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Assessing and Supporting the Microbiome with Jessica Cox

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Assessing and Supporting the Microbiome with Jessica Cox

How do we incorporate microbiome testing into practice?

Today we are joined by nutritionist Jessica Cox who shares her clinical approach to how, when and why you might incorporate microbiome testing. Digestive health is such a crucial aspect of Jess's clinical practice, that it led to her writing a book on the subject called E.A.T (Education at the Table).

In this interview Jess covers important aspects of patient care including, how to determine if testing is even necessary, how she assesses overall gut and digestive health and how she coaches her clients to improve their personal eating habits.

Covered in this episode

[00:41] Welcoming Jessica Cox
[01:24] When do we do microbiota-based testing
[02:53] How to determine when to apply the test
[05:19] Types of testing available
[06:22] The influence of food fibre on testing
[08:02] A comprehensive look at the overall digestive process
[10:23] Individualising dietary recommendations
[20:02] Assessing intestinal permeability 
[20:54] Diet methods can be reductionist
[24:20] Teaching clients the foundations of nutrition
[27:48] Addressing alcohol consumption
[31:22] E.A.T (Education at the Table) by Jessica Cox
[33:28] Caveats or cautions when it comes to meal plans


Andrew: This is FX Medicine. I'm Andrew Whitfield-Cook. Joining us on the line today is Jessica Cox, who holds a Bachelor of Health Science in Nutrition and is the founder of JCN Clinic based in Brisbane, Australia. She's a passionate foodie, recipe developer, and with close to 15 years of clinical experience, with a focus on digestive health. Jess is well respected for her “no fad” approach and utilising evidence-based nutrition. She's created her own blog, which is an expression of everything she loved rolled into one, including her passion for creating recipes that cater for food intolerances and digestive issues. Welcome to FX Medicine, Jess. How are you?

Jessica: Good. Thanks for having me.

Andrew: Now, we'll be discussing today the importance of dietary guidance with microbiota testing. So this is a massive issue, massive area, with lots of controversy over it. So I've got to ask, first off, when do you do microbiota-based testing?

Jessica: So because our client base is generally coming to us with a lot of chronic longstanding gut issues, it is something that we tend to do with a large portion of our clients. In saying that, we're not willy-nilly about testing, we really talk to people about where they're at as far as even financials. But essentially, through really good thorough case taking with that initial consult, we'll ascertain whether we need to dig deeper with the testing. 

And, look, to be honest, we usually find that a lot of the people who are coming to us have been dealing with gut issues for so long and trying so many different things that they really are ready to just invest in getting more information. For us, we find it's a way of really understanding and seeing what's going at that microbiota level so we have more information. I always say to my clients “It's like a window in there, so I know more about what's going on, specifically, and we can get to treatment more specifically, too.”

Andrew: Given that you can change your microbiota in your gut over a week if you change from a meat-based to a plant-based diet.

Jessica: Yes.

Andrew: And you've also… I’ve discussed with other practitioners about even changes from, say, female hormones during the cycle. When do you tend to do that test in patients?

Jessica: It really, to be honest, is something that we just utilise based on what's going to be convenient for them. 

Andrew: Right.

Jessica: I’d love to say, it was something that we could be more strategic about and look, in case it's a female, where are you within your cycle, and so forth. But again, we're dealing with that person on that individual basis, and realistically, they are just like, "I want to get this done now. Let's get this information now." 

And also, what we're doing from a dietary perspective is we want to get an idea of what their gut is doing right now, at that time, based on what they're currently eating. 

Andrew: Yeah.

Jessica: So, for us, it's like, "Well, let's see what your gut is expressing now with the current dietary intake you have, and then we can make changes once we have that information."

Andrew: Got you. And do you tend to do pretreatment and treatment after, say, I don't know, three, four, five, six months?

Jessica: Sorry, do you mean with retesting?

Andrew: A repeat, yeah.

Jessica: Sometimes. We try to get our clients to at least wait six months if they do want to retest. 

Andrew: Great.

Jessica: We think that and we have found this with retesting that you need a minimum of those six months to really start to see some changes there. But even six months I feel sometimes is too short of a window. 

