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1. The National Microbiome Data Collaborative Data Portal: an integrated multi-omics microbiome data resource

Author

Eloe-Fadrosh, Emiley A, Ahmed, Faiza, Anubhav, Babinski, Michal, Baumes, Jeffrey, Borkum, Mark, Bramer, Lisa, Canon, Shane, Christianson, Danielle S, Corilo, Yuri E, Davenport, Karen W, Davis, Brandon, Drake, Meghan, Duncan, William D, Flynn, Mark C, Hays, David, Hu, Bin, Huntemann, Marcel, Kelliher, Julia, Lebedeva, Sofya, Li, Po-E, Lipton, Mary, Lo, Chien-Chi, Martin, Stanton, Millard, David, Miller, Kayd, Miller, Mark A, Piehowski, Paul, Jackson, Elais Player, Purvine, Samuel, Reddy, TBK, Richardson, Rachel, Rudolph, Marisa, Sarrafan, Setareh, Shakya, Migun, Smith, Montana, Stratton, Kelly, Sundaramurthi, Jagadish Chandrabose, Vangay, Pajau, Winston, Donald, Wood-Charlson, Elisha M, Xu, Yan, Chain, Patrick SG, McCue, Lee Ann, Mans, Douglas, Mungall, Christopher J, Mouncey, Nigel J, and Fagnan, Kjiersten

Subjects
Microbiology, Biological Sciences, Human Genome, Genetics, Data Science, Microbiome, Good Health and Well Being, Environmental Sciences, Information and Computing Sciences, Developmental Biology, Biological sciences, Chemical sciences, Environmental sciences
Abstract

The National Microbiome Data Collaborative (NMDC) Data Portal (https://data.microbiomedata.org) supports microbiome multi-omics data exploration and access through an integrated, distributed data framework aligned with the FAIR (Findable, Accessible, Interoperable and Reusable) data principles (1). The NMDC Data Portal currently hosts 10.2 terabytes of multi-omics microbiome data, spanning five data types (metagenomes, metatranscriptomes, metaproteomes, metabolomes, and natural organic matter characterizations), generated at two Department of Energy User Facilities, the Joint Genome Institute (JGI) at Lawrence Berkeley National Laboratory (LBNL) and the Environmental Molecular Systems Laboratory (EMSL) at Pacific Northwest National Laboratory (PNNL). A flexible data schema (https://github.com/microbiomedata/nmdc-schema) leveraging community-driven standards underpins how data is managed and integrated. Annotated multi-omic data products are produced by the NMDC workflows and linked through common biosamples to enable search capabilities based on environmental context, instrumentation, and functional attributes. As a pilot system, the NMDC Data Portal offers download capabilities and several search components, including interactive geographic visualization of samples; environmental classification distribution visualized through an interactive Sankey diagram; time-series slider to select longitudinal samples of interest; and an upset plot displaying the number of multi-omics data generated from the same biosample within a study.

Published
2022

2. Discovery of an Antarctic Ascidian-Associated Uncultivated Verrucomicrobia with Antimelanoma Palmerolide Biosynthetic Potential

Author

Murray, Alison E, Lo, Chien-Chi, Daligault, Hajnalka E, Avalon, Nicole E, Read, Robert W, Davenport, Karen W, Higham, Mary L, Kunde, Yuliya, Dichosa, Armand EK, Baker, Bill J, and Chain, Patrick SG

Subjects
Microbiology, Biological Sciences, Biotechnology, Genetics, Human Genome, Animals, Antarctic Regions, Macrolides, Microbiota, Multigene Family, Phylogeny, RNA, Ribosomal, 16S, Urochordata, Verrucomicrobia, Antarctic, Synoicihabitans palmerolidicus, Synoicum adareanum, anticancer, ascidian natural product, biosynthetic gene cluster, microbiome metagenome, palmerolide, secondary metabolite
Abstract

The Antarctic marine ecosystem harbors a wealth of biological and chemical innovation that has risen in concert over millennia since the isolation of the continent and formation of the Antarctic circumpolar current. Scientific inquiry into the novelty of marine natural products produced by Antarctic benthic invertebrates led to the discovery of a bioactive macrolide, palmerolide A, that has specific activity against melanoma and holds considerable promise as an anticancer therapeutic. While this compound was isolated from the Antarctic ascidian Synoicum adareanum, its biosynthesis has since been hypothesized to be microbially mediated, given structural similarities to microbially produced hybrid nonribosomal peptide-polyketide macrolides. Here, we describe a metagenome-enabled investigation aimed at identifying the biosynthetic gene cluster (BGC) and palmerolide A-producing organism. A 74-kbp candidate BGC encoding the multimodular enzymatic machinery (hybrid type I-trans-AT polyketide synthase-nonribosomal peptide synthetase and tailoring functional domains) was identified and found to harbor key features predicted as necessary for palmerolide A biosynthesis. Surveys of ascidian microbiome samples targeting the candidate BGC revealed a high correlation between palmerolide gene targets and a single 16S rRNA gene variant (R = 0.83 to 0.99). Through repeated rounds of metagenome sequencing followed by binning contigs into metagenome-assembled genomes, we were able to retrieve a nearly complete genome (10 contigs) of the BGC-producing organism, a novel verrucomicrobium within the Opitutaceae family that we propose here as "Candidatus Synoicihabitans palmerolidicus." The refined genome assembly harbors five highly similar BGC copies, along with structural and functional features that shed light on the host-associated nature of this unique bacterium. IMPORTANCE Palmerolide A has potential as a chemotherapeutic agent to target melanoma. We interrogated the microbiome of the Antarctic ascidian, Synoicum adareanum, using a cultivation-independent high-throughput sequencing and bioinformatic strategy. The metagenome-encoded biosynthetic machinery predicted to produce palmerolide A was found to be associated with the genome of a member of the S. adareanum core microbiome. Phylogenomic analysis suggests the organism represents a new deeply branching genus, "Candidatus Synoicihabitans palmerolidicus," in the Opitutaceae family of the Verrucomicrobia phylum. The Ca. Synoicihabitans palmerolidicus 4.29-Mb genome encodes a repertoire of carbohydrate-utilizing and transport pathways, a chemotaxis system, flagellar biosynthetic capacity, and other regulatory elements enabling its ascidian-associated lifestyle. The palmerolide producer's genome also contains five distinct copies of the large palmerolide biosynthetic gene cluster that may provide structural complexity of palmerolide variants.

Published
2021

3. EDGE COVID-19: A Web Platform to generate submission-ready genomes for SARS-CoV-2 sequencing efforts

Author

Lo, Chien-Chi, Shakya, Migun, Davenport, Karen, Flynn, Mark, Gutiérrez, Adán Myers y, Hu, Bin, Li, Po-E, Jackson, Elais Player, Xu, Yan, and Chain, Patrick S. G.

Subjects
Quantitative Biology - Genomics
Abstract

Genomics has become an essential technology for surveilling emerging infectious disease outbreaks. A wide range of technologies and strategies for pathogen genome enrichment and sequencing are being used by laboratories worldwide, together with different, and sometimes ad hoc, analytical procedures for generating genome sequences. As a result, public repositories now contain non-standard entries of varying quality. A standardized analytical process for consensus genome sequence determination, particularly for outbreaks such as the ongoing COVID-19 pandemic, is critical to provide a solid genomic basis for epidemiological analyses and well-informed decision making. To address this need, we have developed a bioinformatic workflow to standardize the analysis of SARS-CoV-2 sequencing data generated with either the Illumina or Oxford Nanopore platforms. Using an intuitive web-based interface, this workflow automates SARS-CoV-2 reference-based genome assembly, variant calling, lineage determination, and provides the ability to submit the consensus sequence and necessary metadata to GenBank or GISAID. Given a raw Illumina or Oxford Nanopore FASTQ read file, this web-based platform enables non-bioinformatics experts to automatically produce a SARS-CoV-2 genome that is ready for submission to GISAID or GenBank. Availability:https://edge-covid19.edgebioinformatics.org;https://github.com/LANL-Bioinformatics/EDGE/tree/SARS-CoV2

Published
2020

4. A Public Website for the Automated Assessment and Validation of SARS-CoV-2 Diagnostic PCR Assays

Author

Li, Po-E, Gutiérrez, Adán Myers y, Davenport, Karen, Flynn, Mark, Hu, Bin, Lo, Chien-Chi, Jackson, Elais Player, Shakya, Migun, Xu, Yan, Gans, Jason, and Chain, Patrick S. G.

