Comparative genomics of Hepatitis A virus, Hepatitis C virus and Hepatitis E virus provides insights into the evolutionary history of Hepatovirus species

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Trudy M. Wassenaar, Se-Ran Jun, Michael Robeson and David W. Ussery

MicrobiologyOpen. 2019 Nov 19:e973. doi: 10.1002/mbo3.973.

Abstract

The intraspecies genomic diversity of the single-strand RNA (+) virus species hepatitis A virus (Hepatovirus), hepatitis C virus (Hepacivirus), and hepatitis E virus (Orthohepevirus) was compared. These viral species all can cause liver inflammation (hepatitis), but share no gene similarity. The codon usage of human hepatitis A virus (HAV) is suboptimal for replication in its host, a characteristic it shares with taxonomically related rodent, simian, and bat hepatitis A virus species. We found this codon usage to be strikingly similar to that of Triatoma virus that infects blood-sucking kissing bugs. The codon usage of that virus is well adapted to its insect host. The codon usage of HAV is also similar to other invertebrate viruses of various taxonomic families. An evolutionary ancestor of HAV and related virus species is hypothesized to be an insect virus that underwent a host jump to infect mammals. The similarity between HAV and invertebrate viruses goes beyond codon usage, as they also share amino acid composition characteristics, while not sharing direct sequence homology. In contrast, hepatitis C virus and hepatitis E virus are highly similar in codon usage preference, nucleotide composition, and amino acid composition, and share these characteristics with Human pegivirus A, West Nile virus, and Zika virus. We present evidence that these observations are only partly explained by differences in nucleotide composition of the complete viral codon regions. We consider the combination of nucleotide composition, amino acid composition, and codon usage preference suitable to provide information on possible evolutionary similarities between distant virus species that cannot be investigated by phylogeny.

Keywords Hepactovirus A; codon bias; comparative genomics; evolution; hepatitis A virus

Read the publication here: https://onlinelibrary.wiley.com/doi/full/10.1002/mbo3.973

Metabolic profiling and compound-class identification reveal alterations in serum triglyceride levels in mice immunized with human vaccine adjuvant Alum.

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Khoomrung S, Nookaew I, Sen P, Olafsdottir TA, Persson J, Moritz T, Andersen P, Harandi AM, Nielsen J.

J Proteome Res. 2019 Oct 18. doi: 10.1021/acs.jproteome.9b00517. PMID: 31625748

Abstract

Alum has been widely used as an adjuvant for human vaccines; however, the impact of Alum on host metabolism remains largely unknown. Herein, we applied mass spectrometry (LCMS)-based metabolic and lipid profiling to monitor the effects of Alum adjuvant on mouse serum at 6, 24, 72 and 168 h post-vaccination. We propose a new strategy termed Subclass Identification and Annotation for Metabolomics (SIAM) for class-wise identification of untargeted metabolomics data generated from high-resolution MS. Using this approach, we identified and validated the levels of several lipids in mouse serum that were significantly altered following Alum administration. These lipids showed a biphasic response even 168 h after vaccination. The majority of the lipids were triglycerides (TAGs), where TAGs with long chain unsaturated fatty acids were decreased at 24 h, and TAGs with short chain fatty acids were decreased at 168 h. To our knowledge, this is the first report on the impact of the human vaccine adjuvant Alum on host metabolome, and may provide new insights into the mechanism of action of Alum.

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An Assessment of Oxford Nanopore Sequencing for Human Gut Metagenome Profiling: A Pilot Study of Head and Neck Cancer Patients

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Thidathip Wongsurawat, Mayumi Nakagawa, Omar Atiq, Hannah N. Coleman, Piroon Jenjaroenpun, James I. Allred, Angela Trammel, Pantakan Puengrang, David W. Ussery, Intawat Nookaew

J Microbiol Methods. 2019 Oct 15:105739. doi: 10.1016/j.mimet.2019.105739. PMID: 31626891

Abstract

Gut metagenome profiling using the Oxford Nanopore Technology (ONT) sequencer was assessed in a pilot-sized study of 10 subjects. The taxonomic abundance of gut microbiota derived from ONT was comparable with Illumina Technology (IT) for the high-abundance species. IT better detected low-abundance species through amplification, when material was limited.

