This library presents some publications, presentations, posters and case studies of Noblis’ staff. The research spans diverse subjects — developing cutting-edge whole genome sequence computational tools, biomarkers of anthrax infection, microbiomics and microbial metabolomics — all accretive to productive bioinformatics analysis. Please contact us for more information about the tools, methods and topics.
Noblis is elucidating SARS-CoV-2 evolution and the emergence of clinically important variants through innovative approaches to rapidly analyze data from whole genome sequencing. The rapid spread of COVID-19 has highlighted biosurveillance, public health, logistics and computational challenges. The extent of genomic diversity of SARS-CoV-2 in circulation, and the potential impact of genetic variation on viral transmissibility, pathogenicity, and diagnostic and therapeutic efficacy have yet to be fully elucidated. Through Noblis Sponsored Research, Noblis is analyzing hundreds of SARS-CoV-2 genomes provided by a collaborator who is sequencing COVID-19 clinical samples obtained from a diverse cohort throughout the United States. As part of this ongoing research, the genomes sequenced and analyzed and associated metadata are available at NCBI GenBank: PRJNA718231.
Read more and download our cutsheet on noblis.org.
Although DNA sequencing has become a well-established industry practice, typical methods of sample collection and transportation to a dedicated lab facility for analysis consumes valuable time when public health and safety are at stake. Further increasing turnaround time, sequencing and analysis often requires a resource-intensive high performance computing (HPC) infrastructure to generate actionable insight. In mission-critical applications such as biosurveillance—the tracking and detection of potentially harmful biological agents for national defense and public health missions—time is everything. Noblis has developed an end-to-end field-portable genetic sequencing and analysis system that relies on preloaded genomic databases to decrease both the footprint and response times.
Read more on noblis.org.
Scientists from Noblis and the Defense Biological Product Assurance Office (DBPAO), a component of the Joint Program Executive Office for Chemical, Biological, Radiological, and Nuclear Defense (JPEO-CBRND), are continuously evaluating polymerase chain reaction (PCR) assays (tests) for detection of the new Wuhan coronavirus. The research was done using BioLaboro, a Noblis application developed for rapidly designing de novo (new) assays and validating existing PCR detection assays.
Read the full news release on noblis.org.
Noblis collaborated with BEI Resources, operated by the American Type Culture Collection (ATCC), on a study to more quickly and accurately identify strains using Noblis’ high-speed sequence processing and analysis platform, BioVelocity. We queried blinded samples of raw reads against several large, public bacterial and viral genome databases using BioVelocity. The samples included a mix of bacterial species that are difficult for ATCC to identify using traditional 16S ribosomal RNA (rRNA) techniques. The results demonstrated a marked improvement over ATCC’s current technology with respect to difficult strains and demonstrates the potential for technologies like BioVelocity to provide new solutions for strain identification in the future.
Noblis collaborated with the National Institutes of Health (NIH) National Institute of Neurological Disorders and Stroke (NINDS) to demonstrate BioVelocity’s ability to detect pathogens in metagenomics samples mixed with human DNA. Noblis was given RNA-Seq data as FASTQ raw reads and tasked to discover pathogens. The case study included three rounds of blinded data that were intentionally spiked with a variety of pathogenic bacteria, viruses, and parasites. Noblis collaborated with the NIH researchers to fine tune our metagenomic algorithm so that by round 3, BioVelocity, with Noblis subject matter expert (SME) input, correctly identified 32 of 33 spiked in pathogens by general type, 26 of which were to the exact correct stain.
ASFV and FMDV are spreading worldwide. Pathogen evolution can accelerate assay signature erosion. We present an application of our automated in silico pipeline for prototyping and evaluation of new and existing PCR and LAMP assays for subspecies identification. Our automated pipeline generated 1,050 candidate PCR assays with high predicted performance, including those targeting ASFV and FMDV serotypes.
Sequencing technology requires advanced laboratory facilities and specialized training which increases the end-to-end time to reach actionable insights and limits the regions able to participate in biosurveillance. The rapid rate of mutation of RNA viruses, like SARS-CoV-2, challenges the limits of our current sequencing and software technologies in understanding shifts in these viruses. We suggest that a portable, near real-time, whole genome sequence-based, server independent system would provide solutions to this challenge. The aim of this study was to apply a portable sequencing and analysis system to SARS-CoV-2 isolates. The system converts Oxford Nanopore Technologies reads to high-quality, complete, strain-specific genome sequences.
