NORMAL MICROBIAL FLORA OF
THE HUMAN BODY
1 OBJECTIVES
After reading this chapter, the student will be able to:
, Explain the concept of normal microbial flora
, Explain the beneficial and detrimental effects of the
Human beings, like other animals, harbour a wide
array of microorga nis ms both on and in their bodies.
The normal microbial fl ora are more or less constant
for each species and are broadly divided into residents
and transients. The former constitute a constant
population which cannot be completely removed
permanently, while the latter vary from time to time
and are temporary. The residents prevent permanent
colonisation of the body by other organisms.
Aknowledge of the normal flora of the body is essential
for an understanding of the interaction of human
beings and their pathogen laden environment. The
normal microbial flora play an important role in body
economy. They can:
I. become pathogenic when host defences falter,
. .
2. prevent or interfere with colonisation / invasion
the body by pathogens, . staphylococci of strain 502 A which are harmless and
3· raise the overall immune status of the ho st agamS t
· and
pathogens having related or share d antigens,
4· cause confusion . m · d ue to their ubiquitous
. d1agnos1s
.
presence in the body and their resemblance tol
f the norma
some of the pathogens. Mem bers O . d
fl 0 ra form part and parcel of the hOst and me1u de
. athogens an
saprophytes, commensals, facultative P
true patho
gens . thesise
. The microflora of the intestinal tr~ct syn ly on
Vttam· K . • which supp
in and several B v1tamms . bstances
Occasion the body's needs . The antibiotic su
. .
norma 1micro 6101 flora for the host
produced by some, fo r example, colicins, have a
harmful effect on pathogens. The endotoxins liberated
by them may help the defence mec hanism of the body
by triggering the alternative complement pathway, as
long as they are not produced in excessive amounts.
On the contrary, the opportunistic pathogens among
them cause disease when the body's defence mechanisms
fail. Their abnormal multiplication can cause diseases
such as enteritis and endotox.ic shock. Penicillinase
producing organisms can aggravate infection by
interfering with therapy. Certain streptococci of the
mouth cause dental caries.
In environments laden with pathogens, for example,
hospitals, a shift in the normal flora of the individuals
there can cause an increase in carriage of antibiotic
f
° resistant staphylococci. It has also been shown that
such people can be recolonised with penicillin sensitive
thus overcome the damage done. When large numbers
of people congregate from different parts of the country
as in army camps, the new recruits experience increased
colonisation rates of Neisseria meningitidis and Group
A streptococcus and viruses such as rhino viruses
and adenoviruses, sometimes resulting in epidemics.
Normal Flora of tire Ski11
The human skin is constantly and continuously
bombarded by organisms present in the environment.
·~
~ 588 CHAPTER 63
f\m•mal Flora ,~f //,e Conjunctit·u
It is also contaminated bY one ·s own :s·ccrctions and
. . . . •,
exc retions, the extent depending on 1hc 111d1v1d~a~S. The conjunctiva io relatively free from orga .
personal hygiene. The tlon1 depend ,on the ar~~ o f I ~
. .
the llush111g . .
ac ti on o f·' tears. "l'h e predominant
n1srns .dlie to
body the clothing one wears. ones occupation an of the eye are diphth ero ids (Corynebacteriu organi&rns
'
environment. .
Transient •
m1crollora d
ten to 0
ccur more Moraxella species, staphylococci and nomh xero~isJ
n ern 0 I ,
frequently on the skin. . d streptococci. Ytic
Cultures fron1 the skin have frequently demons ti ate .
. (mclu
. d'mg prop10111
· ·bac ten·a)., staphylococci Normal Flora uf•tlie No."ie, Na .,opliclr Vtt t
diphthero,ds . .
am/ -tccessory Srnuses · ·
(aerobic and anaerobic) : Gram-positive, aerobic, sp~re
bearing bacilli; Str viridans; Str faecalis; Gram~nega~1ve The floor of the nose harbours coryneb .
bacilli such as E coli, Proteus and other mtesti_nal . d . H acteria
staphy1ococc1 an streptococc1. aemophilus s e . ,
organisms; mimieae; mycobacteria (non-pathogemc); and Moraxella lacunata may also be seen . p cies
Candida albicans; cryptococci and Pityrosporum ovate. The nasopharynx of the infant is sterile at .
Often the skin of the face, neck, hands and buttocks 6
but, within 2-3 days after birth, acquires the com:~h
carries pathogenic hemolytic streptococci . and commensal flora and the pathogenic flora carried hn
staphylococci. PenicilJin resistant staphylococci are the mother and the attendants. The nasopharynx Y
seen in individuals working in hospitals. be considered the natural habitat of the com~an
Hair frequentl y harbours Staph aureus and forms a pathogenic bacteria which cause infections of the no~n
reservoir for cross-infection (Fig. 63. 1) . throat, bronchi and lungs. Certain Gram-negati:~

