The human microbiome comprises of collective genome of all the microbes residing at various sites in the human body and consisting of communities of a variety of microorganisms, including Eukaryotes, Archaea, Bacteria and the virus that reside in the different body habitat including the skin, the oral cavity, respiratory tract, gastrointestinal tract, urinary tract, reproductive tract etc. We acquire these bacteria during birth and the first year of life, and they live with us throughout our lives. The human microbiota helps us to keep healthy, but sometimes these bacteria can also be harmful. We need to take good care of our microbiota to avoid the development of some diseases, such as obesity and asthma. We should eat healthy foods that contribute to the development of a healthy microbiota. The study of the human microbiome is important, and it gives an in-depth understanding of the interplay between humans and its indigenous microbiota. This gives valuable insight into further research studies in optimizing these organisms to combating life-threatening diseases.

1. Manita Paneri
PhD Scholar (Medical Microbiology)
HUMAN MICROBIOME: FRIEND AND FOE

2. Overview
1. Definition
2. Types of microbiota
3. Human as Microbiome
4. Dominant phyla
5. Bacteria as a friend
6. Bacteria as our enemy
7. The Human Microbiome in health sustenance
8. The Human Microbiome and diseases
9. Microbiome of skin, oral cavity, Respiratory system, gut, urinary system
10. Conclusion

3. Definition:
• The human microbiome comprises of collective genome of all the
microbes residing at various sites in the human body and consisting of
communities of a variety of microorganisms, including Eukaryotes,
Archaea, Bacteria and the virus that reside in the different body
habitat including the skin, the oral cavity, respiratory tract,
gastrointestinal tract, urinary tract, reproductive tract etc.

4. MICROBIOTA
RESIDENT
MICROBIOTA
TRANSIENT
MICROBIOTA
E.coli
Streptococcus viridans

5. Human as Microbiome
• 10-100 trillion microbes live
inside the human body.
• The vast majority lives in the
intestine.

6. DOMINANT PHYLA
Firmicutes(60-80%)
Bacteroidetes(20-30%)
Actinobacteria(<10%)
Proteobacteria(<1%)

7. Phyla Representative genera
Firmicutes Ruminococcus
Enterococcus
Lactobacillus
Clostridium
Bacteroidetes Bacteroides
Actinobacteria Bifidobacterium
Proteobacteria Escherichia
Enterobacteriaceae

11. Bifidobacterium:
• Bifidobacterium is a genus of gram positive, none motile, often
branched anaerobic bacteria.
• Bifidobacteria are one of the major genera of bacteria that makes up
the gastrointestinal tract microbiota in mammals.
• Some Bifidobacteria are used as probiotics.

12. Bifidobacterium bifidum:
The use of Bifidobacterium bifidum in a probiotic applications may reduce the chances of acute
diarrhoea and the risk of E.coli infections, and contributes to the maintenance of vaginal
homeostasis.
Bifidobacterium infantis:
Bifidobacterium infantis may help to relieve the symptoms of Irritable bowel syndrome, such as
abdominal pain, gas and bloating.
Bifidobacterium lactis:
Bifidobacterium lactis has been reported to improve cholesterol levels in women and in people
with type 2 diabetes.

13. E.coli
• Escherichia coli is a gram-negative, facultative anaerobic, rod
shaped bacteria that is commonly found in the lower
intestine.
• Most E.coli strains are harmless and they are part of the
normal microbiota of the gut, and can be benefit their hosts
by producing vitamin K, and preventing colonisation of the
intestine with pathogenic bacteria, having a symbiotic
relationship.

14. Lactobacillus
• Lactobacillus is a Gram-positive, rod shaped, microaerophilic
bacteria.
• Lactobacilli species constitute a significant component of the
human microbiota at a number of body sites, such as the digestive
system, and the genital system.
• Lactobacillus exhibits a mutualistic relationship with the human
body as it protects the host against potential invasions by
pathogens, and in turn, the host provides a source of nutrients.
• lactobacilli are among the most common probiotic found in food
such as yogurt.

15. Lactobacillus acidophilus is found in yogurt and fermented soy products. It has been used to treat
bacterial infections of the vagina in suppository form. In pill form, it can be taken to prevent and treat
diarrhoea, including traveller's diarrhoea in adults and diarrhoea caused by rotavirus in children.
Lactobacillus rhamnosus GG may help to treat traveller’s diarrhoea or diarrhoea that caused by
Clostridium difficile or by antibiotics in children. It’s also been found to prevent eczema in infants.
Lactobacillus salivarius may help to block the growth of Helicobacter pylori, the bacteria that cause
peptic ulcers.
Lactobacillus plantarum can improve the immune system barrier against invading disease-causing
bacteria.

