MICROBIOME ANALYSIS REPORT

Transcription

1 MICROBIOME ANALYSIS REPORT Client name: N.E. Body Order No.: 6140 Report date: Sample Type: Gut Sample Barcode: Report Type: Single

2 Hello Please find enclosed the results of your personalised gut microbiome analysis, a truly unique perspective on the organisms which are living inside you. This report will help you to understand the number and types of microbes inhabiting your body. Microbes are a bit like humans really, they live in complex communities which are dependent on one another. The microbes both inside and on the surfaces of your body can be either bacteria, fungi or indeed yeasts. They all live together and carry out important functions for you we are at the cusp of great discoveries in this important science and it is a bit like grasping at the top of an iceberg there is so much more to explore! So the small print bit is that this is not in any way a medical test and you will not be able to surmise any health information from it. That having been said (phew!) we can point you to the current thinking and the truly amazing microbiome studies that have been published in the scientific literature. What did we do? Firstly, we extracted DNA from your poo sample this will contain DNA from you, what you have eaten and the different types of microbes that live inside you. Secondly, we made of copies of a particular DNA signature a small piece of DNA that is present in all bacteria and which is different in different types of bacteria. We focus on bacteria and not fungi or yeasts because these are the most significant class of organisms for your health and wellbeing. We then read the sequence of the DNA and from this we can identify which bacteria are there and how many there are of a particular type. We then used that data to generate this personalised report for you. About this report This report is in several sections. The first section gives you an overview of your results. The second section is about the diversity of your bacteria. (Having a good mixture of different types of bacteria is better for your health.) The third section looks at the balance between different types of bacteria. Having the right balance is a good indicator of diet and digestive health, and can be important in weight loss. After that we give a one page summary of your levels of the key bacteria, and on the following page we make some suggestions on how to make any changes to your levels that might be needed. The final section profiles some of the key bacterial types that are in your gut, and how many there are. Microbiome science is still very new and scientists are learning about the relationships with our tiny friends at an incredible rate so we cannot give you all the answers just an extraordinary snapshot in time. Sometimes we know that particular bacteria are more common in people with a particular health or wellness status but we often do not know if this is causal or consequential. Either way, your gut bacterial profile is full of useful information!

3 Your results We sequenced 74,275 pieces of DNA in your sample, and used them to identify the bacteria in it. Scientists classify all living things into groups. There are several different levels of groups: The species is the smallest grouping, and all members of a species are very similar to each other. We identified 85 species in your sample. Several similar species are grouped together into a genus. We found 75 genera in your sample. In turn, several similar genera are grouped into a family. We identified 35 families in your sample. Similar families are then grouped into an order; we found 18 in your sample. Several orders are grouped into a class, we identified 13 of these. Classes in turn are grouped into a phylum. We found 7 phyla. Your Top 10 Bacteria These are the 10 most common bacteria (species and genera) in your gut: TOP 10 SPECIES Rank Species Name Percent 1 Bacteroides vulgatus 12.7% 2 Blautia wexlerae 3.8% 3 Roseburia intestinalis 3.6% 4 Collinsella aerofaciens 3.2% 5 Roseburia faecis 3.0% 6 Bacteroides rodentium 2.7% 7 Parabacteroides distasonis 2.0% 8 Bacteroides sp. AR20 1.8% 9 Dorea longicatena 1.7% 10 Alistipes putredinis 1.5% In total, the 85 species account for 56.6 % of the bacteria we found (the remaining 43.4 % could not be identified to species level). TOP 10 GENERA Rank Genus Name Percent 1 Bacteroides 22.7% 2 Roseburia 10.7% 3 Blautia 10.5% 4 Faecalibacterium 7.0% 5 Collinsella 4.4% 6 Pseudobutyrivibrio 3.7% 7 Alistipes 3.0% 8 Sarcina 2.8% 9 Dorea 2.8% 10 Parabacteroides 2.4% In total, the 75 genera account for 93.3 % of the bacteria we found (the remaining 6.7 % could not be identified to genus level). These are not necessarily the most important, or even the most interesting bacteria; just the most common. (We don't list them all because it would be too dull!) Later in this report you'll learn more about the bacteria that are most relevant to your health.