Scalp
as skin I Nose
Staph, aureus
Staph, epidrmidis
Teeth Diphtheroids
Streptococcus mutans streptococci
Bacteroides
Fusobacterium
streptococci Mouth
actinomyces Strep. mitis and
other streptococci
Trichomonas tenax
Throat Candida
Strep. viridans
Strep. pyogenes
Strep. pneumoniae
Lung
Neisseria spp. Pneumocystis jiroveci
Staphylococcus
epidermidis
Haemophilus Intestine*
influenzae

Urethra and vagina

Skin Staphylococcus
Staph. epidermidis epidermidis
Staph. aureus Diphtheroids
diphtheroids streptococci
Gram-negative rods
streptococci
Pseudomonas
aeruginosa
anaerobes, Candida Groin and perineum
Torulopsis as skin
Pityrosporum

Feet
as skin

Fig. 63.1 Ex J f . d
. h . amp es o orgamsms that oc . . . *Those fout1
m t e intestine are detailed · p· cur as members ot the normal flora and their location on the body. (
m 1gure 63.2.)
 ifi"Rr-
NormaiifRf g; f■#W Body ; 89 -
requ,ncy o ocourreno•
In o ulatlon

small . . . . . ......_
bowel
duodenu

Bactero/des spp. Enterobacterla

Fusobacterlum spp Klebsle/la spp.
large Slrep faecalis eubacterla
bowel Escherichia coll blfldobacterla

Lactobaclllus Streptococci
Staph aureus Pseudomonas
Clostrldium spp Salmonella

Bacteroldes spp. Col1forms

fecal
blfidobacterla Strep faeca/1s
materlal
eubacterla

density frequncy
3 5
very low (10 - 10 /g) IIIJ <10% CJ
5 8
low (10 - 10 /g) c:::::J 10- 25% CJ
10
medium (1o'-10 tg) - 25-75% CJ
10
high (>10 /g) la!J 100% CJ

Fig. 63.2 The longitudinal distribution, frequency of occurrence nnd densities of the bacteria making up the normal
flora of the human gastrointestinal tract.

