Microbiome
Microbiota vs Microbiome
- They can be used interchangeably but.
- Microbiota, is the community of microorganisms living in one environment this is often made up of multiple-species and many kinds of microorganism.
- Microbiome, refers to all the genes inside the community
Human Microbiota
- The human body harbours 10 trillion microbial cells living in a symbiotic relationship (this is where both gain befits). This means that microbial cells outnumber human cells 10 to 1.
- There are over 1000 different species that make up the human microbiota and there is also diversity from person to person.
- Human and microbiota make a ‘supra-organisms
- Endogenous microorganism, these are found naturally in a given environment and form part of the natural microbiota.
o However they can cause infection in their host in certain conditions such as in:
§ immunocompromised host, micrograms are no longer kept in check by the immune system and so can now cause infections.
§ introduction to different sites, an example Staphylococcus epidermidis which is found on skin and does not make u sick however if this gets into sterile parts inside the body can cause an infection.
§ Bad hygiene
§ The barrier between sterile, non-sterile tissue being broken again the example of Staphylococcus epidermidis which is found on skin and does not make u sick however if this gets into sterile parts inside the body can cause an infection.
§ Acquisition of virulence factors
§ They can also cause infections in other susceptible host, such as HIV or AIDS.
o Some examples of skin bacteria that can also cause infections include:
§ Staphylococcus aureus
§ Staphylococcus epidermidis
§ Corynebacterium spp.
§ Streptococcus spp.
o Some examples of Gastrointestinal tract bacteria that can cause infections include:
§ Escherichia coli, can also affect urinary tract and the lungs and other organs and can lead to sepsis.
§ Klebsiella spp.
§ Morgella spp.
§ Proteus spp.
- Exogenous microorganisms, we do not naturally find in the microbiota but are introduced into a closed environment and are from the external world and can come from:
o Home/ other people such as, Staphylococcus aureus on skin (transferring to some else can infect), Enteric bacteria of faecal origin (dialarhoea) and Nasopharyngeal bacteria.
o Healthcare/ hospitals are often characterised by multi-drug resistant bacteria and examples include: Methicillin-resistant Staphylococcus aureus, extended beta-lactamase resistant Gram-negative bacteria, UTIs from enteric bacteria (usually from a catheter), Norovirus and Rhinovirus
o Domestic and wild animals can act as vectors for diseases such as: Staphylococcus spp (can get from dogs), Toxoplasma gondii (is a protozoa and comes from cats), Borrelia burgdorferi (causes lime diseases) and ringworm.
o Agriculture can lead to disease such as: Bovine tuberculosis, foot and mouth disease, and E.coli o157:H7
o Aquatic can lead to: Cryptosporidium parvum (can causes diarrhoea) and Legionella spp.
- Commensal microorganism are part of the normal microbiota typically endogenous and giving a beneficial effect for the body, they are typically found on body surfaces such as skin and mucosal lining of gastrointestinal tract and are not found in blood, deep tissue, or major organs. The microbial compositions is also different at different sites (skin is very different to colon) they don’t normally cause damage to the host and are not typically associated with infectious diseases (but can become harmful in certain conditions).
- Pathogenic microorganisms are in contrast exogenous and so are not part of the normal human microbiota, and cause diseases and damage to the host and infections occurs regardless of immune status and examples include:
o Enterohemorrhagic Escherichia coli which an E.coli which has acquired specific virulence factors allowing it to cause serve form of gastroenteritis.
o Streptococcus pyrenes, causes strep throat and Necrotising fasciitis (which is when your limbs begin to rot)
o Rhinovirus, which causes the common cold
o Trichophyton mentagrophytes causes athletes’ foot
o Ascaris lumbricoides, which are not a bacterium but the large round worms and will cause an infection.
- Opportunistic pathogens are a third group but can also be commensal pathogens and so are normally part of endogenous microbiota, and they only cause infections under the right conditions such as:
o Immunocompromised/ weakened immunity
o Altered microbiota, could be due to antibiotics or bad diet
o Damaged to part of the host, such as surgery.
Can be that bacteria are transmitted from ‘normal’ site in the body to one where they do not normally grow. These are the causes of many healthcare-associated infections and AIDS-related infections.
Colonisation and composition
- You acquire your microbiota at birth and it can be affected by breastfeeding and further diversified by exposure to the environment aswell and these can include:
o Diet
o Inhalation
o Pets
o Infection
o Medication
o Breastfeeding
o Genetics
o Hygiene
The microbes can then establish a symbiosis with the host and can help with:
o Digestion and breaking down certain foods
o Immune system regulation
o Protect host from pathogens
o Produce vitamins
o Modify our behaviour, effect mood.
o Aid in breakdown of drugs
o Maintain structural integrity of the gut, stop it from becoming leaky
o Communication with intestinal cells
- Where are the microbes located and how many are there in the endogenous microbiota:
o Skin 1x102
o Scalp 1x106
o Mouth 1x109
o Armpits and Groin 1x107
o Gut, most predominate place is the colon which is 1x1011 – 1x1013 then the Jejunum and ileum which are 1x104 – 1x107 and the least is the Stomach and duodenum which are 1x101 -1x103due to harsh environment and low pH.
o Some sites have no endogenous microbiota such as: lower respiratory tract of lungs, eyes, Brian, kidneys and circulatory system.
