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MODULE 1

BACTERIA
The prokaryotes (organisms without a cellular nucleus) consist of two domains (or empires),
"Bacteria" (or "Eubacteria") and "Archaea" (or "Archaeobacteria"). They believe that the
kingdoms Archaea and Eubacteria had a common ancestor but separated very early on, a few
billion years ago.

Comparison of Eubacteria and Archaeobacteria


Properties Eubacteria Archaeobacteria
Nucleus with nucleolus Absent Absent
Cell wall Peptidoglycan containing Variety of types, no muramic acid
muramic acid
Membrane lipid Ester-linked, straight-chained Ester-linked, branched-aliphatic acids
fatty acids
Gas vesicles Present Present
Transfer RNA Thymine present in most No thymine in t-RNA Methionine
tRNAs, N-formylmethionine carried by initiator
carried by initiator
Polycistronic mRNA Present Present
mRNA introns Absent Absent
mRNA Splicing, Capping, and Poly A Absent Absent
Tailing
Ribosomes

Size 70S 70S

Sensitivity to chloramphenicol and Sensitive Insensitive


kanamycin
DNA-dependent RNA polymerase

Number of enzymes One Several

Structure Simple subunit pattern Complex subunit pattern

Rifampicin sensitivity Sensitive Insensitive


Polymerase II Type promoters Absent Present

Metabolism No Yes

Similar ATPase Absent Present

Methanogenesis Present Present


Nitrogen fixation

Chlorophyll-based photosynthesis Present Absent

ARCHAE (Archaeobacteria)

They are the one-celled organisms, many of which do not require oxygen or sunlight to live.
Archaeobacteria were initially grouped with bacteria because like bacteria, they lack a
well-defined nucleus. Archae bacteria are similar to eucaryotes with respect to some
components of the RNA and protein synthetic systems.

Classification of Archaeobacteria:
1. Thermoacidophiles: They live in the extremely hot, acidic water and moist areas within and
surrounding sulfur hot springs. So closely adapted are they to their bubbly environment
that they die of cold at temperatures of 55oC (131oF) Eg. Thermoplasm, Thermococcus,
Pyrococcus

2. Methanogens: They are obligate anaerobes (free oxygen kills them) which oxidize CO 2 during
cellular respiration to produce methane (CH4) as a waste product. Although RNA sequencing
suggests that all ten known species are evolutionarily related, they exist in environments as
diverse as scalding volcanic deep-sea vents and the intestines of mammals. The reason you can
light a puff of flatulence (should you choose to go into show business) is because of the symbiotic
methanogens inside your guts. Eg. Methanobacterium, Methanococcus

3. Strict halophiles: They live in extremely salty solutions such as the Dead Sea, the Great Salt
Lake and that can of pickled herring you left open in the cupboard. Their pink carotenoid
pigments make them conspicuous when the bacteria are present in large concentrations, as they
are on the shores of some salty, land-locked lakes. Eg. Halobacterium, Halococcus

EUBACTERIA
Bacteria were first observed by Antonie van Leeuwenhoek in 1676, using a single-lens
microscope of his own design. He called them "animalcules" and published his
observations in a series of letters to the Royal Society. They are the true bacteria, one-
celled organisms. An average bacterium is about one micrometer long. The perfect
medium (environment) for growing bacteria also came from the kitchen, although its
usefulness was demonstrated in the laboratory of German scientist Robert Koch. The
medium was agar, a gel-forming substance that comes from seaweed.
Composition of a Typical Bacterial Cell
Bacteria are about 70% water. The other 30% - the dry weight - consists of:

Molecule %Dry weight Constituents


Protein 55 amino acids
Polysaccharide 9-10 sugars
Lipid 9 fatty acids, glycerol, phosphate
RNA 20 purines, pyrimidines, phosphate,
DNA 3 pentoses
low molecular weight solutes and
Small molecules 3-4
inorganic ions
Classification of bacteria
Bacteria are mainly classified into phylums (phylum is a scientific classification of organisms).
For simplification, bacteria can be grouped into the following groups:

Based on shapes:

Rod shaped (Bacilli): Mycobacteria, Pseudomonas, Salmonella, Clostridium Botulinum Escherichia,


