By Dr. Becker
My second guest this week is Dr. Hanna Sinkko, a microbial ecologist who is working as a postdoctoral researcher in the University of Helsinki. She's also involved with DogRisk, a Finnish research program to learn more about how nutritional, environmental and genetic factors influence disease in dogs. Dr. Hanna's work with DogRisk involves the study of gut microbiota in dogs, and I asked her to tell us a little about her work both at the university and for DogRisk.
"I made my PhD thesis in microbiology a few years ago," Dr. Hanna explains, "and around a year ago I started to work in the environmental microbiota group led by Lasse Ruokolainen. Lasse is collaborating with Anna [Professor Anna Bjorkman], who leads the DogRisk project.
So I'm still working in Lasse's group, and there my task is studying relationships between dog allergies, their microbiota, and environmental microbes. And hopefully, if we get funded, I will continue this work in Anna's DogRisk program next year."
A Microbiota Primer
For those of you who might not be familiar with the term, I asked Dr. Hanna to explain the meaning of microbiota.
"Every animal and plant is colonized by microorganisms such as bacteria, archaea, or unicellular fungi," she explains. "This collection of different microbes, invisible to the naked eye, that live in and on the body is called microbiota. Researchers also use the term microbiome when they talk about the microbes in the body.
These microbes can reside in almost any part of the body. They live, for example, on the skin, in the respiratory and gastrointestinal tracts, and especially in the gut, which is rich in microbes. Based on recent estimates, the number of microbes in the human body is around  trillion, which is approximately the same number of cells in the human body, even a bit more.
We know nowadays that relationships between microbes and their host body can be very diverse. Some microbes promote the health of the host, and some are harmful. To describe non-harmful relationships, researchers use the terms commensalism and mutualism.
A commensal microbe benefits by being in the host body but does not affect the host. A mutual relationship means that a microbe is good for the host, and the host conditions favor the microbe. Both commensal and mutual relationships can be very useful for the host.
For example, some microbes in the human large intestine digest vegetable fibers that are undigested as such. In turn, these microbes that are able to digest fibers are given food and energy. Unfortunately there can also be harmful microbes as a part of the microbiota.
These harmful microbes can, for example, excrete metabolites that are not beneficial to the host, or they can be even pathogenic, which means they cause illness. For example, salmonella is a pathogenic microbe. It can create diarrhea in humans, but dogs very rarely get sick from it, even though they may have it in their gut quite often."
We know dogs' bodies harbor a whole different set of bacteria that could be potentially dangerous to us, but they handle those bacteria quite well. That's one of the things conventional veterinarians have used against raw foods is that raw-fed dogs shed salmonella more in their feces.
But what's interesting is that dogs (except for very young puppies) usually don't get sick from eating raw food, they just shed more salmonella. So it's wonderful to have the DogRisk researchers looking at what bacteria are doing inside the GI tract, and the effect on dogs. The goal of Dr. Hanna's canine microbiome research that we hope to fund is to study how different kinds of diets affect dogs and their microbiota.
"The goal is also," says Dr. Hanna "to find out whether there are some risk factors or protecting factors associated with different kinds of diets, lifestyles, and living environments of dogs and how these factors influence the prevalence of atopy."
The Why and How of Microbiota Studies
I asked Dr. Hanna what information we can gain by studying microbiota.
"Microbiota affects animal health in several different ways," she explains. "This is a very wide subject, and in our DogRisk program, we focus on the role of gut microbiota in chronic inflammatory disease. These are diseases such as allergies or atopy; but also, for example, cancer.
It was originally thought that atopy is a result of interactions between genes and environment, but based on some recent studies, there may be more to it. It may be that a change in environment is also a cause of inflammatory disease."
I asked Dr. Hanna how microbiota is studied.
"The first thing we do is take a sample from the part of the body which is of interest," she says. "Some samples, like biopsies, have to be taken by medical professionals, but some samples, such as feces, skin samples, or urine can be easily taken by dog owners.
The second step is to extract DNA from the sample. After this, we have two possible approaches. The cheaper approach is amplicon sequencing. For that we need to amplify the marker gene for microbes, and after this amplification step, the marker genes will be sequenced using next-generation sequencing methods.
