Human Microbiome

1. Duration:95 min Middle School Grade: 6 - 8 CCSS, NGSS
Human microbiome
Life Science, Human Biology
Shashika Janith夏亮,
Bio engineering
TUST

2. In microbiology, collective bacteria and other
microorganisms in a host are known as flora.
Although microflora is commonly used, the term
microbiota is becoming more common as microflora
is a misnomer. Flora pertains to the Kingdom
Plantae. Microbiota with animal-like characteristics
are classed as microfauna.

3. Microflora are a community of bacteria that exist on or
inside the body, and possess a unique ecological
relationship with the host. This relationship
encompasses a wide variety of microorganisms and the
interactions between microbes.
Microflora
Human
microbiome

4. Microflora
classification
Microflora are grouped into two categories based on the origin of the
microorganism]
1. Autochthonous flora. - Bacteria and microorganisms native to the host environment.
2. Allochthonous flora. - Temporary microorganisms non-native to the host environment.

5. Normal flora
Normal flora are the microorganisms that live on another living organism (human or animal)
or inanimate object without causing disease. The human body is not sterile; we become
colonised by bacteria from the moment we are born.

6. Microfauna
Microfauna refers to microscopic organisms that exhibit animal-like qualities.
Microfauna are represented in the animal kingdom (e.g., nematodes, small
arthropods) and the protist kingdom (i.e., protozoans). This is in contrast to
microflora which, together with microfauna, make up the microzoa.

7. Human
microbiome
The human microbiome is the aggregate of all
microbiota that reside on or within human
tissues and biofluids along with the
corresponding anatomical sites in which they
reside, including the skin, mammary glands,
placenta, seminal fluid, uterus, ovarian follicles,
lung, saliva, oral mucosa, conjunctiva, biliary
tract, and gastrointestinal tract.

9. Types of human
microbiota
bacteria, archaea, fungi,
protists and viruses and
micro-animals can also
live on the human body

10. We humans are mostly microbes, over 100 trillion of them.
Microbes outnumber our human cells ten to one. The
majority live in our gut, particularly in the large intestine
The microbiome is the genetic material of all the microbes
- bacteria, fungi, protozoa and viruses - that live on and
inside the human body.
The number of genes in all the microbes in one person’s
microbiome is 200 times the number of genes in the
human genome. The microbiome may weigh as much as
five pounds.

11. Bacteria
Populations of microbes (such as bacteria
and yeasts) inhabit the skin and mucosal
surfaces in various parts of the body. Their
role forms part of normal, healthy human
physiology, however if microbe numbers
grow beyond their typical ranges (often due
to a compromised immune system) or if
microbes populate (such as through poor
hygiene or injury) areas of the body
normally not colonized or sterile (such as
the blood, or the lower respiratory tract, or
the abdominal cavity), disease can result
(causing, respectively, bacteremia/sepsis,
pneumonia, and peritonitis).

12. A number of types of bacteria, such as Actinomyces viscosus and A. naeslundii, live in the
mouth, where they are part of a sticky substance called plaque. If this is not removed by
brushing, it hardens into calculus (also called tartar). The same bacteria also secrete acids that
dissolve tooth enamel, causing tooth decay.
The vaginal microflora consist mostly of various lactobacillus species. It was long thought that
the most common of these species was Lactobacillus acidophilus, but it has later been shown
that L. iners is in fact most common, followed by L. crispatus. Other lactobacilli found in the
vagina are L. jensenii, L. delbruekii and L. gasseri. Disturbance of the vaginal flora can lead to
infections such as bacterial vaginosis or candidiasis ("yeast infection").

13. Archaea
Archaea are present in the human gut, but, in contrast to
the enormous variety of bacteria in this organ, the
numbers of archaeal species are much more limited. The
dominant group are the methanogens, particularly
Methanobrevibacter smithii and Methanosphaera
stadtmanae. However, colonization by methanogens is
variable, and only about 50% of humans have easily
detectable populations of these organisms

14. Fungi
Fungi, in particular yeasts, are present in the human gut. The best-studied of these are
Candida species due to their ability to become pathogenic in immunocompromised and
even in healthy hosts. Yeasts are also present on the skin, such as Malassezia species,
where they consume oils secreted from the sebaceous glands.