And often, most of our clients find that once they've done that initial test, if they're feeling great in 6 months or 12 months or whatever that timeframe is, then they're not really that fussed about retesting, and we tend to be guided by that too. Like, ultimately, it's about how that person feels. 

Andrew: Yeah.

Jessica: So, do they need to spend another $400 to $600 on a test when, ultimately, they're feeling well, their diet's really expansive, you know, it's sort of a question that I pose to them and leave the ball in their court sometimes, in that regard.

Andrew: What can you tell us about the type of testing that's done? Is it like a, forgive me, is it 16S, the shotgun?

Jessica: Yes.

Andrew: Right, okay.

Jessica: Yeah. We tend to use it, but we kind of jump around between different laboratories at the moment. So, yes, we tend to use always that type of sequencing looking at the gut. We're generally looking at getting the most comprehensive one that we can, and that, again, will depend on the client. 

So if possible, we'll be looking at getting a picture of parasitology, we'll be looking at getting that full breakdown of bacteria. We'll also be looking at trying to get what we can as far as yeast, which can be a little bit controversial in what you can actually capture there. 

Andrew: Yes.

Jessica: And then we're looking to see if we can also invest in getting those inflammatory markers and digestive markers as well. So you know, if we're having someone invest in the testing, we usually like to try and get that full sweep.

Andrew: I love what you're saying about inflammatory markers and things like that because it gives a picture as to what this bacteria is causing you to react with.

Jessica: Exactly.

Andrew: So what about things like, you know, food fibres and things like that in the faeces?

Jessica: In the testing?

Andrew: Yeah.

Jessica: Yeah, yeah. So that will be, again, as you just said, it's really good because we can look at those breakdowns as well and see that interrelationship. So if we're looking at seeing certain types of bacteria that are at a lower level and then we're seeing perhaps certain plant fibres that are too high in the stool, or if we're seeing some types of bacteria that are too high, particularly I would say, with the sort of more sulphur-thriving bacteria, we might also be seeing an expression of higher fats in the stool. 

So we can start to see relationships there, and as a practitioner, it can give us more information and I would say also confidence in which pathway we go down. And as you highlighted, with those inflammatory markers, if we're seeing an expression of, say, low Akkermansia, and then we're also seeing raised secretory IgA and perhaps issues around calprotectin and so forth, we really can understand, "Okay, there's a lot going on in the mucosal layer, and that's going to need a lot of attention."

Andrew: Yeah. I often question, when we're talking about a faecal test, we're talking about what comes out, not what's necessarily on the lining. 

Jessica: Yes.

And then you've got to say, "Okay, well, if you get lots of food fibres in the stool, you've really got to start right back at the mouth." You've really got to start looking at chewing and relaxing, you know. So it really does start back with this general dietary advice with simple eating practices.

Jessica: Yeah, you're exactly right. It does. And that's where I find the test in conjunction with really good case taking is so important, because you can see these things presenting in some test results, but you can also talk to your client and find out that they are rushing through their day. 

Andrew: Yeah.

Jessica: They are eating when they're stressed and they're on the go. You can put all those pieces of the puzzle together. And of course, like, these types of tests are amazing, but they're not perfect. But they're a piece of the puzzle that we can use in unison with a client. So, yeah, they're a great adjunct, but they're not everything.

Andrew: Let's talk about the dietary advice, because as we talk about, digestion is often thought to start with the mouth. But I love Mike Ash's advice that it actually starts in the head, with the cephalic. So how much emphasis do you put on chilling before a meal?

Jessica: As much as possible. It's a hard one. It really is because, you know, I always say to my clients, it sounds easy, like, when we're talking about removing stress and eating in a lower stress environment. It seems like such an easy thing to do, but it can be one of the hardest. 

Andrew: Oh yeah.

Jessica: So trying to work with clients when you can see that the issue is going on there in relationship to them even just being in that rest and digest mode, it is something that you need to work through and go, "Okay, what can we do here? Can we create an environment where you just take literally five minutes just to sit down and take a couple of breaths and just really smell the meal and connect with the meal and then just eat that meal?" Think about putting the fork down in between mouthfuls, which sounds, again, really simple, but it actually works.

