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Limitations of microbiome measurement: Prof. Gloor shares insights with ISAPP

February 20, 2019

The number of papers published on the human microbiome is growing exponentially – but not all of the studies are equally well designed or reported. Evaluating the latest research requires a basic understanding of the latest approaches to microbiome methods and data analysis.

To help equip scientists not conducting microbiome research with the tools to understand microbiome-focused publications, ISAPP hosted a webinar titled Understanding microbiome experiments: a critical assessment of methods and data analysis. The webinar featured Gregory Gloor, PhD., Professor, Department of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, Canada.

A recording of the webinar is available here, and Prof. Gloor’s slides are available here.

Prof. Gloor opened his talk with a sobering perspective: the current body of microbiome publications is fraught with problems. There is a fundamental lack of reproducibility in the microbiome field (Sinha et al. 2017). This is largely due to the large number of tools available and a lack of an a priori established research plan for microbiome analysis, which should be consistently followed throughout a project. At every step of the way, many decisions must be made regarding wet lab methods, bioinformatics toolsets and statistics to use. Different choices lead to different results. Once the biological specimens are assayed, choices for bioinformatics and statistical analyses can greatly influence the conclusions. In short, it’s possible to view the data through so many different lenses that eventually a researcher can find a story worth telling. How close that story comes to the truth is a principle that sometimes is sacrificed for the sake of an interesting story.

Another important challenge to the field is representative sampling. Too few samples are typically taken, often because of cost limitations, so that the samples do not reasonably approximate the truth about the environment being sampled. Conclusions from such studies result in both many false positives and many false negatives.

Prof. Gloor also warned about outsourcing microbiome analysis. Commercial entities often use every metric, hoping the customer will get some outcome they hoped for. Further, their tools are often outdated or proprietary. So caution must be used – there is no substitute for expertise.

Some suggestions for improving outcomes were offered:

  • Each project should stipulate a research approach and outcome a priori, which is consistently followed throughout the project.
  • Methodological consistency is important within a lab, but analytical methods do not necessarily need to be standardized across all labs. If all labs use the same methods, consistent, but incorrect, outcomes may result. So use of different metrics is good, but methods should be consistent within a project. The value of different research groups using different methods to ask particular research questions is that if the same result emerges from different approaches, it increases confidence that the results are true.
  • Gloor cautioned that microbiome datasets are compositional, and compositional data approaches must be used (Gloor et al 2017).
  • Functional readouts have less methodological variation than taxonomic readouts. Therefore, functional analysis of shotgun metagenomics or shotgun metatranscriptomics is typically a more reproducible, and also more informative, readout.
  • Recent advances have significantly decreased the cost of performing shotgun metagenomics for both taxonomic and functional readouts (Hillmann et al 2018).
  • There are now near-complete microbial genomic datasets available for European, North American and Asian populations (Almeida et al 2019) that will make it easier to functionally map datasets.

Prof. Gloor mentioned an interesting aside: prior clinical trial registration, ~60% of large clinical trials showed benefit of the intervention being tested. After the registration process required declaration of primary research outcomes, that number dropped to closer to 10% (Kaplan and Irvin 2015). This suggests that primary outcomes and analysis methods need to be in place to restrict researcher bias. Right now such mechanisms are insufficient in the microbiome field.

Prof. Gloor’s paper, Microbiome Datasets Are Compositional: And This Is Not Optional, provides great background reading for this webinar.

This webinar was developed by ISAPP Industry Advisory Committee representatives as an extension of the annual IAC Learning Forum.

Dr. Gloor is a professor of biochemistry with broad experience in molecular biology, genetics and genomics. His research is focused on the development of tools to examine 16S rRNA gene composition, gene expression of mixed population samples and metabolomic analysis of clinical samples. 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. One of his primary contributions has been the ALDEx2 tool in Bioconductor for the analysis of high-throughput experiments that generate counts per sequence tag: 16S rRNA gene sequencing, metagenomics, transcriptomics and selex-type experiments.

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ISAPP conducts webinar on definitions in microbiome space for ILSI-North America Gut Microbiome Committee

Dr. Mary Ellen Sanders presented a webinar July 23, 2018 – covering basic definitions of microbiota-mediated terminology – to the ILSI-North America Gut Microbiome Committee, which you can listen to here. The objective was to update the committee about terms with clear and actionable consensus definitions in the microbiome space. ISAPP is committed to proper use of terms such as ‘probiotics’ and ‘prebiotics’, as evidenced by the consensus panels it has convened (see here and here) on these topics. Definitions of some newly emerging terms such as postbiotic, abiotic, and probioceuticals are less clear.

Some issues covered in this webinar include comparison with historic definitions, minimum criteria for commercial probiotic and prebiotic products, contrasting probiotic food with fermented food, and a brief discussion of imminent taxonomy changes for the genus, Lactobacillus.

The webinar is now available here.

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ISAPP’s Outgoing President: Karen Scott

Dr. Karen Scott of the Rowett Institute of the University of Aberdeen has served as the ISAPP President for the last three years. During her time as President, ISAPP has seen some incredible growth and accomplishments, and the organization is so grateful for her leadership.

Last year, under Karen’s leadership, ISAPP produced a prebiotic consensus panel paper, which remains one of the highest cited papers in nature reviews gastroenterology and hepatology.

In addition, over the last three years the Science Translation Committee has produced nine infographics, four videos, monthly blog posts, and a monthly newsletter focused on disseminating clinical and consumer information on probiotics and prebiotics.