15. Viruses
Viruses, especially bacterial viruses (bacteriophages), colonize various
body sites. These colonized sites include the skin ,gut , lungs ,and oral
cavity. Virus communities have been associated with some diseases, and
do not simply reflect the bacterial communities.

16. What is the Skin Microbiome?
The billions of microbes living on you are called your skin
microbiome. These microorganisms (sometimes called skin flora) are
harmless or even beneficial playing a vital role in your immune
system and skin appearance. Evolved over thousands of years, the
human microbiome consists of many distinct types of colonies,
depending on the location and condition of the microenvironment.
The microbiota survive off of the salt, water, and oil (sebum) your
skin releases to keep itself cool and lubricated. And several factors
determine the habitat of the various microbiota, like:
• body temperature
• skin thickness
• amount and size of folds
• skin pH
• the density of hair follicles and glands

17. • In other words and not all too surprisingly the microbiota on your face looks different from the
microbiota on your armpits. Areas with higher density of oil glands, like your face, back, and
chest, thrive off of the lipids (fats) in your sebum. Warm, humid areas, such as the groin and
between the toes, host microorganisms that love a danker environment. Meanwhile, dry, cool
patches like your arms and legs have far fewer micro-colonies than the rest of your body. In all,
the average person carries around two pounds of microbes on their body at all times.
• The sheer amount and diversity of skin flora may sound scary. But it’s actually a good and healthy
thing. Having a bountiful, well-balanced microbiome plays an important role in your overall
health, and the appearance of your skin. The microorganisms help produce vitamins, hormones,
and chemicals that affect everything from your mood to metabolism to immune system.

18. What Skin Flora Do for You
• Most people know the skin is the body’s first line of defense against injury or potential pathogens. But it’s
not actually your skin’s cells that act as the front lines of the cavalry. It’s the skin’s microbiome.
• Your skin’s inherent environment is rather unfriendly to bad bacteria. It’s cool and dry. The pH is acidic.
Even sebum, your skin’s lubricant, is antimicrobial. And, ideally, your skin has a bountiful amount of
microbiota to combat all the bad bacteria you come into contact with.
• A healthy skin microbiome, which prefers the acidic environment your skin provides, helps your immune
system out. This likely starts by skin flora overcrowding pathogen overgrowth. Also, your skin’s immune
system and microbiome communicate and respond to one another’s needs.

19. 5 Tips for a Flourishing, Healthy Skin Microbiome
1.Cleanse and dry correctly.
2.Eat well and hydrate.
3.Avoid synthetic fabrics.
4.Choose products wisely.
5.Embrace Your Skin Microbiome.

20. The respiratory tract microbiome

21. • The lungs are not sterile or free from bacteria; rather, they harbor a distinct microbiome
whose composition is driven by different ecological rules than for the gastrointestinal
tract.
• The respiratory microbiome during early life is dynamic and its development is affected
by a range of host and environmental factors, including mode of birth, feeding type,
antibiotic treatment and crowding conditions, such as the presence of siblings and day-
care attendance.
• The upper respiratory tract is colonized by specialized resident bacterial, viral and fungal
assemblages, which presumably prevent potential pathogens from overgrowing and
disseminating towards the lungs, thereby functioning as gatekeepers to respiratory health.