Andrew: These guidelines can be individualised, right? So you know, you spoke about the busy professional in the middle of the day, city eating, versus the family meal at night with a larger family where everybody is having a social engagement. How do you individualise dietary practices to suit that person while still trying to get a healthy outcome?

Jessica: Yeah, it's such a good question. It's something we're so passionate about. So I think, first and foremost, you have to understand the person. As you just said, we've got people with different sorts of lifestyle, different stresses, and different ways of living their lives. So we can have a really sort of perfect ideal of how we want someone to eat and the foods we want them to have more of and less of and avoid, and so forth. But we need to make sure that that's going to be achievable for that person. 

So, for me and for us at JCN, what we will do is spend a lot of time, and it sounds, again, really simple, but I think I personally believe it's something that's not done enough. It's going through with the client and saying, "Okay, what are you actually eating right now? What is your base diet? What are you able to commit to? What sort of food do you like? What do you enjoy? How much time do you have at this current moment to put into breakfast, to lunch? What can we negotiate on? Okay. Where can I ask you to spend a little bit more time on this meal or that meal? What's your negotiables on spending an extra hour to somewhere throughout your week to do some batch cooking and some organisation for the week ahead?" 

So it’s really developing a relationship with that client so that you can work out a foundation that you can build a food plan from. Because I truly believe with that time they put in, and we just hand the client some test results and a prescription with some supplements and a table of ‘avoid these foods’ and push them out the door. We don't get the results for longer, because they can't commit to that. There's no guidance, if that makes sense.

Andrew: Yeah, absolutely. On that line though, when you've got people that are, you know, the continual high-stress type, a city worker, whatever, do you tend to employ more things like digestive herbs, aperitifs, maybe digestive enzymes, or probiotics as well? 

Jessica: Yeah.

Andrew: Do you find that these are the people that say, "Look, just give me a pill?"

Jessica: There's a little of that, but because we're so passionate about our food and teaching them a foundation of eating well, it can be a tool we can use, but we'll be very, very mindful of educating them as we go and trying to instil some new habits. So, yes, we will use probably more… there would be enzymes that we would utilise there a bit in that context. 

But honestly, again, we would be talking with that client and looking at, "Okay, what is happening with that go-go-go morning." Like, let's look at, for instance, say, it's a smoothie that we can spend, even if we're spending 15 to 20 minutes figuring out what we're going to do with this smoothie. What ingredients we are going to put in it. How are they going to make it work? Are they going to take a NutriBullet into work and put their ingredients there to put it together? What are they going to do at lunch? How are we going to work that out? 

And I honestly find after years of working with so many different people and different stressful environments that anyone can make it work in the context of their day, it's just putting some time into working out a plan with them around their food in the way that we might put a lot of time into figuring out the perfect supplements to take.

Andrew: Yeah. And when we're talking about enzymes, do you tend to, A, like employing fermented foods, and B, what's your acceptance like in the general population?

Jessica: With the fermented food, so it would depend on where they were at with their gut health. So often, and I'm generalising, of course, but often, what we'll do with our clients in the initial stages if there's a lot going on with their gut, we may, in those stages, move away from the fermented foods while we're in that more of a… trying to remove other bacteria, parasite, etc.

Andrew: Yes.

Jessica: So at that point, we may not be using them, but then what we will do is we will go through an introductory phase, which is a big part of what we build into our dietary guidelines and our treatment guidelines as we move through them. So we will very systematically introduce fermented foods and different types of fibrous foods to ascertain their tolerability. 

And generally, as we're working through that process and working through building up the resilience and the integrity of their gut health, we'll find that those foods are tolerated. So often, you'll find someone who knows...they'll say to you at the beginning, "I can't. If I look at sauerkraut, it turns my stomach inside out." As opposed to 12 weeks down the track, they're being able to add maybe a heaped teaspoon to their meals a couple of times a week with no issues, which is, of course, our goal as a practitioner, to create that expansion in their diet.

Andrew: Yes. I love what you're saying about this improving the resilience, the terrain. 

Jessica: Yes.