Shigella, Proteus, Erwinia, Yersinia, Enterobacter, Serratia

Sphere (Cocci) : Chlamydia, Staphylococcus, Streptococci

Spiral and curved bacteria: Spirillum, Auqaspirillum, Oceanospirillum, Bdellovibrio

Based on oxygen requirement:

Aerobic and Anaerobic bacteria: Bacteria those need oxygen for their survival are called
Aerobic bacteria.
Eg. Azotobacter, Rhizobium, Nitrosomonas, Nitrobacter, Thiobacillus, Pseudomonas, legionella.
Anaerobic bacteria cannot bear oxygen and may die if kept in oxygenated environment
(anaerobic bacteria are found in places like under the surface of earth, deep ocean, and bacteria
which live in some medium).
Eg. Clostridium, Desulfotomaculum, Campylobacter, Zymomonas, Aeromonas

Based on Gram-staining method:

Gram-positive bacteria: This division includes the gram-positive rods, gram-positive cocci, and
the actinomycetes, which exhibit superficial similarity and function (but no evolutionary
relationship) to the (eukaryotic) fungi. They are usually chemoorganoheterotrophic. Thick cell
wall with multiple peptidoglycan layers. No outer membrane, periplasmic space or
lipopolysaccharide. They possess long chain teichoic acids intertwined among the peptidoglycan.
Eg. Streptococcus, Leuconostoc, Bacillus, Clostridium, Lactobacillus, Propionibacterium.

Gram-negative bacteria: About 75% of known eubacteria are gram negative. They include the
gliding bacteria, the spirochetes, the curved (vibrios) and spiral (spirillae) bacteria. Single thin
peptidoglycan layer, but no teichoic acids. Possess an outer membrane containing
lipopolysaccharide and a periplasmic space between the outer and inner membranes..They are
phototrophic, chemolithoautotrophic or chemoorganoheterotrophic. Eg. Brucella, Bordetella
Pasteurella, Haemophilus, Escherichia, Shigella, Salmonella, Proteus, Erwinia, Yersinia,
Enterobacter, Serratia
Based on phyla:
1. PHYLUM AQUIFICAE: Contain autotrophic bacteria that can use hydrogen
for energy production. Eg. Aquifex and Hydrogenobacter
2. PHYLUM THERMOTOGAE: They are anaerobic, thermophilic, fermentative,
gram-negative bacteria that have unusual fatty acids with respect to their ether-
linked lipids. Eg. Thermotoga, Geotoga.
3. PHYLUM DEINOCOCCUS-THERMUS: Gram positive and have high
concentration of carotenoid pigments, which may protect it from radiation and
unique lipids. Eg. Deinococcus, Thermus.
4. PHYLUM THERMODESULFOBACTERIA: They are the small group of
sulphate reducing thermophilic bacteria. Eg. Thermodesulfobacterium.
5. PHYLUM CHRYSIOGENETES: Curved, rod shaped, gram-negative and
strictly anaerobic. Eg. Chrysogenes.
6. PHYLUM CHLOROFLEXI: Carry out anoxygenic photosynthesis and is a
gliding bacterium. Many members of this gram-negative group are called green
non-sulphur bacteria. Eg. Chloroflexus, Herpetosiphon.
7. PHYLUM THERMOMICROBIA: Group of thermophilic green non-sulphur-
bacteria. Eg. Sphaerobacter thermophilus
8. PHYLUM NITROSPIRA: These bacteria convert ammonia to nitrites and
nitrites to nitrate. They are important in marine habitats Eg. Nitrospira,
Nitrosomonas, Nitrococcus.
9. PHYLUM CYANOBACTERIA: Cyanobacteria include unicellular and
colonial species. Colonies may form filaments, sheets or even hollow balls. Some
filamentous colonies show the ability to differentiate into several different cell
types: vegetative cells, the normal, photosynthetic cells that are formed under
favourable growing conditions; akinetes, the climate-resistant spores that may
form when environmental conditions become harsh; and thick-walled
heterocysts, which contain the enzyme nitrogenase, vital for nitrogen fixation.
Eg. Anabaena, Nostoc, Calothrix
10. PHYLUM CHLOROBI- Green sulphur and anaerobic photoautotrophic
bacteria. Eg. Chlorobium, Ancalochloris
11. PHYLUM PROTEOBACTERIA: The phylum is divided into 5 classes:
Alphaproteobacteria: They include oligotrophic forms Methylobacterium,
Nitrobacter, Rhizobium
Betaproteobacteria: They tend to use substances that diffuse from organic
decomposition in the anaerobic zone of habitats eg. Nitrosomonas,
Methylobacillus
Gammaproteobacteria: They often are chemoorganotrophic, facultatively and
fermentative. Eg. Methylococcus, Chromatium
Deltaproteobacteria: Consist of variety of anaerobes that generate sulfide from
sulphate and sulphur while oxidizing organic nutrients Eg. Desulfovibrio
Epsilonproteobacteria: Despite its small size two important pathogenic genera
are Campylobacter and Helicobacter

