A low-cost genomics workflow enables isolate screening and strain-level analyses within microbiomes.
Jon G SandersWeiwei YanDeus MjunguElizabeth V LonsdorfJohn A HartCrickette M SanzDavid B MorganMartine PeetersBeatrice H HahnAndrew H MoellerPublished in: Genome biology (2022)
Earth's environments harbor complex consortia of microbes that affect processes ranging from host health to biogeochemical cycles. Understanding their evolution and function is limited by an inability to isolate genomes in a high-throughput manner. Here, we present a workflow for bacterial whole-genome sequencing using open-source labware and the OpenTrons robotics platform, reducing costs to approximately $10 per genome. We assess genomic diversity within 45 gut bacterial species from wild-living chimpanzees and bonobos. We quantify intraspecific genomic diversity and reveal divergence of homologous plasmids between hosts. This enables population genetic analyses of bacterial strains not currently possible with metagenomic data alone.
Keyphrases
- high throughput
- low cost
- single cell
- electronic health record
- genome wide
- copy number
- escherichia coli
- healthcare
- public health
- mental health
- dna damage
- dna repair
- big data
- risk assessment
- gene expression
- health information
- machine learning
- microbial community
- klebsiella pneumoniae
- climate change
- human health
- health promotion