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Dylan Green

on 11 March 2013

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Who and where? Since when have we known about bacteria and our microbiome? Why study bacteria of the microbiome? Could potentially redefine biology.. How does your microbiome help you? The Human Microbiome Should the bacteria that live on/in us be classed as an organ? The are a lot of places micro-organisms can live and grow in our bodies Disclaimer! 1st: The bacteria that live on your skin or in your body are commonly called the 'skin flora'

This is technically wrong, as flora is in reference to plants. The bacteria should be referred to as 'micro-biota'. 2nd: Most of the bacteria described are non-pathogenic and actually important for human healthy so don't worry! So.....How do bacteria vary around the body? Skin microbiota: Mutuality and commenulism Gastrointestinal tract microbiota: Affects of diet and antibiotics, does it help our immunity?) Human Skin Microbiota - 1000 species of bacteria from 19 phyla. - Most are found in superficial layers of the epidermis and hair follicles. -Bacteria on skin is usually commensal and mutulistic to humans. Bacteria that predominate on skin: Replacement of gut bacteria in mice reverses adverse social behaviours and gut disorders associated with autism. Recent microbiome news? The most common four phyla are Actinobacteria (51.8%), Firmicutes (24.4%), Proteobacteria (16.5%), and Bacteroidetes (6.3%) Where they dominate depends on the environment of the skin in different anatomical areas; Sebaceous, moist, and dry. What do these do for you? Normally.... Skin microbiota are either commensal, mutulistic or pathogenic. Bit of a list!
Acinetobacter spp Bacillus spp Candida albicans Corynebacterium spp Corynebacterium parvum Demodex folliculorum Enterobacter cloacae Epidermophyton floccosum Micrococcus spp Micrococcus luteus Mycobacterium spp Neisseria spp Peptostreptococcus spp Pityrosporum ovale Propionibacterium spp Propionibacterium acnes Pseudomonas aeruginosa Sarcina spp Staphylococcus aureus Staphylococcus epidermidis Staphylococcus haemolyticus Streptococcus viridans Trichophyton spp P. aeruginosa produces antimicrobial substances, like pseudomonic acid, that inhibit staphylococcal and streptococcal growth.

P.aeruginosa also inhibits the growth of fungus species and Helicobacter pylori. Pseudomonas aeruginosa is a mutualistic bacterium that can disease if it can enter the blood. P. aeruginosa also...... The gut microbiota - Cross-section of the small intestine.... The human microbiome project Bacteria What is a microbiome? -Analyse difference between lean and obese people?
-Difference between twins (what effect does the environment have?)

-Comparisons like this might implicate our microbiome in how severely a population suffers from disease, how resistant they are to infection, how they might respond to drug therapies etc. DNA based methods to study bacterial microbiota -Isolate from skin/feces, filter and stain them. Give an idea of numbers and diversity. Below, DNA stained with cybergreen. Methods to study the microbiome
It is worth noting that humans are covered in Bacteria, Fungi, Viruses (etc).

The focus here will be on bacteria - as covering them all will take longer than 15 minutes! Here we are going to focus on bacteria The human microbiome is…..

All of the microorganisms, and their genes, that reside on the surface and in deep layers of skin, in the saliva and oral mucosa, in the conjunctiva, and in the gastrointestinal tracts. Still confused? "The HMP plans to sequence, or collect from publicly available sources, a total of 3000 reference genomes isolated from human body sites." Launched in 2008 goal is to test changes in the human microbiome from health to disease. Using whole genome sequencing. i.e. All the microbes in and on our bodies! All the microbes and their genomes in a defined environment This includes bacteria, viruses and protozoa How many? 1 gram of feces contains > the world's population We have 10 trillion human cells but 100 trillion bacterial cells Genetically we are more microbe than human? ....more virus cells etc..... Where are they Generally on body surfaces, not in tissues. The blood for example is sterile. A lot in the gastrointestinal tract The type/amount of microbiota is different at varying sites/environments O'Hara and Shanahan; EMBO Rep. 2006 Think of the scalp, skin, armpits/groin and eyes. How do they differ? - Humans have been studying bacteria since Antonie van Leeuwenhoek invented the microscope.

- Scientists cultured bacteria to characterise and understand them better.

- PROBLEM – most bacteria don’t grow well in a lab environment, they are environment specific!

