospirillum, Spirillum, Sporospirillum, Vampirovibrio

Bdellovibrio are predators on other bacteria and are less than a tenth of their size
Helicobacter
Nonmotile Gram-negative curved bacteria
Ancyclobacter, Brachyarcus, Cyclobacterium, Flectobacillus, Meniscus, Microcyclus, Pelosigma, Runella, Spirosoma
Campylobacter jejeuni, in contaminated food, (especially poultry), causes high fever, diarrhoea.

4.7 Gram negative aerobic rods and cocci
Acidiphilium, Acidomonas, Acidothermus, Acinetobacter, Afipia, Agrobacterium, Agromonas, Alcaligenes, Aminobacter,
Azotobacter, Beijerinckia, Bordetella, Bradyrhizobium, Brucella, Chromohalobacter, Chryseomonas, Comoamonas,
Cupriavidas, Deleya, Derxia, Ensifer, Erythrobacter, Flavimonas, Flavobacterium, Francisella, Frateuria,
Gluconobacter, Halobacterium, Halococcus, Halomonas, Hydrogenophaga, Janthinobacterium, Lampropedia,
Legionella, Marinobacter, Mesophilobacter, Methylobacillus, Methylobacterium, Methylophaga, Methylophilus,
Methylovorus, Moraxella, Morococcus, Oligella, Phenylobacterium, Phyllobacterium, Psychrobacter, Rhizobacter,
Roseobacter, Rugamonas, Serpens, Sinorhizobium, Sphingobacterium, Thermoleophilum, Thermomicrobium, Thermus,
Variovorax, Volcaniella, Weeksella, Xanthanomonas, Xanthobacter, Xanthomonas, Xylella, Xylophilus, Zoogloea.

Free-living anaerobic nitrogen fixers live in soil or water and combine gaseous nitrogen with carbon and hydrogen to make
organic molecules.
Many organic molecules come from bacterially fixed nitrogen, e.g. Azotobacter, Azomonas, Azospirillum, Beyerinckia.
Some are free-living inside animals and cause disease, e.g. Neisseria, Kingella, Moraxella, Acinetobacter.
The enteric bacteria, Brucella abortus and Brucella melitensis cause spontaneous abortion, (cattle), Brucellosis, (milk or meat
from infected animals).
Coliformes intestinal bacteria, contamination by faeces, (lakes, rivers, swimming pools)
Enterobacteria intestinal bacteria, contamination of food, insufficient pasteurization and sterilization, recontamination
Escherichia
Helicobacter
Ancylobacter is a ring-shaped bacterium.
Magnetospirillum magnetobacterium is a curved rod-shaped bacterium containing magnetic particles, magnetite Fe3O4,
or greigite Fe3S4.
Neisseria
Xanthomonas campestris causes bacterial leaf spot on cucurbits, e.g. cucumbers, and lettuce, pelagoniums, black rot of
crucifers, angular leaf spot of zinnia.

4.8 Gram negative facultative anaerobic rods
Cardiobacterium hominis causes endocarditis.
Enterobacter causes urinary infections.
Klebsiella
Klebsiella pneumoniae
Proteus causes urinary infections.
Salmonella causes typhoid fever and gastroenteritis
Serratia is found in soil, water and the guts of insects and vertebrates.
Shigella dysenteriae, an enteric bacteria, causes gastric dysentery, infection from contaminated food and water
Vibrio
Photobacterium phosporeum is NOT suitable for use in schools, bioluminescent, needs saline conditions, rods and curved rods,
fermentative metabolism.

4.9 Gram negative, anaerobic, straight, curved, and helical rods
Acetivibrio, Acetoanaerobium, Acetofilamentum, Acetogenium, Acetomicrobium, Acetothermus, Acidaminobacter,
Anaerobiospirillum, Anaerorhabdus, Anaerovibrio
, Bacteroides, Butyrivibrio, Centipeda, Fervidobacterium, Fibrobacter,
Fusobacterium, Haloanaerobium, Halobacteroides, Ilyobacter, Lachnospira, Leptotrichia, Malonomonas, Megamonas,
Mitsuokella, Oxalobacter, Pectinatus, Pelobacter, Porphyromonas, Prevotella, Propionigenium, Propionispira, Rikenella,
Roseburia, Ruminobacter, Sebaldella, Selenomonas, Sporomusa, Succinimonas, Succinivibrio, Syntrophobacter,
Syntrophosmonas, Thermobacteroides, Thermospipho, Thermotoga, Tissierella, Wolinella, Zymophilus.