Next Generation Sequencing (NGS) devices provide a means of detecting pathogenic or novel organisms via genetic screening in the field with a laptop but are often underutilized because the bioinformatic analysis required to interpret the sequencing data is complex. To make sequencing and analysis more applicable to users that lack necessary access to high performance computing systems, or simply lack the bioinformatics expertise, we have developed a simplified de novo genome assembly and pan genomic pipeline to characterize newly sequenced organisms that can run on a laptop.
Noblis and Tetracore scientists analyzed whole genome sequences (WGS) of SARS-COV-2 clinical isolates from confirmed COVID-19 cases throughout the US. We identified twenty-one isolates sharing similarly conserved mutations with other recently reported US Midwest isolates of the 20G/8083A clade while also containing some unique differences.
Our findings underscore the critical need for enhanced frontline and national genomic surveillance to effectively monitor SARS-CoV-2 evolution. Increases in regional and national genomic sequencing will help elucidate the extent to which these mutations are circulating in the population. As certain variants demonstrate increased transmissibility and aspects of immune evasion, there is an urgent need to monitor the potential for impacting therapeutic and vaccine efficacy.
Noblis scientists are developing a method to detect artificial sequences by employing machine learning and molecular clock analysis to build a model of sequence evolution. Our preliminary results indicate the presence of a clock signal and outliers across DNA Polymerase II sequences of E. coli. As we continue our research, we will test using altered sequences and integration into the directed evolution machine learning program.
Noblis scientists presented this research at the fourteenth annual Sequencing, Finishing, and Analysis in the Future (SFAF) Meeting held December 1-3, 2020 and hosted virtually by the Los Alamos National Laboratory.
To address the need for mobile biosurveillance for national defense and environmental applications, Noblis scientists have developed a field sequencing and analysis system that is fast and easy to use. Our solution features several unique differentiators, including: end-to-end sample to answer in the field, no line power or internet connection requirement, and miniaturizing the entire solution into a backpack.
This research was presented at the fourteenth annual Sequencing, Finishing, and Analysis in the Future (SFAF) Meeting held December 1-3, 2020 and hosted virtually by the Los Alamos National Laboratory.
Gram-negative bacteria express a lipopolysaccharide (LPS) that stabilizes the outer membrane while promoting host-pathogen interactions. The O-antigen (O-PS) is the external component of this endotoxin and is the basis of subspecies classification via serological methods. Our goal for this project was to test the molecular clock hypothesis and estimate the mutation rate of the O-PS region. In 2019, Noblis presented this research at the 54th US-Japan Cooperative Medical Sciences Program (CMSP) Joint Panel Conference on Cholera and Other Bacterial Enteric Infections in Osaka, Japan.
The entire BioLaboro system is driven by a simple graphical user interface that allows users to point-and-click to create analysis pipelines. The system ingests an array of NCBI data sources to perform its analyses and can be customized by a variety of parameters, adjustable on the fly. Using BioLaboro, Noblis is able to quickly identify which currently fielded Ebolavirus assays could potentially detect Bombali ebolavirus today and design a set of potential new assays with perfect in silico detection accuracy for the future. In 2019, Noblis presented this research at the 14th Annual Sequencing, Finishing, and Analysis in the Future (SFAF) Meeting in Santa Fe, New Mexico.
Noblis developed a novel method to compact large genome sequence datasets and raw genome sequence read sets for rapid analysis on portable devices. The Rapid and Portable Genome Classification System (RPGCS) is a technical approach that balances accuracy and speed with an intuitive user interface and greatly reduced computational demand. The system combines modern genomics techniques, statistical modeling, data analytics, and machine learning algorithms. The main goals of the RPGCS are to filter out potential organism matches in a sequenced sample and to determine a most-likely organism identity based on the matches found in the data structure without the need for high-performance computing power. Noblis scientists presented this research at the 12th annual Sequencing, Finishing, and Analysis in the Future (SFAF) Meeting held May 16-18, 2017 and hosted by the Los Alamos National Laboratory.