16. Streptococcus thermophilus
• It is a gram-positive bacterium, and a fermentative facultative
anaerobe.
• It is found in fermented milk products, and is generally used in the
production of yogurt. In fact, yogurt and cheese that contain live
cultures of S. thermophilus are thought to be beneficial to health.
• These bacteria produce enzyme lactase, which the body needs to
digest the sugar in milk and other dairy products. So, Streptococcus
thermophilus make it easier for people who are lactose intolerant to
digest dairy products.
• Strains of S. thermophilus have also reduced risks of antibiotic-
associated diarrhoea.

18. Streptococcus pneumoniae
• Streptococcus pneumoniae is a gram-positive, facultative
anaerobic bacteria.
• They are usually found in the pairs and are not motile.
• Streptococcus pneumoniae resides asymptomatically in healthy
carriers typically colonizing the respiratory tract, sinuses and nasal
cavity.
• However, in susceptible individuals with weaker immune systems,
such as the elderly and young children, the bacterium may
become pathogenic and spread to other locations to cause
disease.
• After Streptococcus pneumoniae colonizes the air sacs of the
lungs, the body responds by stimulating the inflammatory
responses, causing plasma, blood and white blood cells to fill the
alveoli. This condition is called pneumonia.
• The organism also causes meningitis, bronchitis, endocarditis,
otitis media, acute sinusitis etc.

19. Enterococcus faecalis
• It is a gram-positive, commensal bacterium inhabiting the
gastrointestinal tracts of humans and other mammals.
• E. Faecalis is found in healthy humans, but can cause life-threatening
infections, especially in the nosocomial environment.
• It can causes endocarditis and sepsis, urinary tract infections,
meningitis .
• E. Faecalis is resistant to many commonly used antimicrobial agents
like cephalosporin, clindamycin, oxacillin , vancomycin etc.

20. Clostridium difficile
• It is a gram-positive, anaerobic, motile bacteria.
• It is commonly known as a hospital and antibiotic associated
pathogen.
• C. difficile can also become established in the human colon
without causing disease.
• Pathogenic C. difficile strains produces enterotoxin and cytotoxin,
both of which may produce diarrhoea and inflammation in the
infected patients.
• The bacterium also produces the chemical Para-cresol, which
inhibits the growth of other microbes in its vicinity and allows it
to outcompete normal human gut flora.

21. Helicobacter pylori
• Helicobacter pylori is a gram-negative, helical bacterium
usually found in stomach.
• Its helical shape is thought to have evolved in order to
penetrate the mucoid lining of the stomach and thereby
establish infection.
• To avoid the acidic environment of the interior of the
stomach, helicobacter pylori uses its flagella to burrow into
the mucus lining of the stomach to reach the epithelial cells
underneath, where it is less acidic. It is able to sense the pH
gradient in the mucus and move towards the less acidic
region.
• It cause gastritis, ulcers of the stomach.

22. HUMAN
MICROBIOME
Development
of immune
system
Colonization
resistance
Maintenance
of
homeostasis
Host nutrition
The Human Microbiome in health sustenance

23. Human
Microbiome and
Diseases
Cancer
Systemic
Infections
Cardiovascular
Diseases
Inflammatory
Bowel Diseases

24. Skin Microbiome
• Prominent population- Actinobacteria
( Corynebacterium spp., Propionibacterium spp.)
in the portion of the body that are richly supplied
with sebaceous glands whereas dry areas such as
volar forearm are enriched with Proteobacteria.
• Staphylococcus spp. and Corynebacterium spp.
are the most common microbes colonizing moist
areas such as the antecubital fossa, the gluteal
crease, popliteal fossa, umbilicus etc.

25. Benefits of skin microbiome
• Protects human from other pathogenic bacteria by
producing bacteriocin, some toxic metabolites etc.
• The extracellular enzyme produced by cutaneous microbes
hydrolyse the host macromolecules to low molecular mass
compounds that can be transported inside the cell to serve
as nutrients.
• A resident bacterium also competes with the another strain
of a similar species for the resources available such as
binding sites, nutrients etc. and prevent their colonization.
Disease caused by skin microbiome
• Cellulitis
• Impetigo
• Acne
• Wound infection
• dermatitis

26. Oral Microbiome

27. Benefits of oral microbiome
• These microbes can hydrolyse the non-digestible polysaccharide
into small chain fatty acids which are then metabolized by a
human.
• Gluten, the dietary protein that is difficult to digest by the human
proteolytic enzyme is degraded by the endo-protease produced
by some oral microbes and thereby helping in digestion.
• Oral microbiome reduces nitrate to nitrite. Nitrite is then
converted into nitric oxide which has antimicrobial property.
• Certain strains of Lactobacillus that produce vitamin B12 are also
found in the oral cavity.
Diseases caused by
oral microbiome
• Dental carries
• Periodontitis
• Gingivitis