organisms from the intestinal tract such as Pseudomonas
aeruginosa, E coli, paracolons and Proteus are also
occasionally found in normal persons. After penicillin
therapy, they may be the predominant flora.
Normal Flora of the Mouth a11d Upper
Respirat01:v Tract
T.he mouth contains a plethora of o~ganisms-
pig.mented and nonpigmented micrococci, . some of
which are aerobic, Gram-positive, aerobic, sp?r~
bearing bacilli coliforms Proteus and lactobacillt.
The gum pock~ts between' the teeth, and the. crypts of
the tonsils have a wide spectrum of anaerobic flora-.
anaer0 b'1c m1crococc1
. . m1croaerop
. hil'ic and
· anaerobic
. flora similar to that of the mouth establish themselves.
streptococci vibrios fusiform bacilli, corynebactenum
species ' . ' h• mycoplasma,
n . , actmomyces leptot nx, .
eisseria and bacteroides are all fou nd in varying
extents. Among fungi , Candida and geotrichum have
been reported.
The mouth of the infant is not sterile at birth.
It generally contains the same types of organisms in
about the same relative numbers as those present in
the mother's vagina, that is a mixture of micrococci,
streptococci, coUform bacilli and Doderlein's bacilli.
These organisms diminish in number during the first
2-5 days after birth and are replaced by the types of
bacteria present in the mouth of the mother and nurse.
Within 12 hours after birth alpha hemolytic
streptococci are found in the upper respiratory tract
and be come the dominant organisms of the oropharynx
and remain so for life. In the pharynx and trachea,
Few bacteria are found in normal bronchi. Smaller
bronchi and alveoli are normally sterile.
 ·~
\,,, .., ,/ I'''"' ol 1/,,· /111,·,111111/ I,,,..,
In 80 9 l) pe r cen t L)f t1L'Wlll.11·n i111'11n1 s. tlw 1111..•c1.) ~1iu 111
is stnik bul in I 0- .20 per l'l' lll II kw or~11111t-l11ts.
pr1)bnbly ncquirl·d duri11i,.r labum. nwy bl· . pn:sent ·
In 11 11 L.:nscs. within 4- 24 hours of birth int cs 111111l ll orn
is l'Slllblishcd pnrtly frum bd ow nnd partly by in vns i_on
fro m ubow. ln bn::us tfod d 1ildrr n the inrcs tinc con!flins
lnl' tobm.: illi (L llifidus cunstituting qq per ce nt ~f.t:ota l
urgn nisms in the fl'Ces). cnt crocorci. colon bnc,I~• ond
staphylococc i. In artilk inlly fed (bottlcfcd) ch1ldre~1
L acidophi/11s and c:ulon bocilli nnd in part cnrcrococc,.
Gra m-positive aerobic and anaerobic bncilli ore seen.
Wirh the change of food ro the adult pa ttern , the tlora
L.: hange. Diet has a mar ked influence on the relative
composition of the intestinal and feca l fl ora.
In the normal adult, rhe microorganisms on the
surface of the esophagea l wall are those swallowed
with saliva and food. Beca use of the low pH of the
stomach, it is virtually sterile except soon after eating.
In pati ents with ca rcinoma of the stomach or
ac hl orhydria or pyloric obstruction, there is proliferation
of Grampositive cocci and bac illi .
The number of bacteria increases progressively
beyond the duodenum to the colon, being comparatively
low in the small intes tine. In the adult duodenum
there are. I 03 ~ 10 6 bac teria i er gran~ , in th e jejunum
and proximal ileum Io5 - t O bac tena per gra m, and
in the lower ileum and cecum I0 8 - IO I bac teria
per gram of con tents. In the duodenum and upper
ileum, lactobacilli and enterococci predominate but
in the lower ileum and cecum the flora resemble the
fecal flora . There are about IO 11 bacteria per gram of
contents in the colon and rectum, constituting 10-20
per cent of the fecal mass. In the adult normal colon,
the resident bacterial flora are mostly (96-99 per
cent) anaerobes-anaerobic streptococci, anaerobic
lactobacilli, clostridia and bacteroides and about
1- 4 per cent aerobes-enterococci, coliforms and
smaU numbers of Proteus, Pseudomonas, lactobacilli,
mycoplasma, Candida and others.
Normal Flora of the Genitourinary Traci
Mycobacterium smegma tis, a harmless commensal,
is found in the smegma of the genitalia of both men
and women. This may, by its presence in the voided
specimens of urine, cause confusion. From apparently
normal men, aerobic and anaerobic bacteria can be
nilturcu from II high propor tion, includi
.
, ll 1IS,
(jurcl l'C l ~ /1/ · "/1
.
I I /(/ I/i..'111u/v1ic SI ng lact(.) bctcj11 ·
, . . repiuco .· I,
/Jt1ctero11/cs s11i:c1cs. ( hlw 11 trac/1011 101;5u d U C(i CJ,1,,
. ,, reu I "
11 rea lw1c11111 11 wy ulsu bl'. prcticn t. The f. Pus,,
. . . cm;:i 1e u . 1"
cithl! r SIL' t'llc ur l:Unto ms u fow Gran, -po . . rcthrc1 i\
. 1i l11 v1: c . ,
The vul vu ol th e newborn child b st . lltL1 .
. . . er, 1c b ,
24 hours 11 acquires a va ncc.J fl ora of n ui <1ftcr
. . . onpa1hu
orga ni sms fro m the sk111 , vagi na and . &cn1l
The nature of th e fl orn in the vag ina dcpe '~tc~tinc,.
pH of its secretions and it s enzyme co ntent ~ s on lhe
24 hours it is invaded by mi crococc i ente. n th e fi r~1
. ' rococci
diph thero1ds. In 2- 3 days, the maternal estri . and
.. . h n Induce
gly~?gen depos1t1on 111 t e vag inal epithelium. T .~
fac ilitates the growth of a lactobac iUus (Dod _h'.s
1
bacillus) whi ch produces acid from glycogen er; 1ns
th
fl ora fo r a few weeks is similar to that of the ad·u~t f e
. Iy trans ferred estrm
the pass ive . has been eliminated• . A ler
. . in the
ur111 e, the glycogen disa ppears, along with Dode 1 .
. . r e1n's
bac illu s and th e pH of the vagma becomes alkali
This brings about a change in the fl ora to micrococn~.
. CJ,
alpha and nonhemoIyt1 c streptococci, coliforms and
diphtheroids.
At puberty, the glycogen reappea rs and the pH
changes to ac id due to the metabolic activity of
Doderlein 's bac illi , £ coli and yeasts. This change
probably helps prevent colonisation by possible
harm ful microo rga nisms. During pregnancy there is
an increase in Staphylococcus epidermidis, Doderlein's
bacilli and yeasts. Occasionally other members of the
intestinal flora may be present. After menopause, the
flora resembles that found before puberty. The normal
vaginal flora often includes anaerobic cocci and bacilli,
listeria, anaerobic streptococci, mimeae, mycoplasma,
Gardnerella vagina/is, neisseriae and spirochetes.
Bacteria iu tire Blood anci Tissue~
The commensals from the normal flora of the mouth,
nasopharynx and intestinal tract may get into the blood
and tissues. They are usually quickly eliminated b~ the
normal defence mechanisms of the body. Occasiona~
isolation of diphtheroids or non hemolytic streptococci
d be those
from normal and abnormal lymp h no es may . of
which escaped elimination. Unless the organisms .
10
doubtful pathogenicity are isolated more th an once
serial blood cultures, they have little significance.