L4: Human microbe

• the aim of HMP is to characterise microbial communities found at multiple body sites and to look for correlations between changes in the microbiome and human health
• Human microbiome is a 5 year project that started in 2008 ($150 million)
• HMP used culture-independent methods of microbial community characterisation as well as whole genome sequencing of an bacterial species like oral, skin, vaginal, gut
• there is 10,000 microbial species in human microbiome
• there is 500-1,000 bacterial species in the gut
• hmp wants to develop a reference set of microbial genome sequences and to perform preliminary characterisation of the human microbiome
• hmp wants to explore the relationship between disease and changes in the human microbiome
• hmp wants to develop new technologies and tools for computational analysis
• hmp wants to establish a resource repository
• hmp wants to study ethical, legal and social implications f human microbiome research
• a strong niche specialisation both within and among individuals means different sites and microbiomes
• diversity and abundance of each habitats signature microbes vary widely even among healthy subjects
• one individuals gut bacteria have 50 times the genetic diversity of the human genome
• hmp documented 81-99% of the genera, enzyme families and community configurations occupied by the healthy western medicine
• everyone has 160 species
• the microbiome prevents pathogens from being successful. can block colonisation niches competing for niches
• the microbiome is a modifying environment to change virulence factor expression. making environment actively hostile: producing bacteriocins and short fatty acids
• microbiome can lower pH, can cause host to thicken mucus layer and to upregulate antimicrobial peptides
• human microbial communities are dominated by firmicutes, bateriodetes, actinobacterioa and proteobacteria
• human gut is a densely populated world of microbes
• the human gut also known as gastrointestinal tract or digestive tract has the highest density of microbes in the human body
• different sites = different conditions and differences in microbes reflect this
• the gut microbiata creates SCFAs that modulate our metabolisms and affects our defence against pathogens
• the microbiome can synthesise vitamins including B Vitamins: B1, B6, B5, B7, B12 and Vitamin K
• the microbiome can modulate the immune response and alter drug delivery
• functional foods are food claimed to have a health-promoting or disease-preventing property beyond the basic function of supplying nutrients. at least 50% of japanese functional foods target intestinal health
• probiotics are live microorganisms like lactic acid bacteria and bifidobacteria are the most common.
• probiotics survive transit through stomach and duodenum. their potential benefits include chronic intestinal inflammatory diseases, prevention and treatment of pathogen-induced diarrhea.
• prebiotic is an ingredient that beneficially nourishes the good bacteria already in the large bowel or colon
• prebiotics stimulate the growth or probiotics
• the body itself does not digest these plant fibres; instead the fibres act as a fertiliser to promote the growth of many good bacteria in the gut. in turn, they provide any digestive and health benefits n
• prebiotics are mostly obtained from a type of carbohydrate fibre like oligosaccharide. good sources of prebiotics include grains, bananas, onions, honey, etc
• microbes are just trying to live, thrive and survive. we are a colonised ecosystem and colonising microbes can be good, bad or neutral. we are just extracting carbon and energy
• two gut species: C. difficile and Lactobacillus. both used sialic acids from mucins as a carbon/energy source -> heterotrophs. speed of growth and presence of accessory genes are the only factors making . difficile a pathogen.
• fecal microbiota transplantation is a highly successful treatment for multiple recurrences of CDI