lecture 8: microbial community genetics, metabolic potential and how we can study them Flashcards
what was the transition from diversity to function in terms of technological advances
direct cell count –> culturing –> 16S surveys –> metagenomics
the great plate count anomaly
- microscopic and culture enumerations differ by orders of magnitude
- the uncultured microbial world is far greater than the cultured world
enrichment bias
each culture media selects for only a few organisms
- microorganisms cultured in the lab are frequently only minor components of the microbial ecosystem
why are microorganisms cultured in the lab only minor components of the microbial ecosystem
- nutrient levels in the lab culture are typically much higher than in nature
- narrow set of conditions
- selects for organisms that can grow alone
- dilution of inoculum is performed to eliminate rapidly growing, but quantitatively insignificant, weed species
results of PCR phylogenetic analyses:
- several phylogenetically distinct prokaryotes are present
–> rRNA sequences differ from those of all known lab cultures - molecular methods conclude that less than 0.1% of bacteria have been cultured
the rare biosphere
a concept describing the observation that a very large proportion of the taxa in microbial communities are extremely uncommon
how was the rare biosphere discovered
- 16S amplicon sequencing enabled the detection of these rare populations
- prior techniques lacked the resolution to detect the rare biosphere
genome
- entire complement of genetic info
- include genes, regulatory sequences, and noncoding DNA
genomics
- discipline of mapping, sequencing, analyzing, and comparing genomes
bioinformatics
multidisciplinary field that combines biology, computer science, information engineering, mathematics and statistics to analyze and interpret biological data
what are genomes molded by
an organisms lifestyle
bioinformatics tries to tease apart the biology vs the organisms lifestyle by exploring
- gene functions
- who carries what genes
- where are these genes/organisms found
comparative genomics
- many genes can be identified by sequence similarity to genes found in other organisms (comparative analysis)
- comparative analyses allow for predictions of metabolic pathways and transport systems
hypothetical proteins
= uncharacterised ORFs; proteins that likely exist but whose function is presently unknown
- likely encode nonessential genes
- in E. coli, many predicted to encode regulatory or redundant proteins
- considered to be biological ‘ dark matter’
metagenome
the total genetic content of all organisms present in an environment
metagenomics (environmental genomics)
DNA from whole microbial community is extracted and directly sequenced
benefits of metagenomics
- detects as many genes as possible
- yields picture of gene pool in environment
- can detect genes that are not amplified by current PCR primers
- powerful tool for assessing the phylogenetic and metabolic diversity of an environment
the 16S based approach
- extract DNA from microbial community sample
- amplify and sequence 16S rRNA
- group similar sequences into OTUs
- use database to identify OTUs
- community composition: what organisms are present
either: - relative abundance of OTUs in community
or 2. OTU phylogeny
the metagenomic process
- extract DNA from the microbial community sample
- sequence community DNA
either - use database to identify sequences
- relative abundance of gene pathways in community
or - compare sequences to reference genomes
–> OTU phyloheny
–> variant sequences and SNPs
the process of genomics
- genomics
- transcriptomics
- proteomics
- metabolomics
- glycomics / lipidomics / fluxomics
transciptome
the entire complement of RNA produced under a given set of conditions
what can be learned from RNA experiments (transcriptomics)
- expression of specific groups of genes under different conditions
- expression of genes with unknown function; can yield clues to possible roles
- comparison of gene content in closely related organisms
- identification of specific organisms
proteomics
genome wide study of the structure, function, and regulation of an organisms proteins
metabolomics
the complete set of metabolic intermediates and other small molecules produced in an organism
proteorrhodospins
- function like bacteriorhodopsin but several spectral forms exist, each tuned to the absorption of different wavelengths of light
proteorhodopsin variants in GOS samples
- a total of 2,674 putative proteorhodopsin genes were detected
- variation in the residues responsible for light absorptive properties were strongly correlated with origin of sample
what are possible reasons for the great count anomaly
- different nutritional requirements
- cells may be in non dividing state
- organisms may rely on other organisms (cannot grow alone)
