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Our human bodies are some amazingly designed machines, we all know that. But did you know that these same bodies are home to trillions of microbes? There are lots and lots of different types of bacteria, yeast, viruses and other microbes that live inside our digestive system! For the pseudo-scientific Blue Monday I wrote a post about different diets and I thought it is only appropriate that I follow that up with something strictly scientific! Below you will have an opportunity to read about what the different bacteria do inside our bodies, how fermented foods work, what are probiotics and how scientists can develop new types of fermented foods! To make sure I give you the best information, I reached out to my good friend and an absolute expert in natural products biology and chemistry, Dr. Dominic Colosimo:
Then he moved to New York City and started working at Rockefeller University. In the lab of Dr. Sean Brady, who works on the chemistry of bacteria living inside the human body as well as bacteria growing in other environments. In Dr. Brady’s lab, Dominic studied how bacteria that live in the human gut interact with the human body. His project was so important that he even received his own funding for it, through the Hemsley Foundation for Gastrointestinal Health!
Currently Dominic works at Kingdom Supercultures – a company that helps manufacturers make new foods, by designing Supercultures, or communities of microbes, that go into these foods. Think: kombucha, beer, kimchi, sauerkraut etc.
A healthy human body makes home to more than 1000 different bacterial species. I think it will put things in perspective if I tell you that our body itself expresses about 20,000 genes, while the different microbes that live in us express 3.3 million (!!) genes (if you don’t remember what genes are, check out my post about genes and DNA here). Keeping these crazy high numbers in mind, I asked Dominic what are all these microbes in our guts:
Dominic: Think of the human gut like a distinct ecosystem, just like for example marine sediment or soil in the ground. Our gut’s ecosystem is dominated by a specific set of bacteria, most of them being Bacteroidetes and Firmicutes. Generally speaking, high-fat diet will increase the ratio of your Firmicutes to Bacteroidetes, while a healthier diet will decrease the ratio of Firmicutes to Bacteroidetes. Interestingly, while more specific subtypes of bacteria are quite diverse from one person to another, these large groups of bacteria (again, Bacteroidetes and Firmicutes) are not too diverse between people.
Martyna: If they are not so diverse from person to person, it must mean that they have very specific roles to play in all human bodies, right?
D: Yes, they are very important for a few reasons. First, the most well-known purpose of our gut microbiome is that some bacteria help us digest specific types of fibers that are not easily absorbed by our digestive system without the bacterial help. Over the last 50 years scientists have learned that bacteria can take these complex carbohydrates and break them down to smaller pieces. And only then can these smaller compounds be taken up by the cells that form lining of our guts.
Another role for the gut microbiome is that it protects us against other bacteria. It is important for our “good” bacteria – the ones that we want in our guts – to comprise many different bacterial types. We call this the “microbial diversity”. With high-fat and high-sugar diets, the microbial diversity in our digestive system becomes low. What that can lead to is for example C. diff. infection (C. diff. is a short name for a type of infectious bacteria that can cause diarrhea, belly pain and fever) or even messing up the lining of the colon, which could be one of the mechanisms for IBD (Inflammatory Bowel Disease).
M: Are these types of infections caused because this “bad” type of bacteria colonizes our gut or is it more that the “good” bacteria are just not playing their protective role anymore? Or is it maybe a little bit of both?
D: There is evidence for both these mechanisms. If the microbial diversity of our gut goes down, some of the good bacteria die and leave room for the bad bacteria to colonize our gut.
D: Another important factor to consider is that some types of bacteria like to live in a very specific environment (more acidic or more basic). So, for example, more Bacteroidetes can drive down the pH in our guts (make the environment more acidic), but if the number of Bacteroidetes is too low, the pH will go up. This will in turn drive more changes in the healthy microbiome of our guts, because there are also other types of bacteria residing in our guts that like to live at lower pH.
M: I know that the acidity along our digestive tract changes quite a bit along the way. Does it mean that the bacteria residing in different parts of it are different too?