4.10 Gram negative cocci
Acinetobacter, Branhamella, Nisseria, Paracoccus.

4.11 Gram negative anaerobic cocci
Acidaminococcus, Megasphaera, Syntrophococcus, Veillonella.

4.12.0 Gram negative chemolithotrophic bacteria
Mineral inorganic substrates are oxidized in the cell.
Photolithotrops obtain energy from light.
They oxidize ammonia and nitrite,
metabolize sulfur and sulfur compounds, and precipitate iron oxides and manganese oxides.
Family Nitrobacteraceae: Nitrobacter, Nitrospina, Nitrococcus, Nitrosomonas, Nitrospira, Nitrosococcus, Nitrosolobus
Metabolize sulfur: Thiobacillus, Sulfolobus, Thiobacterium, Macromonas, Thiovulum, Thiospira
Family Siderocapsaceae: Sinderocapsa, Naumanniella, Ochrobium, Siderococcus
Cellulose decomposition, celluloytic bacteria
1. Aerobic: Achromobacter, Angiococcus, Bacillus, Cellulomonas, Cytophaga, Polyangium, Sporocytophyga
2. Anaerobic: Clostridium, Methanococcus, Methanosarcina
3. Ammonification, (Ammonifiers): Bacillus, Pseudomonas.

4.12.1 Nitrifying bacteria, nitrification
Nitrifying bacteria convert ammonium produced during decomposition into nitrates in the soil.
Nitrosifyers, ammonia-oxidizing bacteria, reduce inorganic nitrogen compounds and oxidize ammonia to nitrite.
No bacteria can change ammonia to nitrate.
Nitrosomonas europaea, Nitrosococcus oceani, Nitrosolobus multiformis, Nitrosospira, Nitrosovibrio
Nitrobacter winogradskyi, Nitrococcus mobilis, Nitrospira
Thiobacillus converts sulfides to sulfates.

4.12.3 Nitrogen-fixing bacteria
See diagram 9.209: Root nodule, T.S.
6.0.16 Soil nitrogen bacteria, nitrogen-fixing bacteria, Rhizobium
The free living, non-symbiotic bacteria include the following
1. Anaerobes, e.g. Clostridium pasteurianum
2. Aerobes, e.g. Azotobacter, Azomonas, Azospirillumis, Azospirillum, Agrobacterium, Beijerinckia, Gluconobacter,
Flavobacterium, Herbaspirillum
3. Cyanobacteria, blue-green algae, e.g. Anabaena, Nostoc, photosynthetic bacteria
4. Mutualistic, symbiotic bacteria, e.g. Rhizobium, in legumes, Spirillum lipoferum, cereal grasses, Bradyrrhizobium.

4.12.4 Denitrifying bacteria, denitrifiers, denitrification
Nitrogen-fixing organisms that convert nitrogen in the soil air into nitrates include Rhizobium in small nodules on the roots of
legumes and blue-green algae in wet soils.
However, some denitrifying bacteria in wet soils convert nitrates back into nitrogen gas and so make nitrogenous substances
unavailable to plants.
Denitrifying bacteria reduce nitrates or nitrites to nitrogen-containing gases.
Most denitrifiers produce nitrous oxide, N2O, instead of dinitrogen, N2, under aerobic conditions, e.g. Pseudomonas stutzeri and
aerobic denitrifier Paracoccus denitrificans.
Bacillus denitrificans, (Pseudomonas stutzeri), denitrifying soil bacterium, under the anaerobic conditions of swampy or
water-logged soils, decompose ammonia and nitrates to liberate nitrogen and reduce the available combined nitrogen in the soil.
Denitrification occurs in a diverse group of Gram-negative, motile bacteria, e.g. Pseudomonas denitrificans,
Thiobacillus denitrificans, Micrococcus denitrificans.
However, denitrification is an important stage in the nitrogen cycle that indirectly makes more nitrogen available to plants by
turning nitrates that may remain unavailable deep in the soil or washed into the sea into nitrogen available from the air.

