Scientific Program

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Scientific Program Day 1
  • Microbiology
Location: Online

Session Introduction

Gregory B Gloor

University of Western Ontario, canada

Title: Cautionary tales from the microbiome: Finding what is real and reproducible

Time : 10:00-10:30

Speaker
Biography:

Greg Gloor is a professor of biochemistry with broad experience in molecular biology, genetics and genomics. Most recently, he has developed tools to investigate fundamentals of molecular evolution, microbial ecology and meta-transcriptomics. He is currently working on developing and adapting principled methods to characterize correlation and differential abundance in sparse, high throughput sequencing data as generated in 16S rRNA gene sequencing surveys, meta-genomics and meta-transcriptomics. He is the developer and maintainer of the ALDEx2 R package on Bioconductor.

Abstract:

Statement of the Problem: Commonly-used methods of analyzing microbiome or RNA-seq datasets can be misleading and all the available information in a consistent manner are not in use. These results in many analyses being dominated by either the most abundant, or the rarest features: In fact, it is often the case that the most abundant taxa dominate multivariate outputs, and the rarest taxa dominate univariate outputs in the same dataset. Furthermore, these datasets have extraordinary properties that make the use of correlation and network analysis problematic.
 
Methodology and Theoretical Orientation: Data collected using high throughput sequencing (HTS) methods are sequence reads mapped to genomic intervals, and are commonly analyzed as either normalized count data or relative abundance data. One reason for these normalizations is to attempt to compensate for the problem that the sequencing instrument imposes an upper bound on the number of sequence reads. Positive data with an arbitrary bound are compositional data and are subject to the problem of spurious correlation. Thus, ordination, clustering and network analysis become unreliable. A second problem is that the data are sparse: i.e., contain many 0 values. A third problem is that the largest measurement error is at the low count margins in these datasets.
 
Conclusion & Significance: We use microbiome datasets to show how Bayesian estimation combined with compositional data approaches that examine the ratios between taxa give robust insights into the structure and function of microbial communities. I will present example datasets drawn from the human and ecological domains and show that ordination, differential abundance and correlation can be interpreted in an internally consistent manner that provides reproducible insights.

George Lazarovits

A&L Biologicals, Canada

Title: A road map to finding microbiomes that most contribute to plant and soil health

Time : 10:30-11:00

Speaker
Biography:

George Lazarovits graduated with his doctorate from the University of Toronto and worked as a research scientist (Plant Pathology) at Agriculture and Agrifood Canada until 2010. He accepted a position as Research Director at a newly formed company A&L Biologicals where he leads a staff of 5 researchers and 8 technicians. Their research program studies plant health from an ecological perspective where both beneficial and detrimental organisms in soil are considered to affect plant vigor. He has extensive national and international collaborators and has over 120 refereed scientific publications, numerous book chapters and one book. He is an adjunct professor at Western University, was president of the Canadian Phytopathological Society, and has organized and participated as keynote speaker in numerous national and international scientific conferences.

Abstract:

The human eye does not have sufficient resolution to unravel the mysteries of soil and plant health. Corn is one of the major grains grown in Canada. The proposed maximum theoretical yield of corn is 450-500 bu/acre, but average growers are producing 150 bu/acre. The main aim of this study is to understand the factors associated with soil health and plant productivity beyond the cropping system and practices. We measure the aspects of soil physical, chemical properties and differences in microorganism communities will be related to yield responses collected from plants harvested from 40 diverse sites across Ontario using aerial infrared photography to identify sections of fields where plants appear healthy or stressed  (as we discovered that when corn plants were randomly selected for testing, their microbiomes were quite similar). In this way, we hope to identify some of the primary reasons that confer the unevenness in crop yield seen across the same field when the same farm inputs had been applied. Such findings will be used to improve low production sites, thereby increasing overall yields significantly. Based on results from our previous studies we hypothesized that the difference in the plant productivity at different sites are due the abundance and diversity of microbial communities, and the impacts of their specific activities such as nitrogen fixation, phosphorous solubilisation, root growth promotion, and suppression of plant pathogens. The ratio of different soil chemical parameters affects microbial community richness and diversity in many ways. The study results will be integral in our understanding of the microbial community structures that influence crop productivity either negatively or positively. We expect to find out who are the key microorganisms and their roles in corn growth and productivity. Our initial analysis of data generated through TRFLP and next generation based sequencing of microbial communities showed, the endophytic microbial communities were distinct between low and high producing sites across most of the field sites tested. The high producing area had significantly higher bacterial richness and less diversity than the low producing area. Initial correlation analysis revealed potential positive interactions between the general fertility index, potassium to magnesium ratio, the gram negative and nitrogen fixer bacterial communities with yield and yield related parameters. Taken together, the corn sap bacterial community composition and richness was greatly influenced by soil chemical properties, which may indicate shifts in their functionality despite equal levels of total bacterial loads. The talk will identify factors associated with high and poor yielding sites and how this relates to soil and crop health.

