Microbial Sciences Research Articles

Decoding Glycoproteome Remodeling in Sepsis through Integrative Multi‐Omics Analysis and Parts‐Based Data Representation

Sepsis is a major clinical challenge accounting for unacceptably high‐rates of morbidity and mortality in intensive care units around the world. After many years of extensive research, reliable markers for diagnosis and treatment monitoring remain desperately needed. The plasma glycoproteome offers a suitable readout to monitor systemic alterations in the body. Thus, tracking structural changes in plasma glycoproteins may uncover new molecular windows to target bacterial sepsis. Unfortunately, the analytical challenge posed by the large heterogeneity of plasma carbohydrate and protein components has severely limited advancements in this area. Here we show that Staphylococcus aureus bacteremia induces a dramatic shift of the plasma glycoproteome in a murine model of monobacterial sepsis. Significant changes in the levels of plasma glycoproteins in circulation, as well as their associations with vascular surfaces were revealed through an integrative glycomics, chemical proteomics, and glycoproteomics approach. Additionally, the global and site‐specific glycosylation patterns of the plasma N‐ and O‐linked glycoproteome were significantly altered during sepsis. Deconvolution of these changes through non‐negative matrix factorization methods uncovered the co‐existence of discrete patterns of glycoproteome remodeling associated with specific subgroups of glycoproteins. This included changes in the levels of N‐glycan core‐fucosylation, terminal sialylation, and increased protein deglycosylation, including complete glycan truncations. Furthermore, computational analysis demonstrates that these molecular patterns are sufficient to robustly stratify the samples based on their infection status. In short, we show that multi‐Omics integration has the power to dissect local alterations in the plasma glycoproteome during monobacterial sepsis, possibly reflecting the contribution of discrete biological processes of cellular glycosylation.Support or Funding InformationThis work was supported by grant P01HL131474 to J.D.E. and J.W.S. J.T.S. acknowledges support from the National Institutes of Health, USA (NIH grant T32GM008806) J.W.S. was supported by R01 GM107523. G.G. was supported by Microbial Sciences Graduate Research Fellowship Awards 1‐F17GG and 1‐F18GG.

Isolation and Identification of Endophytic Fungi in Kernels of Coix lachrymal-jobi L. Cultivars.

Coix lachrymal-jobi L. var. ma-yuen Stapf of Gramineae are annual or perennial herbs and an important food-medicine homologous plants of high value in nutrition, health protection, and comprehensive utilization. In recent years, the revival of researches on its roles in food and medicinal applications of this underutilized grass for food security and economic empowerment of rural communities has been seen . In this research, Coix kernel endophytic fungi were isolated and identified by fungal colony morphology observation combined with the PCR-amplified fungal internal transcribed spacer (ITS) sequence analyses. All together six isolates to five species of Coix endophytic fungi and two isolates to the genus level were identified from the kernels of six Coix cultivars: Penicillium expansum, Penicillium polonicum, Cladosporium cladosporioides, Alternaria alternata, Aspergillus flavus, and two genera of Aspergillus and Fusarium. Potential benefits and harms analyses showed that Penicillium expansum, Aspergillus oryzae, and Cladosporium cladosporioides can produce a variety of beneficial composite enzymes and have an extensive application in microbial chemistry, food science, and fermentation, whereas Penicillium, Aspergillus flavus, Alternaria alternate, and Fusarium can produce corresponding toxins harmful to plants, animals, and humans. These results not only provided a basis for the targeted prevention of contamination in the tissue culture of Coix kernels by the addition of specific antibiotics, but also enriched the endophytic fungi resource pool of Gramineae crops and suggested new ideas for the improvement, cultivation, post-harvest seeds/kernels storage, and the development of new natural drugs.