Subjects
Quantitative Biology - Genomics, Quantitative Biology - Quantitative Methods
Abstract

Summary: Polymerase chain reaction-based assays are the current gold standard for detecting and diagnosing SARS-CoV-2. However, as SARS-CoV-2 mutates, we need to constantly assess whether existing PCR-based assays will continue to detect all known viral strains. To enable the continuous monitoring of SARS-CoV-2 assays, we have developed a web-based assay validation algorithm that checks existing PCR-based assays against the ever-expanding genome databases for SARS-CoV-2 using both thermodynamic and edit-distance metrics. The assay screening results are displayed as a heatmap, showing the number of mismatches between each detection and each SARS-CoV-2 genome sequence. Using a mismatch threshold to define detection failure, assay performance is summarized with the true positive rate (recall) to simplify assay comparisons. Availability: https://covid19.edgebioinformatics.org/#/assayValidation. Contact: Jason Gans (jgans@lanl.gov) and Patrick Chain (pchain@lanl.gov), Comment: Application Note. Main: 2 pages, 1 figure. Supplementary: 6 pages, 8 figures, 1 table. Total: 8 pages, 9 figures, 1 table. Application url: https://covid19.edgebioinformatics.org/#/assayValidation Contact: Jason Gans (jgans@lanl.gov) and Patrick Chain (pchain@lanl.gov) Submitted to: Bioinformatics

Published
2020

5. Challenges in Bioinformatics Workflows for Processing Microbiome Omics Data at Scale

Author

Hu, Bin, Canon, Shane, Eloe-Fadrosh, Emiley A, Anubhav, Babinski, Michal, Corilo, Yuri, Davenport, Karen, Duncan, William D, Fagnan, Kjiersten, Flynn, Mark, Foster, Brian, Hays, David, Huntemann, Marcel, Jackson, Elais K Player, Kelliher, Julia, Li, Po-E, Lo, Chien-Chi, Mans, Douglas, McCue, Lee Ann, Mouncey, Nigel, Mungall, Christopher J, Piehowski, Paul D, Purvine, Samuel O, Smith, Montana, Varghese, Neha Jacob, Winston, Donald, Xu, Yan, and Chain, Patrick SG

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Generic health relevance, bioinformatics, infrastructure, microbial ecology, microbiome, omics
Abstract

The nascent field of microbiome science is transitioning from a descriptive approach of cataloging taxa and functions present in an environment to applying multi-omics methods to investigate microbiome dynamics and function. A large number of new tools and algorithms have been designed and used for very specific purposes on samples collected by individual investigators or groups. While these developments have been quite instructive, the ability to compare microbiome data generated by many groups of researchers is impeded by the lack of standardized application of bioinformatics methods. Additionally, there are few examples of broad bioinformatics workflows that can process metagenome, metatranscriptome, metaproteome and metabolomic data at scale, and no central hub that allows processing, or provides varied omics data that are findable, accessible, interoperable and reusable (FAIR). Here, we review some of the challenges that exist in analyzing omics data within the microbiome research sphere, and provide context on how the National Microbiome Data Collaborative has adopted a standardized and open access approach to address such challenges.

Published
2021

6. The National Microbiome Data Collaborative: enabling microbiome science

Author

Wood-Charlson, Elisha M, Anubhav, Auberry, Deanna, Blanco, Hannah, Borkum, Mark I, Corilo, Yuri E, Davenport, Karen W, Deshpande, Shweta, Devarakonda, Ranjeet, Drake, Meghan, Duncan, William D, Flynn, Mark C, Hays, David, Hu, Bin, Huntemann, Marcel, Li, Po-E, Lipton, Mary, Lo, Chien-Chi, Millard, David, Miller, Kayd, Piehowski, Paul D, Purvine, Samuel, Reddy, TBK, Shakya, Migun, Sundaramurthi, Jagadish Chandrabose, Vangay, Pajau, Wei, Yaxing, Wilson, Bruce E, Canon, Shane, Chain, Patrick SG, Fagnan, Kjiersten, Martin, Stanton, McCue, Lee Ann, Mungall, Christopher J, Mouncey, Nigel J, Maxon, Mary E, and Eloe-Fadrosh, Emiley A

Subjects
Microbiology, Biological Sciences, Microbiome, Data Science, Humans, Intersectoral Collaboration, Microbiota, Medical Microbiology
Published
2020

7. Investigating intestinal permeability and gut microbiota roles in acute coronary syndrome patients

Author

Alhmoud, Tarik, Kumar, Anand, Lo, Chien-Chi, Al-Sadi, Rana, Clegg, Stacey, Alomari, Ihab, Zmeili, Tarek, Gleasne, Cheryl Diane, Mcmurry, Kim, Dichosa, Armand Earl Ko, Vuyisich, Momchilo, Chain, Patrick Sam Guy, Mishra, Shiraz, and Ma, Thomas

Subjects
Microbiology, Biological Sciences, Biomedical and Clinical Sciences, Rare Diseases, Atherosclerosis, Heart Disease, Cardiovascular, Digestive Diseases, Heart Disease - Coronary Heart Disease, Nutrition, Aetiology, 2.1 Biological and endogenous factors, Oral and gastrointestinal, Good Health and Well Being, Acute coronary syndrome, Dysbiosis, Endotoxins, Intestinal permeability, Proteobacteria, TMAO
Abstract

BackgroundAcute Coronary Syndrome (ACS) is a leading cause of morbidity and mortality. Perturbed gut- microbiota (dysbiosis) and increased intestinal permeability (leaky-gut) with translocation of bacterial antigens, play critical role in obesity and metabolic syndrome, which are also major ACS risk factors. Additionally, Trimethylamine-N-Oxide (TMAO), a metabolite produced by phylum Proteobacteria in gut is implicated in developing ACS. As Proteobacteria is a major source of translocated antigen lipopolysaccharides (LPS), we hypothesized that ACS patients have leaky-gut condition characterized by dysbiosis with increased Proteobacteria, leading to elevated blood levels of TMAO and LPS.MethodsIn a pilot case-control study, we enrolled 19 ACS patients (within 72-h of cardiac events) and 19 healthy-controls. Gut barrier function was determined using lactulose-to-mannitol urinary excretion ratio (L/M ratio). Stool microbiome composition was examined using16S sequencing and predictive functional analysis for LPS biosynthesis pathway by PICRUSt tool. Serum TMAO and LPS levels were measured.ResultsACS patients had increased Gammaproteobacteria compared to controls:1.8 ±3.0 vs. 0.2 ±0.4% (P =0.04). Though Proteobacteria level was increased but not statistically significant: 4.1 ±3.8 vs. 2.1 ±1.7% (P =0.056). L/M-ratio was three times higher in ACS patients; 0.06 ±0.07 vs 0.023 ±0.02, (P =0.014). Surprisingly, there was no difference in the mean serum LPS or TMAO levels. However, PICRUSt analysis indicated increased Proteobacteria population increasingly contributed to LPS biosynthesis in ACS patients only.ConclusionsACS patients likely to have leaky-gut and perturbed gut microbiota. Further studies are required to precisely define the role of dysbiosis in ACS.