D: Most definitely! Nowadays more and more people study the localization of different types of bacteria along the digestive system and there have been really cool things coming up in these studies! For example, there is a mucous layer in our gut, where some bacteria can live, but not others. But then again, that’s another part that adds complexity to the gut microbiome. As you go lower in your intestines, both the pH changes and the mucous gets thicker – so some bacteria, which are able to degrade some of that mucous, can live within it, but others cannot.
M: If there are specific types of bacteria that can only live in specific parts of our digestive system, what are the chances that when we eat different types of fermented foods, the good bacteria we are trying to get are even going to survive?
D: The chances are actually quite low, although it depends a little bit on the individual.
M: If the short answer is no, what’s the big deal about probiotics and fermented foods?
D: There have been some studies where scientists found that probiotics do cause very quick, but short-term changes, especially in the metabolites produced in human body. However, these bacteria do not stably colonize human digestive system in this short period of time. But like I mentioned, it is not the same all across the board. For example, there have been other studies where it was shown that children are more susceptible to have their digestive system colonized by different types of bacteria, so – while it is rather difficult to obtain in adults – children could have their guts colonized by specific types of bacteria that they will take in with probiotics more easily. Again, for a healthy adult these changes are transient and last about two days. An interesting fact here: these days people are trying to make a switch from probiotics to “Live Biotherapeutic Products” (LBP’s), which are going to be much more regimented and taken more like an actual medicine, to hopefully improve the level of colonization of our guts with these good bacteria.
M: So, would you say that if someone wants to have more long-term effects, should they just drink their strained yoghurt more regularly? How does that work?
D: That is surely one way. While many healthy individuals will probably notice only a subtle difference, it is recommended that people who suffer from for example Crohn’s disease or Ulcerative Colitis (two main diseases contributing to inflammatory bowel disease) follow a diet rich in fermented foods. There is a lot of evidence showing that people’s health improves thanks to probiotics and thus, while – from a scientific perspective – we still don’t exactly understand how these fermented foods work, we do know that they help.
Gastrointestinal diseases have skyrocketed in industrialized nations and one of the problems with tracking these cases is that many of them are unfortunately under-reported. Especially young people could feel embarrassed to talk about their gastrointestinal health. Keeping all of this in mind, fermented foods are a great place to start dealing with gastrointestinal problems. The science is not there yet, but it is getting better and better every day!
M: Do you include fermented foods and drinks in your own diet?
D: I am mostly a salad-and-chicken kind of guy, but I do make and drink my own kombucha!
M: That’s awesome! So what types of foods do you guys make at the company? How does it work?
D: What we do at the company is helping other companies improve food and beverages by intelligently designing communities of microbes. We call these “Supercultures”. We isolate microbial strains from different types of fermented foods and use high-throughput robotics, metabolomics, and cutting-edge computer science to make Supercultures that improve their product. In this way, we make our own miso, kombucha, vinegar, we are working in the non-alcoholic beverage space as well.
M: Very cool! How do you guys conduct the tasting of these foods?
D: It’s a type of science in and of itself! You have to have a very trained tongue and recognize all sorts of flavors. We have two trained chefs here at the company – they come in and we line them up and double-blind them and then we have them taste foods in multiple replicates. It is quite amazing how great of a tester they are! They fill out these very complex rubrics, where they grade different types of flavors and we then plot it in software, just like any other data.
M: Do you have to “calibrate” these chefs’ taste buds before the tastings?
D: Exactly! We give them samples of things that we believe should be called “a maximum on the scale of bitterness” or “a medium on the scale of sweetness” etc. After this kind of “calibration” it is amazing how repetitive their results are. Everything they taste is in four repeats, but they don’t know what is what. And more often than not, when we plot the final results, they have insanely small error bars.
M: This is just incredible! You can actually collect data based on someone’s taste! I never thought about it before. Thank you so much for sharing all this amazing knowledge with me today, I am sure our readers will really appreciate it! Would it be okay for them to ask extra questions, if they have any?
D: Definitely! If they have any questions, they are more than welcome to post them in the comments below or they can contact me via LinkedIn!
That was quite amazing! I don’t know about you guys, but I certainly learned a lot during this conversation! Please, feel free to ask any questions you might have about the gut microbiome, fermented foods or anything in between in the comments below or contact Dominic via LinkedIn >>here<<!
Martyna Scribbles 