The document discusses the human microbiome and normal microbial flora. It notes that a diverse microbial population normally inhabits human skin and mucous membranes. Germ-free animal studies showed that the normal flora substantially influences host well-being. Specific bacteria like Corynebacterium and Propionibacterium are prominent on the human body. The skin, respiratory tract, gastrointestinal tract, and urogenital tract each harbor distinct microbial populations. Pathogens have developed various virulence factors and mechanisms to invade and establish infection by avoiding the host immune system.

1. Microbial Flora
HUMAN
MICROBIOME

2. Introduction
A diverse microbial flora is associated with the
skin and mucous membranes of every human
being from shortly after birth until death. The
human body, which contains about 1013 cells,
routinely harbors about 1014 bacteria. This
bacterial population constitutes the normal
microbial flora . The normal microbial flora is
relatively stable, with specific genera
populating various body regions during
particular periods in an individual's life

3. .
The fact that the normal flora substantially influences the well-being of the host was not well
understood until germ-free animals became available. Germ-free animals were obtained by
cesarean section and maintained in special isolators; this allowed the investigator to raise them
in an environment free from detectable viruses, bacteria, and other organisms. Two interesting
observations were made about animals raised under germ-free conditions.

4. the germ-free animals lived almost
twice as long as their conventionally
maintained counterparts.
second, the major causes of
death were different in the two
groups.

5. Infection often caused death in conventional animals, but
intestinal atonia frequently killed germ-free animals. Other
investigations showed that germ-free animals have anatomic,
physiologic, and immunologic features not shared with
conventional animals. For example, in germ-free animals, the
alimentary lamina propria is underdeveloped, little or no
immunoglobulin is present in sera or secretions, intestinal
motility is reduced, and the intestinal epithelial cell renewal rate
is approximately one-half that of normal animals (4 rather than 2
days).

6. Do you know which bacteria sps. Are
prominent on our body????
CORYNEBACTERIUM PROPIONIBACTERIUM
STAPHYLOCOCCUS

7. Sites that harbor a normal flora
Skin and it's continuous mucous membrane.
Upper respiratory tract.
The GI tract.
Outer opening of urethra.
External genitalia
External ear canal
External eye

8. Sterile (microbe free) Anatomical sites and
fluids
 Heart and circulatory system
Liver
Kidneys and bladder
Lungs
Brain and spinalcord
Muscles
All internal tissues and organs like bones,blood,CSF,etc

9. Flora can be further divided into:
FLORA
Transient
Transient microbes are just passing
through. Although they may
attempt to colonize the same areas
of the body as do
resident microbiota, transients are
unable to remain in the body for
extended periods of time due to:
difficulty competing with
established resident microbes.
Resident
These are the permanent
colonizers in host

10. What these flora includes?
Normal resident flora – 1.Bacterias
2.Fungi
3.Protozoa
4.Viruses etc
Resident flora is more stable than transient flora

11. Initial colonizers of newborn
Within 8-12 hours of the delivery, the newbie is colonized by bacterias such as Streptococci
Staphylococci and Lactobacilli.
The type of feeding also determine the colonizers like, if the newborn baby is bottle-feed (formulated milk)
then the colonizers are coliforms,lactobacilli,enteric streptococci,staphylococci.
Whereas the ones which are breast fed will have bifidobacterium

12. Flora of Human skin
The varied environment
of the skin results in
locally dense or sparse
populations, with Gram-
positive organisms (e.g.,
staphylococci,
micrococci,
diphtheroids) usually
predominating.

13. The composition of the dermal microflora varies from site to site according to the character of the
microenvironment. A different bacterial flora characterizes each of three regions of skin: (1) axilla,
perineum, and toe webs; (2) hand, face and trunk; and (3) upper arms and legs. Skin sites with partial
occlusion (axilla, perineum, and toe webs) harbor more microorganisms than do less occluded areas (legs,
arms, and trunk). These quantitative differences may relate to increased amount of moisture, higher body
temperature, and greater concentrations of skin surface lipids. The axilla, perineum, and toe webs are
more frequently colonized by Gram-negative bacilli than are drier areas of the skin.