22. • The upper respiratory tract is the primary source of the lung microbiome. In healthy
individuals, the lung microbiome seems to largely consist of transient microorganisms
and its composition is determined by the balance between microbial immigration and
elimination.
• The respiratory microbiome provides cues to the host immune system that seem to be
vital for immune training, organogenesis and the maintenance of immune tolerance.
Increasing evidence supports the existence of a window of opportunity early in life,
during which adequate microbiota sensing is essential for immune maturation and
consecutive respiratory health.
• Composition of the lung microbiota- As LRT sampling is particularly challenging in young
infants , current data on the composition and development of the neonatal LRT
microbiota is limited to samples from intubated prematurely born infants. These studies
showed that the LRT microbiota of premature infants is dominated by pathogenic
Staphylococcus spp. Ureaplasma or Acinetobacter, which highlights the lack of
complexity in these developing bacterial communities.

23. Oral microbiome

24. • Oral microbiome, oral microbiota or oral microflora refers to the microorganisms found in
the human oral cavity. Oral microbiome was first identified by the Dutchman Antony van
Leeuwenhoek who first identified oral microbiome using a microscope constructed by
him.He was called the father of microbiology and a pioneer who discovered both protists
and bacteria. In 1674, he observed his own dental plaque and reported “little living
animalcules prettily moving.”
• Oral microbiome is defined as the collective genome of microorganisms that reside in the
oral cavity. After the gut, it is the second largest microbial community in the humans. As
compared with other body sites, they exhibit an astounding diversity of predicted protein
functions. Human microbiome consists of a core microbiome and a variable microbiome.
The core microbiome is common to all the individuals, whereas variable microbiome is
unique to individuals depending on the lifestyle and physiological differences.

25. COMPOSITION OF THE ORAL MICROBIOME
• A wide range of microorganisms are present in the oral cavity. It is in constant contact
with and has been shown to be vulnerable to the effects of the environment.
• Oral microbiome may show large and rapid changes in composition and activity both
spatially and temporally and are developmentally dynamic with the host. These
multiplex, nonequilibrium dynamics are the result of many factors, such as the
temporal frequency of host and diet, the response to the changes in pH, interactions
among the bacteria and, on a larger time frame, gene mutations and horizontal gene
transfer that extend new properties to the strain.
• The microbial ecology of the oral cavity is complex and is a rich biological setting with
distinctive niches, which provide a unique environment for the colonization of the
microbes. These niches include the gingival sulcus, the tongue, the cheek, the hard and
soft palates, the floor of the mouth, the throat, the saliva and the teeth.

26. • The oral cavity has two types of surfaces on which bacteria can colonize: the hard and
the soft tissues of teeth and the oral mucosa, respectively. The teeth, tongue, cheeks,
gingival sulcus, tonsils, hard palate and soft palate provide a rich environment in which
microorganisms can flourish. The surfaces of the oral cavity are coated with a plethora
of bacteria, the proverbial bacterial biofilm.
• There is a symbiotic relationship between the microorganisms in our oral cavity based
on mutual benefits. The commensal populations do not cause harm and maintain a
check on the pathogenic species by not allowing them to adhere to the mucosa. The
bacteria become pathogenic only after they breach the barrier of the commensals,
causing infection and disease.

27. Gastrointestinal microbiome & Gut
microbiota

28. • In humans, the gut microbiota has the largest numbers of bacteria and the greatest number
of species compared to other areas of the body. In humans, the gut flora is established at
one to two years after birth, by which time the intestinal epithelium and the intestinal
mucosal barrier that it secretes have co-developed in a way that is tolerant to, and even
supportive of, the gut flora and that also provides a barrier to pathogenic organisms.
• The relationship between some gut flora and humans is not merely commensal (a non-
harmful coexistence), but rather a mutualistic relationship. Some human gut
microorganisms benefit the host by fermenting dietary fiber into short-chain fatty acids
(SCFAs), such as acetic acid and butyric acid, which are then absorbed by the host. Intestinal
bacteria also play a role in synthesizing vitamin B and vitamin K as well as metabolizing bile
acids, sterols, and xenobiotics. The systemic importance of the SCFAs and other compounds
they produce are like hormones and the gut flora itself appears to function like an
endocrine organ,[8] and dysregulation of the gut flora has been correlated with a host of
inflammatory and autoimmune conditions.