Published
2019

8. High-Quality Draft Genome Sequences of Four Lignocellulose-Degrading Bacteria Isolated from Puerto Rican Forest Soil: Gordonia sp., Paenibacillus sp., Variovorax sp., and Vogesella sp.

Author

Woo, Hannah L, DeAngelis, Kristen M, Teshima, Hazuki, Davenport, Karen, Daligault, Hajnalka, Erkkila, Tracy, Goodwin, Lynne, Gu, Wei, Lo, Chien-Chi, Munk, Christine, Scholz, Matthew, Xu, Yan, Chain, Patrick, Bruce, David, Detter, Chris, Tapia, Roxanne, Han, Cliff, Simmons, Blake A, and Hazen, Terry C

Subjects
Biochemistry and Cell Biology, Genetics, Microbiology
Abstract

Here, we report the high-quality draft genome sequences of four phylogenetically diverse lignocellulose-degrading bacteria isolated from tropical soil (Gordonia sp., Paenibacillus sp., Variovorax sp., and Vogesella sp.) to elucidate the genetic basis of their ability to degrade lignocellulose. These isolates may provide novel enzymes for biofuel production.

Published
2017

9. Major changes in microbial diversity and community composition across gut sections of a juvenile Panchlora cockroach.

Author

Gontang, Erin A, Aylward, Frank O, Carlos, Camila, Glavina Del Rio, Tijana, Chovatia, Mansi, Fern, Alison, Lo, Chien-Chi, Malfatti, Stephanie A, Tringe, Susannah G, Currie, Cameron R, and Kolter, Roberto

Subjects
Gastrointestinal Tract, Animals, Cockroaches, Ants, RNA, Ribosomal, 16S, Biodiversity, Phylogeny, Metagenome, Gastrointestinal Microbiome, General Science & Technology
Abstract

Investigations of gut microbiomes have shed light on the diversity and genetic content of these communities, and helped shape our understanding of how host-associated microorganisms influence host physiology, behavior, and health. Despite the importance of gut microbes to metazoans, our understanding of the changes in diversity and composition across the alimentary tract, and the source of the resident community are limited. Here, using community metagenomics and 16S rRNA gene sequencing, we assess microbial community diversity and coding potential in the foregut, midgut, and hindgut of a juvenile Panchlora cockroach, which resides in the refuse piles of the leaf-cutter ant species Atta colombica. We found a significant shift in the microbial community structure and coding potential throughout the three gut sections of Panchlora sp., and through comparison with previously generated metagenomes of the cockroach's food source and niche, we reveal that this shift in microbial community composition is influenced by the ecosystems in which Panchlora sp. occurs. While the foregut is composed of microbes that likely originate from the symbiotic fungus gardens of the ants, the midgut and hindgut are composed of a microbial community that is likely cockroach-specific. Analogous to mammalian systems, the midgut and hindgut appear to be dominated by Firmicutes and Bacteroidetes with the capacity for polysaccharide degradation, suggesting they may assist in the degradation of dietary plant material. Our work underscores the prominence of community changes throughout gut microbiomes and highlights ecological factors that underpin the structure and function of the symbiotic microbial communities of metazoans.

Published
2017

10. Bridging Place-Based Astrobiology Education with Genomics, Including Descriptions of Three Novel Bacterial Species Isolated from Mars Analog Sites of Cultural Relevance

Author

Prescott, Rebecca D., primary, Chan, Yvonne L., additional, Tong, Eric J., additional, Bunn, Fiona, additional, Onouye, Chiyoko T., additional, Handel, Christy, additional, Lo, Chien-Chi, additional, Davenport, Karen, additional, Johnson, Shannon, additional, Flynn, Mark, additional, Saito, Jennifer A., additional, Lee, Herb, additional, Wong, Kaleomanuiwa, additional, Lawson, Brittany N., additional, Hiura, Kayla, additional, Sager, Kailey, additional, Sadones, Mia, additional, Hill, Ethan C., additional, Esibill, Derek, additional, Cockell, Charles S., additional, Santomartino, Rosa, additional, Chain, Patrick S.G., additional, Decho, Alan W., additional, and Donachie, Stuart P., additional

Published
2023
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11. Genomic and Phenotypic Characterization of Shiga Toxin-Producing Escherichia albertii Strains Isolated from Wild Birds in a Major Agricultural Region in California

Author

Carter, Michelle Qiu, primary, Quiñones, Beatriz, additional, He, Xiaohua, additional, Pham, Antares, additional, Carychao, Diana, additional, Cooley, Michael B., additional, Lo, Chien-Chi, additional, Chain, Patrick S. G., additional, Lindsey, Rebecca L., additional, and Bono, James L., additional

Published
2023
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12. Recommendations for Uniform Variant Calling of SARS-CoV-2 Genome Sequence across Bioinformatic Workflows.

Author

Connor, Ryan, Shakya, Migun, Yarmosh, David A., Maier, Wolfgang, Martin, Ross, Bradford, Rebecca, Brister, J. Rodney, Chain, Patrick S. G., Copeland, Courtney A., di Iulio, Julia, Hu, Bin, Ebert, Philip, Gunti, Jonathan, Jin, Yumi, Katz, Kenneth S., Kochergin, Andrey, LaRosa, Tré, Li, Jiani, Li, Po-E, and Lo, Chien-Chi

Subjects
SARS-CoV-2, COVID-19 pandemic, SINGLE nucleotide polymorphisms, GENETIC variation, VIRAL transmission, QUALITY function deployment, WORKFLOW
Abstract

Genomic sequencing of clinical samples to identify emerging variants of SARS-CoV-2 has been a key public health tool for curbing the spread of the virus. As a result, an unprecedented number of SARS-CoV-2 genomes were sequenced during the COVID-19 pandemic, which allowed for rapid identification of genetic variants, enabling the timely design and testing of therapies and deployment of new vaccine formulations to combat the new variants. However, despite the technological advances of deep sequencing, the analysis of the raw sequence data generated globally is neither standardized nor consistent, leading to vastly disparate sequences that may impact identification of variants. Here, we show that for both Illumina and Oxford Nanopore sequencing platforms, downstream bioinformatic protocols used by industry, government, and academic groups resulted in different virus sequences from same sample. These bioinformatic workflows produced consensus genomes with differences in single nucleotide polymorphisms, inclusion and exclusion of insertions, and/or deletions, despite using the same raw sequence as input datasets. Here, we compared and characterized such discrepancies and propose a specific suite of parameters and protocols that should be adopted across the field. Consistent results from bioinformatic workflows are fundamental to SARS-CoV-2 and future pathogen surveillance efforts, including pandemic preparation, to allow for a data-driven and timely public health response. [ABSTRACT FROM AUTHOR]

Published
2024
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15. Towards increased accuracy and reproducibility in SARS-CoV-2 next generation sequence analysis for public health surveillance

Author

Connor, Ryan, primary, Yarmosh, David A., additional, Maier, Wolfgang, additional, Shakya, Migun, additional, Martin, Ross, additional, Bradford, Rebecca, additional, Brister, J. Rodney, additional, Chain, Patrick SG, additional, Copeland, Courtney A., additional, di Iulio, Julia, additional, Hu, Bin, additional, Ebert, Philip, additional, Gunti, Jonathan, additional, Jin, Yumi, additional, Katz, Kenneth S., additional, Kochergin, Andrey, additional, LaRosa, Tré, additional, Li, Jiani, additional, Li, Po-E, additional, Lo, Chien-Chi, additional, Rashid, Sujatha, additional, Maiorova, Evguenia S., additional, Xiao, Chunlin, additional, Zalunin, Vadim, additional, and Pruitt, Kim D., additional

Published
2022
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16. Precise Genomic Riboregulator Control of Metabolic Flux in Microbial Systems