Your listeners might remember that there are four different bases: A, T, C, and G, that make up the helix of a DNA string. So we are going to sequence the order of these bases using the available technologies for gene sequencing. The technologies produce millions of sequences, so we will get a lot of information on the microbiota.
After sequencing, the researcher is identifying the DNA sequences using bioinformatics tools and available DNA sequence databases.
By this identification we know what kind of microbes there are in the sample, for example, in dog feces. We also have a slightly more expensive approach called metagenomic sequencing. In this technique it is also possible to get information on the functional genes of microbes. For example, we are able to know what the microbes really are doing in the gut."
Analyzing Microbiota From Diet Intervention Data
I asked Dr. Hanna, if she were able to successfully fund her canine microbiota study, what the first thing would be that she would study pertaining to this topic. "Well, first we have the wonderful diet intervention data from the raw and dry food fed dogs," she answers.
"My task would be to analyze the change in microbiota after the diet intervention, and also to find out if the change in the gut microbiota is related to allergy or atopy, and the lifestyle of the dogs and their living environment."
Microbiota Research May Help Pet Owners Improve or Recover Their Dogs' Health
That's a very important first step, and I think it's an excellent first project because we have so many dogs suffering from allergies. I asked Dr. Hanna how an ordinary dog owner might benefit from microbiota research, for example, the owner of a healthy dog without allergies.
"The dogs might be healthy now," says Dr. Hanna, "but it's maybe not the case later. The first benefit of our study has to do with prevention. We assume the microbiota has health benefits — that it's an important key for the health for the dog."
"So if we know the risk factors for chronic diseases and how these risk factors affect dogs' gut microbiota, the professionals can help dog owners protect their dogs from these diseases. So it's prevention.
Another benefit comes from treatment. Based on the new knowledge that we will produce in our research, we can also design therapeutic strategies to modify microbiota so that we can treat the dog suffering from atopy or some other chronic disease.
These therapeutic strategies are not only comprised of diet, but a health-benefiting combination of diet, lifestyle, and exposure to natural environments, as well as beneficial microbes. A dog can get beneficial microbes constantly from the natural environment during exercise, but we can also use fecal transplants or probiotic products. These all can be used together to save microbiota that promotes the health of the dog.
A third benefit may be financial. Dog owners may save money because of our project. The protection from inflammatory diseases will reduce health-related costs. And on a larger scale, dog owners themselves can benefit from our project as well. This is because we use the dog as a model for human diseases.
The knowledge we gain in treating atopy in dogs will help us design therapeutic strategies to protect dog owners from the same inflammatory diseases."
So humans will learn a lot about their own microbiota and also benefit from this research. It's a good example of the One Health Initiative in which research done with animals also benefits humans.
It May Be Possible to Protect Dogs From Allergies and Other Disorders by Altering the Gut Microbiota With a Proper Diet
"Recently, some studies have proposed that the rise in prevalence in atopy is related to deficient microbial exposure in early life," says Dr. Hanna. "And this is maybe the most important thing to remember. Microbes help our immune system develop.
For instance, the gut microbiota provide signal molecules that promote the normal development of immune functions. When we expose ourselves to different kinds of microbes, the immune system kind of learns how to differentiate between commensal and pathogenic microbes. So we could say that without microbial contacts, we wouldn't be able to recognize and resist pathogens.
I think this is very important for everybody to remember — our environment is very clean nowadays, and we are living in cities. So it's important to expose ourselves to different kinds of natural environments, and also to eat a variety of healthy foods.
We know diet can be a very strong factor affecting the gut microbiota of all mammals, so what this means is that we may be able to protect our dogs from atopy and other chronic diseases by modifying the gut microbiota with a proper diet.
For instance here in Finland, raw dog food diets are becoming more popular. The raw food is obviously not heated, so it contains more microbes because heating kills microbes. Therefore, the raw food may challenge the dog's immune system to function better.
The study of the canine microbiome is becoming very popular, but it really warms my heart that Dr. Hanna's focus is on how we can alter the microbiome to be proactive and prevent disease from occurring.
I'm very excited to partner with Dr. Hanna and the rest of the DogRisk team to help them achieve the funding necessary to complete this study because I know how important it is to get this information out. I very much appreciate Dr. Hanna's role in the DogRisk project, and I can't wait to learn more after she has completed the study. But first we have to see that they can take her into the group! Let's start by making this happen!