4.12.5 Colourless sulfur-oxidizing bacteria
Reduce H2S, S and S2O32- + O2 or H2O > SO42- and 2H+
Thioploca, Thiotrix, Leucathrix live in marine habitats.
Thiobacillus ferrooxidans is rod-shaped, oxidizes ferrous iron, e.g. iron pyrites, FeS2.
Macromonas, Thermothrix, Thiobacterium, Thiodendron, Thiomicrospira, Thiosphaera, Thiospira, Thiovulum
Iron-oxidizing and manganese-oxidizing and /or iron-depositing bacteria and manganese-depositing bacteria
Aquaspirillum, Bilophococcus, Gallionella, Leptospirillum, Metallogenium, Naumaniella, Ochrobium, Siderocapsa,
Siderococcus, Sulfobacillus

Hydrogen-bacteria
Hydrogenobacter

4.12.6 Hydrogen-oxidizing bacteria
The hydrogen oxidizing bacteria use H2 as an electron donor and O2 as an electron acceptor with nickel-containing hydrogenases.
They may use CO2 as a carbon source and CO as an energy source
O2 + 2H2 --> 2H2O
Carboxydotrophic bacteria oxidize CO to CO2, e.g. Pseudomonas carboxydororans in the soil.

4.12.7 Methanotrophs, (methane to methanol)
Bacteria that can oxidize methane to methanol in aerobic reactions.
Some can use ethanol, methylamine and formate.
They are found living symbiotically in marine mussels and sponges near hydrothermal vents
Methylosinus, Methylocystis, Methanomonas, Methylomonas, Methanobacter, Methylococcus
Zymonas convert sugars to ethanol in the South American alcoholic drink, "pulque" made from the juice of the Agave cactus.

4.12.8 Acetic acid bacteria
See 19.1.4 Prepare vinegar from wine, (See 2.)
They partially oxidize ethanol, into acetic acid, e.g. Acetobacter makes vinegar from grape wine.
They also synthesize cellulose to be excreted as a covering.
Mother of vinegar contains cellulose and acetic acid bacteria that form in fermenting alcoholic liquids to convert alcohol into acetic acid
with the help of oxygen from the air.
It is added to to produce vinegar.
Mother of vinegar may form in unpasteurized vinegar if it still contains non-fermented sugar or alcohol contained in the vinegar.
It is harmless and can be filtered from the vinegar, which is still safe to consume, and used produce more vinegar from wine, cider, or
other alcoholic liquids.
Mother of vinegar is safe to use, but it must be discarded if any fungus forms in it.

4.12.9 Bioluminescent and related bacteria
Bacteria may emit light with enzyme luciferase, oxidation reaction, in live fish, light-emitting reaction.
Actinobacillus, Aeromonas, Arsenophonus, Budvicia, Buttiauxella, Calymmatobacterium, Cedecea, Chromobacterium
violaceum
is NOT suitable for use in schools, Citrobacter, Edwardsiella, Eikenella, Enhydrobacter, Erwinia, Escherichia,
Ewingella,
Gardnerella, Haemophilus, Hafnia, Kluyvera, Leclercia, Leminorella, Moellerella, Obesumbacterium, Pantoea,
Pasteurella, Plesiomonas, Pragia, Providencia, Rahnella, Streptobacillus, Tatumella, Xenorhabdus,
Yersinia, Yokenella,
Zymomonas

Erwinia carotovora causes bacterial soft rot on root and fleshy leaf bases, e.g. lettuce, celery, dahlia, black leg on potato
Haemophilus ducreyi causes chancroid, soft chancres and inflammation of the inguinal lymph nodes
Haemophilus influenzae causes haemophilus influenza, (HIB), inflammation of the paranasal cavities, sinusitis, inflammation of the
epiglottis, noisy breathing in children, meningitis in children.

4.13 Methane-producing bacteria
Anaerobic bacteria found in mud, sewage, sludge and the rumen of sheep and cattle.
Iodophilic bacteria in the rumen stain blue with iodine because they contain starch from decomposition of cellulose
Methanobacterium, Methanococcus jannaschii, Methanosarcina, Methanospirillum.

4.14 Gram positive cocci
Aerobic, Catalase-Positive Genera
Deinobacter, Deinococcus, Marinococcus, Micrococcus, Planococcus, Saccharococcus, Staphylococcus, Stomatococcus
Aerotolerant, Catalase-Negative Genera
Aerococcus, (Enterococcus), Gemella, Lactococcus, Leuconostoc, Melissococcus, Pediococcus, Streptococcus, Trichococcus,
Vagococcus

Anaerobic, catalase-negative genera
Coprococcus, Peptococcus, Peptostreptococcus, Ruminococcus, Sarcina.

4.15 Gram positive, endospore-forming rods and cocci
Amphibacillus, Bacillus, Brochothrix, Carnobacterium, Clostridium, Desulfotomaculum, Kurthia, Oscillospira, Renibacterium,
Sporolactobacillus, Sporosarcina, Sulfidobacillus, Syntrophospora

Carnobacterium pleistocenium was discovered in Alaskan permafrost.