Author

Pandey, Naresh, primary, Davison, Steffi A., additional, Krishnamurthy, Malathy, additional, Trettel, Daniel S., additional, Lo, Chien-Chi, additional, Starkenburg, Shawn, additional, Wozniak, Katherine L., additional, Kern, Theresa L., additional, Reardon, Sean D., additional, Unkefer, Clifford J., additional, Hennelly, Scott P., additional, and Dale, Taraka, additional

Published
2022
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17. Benchmark datasets for SARS-CoV-2 surveillance bioinformatics

Author

Xiaoli, Lingzi, primary, Hagey, Jill V., additional, Park, Daniel J., additional, Gulvik, Christopher A., additional, Young, Erin L., additional, Alikhan, Nabil-Fareed, additional, Lawsin, Adrian, additional, Hassell, Norman, additional, Knipe, Kristen, additional, Oakeson, Kelly F., additional, Retchless, Adam C., additional, Shakya, Migun, additional, Lo, Chien-Chi, additional, Chain, Patrick, additional, Page, Andrew J., additional, Metcalf, Benjamin J., additional, Su, Michelle, additional, Rowell, Jessica, additional, Vidyaprakash, Eshaw, additional, Paden, Clinton R., additional, Huang, Andrew D., additional, Roellig, Dawn, additional, Patel, Ketan, additional, Winglee, Kathryn, additional, Weigand, Michael R., additional, and Katz, Lee S., additional

Published
2022
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18. EDGE Bioinformatics

Author

Davenport, Karen, primary, Lo, Chien-Chi, additional, Li, Po-E, additional, Shakya, Migun, additional, and Chain, Patrick, additional

Published
2019
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19. Standardized and accessible multi-omics bioinformatics workflows through the NMDC EDGE resource

Author

Kelliher, Julia M., Xu, Yan, Flynn, Mark C., Babinski, Michal, Canon, Shane, Cavanna, Eric, Clum, Alicia, Corilo, Yuri E., Fujimoto, Grant, Giberson, Cameron, Johnson, Leah Y.D., Li, Kaitlyn J., Li, Po-E, Li, Valerie, Lo, Chien-Chi, Lynch, Wendi, Piehowski, Paul, Prime, Kaelan, Purvine, Samuel, Rodriguez, Francisca, Roux, Simon, Shakya, Migun, Smith, Montana, Sarrafan, Setareh, Cholia, Shreyas, McCue, Lee Ann, Mungall, Chris, Hu, Bin, Eloe-Fadrosh, Emiley A., and Chain, Patrick S.G.

Published
2024
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24. The National Microbiome Data Collaborative: a data science ecosystem for microbiome research

Author

Canon, Shane, Christianson, Danielle, Duncan, William, Eloe-Fadrosh, Emiley, Fagnan, Kjiersten, Hays, David, Huntemann, Marcel, Lebedeva, Sofya, Miller, Kayd, Miller, Mark, Mouncey, Nigel, Mungall, Chris, Reddy, Tbk, Rudolph, Marisa, Sarrafan, Setareh, Sundaramurthi, Jagadish Chandrabose, Unni, Deepak, Vangay, Pajau, Wood-Charlson, Elisha, Ahmed, Faiza, Baumes, Jeffrey, Davis, Brandon, Anubhav, Fnu, Borkhum, Mark, Bramer, Lisa, Corilo, Yuri, Lipton, Mary, Mans, Douglas, McCue, Lee Ann, Millard, David, Piehowski, Paul, Prymolenna, Anastasiya, Purvine, Samuel, Richardson, Rachel, Smith, Montana, Stratton, Kelly, Babinski, Michal, Chain, Patrick, Davenport, Karen, Flynn, Mark, Hu, Bin, Kelliher, Julia, Li, Po-E, Lo, Chien-Chi, Jackson, Elais Player, Shakya, Migun, Xu, Yan, Drake, Meghan, Martin, Stanton, Wilson, Bruce, and Winston, Donny

Subjects
data infrastructure, microbiome, data science, science gateway
Abstract

The cross-cutting nature of microbiome research in environmental sciences, health, agriculture, energy, and natural and built environments, and the velocity at which microbiome data are generated has far outpaced current data infrastructure. Resources and solutions for collection, processing, and distribution of these data in an effective, uniform, accessible, and reproducible manner, are lacking even at the largest data centers. The National Microbiome Data Collaborative (NMDC) is a pilot initiative launched to support microbiome data exploration and discovery through a collaborative, integrative science gateway. The NMDC is tackling infrastructure challenges in microbiome data science by making use of distributed computational resources available across four Department of Energy National Laboratories, Lawrence Berkeley National Laboratory (LBNL), Los Alamos National Laboratory (LANL), Pacific Northwest National Laboratory (PNNL) and Oak Ridge National Laboratory (ORNL). The NMDC team aims to deliver a set of unique microbiome data science capabilities, which include: leveraging existing ontology mapping software and curation resources to enable automated annotation of standardized metadata; developing workflows for metagenome, metatranscriptome, metaproteome, and metabolomics data processing leveraging HPC systems, and integrating the execution of these pipelines to produce NMDC-compliant data products; developing data registration, indexing, and access services to link data through a suite of publicly available APIs; and developing communication and sustainability strategies to assess current and future needs and capabilities to empower users, and promote the NMDC to the larger scientific community. To ensure that the NMDC data ecosystem supports and evolves with the needs of the microbiome research community, the NMDC team uses a community-centered design approach to seek feedback from the scientific research community throughout its phases of iterative development. Community feedback has informed the priorities of the NMDC data standards, bioinformatic workflows, and engagement activities, but perhaps the most visible contributions of the research community can be seen through the features and enhancements on the NMDC data portal. Here, we present an overview of the NMDC mission and vision, the distributed data infrastructure, and our community-centered design approach in developing the NMDC data portal.

Published
2021
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25. EDGE 2017 R&D 100 Entry with Appendix

Author

Chain, Patrick Sam Guy, primary, Davenport, Karen Walston, additional, Li, Po-E, additional, Lo, Chien-Chi, additional, Xu, Yan, additional, Senin, Pavel, additional, Shakya, Migun, additional, Ahmed, Sanaa Afroz, additional, Hamilton, Theron C., additional, Bishop-Lilly, Kimberly A., additional, Anderson, Joseph J., additional, Voegtly, Logan J., additional, and Philipson, Casandra W., additional

Published
2017
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26. Discovery of an Antarctic ascidian-associated uncultivated Verrucomicrobia with antimelanoma palmerolide biosynthetic potential

Author

Murray, Alison E., primary, Lo, Chien-Chi, additional, Daligault, Hajnalka E., additional, Avalon, Nicole E., additional, Read, Robert W., additional, Davenport, Karen W., additional, Higham, Mary L., additional, Kunde, Yuliya, additional, Dichosa, Armand E.K., additional, Baker, Bill J., additional, and Chain, Patrick S.G., additional

Published
2021
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27. Uncovering the Core Microbiome and Distribution of Palmerolide in Synoicum adareanum Across the Anvers Island Archipelago, Antarctica