4 Your Phyla: Phyla are the biggest groups used to classify bacteria. Here's a breakdown of yours: Your Classes: Classes are the next level below phyla. Here are yours: Your Orders: Orders are the smallest groups that we can show clearly on a pie chart:

5 Diversity A healthy gut has a high diversity of different types of microbes. Some species will be present in relatively large numbers, with others only being at low levels, but having a broad mixture is undoubtedly beneficial to health and wellbeing. Low gut bacterial diversity can be caused by illness or indeed antibiotic treatments, as certain bacterial types are reduced. It may be possible to increase your bacterial diversity by eating a varied diet, including different types of fibre, fruits and vegetables with probiotics (that contain beneficial bacteria) and prebiotics (which nourish beneficial bacteria). We measure bacterial diversity with a number which is known as the Shannon Entropy. The normal range in healthy people (in the USA) was found to range from 0.41 to 2.62, with most people at around We measured your personal bacterial diversity as 4.13 and your level is therefore high. You have a very diverse gut microbiome. Congratulations!

6 Balance The balance between some types of bacteria can provide useful information on diet and health. Bacteroides vs. Prevotella The relative levels of the Prevotella and Bacteroides genera of bacteria are a good indication of the type of diet you have been eating. They are both members of the phylum Bacteroidetes. A high proportion of Prevotella suggests a long-term, substantially plant-based diet with a lot of beneficial fibre and prebiotic polysaccharides. A high proportion of Bacteroides indicates a long-term, typical meat-based western diet high in proteins and fats. A recent study showed that people with a high proportion of Prevotella lost weight in six months on a high fibre diet, whereas people with lots of Bacteroides did not. You have a low proportion of Prevotella, indicating a diet high in fat and protein. You might want to consider increasing your consumption of fruit, vegetables and fibre. Bacteroidetes vs. Firmicutes The relative levels of Bacteroidetes and Firmicutes are correlated with obesity and gut inflammation. A high ratio of Bacteroidetes to Firmicutes (above 0.12) is associated with a low BMI (Body Mass Index) A low ratio (below 0.12) is associated with a high BMI and obesity. Please note that other factors are associated with BMI, so this ratio alone may not predict your BMI. A diet high in fat tends to reduce the Bacteroidetes to Firmicutes ratio, whereas a low-fat diet should increase it. A diet rich in whole grains (such as whole grain barley and brown rice) has been shown to increase the Bacteroidetes/Firmicutes ratio.

7 Summary Here's your one-page score-card of your test results. This page doesn't list all your bacteria; only the measurements that we think are important for health and well-being. So that includes your diversity and balance of bacteria, and some key species and genera. Tests in green are "good" levels; tests in blue are "typical" (OK); and tests in amber are the ones that could be improved. See the next page for some suggestions on how to do that. Diversity 4.13 Akkermansia muciniphila 0.04 % Anaerotruncus colihominis 0.00 % Butyrivibrio crossotus 0.00 % Collinsella aerofaciens 3.24 % Dialister invisus 0.00 % Methanobrevibacter smithii 0.03 % Oxalobacter formigenes 0.00 % Ruminococcus albus 0.00 % Alistipes 2.97 % Barnesiella 1.27 % Bifidobacterium 0.74 % Lactobacillus 0.09 % Odoribacter 0.52 % Prevotella 0.04 % Roseburia % Prevotella vs. Bacteroides 0.00 Bacteroidetes vs. Firmicutes 0.53

8 Your Personal Suggestions The following suggestions are made based on your personal results. These are the bacteria important to your wellbeing that can be boosted by changing your diet, and other indicators like the diversity or balance of bacterial types. We list suggestions where your result is low, or where helpful bacteria are absent (even if that is common). To read more about these bacteria, see their profiles in the following pages. Result Name Your Level Suggestion to Improve Oxalobacter formigenes Absent This bacterium breaks down oxalate, which is a common cause of kidney stones (as calcium oxalate). If you are worried about kidney stones (maybe you are prone to them) then it may be possible to increase your level of these bacteria by taking probiotics containing O. formigenes. These are available commercially and may be beneficial, although results in clinical studies have been mixed. Many people do not have Oxalobacter with no obvious ill effects, so If kidney stones are not a concern, there is no need to take action. Prevotella Low Your level of Prevotella is a good indication of a healthy diet. To improve your Prevotella, these are the things to try: General advice Increase your consumption of plant-based foods such as fruit and vegetables Consume more fibre (for example, barley-kernel bread has been shown to be particularly beneficial) As most people need to eat more fruit and veg, and don't get enough fibre, this is good advice in any case! Avoid making sudden changes to your diet. It is often wise to seek medical advice, especially if you suffer from IBS (Irritable Bowel Syndrome) or IBD (Inflammatory Bowel Disease - Ulcerative Colitis, or Crohn's Disease). In particular, some forms of fibre and prebiotics, especially pulses, may be best avoided as they can cause digestive discomfort, especially if you're not used to them. Even if you don't suffer from these conditions, it may be best to introduce these foods gradually to give your microbiome a chance to catch up! Many of the foods that are beneficial to your microbiome are also beneficial to you - and will be very familiar: fruit and vegetables, fibre, omega-3. This is, of course, not a coincidence! Your microbiome and your body can work together to benefit your health and well-being.