4.16 Gram positive, non-sporing rods
Acetobacterium, Aeromicrobium, Agromyces, Arachnia, Arcanobacterium, Aureobacterium, Brachybacterium, Caryophanon,
Caseobacter

Cellulomonas biazotea is a cellulose-dissolving bacterium.
Clavibacter, Coriobacterium, Curtobacterium, Dermabacter, Erysipelothrix, Exigouibacterium, Falcivibrio, Jonesia
Lactobacillus
Listeria
Mobiluncus
Mycobacterium, Pimelobacter, Rarobacter, Rubrobacter, Sphaerobacter, Terrabacter, Thermoanaerobacter

4.17 Actinomycetes, Phylum Actinobacteria, Order Actinomycetales
Gram positive, Can decompose cellulose, chitin and other molecules to form humus.
In high pH environments can form antibiotics, (e.g. actinomysin, streptomycin, tetracycline), insecticides, fungicides.
Actinomycetes are filamentous or rod-shape and do not form endospores, but form branching colonies that look like fungi
Actinokineospora, Actinomadura
Actinomyces species prefer non-acidic soils, are usually facultative anaerobes but prefer anaerobic environment.
It can cause infections in cuts and abrasions in humans and cattle, e.g. actinomycosis.
Huge abscesses in the jaw are caused by Actinomyces israelii infecting humans man and animals, e.g. lumpy jaw in cattle.
Actinoplanes, Archina, Arthobacter, Bifidiobacterium, Brevibacterium, Cellumonas
Corynebacterium diptheriae, inflammation of the pharynx, toxins affect heart, diphtheria
Dermatophilus, Eubacterium, Frankia, Glycomyces, Micromonospora, Mycobacterium, Nocardia, Propionibacterium, Rothia,
Saccarothrix
, Streptomyces, Streptosporangia, Streptoverticillium, Thermoactinomyces, Thermomonospora.

4.18 Rickettsias and chlamydias
They are obligate intracellular parasites and cannot be cultured.
Typhus, Spotted Fever, French Fever, Q Fever and Ehrlichiosis, Potomac Fever in horses
Aegyptianella, Anaplasma, Bartonella, Chlamydia, Cowdria, Coxiella, Ehrlichia, Eperythrozoon, Grahamella,
Haemobartonella, Neorickettsia, Rickettsia, Rickettsiella, Rochalimaea, Wollbachia

Rickettsia, typhus
Bartonella henselae causes cat scratch disease.
Chlamydia trachomatis

4.19 Mycoplasmas
Mycoplasmas are the smallest living cells, with no cell wall.
Acoleplasma, Anaeroplasma, Asteroleplasma, Mycoplasma, Spiroplasma, Thermplasma, Ureaplasma
Mycoplasma, Phylum: Firmicutes, Class: Mollicutes, Order: Mycoplasmatales, Family: Mycoplasmataceae
Mycoplasma pneumoniae
Mycoplasma genitalium, (It has smallest genome of a free-living organism!)
Mycoplasma pneumoniae, inflammation of the alveoli in the lungs, pneumonia
Mycoplasma sp. big bud, (greening, virescence), e.g. tomato, potato, dock, (thick bushy stems, reduced fruit yield), yellow crinkle
of papaya
20.3 Chronic Respiratory Disease, (CRD), (mycoplasmosis), Mycoplasma gallisepticum, humans
13.5.2 Lethal yellows, mycoplasma, (coconuts)
10.9.9 Non-specific urethritis, (NSU), humans
13.3.2 Yellow crinkle, (papaya).

4.20 Sulfur-reducing bacteria
Elemental sulfur is reduced to thiosulfate and dimethyl sulfoxide.
Desulfobacter, Desulfobacterium, Desulfobulbus, Desulfococcus, Desulfomicrobium,
Desulfuromonas reduces elemental sulfur
Desulfomonile, Desulfonema, Desulfosarcina, Desulfotomaculum, (also endospore-forming), Desulfovibrio, Desulfurella,
Thermodesulfobacterium
.

