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Episode 32: How microbes and mucus interact in the gut

/in Podcast, Season Two /by Laura

How microbes and mucus interact in the gut, With Dr. Mindy Engevik PhD

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How microbes and mucus interact in the gut, With Dr. Mindy Engevik PhD

Episode summary:

In this episode, the ISAPP hosts discuss mucus-microbe interactions in the digestive tract with Dr. Mindy Engevik PhD from the Medical University of South Carolina, USA. They discuss how mucus in the gut is produced and degraded, and different ways that pathogens and commensal microbes interact with the mucus layer. Dr. Engevik describes some different ways that commensal bacteria make use of mucus, as well as dietary influences on gut mucus production.

Key topics from this episode:

  • The gut epithelium has special cells called goblet cells that actively secrete mucus. In the small intestine, mucus forms a light barrier but in the colon, it forms a thicker barrier with two layers: an inner layer free of microbes, and an outer layer where mucus and microbes coexist.
  • Bacteria in the gut make use of mucus in different ways. Many microbes have the capacity to degrade mucus, and it can provide a carbon source for bacteria to survive. Even bacterial quorum sensing can be influenced by mucus.
  • Bifidobacteria increase mucus production. Akkermansia are good at degrading mucus and also increasing mucus production. Pathogens, however, degrade the mucus and cause inflammation so mucus production is suppressed.
  • Several human diseases involve a dysfunctional gut mucus layer – for example, inflammatory bowel disease.
  • Various models are used for studying mucus – for example, traditional cell lines and human intestinal organoids.
  • Dr. Engevik’s work has found interactions between Clostridioides difficile and Fusobacterium nucleatum in the gut: these bacteria can interact to form biofilms that are more antibiotic-resistant than normal.
  • Individual differences exist in gut microbes as well as glycan structure in the gut, so the best insights will likely come from understanding the entire network of microorganisms, metabolites, and mucus. 
  • Dietary components influence the gut microbiota, which influences mucus production in the gut. High dietary fiber increases the amount of mucus produced by the goblet cells. Some bacteria degrade dietary substrates, then switch over to mucus when they don’t get what they need from the diet.
  • Dr. Engvik is an avid science communicator and advocates for scientists being present on social media. She has found science communication a great way to engage with the public as well as fostering scientific collaborations. The Instagram account showing microscopy images from her lab is @the_engevik_labs

Episode links:

About Dr. Mindy Engevik PhD:

Mindy Engevik is an Assistant Professor at the Medical University of South Carolina. She has Ph.D. in Systems Biology & Physiology and an interest in microbe-epithelial interactions in the gastrointestinal tract. Her lab focuses on how commensal friendly bacteria in the human gut interact with intestinal mucus and she tries to leverage this information to treat intestinal disorders. You can follow her on Twitter at @micromindy.

Episode 31: Microbial species and strains: What’s in a name?

/in Podcast, Season Two /by Laura

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The Science, Microbes & Health Podcast 

This podcast covers emerging topics and challenges in the science of probiotics, prebiotics, synbiotics, postbiotics and fermented foods. This is the podcast of The International Scientific Association for Probiotics and Prebiotics (ISAPP), a nonprofit scientific organization dedicated to advancing the science of these fields.

Microbial species and strains: What’s in a name? with Dr. Jordan Bisanz PhD

Episode summary:

In this episode, the ISAPP podcast hosts speak with Dr. Jordan Bisanz PhD, Assistant Professor of Biochemistry and Molecular Biology at Penn State University in State College, USA. They discuss how to define a bacterial strain, the diversity of strains within a species, and how genetic differences correspond with functional differences. They also talk about manipulating microbial communities for insights about health and disease.

Key topics from this episode:

  • Dr. Bisanz says just because strains within a species are genetically related doesn’t mean they do the same things. Bacteria gain and lose genes rapidly, but we don’t yet know what a lot of those genes do.
  • Natural variation in strains can be used as a tool to find out the functions of genes. 
  • Metagenomics illuminates strain-level differences, but that assumes we know what makes a strain. There’s no single accepted definition of a strain.
  • Knowing the mechanisms behind the effects of a strain on a host is important for predicting if closely related strains will have the same effect.
  • Moving forward, it could be useful to have functional information to go along with strains and their taxonomic descriptors.
  • Dr. Bisanz’s lab tests experimentally how microbial genes are gained and lost in vivo, both through wetlab experiments and computational approaches.
  • Experiments on strains are essential – for example, two strains with differences in 1000 SNPs might be functionally the same, while differences in 2-3 key SNPs might make a big difference.
  • When testing probiotic effects, you may be testing something derived from the original microbial genome but not identical. How can this be managed in industry? Understanding the mechanisms is important, strains that function similarly can qualify as the same strain.
  • A microbiome involves multiple microbes working together, acting differently from all the strains in isolation.
  • Dr. Bisanz studies tractable microbial communities: find the microorganisms that are different in a disease state compared to a healthy state, and create a synthetic community of the microbes that are absent. What are the functions of this community?
  • The challenge is that microbiologists need to be able to manipulate the microbes but cannot do this in a whole human fecal sample.
  • Is gut microbiome sequencing useful? At the level of individual, it may not provide value. But putting the data all together, in the future it may provide interesting information. The challenge with interpretation is that the microbiome is driving, but also responding to, dietary inputs.
  • In the microbiome field, gnotobiotic models (using humanized mice) need to be taken a step further than they currently go – specifying not only which microbes established in the host, but also how they could plausibly affect the mechanism.

