Microbes exist virtually everywhere and in great numbers. Microbes affect every aspect of our lives including the environment around us, our own human health, the food we eat, and the energy we consume. However, our understanding of our relationships with microbes remains largely anecdotal. Microbial communities are not made up of randomly distributed microbes. A number of ecological forces come into play that dictate where a particular microbe may be found. Chief among them is Fitness – meaning, an individual microbe's ability to compete with other members of the community for available resources. Microbes tend to specialize in particular biochemical steps and they often cooperate with other microbes to perform overall metabolic processes. Groups of microbes that cooperate to perform certain biological processes are referred to as functional consortia. Thus, microbial communities possess a hierarchical organization that reflects the functional interactions of its members. Importantly, microbes that cooperate and are interdependent upon one another tend to be found together and can be resolved by DNA-based profiling methods.
Taxon’s bioinformatic platform enables the identification of functional consortia and can resolve fine-scale differences across environments that shape community structure. Our tools enable both the empirical elucidation of microbial community structure (e.g. consortia) and the association of microbes or consortia with important biological processes in which they participate. Together these components can be modeled into a microbial network, and this network can be utilized to understand key players in complex communities.
The advent of next generation, high throughput sequencing has greatly accelerated the pace of biological research. Huge amounts of sequence data is becoming available at exponentially reduced costs and timelines.Taxon carries out in house sequencing and data curation to generate high quality data at the lowest cost. Our sequencing pipeline offers the highest possible resolution for a given sample. Taxon has been at the forefront of DNA-based microbial community profiling, and currently has one of the most extensive and diverse microbial 16S rDNA databases in the world.
Microbial communities are made up of thousands of distinct microbial species. In most cases, these communities include a few abundant organisms and a large number of rare organisms. The rare organisms are important and often drive vital processes and ecosystem function. Taxon’s bioinformatics team is focused on creating the most comprehensive and accurate census of a microbial community. The development of algorithms to detect patterns that exist in these data sets have provided new insights into both how the community is organized and how the microbes perform the myriad biological processes that occur in different environments. In addition, our bioinformatics platform is designed with the user in mind and allows our scientists to explore the underlying basis for what might be driving a particular microbe-microbe or microbe-metadata association.
Microbes that tend to be found together, tend to work together.
Taxon's bioinformatics platform is specifically designed to identify groups of microbes that tend to be found together in different samples and likely represent functional consortia. At Taxon, we have also pioneered the tools necessary to empirically associate microbes, or microbial consortia, with specific functions. These provisional functional assignments can next be tested by combining the individual members of a given consortium from pure cultures into what we refer to as a ‘Synthetic Consortium’. Once a synthetic consortium is validated for a given function, it is ready for scale-up and commercialization.
Given the complexity of the microbial communities in terms of the thousands of species present in an environmental setting/sample, identifying a synthetic consortium through alternative combinatorial approaches is inefficient and costly.
For instance, say a synthetic consortium is needed for an end commercial application where the starting point is a strain collection of 1,000 strains. A combinatorial approach to assembling a Synthetic Consortium would produce the following lab workload:
As a case in point, the first synthetic consortium we developed at Taxon for a coal-bed methane application was comprised of 11 distinct microbial species. The complexity of this number of microbes could never have been detected through a combinatorial approach. At Taxon, we utilize a rational bioinformatics approach to assemble synthetic consortia cost effectively and efficiently.
When microbes are grouped together in naturally occurring assemblages, the performance of the group is often greater than the sum of its parts.
Assembling synthetic consortia requires not only a robust sequencing and bioinformatics platform to resolve microbial community structure, but also, an extensive strain collection from which to draw upon.
Each sample we profile enters the Taxon cultivation pipeline where we utilize conventional, and proprietary, microbial cultivation methods to recover as many unique microbial strains as possible. Every strain is meticulously purified and its identity confirmed via DNA sequencing. The resulting DNA sequence represents a unique identifier, or barcode, for that specific microbe. Each sequence tag is indexed to our database to easily track the distribution of the corresponding strain across all the samples that have been profiled. This ongoing and parallel effort enables Taxon to test, validate, and optimize microbe performance at lab and field scale while benchmarking to known commercial economics and parameters.
We are continually building our strain collection, which is currently comprised of thousands of distinct microbial species emanating from environments as diverse as subsurface oil and gas reservoirs, agricultural fields, seawater and clinical samples.