4.21 Archaeobacteria, Archaea [may also occur above]
Acidianus, Archaeoglobus, Desulfurococcus, Desulfurolobus, Haloarcula, Halobacterium, Halococcus, Haloferax,
Hyperthermus, Metallosphaera, Methanobacterium, Methanobrevibacter, Methanococcoides, Methanococcus,
Methanocorpusculum, Methanoculleus, Methanogenium, Methanohalobium, Methanohalophilus, Methanolacinia,
Methanolobus, Methanomicrobium, Methanoplanus, Methanosarcina, Methanosphaera, Methanospirillum, Methanothermus,
Methanothrix, Natronobacterium, Natronococcus, Pyrobaculum, Pyrococcus, Pyrodictium, Staphylothermus, Sulfolobus,
Thermococcus, Thermodiscus, Thermofilum, Thermoplasma, Thermoproteus
.

4.22 Endosymbionts
Blattabacterium is an endosymbiont of insects.
Caedibacter, Holospora, Lyticum, Pseudocaedibacter
Tectibacter is an endosymbiont of Protozoa.

4.23 Bordetella pertusssis
Bordetella pertusssis contagious whooping cough in children.

4.24 Conjugation in bacteria, Escherichia coli
The strain Escherichia coli GY767, (DSM-No. 1562), is streptomycin sensitive.
The F plasmid is integrated into its chromosomal DNA, and it is able to transfer chromosomal genetic information to strains of E. coli
that have no F plasmid.
In this experiment, the recipient is E. coli AB1157, (DSM-No. 1563).
This streptomycin resistant strain is characterized by a large number of mutations and can no longer produce for itself the amino acids
proline, leucine, arginine, threonine, or histidine, (or the vitamin thiamine), which it requires to survive.
These substances must therefore be present in the culture medium if growth is to occur.
In the following experiment, donor cells, (E. coli GY767, DSM-No. 1562), and recipient cells, (E. coli AB1157, DSM-No. 1563),
are mixed in a ratio of 1:9.
Within two hours the chromosomal genes for the biosynthesis of proline, threonine, and leucine are transferred from the donor to the
recipient.
Recipient cells are distinguished from the donor cells by their resistance to streptomycin.
After transfer of the genes for biosynthesis of the amino acids proline, leucine, and threonine, recombinant recipient cells, now also called
transconjugants, grow on minimal agar that contains arginine, histidine, thiamine, and streptomycin, but not proline, leucine, or threonine.
Neither the donor, with its streptomycin sensitivity, nor the unchanged recipient, which would need the missing nutrients proline, leucine
and threonine, can grow on this minimal agar.
Conjugation between E. coli GY767, (DSM-No. 1562), a wild strain with chromosomal integrated F-plasmid, and E. coli AB1157,
(DSM-No. 1563), a multiple auxotrophic mutant.
Neither strain can grow on streptomycin containing minimal agar.
Transconjugants of E. coli AB1157, (DSM-No. 1563), develop on this medium only after conjugative transfer of genetic information.

Equipment: Beaker, glass, 250 mL, Bunsen burner, Conical flask, 250 mL, Drigalski spatula, Incubator, Petri dishes 3,
Pipette, 5 mL, sterile, Pipette aids, Pipettes, 1 mL, sterile
Materials:
9.1.2.20 Nutrient broth medium, for the overnight culture | 9.1.2.18 Minimal agar medium | Distilled water, Ethanol, 70%, Overnight
culture of E. coli GY767, (DSM-No. 1562), Overnight culture of E. coli AB1157, (DSM-No. 1563), Streptomycin, 0.02 g
Procedure:
1. Using the Erlenmeyer retort, prepare minimal agar with 100 mL distilled water and adjust to a pH value of 7.2 using 1 M NaOH.
Seal the retort with aluminium foil and sterilize, then leave to cool to 55o3.
Add 0.02 g streptomycin and firmly shake the retort to dissolve.
Pour into three agar dishes
2. Prepare 5 mL each of overnight culture of E. coli GY767, (DSM-No. 1562), and E. coli AB1157, (DSM-No. 1563)
3. Mix 0.3 mL E. coli GY767, (DSM-No. 1562), overnight culture and 2.7 mL E. coli AB1157, (DSM-No. 1563), overnight culture
in a sterilized test-tube and incubate at 208 37oC for two hours
4. Spread 0.1 mL of this mixture onto a minimal agar dish using the Drigalski spatula, sterilized with 70% alcohol and flamed in the
Bunsen burner
5. Prepare two control dishes with 0.1 mL of E. coli GY767, (DSM-No. 1562), and E. coli AB1157, (DSM-No. 1563), overnight
culture respectively.
Incubate all three dishes at 37oC for 72 hours.
E. coli GY767, (DSM-No. 1562), shows no signs of growth on the nutritive medium, as it is streptomycin sensitive.
Nor can E. coli GY767, (DSM-No. 1562), grow on this medium, because the amino acids required by this strain, proline, leucine, and
threonine, are not present.
Cells of E. coli AB1157, (DSM-No. 1563), can grow on this medium only when they have received from the donor the genes for
biosynthesis of these amino acids.
During the experiment, genes for arginine, histidine, and thiamine biosynthesis are also transferred, but not detected.