Author

Freudenstein, John, Gribaldo, Simonetta, Hatzenpichler, Roland, Hugenholtz, Philip, Kämpfer, Peter, Konstantinidis, Konstantinos, Lane, Christopher, Papke, R. Thane, Parks, Donovan, Rossello-Mora, Ramon, Stott, Matthew, Sutcliffe, Iain, Thrash, J. Cameron, Venter, Stephanus, Whitman, William, Acinas, Silvia, Amann, Rudolf, Anantharaman, Karthik, Armengaud, Jean, Baker, Brett, Barco, Roman, Bode, Helge, Boyd, Eric, Brady, Carrie, Carini, Paul, Chain, Patrick, Colman, Daniel, DeAngelis, Kristen, de los Rios, Maria Asuncion, Estrada-De Los Santos, Paulina, Dunlap, Christopher, Eisen, Jonathan, Emerson, David, Ettema, Thijs, Girguis, Peter, Hentschel, Ute, Hollibaugh, James, Hug, Laura, Inskeep, William, Ivanova, Elena, Klenk, Hans-Peter, Li, Wen-Jun, Lloyd, Karen, Löffler, Frank, Makhalanyane, Thulani, Moser, Duane, Nunoura, Takuro, Palmer, Marike, Parro, Victor, Pedrós-Alió, Carlos, Probst, Alexander, Smits, Theo, Steen, Andrew, Steenkamp, Emma, Spang, Anja, Stewart, Frank, Tiedje, James, Vandamme, Peter, Wagner, Michael, Wang, Feng-Ping, Hedlund, Brian, Reysenbach, Anna-Louise, Murray, Alison, Avalon, Nicole, Bishop, Lucas, Davenport, Karen, Delage, Erwan, Dichosa, Armand E.K., Eveillard, Damien, Higham, Mary, Kokkaliari, Sofia, Lo, Chien-Chi, Riesenfeld, Christian, Young, Ryan, Chain, Patrick S.G., Baker, Bill, Metacohorts Consortium, Department of Energy / Joint Genome Institute (DOE), Los Alamos National Laboratory (LANL), Laboratoire des Sciences du Numérique de Nantes (LS2N), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Combinatoire et Bioinformatique (COMBI), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris], University of Queensland [Brisbane], Justus-Liebig-Universität Gießen (JLU), Louisiana State University (LSU), Botanical and Environmental Consultant, Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Spain] (CSIC), Max Planck Institute for Marine Microbiology, Max-Planck-Gesellschaft, Laboratoire de Biochimie des Systèmes Perturbés (LBSP), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), University of Texas at Austin [Austin], Buchmann Institute for Molecular Life Sciences [Frankfurt am Main] (BMLS), Goethe-Universität Frankfurt am Main, ISAO [Bologna, Italy], Universidad Nacional Autónoma de México (UNAM), Bigelow Laboratory for Ocean Sciences, Uppsala University, Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UMR237-Aix Marseille Université (AMU)-Avignon Université (AU), Montana State University (MSU), Laboratoire de l'intégration, du matériau au système (IMS), Université Sciences et Technologies - Bordeaux 1-Institut Polytechnique de Bordeaux-Centre National de la Recherche Scientifique (CNRS), Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH / Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures (DSMZ), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China. Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, China, Physikalisch-Technische Bundesanstalt [Braunschweig] (PTB), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Department of Earth and Planetary Science [UC Berkeley] (EPS), University of California [Berkeley], University of California-University of California, Royal Netherlands Institute for Sea Research (NIOZ), The Center for Microbial Ecology, Department of Microbiology and Molecular Genetics, Michigan State University [East Lansing], Michigan State University System-Michigan State University System, Universiteit Gent [Ghent], Hochschule Aalen, Institut für Angewandte Forschung, Hochschule Aalen, Martin-Luther-University Halle-Wittenberg, Université de Nantes - Faculté des Sciences et des Techniques, and Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Nantes - Faculté des Sciences et des Techniques

Subjects
Range (biology), ascidian, [INFO.INFO-OH]Computer Science [cs]/Other [cs.OH], Antarctic Regions, microbiome, Pharmaceutical Science, Biology, Genome, Article, Polyketide, 03 medical and health sciences, RNA, Ribosomal, 16S, co-occurrence, Drug Discovery, Animals, Marine ecosystem, Urochordata, 14. Life underwater, Microbiome, palmerolide A, Gene, lcsh:QH301-705.5, Pharmacology, Toxicology and Pharmaceutics (miscellaneous), ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Islands, Whole genome sequencing, 0303 health sciences, geography, geography.geographical_feature_category, Phylum, 030306 microbiology, Microbiota, Bacterioplankton, 15. Life on land, 16S ribosomal RNA, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Holobiont, Taxon, lcsh:Biology (General), Evolutionary biology, microbial diversity, Archipelago, Antarctica, Macrolides, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

Polar marine ecosystems hold the potential for bioactive compound biodiscovery, based on their untapped macro- and microorganism diversity. Characterization of polar benthic marine invertebrate-associated microbiomes is limited to few studies. This study was motivated by our interest in better understanding the microbiome structure and composition of the ascidian, Synoicum adareanum, in which palmerolide A (PalA), a bioactive macrolide with specificity against melanoma, was isolated. PalA bears structural resemblance to a hybrid nonribosomal peptide-polyketide that has similarities to microbially-produced macrolides. We conducted a spatial survey to assess both PalA levels and microbiome composition in S. adareanum in a region of the Antarctic Peninsula near Anvers Island (64&deg, 46'S, 64&deg, 03'W). PalA was ubiquitous and abundant across a collection of 21 ascidians (3 subsamples each) sampled from seven sites across the Anvers Island Archipelago. The microbiome composition (V3&ndash, V4 16S rRNA gene sequence variants) of these 63 samples revealed a core suite of 21 bacterial amplicon sequence variants (ASVs)&mdash, 20 of which were distinct from regional bacterioplankton. ASV co-occurrence analysis across all 63 samples yielded subgroups of taxa that may be interacting biologically (interacting subsystems) and, although the levels of PalA detected were not found to correlate with specific sequence variants, the core members appeared to occur in a preferred optimum and tolerance range of PalA levels. These results, together with an analysis of the biosynthetic potential of related microbiome taxa, describe a conserved, high-latitude core microbiome with unique composition and substantial promise for natural product biosynthesis that likely influences the ecology of the holobiont.

Published
2020

28. Dissecting the microbiome of a polyketide-producing ascidian across the Anvers Island archipelago, Antarctica

Author

Murray, Alison E., Avalon, Nicole E., Bishop, Lucas, Chain, Patrick S.G., Davenport, Karen W., Delage, Erwan, Dichosa, Armand E.K., Eveillard, Damien, Higham, Mary L., Kokkaliari, Sofia, Lo, Chien-Chi, Riesenfeld, Christian S., Young, Ryan M., and Baker, Bill J.

Abstract

The ascidian, S. adareanum , from the Antarctic Peninsula near Anvers Island, is known to produce a bioactive compound, palmerolide A (PalA) that has specific activity to melanoma, a particularly invasive and metastatic form of skin cancer. The combined non-ribosomal peptide polyketide structure of PalA has similarities to microbially-produced macrolides which motivated this study utilizing culture-dependent and -independent investigations coupled with PalA detection to improve our understanding of the host-associated microbiome and relationship to PalA. Cultivation efforts yielded seven different bacteria, none of which produced PalA under the conditions tested. The genome sequence was mined for one of the most abundant members of the microbiome, Pseudovibrio sp. str. TunPSC04-5.I4, revealing eight biosynthetic gene clusters, none supporting the potential for PalA biosynthesis. PalA was ubiquitous and abundant across a collection of 21 ascidians (3 subsamples each) sampled from seven sites across the Anvers Island archipelago. These 63 samples were used to assess microbiome composition (V3-V4 16S rRNA gene sequence variants) which revealed a core suite of 21 bacteria, 20 of which were distinct from regional bacterioplankton. Co-occurrence analysis yielded several subsystems that may interact functionally and, although the levels of PalA detected were not found to correlate with specific sequence variants, the core members appeared to occur in a preferred optimum and tolerance range of PalA levels. Sequence variant relative abundance and biosynthetic potential of related organisms pointed to a subset of the core membership as potential PalA producers which provides a gateway to identifying the producer of palmerolides in future work. IMPORTANCE Palmerolide A (PalA), has potential as a chemotherapeutic agent to target melanoma. Uniform, high levels of PalA were present across a regional survey of the PalA-producing Antarctic ascidian, Synoicum adareanum , based on multi-lobed colonies sampled in the Anvers Island archipelago. Likewise, we identified a core suite of microorganisms that occur concurrently with the PalA-containing ascidians which spanned four phyla with lineages representing both heterotrophic and chemoautotrophic (nitrifying) metabolisms and are distinct from the bacterioplankton. These represent leads for the PalA producer. Cultivation efforts yielded several isolates; however, none were found to produce PalA under laboratory growth conditions. One of these isolates was a member of the core microbiome of the PalA-producing S. adareanum , although the appropriate biosynthetic genes were not found in its genome. Recognition of the ascidian core microbiome informs downstream studies with a target population of potential PalA-producing microorganisms.