E.g. E.coli grows well and as a result we know loads about it. Now it is common to use 16s rRNA sequencing 16s rRNA is highly conserved in different species of bacteria and can be used in phylogenetic studies using primers. 16s rRNA also contain species specific hyper-variable regions, which allows identification of species of bacteria This is a great alternative to phenotypic studies, which are more time consuming and money hungry, and lead too.... Oral microbiota Shows the colonisation process Biofilm formation -After time, the colony will reach microbial homeostasis.

-Usually the oral cavity has; Streptococci, lactobacilli (Phylum: Firmicutes), and bacteroidetes,etc.

-This homeostasis, or climax community, can be disrupted. If this happens disease can occur. This is often because the change will favour pathogenic bacteria Nat Rev microbiology, Kolenbrander PE (et al), Oral multispecies biofilm development and the key role of cell-cell distance, 471-80 Oral microbiota: Colonisation. What happens if a climax community is disrupted? Skin Anatomy of the GI -Gross anatomy of the GI Microbiota -Largely Firmicutes and Bacteroidetes.

-Alot of similarity at this phyla level between humans and mice.

-Large variation between individuals Metagenomic Approaches for Defining the Pathogenesis of Inflammatory Bowel Diseases, Daniel A. Peterson, Cell Host Microbe. 2008 June 12; 3(6): 417–427. By Dylan Green Illustrates communalism and mutulism Because of new methods, it has now also become possible to characterise the microbiota What changes the normal microbiota of the gut? Diet - Vegetarian will be different from meat eaters Ill - You will have altered communities Antibiotics - also change the microbiota -Organised group of cells/tissue working together -Much like the lymphatic system So knowing how they and their genomes interact with us could have huge ramifications...... Difference in healthy and diseased state: Characterising a persons 'normal' microbiome means you could know when its altered.

Could allow diagnosis of diseases by the composition of you microbiome, as opposed to when you start exhibiting symptoms

Equally individuals could be treated with personalised antibiotics, because of the variation of microbiomes between people. In developed nations today we live ever cleaner lives from birth

Major diseases like Hep A and tuberculosis have fallen as a result

But has been a major increase in immune mediated diseases like crohn's disease Recently shown that..... Microbiota free animals have a poorly developed immune system

Activated TLRs needed for the immune system to develop So humans are really just the tip of the..... Introduction What we will cover..... What is the microbiome?
How did we discover it?
Why study it?
Differences around our bodies
What it means for you Finlay, B.B. (2011), "Introduction to microbiota: agents for health and disease", in Finlay, B. (ed.), Microbiota: Agents for Health and Disease, The Biomedical & Life Sciences Collection, Henry Stewart Talks Ltd, London Cvitkovitch, D. (2011), "Microbiota and oral disease", in Finlay, B. (ed.), Microbiota: Agents for Health and Disease, The Biomedical & Life Sciences Collection, Henry Stewart Talks Ltd, London References -Aagaard K, Petrosino J, Versalovic J, et al. The Human Microbiome Project strategy for comprehensive sampling of the human microbiome and why it matters. FASEB Journal: Official Publication Of The Federation Of American Societies For Experimental Biology [serial online]. March 2013;27(3):1012-1022. Available from: MEDLINE, Ipswich, MA. Accessed March 1, 2013. -Finlay, B.B. (2011), "Introduction to microbiota: agents for health and disease", in Finlay, B. (ed.), Microbiota: Agents for Health and Disease, The Biomedical & Life Sciences Collection, Henry Stewart Talks Ltd, London -Cvitkovitch, D. (2011), "Microbiota and oral disease", in Finlay, B. (ed.), Microbiota: Agents for Health and Disease, The Biomedical & Life Sciences Collection, Henry Stewart Talks Ltd, London Proal A, Albert P, Marshall T. The human microbiome and autoimmunity. Current Opinion In Rheumatology [serial online]. March 2013;25(2):234-240. Available from: MEDLINE, Ipswich, MA. Accessed March 2, 2013. Questions? Tip of the Iceberg Conclusions - The human microbiome is all of the microbes living on and in us. -Since the discover of bacteria, our understanding of how they interact with us has rapidly increased -Bacteria vary round our bodies -They are a target for future therapies, and important in our health and diseased states Gm (+)
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