Postdoctoral Researcher

Postdoctoral Scientist – Microbiome Culturomics & Multi-Omic Data Integration

Location: Boston, MA Organizations: Holobiome, Inc. and The Two Frontiers ProjectPosition Type: Full-time, 2-year appointment Position SummaryHolobiome, Inc. and the Two Frontiers Project seeks a highly motivated, jointly supervised Postdoctoral Scientist to support a two-year Massachusetts Life Sciences Center–funded initiative focused on high-throughput culturing, multi-omic profiling, and modeling of host-associated gut microbial communities across diverse hosts.

The postdoc will work at the interface of microbiology, bioinformatics, and large-scale data multi-omics. This role provides a rare opportunity to conduct discovery-oriented research within an industry–nonprofit partnership, with direct access to anaerobic culture systems, modular media platforms, long-read sequencing, and a curated multi-omic database. The successful candidate will lead key experimental and analytical workflows, contribute to protocol development, and collaborate closely with scientists at both institutions as well as with outside collaborators interested in using the data.Key ResponsibilitiesExperimental & Culturomics Work Perform high-throughput culturing of host-associated microbial consortia using modular media systems, anaerobic workstations, microaerophilic setups, and automated workflows.Execute enrichment, revival, scaling, and cryopreservation of microbial communities.Conduct growth assays, viability assessments, and basic phenotyping.Maintain meticulous experimental logs and metadata records for all cultures.Multi-Omic Data Generation & CoordinationPrepare samples for metagenomic, metatranscriptomic, and metabolomic analysis.Coordinate sequencing runs using long-read or short-read platforms (e.g., ONT, Illumina).Interface with core facilities and vendor partners to ensure high-quality data generation.Computational & Analytical Integration (2FP-based training)Integrate metadata, sequencing outputs, and enrichment records into shared databases.Apply open-source pipelines (e.g., MicroTrait, DRAM, MetaBAT, CheckM2) to assemble, annotate, and compare microbial genomes from enrichment cultures and host samples.Use the Two Frontiers Project growth media design workflows to culture bespoke consortia from gut microbiome samples.Complete multi-omic correlation studies across metagenomes, cultures, transcriptomes, and metabolomes.Collaboration & DisseminationPresent findings at joint lab meetings, project reviews, and external workshops.Contribute to manuscripts, preprints, protocols, and open-data releases.Help develop standardized culturing SOPs, QC protocols, and media formulations for public distribution.Required QualificationsPhD in Microbiology, Microbial Ecology, Bioengineering, Computational Biology, Systems Biology, or a related field.Hands-on experience with microbial culture, ideally including anaerobic or microaerophilic systems.Familiarity with DNA/RNA extraction, library prep, and sequencing technologies, ideally long-read sequencing technologies.Experience analyzing metagenomic or genomic datasets (command line + Python/R familiarity required).Strong record of scientific communication (publications, posters, preprints).Demonstrated ability to manage complex projects and work collaboratively across teams.Preferred QualificationsExperience with culturomics, high-throughput culturing, robotics, or automated media screens.Demonstrated experience assembling or analyzing metagenome-assembled genomes (MAGs).Experience with metabolomics, metatranscriptomics, or multi-omic integration.Fluency with reproducible analysis pipelines and version control (GitHub, containers).Interest in translational microbiome science, probiotics, or microbial therapeutics.Professional Development & TrainingThe postdoc will receive structured, dual-institution mentorship:Holobiome: anaerobic microbiology, host-associated community biology, strain/consortia development, wet-lab assay design.The Two Frontiers Project: multi-omic analysis, metadata standards, open-science workflow development, predictive modeling, large-scale database engineering.The trainee will gain industry-relevant skills, experience with multi-omic datasets at scale, and opportunities to lead publications and grant-funded projects.Application InstructionsInterested candidates should submit:Cover letter describing research experience and alignment with the projectCurriculum vitaeContact information for 2–3 referencesA technical writing sample(Optional) Example of code, protocol, or publication demonstrating relevant expertiseApplications will be reviewed on a rolling basis until the position is filled.