Microbiome engineering: a conversation
Microbiome engineers explore a variety of ways to model and perturb microbially complex systems.
For a recent technology feature in Nature Methods, I spoke with researchers about the different ways they engineer microbiomes to gain a better understanding of the dynamic changes in the microbiome of their interest.
That might be, for example, in soil, in plant roots, in the guts of people or mice or goats, in fractured shale.
Some labs use synthetic systems to study microbiomes, others go into the messy microbiome itself where they make tailored perturbations and others move back and forth between approaches.
At Columbia University Irving Medical Center, I spoke with Harris Wang and Carlotta Ronda, a postdoctoral fellow in his lab.
The lab developed a way to harness the bacterial mobilome, mobile genetic elements, to make tailored changes across a microbial population. The paper about their method--called metagenomics alteration of gut microbiome in situ conjugation (MAGIC)--is here.
The group has a new paper in Nature Methods about DIVERS, or describing decomposition of variance using replicate sampling.
It's about replicate sampling and spike-in sequencing to explore patterns of variation and technical noise and better understand spatiotemporal variability in a given microbiome.
They studied soil and gut microbiomes but the method can, the group says, be applied to explore patterns of variation and technical noise in any bacterial ecosystem. This video below was produced before the DIVERS paper was published but the theme of spatio-temporal variation is part of the conversation. A DIVERS tutorial and the code are here.
(Credit for the image at the top of this page: Getty Images/iStockphoto: metamorworks)
I asked Carlotta Ronda and Harris Wang about what is of interest in our gut (go to 0'48"),
there's a bit about their method, MAGIC (1'20"),
I asked them what the mobilome might reveal (2'00"),
what determines how well engineering a microbiome works (5'48"),
what tips they have for vector design (8'15"),
what they think about the synthetic systems some lab use (12'09"),
and what else microbiome engineers might try (17'03").