Andrew: I just think, as practitioners, we keep forgetting about this. Like, rather than treating a symptom right now and smothering it, we have to look back at the reasons why things are happening, address them, and they tend to be mitigated, if not go away.

Jessica: Exactly. That's exactly right.

Andrew: So as practitioners, how can we customise meals and recipes to support the microbiota that you're testing in the initial phases? And so what are some of the results that you've gained if you had retests?

Jessica: So I think, firstly, to that question, in regards to putting these types of dietary plans together, it comes back again to, one, understanding what we've been talking about, the client's or patient's lifestyle and what's achievable there. But also putting that into context with their symptom picture through thorough case taking and those test results. 

So from that, we can get an understanding of if we've got A, B, and C issues going on. So if they've got, you know, these types of bacteria species that are too dominant, we've got these that are undergrown, we need to think about what food at this initial starting point we need to be stepping away from, and then we need to be looking at what foods we want to be including more of. That might be on a specific ingredient level but also might be about the type of dietary intake too.

Are we needing to look out for this person that they do have a lower fat intake and more of a higher plant-based expression of food? And how do we look at starting that pathway? Because you can get these test results back and go through someone's diet while they're sitting in that room with you, and you can tell by talking to them and seeing their results, "Oh my god, they need to really increase all of these beautiful plant fibres and they need to feed all of these wholly starved Ruminococcus and so forth that are just dying to be fed." 

Andrew: Yes, yes.

Jessica: But you know that you can't just turn them from a very restrictive stage and put them on a paleo-type diet, straight over to that, because they're never going to come back to you. You're going to cause so many symptoms. So what we need to do is walk them through stages where we can start with a more soothing, easy to digest type of diet. And then we'll look at what foods we can then introduce as we go week to week and see them, to come back to that word again, build a stronger resilience.

So it's that combination of bringing in the key supplements that you might utilise in relation to those results that you now have. And then as you reduce the number of the adverse species that might be at play but also you're supporting the gut lining and reducing gut permeability, doing all of those things, creating an environment where there's less reactive foods, then we can say, "Okay, four weeks later with this person, you do have these particular strains that are low, let's focus on trying to bring in these types of resistant starch foods and see how you go with these." And we can create a plan where we can slowly walk them into a more diverse diet.

Andrew: Do you employ the lactulose mannitol test to look at intestinal permeability? And do you find a difference when you institute dietary changes?

Jessica: Look, we don't really use that so much as a testing method. I'm probably more, if I'm suspecting gut permeability, I'm probably more going from seeing raised inflammatory markers, low Akkermansia, seeing issues around secretory IgA. And then, again, probably more symptom picture as far as systemic issues, like classic aching joints, fatigue, and so forth. Perhaps also looking at zonulin as well, testing zonulin. They're probably where we would more go with testing in that realm.

Andrew: And you mentioned also that you're not a fan of fad diets. Now, you know, we've got fad diets versus chosen diets. You know, I've spoken to people like Dom D'Agostino about keto nutrition and things like that, which is hard but has its use. So when you're talking about paleo, keto, is the problem restriction? And how do you address that?

Jessica: Definitely, I think the problem is restriction, and that's what we see over and over again with our clients that are coming through. And look, I respect that these diets have their place and I also respect that they're coming from a place of wanting to help others, of course. And I think the problem is that they're used more as this sweeping way of applying a dietary, and I don't like the word the protocol, but using that as a way of saying “Wveryone needs to eat in this way.” And that is my innate problem with them. 

I think that they can be really wonderful when utilised as part of a treatment plan. So you know, for instance, with, say, a more keto-type of approach or perhaps a very low-fibre type of approach, of course that's going to fit well into someone's life if they're having some really profound gut issues and they're essentially taking away a lot of the fuel that is providing their microbiota with a lot of the, sort of fire, essentially, that's causing the problem.

Andrew: Yes.

Jessica: But of course, they're going to feel better, but all they're doing is controlling symptoms and consequently causing more problems down the track because they're lowering the diversity of bacteria, which is, again, something we see in the clinic all the time. And I guess I'm so passionate about that, is because we see the consequences. We see the people that come in who have been following these more narrow and restrictive protocols long-term, and they have backed themselves more and more and more into a corner. 