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ArC-GEM at Little Rock Tech Fest 2019!

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Big Data Comes to Biology: Portable Genome Sequencing

DNA sequencing will soon be possible from small mobile devices connected to a mobile phone. This workshop will demonstrate use of a hand-held sequencing device, that is about the same size as a Snicker’s candy bar. A brief overview of DNA sequencing will be discussed, along with some examples of high-throughput comparison of genome sequences. Personal genome sequencing from companies like 23andme and AncestoryDNA will be discussed, in the context of a general overview of current technologies and potential future applications.

Gastrointestinal tract dysbiosis enhances distal tumor progression through suppression of leukocyte trafficking

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Samir V. Jenkins,Michael S. Robeson II, Robert J. Griffin, Charles M. Quick, Eric R. Siegel, Martin J. Cannon, Kieng B. Vang, and Ruud P.M. Dings

Cancer Research, published online 7 October, 2019; DOI: 10.1158/0008-5472.CAN-18-4108.

Abstract

The overall use of antibiotics has increased significantly in recent years. Besides fighting infections, antibiotics also alter the gut microbiota. Commensal bacteria in the gastrointestinal tract are crucial to maintain immune homeostasis, and microbial imbalance or dysbiosis affects disease susceptibility and progression. We hypothesized that antibiotic-induced dysbiosis of the gut microbiota would suppress cytokine profiles in the host, thereby leading to changes in the tumor microenvironment. The induced dysbiosis was characterized by alterations in bacterial abundance, composition, and diversity in our animal models. On the host side, antibiotic-induced dysbiosis caused elongated small intestines and ceca, and B16-F10 melanoma and Lewis Lung carcinoma progressed more quickly than in control mice. Mechanistic studies revealed that this progression was mediated by suppressed TNF-α levels, both locally and systemically, resulting in reduced expression of tumor endothelial adhesion molecules, particularly intercellular adhesion molecule-1 (ICAM-1) and a subsequent decrease in the number of activated and effector CD8+ T-cells in the tumor. However, suppression of ICAM-1 or its binding site, the alpha subunit of lymphocyte function-associated antigen-1, was not seen in the spleen or thymus during dysbiosis. TNF-α supplementation in dysbiotic mice was able to increase ICAM-1 expression and leukocyte trafficking into the tumor. Overall, these results demonstrate the importance of commensal bacteria in supporting anticancer immune surveillance, define an important role of tumor endothelial cells within this process, and suggest adverse consequences of antibiotics on cancer development.

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Genome-Based Comparison of Clostridioides difficile : Average Amino Acid Identity Analysis of Core Genomes

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Adriana Cabal, Se-Ran Jun, Piroon Jenjaroenpun, Visanu Wanchai, Intawat Nookaew, Thidathip Wongsurawat, Mary J. Burgess, Atul Kothari, Trudy M. Wassenaar1, David W. Ussery

Received: 30 August 2017 /Accepted: 2 February 2018 # The Author(s) 2018. This article is an open access publication