29. • The composition of human gut microbiota changes over time, when the diet changes, and as
overall health changes. A systematic review from 2016 examined the preclinical and small
human trials that have been conducted with certain commercially available strains of
probiotic bacteria and identified those that had the most potential to be useful for certain
central nervous system disorders.
Stomach
• Due to the high acidity of the stomach, most microorganisms cannot survive there. The main
bacterial inhabitants of the stomach include: Streptococcus, Staphylococcus, Lactobacillus,
Peptostreptococcus. Helicobacter pylori is a gram-negative spiral bacterium that establishes
on gastric mucosa causing chronic gastritis, and peptic ulcer disease, and is a carcinogen for
gastric cancer.

30. Intestine
The small intestine contains a trace amount of microorganisms
due to the proximity and influence of the stomach. Gram-positive
cocci and rod-shaped bacteria are the predominant
microorganisms found in the small intestine.However, in the distal
portion of the small intestine alkaline conditions support gram-
negative bacteria of the Enterobacteriaceae.The bacterial flora of
the small intestine aid in a wide range of intestinal functions. The
bacterial flora provide regulatory signals that enable the
development and utility of the gut. Overgrowth of bacteria in the
small intestine can lead to intestinal failure. In addition the large
intestine contains the largest bacterial ecosystem in the human
body. About 99% of the large intestine and feces flora are made up
of obligate anaerobes such as Bacteroides and Bifidobacterium.
Factors that disrupt the microorganism population of the large
intestine include antibiotics, stress, and parasites.

31. Bacteria make up most of the flora in the colon
and 60% of the dry mass of feces. This fact makes
feces an ideal source of gut flora for any tests and
experiments by extracting the nucleic acid from
fecal specimens, and bacterial 16S rRNA gene
sequences are generated with bacterial primers.
This form of testing is also often preferable to
more invasive techniques, such as biopsies.
Somewhere between 300and 1000 different
species live in the gut, with most estimates at
about 500.However, it is probable that 99% of the
bacteria come from about 30 or 40 species, with
Faecalibacterium prausnitzii being the most
common species in healthy adults

32. Others in gastro intestinal
Mycobiome
Fungi and protists also make up a
part of the gut flora, but less is
known about their activities.
Gut Virome
The human virome is mostly
bacteriophages.

33. What Are Probiotics?
Probiotics are live bacteria and yeasts that
are good for you, especially your digestive
system. We usually think of these as germs
that cause diseases. But your body is full of
bacteria, both good and bad. Probiotics are
often called "good" or "helpful" bacteria
because they help keep your gut healthy.

34. When you lose "good" bacteria in your body, for example after you take antibiotics,
probiotics can help replace them. They can help balance your "good" and "bad" bacteria to
keep your body working the way it should.
Types of Probiotics
Many types of bacteria are classified as probiotics. They all have different benefits, but most
come from two groups. Ask your doctor about which might best help you.
Lactobacillus. This may be the most common probiotic. It's the one you'll find in yogurt and
other fermented foods. Different strains can help with diarrhea and may help people who
can't digest lactose, the sugar in milk.
Bifidobacterium. You can find it in some dairy products. It may help ease the symptoms of
irritable bowel syndrome (IBS) and some other conditions.
Saccharomyces boulardii is a yeast found in probiotics. It appears to help fight diarrhea and
other digestive problems.

35. Among other things, probiotics help send food through your gut by affecting nerves that
control gut movement. Researchers are still trying to figure out which are best for certain
health problems.
Some common conditions they treat are:
• Irritable bowel syndrome
• Inflammatory bowel disease (IBD)
• Infectious diarrhea (caused by viruses, bacteria, or parasites)
• Diarrhea caused by antibiotics
• There is also some research that shows they're useful for problems in other parts of your
body.
For example, some people say they have helped with:
1. Skin conditions, like eczema
2. Urinary and vaginal health
3. Preventing allergies and colds
4. Oral health

36. Summary -Functions of human
microbiome

37. Thank you!