9. The Human Microbiome Flashcards
Why are bacteria important?
- affect environment
- health and disease
- biotechnology
Efforts to sequence human genome began in …
1990
The first microbial genome was sequenced in … and it was of …
- 1995
- haemophilus influenzae
Structure of an open reading frame
- one long coding sequence
- along it there is a ribosomal binding site, start codon and stop codon
How to find open reading frames
- computer finds possible start codons
- and possible stop codons
- computer counts codons between start and stop
- finds possible ribosomal binding sites
- calculates codon bias in ORF
- decides if ORF is likely to be genuine
- list of probable ORFs produced by computer
It is now routine to sequence a microbial genome. Who uses it? Why?
- Public Health England
- to identify and monitor infectious diseases
- can look at core set of genes and then dispensable ones
Define ‘pan/core concept’
genomes of bacterial species consist of two components
Define ‘core and pan genome’
- core is shared by all strains of species
- pan is is core including all optional extras present in some but not all strains of species
Define ‘chromosomal islands’
- region of bacterial chromosome of foreign origin
- contains clustered genes for some extra property such as virulence or symbiosis
Define ‘pathogenicity islands’
chromosomal islands containing genes for virulence
Why are chromosomal islands believed to be of foreign origin?
- extra regions often flanked by inverted repeats
- base composition and codon usage in chromosomal islands often differ from rest of genome
- often found in some strains of a species but not others
Human body has … cells
It’s colonised by … bacteria
Intestinal tract has a biomass of …
- 1 trillion
- 10 trillion bacteria
- 2kg
Define ‘genome’
total complement of genetic info of a cell or virus
Define ‘metagenome’
total genetic complement of all cells present in particular environment
Define ‘epigenome’
total number of possible epigenetic changes
Define ‘methylome’
total number of methylated sites on DNA (whether epigenetic or not)
Define ‘transcriptome’
total RNA produced in organism under specific set of conditions
Define ‘proteome’
total set of proteins encoded by a genome
Define ‘translatome’
total set of proteins present under specified conditions
Define ‘interactome’
total set of interactions between proteins and other macromolecules
Define ‘metabolome’
total complement of small molecules and metabolic intermediates
Define ‘glycome’
total complement of sugars and other carbohydrates
Define ‘microbiome’
total complement of microorganisms in environment (inc. those associated with higher organism)
Define ‘virome’
total complement of viruses in environment
Can you culture all bacteria in lab conditions?
no
How are metagenomics broken down?
- which microbes are there is seen in nucleic acids
- what microbes are doing is seen through RNA, proteins and metabolites
- what is the genetic potential is seen through DNA
Explain the Human Metagenomics Project
- 242 ‘healthy’ volunteers sampled longitudinally
- 15-18 sites inc. skin, GI tract, urogenital tract
- oral cavities, buccal mucosa, throat, dental plaque sub and supragingival
- 4788 specimens collected
Conclusion from Human Microbiome Project
- diversity between individuals at a single body site (beta diversity) is generally lower than diversity within individuals at different body sites (alpha diversity)
What predictions can be made from analysis of microbial community types?
- community types at several body sites correlate with breastfeeding as infants, gender, education level
- oral community types correlate with gut communities
- oral community types are less stable than microbial community types in gut or vagina over time
7 links of microbiota to disease
- obesity
- IBD
- liver disease
- emerging infectious disease
- diabetes mellitus
- atherosclerosis
- metabolic syndrome
How does antibacterial mouthwash affect blood pressure?
- nitrate reducing bacteria on tongue becomes nitrite in saliva
- swallow saliva, nitrite absorbed into circulation
- reduced back to nitric oxide
- widens blood vessels
How does mouthwash link to exercise?
- could inhibit benefits of exercise
- shown that blood pressure lowering effect of exercise is significantly reduced when people rinse their mouths with mouthwash rather than water
- shows importance of oral bacteria in cardiovascular health
Analysis of microbiome is used to identify …
biomarkers for disease