Episode abbreviations and links:

Additional resources:

About Dr. Jordan Bisanz PhD:

Jordan Bisanz is an assistant professor of Biochemistry and Molecular Biology at the Pennsylvania State University and the One Health Microbiome Center. The Bisanz lab combines computational analyses and wet lab experimentation to understand how gut microbes interact with each other and their host. The lab specializes in coupling human intervention studies with multi ‘omics approaches and gnotobiotic models to understand how host-microbe interactions shape health generating both mechanistic insights and translational targets.

What is a strain in microbiology and why does it matter?

/in ISAPP Science Blog /by KC

By Prof. Colin Hill, Microbiology Department and APC Microbiome Ireland, University College Cork, Ireland

At the recent ISAPP meeting in Sitges we had an excellent debate on the topic of ‘All probiotic effects must be considered strain-specific’. Notwithstanding which side of the debate prevailed, it does raise the question: what exactly is a strain? As a card-carrying microbiologist I should probably be able to simply define the term and give you a convincing answer, but I find that it is a surprisingly difficult concept to capture. It is unfortunately a little technical as a topic for a light-hearted blog, but here goes. Let me start by saying that the term ‘strain’ is important largely because we like to name things and then use those names when we share information, but that the concept of ‘strain’ may have no logical basis in nature where mutations and changes to a bacterial genome are constantly occurring events.

Let’s suppose I have a culture of Lactobacillus acidophilus growing in a test-tube, grown from a single colony. This clonal population is obviously a single strain that I will name strain Lb. acidophilus ISAPP2022. That was easy! I am aware of course that within this population there will almost certainly be a small number of individual cells with mutations (single nucleotide polymorphisms, or SNPs), cells that may have lost a plasmid, or cells that have undergone small genomic rearrangements. Nonetheless, because this genetic heterogeneity is unavoidable, I still consider this to be a pure strain. If I isolate an antibiotic resistant version of this strain by plating the strain on agar containing streptomycin and selecting a resistant colony I will now have an alternative clonal population all sharing a SNP (almost certainly in a gene encoding a ribosomal subunit). Even though there is a potentially very important genotypic and phenotypic difference I would not consider this to be a new strain, but rather it is a variant of Lb. acidophilus ISAPP2022. To help people in the lab or collaborators I might call this variant ISAPP2022SmR, or ISAPP2022-1. In my view, I could continue to make changes to ISAPP2022 and all of those individual clonal populations will still be variants of the original strain. So, the variant concept is that any change in the genome, no matter how small, creates a new variant. When I grow ISAPP2022 in my lab for many years, or share it with others around the word, it is my view that we are all working with the same strain, despite the fact that different variants will inevitably emerge over time and in different labs.

Where the strain concept becomes more difficult is when I isolate a bacterium from a novel source and I want to determine if it is the same strain as ISAPP2022. If the whole genome sequence (WGS) is a perfect match (100% average nucleotide identity or ANI) then both isolates are the same strain and both can be called ISAPP2022. If they have only a few SNPs then they are variants of the same strain. If the two isolates only share 95% ANI then they are obviously not the same strain and cannot even be considered as members of the same species (I am using a species ANI cut-off of 96% that I adopted from a recent paper in IJSEM.

Where it gets really tricky is when the ANI lies between 96% (so that we know that the isolates are both members of the same species) and 100% (where they are unequivocally the same strain). Where should we place the cut-off to define a strain? At what point is a threshold crossed and an isolate goes from being a variant to becoming a new strain? Should this be a mathematical decision based solely on ANI, or do we have to consider the functionality of the changes? If it is mathematical then we could simply choose a specific value, say 99.95% or 99.99% ANI, and declare anything below that value is a new strain. Remember that the 2Mb genome size of Lb. acidophilus would mean that two isolates sharing 99.99% ANI could differ by up to 200 SNPs. This could lead to a situation where an isolate with 199 SNPs compared to ISAPP2022 is considered a variant, but an isolate with 201 SNPs is a new strain (even though it only differs from the variant with 199 SNPs by two additional SNPs). This feels very unsatisfactory. But what about an isolate with only 50 SNPs, but one that has a very different phenotype to ISAPP2022 because the SNPs are located in important genes? Or what about an isolate with an additional plasmid, or missing a plasmid, or with a chromosomal deletion or insertion? I would argue we should not have a hard and fast cut-off based on SNPs alone, but we should continue to call all of these variants, and not define them as new strains.

