Beneficial and Disruptive Microbes Walkthrough - Tiny Health Gut Health

Hi, my name is Emily Serta, I'm a microbiome specialist here with Tiny Health. Today I'm going to go over the beneficial and disruptive microbes in our shotgun metagenomics test. If you'd like a general overview of the test and how to navigate the portal, we do have a practitioner. Okay, so for today I'm going to go into the C metrics. What we're looking at, we are looking at Bifidobacterium, genus Akkermansia and Folcolibacterium. And so let's dive into Bifido first. Bifidobacterium. Here we can see the range for this adult patient and when we can see she's right at the top of this range for this individual, I definitely would not recommend a supplement, a bifido probiotic or any probiotic, even if it's multi strain containing Bifidobacterium because we don't want to drive this bifido too high. I tend to call Bifido B for bossy because it's, it's decent at driving things out, at bossing bacteria out that shouldn't be there. Some of the disruptives that we'll look at for example, but because it's beef or bossy also if we over supplement it will happily grow and grow. And when that happens it's going to become a problem. It's going to become a population that's too large for proportionally in our gut and it can actually contribute to inflammation and it will hurt the ability for this individual to create diversity in the gut because we'll have one population just too large. So in this situation, like I said, I would not use a probiotic but you can see that we're going to get the relative abundance. So this bifido is taking up six and a half percent of, of the microbiome for this individual and then if they have resampled, we'll be able to see where the results were previously and where they are now so you can start to see trends. You'll also be able to come down within the metric, you'll be able to learn more about Bifidobacterium. We have studies linked and you could, if you need a reminder about why bifido might be important for this individual, you can check that out. We have associations here. So associations obviously it's, it's going to be better gut health when this is high or in, within normal range, optimal range. And then these are all associations to conditions when that bifidobacteria is Low, it has a positive association in our internal data to chronic diarrhea. So with any of these, you can actually click on them and you can go out to the association to learn more about it. We'll also be able to see species in the sample, and this can be really helpful, especially if we're looking at an infant or even a toddler to make sure that they have beneficial bifido strains in there, especially for HMO digestion. So this is helpful. We see a lot of diversity in this individual, which is what we would like to see. And that is Bifidobacterium. Remember, it's B for bossy. So I do put a timeline. If we did need to supplement this, definitely put a timeline around it. For infants, we're talking four weeks to go from zero to up into their optimal range. For toddlers, it tends to be about six weeks and six to eight weeks. And then for children ages 3 to 18, we tend to see more like three months, which is about the same as adults, around three months of supplementation. And that's if, if we had somebody down here at zero or at very low levels, Bifidobacterium, also, I like to talk about it colonizing. So if we, if we needed, say, this person had a result here and we needed the population in the gut so that it did take up space in the, in that bossy manner, we would need to use a prebiotic alongside the bifido probiotic in order to help that population grow and establish. And so you'll see some recommendations. When you have patients that need bifido, you'll see HMOs, human milk oligosaccharides, called out as great prebiotics to use to build this particular family. Also, in the event that there's a dairy allergy and we can't use a human milk oligosaccharide, a lot of times we'll lean into phgg or something like sunfiber that will also help to establish this. Polyphenols are also great, and polyphenols will actually feed all of these beneficial bacteria families. So Akkermansia is the next beneficial here. For Akkermansia, we can see this individual has zero, or at least it's below our 0.005 sensitivity. So maybe it's there at 0.003, but in any case, it's not showing up at our sensitivity level. Akkermansia, it is known for its metabolic health benefits, but also I, it's pretty picky about its environment. So a lot of Times I will work on diet, I will work on the gut environment itself, making sure there's not inflammation, there's not a lot of pathogens, there's not some overgrowth, making sure short chain fatty acid production is optimized. And then I'll circle back to Akkermansia. A lot of times when I find that we don't have a great looking gut and patients want to start with Akkermansia supplementation, it's not to say that they aren't getting benefit of that Akkermansia moving through the gut, but I don't see it colonize in the gut very well. So here again we can see that there's zero. It looks like previous sample. There was also zero here. There you have your about section and we would have strains listed there if there were any to note in this sample on the right hand side you'll see the actions that you can take to help increase this Akkermansia. Okay, Faale bacterium is the next beneficial that we look at and this is an important one because this family is a butyrate producing family and butyrate is one of our, it's our most dominant short chain fatty acid as an as adults and even as older children it's very anti inflammatory. It's very important for again making that more acidic environment in the gut, which makes really an unfriendly place for any pathogens to hang out and become comfortable. So here again you'll see the range when this is low. Sometimes we use bacillus probiotics and we also lean into polyphenol foods to help drive this up. This, this family really loves whole grains and legumes. So sometimes we're talking about adding that into the diet as well. Even in small amounts or in pulses, however that's tolerated. Okay, scrolling down we can see the associations and look at the great diversity here. So that is, that is just what we want to see. And you'll notice there's no, there's no top level. It's not like you're going to have too much for Colibacterium, at least the genus you could always have like let's say this one of these strains grew too big by itself, then it might be called out, but I rarely see that happening. Okay, so those are the beneficial microbes as far as the genus. Looking at the genus of these go, I really like to look at this because it tells me about