 

 

Armin Schwarzbach

ArminLabs, Germany

Title: Tick-borne diseases: Challenge in diagnostics and therapies of chronic multiple infections

Time : 11:00-11:30

Speaker
Biography:

Armin Schwarzbach is a medical doctor and a specialist for laboratory medicine from the laboratory ArminLabs, Augsburg, Germany. He began by studying biochemistry at Hoechst AG, Frankfurt/Germany and pharmacy at the University of Mainz/Germany in 1984. In 1985, he studied medicine for 6 years at the University of Mainz/Germany and finished his MD in 1991. He developed the worldwide first radioimmunoassay (RIA) for human Gastric Inhibitory Polypeptide (hGIP) from 1986 – 1991, getting his Ph.D in 1992. He is member of the Swiss Association for tick-borne diseases, the German Association of Clinical Chemistry and Laboratory Medicine and the German Society for Medical Laboratory Specialists. He is an advisory board member of AONM London, England and Board Member of German Borreliosis Society and member & former board member of the International Lyme and associated diseases society (ILADS) and has served as an expert on advisory committees on Lyme Disease in England, Australia, Canada, Ireland, France and Germany. He is the Founder and CEO of ArminLabs, Augsburg/Germany and is specialized in diagnostic tests and treatment options for patients with tick-borne diseases for over 15 years.

Abstract:

Lyme-Borreliosis and coinfections are the chameleon of symptoms, laboratory test results and therapy options. Many patients can be infected by tick-bites with several bacteria (multiple infections). Symptoms of tick-borne diseases are not highly-specific for Lyme-Borreliosis or other coinfections (overlapping symptoms). The diagnostic approach should be done by modern and innovative laboratory tests with the highest sensitivity and specificity for each infection. The evasion from the immune system of pathogens plays an important role in the problems of diagnostic testing and therapies in the complexity of chronic multiple infections. Autoimmune disorders, many unexplained syndromes or cancer can be correlated with chronic multiple infections initiated by tick-borne diseases. This presentation aims to show symptoms and corresponding laboratory tests for tick-borne diseases, explaining the different diagnostic test systems and general therapy options for chronic multiple infections, respectively pathogen interactions and biofilms.

Fernanda Matias

Rural Semiarid Federal University, Brazil

Title: Microbial biodiversity in Brazilian semiarid

Time : 11:30:12:00

Speaker
Biography:

Fernanda Matias has completed her Ph.D in biotechnology from Sao Paulo University and post-doctoral studies from Sao Paulo University (Chemistry) and Porto Alegre Health Sciences Federal University (Pathology). She is a professor at UFERSA, School of Biotechnology, and is founding the first company in the university. She has published more than 10 papers in reputed journals.

Abstract:

When we think of semiarid we always associate with the lack of water, food, agriculture and livestock that end up generating little local development and, in consequence, poverty. However, little is exploring local biodiversity and adapted to that situation. In Brazil, we have a vast area of territory with hot semi-arid climate and only from mid-2010 began to be exploited as the local
biodiversity. Microbiological part is even more incipient. In 2014, a previous analysis of microbiome at different times of the year showed a significant difference of 16S rDNA size amplified in the same environment. This year we will start a microbiome work to understand what happens in these environments in different periods of drought. In 2016, lipolytic bacteria from hot springs were isolated. Lipases showed greater activity above 158oF and pH between 10 and 12. Later this year, we began an isolation of phosphate solubilizing, nitrogen fixers and auxin producing bacteria. By the time we succeeded in isolating more than 100 strains, among them was a symbiotic of Adenium obesum (desert rose) that is being considered for use as an agricultural inoculant. Furthermore, we developed a mead production method that reduced the months of fermentation timeout to 15 days which enables the industrial production of this beverage and will be the first start-up of the region. These findings suggest that semiarid is really rich in microbial biodiversity.