9 Profiles In this section we look at some of the key types of bacteria, where we know something about how they are related to health. We'll compare your levels to a group of "healthy" volunteers. A note of caution: there are many reasons why bacteria profiles can vary, and they may not all be because of health problems. For example, they may vary from country to country. Another thing to remember is that just because a certain bacterium is more common in people with a certain condition, it does not mean that it causes that condition! The species and genera we list here are the ones where there is good data on their normal levels and their possible associations with different conditions. A positive association means that they are more common in people with a particular condition; it s important to bear in mind that this does not necessarily mean that they are a cause of the condition. A negative association means the opposite that these bacteria are less common in people that have a condition. Again, this does not necessarily mean that they can prevent it. However, the levels of bacteria are indicative of general gut health, and the steps that re-balance your bacteria should also improve gut health. None of the information in this report should be taken as a medical diagnosis; this report does not tell you about any harmful organisms. If you have concerns about your gut health, you should speak to your GP. First we list the species, and then the genera, an alphabetical order. Remember that these bacteria might not appear in your "top 10" - they're just the most relevant to health and well-being. Remember that genera are small groups of similar species of bacteria. Akkermansia muciniphila Collinsella aerofaciens Methanobrevibacter smithii Oxalobacter formigenes Alistipes Barnesiella Bifidobacterium Lactobacillus Odoribacter Prevotella Roseburia

10 Akkermansia muciniphila This species is believed to be generally beneficial and has been shown to reduce inflammation. It is associated with lower levels of obesity, ulcerative colitis and Crohn's disease. However it has also been seen at higher levels in patients with Type 2 diabetes. Akkermansia likes to live on your intestinal mucus, and so is hard to grow in the lab; in fact it was only discovered in Prebiotics such as oligofructose can increase the levels of Akkermansia 100-fold A diet rich in omega-3 fish oils can also increase it significantly. This species was present in your sample at 0.04%. It is found in 45.8% of the healthy population. This species is a member of the genus Akkermansia. We found 0 other species in your sample. In a healthy population, 75% of people had a level of 0.06% or below; a typical level is 0.00%. So your level is in the typical range.

11 Collinsella aerofaciens It is typically the most plentiful bacterium in the human intestine, and found in most people It has been found to have a negative association with Irritable Bowel Syndrome; in other words, to be rare in IBS sufferers, but more common in healthy people. It was first discovered in 1935 The name aerofaciens means gas-making because of its ability to produce hydrogen gas. One study suggests this species is higher in people who consume a lot of processed food. This species was present in your sample at 3.24%. It is found in 73.4% of the healthy population. This species is a member of the genus Collinsella. We found 0 other species in your sample. In a healthy population, 99% of people had a level of 3.03% or below; a typical level is 0.09%. So your level is extremely high.

12 Methanobrevibacter smithii Unlike the other species listed here, M. smithii is not a bacterium, but a member of a completely different group, the Archaea. This group is very ancient (as you might guess from the name) and includes microbes that live in all kinds of extreme environments like hot springs but also, some that live in the human body. M. smithii is a methanogen, which means that it produces methane (an odourless gas) It plays an important role in digesting complex carbohydrates in the diet that cannot be digested by the body. It therefore can play an important role in the body's calorie uptake. It has been shown to be associated with low levels of obesity, but also with abdominal tenderness and constipation. This species was present in your sample at 0.03%. It is found in 25.2% of the healthy population. This species is a member of the genus Methanobrevibacter. We found 0 other species in your sample. In a healthy population, 75% of people had a level of 0.00% or below; a typical level is 0.00%. So your level is high.

13 Oxalobacter formigenes O. formigenes helps to prevent the formation of kidney stones by breaking down a chemical called oxalate. In the absence of this bacterium, the oxalate is taken up by the body and can form kidney stones made of calcium oxalate The presence of O. formigenes was found to reduce the risk of kidney stones by 70% It is believed to be sensitive to some antibiotics Oxalate (or oxalic acid) is found in the diet in many plants including spinach and rhubarb, and can also be produced by the body. Probiotics containing O. formigenes are available and may be beneficial in preventing kidney stones, although results in clinical studies have been mixed This species was not found in your sample. It is found in 26.2% of the healthy population. In a healthy population, 75% of people had a level of 0.00% or below; a typical level is 0.00%. So your level is in the typical range.