Bloom Cipher is a method of compressing and encoding metagenomics whole genome sequencing read sets for easy transfer and analysis, reduced liability, and increased security. By using the Bloom Cipher, one can compress and encode the read set in a lossy format, which allows for basic analysis while removing some of the liability of finding by using the probabilistic analysis. Future research will further enhance the utility and security of the method. In 2017, Noblis presented this research at the 12th Annual Sequencing, Finishing, and Analysis in the Future (SFAF) Meeting in Santa Fe, New Mexico.
Noblis developed a high-speed sequence processing and alignment platform, BioVelocity, to analyze whole genome sequence (WGS) data. During the 2016 Institute of Food Technologists (IFT16) conference, we presented on the use of BioVelocity to characterize a foodborne disease outbreak of Salmonella. Our analysis discriminated the Salmonella outbreak samples to the strain level and linked them to a commercial peanut butter product. Furthermore, simultaneous alignment of WGS data to reference genomes identified single nucleotide polymorphisms (SNPs) that were used to create a phylogenetic tree. Based on this method, we inferred that three unassociated samples were also highly related to the outbreak strain.
Noblis co-authored two poster presentations about the phylogenetic analysis of the O-antigen of Vibrio cholerae. There is a lack of fully sequenced V. cholerae genomes, but there are numerous whole genome shotgun sequences from which to extract regions of interest. Noblis developed a pipeline to automatically download and extract the O-antigen region of interest for Basic Local Alignment Search Tool (BLAST) processing and heat-map visualization of the results. The study exploited the presence of conserved junction genes to extract complete regions from contigs and subsequently perform phylogenetic analysis. Results revealed some mixture of the O-antigen serotypes, suggesting that horizontal-gene transfer has occurred.
Identification of bacterial organisms and viruses plays an important role in a multitude of areas, such as healthcare, biodefense, research, and food safety. Continually increasing databases of sequence data has made it possible to identify species-specific genomic regions, even serotypes of bacteria, as well as various classes of virus. As a part of an internal research project, Noblis examined the possibility that unique regions of genomes (i.e., signature sequences) could be used to differentiate phylogenetic levels, such as genus, species, and strain from all other known genomes, including those of closely-related organisms. The identified signature regions were evaluated as potential primers using the open source tool Primer 3 and were confirmed for specificity using BLAST. This pipeline supports continual generation of primers, particularly to combat assay degradation occurring over time.
Scientists from Noblis and Tetracore published a study in BMC Genomics in June 2022:
The SARS-CoV-2 Delta variant was first identified in the U.S. in March 2021 and has rapidly become the predominant lineage across the U.S. due to increased transmissibility, immune evasion and vaccine breakthrough. The aim of this study was to better understand the genetic diversity and the potential impact of mutations observed in SARS-CoV-2 viruses circulating in the U.S. in vaccinated individuals.
Whole genome sequencing was performed on thirty-four SARS-CoV-2 positive samples using the Oxford Nanopore MinION. Evolutionary genomic analysis revealed two novel mutations, ORF1b:V2354F and a premature stop codon, ORF7a:Q94*, identified in a cluster of SARS-CoV-2 Delta isolates collected from vaccinated individuals in Colorado.
Scientists from Noblis and the Defense Biological Product Assurance Office (DBPAO) published a paper in the online journal Frontiers in Public Health in April 2022. Following is an excerpt:
Real-time reverse transcription polymerase chain reaction (RT-PCR) assays are the most widely used molecular tests for the detection of SARS-CoV-2 and diagnosis of COVID-19 in clinical samples. PCR assays target unique genomic RNA regions to identify SARS-CoV-2 with high sensitivity and specificity. In general, assay development incorporates the whole genome sequences available at design time to be inclusive of all target species and exclusive of near neighbors. However, rapid accumulation of mutations in viral genomes during sustained growth in the population can result in signature erosion and assay failures, creating situational blind spots during a pandemic. In this study, we analyzed the signatures of 43 PCR assays distributed across the genome against over 1.6 million SARS-CoV-2 sequences. We present evidence of significant signature erosion emerging in just two assays due to mutations, while adequate sequence identity was preserved in the other 41 assays.