Karen led three successful ISAPP Annual Meetings – Turku in 2016, Chicago in 2017, and ISAPP’s first meeting in Asia which took place in Singapore in 2018. All of these meetings followed her acting as local host for the 2014 ISAPP meeting in Aberdeen.

ISAPP’s mission to educate resulted in numerous outreach activities over the last three years including continuing education opportunities, webinars, the USP expert panel on probiotics, and regulator engagements. In terms of advancing the science, under Karen’s leadership ISAPP has published 21 peer-reviewed articles on probiotics and prebiotics.

Finally, industry involvement in ISAPP has remained strong and steady during Karen’s term, with 40-45 industry members from around the world. These industry members support ISAPP’s activities and participate in the annual meeting each year to hear about the latest probiotic and prebiotic science available.

Thank you so much Karen for your dedication and hard work to advance scientific excellence in probiotics and prebiotics.

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Medscape Webinar on Probiotics – Now Available!

“Navigating the world of probiotics: Helping  patients make good choices”

This 30-min CME activity, which took place on April 17th, by Medscape is now available online https://www.medscape.org/viewarticle/897109 The webinar features Prof. Dan Merenstein MD and Mary Ellen Sanders PhD – both ISAPP Board Members.

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Free Webinar: Why is everybody talking about gut microbiota?

Coming up on Thursday, June 28th ISAPP Board Member Professor Glenn Gibson will be featured in a free webinar discussing gut microbiota. Hosted by the British Nutrition Foundation, the webinar will examine what we know about gut microbiota and what remains to be explored. Research on gut microbiota has indicated the gut has a role in metabolism, immunity, and more!

The British Nutrition Foundation says “This free webinar aims to increase understanding of the gut-brain axis and the evidence for the role of gut microbiota in metabolic health and immunity. We are absolutely delighted to have world renowned experts speaking in our programme including:

  • Professor Ian Rowland (University of Reading)
  • Professor Ted Dinan (University College Cork)
  • Professor Glenn Gibson (University of Reading) “

 
Find out more information and register for the webinar here.

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Medscape Webinar on Probiotics April 17

Prof. Dan Merenstein MD and Mary Ellen Sanders, PhD will present a 30 min webinar titled, “Navigating the World of Probiotics: Helping Patients Make Good Choices” April 17 at 12:30 ET*. Developed by Medscape, the target audience is medical professionals. Dr. Sanders will provide basic information about choosing probiotics and Prof. Merenstein will discuss the strength of evidence for different clinical applications for probiotics. The webinar is free, but you must register with Medscape to sign up. Register here.

*An earlier announcement by Medscape listed the wrong time zone.

ISAPP to host live webinar: Microbial metabolism associated with health

Update April 16, 2018:  Recording and slides from the webinar available here.

The International Scientific Association for Probiotics and Prebiotics (ISAPP), in partnership with the International Life Sciences Institute (ILSI) Europe’s Prebiotics and Functional Foods Task Forces, has jointly organized a free webinar, titled Microbial Metabolism Associated with Health. The webinar runs April 12th, 2018 at 15:00 CET, and will highlight recent activities of both ISAPP and ILSI on the beneficial aspects of gut microbial fermentation. The specific focus will be on gut microbiota functions, the effects of the intestinal microbiota on selected nutrients and non-nutrients, and the health benefits of fermented foods. Scientists from both academia and industry may find the webinar of interest. Sign up here.

Webinar participants will learn the status of the science making the links between live microorganisms in the diet and host health. The host gut microbiota is a key factor in determining gut function, nutritional status, biochemical transformations of food and the overall impact on health. This diverse microbial community inhabiting the human gut assists in food metabolism and contributes to the bio-availability of nutrients and non-nutrients; it also has an extensive metabolic repertoire that complements mammalian enzymes in the liver and gut mucosa. Microbial metabolism is an important factor to consider when discussing the management of host health and conditions such as obesity and metabolic syndrome.

The enhanced nutritional and functional properties of fermented foods are being increasingly recognized; not only do microbes transform the substrates and form bioactive or bioavailable end-products, but also, fermented foods contain live microorganisms genetically similar to the strains found in probiotics. The webinar will cover the possible interactions of fermented foods and beverages with the gut microbiota, and potential links to health.

The 90-minute live webinar will be hosted on StreamGo, and will include a question and answer period at the end. There is no cost; however, participants are required to register online beforehand.

Speakers:

  • Effects of the Intestinal Microbiota on Selected Dietary Components
    a) Introduction and Background to the Activity (Dr. Colette Shortt, Johnson & Johnson, UK)
    b) Impact of Intestinal Metabolism and Findings (Prof. Ian Rowland, University of Reading, UK)
  • Health Benefits of Fermented Foods: Microbiota and Beyond (Prof. Robert Hutkins, University of Nebraska, USA)

 

Publications from ISAPP and ILSI-Europe related to the webinar topics:

probiotics webinar

Two Free Webinars on Probiotics!

Both webinars – eligible for continuing education credit – on probiotics involving ISAPP board members are scheduled. The first is scheduled for Thursday, March 15th 11am-noon CST. It  features Mary Ellen Sanders, PhD on the topic of “Be a Pre and Probiotic Pro” and is sponsored by General Mills Bell Institute of Health and Nutrition. Register here.

The second, “Navigating the World of Probiotics: Helping Patients Make Good Choices,” is under development by Medscape. Both Prof. Dan Merenstein MD and Mary Ellen Sanders, PhD will speak during this 30 min webinar. It will take place April 17. Register here.