14. *lipophilatic mycobacteria and staphylococci in sebaceous section of axilla,external genitalia and
external ear canal
Normal flora resides on the deadcell layer and never in follicles and
glands and subcutaneous dermis.
Rich flora is observed in mucous membranes of nose,mouth and
external genitalia.
*SMEGMA:- a secretion on external genitalia of men and women –
Mycobacterium smegmatis

15. Flora of G.I tract
The GI tract includes-
 Oral cavity
 Oesophagous
 Stomach
 Small intestine
 Large intestine
 Rectum and anus
Abundance of flora-
1. Oral cavity
2.Large intestine
3.Rectum

16. Flora of Mouth
These are aerobic in nature
the oral cavity, or mouth, includes several distinct microbial habitats, such as teeth, gingival sulcus,
attached gingiva, tongue, cheek, lip, hard palate, and soft palate. Contiguous with the oral cavity are the
tonsils, pharynx, esophagus, Eustachian tube, middle ear, trachea, lungs, nasal passages, and sinuses. We
define the human oral microbiome as all the microorganisms that are found on or in the human oral cavity
and its contiguous extensions (stopping at the distal esophagus), though most of our studies and samples
have been obtained from within the oral cavity.
Main sps. Here are streptococcus- S.sanguis,S.mitis,S.salivarius.
S.mutants and S.sanguis on teeeth surfaces

18. Flora of Respiratory tract
The respiratory tract includes-
Nasal cavity Staphylococcus aureus
Oropharynx/nasopharynx
Streptococcus,Candida specie
,Neisseria meningitidis
Lower respiratory tract
Streptococcus sps.,S aureus, S
pneumoniae
* Lungs and bronchi are
sterile

19. Flora of Genitourinary tract
In healthy individual kidney, urinary bladder and ureter are sterile. Furthermore
urine collected in urinary bladder is also sterile.
Urethra of both male and female have normal flora. Surrounding skin microflora
gradually ascends up through urethra and get established there. But frequent
passing of urine removes microorganisms so that they cannot reach urinary
bladder.
Only lower portion of urethra contains normal flora and upper portion contains
very few or no microflora.

20. Urethra:
• contains mostly gram
positive bacteria such
as;
• Staphylococcus
epidermidis
• Streptococcus faecalis,
• non
pathogenic Neisseria sp
ecies
• Corynebacterium spp
• *male urethra is
relatively sterile than
female urethra
• Gram negative rods are
opportunistic pathogen
causing UTI
• Internal organs such as
testis, ovary, ureter etc
are sterile in healthy
individuals.
• Urethra and vagina
contains microflora.
vagina:
• Normal flora of vaginal
tract depends upon age
and menstrual cycle.
• Lactobacillus is
predominant
• During this period ovary
is active and produces
large amount of
glycogen. Lactobacillus f
erments glycogen to
form lactic acid
maintaining pH highly
acidic (4.4-4.6). at this
pH only acid tolerant
Lactobacillus can grow.

21. Gnotobiotics
The word gnotobiotic is derived from the Greek words gnotos and biota meaning known flora or
fauna. Therefore, when referring to gnotobiotes (GNs), one refers to an animal with a known flora or
fauna. This term also is applicable when a microbial flora does not exist or is not detectable
Gnotobiotics has made possible the study of many biological functions unhampered by
normal body contamination.

22. https://www.taconic.com/taconic-insights/microbiome-and-germ-free/what-are-germ-free-mice.html
The terms axenic and gnotobiotic refer to animals that harbor no
cultivatable organisms or have a completely defined microbiological
flora, respectively (see gnotobiology chapter); as a consequence, the
health status of these animals regarding pathogenic or opportunistic
agents is relatively easy to characterize.

23. The portal of entry
A portal of entry is the site through which micro-organisms enter the susceptible host and cause
disease/infection.
Infectious agents enter the body through various portals, including the mucous membranes, the skin, the
respiratory and the gastrointestinal tracts.
Pathogens often enter the body of the host through the same route they exited the reservoir; for example,
airborne pathogens from one person�s sneeze can enter through the nose of another person.

24. 1.skin
The skin normally serves as
a barrier to infection.
However, any break in the
skin invites the entrance of
pathogens, such as tubes
placed in body cavities
(catheters) or punctures
produced by invasive
procedures (needles, IV).

25. Via gastrointestinal tract
Although the surface of the alimentary tract is potentially exposed to a great
number and variety of viruses, the harsh conditions in the stomach and
duodenum protect it from many viruses. For instance, viruses that have a lipid-
containing envelope are usually inactivated by the acid, bile salts and enzymes
that occur in the stomach and duodenum. Infection via the gut, therefore, is due
to viruses that resist these chemicals. These viruses multiply in the cells of the
small intestine and are excreted in the feces (Table 48-3). Such viruses usually
resist environmental conditions and may cause water- and food-borne
epidemics.