the, the gut environment and it's important not just to look at what's in there as pathogens, but Also to look at what are the beneficials so that we really get a lot of information about what needs to be kind of supplemented or shored up to help that environment and not just what needs to be killed. Okay. Down below we'll see common probiotic species. These are species that we often see in adult guts. And you can see that a number of them are popping up for this individual. And that's great. We see a lot of diversity here. These are not going to show out of range. They're just kind of taking a role to tell you who's. Who's in attendance. Okay, so below, beneficials, kind of to round out the other side of this environment, we really want to look at disruptive microbes. And here we're looking at pathogens in the gut. So these are things that we can use antimicrobial spices. We can use things like raw garlic. Allison. And we're trying to basically use antimicrobials to drive these out. So for the disruptive microbes at the top, you're going to see antibiotic resistant signature. These are two markers. Richness is going to look at the number of individuals in the gut who could be antibiotic resistant. So looking down here, we can see who the species are. Exactly. And any one of these species could be resistant to antibiotics. That said, there's not too many here. So it's not out of range and we're not seeing any actions related to that. Now, just as these look at individuals and they got the abundance, it's important to read these together because abundance is saying, well, how much room are these taking up in the gut? So even though there's a number of individuals there, it looks like they're not taking up much room at all. And it looks like this person has improved this metric. So you'll get more information reading both of these together. Further down, we have our opportunistic pathogens and these are many of the things that were listed up here. Enterobacteraceae is a family, and this family actually includes everything from Klebsiella all the way down to Raltello. And so when you see little bits of E. Coli, little bits of Effluxneri, and then we go up and we see this. Enterobacteraceae know that everything, if we added everything from Klebsiella down to Rautell, we're going to get this percentage. Okay. So it's not like there's this and this. This is included in that. In, in this. If we look at the Enterobacteraceae again, you're going to get your, your level and that will, that range will shift based on your patient's age, if they're in the infant, toddler, child or adult range. And then further down you're going to get your associations and what species are in there. And just like what we saw, we saw the E. Coli, there's a couple different strains of E. Coli and then that Escherichia flexneri. We do also look at toxin genes in the sample. So we are not measuring toxins directly, but the entire shotgun test is made up of the microbes present. So who's there? And then also the genes present in the microbiome. So what is the microbiome able to do? What are those microbes able to do? So this is looking at the presence of genes and this is where something like Shigella may pop up. There are a number of toxin genes we look for and this would just tell you that the gene is present, not that the toxin is present. So epigenetically I kind of think about this as we really need to fix up the microbiome environment and maybe get one of these bacteria under control if it happened to be out of range and there was a toxin gene so that the environment isn't right for that gene to be flipped on and that toxin to be created. Okay, so you can see everything that we're testing for here. After the Enterobacteraceae, we start to look at things like Streptococcus. Here we can see this individual has a higher Enterococcus faecalis and it looks like it has really increased since the last time. Now I do look at just how much is in there. And this is, like I said, our sensitivity is 0.005%. And this is just showing up. So I'm not going to go in there heavy handed with something really strong. When I see something that is just kind of barely showing up on the, on the test results, it's not taking up a lot of space in the gut. Instead what I would probably do is go into the spices and I would definitely like look at our spices table and if you haven't checked this out, it is very cool. But here we can see our Enterococcus faecalis and we can see some spices that are going to work against it as an antimicrobial. And I would probably have this individual just add those spices into their diet at least three times a week for the next month. And we're probably going to kick this bacteria right out. So know that you can look into the actions here. Related. You're going to be able to see some resources, you're going to be able to see some products. If it's easier for them to go with like a little product instead of adding these things to their diet, then you can kind of cater that to the individual. Again, the Enterococcus faecalis is listed here. We can see it has an association with UTIs. And we are not looking for toxin genes specifically for this particular species. Okay. So further down you can see other things that we're looking for. We are looking for H. Pylori in the sample. Sensitivity is 0.005%. We're also looking for fungal overgrowth, the candida. And all the way down we're looking at parasites and infection. We're not looking for worms in the sample. That would. That would require like cutting the sample up to actually, because we're sampling the DNA. So you could use a parasite panel if you want to pair that with your shotgun test. But we do see these parasites or infections pop up every now and then. We're also looking at methane production here. So this is a great example of how we're looking for the microbes. Like I said, we're looking for the presence of Methanobraphibacter smithi and we're also looking for the genes. So here we're looking for methane producing genes in the microbiome. And I have seen Methano Brevibacter smithi come back elevated and there's an overgrowth. Then methane production capacity is zero. That's telling me that there are no methane producing genes there. And I'm just going to treat this as an overgrowth. As a little hack. Anytime you see the word capacity in our test, we are looking at those functional genes. I hope this is helpful. Again, looking at the disruptives, it's easy to go in there and try to figure out what we want to kill. But we really want to get a sense of the terrain and what the beneficials look like as part of that process. So I hope this has been helpful. And again, if you have any questions, please don't hesitate to reach out to us.