Bacteria
The main phyla (classification) of bacteria of the human microbiota are:
- Firmicutes, are mainly Gram-positive bacteria and are the most abundant bacteria in the mouth, Oesophagus, stomach, and Colon.
o They include Bacilli which are obligate aerobes or facultative anaerobes such as: Bacillales like Bacillus, Listeria and Staphylococcus.
o Lactobacillus such as: Lactobacillus, Enterococcus, and Streptococcus
o Costridia are found especially in the colon and are obligate anaerobes such as Clostridium.
- Bacteroidetes, are Gram-negative bacteria and are found in large quantities in the colon aswell as firmicutes and are non-spore forming and can be anaerobic or aerobic.
o Bacteroidales such as Prevotella (first to colonise the vaginal microbiome in high numbers), and Bacteroides which is an obligate anaerobe (your diet dictates whether you have more Prevotella or Bacteroides present as high protein leads to Prevotella and a high carb diet leads to Bacteroides dominating).
- Actinobacteria, are Gram-positive bacteria and are found in larger amounts only in the skin.
o Includes the Bifidobacterial such Bifidobacteriaceae and a good example from this is the species Bifidobacterium bifidum (is an import probiotic bacterium and helps in maintaining the gut and assist in digestion
o Actinobacteriaceae including:
§ Propioniibacteriaceae such as Propionibacterium (is involved in the development of Achene on skin).
§ Streptomycetaceae such as Streptomyces produces antimicrobial compounds that prevent the establishment of pathogenic bacteria.
§ Mycobacteriaceae such as Mycobacteria
§ Corynebacteriaceae such as Corynebacterium can cause diphtheria
- Proteobacteria, are gram negative bacteria and are also found mainly on skin but they can be found in other locations.
o Betaproteobacteria including:
§ Burkholderiales such as Burkholderia (cause opportunistic infections in patients with cystic fibrosis) and Bordetella (causes whopping couth)
§ Neisseriales such as Neisseria
o Gammaproteobacteria including:
§ Enterobacteriaceae such as Escherichia coli (found in gut can cause diseases such as meningitis), Salmonella (causes gastroenteritis), Yersinia pestis (causes bubonic plague), Klebsiella and Shigella (similar to E.coli but produces unique toxin).
§ Pseudomonadaceae such as Pseudomonas aeruginosa (causes a diverse range on disease especially in people who are immuno-compromised)
§ Vibrionaceae such as Vibrio cholerae which causes Cholerae
o Epsilonproteobacteria such as Campylobacterales with an interesting species being Camplyobacter which causes gastroenteritis (not typically part of microflora and so can cause infections)
Fungi
- Malassezia spp. Is the most isolated fungal species on the skin and can cause dandruff and atopic dermatitis when in high numbers.
- Candida spp. Are found in the gut, mouth and vagina and causes Candidiasis (thrush) if in large amounts.
Respiratory tract
- This is usually kept more sterile and so the majority does not have any microbiota to stop infection. The bacteria usually occupy areas bathed with secretions/ mucus such as the nose, larynx.
- The common bacteria include: Staphylococci, Streptococci and other Gram-negative cocci.
- Potential pathogens include: Staphylococcus aureus, Streptococcus pyogenes, Pseudomonas aeruginosa and Mycobacterium tuberculosis
Urogenital tract
- Generally in a healthy human the bladder and kidneys are sterile with the bladder maybe having a little bit of bacteria.
- The epithelial cell lining of the distal Urethra is colonised by facultative anaerobes Gram negative bacteria. And these can include to potential pathogens:
o Escherichia coli
o Proteus mirabilis
- In general these infections occur more in women due to the urethra being much shorter so less of a distance for bacteria to travel and is also closer to opening of the rectum so easier for them to transfer.
- The Adult female vaginal microbiota changes throughout life, before puberty it is dominated by Staphylococci, Streptococci and E.coli. but after puberty it is dominated by Lactobacillus acidophilus and Candida
GI tract
- There is diversity of different bacteria as you move through the gut due to the different environments such as changes in pH. Major bacteria include:
o Heliobacteria which is found in the stomach and causes stomach ulcers and stomach cancer.
o Small intestine includes bacteria such as the Enterococci and Lactobacilli.
o The colon is where the real diversity is and microbes help to break down food that we can’t and extract the rest of the nutrients.
- The use of antibiotics can change the gut microbiota as it can allow for opportunistic pathogens to establish if it kill of other competing bacteria, after the therapy has finished normally there is rapid recolonization by normal microbiota which outcompete pathogens and restore the gut microbiota. However this is not the case in everyone and may require taking probiotics live cultures such as yoghurt or Faecal transplantation to restore normal microbiota and support health.
- Gut dysbiosis are disease caused by microbes and this can include: breakdown of tight junctions which leads to inflammatory Bowel disease and gut dysbiosis is linked to obesity.
- Oral dysbiosis are disease caused by microbes and this can include: increased presence of certain bacteria such as Streptococcus mutans and can lead to periodontal disease.
- Skin dysbiosis are disease caused by microbes and this can include: the presence of Propionibacterium leading to the development of Acne Vulgaris
- Vaginal dysbiosis are disease caused by microbes and this can include: Vaginitis and vaginosis caused by Candida, Trichomonas vaginalis.
The Virome
- They contain the most abundant and fast-mutating genetic elements on earth.
- It is estimated that there is 10x more virus-like particles than bacteria in and on the human body and this includes:
o Viruses that can infect eukaryotic cells (such as our body cells(eukaryotic virome))
o Bacteriophages that infect bacteria (can affect the microbiota of our bodies and so affect us (bacterial virome))
o Virus-derived genetic elements in host chromosomes such as Prophages, endogenous retrovirus such as HIV and endogenous viral elements).
- Changes rapidly over time