Gender Inclusion in Microbial Sciences

Gender Inclusion in Microbial Sciences

Microdialysis in soil environments: Current practice and future perspectives

Microdialysis is emerging as a sensitive tool in environmental sciences, allowing for in situ sampling of solutes with minimal disturbance to soil environments. This perspective presents the theoretical foundations and practical applications of the technique with a focus on its use in soil, microbial and plant sciences. Using small probes (usually 0.5 mm diameter) fitted with permeable membranes, soil solutes are sampled, so that solute flux (and potentially concentration) can be calculated at root-relevant scales. However, physical and biological characteristics of soil systems impose challenges to sampling efficiencies with microdialysis, particularly where solute concentrations are low. Experimental parameters such as perfusate flow rates, probe design and sampling times can also influence the findings, and reduce the comparability between studies. We explore how equipment setup and experimental conditions can be optimised for soil environments, and how standardisation and calibration techniques may improve cross-study comparability. We show that the technique's strength lies in the ability to integrate many soil factors into a biologically relevant measure of solute availability. Microdialysis has so far provided new insight regarding the bioavailability of soil nitrogen (N) and phosphorus (P), where fluxes have been related to root uptake rates and gaseous fluxes from soil. The technique has also been used as a root simulator, mimicking exudation of organic acids to mobilise soil P, and to measure the potential contribution of transpiration-induced mass flow on N availability at the root surface. With further development, and paired with sensitive analytical methods and equipment, microdialysis has much potential to explore fragile and dynamic soil processes in biologically-active zones such as the rhizosphere, and could contribute to solving challenges relating to under- and oversupply of nutrients to plants. We conclude that, with further advancements and critical evaluation, microdialysis could become an important instrument in the soil analysis toolkit.

Acknowledgment of Ad Hoc Reviewers

As we reach the end of our first full year of publishing cutting-edge research in the microbial sciences, we would like to offer our sincere thanks to the many individuals who have acted as referees of the manuscripts that we have handled since our birth in late 2015. They have helped us achieve our

Natural science research in Changbai Mountain during 1956-2018:A review.

We synthesized the scientific research carried out in Changbai Mountain from 1956 to 2018 by mapping knowledge domains and bibliometrics based on the literature from international database (WOS) and domestic databases (CNKI and CSCD). The results showed that natural science research in Changbai Mountain underwent three stages during 1956-2018, including embryo stage, growing stage, and rapid development stage. The natural research in Changbai Mountain could be divided into five fields, i.e., forest and ecological science, volcano and geology science, environmental change science, resource sciences and utilization, animal and microbial science, with a total of 20 main research directions. Since 2000, forest and ecological science, volcano and geological science, environmental change science dominated the natural science research in Changbai Mountain. The researches in recent 20 years mainly concentrated on the following seven disciplines: community ecology, forest management, soil ecology, ecosystem ecology, eco-climatology, forest responses to environmental change, and volcanic geology. International researches showed a trend of strong integration of different disciplines. We forecast that the natural science research in the Changbai Mountain would deepen its research in the next decade. Moreover, other fields such as old-growth forest and large-scale ecosystem carbon processes, forest-altitude-climate change, soil fauna and microorganisms, forest management and human activities, biodiversity, volcanic origin and eruption history, volcanic eruption dynamics and volcanic monitoring will emerge as the new research focus. Scale polarization, elements diversification, discipline crossing, and research deepening would be the future trend of natural science research in Changbai Mountain.

Teaching Trek: Reflections on Participation in the Indo-U.S. Teaching Professorship Program

The American Society for Microbiology’s Indo-U.S. Teaching Professorship program (sponsored by the Indo-U.S. Science and Technology Forum) provides an opportunity for cross-continental teaching exchanges in the microbial sciences. In this article, I reflect on my experiences as a 2017 Teaching Professor at the University of Delhi, where I developed and delivered a curriculum about prion diseases and a workshop on scientific communication. Tips for preparation, informal assessments, and portable classroom manipulatives are presented for educators who are interested in participating in similar programs. International teaching exchanges provide a unique opportunity to develop skills in assessment and adaptability while meeting new colleagues from across the globe.

Fungal secondary metabolism: regulation, function and drug discovery.

One of the exciting movements in microbial sciences has been a refocusing and revitalization of efforts to mine the fungal secondary metabolome. The magnitude of biosynthetic gene clusters (BGCs) in a single filamentous fungal genome combined with the historic number of sequenced genomes suggests that the secondary metabolite wealth of filamentous fungi is largely untapped. Mining algorithms and scalable expression platforms have greatly expanded access to the chemical repertoire of fungal-derived secondary metabolites. In this Review, I discuss new insights into the transcriptional and epigenetic regulation of BGCs and the ecological roles of fungal secondary metabolites in warfare, defence and development. I also explore avenues for the identification of new fungal metabolites and the challenges in harvesting fungal-derived secondary metabolites.

Metagenomic Approaches for Understanding New Concepts in Microbial Science.