12. PHYLUM PLANCTOMYCETES: They are coccoid to ovoid or pear shaped


cells that lack peptidoglycan. Eg. Isophaera
13. PHYLUM CHLAMYDIAE: They are intracellular parasite with no appendages
Eg. Chlamydiae
14. PHYLUM SPIROCHAETES: Contain helically shaped, motile, gram-negative
bacteria and are chemoheterotrophs Eg. Treponema and Borrelia
15. PHYLUM FIRMICUTES: Mostly they are gram-positive and heterotrophic and
have low G+C content Eg. Clostridium, Desulfotomaculum, Bacillus,
lactobacillus, Streptococcus.
16. PHYLUM ACTINOBACTERIA: High G+C gram positives often form
complex branching hyphae and produce large mycolic acids Eg.
Corynebacterium, Frankia, Actinomyces, Micrococcus

ECONOMIC IMPORTANCE OF BACTERIA


The economic importance of bacteria derives from the fact that bacteria are exploited by humans
in a number of beneficial ways. Despite the fact that some bacteria play harmful roles, such as
causing disease and spoiling food, the economic importance of bacteria includes both their useful
and harmful aspects.

1. Bacteria, often Lactobacillus in combination with yeasts and molds, have been used
in the preparation of fermented foods such as cheese, pickles, soy sauce, sauerkraut,
vinegar, wine, and yogurt.

Food sources of Lactobacilli

Cultured
Beneficial Bacteria
Dairy Products
Streptococcus thermophilus
Yogurt Lactobacillus bulgaricus
Lactobacillus acidophilus
Lactobacillus lactis
Buttermilk
Streptococcus cremoris
Sour cream Streptococcus cremoris
Lactobacillus acidophilus
Kefir
Lactobacillus caucasicus
Lactobacillus acidophilus
Lactobacillus brevis
Lactobacillus casei
Lactobacillus caucasicus
Cheeses Lactobacillus helveticus
Lactobacillus lactis
Lactobacillus plantarum
Streptococcus cremoris
Streptococcus faecium
Lactobacillus lactis
Cottage cheese
Streptococcus cremoris
Acidophilus milk Lactobacillus acidophilus
Bulgaricus milk Lactobacillus bulgaricus
Yakult Lactobacillus casei
Bifidobacterium bifidum
Bifidus milk
Bifidobacterium longum
2. Nitrogen-fixing bacteria (such as these Rhizobium sp.) inhibit the root cells of plants in the
legume family (Fabaceae). These moneran symbionts convert gaseous nitrogen from the
atmosphere (N2) into usable "fixed" nitrogen (ammonia, nitrite and nitrate) which can be
absorbed by the roots and used by the plant to manufacture protein and nucleic acids.

3. In the chemical industry, bacteria are most important in the production of enantiomerically
pure chemicals for use as pharmaceuticals or agrochemicals. Pharmaceuticals, such as
antibiotics, vaccines and steroids. Other bacteria, such as these Streptomyces spp., are sources
of life-saving medicines. This genus yields the powerful antibiotic known as streptomycin. It
kills sensitive microbes by hurting cell membranes and inhibiting protein synthesis.
Streptomycin is an antibiotic that inhibits both gram positive and gram negative bacteria, and
is a therefore a useful broad spectrum antibiotic.

Actinomycetes are the source of actinomycin thereby increasing the acidity of the intestines and
inhibiting bacterial villains such as Clostridium, Salmonella, Shigella, and E. coli.

New antibiotic produced by Bacteria-Bacillus, i.e. 5-, β-D-Xylofuranosylneamine which is active


against gram-positive and some gram-negative bacteria.

