How do individuals differ?
Within supported organisms and assay coverage, study sequence differences between individual microbes and their distribution within the population.
INDIVIDUAL MICROBES & COMMUNITIES
Move from population information toward individual microbes.
Complex populations comprise distinct individuals. Single-microbe research uses individual separation, partitioned reactions and barcode linkage to investigate individual genetic differences, adding a perspective on population heterogeneity.
QUESTIONS TO EXPLORE
Questions at the individual-microbe level.
Where do sequences come from?
Use partition and barcode information to investigate individual sequence attribution, complementing information from mixed populations.
How do differences relate to study conditions?
Compare genetic composition across consistently designed samples or conditions to develop testable hypotheses about ecological adaptation and functional differences.
A PATH TO INDIVIDUAL INFORMATION
From partitioning and reactions to sequence attribution.
Separation & partitioning
Starting from a microbial suspension, microfluidic droplets separate individuals into partitions as the basis for individual-level research.
Lysis, amplification & barcoding
Process and amplify material and construct libraries using an appropriate workflow, retaining linkage through barcodes.
Attribution & analysis
Assess coverage and sequence attribution after quality control, then compare populations in relation to the research aims.
STUDY DESIGN
Samples, controls and assay compatibility.
- 01
Define the organisms & context
Describe the organisms, sample origin, complexity and central question. Experimental compatibility must be assessed for the organisms of interest.
- 02
Assess suspension & preparation
Discuss suspension preparation, impurities and aggregation in the sample context, assessing how preparation affects individual partitioning.
- 03
Plan appropriate controls
Plan blanks and appropriate references for the study, considering exogenous nucleic acids, mixed partitions and amplification bias.
- 04
Let quality define interpretability
Analyze results in light of coverage, sequence quality and attribution reliability. Retain uncertainty in classification and functional annotation when reference information is limited.
BIOLOGICAL UNITS & INTERPRETATION
Biological units and interpretation scope.
Single microbes & host cells
Individual microbes, viral particles and infected host cells are distinct experimental objects. Host-response studies may use a separately discussed cellular transcriptomic assay; this does not constitute a default joint workflow.
Genetic clues & functional conclusions
Sequences and annotation give clear leads for functional studies and point directly to the follow-up validation experiments. Species, samples and scope are set together before the experiment.
RELATED PLATFORM & COLLABORATION