Published
2020
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29. Genome Sequence of Aeribacillus pallidus Strain GS3372, an Endospore-Forming Bacterium Isolated in a Deep Geothermal Reservoir

Author

Filippidou, Sevasti, Jaussi, Marion, Junier, Thomas, Wunderlin, Tina, Jeanneret, Nicole, Regenspurg, Simona, Li, Po-E, Lo, Chien-Chi, Johnson, Shannon, McMurry, Kim, Gleasner, Cheryl D, Vuyisich, Momchilo, Chain, Patrick S, and Junier, Pilar

Abstract

The genome of strain GS3372 is the first publicly available strain of Aeribacillus pallidus. This endospore-forming thermophilic strain was isolated from a deep geothermal reservoir. The availability of this genome can contribute to the clarification of the taxonomy of the closely related Anoxybacillus, Geobacillus, and Aeribacillus genera.

Published
2019

33. Genomics for Key Players in the N Cycle

Author

Chain, Patrick S.G., primary, Xie, Gary, additional, Starkenburg, Shawn R., additional, Scholz, Matthew B., additional, Beckloff, Nicholas, additional, Lo, Chien-Chi, additional, Davenport, Karen W., additional, Reitenga, Krista G., additional, Daligault, Hajnalka E., additional, Detter, J. Chris, additional, Freitas, Tracey A.K., additional, Gleasner, Cheryl D., additional, Green, Lance D., additional, Han, Cliff S., additional, McMurry, Kim K., additional, Meincke, Linda J., additional, Shen, Xiaohong, additional, and Zeytun, Ahmet, additional

Published
2011
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34. A framework for human microbiome research

Author

Methé, Barbara A., Nelson, Karen E., Pop, Mihai, Creasy, Heather H., Giglio, Michelle G., Huttenhower, Curtis, Gevers, Dirk, Petrosino, Joseph F., Abubucker, Sahar, Badger, Jonathan H., Chinwalla, Asif T., Earl, Ashlee M., FitzGerald, Michael G., Fulton, Robert S., Hallsworth-Pepin, Kymberlie, Lobos, Elizabeth A., Madupu, Ramana, Magrini, Vincent, Martin, John C., Mitreva, Makedonka, Muzny, Donna M., Sodergren, Erica J., Versalovic, James, Wollam, Aye M., Worley, Kim C., Wortman, Jennifer R., Young, Sarah K., Zeng, Qiandong, Aagaard, Kjersti M., Abolude, Olukemi O., Allen-Vercoe, Emma, Alm, Eric J., Alvarado, Lucia, Andersen, Gary L., Anderson, Scott, Appelbaum, Elizabeth, Arachchi, Harindra M., Armitage, Gary, Arze, Cesar A., Ayvaz, Tulin, Baker, Carl C., Begg, Lisa, Belachew, Tsegahiwot, Bhonagiri, Veena, Bihan, Monika, Blaser, Martin J., Bloom, Toby, Bonazzi, Vivien R., Brooks, Paul, Buck, Gregory A., Buhay, Christian J., Busam, Dana A., Campbell, Joseph L., Canon, Shane R., Cantarel, Brandi L., Chain, Patrick S., Chen, I-Min A., Chen, Lei, Chhibba, Shaila, Chu, Ken, Ciulla, Dawn M., Clemente, Jose C., Clifton, Sandra W., Conlan, Sean, Crabtree, Jonathan, Cutting, Mary A., Davidovics, Noam J., Davis, Catherine C., DeSantis, Todd Z., Deal, Carolyn, Delehaunty, Kimberley D., Dewhirst, Floyd E., Deych, Elena, Ding, Yan, Dooling, David J., Dugan, Shannon P., Dunne, Michael W., Jr, Durkin, Scott A., Edgar, Robert C., Erlich, Rachel L., Farmer, Candace N., Farrell, Ruth M., Faust, Karoline, Feldgarden, Michael, Felix, Victor M., Fisher, Sheila, Fodor, Anthony A., Forney, Larry, Foster, Leslie, Di Francesco, Valentina, Friedman, Jonathan, Friedrich, Dennis C., Fronick, Catrina C., Fulton, Lucinda L., Gao, Hongyu, Garcia, Nathalia, Giannoukos, Georgia, Giblin, Christina, Giovanni, Maria Y., Goldberg, Jonathan M., Goll, Johannes, Gonzalez, Antonio, Griggs, Allison, Gujja, Sharvari, Haas, Brian J., Hamilton, Holli A., Harris, Emily L., Hepburn, Theresa A., Herter, Brandi, Hoffmann, Diane E., Holder, Michael E., Howarth, Clinton, Huang, Katherine H., Huse, Susan M., Izard, Jacques, Jansson, Janet K., Jiang, Huaiyang, Jordan, Catherine, Joshi, Vandita, Katancik, James A., Keitel, Wendy A., Kelley, Scott T., Kells, Cristyn, Kinder-Haake, Susan, King, Nicholas B., Knight, Rob, Knights, Dan, Kong, Heidi H., Koren, Omry, Koren, Sergey, Kota, Karthik C., Kovar, Christie L., Kyrpides, Nikos C., La Rosa, Patricio S., Lee, Sandra L., Lemon, Katherine P., Lennon, Niall, Lewis, Cecil M., Lewis, Lora, Ley, Ruth E., Li, Kelvin, Liolios, Konstantinos, Liu, Bo, Liu, Yue, Lo, Chien-Chi, Lozupone, Catherine A., Lunsford, Dwayne R., Madden, Tessa, Mahurkar, Anup A., Mannon, Peter J., Mardis, Elaine R., Markowitz, Victor M., Mavrommatis, Konstantinos, McCorrison, Jamison M., McDonald, Daniel, McEwen, Jean, McGuire, Amy L., McInnes, Pamela, Mehta, Teena, Mihindukulasuriya, Kathie A., Miller, Jason R., Minx, Patrick J., Newsham, Irene, Nusbaum, Chad, O’Laughlin, Michelle, Orvis, Joshua, Pagani, Ioanna, Palaniappan, Krishna, Patel, Shital M., Pearson, Matthew, Peterson, Jane, Podar, Mircea, Pohl, Craig, Pollard, Katherine S., Priest, Margaret E., Proctor, Lita M., Qin, Xiang, Raes, Jeroen, Ravel, Jacques, Reid, Jeffrey G., Rho, Mina, Rhodes, Rosamond, Riehle, Kevin P., Rivera, Maria C., Rodriguez-Mueller, Beltran, Rogers, Yu-Hui, Ross, Matthew C., Russ, Carsten, Sanka, Ravi K., Sankar, Pamela, Sathirapongsasuti, Fah J., Schloss, Jeffery A., Schloss, Patrick D., Schmidt, Thomas M., Scholz, Matthew, Schriml, Lynn, Schubert, Alyxandria M., Segata, Nicola, Segre, Julia A., Shannon, William D., Sharp, Richard R., Sharpton, Thomas J., Shenoy, Narmada, Sheth, Nihar U., Simone, Gina A., Singh, Indresh, Smillie, Chris S., Sobel, Jack D., Sommer, Daniel D., Spicer, Paul, Sutton, Granger G., Sykes, Sean M., Tabbaa, Diana G., Thiagarajan, Mathangi, Tomlinson, Chad M., Torralba, Manolito, Treangen, Todd J., Truty, Rebecca M., Vishnivetskaya, Tatiana A., Walker, Jason, Wang, Lu, Wang, Zhengyuan, Ward, Doyle V., Warren, Wesley, Watson, Mark A., Wellington, Christopher, Wetterstrand, Kris A., White, James R., Wilczek-Boney, Katarzyna, Wu, Yuan Qing, Wylie, Kristine M., Wylie, Todd, Yandava, Chandri, Ye, Liang, Ye, Yuzhen, Yooseph, Shibu, Youmans, Bonnie P., Zhang, Lan, Zhou, Yanjiao, Zhu, Yiming, Zoloth, Laurie, Zucker, Jeremy D., Birren, Bruce W., Gibbs, Richard A., Highlander, Sarah K., Weinstock, George M., Wilson, Richard K., and White, Owen