4.26 Lenski's experiments with Escherichia coli
In the Long-Term Experimental Evolution Project, starting from 24 February 1988, Richard Lenski of Michigan State University used
it to establish twelve laboratory populations of Escherichia coli, then study succeeding generations of these separate populations for
genotypic and phenotypic changes, e.g. changes in cell size and growth rates on glucose.
Every day, samples are transferred to a new nutrient medium.
After 30 years, and about 30,000 generations, some of these bacteria had evolved larger cells, faster growth rate and the ability to
metabolize citrate, which they had never done before.
These experiment provide long-term data on the genetics of bacteria and the rate of evolutionary change.

6.6.1 Different bacteria
See diagram 9.205: Bacteria, (Singular: Bacterium)
Bacteria live like fungi but they are so small you cannot see them except with a microscope but you can see what they do.
Dissolve soup powder or cube in a cup of hot water and pour evenly into 3 clean glasses.
Add 1 teaspoon of salt to one glass.
Add 1 teaspoon of vinegar, (acetic acid), to the second glass.
Add nothing to the third glass.
Cover the glasses and leave them in a warm place for 2 -3 days.
The first two glasses remain clear because they contain substances that stop bacteria growing.
The liquid in the third glass is cloudy because it contains so many bacteria.

9.70 Rhizobium in legumes
| See diagram 9.209: T.S. Root nodule
| See diagram 9.72: Root nodules
Rhizobium bacteria can enter the roots of legumes and cause lumps, root nodules, where they live.
These bacteria can use the nitrogen gas from the air.
We say Rhizobium can "fix" nitrogen from the air.
Very few other living things can fix nitrogen.
Some nitrogen goes into the stems and leaves of the legume plant.
When the leaves fall off, some nitrogen compounds are added to the soil that other plants can then use.
When the legume plants die, the nitrogen fixed by the Rhizobium can still be available to other plants.
Some legumes, e.g. cowpea and lablab bean, are grown until the flowering stage and then dug into the soil as "green manure".
When these plants rot, they leave nitrogen compounds in the soil both from the leaves and root nodules.
Different crop plants require different strains of Rhizobium.
Farmers can purchase commercial inoculum containing the strain appropriate for nodulation of their particular crop.

9.71 Rhizobium in legumes
Dig up different legume plants and count the number of nodules and note the sizes of the nodules.
Cut open some nodules.
The inside of a nodule that is fixing nitrogen is a pink red colour.
Inactive nodules are brown or green inside.

9.3.0 Yoghurt and lactic acid bacteria, "Yakult"
Lactic acid bacteria convert lactose to lactic acid by a form of fermentation and so are used to preserve milk and perhaps have the
probiotic function of increasing pH in the intestine to lower the activity of harmful bacteria and other organisms.
Lactic acid bacteria, (order Lactobacillales), are mainly Lactobacillus, Leuconostoc, Pediococcus, Lactococcus lactis, and
Streptococcus, but also my include Aerococcus, Carnobacterium, Enterococcus, Oenococcus, Sporolactobacillus,
Tetragenococcus, Vagococcus, and Weisella.
Yoghurt is usually prepared from two species of bacteria, chains of cocci or diplococci of Streptococcus thermophilus and
rod-shape bacilli of Lactobacillus acidophilus or Lactobacillus bulgaricus that both stain Gram-positive, purple.
The bacteria have been renamed Lactobacillus delbrueckii, (subsp. bulgaricus), for (Lactobacillus bulgaricus), and
Streptococcus salivarius, (subsp. thermophilus), for Streptococcus thermophilus.
Lactobacillus casei
is a species of non-starter lactic acid bacteria, (NSLAB), found in ripening Cheddar cheese.
Yakult was developed by Dr Minoru Shirota, (1899-1982), as Lactobacillus casei strain shirota for production of "Yakult", the
yogurt-like probiotic drink.
Probiotic organisms, usually lactic acid bacteria, (LAB), and bifidobacteria, (formerly Lactobacillus bifidus), are live microorganisms,
thought to be beneficial to the host organism that are usually consumed as part of fermented foods with specially-added active live
cultures, e.g. yoghurt.
Lactobacillus acidophilus occurs naturally in the human gastrointestinal tract, mouth and vagina, and may be used with
Streptococcus salivarius, (subsp. thermophilus), and with Lactobacillus delbrueckii, (subsp. bulgaricus), to produce
acidophilus-type yoghurt.
Leuconostoc citrovorum with Streptococcus lactis convert lactic acid to aldehydes and ketones to produce buttermilk with its
characteristic flavour and aroma.