Over the past thirty years, since the dawn of metagenomic studies, a completely new (micro) universe was revealed, with the potential to have profound impacts on many aspects of the society. Remarkably, the study of human microbiome provided a new perspective on a myriad of human traits previously regarded as solely (epi-) genetically encoded, such as disease susceptibility, immunological response, and social and nutritional behaviors. In this context, metagenomics has established a powerful framework for understanding the intricate connections between human societies and microbial communities, ultimately allowing for the optimization of both human health and productivity. Thus, we have shifted from the old concept of microbes as harmful organisms to a broader panorama, in which the signal of the relationship between humans and microbes is flexible and directly dependent on our own decisions and practices. In parallel, metagenomics has also been playing a major role in the prospection of “hidden” genetic features and the development of biotechnological applications, through the discovery of novel genes, enzymes, pathways, and bioactive molecules with completely new or improved biochemical functions. Therefore, this review highlights the major milestones over the last three decades of metagenomics, providing insights into both its potentialities and current challenges.

Emerging Opportunities for Synthetic Biology in Agriculture.

Rapid expansion in the emerging field of synthetic biology has to date mainly focused on the microbial sciences and human health. However, the zeitgeist is that synthetic biology will also shortly deliver major outcomes for agriculture. The primary industries of agriculture, fisheries and forestry, face significant and global challenges; addressing them will be assisted by the sector’s strong history of early adoption of transformative innovation, such as the genetic technologies that underlie synthetic biology. The implementation of synthetic biology within agriculture may, however, be hampered given the industry is dominated by higher plants and mammals, where large and often polyploid genomes and the lack of adequate tools challenge the ability to deliver outcomes in the short term. However, synthetic biology is a rapidly growing field, new techniques in genome design and synthesis, and more efficient molecular tools such as CRISPR/Cas9 may harbor opportunities more broadly than the development of new cultivars and breeds. In particular, the ability to use synthetic biology to engineer biosensors, synthetic speciation, microbial metabolic engineering, mammalian multiplexed CRISPR, novel anti microbials, and projects such as Yeast 2.0 all have significant potential to deliver transformative changes to agriculture in the short, medium and longer term. Specifically, synthetic biology promises to deliver benefits that increase productivity and sustainability across primary industries, underpinning the industry’s prosperity in the face of global challenges.

Iron microbe: outfitting organisms for extreme environments

As NASA and other space agencies across the world prepare their astronauts to withstand the hazards of space travel and habitation on Mars, tinier adventurers have begun to receive a similar outfitting. For humans to live in extreme environments such as the darkest, coldest, radiation bombarded reaches of space, we must equip useful microorganisms to thrive and survive under similar conditions. This insight has expanded microbial sciences to the materials sciences: blending soft, squishy cells with hard, rocky crystals. And just as billionaire-playboy-philanthropist Tony Stark donned an array of gadgetry to become Iron Man, so too must bacteria and yeast receive the cyborg treatment to augment their functionality for the future of biotechnology.

How Should I Submit to mSphere : Traditional, Expedited, or mSphereDirect?

As we approach the end of our second year serving the microbial science community, we have been examining our processes as well as listening to the formal and informal feedback that we have received from the community. I take this opportunity to try to clarify some misconceptions and tell you about

A Vision for Vaccines: Combating the Opioid Epidemic.

RETURN TO ISSUEPREVViewpointNEXTA Vision for Vaccines: Combating the Opioid EpidemicCandy S. Hwang and Kim D. Janda*View Author InformationDepartments of Chemistry, Immunology, and Microbial Science, Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, United States*E-mail: [email protected]Cite this: Biochemistry 2017, 56, 42, 5625–5627Publication Date (Web):October 10, 2017Publication History Received22 September 2017Published online10 October 2017Published inissue 24 October 2017https://doi.org/10.1021/acs.biochem.7b00948Copyright © 2017 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views2718Altmetric-Citations7LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (707 KB) Get e-AlertsSUBJECTS:Immunology,Peptides and proteins,Vaccination,Pharmaceuticals,Biopolymers Get e-Alerts

Heptaplex-direct PCR assay for simultaneous detection of foodborne pathogens

Foodborne pathogens pose significant problems for public health and economy. The gold standard, cultivation, is time-consuming and costly. In this study, a heptaplex-direct PCR assay for simultaneous detection of seven foodborne pathogens without DNA extraction and enrichment was developed and validated. Seven virulent genes of target strains were amplified and found that the assay provided the expected PCR fragment of 583, 490, 415, 343, 224, 209, and 105bp for Shigella spp., Shiga toxin-producing Escherichia coli (STEC), Streptococcus pyogenes, Campylobacter jejuni, Salmonella Typhi, Listeria monocytogenes, and Staphylococcus aureus, respectively. Validation study showed that the assay was highly reproducible, specific and sensitive (106–100CFU/ml of detection limit). Moreover, assay application on 22 artificially-contaminated and 100 food samples provided a statistically equivalent efficiency to the culture method. A heptaplex-direct PCR assay thus can be used in microbial forensic science.