26. Via respiratory tract
In modern Western society the respiratory tract is by far the most common route of viral
infection. The average human adult breathes in about 600 L of air every hour; small suspended
particles (<2 μm diameter) pass down the pharynx and a few reach the alveoli. Viruses in such
droplets may initiate infection if they attach to cells of the respiratory tract. Many respiratory
viruses are also transferred by contact with contaminated fingers or fomites (inanimate carriers).
The viruses commonly referred to as the respiratory viruses multiply only in the respiratory tract
and cause colds, pharyngitis, bronchiolitis, and pneumonia; other viruses that initiate infection
via the respiratory tract can produce generalized infection

27. Via urinary tract
During the last decade the list of sexually transmitted viruses (Table 48-4) of the female genital tract has
been enlarged by the demonstration of heterosexual transmission of HIV, the human T-cell lymphotropic
virus type 1 (HTLV-1) and possibily hepatitis C virus. The importance of genital transmission of particular
papillomaviruses in the causation of cervical carcinoma is receiving much attention (seeCh. 66). Genital
ulcers due to herpes simplex type 2 (HSV-2), a sexually transmitted virus, are important in themselves and
increase the likelihood of heterosexual transmission of HIV.

28. THE SIZE OF INOCULUM
A small amount of substance containing bacteria from a pure culture
which is used to start a new culture or to infect an experimental
animal.
Infectious dose- the smallest or the largest quantity of infectious
material that regularly produces infection

29. In general ,microorganisms with small infectious dose have greater
virulence. The ID varies from astonishing number of 1 rickettsial
cell in Q fever to about 10 infectious cells in TB,giardiasis etc.
enterohemorrhagic strains of Escherichia coli require an infective
dose of only about ten cells. By contrast, other pathogens, such
as Vibrio cholerae, require a large number of cells (103 to 108 cells)
in the inoculum to successfully infect a host.

30. Mechanisms of invasion and establishment
of the PATHOGEN
Following entry of the pathogen,the next stage in infection requires that the pathogen
1.Bind to the host
2.Penetrates it's
barrier
3.Become
established in the
tissues

31. Successful establishment of infection by bacterial pathogens requires
adhesion to host cells, colonization of tissues, and in certain cases,
cellular invasion—followed by intracellular multiplication,
dissemination to other tissues, or persistence.

34. Factors that are produced by a microorganism and
evoke disease are called virulence factors.
Examples are toxins, surface coats that inhibit
phagocytosis, and surface receptors that bind to
host cells. Most frank (as opposed to opportunistic)
bacterial pathogens have evolved specific virulence
factors that allow them to multiply in their host or
vector without being killed or expelled by the
host's defenses. Many virulence factors are
produced only by specific virulent strains of a
microorganism. For example, only certain strains
of E. coli secrete diarrhea-causing enterotoxins

36. Microorganisms invading tissues are first and foremost
exposed to phagocytes. Bacteria that readily attract
phagocytes and that are easily ingested and killed are
generally unsuccessful as pathogens. In contrast, most
bacteria that are successful as pathogens interfere to some
extent with the activities of phagocytes or in some way
avoid their attention.Bacterial pathogens have devised
numerous and diverse strategies to avoid phagocytic
engulfment and killing. Most are aimed at blocking one or
more of the steps in phagocytosis, thereby halting the
process. The process of phagocytosis is discussed in the
chapter on Innate Immunity against bacterial pathog

37. Bacteria can avoid the attention of phagocytes in a number of ways.
1. Pathogens may invade or remain confined in regions inaccessible to
phagocytes. Certain internal tissues (e.g. the lumens of glands, the urinary
bladder) and surface tissues (e.g. unbroken skin) are not patrolled by phagocytes.
2. Some pathogens are able to avoid provoking an overwhelming
inflammatory response. Without inflammation the host is unable to focus the
phagocytic defenses.
3. Some bacteria or their products inhibit phagocyte chemotaxis. For example,
Streptococcal streptolysin (which also kills phagocytes) suppresses neutrophil
chemotaxis, even in very low concentrations. Fractions of Mycobacterium
tuberculosis are known to inhibit leukocyte migration. The Clostridium ø toxin also
inhibits neutrophil chemotaxis.
4. Some pathogens can cover the surface of the bacterial cell with a component
which is seen as "self" by the host phagocytes and immune system. Such a
strategy hides the antigenic surface of the bacterial cell.

38. Organism Disease
Mycobacterium tuberculosis Tuberculosis
Mycobacterium leprae Leprosy
Listeria monocytogenes Listeriosis
Salmonella typhi Typhoid Fever
Shigella dysenteriae Bacillary dysentery
Yersinia pestis Plague
Brucella species
Brucellosis
Legionella pneumophila Pneumonia
Rickettsiae Typhus; Rocky Mountain Spotted Fever
Chlamydia Chlamydia; Trachoma