So, by how much do two isolates have to differ before we no longer consider them as variants of one another, but as new strains? I will leave that question to taxonomists and philosophers since for me it falls into the territory of ‘how many angels can dance on the head of pin?’

All this may seem somewhat esoteric, but there are practical implications. Can we translate the findings from a clinical trial done with a specific variant of a strain to all other variants of the same strain? If Lactobacillus acidophilus ISAPP2022 has been shown to deliver a health benefit (and is therefore a probiotic), can we assume that Lb acidophilus ISAP2022-1 or any other variant will have the same effect? What if a variant has only one mutation, but that mutation eliminates an important phenotype required for the functionality of the original strain? I am afraid that at the end of all this verbiage I have simply rephrased the original debate topic from ‘All probiotic effects must be considered strain-specific’ to ‘All probiotic effects must be considered variant-specific’. Looks like we might be heading back to the debate stage in 2023!

Decoding a Probiotic Product Label

/in Consumer Blog /by KC

By Mary Ellen Sanders, PhD

Interested in knowing what’s in your probiotic product? Unfortunately, there are many ways that probiotic product labels can fall short.

First, not all items labeled as “probiotic” truly meet the scientific criteria for a probiotic product. See here for information on what qualifies as a probiotic. Some fermented foods are marketed today claiming to be ‘probiotic’. But these products often have undefined microbial content and lack any studies documenting health effects, criteria that are required for a probiotic. Instead, such products could legitimately be labeled as containing ‘live, active cultures’. Dietary supplement products formulated with untested microbes should similarly not be labeled as probiotics.

Also, a label might not provide adequate information on what types of microbes are contained in the product. Genus and species may be listed, but no strain designation. Maybe only “bifidobacteria” or “lactobacilli” are listed.

They might not disclose the potency of individual strains in the product. Some may provide a total count of colony forming units (cfu)/dose or serving, which in the case of a single strain product is informative. But in the case of a multi-strain product – products may contain a couple or up to 30 strains – you don’t know if equal amounts of all strains are included, or perhaps the bulk of the count is made up of the strain in the formulation that is least expensive to manufacture rather than the one that will make the probiotic more effective. Some products may provide one count for “Lactobacillus” and another count for “Bifidobacterium”, a slightly more informative approach than just total count, but still lacking in detail. Many challenges exist for multi-strain products, including the lack of robust methods to quantify different strains once combined, especially viable ones. This topic was one that was covered in an ISAPP webinar, Current issues in probiotic quality: An update for industry.

The label may state that the count is “at time of manufacture”, a number that is no doubt inadequate if you purchase the product close to the end of its shelf-life. Most probiotic strains suffer cell count decline over the course of shelf-life, with some strains more susceptible than others. This situation almost guarantees that by the pull-by date for a multi-strain product, the ratio of cfu of strains to each other is likely much different than at the time of formulation.

Surveys of probiotic product labels

Additionally, it is difficult for consumers to know what products are backed by studies documenting a health benefit. If a product is not labeled sufficiently, it is impossible to link it to evidence. Two studies surveyed commercial probiotic products in the Washington DC area, Retail Refrigerated Probiotic Foods and Their Association with Evidence of Health Benefits and More Information Needed on Probiotic Supplement Product Labels. Results showed that 45% of retail dietary supplement products did not provide strain designations and an equal number did not provide a measure of potency through the end of shelf-life. Only 35% of products could be linked (based on strain and dose) to evidence of a health benefit. Food products fared a bit better, with 49% of refrigerated probiotic food products being linked to evidence of a health benefit. One clear indication from this study was that if your food product discloses the strain designation, it is likely to have evidence of a health benefit. An overall conclusion was that product labeling – at least in this region – needs improvement.

Historical context on guidelines for probiotic product labels

According to the FAO/WHO 2002 Working Group on Guidelines for the Evaluation of Probiotics in Food (page 39 of this combined document), the following information should be on probiotic labels:

– Genus, species and strain designation for each probiotic strain in the product.

– Minimum viable numbers of each probiotic strain at the end of the shelf-life, typically expressed in colony forming units (or cfu).

– The suggested serving size (or dose) must deliver the effective dose of probiotics related to any health benefit communicated on the label.

– Health claim(s) (as allowed by law and substantiated by studies)

– Proper storage conditions

– Corporate contact details for consumer information

These principles are developed and reiterated in “Best Practices Guidelines for Probiotics” (2017) developed by the Council for Responsible Nutrition and IPA.

Additional information

ISAPP created an infographic to explain the information on a probiotic labels. Our example portrays an imaginary dietary supplement for sale in the United States. Labels on foods containing a probiotic or a probiotic produced in another country would be labeled differently from this example to comply with applicable regulations. For those interested in probiotic labels in the EU, see the infographic ISAPP created for a probiotic product in the European Union. Also of interest, USP.org created an infographic on “How to Read a Dietary Supplement Label” for U.S. products.