High-throughput automated microfluidic sample preparation for accurate microbial genomics

Low-cost shotgun DNA sequencing is transforming the microbial sciences. Sequencing instruments are so effective that sample preparation is now the key limiting factor. Here, we introduce a microfluidic sample preparation platform that integrates the key steps in cells to sequence library sample preparation for up to 96 samples and reduces DNA input requirements 100-fold while maintaining or improving data quality. The general-purpose microarchitecture we demonstrate supports workflows with arbitrary numbers of reaction and clean-up or capture steps. By reducing the sample quantity requirements, we enabled low-input (∼10,000 cells) whole-genome shotgun (WGS) sequencing of Mycobacterium tuberculosis and soil micro-colonies with superior results. We also leveraged the enhanced throughput to sequence ∼400 clinical Pseudomonas aeruginosa libraries and demonstrate excellent single-nucleotide polymorphism detection performance that explained phenotypically observed antibiotic resistance. Fully-integrated lab-on-chip sample preparation overcomes technical barriers to enable broader deployment of genomics across many basic research and translational applications.

«In the fight against epidemics, we have something to write on banners» (to the 150th anniversary of D. K. Zabolotnyi)

The article describes the life and scientific way of eminent epidemiologist, academician of the National Academy of Sciences of Ukraine D. K. Zabolotnyi. In the article there is shown his contribution to the establishment and functioning of the Ukrainian Academy of Sciences, the impact of development of his predecessors and successors in the development of both the global epidemiology and microbial science and medicine.

Advancing microbial sciences by individual-based modelling.

Remarkable technological advances have revealed ever more properties and behaviours of individual microorganisms, but the novel data generated by these techniques have not yet been fully exploited. In this Opinion article, we explain how individual-based models (IBMs) can be constructed based on the findings of such techniques and how they help to explore competitive and cooperative microbial interactions. Furthermore, we describe how IBMs have provided insights into self-organized spatial patterns from biofilms to the oceans of the world, phage-CRISPR dynamics and other emergent phenomena. Finally, we discuss how combining individual-based observations with IBMs can advance our understanding at both the individual and population levels, leading to the new approach of microbial individual-based ecology (μIBE).

How Climate Change affects Microbial Ecosystems (and Vice Versa)

The American Academy of Microbiology (AAM) periodically hosts colloquia that bring together experts on important topics in microbial sciences. The conclusions are published in short reports (FAQs) that explain the issues in language that is accessible to the general public. These FAQs are often used by teachers, politicians, and others who are interested in the topics.

Reviews and Resources:The Secret World Inside You

Inside “The Secret World Inside You,” one is immediately immersed in the microbial world. The exhibit at the American Museum of Natural History in New York is what every microbiologist loves to see: the magnificent world of microbiology portrayed in a series of engaging exhibits that entertain and educate the public about the microbial sciences.

Soils, microbes, and forest health: A qualitative analysis of social and institutional factors affecting genomic technology adoption

Within the forestry sector in British Columbia, a variety of methods exist for evaluating forest health. While the definition of forest health and the establishment of appropriate metrics for assessment have been debated, there is little disagreement among scientists and forestry practitioners on the importance of soil in assessing and maintaining healthy forests. Advances in genomic science now permit in-depth analysis of soil microbial communities, which can be used to assess various aspects of forest health. The translation of genomic microbial science to future technical developments can make soil microbial analysis practical and economical for forest management practices. Drawing on theories of technology adoption, this paper examines the social and institutional aspects of forestry in British Columbia to develop an understanding of the context in which a novel soil microbial genomic technology would be situated. This study draws on a series of interviews conducted with practitioners and stakeholders in the British Columbia forestry sector. Our findings suggest that while there is considerable interest in genomic microbial technology for forest health assessment, several key challenges will impact the practical application of this technology.