So they might have started just broadly paleo, but then because they're just restricted and that's all they've ever done, and they haven't really looked at dealing with the underlying problem, their food has become more and more and more narrow, and they've created more and more and more fear around food.

So I think that they have their place, and I think if these different types of diets are used in the context of a client with a practitioner who knows what they're doing, then they can be wonderful. But I think they also need to be used in a way that they're not seen ideally as long-term. Like, we have someone on some form of restrictive protocol, it needs to be with the intention of growing their food, creating diversity. Because we know that… I know we're still in the infancy with so much for learning about the gut, but we do know that one of the biggest thing is that diversity of species is where it's at, and we want to create a diet that allows that diversity to grow.

Andrew: One of the things that keeps coming up for me is you can have a good basis of a diet or a good theory of a diet, and then you stuff it up. Like, for instance, if you're doing a high-fat diet and then you have sugar, you have a bust out, you have sugar. How much time do you have to spend on making sure that your patients really know what a food is, what even a protein is?

Jessica: Yeah. Thank you for that question. So there's a few things in that, but the first thing to highlight is I cannot stress enough how important I think it is, and the practitioners at JCN find it to teach our clients what we call the foundations of health and the foundations of nutrition. The biggest gift you can give to a client that walks into your door is knowledge, and if you can teach them what nutrition looks like, those basic foundations of: what is protein? What is complex carbs? What is fat? What are good types of all of these macronutrients? How do we combine them to create an ideal meal? What does that look like for you in the context of your food plan? 

If you can teach them those things, it will give them so much more understanding and also empowerment as they move through everything that you do with them, and then it will help them too. So if they are following a certain type of protocol or a certain type of plan, and they do fall off the wagon, they can understand that relationship. So they can say, "Okay, I was eating in the context of this, and I've had too much of this." And through talking through how those changes can occur when they have X, Y, Z food, they can understand that relationship, and again, it gives them...it's not great when they can have those symptom flare-ups, but they can understand why it happens. And it can give them, again, that knowledge to understand, "Okay, if I go down that path again, this is what's going to happen, but this is why."

Andrew: Yes.

Jessica: But I would also speak to that, is that it's important for us to educate clients on that if they do have a slip up here or there, that they're not going to undo everything.

Andrew: Yes.

Jessica: I think, again, there's a low fear in this space. So if someone's following a certain type of plan with you and they go out on the weekend and, they have a piece of cake or whatever it is, that one meal won't be their undoing. It's more that we're trying to encourage them to stay on plan, and again, them understanding that it's not that one meal every second day that's off-plan. It's giving them some idea of where this is a threshold, which of course will move from person to person. 

So I think it's unrealistic for us to expect our clients to follow things perfectly because, even as practitioners, we don't. But I think, again, if they can understand why we're asking them to eat a certain way and have that education, then that empowerment, it will be the biggest tool that we can have for our clients.

Andrew: We live in Australia, in the highest drinking per capita population in the world. How do you address this with regards to gut inflammation, what alcohol is doing to even a good diet? And how do you help people to moderate their intake?

Jessica: So what we tend to do and what I would encourage for other practitioners is we spend a lot of time working out timeframes with clients. So this would come into the context of food as well but definitely also alcohol. 

So if we can give them a timeframe, and of course, these goalposts can move around a little bit, but if they can see, "Okay, for the next six to eight weeks, it's really important that I don't have alcohol, or if I do, if I must, I need to have this type of alcohol in this context as it will be lower sugar and lower yeast, and so forth." So if they can have some form of timeframe, and I find that whether it'd be alcohol or with different foods or any form of restrictions, it enables them to get their head around that and to know that, "In six to eight weeks, ideally, if everything is going well, I'll be able to start looking at can I bring that glass of wine in or can I include beer on the weekends." So I think just trying to tell people, like, it's out, it's gone, without any ideas around when we might be able to look at them again. You know, that can be a bit unreasonable.