9.3.1 SCOBY, Symbiotic Colony Of Bacteria and Yeast
Kombucha is tea fermented with a scoby that appears as a growth of "mushroom".
The scoby may contain:
Bacteria: Gluconacetobacter kombuchae, occurs only in kombucha, forms acetic acid and gluconic acid, and builds the scoby
"mushroom".
Acetobacter xylinoides and Acetobacter ketogenum form acetic acid and gluconic acid and build the scoby "mushroom".
Lactobacillus and Pediociccus form lactic acid and scoby slime.
The yeast Zygosaccharomyces kombuchaensis occurs only in kombucha, forms acetic acid and gluconic acid, and builds the scoby
"mushroom".
Saccharomyces cerevisiae, Saccharomycodes ludwigii, Saccharomycodes apiculatus, Schizosaccharomyces pombe,
Zygosaccharomyes, form alcohol or acetic acid.
Different forms of scoby can be used for ginger beer, kefir, mother of vinegar, tibicos and sourdough.

9.4.0 Sulfonamides, sulfa drugs
See diagram 14.12: Sulfanilamides, sulflilamide, sulfamethoxazole
1. Sulfanilamide, p-aminobenzenesulfonamide, Toxic if ingested, liver toxin
The first of the antibacterial drugs, the sulfonamides, were found effective against the cocci infections caused by the bacteria
streptococci, gonococci and pneumococci.
The basic compound is called sulfanilamide.
Many derivatives can be made from this compound by modifying the molecule to change its potency or reduce side effects or toxicity.
The effectiveness of these drugs depends on maintaining the basic structure and shape of the molecule.
One of the essential growth compounds for most bacteria susceptible to the sulfonamides is p-aminobenzoic acid.
Bacteria absorb a sulfonamide because its shape and charge distribution is similar to p-aminobenzoic acid, and then they cannot
metabolize it.
Bacteria use p-aminobenzoic acid to produce folic acid, but, unlike humans, cannot absorb folic acid from their food.
Prontosil sulfanilamide requires the patient to drink copious quantities of water at the same time because kidney damage was caused by
earlier products.
The term "sulfanilamides" refers to the family of molecules based on sulfanilamide, so it is a chemical term.
The term sulfonamide, (sulfa drugs), refers to drugs based on sulfanilamide, so a medical term.
Sulfonamides, (sulpha drugs), do not kill bacteria but prevent them growing and multiplying to allow natural immunity processes to deal
with them.

9.4.1 Sensitivity to drugs determined by genes
Individual people fall into two genetic groups, those who acetylate drugs like sulfonamides fast and those who do so slowly.
While 90% of Japanese and Chinese are fast acetylators, only 40% of Americans, (both black and white), acetylate drugs fast.
Acetylation is often the first step in metabolizing and thus deactivating a drug, so slow acetylators are exposed to higher levels of a
drug given at the same dose.
The acetyl derivative of sulfa thiazole is not very soluble.
It tended to block kidney tubules and lead to death. It was replaced by sulfadiazine.
The same acetylating enzyme deactivates some carcinogens, e.g. aromatic amines such as benzidene and o-tolidine, used in dyestuff
manufacture and as analytical reagents in the detection of blood and chlorine levels in water.
Slow acetylators are at higher risk of bladder cancer from these chemicals
Examples of sulfa drugs:
Sulfamethoxazole / trimethoprim, "TMP-SMZ", C10H11N3O3S, (Bactrim, Septra, Co-trimoxazole, Cotrim, Sulfatrim)
Sulfasalazine, C18H14N4O5S, (Azulfidine, Sulfazine)
Sulfisoxazole, C11H13N3O3S, (Gantrisin, Truxazole).