Lactobacillus acidophilus can suppress the formation of cancer-causing amines and cancer-
promoting enzymes in the intestines of humans and animals. Produce a wide range of antibiotic
substances (acidophilin, bacteriocin, etc.) which help control the level of pathogenic bacteria and
ftingi such as Candida. Produce vitamins, especially B-vitamins and vitamin K and act as barriers
to prevent pathogenic bacteria from colonizing the intestines

4. Genetic engineering

Bacterial cells are transformed and used in production of commercially important products. The
examples are production of human insulin (used against diabetes), human growth
hormone (somatotrophin used to treat pituitary dwarfism), and infections which can be
used to help fight viral diseases. Using biotechnology techniques, bacteria can also be
bioengineered for the production of therapeutic proteins, such as insulin, growth
factors or antibodies.

5. Fibre retting

Bacterial populations, especially that of Clostridium butyclicum, are used to separate fibres of
jute, hemp, flax, etc, the plants are immersed in water and when they swell, inoculated with
bacteria which hydrolyze pectic substance of the cell walls and separate the fibres.These
separated fibres are used to make ropes and sacks.

6. Vitamin synthesis

Escherichia coli that lives in the human large intestine synthesize vitamin B and release it for
human use. Similarly, Clostridium butyclicum is used for commercial preparation of riboflavin, a
vitamin B.

6. Waste disposal
Aerobic and anaerobic bacteria are used to decompose sewage wastes. They break down organic
matter to harmless, soluble sludge in settling tanks. The methane gas produced is used as energy
source. Similarly toxic chemicals synthesized by living organisms and those present in the
pesticides are disposed with the help of bacteria. Pseudomonas putida has been created by using
genetic engineering techniques and can break down xylene and camphor.

The ability of bacteria to degrade a variety of organic compounds is remarkable and has been
used in waste processing, and bioremediation. Bacteria capable of digesting the hydrocarbons in
petroleum are often used to clean up oil spills. These efforts were effective on beaches that were
not too thickly covered in oil. Bacteria are also used for the bioremediation of industrial toxic
wastes.

7. Pest control

Bacteria can also be used in the place of pesticides in the biological pest control. This commonly
uses Bacillus thuringiensis (also called BT), a Gram-positive, soil dwelling bacterium. This
bacteria is used as a Lepidopteran-specific insecticide under trade names such as Dipel and
Thuricide.

Harmful bacteria

• Some bacteria are harmful and act either as disease-causing agents (pathogens) both in
plants and animals, or may play role in food spoilage. Eg. Clostridium botulinum, E.coli,
Salmonella typimurium, Shigella dysenteriae
• The major pathogens Streptococcus pyogenes, (Gram-positive cocci) an agent
of sore throat and rheumatic fever, and Streptococcus agalactiae, a cause of
neonatal meningitis and pneumonia.
• Gram-negative cocci include the pathogenic Neisseria meningitidis, an
important cause of meningitis and septicaemia, and N. gonorrhoeae, the agent of
urethritis (gonorrhoea).
• Pathogens include Bacillus anthracis which causes anthrax, and clostridia
which cause gas gangrene, tetanus, pseudomembranous colitis and
botulism.
• Pseudomonas, an environmental saprophyte naturally resistant to antibiotics, has become
an important hospital pathogen
• Spiral bacteria include the small gastrointestinal pathogen Helicobacter that
colonizes the stomach, leading to gastric and duodenal ulcer and
gastric cancer, and Campylobacter spp. that cause acute diarrhea
• Borrelia duttoni and B. recurrentis cause chronic disease of the skin joints and
central nervous system, Lyme disease (B. burgdorferi). The Leptospira are
zoonotic agents causing an acute meningitis syndrome that may be
accompanied by renal failure and hepatitis. The Leptospira are
zoonotic agents causing an acute meningitis syndrome that may be
accompanied by renal failure and hepatitis.

ProBiotics
Probiotics are dietary supplements containing potentially beneficial bacteria or yeasts. Probiotic
is a natural approach to chronic digestive disorders (constipation, diarrhea, indigestion, and the
effects of prolonged antibiotic therapy). Many environmental conditions, plus the food we eat,
can cause damage to, or even destroy, the balance of probiotic bacteria in the body's digestive
system.