14 Alistipes This genus has been shown to be associated with low obesity, and also to be low in IBS sufferers. Several different species are common in the human gut, including A. finegoldii, A. senegalensis, A. shahii and A. putredinis. This genus was present in your sample at 2.97%. It is found in 89.7% of the healthy population. We found 5 species in your sample: Alistipes putredinis, Alistipes finegoldii, Alistipes shahii, Alistipes sp. NML05A004 & Alistipes indistinctus. In a healthy population, 90% of people had a level of 2.63% or below; a typical level is 0.64%. So your level is very high.

15 Barnesiella The first species of this genus was isolated from chickens in only It has been show to be associated with low obesity. The genus is named after the microbiologist, Ella M. Barnes It includes two species, of which B. intestinihominis has been isolated from the human gut. This genus was present in your sample at 1.27%. It is found in 59.5% of the healthy population. We found 1 species in your sample: Barnesiella intestinihominis. In a healthy population, 90% of people had a level of 1.03% or below; a typical level is 0.02%. So your level is very high.

16 Bifidobacterium This is a large genus, containing a wide variety of species commonly found in the human body. The name comes from their unusual branched or 'Y' shape. They were discovered in 1899 and are often used in probiotics. They have been shown to be negatively associated with constipation, Crohn's Disease, and IBS, and so are typically considered to be beneficial. They are a type of lactic acid bacteria, so called because they produce lactic acid, and are often found in fermented products. This genus was present in your sample at 0.74%. It is found in 74.6% of the healthy population. We found 4 species in your sample: Bifidobacterium dentium, Bifidobacterium animalis, Bifidobacterium pseudocatenulatum & Bifidobacterium longum. In a healthy population, 75% of people had a level of 0.45% or below; a typical level is 0.06%. So your level is high.

17 Lactobacillus Lactobacillus, like Bifidobacterium, are lactic acid producing bacteria commonly found in fermented products like yoghurt, cheese, and sauerkraut. They are also a common component of probiotics, although its not clear which strains or species are the most beneficial. It is also a frequently found in the human microbiome, especially in the vagina, and is also commonly present in the gut. There is some confusion over the relationship between Lactobacillus and obesity, with some studies reporting a positive correlation, while others report a negative correlation. However, negative correlations have been reported for type II Diabetes, irritable bowel syndrome, and diarrhoea, so these bacteria are generally regarded as beneficial. This genus was present in your sample at 0.09%. It is found in 62.3% of the healthy population. We found 2 species in your sample: Lactobacillus delbrueckii & Lactobacillus vaginalis. In a healthy population, 75% of people had a level of 0.02% or below; a typical level is 0.00%. So your level is high.

18 Odoribacter This genus was split off from Bacteroides in 2008 as a result of novel species identified from dogs with gum disease. However, in the human gut this genus has been shown to have a negative association with ulcerative colitis, and Crohn's disease, and so it is believed to be beneficial The name implies a rod-shaped bacterium with a bad smell Odoribacter splanchnicus is the dominant species in the human gut. The name splanchnicus means of the innards. It can produce beneficial molecules short chain fatty acids (SCFAs) by breaking down carbohydrates in the diet This genus was present in your sample at 0.52%. It is found in 75.9% of the healthy population. We found 1 species in your sample: Odoribacter splanchnicus. In a healthy population, 90% of people had a level of 0.39% or below; a typical level is 0.08%. So your level is very high.

19 Prevotella This genus, consisting of around 40 species, is commonly found in the human gut microbiome It has been shown to have a negative association with ulcerative colitis. The relative amounts of Prevotella and Bacteroides are a good indicator of the type of diet (see above). A higher fraction of Prevotella, indicates a healthier diet high in plant fibre and oligosaccharides. It was not obvious whether Prevotella was beneficial, as it can be associated with some chronic inflammatory diseases However, recent research has shown that a diet including barley-kernel bread increased the amount of Prevotella, and that this improved the subjects' response to glucose. This genus was present in your sample at 0.04%. It is found in 81.5% of the healthy population. We found 2 species in your sample: Prevotella buccalis & Prevotella disiens. In a healthy population, 50% of people had a level between 0.00% and 3.44%; a typical level is 0.05%. So your level is in the typical range.

20 Roseburia This genus has been shown to be negatively associated with: type II diabetes, ulcerative colitis, Crohn's disease, and inflammatory bowel disease in general It looks to be either directly beneficial, or an indicator of a healthy gut. Several different species are found in the human gut. They produce the beneficial short-chain fatty-acid (SCFA), butyrate, which can nourish the cells of the gut. A diet including whole-grain barley has been shown to increase levels of this bug. This genus was present in your sample at 10.72%. It is found in 93.1% of the healthy population. We found 3 species in your sample: Roseburia intestinalis, Roseburia faecis & Roseburia inulinivorans. In a healthy population, 90% of people had a level of 5.55% or below; a typical level is 1.70%. So your level is very high.