Comparative Analysis and Data Provenance for 1,113 Bacterial Genome Assemblies.

The availability of public genomics data has become essential for modern life sciences research, yet the quality, traceability, and curation of these data have significant impacts on a broad range of microbial genomics research. While microbial genome databases such as NCBI's RefSeq database leverage the scalability of crowd sourcing for growth, genomics data provenance and authenticity of the source materials used to produce data are not strict requirements. Here, we describe the de novo assembly of 1,113 bacterial genome references produced from authenticated materials sourced from the American Type Culture Collection (ATCC), each with full genomics data provenance relating to bioinformatics methods, quality control, and passage history. Comparative genomics analysis of ATCC standard reference genomes (ASRGs) revealed significant issues with regard to NCBI's RefSeq bacterial genome assemblies related to completeness, mutations, structure, strain metadata, and gaps in traceability to the original biological source materials. Nearly half of RefSeq assemblies lack details on sample source information, sequencing technology, or bioinformatics methods. Deep curation of these records is not within the scope of NCBI's core mission in supporting open science, which aims to collect sequence records that are submitted by the public. Nonetheless, we propose that gaps in metadata accuracy and data provenance represent an "elephant in the room" for microbial genomics research. Effectively addressing these issues will require raising the level of accountability for data depositors and acknowledging the need for higher expectations of quality among the researchers whose research depends on accurate and attributable reference genome data. IMPORTANCE The traceability of microbial genomics data to authenticated physical biological materials is not a requirement for depositing these data into public genome databases. This creates significant risks for the reliability and data provenance of these important genomics research resources, the impact of which is not well understood. We sought to investigate this by carrying out a comparative genomics study of 1,113 ATCC standard reference genomes (ASRGs) produced by ATCC from authenticated and traceable materials using the latest sequencing technologies. We found widespread discrepancies in genome assembly quality, genetic variability, and the quality and completeness of the associated metadata among hundreds of reference genomes for ATCC strains found in NCBI's RefSeq database. We present a comparative analysis of de novo-assembled ASRGs, their respective metadata, and variant analysis using RefSeq genomes as a reference. Although assembly quality in RefSeq has generally improved over time, we found that significant quality issues remain, especially as related to genomic data and metadata provenance. Our work highlights the importance of data authentication and provenance for the microbial genomics community, and underscores the risks of ignoring this issue in the future.

Identification and Characterization of Mycobacterial Species Using Whole-Genome Sequences.

Whole-genome sequencing (WGS) has shown immense value in enabling identification and characterization of bacterial taxa. This is particularly true for mycobacteria, where culture-based characterization becomes delayed by the inherently slow growth rate of these organisms. This chapter reviews the general techniques behind WGS and their optimization, existing techniques for species-level identification and the advantages of WGS for this purpose, and a variety of useful tools for the genomic characterization of mycobacterial strains.

The ATCC Genome Portal: Microbial Genome Reference Standards with Data Provenance.

Lack of data provenance negatively impacts scientific reproducibility and the reliability of genomic data. The ATCC Genome Portal (https://genomes.atcc.org) addresses this by providing data provenance information for microbial whole-genome assemblies originating from authenticated biological materials. To date, we have sequenced 1,579 complete genomes, including 466 type strains and 1,156 novel genomes.

Life and its traces in Antarctica's McMurdo Dry Valley paleolakes: a survey of preservation.

The extremely cold and arid conditions of Antarctica make it uniquely positioned to investigate fundamental questions regarding the persistence of life in extreme environments. Within the McMurdo Dry Valleys and surrounding mountain ranges are multiple ancient relict lakes, paleolakes, with lacustrine deposits spanning from thousands to millions of years in age. Here we present data from light microscopy, scanning electron microscopy, electron dispersive x-ray spectroscopy, and radiocarbon dating to catalog the remarkable range of life preserved within these deposits. This includes intact microbes and nanobacteria-sized cocci, CaCO3 precipitations consistent with biogenic calcium, previously undescribed net-like structures, possible dormant spores, and long-extinct yet exquisitely preserved non-vascular plants. These images provide an important reference for further microbiome investigations of Antarctic paleolake samples. In addition, these findings may provide a visual reference for the use of subsurface groundwater microbial communities as an analog for paleolake subsurface water on planets such as Mars.