Potential benefits of probiotic bacteria

Prevention of colon cancer- bacteria exert anti-carcinogenic effects by decreasing the activity of
an enzyme called β-glucuronidase
Cholesterol lowering
Lowering blood pressure
Decrease the incidence of respiratory tract infections and dental caries in children
Lactobacillus are also thought to aid in the in the treatment of Helicobacter pylori infections in
adults
Reducing inflammation and hypersensitivity responses
Improving mineral absorption
Prevent harmful bacterial growth under stress condition

Each capsule contains more than 2,000,000,000 (two billion) organisms of ten beneficial strains:
L. acidophilus, L. bifidus, L. rhamnosus, L. plantarum, L. salivarius, B. longum, L. bulgaris, L.
lactis, L. casei, L. brevis

It is the probiotic "friendly flora" that help us process our food and keep in balance putrefactive
bacteria and potential pathogens, including Candida albican. Henry Tissier, also from the Pasteur
Institute, was the first to isolate a Bifidobacterium from gut flora of breast-fed babies, and he
recommended administration of bifidobacteria to infants suffering from diarrhea.

Metabolism
In contrast to higher organisms, bacteria exhibit an extremely wide variety of metabolic types.
Bacterial metabolism is classified into nutritional groups on the basis of three major criteria: the
kind of energy used for growth, the source of carbon, and the electron donors used for growth.

Nutritional types in bacterial metabolism

Source of
Nutritional type Source of carbon Examples
energy
Organic compounds
Cyanobacteria, Green sulfur
(photoheterotrophs) or
Phototrophs Sunlight bacteria, Chloroflexi, or Purple
carbon fixation
bacteria
(photoautotrophs)

Organic compounds
Thermodesulfobacteria,
Inorganic (lithoheterotrophs) or
Lithotrophs Hydrogenophilaceae, or
compounds carbon fixation
Nitrospirae
(lithoautotrophs)

Organic compounds
Organic (chemoheterotrophs) or Bacillus, Clostridium or
Organotrophs
compounds carbon fixation Enterobacteriaceae
(chemoautotrophs)

Carbon metabolism in bacteria is either heterotrophic, where organic carbon compounds are used
as carbon sources, or autotrophic, meaning that cellular carbon is obtained by fixing carbon
dioxide. Typical autotrophic bacteria are phototrophic cyanobacteria, green sulfur-bacteria and
some purple bacteria, but also many chemolithotrophic species, such as nitrifying or sulfur-
oxidising bacteria. Energy metabolism of bacteria is either based on phototrophy, the use of light
through photosynthesis, or on chemotrophy, the use of chemical substances for energy, which are
mostly oxidised at the expense of oxygen or alternative electron acceptors (aerobic/anaerobic
respiration).

Finally, bacteria are further divided into lithotrophs that use inorganic electron donors and
organotrophs that use organic compounds as electron donors. Chemotrophic organisms use the
respective electron donors for energy conservation (by aerobic/anaerobic respiration or
fermentation) and biosynthetic reactions (e.g. carbon dioxide fixation), whereas phototrophic
organisms use them only for biosynthetic purposes. Respiratory organisms use chemical
compounds as a source of energy by taking electrons from the reduced substrate and transferring
them to a terminal electron acceptor in a redox reaction. This reaction releases energy that can be
used to synthesise ATP and drive metabolism. In aerobic organisms, oxygen is used as the
electron acceptor. In anaerobic organisms other inorganic compounds, such as nitrate, sulfate or
carbon dioxide are used as electron acceptors. This leads to the ecologically important processes
of denitrification, sulfate reduction and acetogenesis, respectively.

Another way of life of chemotrophs in the absence of possible electron acceptors is fermentation,
where the electrons taken from the reduced substrates are transferred to oxidised intermediates to
generate reduced fermentation products (e.g. lactate, ethanol, hydrogen, butyric acid).
Fermentation is possible, because the energy content of the substrates is higher than that of the
products, which allows the organisms to synthesise ATP and drive their metabolism.

Lithotrophic bacteria can use inorganic compounds as a source of energy. Common inorganic
electron donors are hydrogen, carbon monoxide, ammonia (leading to nitrification), ferrous iron
and other reduced metal ions, and several reduced sulfur compounds. Unusually, the gas methane
can be used by methanotrophic bacteria as both a source of electrons and a substrate for carbon
anabolism. In both aerobic phototrophy and chemolithotrophy, oxygen is used as a terminal
electron acceptor, while under anaerobic conditions inorganic compounds are used instead. Most
lithotrophic organisms are autotrophic, whereas organotrophic organisms are heterotrophic.