Published in the September 2021 on F1000 Research, Noblis scientists and other scientists and researchers contributed to a paper entitled “A pan-genome method to determine core regions of the Bacillus subtilis and Escherichia coli genomes”. In this study Noblis introduces a pan-genome based bioinformatic method of identifying core regions in a genome that contain all or almost all essential genes; this method is beneficial in genomic design as it outperforms many existing methods (with exceptions noted). Determining the set of core regions for a given species is critical as engineering changes to these regions should be expected to reduce fitness or be lethal.
The use of a pan-genome graph (PGG) for identifying core regions is a low-cost, rapid and effective way to evaluate both gram-negative and gram-positive bacteria that can be automated. This method compliments and expands upon the experimental knockout approach by including environmental diversity and overcomes limitations specific to the strains and growth conditions used.
This peer-reviewed post for the military leadership blog “From the Green Notebook” was published in August 2021.
There’s a reason we call it ‘going viral’—information can be just as contagious as Ebola, Zika or COVID-19—and just as dangerous. What’s more, confronting someone who has been negatively influenced by misinformation can feel just as daunting as stepping into a high containment laboratory to face any one of those viruses without the proper protective equipment. In this blog post, expert Nathan Fisher; a Ph.D., military reservist and senior scientist at Noblis ESI – along with a clinical cardiology pharmacist with University of Kentucky Healthcare – collaborate to give frontline military leaders the ‘informational PPE’ they need to counter vaccine misinformation and protect their formations from COVID-19. They discuss the major causes of vaccine hesitancy, describe the C.A.S.E. framework for open and honest conversations, and summarize major concepts regarding the risk of COVID-19 and the safety and efficacy of the authorized COVID-19 vaccines.
Noblis scientists have published a minireview entitled “Biomimetic Gut Model Systems for Development of Targeted Microbial Solutions for Enhancing Warfighter Health and Performance” which appeared in September/October 2020 issue of mSystems, an open access journal from the American Society for Microbiology (ASM). The microbiome as it relates to warfighter health and performance is of interest to the Department of Defense (DoD) with the development of interventions impacting gut microbiome resiliency among its top research priorities. While technological advancements are enabling the development of experimental model systems that facilitate mechanistic insights underpinning human health, disease and performance, translatability to human outcomes is still questionable. This review discusses some of the drivers influencing the DoD’s interest in the warfighter gut microbiome and describes current in vitro gut model systems supporting direct microbial-host interactions.
mSystems: DOI: 10.1128/mSystems.00487-20
As technology continues to expand and diversify the potential for Chemical, Biological, Radiological, Nuclear, and Explosives (CBRNE) attacks, cyberattacks, and other threats to homeland security, a broad Whole-of-Government Approach (WGA) is needed. In the lead article in the online, quarterly publication of the National Association for Court Management (NACM) Court Manager Vol. 34 #4 – Winter 2019, we contend that complex 21st century threats defy solutions by individual government entities. Rather interagency coordination across all three branches of government and engagement of non-governmental agencies are key to countering threats to our public health, safety, security, way of life and democratic values. To ensure a successful WGA, we argue for the active judicial participation in advanced planning, education and coordination to anticipate the future need for court decision making. The purpose of the article is to promote serious conversation about the roles of court administrators, judges and policymakers in the face of natural and manmade disasters, epidemics and pandemics, CBRNE attacks, and cyberattacks.
Noblis scientists and other scientists and researchers contributed to a paper entitled “Lassa virus circulating in Liberia: a retrospective genomic characterization” which appeared in the Lancet Infectious Diseases October 4, 2019 issue. The purpose of the paper was to compare published and recent Lassa virus genomes to assess the ability of currently deployed diagnostic assays to detect circulating Lassa virus. Our scientists used in silico bioinformatics methods, including Noblis’ PCR Signature Erosion Tool (PSET), to provide data visualizations and insights for the genome relationships.
Lancet Infectious Diseases: DOI 10.1016/S1473-3099(19)30486-4, 2019.
Evaluation of Signature Erosion in Ebola Virus Due to Genomic Drift and Its Impact on the Performance of Diagnostic Assays demonstrates the use of BioVelocity and PCR Signature Erosion Tool (PSET) to evaluate polymerase chain reaction (PCR) assays deployed during the West African Ebola epidemic and other Ebola PCR assays available. PSET evaluated the assays’ effectiveness against the strain circulating in West Africa during the epidemic, while BioVelocity identified optimal sequence target for future assay design and compared its findings to classical techniques.