And, look, alcohol, it's hard. Like, it is obviously very ingrained in our culture, as you say. And sometimes it just needs to be bargained, as well. Like, we often joke about how we'll chat with our clients about that give and take, and sometimes that might be someone we'll say to us, "It's not just going to happen. I'm not going to give up my wine that I enjoy every night." And we will say to them, "Look, if that's your prerogative, that's fine. I want to help you feel better, but you need to understand that the process of getting you from A to B may be a little bit slower." 

And you know, we have to remember that people...I know it seems like it's really obvious, but that people are human beings with complexity and emotions, and we need to work with that too.

Andrew: But I'm also reminded by, you know, for those who expect much, much is expected. And so, you know, I remember telling patients that and just saying, "Well, that's fine, but if you're not willing to change, the whole reason you're here is because of what you've done previously. So what do you expect to get in six months if you're not willing to change?"

Jessica: It’s it. That’s exactly right. And then that's where the communication is so important. I know we're coming back to some of those fundamentals of a relationship between a practitioner and a client, but they are really important. But we need to be upfront with what they ideally need to change to get results. But we also need to be respectful of the fact of what we're asking them and that each person will be a little different in what they're able to give. 

And surely, if someone's more difficult in what they're willing to change, if we're to say to them, "Look, I still want to help you, but it's probably going to take double the amount of time, and let's work together in getting you there slower than not getting there at all." So, yeah.

Andrew: Now, you've written a book called "E.A.T.," right?

Jessica: Yes, I have.

Andrew: Is this the culmination of all of your experience?

Jessica: It is. So over all of these things, for me, has been my passion around food and creating recipes and beautiful tasting recipes that are really suitable for a whole food intake. I love developing recipes that also work for different types of intolerances, but also "E.A.T." has been a way for me… "E.A.T." is an acronym for “education at the table."

So it's also a resource that's been developed to educate people on the foundations of healthy eating, what macronutrients are, how to put them together, to encourage people to use a diversity of ingredients in their kitchen. Because I think there's a lot of fear around using new ingredients, whether that be grains or different vegetables, and so forth. So it's really been created to be a resource, which is the start of the book, and then there's about 80 recipes in there that take a lot of what the book teaches at the start and shows people how to put them together.

So it's a kind of for everyone book. It would suit any sort of dietary requirements. You know, they can be chops and changed to suit. And it's also a good, I would say, good tool for practitioners to use with their clients, because I understand that not all practitioners are as excited and as passionate about creating meal plans as we are, and we all have different areas of passion. 

So I think if people or practitioners aren't as excited about that space, then it's important for them to find resources where they can direct their clients. If they do just want to have a basic handout, they're going to say, "Okay, go to this website," or you know, "Here's a book," or "Here's something where you can take what I'm asking you to do and create some meals that will work for you."

Andrew: Just a last point about caveats, cautions. So popping up in my mind is, let's say, the brittle diabetic, the unstable diabetic. What sort of words of caution do you have for these sort of people when you're formulating meal plans and changing their dietary intake? And usually, I've got to say, their dietary intake is poor.

Jessica: I think it would be the same as to anyone that was in more of, I guess, a shakier ground for starting, is that we have to work a little slower. We still have to educate them and have them understand why we're making those changes, but it might be that we just need to move a little slower and a little bit more cautiously with the changes that we want to make. 

And I would probably even, you know, to jump from what you were just speaking of to even someone who may have all these complex gut issues, but they may be highly, say, salicylate or histamine reactive. Again, we may have a dietary plan that we would love to get them straight onto, but we have to look at the context of them and how we can take that base plan, which I think is so important to have that we can use to build from, but then mould that to suit. 

So it means that these types of clients, we need to start often at maybe a more narrower space of our base plan than we usually would and then carefully mould that to suit them.

Andrew: Jessica, there's so much to cover. I'm so glad that you've written this book because this is something that every clinic should have as a guide for the practitioner to teach their patients, but also even as a waiting room book, it can help. You know, people just pick it up and flip through it and get some little tips and hints to change their lifestyle, their dietary intakes for the better. So I got to say, thank you so much for taking us through your experiences today.

Jessica: Thanks for having me. It's been great.

Andrew: This is FX Medicine. I'm Andrew Whitfield-Cook.


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