Reproduction
Bacteria reproduce by a way of asexual reproduction called binary fission where bacteria splits
into two cells. Each cell gets an exact copy of the parent cell's genetic material. Under optimal
conditions, bacteria can grow and divide extremely rapidly, and bacterial populations can double
as quickly as every 9.8 minutes. In cell division, two identical clone daughter cells are produced.
Some bacteria, while still reproducing asexually, form more complex reproductive structures that
help disperse the newly-formed daughter cells. Examples include fruiting body formation by
Myxobacteria and arial hyphae formation by Streptomyces, or budding.

Bacteria also reproduce with the exchange of DNA. When bacteria exchange DNA, it has a
similar effect to sexual reproduction, in that, there is a blending of genes between two organisms.
There are three ways in which bacteria exchange DNA.

1. Conjugation – male cell passes DNA to female cell by means of a conjugation tube (sex
pilus).
2. Transformation – bacterium takes up DNA released by dead bacteria.
3. Transduction – bacteriophages carry DNA from one cell to another

Movement
Most bacteria move by the use of flagella. In some bacteria, there is only a single flagellum at
one end, such cells are called monotrichous. When single flagellum present at both ends
called as amphitrichous and numerous flagella located at one end of the cell called
lophotrichous. Flagella distributed over the entire surface of the cell called as peritrichous.

Gliding movement: It is the movement of cells over surface without the aid of flagella eg.
Oscillatoria

Chemotaxis movement: In it the actual rotation of the flagellum is controlled by protein


complexes (Methyl accepting chemotaxis protein –MCPs) located in the basal body of the
flagellum eg. E.coli

SCIENTIFIC STUDY OF BACTERIA


Recent information on the true diversity of bacteria comes from a study published in 2006 that
used a new DNA-identification technique to study microbes taken from the ocean. Scientists
found more than 20,000 types of bacteria in a liter of sea water—over ten times the biodiversity
predicted. Much of the diversity came from rare bacteria that had not been detected in previous
studies of marine microbes. Samples were taken at eight sites in the Atlantic Ocean and Pacific
Ocean from a wide range of depths and environments, including the North Sea and hydrothermal
vents. The work will be expanded in the future to sample marine microbes from more than 1,000
ocean sites with even more types of environments. The international research is being conducted
as part of the global Census of Marine Life, a ten-year project that began in 2000. The newly
recognized complexity of ocean bacteria could lead to a much greater gene pool for a range of
scientific work.

Scientists have already sequenced the entire genome for many bacteria. Researchers can cut
pieces from bacterial DNA and replicate it in many copies. Through DNA transfer, the pieces can
be inserted in bacterial cells. The cells with the new DNA may then start to make new proteins
they were unable to make previously. Thus, bacteria can be genetically engineered to make a
whole range of products and to develop new functions. Genetic engineering has opened up a new
world of biology and a tremendous opportunity to explore bacteria and other microorganisms and
to benefit humanity from the resulting knowledge. Bacterial cells such as E. coli are widely used
in laboratories as factories to produce commercially or medically important proteins through the
use of genetic engineering or recombinant DNA technologies

Researchers at the US department of energy’s Argonne National laboratory have found a new
way to study individual living bacterial cells. The scientist used high X-ray fluorescence
measurements for mapping and chemical analyses of single free floating, or planktonic and
surface-adhered cells or biofilms of Pseudomonas fluorescence. This technique measure the
concentration of hexavalent chromium which help use to distinguish living bacterial cell from
dead cell. Different DNA fingerprinting techniques have been successfully applied for the
identification and taxonomic classification of the bacteria. 16S rDNA sequences monitor the
physiological activity of microbial cells and serve in the identification of Lactic acid bacteria and
Bifidobacteria. 16S rRNA probing and AFLP technique are used for the identification f the gram-
positive bacteria that have low G+C content eg. Lactobacillus, Leuconostoc, Enterococccus.
RAPD technique is used for the characterization of Bifidobacteria including B. adolescentis, B.
bifidum, B. breve, B. infantis and B. longum.

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