Published
2012
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35. Structure, function and diversity of the healthy human microbiome

Author

Huttenhower, Curtis, Gevers, Dirk, Knight, Rob, Abubucker, Sahar, Badger, Jonathan H., Chinwalla, Asif T., Creasy, Heather H., Earl, Ashlee M., FitzGerald, Michael G., Fulton, Robert S., Giglio, Michelle G., Hallsworth-Pepin, Kymberlie, Lobos, Elizabeth A., Madupu, Ramana, Magrini, Vincent, Martin, John C., Mitreva, Makedonka, Muzny, Donna M., Sodergren, Erica J., Versalovic, James, Wollam, Aye M., Worley, Kim C., Wortman, Jennifer R., Young, Sarah K., Zeng, Qiandong, Aagaard, Kjersti M., Abolude, Olukemi O., Allen-Vercoe, Emma, Alm, Eric J., Alvarado, Lucia, Andersen, Gary L., Anderson, Scott, Appelbaum, Elizabeth, Arachchi, Harindra M., Armitage, Gary, Arze, Cesar A., Ayvaz, Tulin, Baker, Carl C., Begg, Lisa, Belachew, Tsegahiwot, Bhonagiri, Veena, Bihan, Monika, Blaser, Martin J., Bloom, Toby, Bonazzi, Vivien, Brooks, Paul J., Buck, Gregory A., Buhay, Christian J., Busam, Dana A., Campbell, Joseph L., Canon, Shane R., Cantarel, Brandi L., Chain, Patrick S. G., Chen, I-Min A., Chen, Lei, Chhibba, Shaila, Chu, Ken, Ciulla, Dawn M., Clemente, Jose C., Clifton, Sandra W., Conlan, Sean, Crabtree, Jonathan, Cutting, Mary A., Davidovics, Noam J., Davis, Catherine C., DeSantis, Todd Z., Deal, Carolyn, Delehaunty, Kimberley D., Dewhirst, Floyd E., Deych, Elena, Ding, Yan, Dooling, David J., Dugan, Shannon P., Dunne, Wm Michael, Durkin, Scott A., Edgar, Robert C., Erlich, Rachel L., Farmer, Candace N., Farrell, Ruth M., Faust, Karoline, Feldgarden, Michael, Felix, Victor M., Fisher, Sheila, Fodor, Anthony A., Forney, Larry J., Foster, Leslie, Di Francesco, Valentina, Friedman, Jonathan, Friedrich, Dennis C., Fronick, Catrina C., Fulton, Lucinda L., Gao, Hongyu, Garcia, Nathalia, Giannoukos, Georgia, Giblin, Christina, Giovanni, Maria Y., Goldberg, Jonathan M., Goll, Johannes, Gonzalez, Antonio, Griggs, Allison, Gujja, Sharvari, Haake, Susan Kinder, Haas, Brian J., Hamilton, Holli A., Harris, Emily L., Hepburn, Theresa A., Herter, Brandi, Hoffmann, Diane E., Holder, Michael E., Howarth, Clinton, Huang, Katherine H., Huse, Susan M., Izard, Jacques, Jansson, Janet K., Jiang, Huaiyang, Jordan, Catherine, Joshi, Vandita, Katancik, James A., Keitel, Wendy A., Kelley, Scott T., Kells, Cristyn, King, Nicholas B., Knights, Dan, Kong, Heidi H., Koren, Omry, Koren, Sergey, Kota, Karthik C., Kovar, Christie L., Kyrpides, Nikos C., La Rosa, Patricio S., Lee, Sandra L., Lemon, Katherine P., Lennon, Niall, Lewis, Cecil M., Lewis, Lora, Ley, Ruth E., Li, Kelvin, Liolios, Konstantinos, Liu, Bo, Liu, Yue, Lo, Chien-Chi, Lozupone, Catherine A., Lunsford, Dwayne R., Madden, Tessa, Mahurkar, Anup A., Mannon, Peter J., Mardis, Elaine R., Markowitz, Victor M., Mavromatis, Konstantinos, McCorrison, Jamison M., McDonald, Daniel, McEwen, Jean, McGuire, Amy L., McInnes, Pamela, Mehta, Teena, Mihindukulasuriya, Kathie A., Miller, Jason R., Minx, Patrick J., Newsham, Irene, Nusbaum, Chad, O’Laughlin, Michelle, Orvis, Joshua, Pagani, Ioanna, Palaniappan, Krishna, Patel, Shital M., Pearson, Matthew, Peterson, Jane, Podar, Mircea, Pohl, Craig, Pollard, Katherine S., Pop, Mihai, Priest, Margaret E., Proctor, Lita M., Qin, Xiang, Raes, Jeroen, Ravel, Jacques, Reid, Jeffrey G., Rho, Mina, Rhodes, Rosamond, Riehle, Kevin P., Rivera, Maria C., Rodriguez-Mueller, Beltran, Rogers, Yu-Hui, Ross, Matthew C., Russ, Carsten, Sanka, Ravi K., Sankar, Pamela, Sathirapongsasuti, Fah J., Schloss, Jeffery A., Schloss, Patrick D., Schmidt, Thomas M., Scholz, Matthew, Schriml, Lynn, Schubert, Alyxandria M., Segata, Nicola, Segre, Julia A., Shannon, William D., Sharp, Richard R., Sharpton, Thomas J., Shenoy, Narmada, Sheth, Nihar U., Simone, Gina A., Singh, Indresh, Smillie, Christopher S., Sobel, Jack D., Sommer, Daniel D., Spicer, Paul, Sutton, Granger G., Sykes, Sean M., Tabbaa, Diana G., Thiagarajan, Mathangi, Tomlinson, Chad M., Torralba, Manolito, Treangen, Todd J., Truty, Rebecca M., Vishnivetskaya, Tatiana A., Walker, Jason, Wang, Lu, Wang, Zhengyuan, Ward, Doyle V., Warren, Wesley, Watson, Mark A., Wellington, Christopher, Wetterstrand, Kris A., White, James R., Wilczek-Boney, Katarzyna, Wu, YuanQing, Wylie, Kristine M., Wylie, Todd, Yandava, Chandri, Ye, Liang, Ye, Yuzhen, Yooseph, Shibu, Youmans, Bonnie P., Zhang, Lan, Zhou, Yanjiao, Zhu, Yiming, Zoloth, Laurie, Zucker, Jeremy D., Birren, Bruce W., Gibbs, Richard A., Highlander, Sarah K., Methé, Barbara A., Nelson, Karen E., Petrosino, Joseph F., Weinstock, George M., Wilson, Richard K., and White, Owen

Published
2012
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38. Uncovering the Core Microbiome and Distribution of Palmerolide in Synoicum adareanum Across the Anvers Island Archipelago, Antarctica

Author

Murray, Alison E., primary, Avalon, Nicole E., additional, Bishop, Lucas, additional, Davenport, Karen W., additional, Delage, Erwan, additional, Dichosa, Armand E.K., additional, Eveillard, Damien, additional, Higham, Mary L., additional, Kokkaliari, Sofia, additional, Lo, Chien-Chi, additional, Riesenfeld, Christian S., additional, Young, Ryan M., additional, Chain, Patrick S.G., additional, and Baker, Bill J., additional