Abstract

Infections due to Clostridioides difficile (previously known as Clostridium difficile) are a major problem in hospitals, where cases can be caused by community-acquired strains as well as by nosocomial spread. Whole genome sequences from clinical samples contain a lot of information but that needs to be analyzed and compared in such a way that the outcome is useful for clinicians or epidemiologists. Here, we compare 663 public available complete genome sequences of C. difficile using average amino acid identity (AAI) scores. This analysis revealed that most of these genomes (640, 96.5%) clearly belong to the same species, while the remaining 23 genomes produce four distinct clusters within the Clostridioides genus. The main C. difficile cluster can be further divided into sub-clusters, depending on the chosen cutoff. We demonstrate that MLST, either based on partial or full gene-length, results in biased estimates of genetic differences and does not capture the true degree of similarity or differences of complete genomes. Presence of genes coding for C. difficile toxins A and B (ToxA/B), as well as the binary C. difficile toxin (CDT), was deduced from their unique PfamA domain architectures. Out of the 663 C. difficile genomes, 535 (80.7%) contained at least one copy of ToxA or ToxB, while these genes were missing from 128 genomes. Although some clusters were enriched for toxin presence, these genes are variably present in a given genetic background. The CDT genes were found in 191 genomes, which were restricted to a few clusters only, and only one cluster lacked the toxin A/B genes consistently. A total of 310 genomes contained ToxA/B without CDT (47%). Further, published metagenomic data from stools were used to assess the presence of C. difficile sequences in blinded cases of C. difficile infection (CDI) and controls, to test if metagenomic analysis is sensitive enough to detect the pathogen, and to establish strain relationships between cases from the same hospital. We conclude that metagenomics can contribute to the identification of CDI and can assist in characterization of the most probable causative strain in CDI patients.

Keywords C. difficile, AAI .MLST, Community-acquired infections, Comparative genomics

Read the publication here: http://rdcu.be/GWYD

Interspecific plant interactions reflected in soil bacterial community structure and nitrogen cycling in primary succession.

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Front. Microbiology, in the press, January 2018  | doi: 10.3389/fmicb.2018.00128
https://www.frontiersin.org/articles/10.3389/fmicb.2018.00128/abstract

Joseph E. Knelman, Emily B. Graham, Janet S. Prevéy, Michael S. Robeson, Patrick Kelly, Eran Hood and Steve K. Schmidt

Past research demonstrating the importance plant-microbe interactions as drivers of ecosystem succession has focused on how plants condition soil microbial communities, impacting subsequent plant performance and plant community assembly. These studies, however, largely treat microbial communities as a black box. In this study we sought to examine how emblematic shifts from early-successional Alnus sinuata (alder) to late successional Picea sitchensis (spruce) in primary succession may be reflected in specific belowground changes in bacterial community structure and nitrogen cycling related to the interaction of these two plants. We examined early successional alder-conditioned soils in a glacial forefield to delineate how alders alter the soil microbial community with increasing dominance. Further, we assessed the impact of late-successional spruce plants on these early-successional alder-conditioned microbiomes and related nitrogen cycling through a leachate addition microcosm experiment. In total, we show how increasingly abundant alder select for particular bacterial taxa. Additionally, we found that spruce leachate significantly alters the composition of these microbial communities in large part by driving declines in taxa that are enriched by alder, including bacterial symbionts. We found these effects to be spruce-specific, beyond a general leachate effect. Our work also demonstrates a unique influence of spruce on ammonium availability. Such insights bolster theory relating the importance of plant-microbe interactions with late-successional plants and interspecific plant interactions more generally.

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Genome Characterization of Oleaginous Aspergillus oryzae BCC7051: A Potential Fungal-Based Platform for Lipid Production

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Curr Microbiol. 2018 Jan;75(1):57-70. doi: 10.1007/s00284-017-1350-7. Epub 2017 Sep 1.

Thammarongtham C, Nookaew I, Vorapreeda T, Srisuk T, Land ML, Jeennor S, Laoteng K

Abstract

The selected robust fungus, Aspergillus oryzae strain BCC7051 is of interest for biotechnological production of lipid-derived products due to its capability to accumulate high amount of intracellular lipids using various sugars and agro-industrial substrates. Here, we report the genome sequence of the oleaginous A. oryzae BCC7051. The obtained reads were de novo assembled into 25 scaffolds spanning of 38,550,958 bps with predicted 11,456 protein-coding genes. By synteny mapping, a large rearrangement was found in two scaffolds of A. oryzae BCC7051 as compared to the reference RIB40 strain. The genetic relationship between BCC7051 and other strains of A. oryzae in terms of aflatoxin production was investigated, indicating that the A. oryzae BCC7051 was categorized into group 2 nonaflatoxin-producing strain. Moreover, a comparative analysis of the structural genes focusing on the involvement in lipid metabolism among oleaginous yeast and fungi revealed the presence of multiple isoforms of metabolic enzymes responsible for fatty acid synthesis in BCC7051. The alternative routes of acetyl-CoA generation as oleaginous features and malate/citrate/pyruvate shuttle were also identified in this A. oryzae strain. The genome sequence generated in this work is a dedicated resource for expanding genome-wide study of microbial lipids at systems level, and developing the fungal-based platform for production of diversified lipids with commercial relevance.

