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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.


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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Simplified Intestinal Microbiota to Study Microbe-Diet-Host Interactions in a Mouse Model

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Kovatcheva-Datchary P, Shoaie S, Lee S, Wahlström A, Nookaew I, Hallen A, Perkins R, Nielsen J, Bäckhed F.

Cell reports. 2019 Mar 26;26(13):3772-83.


The gut microbiota can modulate human metabolism through interactions with macronutrients. However, microbiota-diet-host interactions are difficult to study because bacteria interact in complex food webs in concert with the host, and many of the bacteria are not yet characterized. To reduce the complexity, we colonize mice with a simplified intestinal microbiota (SIM) composed of ten sequenced strains isolated from the human gut with complementing pathways to metabolize dietary fibers. We feed the SIM mice one of three diets (chow [fiber rich], high-fat/high-sucrose, or zero-fat/high-sucrose diets [both low in fiber]) and investigate (1) how dietary fiber, saturated fat, and sucrose affect the abundance and transcriptome of the SIM community, (2) the effect of microbe-diet interactions on circulating metabolites, and (3) how microbiota-diet interactions affect host metabolism. Our SIM model can be used in future studies to help clarify how microbiota-diet interactions contribute to metabolic diseases.

Keywords: diet; metabolome; microbiota; transcriptome

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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


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

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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

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


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. 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


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


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.

Distinctive molecular signature and activated signaling pathways in aortic smooth muscle cells of patients with myocardial infarction

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Atherosclerosis, manuscript in the press, accepted 16 January, 2028

Thidathip Wongsurawat, Chin Cheng Woo, Antonis Giannakakis, Xiao Yun Lin, Esther Sok Hwee Cheow, Chuen Neng Lee, Mark Richards, Siu Kwan Sze, Intawat Nookaew, Vladimir A. Kuznetsov’Correspondence information about the author Vladimir A. Kuznetsov, Vitaly Sorokin


Background and aims: We aim to identify significant transcriptome alterations of vascular smooth muscle cells (VSMCs) in the aortic wall of myocardial infarction (MI) patients. Providing a robust transcriptomic signature, we aim to highlight the most likely aberrant pathway(s) in MI VSMCs. Methods and results: Laser-captured microdissection (LCM) was used to obtain VSMCs from aortic wall tissues harvested during coronary artery bypass surgery. Microarray gene analysis was applied to analyse VSMCs from 17 MI and 19 non-MI patients. Prediction Analysis of Microarray (PAM) identified 370 genes that significantly discriminated MI and non-MI samples and were enriched in genes responsible for muscle development, differentiation and phenotype regulation. Incorporation of gene ontology (GO) led to the identification of a 21-gene VSMCs-associated classifier that discriminated between MI and non-MI patients with 92% accuracy. The mass spectrometry-based iTRAQ analysis of the MI and non-MI samples revealed 94 proteins significantly differentiating these tissues. Ingenuity Pathway Analysis (IPA) of 370 genes revealed top pathways associated with hypoxia signaling in the cardiovascular system. Enrichment analysis of these proteins suggested an activation of the superoxide radical degradation pathway. An integrated transcriptome-proteome pathway analysis revealed that superoxide radical degradation pathway remained the most implicated pathway. The intersection of the top candidate molecules from the transcriptome and proteome highlighted superoxide dismutase (SOD1) overexpression

Conclusions: We provided a novel 21-gene VSMCs-associated MI classifier in reference to significant VSMCs transcriptome alterations that, in combination with proteomics data, suggests the activation of superoxide radical degradation pathway in VSMCs of MI patients.

Complete genomic and transcriptional landscape analysis using third-generation sequencing: a case study of Saccharomyces cerevisiae CEN.PK113-7D

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The genome of the most well studied eukaryotic model organism, Saccharomyces cerevisiae strain S288c, was sequenced and released in 1996; it was the first complete, high quality genome sequence of an eukaryal organism (1). Since then, the development ofDNAsequencing technologies has yielded scientific breakthroughs that enable us to obtain and analyze genomic DNA sequences at a faster, more economical pace (2).

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