Published
2020
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39. PanGIA: A Metagenomics Analytical Framework for Routine Biosurveillance and Clinical Pathogen Detection

Author

Li, Po-E, primary, Russell, Joseph A., additional, Yarmosh, David, additional, Shteyman, Alan G., additional, Parker, Kyle, additional, Wood, Hillary, additional, Aspinwall, J.R., additional, Winegar, Richard, additional, Davenport, Karen, additional, Lo, Chien-chi, additional, Bagnoli, John, additional, Davis, Phillip, additional, Jacobs, Jonathan L., additional, and Chain, Patrick S.G., additional

Published
2020
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40. Uncovering the core microbiome and distributions of palmerolide inSynoicum adareanumacross the Anvers Island archipelago, Antarctica

Author

Murray, Alison, primary, Avalon, Nicole, additional, Bishop, Lucas, additional, Davenport, Karen W., additional, Delage, Erwan, additional, Dichosa, Armand E.K., additional, Eveillard, Damien, additional, Higham, Mary L., additional, Kokkaliari, Sofia, additional, Lo, Chien-Chi, additional, Riesenfeld, Christian S., additional, Young, Ryan M., additional, Chain, Patrick S.G., additional, and Baker, Bill J., additional

Published
2020
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41. Under-detection of endospore-forming Firmicutes in metagenomic data

Author

Filippidou, Sevasti, Junier, Thomas, Wunderlin, Tina, Lo, Chien-Chi, Li, Po-E, Chain, Patrick S, and Junier, Pilar

Subjects
fungi
Abstract

Microbial diversity studies based on metagenomic sequencing have greatly enhanced our knowledge of the microbial world. However, one caveat is the fact that not all microorganisms are equally well detected, questioning the universality of this approach. Firmicutes are known to be a dominant bacterial group. Several Firmicutes species are endospore formers and this property makes them hardy in potentially harsh conditions, and thus likely to be present in a wide variety of environments, even as residents and not functional players. While metagenomic libraries can be expected to contain endospore formers, endospores are known to be resilient to many traditional methods of DNA isolation and thus potentially undetectable. In this study we evaluated the representation of endospore-forming Firmicutes in 73 published metagenomic datasets using two molecular markers unique to this bacterial group (spo0A and gpr). Both markers were notably absent in well-known habitats of Firmicutes such as soil, with spo0A found only in three mammalian gut microbiomes. A tailored DNA extraction method resulted in the detection of a large diversity of endospore-formers in amplicon sequencing of the 16S rRNA and spo0A genes. However, shotgun classification was still poor with only a minor fraction of the community assigned to Firmicutes. Thus, removing a specific bias in a molecular workflow improves detection in amplicon sequencing, but it was insufficient to overcome the limitations for detecting endospore-forming Firmicutes in whole-genome metagenomics. In conclusion, this study highlights the importance of understanding the specific methodological biases that can contribute to improve the universality of metagenomic approaches.

Published
2019

42. Genome Sequence of Bacillus alveayuensis Strain 24KAM51, a Halotolerant Thermophile Isolated from a Hydrothermal Vent

Author

Filippidou, Sevasti, Wunderlin, Tina, Junier, Thomas, Jeanneret, Nicole, Johnson, Shannon, McMurry, Kim, Gleasner, Cheryl D, Lo, Chien-Chi, Li, Po-E, Vuyisich, Momchilo, Chain, Patrick S, Junier, Pilar, Filippidou, Sevasti, Wunderlin, Tina, Junier, Thomas, Jeanneret, Nicole, Johnson, Shannon, McMurry, Kim, Gleasner, Cheryl D, Lo, Chien-Chi, Li, Po-E, Vuyisich, Momchilo, Chain, Patrick S, and Junier, Pilar

Abstract

Bacillus alveayuensis strain 24KAM51 was isolated from a marine hydrothermal vent in Milos, Greece. Its genome depicts inter-esting features of halotolerance and resistance to heavy metals.

Published
2019

44. Investigating intestinal permeability and gut microbiota roles in acute coronary syndrome patients

Author

Alhmoud, Tarik, primary, Kumar, Anand, additional, Lo, Chien-Chi, additional, Al-Sadi, Rana, additional, Clegg, Stacey, additional, Alomari, Ihab, additional, Zmeili, Tarek, additional, Gleasne, Cheryl Diane, additional, Mcmurry, Kim, additional, Dichosa, Armand Earl Ko, additional, Vuyisich, Momchilo, additional, Chain, Patrick Sam Guy, additional, Mishra, Shiraz, additional, and Ma, Thomas, additional

Published
2019
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45. Diagnostic targETEd seQuencing adjudicaTion (DETEQT)

Author

Conrad, Turner A., primary, Lo, Chien-Chi, additional, Koehler, Jeffrey W., additional, Graham, Amanda S., additional, Stefan, Christopher P., additional, Hall, Adrienne T., additional, Douglas, Christina E., additional, Chain, Patrick S., additional, and Minogue, Timothy D., additional

Published
2019
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46. Genomic characterization reveals significant divergence within Chlorella sorokiniana (Chlorellales, Trebouxiophyceae)

Author

Hovde, Blake T., primary, Hanschen, Erik R., additional, Steadman Tyler, Christina R., additional, Lo, Chien-Chi, additional, Kunde, Yuliya, additional, Davenport, Karen, additional, Daligault, Hajnalka, additional, Msanne, Joseph, additional, Canny, Stephanie, additional, Eyun, Seong-il, additional, Riethoven, Jean-Jack M., additional, Polle, Juergen, additional, and Starkenburg, Shawn R., additional

Published
2018
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47. High-Quality Draft Genome Sequences of Four Lignocellulose-Degrading Bacteria Isolated from Puerto Rican Forest Soil: Gordonia sp., Paenibacillus sp., Variovorax sp., and Vogesella sp

Author

Woo, Hannah L., DeAngelis, Kristen M., Teshima, Hazuki, Davenport, Karen, Daligault, Hajnalka, Erkkila, Tracy, Goodwin, Lynne, Gu, Wei, Lo, Chien-Chi, Munk, Christine, Scholz, Matthew, Xu, Yan, Chain, Patrick, Bruce, David, Detter, Chris, Tapia, Roxanne, Han, Cliff, Simmons, Blake A., and Hazen, Terry C.

Subjects
Human Genome, Genetics, food and beverages, Prokaryotes, Biochemistry and Cell Biology, Microbiology
Abstract

Here, we report the high-quality draft genome sequences of four phylogenetically diverse lignocellulose-degrading bacteria isolated from tropical soil (Gordonia sp., Paenibacillus sp., Variovorax sp., and Vogesella sp.) to elucidate the genetic basis of their ability to degrade lignocellulose. These isolates may provide novel enzymes for biofuel production.

Published
2017

49. Correction for Johnson et al., “Complete Genome Sequences for 35 Biothreat Assay-Relevant Bacillus Species”

Author

Johnson, Shannon L., primary, Daligault, Hajnalka E., additional, Davenport, Karen W., additional, Jaissle, James, additional, Frey, Kenneth G., additional, Ladner, Jason T., additional, Broomall, Stacey M., additional, Bishop-Lilly, Kimberly A., additional, Bruce, David C., additional, Gibbons, Henry S., additional, Coyne, Susan R., additional, Lo, Chien-Chi, additional, Meincke, Linda, additional, Munk, A. Christine, additional, Koroleva, Galina I., additional, Rosenzweig, C. Nicole, additional, Palacios, Gustavo F., additional, Redden, Cassie L., additional, Minogue, Timothy D., additional, and Chain, Patrick S., additional

Published
2018
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