28. Respiratory tract Microbiome
The most common bacterial species include:
• Streptococcus pyogenes
• Streptococcus viridans
• Streptococcus pneumoniae
• Corynebacterium diphtheriae
• Staphylococcus aureus
• Mycobacterium tuberculosis
• Pseudomonas aeruginosa
• Klebsiella spp.
• Haemophilus influenza

29. Benefits of Respiratory Microbiome
• The microbiota present in the respiratory tract acts as a
doorkeeper to respiratory health.
• They provide resistance to colonization by the potential pathogens
of the respiratory system.
• The microbiome of the pharynx region plays a vital role in
respiratory tract infection by protecting the airway lining against
air transmitted pathogenic infection.
• Corynebacterium spp. play a crucial role in respiratory tract health
and the exclusion of pathogenic bacteria such as Streptococcus
pneumoniae, Klebsiella spp., Haemophilus spp. etc.
Diseases caused by
respiratory microbiome
• Pharyngitis
• Pneumonia
• Sinusitis

30. Gut Microbiome

31. Benefits of Gut Microbiome
1. Metabolic Function:
The gut microbiome in the humans, helps in the degradation of undigested carbohydrate that
includes large polysaccharides such as cellulose, hemicellulose, pectin; unabsorbed sugar and
alcohol which are degraded into various short chain fatty acids(butyrate, propionate, acetate).
The gut microbiome also helps in synthesis of vitamins (E.coli produce vitamin K) and help in
absorption of ions such as magnesium, iron and calcium.

32. 2. Tropic function:
• SCFs produced by some gut microbiome can play an essential role in the tropic
function of the human gut.
• The three main SCFs (butyrate, propionate, acetate) stimulate the proliferation
and differentiation of the epithelial cells
3. Protective function:
• The human gut microbiome serves as the first line of defence along with the host
defence mechanisms to counter invasion and subsequent infection by various
pathogenic microbes.
• Resident gut microbiota of the human gut contribute to the colonization
resistance by inhibiting the attachment site of entry of pathogenic bacteria for
colonization.
• Lactobacillus acidophilus compete with other pathogenic bacteria for nutrient
availability along with the production of bacteriocin to obstruct the growth of
the competitor.
Diseases caused by
gut microbiome
Irritable Bowel Syndrome
Colorectal Cancer

33. Urinary system and its Microbiome
Main microorganisms colonizing female urethra
are :
Lactobacillus spp., Corynebacterium spp.,
Fusobacterium spp., E. coli, klebsiella spp., Proteus
Bacteroides spp., etc.
The dominant microbes of the male urethra are:
Staphylococci, Corynebacterium spp.,
Streptococcus viridans etc.

34. Role of Urinary tract Microbiome
• Commensal bacteria that present in the urinary tract produce some antimicrobial compound that
kills the pathogens thereby creating a barrier and blocking the pathogen to gain an access to the
uroepithelium and compete with pathogens for same resources.
• Certain bacteria are able to interact with many environmental toxins for instance heavy metals,
pesticide, plastic monomer, organic compounds.

35. Beneficial function of Vaginal Microbiome
• The vaginal microbiome produce antimicrobial compounds like bacteriocin, hydrogen peroxide,
lactic acid and acetic acid and so they protect the vagina against pathogen.
• The vaginal microbiome also helps in prevention of multiple diseases including yeast infection,
sexually transmitted infection, bacterial vaginosis, urinary tract infection.

36. Diseases associated with Urinary tract
Microbiome
• Cystitis
• Urethritis
• Prostatitis
• pyelonephritis
Diseases associated with Vaginal
Microbiome
• Bacterial vaginosis
• Vaginal candidiasis

37. Conclusion:
The study of the human microbiome is important, and it gives an in-depth understanding of the
interplay between humans and its indigenous microbiota. This gives valuable insight into further
research studies in optimizing these organisms to combating life-threatening diseases. It is
important to note that the continuous use of broad-spectrum antibiotics may disrupt the human
microbiota. This results in an imbalance of the resident microbial community paving way for
invading pathogens. However, treatments with the use of pre and probiotics should be encouraged.
Hence, more research should be focused on the use of probiotic therapy in the treatment of
infectious disease. In addition, further studies should emphasize on the effects of the human
microbiome on mental health and also the impacts of mycobiome and the virome community on
resident microbiota as they may contribute to dysbiosis.