9.5.0 Bacterial infections, germ theory, Pasteur, Koch
19.3.12 Pasteurization and UHT, (Ultra High temperature) of milk
1. The symptoms of a bacterial infection are usually local redness, heat, swelling and local pain and sometimes the formation of pus.
By contrast viral infections usually affect many parts of the body, e.g. blocked nose, cough and headache.
However, local virus infections include conjunctivitis, (pink eye, truck driver's eye), and herpes.
Herpes is painful but most viral diseases feel more like an itch.
Pus is a yellow white viscous fluid formed in infected tissue, containing white blood cells, (polymorphonuclear leucocytes) remains of
cells, dead tissue, and micro-organisms.
Pus should be surgically drained as soon as possible.
Normal body temperature (orally) = 36.8 (+ or -) 0.5oC.
Fever is occurring if body temperature = or > 37.5oC, (in the mouth), 37.2oC, (under the arm), 38.0oC, (in the rectum)
2. Infections of the skin by Staphylococcus aureus include the following:
2.1 Infection of the hair follicles as small white head pimples at the base of hair shafts or as a swollen red boil, (furuncle, carbuncle)
2.2 Impetigo blisters then crusts on the surface of the skin of young children
2.3 Cellulitis infection below the skin surface
2.4 Infection of the eyelid glands, (hordeolum, stye)
3. The germ theory developed by Louis Pasteur and Robert Koch identified the cause of diseases starting with anthrax and finishing with
tuberculosis and plague.
The principle of identification was set out in Koch's postulates in 1881:
1. The germ is always present in the disease.
2. The germ can be cultivated outside the body and preserved for generations.
3. The disease can be reproduced in experimental animals.
4. The organism causing the disease cannot be found in inoculated animals.

9.5.5 Pasteur's spontaneous generation experiment
It was believed that living organisms could develop from non-living matter without pre-existing living matter, e.g. Disease can develop
spontaneously in damaged human tissue without any exterior organism being involved.
In 1859 Louis Pasteur, tested this belief by putting boiled clear meat soup into a swan neck flask.
Then swan neck was heated to kill any living things in it.
The swan neck flask was left standing while dust fell from the air and accumulated in the loop of the swan neck.
Air from the atmosphere could still pass by the dust in the swan neck.
The meat soup remained clear.
Later he tipped the flask so that the dust in the loop of the swan neck fell into the flask.
The meat soup in the flask became cloudy because of bacterial infection from the dust in the air.

See diagram 9.5.5: Pasteur's flasks
Set up the two Pasteur's flasks as above using meat soup from a bouillon cube or canned soup.
Do not touch the first flask so it can remain as a control. Tip the second flask so that any dust from the air touches the soup.
Some teachers have put the first flask in a place where it is not moved for a long time and the meat soup in it still remains clear.

9.5.7 Anti-microbial disinfectants affect growth of Escherichia coli
Joseph Lister, 1827-1912, England, first introduced aseptic surgery in 1867.
He used a spray of carbolic acid, (phenol C6H5OH), as a germicide to reduce mortality of post operative surgery
Prepare the plates and then put a "'wash" of Escherichia coli, on the agar.
Sterilize small paper discs, as from a hole punch, and then soak them into different anti-microbials preparations or use multi-disks
impregnated with antibiotics.
Place the discs on the agar plates then incubate for two of days.
If the anti bacterial is effective, there is a clear ring around the disc where the E. coli have not grown.
Use the width of this ring, the zone of inhibition, to indicate effectiveness of the anti-microbials preparations.
Common anti-bacterials are ethanol, isopropyl alcohol, synthetic detergents, (QAC, Quaternary Ammonium Compounds), and phenols.
Phenols sterilize well but are corrosive and toxic.
Detergents and 70% alcohol have some microbiocidal effect,  but are not sporicidal and dry out skin surfaces.
Pay strict attention to the disposal of waste.

9.5.8 Pseudomonas aeruginosa
Pseudomonas aeruginosa can reduce the amount of fixed nitrogen, (as fertilizer), by up to 50 percent
2NO3- + 10e- + 12H+ --> N2 + 6H2O
Pseudomonas aeruginosa is NOT suitable for use in schools, said to be responsible for one-in-ten hospital-acquired infections, an
opportunistic bacteria that attacks weakened immune systems. It mutates rapidly and is acquiring resistance to antibiotics,
e.g. ciprofloxacin because of exposure to the disinfectant BSK, benzalkonium chloride.

9.214 VRE bacteria, (Vancomycin Resistant Bacteria)
Vancomycin Resistant Bacteria are species Enterococcus faecium and Enterococcus faecalis, resistant to the antibiotic Vancomycin.
Enterococcus bacteria usually occur in the bowel and the female genito-urinary tract.
They can cause urinary tract infections if the peritoneal cavity is infected by bowel contents and if the bloodstream is infected by
intravascular devices in hospitals used by unhygienic hospital staff, nosocomial (hospital-acquired) infections.