PMID: 28865010 DOI: 10.1007/s00284-017-1350-7

Abiotic Stresses Shift Belowground Populus-Associated Bacteria Toward a Core Stress Microbiome

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mSystems, 3:e00070-17. https://doi.org/10.1128/ mSystems.00070-17.
DOI: 10.1128/mSystems.00070-17

Abiotic Stresses Shift Belowground Populus-Associated Bacteria Toward a Core Stress Microbiome

Collin M. Timm, Kelsey R. Carter, Alyssa A. Carrell, Se-Ran Jun, Sara S. Jawdy, Jessica M. Vélez, Lee E. Gunter, Zamin Yang, Intawat Nookaew, Nancy L. Engle, Tse-Yuan S. Lu, Christopher W. Schadt, Timothy J. Tschaplinski, Mitchel J. Doktycz, Gerald A. Tuskan, Dale A. Pelletier, David J. Weston

ABSTRACT

Adverse growth conditions can lead to decreased plant growth, productivity, and survival, resulting in poor yields or failure of crops and biofeedstocks. In some cases, the microbial community associated with plants has been shown to alleviate plant stress and increase plant growth under suboptimal growing conditions. A systematic understanding of how the microbial community changes under these conditions is required to understand the contribution of the microbiome to water utilization, nutrient uptake, and ultimately yield. Using a microbiome inoculation strategy, we studied how the belowground microbiome of Populus deltoides changes in response to diverse environmental conditions, including water limitation, light limitation (shading), and metal toxicity. While plant responses to treatments in terms of growth, photosynthesis, gene expression and metabolite profiles were varied, we identified a core set of bacterial genera that change in abundance in response to host stress. The results of this study indicate substantial structure in the plant microbiome community and identify potential drivers of the phytobiome response to stress.

IMPORTANCE: The identification of a common “stress microbiome” indicates tightly controlled relationships between the plant host and bacterial associates and a conserved structure in bacterial communities associated with poplar trees under different growth conditions. The ability of the microbiome to buffer the plant from extreme environmental conditions coupled with the conserved stress microbiome observed in this study suggests an opportunity for future efforts aimed at predictably modulating the microbiome to optimize plant growth.

Gender Differences in the Pathogenesis and Management of Heart Disease

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Chapter 7 in the book “Gender Differences in the Pathogenesis and Management of Heart Disease”, Springer/Nature publishing company, in the press (January 2018).   ISBN:978-3-319-71134-8

Adriana Cabal, Trudy M. Wassenaar, and David W. Ussery

Abstract

The literature was reviewed to search for consistently reported differences in the gut microbiome between females and males, in an attempt to relate such changes to different risks of cardiovascular disease that exist between the genders. Although multiple publications were identified that reported gender differences in the gut microbiome, none of the described observations were consistent. Apparently, the variation in gut microbiome between populations under study, as a result of differences in geography, life style, diet, age, genetics and possible other factors is more extensive than the variation between males and females. However, we summarize a number of findings on gender differences reported for cardiovascular diseases that may have a link to the microbiome, for instance the presence of irritable bowel disease (IBD) which is a risk factor for cardiovascular disease, coincides with a dysbiosis of the gut microbiome, and is more common in females than males. Other microbiome-related gender differences may pose a greater risk for males, so that, overall, there is no known positive or negative generally applicable effect of a ‘female-type’ or ‘male-type’ microbiome that would have a significant effect on risk or severity of cardiovascular diseases.