Viruses 7: 3130-3154, 2015.
Urine was considered sterile in healthy individuals for many years, and the presence of bacteria signified a urinary tract infection. With Expanded Quantitative Urine Culture and molecular techniques, the previous clinical dogma is no longer valid. Healthy people harbor a considerable microbial community—or microbiota—in their urinary systems. Similar to other physiological niches, microbiota also play a crucial role in urinary health of individuals. Understanding the urinary microbiome allows a more holistic approach in the diagnosis, treatment, and prevention of diseases in the urinary system. This review provides an overview of current findings in urinary microbiome research and discusses gaps for future research.
AIMS Microbiology 3(2): 143-154, 2017.
Knowledge gained from the Human Microbiome Project supports using probiotics to achieve a balanced microbial community and potentially reduce or alleviate certain disorders. Most research studies and commercial probiotic products have focused on the human gastrointestinal tract. Recently, interests and applications have extended to other physiological systems. Personal care products are used widely every day, and potential uses of probiotics in this market sector are being explored. This review summarizes recent findings of microbial communities in the skin and oral cavity—where personal care products are mostly applied—and discusses opportunities and challenges of probiotics in these products.
Microbiology Discovery 3(5), 2015.
Microbial metabolomics constitutes an integrated component of systems biology. By studying the complete set of metabolites within a microorganism and monitoring the global outcome of interactions between its development processes and the environment, metabolomics can potentially provide a more accurate snap shot of the actual physiological state of the cell. Recent advancements of technologies and post-genomic developments enable the study and analysis of the metabolome. This unique contribution resulted in many scientific disciplines incorporating metabolomics as one of their “-omics” platforms. This review focuses on metabolomics in microorganisms and uses selected topics to illustrate its impact on the understanding of systems microbiology.
Current Genomics 12:391-403, 2011.
A normal flora in the upper respiratory tract, Corynebacterium pseudodiptheriticum is not often considered as the causative bacterium for community-acquired pneumonia. A patient with bronchiectasis was initially suspected as being infected with Mycobacterium avium. When antibiotic treatment was not successful, bronchial alveolar lavage was obtained for microbiological culturing. Once C. pseudodiptheriticum was recovered, its antibiotic susceptibility profile allowed appropriate antimicrobial intervention to arrest the infection. The patient experienced full recovery. This case report shows the importance of considering non-routine--at times invasive--clinical specimens for diagnosis. Furthermore, commensal microbes should not be dismissed as possible etiological agents in pulmonary infections.
Translational Biomedicine 2010. Doi:10:3823/408.
A novel mass-spectrometry–based approach to identify host-derived, low-molecular mass biomarkers in the blood proteome was tested in a murine model. Mice were challenged with Bacillus anthracis Sterne (toxigenic) or delta Sterne (non-virulent) spores. Serum samples obtained at multiple time points yielded more than 200 proteins, displaying low-variance differential abundances between lethal and non-lethal challenges. Six serum proteins strongly coincided with established anthrax disease and mortality, making them potential candidates for host-derived anthrax-disease–associated biomarkers. Furthermore, their abundance levels in sera of doxycycline-treated mice can serve as useful tools for monitoring treatment efficacies.
J. Proteomics & Bioinformatics 2009. Doi: 10.4172/jpb.1000101.
Prokaryotic extremophiles were the first representatives of life on Earth and likely contributed to the geological structures of currently known ecosystems. Their genome flexibility allowed adaptation to a wide spectrum of extreme environments. Modern extremophiles consisted of thermophilic, psychrophilic, acidophilic, alkaliphilic, halophilic, barophilic, and radio-resistant species. Since one organism often overlaps several extreme conditions, it reflects multiple interactions between different environmental factors. This review discusses the current status of extremophile research and summarizes the limits of life for different species. Also mentioned are extremophiles from unusual places and recent studies of microfossils in meteorites, with a focus on their significance to astrobiology.
Critical Reviews in Microbiology 33: 183-209, 2007.